Sda

Establishing connection to ws://127.0.0.1:57531/ ...
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<== ["#6#","!","R is free software and comes with ABSOLUTELY NO WARRANTY.\nYou are
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<== ["#8#","!","R is a collaborative project with many contributors.\nType

'contributors()' for more information and\n'citation()' on how to cite R or R
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<== ["#10#","!","Type 'demo()' for some demos, 'help()' for on-line help,
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<== ["#12#","!","Check out Microsoft's enhanced R distribution at
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Maps.","Imports":"MASS","LibPath":"C:\/Program Files\/R\/R-
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either in memory, on disk, or streaming via the callback or connection\n
interfaces. Some knowledge of libcurl is recommended; for a more-user-friendly\n
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(>= 0.4), utils, tools, methods, memoise, whisker,\ndigest, rstudioapi (>= 0.2.0),
jsonlite, stats, git2r (>=\n0.11.0),
withr","LibPath":"C:\/Users\/pminaev\/Documents\/R\/win-
2)","NeedsCompilation":"yes","Package":"devtools","Suggests":"curl (>= 0.9),
testthat (>= 0.7), BiocInstaller, Rcpp (>=\n0.10.0), MASS, rmarkdown, knitr, lintr
(>= 0.2.1), bitops,\nroxygen2 (>= 5.0.0), evaluate, rversions","Title":"Tools to
Make Developing R Packages Easier","Version":"1.10.0"},"dichromat":
{"Author":"Thomas Lumley [aut, cre], Ken Knoblauch [ctb], Scott Waichler\n
[ctb], Achim Zeileis [ctb]","Built":"3.2.3","Depends":"R (>= 2.10),
stats","Description":"Collapse red-green or green-blue distinctions to simulate\n
the effects of different types of color-
blindness.","LibPath":"C:\/Users\/pminaev\/Documents\/R\/win-
library\/3.2","License":"GPL-2","Package":"dichromat","Title":"Color Schemes for
Dichromats","Version":"2.0-0"},"digest":{"Author":"Dirk Eddelbuettel
<edd@debian.org> with contributions \n by Antoine Lucas, Jarek Tuszynski, Henrik
Bengtsson, Simon Urbanek,\n Mario Frasca, Bryan Lewis, Murray Stokely, Hannes
Muehleisen,\n Duncan Murdoch, Jim Hester, Wush Wu and Thierry
Onkelinx.","Built":"3.2.4","Depends":"R (>= 2.4.1)","Description":"Implementation
of a function 'digest()' for the creation \n of hash digests of arbitrary R objects
(using the md5, sha-1, sha-256, \n crc32, xxhash and murmurhash algorithms)
permitting easy comparison of R\n language objects, as well as a function 'hmac()'
to create hash-based\n message authentication code.\n\n The md5 algorithm by Ron
Rivest is specified in RFC 1321, the sha-1 \n and sha-256 algorithms are specified
in FIPS-180-1 and FIPS-180-2, \n and the crc32 algorithm is described in \n
ftp:\/\/ftp.rocksoft.com\/cliens\/rocksoft\/papers\/crc_v3.txt.\n\n For md5, sha-
1, sha-256 and aes, this package uses small standalone\n implementations that were
provided by Christophe Devine. For crc32, code\n from the zlib library is used. For
sha-512, an implementation by Aaron\n D. Gifford is used. For xxhash, the
implementation by Yann Collet is used.\n For murmurhash, an implementation by Shane
Day is used.\n\n Please note that this package is not meant to be deployed for \n
cryptographic purposes for which more comprehensive (and widely \n tested)
libraries such as OpenSSL should be
used.","LibPath":"C:\/Users\/pminaev\/Documents\/R\/win-
2","NeedsCompilation":"yes","Package":"digest","Suggests":"knitr,
rmarkdown","Title":"Create Compact Hash Digests of R
Objects","Version":"0.6.9"},"dplyr":{"Author":"Hadley Wickham [aut, cre],\n Romain
Francois [aut],\n RStudio [cph]","Built":"3.2.3","Depends":"R (>=
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objects,\n both in memory and out of memory.","Imports":"assertthat, utils, R6,
Rcpp, magrittr, lazyeval (>= 0.1.10),\nDBI (>=
0.3)","LibPath":"C:\/Users\/pminaev\/Documents\/R\/win-library\/3.2","License":"MIT
+ file LICENSE","LinkingTo":"Rcpp (>= 0.12.0), BH (>= 1.58.0-
1)","NeedsCompilation":"yes","Package":"dplyr","Suggests":"RSQLite (>= 1.0.0),
RMySQL, RPostgreSQL, data.table,\ntestthat, knitr, microbenchmark, ggplot2, mgcv,
Lahman (>=\n3.0-1), nycflights13, methods","Title":"A Grammar of Data
Manipulation","Version":"0.4.3"},"evaluate":{"Author":"Hadley Wickham [aut],\n
Yihui Xie [cre, ctb],\n Michael Lawrence [ctb],\n Thomas Kluyver [ctb],\n Barret
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and evaluation tools that make it easy to recreate the\n command line behaviour
of R.","Imports":"methods, stringr (>=
LICENSE","NeedsCompilation":"no","Package":"evaluate","Suggests":"testthat,
lattice, ggplot2","Title":"Parsing and Evaluation Tools that Provide More Details
than the\nDefault","Version":"0.8.3"},"foreign":{"Author":"R Core Team [aut, cph,
cre],\n Roger Bivand [ctb, cph],\n Vincent J. Carey [ctb, cph],\n Saikat DebRoy
[ctb, cph],\n Stephen Eglen [ctb, cph],\n Rajarshi Guha [ctb, cph],\n Nicholas
Lewin-Koh [ctb, cph],\n Mark Myatt [ctb, cph],\n Ben Pfaff [ctb],\n Brian
Quistorff [ctb],\n Frank Warmerdam [ctb, cph],\n Stephen Weigand [ctb, cph],\n
Free Software Foundation, Inc. [cph]","Built":"3.2.3","Depends":"R (>=
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versions of\n\tEpi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka\n\tand for
reading and writing some dBase files.","Imports":"methods, utils,
stats","LibPath":"C:\/Program Files\/R\/R-3.2.3\/library","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"foreign","Priority":"recommended","Title":"
Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat,
Weka,\ndBase, ...","Version":"0.8-66"},"formatR":{"Author":"Yihui
Xie","Built":"3.2.4","Depends":"R (>= 3.0.2)","Description":"Provides a function
tidy_source() to format R source code. Spaces\n and indent will be added to the
code automatically, and comments will be\n preserved under certain conditions,
so that R code will be more\n human-readable and tidy. There is also a Shiny app
as a user interface in\n this package (see
tidy_app()).","LibPath":"C:\/Users\/pminaev\/Documents\/R\/win-
library\/3.2","License":"GPL","NeedsCompilation":"no","Package":"formatR","Suggests
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Automatically","Version":"1.3"},"ggplot2":{"Author":"Hadley Wickham [aut, cre],\n
Winston Chang [aut],\n RStudio [cph]","Built":"3.2.4","Depends":"R (>=
3.1)","Description":"An implementation of the grammar of graphics in R. It combines
the\n advantages of both base and lattice graphics: conditioning and shared
axes\n are handled automatically, and you can still build up a plot step by
step\n from multiple data sources. It also implements a sophisticated\n
multidimensional conditioning system and a consistent interface to map\n data to
aesthetic attributes. See http:\/\/ggplot2.org for more information,\n
documentation and examples.","Enhances":"sp","Imports":"digest, grid, gtable (>=
0.1.1), MASS, plyr (>= 1.7.1),\nreshape2, scales (>= 0.3.0),
stats","LibPath":"C:\/Users\/pminaev\/Documents\/R\/win-
2","NeedsCompilation":"no","Package":"ggplot2","Suggests":"covr, ggplot2movies,
hexbin, Hmisc, lattice, mapproj, maps,\nmaptools, mgcv, multcomp, nlme, testthat
(>= 0.11.0), quantreg,\nknitr, rpart, rmarkdown, svglite","Title":"An
Implementation of the Grammar of Graphics","Version":"2.1.0"},"git2r":
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implementation of the 'Git' core methods. Provides access to 'Git'\n
repositories to extract data and running some basic 'Git'\n
commands.","Imports":"graphics,
2","NeedsCompilation":"yes","Package":"git2r","Title":"Provides Access to Git
Repositories","Version":"0.14.0"},"glmnet":{"Author":"Jerome
Friedman, Trevor Hastie, Noah Simon, Rob
Tibshirani","Built":"3.2.3","Depends":"Matrix (>= 1.0-6), utils,
foreach","Description":"Extremely efficient procedures for fitting the entire lasso
or elastic-net regularization path for linear regression, logistic and multinomial
regression models, Poisson regression and the Cox model. Two recent additions are
the multiple-response Gaussian, and the grouped multinomial. The algorithm uses
cyclical coordinate descent in a path-wise fashion, as described in the paper
linked to via the URL below. ","LibPath":"C:\/Users\/pminaev\/Documents\/R\/win-
2","NeedsCompilation":"yes","Package":"glmnet","Suggests":"survival, knitr,
lars","Title":"Lasso and Elastic-Net Regularized Generalized Linear
Models","Version":"2.0-2"},"grDevices":{"Author":"R Core Team and contributors
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grid graphics.","LibPath":"C:\/Program Files\/R\/R-3.2.3\/library","License":"Part
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3.2.3","Package":"grDevices","Priority":"base","Suggests":"KernSmooth","Title":"The
R Graphics Devices and Support for Colours and
Fonts","Version":"3.2.3"},"graphics":{"Author":"R Core Team and contributors
worldwide","Built":"3.2.3","Description":"R functions for base
graphics.","Imports":"grDevices","LibPath":"C:\/Program Files\/R\/R-
3.2.3\/library","License":"Part of R
3.2.3","Package":"graphics","Priority":"base","Title":"The R Graphics
Package","Version":"3.2.3"},"grid":{"Author":"Paul Murrell
<paul@stat.auckland.ac.nz>","Built":"3.2.3","Description":"A rewrite of the
graphics layout capabilities, plus some\n support for
interaction.","Imports":"grDevices","LibPath":"C:\/Program Files\/R\/R-
3.2.3","Package":"grid","Priority":"base","Suggests":"lattice","Title":"The Grid
Graphics Package","Version":"3.2.3"},"gridExtra":{"Author":"Baptiste Auguie [aut,
cre],\n Anton Antonov [ctb]","Built":"3.2.4","Description":"Provides a number of
user-level functions to work with \"grid\" graphics, notably to arrange multiple
grid-based plots on a page, and draw tables.","Imports":"gtable, grid, grDevices,
graphics, utils","LibPath":"C:\/Users\/pminaev\/Documents\/R\/win-
2)","NeedsCompilation":"no","Package":"gridExtra","Suggests":"ggplot2, lattice,
knitr, testthat","Title":"Miscellaneous Functions for \"Grid\"
Graphics","Version":"2.2.1"},"gtable":{"Author":"Hadley Wickham
<h.wickham@gmail.com>","Built":"3.2.3","Depends":"R (>= 2.14),
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grobs.","LibPath":"C:\/Users\/pminaev\/Documents\/R\/win-
library\/3.2","License":"GPL-2","Package":"gtable","Suggests":"testthat,
plyr","Title":"Arrange grobs in tables.","Version":"0.1.2"},"highr":
{"Author":"Christopher Gandrud [ctb],\n Qiang Li [ctb],\n Yixuan Qiu [aut],\n
Yihui Xie [aut, cre]","Built":"3.2.4","Depends":"R (>=
3.0.2)","Description":"Provides syntax highlighting for R source code. Currently
it\n supports LaTeX and HTML output. Source code of other languages is
supported\n via Andre Simon's highlight package (http:\/\/www.andre-
simon.de).","LibPath":"C:\/Users\/pminaev\/Documents\/R\/win-
library\/3.2","License":"GPL","NeedsCompilation":"no","Package":"highr","Suggests":
"knitr, testit","Title":"Syntax Highlighting for R Source
Code","Version":"0.5.1"},"htmltools":{"Author":"RStudio,
Inc.","Built":"3.2.3","Depends":"R (>= 2.14.1)","Description":"Tools for HTML
generation and output.","Enhances":"knitr","Imports":"utils,
digest","LibPath":"C:\/Users\/pminaev\/Documents\/R\/win-
2)","NeedsCompilation":"no","Package":"htmltools","Suggests":"markdown,
testthat","Title":"Tools for HTML","Version":"0.3"},"htmlwidgets":
{"Author":"Ramnath Vaidyanathan [aut, cph],\n Yihui Xie [aut],\n JJ Allaire [aut,
cre],\n Joe Cheng [aut],\n Kenton Russell [aut, cph],\n RStudio
[cph]","Built":"3.2.3","Description":"A framework for creating HTML widgets that
render in various\n contexts including the R console, 'R Markdown' documents,
and 'Shiny'\n web applications.","Enhances":"shiny (>=
0.12)","Imports":"htmltools (>= 0.2.6), jsonlite (>= 0.9.16),
yaml","LibPath":"C:\/Users\/pminaev\/Documents\/R\/win-library\/3.2","License":"MIT
+ file LICENSE","NeedsCompilation":"no","Package":"htmlwidgets","Suggests":"knitr
(>= 1.8)","Title":"HTML Widgets for R","Version":"0.5"},"httpuv":
{"Author":"RStudio, Inc.","Built":"3.2.3","Depends":"R (>= 2.15.1),
methods","Description":"Provides low-level socket and protocol support for
handling\n HTTP and WebSocket requests directly from within R. It is primarily\n
intended as a building block for other packages, rather than making it\n
particularly easy to create complete web applications using httpuv alone.\n
httpuv is built on top of the libuv and http-parser C libraries, both of\n which
were developed by Joyent, Inc. (See LICENSE file for libuv and\n http-parser
license information.)","Imports":"Rcpp (>= 0.11.0),
library\/3.2","License":"GPL-3 | file
LICENSE","LinkingTo":"Rcpp","NeedsCompilation":"yes","Package":"httpuv","Title":"HT
TP and WebSocket Server Library","Version":"1.3.3"},"httr":{"Author":"Hadley
Wickham [aut, cre],\n RStudio [cph]","Built":"3.2.4","Depends":"R (>=
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(GET(), POST(), etc). Configuration functions make it easy to control\n
additional request components (authenticate(), add_headers() and so
on).","Imports":"jsonlite, mime, curl (>= 0.9.1), openssl (>= 0.8),
R6","LibPath":"C:\/Users\/pminaev\/Documents\/R\/win-library\/3.2","License":"MIT +
file LICENSE","NeedsCompilation":"no","Package":"httr","Suggests":"httpuv, jpeg,
knitr, png, testthat (>= 0.8.0), readr, xml2","Title":"Tools for Working with URLs
and HTTP","Version":"1.1.0"},"inline":{"Author":"Oleg Sklyar, Duncan Murdoch, Mike
Smith, Dirk Eddelbuettel, \n Romain Francois, Karline
Soetaert","Built":"3.2.4","Depends":"R (>= 2.4.0),
methods","Description":"Functionality to dynamically define R functions and S4
methods\n with inlined C, C++ or Fortran code supporting .C and .Call calling
conventions.","LibPath":"C:\/Users\/pminaev\/Documents\/R\/win-
library\/3.2","License":"LGPL","NeedsCompilation":"no","Package":"inline","Suggests
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from R","Version":"0.3.14"},"jsonlite":{"Author":"Jeroen Ooms, Duncan Temple Lang,
Lloyd Hilaiel","Built":"3.2.3","Depends":"methods","Description":"A fast JSON
parser and generator optimized for statistical data\n and the web. Started out
as a fork of 'RJSONIO', but has been completely\n rewritten in recent versions.
The package offers flexible, robust, high\n performance tools for working with
JSON in R and is particularly powerful\n for building pipelines and interacting
with a web API. The implementation is\n based on the mapping described in the
vignette (Ooms, 2014). In addition to\n converting JSON data from\/to R objects,
'jsonlite' contains functions to\n stream, validate, and prettify JSON data. The
unit tests included with the\n package verify that all edge cases are encoded
and decoded consistently for\n use with dynamic data in systems and
applications.","LibPath":"C:\/Users\/pminaev\/Documents\/R\/win-
LICENSE","NeedsCompilation":"yes","Package":"jsonlite","Suggests":"curl (>= 0.5),
plyr, testthat, knitr, rmarkdown, R.rsp","Title":"A Robust, High Performance JSON
Parser and Generator for R","Version":"0.9.19"},"knitr":{"Author":"Yihui Xie [aut,
cre],\n Adam Vogt [ctb],\n Alastair Andrew [ctb],\n Alex Zvoleff [ctb],\n Andre
Simon [ctb] (the CSS files under inst\/themes\/ were derived from\n the
Highlight package http:\/\/www.andre-simon.de),\n Aron Atkins [ctb],\n Aaron
Wolen [ctb],\n Ashley Manton [ctb],\n Ben Baumer [ctb],\n Brian Diggs [ctb],\n
Cassio Pereira [ctb],\n David Robinson [ctb],\n Donald Arseneau [ctb, cph] (the
framed package at inst\/misc\/framed.sty),\n Doug Hemken [ctb],\n Duncan Murdoch
[ctb],\n Fabian Hirschmann [ctb],\n Fitch Simeon [ctb],\n Frank E Harrell Jr
[ctb] (the Sweavel package at inst\/misc\/Sweavel.sty),\n Gregoire Detrez [ctb],\n
Hadley Wickham [ctb],\n Heewon Jeon [ctb],\n Henrik Bengtsson [ctb],\n Hiroaki
Yutani [ctb],\n Jake Burkhead [ctb],\n James Manton [ctb],\n Jared Lander
[ctb],\n Jason Punyon [ctb],\n Jeff Arnold [ctb],\n Jeremy Ashkenas [ctb, cph]
(the CSS file at\n inst\/misc\/docco-classic.css),\n Jeremy Stephens [ctb],\n
Jim Hester [ctb],\n Joe Cheng [ctb],\n Johannes Ranke [ctb],\n John Honaker
[ctb],\n John Muschelli [ctb],\n Jonathan Keane [ctb],\n JJ Allaire [ctb],\n
Johan Toloe [ctb],\n Joseph Larmarange [ctb],\n Julien Barnier [ctb],\n Kaiyin
Zhong [ctb],\n Kevin K. Smith [ctb],\n Kirill Mueller [ctb],\n Kohske Takahashi
[ctb],\n Michael Friendly [ctb],\n Michal Bojanowski [ctb],\n Michel Kuhlmann
[ctb],\n Nacho Caballero [ctb],\n Nick Salkowski [ctb],\n Noam Ross [ctb],\n
Qiang Li [ctb],\n Ramnath Vaidyanathan [ctb],\n Richard Cotton [ctb],\n Robert
Krzyzanowski [ctb],\n Romain Francois [ctb],\n Scott Kostyshak [ctb],\n
Sebastian Meyer [ctb],\n Sietse Brouwer [ctb],\n Simon de Bernard [ctb],\n
Taiyun Wei [ctb],\n Thibaut Assus [ctb],\n Thibaut Lamadon [ctb],\n Thomas
Leeper [ctb],\n Tom Torsney-Weir [ctb],\n Trevor Davis [ctb],\n Viktoras Veitas
[ctb],\n Weicheng Zhu [ctb],\n Wush Wu [ctb],\n Zachary Foster
[ctb]","Built":"3.2.4","Depends":"R (>= 3.0.2)","Description":"Provides a general-
purpose tool for dynamic report generation in R\n using Literate Programming
techniques.","Imports":"evaluate (>= 0.8), digest, formatR, highr, markdown,
stringr\n(>= 0.6), yaml (>= 2.1.5), methods,
tools","LibPath":"C:\/Users\/pminaev\/Documents\/R\/win-
library\/3.2","License":"GPL","NeedsCompilation":"no","Package":"knitr","Suggests":
"testit, rgl (>= 0.95.1201), codetools, rmarkdown, tikzDevice\n(>= 0.9), XML,
RCurl","Title":"A General-Purpose Package for Dynamic Report Generation in
R","Version":"1.12.3"},"labeling":{"Author":"Justin
Talbot","Built":"3.2.3","Description":"Provides a range of axis labeling
algorithms","LibPath":"C:\/Users\/pminaev\/Documents\/R\/win-
library\/3.2","License":"MIT + file LICENSE |
Unlimited","NeedsCompilation":"no","Package":"labeling","Title":"Axis
Labeling","Version":"0.3"},"lattice":{"Author":"Deepayan Sarkar <deepayan.sarkar@r-
project.org>","Built":"3.2.3","Depends":"R (>= 3.0.0)","Description":"A powerful
and elegant high-level data visualization\n system inspired by Trellis graphics,
with an emphasis on\n multivariate data. Lattice is sufficient for typical
graphics needs,\n and is also flexible enough to handle most nonstandard
requirements.\n See ?Lattice for an
introduction.","Enhances":"chron","Imports":"grid, grDevices, graphics, stats,
utils","LibPath":"C:\/Program Files\/R\/R-3.2.3\/library","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"lattice","Priority":"recommended","Suggests
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33"},"lazyeval":{"Author":"Hadley Wickham [aut, cre],\n RStudio
[cph]","Built":"3.2.3","Depends":"R (>= 3.1.0)","Description":"A disciplined
approach to non-standard
evaluation.","LibPath":"C:\/Users\/pminaev\/Documents\/R\/win-
3","NeedsCompilation":"yes","Package":"lazyeval","Suggests":"knitr, rmarkdown (>=
0.2.65), microbenchmark, testthat","Title":"Lazy (Non-Standard)
Evaluation","Version":"0.1.10"},"leaflet":{"Author":"Joe Cheng [aut, cre],\n Yihui
Xie [aut],\n Hadley Wickham [ctb],\n jQuery Foundation and contributors [ctb,
cph] (jQuery library),\n Vladimir Agafonkin [ctb, cph] (Leaflet library),\n
CloudMade [cph] (Leaflet library),\n Leaflet contributors [ctb] (Leaflet
library),\n Leaflet Providers contributors [ctb, cph] (Leaflet Providers
plugin),\n RStudio [cph]","Built":"3.2.3","Description":"Create and customize
interactive maps using the 'Leaflet' JavaScript\n library and the 'htmlwidgets'
package. These maps can be used directly from\n the R console, from 'RStudio',
in Shiny apps and R Markdown documents.","Imports":"base64enc, htmlwidgets,
htmltools, magrittr, markdown, png,\nRColorBrewer, raster, scales (>= 0.2.5),
sp","LibPath":"C:\/Users\/pminaev\/Documents\/R\/win-library\/3.2","License":"GPL-3
| file LICENSE","NeedsCompilation":"no","Package":"leaflet","Suggests":"knitr,
maps, shiny, testit (>= 0.4), rgdal, R6, RJSONIO","Title":"Create Interactive Web
Maps with the JavaScript 'Leaflet'\nLibrary","Version":"1.0.0"},"lme4":
{"Author":"Douglas Bates [aut], Martin Maechler [aut],\n\tBen Bolker [aut, cre],
Steven Walker [aut],\n Rune Haubo Bojesen Christensen [ctb],\n\tHenrik
Singmann [ctb], Bin Dai [ctb],\n Gabor Grothendieck
[ctb]","Built":"3.2.3","Depends":"R (>= 3.0.2), Matrix (>= 1.1.1), methods,
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The models and their components are represented using S4 classes and\n methods.
The core computational algorithms are implemented using the\n 'Eigen' C++
library for numerical linear algebra and
'RcppEigen' \"glue\".","Imports":"graphics, grid, splines, utils, parallel, MASS,
nlme, lattice,\nminqa (>= 1.1.15), nloptr (>=
library\/3.2","License":"GPL (>= 2)","LinkingTo":"Rcpp (>= 0.10.5),
RcppEigen","NeedsCompilation":"yes","Package":"lme4","Suggests":"knitr, boot,
PKPDmodels, MEMSS, testthat (>= 0.8.1), ggplot2,\nmlmRev, optimx (>= 2013.8.6),
gamm4, pbkrtest, HSAUR2, numDeriv","Title":"Linear Mixed-Effects Models using
'Eigen' and S4","Version":"1.1-10"},"lmtest":{"Author":"Torsten Hothorn [aut],\n
Achim Zeileis [aut, cre],\n Richard W. Farebrother [aut] (pan.f),\n Clint Cummins
[aut] (pan.f),\n Giovanni Millo [ctb],\n David Mitchell
[ctb]","Built":"3.2.3","Depends":"R (>= 2.10.0), stats, zoo","Description":"A
collection of tests, data sets, and examples\n for diagnostic checking in linear
regression models. Furthermore,\n some generic tools for inference in parametric
models are
provided.","Imports":"graphics","LibPath":"C:\/Users\/pminaev\/Documents\/R\/win-
3","NeedsCompilation":"yes","Package":"lmtest","Suggests":"car, strucchange,
sandwich, dynlm, stats4, survival, AER","Title":"Testing Linear Regression
Models","Version":"0.9-34"},"magrittr":{"Author":"Stefan Milton Bache
<stefan@stefanbache.dk> and\n Hadley Wickham
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chaining commands with a\n new forward-pipe operator, %>%. This operator will
forward a\n value, or the result of an expression, into the next function\n
call\/expression. There is flexible support for the type\n of right-hand side
expressions. For more information, see\n package vignette.\n To quote Rene
Magritte, \"Ceci n'est pas un
pipe.\"","LibPath":"C:\/Users\/pminaev\/Documents\/R\/win-
LICENSE","NeedsCompilation":"no","Package":"magrittr","Suggests":"testthat,
knitr","Title":"A Forward-Pipe Operator for R","Version":"1.5"},"markdown":
{"Author":"JJ Allaire, Jeffrey Horner, Vicent Marti, and Natacha
Porte","Built":"3.2.1","Depends":"R (>= 2.11.1)","Description":"Provides R bindings
to the 'Sundown' 'Markdown' rendering library\n
(https:\/\/github.com\/vmg\/sundown). 'Markdown' is a plain-text formatting\n
syntax that can be converted to 'XHTML' or other formats. See\n
http:\/\/en.wikipedia.org\/wiki\/Markdown for more information about
'Markdown'.","Imports":"mime (>=
0.3)","LibPath":"C:\/Users\/pminaev\/Documents\/R\/win-
2","NeedsCompilation":"yes","Package":"markdown","Suggests":"knitr,
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{"Author":"Hadley Wickham [aut],\n Jim Hester [aut, cre],\n Kirill Müller
[aut]","Built":"3.2.4","Description":"Cache the results of a function so that when
you call it\n again with the same arguments it returns the pre-computed
value.","Imports":"digest (>=
LICENSE","NeedsCompilation":"no","Package":"memoise","Suggests":"testthat","Title":
"Memoisation of Functions","Version":"1.0.0"},"methods":{"Author":"R Core
Team","Built":"3.2.3","Description":"Formally defined methods and classes for R
objects,\n plus other programming tools, as described in the
reference.","Imports":"utils","LibPath":"C:\/Program Files\/R\/R-
3.2.3","Package":"methods","Priority":"base","Suggests":"codetools","Title":"Formal
Methods and Classes","Version":"3.2.3"},"mgcv":{"Author":"Simon Wood <simon.wood@r-
project.org>","Built":"3.2.3","Depends":"R (>= 2.14.0), nlme (>= 3.1-
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multiple smoothing parameter estimation by GCV, REML or UBRE\/AIC. \n
Includes a gam() function, a wide variety of smoothers, JAGS \n support
and distributions beyond the exponential family.","Imports":"methods, stats,
graphics, Matrix","LibPath":"C:\/Users\/pminaev\/Documents\/R\/win-
2)","NeedsCompilation":"yes","Package":"mgcv","Priority":"recommended","Suggests":"
splines, parallel, survival, MASS","Title":"Mixed GAM Computation Vehicle with
GCV\/AIC\/REML Smoothness\nEstimation","Version":"1.8-11"},"mime":
{"Author":"Jeffrey Horner [ctb],\n Yihui Xie [aut,
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techniques, data sets, summary and inference\n procedures aimed particularly
at categorical data. Special\n emphasis is given to highly extensible grid
graphics. The\n package was package was originally inspired by the book
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support package for a new book, \n\t\"Discrete Data Analysis with R\" by Michael
Friendly and \n\tDavid Meyer (2015).","Imports":"stats, utils, MASS, grDevices,
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dependencies\n to provide access to these functions.","Imports":"stats,
graphics","LibPath":"C:\/Users\/pminaev\/Documents\/R\/win-
2)","NeedsCompilation":"no","Package":"withr","Suggests":"testthat","Title":"Run
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allowing for user level customization and extension, while simplifying cross-class
interoperability.","LibPath":"C:\/Users\/pminaev\/Documents\/R\/win-
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R.","LibPath":"C:\/Users\/pminaev\/Documents\/R\/win-
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observations. It is particularly aimed at irregular time series\n of
numeric vectors\/matrices and factors. zoo's key design goals\n are
independence of a particular index\/date\/time class and\n consistency
with ts and base R by providing methods to extend\n standard
generics.","Imports":"utils, graphics, grDevices, lattice (>= 0.20-
27)","LibPath":"C:\/Users\/pminaev\/Documents\/R\/win-library\/3.2","License":"GPL-
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fts, its, ggplot2, mondate, scales,\nstrucchange, timeDate, timeSeries, tis,
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Roe","Depends":"R (>= 2.15.0), xtable, pbapply","Description":"Supplies tools for
tabulating and analyzing the results of predictive models. The methods employed are
applicable to virtually any predictive model and make comparisons between different
methodologies straightforward.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"A3","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"randomForest, e1071","Title":"Accurate, Adaptable, and
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{"Author":"Michael Thrun, Jorn Lotsch, Alfred Ultsch","Depends":"R (>=
2.10)","Description":"For a given data set, the package provides a novel method of
computing precise limits to acquire subsets which are easily interpreted. Closely
related to the Lorenz curve, the ABC curve visualizes the data by graphically
representing the cumulative distribution function. Based on an ABC analysis the
algorithm calculates, with the help of the ABC curve, the optimal limits by
exploiting the mathematical properties pertaining to distribution of analyzed
items. The data containing positive values is divided into three disjoint subsets
A, B and C, with subset A comprising very profitable values, i.e. largest data
values (\"the important few\"), subset B comprising values where the yield equals
to the effort required to obtain it, and the subset C comprising of non-profitable
values, i.e., the smallest data sets (\"the trivial many\"). Package is based on
Ultsch. A ., Lotsch J.: Computed ABC Analysis for rational Selection of most
informative Variables in multivariate Data, PLoS One, 2015.","Imports":"Hmisc,
plotrix","License":"GPL-
3","NeedsCompilation":"no","Package":"ABCanalysis","Repository":"http:\/\/cran.csir
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Artificial Bee Colony Optimization algorithm. This (working) version is a Work-in-
progress, which is why it has been implemented using pure R code. This was
developed upon the basic version programmed in C and distributed at the algorithm's
official website.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"ABCoptim","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Implementation of Artificial Bee Colony (ABC)
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estimates the proportional paternity of the second male (P2) based on the best fit
distribution.","License":"GPL-
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3","NeedsCompilation":"no","Package":"ABHgenotypeR","Repository":"http:\/\/cran.csi
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breakpoints in series.","Imports":"graphics, grDevices, stats,
utils","License":"GPL","NeedsCompilation":"no","Package":"ACA","Repository":"http:\
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indicates by TRUE\/FALSE (false by\ndefault) if the source CSV file has a head row
or not. The data\nset should contain only one independent variable (X) and
one\ndependent varialbe (Y) and can contain a weight for
each\nobservation","License":"GPL-
2","NeedsCompilation":"no","Package":"ACCLMA","Repository":"http:\/\/cran.csiro.au\
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responses","License":"GPL (>=
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tests them.","Imports":"plyr, dplyr, ggplot2, Rsolnp, zoo, graphics","License":"GPL
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of the variance components in the classical twin models with respect to age using
B-splines and P-splines.","Imports":"Rcpp (>= 0.11.1), splines,
MASS","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ACEt","Repository":"http:\/\/cran.csiro.au\
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maps from the Atlas of Cancer Signalling Networks (ACSN) or user imported
maps.\nUser imported maps must be complying with the GMT format as defined by the
Broad Institute, that is to say that the file should be tab-separated, that the
first column should contain the module name, the second column can contain comments
that will be overwritten with the number of genes in the module, and subsequent
columns must contain the list of genes (HUGO symbols; tab-separated) inside the
module.\nThe gene set enrichment can be run with hypergeometric test or Fisher
exact test, and can use multiple corrections.\nVisualization of data can be done
either by barplots or heatmaps.","License":"GPL-
2","NeedsCompilation":"no","Package":"ACSNMineR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr, rmarkdown,","Title":"Gene Enrichment Analysis
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2","NeedsCompilation":"no","Package":"ACSWR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"A Companion Package for the Book \"A Course in Statistics
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Jersey)","Depends":"R (>= 2.15.1), R.methodsS3","Description":"This package
includes functions used to perform cluster analysis for cognitive\ndiagnosis based
on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009). Given
the\nsample statistic of sum-scores and the item-by-attribute association matrix
(Q-matrix; Tatsuoka, 1985),\ncluster analysis techniques can be used to classify
examinees into latent\nclasses based on their attribute patterns. In addition to
the algorithms used to classify data, three\nlabeling approaches are proposed to
label clusters so that examinees' attribute profiles can be
obtained.","License":"GPL (>=
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\/src\/contrib","Title":"Asymptotic Classification Theory for Cognitive
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materials. Based on the collected data, a thermal index
(TI) is estimated. The TI can be useful for material rating and comparison. This
package performs the least squares (LS) and maximum likelihood (ML) procedures for
estimating TI for polymeric materials. The LS approach is a two-step approach that
is currently used in industrial standards, while the ML procedure is widely used in
the statistical literature. The ML approach allows one to do statistical inference
such as quantifying uncertainties in estimation, hypothesis testing, and
predictions. Two publicly available datasets are provided to allow users to
experiment and practice with the functions.","License":"GPL-
2","NeedsCompilation":"no","Package":"ADDT","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"A Package for Analysis of Accelerated Destructive
Degradation\nTest Data","Version":"1.0"},"ADGofTest":{"Author":"Carlos J. Gil
Bellosta","Description":"Anderson-Darling GoF test with p-value calculation based
on Marsaglia's 2004 paper \"Evaluating the Anderson-Darling
Distribution\"","License":"GPL","NeedsCompilation":"no","Package":"ADGofTest","Repo
sitory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Anderson-Darling GoF
test","Version":"0.3"},"ADM3":{"Author":"Tomas William
Fitzgerald","Description":"Robust change point detection using ADM3
algorithm.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ADM3","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"An Interpretation of the ADM method - automated
detection\nalgorithm","Version":"1.3"},"ADMMnet":{"Author":"Xiang Li, Shanghong
Xie, Donglin Zeng and Yuanjia Wang","Depends":"Matrix (>= 1.2-
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forms, such as adaptive lasso and net adjusting for signs of linked coefficients.
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parameter and simultaneously selects with the regularization parameter. The package
uses one-step coordinate descent algorithm and runs extremely fast by taking into
account the sparsity structure of coefficients.","Imports":"Rcpp (>=
0.12.2)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ADMMnet","Repository":"http:\/\/cran.csiro.
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Zeros","Version":"0.1"},"ADPclust":{"Author":"Yifan \"Ethan\" Xu [aut, cre],\nXiao-
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automatic centroids selection and\nparameter optimization algorithm, which finds
the number of clusters and cluster\ncentroids by comparing average silhouettes on a
grid of testing clustering\nresults; It also includes an user interactive algorithm
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dimensional \"density-distance\nplot\".","Imports":"dplyr, cluster, fields,
knitr","License":"GPL (>=
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signal","License":"GPL-
3","NeedsCompilation":"no","Package":"AEDForecasting","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"R.rsp","Title":"Change Point Analysis in ARIMA
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vignette for a package overview.)","Imports":"stats, Formula (>= 0.2-
0)","License":"GPL-2 | GPL-
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c\/contrib","Suggests":"boot, dynlm, effects, foreign, ineq, KernSmooth,
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ROCR,\nsampleSelection, scatterplot3d, strucchange, systemfit, rgl,\ntruncreg,
tseries, urca","Title":"Applied Econometrics with R","Version":"1.2-4"},"AF":
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graphics, survival, drgee, R (>= 3.0.0),\ndata.table","Description":"Estimates the
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confounders using logistic regression (cross-sectional and case-control designs),
conditional logistic regression (matched case-control design) and Cox proportional
hazard regression (cohort design with time-to-event outcome). The variance of the
estimator is obtained by combining the delta method with the the sandwich
formula.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"AF","Repository":"http:\/\/cran.csiro.au\/src
\/contrib","Title":"Model-Based Estimation of Confounder-Adjusted
Attributable\nFractions","Version":"0.1.2"},"AFLPsim":{"Author":"Francisco Balao
[aut, cre],\nJuan Luis García-Castaño [aut]","Depends":"R (>=
2.15.0)","Description":"Hybrid simulation functions for dominant genetic data and
genome scan methods.","Imports":"adegenet, introgress","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"AFLPsim","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"R.rsp","Title":"Hybrid Simulation and Genome Scan for
Dominant Markers","URL":"http:\/\/www.r-
project.org,\nhttp:\/\/personal.us.es\/fbalao\/software.html","Version":"0.4-
2"},"AFM":{"Author":"Mathieu Beauvais [aut, cre],\nIrma Liascukiene [aut],\nJessem
Landoulsi [aut]","Depends":"R (>= 3.1.3)","Description":"Provides Atomic Force
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lengthscale, variogram and variance,\nfractal dimension and scale. The AFM images
can be exported to STL format for 3D\nprinting.","Imports":"data.table(>=
1.9.6),stringr(>= 1.0.0),gstat(>=\n1.0-26),fractaldim(>= 0.8-4),rgl(>=
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c\/contrib","Title":"Atomic Force Microscope Image
Analysis","Version":"1.2.0"},"AGD":{"Author":"Stef van Buuren
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Rotterdam.","Imports":"gamlss, gamlss.dist","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"AGD","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Analysis of Growth
Data","URL":"http:\/\/www.stefvanbuuren.nl,\nhttp:\/\/nihes.nl\/courses\/analysis-
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Brannath, Matthias Brueckner","Description":"Calculation of repeated confidence
intervals as well as confidence\nintervals based on the stage-wise ordering in
group sequential designs and\nadaptive group sequential designs. For adaptive group
sequential designs\nthe confidence intervals are based on the conditional rejection
probability\nprinciple. Currently the procedures do not support the use of
futility\nboundaries or more than one adaptive interim analysis.","Imports":"stats,
graphics, grDevices, ldbounds","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"AGSDest","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Estimation in Adaptive Group Sequential
Trials","Version":"2.3"},"AHR":{"Author":"Matthias Brueckner <mwb@math.uni-
bremen.de>","Depends":"survival","Description":"Methods for estimation of
multivariate average hazard ratios as\ndefined by Kalbfleisch and Prentice. The
underlying survival functions of the\nevent of interest in each group can be
estimated using either the (weighted)\nKaplan-Meier estimator or the Aalen-Johansen
estimator for the transition\nprobabilities in Markov multi-state models. Right-
censored and left-truncated\ndata is supported. Moreover, the difference in
restricted mean survival can be\nestimated.","Imports":"stats, MASS, etm,
Rcpp","License":"GPL (>=
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src\/contrib","Suggests":"testthat","Title":"Estimation and Testing of Average
Hazard Ratios","Version":"1.4"},"AICcmodavg":{"Author":"Marc J. Mazerolle
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to implement model selection and multimodel inference based on Akaike's information
criterion (AIC) and the second-order AIC (AICc), as well as their quasi-likelihood
counterparts (QAIC, QAICc) from various model object classes. The package
implements classic model averaging for a given parameter of interest or predicted
values, as well as a shrinkage version of model averaging parameter estimates or
effect sizes. The package includes diagnostics and goodness-of-fit statistics for
certain model types including those of 'unmarkedFit' classes estimating demographic
parameters after accounting for imperfect detection probabilities. Some functions
also allow the creation of model selection tables for Bayesian
models of the 'bugs' and 'rjags' classes. Objects following model selection and
multimodel inference can be formatted to LaTeX using 'xtable' methods included in
the package.","Imports":"methods, stats, graphics, lattice, MASS, Matrix, nlme,
stats4,\nsurvival, unmarked, VGAM, xtable","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"AICcmodavg","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"betareg, coxme, fitdistrplus, lavaan, lme4,
maxlike, nnet,\nordinal, pscl, R2jags, R2OpenBUGS, R2WinBUGS","Title":"Model
Selection and Multimodel Inference Based on (Q)AIC(c)","Version":"2.0-4"},"AID":
{"Author":"Osman Dag, Ozgur Asar, Ozlem Ilk","Depends":"R (>=
3.1.1)","Description":"Power transformation parameter is estimated for different
purposes.","Imports":"MASS, tseries, nortest","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"AID","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Estimation of Box-Cox Power Transformation
Parameter","Version":"1.5"},"AIM":{"Author":"L. Tian and R.
Tibshirani","Depends":"survival","Description":"R functions for adaptively
constructing index models for\ncontinuous, binary and survival outcomes.
Implementation\nrequires loading R-
pacakge \"survival\"","Imports":"survival","License":"LGPL-
2","NeedsCompilation":"no","Package":"AIM","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"AIM: adaptive index model","Version":"1.01"},"ALDqr":
{"Author":"Luis Benites Sanchez <lsanchez@ime.usp.br>,\nVictor Lachos
<hlachos@ime.unicamp.br>","Depends":"R (>= 2.15.0)","Description":"EM algorithm for
estimation of parameters and other methods in a quantile
regression.","Imports":"HyperbolicDist","License":"GPL (>=
3.0)","NeedsCompilation":"no","Package":"ALDqr","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Quantile Regression Using Asymmetric Laplace
Distribution","Version":"0.5"},"ALKr":{"Author":"Jose Francisco Loff, Alberto
Murta, Laurence Kell","Depends":"R (>= 2.15.2)","Description":"A collection of
functions that implement several algorithms for\ngenerating age-length keys for
fish populations from incomplete data.","Imports":"MASS, methods, Rcpp (>=
0.10.2)","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"yes","Package":"ALKr","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Generate Age-Length Keys for fish
populations","URL":"http:\/\/www.github.com\/ALKr","Version":"0.5.3.1"},"ALS":
{"Author":"Katharine M. Mullen","Depends":"nnls (>= 1.1), Iso, R (>=
2.10)","Description":"Alternating least squares is often used to
resolve\ncomponents contributing to data with a bilinear structure; the\nbasic
technique may be extended to alternating constrained\nleast squares. Commonly
applied constraints include\nunimodality, non-negativity, and normalization of
components.\nSeveral data matrices may be decomposed simultaneously by\nassuming
that one of the two matrices in the bilinear\ndecomposition is shared between
datasets.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ALS","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Multivariate Curve Resolution Alternating Least
Squares\n(MCR-ALS)","Version":"0.0.6"},"ALSCPC":{"Author":"Dariush
Najarzadeh","Description":"Using of the accelerated line search algorithm for
simultaneously diagonalize a set of symmetric positive definite
matrices.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ALSCPC","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Accelerated line search algorithm for simultaneous
orthogonal\ntransformation of several positive definite symmetric matrices\nto
nearly diagonal form","Version":"1.0"},"ALTopt":{"Author":"Kangwon Seo [aut,
cre],\nRong Pan [aut]","Depends":"R (>= 3.0.0)","Description":"Creates the optimal
(D, U and I) designs for the accelerated life\ntesting with right censoring or
interval censoring. It uses generalized\nlinear model (GLM) approach to derive the
asymptotic variance-covariance\nmatrix of regression coefficients. The failure time
distribution is assumed\nto follow Weibull distribution with a known shape
parameter and log-linear\nlink functions are used to model the relationship between
failure time\nparameters and stress variables. The acceleration model may have
multiple\nstress factors, although most ALTs involve only two or less stress
factors.\nALTopt package also provides several plotting functions including contour
plot,\nFraction of Use Space (FUS) plot and Variance Dispersion graphs of Use
Space\n(VDUS) plot.","Imports":"cubature (>= 1.0), lattice (>=
0.20)","License":"GPL-
3","NeedsCompilation":"no","Package":"ALTopt","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Optimal Experimental Designs for Accelerated Life
Testing","Version":"0.1.1"},"AMAP.Seq":{"Author":"Yaqing Si","Description":"An
Approximated Most Average Powerful Test with Optimal\nFDR Control with Application
to RNA-seq Data","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"AMAP.Seq","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Compare Gene Expressions from 2-Treatment RNA-Seq
Experiments","Version":"1.0"},"AMCP":{"Author":"Scott Maxwell [aut],\nHarold
Delaney [aut],\nKen Kelley [aut, cre]","Description":"Accompanies \"Designing
experiments and analyzing data: A model comparison perspective\"\" (3rd ed.)
Maxwell, Delaney, & Kelley (forthcoming). This package contains all of the data
sets in the book. Information about the book is available here
<http:\/\/www.DesigningExperiments.com>.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"AMCP","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"A Multiple Comparison
Perspective","Version":"0.0.2"},"AMGET":{"Author":"Benjamin
Guiastrennec","Description":"AMGET allows to simply and rapidly creates highly
informative diagnostic plots for ADAPT 5 models. Features include data analysis
prior any modeling form either NONMEM or ADAPT shaped dataset, goodness-of-fit
plots (GOF), posthoc-fits plots (PHF), parameters distribution plots (PRM) and
visual predictive check plots (VPC) based on ADAPT output.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"AMGET","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Post-processing tool for ADAPT
5","Version":"1.0"},"AMOEBA":{"Author":"Guillermo Valles","Depends":"snowfall,
rlecuyer, spdep","Description":"A function to calculate spatial clusters using the
Getis-Ord local statistic. It searches\nirregular clusters (ecotopes) on a
map.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"AMOEBA","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"maptools, plotrix,","Title":"A Multidirectional Optimum
Ecotope-Based Algorithm","Version":"1.1"},"AMORE":{"Author":"Manuel Castejon Limas,
Joaquin B. Ordieres Mere, Ana Gonzalez\nMarcos, Francisco Javier Martinez de Pison
Ascacibar, Alpha V.\nPernia Espinoza, Fernando Alba Elias, Jose Maria Perez
Ramos","Description":"This package was born to release the TAO robust
neural\nnetwork algorithm to the R users. It has grown and I think it\ncan be of
interest for the users wanting to implement their own\ntraining algorithms as well
as for those others whose needs lye\nonly in the \"user space\".","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"AMORE","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"A MORE flexible neural network
package","URL":"http:\/\/rwiki.sciviews.org\/doku.php?
id=packages:cran:amore","Version":"0.2-15"},"ANOM":{"Author":"Philip
Pallmann","Depends":"R (>= 3.0.0)","Description":"Analysis of means (ANOM) as used
in technometrical computing. The package takes results from multiple comparisons
with the grand mean (obtained with 'multcomp', 'SimComp', 'nparcomp', or 'MCPAN')
or corresponding simultaneous confidence intervals as input and produces ANOM
decision charts that illustrate which group means deviate significantly from the
grand mean.","Imports":"ggplot2, MCPAN, multcomp, nparcomp, SimComp","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"ANOM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr, lme4, nlme, sandwich","Title":"Analysis of
Means","URL":"https:\/\/github.com\/PhilipPallmann\/ANOM","Version":"0.4.3"},"APSIM
":{"Author":"Justin Fainges","Description":"Contains functions designed to
facilitate the loading\nand transformation of 'Agricultural Production Systems
Simulator'\noutput files <https:\/\/www.apsim.info>. Input meteorological
data\n(also known as \"weather\" or \"met\") files can also be generated\nfrom user
supplied data.","Imports":"data.table (>= 1.9.4), lubridate (>= 1.3.3), stringr
(>=\n0.6.2), plyr (>= 1.8.1), sirad, methods, utils","License":"GPL-
3","NeedsCompilation":"no","Package":"APSIM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"General Utility Functions for the 'Agricultural
Production\nSystems
Simulator'","URL":"https:\/\/www.apsim.info","Version":"0.8.3"},"APSIMBatch":
{"Author":"Bangyou Zheng","Description":"Run APSIM in Batch mode","License":"GPL-
3","NeedsCompilation":"no","Package":"APSIMBatch","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Analysis the output of Apsim
software","Version":"0.1.0.2374"},"AR1seg":{"Author":"S. Chakar, E. Lebarbier, C.
Levy-Leduc, S. Robin","Depends":"Segmentor3IsBack","Description":"This package
corresponds to the implementation of the robust approach for estimating change-
points in the mean of an AR(1) Gaussian process by using the methodology described
in the paper arXiv 1403.1958","License":"GPL-
2","NeedsCompilation":"no","Package":"AR1seg","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Segmentation of an autoregressive Gaussian process of order
1","Version":"1.0"},"ARPobservation":{"Author":"James E. Pustejovsky, with
contributions from Daniel M. Swan","Description":"Tools for simulating data
generated by direct observation\nrecording.
Behavior streams are simulated based on an alternating renewal\nprocess, given
specified distributions of event durations and interim\ntimes. Different procedures
for recording data can then be applied to the\nsimulated behavior streams.
Functions are provided for the following\nrecording methods: continuous duration
recording, event counting, momentary\ntime sampling, partial interval recording,
and whole interval recording.","License":"GPL-
3","NeedsCompilation":"no","Package":"ARPobservation","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"plyr, reshape2, ggplot2, knitr,
testthat","Title":"Tools for Simulating Direct Behavioral Observation
Recording\nProcedures Based on Alternating Renewal
Processes","Version":"1.1"},"ART":{"Author":"Pablo J. Villacorta
<pjvi@decsai.ugr.es>","Description":"An implementation of the Aligned Rank
Transform technique for\nfactorial analysis (see references below for details)
including models with\nmissing terms (unsaturated factorial models). The function
first\ncomputes a separate aligned ranked response variable for each effect of
the\nuser-specified model, and then runs a classic ANOVA on each of the
aligned\nranked responses. For further details, see Higgins, J. J. and Tashtoush,
S.\n(1994). An aligned rank transform test for interaction. Nonlinear World 1\n(2),
pp. 201-211. Wobbrock, J.O., Findlater, L., Gergle, D. and\nHiggins,J.J. (2011).
The Aligned Rank Transform for nonparametric factorial\nanalyses using only ANOVA
procedures. Proceedings of the ACM Conference on\nHuman Factors in Computing
Systems (CHI '11). New York: ACM Press, pp.\n143-146.
<doi:10.1145\/1978942.1978963>.","Imports":"stats, car","License":"LGPL (>=
3)","NeedsCompilation":"no","Package":"ART","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Aligned Rank Transform for Nonparametric Factorial
Analysis","URL":"http:\/\/decsai.ugr.es\/~pjvi\/r-
packages.html","Version":"1.0"},"ARTIVA":{"Author":"S. Lebre and G.
Lelandais.","Depends":"MASS, igraph, gplots","Description":"Reversible Jump MCMC
(RJ-MCMC)sampling for approximating the posterior\ndistribution of a time varying
regulatory network, under the Auto Regressive TIme VArying\n(ARTIVA) model (for a
detailed description of the algorithm, see Lebre et al. BMC Systems\nBiology,
2010). Starting from time-course gene expression measurements for a gene
of\ninterest (referred to as \"target gene\") and a set of genes (referred to
as \"parent genes\")\nwhich may explain the expression of the target gene, the
ARTIVA procedure identifies\ntemporal segments for which a set of interactions
occur between the \"parent genes\" and the\n\"target gene\". The time points that
delimit the different temporal segments are referred to\nas changepoints
(CP).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ARTIVA","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Time-Varying DBN Inference with the ARTIVA (Auto
Regressive TIme\nVArying) Model","Version":"1.2.3"},"ARTP":{"Author":"Kai Yu,
Qizhai Li and William Wheeler","Description":"A package for calculating gene and
pathway p-values using the Adaptive Rank Truncated Product test","License":"GPL-
2","NeedsCompilation":"yes","Package":"ARTP","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Gene and Pathway p-values computed using the Adaptive
Rank\nTruncated Product","Version":"2.0.4"},"ARTP2":{"Author":"Han Zhang, Bill
Wheeler, Kai Yu, Yifan Yang","Depends":"R (>= 2.10), Formula, data.table, stats,
utils, parallel","Description":"Pathway and gene level association test using raw
data or summary statistics.","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"ARTP2","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Pathway and Gene-Level Association
Test","URL":"https:\/\/github.com\/zhangh12\/ARTP2","Version":"0.9.22"},"ARTool":
{"Author":"Matthew Kay [aut, cre],\nJacob O. Wobbrock [aut]","Depends":"R (>=
3.2)","Description":"The Aligned Rank Transform for nonparametric\nfactorial ANOVAs
as described by J. O. Wobbrock,\nL. Findlater, D. Gergle, & J. J. Higgins, \"The
Aligned\nRank Transform for nonparametric factorial analyses\nusing only ANOVA
procedures\", CHI 2011 <DOI:10.1145\/1978942.1978963>.","Imports":"lme4, car (>=
2.0-24), plyr, magrittr, dplyr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ARTool","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat (>= 0.10.0), lsmeans (>= 2.22), knitr,
rmarkdown,\nggplot2, tidyr, pander, Cairo, DescTools","Title":"Aligned Rank
Transform","URL":"https:\/\/github.com\/mjskay\/ARTool","Version":"0.10.2"},"ASMap"
:{"Author":"Julian Taylor <julian.taylor@adelaide.edu.au>, David
Butler\n<david.butler@daff.qld.gov.au>.","Depends":"R (>= 2.10), qtl, gtools,
fields, RColorBrewer, lattice","Description":"Functions for Accurate and Speedy
linkage map construction, manipulation and diagnosis of Doubled Haploid, Backcross
and Recombinant Inbred 'R\/qtl' objects. This includes extremely fast linkage map
clustering and optimal marker ordering using 'MSTmap' (see Wu et
al.,2008).","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ASMap","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr","Title":"Linkage Map Construction using the
MSTmap Algorithm","Version":"0.4-5"},"ASPBay":{"Author":"Claire Dandine-
Roulland","Depends":"hexbin, Rcpp","Description":"This package allows to make
inference on the properties of causal genetic\nvariants in linkage disequilibrium
with genotyped markers. In a first step,\nwe select a subset of variants using a
score statistic for affected\nsib-pairs. In a second step, on the selected subset,
we make\ninference on causal genetic variants in the considered
region.","License":"GPL-
2","NeedsCompilation":"yes","Package":"ASPBay","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Bayesian Inference on Causal Genetic Variants using
Affected\nSib-Pairs Data","Version":"1.2"},"ATE":{"Author":"Asad Haris
<aharis@uw.edu> and Gary Chan <kcgchan@uw.edu>","Description":"Nonparametric
estimation and inference for average treatment effects based on covariate
balancing.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ATE","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Inference for Average Treatment Effects using
Covariate\nBalancing","Version":"0.2.0"},"ATmet":{"Author":"S.Demeyer,
A.Allard","Depends":"R (>= 2.7.0), DiceDesign, lhs, metRology, msm,
sensitivity","Description":"This package provides functions for smart sampling and
sensitivity analysis for metrology applications, including computationally
expensive problems.","License":"GPL-
3","NeedsCompilation":"no","Package":"ATmet","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Advanced Tools for Metrology","Version":"1.2"},"AUC":
{"Author":"Michel Ballings and Dirk Van den Poel","Description":"This package
includes functions to compute the area under the curve of selected measures: The
area under the sensitivity curve (AUSEC), the area under the specificity curve
(AUSPC), the area under the accuracy curve (AUACC), and the area under the receiver
operating characteristic curve (AUROC). The curves can also be visualized. Support
for partial areas is provided.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"AUC","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Threshold independent performance measures for
probabilistic\nclassifiers","Version":"0.3.0"},"AUCRF":{"Author":"Victor Urrea,
M.Luz Calle","Depends":"R (>= 2.11.0), randomForest","Description":"Variable
selection using Random Forest based on optimizing\nthe area-under-the ROC curve
(AUC) of the Random Forest.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"AUCRF","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Variable Selection with Random Forest and the Area Under
the\nCurve","Version":"1.1"},"AUtests":{"Author":"Arjun Sondhi, Ken
Rice","Depends":"R (>= 3.1.2)","Description":"Performs approximate unconditional
and permutation testing for\n2x2 contingency tables. Motivated by testing for
disease association with rare\ngenetic variants in case-control studies. When
variants are extremely rare,\nthese tests give better control of Type I error than
standard tests.","Imports":"logistf","License":"GPL-
2","NeedsCompilation":"no","Package":"AUtests","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr","Title":"Approximate Unconditional and
Permutation Tests","Version":"0.97"},"AbsFilterGSEA":{"Author":"Sora Yoon
<yoonsora@unist.ac.kr>","Depends":"stats, limma","Description":"Gene-set enrichment
analysis (GSEA) is popularly used to assess the enrichment of differential signal
in a pre-defined gene-set without using a cutoff threshold for differential
expression. The significance of enrichment is evaluated through sample- or gene-
permutation method. Although the sample-permutation approach is highly recommended
due to its good false positive control, we must use gene-permuting method if the
number of samples is small. However, such gene-permuting GSEA (or preranked GSEA)
generates a lot of false positive gene-sets as the inter-gene correlation in each
gene set increases. These false positives can be successfully reduced by filtering
with the one-tailed absolute GSEA results. This package provides a function that
performs gene-permuting GSEA calculation with or without the absolute filtering.
Without filtering, users can perform (original) two-tailed or one-tailed absolute
GSEA.","Imports":"Rcpp, DESeq","License":"GPL-
2","NeedsCompilation":"yes","Package":"AbsFilterGSEA","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Improved False Positive Control of Gene-Permuting
GSEA with\nAbsolute Filtering","Version":"1.2.1"},"AcceptanceSampling":
{"Author":"Andreas Kiermeier <Andreas.Kiermeier@gmail.com>","Depends":"methods,
R(>= 2.4.0),
stats","Description":"Provides functionality for creating and\nevaluating
acceptance sampling plans. Sampling plans can be single,\ndouble or
multiple.","Imports":"graphics, utils","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"AcceptanceSampling","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Title":"Creation and Evaluation of Acceptance Sampling
Plans","Version":"1.0-4"},"Actigraphy":{"Author":"William Shannon, Tao Li, Hong
Xian, Jia Wang, Elena Deych, Carlos Gonzalez","Depends":"R (>= 2.14.0),
fda","Description":"Functional linear modeling and analysis for actigraphy
data.","Imports":"SDMTools","License":"Apache License (==
2.0)","NeedsCompilation":"no","Package":"Actigraphy","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"lattice","Title":"Actigraphy Data
Analysis","Version":"1.3.2"},"ActuDistns":{"Author":"Saralees
Nadarajah","Depends":"R (>= 2.15.0), reliaR, actuar,
hypergeo","Description":"Computes the probability density function, hazard
rate\nfunction, integrated hazard rate function and the quantile\nfunction for 44
commonly used survival models","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ActuDistns","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Functions for actuarial
scientists","Version":"3.0"},"AdMit":{"Author":"David Ardia, Lennart F. Hoogerheide
and Herman K. van Dijk","Depends":"mvtnorm","Description":"This package provides
functions to perform the fitting of an\nadaptive mixture of Student-t distributions
to a target density through its kernel function.\nThe mixture approximation can
then be used as the importance density\nin importance sampling or as the candidate
density in the Metropolis-Hastings algorithm to\nobtain quantities of interest for
the target density itself.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"AdMit","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"coda","Title":"Adaptive Mixture of Student-t
distributions","URL":"http:\/\/perso.unifr.ch\/david.ardia\/","Version":"2.0.1"},"A
dapEnetClass":{"Author":"Hasinur Rahaman Khan and Ewart Shaw","Depends":"imputeYn,
glmnet, lars, quadprog, R (>= 3.0.2)","Description":"Provides new approaches to
variable selection for AFT model.","License":"GPL-
2","NeedsCompilation":"no","Package":"AdapEnetClass","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"A Class of Adaptive Elastic Net Methods for Censored
Data","Version":"1.2"},"AdaptFit":{"Author":"Tatyana Krivobokova
<tkrivob@gwdg.de>","Depends":"SemiPar, MASS, nlme, cluster","Description":"Based on
the function \"spm\" of the SemiPar package fits\nsemiparametric regression models
with spatially adaptive\npenalized splines.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"AdaptFit","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Adaptive Semiparametic Regression","Version":"0.2-
2"},"AdaptFitOS":{"Author":"Manuel Wiesenfarth and Tatyana
Krivobokova","Depends":"nlme, MASS, splines","Description":"Fits semiparametric
regression models with spatially adaptive penalized splines and computes
simultaneous confidence bands.","Imports":"mgcv, SemiPar","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"AdaptFitOS","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Adaptive Semiparametric Regression with Simultaneous
Confidence\nBands","Version":"0.62"},"AdaptGauss":{"Author":"Michael Thrun, Onno
Hansen-Goos, Rabea Griese, Catharina Lippmann, Jorn Lotsch, Alfred
Ultsch","Depends":"R (>= 2.10)","Description":"Multimodal distributions can be
modelled as a mixture of components. The model is derived using the Pareto Density
Estimation (PDE) for an estimation of the pdf. PDE has been designed in particular
to identify groups\/classes in a dataset. Precise limits for the classes can be
calculated using the theorem of Bayes. Verification of the model is possible by QQ
plot, Chi-squared test and Kolmogorov-Smirnov test.","Imports":"shiny, caTools,
mclust, methods, ggplot2, grid","License":"GPL-
3","NeedsCompilation":"no","Package":"AdaptGauss","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Gaussian Mixture Models
(GMM)","Version":"1.2.0"},"AdaptiveSparsity":{"Author":"Kristen Zygmunt, Eleanor
Wong, Tom Fletcher","Depends":"R (>= 3.0.2), Rcpp (>=
0.8.0)","Description":"Implements Figueiredo EM algorithm for adaptive sparsity
(Jeffreys prior) (see Figueiredo, M.A.T.; , \"Adaptive sparseness for supervised
learning,\" Pattern Analysis and Machine Intelligence, IEEE Transactions on ,
vol.25, no.9, pp. 1150- 1159, Sept. 2003) and Wong algorithm for adaptively sparse
gaussian geometric models (see Wong, Eleanor, Suyash Awate, and P. Thomas Fletcher.
\"Adaptive Sparsity in Gaussian Graphical Models.\" In Proceedings of the 30th
International Conference on Machine Learning (ICML-13), pp. 311-319.
2013.)","License":"LGPL (>=
3.0)","NeedsCompilation":"yes","Package":"AdaptiveSparsity","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Suggests":"MASS, Matrix","Title":"Adaptive Sparsity
Models","Version":"1.4"},"AdequacyModel":{"Author":"Pedro Rafael Diniz Marinho
[aut, cre], Marcelo Bourguignon [aut, ctb], Cicero Rafael Barros Dias [aut,
ctb]","Description":"This package provides some useful functions for calculating
quality\nmeasures for\nadjustment, including statistics Kolmogorov-Smirnov, Cramer-
von Mises and Anderson-Darling.\nThese statistics are often used to compare models
not equipped. Also provided are other measures\nof fitness, such as AIC, CAIC, BIC
and HQIC. The package also provides functions for generating\npseudo-random number
of random variables that follow the following probability distributions:
Kumaraswamy Birnbaum-Saunders, Kumaraswamy Pareto, Exponentiated Weibull\nand
Kumaraswamy Weibull.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"AdequacyModel","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Adequacy of probabilistic models and generation of
pseudo-random\nnumbers","URL":"http:\/\/www.r-
project.org","Version":"1.0.8"},"AdvBinomApps":{"Author":"Daniel Kurz [aut], Horst
Lewitschnig [aut, cre]","Depends":"GenBinomApps,
rootSolve","Description":"Functions to compute upper Clopper-Pearson confidence
limits of early life failure probabilities and required sample sizes of burn-in
studies under further available information, e.g. from other products or
technologies.","License":"GPL-
3","NeedsCompilation":"no","Package":"AdvBinomApps","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Upper Clopper-Pearson Confidence Limits for Burn-in
Studies\nunder Additional Available Information","Version":"1.0"},"AggregateR":
{"Author":"Matthias Bogaert, Michel Ballings, Dirk Van den
Poel","Description":"Convenience functions for aggregating data frame. Currently
mean, sum and variance are supported. For Date variables, recency and duration are
supported. There is also support for dummy variables in predictive
contexts.","Imports":"dummy, stats, utils, methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"AggregateR","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Aggregate Numeric, Date and Categorical Variables by
an ID","Version":"0.0.2"},"Agreement":{"Author":"Yue Yu AND Lawrence
Lin","Depends":"R (>= 2.1.0), R2HTML","Description":"This package computes several
statistics for measuring\nagreement, for example, mean square deviation (MSD),
total\ndeviation index (TDI) or concordance correlation coefficient\n(CCC). It can
be used for both continuous data and categorical\ndata for multiple raters and
multiple readings cases.","License":"GPL-
2","NeedsCompilation":"no","Package":"Agreement","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Statistical Tools for Measuring
Agreement","URL":"http:\/\/imyy.net","Version":"0.8-1"},"Ake":{"Author":"W. E.
WansouwÃ©, S. M. SomÃ© and C. C. Kokonendji","Description":"Continuous and discrete
(count or categorical) estimation of density, probability mass function (p.m.f.)
and regression functions are performed using associated kernels. The cross-
validation technique and the local Bayesian procedure are also implemented for
bandwidth selection.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Ake","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Associated Kernel Estimations","URL":"www.r-
project.org","Version":"1.0"},"AlgDesign":{"Author":"Bob Wheeler
<bwheelerg@gmail.com>","Description":"Algorithmic experimental designs. Calculates
exact and\napproximate theory experimental designs for D,A, and I\ncriteria. Very
large designs may be created. Experimental\ndesigns may be blocked or blocked
designs created from a\ncandidate list, using several criteria. The blocking can
be\ndone when whole and within plot factors interact.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"AlgDesign","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Algorithmic Experimental
Design","URL":"https:\/\/github.com\/jvbraun\/AlgDesign","Version":"1.1-
7.3"},"AlgebraicHaploPackage":{"Author":"Jan Wolfertz","Depends":"R (>=
3.1.3)","Description":"Two unordered pairs of data of two different snips positions
is haplotyped by resolving a small number ob closed equations.","License":"GPL-
2","NeedsCompilation":"no","Package":"AlgebraicHaploPackage","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Suggests":"compiler","Title":"Haplotype Two Snips
Out of a Paired Group of Patients","Version":"1.2"},"AlignStat":{"Author":"Thomas
Shafee, Ira Cooke","Depends":"R (>= 2.10)","Description":"Methods for comparing two
alternative multiple\nsequence alignments (MSAs) to determine whether they align
homologous residues in\nthe same columns as one another. It then classifies
similarities and differences\ninto conserved gaps, conserved sequence, merges,
splits or shifts of one MSA relative\nto the other. Summarising these categories
for each
MSA column yields information\non which sequence regions are agreed upon my both
MSAs, and which differ. Several\nplotting functions enable easily visualisation of
the comparison data for analysis.","Imports":"Rcpp (>= 0.11.6), seqinr, ggplot2,
reshape2","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"AlignStat","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat","Title":"Comparison of Alternative
Multiple Sequence Alignments","Version":"1.1.3"},"AllPossibleSpellings":
{"Author":"Antoine Tremblay, IWK Health Center","Description":"Contains functions
possSpells.fnc and\nbatch.possSpells.fnc.","License":"GPL-
2","NeedsCompilation":"no","Package":"AllPossibleSpellings","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Title":"Computes all of a word's possible
spellings","Version":"1.1"},"AlleleRetain":{"Author":"Emily Weiser","Depends":"R
(>= 2.11.0)","Description":"Simulate the effect of management or demography on
allele\nretention and inbreeding accumulation in bottlenecked\npopulations of
animals with overlapping generations.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"AlleleRetain","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"pedigree","Title":"Allele Retention, Inbreeding,
and
Demography","URL":"https:\/\/sites.google.com\/site\/alleleretain\/","Version":"1.3
.1"},"Amelia":{"Author":"James Honaker <jhonaker@iq.harvard.edu>,\nGary King
<king@harvard.edu>,\nMatthew Blackwell <mblackwell@gov.harvard.edu>","Depends":"R
(>= 3.0.2), Rcpp (>= 0.11)","Description":"A tool that \"multiply imputes\" missing
data in a single cross-section\n(such as a survey), from a time series (like
variables collected for\neach year in a country), or from a time-series-cross-
sectional data\nset (such as collected by years for each of several
countries).\nAmelia II implements our bootstrapping-based algorithm that
gives\nessentially the same answers as the standard IP or EMis approaches,\nis
usually considerably faster than existing approaches and can\nhandle many more
variables. Unlike Amelia I and other statistically\nrigorous imputation software,
it virtually never crashes (but please\nlet us know if you find to the contrary!).
The program also\ngeneralizes existing approaches by allowing for trends in time
series\nacross observations within a cross-sectional unit, as well as priors\nthat
allow experts to incorporate beliefs they have about the values\nof missing cells
in their data. Amelia II also includes useful\ndiagnostics of the fit of multiple
imputation models. The program\nworks from the R command line or via a graphical
user interface that\ndoes not require users to know R.","Imports":"foreign, utils,
grDevices, graphics, methods, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"Amelia","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"tcltk, Zelig","Title":"A Program for Missing
Data","URL":"http:\/\/gking.harvard.edu\/amelia","Version":"1.7.4"},"AmericanCallOp
t":{"Author":"Paolo Zagaglia","Depends":"R (>= 2.0.0)","Description":"This package
includes a set of pricing functions for\nAmerican call options. The following cases
are covered: Pricing\nof an American call using the standard binomial
approximation;\nHedge parameters for an American call with a standard
binomial\ntree; Binomial pricing of an American call with continuous\npayout from
the underlying asset; Binomial pricing of an\nAmerican call with an underlying
stock that pays proportional\ndividends in discrete time; Pricing of an American
call on\nfutures using a binomial approximation; Pricing of a currency\nfutures
American call using a binomial approximation; Pricing\nof a perpetual American
call. The user should kindly notice\nthat this material is for educational purposes
only. The codes\nare not optimized for computational efficiency as they are\nmeant
to represent standard cases of analytical and numerical\nsolution.","License":"GPL-
3","NeedsCompilation":"no","Package":"AmericanCallOpt","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"This package includes pricing function for
selected American\ncall options with underlying assets that generate
payouts","Version":"0.95"},"AmpliconDuo":{"Author":"Anja Lange [aut, cre], Daniel
Hoffmann [aut]","Depends":"R (>= 2.10), stats, ggplot2,
xtable","Description":"Increasingly powerful techniques for high-throughput
sequencing open the possibility to comprehensively characterize microbial
communities, including rare species. However, a still unresolved issue are the
substantial error rates in the experimental process generating these sequences. To
overcome these limitations we propose an approach, where each sample is split and
the same amplification and sequencing protocol is applied to both halves. This
procedure should allow to detect likely PCR and sequencing artifacts, and true rare
species by comparison of the results of both parts. The AmpliconDuo package,
whereas amplicon duo from here on refers to the two amplicon data sets of a split
sample, is intended to help interpret the obtained read frequency distribution
across split samples, and to filter the false positive reads.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"AmpliconDuo","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Statistical Analysis of Amplicon Data of the Same
Sample to\nIdentify Artefacts","Version":"1.1"},"AnDE":{"Author":"Sai Teja Ranuva &
Nayyar Zaidi","Depends":"R (>= 2.14.0),discretization,
functional,foreign,stringr","Description":"AODE achieves highly accurate
classification by averaging over all\nof a small space.","License":"GPL-
3","NeedsCompilation":"no","Package":"AnDE","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"An extended Bayesian Learning Technique developed by Dr.
Geoff\nWebb","Version":"1.0"},"AnalyzeFMRI":{"Author":"P Lafaye de Micheaux
<lafaye@dms.umontreal.ca>, J L
Marchini\n<marchini@stats.ox.ac.uk>","Depends":"tcltk, R.matlab,
fastICA","Description":"Functions for I\/O, visualisation and analysis
of\nfunctional Magnetic Resonance Imaging (fMRI) datasets stored in\nthe ANALYZE or
NIFTI format.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"AnalyzeFMRI","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Functions for analysis of fMRI datasets stored in
the ANALYZE or\nNIFTI format","Version":"1.1-16"},"AnalyzeTS":{"Author":"Tran Thi
Ngoc Han <tranthingochan01011994@gmail.com>_ Doan Hai Nghi
<Hainghi1426262609121094@gmail.com> _ Mai Thi Hong Diem <maidiemks@gmail.com> _
Nguyen Thi Diem My <myntdhg@gmail.com> _ Hong Viet Minh
<hongvietminh@gmail.com>","Depends":"MASS,TSA,TTR,tseries","Description":"Main
function of package is helped to analyze time series, peculiar is fuzzy time
series. The package can calculate AIC value of common time series models and
propose the best models according AIC values. To fuzzy time series
by \"Chen\", \"Sing\", \"Heuristic\" and \"Chen-Hsu\" models, also can fuzzy and
forecast time series by Abbasov-Mamedova model.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"AnalyzeTS","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Analyze Time
Series","Version":"1.8"},"AncestryMapper":{"Author":"Tiago R Magalhaes, Darren J
Fitzpatrick, Eoghan O'Halloran","Description":"Assigns genetic ancestry to an
individual, relating to well studied populations, with world-wide coverage, and
studies relationships between local and global populations.","License":"GPL-
2","NeedsCompilation":"no","Package":"AncestryMapper","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"knitr","Title":"Assigning Ancestry Based on
Population References","Version":"1.2"},"AnglerCreelSurveySimulation":
{"Author":"Steven Ranney","Depends":"R (>= 3.0.2)","Description":"Create an angler
population, sample the population with a user-specified survey times, and calculate
metrics from a bus route-type creel survey.","License":"GPL-
3","NeedsCompilation":"no","Package":"AnglerCreelSurveySimulation","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"Simulate a Bus Route Creel Survey of
Anglers","Version":"0.2.1"},"AnnotLists":{"Author":"Nicolas
Cagnard","Depends":"tcltk","Description":"Annotate multiple lists from a specific
annotation
file.","License":"GPL","NeedsCompilation":"no","Package":"AnnotLists","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Title":"AnnotLists: A tool to annotate
multiple lists from a specific\nannotation file","Version":"1.2"},"AntWeb":
{"Author":"'Karthik Ram' [aut, cre]","Depends":"R (>= 3.0.1)","Description":"A
complete programmatic interface to the AntWeb database from the\nCalifornia Academy
of Sciences.","Imports":"rjson, plyr, assertthat, httr, leafletR (>= 0.1-
1)","License":"CC0","NeedsCompilation":"no","Package":"AntWeb","Repository":"http:\
/\/cran.csiro.au\/src\/contrib","Title":"programmatic interface to the
AntWeb","URL":"https:\/\/github.com\/ropensci\/AntWeb","Version":"0.7"},"AnthropMMD
":{"Author":"Frederic Santos","Depends":"R (>= 3.0.1), tcltk,
tcltk2","Description":"Offers a complete and interactive GUI to work out Mean
Measures of Divergence, especially for anthropologists.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"AnthropMMD","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"A GUI for Mean Measures of
Divergence","Version":"1.0.1"},"Anthropometry":{"Author":"Guillermo Vinue, Irene
Epifanio, Amelia Simo, M. Victoria Ibanez, Juan Domingo, Guillermo
Ayala","Depends":"R (>= 3.0.0)","Description":"Statistical methodologies especially
developed to analyze anthropometric data. These methods are aimed \t\tat providing
effective solutions to some commons problems related to Ergonomics and
Anthropometry. They are based on clustering, the \t\tstatistical concept of data
depth, statistical shape analysis and archetypal analysis.","Imports":"shapes,
rgl, archetypes, nnls, depth, FNN, ICGE, cluster,\nbiclust","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"Anthropometry","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"knitr, calibrate, mvtnorm, SportsAnalytics,
RColorBrewer,\nplotrix, abind","Title":"Statistical Methods for Anthropometric
Data","URL":"http:\/\/www.r-project.org,
http:\/\/www.uv.es\/vivigui","Version":"1.7"},"ApacheLogProcessor":{"Author":"Diogo
Silveira Mendonca","Description":"Provides a function to process Apache Log
Combined files. The main functionality is to extract data from log files to data
frames.","Imports":"foreach, parallel, doParallel","License":"LGPL-
3","NeedsCompilation":"no","Package":"ApacheLogProcessor","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Process the Apache Web Server Log Combined
Files","URL":"https:\/\/github.com\/diogosmendonca\/ApacheLogProcessor","Version":"
0.1.5"},"AppliedPredictiveModeling":{"Author":"Max Kuhn, Kjell
Johnson","Depends":"R (>= 2.10)","Description":"A few functions and several data
set for the Springer book 'Applied Predictive Modeling'","Imports":"CORElearn,
MASS, plyr,
reshape2","License":"GPL","NeedsCompilation":"no","Package":"AppliedPredictiveModel
ing","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"caret (>= 6.0-
22), lattice, ellipse","Title":"Functions and Data Sets for 'Applied Predictive
Modeling'","URL":"http:\/\/appliedpredictivemodeling.com\/","Version":"1.1-
6"},"AquaEnv":{"Author":"Andreas F. Hofmann, Karline Soetaert, Filip J.R.
Meysman","Depends":"minpack.lm, deSolve","Description":"AquaEnv is an integrated
development toolbox for aquatic\nchemical model generation focused on (ocean)
acidification and\nCO2 air-water exchange. It contains all elements necessary
to\nmodel the pH, the related CO2 air-water exchange, as well as\naquatic acid-base
chemistry in general for an arbitrary marine,\nestuarine or freshwater system. Also
chemical batches can be\nmodelled. Next to the routines necessary to calculate
desired\ninformation, AquaEnv also contains a suite of tools to\nvisualize this
information. Furthermore, AquaEnv can not only\nbe used to build dynamic models of
aquatic systems, but it can\nalso serve as a simple desktop tool for the
experimental\naquatic chemist to generate and visualize all possible
derived\ninformation from a set of measurements with one single easy to\nuse R
function. Additionally, the sensitivity of the system to\nvariations in the input
variables can be visualized. The\ncorresponding publication in Aquatic Geochemistry
can be found\nat
http:\/\/www.springerlink.com\/content\/l4747417w0k50463\/","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"AquaEnv","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"AquaEnv - an integrated development toolbox for aquatic
chemical\nmodel generation","Version":"1.0-3"},"ArArRedux":{"Author":"Pieter
Vermeesch [aut, cre]","Depends":"R (>= 3.0.2)","Description":"Processes noble gas
mass spectrometer data to determine the isotopic composition of argon (comprised of
Ar36, Ar37, Ar38, Ar39 and Ar40) released from neutron-irradiated potassium-bearing
minerals. Then uses these compositions to calculate precise and accurate
geochronological ages for multiple samples as well as the covariances between them.
Error propagation is done in matrix form, which jointly treats all samples and all
isotopes simultaneously at every step of the data reduction process. Includes
methods for regression of the time-resolved mass spectrometer signals to t=0 ('time
zero') for both single- and multi-collector instruments, blank correction, mass
fractionation correction, detector intercalibration, decay corrections,
interference corrections, interpolation of the irradiation parameter between
neutron fluence monitors, and (weighted mean) age calculation. All operations are
performed on the logs of the ratios between the different argon isotopes so as to
properly treat them as 'compositional data', sensu Aitchison [1986, The Statistics
of Compositional Data, Chapman and Hall].","Imports":"utils, stats, methods,
graphics, grDevices","License":"GPL-
2","NeedsCompilation":"no","Package":"ArArRedux","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Rigorous Data Reduction and Error Propagation of Ar40 \/
Ar39\nData","Version":"0.2"},"ArDec":{"Author":"Susana
Barbosa","Description":"Package ArDec implements autoregressive-
based\ndecomposition of a time series based on the constructive\napproach in West
(1997). Particular cases include the\nextraction of trend and seasonal
components.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ArDec","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Time series autoregressive-based
decomposition","Version":"2.0"},"ArfimaMLM":{"Author":"Patrick Kraft [aut,
cre],\nChristopher Weber [ctb]","Depends":"R (>= 3.0.0), lme4,
fractal","Description":"Functions to facilitate the estimation of Arfima-MLM models
for repeated cross-sectional data and pooled cross-sectional time-series data (see
Lebo and Weber 2015). The estimation procedure uses double filtering with Arfima
methods to account for autocorrelation in repeated cross-sectional data followed by
multilevel modeling (MLM) to estimate aggregate as well as individual-level
parameters simultaneously.","Imports":"fracdiff","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ArfimaMLM","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Arfima-MLM Estimation For Repeated Cross-Sectional
Data","URL":"https:\/\/github.com\/pwkraft\/ArfimaMLM","Version":"1.3"},"ArgumentCh
eck":{"Author":"Benjamin Nutter","Depends":"R (>= 3.0.0)","Description":"The
typical process of checking arguments in functions is\niterative. In this process,
an error may be returned and the user may fix\nit only to receive another error on
a different argument. 'ArgumentCheck'\nfacilitates a more helpful way to perform
argument checks allowing the\nprogrammer to run all of the checks and then return
all of the errors and\nwarnings in a single message.","License":"GPL-
3","NeedsCompilation":"no","Package":"ArgumentCheck","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"knitr, testthat","Title":"Improved Communication
to Users with Respect to Problems in\nFunction
Arguments","URL":"https:\/\/github.com\/nutterb\/ArgumentCheck","Version":"0.10.2"}
,"ArrayBin":{"Author":"Ed Curry","Depends":"R (>= 2.15.0),
SAGx","Description":"Fast adaptive binarization for numeric data
arrays,\nparticularly designed for high-throughput biological datasets.\nIncludes
options to filter out rows of the array with\ninsufficient magnitude or variation
(based on gap statistic).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ArrayBin","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Binarization of numeric data
arrays","URL":"http:\/\/www.r-
project.org,\nhttp:\/\/www1.imperial.ac.uk\/medicine\/people\/e.curry\/","Version":
"0.2"},"AsioHeaders":{"Author":"Dirk Eddelbuettel","Description":"'Asio' is a
cross-platform C++ library for network and low-level\nI\/O programming that
provides developers with a consistent asynchronous model\nusing a modern C++
approach.\n\n'Asio' is also included in Boost but requires linking when used
with\nBoost. Standalone it can be used header-only provided a recent-
enough\ncompiler. 'Asio' is written and maintained by Christopher M.
Kohlhoff.\n'Asio' is released under the 'Boost Software License', Version
1.0.","License":"BSL-
1.0","NeedsCompilation":"no","Package":"AsioHeaders","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"'Asio' C++ Header Files","Version":"1.11.0-
1"},"AssetPricing":{"Author":"Rolf Turner <r.turner@auckland.ac.nz>","Depends":"R
(>= 0.99)","Description":"Calculates the optimal price of assets (such as\nairline
flight seats, hotel room bookings) whose value\nbecomes zero after a fixed `èxpiry
date''. Assumes\npotential customers arrive (possibly in groups) according\nto a
known inhomogeneous Poisson process. Also assumes a\nknown time-varying elasticity
of demand (price sensitivity)\nfunction. Uses elementary techniques based on
ordinary\ndifferential equations. Uses the package deSolve to effect\nthe solution
of these differential equations.","Imports":"polynom, deSolve","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"AssetPricing","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Optimal pricing of assets with fixed expiry
date","URL":"http:\/\/www.stat.auckland.ac.nz\/~rolf\/","Version":"1.0-
0"},"AssocTests":{"Author":"Lin Wang [aut],\nWei Zhang [aut],\nQizhai Li
[aut],\nWeicheng Zhu [ctb]","Depends":"cluster, mvtnorm, combinat, fExtremes, R(>=
2.10.0)","Description":"Some procedures including EIGENSTRAT (a procedure
for\ndetecting and correcting for population stratification through\nsearching for
the eigenvectors in genetic association studies),\nPCoC (a procedure for correcting
for population stratification\nthrough calculating the principal coordinates and
the clustering\nof the subjects), Tracy-Wisdom test (a procedure for detecting\nthe
significant eigenvalues of a matrix), distance regression (a\nprocedure for
detecting the association between a distance matrix\nand some independent variants
of interest), single-marker test (a\nprocedure for identifying the association
between the genotype at\na biallelic marker and a trait using the Wald test or the
Fisher\nexact test), MAX3 (a procedure for testing for the association\nbetween a
single nucleotide polymorphism and a binary phenotype\nusing the maximum value of
the three test statistics derived for\nthe recessive, additive, and dominant
models), nonparametric trend\ntest (a procedure for testing for the association
between a genetic\nvariant and a non-normal distributed quantitative trait based on
the\nnonparametric risk), and nonparametric
MAX3 (a procedure for testing\nfor the association between a biallelic single
nucleotide polymorphism\nand a quantitative trait using the maximum value of the
three\nnonparametric trend tests derived for the recessive, additive, and\ndominant
models), which are commonly used in genetic association studies.","License":"GPL-
2","NeedsCompilation":"no","Package":"AssocTests","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Genetic Association Studies","Version":"0.0-
3"},"AssotesteR":{"Author":"Gaston Sanchez","Depends":"mvtnorm","Description":"R
package with statistical tests and methods for genetic\nassociation studies with
emphasis on rare variants and binary (dichotomous)\ntraits","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"AssotesteR","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Statistical Tests for Genetic Association
Studies","URL":"http:\/\/www.gastonsanchez.com","Version":"0.1-10"},"AsynchLong":
{"Author":"Hongyuan Cao, Donglin Zeng, Jialiang Li, Jason P. Fine, and Shannon T.
Holloway","Depends":"compiler, parallel, stats, graphics,
methods","Description":"Estimation of regression models for sparse asynchronous
longitudinal observations, where time-dependent response and covariates are
mismatched and observed intermittently within subjects. Kernel weighted estimating
equations are used for generalized linear models with either time-invariant or
time-dependent coefficients.","License":"GPL-
2","NeedsCompilation":"no","Package":"AsynchLong","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Regression Analysis of Sparse Asynchronous Longitudinal
Data","Version":"2.0"},"AtelieR":{"Author":"Yvonnick Noel","Depends":"R (>= 2.10),
proto, cairoDevice, gWidgetsRGtk2, partitions","Description":"A collection of
statistical simulation and computation tools with a GTK GUI, to help teach
statistical concepts and compute probabilities. Two domains are covered: I.
Understanding (Central-Limit Theorem and the Normal Distribution, Distribution of a
sample mean, Distribution of a sample variance, Probability calculator for common
distributions), and II. Elementary Bayesian Statistics (bayesian inference on
proportions, contingency tables, means and variances, with informative and
noninformative priors).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"AtelieR","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"A GTK GUI for teaching basic concepts in statistical
inference,\nand doing elementary bayesian tests","Version":"0.24"},"AtmRay":
{"Author":"Jake Anderson","Description":"Calculates acoustic traveltimes and ray
paths in 1-D,\nlinear atmospheres. Later versions will support arbitrary 1-
D\natmospheric models, such as radiosonde measurements and\nstandard reference
atmospheres.","License":"GPL","NeedsCompilation":"yes","Package":"AtmRay","Reposito
ry":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"RSEIS","Title":"Acoustic
Traveltime Calculations for 1-D Atmospheric Models","Version":"1.31"},"AutoModel":
{"Author":"Alex Lishinski","Depends":"R (>= 3.1.3),","Description":"A set of
functions that automates the process and produces reasonable output for
hierarchical multiple regression models. It allows you to specify predictor
blocks, from which it generates all of the linear models, and checks the
assumptions of the model, producing the requisite plots and statistics to allow you
to judge the suitability of the model.","Imports":"lmtest, car, MASS, broom, rowr,
ROCR, dplyr, BaylorEdPsych,\naod, gtools","License":"GPL-
3","NeedsCompilation":"no","Package":"AutoModel","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr, xtable, testthat","Title":"Automated
Hierarchical Multiple Regression with
Assumptions\nChecking","URL":"https:\/\/github.com\/alishinski\/AutoModel","Version
":"0.4.9"},"AutoSEARCH":{"Author":"Genaro Sucarrat","Depends":"R (>= 2.4.1), zoo,
lgarch","Description":"General-to-Specific (GETS) modelling of the mean and
variance of a regression. NOTE: The package has been succeeded by gets, also
available on the CRAN, which is more user-friendly, faster and easier to extend.
Users are therefore encouraged to consider gets instead.","License":"GPL-
2","NeedsCompilation":"no","Package":"AutoSEARCH","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"General-to-Specific (GETS)
Modelling","Version":"1.5"},"AutoregressionMDE":{"Author":"Jiwoong Kim [aut,
cre]","Depends":"R (>= 3.2.2)","Description":"Consider autoregressive model of
order p where the distribution function of innovation is unknown, but innovations
are independent and symmetrically distributed. The package contains a function
named ARMDE which takes X (vector of n observations) and p (order of the model) as
input argument and returns minimum distance estimator of the parameters in the
model.","License":"GPL-
2","NeedsCompilation":"no","Package":"AutoregressionMDE","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Minimum Distance Estimation in Autoregressive
Model","Version":"1.0"},"AzureML":{"Author":"Andrie de Vries [aut, cre],\nMicrosoft
Corporation [cph],\nRevolution Analytics [cph] (Code adapted from the foreach
package)","Description":"Functions and datasets to support Azure Machine Learning.
This\nallows you to interact with datasets, as well as publish and consume R
functions\nas API services.","Imports":"jsonlite(>= 0.9.16), curl(>= 0.8), foreign,
codetools,\nbase64enc, miniCRAN, uuid","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"AzureML","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat, knitr, rmarkdown, lme4, gbm,
MASS","Title":"Interface with Azure Machine Learning Datasets, Experiments and\nWeb
Services","URL":"https:\/\/github.com\/RevolutionAnalytics\/AzureML","Version":"0.2
.10"},"B2Z":{"Author":"Joao Vitor Dias Monteiro <monte092@umn.edu>, Sudipto
Banerjee\n<baner009@umn.edu>, Gurumurthy Ramachandran
<ramac002@umn.edu>","Depends":"numDeriv, coda, mvtnorm","Description":"This package
fits the Bayesian two-Zone Models.","License":"GPL-
2","NeedsCompilation":"no","Package":"B2Z","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Bayesian Two-Zone Model","Version":"1.4"},"BACA":
{"Author":"Vittorio Fortino and Dario Greco","Depends":"R (>=
3.0.0)","Description":"R-based graphical tool to concisely visualise and compare
biological annotations queried from the DAVID web service. It provides R functions
to perform enrichment analysis (via DAVID - http:\/\/david.abcc.ncifcrf.gov) on
several gene lists at once, and then visualizing all the results in one generated
figure that allows R users to compare the annotations found for each
list.","Imports":"RDAVIDWebService, ggplot2, rJava","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BACA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr","Title":"Bubble Chart to Compare Biological
Annotations by using DAVID","Version":"1.3"},"BACCO":{"Author":"Robin K. S.
Hankin","Depends":"emulator (>= 1.2-13), calibrator (>= 1.2-5), approximator
(>=\n1.2-6)","Description":"The BACCO bundle of packages is replaced by the
BACCO\npackage, which provides a vignette that illustrates the
constituent\npackages (emulator, approximator, calibrator) in
use.","License":"GPL","NeedsCompilation":"no","Package":"BACCO","Repository":"http:
\/\/cran.csiro.au\/src\/contrib","Title":"Bayesian Analysis of Computer Code Output
(BACCO)","Version":"2.0-9"},"BACprior":{"Author":"Denis Talbot, Geneviève Lefebvre,
Juli Atherton","Depends":"mvtnorm, leaps, boot","Description":"The BACprior package
provides an approximate sensitivity analysis of the\nBayesian Adjustment for
Confounding (BAC) algorithm (Wang et al., 2012) with regards to the\nhyperparameter
omega. The package also provides functions to guide the user in their choice\nof an
appropriate omega value. The method is based on Lefebvre, Atherton and Talbot
(2014).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BACprior","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Choice of the Hyperparameter Omega in the Bayesian
Adjustment\nfor Confounding (BAC) Algorithm","Version":"2.0"},"BAEssd":
{"Author":"Eric M. Reyes and Sujit K.
Ghosh","Depends":"mvtnorm","Description":"Implements sample size calculations
following the approach\ndescribed in \"Bayesian Average Error Based Approach
to\nHypothesis Testing and Sample Size Determination.\"","License":"GPL-
2","NeedsCompilation":"no","Package":"BAEssd","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Bayesian Average Error approach to Sample Size
Determination","Version":"1.0.1"},"BAMMtools":{"Author":"Dan Rabosky, Mike
Grundler, Pascal Title, Carlos Anderson, Jeff Shi, Joseph Brown, Huateng Huang, Jon
Mitchell","Depends":"ape, R (>= 2.10)","Description":"Provides functions for
analyzing and visualizing complex macroevolutionary dynamics on phylogenetic trees.
It is a companion package to the command line program BAMM (Bayesian Analysis of
Macroevolutionary Mixtures) and is entirely oriented towards the analysis,
interpretation, and visualization of evolutionary rates. Functionality includes
visualization of rate shifts on phylogenies, estimating evolutionary rates through
time, comparing posterior distributions of evolutionary rates across clades,
comparing diversification models using Bayes factors, and
more.","Imports":"methods","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"BAMMtools","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"parallel","Title":"Analysis and Visualization of
Macroevolutionary Dynamics on\nPhylogenetic Trees","URL":"http:\/\/www.bamm-
project.org","Version":"2.1.1"},"BANFF":{"Author":"Zhou Lan, Yize Zhao, Jian Kang,
Tianwei Yu","Depends":"R (>= 3.0.3), foreach, doParallel","Description":"Provides a
full package of posterior inference, model comparison, and graphical illustration
of model fitting. A parallel computing algorithm for the Markov chain Monte Carlo
(MCMC) based posterior inference and an Expectation-Maximization (EM) based
algorithm for posterior approximation are are developed, both of which greatly
reduce the computational time for model inference.","Imports":"DPpackage, igraph,
mclust, pscl, tmvtnorm, network, coda,\ngraphics, methods, stats,
utils","License":"GPL-
2","NeedsCompilation":"no","Package":"BANFF","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Bayesian Network Feature Finder","Version":"1.0"},"BANOVA":
{"Author":"Chen Dong, Michel Wedel","Depends":"R (>= 3.0.1), rjags(>= 3-13),
runjags (>= 1.2.1-0), coda (>=\n0.16-1)","Description":"It covers several Bayesian
Analysis of Variance (BANOVA) models used in analysis of experimental designs in
which both within- and between- subjects factors are manipulated. They can be
applied to data that are common in the behavioral sciences and related fields. The
package includes: Hierarchical Bayes ANOVA models with normal response, t response,
Binomial(Bernoulli) response, Poisson response, ordered multinomial response and
multinomial response variables. All models accommodate unobserved heterogeneity by
including a normal distribution of the parameters across individuals. Outputs of
the package include tables of sums of squares, effect sizes and p-values, and
tables of means, which are easily interpretable for behavioral researchers. BANOVA
uses JAGS as the computational platform.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BANOVA","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Hierarchical Bayesian ANOVA
Models","Version":"0.5"},"BAS":{"Author":"Merlise Clyde [aut, cre, cph],\nMichael
Littman [ctb],\nQuanli Wang [ctb],\nJoyee Ghosh [ctb],\nYingbo Li
[ctb]","Depends":"R (>= 3.0), stats, graphics","Description":"Package for Bayesian
Model Averaging in linear models and\ngeneralized linear models using stochastic
or\ndeterministic sampling without replacement from posterior\ndistributions.
Prior distributions on coefficients are\nfrom Zellner's g-prior or mixtures of g-
priors\ncorresponding to the Zellner-Siow Cauchy Priors or the\nmixture of g-priors
from\nLiang et al (2008)\n<http:\/\/dx.doi.org\/10.1198\/016214507000001337>\nfor
linear models or mixtures of\ng-priors in GLMs of Li and Clyde
(2015)\n<http:\/\/arxiv.org\/abs\/1503.06913 >. Other model\nselection criteria
include AIC and BIC. Sampling\nprobabilities may be updated based on the sampled
models\nusing Sampling w\/out Replacement or an MCMC algorithm\nsamples models
using the BAS tree structure as an efficient\nhash table. Allows uniform or beta-
binomial prior distributions on\nmodels and for large p truncated priors on the
model\nspace. The user may force variables to always be included.","License":"GPL
(>=
3)","NeedsCompilation":"yes","Package":"BAS","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"MASS","Title":"Bayesian Model Averaging using Bayesian
Adaptive Sampling","URL":"http:\/\/www.r-project.org,
http:\/\/github.com\/merliseclyde\/BAS","Version":"1.1.0"},"BASIX":
{"Author":"Bastian Pfeifer","Depends":"R (>= 2.14.2), methods","Description":"BASIX
provides some efficient C\/C++ implementations to speed up calculations in
R.","License":"GPL-
2","NeedsCompilation":"yes","Package":"BASIX","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"BASIX: An efficient C\/C++ toolset for
R","Version":"1.1"},"BAT":{"Author":"Pedro Cardoso, Francois Rigal, Jose Carlos
Carvalho","Depends":"R (>= 3.0.0), graphics, nls2, spatstat, stats,
vegan","Description":"Includes algorithms to assess alpha and beta\ndiversity in
all their dimensions (taxon, phylogenetic and functional\ndiversity), whether
communities are completely sampled or not. It allows\nperforming a number of
analyses based on either species identities or\nphylogenetic\/functional trees
depicting species relationships.","License":"GPL-
3","NeedsCompilation":"no","Package":"BAT","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Biodiversity Assessment Tools","Version":"1.4.0"},"BAYSTAR":
{"Author":"Cathy W. S. Chen, Edward M.H. Lin, F.C. Liu, and
Richard\nGerlach","Depends":"R (>= 3.0.1), mvtnorm, coda","Description":"The
manuscript introduces the BAYSTAR package, which\nprovides the functionality for
Bayesian estimation in\nautoregressive threshold models.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BAYSTAR","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"On Bayesian analysis of Threshold autoregressive model
(BAYSTAR)","Version":"0.2-9"},"BB":{"Author":"Ravi Varadhan [aut, cph, trl],\nPaul
Gilbert [aut, cre],\nMarcos Raydan [ctb] (with co-authors, wrote original
algorithms in\nfortran. These provided some guidance for implementing R code
in\nthe BB package.),\nJM Martinez [ctb] (with co-authors, wrote original
algorithms in\nfortran. These provided some guidance for implementing R code
in\nthe BB package.),\nEG Birgin [ctb] (with co-authors, wrote original algorithms
in fortran.\nThese provided some guidance for implementing R code in the
BB\npackage.),\nW LaCruz [ctb] (with co-authors, wrote original algorithms in
fortran.\nThese provided some guidance for implementing R code in the
BB\npackage.)","Depends":"R (>= 2.6.1)","Description":"Barzilai-Borwein spectral
methods for solving nonlinear\nsystem of equations, and for optimizing nonlinear
objective\nfunctions subject to simple constraints. A tutorial style\nintroduction
to this package is available in a vignette on the\nCRAN download page or, when the
package is loaded in an R\nsession, with vignette(\"BB\").","Imports":"stats,
quadprog","License":"GPL-
3","NeedsCompilation":"no","Package":"BB","Repository":"http:\/\/cran.csiro.au\/src
\/contrib","Suggests":"setRNG, survival, Hmisc, numDeriv","Title":"Solving and
Optimizing Large-Scale Nonlinear
Systems","URL":"\nhttp:\/\/www.jhsph.edu\/agingandhealth\/People\/Faculty_personal_
pages\/Varadhan.html","Version":"2014.10-1"},"BBEST":{"Author":"Anton Gagin and
Igor Levin with contributions from Charles R. Hogg III","Description":"We
implemented a Bayesian-statistics approach for\nsubtraction of incoherent
scattering from neutron total-scattering data.\nIn this approach, the estimated
background signal associated with\nincoherent scattering maximizes the posterior
probability, which combines\nthe likelihood of this signal in reciprocal and real
spaces with the prior\nthat favors smooth lines.","Imports":"DEoptim, wmtsa, grid,
ggplot2, reshape2, shiny, methods","License":"GPL-
3","NeedsCompilation":"no","Package":"BBEST","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Bayesian Estimation of Incoherent Neutron Scattering
Backgrounds","Version":"0.1-6"},"BBMM":{"Author":"Nielson, R. M., H. Sawyer, and T.
L. McDonald (WEST, Inc.,\nwww.west-inc.com)","Description":"The model provides an
empirical estimate of a movement\npath using discrete location data obtained at
relatively short\ntime intervals.","License":"GNU General Public
License","NeedsCompilation":"no","Package":"BBMM","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Brownian bridge movement
model","Version":"3.0"},"BBRecapture":{"Author":"Luca Tardella and Danilo Alunni
Fegatelli","Depends":"R (>= 3.0.2), HI, locfit, lme4, secr","Description":"Model
fitting of flexible behavioural recapture models based on conditional probability
reparameterization and meaningful partial capture history quantification also
referred to as meaningful behavioural covariate","License":"GPL-
2","NeedsCompilation":"no","Package":"BBRecapture","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Bayesian Behavioural Capture-Recapture
Models","Version":"0.1"},"BBmisc":{"Author":"Bernd Bischl [aut, cre],\nMichel Lang
[aut],\nJakob Bossek [aut],\nDaniel Horn [aut],\nJakob Richter
[aut]","Description":"Miscellaneous helper functions for and from B. Bischl
and\nsome other guys at TU Dortmund, mainly for package
development.","Imports":"stats, checkmate","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"yes","Package":"BBmisc","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat, microbenchmark,
codetools","Title":"Miscellaneous Helper Functions for B.
Bischl","URL":"https:\/\/github.com\/berndbischl\/BBmisc","Version":"1.9"},"BCA":
{"Author":"Dan Putler <putler@yahoo.com>","Depends":"R (>=
3.0.0)","Description":"Underlying support functions for RcmdrPlugin.BCA and
a\ncompanion to the book Customer and Business Analytics: Applied\nData Mining for
Business Decision Making Using R by Daniel S.\nPutler and Robert E.
Krider","Imports":"RcmdrMisc (>= 1.0-1), Rcmdr (>= 2.1-0), car (>= 2.0-21),\nrpart,
flexclust, clv","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BCA","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"rgl","Title":"Business and Customer
Analytics","URL":"http:\/\/www.customeranalyticsbook.com","Version":"0.9-
3"},"BCBCSF":{"Author":"Longhai Li <longhai@math.usask.ca>","Depends":"R (>=
2.13.1), abind","Description":"Fully Bayesian Classification with a subset of high-
dimensional features, such as expression levels of genes. The data are modeled with
a hierarchical Bayesian models using heavy-tailed t distributions as priors. When a
large number of features are available, one may like to select only a subset of
features to use, typically those features strongly correlated with the response in
training cases. Such a feature selection procedure is however invalid since the
relationship between the response and the features has be exaggerated by feature
selection. This package provides a way to avoid this bias and yield better-
calibrated predictions for future cases when one uses F-statistic to select
features.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"BCBCSF","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Bias-Corrected
Bayesian Classification with Selected Features","URL":"http:\/\/www.r-project.org,
http:\/\/math.usask.ca\/~longhai","Version":"1.0-1"},"BCDating":{"Author":"Majid
Einian [aut, cre]","Depends":"methods","Description":"Tools for Dating Business
Cycles using Harding-Pagan (Quarterly Bry-Boschan) method and various plotting
features.","License":"GPL-
2","NeedsCompilation":"no","Package":"BCDating","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Business Cycle Dating and Plotting
Tools","Version":"0.9.7"},"BCE":{"Author":"Karel Van den Meersche
<karel.van_den_meersche@cirad.fr>, Karline Soetaert
<karline.soetaert@nioz.nl>","Depends":"R (>= 2.0.1), FME, limSolve,
Matrix","Description":"Function to estimates taxonomic compositions from biomarker
data, using a Bayesian approach.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BCE","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Bayesian composition estimator: estimating sample
(taxonomic)\ncomposition from biomarker data","Version":"2.1"},"BCEA":
{"Author":"Gianluca Baio, Andrea Berardi, Anna Heath","Depends":"R (>=
2.10)","Description":"Produces an economic evaluation of a Bayesian model in the
form of MCMC simulations. Given suitable variables of cost and effectiveness \/
utility for two or more interventions, This package computes the most cost-
effective alternative and produces graphical summaries and probabilistic
sensitivity analysis.","Imports":"MASS","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BCEA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"R2jags, R2OpenBUGS, ggplot2, grid, INLA, splancs,
mgcv","Title":"Bayesian Cost Effectiveness
Analysis","URL":"http:\/\/www.statistica.it\/gianluca\/BCEA,\nhttp:\/\/www.statisti
ca.it\/gianluca","Version":"2.2-2"},"BCEE":{"Author":"Denis Talbot, Geneviève
Lefebvre, Juli Atherton.","Depends":"BMA","Description":"Implementation of the
Bayesian Causal Effect Estimation algorithm,\na data-driven method for the
estimation of the causal effect of an exposure\non a continuous outcome. For more
details, see Talbot et al. (2015) DOI:10.1515\/jci-2014-0035.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BCEE","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"The Bayesian Causal Effect Estimation
Algorithm","Version":"1.1"},"BCEs0":{"Author":"Gianluca
Baio","Description":"Implements a full Bayesian cost-effectiveness analysis in the
case where the cost variable is characterised by structural zeros. The package
implements the Gamma, log-Normal and Normal models for the cost variable and the
Gamma, Beta, Bernoulli and Normal models for the measure of clinical
effectiveness.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BCEs0","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"R2jags","Title":"Bayesian Models for Cost-Effectiveness
Analysis in the Presence\nof Structural Zero Costs","Version":"1.1-1"},"BCRA":
{"Author":"Fanni Zhang","Description":"Functions provide risk projections of
invasive breast cancer based on Gail model according to National Cancer Institute's
Breast Cancer Risk Assessment Tool algorithm for specified race\/ethnic groups and
age intervals.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BCRA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Breast Cancer Risk Assessment","Version":"1.0"},"BDWreg":
{"Author":"Hamed Haselimashhadi <hamedhaseli@gmail.com>","Depends":"R (>=
3.0)","Description":"A Bayesian regression model for discrete response, where the
conditional distribution is modelled via a discrete Weibull distribution. This
package provides an implementation of Metropolis-Hastings and Reversible-Jumps
algorithms to draw samples from the posterior. It covers a wide range of
regularizations through any two parameter prior. Examples are Laplace (Lasso),
Gaussian (ridge), Uniform, Cauchy and customized priors like a mixture of priors.
An extensive visual toolbox is included to check the validity of the results as
well as several measures of goodness-of-fit.","Imports":"coda, parallel, foreach,
doParallel, MASS, methods, graphics,\nstats, utils","License":"LGPL (>=
2)","NeedsCompilation":"no","Package":"BDWreg","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Bayesian Inference for Discrete Weibull
Regression","URL":"http:\/\/hamedhaseli.webs.com","Version":"1.0.0"},"BDgraph":
{"Author":"Abdolreza Mohammadi and Ernst Wit","Depends":"R (>= 3.0.0), Matrix,
igraph","Description":"Provides statistical tools for Bayesian structure learning
in undirected graphical models with either continuous or discrete
variables.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"BDgraph","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Bayesian Graph Selection Based on Birth-Death MCMC
Approach","URL":"http:\/\/www.math.rug.nl\/stat\/Main\/Research","Version":"2.26"},
"BEANSP":{"Author":"Chong He, Yiqun Yang, Jing Cao","Description":"Computing age
specific nest survival rates based on a Bayesian hierarchical model. This package
can handle unknown nest age, irregular visiting schedule and nest-specific
covariates.","License":"GPL-
2","NeedsCompilation":"yes","Package":"BEANSP","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Bayesian Estimate of Age-specific Nest Survival
Probabilities","Version":"1.0"},"BEDASSLE":{"Author":"Gideon
Bradburd","Description":"provides functions that allow users to quantify the
relative\ncontributions of geographic and ecological distances to empirical
patterns of genetic\ndifferentiation on a landscape. Specifically, we use a custom
Markov chain\nMonte Carlo (MCMC) algorithm, which is used to estimate the
parameters of the\ninference model, as well as functions for performing MCMC
diagnosis and assessing\nmodel adequacy.","Imports":"MASS, matrixcalc,
emdbook","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BEDASSLE","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Quantifies effects of geo\/eco distance on
genetic\ndifferentiation","Version":"1.5"},"BEDMatrix":{"Author":"Alexander
Grueneberg [aut, cre],\nLian Lian [ctb],\nGustavo de los Campos [ctb]","Depends":"R
(>= 3.0.0)","Description":"A matrix-like data structure that allows for
efficient,\nconvenient, and scalable subsetting of binary genotype\/phenotype
files\ngenerated by PLINK (http:\/\/pngu.mgh.harvard.edu\/~purcell\/plink\/), the
whole\ngenome association analysis toolset, without loading the entire file
into\nmemory.","Imports":"methods, Rcpp (>= 0.12.1)","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"BEDMatrix","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Matrices Backed by Binary
PED Files
(PLINK)","URL":"https:\/\/github.com\/QuantGen\/BEDMatrix","Version":"1.2.0"},"BEQI
2":{"Author":"Willem van Loon [aut, cph],\nDennis Walvoort [aut, cre]","Depends":"R
(>= 3.0.2), methods","Description":"Tool for analysing benthos data. It estimates
several quality\nindices like the total abundance of species, species
richness,\nMargalef's d, AZTI Marine Biotic Index (AMBI), and the BEQI-2
index.\nFurthermore, additional (optional) features are provided that enhance
data\npreprocessing: (1) genus to species conversion, i.e.,taxa counts at
the\ntaxonomic genus level can optionally be converted to the species level
and\n(2) pooling: small samples are combined to bigger samples with a\nstandardized
size to (a) meet the data requirements of the AMBI,\n(b) generate comparable
species richness values and\n(c) give a higher benthos signal to noise
ratio.","Imports":"knitr, markdown, jsonlite, xtable, plyr,
3)","NeedsCompilation":"no","Package":"BEQI2","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat","Title":"Benthic Ecosystem Quality Index
2","Version":"2.0-0"},"BEST":{"Author":"John K. Kruschke and Mike
Meredith","Description":"An alternative to t-tests, producing posterior
estimates\nfor group means and standard deviations and their differences
and\neffect sizes.","Imports":"coda, jagsUI (>= 1.3.6)","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"BEST","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Bayesian Estimation Supersedes the t-
Test","Version":"0.4.0"},"BGLR":{"Author":"Gustavo de los Campos, Paulino Perez
Rodriguez,","Depends":"R (>= 3.1.3)","Description":"Bayesian Generalized Linear
Regression.","License":"GPL-
3","NeedsCompilation":"yes","Package":"BGLR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Bayesian Generalized Linear
Regression","Version":"1.0.4"},"BGPhazard":{"Author":"L. E. Nieto-Barajas and J. A.
Garcia Bueno","Depends":"R(>= 3.1.2)","Description":"Computes the hazard rate
estimate as described by Nieto-Barajas and Walker (2002) and Nieto-Barajas
(2003).","Imports":"survival","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BGPhazard","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Markov Beta and Gamma Processes for Modeling Hazard
Rates","Version":"1.2.3"},"BGSIMD":{"Author":"Kwang Woo Ahn <kwooahn@mcw.edu>,
Kung-Sik Chan\n<kung-sik-chan@uiowa.edu>","Description":"Implement an efficient
block Gibbs sampler with incomplete\ndata from a multinomial distribution taking
values from the k\ncategories 1,2,...,k, where data are assumed to miss at
random\nand each missing datum belongs to one and only one of m\ndistinct non-empty
proper subsets A1, A2,..., Am of 1,2,...,k\nand the k categories are labelled such
that only consecutive\nA's may overlap.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BGSIMD","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Block Gibbs Sampler with Incomplete Multinomial
Distribution","Version":"1.0"},"BH":{"Author":"Dirk Eddelbuettel, John W. Emerson
and Michael J. Kane","Description":"Boost provides free peer-reviewed portable
C++ source\nlibraries. A large part of Boost is provided as C++ template
code\nwhich is resolved entirely at compile-time without linking. This\npackage
aims to provide the most useful subset of Boost libraries\nfor template use among
CRAN package. By placing these libraries in\nthis package, we offer a more
efficient distribution system for CRAN\nas replication of this code in the sources
of other packages is\navoided.\n\nAs of release 1.60, the following Boost libraries
are included:\nalgorithm any bind circular_buffer concept config
container\ndate_time detail dynamic_bitset exception filesystem foreach\nfunctional
fusion geometry graph heap integer interprocess\nintrusive io iostreams iterator
math move mpl multiprcecision\nnumeric pending phoenix preprocessor random range
smart_ptr\nspirit tuple type_trains typeof unordered utility uuid.","License":"BSL-
1.0","NeedsCompilation":"no","Package":"BH","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Boost C++ Header Files","Version":"1.60.0-1"},"BHH2":
{"Author":"Ernesto Barrios","Depends":"R (>= 2.0.0)","Description":"Functions and
data sets reproducing some examples in\nBox, Hunter and Hunter II. Useful for
statistical design\nof experiments, especially factorial
experiments.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BHH2","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"FrF2","Title":"Useful Functions for Box, Hunter and
Hunter II","Version":"2015.06.25"},"BIFIEsurvey":{"Author":"\nBIFIE","Depends":"R
(>= 2.15.0)","Description":"\nContains tools for survey statistics (especially in
educational\nassessment) for datasets with replication designs
(jackknife,\nbootstrap, replicate weights). Descriptive statistics, linear\nand
logistic regression, path models for manifest variables\nwith measurement error
correction and two-level hierarchical\nregressions for weighted samples are
included. Statistical\ninference can be conducted for multiply imputed datasets
and\nnested multiply imputed datasets.\nThis package is developed by BIFIE (Federal
Institute for\nEducational Research, Innovation and Development of the
Austrian\nSchool System; Salzburg, Austria).","Imports":"graphics, grDevices,
methods, miceadds, mitools, Rcpp, stats,\nutils, TAM","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"BIFIEsurvey","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"car, Hmisc, intsvy, lavaan.survey, lme4, survey,
svyPVpack","Title":"Tools for Survey Statistics in Educational
Assessment","URL":"http:\/\/www.bifie.at","Version":"1.8-0"},"BIGDAWG":
{"Author":"Derek Pappas <dpappas@chori.org>, Steve Mack <sjmack@chori.org>,
Jill\nHollenbach <Jill.Hollenbach@ucsf.edu>","Depends":"R (>=
2.10)","Description":"Data sets and functions for chi-squared Hardy-Weinberg and
case-control\nassociation tests of highly polymorphic genetic data [e.g., human
leukocyte antigen\n(HLA) data]. Performs association tests at multiple levels of
polymorphism\n(haplotype, locus and HLA amino-acids) as described in Pappas DJ,
Marin W, Hollenbach\nJA, Mack SJ (2016) <doi:10.1016\/j.humimm.2015.12.006>.
Combines rare variants to a\ncommon class to account for sparse cells in tables as
described by Hollenbach JA,\nMack SJ, Thomson G, Gourraud PA (2012)
<doi:10.1007\/978-1-61779-842-9_14>.","Imports":"XML, haplo.stats,
parallel","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"BIGDAWG","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr","Title":"Case-Control Analysis of Multi-Allelic
Loci","URL":"http:\/\/tools.immunogenomics.org\/","Version":"1.3.4"},"BIOM.utils":
{"Author":"Daniel T. Braithwaite [aut, cre]","Depends":"R (>= 3.0),
utils","Description":"Provides utilities to facilitate import, export and
computation with the\nBIOM (Biological Observation Matrix) format (http:\/\/biom-
format.org).","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"BIOM.utils","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"RJSONIO, MGRASTer","Title":"Utilities for the
BIOM (Biological Observation Matrix)
Format","URL":"https:\/\/github.com\/braithwaite\/BIOM.utils\/","Version":"0.9"},"B
IOdry":{"Author":"Wilson Lara <wilarhen@gmail.com>, Felipe Bravo
<fbravo@pvs.uva.es>","Depends":"nlme, ecodist","Description":"Multilevel data
frames of tree rings and climate are modeled into normalized fluctuations of tree
growth and aridity. Modeled fluctuations (model frames) are compared with Mantel
correlograms on multiple levels defined by sample design. Package implementation
can be understood by running examples in functions ringApply(), modelFrame(), and
muleMan().","License":"GPL-
3","NeedsCompilation":"no","Package":"BIOdry","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Multilevel Modeling of Dendroclimatical
Fluctuations","Version":"0.3"},"BIPOD":{"Author":"Anders Chr.
Jensen","Depends":"R(>= 3.0.2)","Description":"Bayesian parameter estimation for
(partially observed)\ntwo-dimensional diffusions.","Imports":"Rcpp (>=
0.11.1)","License":"GPL-
3","NeedsCompilation":"yes","Package":"BIPOD","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"BIPOD (Bayesian Inference for Partially Observed
diffusions)","Version":"0.2.1"},"BKPC":{"Author":"K. Domijan","Depends":"R (>=
2.10)","Description":"Bayesian kernel projection classifier is a nonlinear
multicategory classifier which performs the classification of the projections of
the data to the principal axes of the feature space. A Gibbs sampler is implemented
to find the posterior distributions of the
parameters.","Imports":"kernlab","License":"GPL-
2","NeedsCompilation":"yes","Package":"BKPC","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Bayesian Kernel Projection
Classifier","Version":"1.0"},"BLCOP":{"Author":"Francisco Gochez, Richard Chandler-
Mant, Suchen Jin, Jinjing Xie","Depends":"methods, MASS,
quadprog","Description":"An implementation of the Black-Litterman Model and
Atilio\nMeucci's copula opinion pooling framework.","Imports":"RUnit (>= 0.4.22),
timeSeries, fBasics, fMultivar, fPortfolio\n(>= 3011.81)","License":"GPL-
3","NeedsCompilation":"no","Package":"BLCOP","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"sn, corpcor, mnormt","Title":"Black-Litterman and Copula
Opinion Pooling Frameworks","Version":"0.3.1"},"BLR":{"Author":"Gustavo de los
Campos, Paulino Perez Rodriguez,","Depends":"R (>= 3.1.2),
SuppDists","Description":"Bayesian Linear Regression","License":"GPL-
2","NeedsCompilation":"yes","Package":"BLR","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Bayesian Linear Regression","Version":"1.4"},"BMA":
{"Author":"Adrian Raftery <raftery@uw.edu>, Jennifer Hoeting,\nChris Volinsky, Ian
Painter, Ka Yee Yeung","Depends":"survival, leaps, robustbase, inline,
rrcov","Description":"Package for Bayesian model averaging and variable selection
for linear models,\ngeneralized linear models and survival models
(cox\nregression).","Imports":"methods","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"BMA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"MASS, forward","Title":"Bayesian Model
Averaging","URL":"http:\/\/www.r-
project.org,\nhttp:\/\/www.research.att.com\/~volinsky\/bma.html","Version":"3.18.6
"},"BMN":{"Author":"Holger Hoefling","Depends":"R (>= 2.6.0)","Description":"This
package implements approximate and exact methods for\npairwise binary markov
models. The exact method uses an\nimplementation of the junction tree algorithm for
binary\ngraphical models. For more details see the help files","License":"GPL-
2","NeedsCompilation":"yes","Package":"BMN","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"The pseudo-likelihood method for pairwise binary markov
networks","Version":"1.02"},"BMRV":{"Author":"Liang He","Depends":"R (>= 3.1.1),
stats","Description":"Provides two Bayesian models for detecting the association
between rare variants and traits that can be continuous, ordinal or binary.
Bayesian latent variable collapsing model (BLVCM) detects interaction effect and is
dedicated to twin design while it can also be applied to independent samples.
Hierarchical Bayesian multiple regression model (HBMR) incorporates genotype
uncertainty information and can be applied to either independent or family samples.
Furthermore, it deals with continuous, binary and ordinal traits.","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"BMRV","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Bayesian Models for Rare Variant Association
Analysis","Version":"1.31"},"BMS":{"Author":"Martin Feldkircher and Stefan
Zeugner","Depends":"R (>= 2.5)","Description":"Bayesian model averaging for linear
models with a wide choice of (customizable) priors. Built-in priors include
coefficient priors (fixed, flexible and hyper-g priors), 5 kinds of model priors,
moreover model sampling by enumeration or various MCMC approaches. Post-processing
functions allow for inferring posterior inclusion and model probabilities, various
moments, coefficient and predictive densities. Plotting functions available for
posterior model size, MCMC convergence, predictive and coefficient densities, best
models representation, BMA comparison.","Imports":"graphics, methods,
stats","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"BMS","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Bayesian Model Averaging
Library","URL":"http:\/\/bms.zeugner.eu\/","Version":"0.3.4"},"BMhyd":
{"Author":"Dwueng-Chwuan Jhwueng <djhwueng@umail.iu.edu> and Brian O'Meara
<omeara.brian@gmail.com>","Description":"The BMhyd package analyzes the phenotypic
evolution of species of hybrid origin on a phylogenetic network. This package can
detect the hybrid vigor effect, a burst of variation at formation, and the relative
portion of heritability from its parents. Parameters are estimated
by maximum likelihood. Users need to enter a comparative data set, a phylogeny,
and information on gene flow leading to hybrids.","Imports":"corpcor, numDeriv,
geiger, ape, TreeSim, phytools, phylobase,\nmvtnorm, grDevices, graphics, methods,
stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BMhyd","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"PCM for Hybridization","Version":"1.2-
8"},"BNDataGenerator":{"Author":"Jae-seong Yoo","Depends":"R (>=
3.0.0)","Description":"Data generator based on Bayesian network
model","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BNDataGenerator","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"bnlearn","Title":"Data Generator based on
Bayesian Network
Model","URL":"http:\/\/www.github.com\/praster1\/BN_Data_Generator","Version":"1.0"
},"BNPTSclust":{"Author":"Martell-Juarez, D.A. & Nieto-Barajas,
L.E.","Depends":"R(>= 3.1.2), mvtnorm, MASS","Description":"Performs the algorithm
for time series clustering described in Nieto-Barajas and Contreras-Cristan
(2014).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BNPTSclust","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"A Bayesian Nonparametric Algorithm for Time Series
Clustering","Version":"1.1"},"BNPdensity":{"Author":"Ernesto Barrios, Antonio
Lijoi, Luis E. Nieto-Barajas and Igor PrÃ¼nster. R implementation by Ernesto
Barrios and Luis E. Nieto-Barajas.","Depends":"R(>=
2.14.0)","Description":"Modeling mixtures with normalized random measures by a
Ferguson-Klass type algorithm for posterior normalized random
measures.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BNPdensity","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Ferguson-Klass Type Algorithm for Posterior Normalized
Random\nMeasures","Version":"2015.5"},"BNSP":{"Author":"Georgios
Papageorgiou","Depends":"R (>= 3.1.0)","Description":"Markov chain Monte Carlo
algorithms for non- and semi-parametric models.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"BNSP","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"mvtnorm","Title":"Bayesian Non- and Semi-Parametric
Model
Fitting","URL":"http:\/\/www.bbk.ac.uk\/ems\/faculty\/papageorgiou\/BNSP","Version"
:"1.1.0"},"BOG":{"Author":"Jincheol Park (Keimyung University, South Korea), Cenny
Taslim, Shili Lin (The Ohio State University, USA)","Depends":"R(>= 3.1.2), hash,
DIME","Description":"An implementation of three statistical tests for
identification of COG (Cluster of Orthologous Groups) that are over represented
among genes that show differential expression under conditions. It also provides
tabular and graphical summaries of the results for easy visualisation and
presentation.","License":"GPL-
3","NeedsCompilation":"no","Package":"BOG","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Bacterium and Virus Analysis of Orthologous Groups (BOG) is
a\nPackage for Identifying Differentially Regulated Genes in the\nLight of Gene
Functions","Version":"2.0"},"BOIN":{"Author":"Ying Yuan and Suyu
Liu","Description":"The Bayesian optimal interval (BOIN) design is a novel phase
I\nclinical trial design for finding the maximum tolerated dose (MTD). It can
be\nused to design both single-agent and drug-combination trials. The BOIN
design\nis motivated by the top priority and concern of clinicians when testing a
new\ndrug, which is to effectively treat patients and minimize the chance of
exposing\nthem to subtherapeutic or overly toxic doses. The prominent advantage of
the\nBOIN design is that it achieves simplicity and superior performance at the
same\ntime. The BOIN design is algorithm-based and can be implemented in a
simple\nway similar to the traditional 3+3 design. The BOIN design yields an
average\nperformance that is comparable to that of the continual reassessment
method\n(CRM, one of the best model-based designs) in terms of selecting the MTD,
but\nhas a substantially lower risk of assigning patients to subtherapeutic or
overly\ntoxic doses.","Imports":"Iso","License":"GPL-
2","NeedsCompilation":"no","Package":"BOIN","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Bayesian Optimal INterval (BOIN) Design for Single-Agent
and\nDrug- Combination Phase I Clinical Trials","Version":"2.1"},"BPEC":
{"Author":"Ioanna Manolopoulou, Axel
Hille","Depends":"ape,maps,igraph","Description":"Model-based clustering for
phylogeographic data comprising mtDNA sequences and geographical locations along
with optional environmental characteristics, aiming to identify migration events
that led to homogeneous population
clusters.","Imports":"mvtnorm,maptools,sp,R2G2,phytools,fields,coda,methods","Licen
se":"GPL-
2","NeedsCompilation":"yes","Package":"BPEC","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Bayesian Phylogeographic and Ecological
Clustering","Version":"1.0"},"BRugs":{"Author":"OpenBUGS was developed by Andrew
Thomas, Dave Lunn, David Spiegelhalter and Nicky Best. R interface developed by
Uwe Ligges, Sibylle Sturtz, Andrew Gelman, Gregor Gorjanc and Chris Jackson. Linux
port and most recent developments by Chris Jackson.","Depends":"R (>=
2.11.0)","Description":"Fully-interactive R interface to the 'OpenBUGS' software
for Bayesian analysis using MCMC sampling. Runs natively and stably in 32-bit R
under Windows. Versions running on Linux and on 64-bit R under Windows are
in \"beta\" status and less efficient.","Imports":"utils, coda, grDevices,
graphics, stats","License":"GPL-
2","NeedsCompilation":"yes","Package":"BRugs","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Interface to the 'OpenBUGS' MCMC
Software","URL":"http:\/\/www.openbugs.net\/","Version":"0.8-6"},"BSDA":
{"Author":"Alan T. Arnholt","Depends":"e1071, lattice","Description":"Data sets for
book \"Basic Statistics and Data Analysis\" by\nLarry J. Kitchens","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"BSDA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Basic Statistics and Data
Analysis","Version":"1.01"},"BSGS":{"Author":"Kuo-Jung Lee and Ray-Bin
Chen","Depends":"R (>= 3.1.1), MASS, compiler, pscl, plyr,
batchmeans","Description":"The integration of Bayesian variable and sparse group
variable selection approaches for regression models.","License":"GPL-
2","NeedsCompilation":"no","Package":"BSGS","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Bayesian Sparse Group Selection","Version":"2.0"},"BSGW":
{"Author":"Alireza S. Mahani, Mansour T.A. Sharabiani","Depends":"survival,
MfUSampler","Description":"Bayesian survival model using Weibull regression on both
scale and shape parameters. Dependence of shape parameter on covariates permits
deviation from proportional-hazard assumption, leading to dynamic - i.e. non-
constant with time - hazard ratios between subjects. Bayesian Lasso shrinkage in
the form of two Laplace priors - one for scale and one for shape coefficients -
allows for many covariates to be included. Cross-validation helper functions can be
used to tune the shrinkage parameters. Monte Carlo Markov Chain (MCMC) sampling
using a Gibbs wrapper around Radford Neal's univariate slice sampler (R package
MfUSampler) is used for coefficient estimation.","Imports":"foreach,
doParallel","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BSGW","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Bayesian Survival Model with Lasso Shrinkage Using
Generalized\nWeibull Regression","Version":"0.9.1"},"BSSasymp":{"Author":"Jari
Miettinen, Klaus Nordhausen, Hannu Oja, Sara Taskinen","Description":"Functions to
compute the asymptotic covariance matrices of mixing and unmixing matrix estimates
of the following blind source separation (BSS) methods: symmetric and squared
symmetric FastICA, regular and adaptive deflation-based FastICA, FOBI, JADE, AMUSE
and deflation-based and symmetric SOBI. Also functions to estimate these
covariances based on data are available.","Imports":"fICA (>= 1.0-2),
JADE","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"BSSasymp","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Asymptotic Covariance Matrices of Some BSS Mixing and
Unmixing\nMatrix Estimates","Version":"1.1-2"},"BSagri":{"Author":"Frank
Schaarschmidt","Depends":"gamlss, multcomp, MCPAN","Description":"Collection of
functions, data sets and code examples\nfor evaluations of field trials with the
objective of equivalence assessment.","Imports":"mvtnorm, boot,
mratios","License":"GPL-
2","NeedsCompilation":"no","Package":"BSagri","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Statistical methods for safety assessment in agricultural
field\ntrials","Version":"0.1-8"},"BSquare":{"Author":"Luke Smith & Brian
Reich","Depends":"quadprog, quantreg, VGAM","Description":"This package models the
quantile process as a function of\npredictors.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"BSquare","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"survival","Title":"Bayesian Simultaneous Quantile
Regression","Version":"1.1"},"BTLLasso":{"Author":"Gunther
Schauberger","Depends":"Matrix, parallel","Description":"Performs 'BTLLasso', a
method to model heterogeneity in paired comparison data. Subject-specific
covariates are allowed to have an influence on the attractivity\/strength of the
objects. An L1 penalty on the pairwise differences between the object-specific
parameters allows for both clustering of objects with regard to covariates and
elimination of irrelevant covariates.","Imports":"Rcpp (>= 0.11.3),
stringr","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"BTLLasso","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Modelling Heterogeneity in Paired Comparison
Data","Version":"0.1-2"},"BTSPAS":{"Author":"Carl J Schwarz <cschwarz@stat.sfu.ca>
and\nSimon J Bonner <simon.bonner@uky.edu>","Description":"BTSPAS
provides advanced Bayesian methods to estimate\nabundance and run-timing from
temporally-stratified\nPetersen mark-recapture experiments. Methods
include\nhierarchical modelling of the capture probabilities\nand spline smoothing
of the daily run size. This version\nuses JAGS to sample from the posterior
distribution.","Imports":"coda, splines, actuar, rjags, R2OpenBUGS, ggplot2,
plyr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BTSPAS","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"BRugs","Title":"Bayesian Time-Strat. Population
Analysis","URL":"http:\/\/www.stat.sfu.ca\/~cschwarz\/Consulting\/Trinity\/Phase2",
"Version":"2014.0901"},"BTYD":{"Author":"Lukasz Dziurzynski [aut],\nEdward
Wadsworth [aut],\nPeter Fader [ctb],\nElea McDonnell Feit [ctb],\nDaniel McCarthy
[aut, cre, ctb],\nBruce Hardie [ctb],\nArun Gopalakrishnan [ctb],\nEric Schwartz
[ctb],\nYao Zhang [ctb]","Depends":"hypergeo","Description":"This package contains
functions for data preparation, parameter estimation, scoring, and plotting for the
BG\/BB, BG\/NBD and Pareto\/NBD models.","Imports":"Matrix","License":"GPL-
3","NeedsCompilation":"no","Package":"BTYD","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"knitr","Title":"Implementing Buy 'Til You Die
Models","URL":"wcai.wharton.upenn.edu","Version":"2.4"},"BVS":{"Author":"Melanie
Quintana <maw27.wilson@gmail.com>","Depends":"MASS, msm, haplo.stats, R (>=
2.14.0)","Description":"The functions in this package focus on analyzing\ncase-
control association studies involving a group of genetic\nvariants. In particular,
we are interested in modeling the\noutcome variable as a function of a multivariate
genetic\nprofile using Bayesian model uncertainty and variable
selection\ntechniques. The package incorporates functions to analyze data\nsets
involving common variants as well as extensions to model\nrare variants via the
Bayesian Risk Index (BRI) as well as\nhaplotypes. Finally, the package also allows
the incorporation\nof external biological information to inform the
marginal\ninclusion probabilities via the
iBMU.","License":"Unlimited","NeedsCompilation":"no","Package":"BVS","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Title":"Bayesian Variant Selection: Bayesian
Model Uncertainty\nTechniques for Genetic Association
Studies","Version":"4.12.1"},"BWStest":{"Author":"Steven E. Pav [aut,
cre]","Description":"Performs the 'Baumgartner-Weiss-Schindler' two-sample test of
equal\nprobability distributions.","Imports":"Rcpp (>= 0.12.3)","License":"LGPL-
3","NeedsCompilation":"yes","Package":"BWStest","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"testthat","Title":"Baumgartner Weiss Schindler Test of
Equal
Distributions","URL":"https:\/\/github.com\/shabbychef\/BWStest","Version":"0.1.0"}
,"BaBooN":{"Author":"Florian Meinfelder [aut, cre],\nThorsten Schnapp
[aut]","Depends":"R (>= 3.1.0), Rcpp (>= 0.11.2)","Description":"Included are two
variants of Bayesian Bootstrap\nPredictive Mean Matching to multiply impute missing
data. The\nfirst variant is a variable-by-variable imputation combining\nsequential
regression and Predictive Mean Matching (PMM) that\nhas been extended for unordered
categorical data. The Bayesian\nBootstrap allows for generating approximately
proper multiple\nimputations. The second variant is also based on PMM, but
the\nfocus is on imputing several variables at the same time. The\nsuggestion is to
use this variant, if the missing-data pattern\nresembles a data fusion situation,
or any other\nmissing-by-design pattern, where several variables have\nidentical
missing-data patterns. Both variants can be run as\n'single imputation' versions,
in case the analysis objective is\nof a purely descriptive
nature.","Imports":"Hmisc, MASS, nnet, coda","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"BaBooN","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"mice, lattice, norm","Title":"Bayesian Bootstrap
Predictive Mean Matching - Multiple and\nSingle Imputation for Discrete
Data","URL":"http:\/\/www.r-project.org","Version":"0.2-0"},"BaM":{"Author":"Jeff
Gill <jgill@wustl.edu>","Depends":"R (>= 1.4.1), bayesm, coda, MASS, stats, mice,
survival,\nforeign,nnet","Description":"Books is \"Bayesian Methods: A Social and
Behavioral\nSciences Approach, Second Edition published by CRC Press,
2007\"","License":"GPL","NeedsCompilation":"no","Package":"BaM","Repository":"http:
\/\/cran.csiro.au\/src\/contrib","Title":"Functions and datasets for books by Jeff
Gill","URL":"jgill.wustl.edu","Version":"0.99"},"BaSTA":{"Author":"Fernando
Colchero, Owen Jones, Maren Rebke","Depends":"R (>= 2.10)","Description":"Estimates
survival and mortality with covariates from capture-recapture\/recovery data in a
Bayesian framework when many individuals are of unknown age. It includes tools for
data checking, model diagnostics and outputs such as life-tables and
plots.","Imports":"snowfall","License":"GPL","NeedsCompilation":"no","Package":"BaS
TA","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Age-Specific
Survival Analysis from Incomplete\nCapture-Recapture\/Recovery
Data","Version":"1.9.4"},"BacArena":{"Author":"Eugen Bauer [aut],\nJohannes
Zimmermann [aut, cre]","Depends":"R (>= 3.0.0), sybil (>= 1.3.0), ReacTran (>=
1.4.2), deSolve\n(>= 1.12), Matrix (>= 1.2)","Description":"Can be used for
simulation of organisms living in\ncommunities. Each organism is represented
individually and genome scale\nmetabolic models determine the uptake and release of
compounds. Biological\nprocesses such as movement, diffusion, chemotaxis and
kinetics are available\nalong with data analysis techniques.","Imports":"igraph,
methods, utils, stats, graphics, Rcpp","License":"GPL-
3","NeedsCompilation":"yes","Package":"BacArena","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"glpkAPI, sybilSBML, knitr,
rmarkdown","Title":"Modeling Framework for Cellular Communities in
their\nEnvironments","URL":"https:\/\/github.com\/euba\/BacArena","Version":"1.0.1"
},"Bagidis":{"Author":"Catherine Timmermans","Depends":"abind","Description":"This
is the companion package of a PhD thesis entitled \"Bases Giving Distances. A new
paradigm for investigating functional data with applications for spectroscopy\" by
Timmermans (2012). See references for details and related publications. The core of
the BAGIDIS methodology is a functional wavelet based semi-distance that has been
introduced by Timmermans and von Sachs (2010, 2015) and Timmermans, Delsol and von
Sachs (2013). This semi-distance allows for comparing curves with sharp local
patterns that might not be well aligned from one curve to another. It is data-
driven and highly adaptive to the curves being studied. Its main originality is
its ability to consider simultaneously horizontal and vertical variations of
patterns, which proofs highly useful when used together with clustering algorithms
or visualization method. BAGIDIS is an acronym for BAsis GIving DIStances. The
extension of BAGIDIS to image data relies on the same principles and has been
described in Timmermans and Fryzlewicz (2012), Fryzlewicz and Timmermans
(2015).","License":"GPL","NeedsCompilation":"no","Package":"Bagidis","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Title":"BAses GIving
DIStances","Version":"1.0"},"BalancedSampling":{"Author":"Anton GrafstrÃ¶m,
Jonathan Lisic","Description":"Select balanced and spatially balanced probability
samples in multi-dimensional spaces with any prescribed inclusion probabilities. It
contains fast (C++ via Rcpp) implementations of the included sampling methods. The
local pivotal method and spatially correlated Poisson sampling (for spatially
balanced sampling) are included. Also the cube method (for balanced sampling) and
the local cube method (for doubly balanced sampling) are included.","Imports":"Rcpp
(>= 0.11.1)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"BalancedSampling","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Balanced and Spatially Balanced
Sampling","URL":"http:\/\/www.antongrafstrom.se\/balancedsampling","Version":"1.5.1
"},"Barnard":{"Author":"Kamil Erguler","Description":"Barnard's unconditional test
for 2x2 contingency tables.","License":"GPL-
2","NeedsCompilation":"yes","Package":"Barnard","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Barnard's Unconditional
Test","URL":"https:\/\/github.com\/kerguler\/Barnard","Version":"1.6"},"BatchExperi
ments":{"Author":"Bernd Bischl <bernd_bischl@gmx.net>,\nMichel Lang
<michellang@gmail.com>,\nOlaf Mersmann <olafm@p-value.net>","Depends":"R (>=
2.15.0), BatchJobs (>= 1.6)","Description":"Extends the BatchJobs package to run
statistical experiments on\nbatch computing clusters. For further details see the
project web page.","Imports":"checkmate (>= 1.5), BBmisc (>= 1.8), DBI, RSQLite (>=
1.0.0),\nplyr","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"BatchExperiments","Repository":"http:\/
\/cran.csiro.au\/src\/contrib","Suggests":"randomForest, rpart,
testthat","Title":"Statistical Experiments on Batch Computing
Clusters","URL":"https:\/\/github.com\/tudo-
r\/BatchExperiments","Version":"1.4.1"},"BatchJobs":{"Author":"Bernd Bischl
<bernd_bischl@gmx.net>,\nMichel Lang <michellang@gmail.com>,\nHenrik Bengtsson
<henrikb@braju.com>","Depends":"R (>= 2.15.0), BBmisc (>= 1.9),
methods","Description":"Provides Map, Reduce and Filter variants to generate jobs
on batch\ncomputing systems like PBS\/Torque, LSF, SLURM and Sun Grid
Engine.\nMulticore and SSH systems are also supported. For further details see
the\nproject web page.","Imports":"brew, checkmate (>= 1.5.1), DBI, digest, fail
(>= 1.2),\nparallel, RSQLite (>= 1.0.0), sendmailR, stats, stringr,
utils","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"BatchJobs","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"MASS,
testthat","Title":"Batch Computing with R","URL":"https:\/\/github.com\/tudo-
r\/BatchJobs","Version":"1.6"},"BayClone2":{"Author":"Juhee Lee, Peter Mueller,
Subhajit Sengupta, Kamalakar Gulukota, Yuan Ji","Depends":"R (>= 2.0.1),
combinat","Description":"A Bayesian feature allocation model is implemented for
inference on tumor heterogeneity using next-generation sequencing data. The model
identifies the subclonal copy number and single nucleotide mutations at a selected
set of loci and provides inference on genetic tumor variation.","License":"GPL-3 |
file
LICENSE","NeedsCompilation":"yes","Package":"BayClone2","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Bayesian Feature Allocation Model for Tumor
Heterogeneity","Version":"1.1"},"BayHap":{"Author":"Raquel Iniesta and Victor
Moreno","Depends":"boa","Description":"The package BayHap performs simultaneous
estimation of\nuncertain haplotype frequencies and association with
haplotypes\nbased on generalized linear models for quantitative, binary
and\nsurvival traits. Bayesian statistics and Markov Chain Monte\nCarlo techniques
are the theoretical framework for the methods\nof estimation included in this
package. Prior values for model\nparameters can be included by the user.
Convergence diagnostics\nand statistical and graphical analysis of the sampling
output\ncan be also carried out.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"BayHap","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Bayesian analysis of haplotype association using Markov
Chain\nMonte Carlo","Version":"1.0.1"},"BayHaz":{"Author":"Luca La
Rocca","Depends":"R (>= 1.8.0), splines","Description":"A suite of R functions for
Bayesian estimation of smooth\nhazard rates via Compound Poisson Process (CPP) and
Bayesian\nPenalized Spline (BPS) priors.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BayHaz","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"coda","Title":"R Functions for Bayesian Hazard Rate
Estimation","URL":"http:\/\/www-dimat.unipv.it\/luca\/bayhaz.htm","Version":"0.1-
3"},"BaySIC":{"Author":"Nicholas B. Larson","Depends":"R (>= 2.10), rjags, fields,
poibin","Description":"This R package is the software implementation of
the\nalgorithm BaySIC, a Bayesian approach toward analysis of\nsignificantly
mutated genes in cancer data.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BaySIC","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Bayesian Analysis of Significantly Mutated Genes in
Cancer","Version":"1.0"},"BayesBD":{"Author":"Meng Li","Depends":"R(>=
2.10.0)","Description":"It estimate the boundaries in an image adaptively to the
smoothness\nlevel of the boundary.The method is applicable to images with binary
noise,\nGaussian noise or Poisson noise.","Imports":"plotrix","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"BayesBD","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Bayesian Boundary Detection in
Images","Version":"0.1"},"BayesBridge":{"Author":"Nicholas G. Polson, James G.
Scott, and Jesse Windle","Depends":"R (>= 2.10)","Description":"Bayesian bridge
regression.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"BayesBridge","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Bridge Regression","Version":"0.6"},"BayesCR":
{"Author":"Aldo M. Garay <medina_garay@yahoo.com>,\nMonique B. Massuia
<moniquemassuia@gmail.com>\nVictor H. Lachos
<hlachos@ime.unicamp.br>","Depends":"R(>= 3.1.2)","Description":"Propose a
parametric fit for censored linear regression models based on SMSN distributions,
from a Bayesian perspective. Also, generates SMSN random
variables.","Imports":"mvtnorm, Rlab, truncdist, mnormt, rootSolve","License":"GPL
(>=
3.1.2)","NeedsCompilation":"no","Package":"BayesCR","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Bayesian Analysis of Censored Regression Models Under
Scale\nMixture of Skew Normal Distributions","Version":"2.0"},"BayesComm":
{"Author":"Nick Golding and David J. Harris","Description":"Bayesian multivariate
binary (probit) regression\nmodels for analysis of ecological
communities.","Imports":"Rcpp (>= 0.11.6), abind, coda, mvtnorm","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"BayesComm","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Bayesian Community Ecology Analysis","Version":"0.1-
2"},"BayesDA":{"Author":"Compiled by Kjetil Halvorsen","Depends":"stats, R (>=
2.2.0)","Description":"Functions for Bayesian Data Analysis, with datasets
from\nthe book \"Bayesian data Analysis (second edition)\" by Gelman,\nCarlin,
Stern and Rubin. Not all datasets yet, hopefully\ncompleted soon.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"BayesDA","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"MCMCpack","Title":"Functions and Datasets for the book
\"Bayesian Data Analysis\"","Version":"2012.04-1"},"BayesFactor":{"Author":"Richard
D. Morey [aut, cre],\nJeffrey N. Rouder [aut],\nTahira Jamil [ctb]","Depends":"R
(>= 3.0.2), coda, Matrix (>= 1.1-1)","Description":"A suite of functions for
computing\nvarious Bayes factors for simple designs, including contingency
tables,\none- and two-sample designs, one-way designs, general ANOVA designs,
and\nlinear regression.","Imports":"pbapply, mvtnorm, stringr, utils, graphics,
gtools,\nMatrixModels, Rcpp (>= 0.11.2), methods","License":"GPL-
2","NeedsCompilation":"yes","Package":"BayesFactor","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"doMC, foreach, testthat, knitr, markdown, arm,
lme4, xtable,\nlanguageR","Title":"Computation of Bayes Factors for Common
Designs","URL":"http:\/\/bayesfactorpcl.r-forge.r-project.org\/","Version":"0.9.12-
2"},"BayesGESM":{"Author":"Luz Marina Rondon <lumarp@gmail.com> and Heleno
Bolfarine","Depends":"splines, GIGrvg, normalp, Formula","Description":"Set of
tools to perform the statistical inference based on the Bayesian approach for
regression models under the assumption that independent additive errors follow
normal, Student-t, slash, contaminated normal, Laplace or symmetric hyperbolic
distributions, i.e., additive errors follow a scale mixtures of normal
distributions. The regression models considered in this package are: (i)
Generalized elliptical semi-parametric models, where both location and dispersion
parameters of the response variable distribution include non-parametric additive
components described by using B-splines; and (ii) Flexible measurement error models
under the presence of homoscedastic and heteroscedastic random errors, which admit
explanatory variables with and without measurement additive errors as well as the
presence of a non-parametric components approximated by using B-
splines.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"BayesGESM","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"ssym","Title":"Bayesian Analysis of Generalized
Elliptical Semi-Parametric\nModels and Flexible Measurement Error
Models","Version":"1.4"},"BayesH":{"Author":"Renato Rodrigues Silva","Depends":"R
(>= 2.10)","Description":"Functions to performs Bayesian regression model with
mixture of two scaled inverse\nchi square as hyperprior distribution for variance
of each regression coefficient.","License":"GPL-
3","NeedsCompilation":"yes","Package":"BayesH","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Bayesian Regression Model with Mixture of Two Scaled
Inverse Chi\nSquare as Hyperprior","Version":"1.0"},"BayesLCA":{"Author":"Arthur
White [aut, cre] (Previous email address:\narthur.white@ucdconnect.ie),\nThomas
Brendan Murphy [aut, ths]","Depends":"e1071, coda","Description":"Bayesian Latent
Class Analysis using several different\nmethods.","Imports":"fields, nlme,
MCMCpack","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BayesLCA","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Bayesian Latent Class
Analysis","Version":"1.7"},"BayesLogit":{"Author":"Nicholas G. Polson, James G.
Scott, and Jesse Windle","Depends":"R (>= 2.14.0)","Description":"The BayesLogit
package does posterior simulation for binomial and\nmultinomial logistic regression
using the Polya-Gamma latent variable\ntechnique. This method is fully automatic,
exact, and fast. A routine to\nefficiently sample from the Polya-Gamma class of
distributions is included.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"BayesLogit","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Logistic Regression","Version":"0.5.1"},"BayesMAMS":
{"Author":"Philip Pallmann, Amanda Turner","Description":"Calculating Bayesian
sample sizes for multi-arm trials where several experimental treatments are
compared to a common control, perhaps even at multiple
stages.","Imports":"mvtnorm","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BayesMAMS","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"MAMS, knitr","Title":"Designing Bayesian Multi-Arm
Multi-Stage
Studies","URL":"https:\/\/github.com\/PhilipPallmann\/BayesMAMS","Version":"0.1"},"
BayesMed":{"Author":"Michele B. Nuijten, Ruud Wetzels, Dora Matzke, Conor V. Dolan,
and Eric-Jan Wagenmakers","Depends":"R (>= 2.12.1), R2jags, QRM, polspline,
MCMCpack","Description":"Default Bayesian hypothesis tests for correlation, partial
correlation, and mediation","License":"GPL-
2","NeedsCompilation":"no","Package":"BayesMed","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Default Bayesian Hypothesis Tests for Correlation,
Partial\nCorrelation, and Mediation","Version":"1.0.1"},"BayesMixSurv":
{"Author":"Alireza S. Mahani, Mansour T.A.
Sharabiani","Depends":"survival","Description":"Bayesian Mixture Survival Models
using Additive Mixture-of-Weibull Hazards, with Lasso Shrinkage and
Stratification","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BayesMixSurv","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Bayesian
Mixture Survival Models using Additive\nMixture-of-Weibull Hazards, with Lasso
Shrinkage and\nStratification","Version":"0.9"},"BayesNI":{"Author":"Sujit K Ghosh,
Muhtarjan Osman","Description":"A Bayesian testing procedure for noninferiority
trials\nwith binary endpoints. The prior is constructed based on\nBernstein
polynomials with options for both informative and\nnon-informative prior. The
critical value of the test statistic\n(Bayes factor) is determined by minimizing
total weighted error\n(TWE) criteria","License":"GPL-
2","NeedsCompilation":"no","Package":"BayesNI","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"BayesNI: Bayesian Testing Procedure for Noninferiority
with\nBinary Endpoints","Version":"0.1"},"BayesSAE":{"Author":"Chengchun Shi, with
contributions from Peng Zhang","Depends":"Formula, coda,
lattice","Description":"This package provides a variety of functions to deal with
several specific small area area-\nlevel models in Bayesian context. Models
provided range from the basic Fay-Herriot model to\nits improvement such as You-
Chapman models, unmatched models, spatial models and so on.\nDifferent types of
priors for specific parameters could be chosen to obtain MCMC posterior\ndraws. The
main sampling function is written in C with GSL lab so as to facilitate
the\ncomputation. Model internal checking and model comparison criteria are also
involved.","License":"GPL-
2","NeedsCompilation":"yes","Package":"BayesSAE","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Bayesian Analysis of Small Area
Estimation","Version":"1.0-1"},"BayesSingleSub":{"Author":"Richard D. Morey, Rivka
de Vries","Depends":"R (>= 3.0.0)","Description":"The BayesSingleSub package is a
suite of functions for computing various Bayes factors for interrupted time-series,
based on the models described in de Vries and Morey (2013).","Imports":"coda,
mvtnorm, MCMCpack","License":"GPL-
2","NeedsCompilation":"yes","Package":"BayesSingleSub","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"knitr","Title":"Computation of Bayes factors
for interrupted time-series designs","Version":"0.6.2"},"BayesSummaryStatLM":
{"Author":"Evgeny Savel'ev, Alexey Miroshnikov, Erin Conlon","Depends":"R (>=
3.1.1), mvnfast, ff","Description":"Methods for generating Markov Chain Monte Carlo
(MCMC) posterior samples of Bayesian linear regression model parameters that
require only summary statistics of data as input. Summary statistics are useful for
systems with very limited amounts of physical memory. The package provides two
functions: one function that computes summary statistics of data and one function
that carries out the MCMC posterior sampling for Bayesian linear regression models
where summary statistics are used as input. The function read.regress.data.ff
utilizes the R package 'ff' to handle data sets that are too large to fit into a
user's physical memory, by reading in data in chunks.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BayesSummaryStatLM","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Title":"MCMC Sampling of Bayesian Linear Models via
Summary Statistics","Version":"1.0-1"},"BayesTree":{"Author":"Hugh Chipman
<hugh.chipman@gmail.com>, Robert
McCulloch\n<robert.e.mcculloch@gmail.com>","Description":"This is an implementation
of BART:Bayesian Additive Regression Trees,\nby Chipman, George, McCulloch
(2010).","Imports":"nnet","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"BayesTree","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Bayesian Additive Regression
Trees","URL":"http:\/\/www.r-project.org, http:\/\/www.rob-
mcculloch.org","Version":"0.3-1.3"},"BayesValidate":{"Author":"Samantha Cook
<cook@stat.columbia.edu>.","Depends":"R (>= 2.0.1)","Description":"BayesValidate
implements the software validation method\ndescribed in the paper \"Validation of
Software for Bayesian\nModels using Posterior Quantiles\" (Cook, Gelman, and
Rubin,\n2005). It inputs a function to perform Bayesian inference as\nwell as
functions to generate data from the Bayesian model\nbeing fit, and repeatedly
generates and analyzes data to check\nthat the Bayesian inference program works
properly.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BayesValidate","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"BayesValidate
Package","Version":"0.0"},"BayesVarSel":{"Author":"Gonzalo Garcia-Donato and Anabel
Forte","Depends":"R (>= 3.0), parallel, MASS","Description":"Conceived to calculate
Bayes factors in linear models and then to provide a formal Bayesian answer to
testing and variable selection problems. From a theoretical side, the emphasis in
the package is placed on the prior distributions and BayesVarSel allows using a
wide range of them: Jeffreys (1961); Zellner and
Siow(1980)<DOI:10.1007\/bf02888369>; Zellner and Siow(1984); Zellner
(1986)<DOI:10.2307\/2233941>; Fernandez et al. (2001)<DOI:10.1016\/s0304-
4076(00)00076-2>; Liang et al. (2008)<DOI:10.1198\/016214507000001337> and Bayarri
et al. (2012)<DOI:10.1214\/12-aos1013>. The interaction with the package is through
a friendly interface that syntactically mimics the well-known lm() command of R.
The resulting objects can be easily explored providing the user very valuable
information (like marginal, joint and conditional inclusion probabilities of
potential variables; the highest posterior probability model, HPM; the median
probability model, MPM) about the structure of the true -data generating- model.
Additionally, \"BayesVarSel\" incorporates abilities to handle problems with a
large number of potential explanatory variables through parallel and heuristic
versions of the main commands, Garcia-Donato and Martinez-Beneito
(2013)<DOI:10.1080\/01621459.2012.742443>.","License":"GPL-
2","NeedsCompilation":"yes","Package":"BayesVarSel","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Bayes Factors, Model Choice and Variable Selection in
Linear\nModels","Version":"1.6.2"},"BayesX":{"Author":"Thomas Kneib, Felix Heinzl,
Andreas Brezger, Daniel Sabanes Bove, Nadja
Klein","Depends":"shapefiles","Description":"This package provides functionality
for exploring and visualising estimation results\nobtained with the software
package BayesX for structured additive regression. It also provides\nfunctions that
allow to read, write and manipulate map objects that are required in spatial
analyses\nperformed with BayesX, a free software for estimating structured additive
regression models\n(http:\/\/www.bayesx.org).","Imports":"sp, maptools, colorspace
(>= 0.97), coda, splines","License":"GPL-
2","NeedsCompilation":"no","Package":"BayesX","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"spdep, akima, gpclib, rgeos","Title":"R Utilities
Accompanying the Software Package BayesX","Version":"0.2-9"},"BayesXsrc":
{"Author":"Daniel Adler [aut, cre],\nThomas Kneib [aut],\nStefan Lang
[aut],\nNikolaus Umlauf [aut],\nAchim Zeileis [aut]","Depends":"R (>=
2.7.0)","Description":"BayesX performs Bayesian inference in structured additive
regression (STAR) models.\nThe R package BayesXsrc provides the BayesX command line
tool for easy installation.\nA convenient R interface is provided in package
R2BayesX.","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"BayesXsrc","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"R2BayesX","Title":"R Package Distribution of the
BayesX C++ Sources","URL":"http:\/\/www.BayesX.org\/","Version":"2.1-
2"},"BayesianAnimalTracker":{"Author":"Yang (Seagle) Liu [aut, cre],\nBrian C.
Battaile [ctb]","Depends":"R (>= 2.10),
TrackReconstruction","Description":"Bayesian melding approach to combine the GPS
observations and Dead-Reckoned path for an accurate animal's track, or
equivalently, use the GPS observations to correct the Dead-Reckoned path. It can
take the measurement errors in the GPS observations into account and provide
uncertainty statement about the corrected path. The main calculation can be done by
the BMAnimalTrack function.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BayesianAnimalTracker","Repository":"http:\/
\/cran.csiro.au\/src\/contrib","Title":"Bayesian Melding of GPS and DR Path for
Animal Tracking","Version":"1.2"},"Bayesianbetareg":{"Author":"The code in R and
guide document were prepared by Margarita Marin,\nJavier Rojas, Daniel Jaimes and
Hugo Andres Gutierrez Rojas, under the\ndirection of professor Edilberto Cepeda-
Cuervo and with collaboration of\nMartha Corrales, Maria Fernanda Zarate, Ricardo
Duplat and Luis F\nVillarraga.","Depends":"R (>= 2.12.1), mvtnorm,
betareg","Description":"This package performs beta regression","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Bayesianbetareg","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Bayesian Beta regression: joint mean and
precision modeling","Version":"1.2"},"Bayesthresh":{"Author":"Fabio Mathias Correa
<fmcorrea@uesc.br> and Julio Silvio de\nSousa Bueno Filho
<juliobuenof@gmail.com>","Depends":"R(>= 2.15.2), lme4 (>= 0.999375-35), MASS,
VGAM, mvtnorm,\nmatrixcalc, coda","Description":"This package fits a linear mixed
model for ordinal\ncategorical responses using Bayesian inference via Monte
Carlo\nMarkov Chains. Default is Nandran & Chen algorithm using\nGaussian link
function and saving just the summaries of the\nchains. Among the options, package
allow for two other options\nof algorithms, for using Student's \"t\" link function
and for\nsaving the full chains.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"Bayesthresh","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Bayesian thresholds mixed-effects models for
categorical data","Version":"2.0.1"},"BaylorEdPsych":{"Author":"A. Alexander
Beaujean","Description":"Functions and data used for Baylor University
Educational\nPsychology Quantitative Courses","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BaylorEdPsych","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"mvnmle, moments","Title":"R Package for Baylor
University Educational Psychology\nQuantitative Courses","Version":"0.5"},"BcDiag":
{"Author":"Aregay Mengsteab, Martin Otava, Tatsiana Khamiakova, Ewoud De
Troyer","Depends":"R (>= 2.10)","Description":"Diagnostic tools based on two-
way\nanova and median-polish residual plots for Bicluster output\nobtained from
packages; \"biclust\" by Kaiser et al.(2008),\"isa2\"\nby Csardi et al. (2010)
and \"fabia\" by Hochreiter et al.\n(2010). Moreover, It provides visualization
tools for bicluster\noutput and corresponding non-bicluster rows- or
columns\noutcomes. It has also extended the idea of Kaiser et al.(2008)\nwhich is,
extracting bicluster output in a text format, by\nadding two bicluster methods from
the fabia and isa2 R\npackages.","Imports":"fabia, methods, graphics,
stats","License":"GPL-
3","NeedsCompilation":"no","Package":"BcDiag","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"biclust, isa2","Title":"Diagnostics Plots for Bicluster
Data","Version":"1.0.10"},"Bchron":{"Author":"Andrew
Parnell","Depends":"inline","Description":"Enables quick calibration of radiocarbon
dates under various calibration curves (including user generated ones); Age-depth
modelling as per the algorithm of Haslett and Parnell (2008); Relative sea level
rate estimation incorporating time uncertainty in polynomial regression models; and
non-parametric phase modelling via Gaussian mixtures as a means to determine the
activity of a site (and as an alternative to the Oxcal function SUM). The package
includes a vignette which can be accessed via
vignette(â€˜Bchronâ€™).","Imports":"hdrcde, utils, MASS, ellipse, coda,
mclust","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Bchron","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr","Title":"Radiocarbon Dating, Age-Depth
Modelling, Relative Sea Level Rate\nEstimation, and Non-Parametric Phase
Modelling","Version":"4.1.2"},"Bclim":{"Author":"Andrew Parnell, Thinh Doan and
James Sweeney","Depends":"MASS, mclust","Description":"This package takes
pollen\/time data from lake cores and produces a Bayesian posterior distribution of
palaeoclimate from that location after fitting a non-linear non-Gaussian state-
space model.","Imports":"hdrcde, statmod","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"Bclim","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"Bchron, doMC, foreach","Title":"Bayesian Palaeoclimate
Reconstruction from Pollen","Version":"2.3.1"},"Benchmarking":{"Author":"Peter
Bogetoft and Lars Otto","Depends":"lpSolveAPI, ucminf","Description":"Methods for
frontier\nanalysis, Data Envelopment Analysis (DEA), under different\ntechnology
assumptions (fdh, vrs, drs, crs, irs, add\/frh, and fdh+),\nand using different
efficiency measures (input based, output based,\nhyperbolic graph, additive, super,
and directional efficiency). Peers\nand slacks are available, partial price
information can be included,\nand optimal cost, revenue and profit can be
calculated. Evaluation of\nmergers is also supported. Methods for graphing the
technology sets\nare also included. There is also support comparative methods
based\non Stochastic Frontier Analyses (SFA). In general, the methods can be\nused
to solve not only standard models, but also many other model\nvariants. It
complements the book, Bogetoft and Otto,\nBenchmarking with DEA, SFA, and R,
Springer-Verlag, 2011, but can of\ncourse also be used as a stand-alone
package.","Imports":"methods, stats, graphics, grDevices","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Benchmarking","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Benchmark and Frontier Analysis Using DEA and
SFA","Version":"0.26"},"BenfordTests":{"Author":"Dieter William Joenssen [aut, cre,
cph],\nThomas Muellerleile [ctb]","Depends":"R (>= 3.0.0), grDevices, graphics,
stats","Description":"Several specialized statistical tests and support
functions\nfor determining if numerical data could conform to Benford's
law.","License":"GPL-
3","NeedsCompilation":"yes","Package":"BenfordTests","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Statistical Tests for Evaluating Conformity to
Benford's Law","URL":"https:\/\/cran.r-
project.org\/package=BenfordTests,\nhttps:\/\/www.researchgate.net\/profile\/Dieter
_Joenssen","Version":"1.2.0"},"Bergm":{"Author":"Alberto Caimo [aut, cre], Nial
Friel [ctb]","Depends":"ergm, network, coda, mvtnorm","Description":"Set of tools
to analyse Bayesian exponential random graph models","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Bergm","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Bayesian analysis for exponential random graph
models","URL":"http:\/\/tiny.cc\/Bergm-info","Version":"3.0.1"},"BerlinData":
{"Author":"Kate McCurdy, Dirk Schumacher","Depends":"R (>=
2.13.0)","Description":"This package provides easy access to
http:\/\/daten.berlin.de\nIt allows you to search through the data catalogue and to
download\nthe data directly from within R.","Imports":"XML (>= 3.95), stringr,
rjson","License":"GPL-3 + file
LICENSE","NeedsCompilation":"no","Package":"BerlinData","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Easy access to Berlin
related
data","URL":"http:\/\/dirkschumacher.github.io\/RBerlinData","Version":"1.0.1"},"Be
ssel":{"Author":"Martin Maechler","Depends":"Rmpfr","Description":"Bessel Function
Computations for complex and real numbers;\nnotably interfacing TOMS 644;
approximations for large arguments,\nexperiments, etc.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"Bessel","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"gsl","Title":"Bessel -- Bessel Functions Computations
and Approximations","URL":"http:\/\/specfun.r-forge.r-
project.org\/","Version":"0.5-5"},"Bhat":{"Author":"Georg Luebeck
<gluebeck@fhcrc.org> and Rafael Meza\n<rmeza@umich.edu>","Description":"Functions
for MLE, MCMC, CIs (originally in Fortran)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Bhat","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"General likelihood exploration","Version":"0.9-
10"},"BiDimRegression":{"Author":"Claus-Christian Carbon","Depends":"R (>= 1.8.0),
nlme","Description":"An S3 class with a method for calculates the bidimensional
regression between two 2D configurations following the approach by Tobler
(1965).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BiDimRegression","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"MASS","Title":"Calculates the bidimensional
regression between two 2D\nconfigurations","URL":"http:\/\/www.r-project.org,
http:\/\/www.experimental-psychology.de","Version":"1.0.6"},"BiSEp":{"Author":"Mark
Wappett","Depends":"R (>= 3.0.1), mclust (>= 4.2.0), GOSemSim (>=
1.20.0)","Description":"Enables the user to infer potential synthetic lethal
relationships\nby analysing relationships between bimodally distributed gene pairs
in big\ngene expression datasets. Enables the user to visualise these
candidate\nsynthetic lethal
relationships.","Imports":"AnnotationDbi","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"BiSEp","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"GO.db(>= 2.10.1), org.Hs.eg.db (>=
2.10.1)","Title":"Toolkit to Identify Candidate Synthetic
Lethality","Version":"2.0.1"},"BiTrinA":{"Author":"Stefan Mundus, Christoph
MÃ¼ssel, Florian Schmid, Ludwig Lausser, Tamara J. BlÃ¤tte, Martin Hopfensitz, Hans
A. Kestler","Depends":"methods, diptest","Description":"Provides methods for the
binarization and trinarization of one-dimensional data and some visualization
functions.","Imports":"graphics, stats","License":"Artistic-
2.0","NeedsCompilation":"yes","Package":"BiTrinA","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Binarization and Trinarization of One-Dimensional
Data","Version":"1.1"},"BiasedUrn":{"Author":"Agner Fog","Description":"Statistical
models of biased sampling in the form of\nunivariate and multivariate noncentral
hypergeometric distributions,\nincluding Wallenius' noncentral hypergeometric
distribution and\nFisher's noncentral hypergeometric distribution\n(also called
extended hypergeometric distribution).\nSee vignette(\"UrnTheory\") for explanation
of these distributions.","License":"GPL-
3","NeedsCompilation":"yes","Package":"BiasedUrn","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Biased Urn Model
Distributions","URL":"http:\/\/www.agner.org\/random\/ http:\/\/www.r-
project.org","Version":"1.07"},"BigTSP":{"Author":"Xiaolin Yang,Han
Liu","Depends":"glmnet,tree,randomForest,gbm","Description":"This package is trying
to implement Top Scoring Pair based\nmethods for classification including LDCA,
TSP-tree, TSP-random\nforest and TSP gradient boosting algorithm.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"BigTSP","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Top Scoring Pair based methods for
classification","Version":"1.0"},"BinNonNor":{"Author":"Gul Inan, Hakan
Demirtas","Depends":"BB, corpcor, mvtnorm, Matrix","Description":"Generation of
multiple binary and continuous non-normal variables simultaneously\ngiven the
marginal characteristics and association structure based on the
methodology\nproposed by Demirtas et al. (2012).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BinNonNor","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Data Generation with Binary and Continuous Non-Normal
Components","Version":"1.2"},"BinNor":{"Author":"Anup Amatya, Hakan
Demirtas","Depends":"mvtnorm, corpcor, psych, Matrix","Description":"Generating
multiple binary and normal variables\nsimultaneously given marginal characteristics
and association\nstructure based on the methodology proposed by Demirtas
and\nDoganay (2012).","License":"GPL-
2","NeedsCompilation":"no","Package":"BinNor","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Simultaneous generation of multivariate binary and
normal\nvariates","Version":"2.0"},"BinOrdNonNor":{"Author":"Yue Wang, Hakan
Demirtas","Depends":"GenOrd, OrdNor","Description":"Generation of samples from a
mix of binary, ordinal and continuous random variables with a pre-specified
correlation matrix and marginal distributions.","Imports":"BB, corpcor, Matrix,
mvtnorm","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BinOrdNonNor","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Concurrent Generation of Binary, Ordinal and
Continuous Data","Version":"1.0"},"Binarize":{"Author":"Stefan Mundus, Christoph
MÃ¼ssel, Florian Schmid, Ludwig Lausser, Tamara J. BlÃ¤tte, Martin Hopfensitz, Hans
A. Kestler","Depends":"methods, diptest","Description":"Provides methods for the
binarization of one-dimensional data and some visualization
functions.","Imports":"graphics, stats","License":"Artistic-
2.0","NeedsCompilation":"yes","Package":"Binarize","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Binarization of One-Dimensional
Data","Version":"1.1"},"BinaryEMVS":{"Author":"John Snyder [aut, cre]","Depends":"R
(>= 3.1.3)","Description":"Implements variable selection for high dimensional
datasets with a binary response\nvariable using the EM algorithm. Both probit and
logit models are supported. Also included\nis a useful function to generate high
dimensional data with correlated variables.","License":"GPL-
3","NeedsCompilation":"no","Package":"BinaryEMVS","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Variable Selection for Binary Data Using the EM
Algorithm","Version":"0.1"},"BinaryEPPM":{"Author":"David M Smith, Malcolm J
Faddy","Description":"Modeling under- and over-dispersed binary data using extended
Poisson process models (EPPM).","Imports":"Formula, expm, numDeriv","License":"GPL-
2","NeedsCompilation":"no","Package":"BinaryEPPM","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Mean and Variance Modeling of Binary
Data","Version":"1.0"},"BioFTF":{"Author":"Fabrizio Maturo [aut, cre],\nFrancesca
Fortuna [aut],\nTonio Di Battista [aut]","Depends":"R (>=
3.1.0)","Description":"The main drawback of the most common biodiversity indices is
that different measures may lead to different rankings among communities . This
instrument overcomes this limit using some functional tools with the diversity
profiles. In particular, the derivatives, the curvature, the radius of curvature,
the arc length, and the surface area are proposed. The goal of this method is to
interpret in detail the diversity profiles and obtain an ordering between different
ecological communities on the basis of diversity. In contrast to the typical
indices of diversity, the proposed method is able to capture the multidimensional
aspect of biodiversity, because it takes into account both the evenness and the
richness of the species present in an ecological community.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BioFTF","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"MASS","Title":"Biodiversity Assessment Using Functional
Tools","URL":"https:\/\/www.r-project.org","Version":"1.0-0"},"BioGeoBEARS":
{"Author":"Nicholas J. Matzke [aut, cre, cph]","Depends":"rexpokit, cladoRcpp, ape,
phylobase, methods","Description":"BioGeoBEARS allows probabilistic inference of
both historical biogeography (ancestral geographic ranges on a phylogeny) as well
as comparison of different models of range evolution. It reproduces the model
available in LAGRANGE (Ree and Smith 2008), as well as making available numerous
additional models. For example, LAGRANGE as typically run has two free parameters,
d (dispersal rate, i.e. the rate of range addition along a phylogenetic branch) and
e (extinction rate, really the rate of local range loss along a phylogenetic
branch). LAGRANGE also has a fixed cladogenic model which gives equal probability
to a number of allowed range inheritance events, e.g.: (1) vicariance, (2) a new
species starts in a subset of the ancestral range, (3) the ancestral range is
copied to both species; in all cases, at least one species must have a starting
range of size 1. LAGRANGE assigns equal probability to each of these events, and
zero probability to other events. BioGeoBEARS adds an additional cladogenic event:
founder-event speciation (the new species jumps to a range outside of the ancestral
range), and also allows the relative weighting of the different sorts of events to
be made into free parameters, allowing optimization and standard model choice
procedures to pick the best model. The relative probability of different descendent
range sizes is also parameterized and thus can also be specified or estimated. The
flexibility available in BioGeoBEARS also enables the natural incorporation of (1)
imperfect detection of geographic ranges in the tips, and (2) inclusion of fossil
geographic range data, when the fossils are tips on the phylogeny. Bayesian
analysis has been implemented through use of the \"LaplacesDemon\" package, however
this package is now maintained off of CRAN, so its usage is not formally included
in BioGeoBEARS at the current time. CITATION INFO: This package is the result of
my Ph.D. research, please cite the package if you use it! Type:
citation(package=\"BioGeoBEARS\") to get the citation
information.","Imports":"optimx, FD, parallel, xtable, plotrix,
gdata","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BioGeoBEARS","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"BioGeography with Bayesian (and Likelihood)
Evolutionary\nAnalysis in R
Scripts","URL":"http:\/\/phylo.wikidot.com\/biogeobears","Version":"0.2.1"},"BioMar
k":{"Author":"Ron Wehrens, Pietro Franceschi","Depends":"pls, glmnet, MASS, st (>=
1.1.6)","Description":"Variable selection methods are provided for several
classification methods: the lasso\/elastic net, PCLDA, PLSDA, and several t-tests.
Two approaches for selecting cutoffs can be used, one based on the stability of
model coefficients under perturbation, and the other on higher
criticism.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BioMark","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Find Biomarkers in Two-Class Discrimination
Problems","Version":"0.4.5"},"BioPhysConnectoR":{"Author":"Franziska Hoffgaard
<hoffgaard@bio.tu-darmstadt.de>, with\ncontributions from Philipp Weil
<weil@bio.tu-darmstadt.de> and\nKay Hamacher <hamacher@bio.tu-
darmstadt.de>","Depends":"R (>= 2.11.0), snow, matrixcalc","Description":"Utilities
and functions to investigate the relation\nbetween biomolecular structures, their
interactions, and the\nevolutionary information revealed in sequence alignments
of\nthese molecules.","License":"GPL-
2","NeedsCompilation":"yes","Package":"BioPhysConnectoR","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"BioPhysConnectoR","Version":"1.6-
10"},"BioStatR":{"Author":"Frederic Bertrand <frederic.bertrand@math.unistra.fr>,
Myriam Maumy-Bertrand <myriam.maumy-bertrand@math.unistra.fr>.","Depends":"R (>=
2.8.0)","Description":"This packages provides datasets and functions for the
book \"Initiation Ã la Statistique avec R\", Dunod, 2ed,
2014.","Imports":"ggplot2","License":"GPL-
3","NeedsCompilation":"no","Package":"BioStatR","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Initiation Ã la Statistique avec R","URL":"http:\/\/www-
irma.u-strasbg.fr\/~fbertran\/","Version":"2.0.0"},"Biocomb":{"Author":"Natalia
Novoselova,Junxi Wang,Frank Pessler,Frank Klawonn","Depends":"R (>=
2.13.0),gtools,Rcpp (>= 0.12.1)","Description":"Contains functions for the data
analysis with the emphasis on biological data, including several algorithms for
feature ranking, feature selection, classification\nalgorithms with the embedded
validation procedures.\nThe functions can deal with numerical as well as with
nominal features. Includes also the functions for calculation\nof feature AUC (Area
Under the ROC Curve) and HUM (hypervolume under manifold) values and construction
2D- and 3D- ROC curves.\nBiocomb provides the calculation of Area Above the RCC
(AAC) values and construction of Relative Cost Curves\n(RCC) to estimate the
classifier performance under unequal misclassification costs problem.\nBiocomb has
the special function to deal with missing values, including different imputing
schemes.","Imports":"rgl, MASS, e1071, randomForest, pROC, ROCR,
discretization,\narules, pamr, class, nnet, rpart, FSelector, RWeka,
grDevices,\ngraphics, stats, utils","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"Biocomb","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Feature Selection and Classification with the
Embedded\nValidation Procedures for Biomedical Data
Analysis","Version":"0.2"},"Biodem":{"Author":"Alessio Boattini and Federico C. F.
Calboli; Vincente Canto Cassola together with Martin Maechler authored the function
mtx.exp.","Description":"The Biodem package provides a number of functions for
Biodemographic analysis.","License":"GPL-
2","NeedsCompilation":"no","Package":"Biodem","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Biodemography Functions","Version":"0.4"},"BiodiversityR":
{"Author":"Roeland Kindt","Depends":"R (>= 3.2.2), tcltk, vegan (>= 2.2-
0)","Description":"Graphical User Interface (via the R-Commander) and utility
functions (often based on the vegan package) for statistical analysis of
biodiversity and ecological communities, including species accumulation curves,
diversity indices, Renyi profiles, GLMs for analysis of species abundance and
presence-absence, distance matrices, Mantel tests, and cluster, constrained
and unconstrained ordination analysis. A book on biodiversity and community
ecology analysis is available for free download from the website. In 2012, methods
for (ensemble) suitability modelling and mapping were expanded in the
package.","Imports":"Rcmdr (>= 2.2-1)","License":"GPL-
2","NeedsCompilation":"no","Package":"BiodiversityR","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"permute, lattice, MASS, mgcv, cluster, car,
RODBC, rpart,\neffects, multcomp, ellipse, maptree, sp, splancs, spatial,\nakima,
nnet, dismo, raster (>= 2.0-31), rgdal, gbm,\nrandomForest, gam, earth, mda,
kernlab, e1071, tools, methods,\nbootstrap, PresenceAbsence,
geosphere","Title":"Package for Community Ecology and Suitability
Analysis","URL":"http:\/\/www.r-
project.org,\nhttp:\/\/www.worldagroforestry.org\/resources\/databases\/tree-
diversity-analysis","Version":"2.7-0"},"Biograph":{"Author":"Frans
Willekens","Depends":"R (>= 3.0.0)","Description":"Transition rates are computed
from transitions and exposures.Useful graphics and life-course indicators are
computed. The package structures the data for multistate statistical and
demographic modeling of life
histories.","Imports":"\nmvna,etm,msm,Epi,lubridate,reshape,plyr,survival,mstate,gg
plot2,\ngrDevices,graphics,stats","License":"GPL-
2","NeedsCompilation":"no","Package":"Biograph","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Explore Life Histories","Version":"2.0.6"},"BiplotGUI":
{"Author":"Anthony la Grange, with some Fortran code adapted by NJ le Roux\nfrom
the original by PJ Rousseeuw, I Ruts and JW Tukey","Depends":"R (>= 2.15.2),
colorspace (>= 1.2-1), deldir, rgl (>= 0.93),\ntcltk, tcltk2 (>= 1.2-5), tkrplot
(>= 0.0-23)","Description":"Provides a GUI with which users can construct and
interact\nwith biplots.","Imports":"colorspace, KernSmooth, MASS","License":"GPL
(>=
3)","NeedsCompilation":"yes","Package":"BiplotGUI","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Interactive Biplots in R","URL":"http:\/\/biplotgui.r-
forge.r-project.org\/","Version":"0.0-7"},"BivarP":{"Author":"Josef
Brejcha","Depends":"dfoptim, survival, copula","Description":"Parameter estimation
of bivariate distribution functions\nmodeled as a Archimedean copula function. The
input data may contain\nvalues from right censored. Used marginal distributions are
two-parameter.\nMethods for density, distribution, survival, random sample
generation.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"BivarP","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Estimating the Parameters of Some Bivariate
Distributions","Version":"1.0"},"BlakerCI":{"Author":"Jan
Klaschka","Description":"Fast and accurate calculation of Blaker's binomial
confidence limits (and some related stuff).","License":"GPL-
3","NeedsCompilation":"no","Package":"BlakerCI","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Blaker's Binomial Confidence Limits","Version":"1.0-
5"},"BlandAltmanLeh":{"Author":"Bernhard Lehnert","Description":"Bland-Altman Plots
using either base graphics or ggplot2,\naugmented with confidence intervals, with
detailed return values and\na sunflowerplot option for data with
ties.","License":"GPL","NeedsCompilation":"no","Package":"BlandAltmanLeh","Reposito
ry":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"ggplot2, knitr,
ggExtra","Title":"Plots (Slightly Extended) Bland-Altman
Plots","Version":"0.3.1"},"Blaunet":{"Author":"Cheng Wang*, Michael Genkin*, George
Berry, Liyuan Chen, Matthew Brashears *Both authors contributed equally to this
work and their names are randomly ordered","Depends":"R (>= 3.0.0), network (>=
1.7.1)","Description":"An integrated set of tools to calculate and analyze Blau
statuses quantifying social distance between individuals belonging to
organizations. Relational (network) data may be incorporated for additional
analyses.","License":"GPL-
3","NeedsCompilation":"no","Package":"Blaunet","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Calculate and Analyze Blau Status for Measuring Social
Distance","URL":"https:\/\/www.facebook.com\/groups\/425015561030239\/","Version":"
2.0.3"},"BlockMessage":{"Author":"Elliot Noma, Aliona
Manvae","Description":"Creates strings that show a text message in 8 by 8
block\nletters","License":"GPL-
2","NeedsCompilation":"no","Package":"BlockMessage","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Creates strings that show a text message in 8 by 8
block letters","Version":"1.0"},"Blossom":{"Author":"Marian Talbert, Jon Richards,
Paul Mielke, and Brian Cade","Depends":"methods, R (>=
2.10)","Description":"Provides tools for making statistical comparisons with
distance-function based permutation tests developed by P. W. Mielke, Jr. and
colleagues at Colorado State University (Mielke, P. W. & Berry, K. J. Permutation
Methods: A Distance Function Approach (Springer, New York, 2001)) and for testing
parameters estimated in linear models with permutation procedures developed by B.
S. Cade and colleagues at the Fort Collins Science Center, U. S. Geological
Survey.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"Blossom","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Statistical Comparisons with Distance-Function Based
Permutation\nTests","Version":"1.4"},"Bmix":{"Author":"Matt Taddy
<taddy@chicagobooth.edu>","Depends":"mvtnorm","Description":"This is a bare-bones
implementation of sampling algorithms\nfor a variety of Bayesian stick-breaking
(marginally DP)\nmixture models, including particle learning and Gibbs
sampling\nfor static DP mixtures, particle learning for dynamic BAR\nstick-
breaking, and DP mixture regression. The software is\ndesigned to be easy to
customize to suit different situations\nand for experimentation with stick-breaking
models. Since\nparticles are repeatedly copied, it is not an especially\nefficient
implementation.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"Bmix","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Bayesian Sampling for Stick-Breaking
Mixtures","URL":"http:\/\/faculty.chicagobooth.edu\/matt.taddy","Version":"0.6"},"B
oSSA":{"Author":"Pierre Lefeuvre","Description":"Sort sequence from genbank.
Retrieve sequence information\nfrom genbank (designed for viruses sequences and
retrieve\ninformation such as isolation date and host). BLAST sequence\nand
accession numbers. Detect group of sequences presenting\nphylogeography signal.
Read PDB file (protein 3D structure\nfile).","Imports":"ape,
SoDA","License":"GPL","NeedsCompilation":"no","Package":"BoSSA","Repository":"http:
\/\/cran.csiro.au\/src\/contrib","Title":"a Bunch of Structure and Sequence
Analysis","Version":"1.2"},"Bolstad":{"Author":"James Curran [aut,
cre]","Depends":"R (>= 3.2.0)","Description":"A set of R functions and data sets
for the book Introduction to\nBayesian Statistics, Bolstad, W.M. (2007), John Wiley
& Sons ISBN 0-471-27020-2.","Imports":"mvtnorm","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Bolstad","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Functions for Elementary Bayesian
Inference","Version":"0.2-33"},"Bolstad2":{"Author":"James M. Curran
<j.curran@auckland.ac.nz>","Description":"A set of R functions and data sets for
the book\nUnderstanding Computational Bayesian Statistics, Bolstad, W.M.\n(2009),
John Wiley & Sons ISBN 978-0470046098","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Bolstad2","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Bolstad
functions","URL":"http:\/\/www.waikato.ac.nz\/Staff\/bolstad","Version":"1.0-
28"},"BonEV":{"Author":"Dongmei Li","Depends":"R (>= 3.2.0),
qvalue","Description":"An improved multiple testing procedure for controlling false
discovery rates which is developed based on the Bonferroni procedure with
integrated estimates from the Benjamini-Hochberg procedure and the Storey's q-value
procedure. It controls false discovery rates through controlling the expected
number of false discoveries.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BonEV","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"An Improved Multiple Testing Procedure for Controlling
False\nDiscovery Rates","Version":"1.0"},"BoolNet":{"Author":"Christoph MÃ¼ssel
[aut],\nMartin Hopfensitz [aut],\nDao Zhou [aut],\nHans A. Kestler [aut,
cre],\nArmin Biere [ctb] (contributed PicoSAT code),\nTroy D. Hanson [ctb]
(contributed uthash macros)","Description":"Provides methods to reconstruct and
generate synchronous,\nasynchronous, probabilistic and temporal Boolean networks,
and to\nanalyze and visualize attractors in Boolean networks.","Imports":"igraph
(>= 0.6), XML","License":"Artistic-
2.0","NeedsCompilation":"yes","Package":"BoolNet","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Construction, Simulation and Analysis of Boolean
Networks","Version":"2.1.1"},"Boom":{"Author":"Steven L. Scott is the sole author
and creator of the BOOM\nproject. Some code in the BOOM libraries has been
modified from\nother open source projects. These include Cephes (obtained
from\nNetlib, written by Stephen L. Moshier), NEWUOA (M.J.D Powell,\nobtained from
Powell's web site), and a modified version of the R\nmath libraries (R core
development team). Original copyright\nnotices have been maintained in all source
files. In these cases,\ncopyright claimed by Steven L. Scott is limited to
modifications\nmade to the original code.","Depends":"MASS, R(>=
3.1.0)","Description":"A C++ library for Bayesian modeling, with an emphasis
on\nMarkov chain Monte Carlo. Although boom contains a few R utilities\n(mainly
plotting functions), its primary purpose is to install the\nBOOM C++ library on
your system so that other packages can link\nagainst it.","License":"LGPL-2.1 |
file
LICENSE","NeedsCompilation":"yes","Package":"Boom","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Bayesian
Object Oriented Modeling","Version":"0.3"},"BoomSpikeSlab":{"Author":"Steven L.
Scott <stevescott@google.com>","Depends":"Boom (>= 0.3) , R (>=
3.1.0)","Description":"Spike and slab regression a la McCulloch and George
(1997).","License":"LGPL-2.1 | file
LICENSE","NeedsCompilation":"yes","Package":"BoomSpikeSlab","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Suggests":"MASS","Title":"MCMC for Spike and Slab
Regression","Version":"0.5.3"},"BootPR":{"Author":"Jae. H.
Kim","Description":"Bias-Corrected Forecasting and Bootstrap Prediction Intervals
for Autoregressive Time Series","License":"GPL-
2","NeedsCompilation":"no","Package":"BootPR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Bootstrap Prediction Intervals and Bias-Corrected
Forecasting","Version":"0.60"},"Boruta":{"Author":"Miron Bartosz Kursa [aut,
cre],\nWitold Remigiusz Rudnicki [aut]","Depends":"ranger","Description":"An all-
relevant feature selection wrapper algorithm.\nIt finds relevant features by
comparing original attributes'\nimportance with importance achievable at random,
estimated\nusing their permuted copies.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Boruta","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"mlbench, rFerns, randomForest","Title":"Wrapper
Algorithm for All-Relevant Feature
Selection","URL":"https:\/\/m2.icm.edu.pl\/boruta\/","Version":"5.0.0"},"BradleyTer
ry2":{"Author":"Heather Turner and David Firth","Depends":"R (>= 2.10), lme4 (>=
1.0)","Description":"Specify and fit the Bradley-Terry model, including structured
versions in which the parameters are related to explanatory variables through a
linear predictor and versions with contest-specific effects, such as a home
advantage.","Enhances":"gnm","Imports":"brglm, gtools, stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"BradleyTerry2","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"prefmod","Title":"Bradley-Terry
Models","URL":"http:\/\/bradleyterry2.r-forge.r-project.org","Version":"1.0-
6"},"BrailleR":{"Author":"A. Jonathan R. Godfrey [aut, cre], Duncan Murdoch [ctb],
Greg Snow\n[ctb], Henrik Bengtsson [ctb], James Curtis [ctb], Paul Murrell [ctb],
Timothy Bilton [ctb], Yihui Xie\n[ctb]","Depends":"R (>= 3.2.0),
knitr","Description":"Blind users do not have access to the graphical output from
R\nwithout printing the content of graphics windows to an embosser of some kind.
This\nis not as immediate as is required for efficient access to statistical
output.\nThe functions here are created so that blind people can make even better
use\nof R. This includes the text descriptions of graphs, convenience functions\nto
replace the functionality offered in many GUI front ends, and
experimental\nfunctionality for optimising graphical content to prepare it for
embossing as\ntactile images.","Imports":"devtools, extrafont, grid, gridGraphics,
gridSVG, moments,\nnortest, pander, rmarkdown, utils, xtable","License":"GPL-
2","NeedsCompilation":"no","Package":"BrailleR","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Improved Access for Blind
Users","URL":"http:\/\/github.com\/ajrgodfrey\/BrailleR","Version":"0.24.2"},"Brobd
ingnag":{"Author":"Robin K. S. Hankin","Depends":"R (>= 2.13.0),
methods","Description":"Handles very large numbers in R. Real numbers are
held\nusing their natural logarithms, plus a logical flag indicating\nsign. The
package includes a vignette that gives a\nstep-by-step introduction to using S4
methods.","License":"GPL","NeedsCompilation":"no","Package":"Brobdingnag","Reposito
ry":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Very large numbers in
R","Version":"1.2-4"},"BsMD":{"Author":"Ernesto Barrios based on Daniel Meyer's
code.","Depends":"R(>= 2.14.0)","Description":"Bayes screening and model
discrimination follow-up designs.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"BsMD","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Bayes Screening and Model
Discrimination","Version":"2013.0718"},"BurStFin":{"Author":"Burns
Statistics","Depends":"stats","Description":"A suite of functions for finance,
including the estimation\nof variance matrices via a statistical factor model
or\nLedoit-Wolf
shrinkage.","License":"Unlimited","NeedsCompilation":"no","Package":"BurStFin","Rep
ository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Burns Statistics
Financial","URL":"http:\/\/www.burns-stat.com\/","Version":"1.02"},"BurStMisc":
{"Author":"Burns Statistics","Description":"corner, genetic optimization,
permutation
tests","License":"Unlimited","NeedsCompilation":"no","Package":"BurStMisc","Reposit
ory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Burns Statistics
miscellaneous","Version":"1.00"},"C50":{"Author":"Max Kuhn, Steve Weston, Nathan
Coulter, Mark Culp. C code for C5.0 by R. Quinlan","Depends":"R (>=
2.10.0)","Description":"C5.0 decision trees and rule-based models for pattern
recognition.","Imports":"partykit","License":"GPL-
3","NeedsCompilation":"yes","Package":"C50","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"C5.0 Decision Trees and Rule-Based Models","Version":"0.1.0-
24"},"CADFtest":{"Author":"Claudio Lupi","Depends":"dynlm, sandwich, tseries,
urca","Description":"This package performs Hansen's (1995) Covariate-
Augmented\nDickey-Fuller (CADF) test. The only required argument is y, the\nTx1
time series to be tested. If no stationary covariate X is\npassed to the procedure,
then an ordinary ADF test is\nperformed. The p-values of the test are computed
using a\nprocedure proposed in Costantini, Lupi and Popp (2007),\nillustrated in
Lupi (2009).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CADFtest","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"fUnitRoots","Title":"This package performs the CADF
unit root test proposed in
Hansen\n(1995)","URL":"http:\/\/www.jstatsoft.org\/v32\/i02","Version":"0.3-
2"},"CALF":{"Author":"Stephanie Lane [aut, cre], Clark Jeffries [aut], Diana
Perkins [aut]","Description":"Contains a greedy algorithm for coarse approximation
linear function.","Imports":"ggplot2","License":"GPL-
2","NeedsCompilation":"no","Package":"CALF","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Coarse Approximation Linear
Function","Version":"0.1.2"},"CALIBERrfimpute":{"Author":"Anoop Shah [aut,
cre],\nJonathan Bartlett [ctb],\nHarry Hemingway [ths],\nOwen Nicholas
[ths],\nAroon Hingorani [ths]","Depends":"mice (>= 2.20)","Description":"Functions
to impute using Random Forest under Full Conditional Specifications (Multivariate
Imputation by Chained Equations). The CALIBER programme is funded by the Wellcome
Trust (086091\/Z\/08\/Z) and the National Institute for Health Research (NIHR)
under its Programme Grants for Applied Research programme (RP-PG-0407-10314). The
author is supported by a Wellcome Trust Clinical Research Training Fellowship
(0938\/30\/Z\/10\/Z).","Imports":"mvtnorm, randomForest","License":"GPL-
3","NeedsCompilation":"no","Package":"CALIBERrfimpute","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"missForest, rpart, survival,
xtable","Title":"Multiple imputation using MICE and Random Forest","Version":"0.1-
6"},"CAM":{"Author":"Jonas Peters and Jan Ernest","Depends":"glmnet, mboost,
Matrix, parallel, mgcv","Description":"The code takes an n x p data matrix and fits
a Causal Additive Model (CAM) for estimating the causal structure of the underlying
process. The output is a p x p adjacency matrix (a one in entry (i,j) indicates an
edge from i to j). Details of the algorithm can be found in: P. BÃ¼hlmann, J.
Peters, J. Ernest: \"CAM: Causal Additive Models, high-dimensional order search and
penalized regression\", Annals of Statistics 42:2526-2556,
2014.","License":"FreeBSD","NeedsCompilation":"no","Package":"CAM","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"Causal Additive Model
(CAM)","Version":"1.0"},"CAMAN":{"Author":"Peter Schlattmann
<peter.schlattmann@mti.uni-jena.de>, Johannes\nHoehne, Maryna Verba","Depends":"R
(>= 2.10), methods, sp, mvtnorm","Description":"Tools for the analysis of finite
semiparametric mixtures.\nThese are useful when data is heterogeneous, e.g.
in\npharmacokinetics or meta-analysis. The NPMLE and VEM algorithms\n(flexible
support size) and EM algorithms (fixed support size)\nare provided for univariate
and bivariate data.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"CAMAN","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Finite Mixture Models and Meta-Analysis Tools - Based on
C.A.MAN","Version":"0.73"},"CANSIM2R":{"Author":"Marco Lugo
<marco.lugo.rodriguez@umontreal.ca>","Depends":"R (>=
3.2.2)","Description":"Extract CANSIM (Statistics Canada) tables and transform them
into readily usable data in panel (wide) format. It can also extract more than one
table at a time and produce the resulting merge by time period and geographical
region.","Imports":"reshape2, Hmisc, utils","License":"GPL-
3","NeedsCompilation":"no","Package":"CANSIM2R","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Directly Extracts Complete CANSIM Data
Tables","Version":"0.11"},"CARBayes":{"Author":"Duncan Lee","Depends":"MASS, R (>=
2.10.0), Rcpp (>= 0.10.6)","Description":"Implements a class of spatial generalised
linear mixed models for areal unit data, with inference in a Bayesian setting using
Markov chain Monte Carlo (McMC) simulation. The response variable can be binomial,
Gaussian or Poisson. The spatial autocorrelation is modelled by a set of random
effects, which are assigned a conditional autoregressive (CAR) prior distribution.
A number of different CAR priors are available for the random effects, and full
details are given in the vignette accompanying this package. The initial creation
of this package was supported by the Economic and Social Research Council (ESRC)
grant RES-000-22-4256,
and on-going development was supported by the Engineering and Physical Science
Research Council (EPSRC) grant EP\/J017442\/1.","Imports":"CARBayesdata, coda, sp,
spam, spdep, stats, truncdist, utils","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"CARBayes","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"boot, deldir, foreign, grid, maptools, Matrix,
nlme,\nshapefiles, splines","Title":"Spatial Generalised Linear Mixed Models for
Areal Unit Data","Version":"4.4"},"CARBayesST":{"Author":"Duncan Lee, Alastair
Rushworth and Gary Napier","Depends":"MASS, R (>= 3.0.0), Rcpp (>=
0.11.5)","Description":"Implements a class of spatio-temporal generalised linear
mixed models for areal unit data, with inference in a Bayesian setting using Markov
chain Monte Carlo (McMC) simulation. The response variable can be binomial,
Gaussian or Poisson. The spatio-temporal autocorrelation is modelled by random
effects, which are assigned conditional autoregressive (CAR) prior distributions.
A number of different random effects structures are available, and full details are
given in the vignette accompanying this package and the references below. The
creation of this package was supported by the Engineering and Physical Science
Research Council (EPSRC) grant EP\/J017442\/1 and the Medical Research Council
(MRC) grant MR\/L022184\/1.","Imports":"spam, truncdist, coda, stats, spdep,
utils","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"CARBayesST","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Spatio-Temporal Generalised Linear Mixed Models for
Areal Unit\nData","Version":"2.2"},"CARBayesdata":{"Author":"Duncan
Lee","Depends":"R (>= 2.10.0)","Description":"Three spatial data sets from Scotland
used in the vignette accompanying the CARBayes package. These include a lip cancer
data set for all of Scotland, and property price and respiratory hospitalisation
data sets from the Greater Glasgow and Clyde health board.","Imports":"sp,
shapefiles","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CARBayesdata","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Data Sets Used in the Vignette Accompanying the
CARBayes Package","Version":"1.0"},"CARE1":{"Author":"T.C.
Hsieh","Description":"The R package CARE1, the first part of the program
CARE\n(Capture-Recapture) in\nhttp:\/\/chao.stat.nthu.edu.tw\/softwareCE.html, can
be used to\nanalyze epidemiological data via sample coverage approach (Chao\net al.
2001a). Based on the input of records from several\nincomplete lists (or samples)
of individuals, the R package\nCARE1 provides output of population size estimate
and related\nstatistics.","License":"GPL-
3","NeedsCompilation":"no","Package":"CARE1","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Statistical package for population size estimation
in\ncapture-recapture models","Version":"1.1.0"},"CARLIT":{"Author":"Danilo
Pecorino, Gina de la Fuente Mancebo, Xavier Torras","Description":"Functions to
calculate and plot ecological quality ratios (EQR) as specified by Ballesteros et
al. 2007.","License":"GPL-
2","NeedsCompilation":"no","Package":"CARLIT","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Ecological Quality Ratios Calculation and
Plot","Version":"1.0"},"CARrampsOcl":{"Author":"Kate Cowles and Michael Seedorff
and Alex Sawyer","Description":"This package fits Bayesian conditional
autoregressive models for spatial and spatiotemporal data on a lattice. It uses
OpenCL kernels running on GPUs to perform rejection sampling to obtain independent
samples from the joint posterior distribution of model
parameters.","Imports":"OpenCL, fields","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"CARrampsOcl","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"coda","Title":"Reparameterized and marginalized
posterior sampling for\nconditional autoregressive models, OpenCL
implementation","Version":"0.1.4"},"CAvariants":{"Author":"Rosaria Lombardo and
Eric J Beh","Depends":"R (> 3.0.1), methods","Description":"Provides six variants
of two-way correspondence analysis (ca):\nsimple ca, singly ordered ca, doubly
ordered ca, non-symmetrical ca,\nsingly ordered non symmetrical ca, and doubly
ordered non symmetrical\nca.","License":"GPL (>
2)","NeedsCompilation":"no","Package":"CAvariants","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Correspondence Analysis
Variants","URL":"http:\/\/www.r-project.org","Version":"3.1"},"CBPS":
{"Author":"Christian Fong <christianfong@stanford.edu>, Marc Ratkovic
<ratkovic@princeton.edu>, Chad Hazlett <chazlett@ucla.edu>, Kosuke Imai
<kimai@princeton.edu>","Depends":"R (>= 2.14), MASS, MatchIt, nnet,
numDeriv","Description":"Implements the covariate balancing propensity score (CBPS)
proposed by Imai and Ratkovic (2014; JRSSB). The propensity score is estimated such
that it maximizes the resulting covariate balance as well as the prediction of
treatment assignment. The method, therefore, avoids an iteration between model
fitting and balance checking. The package also implements several extensions of
the CBPS beyond the cross-sectional, binary treatment setting. The current version
implements the CBPS for longitudinal settings so that it can be used in conjunction
with marginal structural models (Imai and Ratkovic, 2014), treatments with three-
and four-valued treatment variables, continuous-valued treatments (Fong, Hazlett,
and Imai, 2015), and the situation with multiple distinct binary treatments
administered simultaneously. In the future it will be extended to other settings
including the generalization of experimental and instrumental variable
estimates.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CBPS","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Covariate Balancing Propensity
Score","Version":"0.10"},"CCA":{"Author":"Ignacio González, Sébastien
Déjean","Depends":"fda, fields","Description":"The package provide a set of
functions that extend the\ncancor function with new numerical and graphical
outputs. It\nalso include a regularized extension of the cannonical\ncorrelation
analysis to deal with datasets with more variables\nthan
observations.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CCA","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Canonical correlation analysis","Version":"1.2"},"CCAGFA":
{"Author":"Seppo Virtanen [aut, cre],\nEemeli Leppaaho [aut],\nArto Klami
[aut]","Description":"Variational Bayesian algorithms for learning canonical
correlation analysis (CCA), inter-battery factor analysis (IBFA), and group factor
analysis (GFA). Inference with several random initializations can be run with the
functions CCAexperiment() and GFAexperiment().","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CCAGFA","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Bayesian Canonical Correlation Analysis and Group
Factor\nAnalysis","URL":"http:\/\/research.ics.aalto.fi\/mi\/","Version":"1.0.8"},"
CCM":{"Author":"Garrett M. Dancik and Yuanbin Ru","Description":"Classification
method that classifies a sample according\nto the class with the maximum mean (or
any other function of)\ncorrelation between the test and training samples with
known\nclasses.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CCM","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Correlation classification method
(CCM)","Version":"1.1"},"CCMnet":{"Author":"Ravi Goyal, with contributions from
Mark S. Handcock (ergm R package), David R. Hunter (ergm R package), Carter T.
Butts (ergm R package), Steven M. Goodreau (ergm R package), Pavel N. Krivitsky
(ergm R package), Martina Morris (ergm R package), Nicole Bohme Carnegie (ergm-user
term degmix)","Depends":"sna, network, ergm, R(>= 2.12.2)","Description":"Tools to
simulate networks based on Congruence Class models.","License":"GPL-3 + file
LICENSE","NeedsCompilation":"yes","Package":"CCMnet","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Simulate Congruence Class Model for
Networks","Version":"0.0-3"},"CCP":{"Author":"Uwe
Menzel","Description":"Significance tests for canonical correlation
analysis,\nincluding asymptotic tests and a Monte Carlo
method","License":"GPL","NeedsCompilation":"no","Package":"CCP","Repository":"http:
\/\/cran.csiro.au\/src\/contrib","Title":"Significance Tests for Canonical
Correlation Analysis (CCA)","Version":"1.1"},"CCTpack":{"Author":"Royce Anders
<andersr@uci.edu>","Depends":"R2jags (>= 0.04-03)","Description":"A user-friendly
GUI for the application of Cultural Consensus Theory (CCT) models and methods to
consensus data. The models are applied using hierarchical Bayesian inference. The
current package version supports binary, ordinal, and continuous data
formats.","Imports":"tcltk, rjags, psych, mvtnorm, polycor, MASS,
methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CCTpack","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Cultural Consensus Theory applications to
data","Version":"1.4"},"CCpop":{"Author":"Shachar
Kaufman","Depends":"nloptr","Description":"Tests of association between SNPs or
pairs of SNPs and binary phenotypes, in case-control \/ case-population \/ case-
control-population studies.","License":"GPL-
2","NeedsCompilation":"no","Package":"CCpop","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"One and two locus GWAS of binary phenotype with\ncase-
control-population design","Version":"1.0"},"CDFt":{"Author":"Mathieu Vrac
<mathieu.vrac@lsce.ipsl.fr> and Paul-Antoine\nMichelangeli
<pam@climpact.com>","Depends":"R (>= 1.8.0)","Description":"This package proposes a
statistical downscaling method for\ncumulative distribution functions (CDF), as
well as the\ncomputation of the Cram\\èr-von Mises statistics U, and
the\nKolmogorov-Smirnov statistics KS.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CDFt","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Statistical
downscaling through CDF-transform","Version":"1.0.1"},"CDLasso":{"Author":"Edward
Grant, Kenneth Lange, Tong Tong Wu","Description":"Coordinate Descent Algorithms
for Lasso Penalized L1, L2,\nand Logistic Regression","License":"GPL-
2","NeedsCompilation":"yes","Package":"CDLasso","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Coordinate Descent Algorithms for Lasso Penalized L1, L2,
and\nLogistic Regression","Version":"1.1"},"CDM":{"Author":"\nAlexander Robitzsch
[aut, cre], Thomas Kiefer [aut],\nAnn Cathrice George [aut], Ali Uenlue
[aut]","Depends":"R (>= 2.15.0), mvtnorm","Description":"\nFunctions for cognitive
diagnosis modeling\nand multidimensional item response modeling for\ndichotomous
and polytomous data. This package\nenables the estimation of the DINA and DINO
model,\nthe multiple group (polytomous) GDINA model,\nthe multiple choice DINA
model, the general diagnostic\nmodel (GDM), the multidimensional linear
compensatory\nitem response model and the structured latent class\nmodel
(SLCA).","Imports":"graphics, grDevices, lattice, MASS, methods, plyr,
polycor,\npsych, Rcpp, sfsmisc, stats, utils","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"CDM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"BIFIEsurvey, miceadds, mirt, sirt,
TAM","Title":"Cognitive Diagnosis Modeling","Version":"4.8-0"},"CDNmoney":
{"Author":"Paul Gilbert <pgilbert.ttv9z@ncf.ca>","Depends":"R (>=
2.10)","Description":"Components of Canadian Credit Aggregates and Monetary
Aggregates with continuity adjustments.","License":"GPL-2 | file
LICENSE","NeedsCompilation":"no","Package":"CDNmoney","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"tframe (>= 2006.1-1),
tfplot","Title":"Components of Canadian Monetary and Credit
Aggregates","Version":"2012.4-2"},"CDROM":{"Author":"Brent Perry <brp5173@psu.edu>,
Raquel Assis <rassis@psu.edu>","Depends":"R (>=
3.2.0)","Description":"Classification is based on the recently developed
phylogenetic\napproach by Assis and Bachtrog (2013). The method classifies
the\nevolutionary mechanisms retaining pairs of duplicate genes
(conservation,\nneofunctionalization, subfunctionalization, or specialization) by
comparing gene\nexpression profiles of duplicate genes in one species to those of
their single-\ncopy ancestral genes in a sister species.","Imports":"graphics,
grDevices, stats, utils","License":"GPL-
2","NeedsCompilation":"no","Package":"CDROM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Phylogenetically Classifies Retention Mechanisms of
Duplicate\nGenes from Gene Expression Data","Version":"1.0"},"CDVine":
{"Author":"Ulf Schepsmeier, Eike Christian Brechmann","Depends":"R (>=
2.11.0)","Description":"Functions for statistical inference of canonical vine (C-
vine)\nand D-vine copulas. Tools for bivariate exploratory data analysis and for
bivariate\nas well as vine copula selection are provided. Models can be
estimated\neither sequentially or by joint maximum likelihood estimation.\nSampling
algorithms and plotting methods are also included.\nData is assumed to lie in the
unit hypercube (so-called copula\ndata).","Imports":"MASS, mvtnorm, graphics,
igraph, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"CDVine","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Statistical Inference of C- And D-Vine
Copulas","Version":"1.4"},"CEC":{"Author":"Konrad Kamieniecki [aut, cre],
Przemyslaw Spurek [ctb]","Description":"Cross-Entropy Clustering (CEC) divides the
data into Gaussian type clusters. It performs the automatic reduction of
unnecessary clusters, while at the same time allows the simultaneous use of various
type Gaussian mixture models.","License":"GPL-
3","NeedsCompilation":"yes","Package":"CEC","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Cross-Entropy
Clustering","URL":"https:\/\/github.com\/azureblue\/cec","Version":"0.9.3"},"CEGO":
{"Author":"Martin Zaefferer <mzaefferer@gmail.com>","Depends":"R (>=
3.0.0)","Description":"Model building, surrogate model\nbased optimization and
Efficient Global Optimization in combinatorial\nor mixed search
spaces.","Imports":"MASS, stats, DEoptim, graphics","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"CEGO","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"nloptr","Title":"Combinatorial Efficient Global
Optimization","Version":"2.0.0"},"CEoptim":{"Author":"Tim Benham and Qibin Duan and
Dirk P. Kroese and Benoit Liquet","Depends":"MASS, msm, stats,
sna","Description":"Optimization solver based on the Cross-Entropy
method.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"CEoptim","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Cross-Entropy R Package for
Optimization","Version":"1.1"},"CFC":{"Author":"Mansour T.A. Sharabiani, Alireza S.
Mahani","Description":"Numerical integration of cause-specific survival curves to
arrive at cause-specific cumulative incidence functions,\nwith three usage modes:
1) Convenient API for parametric survival regression followed by competing-risk
analysis, 2) API for\nCFC, accepting user-specified survival functions in R, and 3)
Same as 2, but accepting survival functions in C++.","Imports":"Rcpp (>= 0.12.1),
abind, survival, doParallel, foreach","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"CFC","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"BSGW, BayesMixSurv, Hmisc, randomForestSRC,
RcppArmadillo","Title":"Cause-Specific Framework for Competing-Risk
Analysis","Version":"1.0.1"},"CGP":{"Author":"Shan Ba and V. Roshan
Joseph","Description":"Fit composite Gaussian process (CGP) models as described in
Ba and Joseph (2012) \"Composite Gaussian Process Models for Emulating Expensive
Functions\", Annals of Applied Statistics. The CGP model is capable of
approximating complex surfaces that are not second-order stationary. Important
functions in this package are CGP, print.CGP, summary.CGP, predict.CGP and
plotCGP.","License":"LGPL-
2.1","NeedsCompilation":"no","Package":"CGP","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Composite Gaussian process models","Version":"2.0-
2"},"CHAT":{"Author":"Bo Li","Depends":"R (>= 2.10), parallel, DNAcopy,
DPpackage","Description":"CHAT is a collection of tools developed for tumor
subclonality analysis using high density DNA SNP array data and sequencing data.
The pipeline consists of four major compartments: 1) tumor aneuploid genome
proportion (AGP) calculation and ploidy estimation. 2) segment-specific AGP
calculation and absolute copy number estimation for somatic CNAs. 3) cancer cell
fraction correction for somatic SNVs in clonal or subclonal sCNA regions. 4) number
of subclones estimation using Dirichlet process prior followed by MCMC
approach.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CHAT","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Clonal Heterogeneity Analysis
Tool","URL":"http:\/\/sourceforge.net\/p\/clonalhetanalysistool\/wiki\/CHAT\/","Ver
sion":"1.1"},"CHCN":{"Author":"Steven Mosher","Depends":"R (>=
2.11.0),methods,bitops, RCurl","Description":"A compilation of historical through
contemporary climate\nmeasurements scraped from the Environment Canada
Website\nIncluding tools for scraping data, creating metadata and\nformating
temperature files.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CHCN","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Canadian Historical Climate
Network","URL":"http:\/\/stevemosher.wordpress.com\/","Version":"1.5"},"CHNOSZ":
{"Author":"Jeffrey Dick","Depends":"R (>= 3.1.0)","Description":"Functions and data
sets to support chemical thermodynamic modeling in biochemistry\nand low-
temperature geochemistry. The features include calculation of the standard
molal\nthermodynamic properties and chemical affinities of reactions involving
minerals and\/or\nbiomolecules; a database of thermodynamic properties of aqueous,
crystalline and gaseous\nspecies; amino acid group additivity for the standard
molal thermodynamic properties of\nneutral and ionized proteins; use of the revised
Helgeson-Kirkham-Flowers equations of state\nfor aqueous species; construction of
equilibrium activity diagrams as a function of\ntemperature, pressure, and chemical
activities or fugacities of basis species.","Imports":"grDevices, graphics, stats,
2)","NeedsCompilation":"yes","Package":"CHNOSZ","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"limSolve, testthat, knitr","Title":"Chemical
Thermodynamics and Activity Diagrams","URL":"http:\/\/www.chnosz.net\/,
http:\/\/chnosz.r-forge.r-project.org\/","Version":"1.0.7"},"CHsharp":
{"Author":"Douglas Woolford and John Braun","Depends":"scatterplot3d,
KernSmooth","Description":"Functions for use in perturbing data prior to use of
nonparametric smoothers\nand clustering.","License":"GPL-
3","NeedsCompilation":"yes","Package":"CHsharp","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Choi and Hall Style Data
Sharpening","Version":"0.4"},"CIDnetworks":{"Author":"Samrachana Adhikari
[aut],\nBeau Dabbs [cre, aut],\nBrian Junker [aut],\nMauricio Sadinle [aut],\nTracy
Sweet [aut],\nA.C. Thomas [aut]","Depends":"R (>= 3.0.0)","Description":"Generative
models for complex networks with conditionally independent dyadic structure. Now
supports directed arcs!","Imports":"mvtnorm, msm, methods, Rcpp (>= 0.11.0),
igraph, numDeriv,\npbivnorm, MASS","License":"GPL (>
3)","NeedsCompilation":"yes","Package":"CIDnetworks","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Generative Models for Complex Networks with
Conditionally\nIndependent Dyadic Structure","Version":"0.8.1"},"CIFsmry":
{"Author":"Jianing Li","Depends":"R(>= 3.0.1)","Description":"Estimate of
cumulative incidence function in two samples. Provide weighted summary statistics
based on various
methods and weights.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"CIFsmry","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Weighted summary of cumulative incidence
functions","Version":"1.0.1"},"CINID":{"Author":"Aurelie Siberchicot, Adrien
Merville, Marie-Claude Bel-Venner and Samuel Venner","Description":"This package
provides functions to compute a method for identifying the instar of Curculionid
larvae from the observed distribution of the headcapsule size of mature
larvae.","Imports":"graphics, utils, stats","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"CINID","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Curculionidae INstar
IDentification","Version":"1.2"},"CINOEDV":{"Author":"Junliang
Shang","Depends":"R.matlab, igraph, ggplot2, reshape2","Description":"Detecting and
visualizing nonlinear interaction effects of single nucleotide polymorphisms or
epistatic interactions, especially high-order epistatic interactions, are important
topics in bioinformatics because of their significant mathematical and
computational challenges. We present CINOEDV (Co-Information based N-Order
Epistasis Detector and Visualizer) for detecting, visualizing, and analyzing high-
order epistatic interactions by introducing virtual vertices into the construction
of a hypergraph. CINOEDV was developed as an alternative to existing software to
build a global picture of epistatic interactions and unexpected high-order
epistatic interactions, which might provide useful clues for understanding the
underlying genetic architecture of complex diseases.","License":"GPL-
2","NeedsCompilation":"no","Package":"CINOEDV","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Co-Information based N-Order Epistasis Detector and
Visualizer","Version":"2.0"},"CITAN":{"Author":"Marek Gagolewski [aut,
cre]","Depends":"R (>= 3.2.0), agop, RSQLite, RGtk2","Description":"Supports
quantitative\nresearch in scientometrics and bibliometrics. Provides\nvarious tools
for preprocessing bibliographic\ndata retrieved, e.g., from Elsevier's SciVerse
Scopus,\ncomputing bibliometric impact of individuals,\nor modeling many phenomena
encountered in the social sciences.","Imports":"hash, stringi, DBI, grDevices,
graphics, stats, utils","License":"LGPL (>=
3)","NeedsCompilation":"no","Package":"CITAN","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"CITation ANalysis Toolpack","Version":"2015.12-2"},"CLME":
{"Author":"Casey M. Jelsema, Shyamal D. Peddada","Depends":"R (>= 3.0.2), shiny,
lme4","Description":"Estimation and inference for linear models where some or all
of the fixed-effects coefficients are subject to order restrictions. This package
uses the robust residual bootstrap methodology for inference, and can handle some
structure in the residual variance matrix.","Imports":"MASS, nlme, methods,
isotone, stringr, prettyR, stats,\nopenxlsx, graphics","License":"GPL-
3","NeedsCompilation":"no","Package":"CLME","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Constrained Inference for Linear Mixed Effects
Models","Version":"2.0-4"},"CLSOCP":{"Author":"Jason
Rudy","Depends":"Matrix","Description":"This package provides and implementation of
a one step\nsmoothing newton method for the solution of second order
cone\nprogramming problems, originally described by Xiaoni Chi and\nSanyang
Liu.","License":"GPL-
3","NeedsCompilation":"no","Package":"CLSOCP","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"A smoothing Newton method SOCP
solver","Version":"1.0"},"CMC":{"Author":"Michela Cameletti and Valeria
Caviezel","Description":"Calculation and plot of the stepwise Cronbach-Mesbah
Curve","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CMC","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Cronbach-Mesbah Curve","Version":"1.0"},"CMF":{"Author":"Arto
Klami and Lauri VÃ¤re","Description":"Collective matrix factorization (CMF) finds
joint low-rank representations for a collection of matrices with shared row or
column entities. This code learns variational Bayesian approximation for CMF,
supporting multiple likelihood potentials and missing data, while identifying both
factors shared by multiple matrices and factors private for each
matrix.","Imports":"Rcpp","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"CMF","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Collective matrix
factorization","Version":"1.0"},"CMPControl":{"Author":"Kimberly Sellers
<kfs7@georgetown.edu> ; Luis Costa
<lc436@georgetown.edu>","Depends":"compoisson","Description":"The main purpose of
this package is to juxtapose the different control limits obtained by modelling a
data set through the COM-Poisson distribution vs. the classical Poisson
distribution. Accordingly, this package offers the ability to compute the COM-
Poisson parameter estimates and plot associated Shewhart control charts for a given
data set.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"CMPControl","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Control Charts for Conway-Maxwell-Poisson
Distribution","Version":"1.0"},"CMplot":{"Author":"LiLin-Yin","Depends":"R(>=
2.10)","Description":"Manhattan plot, a type of scatter plot, was widely used to
display the association results. However, it is usually time-consuming and
laborious for a\nnon-specialist user to write scripts and adjust parameters of an
elaborate plot. Moreover, the ever-growing traits measured have necessitated
the\nintegration of results from different Genome-wide association study
researches. Circle Manhattan Plot is the first open R package that can lay
out\nGenome-wide association study P-value results in both traditional rectangular
patterns and novel circular ones. United in only one bull's eye style\nplot,
association results from multiple traits can be compared interactively, thereby to
reveal both similarities and differences between signals.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CMplot","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Circle Manhattan
Plot","URL":"https:\/\/github.com\/YinLiLin\/R-
CMplot\/blob\/master\/CMplot.r","Version":"3.0.3"},"CNOGpro":{"Author":"Ola
Brynildsrud, Lars-Gustav Snipen","Depends":"seqinr","Description":"Methods for
assigning copy number states and breakpoints in resequencing experiments of
prokaryotic organisms.","License":"GPL-
2","NeedsCompilation":"no","Package":"CNOGpro","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Copy Numbers of Genes in
prokaryotes","Version":"1.1"},"CNVassoc":{"Author":"Juan R González, Isaac
Subirana","Depends":"R (>= 2.15.0), CNVassocData, mixdist, mclust,
survival","Description":"The CNVassoc package carries out analysis of common\nCopy
Number Variants (CNVs) and imputed Single Nucleotide\nPolymorphisms (SNPs) in
population-based studies.\nIt includes tools for estimating association under a
series\nof study designs (case-control, cohort, etc), using several\ndependent
variables (class status, censored data, counts)\nas response, adjusting for
covariates and considering\nvarious inheritance models. Moreover, it is possible
to\nperform epistasis studies with pairs of CNVs or imputed SNPs.\nIt has been
optimized in order to make feasible the analyses\nof Genome Wide Association
studies (GWAs) with hundreds of\nthousands of genetic variants (CNVs \/ imputed
SNPs). Also,\nit incorporates functions for inferring copy number (CNV\ngenotype
calling). Various classes and methods for generic\nfunctions (print, summary, plot,
anova, ...) have been\ncreated to facilitate the analysis.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"CNVassoc","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"CGHcall, CGHregions, CNVtools, xtable, MASS,
Biobase, CGHbase","Title":"Association Analysis of CNV Data and Imputed
SNPs","URL":"http:\/\/www.creal.cat\/jrgonzalez\/software.htm","Version":"2.1"},"CN
VassocData":{"Author":"Juan R González, Isaac Subirana","Depends":"R (>=
2.15.0)","Description":"This package contains example data sets with Copy Number
Variants and imputed SNPs to be used by CNVassoc package.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CNVassocData","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Example data sets for association analysis of CNV
data","URL":"http:\/\/www.creal.cat\/jrgonzalez\/software.htm","Version":"1.0"},"CN
prep":{"Author":"Alex Krasnitz, Guoli Sun","Depends":"R (>= 2.10), parallel,
mclust, rlecuyer","Description":"This package evaluates DNA copy number data, using
both their initial form (copy number as a noisy function of genomic position) and
their approximation by a piecewise-constant function (segmentation), for the
purpose of identifying genomic regions where the copy number differs from the
norm.","License":"GPL-
2","NeedsCompilation":"no","Package":"CNprep","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Pre-process DNA Copy Number (CN) Data for Detection of CN
Events","Version":"2.0"},"COBRA":{"Author":"Benjamin Guedj
<benjamin.guedj@upmc.fr>","Description":"This package performs prediction for
regression-oriented problems, aggregating in a nonlinear scheme any basic
regression machines suggested by the context and provided by the user. If the user
has no valuable knowledge on the data, four defaults machines wrappers are
implemented so as to cover a minimal spectrum of prediction methods. If necessary,
the computations may be parallelized. The method is described in Biau, Fischer,
Guedj and Malley (2013), \"COBRA: A Nonlinear Aggregation
Strategy\".","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"COBRA","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"snowfall, lars, ridge, tree,
randomForest","Title":"Nonlinear Aggregation of
Predictors","URL":"http:\/\/www.lsta.upmc.fr\/doct\/guedj\/index.html","Version":"0
.99.4"},"COMBIA":{"Author":"Muhammad
Kashif","Depends":"hash, gdata, lattice, latticeExtra, oro.nifti","Description":"A
comprehensive synergy\/antagonism analyses of drug combinations with\nquality
graphics and data. The analyses can be performed by Bliss independence and
Loewe\nadditivity models. COMBIA provides improved statistical analysis and makes
only very weak assumption of data variability\nwhile calculating bootstrap
intervals (BIs). Finally, package saves analyzed data,\n2D and 3D plots ready to
use in research publications. COMBIA does not require manual\ndata entry. Data can
be directly input from wetlab experimental platforms\nfor example fluostar,
automated robots etc. One needs to call a single function only\nto perform all
analysis (examples are provided with sample data).","Imports":"grDevices, stats,
2)","NeedsCompilation":"no","Package":"COMBIA","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Synergy\/Antagonism Analyses of Drug
Combinations","Version":"1.0-4"},"COMMUNAL":{"Author":"Albert Chen [aut, cre],
Timothy E Sweeney [aut], Olivier Gevaert [ths]","Depends":"R (>= 2.10), cluster,
clValid, fpc","Description":"Facilitates optimal clustering of a data set. Provides
a framework to run a wide range of clustering algorithms to determine the optimal
number (k) of clusters in the data. Then analyzes the cluster assignments from each
clustering algorithm to identify samples that repeatedly classify to the same
group. We call these 'core clusters', providing a basis for later class
discovery.","Imports":"methods, grDevices, graphics, stats, utils","License":"GPL-
2","NeedsCompilation":"no","Package":"COMMUNAL","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"RUnit, NMF, ConsensusClusterPlus, rgl,
kohonen","Title":"Robust Selection of Cluster Number
K","Version":"1.1.0"},"COMPoissonReg":{"Author":"Kimberly Sellers
<kfs7@georgetown.edu>, Thomas Lotze
<thomas.lotze@thomaslotze.com>","Depends":"stats","Description":"Fit a CMP
regression model to count data. The code provides functions for model estimation,
dispersion testing, and diagnostics.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"COMPoissonReg","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Conway-Maxwell Poisson (COM-Poisson)
Regression","Version":"0.3.5"},"CONDOP":{"Author":"Vittorio Fortino
<vittorio.fortino@ttl.fi>","Depends":"R (>= 3.0.1)","Description":"An
implementation of the computational strategy for the\ncomprehensive analysis of
condition-dependent operon maps in prokaryotes\nproposed by Fortino et al. (2014)
<DOI:10.1186\/1471-2105-15-145>.\nIt uses RNA-seq transcriptome profiles to improve
prokaryotic operon map inference.","Imports":"stats, utils, mclust, earth, plyr,
seqinr, randomForest,\nrminer, GenomicRanges, GenomeInfoDb, S4Vectors,
IRanges","License":"GPL-
3","NeedsCompilation":"no","Package":"CONDOP","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Condition-Dependent Operon
Predictions","Version":"1.0"},"CORE":{"Author":"Alex Krasnitz, Guoli
Sun","Description":"given a collection of intervals with integer start and end
positions, find recurrently targeted regions and estimate the significance of
finding. Randomization is implemented by parallel methods, either using local host
machines, or submitting grid engine jobs.","Imports":"parallel","License":"GPL-
2","NeedsCompilation":"no","Package":"CORE","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Cores of Recurrent Events","Version":"3.0"},"CORElearn":
{"Author":"Marko Robnik-Sikonja and Petr Savicky with contributions from John
Adeyanju Alao","Description":"This is a suite of machine learning algorithms
written in C++ with R\ninterface. It contains several machine learning model
learning techniques in\nclassification and regression, for example classification
and regression trees with\noptional constructive induction and models in the
leaves, random forests, kNN,\nnaive Bayes, and locally weighted regression. All
predictions obtained with these\nmodels can be explained and visualized with
ExplainPrediction package.\nThe package is especially strong in feature evaluation
where it contains several variants of\nRelief algorithm and many impurity based
attribute evaluation functions, e.g., Gini,\ninformation gain, MDL, and DKM. These
methods can be used for example to discretize\nnumeric attributes.\nIts additional
feature is OrdEval algorithm and its visualization used for evaluation\nof data
sets with ordinal features and class, enabling analysis according to the\nKano
model of customer satisfaction.\nSeveral algorithms support parallel multithreaded
execution via OpenMP.\nThe top-level documentation is reachable through ?
CORElearn.","Imports":"cluster,rpart, stats","License":"GPL-
3","NeedsCompilation":"yes","Package":"CORElearn","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"lattice,MASS,rpart.plot","Title":"Classification,
Regression and Feature Evaluation","URL":"http:\/\/lkm.fri.uni-
lj.si\/rmarko\/software\/","Version":"1.47.1"},"CORM":{"Author":"Li-Xuan Qin
[aut],\nJiejun Shi [cre]","Depends":"R (>= 2.10.0), cluster,
limma","Description":"We proposed a new model-based clustering method, called the
clustering of\nregression models method(CORM), which groups genes that share a
similar\nrelationship to the covariate(s). This method provides a unified
approach\nfor a family of clustering procedures and can be applied to data
collected\nwith various experimental designs. This package includes the
implementation\nfor two such clustering procedures: (1) the Clustering of Linear
Models\n(CLM) method, and (2) the Clustering of Linear Mixed Models (CLMM)
2)","NeedsCompilation":"no","Package":"CORM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"MASS","Title":"The Clustering of Regression Models
Method","URL":"http:\/\/www.r-
project.org,\nhttp:\/\/www.mskcc.org\/mskcc\/html\/60448.cfm","Version":"1.0.2"},"C
OSINE":{"Author":"Haisu Ma","Depends":"R (>= 3.1.0), MASS,genalg","Description":"To
identify the globally most discriminative subnetwork from gene\nexpression profiles
using an optimization model and genetic algorithm","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"COSINE","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"COndition SpecIfic sub-NEtwork","Version":"2.1"},"COUNT":
{"Author":"Joseph M Hilbe <hilbe@asu.edu>","Depends":"R (>= 2.10), msme,
sandwich","Description":"Functions, data and code for Hilbe, J.M. 2011. Negative
Binomial Regression, 2-nd Edition (Cambridge University Press) and Hilbe, J.M.
2014. Modeling Count Data (Cambridge University
Press).","Imports":"MASS","License":"GPL-
2","NeedsCompilation":"no","Package":"COUNT","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Functions, data and code for count
data","Version":"1.3.2"},"COUSCOus":{"Author":"Reda Rawi [aut,cre], Matyas A.
Sustik [aut], Ben Calderhead [aut]","Depends":"R (>= 3.2.2)","Description":"Contact
prediction using shrinked covariance (COUSCOus). COUSCOus is a residue-residue
contact detecting method approaching the contact inference using the glassofast
implementation of Matyas and Sustik (2012, The University of Texas at Austin UTCS
Technical Report 2012:1-3. TR-12-29.) that solves the L_1 regularised Gaussian
maximum likelihood estimation of the inverse of a covariance matrix. Prior to the
inverse covariance matrix estimation we utilise a covariance matrix shrinkage
approach, the empirical Bayes covariance estimator, which has been shown by Haff
(1980) <DOI:10.1214\/aos\/1176345010> to be the best estimator in a Bayesian
framework, especially dominating estimators of the form aS, such as the smoothed
covariance estimator applied in a related contact inference technique
PSICOV.","Imports":"bio3d (>= 2.2-2), matrixcalc (>= 1.0-3), utils (>=
3.2.2)","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"COUSCOus","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"A Residue-Residue Contact Detecting
Method","Version":"1.0.0"},"CP":{"Author":"Andreas Kuehnapfel","Depends":"R(>=
3.0.1)","Description":"Functions for calculating the conditional power\nfor
different models in survival time analysis\nwithin randomized clinical trials\nwith
two different treatments to be compared\nand survival as an
endpoint.","Imports":"survival","License":"GPL-
3","NeedsCompilation":"no","Package":"CP","Repository":"http:\/\/cran.csiro.au\/src
\/contrib","Title":"Conditional Power Calculations","URL":"https:\/\/www.imise.uni-
leipzig.de","Version":"1.5"},"CPE":{"Author":"Qianxing Mo, Mithat Gonen and Glenn
Heller","Depends":"R (>= 2.10.0),survival,rms","Description":"Functions to
calculate concordance probability estimates\nin survival analysis","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"CPE","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Concordance Probability Estimates in Survival
Analysis","Version":"1.4.4"},"CPHshape":{"Author":"Rihong Hui and Hanna Jankowski
<hkj@mathstat.yorku.ca>","Description":"This package computes the maximum
likelihood estimator (MLE) of the shape-constrained hazard baseline and the effect
parameters in the Cox proportional hazards model under IID sampling. We assume
that the data are continuous and allow for right censoring. The function
'find.shapeMLE' allows for four different shape constraints: increasing,
decreasing, unimodal, and u-shaped.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CPHshape","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Find the maximum likelihood estimator of the shape
constrained\nhazard baseline and the effect parameters in the Cox\nproportional
hazards
model","URL":"http:\/\/www.math.yorku.ca\/~hkj","Version":"1.0.1"},"CPMCGLM":
{"Author":"Jeremie Riou, Amadou Diakite, and Benoit Liquet","Depends":"R (>=
2.10.0), mvtnorm, plyr","Description":"We
propose to determine the correction of the significance level after multiple
coding of an explanatory variable in Generalized Linear Model. The different
methods of correction of the p-value are the Single step Bonferroni procedure, and
resampling based methods developped by P.H.Westfall in 1993. Resampling methods are
based on the permutation and the parametric bootstrap procedure. If some
continuous, and dichotomous transformations are performed this package offers an
exact correction of the p-value developped by B.Liquet & D.Commenges in 2005. The
naive method with no correction is also available.","License":"GPL (>
2)","NeedsCompilation":"no","Package":"CPMCGLM","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Correction of the pvalue after multiple
coding","URL":"http:\/\/www.r-project.org","Version":"1.1"},"CR":{"Author":"Emil A.
Cornea, Bahjat F. Qaqish, and Joseph G.
Ibrahim","Depends":"methods","Description":"This package contains R-functions to
perform power\ncalculation in a group sequential clinical trial with
censored\nsurvival data and possibly unequal patient allocation between\ntreatment
and control groups. The fuctions can also be used to\ndetermine the study duration
in a clinical trial with censored\nsurvival data as the sum of the accrual
duration, which\ndetermines the sample size in a traditional sense, and
the\nfollow-up duration, which more or less controls the number of\nevents to be
observed. This package also contains R functions\nand methods to display the
computed results.","License":"GPL-
2","NeedsCompilation":"no","Package":"CR","Repository":"http:\/\/cran.csiro.au\/src
\/contrib","Title":"Power Calculation for Weighted Log-Rank Tests in Cure
Rate\nModels","Version":"1.0"},"CRAC":{"Author":"Jiayi Liu","Description":"R
functions for cosmological research.\nThe main functions are similar to the python
library, cosmolopy.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CRAC","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Cosmology R Analysis Code","Version":"1.0"},"CRF":
{"Author":"Ling-Yun Wu [aut, cre]","Depends":"R (>= 2.12.0)","Description":"This
package implements modeling and computational tools for\nconditional random fields
model (CRF) as well as other probabilistic\nundirected graphical models of discrete
data with pairwise and unary\npotentials.","Imports":"Rglpk (>= 0.3-5), Matrix (>=
1.1-2)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"CRF","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"CRF - Conditional Random Fields","URL":"http:\/\/r-forge.r-
project.org\/projects\/crf\/","Version":"0.3-8"},"CRM":{"Author":"Qianxing
Mo","Depends":"R (>= 2.10.0)","Description":"CRM simulator for Phase I Clinical
Trials","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"CRM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Continual Reassessment Method (CRM) for Phase I Clinical
Trials","Version":"1.1.1"},"CRTSize":{"Author":"Michael A Rotondi
<mrotondi@yorku.ca>","Depends":"R (>= 2.01)","Description":"Sample size estimation
in cluster (group) randomized trials. Contains traditional power-based methods,
empirical smoothing (Rotondi and Donner, 2009), and updated meta-analysis
techniques (Rotondi and Donner, 2012).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CRTSize","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Sample Size Estimation Functions for Cluster Randomized
Trials","Version":"1.0"},"CRTgeeDR":{"Author":"Melanie Prague [aut, cre],\nPaul
Gilbert [ctb] (Author of R package numDeriv, which has been\nacknowledged in
numDeriv.R),\nRavi Varadhan [ctb] (Author of R package numDeriv, which has
been\nacknowledged in numDeriv.R),\nMing Wang [ctb] (Author of R package geesmv,
which has been\nacknowledged in getFay.R),\nLee McDaniel [ctb] (Author of R package
geeM, which has been modified\nand referenced in multiple R files),\nNick Henderson
[ctb] (Author of R package geeM, which has been modified\nand referenced in
multiple R files)","Depends":"Matrix, MASS, ggplot2, grDevices, graphics, stats,
methods","Description":"Implements a semi-parametric GEE estimator accounting for
missing data with Inverse-probability weighting (IPW) and for imbalance in
covariates with augmentation (AUG). The estimator IPW-AUG-GEE is Doubly robust
(DR).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CRTgeeDR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Doubly Robust Inverse Probability Weighted Augmented
GEE\nEstimator","Version":"1.2"},"CTT":{"Author":"John T.
Willse","Description":"Contains common CTT functions","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CTT","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Classical Test Theory Functions","Version":"2.1"},"CTTShiny":
{"Author":"William Kyle Hamilton [aut, cre],\nAtsushi Mizumoto [aut]","Depends":"R
(>= 3.0.3)","Description":"Interactive shiny application for running classical test
theory (item analysis).","Imports":"shiny, shinyAce, CTT, ltm,
psych","License":"GPL-
3","NeedsCompilation":"no","Package":"CTTShiny","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Classical Test Theory via Shiny","Version":"0.1"},"CUB":
{"Author":"Maria Iannario <maria.iannario@unina.it>, Domenico
Piccolo\n<domenico.piccolo@unina.it>","Depends":"R (>=
2.15.2)","Description":"Estimating and testing models for ordinal data within the
family of\nCUB models and their extensions (where CUB stands for Combination of a
discrete Uniform and a shifted Binomial distributions).","Imports":"stats,
graphics","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"CUB","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"A Class of Mixture Models for Ordinal
Data","URL":"http:\/\/www.labstat.it\/home\/wp-
content\/uploads\/2015\/10\/CUB.txt,\nResearchgate DOI:
10.13140\/RG.2.1.1507.2480","Version":"0.0"},"CUFF":{"Author":"Charles-Ã‰douard
GiguÃ¨re","Depends":"R (>= 3.2.2)","Description":"Utility functions that provides
wrapper to descriptive base functions\nlike correlation, mean and table . It makes
use of the formula interface to pass\nvariables to functions. It also provides
operators like to concatenate (%+%), to\nrepeat and manage character vector for
nice display.","Imports":"openxlsx, xtable","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CUFF","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Charles's Utility Function using
Formula","URL":"https:\/\/github.com\/giguerch\/CUFF","Version":"1.0"},"CUMP":
{"Author":"Xuan Liu <liuxuan@bu.edu> and Qiong Yang
<qyang@bu.edu>","Description":"Combining Univariate Association Test Results of
Multiple\nPhenotypes for Detecting Pleiotropy","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CUMP","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Analyze Multivariate Phenotypes by Combining Univariate
results","Version":"1.0"},"CUSUMdesign":{"Author":"Douglas M. Hawkins, David H.
Olwell, Boxiang Wang","Description":"Computation of decision intervals (H) and
average run lengths (ARL) for CUSUM charts.","License":"GPL-
2","NeedsCompilation":"yes","Package":"CUSUMdesign","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Compute Decision Interval and Average Run Length for
CUSUM\nCharts","Version":"1.1.1"},"CVST":{"Author":"Tammo Krueger, Mikio
Braun","Depends":"kernlab,Matrix","Description":"This package implements the fast
cross-validation via sequential testing (CVST) procedure. CVST is an improved
cross-validation procedure which uses non-parametric testing coupled with
sequential analysis to determine the best parameter set on linearly increasing
subsets of the data. By eliminating underperforming candidates quickly and keeping
promising candidates as long as possible, the method speeds up the computation
while preserving the capability of a full cross-validation. Additionally to the
CVST the package contains an implementation of the ordinary k-fold cross-validation
with a flexible and powerful set of helper objects and methods to handle the
overall model selection process. The implementations of the Cochran's Q test with
permutations and the sequential testing framework of Wald are generic and can
therefore also be used in other contexts.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"CVST","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Fast Cross-Validation via Sequential
Testing","Version":"0.2-1"},"CVThresh":{"Author":"Donghoh Kim
<donghoh.kim@gmail.com>, Hee-Seok Oh\n<heeseok@stats.snu.ac.kr>","Depends":"R (>=
2.15.1), wavethresh (>= 4.6.1), EbayesThresh (>= 1.3.2)","Description":"This
package carries out level-dependent cross-validation\nmethod for the selection of
thresholding value in wavelet\nshrinkage. This procedure is implemented by coupling
a\nconventional cross validation with an imputation method due to\na limitation of
data length, a power of 2. It can be easily\napplied to classical leave-one-out and
k-fold cross validation.\nSince the procedure is computationally fast, a level-
dependent\ncross validation can be performed for wavelet shrinkage of\nvarious data
such as a data with correlated errors.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CVThresh","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Level-Dependent Cross-Validation
Thresholding","URL":"http:\/\/dasan.sejong.ac.kr\/~dhkim\/software_cvthresh.html","
Version":"1.1.1"},"CVTuningCov":{"Author":"Binhuan Wang","Description":"This is a
package for selecting tuning parameters based on cross-validation (CV) in
regularized estimators of large covariance matrices. Four regularized methods are
implemented: banding, tapering, hard-thresholding and soft-thresholding. Two types
of matrix norms are applied: Frobenius norm and operator norm. Two types of CV are
considered: K-fold CV and random CV.
Usually K-fold CV use K-1 folds to train a model and the rest one fold to validate
the model. The reverse version trains a model with 1 fold and validates with the
rest with K-1 folds. Random CV randomly splits the data set to two parts, a
training set and a validation set with user-specified sizes.","License":"GPL-
2","NeedsCompilation":"no","Package":"CVTuningCov","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"MASS","Title":"Regularized Estimators of Covariance
Matrices with CV Tuning","Version":"1.0"},"CVcalibration":{"Author":"He Qi and Lu
Tian","Description":"Statistical inferences for estimating the calibration equation
with error-in observations","License":"GPL-
2","NeedsCompilation":"no","Package":"CVcalibration","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Estimation of the Calibration Equation with Error-
in\nObservations","Version":"1.0-1"},"CaDENCE":{"Author":"Alex J.
Cannon","Depends":"pso","Description":"Parameters of a user-specified probability
distribution are modelled by a multi-layer perceptron artificial neural network.
This framework can be used to implement probabilistic nonlinear models including
mixture density networks, heteroscedastic regression models, zero-inflated models,
and the like.","License":"GPL-
2","NeedsCompilation":"no","Package":"CaDENCE","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"boot","Title":"Conditional Density Estimation Network
Construction and\nEvaluation","Version":"1.2.3"},"Cairo":{"Author":"Simon Urbanek
<Simon.Urbanek@r-project.org>, Jeffrey Horner
<jeff.horner@vanderbilt.edu>","Depends":"R (>= 2.4.0)","Description":"Cairo
graphics device that can be use to create high-quality vector (PDF, PostScript and
SVG) and bitmap output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11
and Win32). Since it uses the same back-end for all output, copying across formats
is WYSIWYG. Files are created without the dependence on X11 or other external
programs. This device supports alpha channel (semi-transparent drawing) and
resulting images can contain transparent and semi-transparent regions. It is ideal
for use in server environments (file output) and as a replacement for other devices
that don't have Cairo's capabilities such as alpha support or anti-aliasing.
Backends are modular such that any subset of backends is
supported.","Enhances":"FastRWeb","Imports":"grDevices, graphics","License":"GPL-
2","NeedsCompilation":"yes","Package":"Cairo","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"png","Title":"R graphics device using cairo graphics
library for creating\nhigh-quality bitmap (PNG, JPEG, TIFF), vector (PDF,
SVG,\nPostScript) and display (X11 and Win32)
output","URL":"http:\/\/www.rforge.net\/Cairo\/","Version":"1.5-
9"},"Calculator.LR.FNs":{"Author":"Abbas Parchami (Department of Statistics,
Faculty of Mathematics and Computer, Shahid Bahonar University of Kerman, Kerman,
Iran)","Description":"Arithmetic operations scalar multiplication, addition,
subtraction, multiplication and division of LR fuzzy numbers (which are on the
basis of Zadeh extension principle) have a complicate form for using in fuzzy
Statistics, fuzzy Mathematics, machine learning, fuzzy data analysis and etc.
Calculator for LR Fuzzy Numbers package, i.e. Calculator.LR.FNs package, relieve
and aid applied users to achieve a simple and closed form for some complicated
operator based on LR fuzzy numbers and also the user can easily draw the membership
function of the obtained result by this package.","License":"LGPL (>=
3)","NeedsCompilation":"no","Package":"Calculator.LR.FNs","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Calculator for LR Fuzzy
Numbers","Version":"1.0"},"Canopy":{"Author":"Yuchao Jiang, Nancy R.
Zhang","Depends":"R (>= 3.2), ape, fields","Description":"A statistical framework
and computational procedure for identifying the sub-populations within a tumor,
determining the mutation profiles of each subpopulation, and inferring the tumor's
phylogenetic history. The input are variant allele frequencies (VAFs) of somatic
single nucleotide alterations (SNAs) along with allele-specific coverage ratios
between the tumor and matched normal sample for somatic copy number alterations
(CNAs). These quantities can be directly taken from the output of existing
software. Canopy provides a general mathematical framework for pooling data across
samples and sites to infer the underlying parameters. For SNAs that fall within CNA
regions, Canopy infers their temporal ordering and resolves their phase. When
there are multiple evolutionary configurations consistent with the data, Canopy
outputs all configurations along with their confidence
assessment.","Imports":"grDevices, graphics, stats","License":"GPL-
2","NeedsCompilation":"no","Package":"Canopy","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Accessing Intra-Tumor Heterogeneity and Tracking
Longitudinal\nand Spatial Clonal Evolutionary History by Next-
Generation\nSequencing","URL":"\nhttps:\/\/sites.google.com\/a\/cornell.edu\/yuchao
jiang\/home\/research\/canopy","Version":"1.0.0"},"CarletonStats":{"Author":"Laura
Chihara","Description":"Includes commands for bootstrapping and permutation tests,
a command for created grouped bar plots, and a demo of the quantile-normal plot for
data drawn from different distributions.","License":"GPL-
2","NeedsCompilation":"no","Package":"CarletonStats","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"MASS","Title":"Functions For Statistics Classes
At Carleton College","Version":"1.2"},"CatDyn":{"Author":"Ruben H. Roa-
Ureta","Depends":"R (>= 3.0.0)","Description":"Based on fishery Catch Dynamics
instead of fish Population Dynamics (hence CatDyn) and using high-frequency or
medium-frequency catch in biomass or numbers, fishing nominal effort, and mean fish
body weight by time step, from one or two fishing fleets, estimate stock abundance,
natural mortality rate, and fishing operational parameters. It includes methods for
data organization, plotting standard exploratory and analytical plots, predictions,
for 77 types of models of increasing complexity, and 56 likelihood models for the
data.","Imports":"optimx (>= 2013.8.6), BB","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CatDyn","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Fishery Stock Assessment by Generalized Depletion
Models","Version":"1.1-0"},"CateSelection":{"Author":"Yi Xu and Jixiang
Wu","Depends":"R(>= 2.10)","Description":"A multi-factor dimensionality reduction
based forward selection method for genetic association mapping.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CateSelection","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Categorical Variable Selection
Methods","Version":"1.0"},"CausalFX":{"Author":"Ricardo Silva [cre, aut],\nRobin
Evans [aut]","Description":"Estimate causal effects of one variable on another,
currently for\nbinary data only. Methods include instrumental variable bounds,
adjustment by a\ngiven covariate set, adjustment by an induced covariate set using
a variation of\nthe PC algorithm, and an effect bounding method (the Witness
Protection Program)\nbased on covariate adjustment with observable independence
constraints.","Imports":"igraph, rcdd, rje","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CausalFX","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Methods for Estimating Causal Effects from Observational
Data","URL":"http:\/\/github.com\/rbas2015\/CausalFX","Version":"1.0.1"},"CausalGAM
":{"Author":"Adam Glynn <aglynn@iq.harvard.edu>, Kevin
Quinn\n<kquinn@law.berkeley.edu>","Depends":"R (>= 2.9.0), gam (>=
1.0.1)","Description":"This package implements various estimators for
average\ntreatment effects---an inverse probability weighted (IPW)\nestimator, an
augmented inverse probability weighted (AIPW)\nestimator, and a standard regression
estimator---that make use\nof generalized additive models for the treatment
assignment\nmodel and\/or outcome model.","License":"GPL-
2","NeedsCompilation":"no","Package":"CausalGAM","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Estimation of Causal Effects with Generalized Additive
Models","Version":"0.1-3"},"Causata":{"Author":"Justin Hemann, David Barker,
Suzanne Weller, Jason McFall","Depends":"R (>= 2.15.1)","Description":"The Causata
package provides utilities for\nextracting data from the Causata application,
training binary classification\nmodels, and exporting models as PMML for
scoring.","Imports":"XML, R.utils, rjson, RMySQL, RCurl, stringr, yaml,
boot,\nforeach, data.table, glmnet,
ggplot2","License":"GPL","NeedsCompilation":"no","Package":"Causata","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Suggests":"doMC, testthat, pROC,
knitr","Title":"Analysis utilities for binary classification and Causata
users","URL":"www.causata.com","Version":"4.2-0"},"CePa":{"Author":"Zuguang
Gu","Depends":"R (>= 2.10.0), igraph (>= 0.6), stats, snow","Description":"Use
pathway topology information to assign weight to\npathway nodes.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"CePa","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Centrality-based pathway
enrichment","URL":"http:\/\/mcube.nju.edu.cn\/jokergoo\/","Version":"0.5"},"Cellula
rAutomaton":{"Author":"John Hughes","Depends":"R.oo,
R.methodsS3","Description":"This package is an object-oriented implementation of
one-dimensional cellular automata. It supports many of the features offered by
Mathematica, including elementary rules, user-defined rules, radii, user-defined
seeding, and
plotting.","License":"GPL","NeedsCompilation":"no","Package":"CellularAutomaton","R
epository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"One-Dimensional Cellular
Automata","Version":"1.1-1"},"CensMixReg":{"Author":"Luis Benites
Sanchez, Victor Hugo Lachos","Description":"Fit censored linear regression models
where the random errors follow a finite mixture of Normal or Student-t
distributions.","Imports":"mixsmsn","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CensMixReg","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Censored Linear Mixture Regression
Models","Version":"0.7"},"CensRegMod":{"Author":"Monique Bettio Massuia
<moniquemassuia@gmail.com>,\nLarissa Avila Matos <larissaam@ime.unicamp.br>\nand
Victor Lachos <hlachos@ime.unicamp.br>","Depends":"R (>=
3.1.2)","Description":"Fits univariate censored linear regression model under
Normal or Student-t distribution","License":"GPL (>=
3.0)","NeedsCompilation":"no","Package":"CensRegMod","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Fits Normal and Student-t Censored Regression
Model","Version":"1.0"},"CepLDA":{"Author":"Zeda Li, Robert Krafty","Depends":"R(>=
3.0.1), astsa, MASS, class, multitaper","Description":"Performs cepstral based
discriminant analysis of groups of time series\nwhen there exists Variability in
power spectra from time series within the same group\nas described in R.T. Krafty
(2016) \"Discriminant Analysis of Time Series in the\nPresence of Within-Group
Spectral Variability\" Journal of Time Series Analysis.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CepLDA","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Discriminant Analysis of Time Series in the Presence
of\nWithin-Group Spectral
Variability","URL":"http:\/\/astro.temple.edu\/~tuf28410\/","Version":"1.0.0"},"Cer
ioliOutlierDetection":{"Author":"Christopher G. Green [aut, cre],\nR. Doug Martin
[ths]","Depends":"R (>= 3.0.0)","Description":"This package provides the iterated
RMCD method of Cerioli (2010)\nfor multivariate outlier detection via robust
Mahalanobis distances. It also\nprovides the finite-sample RMCD method discussed in
the paper, as well as\nthe methods provided in Hardin and Rocke (2005) and Green
and Martin (2014).","Imports":"robustbase (>= 0.91-1)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CerioliOutlierDetection","Repository":"http:
\/\/cran.csiro.au\/src\/contrib","Suggests":"rrcov, robust,
mvtnorm","Title":"Outlier detection using the iterated RMCD method of
Cerioli\n(2010)","URL":"http:\/\/christopherggreen.github.io\/CerioliOutlierDetecti
on\/","Version":"1.0.8"},"CfEstimateQuantiles":{"Author":"Maxim
Yurchuk","Description":"Estimate quantiles using formula (18)
from\nhttp:\/\/www.jaschke-net.de\/papers\/CoFi.pdf (Yaschke;
2001)","License":"GPL-
2","NeedsCompilation":"no","Package":"CfEstimateQuantiles","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Title":"Estimate quantiles using any order Cornish-
Fisher expansion","Version":"1.0"},"ChainLadder":{"Author":"Markus Gesmann [aut,
cre],\nDaniel Murphy [aut],\nYanwei (Wayne) Zhang [aut],\nAlessandro Carrato
[aut],\nGiuseppe Crupi [aut],\nChristophe Dutang [ctb],\nArnaud Lacoume
[ctb],\nArthur Charpentier [ctb],\nMario Wuthrich [aut],\nFabio Concina
[aut]","Description":"Various statistical methods and models which are\ntypically
used for the estimation of outstanding claims reserves\nin general insurance,
including those to estimate the claims\ndevelopment result as required under
Solvency II.","Imports":"Matrix, actuar, methods, stats, reshape2, lattice,
grid,\ntweedie, utils, systemfit, statmod, cplm (>= 0.7-3), ggplot2","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"ChainLadder","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"RUnit, MASS","Title":"Statistical Methods and
Models for Claims Reserving in
General\nInsurance","URL":"https:\/\/github.com\/mages\/ChainLadder#chainladder","V
ersion":"0.2.2"},"ChannelAttribution":{"Author":"Davide
Altomare","Description":"Advertisers use a variety of online marketing channels to
reach consumers and they want to know the degree each channel contributes to their
marketing success. It's called the online multi-channel attribution problem. This
package contains a probabilistic algorithm for the attribution problem. The model
uses a k-order Markov representation to identifying structural correlations in the
customer journey data. The package also contains three heuristic algorithms (first-
touch, last-touch and linear-touch approach) for the same problem. The algorithms
are implemented in C++. For customizations or interest in other statistical
methodologies for web data analysis please contact
<davide.altomare@gmail.com>.","Imports":"Rcpp (>= 0.11.4)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ChannelAttribution","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Title":"Markov Model for the Online Multi-Channel
Attribution Problem","URL":"\nhttp:\/\/www.slideshare.net\/adavide1982\/markov-
model-for-the-multichannel-attribution-
problem","Version":"1.5"},"ChannelAttributionApp":{"Author":"Davide
Altomare","Description":"Shiny Web Application for the Multichannel Attribution
Problem. It is basically a user-friendly graphical interface for running and
comparing all the attribution models in package 'ChannelAttribution'. For
customizations or interest in other statistical methodologies for web data analysis
please contact <davide.altomare@gmail.com>.","Imports":"ChannelAttribution, shiny,
data.table, ggplot2, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ChannelAttributionApp","Repository":"http:\/
\/cran.csiro.au\/src\/contrib","Title":"Shiny Web Application for the Multichannel
Attribution Problem","URL":"\nhttp:\/\/www.slideshare.net\/adavide1982\/markov-
model-for-the-multichannel-attribution-problem","Version":"1.1"},"ChaosGame":
{"Author":"Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at>,\nWolfgang
Trutschnig <Wolfgang.Trutschnig@sbg.ac.at>","Depends":"rgl, RColorBrewer,
colorRamps","Description":"The main objective of the package is to enter a word of
at least two letters based on which an Iterated Function System with Probabilities
(IFSP) is constructed, and a two-dimensional fractal containing the chosen word
infinitely often is generated via the Chaos Game. Additionally, the package allows
to project the two-dimensional fractal on several three-dimensional surfaces and to
transform the fractal into another fractal with uniform
marginals.","Imports":"ggplot2, gridExtra, sphereplot, plot3D","License":"GPL-
2","NeedsCompilation":"no","Package":"ChaosGame","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Chaos Game","URL":"http:\/\/www.r-
project.org","Version":"0.2"},"ChargeTransport":{"Author":"Julien IdÃ© and Guido
Raos","Depends":"R (>= 3.0), parallel (>= 3.0)","Description":"This package
provides functions to compute Marcus, Marcus-Levich-Jortner or Landau-Zener charge
transfer rates. These rates can then be used to perform kinetic Monte Carlo
simulations to estimate charge carrier mobilities in molecular materials. The
preparation of this package was supported by the the Fondazione Cariplo (PLENOS
project, ref. 2011-
0349).","License":"GPL","NeedsCompilation":"yes","Package":"ChargeTransport","Repos
itory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Charge Transfer Rates and
Charge Carrier Mobilities","Version":"1.0.2"},"CheckDigit":{"Author":"Justin
Brantley <brantley@uw.edu>","Description":"A set of functions to calculate check
digits according to\nvarious algorithms and to verify whether a string ends in
a\nvalid check digit","License":"GPL-
3","NeedsCompilation":"no","Package":"CheckDigit","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat","Title":"Calculate and verify check
digits","URL":"https:\/\/github.com\/fascinatingfingers\/CheckDigit","Version":"0.1
-1"},"ChemoSpec":{"Author":"Bryan A. Hanson DePauw University, Greencastle Indiana
USA","Depends":"R (>= 3.1)","Description":"A collection of functions for top-down
exploratory data analysis of spectral data obtained via nuclear magnetic resonance
(NMR), infrared (IR) or Raman spectroscopy. Includes functions for plotting and
inspecting spectra, peak alignment, hierarchical cluster analysis (HCA), principal
components analysis (PCA) and model-based clustering. Robust methods appropriate
for this type of high-dimensional data are available. ChemoSpec is designed with
metabolomics data sets in mind, where the samples fall into groups such as
treatment and control. Graphical output is formatted consistently for publication
quality plots. ChemoSpec is intended to be very user friendly and help you get
usable results quickly. A vignette covering typical operations is
available.","Imports":"plyr, rgl, stats, utils, grDevices","License":"GPL-
3","NeedsCompilation":"no","Package":"ChemoSpec","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"mvbutils, sna, knitr, IDPmisc, amap, seriation,
speaq,\nclusterCrit, NbClust, R.utils, RColorBrewer, baseline, js,\njsonlite,
exCon, mclust, gsubfn, lattice, pcaPP, pls, grid,\nrobustbase, MASS,
signal","Title":"Exploratory Chemometrics for
Spectroscopy","URL":"https:\/\/github.com\/bryanhanson\/ChemoSpec","Version":"4.3.1
7"},"ChemometricsWithR":{"Author":"Ron Wehren9","Depends":"ChemometricsWithRData
(>= 0.1.3), MASS, pls, kohonen","Description":"Functions and scripts used in the
book \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
Life Sciences\" by Ron Wehrens, Springer (2011).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ChemometricsWithR","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"nnet, randomForest, ada, rrcov, sfsmisc,
ipred, fastICA, rda,\nTIMP, class, e1071, rpart, cluster, ALS, ptw, dtw, boot,
leaps,\nlars, elasticnet, subselect, signal, mclust","Title":"Chemometrics with R -
Multivariate Data Analysis in the Natural\nSciences and Life
Sciences","Version":"0.1.9"},"ChemometricsWithRData":{"Author":"Ron
Wehrens","Depends":"R (>= 2.10)","Description":"The
package provides data sets used in the book\n\"Chemometrics with R - Multivariate
Data Analysis in the\nNatural Sciences and Life Sciences\" by Ron Wehrens,
Springer\n(2011).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ChemometricsWithRData","Repository":"http:\/
\/cran.csiro.au\/src\/contrib","Title":"Data for package
ChemometricsWithR","Version":"0.1.3"},"ChoiceModelR":{"Author":"Ryan Sermas,
assisted by John V. Colias,
Ph.D.\n<DecisionAnalystR@decisionanalyst.com>","Depends":"R (>=
2.10)","Description":"Implements an MCMC algorithm to estimate a
hierarchical\nmultinomial logit model with a normal heterogeneity\ndistribution.
The algorithm uses a hybrid Gibbs Sampler with a\nrandom walk metropolis step for
the MNL coefficients for each\nunit. Dependent variable may be discrete or
continuous.\nIndependent variables may be discrete or continuous with\noptional
order constraints. Means of the distribution of\nheterogeneity can optionally be
modeled as a linear function of\nunit characteristics variables.","License":"GPL
(>=
3)","NeedsCompilation":"no","Package":"ChoiceModelR","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"bayesm, MASS, lattice, Matrix","Title":"Choice
Modeling in R","URL":"http:\/\/www.decisionanalyst.com","Version":"1.2"},"CircE":
{"Author":"Michele Grassi <grassi.mic@gmail.com>","Depends":"R (>= 1.6.0),
stats","Description":"This package contains functions for fitting
circumplex\nstructural models for correlation matrices (with negative\ncorrelation)
by the method of maximum likelihood.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CircE","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Circumplex models Estimation","Version":"1.1"},"CircNNTSR":
{"Author":"Juan Jose Fernandez-Duran and Maria Mercedes Gregorio-
Dominguez","Depends":"stats","Description":"Functions for the analysis of circular
data using\ndistributions based on Nonnegative Trigonometric Sums
(NNTS).\nFunctions for calculation of densities and distributions, the\nestimation
of parameters, plotting and more","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CircNNTSR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"CircNNTSR: An R package for the statistical analysis of
circular\ndata using nonnegative trigonometric sums (NNTS)
models","Version":"2.1"},"CircOutlier":{"Author":"Azade Ghazanfarihesari, Majid
Sarmad- Ferdowsi University Of Mashhad","Depends":"CircStats,
circular","Description":"Detection of outliers in circular-circular regression
models, modifying its and estimating of models parameters.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CircOutlier","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Detection of Outliers in Circular-Circular
Regression","Version":"3.2.3"},"CircStats":{"Author":"S-plus original by Ulric Lund
<ulund@calpoly.edu>, R port by\nClaudio Agostinelli
<claudio@unive.it>","Depends":"MASS, boot","Description":"Circular Statistics, from
\"Topics in circular Statistics\"\n(2001) S. Rao Jammalamadaka and A. SenGupta,
World Scientific.","License":"GPL-
2","NeedsCompilation":"no","Package":"CircStats","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Circular Statistics, from \"Topics in circular
Statistics\" (2001)","URL":"S-plus original at
http:\/\/statweb.calpoly.edu\/lund\/","Version":"0.2-4"},"CityPlot":
{"Author":"Martin Dugas","Description":"Input: a csv-file for each database table
and a\ncontrolfile describing relations between tables. Output: An\nextended ER
diagram","License":"LGPL","NeedsCompilation":"no","Package":"CityPlot","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Title":"Visualization of structure and
contents of a database","Version":"2.0"},"Ckmeans.1d.dp":{"Author":"Joe Song and
Haizhou Wang","Depends":"R (>= 2.10.0)","Description":"A dynamic programming
algorithm for optimal one-dimensional k-means clustering. The algorithm minimizes
the sum of squares of within-cluster distances. As an alternative to the standard
heuristic k-means algorithm, this algorithm guarantees optimality and
repeatability.","License":"LGPL (>=
3)","NeedsCompilation":"yes","Package":"Ckmeans.1d.dp","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat","Title":"Optimal k-Means Clustering
for One-Dimensional Data","Version":"3.3.1"},"ClamR":{"Author":"Jonathan M.
Lees","Description":"Implementation of the Wilkinson and Ivany (2002) approach to
paleoclimate analysis, applied to isotope data extracted from
clams.","Imports":"stats","License":"GPL","NeedsCompilation":"no","Package":"ClamR"
,"Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Time Series Modeling
for Climate Change Proxies","Version":"2.1-1"},"ClickClust":{"Author":"Volodymyr
Melnykov [aut, cre]","Depends":"R (>= 3.0.0)","Description":"Clustering categorical
sequences by means of finite mixtures with Markov model components is the main
utility of ClickClust. The package also allows detecting blocks of equivalent
states by forward and backward state selection procedures.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ClickClust","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Model-Based Clustering of Categorical
Sequences","Version":"1.1.4"},"ClimClass":{"Author":"Emanuele Eccel [aut,
cre],\nEmanuele Cordano [aut],\nGiambattista Toller [aut],\nFabio Zottele
[ctb]","Depends":"R(>= 2.10.0),geosphere,ggplot2,reshape2,
utils","Description":"Classification of climate according to Koeppen - Geiger, of
aridity\nindices, of continentality indices, of water balance after Thornthwaite,
of\nviticultural bioclimatic indices. Drawing climographs: Thornthwaite,
Peguy,\nBagnouls-Gaussen.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ClimClass","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"stringr","Title":"Climate Classification According
to Several Indices","Version":"2.0.1"},"CluMix":{"Author":"M. Hummel, A. Kopp-
Schneider","Description":"Provides utilities for clustering subjects and variables
of mixed data types. Similarities between subjects are measured by Gower's general
similarity coefficient with an extension of Podani for ordinal variables.
Similarities between variables are assessed by combination of appropriate measures
of association for different pairs of data types. Alternatively, variables can also
be clustered by the 'ClustOfVar' approach. The main feature of the package is the
generation of a mixed-data heatmap. For visualizing similarities between either
subjects or variables, a heatmap of the corresponding distance matrix can be drawn.
Associations between variables can be explored by a 'confounderPlot', which allows
visual detection of possible confounding, collinear, or surrogate factors for some
variables of primary interest. Distance matrices and dendrograms for subjects and
variables can be derived and used for further visualizations and
applications.","Imports":"ClustOfVar, Hmisc, DescTools, extracat, marray, FD,
gplots,\nMatrix","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CluMix","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Clustering and Visualization of Mixed-Type
Data","Version":"0.3"},"ClueR":{"Author":"Pengyi Yang & Raja Jothi","Depends":"R
(>= 2.10.0), e1071","Description":"CLUE is an R package for identifying optimal
number of clusters in a given time-course dataset clustered by cmeans or kmeans
algorithms.","License":"GPL-
3","NeedsCompilation":"no","Package":"ClueR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"Hmisc","Title":"CLUster Evaluation
(CLUE)","Version":"1.1"},"ClustGeo":{"Author":"Amaury Labenne, Marie Chavent,
Vanessa Kuentz-Simonet and Jerome Saracco","Depends":"R(>= 2.10.0), rCarto,
FactoMineR, plyr,","Description":"Functions which allow to integrate geographical
constraints in Ward hierarchical clustering. Geographical maps of typologies
obtained can be displayed with the use of shapefiles.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"ClustGeo","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Clustering of Observations with Geographical
Constraints","Version":"1.0"},"ClustMMDD":{"Author":"Wilson
Toussile","Depends":"Rcpp (>= 0.11.5), R (>= 3.0.0)","Description":"An
implementation of a variable selection procedure in clustering by mixture of
multinomial models for discrete data. Genotype data are examples of such data with
two unordered observations (alleles) at each locus for diploid individual. The two-
fold problem of variable selection and clustering is seen as a model selection
problem where competing models are characterized by the number of clusters K, and
the subset S of clustering variables. Competing models are compared by penalized
maximum likelihood criteria. We considered asymptotic criteria such as Akaike and
Bayesian Information criteria, and a family of penalized criteria with penalty
function to be data driven calibrated.","Imports":"methods","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ClustMMDD","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Variable Selection in Clustering by Mixture Models for
Discrete\nData","Version":"1.0.3"},"ClustOfVar":{"Author":"Marie Chavent and
Vanessa Kuentz and Benoit Liquet and Jerome Saracco","Description":"Cluster
analysis of a set of variables. Variables can be\nquantitative, qualitative or a
mixture of both.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"ClustOfVar","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Clustering of
variables","Version":"0.8"},"ClustVarLV":{"Author":"Evelyne Vigneau, Mingkun
Chen","Depends":"R (>= 3.0.0)","Description":"Functions for the clustering of
variables around Latent Variables. Each cluster of variables, which may be defined
as a local or directional cluster, is associated with a latent variable.\nExternal
variables measured on the same observations or\/and additional information on the
variables can be taken into account.","Imports":"Rcpp (>= 0.11.6)","License":"GPL-
2","NeedsCompilation":"yes","Package":"ClustVarLV","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr","Title":"Clustering of Variables Around
Latent Variables","Version":"1.4.1"},"ClusterStability":{"Author":"Etienne Lord,
Matthieu Willems, Francois-Joseph Lapointe, and Vladimir\nMakarenkov","Depends":"R
(>= 2.2.4), Rcpp, clusterCrit, cluster, copula (>=
0.999),\nWeightedCluster","Description":"Allows one to assess the stability of
individual objects, clusters\nand whole clustering solutions based on repeated runs
of the K-means and K-medoids\npartitioning algorithms.","License":"GPL-
3","NeedsCompilation":"yes","Package":"ClusterStability","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Assessment of Stability of Individual Objects or
Clusters in\nPartitioning Solutions","Version":"1.0.3"},"CoClust":
{"Author":"Francesca Marta Lilja Di Lascio, Simone Giannerini","Depends":"R (>=
2.15.1), methods, copula","Description":"Copula Based Cluster
Analysis.","Imports":"gtools","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CoClust","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Copula Based Cluster Analysis","Version":"0.3-
1"},"CoImp":{"Author":"Francesca Marta Lilja Di Lascio, Simone
Giannerini","Depends":"R (>= 2.15.2), methods, copula","Description":"Copula based
imputation method. A semiparametric imputation procedure for missing multivariate
data based on conditional copula specifications.","Imports":"nnet, gtools,
locfit","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CoImp","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Copula based imputation method","Version":"0.2-
3"},"CoinMinD":{"Author":"Dr M.Subbiah","Depends":"MCMCpack","Description":"Methods
for obtaining simultaneous confidence interval for\nmultinomial proportion have
been proposed by many authors and\nthe present study include a variety of widely
applicable\nprocedures. Seven classical methods (Wilson, Quesenberry and\nHurst,
Goodman, Wald with and without continuity correction,\nFitzpatrick and Scott, Sison
and Glaz) and Bayesian Dirichlet\nmodels are included in the package. The advantage
of MCMC pack\nhas been exploited to derive the Dirichlet posterior directly\nand
this also helps in handling the Dirichlet prior parameters.\nThis package is
prepared to have equal and unequal values for\nthe Dirichlet prior distribution
that will provide better scope\nfor data analysis and associated sensitivity
analysis.","License":"GPL-
2","NeedsCompilation":"no","Package":"CoinMinD","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Simultaneous Confidence Interval for Multinomial
Proportion","Version":"1.1"},"CollapsABEL":{"Author":"Kaiyin Zhong, Fan
Liu","Depends":"R (>= 3.1.0), rJava (>= 0.9-6)","Description":"Implements a
generalized version of the CDH test\n<DOI:10.1371\/journal.pone.0028145> for
detecting compound heterozygosity on a\ngenome-wide level, due to usage of
generalized linear models it allows flexible\nanalysis of binary and continuous
traits with covariates.","Imports":"R.utils, RSQLite, biganalytics, bigmemory,
collUtils, dplyr,\nggplot2, methods, stringr, stats","License":"GPL-
3","NeedsCompilation":"no","Package":"CollapsABEL","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat","Title":"Generalized CDH (GCDH)
Analysis","URL":"https:\/\/bitbucket.org\/kindlychung\/collapsabel2\/overview","Ver
sion":"0.10.8"},"CollocInfer":{"Author":"Giles Hooker <gjh27@cornell.edu>,\nLuo
Xiao <lx42@cornell.edu>,\nJames Ramsay <ramsay@psych.mcgill.ca>","Depends":"R (>=
2.4.0), fda","Description":"These functions implement collocation-inference\nfor
continuous-time and discrete-time stochastic processes.\nThey provide model-based
smoothing, gradient-matching,\ngeneralized profiling and forwards prediction error
methods.","Imports":"MASS, Matrix, spam, deSolve, methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CollocInfer","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"pomp, SparseM, subplex, trust,
maxLik","Title":"Collocation Inference for Dynamic
Systems","URL":"http:\/\/www.bscb.cornell.edu\/~hooker","Version":"1.0.2"},"ColorPa
lette":{"Author":"Carl Ambroselli [aut, cre]","Depends":"R (>=
3.0.0)","Description":"Different methods to generate a color palette based on a
specified base color and a number of colors that should be created.","License":"MIT
+ file
LICENSE","NeedsCompilation":"no","Package":"ColorPalette","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Color Palettes Generator","Version":"1.0-
1"},"ComICS":{"Author":"Yael Steuerman [aut, cre],\nIrit Gat-Viks
[aut]","Depends":"R (>= 3.1.1)","Description":"Provided are Computational methods
for Immune Cell-type Subsets, including:(1) DCQ (Digital Cell Quantifier) to infer
global dynamic changes in immune cell quantities within a complex tissue; and (2)
VoCAL (Variation of Cell-type Abundance Loci) a deconvolution-based method that
utilizes transcriptome data to infer the quantities of immune-cell types, and then
uses these quantitative traits to uncover the underlying DNA
loci.","Imports":"glmnet, stats","License":"GPL-
2","NeedsCompilation":"no","Package":"ComICS","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Computational Methods for Immune Cell-Type
Subsets","URL":"http:\/\/dcq.tau.ac.il\/ ,
http:\/\/csgi.tau.ac.il\/VoCAL\/","Version":"1.0.3"},"CombMSC":{"Author":"Andrew K.
Smith","Depends":"R(>= 2.4.0)","Description":"Functions for computing optimal
convex combinations of\nmodel selection criteria based on ranks, along with
utility\nfunctions for constructing model lists, MSCs, and priors on\nmodel
lists.","License":"GPL-
2","NeedsCompilation":"no","Package":"CombMSC","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"lattice, rgl","Title":"Combined Model Selection
Criteria","Version":"1.4.2"},"CombinS":{"Author":"Mohamed Laib, Imane Rezgui,
Zebida Gheribi-Aoulmi and Herve Monod","Description":"The Combinatory Method (s) to
Construct a series of PBIB designs and we give their associated U-type
design.","License":"GPL-
3","NeedsCompilation":"no","Package":"CombinS","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Construction Methods of some Series of PBIB
Designs","Version":"1.1"},"Combine":{"Author":"Alaa Ali, Marta Padilla and David R.
Bickel","Depends":"R (>= 2.14.0), methods","Description":"Suite of R functions for
combination of probabilities using a game-theoretic method.","License":"GPL-
3","NeedsCompilation":"no","Package":"Combine","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Game-Theoretic Probability
Combination","URL":"http:\/\/www.cran.r-project.org,
http:\/\/www.statomics.com","Version":"1.0"},"CombinePValue":{"Author":"Hongying
Dai","Description":"We offer two statistical tests to combine p-values:
selfcontained.test vs competitive.test. The goal is to test whether a vector of
pvalues are jointly significant when we combine them together.","License":"GPL-
3","NeedsCompilation":"no","Package":"CombinePValue","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Combine a Vector of Correlated p-
values","Version":"1.0"},"CommonJavaJars":{"Author":"Kornelius Rohmeyer (R
package), see COPYRIGHTS file for the authors of the java libraries","Depends":"R
(>= 2.8.0)","Description":"Useful libraries for building a Java based GUI under
R","License":"GPL-
2","NeedsCompilation":"no","Package":"CommonJavaJars","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"rJava","Title":"Useful libraries for building a
Java based GUI under R","URL":"http:\/\/gsrmtp.r-forge.r-
project.org\/","Version":"1.0-5"},"CommonTrend":{"Author":"Fan Yang","Depends":"R
(>= 2.10)","Description":"Directly extract and plot stochastic common trends
from\na cointegration system using different approaches, currently\nincluding Kasa
(1992) and Gonzalo and Granger (1995).\nThe approach proposed by Gonzalo and
Granger, also known as\nPermanent-Transitory Decomposition, is widely used
in\nmacroeconomics and market microstructure literature.\nKasa's approach, on the
other hand, has a nice property that it only\nuses the super consistent estimator:
the cointegration vector\n'beta'.\nThis package also provides functions calculate
P-value\nfrom Johansen Statistics according to the approximation method\nproposed
by Doornik (1998).\nUpdate:\n0.7-1: Fix bugs in calculation alpha. Add formulas and
more explanations.\n0.6-1: Rewrite the description file.\n0.5-1: Add functions to
calculate P-value from Johansen statistic, and vice
versa.","Imports":"methods,MASS,urca","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CommonTrend","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Extract and plot common trends from a cointegration
system.\nCalculate P-value for Johansen Statistics","Version":"0.7-
1"},"CommunityCorrelogram":{"Author":"J. Malia Andrus, Timothy Kuehlhorn, Luis F.
Rodriguez, Angela D. Kent, and Julie L. Zilles","Depends":"vegan,
methods","Description":"The CommunityCorrelogram package is designed for the
geostatistical analysis of ecological community datasets with either a spatial or
temporal distance component.","License":"GPL-
2","NeedsCompilation":"no","Package":"CommunityCorrelogram","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Title":"Ecological Community
Correlogram","Version":"1.0"},"Comp2ROC":{"Author":"Ana C. Braga with contributions
from Hugo Frade and Sara Carvalho","Depends":"R (>= 2.15.1), ROCR,
boot","Description":"Comparison of two ROC curves throughout the methodology
propose by Ana C. Braga.","License":"GPL-
2","NeedsCompilation":"no","Package":"Comp2ROC","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Compare
Two ROC Curves that Intersect","Version":"1.1"},"CompGLM":{"Author":"Jeffrey
Pollock","Description":"The package contains a function (which uses a similar
interface to\nthe `glm' function) for the fitting of a Conway-Maxwell-Poisson GLM.
There\nare also various methods for analysis of the model fit. The package
also\ncontains functions for the Conway-Maxwell-Poisson distribution in a
similar\ninterface to functions `dpois', `ppois' and `rpois'. The functions
are\ngenerally quick, since the workhorse functions are written in C++ (thanks\nto
the Rcpp package).","Imports":"Rcpp (>= 0.11.2), stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"CompGLM","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"RUnit","Title":"Conway-Maxwell-Poisson GLM and
distribution functions","Version":"1.0"},"CompLognormal":{"Author":"Saralees
Nadarajah","Depends":"R (>= 2.15.0), numDeriv","Description":"Computes the
probability density function, cumulative distribution function, quantile function,
random numbers of any composite model based on the lognormal
distribution.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CompLognormal","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Functions for actuarial
scientists","Version":"3.0"},"CompQuadForm":{"Author":"P. Lafaye de
Micheaux","Description":"Computes the distribution function of quadratic forms
in\nnormal variables using Imhof's method, Davies's algorithm,\nFarebrother's
algorithm or Liu et al.'s algorithm.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"CompQuadForm","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Distribution function of quadratic forms in normal
variables","Version":"1.4.1"},"CompR":{"Author":"Michel Semenou","Depends":"R (>=
3.1), methods, utils, MASS, graphics, stats","Description":"Different tools for
describing and analysing paired comparison data are presented. Main methods are
estimation of products scores according Bradley Terry Luce model. A segmentation of
the individual could be conducted on the basis of a mixture distribution approach.
The number of classes can be tested by the use of Monte Carlo simulations. This
package deals also with multi-criteria paired comparison data.","License":"GPL-
2","NeedsCompilation":"no","Package":"CompR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Paired Comparison Data
Analysis","Version":"1.0"},"CompRandFld":{"Author":"Simone Padoan[aut, cre]
<simone.padoan@unibocconi.it>, Moreno Bevilacqua[aut]
<moreno.bevilacqua@uv.cl>","Depends":"R (>= 2.13)","Description":"A set of
procedures for the analysis of Random Fields using likelihood and non-standard
likelihood methods is provided. Spatial analysis often involves dealing with large
dataset. Therefore even simple studies may be too computationally demanding.
Composite likelihood inference is emerging as a useful tool for mitigating such
computational problems. This methodology shows satisfactory results when compared
with other techniques such as the tapering method. Moreover, composite likelihood
(and related quantities) have some useful properties similar to those of the
standard likelihood.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"CompRandFld","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"RandomFields, spam, scatterplot3d, fields,
mapproj","Title":"Composite-Likelihood Based Analysis of Random
Fields","URL":"http:\/\/faculty.unibocconi.it\/simonepadoan","Version":"1.0.3-
4"},"CompareCausalNetworks":{"Author":"Christina Heinze
<heinze@stat.math.ethz.ch>,\nNicolai Meinshausen
<meinshausen@stat.math.ethz.ch>","Depends":"R (>= 3.1.0)","Description":"Unified
interface for the estimation of causal networks,\nincluding the methods 'backShift'
(from package 'backShift'),\n'bivariateANM' (bivariate additive noise
model),\n'bivariateCAM' (bivariate causal additive model),\n'CAM' (causal additive
model) (from package 'CAM'),\n'hiddenICP' (invariant causal prediction with hidden
variables),\n'ICP' (invariant causal prediction) (from package
'InvariantCausalPrediction'),\n'GES' (greedy equivalence search),\n'GIES' (greedy
interventional equivalence search),\n'LINGAM', 'PC' (PC Algorithm),\n'RFCI' (really
fast causal inference)\n(all from package 'pcalg') and
regression.","Imports":"Matrix,
methods","License":"GPL","NeedsCompilation":"no","Package":"CompareCausalNetworks",
"Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"pcalg,
InvariantCausalPrediction, glmnet, backShift, CAM,\nkernlab, mgcv,
testthat","Title":"Interface to Diverse Estimation Methods of Causal
Networks","URL":"https:\/\/github.com\/christinaheinze\/CompareCausalNetworks","Ver
sion":"0.1.4"},"CompareTests":{"Author":"Hormuzd A. Katki and David W.
Edelstein","Description":"A standard test is observed on all specimens. We treat
the second test (or sampled test) as being conducted on only a stratified sample of
specimens. Verification Bias is this situation when the specimens for doing the
second (sampled) test is not under investigator control. We treat the total sample
as stratified two-phase sampling and use inverse probability weighting. We
estimate diagnostic accuracy (category-specific classification probabilities; for
binary tests reduces to specificity and sensitivity, and also predictive values)
and agreement statistics (percent agreement, percent agreement by category, Kappa
(unweighted), Kappa (quadratic weighted) and symmetry tests (reduces to McNemar's
test for binary tests)). See: Katki HA, Li Y, Edelstein DW, Castle PE. Estimating
the agreement and diagnostic accuracy of two diagnostic tests when one test is
conducted on only a subsample of specimens. Stat Med. 2012 Feb 28; 31(5):
10.1002\/sim.4422.","License":"GPL-
3","NeedsCompilation":"no","Package":"CompareTests","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Correct for Verification Bias in Diagnostic Accuracy
& Agreement","URL":"\nhttp:\/\/dceg.cancer.gov\/about\/staff-
directory\/biographies\/A-J\/katki-hormuzd","Version":"1.1"},"Compind":
{"Author":"Francesco Vidoli, Elisa Fusco","Depends":"Benchmarking, psych,
boot","Description":"Contains several functions to enhance approaches to the
Composite Indicators methods, focusing, in particular, on the normalisation and
weighting-aggregation steps.","Imports":"Hmisc, MASS, GPArotation, lpSolve,
nonparaeff","License":"GPL-
3","NeedsCompilation":"no","Package":"Compind","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Composite Indicators
Functions","Version":"1.1"},"ComplexAnalysis":{"Author":"Char
Leung","Description":"Evaluate complex integrals along a disc or a straight
line.\nEvaluate higher-order derivatives by employing the Cauchy integral
formula.\nEvaluate residues.\nSearch for simple poles given a function.\nEvaluate
limits.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ComplexAnalysis","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Numerically Evaluate Integrals and Derivatives
(also Higher\nOrder) of Vector- And Complex-Valued
Functions","Version":"1.0"},"Compositional":{"Author":"Michail Tsagris [aut, cre],
Giorgos Athineou [aut]","Depends":"R (>= 3.2.2)","Description":"A collection of
functions for compositional data analysis.","Imports":"sn, quantreg, mixture, BB,
doParallel, parallel, foreach,\nMASS, fields","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Compositional","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Compositional Data
Analysis","Version":"1.2"},"Compounding":{"Author":"Bozidar V. Popovic, Saralees
Nadarajah, Miroslav M. Ristic","Depends":"R (>= 2.12.0),
hypergeo","Description":"Computing Continuous Distributions Obtained by
Compounding\na Continuous and a Discrete Distribution","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Compounding","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Computing Continuous
Distributions","Version":"1.0.2"},"ConConPiWiFun":{"Author":"Robin
Girard","Depends":"methods, graphics, Rcpp (>= 0.10.3)","Description":"Continuous
convex piecewise linear (ccpl) resp. quadratic (ccpq) functions can be implemented
with sorted breakpoints and slopes. This includes functions that are ccpl (resp.
ccpq) on a convex set (i.e. an interval or a point) and infinite out of the domain.
These functions can be very useful for a large class of optimisation problems.
Efficient manipulation (such as log(N) insertion) of such data structure is
obtained with map standard template library of C++ (that hides balanced trees).
This package is a wrapper on such a class based on Rcpp modules.","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"ConConPiWiFun","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Optimisation with Continuous Convex Piecewise
(Linear and\nQuadratic) Functions","Version":"0.4.6"},"ConSpline":{"Author":"Mary C
Meyer","Depends":"graphics, grDevices, stats, utils, coneproj","Description":"Given
response y, continuous predictor x, and covariate matrix, the relationship between
E(y) and x is estimated with a shape constrained regression spline. Function
outputs fits and various types of inference.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"ConSpline","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Partial Linear Least-Squares Regression using
Constrained\nSplines","Version":"1.1"},"Conake":{"Author":"W. E. WansouwÃ©, F. G.
LibenguÃ© and C. C. Kokonendji","Description":"Continuous smoothing of probability
density function on a compact or semi-infinite support is performed using four
continuous associated kernels: extended beta, gamma, lognormal and reciprocal
inverse Gaussian. The cross-validation technique is also implemented for bandwidth
selection.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Conake","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Continuous
Associated Kernel Estimation","URL":"www.r-
project.org","Version":"1.0"},"CondReg":{"Author":"Sang-Yun Oh <syoh@lbl.gov>,
Joong-Ho Won <wonj@stats.snu.ac.kr>","Description":"Based
on\n\\url{http:\/\/statistics.stanford.edu\/~ckirby\/techreports\/GEN\/2012\/2012-
10.pdf}","License":"GPL-
3","NeedsCompilation":"no","Package":"CondReg","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Condition Number Regularized Covariance
Estimation","Version":"0.20"},"ConjointChecks":{"Author":"Ben Domingue
<ben.domingue@gmail.com>","Depends":"R (>= 2.14.0), parallel,
methods","Description":"Implementation of a procedure (Domingue, 2012; see
also\nKarabatsos, 2001 and Kyngdon, 2011) to test the single and\ndouble
cancellation axioms of conjoint measure in data that is\ndichotomously coded and
measured with error.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ConjointChecks","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"snow, Rmpi","Title":"A package to check the
cancellation axioms of conjoint\nmeasurement","Version":"0.0.9"},"ConnMatTools":
{"Author":"Marco Andrello <marco.andrello@gmail.com>","Description":"ConnMatTools
collects several different methods for analyzing and\nworking with connectivity
matrices in R. Though primarily oriented towards\nmarine larval dispersal, many of
the methods are general and useful for\nterrestrial systems as
well.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ConnMatTools","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"igraph","Title":"Tools for working with
connectivity
matrices","URL":"https:\/\/github.com\/dmkaplan2000\/ConnMatTools.git","Version":"0
.1.5"},"ConsRank":{"Author":"Antonio D'Ambrosio <antdambr@unina.it>, Sonia Amodio
<sonia.amodio@unina.it>","Depends":"MASS,proxy,rgl,gtools","Description":"Compute
the median ranking according the Kemeny's axiomatic approach. Rankings can or
cannot contain ties, rankings can be both complete or incomplete.","License":"GPL-
3","NeedsCompilation":"no","Package":"ConsRank","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Compute the Median Ranking(s) According to the
Kemeny's\nAxiomatic Approach","URL":"http:\/\/www.r-
project.org","Version":"1.0.2"},"ContaminatedMixt":{"Author":"Antonio Punzo, Angelo
Mazza, Paul D. McNicholas","Depends":"R (>= 2.15.0)","Description":"Fits mixtures
of multivariate contaminated normal distributions\n(with eigen-decomposed scale
matrices) via the expectation conditional-\nmaximization algorithm under a
clustering or classification paradigm.","Imports":"mixture, mnormt,
mclust","License":"GPL-
2","NeedsCompilation":"no","Package":"ContaminatedMixt","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Model-Based Clustering and Classification with
the Multivariate\nContaminated Normal
Distribution","Version":"1.0"},"ConvCalendar":{"Author":"Bill J. Gray
(www.projectpluto.com\/calendar) and Thomas Lumley","Description":"Converts between
the Date class and d\/m\/y for several\ncalendars, including Persian, Islamic, and
Hebrew","License":"GPL-
2","NeedsCompilation":"yes","Package":"ConvCalendar","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Converts dates between
calendars","Version":"1.2"},"ConvergenceConcepts":{"Author":"P. Lafaye de Micheaux
<lafaye@dms.umontreal.ca>, B. Liquet <Benoit.Liquet@isped.u-
bordeaux2.fr>.","Depends":"R (>= 2.5.0), tcltk, tkrplot,
lattice","Description":"This package provides a way to investigate various modes of
convergence of random variables.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ConvergenceConcepts","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Title":"Seeing convergence concepts in
action","URL":"http:\/\/www.r-
project.org,\nhttp:\/\/www.biostatisticien.eu\/ConvergenceConcepts\/","Version":"1.
1"},"Copula.Markov":{"Author":"Takeshi Emura and Ting-Hsuan
Long","Description":"Estimation and statistical process control are performed under
copula-based time-series models.","License":"GPL-
2","NeedsCompilation":"no","Package":"Copula.Markov","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Estimation and Statistical Process Control Under
Copula-Based\nTime Series Models","Version":"1.0"},"CopulaDTA":{"Author":"Victoria
N Nyaga [aut, cre]","Depends":"R (>= 3.2.2), rstan (>=
2.8.2)","Description":"Modelling of sensitivity and specificity on their natural
scale\nusing copula based bivariate beta-binomial distribution to yield marginal
mean sensitivity\nand specificity. The intrinsic negative correlation between
sensitivity and\nspecificity is modelled using a copula function. A forest plot can
be obtained\nfor categorical covariates or for the model with intercept
only.","Imports":"methods, ggplot2 (>= 1.0.1), plyr (>= 1.8.3), stats (>=\n3.2.2),
reshape2 (>= 1.4.1), grDevices (>= 3.2.2)","License":"GPL-
2","NeedsCompilation":"no","Package":"CopulaDTA","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Copula Based Bivariate Beta-Binomial Model for
Diagnostic Test\nAccuracy Studies","URL":"https:\/\/cran.r-
project.org\/package=CopulaDTA","Version":"0.0.2"},"CopulaREMADA":
{"Author":"Aristidis K. Nikoloulopoulos <A.Nikoloulopoulos@uea.ac.uk>","Depends":"R
(>= 2.0.0), statmod, matlab, tensor","Description":"It has functions to implement
the copula mixed models for bivariate and trivariate meta-analysis of diagnostic
test accuracy studies in Nikoloulopoulos, A.K. (2015a,b).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CopulaREMADA","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Copula Mixed Effect Models for Bivariate and
Trivariate\nMeta-Analysis of Diagnostic Test Accuracy
Studies","Version":"0.9"},"CopulaRegression":{"Author":"Nicole Kraemer, Daniel
Silvestrini","Depends":"R (>= 2.11.0), MASS, VineCopula","Description":"This R-
packages presents a bivariate, copula-based model\nfor the joint distribution of a
pair of continuous and discrete\nrandom variables. The two marginal random
variables are modeled\nvia generalized linear models, and their joint
distribution\n(represented by a parametric copula family) is estimated
using\nmaximum-likelihood techniques.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"CopulaRegression","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Title":"Bivariate Copula Based Regression
Models","Version":"0.1-5"},"CopyDetect":{"Author":"Cengiz
Zopluoglu","Depends":"irtoys","Description":"CopyDetect contains several IRT and
non-IRT based statistical indices proposed in the literature for detecting answer
copying on multiple-choice examinations. CopyDetect includes the indices that have
been shown as effective and reliable based on the simulation studies. CopyDetect
provides results for the Omega index (Wollack, 1996), Generalized Binomial Test
(van der Linden & Sotaridona, 2006), K index (Holland, 1996), K1 and K2 indices
(Sotaridona & Meijer, 2002), and S1 and S2 indices (Sotaridona & Meijer,
2003).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CopyDetect","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Computing Statistical Indices to Detect Answer Copying
on\nMultiple-Choice
Tests","URL":"http:\/\/sites.education.miami.edu\/zopluoglu\/","Version":"1.1"},"Co
pyNumber450kCancer":{"Author":"Nour-al-dain Marzouka [aut, cre]","Depends":"R (>=
3.1.0)","Description":"The 450k arrays are frequently used in the epigenetic
studies, the copy number calling from the 450k data is possible but it faces some
difficulties in cancer samples regarding the determination of the copy number
status due to the false sample centering and baseline shifting. Without solving
this issue the CN calling will be inaccurate. CopyNumber450kCancer-package was
designed to correct the baseline in cancer samples using the Maximum Density Peak
Estimation (MDPE) method.\nThe main advantages for CopyNumber450kCancer-package
are: Fast (few seconds per sample), high accuracy rate, in-sample correction, no
input parameters needed, low computer sources required, and adaptable for 450k-
similar technologies.","Imports":"methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CopyNumber450kCancer","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Title":"Baseline Correction for Copy Number Data
from Cancer Samples","Version":"1.0.4"},"CorReg":{"Author":"Clement THERY [aut,
cre],\nChristophe BIERNACKI [ctb],\nGaetan LORIDANT [ctb],\nFlorian WATRIN
[ctb],\nQuentin GRIMONPREZ [ctb],\nVincent KUBICKI [ctb],\nSamuel BLANCK
[ctb],\nJeremie KELLNER [ctb]","Depends":"R(>= 3.0)","Description":"Linear
regression based on a recursive structural equation model\n(explicit multiples
correlations) found by a MCMC algorithm. It permits to face\nhighly correlated
covariates. Variable selection is included (by lasso,\nelastic net, etc.). It also
provides some graphical tools for basic\nstatistics (Boxplot with confidence
intervals, etc) and regression trees.","Imports":"Rcpp(>= 0.11.0), lars(>= 1.2),
Rmixmod(>= 2.0.1),\nelasticnet(>= 1.1), corrplot(>= 0.73), Matrix(>= 1.1),
rpart(>=\n4.1-5), glmnet(>= 2.0-2), MASS(>= 7.3-30), mvtnorm(>= 0.9),\nmclust(>=
4.2), methods, graphics, grDevices, utils,
stats","License":"CeCILL","NeedsCompilation":"yes","Package":"CorReg","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"clere(>= 1.1.2), spikeslab(>=
1.1.5), parcor(>= 0.2), missMDA\n(>= 1.7.3), tuneR","Title":"Linear Regression
Based on Linear Structure Between
Covariates","URL":"http:\/\/www.correg.org","Version":"1.1.1"},"CorrBin":
{"Author":"Aniko Szabo [aut, cre]","Depends":"R (>= 2.10)","Description":"This
package implements non-parametric analyses for clustered\nbinary and multinomial
data. The elements of the cluster are assumed\nexchangeable, and identical joint
distribution (also known as marginal\ncompatibility, or reproducibility) is assumed
for clusters of different\nsizes. A trend test based
on stochastic ordering is implemented.","Imports":"boot, combinat, geepack,
dirmult, mvtnorm","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"CorrBin","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"lattice","Title":"Nonparametrics with Clustered
Binary and Multinomial Data","Version":"1.5"},"CorrMixed":{"Author":"Wim Van der
Elst, Geert Molenberghs, Dieter Hilgers, & Nicole
Heussen","Depends":"nlme","Description":"In clinical practice and research settings
in medicine and the behavioral sciences, it is often of interest to quantify the
correlation of a continuous endpoint that was repeatedly measured (e.g., test-
retest correlations, ICC, etc.). This package allows for estimating these
correlations based on mixed-effects models. Part of this software has been
developed using funding provided from the European Union's 7th Framework Programme
for research, technological development and demonstration under Grant Agreement no
602552.","Imports":"psych","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CorrMixed","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Estimate Correlations Between Repeatedly Measured
Endpoints\n(E.g., Reliability) Based on Linear Mixed-Effects
Models","Version":"0.1-12"},"Correlplot":{"Author":"Jan Graffelman","Depends":"R
(>= 1.8.0), calibrate","Description":"Correlplot contains diverse routines for the
construction of different plots for representing correlation
matrices.","Imports":"xtable","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Correlplot","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"A collection of functions for graphing correlation
matrices","URL":"http:\/\/www.r-project.org, http:\/\/www-
eio.upc.es\/~jan","Version":"1.0-2"},"CosmoPhotoz":{"Author":"Rafael S. de Souza,
Alberto Krone-Martins, Jonathan Elliott, Joseph\nHilbe","Depends":"R (>=
3.0)","Description":"User-friendly interfaces to perform fast and reliable
photometric\nredshift estimation. The code makes use of generalized linear models
and\ncan adopt gamma or inverse gaussian families, either from a frequentist or\na
Bayesian perspective. The code additionally provides a Shiny application\nproviding
a simple user interface.","Imports":"ggplot2, ggthemes, arm, COUNT, gridExtra,
pcaPP, mvtnorm,\nshiny","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"CosmoPhotoz","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Photometric redshift estimation using generalized
linear models","Version":"0.1"},"Countr":{"Author":"Tarak Kharrat, Georgi N.
Boshnakov","Depends":"R (>= 3.0.2)","Description":"Flexible univariate and
bivariate count models based on\nthe Weibull distribution. The models may include
covariates and\ncan be specified with familiar formula syntax.","Imports":"Matrix,
Rcpp (>= 0.11.3), flexsurv, Formula, VGAM, optimx,\nnumDeriv, boot, MASS,
car","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"Countr","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"testthat","Title":"Flexible Univariate and Bivariate
Count Process Probability","Version":"3.2.0"},"CountsEPPM":{"Author":"David M
Smith, Malcolm J Faddy","Description":"Modeling under- and over-dispersed count
data using extended Poisson process models (EPPM).","Imports":"Formula, expm,
numDeriv, stats","License":"GPL-
2","NeedsCompilation":"no","Package":"CountsEPPM","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Mean and Variance Modeling of Count
Data","Version":"2.1"},"CovSel":{"Author":"Jenny HÃ¤ggstrÃ¶m, Emma
Persson,","Depends":"dr, np, MASS","Description":"Model-free selection of
covariates under unconfoundedness for situations where the parameter of interest is
an average causal effect. This package is based on model-free backward elimination
algorithms proposed in de Luna, Waernbaum and Richardson (2011). Marginal co-
ordinate hypothesis testing is used in situations where all covariates are
continuous while kernel-based smoothing appropriate for mixed data is used
otherwise.","License":"GPL-
3","NeedsCompilation":"no","Package":"CovSel","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"bindata","Title":"Model-Free Covariate
Selection","Version":"1.2.1"},"CoxBoost":{"Author":"Harald Binder <binderh@uni-
mainz.de>","Depends":"R (>= 2.14.0), survival, Matrix, prodlim","Description":"This
package provides routines for fitting Cox models by\nlikelihood based boosting for
a single endpoint or in presence\nof competing risks","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"CoxBoost","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"parallel, snowfall","Title":"Cox models by
likelihood based boosting for a single survival\nendpoint or competing
risks","Version":"1.4"},"CoxPlus":{"Author":"Jing Peng","Depends":"R (>= 3.1.0),
Rcpp (>= 0.12.0)","Description":"A high performance package estimating Cox Model
when an even has more than one causes. It also supports random and fixed effects,
tied events, and time-varying variables.","Imports":"methods","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"CoxPlus","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Cox Regression (Proportional Hazards Model) with
Multiple Causes\nand Mixed Effects","Version":"1.1.1"},"CoxRidge":{"Author":"Aris
Perperoglou <aperpe@essex.ac.uk>","Depends":"survival,splines","Description":"A
package for fitting Cox models with penalized ridge-type partial likelihood. The
package includes functions for fitting simple Cox models with all covariates
controlled by a ridge penalty. The weight of the penalty is optimised by using a
REML type-algorithm. Models with time varying effects of the covariates can also be
fitted. Some of the covariates may be allowed to be fixed and thus not controlled
by the penalty. There are three different penalty functions, ridge, dynamic and
weighted dynamic. Time varying effects can be fitted without the need of an
expanded dataset.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CoxRidge","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Cox Models with Dynamic Ridge
Penalties","Version":"0.9.2"},"Coxnet":{"Author":"Xiang Li, Donglin Zeng and
Yuanjia Wang","Depends":"Matrix (>= 1.1-5)","Description":"Cox model regularized
with net (L1 and Laplacian), elastic-net (L1 and L2) or lasso (L1) penalty, and
their adaptive forms, such as adaptive lasso and net adjusting for signs of linked
coefficients. Moreover, it treats the number of non-zero coefficients as another
tuning parameter and simultaneously selects with the regularization parameter
\\code{lambda}. In addition, it fits a varying coefficient Cox model by kernel
smoothing, incorporated with the aforementioned penalties. The package uses one-
step coordinate descent algorithm and runs extremely fast by taking into account
the sparsity structure of coefficients.","Imports":"Rcpp (>=
0.11.5)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"Coxnet","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Regularized Cox Model","Version":"0.2"},"CpGFilter":
{"Author":"Jun Chen","Description":"Filter CpGs based on Intra-class Correlation
Coefficients (ICCs) when replicates are available. ICCs are calculated by fitting
linear mixed effects models to all samples including the un-replicated samples.
Including the large number of un-replicated samples improves ICC estimates
dramatically. The method accommodates any replicate design.","License":"GPL-
2","NeedsCompilation":"no","Package":"CpGFilter","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"CpG Filtering Method Based on Intra-class
Correlation\nCoefficients","Version":"1.0"},"CpGassoc":{"Author":"Barfield, R.,
Conneely, K., Kilaru,V","Depends":"R (>= 2.10), nlme, methods","Description":"Is
designed to test for association between methylation at CpG sites across the genome
and a phenotype of interest, adjusting for any relevant covariates. The package can
perform standard analyses of large datasets very quickly with no need to impute the
data. It can also handle mixed effects models with chip or batch entering the model
as a random intercept. Also includes tools to apply quality control filters,
perform permutation tests, and create QQ plots, manhattan plots, and scatterplots
for individual CpG sites.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"CpGassoc","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"qvalue","Title":"Association Between Methylation and
a Phenotype of Interest","Version":"2.55"},"Cprob":{"Author":"Arthur
Allignol","Depends":"prodlim","Description":"Estimates the conditional probability
function of a competing event, and fits, using the temporal process regression or
the pseudo-value approach, a proportional-odds model to the conditional probability
function","Imports":"tpr, geepack, lgtdl, lattice","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Cprob","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Conditional probability function of a competing
event","Version":"1.2.4"},"CreditMetrics":{"Author":"Andreas Wittmann
<andreas_wittmann@gmx.de>","Depends":"R (>= 2.2.0)","Description":"A set of
functions for computing the CreditMetrics risk
model","License":"Unlimited","NeedsCompilation":"no","Package":"CreditMetrics","Rep
ository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Functions for calculating
the CreditMetrics risk model","Version":"0.0-2"},"CrossClustering":{"Author":"Paola
Tellaroli, Michele Donato","Description":"Computes a partial clustering algorithm
that combines\nthe Ward's minimum variance and Complete Linkage algorithms,
providing\nautomatic estimation of a suitable number of clusters and identification
of\noutlier elements.","Imports":"cluster","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"CrossClustering","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"A
Partial Clustering Algorithm with Automatic Estimation of the\nNumber of Clusters
and Identification of Outliers","URL":"https:\/\/CRAN.R-
project.org\/package=CrossClustering","Version":"3.0"},"Crossover":
{"Author":"Kornelius Rohmeyer","Depends":"R (>= 3.0.2), rJava (>= 0.8-3),
CommonJavaJars (>= 1.0.5),\nJavaGD, ggplot2","Description":"Package Crossover
provides different crossover designs from combinatorial or search algorithms as
well as from literature and a GUI to access them.","Imports":"MASS, crossdes (>=
1.1-1), xtable, methods, Matrix, multcomp,\nstats4, digest","License":"GPL-
2","NeedsCompilation":"yes","Package":"Crossover","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr, RUnit, nlme","Title":"Analysis and Search of
Crossover
Designs","URL":"https:\/\/github.com\/kornl\/Crossover\/wiki","Version":"0.1-
15"},"CryptRndTest":{"Author":"Haydar Demirhan","Depends":"MissMech, kSamples,
sfsmisc, Rmpfr, parallel","Description":"Performs cryptographic randomness tests on
a sequence of random\nintegers or bits. Included tests are greatest common divisor,
birthday spacings,\nbook stack, adaptive chi-square, topological binary, and three
random walk\ntests. Tests except greatest common divisor and birthday spacings are
not\ncovered by standard test suites. In addition to the chi-square goodness-of-
fit\ntest, results of Anderson-Darling, Kolmogorov-Smirnov, and Jarque-Bera tests
are\nalso generated by some of the cryptographic randomness
tests.","Imports":"LambertW, gmp, tseries, methods","License":"GPL-
3","NeedsCompilation":"no","Package":"CryptRndTest","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"R.rsp","Title":"Statistical Tests for
Cryptographic Randomness","Version":"1.2.2"},"CrypticIBDcheck":{"Author":"Annick
Joelle Nembot-Simo, Jinko Graham and Brad McNeney","Depends":"R (>= 2.14.0),
rJPSGCS (>= 0.2-5), car (>= 2.0-9), ellipse (>=\n0.3-5)","Description":"Exploratory
tools to identify closely related subjects using autosomal genetic marker
data.","Imports":"chopsticks","License":"GPL-
3","NeedsCompilation":"yes","Package":"CrypticIBDcheck","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"parallel","Title":"Identifying cryptic
relatedness in genetic association studies","Version":"0.3-1"},"Cubist":
{"Author":"Max Kuhn, Steve Weston, Chris Keefer, Nathan Coulter. C code for Cubist
by Ross Quinlan","Depends":"lattice","Description":"Regression modeling using rules
with added instance-based corrections","Imports":"reshape2","License":"GPL-
3","NeedsCompilation":"yes","Package":"Cubist","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"mlbench, caret","Title":"Rule- and Instance-Based
Regression Modeling","Version":"0.0.18"},"D2C":{"Author":"Gianluca Bontempi,
Catharina Olsen, Maxime Flauder","Depends":"R(>= 2.10.0),
randomForest","Description":"The relationship between statistical dependency and
causality lies\nat the heart of all statistical approaches to causal inference. The
D2C\npackage implements a supervised machine learning approach to infer
the\nexistence of a directed causal link between two variables in
multivariate\nsettings with n>2 variables. The approach relies on the asymmetry of
some\nconditional (in)dependence relations between the members of the
Markov\nblankets of two variables causally connected. The D2C algorithm
predicts\nthe existence of a direct causal link between two variables in
a\nmultivariate setting by (i) creating a set of of features of the\nrelationship
based on asymmetric descriptors of the multivariate dependency\nand (ii) using a
classifier to learn a mapping between the features and the\npresence of a causal
link","Imports":"gRbase, lazy, RBGL, MASS, corpcor, methods, Rgraphviz,
foreach","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"D2C","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr","Title":"Predicting Causal Direction from
Dependency Features","Version":"1.2.1"},"D3M":{"Author":"Yusuke Matsui & Teppei
Shimamura","Description":"Two sample test based on Wasserstein metric. This is
motivated from detection of differential DNA-methylation sites based on underlying
distributions.","Imports":"Rcpp (>= 0.11.6), beanplot, stats, parallel,
graphics,\ngrDevices","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"D3M","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Two Sample Test with Wasserstein
Metric","Version":"0.41"},"DAAG":{"Author":"John H. Maindonald and W. John
Braun","Depends":"R (>= 2.10.0), lattice","Description":"Various data sets used in
examples and exercises in the\nbook Maindonald, J.H. and Braun, W.J. (2003, 2007,
2010) \"Data\nAnalysis and Graphics Using R\".","Imports":"latticeExtra,
methods","License":"GPL-
3","NeedsCompilation":"no","Package":"DAAG","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"leaps, oz, lme4, quantreg, knitr, boot, rpart,
randomForest,\nMASS, survival","Title":"Data Analysis and Graphics Data and
Functions","URL":"http:\/\/www.stats.uwo.ca\/DAAG","Version":"1.22"},"DAAGbio":
{"Author":"John Maindonald","Depends":"R (>= 2.10.0), limma (>=
2.9.15)","Description":"Data sets and functions, for the display of
biological\nexpression array (microarray) data, and for demonstrations with\nsuch
data","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"DAAGbio","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"DAAG, locfit","Title":"Data Sets and Functions, for
demonstrations with expression\narrays and gene
sequences","URL":"http:\/\/www.maths.anu.edu.au\/~johnm","Version":"0.62"},"DAAGxtr
as":{"Author":"John Maindonald","Depends":"R (>= 2.10.0)","Description":"various
data sets used in additional exercises for\nthe book Maindonald, J.H. and Braun,
W.J. (3rd edn 2010)\n\"Data Analysis and Graphics Using R\", and for a\n'Data
Mining' course. Note that a number of datasets\nthat were in earlier versions of
this package have been\ntransferred to the DAAG
package.","License":"Unlimited","NeedsCompilation":"no","Package":"DAAGxtras","Repo
sitory":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"DAAG, MASS, lattice,
randomForest","Title":"Data Sets and Functions, supplementary to
DAAG","URL":"http:\/\/www.maths.anu.edu.au\/~johnm","Version":"0.8-4"},"DAGGER":
{"Author":"Jeffrey Endelman","Depends":"Rglpk, quadprog,
Matrix","Description":"Integrates the information from multiple linkage maps
to\ncreate a consensus directed graph, which is then linearized to\nproduce a
consensus map.","License":"GPL-
3","NeedsCompilation":"no","Package":"DAGGER","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Consensus genetic maps","Version":"1.4"},"DAISIE":
{"Author":"Rampal S. Etienne, Luis M. Valente, Albert B. Phillimore & Bart
Haegenan","Depends":"R (>= 3.0.0)","Description":"Simulates and computes the
(maximum) likelihood of a dynamical model of island biota assembly through
speciation, immigration and extinction. See Valente et al. 2015. Ecology Letters
18: 844-852.","Imports":"deSolve, grDevices, graphics, stats,
2","NeedsCompilation":"no","Package":"DAISIE","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Dynamical Assembly of Islands by Speciation, Immigration
and\nExtinction","Version":"1.0.2"},"DAKS":{"Author":"Ali Uenlue [aut, cre], Anatol
Sargin [aut]","Depends":"R (>= 2.15.1), relations, sets","Description":"Functions
and an example dataset for the psychometric\ntheory of knowledge spaces. This
package implements data\nanalysis methods and procedures for simulating data and
quasi\norders and transforming different formulations in knowledge\nspace
theory.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"DAKS","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Data Analysis and Knowledge
Spaces","URL":"http:\/\/www.meb.edu.tum.de\/","Version":"2.1-2"},"DALY":
{"Author":"Brecht Devleesschauwer [aut, cre], Scott McDonald [aut],\nJuanita
Haagsma [aut], Nicolas Praet [aut], Arie Havelaar [aut],\nNiko Speybroeck
[aut]","Depends":"R (>= 3.0.0)","Description":"The DALY Calculator is a free, open-
source Graphical User\nInterface (GUI) for stochastic disability-adjusted life
year\n(DALY) calculation.","Imports":"tcltk, grid, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"DALY","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"DALY Calculator - A GUI for stochastic DALY calculation in
R","URL":"http:\/\/users.ugent.be\/~bdvleess\/DALYcalculator","Version":"1.4.0"},"D
AMOCLES":{"Author":"Rampal S. Etienne & Alex L. Pigot","Depends":"R (>= 3.0),
geiger, caper, ape, deSolve, matrixStats","Description":"Simulates and computes
(maximum) likelihood of a dynamical model of community assembly that takes into
account phylogenetic history.","Imports":"expm, picante","License":"GPL-
2","NeedsCompilation":"no","Package":"DAMOCLES","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Dynamic Assembly Model of Colonization, Local Extinction
and\nSpeciation","Version":"1.1"},"DAMisc":{"Author":"Dave Armstrong (UW-Milwaukee,
Department of Political Science)","Depends":"car, effects,","Description":"This
package contains a miscellaneous set of functions I use in my teaching either at
UWM or the ICPSR Summer Program. Broadly, the functions help with presentation and
interpretation of GLMs.","Imports":"lattice, sm, MASS, nnet, splines, pscl, gdata,
xtable","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"DAMisc","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Dave Armstrong's Miscellaneous
Functions","Version":"1.3"},"DATforDCEMRI":{"Author":"Gregory Z. Ferl","Depends":"R
(>= 2.11.0), xtable, akima, R.oo, R.methodsS3, matlab,\nlattice, locfit, graphics,
grDevices, grid","Description":"This package performs voxel-wise deconvolution
analysis of\nDCE-MRI contrast agent concentration versus time data and\ngenerates
the Impulse Response Function, which can be used to\napproximate commonly utilized
kinetic parameters such as Ktrans\nand ve. An interactive advanced voxel diagnosis
tool (AVDT) is\nalso provided to facilitate easy navigation of voxel-wise
data.","License":"CC BY-NC-SA
3.0","NeedsCompilation":"no","Package":"DATforDCEMRI","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"R.matlab","Title":"Deconvolution Analysis Tool
for Dynamic Contrast Enhanced MRI","Version":"0.55"},"DBGSA":{"Author":"Li Jin,
Huang Meilin","Depends":"R (>= 2.12.2), fdrtool(>= 1.2.6)","Description":"This
package provides methods and examples to support a\nmethod of Gene Set Analysis
(GSA). DBGSA is a novel\ndistance-based gene set enrichment analysis method. We
consider\nthat, the distance between 2 groups with different phenotype by\nfocusing
on the gene expression should be larger, if a certain\ngene functional set was
significantly associated with a\nparticular phenotype.","License":"GPL-
3","NeedsCompilation":"no","Package":"DBGSA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"methods of distance-based gene set functional
enrichment\nanalysis","Version":"1.2"},"DBI":{"Author":"R Special Interest Group on
Databases (R-SIG-DB)","Depends":"R (>= 2.15.0), methods","Description":"A database
interface (DBI) definition for communication\nbetween R and relational database
management systems. All\nclasses in this package are virtual and need to be
extended by\nthe various R\/DBMS implementations.","License":"LGPL (>=
2)","NeedsCompilation":"no","Package":"DBI","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"testthat, RSQLite","Title":"R Database
Interface","URL":"https:\/\/github.com\/rstats-
db\/DBI","Version":"0.3.1"},"DBKGrad":{"Author":"Angelo Mazza [aut, cre],\nAntonio
Punzo [aut]","Depends":"R (>= 2.15.0)","Description":"This package allows for
nonparametric graduation of mortality rates using fixed or adaptive discrete beta
kernel estimator.","Imports":"minpack.lm, SDD, TSA, lattice","License":"GPL-
2","NeedsCompilation":"no","Package":"DBKGrad","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Discrete Beta Kernel Graduation of Mortality
Data","Version":"1.6"},"DCGL":{"Author":"Jing Yang, Hui Yu, Bao-Hong Liu, Zhongming
Zhao, Lei Liu, Liang-Xiao Ma, Yi-Xue Li, Yuan-Yuan Li","Depends":"R (>=
2.10)","Description":"Functions for 1) gene filtration; 2) link filtration; 3)
differential co-expression analysis: DCG (Differential Coexpressed\nGene)
identification and DCL (Differentially Coexpressed Link)\nidentification; and 4)
differential regulation analysis: DRG (Differential Regulated\nGene)
identification, DRL (Differential Regulated Link)\nidentification, DRL
visualization and regulator ranking.","Imports":"igraph, limma","License":"GPL (>
2)","NeedsCompilation":"no","Package":"DCGL","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Differential Co-expression Analysis and Differential
Regulation\nAnalysis of Gene Expression Microarray Data","Version":"2.1.2"},"DCL":
{"Author":"Maria Dolores Martinez-Miranda, Jens Perch Nielsen and Richard
Verrall","Depends":"lattice, latticeExtra","Description":"Statistical modelling and
forecasting in claims reserving in non-life insurance under the Double Chain Ladder
framework by Martinez-Miranda, Nielsen and Verrall (2012).","License":"GPL-
2","NeedsCompilation":"no","Package":"DCL","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Claims Reserving under the Double Chain Ladder
Model","Version":"0.1.0"},"DCODE":{"Author":"Sophie Lebre","Depends":"R (>= 3.1.0),
seqinr","Description":"Traversal graph algorithm for listing linear n-peptide
constraints for overlapping protein regions. (Lebre and Gascuel, The combinatorics
of overlapping genes, freely available from arXiv at :
http:\/\/arxiv.org\/abs\/1602.04971).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"DCODE","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"List Linear n-Peptide Constraints for Overlapping
Protein\nRegions","Version":"1.0"},"DCchoice":{"Author":"Tomoaki Nakatani [aut,
cph] (original developer),\nHideo Aizaki [aut, cre] (code patches),\nKazuo Sato
[ctb] (theoretical part of the manual)","Depends":"R (>= 3.1.0), stats, MASS,
interval, Formula","Description":"Functions for analyzing dichotomous choice
contingent valuation (CV) data. It provides\nfunctions for estimating parametric
and nonparametric models for single- and double-bounded\nCV data.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"DCchoice","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"Ecdat","Title":"Analyzing Dichotomous Choice
Contingent Valuation
Data","URL":"http:\/\/www.agr.hokudai.ac.jp\/spmur\/","Version":"0.0.14"},"DCluster
":{"Author":"Virgilio Gómez-Rubio, Juan Ferrándiz-Ferragud and Antonio\nLópez-
Quílez, with contributions by Roger Bivand.","Depends":"R (>= 1.6.2), boot, spdep,
MASS","Description":"A set of functions for the detection of spatial clusters\nof
disease using count data. Bootstrap is used to estimate\nsampling distributions of
statistics.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"DCluster","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Functions for the Detection of Spatial Clusters of
Diseases","Version":"0.2-7"},"DDD":{"Author":"Rampal S. Etienne & Bart
Haegeman","Depends":"R (>= 3.0.2), deSolve, ape, ade4","Description":"\nImplements
maximum likelihood methods based on the diversity-dependent birth-death process to
test whether speciation or extinction are diversity-dependent.\nSee Etienne et al.
2012, Proc. Roy. Soc. B 279: 1300-1309, <DOI:10.1098\/rspb.2011.1439>.\nAlso
implements maximum likelihood methods to detect various types of key innovations in
the light of diversity-dependence.\nSee Etienne & Haegeman 2012, Am. Nat. 180: E75-
E89, <DOI:10.1086\/667574>.\nFinally, DDD contains a function to simulate the
diversity-dependent process.","Imports":"phytools, subplex, Matrix, expoRkit,
SparseM","License":"GPL-
3","NeedsCompilation":"no","Package":"DDD","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Diversity-Dependent Diversification","Version":"3.2"},"DDHFm":
{"Author":"Efthimios Motakis [aut],\nGuy Nason [aut, cre],\nPiotr Fryzlewicz
[aut]","Depends":"R (>= 2.10)","Description":"The package contains the normalizing
and variance stabilizing\nData-Driven Haar-Fisz algorithm. Also contains related
algorithms\nfor simulating from certain microarray gene intensity models
and\nevaluation of certain transformations.","License":"GPL-
2","NeedsCompilation":"yes","Package":"DDHFm","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"lokern, wavethresh","Title":"Variance Stabilization by
Data-Driven Haar-Fisz (for\nMicroarrays)","Version":"1.1.1"},"DDIwR":
{"Author":"Adrian Dusa [aut, cre]","Depends":"R (>= 3.1.0)","Description":"This
package provides useful functions for various DDI (Data Documentation Initiative)
related outputs.","Imports":"XML, foreign","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"DDIwR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"DDI with R","Version":"0.2-0"},"DDRTree":{"Author":"Xiaojie
Qiu, Cole Trapnell, Qi Mao, Li Wang","Depends":"irlba","Description":"Project data
into a reduced dimensional space and construct a principal graph from the reduced
dimension.","Imports":"Rcpp","License":"Artistic License
2.0","NeedsCompilation":"yes","Package":"DDRTree","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Learning Principal Graphs with
DDRTree","Version":"0.1.3"},"DECIDE":{"Author":"Christiana
Kartsonaki","Description":"Calculates various estimates for measures of
educational\ndifferentials, the relative importance of primary and
secondary\neffects in the creation of such differentials and compares
the\nestimates obtained from two datasets.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"DECIDE","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"DEComposition of Indirect and Direct
Effects","Version":"1.2"},"DEEPR":{"Author":"Mark T Merilo
<mmerilo@uoguelph.ca>","Depends":"R (>= 3.0), dirmult","Description":"Tests for,
and describe differences in event count profiles in groups of reconstructed
cophylogenies","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"DEEPR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Dirichlet-multinomial Evolutionary Event Profile
Randomization\n(DEEPR) test","Version":"0.1"},"DEMEtics":{"Author":"Alexander
Jueterbock, Philipp Kraemer, Gabriele Gerlach and Jana Deppermann","Depends":"R (>=
2.8.0)","Description":"This package allows to calculate the fixation index
Gst\n(Nei, 1973) and the differentiation index D (Jost, 2008) pairwise\nbetween or
averaged over several populations. P-values, stating the\nsignificance of
differentiation, and 95 percent confidence intervals\ncan be estimated using
bootstrap resamplings. In the case that more\nthan two populations are compared
pairwise, the p-values are\nadjusted by bonferroni correction and in several other
ways due to\nthe multiple comparison from one data set.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"DEMEtics","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Evaluating the genetic differentiation between
populations based\non Gst and D values","Version":"0.8-7"},"DEMOVA":
{"Author":"Vinca Prana","Depends":"leaps","Description":"Tool for the development
of multi-linear QSPR\/QSAR models (Quantitative structure-property\/activity
relationship). Theses models are used in chemistry, biology and pharmacy to find a
relationship between the structure of a molecule and its property (such as
activity, toxicology but also physical properties). The various functions of this
package allows: selection of descriptors based of variances, intercorrelation and
user expertise; selection
of the best multi-linear regression in terms of correlation and robustness;
methods of internal validation (Leave-One-Out, Leave-Many-Out, Y-scrambling) and
external using test sets.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"DEMOVA","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat","Title":"DEvelopment (of Multi-Linear
QSPR\/QSAR) MOdels VAlidated using\nTest Set","Version":"1.0"},"DESP":
{"Author":"Arnak Dalalyan [aut], Samuel Balmand [aut, cre]","Description":"Several
estimators of the diagonal elements of a sparse precision\n(inverse covariance)
matrix from a sample of Gaussian vectors for a\ngiven matrix of estimated marginal
regression coefficients.\nTo install package 'gurobi', instructions
at\nhttp:\/\/user.gurobi.com\/download\/gurobi-optimizer
and\nhttp:\/\/www.gurobi.com\/documentation\/6.0\/refman\/r_api_overview.html.","Im
ports":"MASS, Matrix, graph, RBGL, SparseM","License":"GPL-
3","NeedsCompilation":"yes","Package":"DESP","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"Rmosek, gurobi","Title":"Estimation of Diagonal Elements
of Sparse Precision-Matrices","Version":"0.1-6"},"DESnowball":{"Author":"Yaomin Xu
<yaomin.xu@vanderbilt.edu>","Depends":"R (>= 3.0.0)","Description":"This package
implements a statistical data mining method to\ncompare whole genome gene
expression profiles, with respect to the presence\nof a recurrent genetic
disturbance event, to identify the affected target\ngenes.","Imports":"clue,
combinat, MASS, parallel, cluster","License":"GPL-
3","NeedsCompilation":"no","Package":"DESnowball","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Bagging with Distance-based Regression for Differential
Gene\nExpression Analyses","URL":"https:\/\/github.com\/snowball-
project\/DESnowball","Version":"1.0"},"DEoptim":{"Author":"David Ardia
[aut],\nKatharine Mullen [aut, cre],\nBrian Peterson [aut],\nJoshua Ulrich
[aut],\nKris Boudt [ctb]","Description":"Implements the differential evolution
algorithm for global optimization of a real-valued function of a real-valued
parameter vector.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"DEoptim","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"foreach, iterators, parallel","Title":"Global
Optimization by Differential Evolution","Version":"2.2-3"},"DEoptimR":
{"Author":"Eduardo L. T. Conceicao and Martin Maechler [ctb]","Description":"An
implementation of the jDE variant of the Differential Evolution\nstochastic
algorithm for global optimization of nonlinear programming
problems.","Enhances":"robustbase","Imports":"stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"DEoptimR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Differential Evolution Optimization in Pure
R","Version":"1.0-4"},"DFIT":{"Author":"Victor H. Cervantes
<vcervantes@icfes.gov.co, vhcervantesb@unal.edu.co>","Description":"A set of
functions to perform Raju, van der Linden and Fleer's\n(1995) Differential
Functioning of Items and Tests (DFIT) analyses. It includes\nfunctions to use the
Monte Carlo Item Parameter Replication approach\n(Oshima, Raju, & Nanda, 2006) for
obtaining the associated statistical\nsignificance tests cut-off points. They may
also be used for a priori and\npost-hoc power calculations.","Imports":"simex,
mvtnorm, ggplot2","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"DFIT","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Differential Functioning of Items and Tests","Version":"1.0-
2"},"DIFboost":{"Author":"Gunther Schauberger","Description":"Performs detection of
Differential Item Functioning using the method DIFboost as proposed in Schauberger
and Tutz (2015): Detection of Differential item functioning in Rasch models by
boosting techniques, British Journal of Mathematical and Statistical
Psychology.","Imports":"mboost, penalized, stabs","License":"GPL-
2","NeedsCompilation":"no","Package":"DIFboost","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Detection of Differential Item Functioning (DIF) in Rasch
Models\nby Boosting Techniques","Version":"0.1"},"DIFlasso":{"Author":"Gunther
Schauberger","Depends":"grplasso, penalized, miscTools","Description":"A package to
perform DIFlasso, a method to detect DIF (Differential Item Functioning) in Rasch
Models. It can handle settings with many covariates and also metric
2","NeedsCompilation":"no","Package":"DIFlasso","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"A penalty approach to Differential Item Functioning in
Rasch\nModels","Version":"1.0-1"},"DIFtree":{"Author":"Moritz
Berger","Depends":"penalized, plotrix","Description":"Item focused recursive
partitioning for simultaneous selection of\nitems and variables that induce
Differential Item Functioning (DIF) based on the\nRasch Model or the Logistic
Regression Approach for DIF detection.","License":"GPL-
2","NeedsCompilation":"no","Package":"DIFtree","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Item Focused Trees for the Identification of Items
in\nDifferential Item Functioning","Version":"2.0.1"},"DIME":{"Author":"Cenny
Taslim <taslim.2@osu.edu>, with contributions from Dustin Potter, Abbasali Khalili
and Shili Lin <shili@stat.osu.edu>.","Description":"A robust differential
identification method that considers an ensemble of finite mixture models combined
with a local false discovery rate (fdr) to analyze ChIP-seq (high-throughput
genomic)data comparing two samples allowing for flexible modeling of
data.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"DIME","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"DIME (Differential Identification using Mixture
Ensemble)","Version":"1.2"},"DIRECT":{"Author":"Audrey Qiuyan Fu, Steven Russell,
Sarah J. Bray and Simon Tavare","Description":"A Bayesian clustering method for
replicated time series or replicated measurements from multiple experimental
conditions, e.g., time-course gene expression data. It estimates the number of
clusters directly from the data using a Dirichlet-process prior. See Fu, A. Q.,
Russell, S., Bray, S. and Tavare, S. (2013) Bayesian clustering of replicated time-
course gene expression data with weak signals. The Annals of Applied Statistics.
7(3) 1334-1361. <doi:10.1214\/13-AOAS650>.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"DIRECT","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Bayesian Clustering of Multivariate Data Under
the\nDirichlet-Process Prior","Version":"1.0.1"},"DJL":{"Author":"Dong-Joon Lim,
PhD","Depends":"R (>= 3.2.2), car, combinat, lpSolveAPI","Description":"Implements
various decision support tools related to the new product development.\nSubroutines
include combinatorial search (all possible subset regression), productivity
evaluation using distance measures: DDF (directional distance function), DEA (data
envelopment analysis), SBM (slack-based measure), and SF (shortage function),
benchmarking, risk analysis, technology adoption model, new product target setting,
etc.","License":"GPL-
2","NeedsCompilation":"no","Package":"DJL","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Distance Measure Based Judgment and
Learning","Version":"2.1"},"DLMtool":{"Author":"Tom Carruthers and Adrian
Hordyk","Depends":"R (>= 2.10.0), methods, snowfall, boot, MASS,
parallel","Description":"Simulation testing and implementation of data-limited
fishery stock\nassessment methods.","License":"GPL-
2","NeedsCompilation":"no","Package":"DLMtool","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr, rmarkdown","Title":"Data-Limited Methods
Toolkit","Version":"3.1"},"DMR":{"Author":"Aleksandra Maj, Agnieszka Prochenka,
Piotr Pokarowski","Depends":"R (>= 1.8.0), magic","Description":"A backward
selection procedure called delete or merge\nregressors (DMR) combines deleting
continuous variables with\nmerging levels of factors. The method assumes greedy
search\namong linear models with set of constraints of two types:\neither a
parameter for a continuous variable is set to zero or\nparameters corresponding to
two levels of a factor are\ncompared. DMR is a stepwise regression procedure, where
in each\nstep a new constraint is added according to ranking of the\nhypotheses
based on squared t-statistics. As a result a nested\nfamily of linear models is
obtained and the final decision is\nmade according to minimization of the
generalized information\ncriterion (GIC, default BIC). The main function of the
package\nis DMR, which is based on hierarchical clustering. Moreover,\nother
functions for extensions of DMR method are given, such as\nstepDMR which is based
on recalculation of t-statistics in each\nstep and function DMR4glm for generalized
linear models.","License":"GPL-
2","NeedsCompilation":"no","Package":"DMR","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Delete or Merge Regressors for linear model
selection","Version":"2.0"},"DMwR":{"Author":"Luis Torgo","Depends":"R(>= 2.10),
methods, graphics, lattice (>= 0.18-3), grid (>=\n2.10.1)","Description":"This
package includes functions and data accompanying the book\n\"Data Mining with R,
learning with case studies\" by Luis Torgo, CRC Press 2010.","Imports":"xts (>=
0.6-7), quantmod (>= 0.3-8), zoo (>= 1.6-4), abind (>=\n1.1-0), rpart (>= 3.1-46),
class (>= 7.3-1), ROCR (>= 1.0)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"DMwR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Functions and data for \"Data Mining with
R\"","Version":"0.4.1"},"DNAprofiles":{"Author":"Maarten
Kruijver","Depends":"RcppProgress","Description":"Methods for studying forensic DNA
profiling, in particular familial database searches.","Imports":"Rcpp (>= 0.10.3),
bit, parallel","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"DNAprofiles","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"DNAtools,
testthat, knitr","Title":"DNA Profiling Evidence
Analysis","Version":"0.3.1"},"DNAseqtest":{"Author":"Faisal Ababneh, John Robinson,
Lars S Jermiin and Hasinur Rahaman Khan","Description":"Generates DNA sequences
based on Markov model techniques for matched sequences. This can be generalized to
several sequences. The sequences (taxa) are then arranged in an evolutionary tree
(phylogenetic tree) depicting how taxa diverge from their common ancestors. This
gives the tests and estimation methods for the parameters of different models.
Standard phylogenetic methods assume stationarity, homogeneity and reversibility
for the Markov processes, and often impose further restrictions on the
parameters.","License":"GPL-
2","NeedsCompilation":"no","Package":"DNAseqtest","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Generating and Testing DNA
Sequences","Version":"1.0"},"DNAtools":{"Author":"Torben Tvedebrink
<tvede@math.aau.dk> and James Curran <j.curran@auckland.ac.nz>. Mikkel Meyer
Andersen <mikl@math.aau.dk> assisted on the multicore\/CPU
implementation.","Depends":"R (>= 2.10.0), Rsolnp,
multicool","Description":"Computationally efficient tools for comparing all pairs
of profiles in a DNA database. The expectation and covariance of the summary
statistic\nis implemented for fast computing. Routines for estimating proportions
of close related individuals are available. The use of wildcards (also\ncalled F-
designation) is implemented. Dedicated functions ease plotting the
results.","Imports":"Rcpp (>= 0.11.2)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"DNAtools","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Tools for analysing forensic genetic DNA
data","Version":"0.1-21"},"DNMF":{"Author":"Zhilong Jia [aut, cre],\nXiang Zhang
[aut]","Depends":"foreach","Description":"Discriminant Non-Negative Matrix
Factorization aims to extend the Non-negative Matrix Factorization algorithm in
order to extract features that enforce not only the spatial locality, but also the
separability between classes in a discriminant manner. It refers to three article,
Zafeiriou, Stefanos, et al. \"Exploiting discriminant information in nonnegative
matrix factorization with application to frontal face verification.\" Neural
Networks, IEEE Transactions on 17.3 (2006): 683-695. Kim, Bo-Kyeong, and Soo-Young
Lee. \"Spectral Feature Extraction Using dNMF for Emotion Recognition in Vowel
Sounds.\" Neural Information Processing. Springer Berlin Heidelberg, 2013. and Lee,
Soo-Young, Hyun-Ah Song, and Shun-ichi Amari. \"A new discriminant NMF algorithm
and its application to the extraction of subtle emotional differences in speech.\"
Cognitive neurodynamics 6.6 (2012): 525-535.","Imports":"Matrix, gplots, parallel,
2)","NeedsCompilation":"no","Package":"DNMF","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Discriminant Non-Negative Matrix
Factorization","URL":"https:\/\/github.com\/zhilongjia\/DNMF","Version":"1.3"},"DOB
AD":{"Author":"Charles Doss, Vladimir Minin, Marc
Suchard","Depends":"numDeriv","Description":"Provides Frequentist (EM) and Bayesian
(MCMC) Methods for Inference of Birth-Death-Immigration Markov
Chains.","Imports":"methods,lattice","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"DOBAD","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"gtools,MCMCpack","Title":"Analysis of Discretely
Observed Linear\nBirth-and-Death(-and-Immigration) Markov
Chains","Version":"1.0.5"},"DOvalidation":{"Author":"M.L. Gamiz, E. Mammen, M.D.
Martinez-Miranda and J.P. Nielsen","Description":"Local linear estimator for the
univariate hazard (hazard rate) and bandwidth parameter selection using the do-
validation method and the standard least squares cross-validation
method.","License":"GPL-
2","NeedsCompilation":"no","Package":"DOvalidation","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Local Linear Hazard Estimation with Do-Validated
and\nCross-Validated Bandwidths","Version":"0.1.0"},"DPpackage":
{"Author":"Alejandro Jara [aut, cre], Timothy Hanson [ctb], Fernando\nQuintana
[ctb], Peter Mueller [ctb], Gary Rosner [ctb]","Depends":"R (>= 2.10), MASS, nlme,
survival, splines","Description":"This package contains functions to perform
inference via\nsimulation from the posterior distributions for
Bayesian\nnonparametric and semiparametric models. Although the name of\nthe
package was motivated by the Dirichlet Process prior, the\npackage considers and
will consider other priors on functional\nspaces. So far, DPpackage includes models
considering Dirichlet\nProcesses, Dependent Dirichlet Processes, Dependent
Poisson-\nDirichlet Processes, Hierarchical Dirichlet Processes, Polya\nTrees,
Linear Dependent Tailfree Processes, Mixtures of\nTriangular distributions, Random
Bernstein polynomials priors\nand Dependent Bernstein Polynomials. The package
also includes\nmodels considering Penalized B-Splines. Currently the
package\nincludes semiparametric models for marginal and conditional\ndensity
estimation, ROC curve analysis, interval censored data,\nbinary regression models,
generalized linear mixed models, IRT\ntype models, and generalized additive models.
The package also\ncontains functions to compute Pseudo-Bayes factors for
model\ncomparison, and to elicitate the precision parameter of the\nDirichlet
Process. To maximize computational efficiency, the\nactual sampling for each model
is done in compiled FORTRAN. The\nfunctions return objects which can be
subsequently analyzed\nwith functions provided in the coda package.","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"DPpackage","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Bayesian nonparametric modeling in
R","URL":"http:\/\/www.mat.puc.cl\/~ajara","Version":"1.1-6"},"DRIP":
{"Author":"Yicheng Kang <kangx276@umn.edu>","Depends":"R (>= 2.10.0), readbitmap,
caTools, graphics, stats","Description":"This is a collection of functions for
discontinuous regression\nanalysis and image processing.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"DRIP","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Discontinuous Regression and Image
Processing","Version":"1.1"},"DRaWR":{"Author":"Charles Blatti [aut,
cre]","Depends":"R (>= 3.0)","Description":"We present DRaWR, a network-based
method for ranking genes or\nproperties related to a given gene set. Such related
genes or properties are\nidentified from among the nodes of a large, heterogeneous
network of biological\ninformation. Our method involves a random walk with
restarts, performed on\nan initial network with multiple node and edge types,
preserving more of the\noriginal, specific property information than current
methods that operate\non homogeneous networks. In this first stage of our
algorithm, we find the\nproperties that are the most relevant to the given gene set
and extract a\nsubnetwork of the original network, comprising only the relevant
properties. We\nthen rerank genes by their similarity to the given gene set, based
on a second\nrandom walk with restarts, performed on the above
subnetwork.","Imports":"Matrix, ROCR","License":"GPL-
2","NeedsCompilation":"no","Package":"DRaWR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Discriminative Random Walk with
Restart","Version":"1.0.1"},"DSBayes":{"Author":"Ravi Varadhan <rvaradhan@jhmi.edu>
and Wenliang Yao <yaow080@gmail.com>","Depends":"R (>=
2.15.1)","Description":"Calculate posterior modes and credible intervals of
parameters of the Dixon-Simon model for subgroup analysis (with binary covariates)
in clinical trials.","Imports":"BB","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"DSBayes","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Bayesian subgroup analysis in clinical
trials","URL":"\nhttp:\/\/www.jhsph.edu\/agingandhealth\/People\/Faculty_personal_p
ages\/Varadhan.html","Version":"1.1"},"DSL":{"Author":"Ingo Feinerer [aut],\nStefan
Theussl [aut, cre],\nChristian Buchta [ctb]","Description":"An abstract DList class
helps storing large list-type objects in a distributed manner. Corresponding high-
level functions and methods for handling distributed storage (DStorage) and lists
allows for processing such DLists on distributed systems efficiently. In doing so
it uses a well defined storage backend implemented based on the DStorage
class.","Imports":"methods, utils","License":"GPL-
3","NeedsCompilation":"yes","Package":"DSL","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"hive (>= 0.1-14), parallel","Title":"Distributed Storage
and List","Version":"0.1-6"},"DSpat":{"Author":"Devin Johnson, Jeff Laake, Jay
VerHoef","Depends":"R (>= 2.0.0), spatstat (>= 1.22-0),
RandomFields","Description":"Fits inhomogeneous Poisson process spatial models\nto
line transect sampling data and provides estimate of\nabundance within a
region.","Imports":"rgeos, mgcv, sp","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"DSpat","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Spatial Modelling for Distance Sampling
Data","Version":"0.1.6"},"DSsim":{"Author":"Laura Marshall <lhm@st-
and.ac.uk>","Depends":"graphics, splancs, mrds, mgcv, shapefiles,
methods","Description":"Performs distance sampling simulations. It
repeatedly\ngenerates instances of a user defined population within a given
survey\nregion, generates realisations of a survey design (currently these must\nbe
pre-generated using Distance software) and simulates the detection\nprocess. The
data are then analysed so that the results can be compared for\naccuracy and
precision across all replications. This will allow users to\nselect survey designs
which will give them the best accuracy and precision\ngiven their expectations
about population distribution. Any uncertainty in\npopulation distribution or
population parameters can be included
by running\nthe different survey designs for a number of different
population\ndescriptions. An example simulation can be found in the help file\nfor
make.simulation.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"DSsim","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat, parallel","Title":"Distance Sampling
Simulations","Version":"1.0.4"},"DStree":{"Author":"Peter Mayer, Denis Larocque,
Matthias Schmid","Depends":"rpart,pec,Ecdat","Description":"Building discrete-time
survival trees and bagged trees based on\nthe functionalities of the rpart package.
Splitting criterion maximizes the\nlikelihood of a covariate-free logistic discrete
time hazard model.","Imports":"rpart.plot,survival, Rcpp","License":"GPL-
2","NeedsCompilation":"no","Package":"DStree","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Recursive Partitioning for Discrete-Time Survival
Trees","Version":"1.0"},"DSviaDRM":{"Author":"Jing Yang","Depends":"R (>=
2.10)","Description":"Elucidation of human disease similarities has emerged as an
active research area, which is highly relevant to etiology, disease classification,
and drug repositioning. This package was designed and implemented for identifying
disease similarities. It contains five functions which are 'DCEA', 'DCpathway',
'DS', 'comDCGL' and 'comDCGLplot'. In 'DCEA' function, differentially co-expressed
genes and differentially co-expressed links are extracted from disease vs. health
samples. Then 'DCpathway' function assigns differential co-expression values of
pathways to be the average differential co-expression value of their component
genes. Then 'DS' employs partial correlation coefficient of pathways as the disease
similarity for each disease pairs. And 'DS' contains a permutation process for
evaluating the statistical significant of observed disease partial correlation
coefficients. At last, 'comDCGL' and 'comDCGLplot' sort out shared differentially
co-expressed genes and differentially co-expressed links with regulation
information and visualize them.","Imports":"igraph, ppcor","License":"GPL (>
2)","NeedsCompilation":"no","Package":"DSviaDRM","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Exploring Disease Similarity in Terms of
Dysfunctional\nRegulatory Mechanisms","Version":"1.0"},"DT":{"Author":"Yihui Xie
[aut, cre],\nJoe Cheng [ctb],\njQuery contributors [ctb, cph] (jQuery in
htmlwidgets\/lib),\nSpryMedia Limited [ctb, cph] (DataTables in
htmlwidgets\/lib),\nBrian Reavis [ctb, cph] (selectize.js in
htmlwidgets\/lib),\nLeon Gersen [ctb, cph] (noUiSlider in
htmlwidgets\/lib),\nBartek Szopka [ctb, cph] (jquery.highlight.js in
htmlwidgets\/lib),\nRStudio Inc [cph]","Description":"Data objects in R can be
rendered as HTML tables using the\nJavaScript library 'DataTables' (typically via R
Markdown or Shiny). The\n'DataTables' library has been included in this R package.
The package name\n'DT' is an abbreviation of 'DataTables'.","Imports":"htmltools,
htmlwidgets (>= 0.4), magrittr","License":"GPL-3 | file
LICENSE","NeedsCompilation":"no","Package":"DT","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"jsonlite (>= 0.9.16), knitr (>= 1.8), shiny (>=
0.12.0)","Title":"A Wrapper of the JavaScript Library
'DataTables'","URL":"http:\/\/rstudio.github.io\/DT","Version":"0.1"},"DTComPair":
{"Author":"Christian Stock, Thomas Hielscher","Depends":"gee,
PropCIs","Description":"This package contains functions to compare the accuracy of
two binary diagnostic tests in a \"paired\" study design, i.e. when each test is
applied to each subject in the
study.","License":"GPL","NeedsCompilation":"no","Package":"DTComPair","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Title":"Comparison of Binary Diagnostic
Tests in a Paired Study Design","Version":"1.0.3"},"DTDA":{"Author":"Carla Moreira,
Jacobo de Uña-Álvarez and Rosa Crujeiras","Description":"This package implements
different algorithms for analyzing\nrandomly truncated data, one-sided and two-
sided (i.e. doubly)\ntruncated data. Two real data sets are
included.","License":"GPL-
2","NeedsCompilation":"no","Package":"DTDA","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Doubly truncated data analysis","Version":"2.1-1"},"DTK":
{"Author":"Matthew K. Lau","Description":"This package was created to analyze
multi-level one-way\nexperimental designs. It is designed to handle
vectorized\nobservation and factor data where there are unequal sample\nsizes and
population variance homogeneity can not be assumed.\nTo conduct the Dunnett
modified Tukey-Kramer test (a.k.a. the\nT3 Procedure), create two vectors: one for
your observations\nand one for the factor level of each observation. The
function,\ngl.unequal, provides a means to more conveniently produce a\nfactor
vector with unequal sample sizes. Next, use the DTK.test\nfunction to conduct the
test and save the output as an object\nto input into the DTK.plot function, which
produces a\nconfidence interval plot for each of the pairwise comparisons.\nLastly,
the function TK.test conducts the original Tukey-Kramer\ntest.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"DTK","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Dunnett-Tukey-Kramer Pairwise Multiple Comparison Test
Adjusted\nfor Unequal Variances and Unequal Sample
Sizes","Version":"3.5"},"DTMCPack":{"Author":"William Nicholson","Description":"A
series of functions which aid in both simulating and\ndetermining the properties of
finite, discrete-time, discrete\nstate markov chains. Two functions (DTMC,
MultDTMC) produce n\niterations of a Markov Chain(s) based on
transition\nprobabilities and an initial distribution. The function
FPTime\ndetermines the first passage time into each state. The\nfunction statdistr
determines the stationary distribution of a\nMarkov Chain.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"DTMCPack","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Suite of functions related to discrete-time discrete-
state\nMarkov Chains","Version":"0.1-2"},"DTR":{"Author":"Xinyu Tang [aut,
cre],\nMaria Melguizo [aut]","Depends":"R (>= 3.2.3)","Description":"Estimation and
comparison of survival distributions of dynamic treatment regimes (DTRs) from
sequentially randomized clinical trials.","Imports":"survival, ggplot2,
aod","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"DTR","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Estimation and Comparison of Dynamic Treatment
Regimes","URL":"http:\/\/CRAN.R-
project.org\/package=DTR","Version":"1.7"},"DTRlearn":{"Author":"Ying Liu, Yuanjia
Wang, Donglin Zeng","Depends":"kernlab,MASS,glmnet,ggplot2","Description":"Dynamic
treatment regimens (DTRs) are sequential decision rules tailored at each stage by
time-varying subject-specific features and intermediate outcomes observed in
previous stages. This package implements three methods: O-learning (Zhao et. al.
2012,2014), Q-learning (Murphy et. al. 2007; Zhao et.al. 2009) and P-learning (Liu
et. al. 2014, 2015) to estimate the optimal DTRs.","License":"GPL-
2","NeedsCompilation":"no","Package":"DTRlearn","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Learning Algorithms for Dynamic Treatment
Regimes","Version":"1.2"},"DTRreg":{"Author":"Michael Wallace, Erica E M Moodie and
David A Stephens","Description":"Dynamic treatment regime estimation and inference
via G-estimation,\ndynamic weighted ordinary least squares (dWOLS) and Q-learning.
Inference\nvia bootstrap and (for G-estimation) recursive sandwich
estimation.","Imports":"graphics, stats, utils","License":"GPL-
2","NeedsCompilation":"no","Package":"DTRreg","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"DTR Estimation and Inference via G-Estimation, Dynamic
WOLS, and\nQ-Learning","Version":"1.0"},"DVHmetrics":{"Author":"Daniel
Wollschlaeger [aut, cre],\nHeiko Karle [aut],\nHeinz Schmidberger
[ctb]","Depends":"R (>= 3.2)","Description":"Functionality for analyzing dose-
volume histograms (DVH)\nin radiation oncology: Read DVH text files, calculate
DVH\nmetrics as well as generalized equivalent uniform dose (gEUD),\nbiologically
effective dose (BED), equivalent dose in 2 Gy\nfractions (EQD2), normal tissue
complication probability\n(NTCP), and tumor control probability (TCP). Show
DVH\ndiagrams, check and visualize quality assurance constraints\nfor the DVH.
Includes web-based graphical user interface.","Imports":"ggplot2, grid, markdown,
reshape2, shiny, KernSmooth, stats,\nutils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"DVHmetrics","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr","Title":"Analyze Dose-Volume Histograms and
Check
Constraints","URL":"https:\/\/github.com\/dwoll\/DVHmetrics\/","Version":"0.3.5"},"
DWreg":{"Author":"Veronica Vinciotti
<veronica.vinciotti@brunel.ac.uk>","Depends":"R (>= 3.2)","Description":"Regression
for a discrete response, where the conditional distribution is modelled via a
discrete Weibull distribution.","Imports":"maxLik, DiscreteWeibull,
Ecdat","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"DWreg","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Parametric Regression for Discrete
Response","Version":"1.0"},"DYM":{"Author":"Kosei Abe [aut, cre], Richard Cotton
[ctb]","Description":"Add a \"Did You Mean\" feature to the R interactive. With
this\npackage, error messages for misspelled input of variable names or package
names\nsuggest what you really want to do in addition to notification of the
mistake.","Imports":"stats, utils","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"DYM","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat","Title":"Did You
Mean?","Version":"0.2"},"Daim":{"Author":"Sergej Potapov, Werner Adler, Benjamin
Hofner and Berthold Lausen.","Depends":"R (>= 2.15.1),
parallel","Description":"Several functions for evaluating the accuracy
of\nclassification models. The package provides the following\nperformance
measures: repeated k-fold cross-validation,\n0.632 and 0.632+ bootstrap estimation
of the misclassification rate,\nsensitivity, specificity and AUC. If an application
is\ncomputationally intensive, parallel execution can be used\nto reduce the
computational effort.","Imports":"rms","License":"GPL-
2","NeedsCompilation":"yes","Package":"Daim","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"MASS, rpart, ipred, e1071, randomForest, mboost,
TH.data","Title":"Diagnostic accuracy of classification
models","Version":"1.1.0"},"DandEFA":{"Author":"Artur Manukyan, Ahmet Sedef, Erhan
Cene, Ibrahim Demir","Depends":"R(>= 3.2.3), gplots,
polycor","Description":"Contains the function used to create the Dandelion Plot.
Dandelion Plot is a visualization method for R-mode Exploratory Factor
Analysis.","License":"GPL-
2","NeedsCompilation":"no","Package":"DandEFA","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Dandelion Plot for R-Mode Exploratory Factor
Analysis","Version":"1.6"},"Dark":{"Author":"Dr Jeremiah MF
Kelly","Description":"The recovery of visual sensitivity in a dark environment is
known as dark\nadaptation. In a clinical or research setting the recovery is
typically\nmeasured after a dazzling flash of light and can be described by the
Mahroo,\nLamb and Pugh (MLP) model of dark adaptation. The functions in this
package\ntake dark adaptation data and use nonlinear regression to find the
parameters\nof the model that 'best' describe the data. They do this by
firstly,\ngenerating rapid initial objective estimates of data adaptation
parameters,\nthen a multi-start algorithm is used to reduce the possibility of a
local\nminimum. There is also a bootstrap method to calculate parameter
confidence\nintervals. The functions rely upon a 'dark' list or object. This object
is\ncreated as the first step in the workflow and parts of the object are\nupdated
as it is processed.","License":"GPL-
3","NeedsCompilation":"no","Package":"Dark","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"knitr, rmarkdown,testthat","Title":"The Analysis of Dark
Adaptation Data","URL":"https:\/\/github.com\/emkayoh\/Dark,
http:\/\/www.nihr.ac.uk","Version":"0.9.4"},"DatABEL":{"Author":"Yurii Aulchenko,
Stepan Yakovenko, Erik Roos, Marcel Kempenaar, Maksim\nStruchalin, Lennart C.
Karssen","Depends":"R (>= 2.4.0), methods, utils","Description":"Provides an
interface to the C++ FILEVECTOR library\nfacilitating analysis using large (giga-
to tera-bytes) matrices.\nMatrix storage is organized in a way that either columns
or rows\nare quickly accessible. DatABEL is primarily aimed to support\ngenome-wide
association analyses e.g. using GenABEL, MixABEL and\nProbABEL.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"DatABEL","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"GenABEL, RUnit","Title":"File-Based Access to Large
Matrices Stored on HDD in Binary\nFormat","Version":"0.9-6"},"DataClean":
{"Author":"Xiaorui(Jeremy) Zhu","Depends":"R (>= 3.1.0)","Description":"Includes
functions that researchers or practitioners may use to clean\nraw data,
transferring html, xlsx, txt data file into other formats. And it\nalso can be used
to manipulate text variables, extract numeric variables from\ntext variables and
other variable cleaning processes. It is originated from a\nauthor's project which
focuses on creative performance in online education\nenvironment. The resulting
paper of that study will be published soon.","Imports":"xlsx, XML","License":"GPL-
3","NeedsCompilation":"no","Package":"DataClean","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Data Cleaning","Version":"1.0"},"DataCombine":
{"Author":"Christopher Gandrud [aut, cre]","Depends":"R (>=
3.0.2)","Description":"Tools for combining and cleaning data sets,
particularly\nwith grouped and time series data.","Imports":"data.table, dplyr (>=
0.4)","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"DataCombine","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"devtools, testthat","Title":"Tools for Easily
Combining and Cleaning Data Sets","URL":"http:\/\/CRAN.R-
project.org\/package=DataCombine","Version":"0.2.20"},"DataExplorer":
{"Author":"Boxuan Cui [aut, cre]","Depends":"R (>= 3.2.0)","Description":"Data
exploration process for data analysis and model building, so\nthat users could
focus on understanding data and extracting insights. The\npackage automatically
scans through each variable and does data profiling.\nTypical graphical techniques
will be performed for both discrete and\ncontinuous
features.","Imports":"data.table (>= 1.9.4), reshape2 (>= 1.4.1), ggplot2
(>=\n1.0.1), scales (>= 0.3.0), gridExtra (>= 0.9.1), rmarkdown (>=\n0.9.5), stats,
2","NeedsCompilation":"no","Package":"DataExplorer","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Data
Explorer","URL":"https:\/\/github.com\/boxuancui\/DataExplorer","Version":"0.2.4"},
"DataLoader":{"Author":"Srivenkatesh
Gandhi<srivenkateshg@sase.ssn.edu.in>,\nKreshnaa Raam S Bethusamy
<kreshnaaraamsb@sase.ssn.edu.in>","Depends":"readxl, plyr, tools, xlsx,
rChoiceDialogs","Description":"Functions to import multiple files of multiple data
file types ('.xlsx', '.xls', '.csv', '.txt')\nfrom a given directory into R data
frames.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"DataLoader","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat","Title":"Import Multiple File
Types","Version":"1.3"},"Davies":{"Author":"Robin K. S.
Hankin","Description":"Various utilities for the Davies distribution and
the\ngeneralized lambda distribution","License":"GPL-
2","NeedsCompilation":"no","Package":"Davies","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"The Davies quantile function","Version":"1.1-
8"},"DecisionCurve":{"Author":"Marshall Brown","Description":"Decision curves are a
useful tool to evaluate the population impact\nof adopting a risk prediction
instrument into clinical practice. Given one or more\ninstruments (risk models)
that predict the probability of a binary outcome, this\npackage calculates and
plots decision curves, which display estimates of the\nstandardized net benefit by
the probability threshold used to categorize observations\nas 'high risk.' Curves
can be estimated using data from an observational cohort, or\nfrom case-control
studies when an estimate of the population outcome prevalence\nis available.
Confidence intervals calculated using the bootstrap can be displayed and\na wrapper
function to calculate cross-validated curves using k-fold cross-validation is\nalso
provided.","Imports":"reshape, pander, MASS, caret","License":"GPL-
2","NeedsCompilation":"no","Package":"DecisionCurve","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Calculate and Plot Decision
Curves","URL":"http:\/\/mdbrown.github.io\/DecisionCurve\/,\nhttps:\/\/github.com\/
mdbrown\/DecisionCurve","Version":"1.1"},"Deducer":{"Author":"Ian Fellows with
contributions from others (see documentation).","Depends":"R (>= 2.15.0), ggplot2
(>= 2.0.0), JGR(>= 1.7-10), car, MASS","Description":"An intuitive, cross-platform
graphical data analysis system. It uses menus and dialogs to guide the user
efficiently through the data manipulation and analysis process, and has an excel
like spreadsheet for easy data frame visualization and editing. Deducer works best
when used with the Java based R GUI JGR, but the dialogs can be called from the
command line. Dialogs have also been integrated into the Windows
Rgui.","Imports":"rJava, e1071, scales, plyr, foreign, multcomp,
effects","License":"GPL-
2","NeedsCompilation":"no","Package":"Deducer","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"lawstat, Hmisc, XLConnect","Title":"A Data Analysis GUI
for R","URL":"http:\/\/www.deducer.org\/manual.html
http:\/\/www.fellstat.com","Version":"0.7-9"},"DeducerExtras":{"Author":"Ian
Fellows and Helios De Rosario","Depends":"Deducer (>= 0.4-4),
irr","Description":"Added functionality for Deducer. This package
includes\nadditional dialogs for calculating distribution function\nvalues, cluster
analysis and more.","Imports":"rJava","License":"GPL-
2","NeedsCompilation":"no","Package":"DeducerExtras","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"pwr, rgl","Title":"Additional dialogs and
functions for Deducer","Version":"1.7"},"DeducerPlugInExample":{"Author":"Ian
Fellows","Depends":"Deducer (>= 0.5-0)","Description":"A example GUI plug-in
package to serve as a template.","License":"GPL-
2","NeedsCompilation":"no","Package":"DeducerPlugInExample","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Title":"Deducer Plug-in
Example","URL":"http:\/\/www.deducer.org\/pmwiki\/index.php?
n=Main.Development","Version":"0.2-0"},"DeducerPlugInScaling":{"Author":"Alberto
Mirisola, Ian Fellows and Helios De Rosario-Martinez","Depends":"Deducer, psych,
GPArotation, mvnormtest, irr, klaR","Description":"A Deducer plug-in for factor
analysis, reliability\nanalysis and discriminant analysis, using psych,
GPArotation\nand mvnormtest packages.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"DeducerPlugInScaling","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Title":"Reliability and factor analysis
plugin","Version":"0.1-0"},"DeducerSpatial":{"Author":"Ian Fellows and Alex Rickett
with contributions from Neal\nFultz.","Depends":"JavaGD (>= 0.6-0), Deducer (>=
0.7-4), sp, maptools,\nOpenStreetMap, scales, rgdal","Description":"A Deducer plug-
in for spatial data analysis. Includes The\nability to plot and explore open street
map and Bing satellite\nimages.","Imports":"UScensus2010, Hmisc","License":"GPL-
2","NeedsCompilation":"no","Package":"DeducerSpatial","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"UScensus2010","Title":"Deducer
for spatial data analysis","URL":"http:\/\/www.deducer.org\/pmwiki\/pmwiki.php?
n=Main.DeducerSpatial\nhttp:\/\/www.fellstat.com
http:\/\/research.cens.ucla.edu\/","Version":"0.7"},"DeducerSurvival":
{"Author":"Matthew Ockendon, Paul Cool","Depends":"Deducer (>= 0.5-
0)","Description":"Adds Kaplan-Meier Survival Analysis to the Deducer
GUI","License":"GPL-
2","NeedsCompilation":"no","Package":"DeducerSurvival","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Add Survival Dialogue to Deducer","Version":"0.1-
0"},"DeducerText":{"Author":"Alex Rickett and Ian Fellows, with contributions from
Neal Fultz","Depends":"R (>= 2.10.0), Deducer (>= 0.7-0), tm (>= 0.6), wordcloud
(>=\n2.1), RColorBrewer","Description":"A GUI for text
mining","Imports":"SnowballC","License":"LGPL-
2","NeedsCompilation":"no","Package":"DeducerText","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Deducer GUI for Text
Data","URL":"http:\/\/www.deducer.org\/manual.html
http:\/\/www.fellstat.com\nhttp:\/\/research.cens.ucla.edu\/","Version":"0.1-
2"},"Delaporte":{"Author":"Avraham Adler [aut, cph, cre]","Description":"Provides
probability mass, distribution, quantile, random-variate generation, and method-of-
moments parameter-estimation functions for the Delaporte distribution. The
Delaporte is a discrete probability distribution which can be considered the
convolution of a negative binomial distribution with a Poisson distribution.
Alternatively, it can be considered a counting distribution with both Poisson and
negative binomial components. It has been studied in actuarial science as a
frequency distribution which has more variability than the Poisson, but less than
the negative binomial.","Imports":"Rcpp (>= 0.11.0), stats","License":"GPL (>= 2) |
LGPL (>=
3)","NeedsCompilation":"yes","Package":"Delaporte","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat","Title":"Statistical Functions for the
Delaporte
Distribution","URL":"https:\/\/bitbucket.org\/aadler\/delaporte","Version":"2.2-
3"},"Demerelate":{"Author":"Philipp Kraemer [aut, cre],\nGabriele Gerlach
[aut]","Depends":"R (>= 2.15.0), Formula","Description":"Functions to calculate
pairwise relatedness on diploid genetic datasets. Different estimators for
relatedness can be combined with information on geographical distances. Information
on heterozygosity, allele- and genotype diversity as well as genetic F-statistics
are provided for each population.","Imports":"fts, sfsmisc, vegan,
mlogit","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Demerelate","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"MASS","Title":"Functions to calculate relatedness
on diploid genetic data","URL":"http:\/\/www.r-project.org","Version":"0.8-
1"},"DendSer":{"Author":"Catherine B. Hurley and Denise
Earle","Depends":"gclus,seriation","Description":"Re-arranges a dendrogram to
optimize visualisation-based cost functions","License":"GPL-
2","NeedsCompilation":"yes","Package":"DendSer","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Dendrogram seriation: ordering for
visualisation","Version":"1.0.1"},"DensParcorr":{"Author":"Yikai Wang, Jian Kang,
Phebe Brenne Kemmer and Ying Guo","Depends":"R (>= 3.1.0), clime,
gplots","Description":"Provide a Dens-based method for estimating functional
connection in large scale brain networks using partial
correlation.","License":"GPL-
2","NeedsCompilation":"no","Package":"DensParcorr","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Dens-Based Method for Partial Correlation Estimation
in Large\nScale Brain Networks","Version":"1.0"},"Density.T.HoldOut":
{"Author":"Nelo MagalhÃ£es (Univ. Paris Sud 11 - INRIA team Select) and Yves
Rozenholc (Univ. Paris Descartes - INRIA team
Select)","Description":"Implementation in the density framework of the non-
combinatorial algorithm and its greedy version, introduced by MagalhÃ£es and
Rozenholc (2014), for T-estimation Hold-Out proposed in BirgÃ© (2006, Section 9).
The package provide an implementation which uses several families of estimators
(regular and irregular histograms, kernel estimators) which may be used alone or
combined. As a complement, provides also a comparison with other Held-Out derived
from least-squares and maximum-likelihood. This package implements also the T-
estimation Hold-Out derived from the test introduced in Baraud
(2011).","Imports":"histogram","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Density.T.HoldOut","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Density.T.HoldOut: Non-combinatorial T-
estimation Hold-Out for\ndensity estimation","Version":"2.00"},"DepthProc":
{"Author":"Daniel Kosiorowski, Mateusz Bocian, Anna Wegrzynkiewicz and
Zygmunt\nZawadzki from Cracow University of Economics.","Depends":"R (>= 3.0.0),
ggplot2, Rcpp (>= 0.11.2), rrcov, methods, MASS,\nnp","Description":"Data depth
concept offers a variety of powerful and user friendly tools for robust exploration
and inference for multivariate data. The offered techniques may be successfully
used in cases of lack of our knowledge on parametric models generating data due to
their nonparametric nature. The package consist of among others implementations of
several data depth techniques involving multivariate quantile-quantile plots,
multivariate scatter estimators, multivariate Wilcoxon tests and robust
regressions.","Imports":"lattice, sm, geometry, colorspace,","License":"GPL-
2","NeedsCompilation":"yes","Package":"DepthProc","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"mvtnorm, rgl, sn, robustbase, dplyr,
RcppArmadillo","Title":"Statistical Depth Functions for Multivariate
Analysis","Version":"1.0.7"},"Deriv":{"Author":"Andrew Clausen [aut],\nSerguei
Sokol [aut, cre]","Description":"R-based solution for symbolic differentiation. It
admits\nuser-defined function as well as function substitution\nin arguments of
functions to be differentiated. Some symbolic\nsimplification is part of the
work.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"Deriv","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat","Title":"Symbolic
Differentiation","Version":"3.7.0"},"DescTools":{"Author":"Andri Signorell.
Includes R source code and\/or documentation previously published by (in
alphabetical order): Ken Aho, Nanina Anderegg, Tomas Aragon, Antti Arppe, Adrian
Baddeley, Ben Bolker, Frederico Caeiro, Stephane Champely, Daniel Chessel, Leanne
Chhay, Clint Cummins, Michael Dewey, Harold C. Doran, Stephane Dray, Charles
Dupont, Dirk Eddelbuettel, Jeff Enos, Claus Ekstrom, Martin Elff, Kamil Erguler,
Richard W. Farebrother, John Fox, Michael Friendly, Tal Galili, Matthias Gamer,
Joseph L. Gastwirth, Yulia R. Gel, Juergen Gross, Gabor Grothendieck, Frank E.
Harrell Jr, Richard Heiberger, Michael Hoehle, Christian W. Hoffmann, Torsten
Hothorn, Markus Huerzeler, Wallace W. Hui, Pete Hurd, Rob J. Hyndman, Pablo J.
Villacorta Iglesias, Matthias Kohl, Mikko Korpela, Max Kuhn, Detlew Labes,
Friederich Leisch, Jim Lemon, Dong Li, Martin Maechler, Arni Magnusson, Daniel
Malter, George Marsaglia, John Marsaglia, Alina Matei, David Meyer, Weiwen Miao,
Giovanni Millo, Yongyi Min, David Mitchell, Markus Naepflin, Daniel Navarro, Klaus
Nordhausen, Derek Ogle, Hong Ooi, Nick Parsons, Sandrine Pavoine, Tony Plate,
Roland Rapold, William Revelle, Tyler Rinker, Brian D. Ripley, Caroline Rodriguez,
Venkatraman E. Seshan, Greg Snow, Michael Smithson, Werner A. Stahel, Mark
Stevenson, Terry Therneau, Yves Tille, Adrian Trapletti, Kevin Ushey, Jeremy
VanDerWal, Bill Venables, John Verzani, Gregory R. Warnes, Stefan Wellek, Rand R.
Wilcox, Peter Wolf, Daniel Wollschlaeger, Thomas Yee, Achim
Zeileis","Depends":"base, stats, R (>= 3.1.1)","Description":"A collection of basic
statistic functions and convenience wrappers for efficiently describing data. The
author's intention was to create a toolbox, which facilitates the (notoriously time
consuming) first descriptive tasks in data analysis, consisting of calculating
descriptive statistics, drawing graphical summaries and reporting the results. The
package contains furthermore functions to produce documents using MS Word (or
PowerPoint) and functions to import data from Excel. Many of the included functions
can be found scattered in other packages and other sources written partly by Titans
of R. The reason for collecting them here, was primarily to have them consolidated
in ONE instead of dozens of packages (which themselves might depend on other
packages which are not needed at all), and to provide a common and consistent
interface as far as function and arguments naming, NA handling, recycling rules
etc. are concerned. Google style guides were used as naming rules (in absence of
convincing alternatives). The 'camel style' was consequently applied to functions
borrowed from contributed R packages as well.","Imports":"graphics, grDevices,
methods, utils, boot, manipulate,mvtnorm,\nforeign, Rcpp (>=
0.11.5)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"DescTools","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"RDCOMClient, tcltk","Title":"Tools for Descriptive
Statistics","Version":"0.99.16"},"DescribeDisplay":{"Author":"Di Cook [aut,
cre],\nHadley Wickham [aut],\nAndreas Buja [aut],\nBarret Schloerke
[aut]","Description":"Produce publication quality graphics from output of
GGobi's\ndescribe display plugin.","Imports":"reshape2, ggplot2 (>= 2.0.0), plyr,
scales, grid, GGally (>=\n1.0.0)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"DescribeDisplay","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Suggests":"roxygen2 (>= 5.0.1),
testthat","Title":"An Interface to the DescribeDisplay GGobi
Plugin","URL":"https:\/\/github.com\/ggobi\/DescribeDisplay","Version":"0.2.5"},"De
tMCD":{"Author":"Vakili Kaveh [aut, cre],\nMia Hubert [ths]","Depends":"robustbase,
pcaPP","Description":"Implementation of DetMCD, a new algorithm for robust and
deterministic estimation of location and scatter. The benefits of robust and
deterministic estimation are explained in Hubert, M., Rousseeuw, P.J. and Verdonck,
T. (2012),\"A deterministic algorithm for robust location and scatter\", Journal of
Computational and Graphical Statistics, Volume 21, Number 3, Pages 618--
637.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"DetMCD","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"mvtnorm, MASS","Title":"Implementation of the DetMCD
Algorithm (Robust and Deterministic\nEstimation of Location and
Scatter)","Version":"0.0.3"},"DetR":{"Author":"Kaveh Vakili [aut, cre],\nValentin
Todorov [ctb] (modified code originally from the R package\nrobustbase: function
ltscheckout, LTScnp2 and LTScnp2.rew and from\nrobustbase:::.detmcd()),\nPeter
Filzmoser [ctb] (translations of the code for computing the Qn\nfound in package
pcaPP),\nHeinrich Fritz [ctb] (translations of the code for computing the Qn\nfound
in package pcaPP),\nKlaudius Kalcher [ctb] (translations of the code for computing
the Qn\nfound in package pcaPP),\nKjell Konis [ctb] (translations of the code
scaleTau2 found in package\nrobustbase),\nMartin Maechler [ctb] (translations of
the code scaleTau2 found in\npackage robustbase),\nMatias Salibian-Barrera [ctb]
(modified code for the FastS from the\nauthors's website),\nPeter Rousseeuw [ctb]
(modified code originally from the R package\nrobustbase: function ltscheckout,
LTScnp2 and LTScnp2.rew and from\nrobustbase:::.detmcd()),\nKatrien van Driessen
[ctb] (modified code originally from the R package\nrobustbase: function
ltscheckout, LTScnp2 and LTScnp2.rew and
from\nrobustbase:::.detmcd())","Depends":"R (>= 3.1.1),","Description":"DetLTS,
DetMM (and DetS) Algorithms for Deterministic, Robust\nLinear
Regression.","Imports":"robustbase, MASS, pcaPP","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"DetR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"mvtnorm","Title":"Suite of Deterministic and Robust
Algorithms for Linear\nRegression","Version":"0.0.4"},"DetSel":{"Author":"Renaud
Vitalis <vitalis@supagro.inra.fr>.","Depends":"R (>= 2.15), ash","Description":"In
the new era of population genomics, surveys of genetic\npolymorphism (\"genome
scans\") offer the opportunity to\ndistinguish locus-specific from genome wide
effects at many\nloci. Identifying presumably neutral regions of the genome
that\nare assumed to be influenced by genome-wide effects only, and\nexcluding
presumably selected regions, is therefore critical to\ninfer population demography
and phylogenetic history reliably.\nConversely, detecting locus-specific effects
may help identify\nthose genes that have been, or still are, targeted by
natural\nselection. The software package DetSel has been developed to\nidentify
markers that show deviation from neutral expectation\nin pairwise comparisons of
diverging populations.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"DetSel","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"A computer program to detect markers responding to
selection","Version":"1.0.2"},"Devore7":{"Author":"Original by Jay L. Devore,
modifications by Douglas Bates\n<bates@stat.wisc.edu>, modifications for 7th
edition by John Verzani.","Depends":"R(>= 2.4.0), MASS,
lattice","Description":"Data sets and sample analyses from Jay L. Devore
(2008),\n\"Probability and Statistics for Engineering and the Sciences\n(7th ed)\",
Thomson.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Devore7","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Data sets from Devore's \"Prob and Stat for Eng (7th
ed)\"","Version":"0.7.6"},"DiagTest3Grp":{"Author":"Jingqin Luo, Chengjie
Xiong","Depends":"car,KernSmooth,stats, gplots","Description":"The R package
provides utilities to estimate and make inference on two summary measures for
diagnostic tests when there are three ordinal groups ----volume under ROC surface
(VUS) and the extended Youden index, assuming that diagnostic markers increase
monotonically and stochastically with disease severity. Point estimates, variance,
confidence interval and optimal cut-points both under the normal assumption and
also the non-parametric method(s) will be provided for the summary measures.
Statistical tests are implemented to compare multiple diagnostic tests and two
diagnostic test. Sample size is calculated to estimate the summary measures within
a user-specified margin of error for future study planning.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"DiagTest3Grp","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Diagnostic test summary measures for three ordinal
groups","Version":"1.6"},"DiagrammeR":{"Author":"Knut Sveidqvist [aut, cph]
(mermaid.js library in
htmlwidgets\/lib,\nhttp:\/\/github.com\/knsv\/mermaid\/),\nMike Bostock [aut, cph]
(d3.js library in htmlwidgets\/lib,\nhttp:\/\/d3js.org),\nChris Pettitt [aut, cph]
(dagre-d3.js library in htmlwidgets\/lib,\nhttp:\/\/github.com\/cpettitt\/dagre-
d3),\nMike Daines [aut, cph] (viz.js library in
htmlwidgets\/lib,\nhttp:\/\/github.com\/mdaines\/viz.js\/),\nAndrei Kashcha [aut,
cph] (vivagraphjs library in
htmlwidgets\/lib,\nhttps:\/\/github.com\/anvaka\/VivaGraphJS),\nRichard Iannone
[aut, cre] (R interface)","Description":"Create graph diagrams and flowcharts using
R.","Imports":"htmlwidgets (>= 0.5), rstudioapi (>= 0.3.1), stringr (>=\n1.0.0),
visNetwork (>= 0.1.2), scales (>= 0.3.0)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"DiagrammeR","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"knitr, testthat","Title":"Create Graph
Diagrams and Flowcharts Using R","URL":"https:\/\/github.com\/rich-
iannone\/DiagrammeR","Version":"0.8.2"},"DiagrammeRsvg":{"Author":"Richard Iannone
[aut, cre]","Description":"Allows for export of DiagrammeR Graphviz objects to
SVG.","Imports":"V8 (>= 0.10)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"DiagrammeRsvg","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Title":"Export DiagrammeR Graphviz Graphs as
SVG","URL":"https:\/\/github.com\/rich-
iannone\/DiagrammeRsvg","Version":"0.1"},"DiallelAnalysisR":{"Author":"Muhammad
Yaseen [aut, cre],\nKent M. Eskridge [ctb]","Depends":"R (>=
3.1)","Description":"Performs Diallel Analysis with R using Griffing's and Hayman's
approaches. Four different methods (1: Method-I (Parents + F1's + reciprocals); 2:
Method-II (Parents and one set of F1's); 3: Method-III (One set of F1's and
reciprocals); 4: Method-IV (One set of F1's only)) and two methods (1: Fixed
Effects Model; 2: Random Effects Model) can be applied using Griffing's
approach.","Imports":"ggplot2, stats","License":"GPL-
2","NeedsCompilation":"no","Package":"DiallelAnalysisR","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Diallel Analysis with
R","Version":"0.1.1"},"DiceDesign":{"Author":"Jessica Franco, Delphine Dupuy,
Olivier Roustant, Guillaume\nDamblin and Bertrand Iooss.","Description":"Space-
Filling Designs and Uniformity Criteria.","License":"GPL-
3","NeedsCompilation":"yes","Package":"DiceDesign","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"rgl, randtoolbox, lattice","Title":"Designs of
Computer Experiments","URL":"http:\/\/dice.emse.fr\/","Version":"1.7"},"DiceEval":
{"Author":"D. Dupuy and C.
Helbert","Depends":"DiceKriging","Description":"Estimation, validation and
prediction of models of different types : linear models, additive models,
MARS,PolyMARS and Kriging.","License":"GPL-
3","NeedsCompilation":"no","Package":"DiceEval","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"gam, akima, mda, polspline","Title":"Construction and
Evaluation of
Metamodels","URL":"http:\/\/dice.emse.fr\/","Version":"1.4"},"DiceKriging":
{"Author":"Olivier Roustant, David Ginsbourger, Yves Deville. Contributors: Clement
Chevalier, Yann Richet.","Depends":"methods","Description":"Estimation, validation
and prediction of kriging models.\nImportant functions : km, print.km, plot.km,
predict.km.","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"DiceKriging","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"rgenoud, foreach, doParallel,
testthat","Title":"Kriging Methods for Computer
Experiments","URL":"http:\/\/dice.emse.fr\/","Version":"1.5.5"},"DiceOptim":
{"Author":"D. Ginsbourger, V. Picheny, O. Roustant, with contributions by\nC.
Chevalier, S. Marmin, and T. Wagner","Depends":"DiceKriging (>= 1.2), rgenoud,
MASS, lhs, mnormt","Description":"Expected Improvement. EGO algorithm. Multipoint
EI and parallelized versions of EGO. Criteria and algorithms for Noisy Kriging-
based Optimization , including AEI, AKG, EQI, and EI with plugin.","License":"GPL-2
| GPL-
3","NeedsCompilation":"no","Package":"DiceOptim","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Kriging-Based Optimization for Computer
Experiments","URL":"http:\/\/dice.emse.fr\/","Version":"1.5"},"DiceView":
{"Author":"Yann Richet, Yves Deville, Clement Chevalier","Depends":"methods,
DiceKriging, DiceEval, rgl","Description":"View 2D\/3D sections or contours of
computer experiments designs, surrogates or test functions.","License":"GPL-
3","NeedsCompilation":"no","Package":"DiceView","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Plot methods for computer experiments design and
surrogate","URL":"http:\/\/promethee.irsn.org\/","Version":"1.3-1"},"DiffCorr":
{"Author":"Atsushi Fukushima, Kozo Nishida","Depends":"pcaMethods, igraph, fdrtool,
multtest","Description":"A method for identifying pattern changes between 2
experimental\nconditions in correlation networks (e.g., gene co-expression
networks),\nwhich builds on a commonly used association measure, such as
Pearson's\ncorrelation coefficient. This package
includes functions to calculate\ncorrelation matrices for high-dimensional dataset
and to test\ndifferential correlation, which means the changes in the
correlation\nrelationship among variables (e.g., genes and metabolites) between
2\nexperimental conditions.","License":"GPL (>
3)","NeedsCompilation":"no","Package":"DiffCorr","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Analyzing and Visualizing Differential Correlation
Networks in\nBiological Data","Version":"0.4.1"},"DiffusionRgqd":{"Author":"Etienne
A.D. Pienaar [aut, cre],\nMelvin M. Varughese [ctb]","Depends":"R (>=
3.2.1)","Description":"Tools for performing inference and analysis on a class of
quadratic diffusion processes for both scalar and bivariate diffusion systems. For
scalar diffusions, a module is provided for solving first passage time problems for
both time-homogeneous and time-inhomogeneous GQDs.","Imports":"Rcpp, RcppArmadillo,
rgl, colorspace","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"DiffusionRgqd","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"knitr, coda, fptdApprox, Quandl,
R.rsp","Title":"Inference and Analysis for Generalized Quadratic
Diffusions","URL":"https:\/\/github.com\/eta21","Version":"0.1.2"},"DiffusionRjgqd"
:{"Author":"Etienne A.D. Pienaar [aut, cre],\nMelvin M. Varughese
[ctb]","Depends":"R (>= 3.2.1)","Description":"Tools for performing inference and
analysis on a class of quadratic jump diffusion processes.","Imports":"Rcpp,
RcppArmadillo, rgl, colorspace","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"DiffusionRjgqd","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"DiffusionRgqd, knitr, coda, Quandl,
R.rsp","Title":"Inference and Analysis for Jump Generalized Quadratic
Diffusions","URL":"https:\/\/github.com\/eta21","Version":"0.1.0"},"Digiroo2":
{"Author":"Ross Dwyer, Emily Best and Anne Goldizen","Depends":"R (>= 2.14.0),
maptools, spatstat, spdep","Description":"Digiroo2 is an R package developed by
researchers at the\nUniversity of Queensland to investigate association
patterns\nand social structure in wild animal populations. Proximity\nbetween
individuals is generally considered to be an\nappropriate proxy for associations
and pairwise association\nindices are the most widely used technique for analysing
animal\nsocial structure. However, little attention is given to\nidentifying how
patterns of spatial overlap affect these\nassociation patterns. For example, do
individuals associate\nrandomly with others with whom they share home ranges, or
do\nsome individuals go out of their way to associate with or avoid\nparticular
individuals? This program builds a null model of\nrandom associations based on an
individual's space use\ndetermined using home range methodologies. Random points
may be\ngenerated within a specified home range contour or according to\nthe
Utilization Distribution (UD). Expected associations of\nindividuals are extracted
based on probability of occurrence\nand the proximity between home range weighted
random points.\nAssociation matrices can be generated from multiple\npermutations
for analysis using SOCPROG 2.4 (Whitehead 2009) to\ncreate 'expected' pairwise
half-weight association indices\n(HWIs). These may be compared with the 'observed'
HWIs from\nfield observations to reveal whether pairs of animals associate\nmore (=
attraction) or less (= avoidance) than expected by\nchance.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Digiroo2","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"adehabitatHR, raster","Title":"An application
programming interface for generating null models\nof social contacts based on
individuals' space use","Version":"0.6"},"Directional":{"Author":"Michail Tsagris,
Giorgos Athineou","Description":"A collection of R functions for directional data
analysis.","Imports":"MASS, abind, doParallel, parallel, foreach,
fields","License":"GPL-
2","NeedsCompilation":"no","Package":"Directional","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Directional
Statistics","Version":"1.8"},"DirichletReg":{"Author":"Marco Johannes Maier [cre,
aut]","Depends":"R (>= 3.0.0), Formula, rgl","Description":"Implements Dirichlet
regression models in R.","Imports":"stats, graphics, methods,
maxLik","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"DirichletReg","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat","Title":"Dirichlet Regression in
R","URL":"http:\/\/dirichletreg.r-forge.r-project.org\/\nhttp:\/\/r-forge.r-
project.org\/projects\/dirichletreg\/\nhttp:\/\/CRAN.R-
project.org\/package=DirichletReg","Version":"0.6-3"},"Disake":{"Author":"W. E.
WansouwÃ©, C. C. Kokonendji and D. T. Kolyang","Description":"Discrete smoothing of
probability mass function is performed using three discrete associated kernels:
Dirac Discrete Uniform (DiracDU), Binomial and Discrete Triangular. Two automatic
bandwidth selection procedures are implemented: the cross-validation method for the
three kernels and the local Bayesian approach for Binomial kernel. Note that
DiracDU is used for categorical data, Binomial kernel is appropriate for count data
with small or moderate sample sizes, and Discrete Triangular kernel is recommended
for count data with large sample sizes.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Disake","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Discrete associated kernel estimators","URL":"www.r-
project.org","Version":"1.5"},"DiscML":{"Author":"Tane Kim, Weilong
Hao","Depends":"ape","Description":"DiscML performs rate estimation using maximum
likelihood with the\noptions to correct for unobservable data, to implement a
Gamma-distribution\nfor rate variation, and to estimate the prior root
probabilities from the\nempirical data.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"DiscML","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"DiscML: An R package for estimating evolutionary rates
of\ndiscrete characters using maximum
likelihood","Version":"1.0.1"},"DiscreteInverseWeibull":{"Author":"Alessandro
Barbiero, Riccardo Inchingolo, Mario
Samigli","Depends":"Rsolnp","Description":"Probability mass function, distribution
function, quantile function, random generation and parameter estimation for the
discrete inverse Weibull
distribution","License":"GPL","NeedsCompilation":"no","Package":"DiscreteInverseWei
bull","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Discrete inverse
Weibull distribution","Version":"1.0.1"},"DiscreteLaplace":{"Author":"Alessandro
Barbiero <alessandro.barbiero@unimi.it>, Riccardo Inchingolo
<riccardo.arner@libero.it>","Depends":"Rsolnp, stats","Description":"Probability
mass function, distribution function, quantile function, random generation and
estimation for the skew discrete Laplace
distributions.","License":"GPL","NeedsCompilation":"no","Package":"DiscreteLaplace"
,"Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Discrete Laplace
Distributions","Version":"1.1"},"DiscreteWeibull":{"Author":"Alessandro
Barbiero","Depends":"Rsolnp, stats","Description":"Probability mass function,
distribution function, quantile function, random generation and parameter
estimation for the type I and III discrete Weibull
distributions.","License":"GPL","NeedsCompilation":"no","Package":"DiscreteWeibull"
,"Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Discrete Weibull
Distributions (Type 1 and 3)","Version":"1.1"},"DiscriMiner":{"Author":"Gaston
Sanchez [aut, cre],\nCharles Determan [ctb]","Depends":"R (>=
2.15.0)","Description":"Functions for Discriminant Analysis and Classification
purposes\ncovering various methods such as descriptive, geometric, linear,
quadratic,\nPLS, as well as qualitative discriminant analyses","License":"GPL-
3","NeedsCompilation":"no","Package":"DiscriMiner","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"MASS, FactoMineR","Title":"Tools of the Trade for
Discriminant Analysis","URL":"http:\/\/www.gastonsanchez.com","Version":"0.1-
29"},"DisimForMixed":{"Author":"Hasanthi A. Pathberiya","Description":"Implement
the methods proposed by Ahmad & Dey (2007) <doi:10.1016\/j.datak.2007.03.016> in
calculating the dissimilarity matrix at the presence of mixed attributes. This
Package includes functions to discretize quantitative variables, calculate
conditional probability for each pair of attribute values, distance between every
pair of attribute values, significance of attributes, calculate dissimilarity
between each pair of objects.","Imports":"dplyr,
cluster","License":"GPL","NeedsCompilation":"no","Package":"DisimForMixed","Reposit
ory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Calculate Dissimilarity Matrix
for Dataset with Mixed Attributes","Version":"0.1"},"Distance":{"Author":"David
Lawrence Miller","Depends":"R (>= 3.0), mrds (>= 2.1.10)","Description":"A simple
way of fitting detection functions to distance sampling\ndata for both line and
point transects. Adjustment term selection, left and\nright truncation as well as
monotonicity constraints and binning are\nsupported. Abundance and density
estimates can also be calculated (via a\nHorvitz-Thompson-like estimator) if survey
area information is provided.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Distance","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat","Title":"Distance Sampling Detection
Function and Abundance
Estimation","URL":"http:\/\/github.com\/DistanceDevelopment\/Distance\/","Version":
"0.9.4"},"DistatisR":{"Author":"Derek Beaton [aut, com, ctb], Cherise Chin Fatt
[ctb], Herve Abdi [aut, cre]","Depends":"prettyGraphs (>= 2.0.0),
car","Description":"Implement DiSTATIS and CovSTATIS (three-way multidimensional
scaling). For the analysis of multiple distance\/covariance matrices collected on
the same set of observations","License":"GPL-
2","NeedsCompilation":"no","Package":"DistatisR","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"DiSTATIS Three Way Metric Multidimensional
Scaling","URL":"www.utdallas.edu\/~herve","Version":"1.0"},"DistributionUtils":
{"Author":"David Scott <d.scott@auckland.ac.nz>","Depends":"R (>= 2.3.0),
RUnit","Description":"This package contains utilities which are of use in
the\npackages I have developed for dealing with distributions.\nCurrently these
packages are GeneralizedHyperbolic,\nVarianceGamma, and SkewHyperbolic and
NormalLaplace. Each of\nthese packages requires DistributionUtils.
Functionality\nincludes sample skewness and kurtosis, log-histogram, tail\nplots,
moments by integration, changing the point about which a\nmoment is calculated,
functions for testing distributions using\ninversion tests and the Massart
inequality. Also includes an\nimplementation of the incomplete Bessel K
function.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"DistributionUtils","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Suggests":"GeneralizedHyperbolic, VarianceGamma,
SkewHyperbolic","Title":"Distribution Utilities","Version":"0.5-1"},"DivE":
{"Author":"Daniel Laydon, Aaron Sim, Charles Bangham, Becca
Asquith","Depends":"deSolve, FME, rgeos, sp, R (>= 2.15.3)","Description":"R-
package DivE contains functions for the DivE estimator (Laydon, D. et al.,
Quantification of HTLV-1 clonality and TCR diversity, PLOS Comput. Biol. 2014). The
DivE estimator is a heuristic approach to estimate the number of classes or the
number of species (species richness) in a population.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"DivE","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Diversity Estimator","Version":"1.0"},"DivMelt":
{"Author":"David A. Swan <dswan@fhcrc.org> with contributions from Craig A\nMagaret
<cmagaret@fhcrc.org> and Matthew M
Cousins\n<matthew.m.cousins@gmail.com>","Depends":"R(>=
2.12.0),tcltk,glmnet","Description":"This package has tools for analyzing DNA
melting data to\ngenerate HRM scores, the DNA diversity measure output of the\nHRM
Diversity Assay. For additional documentation
visit\nhttp:\/\/code.google.com\/p\/divmelt\/.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"DivMelt","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"HRM Diversity Assay Analysis
Tool","Version":"1.0.3"},"DiversityOccupancy":{"Author":"Derek Corcoran [aut,
cre],\nDylan Kesler [aut],\nElisabeth Webb [aut],\nNicole Michel
[ctb]","Depends":"R (>= 3.2.2), MuMIn, unmarked","Description":"Predictions of
alpha diversity are fitted from presence data, first abundance is modeled from
occupancy models and then, several diversity indices are calculated and finally GLM
models are used to predict diversity in different environments and select priority
areas.","Imports":"dplyr, ggplot2, glmulti, qpcR, raster, vegan","License":"GPL-
3","NeedsCompilation":"no","Package":"DiversityOccupancy","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"knitr, rmarkdown,","Title":"Building
Diversity Models from Multiple Species Occupancy
Models","Version":"1.0.2"},"DiversitySampler":{"Author":"Matthew K.
Lau","Description":"There are two functions in this package, which can be
used\ntogether to estimate the Shannon's Diversity index at different\nlevels of
sample size. A Monte-Carlo procedure is used to\nre-sample a given observation at
each level of sampling. The\nexpectation being that the mean of the re-sampling
will\napproach Shannon's diversity index at that sample level.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"DiversitySampler","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Functions for re-sampling a community matrix to
compute\ndiversity indices at different sampling levels","Version":"2.1"},"DnE":
{"Author":"Junyao Chen, Cuiyi He, Boxian Wei","Description":"The DnE package
involves functions to analyse the distribution of a set of given data. The basic
idea of the analysis is chi-squared test. Functions which have the form
as \"is.xxdistribution\" are used to analyse whether the data obeys the
xxdistrbution. If you do not know which distribution to judge, use function
is.dt().","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"DnE","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Distribution and Equation","Version":"2.1.0"},"DoE.base":
{"Author":"Ulrike Groemping [aut, cre],\nBoyko Amarov [ctb],\nHongquan Xu
[ctb]","Depends":"R(>= 2.10.0), grid, conf.design","Description":"Package DoE.base
creates full factorial experimental designs and designs based on orthogonal arrays
for (industrial) experiments. Additionally, it provides utility functions for the
class design, which is also used by other packages for designed
experiments.","Imports":"stats, utils, graphics, vcd, combinat,
2)","NeedsCompilation":"no","Package":"DoE.base","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Full Factorials, Orthogonal Arrays and Base Utilities
for DoE\nPackages","URL":"http:\/\/prof.beuth-
hochschule.de\/groemping\/DoE\/,\nhttp:\/\/prof.beuth-
hochschule.de\/groemping\/","Version":"0.28"},"DoE.wrapper":{"Author":"Ulrike
Groemping [aut, cre],\nLenth Russ [ctb]","Depends":"R(>= 2.13.0), FrF2(>= 1.6-5),
DoE.base(>= 0.23-4), rsm","Description":"This package creates various kinds of
designs for\n(industrial) experiments. It uses, and sometimes enhances,\ndesign
generation routines from other packages.\nSo far, response surface designs from
package rsm, latin hypercube\nsamples from packages lhs and DiceDesign, and\nD-
optimal designs from package AlgDesign have been implemented.","Imports":"lhs,
DiceDesign, AlgDesign(>= 1.1)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"DoE.wrapper","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Wrapper package for design of experiments
functionality","URL":"http:\/\/prof.beuth-
hochschule.de\/groemping\/","Version":"0.8-10"},"Dodge":{"Author":"Jonathan Godfrey
and Raj Govindaraju","Depends":"R (>= 2.14.0)","Description":"Various sampling
plans are able to be compared using evaluations of their OC, AOQ, ATI
etc.","License":"GPL","NeedsCompilation":"no","Package":"Dodge","Repository":"http:
\/\/cran.csiro.au\/src\/contrib","Title":"Functions for Acceptance Sampling Ideas
originated by H.F. Dodge","Version":"0.8"},"Dominance":{"Author":"Konstanze Krueger
[aut],\nKnut Krueger [cre, aut]","Depends":"R (>= 2.14.0)","Description":"The
package can calculate ADI (Average Dominance Index) and can build social network
graphs with dual directions, can build a Music Notation
Graph","Imports":"igraph,chron,gdata","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Dominance","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"ADI (average dominance index), social network graphs
with dual\ndirections, and music notation graph","URL":"http:\/\/www.r-project.org,
http:\/\/www.Konstanze-Krueger.de\/r","Version":"1.0.0"},"DoseFinding":
{"Author":"Bjoern Bornkamp, Jose Pinheiro, Frank Bretz","Depends":"lattice,
mvtnorm, R (>= 2.15.0)","Description":"The DoseFinding package provides functions
for the design and analysis\nof dose-finding experiments (with focus on
pharmaceutical Phase\nII clinical trials). It provides functions for: multiple
contrast\ntests, fitting non-linear dose-response models (using Bayesian and\nnon-
Bayesian estimation), calculating optimal designs and an\nimplementation of the
MCPMod methodology.","License":"GPL-
3","NeedsCompilation":"yes","Package":"DoseFinding","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"numDeriv, Rsolnp, quadprog, parallel,
multcomp","Title":"Planning and Analyzing Dose Finding Experiments","Version":"0.9-
14"},"DoubleCone":{"Author":"Mary C Meyer, Bodhisattva Sen","Depends":"graphics,
grDevices, stats, utils, coneproj, Matrix, MASS","Description":"Performs hypothesis
tests concerning a regression function in a least-squares model, where the null is
a parametric function, and the alternative is the union of large-dimensional convex
polyhedral cones.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"DoubleCone","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Test against parametric regression
function","Version":"1.0"},"DoubleExpSeq":{"Author":"Sean
Ruddy","Description":"Differential exon usage test for RNA-Seq data via an
empirical Bayes shrinkage method for the dispersion parameter the utilizes
inclusion-exclusion data to analyze the propensity to skip an exon across groups.
The input data consists of two matrices where each row represents an exon and the
columns represent the biological samples. The first matrix is the count of the
number of reads expressing the exon for each sample. The second matrix is the count
of the number of reads that either express the exon or explicitly skip the exon
across the samples, a.k.a. the total count matrix. Dividing the two matrices yields
proportions representing the propensity to express the exon versus skipping the
exon for each sample.","Imports":"numDeriv, datasets, grDevices, graphics, stats,
3","NeedsCompilation":"no","Package":"DoubleExpSeq","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Differential Exon Usage Test for RNA-Seq Data via
Empirical\nBayes Shrinkage of the Dispersion Parameter","Version":"1.1"},"Dowd":
{"Author":"Dinesh Acharya <dines.acharya@gmail.com>","Depends":"R (>= 3.0.0),
bootstrap, MASS, forecast","Description":"'Kevin Dowd's' book Measuring Market Risk
is a widely read book\nin the area of risk measurement by students
and\npractitioners alike. As he claims, 'MATLAB' indeed might have been the
most\nsuitable language when he originally wrote the functions, but,\nwith growing
popularity of R it is not entirely\nvalid. As 'Dowd's' code was not intended to be
error free and were mainly\nfor reference,
some functions in this package have inherited those\nerrors. An attempt will be
made in future releases to identify and correct\nthem. 'Dowd's' original code can
be downloaded from www.kevindowd.org\/measuring-market-risk\/.\nIt should be noted
that 'Dowd' offers both\n'MMR2' and 'MMR1' toolboxes. Only 'MMR2' was ported to R.
'MMR2' is more\nrecent version of 'MMR1' toolbox and they both have mostly
similar\nfunction. The toolbox mainly contains different parametric and
non\nparametric methods for measurement of market risk as well as\nbacktesting risk
measurement
methods.","License":"GPL","NeedsCompilation":"no","Package":"Dowd","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Suggests":"PerformanceAnalytics,
testthat","Title":"Functions Ported from 'MMR2' Toolbox Offered in Kevin
Dowd's\nBook Measuring Market Risk","Version":"0.12"},"DrugClust":
{"Author":"Giovanna Maria Dimitri","Description":"An implementation of a Machine
Learning Framework for prediction of new drugs Side Effects.\nFirstly drugs are
clustered with respect to their features description and secondly predictions are
made, according to Bayesian scores.\nMoreover it can perform protein enrichment
considering the proteins clustered together in the first step of the
algorithm.\nThis last tool is of extreme interest for biologist and drug discovery
purposes, given the fact that it can be used either as a validation of the clusters
obtained, as well as for the possible discovery of new interactions between certain
side effects and non targeted pathways.\nClustering of the drugs in the feature
space can be done using K-Means, PAM or K-Seeds (a novel clustering algorithm
proposed by the author).","Imports":"ROCR, MESS, cclust, cluster, e1071, utils,
base","License":"GPL-
2","NeedsCompilation":"no","Package":"DrugClust","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Implementation of a Machine Learning Framework for
Predicting\nDrugs Side Effects","Version":"0.1"},"DunnettTests":{"Author":"FAN
XIA","Depends":"mvtnorm","Description":"For the implementation of the step-down or
step-up Dunnett testing procedures, the package includes R functions to calculate
critical constants and R functions to calculate adjusted P-values of the test
statistics. In addition, the package also contains functions to evaluate testing
powers and hence the necessary sample sizes specially for the classical problem of
comparisons of several treatments with a control.","License":"GPL-
2","NeedsCompilation":"no","Package":"DunnettTests","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Software implementation of step-down and step-up
Dunnett test\nprocedures","Version":"2.0"},"DynClust":{"Author":"Yves Rozenholc
(MAP5, Univ. Paris Descartes), Christophe Pouzat (MAP5, Univ. Paris Descartes) and
Tiffany Lieury (Cerebral Physiology lab, Univ. Paris Descartes)","Depends":"R (>=
2.10), parallel","Description":"DynClust is a two-stage procedure for the denoising
and clustering of stack of noisy images acquired over time. Clustering only assumes
that the data contain an unknown but small number of dynamic features. The method
first denoises the signals using local spatial and full temporal information. The
clustering step uses the previous output to aggregate voxels based on the knowledge
of their spatial neighborhood. Both steps use a single keytool based on the
statistical comparison of the difference of two signals with the null signal. No
assumption is therefore required on the shape of the signals. The data are assumed
to be normally distributed (or at least follow a symmetric distribution) with a
known constant variance. Working pixelwise, the method can be time-consuming
depending on the size of the data-array but harnesses the power of multicore
cpus.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"DynClust","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Denoising and clustering for dynamical image
sequence (2D or\n3D)+T","Version":"3.13"},"DynNom":{"Author":"Amirhossein Jalali,
Alberto Alvarez-Iglesias, Davood Roshan Sangachin, John
Newell","Description":"Demonstrate the results of an lm(), glm() or coxph() model
object as a dynamic nomogram that can be displayed in an 'RStudio' panel or web
browser.","Imports":"ggplot2, stargazer, shiny, compare, survival (>= 2.38-
3)","License":"GPL-
2","NeedsCompilation":"no","Package":"DynNom","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Dynamic Nomograms for Linear, Generalized Linear
and\nProportional Hazard Models","Version":"2.0"},"DynTxRegime":{"Author":"S. T.
Holloway, E. B. Laber, K. A. Linn, B. Zhang, M. Davidian, and A. A.
Tsiatis","Depends":"methods, modelObj","Description":"A comprehensive toolkit for
estimating Dynamic Treatment Regimes. Available methods include Interactive Q-
Learning, Q-Learning, and value-search methods based on Augmented Inverse
Probability Weighted estimators and Inverse Probability Weighted
estimators.","License":"GPL-
2","NeedsCompilation":"no","Package":"DynTxRegime","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"MASS, rpart, nnet, rgenoud","Title":"Methods for
Estimating Dynamic Treatment Regimes","Version":"2.1"},"DynamicDistribution":
{"Author":"Lei ZHANG, Hao JIANG and Chen XUE(Equally contributed, the order
is\ndecided by the time the author joined the project. )","Depends":"R (>=
3.0.2)","Description":"The package is aimed at dynamically visualizing
probability\ndistributions and their moments and all the commonly used
distributions are\nincluded.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"DynamicDistribution","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Title":"Dynamically visualized probability
distributions and their\nmoments","Version":"1.1"},"EBEN":{"Author":"Anhui
Huang","Depends":"R (>= 2.10)","Description":"Provides the Empirical Bayesian
Elastic Net for handling multicollinearity in generalized linear regression models.
As a special case of the 'EBglmnet'\npackage (also available on CRAN), this package
encourages a grouping effects to select relevant variables and estimate the
corresponding non-zero
effects.","License":"GPL","NeedsCompilation":"yes","Package":"EBEN","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Title":"Empirical Bayesian Elastic
Net","Version":"4.6"},"EBMAforecast":{"Author":"Jacob M. Montgomery, Florian M.
Hollenbach, and Michael D. Ward","Depends":"stats, graphics, separationplot, plyr,
methods, Hmisc, abind","Description":"Ensemble BMA for social science
data.","Imports":"Rcpp (>= 0.11.3)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"EBMAforecast","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Ensemble BMA Forecasting","Version":"0.52"},"EBS":
{"Author":"Alice Cleynen","Depends":"R (>= 2.0.0)","Description":"This package
performs an exact Bayesian segmentation on data and returns the probabilities of
breakpoints, an ICL criteria, comparison of change-point location,
etc","Imports":"methods, MASS","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"EBS","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Exact Bayesian Segmentation","Version":"3.0"},"EBglmnet":
{"Author":"Anhui Huang, Dianting Liu","Depends":"R (>=
2.10)","Description":"Provides empirical Bayesian lasso and elastic net algorithms
for variable selection and effect estimation. Key features include sparse variable
selection and effect estimation via generalized linear regression models, high
dimensionality with p>>n, and significance test for nonzero effects. This package
outperforms other popular methods such as lasso and elastic net methods in terms of
power of detection, false discovery rate, and power of detecting grouping
effects.","License":"GPL","NeedsCompilation":"yes","Package":"EBglmnet","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"knitr,
glmnet","Title":"Empirical Bayesian Lasso and Elastic Net Methods for
Generalized\nLinear
Models","URL":"https:\/\/sites.google.com\/site\/anhuihng\/","Version":"4.1"},"ECOS
olveR":{"Author":"Anqi Fu [aut],\nBalasubramanian Narasimhan [aut,
cre]","Description":"R interface to the Embedded COnic Solver (ECOS), an
efficient\nand robust C library for convex problems. Conic and
equality\nconstraints can be specified in addition to integer and\nboolean variable
constraints for mixed-integer problems. This\nR interface is inspired by the python
interface and has\nsimilar calling conventions.","Imports":"Matrix","License":"GPL
(>=
3)","NeedsCompilation":"yes","Package":"ECOSolveR","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr, rmarkdown, testthat","Title":"Embedded Conic
Solver in
R","URL":"https:\/\/github.com\/bnaras\/ECOSolveR","Version":"0.2"},"ECctmc":
{"Author":"Jon Fintzi [aut, cre]","Description":"Draw sample paths for endpoint-
conditioned continuous time Markov chains via modified rejection sampling or
uniformization.","Imports":"Rcpp (>= 0.12.3)","License":"GPL-
3","NeedsCompilation":"yes","Package":"ECctmc","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr, rmarkdown, testthat","Title":"Simulation from
Endpoint-Conditioned Continuous Time
Markov\nChains","URL":"https:\/\/github.com\/fintzij\/ECctmc","Version":"0.1.0"},"E
DFIR":{"Author":"Alex Bond and Robert Robere","Depends":"R (>= 2.15.3), lpSolve,
geometry, vertexenum, MASS","Description":"Functions for reading in data sets of
prey and predator isotopic measurements and producing estimates for discrimination
factors.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"EDFIR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Estimating Discrimination
Factors","Version":"1.0"},"EDISON":{"Author":"Frank Dondelinger, Sophie
Lebre","Depends":"corpcor, MASS","Description":"Package EDISON (Estimation of
Directed Interactions from\nSequences Of Non-homogeneous gene expression)
runs an MCMC\nsimulation to reconstruct networks from time series data, using\na
non-homogeneous, time-varying dynamic Bayesian network.\nNetworks segments and
changepoints are inferred concurrently,\nand information sharing priors provide a
reduction of the\ninference uncertainty.","License":"GPL-
2","NeedsCompilation":"no","Package":"EDISON","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat","Title":"Network Reconstruction and
Changepoint Detection","Version":"1.1.1"},"EDR":{"Author":"Joerg Polzehl
<joerg.polzehl@wias-berlin.de>","Description":"The library contains R-functions to
estimate the effective\ndimension reduction space in multi-index regression
models.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"EDR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"sm, akima","Title":"Estimation of the effective dimension
reduction (EDR) space","URL":"http:\/\/www.wias-berlin.de\/","Version":"0.6-
5.1"},"EEM":{"Author":"Vipavee Trivittayasil","Depends":"R (>=
3.0.0)","Description":"Read raw EEM data and prepares them for further
analysis.","Imports":"tools, reshape2, graphics, colorRamps, utils, readxl,
R.utils,\nsp","License":"GPL-
3","NeedsCompilation":"no","Package":"EEM","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"stats, pls, knitr, testthat","Title":"Read and Preprocess
Fluorescence Excitation-Emission Matrix\n(EEM) Data","Version":"1.0.4"},"EFDR":
{"Author":"Andrew Zammit-Mangion [aut, cre],\nHsin-Cheng Huang [aut]","Depends":"R
(>= 3.0)","Description":"Enhanced False Discovery Rate (EFDR) is a tool to detect
anomalies\nin an image. The image is first transformed into the wavelet domain
in\norder to decorrelate any noise components, following which the coefficients\nat
each resolution are standardised. Statistical tests (in a multiple\nhypothesis
testing setting) are then carried out to find the anomalies. The\npower of EFDR
exceeds that of standard FDR, which would carry out tests on\nevery wavelet
coefficient: EFDR choose which wavelets to test based on a\ncriterion described in
Shen et al. (2002). The package also provides\nelementary tools to interpolate
spatially irregular data onto a grid of the\nrequired size. The work is based on
Shen, X., Huang, H.-C., and Cressie, N.\n'Nonparametric hypothesis testing for a
spatial signal.' Journal of the\nAmerican Statistical Association 97.460 (2002):
1122-1140.","Imports":"Matrix, foreach (>= 1.4.2), doParallel (>= 1.0.8),
waveslim\n(>= 1.7.5), parallel, gstat (>= 1.0-19), tidyr (>= 0.1.0.9000),\ndplyr
(>= 0.3.0.2), sp (>= 1.0-15)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"EFDR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr, ggplot2, RCurl, fields, gridExtra,
animation","Title":"Wavelet-Based Enhanced FDR for Signal Detection in Noisy
Images","URL":"http:\/\/github.com\/andrewzm\/EFDR","Version":"0.1.1"},"EGRET":
{"Author":"Robert Hirsch [aut],\nLaura DeCicco [aut, cre]","Depends":"R (>=
3.0)","Description":"Statistics and graphics for streamflow history,\nwater quality
trends, and the statistical modeling algorithm: Weighted\nRegressions on Time,
Discharge, and Season (WRTDS).","Imports":"dataRetrieval (>= 2.0.1), survival,
fields, lubridate,\nmethods, utils, graphics, stats,
grDevices","License":"CC0","NeedsCompilation":"no","Package":"EGRET","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Suggests":"xtable, knitr, rmarkdown,
extrafont, testthat, rkt","Title":"Exploration and Graphics for RivEr Trends
(EGRET)","URL":"http:\/\/pubs.usgs.gov\/tm\/04\/a10\/,\nhttps:\/\/github.com\/USGS-
R\/EGRET\/wiki","Version":"2.4.3"},"EGRETci":{"Author":"Robert Hirsch [aut],\nLaura
DeCicco [aut, cre]","Depends":"R (>= 3.0)","Description":"Collection of functions
to evaluate uncertainty of results from water quality analysis using the Weighted
Regressions on Time Discharge and Season (WRTDS) method. This package is an add-on
to the EGRET package that performs the WRTDS analysis.","Imports":"EGRET (>=
2.1.1), binom, lubridate, stats,
graphics","License":"CC0","NeedsCompilation":"no","Package":"EGRETci","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"knitr, testthat, foreach,
doParallel, iterators, rmarkdown","Title":"Exploration and Graphics for RivEr
Trends (EGRET) Confidence\nIntervals","URL":"https:\/\/github.com\/USGS-
R\/EGRETci","Version":"1.0.0"},"EIAdata":{"Author":"Matthew Brigida","Depends":"R
(>= 2.11.0), XML, plyr, xts, zoo","Description":"An R wrapper to allow the user to
query categories and Series IDs, and import data, from the EIA's
API.","License":"GPL-
2","NeedsCompilation":"no","Package":"EIAdata","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"R Wrapper for the Energy Information Administration (EIA)
API","Version":"0.0.3"},"EILA":{"Author":"James J. Yang, Jia Li, Anne Buu, and L.
Keoki Williams","Depends":"R (>= 2.10), class,
quantreg","Description":"Implementation of Efficient Inference of Local
Ancestry\nusing fused quantile regression and k-means classifier","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"EILA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Efficient Inference of Local Ancestry","Version":"0.1-
2"},"EL":{"Author":"Edmunds Cers <edmunds.cers@gmail.com>, Janis Valeinis
<valeinis@lu.lv>","Description":"Empirical likelihood (EL) inference for two-sample
problems. The following statistics are included: the difference of two-sample
means, smooth Huber estimators, quantile (qdiff) and cumulative distribution
functions (ddiff), probability-probability (P-P) and quantile-quantile (Q-Q) plots
as well as receiver operating characteristic (ROC) curves.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"EL","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Two-sample Empirical Likelihood","Version":"1.0"},"ELMR":
{"Author":"Alessio Petrozziello [aut, cre]","Depends":"R (>=
3.2.2)","Description":"Training and prediction functions are provided for the
Extreme Learning Machine algorithm (ELM). The ELM use a Single Hidden Layer
Feedforward Neural Network (SLFN) with random generated weights and no gradient-
based backpropagation. The training time is very short and the online version
allows to update the model using small chunk of the training set at each iteration.
The only parameter to tune is the hidden layer size and the learning
function.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"ELMR","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Extreme Machine Learning (ELM)","Version":"1.0"},"ELT":
{"Author":"Julien Tomas, Frederic Planchet, Wassim Youssef","Depends":"R (>=
2.10.0), locfit, lattice, latticeExtra, xlsx","Description":"Build experience life
tables.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ELT","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Experience Life Tables","Version":"1.6"},"ELYP":
{"Author":"Mai Zhou","Depends":"R (>= 2.15.0), survival","Description":"Empirical
likelihood ratio tests for the Yang and Prentice (short\/long term hazards ratio)
models.\nEmpirical likelihood tests within a Cox model, for parameters defined
via\nboth baseline hazard function and regression parameters.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ELYP","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"emplik","Title":"Empirical Likelihood Analysis for the
Cox Model and\nYang-Prentice (2005)
Model","URL":"http:\/\/www.ms.uky.edu\/~mai\/EmpLik.html","Version":"0.7-3"},"EMA":
{"Author":"Nicolas Servant, Eleonore Gravier, Pierre Gestraud, Cecile Laurent,
Caroline Paccard, Anne Biton, Jonas Mandel, Bernard Asselain, Emmanuel Barillot,
Philippe Hupe","Depends":"R (>= 2.10)","Description":"We propose both a clear
analysis strategy and a selection of tools to investigate microarray gene
expression data. The most usual and relevant existing R functions were discussed,
validated and gathered in an easy-to-use R package (EMA) devoted to gene expression
microarray analysis. These functions were improved for ease of use, enhanced
visualisation and better interpretation of results.","Imports":"siggenes, affy,
multtest, survival, xtable, gcrma,\nheatmap.plus, biomaRt, GSA, MASS, FactoMineR,
cluster,\nAnnotationDbi","License":"GPL-
3","NeedsCompilation":"no","Package":"EMA","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"hgu133plus2.db, lumi, vsn, GOstats, GO.db","Title":"Easy
Microarray data Analysis","Version":"1.4.4"},"EMC":{"Author":"Gopi Goswami
<goswami@stat.harvard.edu>","Depends":"R (>= 1.9.0), mvtnorm, MASS,
graphics","Description":"random walk Metropolis, Metropolis Hasting, parallel
tempering, evolutionary Monte Carlo, temperature ladder construction and
placement","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"EMC","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Evolutionary Monte Carlo (EMC)
algorithm","Version":"1.3"},"EMCluster":{"Author":"Wei-Chen Chen [aut,
cre],\nRanjan Maitra [aut],\nVolodymyr Melnykov [ctb]","Depends":"R (>= 3.0.1),
MASS, Matrix","Description":"EM algorithms and several efficient\ninitialization
methods for model-based clustering of finite\nmixture Gaussian distribution with
unstructured dispersion\nin both of unsupervised and semi-supervised
learning.","Enhances":"PPtree, RColorBrewer","License":"Mozilla Public License
2.0","NeedsCompilation":"yes","Package":"EMCluster","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"EM Algorithm for Model-Based Clustering of Finite
Mixture\nGaussian
Distribution","URL":"http:\/\/maitra.public.iastate.edu\/","Version":"0.2-
5"},"EMD":{"Author":"Donghoh Kim and Hee-Seok Oh","Depends":"R (>= 3.0), fields (>=
6.9.1), locfit (>= 1.5-8)","Description":"This package carries out empirical mode
decomposition and Hilbert spectral\nanalysis. For usage of EMD, see Kim and Oh,
2009 (Kim, D and Oh, H.-S.
(2009) EMD: A Package for Empirical\nMode Decomposition and Hilbert Spectrum, The
R Journal, 1, 40-46).","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"EMD","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Empirical Mode Decomposition and Hilbert Spectral
Analysis","URL":"http:\/\/dasan.sejong.ac.kr\/~dhkim\/software_emd.html","Version":
"1.5.7"},"EMMAgeo":{"Author":"Michael Dietze, Elisabeth Dietze","Depends":"R (>=
3.2.1), GPArotation, limSolve, shape, shiny","Description":"End-member modelling
analysis of grain-size data.","License":"GPL-
3","NeedsCompilation":"no","Package":"EMMAgeo","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"End-Member Modelling of Grain-Size
Data","Version":"0.9.4"},"EMMIXcontrasts":{"Author":"Angus Ng, Geoff McLachlan, Kui
Wang.","Description":"For forming contrasts in the mixed effects for mixtures of
linear mixed models fitted to the gene profiles.","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"EMMIXcontrasts","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Contrasts in mixed effects for EMMIX model with
random effects","Version":"1.0.0"},"EMMIXskew":{"Author":"Kui Wang, Angus Ng and
Geoff McLachlan.","Depends":"lattice,mvtnorm, KernSmooth","Description":"EM
algorithm for Mixture of Multivariate Skew Normal\/T
Distributions","License":"GPL","NeedsCompilation":"yes","Package":"EMMIXskew","Repo
sitory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"The EM Algorithm and Skew
Mixture Distribution","Version":"1.0.1"},"EMMIXuskew":{"Author":"S.X. Lee and G.J.
McLachlan","Depends":"MASS, graphics","Description":"Functions to fit finite
mixture of unrestricted multivariate skew t (FM-uMST) model, random sample
generation, discriminant analysis, 2D and 3D contour
plots","License":"GPL","NeedsCompilation":"yes","Package":"EMMIXuskew","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"rgl, stats, grDevices,
KernSmooth","Title":"Fitting Unrestricted Multivariate Skew t Mixture
Models","Version":"0.11-6"},"EMMREML":{"Author":"Deniz Akdemir, Okeke Uche
Godfrey","Depends":"Matrix, stats","Description":"The main functions are 'emmreml',
and 'emmremlMultiKernel'. 'emmreml' solves a mixed model with known covariance
structure using the 'EMMA' algorithm. 'emmremlMultiKernel' is a wrapper for
'emmreml' to handle multiple random components with known covariance structures.
The function 'emmremlMultivariate' solves a multivariate gaussian mixed model with
known covariance structure using the 'ECM' algorithm.","License":"GPL-
2","NeedsCompilation":"no","Package":"EMMREML","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Fitting Mixed Models with Known Covariance
Structures","Version":"3.1"},"EMP":{"Author":"Cristian Bravo, Seppe vanden Broucke
and Thomas Verbraken","Depends":"R (>= 3.0.0)","Description":"Functions for
estimating EMP (Expected Maximum Profit Measure) in Credit Risk Scoring and
Customer Churn Prediction, according to Verbraken et al (2013,
2014).","Imports":"ROCR","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"EMP","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Expected Maximum Profit Classification Performance
Measure","Version":"2.0.1"},"EMSC":{"Author":"Kristian Hovde Liland","Depends":"R
(>= 2.10)","Description":"Background correction of spectral like data. Handles
variations in\nscaling, polynomial baselines and interferents. Parameters for
corrections are stored\nfor further analysis, and spectra are corrected
accordingly.","Imports":"pracma","License":"GPL-
2","NeedsCompilation":"no","Package":"EMSC","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Extended Multiplicative Signal
Correction","Version":"0.7"},"EMT":{"Author":"Uwe Menzel","Description":"The
package provides functions to carry out a\nGoodness-of-fit test for discrete
multivariate data. It is\ntested if a given observation is likely to have occurred
under\nthe assumption of an ab-initio model. A p-value can be\ncalculated using
different distance measures between observed\nand expected frequencies. A Monte
Carlo method is provided to\nmake the package capable of solving high-dimensional
problems.","License":"GPL","NeedsCompilation":"no","Package":"EMT","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"Exact Multinomial Test: Goodness-of-
Fit Test for Discrete\nMultivariate data","Version":"1.1"},"EMVC":{"Author":"H.
Robert Frost and Jason H. Moore","Description":"Contains logic for the data-driven
optimization of annotations via minimization of the entropy of variable group
members over discrete variable clusters.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"EMVC","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Entropy Minimization over Variable Clusters
(EMVC)","Version":"0.1"},"EMbC":{"Author":"Joan Garriga, John R.B. Palmer, Aitana
Oltra, Frederic Bartumeus","Depends":"move","Description":"Unsupervised,
multivariate, clustering algorithm for meaningful binary clustering and taking into
account the uncertainty in the data. A specific constructor for trajectory movement
analysis yields behavioural annotation of the tracks based on estimated local
measures of velocity and turning angle, eventually with solar position covariate as
a daytime indicator.","Imports":"sp, methods, RColorBrewer, mnormt,
maptools","License":"GPL-3 | file
LICENSE","NeedsCompilation":"no","Package":"EMbC","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"rgl, knitr","Title":"Expectation-Maximization Binary
Clustering","URL":"'Expectation-Maximization Binary Clustering for
Behavioural\nAnnotation', (submitted to PLOS ONE)","Version":"1.9.4"},"ENMeval":
{"Author":"Robert Muscarella, Peter J. Galante, Mariano Soley-Guardia, Robert A.
Boria, Jamie M. Kass, Maria Uriarte and Robert P. Anderson","Depends":"dismo,
methods, rJava (>= 0.5-0), parallel, R (>= 2.10)","Description":"Automatically
partitions data into evaluation bins, executes ecological niche models across a
range of settings, and calculates a variety of evaluation statistics. Current
version only implements ENMs with Maxent (Phillips et al.
2006).","Imports":"doParallel, foreach, utils, graphics, stats, grDevices,
raster","License":"GPL","NeedsCompilation":"no","Package":"ENMeval","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Title":"Automated Runs and Evaluations of
Ecological Niche Models","Version":"0.2.1"},"ENiRG":{"Author":"Fernando Canovas,
Chiara Magliozzi, Jose Antonio Palazon-Ferrando, Frederico Mestre, Mercedes
Gonzalez-Wanguemert","Depends":"ade4, raster, R.utils, sp,
spgrass6","Description":"The package allows to perform the Ecological Niche Factor
Analysis, calculate habitat suitability maps and classify the habitat in
suitability classes. Computations are executed in a throw-away GRASS environment
from R in order to be able to perform analysis with large data
sets.","Imports":"gdata, fgui, miniGUI, tcltk","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ENiRG","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Ecological Niche in R and GRASS","Version":"0.1"},"ENmisc":
{"Author":"Erich Neuwirth [aut, cre]","Depends":"Hmisc, vcd (>= 1.2-11),
RColorBrewer","Description":"The ENmisc package contains utility function for
different\npurposes: mtapply and mlapply (multivariate version of tapply\nand
lapply), wtd.boxplot (a boxplot with weights), and a visual\ninterface to
restructuring mosaic plots.","License":"GPL-
2","NeedsCompilation":"no","Package":"ENmisc","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"Rcmdr, gWidgets (>= 0.0-45), gWidgetstcltk (>= 0.0-
44)","Title":"Neuwirth miscellaneous","Version":"1.2-7"},"EPGLM":{"Author":"James
Ridgway","Depends":"Rcpp, MASS","Description":"The main functions compute the
expectation propagation approximation of a Bayesian probit\/logit models with
Gaussian prior. More information can be found in Chopin and Ridgway (2015). More
models and priors should follow.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"EPGLM","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Gaussian Approximation of Bayesian Binary Regression
Models","Version":"1.1.1"},"EQL":{"Author":"Thorn Thaler
<thorn.thaler@thothal.com>","Depends":"ttutils(>= 0.1-
0)","Description":"Computation of the EQL for a given family of
variance\nfunctions, Saddlepoint-approximations and related auxiliary\nfunctions
(e.g. Hermite polynomials)","Imports":"lattice(>= 0.17-17)","License":"GPL-
2","NeedsCompilation":"no","Package":"EQL","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Extended-Quasi-Likelihood-Function (EQL)","Version":"1.0-
0"},"ERP":{"Author":"David Causeur (Agrocampus, Rennes, France) and Ching-Fan Sheu
(National Cheng-Kung University, Tainan, Taiwan)","Description":"The functions
provided in the package ERP are designed for the significance analysis of ERP data
in a linear model framework. The possible procedures are either the collection of
FDR or FWER controlling methods available in the generic function p.adjust, the
same collection combined with a factor modeling of the time dependence among tests
(see Sheu, Perthame, Lee and Causeur, 2016) and the Guthrie and Buchwald (1991)
test.","Imports":"fdrtool,mnormt","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ERP","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Significance Analysis of Event-Related Potentials
Data","Version":"1.1"},"ES":{"Author":"Meng Hwee Victor Ong, Sanjay
Chaudhuri","Description":"Implementation of the Edge Selection
Algorithm","License":"GPL-
2","NeedsCompilation":"no","Package":"ES","Repository":"http:\/\/cran.csiro.au\/src
\/contrib","Title":"Edge Selection","Version":"1.0"},"ESEA":{"Author":"Junwei Han,
Xinrui Shi, Chunquan Li","Depends":"R (>=
2.10),igraph,XML,parmigene","Description":"The package can identify the
dysregulated canonical
pathways by investigating the changes of biological relationships of pathways in
the context of gene expression data. (1) The ESEA package constructs a background
set of edges by extracting pathway structure (e.g. interaction, regulation,
modification, and binding etc.) from the seven public databases (KEGG; Reactome;
Biocarta; NCI; SPIKE; HumanCyc; Panther) and the edge sets of pathways for each of
the above databases. (2) The ESEA package can can quantify the change of
correlation between genes for each edge based on gene expression data with cases
and controls. (3) The ESEA package uses the weighted Kolmogorov-Smirnov statistic
to calculate an edge enrichment score (EES), which reflects the degree to which a
given pathway is associated the specific phenotype. (4) The ESEA package can
provide the visualization of the results.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ESEA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"Matrix,graph","Title":"ESEA: Discovering the Dysregulated
Pathways based on Edge Set\nEnrichment Analysis","Version":"1.0"},"ESG":
{"Author":"Jean-Charles Croix, Thierry Moudiki, Frédéric Planchet,
Wassim\nYoussef","Depends":"methods","Description":"The package presents
a \"Scenarios\" class containing\ngeneral parameters, risk parameters and
projection results.\nRisk parameters are gathered together into a
ParamsScenarios\nsub-object. The general process for using this package is to\nset
all needed parameters in a Scenarios object, use the\ncustomPathsGeneration method
to proceed to the projection, then\nuse xxx_PriceDistribution() methods to get
asset prices.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ESG","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"ESG - A package for asset
projection","Version":"0.1"},"ESGtoolkit":{"Author":"Jean-Charles Croix, Thierry
Moudiki, Frederic Planchet, Wassim Youssef","Depends":"CDVine, ggplot2, gridExtra,
reshape2, ycinterextra","Description":"Toolkit for Monte Carlo simulations of
financial assets and\ninterest rates models, involved in an Economic Scenario
Generator (ESG).\nThe underlying simulation loops have been implemented in C+
+.","Imports":"Rcpp(>= 0.11.0)","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"ESGtoolkit","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr, fOptions","Title":"Toolkit for the
simulation of financial assets and interest\nrates
models","Version":"0.1"},"ESKNN":{"Author":"Asma Gul, Aris Perperoglou, Zardad
Khan, Osama Mahmoud, Werner Adler, Miftahuddin Miftahuddin, and Berthold
Lausen","Description":"Functions for classification and group membership
probability estimation are given.\nThe issue of non-informative features in the
data is addressed by utilizing the ensemble method.\nA few optimal models are
selected in the ensemble from an initially large set of base k-nearest neighbours
(KNN) models, generated on subset of features from the training data.\nA two stage
assessment is applied in selection of optimal models for the ensemble in the
training function.\nThe prediction functions for classification and class
membership probability estimation returns class outcomes and class membership
probability estimates for the test data.\nThe package includes measure of
classification error and brier score, for classification and probability estimation
tasks respectively.","Imports":"caret,stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ESKNN","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Ensemble of Subset of K-Nearest Neighbours Classifiers
for\nClassification and Class Membership Probability
Estimation","Version":"1.0"},"ETAS":{"Author":"Abdollah Jalilian [aut, cre],
Jiancang Zhuang [ctb]","Depends":"R (>= 3.1.0), maps","Description":"Fitting the
space-time Epidemic Type\nAftershock Sequence (ETAS) model to earthquake
catalogs\nusing a stochastic declustering approach.\nThe ETAS model is a spatio-
temporal marked point process\nmodel and a special case of the Hawcks process.\nThe
package is based on Fortran code by Jiancang Zhuang\n(available at
http:\/\/bemlar.ism.ac.jp\/zhuang\/software.html),\nwhich is translated into C such
that it can be called from R.","Imports":"spatstat","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ETAS","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Modeling Earthquake Data Using ETAS
Model","Version":"0.2"},"ETC":{"Author":"Mario Hasler","Description":"The package
allows selecting those treatments of a one-way layout\nbeing equivalent to a
control. Bonferroni adjusted \"two one-sided t-tests\"\n(TOST) and related
simultaneous confidence intervals are given for both\ndifferences or ratios of
means of normally distributed data. For the case of\nequal variances and balanced
sample sizes for the treatment groups, the\nsingle-step procedure of Bofinger and
Bofinger (1995) can be chosen. For\nnon-normal data, the Wilcoxon test is
applied.","Imports":"mvtnorm","License":"GPL","NeedsCompilation":"no","Package":"ET
C","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"SimComp,
multcomp, mratios","Title":"Equivalence to control","Version":"1.3"},"ETLUtils":
{"Author":"Jan Wijffels","Depends":"ff (>= 2.2-13)","Description":"Provides
functions to facilitate the use of the 'ff' package in\ninteraction with big data
in 'SQL' databases (e.g. in\n'Oracle', 'MySQL', 'PostgreSQL', 'Hive') by allowing
easy importing directly into 'ffdf'\nobjects using 'DBI', 'RODBC' and 'RJDBC'. Also
contains some basic utility\nfunctions to do fast left outer join merging based on
'match', factorisation of data and a basic\nfunction for re-coding
vectors.","Imports":"bit (>= 1.1-12)","License":"GPL-
2","NeedsCompilation":"no","Package":"ETLUtils","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"RSQLite, zoo, DBI, RODBC, RJDBC","Title":"Utility
Functions to Execute Standard Extract\/Transform\/Load\nOperations (using Package
'ff') on Large Data","URL":"https:\/\/github.com\/jwijffels\/ETLUtils,
http:\/\/www.bnosac.be","Version":"1.3"},"EW":
{"Author":"H.R.Law","Description":"Edgeworth Expansion
calculation.","License":"GPL","NeedsCompilation":"no","Package":"EW","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Title":"Edgeworth
Expansion","Version":"1.1"},"EWGoF":{"Author":"Meryam Krit","Description":"An
implementation of a large number of the goodness-of-fit tests for the exponential
and Weibull distributions classified into families: the tests based on the
empirical distribution function, the tests based on the probability plot, the tests
based on the normalized spacings, the tests based on the Laplace transform and the
likelihood-based tests.","Imports":"Rcpp (>= 0.10.3)","License":"GPL (>=
2.0)","NeedsCompilation":"yes","Package":"EWGoF","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Goodness-of-Fit Tests for the Exponential and Two-
Parameter\nWeibull Distributions","Version":"2.1"},"EasyABC":{"Author":"Franck
Jabot, Thierry Faure, Nicolas Dumoulin, Carlo Albert.","Depends":"R (>= 2.14.0),
abc","Description":"Enables launching a series of simulations of a computer code
from the R session, and to retrieve the simulation outputs in an appropriate format
for post-processing treatments. Five sequential sampling schemes and three coupled-
to-MCMC schemes are implemented.","Imports":"pls, mnormt, MASS, parallel, lhs,
tensorA","License":"GPL-
3","NeedsCompilation":"yes","Package":"EasyABC","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Efficient Approximate Bayesian Computation Sampling
Schemes","URL":"http:\/\/easyabc.r-forge.r-
project.org\/","Version":"1.5"},"EasyHTMLReport":{"Author":"Yohei Sato
<yohei0511@gmail.com>","Depends":"base64enc,markdown,knitr(>=
0.7),","Description":"It is a package that can be used to send HTML reports
easily.","Imports":"ggplot2,scales,xtable,reshape2","License":"GPL-
2","NeedsCompilation":"no","Package":"EasyHTMLReport","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"EasyHTMLReport","Version":"0.1.1"},"EasyMARK":
{"Author":"John Waller","Depends":"R (>= 3.0.2)","Description":"Contains a few
utility functions for working with capture-history data, a function for simulating
capture-history data, and a function to fit this data, using a Gibbs
sampler.","Imports":"MASS, stringr, rjags, coda, foreach,
doParallel,random,\nparallel","License":"GPL-
2","NeedsCompilation":"no","Package":"EasyMARK","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Utility functions for working with mark-recapture
data","Version":"1.0"},"EasyStrata":{"Author":"Thomas
Winkler","Depends":"methods,Cairo,plotrix","Description":"This is a pipelining tool
that facilitates\nevaluation and visualisation of stratified genome-
wide\nassociation meta-analyses (GWAMAs) results data. It\nprovides (i) statistical
methods to test and to account\nfor between-strata difference and to clump genome-
wide\nresults into independent loci and (ii) extended graphical\nfeatures (e.g.,
Manhattan, Miami and QQ plots) tailored\nfor stratified GWAMA
results.","License":"GPL-
3","NeedsCompilation":"no","Package":"EasyStrata","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Evaluation of stratified genome-wide association meta-
analysis\nresults","Version":"8.6"},"EbayesThresh":{"Author":"Bernard W.
Silverman","Description":"This package carries out Empirical Bayes
thresholding\nusing the methods developed by I. M. Johnstone and B. W.\nSilverman.
The basic problem is to estimate a mean vector given\na vector of observations of
the mean vector plus white noise,\ntaking advantage of possible sparsity in the
mean vector.\nWithin a Bayesian formulation, the elements of the mean vector\nare
modelled as having, independently, a distribution that is a\nmixture of an atom of
probability at zero and a suitable\nheavy-tailed distribution. The
mixing parameter can be\nestimated by a marginal maximum likelihood approach.
This\nleads to an adaptive thresholding approach on the original\ndata. Extensions
of the basic method, in particular to wavelet\nthresholding, are also implemented
within the package.","Enhances":"wavethresh","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"EbayesThresh","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Empirical Bayes Thresholding and Related
Methods","Version":"1.3.2"},"Ecdat":{"Author":"Yves Croissant
<yves.croissant@let.ish-lyon.cnrs.fr>","Depends":"R (>= 2.10),
Ecfun","Description":"Data sets for econometrics.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Ecdat","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"car, systemfit, sem, lmtest, sandwich, gdata, RCurl,
XML,\ntis, knitr","Title":"Data Sets for Econometrics","URL":"http:\/\/www.r-
project.org","Version":"0.2-9"},"Ecfun":{"Author":"Spencer Graves
<spencer.graves@effectivedefense.org>","Depends":"R (>=
3.0.1)","Description":"Functions to update datasets in Ecdat and to
create,\nmanipulate, plot and analyze those and similar datasets.","Imports":"fda,
gdata, RCurl, XML, tis, jpeg, MASS, TeachingDemos,\nstringi,
2)","NeedsCompilation":"no","Package":"Ecfun","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"BMA, car, DescTools, Ecdat, maps, grid, gridBase,
pryr","Title":"Functions for Ecdat","URL":"http:\/\/www.r-
project.org","Version":"0.1-6"},"EcoGenetics":{"Author":"Leandro Roser, Juan
Vilardi, Beatriz Saidman and Laura Ferreyra","Depends":"R (>= 3.0),
methods","Description":"Geostatistical tools for analyzing spatial patterns
in\npopulation biology. Easy integration of information from multiple sources\nwith
\"ecogen\" objects.","Imports":"ggplot2, party, raster, reshape2, rgdal, rkt, SoDA,
sp,","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"EcoGenetics","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"adegenet","Title":"Spatial Analysis of Phenotypic,
Genotypic and Environmental
Data","URL":"https:\/\/github.com\/cran\/EcoGenetics","Version":"1.2.0-
2"},"EcoHydRology":{"Author":"Fuka DR, Walter MT, Archibald JA, Steenhuis TS, and
Easton ZM","Depends":"R (>= 2.10), operators, topmodel, DEoptim,
XML","Description":"This package provides a flexible foundation for
scientists,\nengineers, and policy makers to base teaching exercises as well as
for\nmore applied use to model complex eco-hydrological
interactions.","License":"GPL-
2","NeedsCompilation":"no","Package":"EcoHydRology","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"A community modeling foundation for Eco-
Hydrology","Version":"0.4.12"},"EcoSimR":{"Author":"Nick Gotelli [aut],\nEdmund
Hart [aut, cre],\nAaron Ellison [aut]","Depends":"MASS","Description":"Given a site
by species interaction matrix, users can make inferences about species interactions
by performance hypothesis comparing test statistics against a null distribution.
The current package provides algorithms and metrics for niche-overlap, body size
ratios and species co-occurrence. Users can also integrate their own algorithms and
metrics within these frameworks or completely novel null models. Detailed
explanations about the underlying assumptions of null model analysis in ecology can
be found at http:\/\/ecosimr.org.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"EcoSimR","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat, knitr","Title":"Null Model Analysis for
Ecological Data","Version":"0.1.0"},"EcoTroph":{"Author":"J. Guitton, M. Colleter,
P. Gatti, and D. Gascuel","Depends":"XML","Description":"EcoTroph is an approach
and software for modelling marine and freshwater ecosystems. It is articulated
entirely around trophic levels. EcoTroph's key displays are bivariate plots, with
trophic levels as the abscissa, and biomass flows or related quantities as
ordinates. Thus, trophic ecosystem functioning can be modelled as a continuous flow
of biomass surging up the food web, from lower to higher trophic levels, due to
predation and ontogenic processes. Such an approach, wherein species as such
disappear, may be viewed as the ultimate stage in the use of the trophic level
metric for ecosystem modelling, providing a simplified but potentially useful
caricature of ecosystem functioning and impacts of fishing. This version contains
catch trophic spectrum analysis (CTSA) function and corrected versions of the
mf.diagnosis and create.ETmain
functions.","License":"GPL","NeedsCompilation":"no","Package":"EcoTroph","Repositor
y":"http:\/\/cran.csiro.au\/src\/contrib","Title":"EcoTroph R
package","URL":"http:\/\/sirs.agrocampus-
ouest.fr\/EcoTroph\/","Version":"1.6"},"EcoVirtual":{"Author":"Alexandre Adalardo
de Oliveira and Paulo Inacio Prado
<ecovirtualpackage@gmail.com>","Depends":"tcltk","Description":"A package for
simulations of classical ecological models as a learning resource.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"EcoVirtual","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Simulation of Ecological
Models","URL":"http\/\/ecovirtual.ib.usp.br","Version":"0.1"},"EditImputeCont":
{"Author":"Quanli Wang, Hang J. Kim, Jerome P. Reiter, Lawrence H. Cox and Alan F.
Karr","Depends":"Rcpp (>= 0.11.5), methods, editrules, graphics,
utils","Description":"An integrated editing and imputation method for continuous
microdata under linear constraints is implemented. It relies on a Bayesian
nonparametric hierarchical modeling approach in which the joint distribution of the
data is estimated by a flexible joint probability model. The generated edit-imputed
data are guaranteed to satisfy all imposed edit rules, whose types include ratio
edits, balance edits and range restrictions.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"EditImputeCont","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Simultaneous Edit-Imputation for Continuous
Microdata","Version":"1.0.1"},"EffectLiteR":{"Author":"Axel Mayer [aut, cre],\nLisa
Dietzfelbinger [ctb]","Depends":"R (>= 3.1.0), lavaan (>= 0.5-
19)","Description":"Use structural equation modeling to estimate average
and\nconditional effects of a treatment variable on an outcome variable, taking
into\naccount multiple continuous and categorical covariates.","Imports":"methods,
shiny (>= 0.11), foreign, ggplot2, nnet, survey,\nlavaan.survey,
2)","NeedsCompilation":"no","Package":"EffectLiteR","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Average and Conditional
Effects","URL":"https:\/\/github.com\/amayer2010\/EffectLiteR","Version":"0.4-
2"},"EffectStars":{"Author":"Gunther
Schauberger","Depends":"VGAM","Description":"Provides functions to visualize
regression models with categorical response. The effects of the variables are
plotted with star plots in order to allow for an optical impression of the fitted
2","NeedsCompilation":"no","Package":"EffectStars","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Visualization of Categorical Response
Models","Version":"1.6"},"EffectTreat":{"Author":"Wim Van der Elst, Ariel Alonso &
Geert Molenberghs","Description":"In personalized medicine, one wants to know, for
a given patient and his or her outcome for a predictor (pre-treatment variable),
how likely it is that a treatment will be more beneficial than an alternative
treatment. This package allows for the quantification of the predictive causal
association (i.e., the association between the predictor variable and the
individual causal effect of the treatment) and related metrics. Part of this
software has been developed using funding provided from the European Union's 7th
Framework Programme for research, technological development and demonstration under
Grant Agreement no 602552.","Imports":"methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"EffectTreat","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Prediction of Therapeutic
Success","Version":"0.2"},"EffectsRelBaseline":{"Author":"Peter N. Steinmetz
<PeterNSteinmetz@steinmetz.org>","Description":"Functions to test for changes of a
response to a stimulus grouping relative\nto a background or baseline
response.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"EffectsRelBaseline","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Suggests":"boot","Title":"Test changes of a grouped
response relative to baseline","Version":"0.5"},"ElemStatLearn":{"Author":"Material
from the book's webpage, R port and packaging by\nKjetil B Halvorsen","Depends":"R
(>= 2.10.0), stats","Description":"Useful when reading the book above mentioned, in
the\ndocumentation referred to as `the book'.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ElemStatLearn","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"gam, splines, MASS, class, leaps, mda, lasso2,
lars, boot,\nprim, earth","Title":"Data Sets, Functions and Examples from the Book:
\"The Elements\nof Statistical Learning, Data Mining, Inference, and\nPrediction\"
by Trevor Hastie, Robert Tibshirani and Jerome\nFriedman","URL":"http:\/\/www-
stat.stanford.edu\/~tibs\/ElemStatLearn\/","Version":"2015.6.26"},"EloChoice":
{"Author":"Christof Neumann","Description":"Allows calculating global scores for
characteristics of visual stimuli. Stimuli are presented as sequence of pairwise
comparisons ('contests'), during each of which a rater expresses preference for
one stimulus over the other. The algorithm for calculating global scores is based
on Elo rating, which updates individual scores after each single pairwise contest.
Elo rating is widely used to rank chess players according to their performance. Its
core feature is that dyadic contests with expected outcomes lead to smaller changes
of participants'
scores than outcomes that were unexpected. As such, Elo rating is an efficient
tool to rate individual stimuli when a large number of such stimuli are paired
against each other in the context of experiments where the goal is to rank stimuli
according to some characteristic of interest.","Imports":"Rcpp","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"EloChoice","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"xtable","Title":"Preference Rating for Visual
Stimuli Based on Elo Ratings","Version":"0.29"},"EloRating":{"Author":"Christof
Neumann & Lars Kulik","Depends":"zoo","Description":"Calculate Elo ratings as means
to describe animal dominance hierarchies","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"EloRating","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Animal Dominance Hierarchies by Elo
Rating","Version":"0.43"},"ElstonStewart":{"Author":"Herve
Perdry","Depends":"kinship2, parallel, digest","Description":"Flexible
implementation of Elston-Stewart algorithm","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ElstonStewart","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Elston-Stewart
Algorithm","Version":"1.1"},"EmpiricalCalibration":{"Author":"Martijn Schuemie,
Marc Suchard","Description":"Routines for performing empirical calibration of
observational\nstudy estimates. By using a set of negative control hypotheses we
can\nestimate the empirical null distribution of a particular observational\nstudy
setup. This empirical null distribution can be used to compute a\ncalibrated p-
value, which reflects the probability of observing an\nestimated effect size when
the null hypothesis is true taking both random\nand systematic error into
account.","Imports":"ggplot2 (>= 2.0.0), MASS","License":"Apache License
2.0","NeedsCompilation":"no","Package":"EmpiricalCalibration","Repository":"http:\/
\/cran.csiro.au\/src\/contrib","Suggests":"knitr, rmarkdown","Title":"Routines for
Performing Empirical Calibration of Observational\nStudy
Estimates","URL":"https:\/\/github.com\/OHDSI\/EmpiricalCalibration","Version":"1.1
.0"},"EnQuireR":{"Author":"Fournier Gwenaelle, Cadoret Marine, Fournier Olivier, Le
Poder\nFrancois, Bouche Jerome, Le Sebastien","Depends":"FactoMineR, SensoMineR,
Rcmdr, MASS","Description":"A package dedicated to questionnaires","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"EnQuireR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"A package dedicated to
questionnaires","Version":"0.10"},"EngrExpt":{"Author":"R port by Douglas Bates
<bates@stat.wisc.edu> and Karen A.F.\nCopeland
<karen@boulderstats.com>","Depends":"R (>= 2.9.0), lattice","Description":"Datasets
from Nelson, Coffin and Copeland \"Introductory\nStatistics for Engineering
Experimentation\" (Elsevier, 2003)\nwith sample code.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"EngrExpt","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Data sets from \"Introductory Statistics for
Engineering\nExperimentation\"","Version":"0.1-8"},"EnsembleBase":
{"Author":"Alireza S. Mahani, Mansour T.A.
Sharabiani","Depends":"kknn,methods","Description":"Extensible S4 classes and
methods for batch training of regression and classification algorithms such as
Random Forest, Gradient Boosting Machine, Neural Network, Support Vector Machines,
K-Nearest Neighbors, Penalized Regression (L1\/L2), and Bayesian Additive
Regression Trees. These algorithms constitute a set of 'base learners', which can
subsequently be combined together to form ensemble predictions. This package
provides cross-validation wrappers to allow for downstream application of ensemble
integration techniques, including best-error selection. All base learner estimation
objects are retained, allowing for repeated prediction calls without the need for
re-training. For large problems, an option is provided to save estimation objects
to disk, along with prediction methods that utilize these objects. This allows
users to train and predict with large ensembles of base learners without being
constrained by system
RAM.","Imports":"\ngbm,nnet,e1071,randomForest,doParallel,foreach,glmnet,bartMachin
e","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"EnsembleBase","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Extensible Package for Parallel, Batch Training of
Base Learners\nfor Ensemble Modeling","Version":"1.0.1"},"EnsembleCV":
{"Author":"Mansour T.A. Sharabiani, Alireza S.
Mahani","Depends":"EnsembleBase","Description":"This package extends the base
classes and methods of EnsembleBase package for cross-validation-based integration
of base learners. Default implementation calculates average of repeated CV errors,
and selects the base learner \/ configuration with minimum average error. The
package takes advantage of the file method provided in EnsembleBase package for
writing estimation objects to disk in order to circumvent RAM bottleneck. Special
save and load methods are provided to allow estimation objects to be saved to
permanent files on disk, and to be loaded again into temporary files in a later R
session. The package can be extended, e.g. by adding variants of the current
implementation.","Imports":"parallel,methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"EnsembleCV","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Extensible Package for Cross-Validation-Based
Integration of\nBase Learners","Version":"0.7.1"},"EnsemblePCReg":
{"Author":"Mansour T.A. Sharabiani, Alireza S.
Mahani","Depends":"EnsembleBase","Description":"Extends the base classes and
methods of EnsembleBase package for Principal-Components-Regression-based (PCR)
integration of base learners. Default implementation uses cross-validation error to
choose the optimal number of PC components for the final predictor. The package
takes advantage of the file method provided in EnsembleBase package for writing
estimation objects to disk in order to circumvent RAM bottleneck. Special save and
load methods are provided to allow estimation objects to be saved to permanent
files on disk, and to be loaded again into temporary files in a later R session.
Users and developers can extend the package by extending the generic methods and
classes provided in EnsembleBase package as well as this
package.","Imports":"parallel,methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"EnsemblePCReg","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"R.rsp","Title":"Extensible Package for
Principal-Component-Regression-Based\nIntegration of Base
Learners","Version":"1.0.0"},"EnsemblePenReg":{"Author":"Mansour T.A. Sharabiani,
Alireza S. Mahani","Depends":"EnsembleBase","Description":"Extending the base
classes and methods of EnsembleBase package for Penalized-Regression-based (Ridge
and Lasso) integration of base learners. Default implementation uses cross-
validation error to choose the optimal lambda (shrinkage parameter) for the final
predictor. The package takes advantage of the file method provided in EnsembleBase
package for writing estimation objects to disk in order to circumvent RAM
bottleneck. Special save and load methods are provided to allow estimation objects
to be saved to permanent files on disk, and to be loaded again into temporary files
in a later R session. Users and developers can extend the package by extending the
generic methods and classes provided in EnsembleBase package as well as this
package.","Imports":"parallel,methods,glmnet","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"EnsemblePenReg","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Extensible Classes and Methods for Penalized-
Regression-based\nIntegration of Base
Learners","Version":"0.6"},"EntropyEstimation":{"Author":"Lijuan Cao
<lcao@jcsu.edu> and Michael Grabchak <mgrabcha@uncc.edu>","Description":"Contains
methods for the estimation of Shannon's entropy, variants of Renyi's entropy,
mutual information, Kullback-Leibler divergence, and generalized Simpson's indices.
The estimators used have a bias that decays exponentially fast.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"EntropyEstimation","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Title":"Estimation of Entropy and Related
Quantities","Version":"1.2"},"EntropyExplorer":{"Author":"Kai Wang, Charles A.
Phillips, Arnold M. Saxton and Michael A. Langston","Depends":"R (>=
3.0)","Description":"Rows of two matrices are compared for Shannon
entropy,\ncoefficient of variation, and expression. P-values can be requested for
all metrics.","License":"GPL-
3","NeedsCompilation":"no","Package":"EntropyExplorer","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Tools for Exploring Differential Shannon Entropy,
Differential\nCoefficient of Variation and Differential
Expression","Version":"1.1"},"EnvNicheR":{"Author":"Cástor Guisande
González","Depends":"R (>= 3.1.1), IDPmisc, stats, utils, graphics,
grDevices","Description":"A plot overlying the niche of multiple species is
obtained, to determine the niche conditions which favor a higher species richness,
to create boxplots with the range of environmental variables of the species, to
obtain a list of species in an area of the niche selected by the user and to
estimate niche overlap among the species. It uses an output file of the software
ModestR, which is available at the web site www.ipez.es\/ModestR.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"EnvNicheR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Niche Estimation","Version":"1.3"},"EnvStats":
{"Author":"Steven P. Millard <EnvStats@ProbStatInfo.com>","Depends":"R (>=
3.0.1)","Description":"Graphical and statistical analyses of environmental data,
with\nfocus on analyzing chemical concentrations and physical parameters, usually
in\nthe context of mandated environmental
monitoring. Major environmental\nstatistical methods found in the literature and
regulatory guidance documents,\nwith extensive help that explains what these
methods do, how to use them,\nand where to find them in the literature. Numerous
built-in data sets from\nregulatory guidance documents and environmental statistics
literature. Includes\nscripts reproducing analyses presented in the
book \"EnvStats: An R Package for\nEnvironmental Statistics\" (Millard, 2013,
Springer).","Imports":"MASS","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"EnvStats","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"lattice, qcc, sp, boot","Title":"Package for
Environmental Statistics, Including US EPA
Guidance","URL":"http:\/\/www.probstatinfo.com","Version":"2.0.2"},"EnviroStat":
{"Author":"Nhu Le, Jim Zidek, Rick White, and Davor Cubranic, with\nFortran code
for Sampson-Guttorp estimation authored by Paul D.\nSampson, Peter Guttorp, Wendy
Meiring, and Catherine Hurley, and\nRunge-Kutta-Fehlberg method implementation by
H.A. Watts and L.F. Shampine.","Description":"Functions and datasets to support the
book by Nhu D Le and James V Zidek, Springer
(2006).","Imports":"MASS","License":"AGPL (>=
3)","NeedsCompilation":"yes","Package":"EnviroStat","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Statistical Analysis of Environmental Space-Time
Processes","Version":"0.4-2"},"Epi":{"Author":"Bendix Carstensen [aut,
cre],\nMartyn Plummer [aut],\nEsa Laara [ctb],\nMichael Hills [ctb]","Depends":"R
(>= 3.0.0), utils","Description":"Functions for demographic and epidemiological
analysis in\nthe Lexis diagram, i.e. register and cohort follow-up data,
in\nparticular representation, manipulation and simulation of multistate\ndata -
the Lexis suite of functions, which includes interfaces to\nmstate, etm and cmprsk
packages.\nAlso contains functions for Age-Period-Cohort modeling and a\nfunction
for interval censored data and some useful functions for\ntabulation and plotting,
as well some epidemiological datasets.","Imports":"cmprsk, etm, splines, MASS,
survival, plyr","License":"GPL-
2","NeedsCompilation":"yes","Package":"Epi","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"mstate, nlme, lme4","Title":"A Package for Statistical
Analysis in
Epidemiology","URL":"http:\/\/BendixCarstensen.com\/Epi\/","Version":"2.0"},"EpiBay
es":{"Author":"Matthew Branan, Marta Remmenga, Lori Gustafson, Jennifer
Hoeting","Depends":"R (>= 3.0.0)","Description":"Hierarchical Bayesian models for
use in disease\nfreedom and disease prevalence studies, designed\nwith
epidemiological applications in mind. The models\nthemselves are in the spirit of
those presented in Branscum\net al. (2006) (see package documentation for
full\nreference). The helper functions and methods were designed\nto make
implementation and processing of the complex model\noutput relatively simple in
application.","Imports":"epiR, compiler, shape, scales, coda","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"EpiBayes","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr","Title":"Implements Hierarchical Bayesian
Models for Epidemiological\nApplications","Version":"0.1.2"},"EpiContactTrace":
{"Author":"Maria Noremark [aut],\nStefan Widgren [aut, cre]","Depends":"R(>=
3.0.2)","Description":"Routines for epidemiological contact tracing\nand
visualisation of network of contacts.","Imports":"graphics, methods, tools,
utils","License":"EUPL","NeedsCompilation":"yes","Package":"EpiContactTrace","Repos
itory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Epidemiological Tool for
Contact
Tracing","URL":"https:\/\/github.com\/stewid\/EpiContactTrace","Version":"0.9.1"},"
EpiDynamics":{"Author":"Oswaldo Santos Baquero [aut, cre],\nFernando Silveira
Marques [aut]","Depends":"R (>= 3.2.2)","Description":"Mathematical models of
infectious diseases in humans and animals.\nBoth, deterministic and stochastic
models can be simulated and plotted.","Imports":"deSolve, reshape2, ggplot2,
grid","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"EpiDynamics","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Dynamic Models in
Epidemiology","URL":"https:\/\/github.com\/oswaldosantos\/EpiDynamics","Version":"0
.3.0"},"EpiEstim":{"Author":"Anne Cori <a.cori@imperial.ac.uk>","Description":"This
package provides tools to quantify transmissibility\nthroughout an epidemic from
the analysis of time series of\nincidence.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"EpiEstim","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"EpiEstim: a package to estimate time varying
reproduction\nnumbers from epidemic curves","Version":"1.1-2"},"EpiModel":
{"Author":"Samuel Jenness [cre, aut],\nSteven M. Goodreau [aut],\nMartina Morris
[aut],\nEmily Beylerian [ctb],\nLi Wang [ctb],\nSkye Bender-deMoll
[ctb]","Depends":"R (>= 3.1), deSolve (>= 1.11), networkDynamic (>= 0.7.1),\ntergm
(>= 3.2.4)","Description":"Tools for simulating mathematical models of infectious
disease.\nEpidemic model classes include deterministic compartmental
models,\nstochastic agent-based, and stochastic network models. Network models
use\nrobust statistical methods of exponential-family random graph models
(ERGMs)\nfrom the Statnet suite of software packages in R. Standard templates for
epidemic\nmodeling include SI, SIR, and SIS disease types. EpiModel features\nan
easy API for extending these templates to address novel scientific
research\naims.","Imports":"graphics, grDevices, stats, utils, doParallel, ergm
(>=\n3.2.4), foreach, network (>= 1.12.0), RColorBrewer, ape","License":"GPL-
2","NeedsCompilation":"no","Package":"EpiModel","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr, ndtv (>= 0.7), rmarkdown, shiny,
testthat","Title":"Mathematical Modeling of Infectious
Disease","URL":"http:\/\/epimodel.org\/","Version":"1.2.5"},"Eplot":{"Author":"Eran
Raviv","Description":"Aim: Adjust the graphical parameters to create
nicer\nlongitudinal series plots. The default set of graphical parameters is
very\ngeneral, and can be improved upon when we are interested in plotting
data\npoints observed over time. Functions facilitate plotting those kind
of\nseries, univariate plots, bivariate plots (with vertical axis on both left\nand
right hand sides), multivariate plots and plots which allow to examine\nwhether a
new observation is 'unusual' via construction and visualization\nof prediction
intervals around it.","License":"GPL-
2","NeedsCompilation":"no","Package":"Eplot","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Plotting longitudinal series","Version":"1.0"},"EstCRM":
{"Author":"Cengiz Zopluoglu","Depends":"Hmisc, lattice","Description":"Estimates
item and person parameters for the Samejima's Continuous Response Model (CRM),
computes item fit residual statistics, draws empirical 3D item category response
curves, draws theoretical 3D item category response curves, and generates data
under the CRM for simulation studies.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"EstCRM","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Calibrating Parameters for the Samejima's Continuous IRT
Model","URL":"http:\/\/sites.education.miami.edu\/zopluoglu\/","Version":"1.4"},"Es
tHer":{"Author":"Anna Bonnet and Celine Levy-Leduc","Depends":"R (>= 2.10), glmnet,
parallel, MASS","Description":"Our method is a variable selection method to select
active components in sparse linear mixed models in order to estimate the
heritability. The selection allows us to reduce the size of the data sets which
improves the accuracy of the estimations. Our package also provides a confidence
interval for the estimated heritability.","Imports":"Rcpp (>=
2","NeedsCompilation":"yes","Package":"EstHer","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Estimation of Heritability in High Dimensional Sparse
Linear\nMixed Models using Variable Selection","Version":"1.0"},"EstSimPDMP":
{"Author":"Romain Azais","Description":"This package deals with the estimation of
the jump rate for piecewise-deterministic Markov processes (PDMPs), from only one
observation of the process within a long time. The main functions provide an
estimate of this function. The state space may be discrete or continuous. The
associated paper has been published in Scandinavian Journal of Statistics and is
given in references. Other functions provide a method to simulate random variables
from their (conditional) hazard rate, and then to simulate PDMPs.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"EstSimPDMP","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Estimation and Simulation for
PDMPs","Version":"1.2"},"EurosarcBayes":{"Author":"Peter Dutton","Depends":"shiny,
VGAM, data.table, plyr, methods, clinfun","Description":"Frequentist and Bayesian
single arm trial design and sample size software.\nDesigns cover one and two binary
endpoints with both single and multi-stage\nmethodology. The research leading to
these results has received funding from the\nEuropean Union Seventh Framework
Programme (FP7\/2007-2013) under grant agreement\nnumber 278742
(Eurosarc).","License":"GPL-
2","NeedsCompilation":"no","Package":"EurosarcBayes","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Bayesian Single Arm Sample Size Calculation
Software","Version":"1.0"},"EvCombR":{"Author":"Alexander
Karlsson","Depends":"methods","Description":"Package for combining pieces of
evidence","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"EvCombR","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Evidence Combination in R","Version":"0.1-
2"},"EvalEst":{"Author":"Paul Gilbert <pgilbert.ttv9z@ncf.ca>","Depends":"R (>=
2.5.0), tfplot, dse (>= 2007.10-1)","Description":"Provides functions for
evaluating (time series)
model\nestimation methods. These facilitate Monte Carlo experiments of
repeated\nsimulations and estimations. Also provides methods for\nlooking at the
distribution of the results from these experiments,\nincluding model roots (which
are an equivalence class invariant).","Imports":"setRNG, tframe (>= 2007.5-
3)","License":"GPL-
2","NeedsCompilation":"no","Package":"EvalEst","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Dynamic Systems Estimation -
Extensions","URL":"http:\/\/tsanalysis.r-forge.r-project.org\/","Version":"2015.4-
2"},"Evapotranspiration":{"Author":"Danlu Guo <danlu.guo@adelaide.edu.au>, Seth
Westra <swestra@civeng.adelaide.edu.au>","Depends":"R (>= 2.10),
zoo","Description":"Uses data and constants to calculate potential
evapotranspiration (PET) and actual evapotranspiration (AET) from 21 different
formulations including Penman, Penman-Monteith FAO 56, Priestley-Taylor and Morton
formulations.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Evapotranspiration","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Title":"Modelling Actual, Potential and Reference
Crop\nEvapotranspiration","Version":"1.9"},"EvoRAG":{"Author":"Jason T.
Weir","Description":"Uses maximum likelihood to estimate rates of trait evolution
across environmental gradients.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"EvoRAG","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Evolutionary Rates Across
Gradients","Version":"2.0"},"Evomorph":{"Author":"Juan Manuel Cabrera, Federico
Giri","Depends":"R (>= 3.2.0)","Description":"Evolutionary process simulation using
geometric morphometric data. Manipulation of landmark data files (TPS), shape
plotting and distances plotting functions.","Imports":"ggplot2, reshape2, geomorph,
2)","NeedsCompilation":"no","Package":"Evomorph","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Evolutionary Morphometric
Simulation","Version":"0.9"},"ExPosition":{"Author":"Derek Beaton, Cherise R. Chin
Fatt, Herve Abdi","Depends":"prettyGraphs (>= 2.1.4)","Description":"ExPosition is
for descriptive (i.e., fixed-effects) multivariate analysis with the singular value
decomposition.","License":"GPL-
2","NeedsCompilation":"no","Package":"ExPosition","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Exploratory analysis with the singular value
decomposition","Version":"2.8.19"},"Exact":{"Author":"Peter
Calhoun","Description":"Performs unconditional exact tests and power calculations
for 2x2 contingency\ntables. Unconditional exact tests are often more powerful than
conditional exact tests and asymptotic tests.","License":"GPL-
2","NeedsCompilation":"no","Package":"Exact","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Unconditional Exact Test","Version":"1.6"},"ExactCIdiff":
{"Author":"Guogen Shan <guogen.shan@unlv.edu>, Weizhen
Wang\n<weizhen.wang@wright.edu>","Depends":"R (>= 1.8.0)","Description":"This is a
package for exact Confidence Intervals for the\ndifference between two independent
or dependent proportions.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ExactCIdiff","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Inductive Confidence Intervals for the difference
between two\nproportions","URL":"http:\/\/www.r-
project.org,\nhttp:\/\/www.wright.edu\/~weizhen.wang\/wanghome.htm,\nhttp:\/\/facul
ty.unlv.edu\/gshan\/","Version":"1.3"},"ExactPath":{"Author":"Dr. Kai
Wang","Depends":"R(>= 2.12), ncvreg, lars","Description":"ExactPath implements an
algorithm for exact LASSO\nsolution. Two methods are provided to print and
visualize the\nwhole solution paths. Use ?ExactPath to see an
introduction.\nPackages ncvreg and lars are required so that their data sets\ncan
be used in examples.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ExactPath","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Exact solution paths for regularized LASSO regressions
with L_1\npenalty","Version":"1.0"},"ExceedanceTools":{"Author":"Joshua
French","Depends":"R (>= 2.12.0)","Description":"Tools for constructing confidence
regions for exceedance regions\nand contour lines.","Imports":"splancs,
SpatialTools","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ExceedanceTools","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"spBayes","Title":"Confidence regions for
exceedance sets and contour lines","Version":"1.2.2"},"ExomeDepth":
{"Author":"Vincent Plagnol","Depends":"R (>= 3.1.0)","Description":"Calls copy
number variants (CNVs) from targeted sequence data, typically exome sequencing
experiments designed to identify the genetic basis of Mendelian
disorders.","Imports":"Biostrings, IRanges, Rsamtools, GenomicRanges (>=
1.16.0),\naod, VGAM (>= 0.8.4), methods, GenomicAlignments","License":"GPL-
3","NeedsCompilation":"yes","Package":"ExomeDepth","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr","Title":"Calls Copy Number Variants from
Targeted Sequence Data","Version":"1.1.8"},"ExpDE":{"Author":"Felipe Campelo [aut,
cre],\nMoises Botelho [aut]","Depends":"R (>= 3.2.0)","Description":"Modular
implementation of the Differential Evolution algorithm for\nexperimenting with
different types of operators.","License":"GPL-
2","NeedsCompilation":"no","Package":"ExpDE","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Modular Differential Evolution for Experimenting with
Operators","Version":"0.1.2"},"ExpDes":{"Author":"Eric Batista Ferreira, Portya
Piscitelli Cavalcanti, Denismar\nAlves Nogueira","Description":"Package for
analysis of simple experimental designs (CRD,\nRBD and LSD), experiments in double
factorial schemes (in CRD\nand RBD), experiments in a split plot in time schemes
(in CRD\nand RBD), experiments in double factorial schemes with an\nadditional
treatment (in CRD and RBD), experiments in triple\nfactorial scheme (in CRD and
RBD) and experiments in triple\nfactorial schemes with an additional treatment (in
CRD and\nRBD), performing the analysis of variance and means comparison\nby fitting
regression models until the third power\n(quantitative treatments) or by a multiple
comparison test,\nTukey test, test of Student-Newman-Keuls (SNK), Scott-
Knott,\nDuncan test, t test (LSD) and Bonferroni t test (protected LSD)\n- for
qualitative treatments.","License":"GPL-
2","NeedsCompilation":"no","Package":"ExpDes","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Experimental Designs
package","Version":"1.1.2"},"ExpDes.pt":{"Author":"Eric Batista Ferreira, Pórtya
Piscitelli Cavalcanti, Denismar\nAlves Nogueira","Description":"Pacote destinado a
analise de delineamentos experimentais\nsimples (DIC, DBC e DQL), experimentos em
esquema de fatorial\nduplo (em DIC e DBC), experimentos em esquema de
parcelas\nsubdivididas no tempo (em DIC e DBC), experimentos em esquema\nde
fatorial duplo com um tratamento adicional (em DIC e DBC),\nexperimentos em esquema
de fatorial triplo (em DIC e DBC) e\nexperimentos em esquema de fatorial triplo com
um tratamento\nadicional (em DIC e DBC); realizando a analise de variancia
e\ncomparacao de medias pelo ajuste de modelos de regressao ate o\nterceiro grau
(tratamentos quantitativos) ou por testes de\ncomparacao multipla: teste de Tukey,
teste de\nStudent-Newman-Keuls (SNK), teste de Scott-Knott, teste de\nDuncan, teste
t (LSD), teste t de Bonferroni (LSD protegido) e\nteste Bootstrap - tratamentos
qualitativos.","License":"GPL-
2","NeedsCompilation":"no","Package":"ExpDes.pt","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Pacote Experimental Designs
(Portuguese)","Version":"1.1.2"},"ExplainPrediction":{"Author":"Marko Robnik-
Sikonja","Depends":"CORElearn (>= 1.47.0),semiArtificial (>=
2.0.0)","Description":"Package contains methods to generate explanations for
individual predictions of\nclassification and regression models. Weighted averages
of individual explanations form explanation of the whole model.\nThe package
extends 'CORElearn' package, but other prediction models can also be explained
using a wrapper.","License":"GPL-
3","NeedsCompilation":"no","Package":"ExplainPrediction","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Explanation of Predictions for Classification
and Regression\nModels","URL":"http:\/\/lkm.fri.uni-
lj.si\/rmarko\/software\/","Version":"1.0.2"},"ExtDist":{"Author":"Haizhen Wu
<h.wu2@massey.ac.nz>,\nA. Jonathan R. Godfrey
<A.J.Godfrey@massey.ac.nz>,\nKondaswamy Govindaraju
<k.govindaraju@massey.ac.nz>,\nSarah Pirikahu
<s.pirikahu@massey.ac.nz>","Description":"A consistent, unified and
extensible\nframework for estimation of parameters for probability distributions,
including\nparameter estimation procedures that allow for weighted samples; the
current set of distributions included are: the standard beta, The four-parameter
beta, Burr, gamma, Gumbel, Johnson SB and SU, Laplace, logistic, normal, symmetric
truncated normal, truncated normal, symmetric-reflected truncated beta, standard
symmetric-reflected truncated beta, triangular, uniform, and Weibull distributions;
decision criteria and selections based on these decision
criteria.","Imports":"numDeriv, optimx","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ExtDist","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"ggplot2, knitr, PerformanceAnalytics, stats,
SuppDists,\ntruncdist, VGAM, xtable","Title":"Extending the Range of Functions for
Probability Distributions","Version":"0.6-3"},"ExtremeBounds":{"Author":"Marek
Hlavac <hlavac@fas.harvard.edu>","Description":"An implementation of Extreme Bounds
Analysis (EBA), a global sensitivity analysis that examines the robustness of
determinants in regression models. The package supports both Leamer's and Sala-i-
Martin's versions of EBA, and allows users to customize all aspects of the
analysis.","Imports":"Formula, graphics, methods,
stats, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ExtremeBounds","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Extreme Bounds Analysis
(EBA)","Version":"0.1.5.1"},"FACTMLE":{"Author":"Koulik Khamaru
<koulik123@gmail.com>, Rahul Mazumder<rahul.mazumder@gmail.com
>","Description":"Perform Maximum Likelihood Factor analysis on a covariance matrix
or data matrix.","Imports":"rARPACK, stats","License":"GPL-
3","NeedsCompilation":"no","Package":"FACTMLE","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"MASS","Title":"Maximum Likelihood Factor
Analysis","Version":"1.1"},"FACTscorer":{"Author":"Ray Baser [aut, cre],\nAyelet
Greenberg [ctb]","Depends":"R (>= 3.1.1)","Description":"Provides functions to
score the Functional Assessment of Cancer\nTherapy (FACT) and Functional Assessment
of Chronic Illness Therapy (FACIT)\nfamily of patient-reported outcome (PRO)
measures. The questionnaires\nthemselves can be downloaded from www.FACIT.org.
For most of the FACIT\nquestionnaires, FACIT.org provides scoring syntax for use
with commercial\nstatistical software (SAS and SPSS). The FACTscorer R package is
intended\nto serve as a free, reliable alternative for those without access to SAS
or\nSPSS. Additionally, it will allow R users to both score and analyze the\nFACT
and FACIT scales in R, avoiding the time-consuming and and error-prone\nprocess of
transferring data back-and-forth between statistical software.\nFinally, use of the
FACTscorer package will prevent many sources of scoring\nerror common when using
SAS and\/or SPSS syntax (e.g., copy-paste errors and\nother accidental
modifications to the syntax).","License":"GPL-
3","NeedsCompilation":"no","Package":"FACTscorer","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Scores the FACT and FACIT Family of Patient-Reported
Outcome\nMeasures","Version":"0.1.0"},"FADA":{"Author":"Emeline Perthame
(Agrocampus Ouest, Rennes, France), Chloe Friguet\n(Universite de Bretagne Sud,
Vannes, France) and David Causeur (Agrocampus\nOuest, Rennes,
France)","Depends":"MASS, elasticnet","Description":"The functions provided in the
FADA (Factor Adjusted Discriminant Analysis) package aim at performing supervised
classification of high-dimensional and correlated profiles. The procedure combines
adecorrelation step based on a\nfactor modeling of the dependence among covariates
and a classification method. The available methods are Lasso regularized logistic
model\n(see Friedman et al. (2010)), sparse linear discriminant analysis
(see\nClemmensen et al. (2011)), shrinkage linear and diagonal
discriminant\nanalysis (see M. Ahdesmaki et al. (2010)). More methods of
classification can be used on the decorrelated data provided by the package
FADA.","Imports":"sparseLDA,sda,glmnet,mnormt,crossval","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"FADA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Variable selection for supervised classification in
high\ndimension","Version":"1.2"},"FAMILY":{"Author":"Asad
Haris","Description":"Fits penalized linear and logistic regression models with
pairwise interaction terms.","Imports":"pheatmap, pROC","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"FAMILY","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"A Convex Formulation for Modeling Interactions with
Strong\nHeredity","Version":"0.1.19"},"FAMT":{"Author":"David Causeur, Chloe
Friguet, Magalie Houee-Bigot, Maela Kloareg","Depends":"mnormt,
impute","Description":"The method proposed in this package takes into account the
impact of dependence on the multiple testing procedures for high-throughput data as
proposed by Friguet et al. (2009). The common information shared by all the
variables is modeled by a factor analysis structure. The number of factors
considered in the model is chosen to reduce the false discoveries variance in
multiple tests. The model parameters are estimated thanks to an EM algorithm.
Adjusted tests statistics are derived, as well as the associated p-values. The
proportion of true null hypotheses (an important parameter when controlling the
false discovery rate) is also estimated from the FAMT model. Graphics are proposed
to interpret and describe the factors.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"FAMT","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Factor Analysis for Multiple Testing (FAMT) : simultaneous
tests\nunder dependence in high-dimensional
data","URL":"http:\/\/famt.free.fr\/","Version":"2.5"},"FAOSTAT":{"Author":"Michael
C. J. Kao <michael.kao@fao.org>, Markus Gesmann, Filippo Gheri","Description":"A
list of functions to download statistics from FAOSTAT (database\nof the Food and
Agricultural Organization of the United Nations) and WDI\n(database of the World
Bank), and to perform some harmonization operations.","Imports":"RJSONIO (>= 0.96-
0), plyr (>= 1.7.1), data.table (>= 1.8.2),\nMASS (>= 7.3-22), classInt (>= 0.1-
19), ggplot2 (>= 0.9.3),\nlabeling (>= 0.1), scales (>= 0.2.3)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"FAOSTAT","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr","Title":"Download Data from the FAOSTAT
Database of the Food and\nAgricultural Organization (FAO) of the United
Nations","URL":"https:\/\/github.com\/mkao006\/FAOSTATpackage","Version":"2.0"},"FA
dist":{"Author":"Francois Aucoin","Description":"Probability distributions that are
sometimes useful in hydrology.","Imports":"stats","License":"GPL-
2","NeedsCompilation":"no","Package":"FAdist","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Distributions that are Sometimes Used in
Hydrology","URL":"https:\/\/github.com\/tpetzoldt\/FAdist","Version":"2.2"},"FAiR":
{"Author":"Ben Goodrich","Depends":"R (>= 2.7.0), methods, rgenoud (>= 5.4-7),
gWidgetsRGtk2 (>=\n0.0-31), stats4, rrcov, Matrix","Description":"This package
estimates factor analysis models using a\ngenetic algorithm, which permits a
general mechanism for\nrestricted optimization with arbitrary restrictions that
are\nchosen at run time with the help of a GUI. Importantly,\ninequality
restrictions can be imposed on functions of multiple\nparameters, which provides a
new avenues for testing and\ngenerating theories with factor analysis models. This
package\nalso includes an entirely new estimator of the common factor\nanalysis
model called semi-exploratory factor analysis, which\nis a general alternative to
exploratory and confirmatory factor\nanalysis. Finally, this package integrates a
lot of other\npackages that estimate sample covariance matrices and thus\nprovides
a lot of alternatives to the traditional sample\ncovariance calculation. Note that
you need to have the Gtk run\ntime library installed on your system to use this
package; see\nthe URL below for detailed installation instructions. Most\nusers
would only need to understand the first twenty-four pages\nof the PDF
manual.","License":"AGPL (>= 3) + file
LICENSE","NeedsCompilation":"yes","Package":"FAiR","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"corpcor, mvnmle, polycor, nFactors, Rgraphviz,
mvnormtest,\nenergy, GPArotation, sem, MASS, psych","Title":"Factor Analysis in
R","URL":"http:\/\/wiki.r-project.org\/rwiki\/doku.php?
id=packages:cran:fair","Version":"0.4-15"},"FAmle":{"Author":"Francois
Aucoin","Depends":"mvtnorm","Description":"Estimate parameters of univariate
probability distributions\nwith maximum likelihood and Bayesian
methods.","Imports":"graphics, stats, utils","License":"GPL-
2","NeedsCompilation":"yes","Package":"FAmle","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"FAdist","Title":"Maximum Likelihood and Bayesian
Estimation of Univariate\nProbability
Distributions","URL":"https:\/\/github.com\/tpetzoldt\/FAmle","Version":"1.3.4"},"F
AwR":{"Author":"Andrew Robinson and Jeff Hamann","Depends":"R (>= 2.10), MASS,
lattice, glpkAPI","Description":"Provides functions and datasets from the
book \"Forest Analytics with R\".","License":"GPL-
3","NeedsCompilation":"no","Package":"FAwR","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Functions and Datasets for \"Forest Analytics with
R\"","Version":"1.1.0"},"FBFsearch":{"Author":"Davide Altomare, Guido Consonni and
Luca La Rocca","Depends":"Rcpp (>= 0.9.13), RcppArmadillo (>=
0.3.2.4)","Description":"We propose an objective Bayesian algorithm for
searching\nthe space of Gaussian directed acyclic graphical models when\nthe
variables are assumed to satisfy a given ordering. The\napproach used is based on
non-local parameter priors and thus\nit is suitable for learning sparse graphs. The
algorithm is\nimplemented in C++ using the open-source library
Armadillo.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"FBFsearch","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Algorithm for searching the space of Gaussian directed
acyclic\ngraphical models through moment fractional Bayes
factors","Version":"1.0"},"FBN":{"Author":"Adrian Andronache
<adi.andronache@gmail.com>, Luca Agnelli\n<luca.agnelli@gmail.com>","Depends":"R
(>= 2.10)","Description":"Normalizes the data from a file containing the raw
values\nof the SNP probes of microarrray data by using the FISH probes\nand their
corresponding CNs.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"FBN","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"FISH Based Normalization and Copy Number inference of
SNP\nmicroarray data","Version":"1.5.1"},"FCGR":{"Author":"Antonio Meneses
<antoniomenesesfreire@hotmail.com>,\nSalvador Naya <salva@udc.es>,\nJavier Tarrio-
Saavedra <jtarrio@udc.es>,\nIgnacio Lopez-Ullibarri <ilu@udc.es>","Depends":"R (>=
3.2.2), KernSmooth, kerdiest, nlme","Description":"Fatigue Crack Growth in
Reliability estimates the distribution\nof material lifetime due to mechanical
fatigue efforts. The FCGR\npackage
provides simultaneous crack growth curves fitting to\ndifferent specimens in
materials under mechanical stress efforts.\nLinear mixed-effects models (LME) with
smoothing B-Splines\nand the linearized Paris-Erdogan law are applied. Once
defined\nthe fail for a determined crack length, the distribution function\nof
failure times to fatigue is obtained. The density function is\nestimated by
applying nonparametric binned kernel density estimate\n(bkde) and the kernel
estimator of the distribution function (kde).\nThe results of Pinheiro and Bates
method based on nonlinear\nmixed-effects regression (nlme) can be also retrieved.
The package\ncontains the crack.growth, PLOT.cg, IB.F, and Alea.A (database)
functions.","Imports":"MASS, mgcv, pspline, sfsmisc","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"FCGR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Fatigue Crack Growth in Reliability","Version":"1.0-
0"},"FCMapper":{"Author":"Shaun Turney and Michael
Bachhofer","Description":"Provides several functions to create and manipulate
fuzzy\ncognitive maps. It is based on 'FCMapper' for Excel, distributed at
<http:\/\/\nwww.fcmappers.net\/joomla\/>, developed by Michael Bachhofer and Martin
Wildenberg.\nMaps are inputted as adjacency matrices. Attributes of the maps and
the\nequilibrium values of the concepts (including with user-defined
constrained\nvalues) can be calculated. The maps can be graphed with a function
that calls\n'igraph'. Multiple maps with shared concepts can be
aggregated.","Imports":"igraph","License":"GPL-
2","NeedsCompilation":"no","Package":"FCMapper","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Fuzzy Cognitive Mapping","Version":"1.1"},"FCNN4R":
{"Author":"Grzegorz Klima <gklima@users.sourceforge.net>","Depends":"R (>= 3.0),
stats, graphics, methods, Rcpp","Description":"Provides an interface to kernel
routines from the FCNN C++ library.\nFCNN is based on a completely new Artificial
Neural Network representation that\noffers unmatched efficiency, modularity, and
extensibility. FCNN4R provides\nstandard teaching (backpropagation, Rprop,
simulated annealing, stochastic\ngradient) and pruning algorithms (minimum
magnitude, Optimal Brain Surgeon),\nbut it is first and foremost an efficient
computational engine. Users can\neasily implement their algorithms by taking
advantage of fast gradient computing\nroutines, as well as network reconstruction
functionality (removing weights\nand redundant neurons, reordering inputs, merging
networks). Networks can be\nexported to C functions in order to integrate them into
virtually any software\nsolution.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"FCNN4R","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Fast Compressed Neural Networks for
R","Version":"0.6.2"},"FD":{"Author":"Etienne Laliberté, Pierre Legendre, Bill
Shipley","Depends":"ade4, ape, geometry, vegan","Description":"FD is a package to
compute different multidimensional FD indices. It implements a distance-based
framework to measure FD that allows any number and type of functional traits, and
can also consider species relative abundances. It also contains other useful tools
for functional ecology.","License":"GPL-
2","NeedsCompilation":"yes","Package":"FD","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Measuring functional diversity (FD) from multiple traits,
and\nother tools for functional ecology","Version":"1.0-12"},"FDGcopulas":
{"Author":"Gildas Mazo, Stephane Girard","Depends":"Rcpp (>= 0.10.6),
methods","Description":"FDG copulas are a class of copulas featuring an interesting
balance between flexibility and tractability. This package provides tools to
construct, calculate the pairwise dependence coefficients of, simulate from, and
fit FDG copulas. The acronym FDG stands for 'one-Factor with Durante Generators',
as an FDG copula is a one-factor copula -- that is, the variables are independent
given a latent factor -- whose linking copulas belong to the Durante class of
bivariate copulas (also referred to as exchangeable Marshall-Olkin or semilinear
copulas).","Imports":"numDeriv, randtoolbox","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"FDGcopulas","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Multivariate Dependence with FDG
Copulas","Version":"1.0"},"FDRreg":{"Author":"James G. Scott, with contributions
from Rob Kass and Jesse Windle","Depends":"fda (>= 2.4.0), splines (>=
3.0.2)","Description":"Tools for FDR problems, including false discovery rate
regression.\nSee corresponding paper: \"False discovery rate regression:
application to\nneural synchrony detection in primary visual cortex.\" James G.
Scott, Ryan\nC. Kelly, Matthew A. Smith, Robert E. Kass.","Imports":"Rcpp (>=
0.11.0), mosaic (>= 0.8-10)","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"FDRreg","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"False discovery rate
regression","Version":"0.1"},"FDRsampsize":{"Author":"Stan Pounds
<stanley.pounds@stjude.org>","Depends":"R (>= 2.15.1)","Description":"Defines a
collection of functions to compute average power and sample size for studies that
use the false discovery rate as the final measure of statistical
significance.","Imports":"stats","License":"GPL-
2","NeedsCompilation":"no","Package":"FDRsampsize","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Compute Sample Size that Meets Requirements for
Average Power\nand FDR","Version":"1.0"},"FDboost":{"Author":"Sarah Brockhaus [aut,
cre],\nDavid Ruegamer [ctb],\nTorsten Hothorn [ctb],\nwith contributions by many
others (see inst\/CONTRIBUTIONS) [ctb]","Depends":"R (>= 3.0.0), methods, mboost
(>= 2.6-0)","Description":"Regression models for functional data, i.e., scalar-on-
function,\nfunction-on-scalar and function-on-function regression models, are
fitted\nby a component-wise gradient boosting algorithm.","Imports":"graphics,
grDevices, utils, stats, Matrix, gamboostLSS (>=\n1.2-1), mgcv, refund, MASS,
zoo","License":"GPL-
2","NeedsCompilation":"no","Package":"FDboost","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"fda, fields, maps, mapdata","Title":"Boosting
Functional Regression Models","Version":"0.1-0"},"FENmlm":{"Author":"Laurent
Berge","Depends":"stats, numDeriv, Matrix, MASS","Description":"Efficient
estimation of fixed-effect maximum likelihood models with, possibly, non-linear
right hand sides.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"FENmlm","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Fixed Effects Nonlinear Maximum Likelihood
Models","Version":"1.0"},"FFD":{"Author":"Ian Kopacka","Depends":"R (>= 2.10),
methods, graphics, tcltk, tkrplot, R2HTML","Description":"Functions, S4
classes\/methods and a graphical user interface (GUI) to design surveys to
substantiate freedom from disease using a modified hypergeometric function (see
Cameron and Baldock, 1997). Herd sensitivities are computed according to sampling
strategies \"individual sampling\" or \"limited sampling\" (see M. Ziller, T.
Selhorst, J. Teuffert, M. Kramer and H. Schlueter, 2002). Methods to compute the a-
posteriori alpha-error are implemented. Risk-based targeted sampling is
supported.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"FFD","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Freedom from Disease","URL":"http:\/\/ffd.r-forge.r-
project.org, http:\/\/www.ages.at","Version":"1.0-6"},"FField":{"Author":"Grigori
Kapoustin","Description":"Force field simulation of interaction of set of
points.\nVery useful for placing text labels on graphs, such
as\nscatterplots.","License":"GPL-
3","NeedsCompilation":"no","Package":"FField","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"ggplot2, gridExtra","Title":"Force field simulation for
a set of points","Version":"0.1.0"},"FGN":{"Author":"A.I. McLeod and Justin
Veenstra","Depends":"R (>= 2.1.0)","Description":"Exact MLE and Whittle MLE
estimation for power law decay models.","Imports":"akima, ltsa","License":"CC BY-
NC-SA
3.0","NeedsCompilation":"yes","Package":"FGN","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Fractional Gaussian Noise and power law decay time series
model\nfitting","URL":"http:\/\/www.stats.uwo.ca\/faculty\/aim","Version":"2.0-
12"},"FGSG":{"Author":"Xiaotong Shen, Yiwen Sun, Julie
Langou","Description":"Implement algorithms for feature grouping and selection over
an undirected graph, solves problems like graph fused lasso, graph OSCAR and so
on.","License":"GPL-
2","NeedsCompilation":"yes","Package":"FGSG","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Feature Grouping and Selection Over an Undirected
Graph","Version":"1.0.2"},"FGalgorithm":{"Author":"Dariush
Najarzadeh","Description":"This is a package for implementation of Flury-
Gautschi\nalgorithms.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"FGalgorithm","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Flury and Gautschi
algorithms","Version":"1.0"},"FHtest":{"Author":"Ramon Oller, Klaus
Langohr","Depends":"interval, KMsurv","Description":"Functions to compare two or
more survival curves with:\na) The Fleming-Harrington test for right-censored data
based on permutations and on counting processes.\nb) An extension of the Fleming-
Harrington test for interval-censored data based on a permutation distribution and
on a score vector distribution.","Imports":"survival, perm, MASS","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"FHtest","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Tests for Right and Interval-Censored Survival Data Based
on the\nFleming-Harrington Class","Version":"1.3"},"FI":{"Author":"David V. Dias
[aut, cre]","Description":"Provide functions for forest inventory
calculations.\nCommon volumetric equations (Smalian, Newton and Huber)
as well\nstacking factor and form","License":"GPL-
3","NeedsCompilation":"no","Package":"FI","Repository":"http:\/\/cran.csiro.au\/src
\/contrib","Title":"Provide functions for forest inventory
calculations","Version":"1.0"},"FIACH":{"Author":"Tim Tierney","Depends":"R (>=
3.2.0)","Description":"Useful functions for fMRI preprocessing.","Imports":"Rcpp
(>= 0.11.4), RNiftyReg (>= 2.0.0),tcltk, tkrplot, utils,\nstats, graphics,
grDevices","License":"GPL-
2","NeedsCompilation":"yes","Package":"FIACH","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Retrospective Noise Control for
fMRI","Version":"0.1.2"},"FITSio":{"Author":"Andrew Harris","Depends":"R (>=
2.0.0)","Description":"Utilities to read and write files in the FITS
(Flexible\nImage Transport System) format, a standard format in astronomy.\nPresent
low-level routines allow: reading, parsing, and modifying\nFITS headers; reading
FITS images (multi-dimensional arrays);\nreading FITS binary tables; and writing
FITS images\n(multi-dimensional arrays). Higher-level functions allow:
reading\nfiles composed of one or more headers and a single
(perhaps\nmultidimensional) image or single bintable; reading bintables into\ndata
frames; generating vectors for image array axes; scaling and\nwriting images as 16-
bit integers. Known incompletenesses are\nreading FITS ASCII table and random
group extensions, as well as\nbit, complex, and array descriptor data types in
binary tables.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"FITSio","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"FITS (Flexible Image Transport System)
utilities","Version":"2.0-0"},"FKF":{"Author":"David Luethi, Philipp Erb, Simon
Otziger","Depends":"R(>= 2.8), RUnit","Description":"This is a fast and flexible
implementation of the Kalman\nfilter, which can deal with NAs. It is entirely
written in C\nand relies fully on linear algebra subroutines contained in\nBLAS and
LAPACK. Due to the speed of the filter, the fitting of\nhigh-dimensional linear
state space models to large datasets\nbecomes possible. This package also contains
a plot function\nfor the visualization of the state vector and
graphical\ndiagnostics of the residuals.","Imports":"graphics","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"FKF","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Fast Kalman Filter","Version":"0.1.3"},"FLIM":
{"Author":"Rune Hoff with contributions from Jon Michael Gran and Daniel
Farewell","Depends":"zoo, MASS","Description":"FLIM fits linear models for the
observed increments in a longitudinal dataset, and imputes missing values according
to the models.","License":"GPL-
2","NeedsCompilation":"no","Package":"FLIM","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Farewellâ€™s Linear Increments
Model","Version":"1.2"},"FLLat":{"Author":"Gen Nowak [aut, cre],\nTrevor Hastie
[aut],\nJonathan R. Pollack [aut],\nRobert Tibshirani [aut],\nNicholas Johnson
[aut]","Description":"Fits the Fused Lasso Latent Feature model, which is used for
modeling multi-sample aCGH data to identify regions of copy number variation (CNV).
Produces a set of features that describe the patterns of CNV and a set of weights
that describe the composition of each sample. Also provides functions for choosing
the optimal tuning parameters and the appropriate number of features, and for
estimating the false discovery rate.","Imports":"graphics, stats,
gplots","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"FLLat","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Fused Lasso Latent Feature Model","Version":"1.2"},"FLR":
{"Author":"Constantinos Mavridis and Ioannis N.
Athanasiadis","Depends":"combinat","Description":"FLR algorithm for
classification","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"FLR","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Fuzzy Logic Rule Classifier","Version":"1.0"},"FLSSS":
{"Author":"Charlie Wusuo Liu","Description":"Solve an approximate Subset Sum
Problem via a recursive compression algorithm","Imports":"Rcpp (>=
2","NeedsCompilation":"yes","Package":"FLSSS","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Fixed Size Subset Sum Solution","Version":"3.1"},"FME":
{"Author":"Karline Soetaert <karline.soetaert@nioz.nl>,\nThomas Petzoldt
<thomas.petzoldt@tu-dresden.de>","Depends":"R (>= 2.6), deSolve, rootSolve,
coda","Description":"Provides functions to help in fitting models to data,
to\nperform Monte Carlo, sensitivity and identifiability analysis. It is\nintended
to work with models be written as a set of differential\nequations that are solved
either by an integration routine from\npackage deSolve, or a steady-state solver
from package\nrootSolve. However, the methods can also be used with other types
of\nfunctions.","Imports":"minpack.lm, MASS","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"FME","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"diagram","Title":"A Flexible Modelling Environment for
Inverse Modelling,\nSensitivity, Identifiability, Monte Carlo
Analysis","Version":"1.3.2"},"FMP":{"Author":"Niels G. Waller
<nwaller@umn.edu>","Depends":"R (>= 3.0)","Description":"Estimates Filtered
Monotonic Polynomial IRT Models as described by Liang and Browne (2015)
<DOI:10.3102\/1076998614556816>.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"FMP","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Filtered Monotonic Polynomial IRT
Models","Version":"1.4"},"FMStable":{"Author":"Geoff Robinson","Description":"This
package implements some basic procedures for dealing\nwith log maximally skew
stable distributions, which are also\ncalled finite moment log stable
distributions.","License":"GPL-
3","NeedsCompilation":"yes","Package":"FMStable","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Finite Moment Stable Distributions","Version":"0.1-
2"},"FMsmsnReg":{"Author":"Luis Benites Sanchez and Rocio Paola Maehara and Victor
Hugo Lachos","Description":"Fit linear regression models where the random errors
follow a finite mixture of of Skew Heavy-Tailed
Errors.","Imports":"mvtnorm","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"FMsmsnReg","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Regression Models with Finite Mixtures of Skew Heavy-
Tailed\nErrors","Version":"1.0"},"FNN":{"Author":"Alina Beygelzimer, Sham Kakadet
and John Langford (cover tree library),\nSunil Arya and David Mount (ANN library
for the kd-tree approach), Shengqiao Li","Depends":"R (>=
2.8.0)","Description":"Cover-tree and kd-tree fast k-nearest neighbor search
algorithms and related applications\nincluding KNN classification, regression and
information measures are implemented.","License":"GPL (>=
2.1)","NeedsCompilation":"yes","Package":"FNN","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"chemometrics, mvtnorm","Title":"Fast Nearest Neighbor
Search Algorithms and Applications","Version":"1.1"},"FPDclustering":
{"Author":"Cristina Tortora and Paul D.
McNicholas","Depends":"ThreeWay","Description":"Probabilistic distance clustering
(PD-clustering) is an iterative, distribution free, probabilistic clustering
method. PD-clustering assigns units to a cluster according to their probability of
membership, under the constraint that the product of the probability and the
distance of each point to any cluster centre is a constant. PD-clustering is a
flexible method that can be used with non-spherical clusters, outliers, or noisy
data. Facto PD-clustering (FPDC) is a recently proposed factor clustering method
that involves a linear transformation of variables and a cluster optimizing the PD-
clustering criterion. It allows clustering of high dimensional data
sets.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"FPDclustering","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"PD-Clustering and Factor PD-
Clustering","Version":"1.0"},"FRACTION":{"Author":"OuYang Ming
<oula2004@163.com>","Description":"This is the package which can help you
turn\nnumeric,dataframe,matrix into fraction form.","License":"GPL-
2","NeedsCompilation":"no","Package":"FRACTION","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Numeric number into fraction","Version":"1.0"},"FRAPO":
{"Author":"Bernhard Pfaff [aut, cre], Miguel Sousa Lobo [ctb] (SOCP),\nLieven
Vandenberghe [ctb] (SOCP), Stephen Boyd [ctb] (SOCP),\nHerve Lebret [ctb]
(SOCP)","Depends":"R (>= 2.11), methods, quadprog, Rglpk,
timeSeries","Description":"Accompanying package of the book 'Financial Risk
Modelling\nand Portfolio Optimisation with R'. The data sets used in the\nbook are
contained in this package.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"FRAPO","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"xts, zoo, Rsolnp","Title":"Financial Risk Modelling and
Portfolio Optimisation with R","Version":"0.3-8"},"FRB":{"Author":"Ella Roelant,
Stefan Van Aelst, Gert Willems","Depends":"corpcor, rrcov (>= 1.3-
01)","Description":"This package performs robust inference based on applying\nFast
and Robust Bootstrap on robust estimators. Available\nmethods are multivariate
regression, PCA and Hotelling tests.","License":"GPL-
2","NeedsCompilation":"no","Package":"FRB","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Fast and Robust Bootstrap","Version":"1.8"},"FRCC":
{"Author":"Raul Cruz-Cano","Depends":"CCP, MASS, calibrate,
corpcor","Description":"This package implements the functions associated with
Fast\nRegularized Canonical Correlation Analysis.","License":"GPL-
2","NeedsCompilation":"no","Package":"FRCC","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Fast Regularized Canonical Correlation
Analysis","Version":"1.0"},"FREGAT":{"Author":"Nadezhda M. Belonogova
<belon@bionet.nsc.ru> and\nGulnara R. Svishcheva <gulsvi@mail.ru>,\nwith
contributions from:\nSeunggeun Lee (kernel functions), Pierre Lafaye de Micheaux
('davies' method),\nThomas Lumley ('kuonen' method), James O. Ramsay (functional
data analysis functions),\nDavid Clayton ('read.plink' function) and Brian Ripley
('ginv' function)","Depends":"R (>= 2.10.0)","Description":"Fast regional
association analysis of quantitative traits for family-based and population
studies.","Imports":"methods, Matrix, splines, parallel","License":"GPL-
3","NeedsCompilation":"yes","Package":"FREGAT","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"doParallel, foreach, GenABEL, seqminer","Title":"Family
REGional Association Tests","Version":"1.0"},"FREQ":{"Author":"Annegret Grimm &
Klaus Henle","Description":"Real capture frequencies will be fitted to various
distributions which provide the basis of estimating population sizes, their
standard error, and symmetric as well as asymmetric confidence
intervalls.","License":"GPL-
2","NeedsCompilation":"no","Package":"FREQ","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"FREQ: Estimate population size from capture
frequencies","Version":"1.0"},"FRESA.CAD":{"Author":"Jose Gerardo Tamez-Pena,
Antonio Martinez-Torteya and Israel Alanis","Depends":"Rcpp (>=
0.10.0),stringr,miscTools,Hmisc,pROC","Description":"Contains a set of utilities
for building and testing formula-based models (linear, logistic or COX) for
Computer Aided Diagnosis\/Prognosis applications. Utilities include data
adjustment, univariate analysis, model building, model-validation, longitudinal
analysis, reporting and visualization.","License":"LGPL (>=
2)","NeedsCompilation":"yes","Package":"FRESA.CAD","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"nlme,rpart,gplots,RColorBrewer,class,cvTools,glmnet
,survival","Title":"Feature Selection Algorithms for Computer Aided
Diagnosis","Version":"2.2.0"},"FSA":{"Author":"Derek Ogle [aut, cre]","Depends":"R
(>= 3.0.0)","Description":"Functions to perform a variety of simple fish stock
assessment\nmethods. Detailed vignettes are available on the fishR website
<http:\/\/derekogle.com\/fishR\/>.","Imports":"graphics, grDevices, stats, tools,
utils, car, dplyr, gdata,\ngplots, Hmisc, plotrix, plyr, sciplot","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"FSA","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"dunn.test, fishmethods, FSAdata, knitr, lmtest,
marked,\nnlstools, Rcapture, relax, testthat, rmarkdown","Title":"Functions for
Simple Fisheries Stock Assessment
Methods","URL":"https:\/\/github.com\/droglenc\/FSA","Version":"0.8.6"},"FSAdata":
{"Author":"Derek Ogle [aut, cre]","Depends":"R (>= 3.0.0)","Description":"The
datasets to support the Fish Stock Assessment (FSA) package.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"FSAdata","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Data to Support Fish Stock Assessment (FSA)
Package","URL":"http:\/\/derekogle.com\/fishR\/,
https:\/\/github.com\/droglenc\/FSAdata","Version":"0.3.2"},"FSInteract":
{"Author":"Hyun Jik Kim, Rajen D. Shah","Depends":"Rcpp (>= 0.11.2), Matrix (>=
1.0)","Description":"Performs fast detection of interactions in large-scale data
using the\nmethod of random intersection trees introduced in\n``Shah, R. D. and
Meinshausen, N. (2014) Random Intersection Trees''. The algorithm\nfinds
potentially high-order interactions in high-dimensional binary\ntwo-class
classification data, without requiring lower order interactions\nto be informative.
The search is particularly fast when the matrices of\npredictors are sparse. It
can also be used to perform market basket analysis\nwhen supplied with a single
binary data matrix. Here it will find collections\nof columns which for many rows
contain all 1's.","License":"GPL-
2","NeedsCompilation":"yes","Package":"FSInteract","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Fast Searches for
Interactions","Version":"0.1.1"},"FSelector":{"Author":"Piotr Romanski, Lars
Kotthoff","Description":"This package provides functions for selecting
attributes\nfrom a given dataset. Attribute subset selection is the process\nof
identifying and removing as much of the irrelevant and\nredundant information as
possible.","Imports":"randomForest, RWeka, digest, entropy","License":"GPL-
2","NeedsCompilation":"no","Package":"FSelector","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"mlbench, rpart","Title":"Selecting
attributes","Version":"0.20"},"FTICRMS":{"Author":"Don
Barkauskas","Depends":"Matrix,lattice,splines","Description":"This package was
developed partially with funding from the\nNIH Training Program in Biomolecular
Technology\n(2-T32-GM08799).","License":"GPL-
2","NeedsCompilation":"no","Package":"FTICRMS","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Programs for Analyzing Fourier Transform-Ion Cyclotron
Resonance\nMass Spectrometry Data","Version":"0.8"},"FUNTA":{"Author":"Andre
Rehage","Description":"Computes the functional tangential angle pseudo-depth and
its robustified version from the paper by Kuhnt and Rehage (2016). See Kuhnt, S.;
Rehage, A. (2016): An angle-based multivariate functional pseudo-depth for shape
outlier detection, JMVA 146, 325-340, <doi:10.1016\/j.jmva.2015.10.016> for
details.","License":"GPL-
3","NeedsCompilation":"no","Package":"FUNTA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Functional Tangential Angle Pseudo-
Depth","Version":"0.1.0"},"FWDselect":{"Author":"Marta Sestelo [aut, cre],\nNora M.
Villanueva [aut],\nJavier Roca-Pardinas [aut]","Depends":"R (>=
3.1.0)","Description":"A simple method\nto select the best model or best subset of
variables using\ndifferent types of data (binary, Gaussian or Poisson)
and\napplying it in different contexts (parametric or non-
parametric).","Imports":"cvTools, mgcv, parallel, graphics, stats","License":"MIT +
file
LICENSE","NeedsCompilation":"no","Package":"FWDselect","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Selecting Variables in Regression
Models","URL":"http:\/\/cran.r-
project.org\/package=FWDselect","Version":"2.1.0"},"FacPad":{"Author":"Haisu
Ma","Depends":"R (>= 2.12.1),Rlab,MASS","Description":"This method tries to explain
the gene-wise treatment response ratios in terms of the latent pathways. It uses
bayesian sparse factor modeling to infer the loadings (weights) of each pathway on
its associated probesets as well as the latent factor activity levels for each
treatment.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"FacPad","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Bayesian Sparse Factor Analysis model for the inference
of\npathways responsive to drug treatment","Version":"3.0"},"FactMixtAnalysis":
{"Author":"Cinzia Viroli","Depends":"R (>= 2.0.1), MASS,
mvtnorm","Description":"The package estimates Factor Mixture Analysis via the
EM\nalgorithm","License":"GPL-
2","NeedsCompilation":"no","Package":"FactMixtAnalysis","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Factor Mixture Analysis with
covariates","Version":"1.0"},"FactoClass":{"Author":"Campo Elias Pardo
<cepardot@unal.edu.co>, Pedro Cesar del Campo\n<pcdelcampon@unal.edu.co> and Camilo
Jose Torres\n<cjtorresj@unal.edu.co>, with the contributions from Ivan
Diaz\n<ildiazm@unal.edu.co>, Mauricio
Sadinle\n<msadinleg@unal.edu.co>.","Depends":"R (>= 2.7.0), ade4,
xtable","Description":"Multivariate exploration of a data table with
factorial\nanalysis and cluster methods.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"FactoClass","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Combination of Factorial Methods and Cluster
Analysis","Version":"1.1.2"},"FactoMineR":{"Author":"Francois Husson, Julie Josse,
Sebastien Le, Jeremy Mazet","Depends":"R (>= 2.12.0)","Description":"Exploratory
data analysis methods such as principal component methods and
clustering.","Imports":"\ncar,cluster,ellipse,flashClust,graphics,grDevices,lattice
,leaps,MASS,scatterplot3d,stats,data.table,dplyr,knitr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"FactoMineR","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"missMDA","Title":"Multivariate Exploratory Data
Analysis and Data
Mining","URL":"http:\/\/factominer.free.fr","Version":"1.32"},"Factoshiny":
{"Author":"Pauline Vaissie, Astrid Monge, Francois
Husson","Depends":"FactoMineR,shiny(>= 0.11)","Description":"Perform factorial
analysis with a menu and draw graphs interactively thanks to FactoMineR and a Shiny
application.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Factoshiny","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Perform Factorial Analysis from FactoMineR with a
Shiny\nApplication","Version":"1.0.2"},"Fahrmeir":{"Author":"compiled by Kjetil B
Halvorsen","Depends":"stats, R (>= 2.1.0)","Description":"Data and functions for
the book \"Multivariate Statistical\nModelling Based on Generalized Linear
Models\", first edition, by\nLudwig Fahrmeir and Gerhard Tutz. Useful when using
the book.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Fahrmeir","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"MASS","Title":"Data from the Book \"Multivariate
Statistical Modelling Based on\nGeneralized Linear Models\", First Edition, by
Ludwig Fahrmeir\nand Gerhard Tutz","Version":"2015.6.25"},"FamEvent":
{"Author":"Yun-Hee Choi, Karen Kopciuk, Wenqing He, Laurent
Briollais","Depends":"R(>= 3.0.0), base, MASS, truncnorm, survival,
kinship2","Description":"Generates time-to-event family data associated with
mutated genes arising from various family study designs such as population-based,
clinic- based, or multi-stage designs and provides functions to fit family data
accounting for the study design and estimate age-dependent penetrance functions. It
also provides carrier probabilities for those with missing genotypes
and penetrance estimations are based on an Expectation-Maximization algorithm when
genotypes are missing.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"FamEvent","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Simulation of Time-to-Event Family Data and
Penetrance\nEstimation","Version":"1.1"},"Familias":{"Author":"Petter Mostad, Thore
Egeland, Ivar Simonsson","Depends":"R (>= 1.8.0), kinship2, paramlink,
Rsolnp","Description":"\nAn interface to the core Familias functions
(www.familias.name),\nwhich are programmed in C++.","License":"GPL-
2","NeedsCompilation":"yes","Package":"Familias","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Probabilities for Pedigrees Given DNA
Data","URL":"http:\/\/www.familias.name,
http:\/\/www.familias.no","Version":"2.4"},"FastBandChol":{"Author":"Aaron Molstad
<molst029@umn.edu>","Description":"Fast and numerically stable estimation of a
covariance matrix by banding the Cholesky factor using a modified Gram-Schmidt
algorithm implemented in RcppArmadilo. See <http:\/\/stat.umn.edu\/~molst029> for
details on the algorithm.","Imports":"Rcpp","License":"GPL-
2","NeedsCompilation":"yes","Package":"FastBandChol","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Fast Estimation of a Covariance Matrix by Banding
the Cholesky\nFactor","Version":"0.1.1"},"FastGP":{"Author":"Giri Gopalan, Luke
Bornn","Description":"Contains Rcpp and RcppEigen implementations of matrix
operations useful for Gaussian process models, such as the inversion of a symmetric
Toeplitz matrix, sampling from multivariate normal distributions, evaluation of the
log-density of a multivariate normal vector, and Bayesian inference for latent
variable Gaussian process models with elliptical slice sampling (Murray, Adams, and
MacKay 2010).","Imports":"Rcpp, MASS, mvtnorm, rbenchmark, stats","License":"GPL-
2","NeedsCompilation":"yes","Package":"FastGP","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Efficiently Using Gaussian Processes with Rcpp and
RcppEigen","Version":"1.2"},"FastHCS":{"Author":"Kaveh Vakili [aut,
cre]","Depends":"R (>= 3.1.1), matrixStats, robustbase","Description":"The FastHCS
algorithm of Schmitt and Vakili (2014) for high-dimensional, robust PCA modelling
and associated outlier detection and diagnostic tools.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"FastHCS","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"mvtnorm","Title":"Robust Algorithm for Principal
Component Analysis","Version":"0.0.5"},"FastImputation":{"Author":"Stephen R.
Haptonstahl","Description":"TrainFastImputation uses training data to describe
a\nmultivariate normal distribution that the data approximates or\ncan be
transformed into approximating and stores this information\nas an object of class
FastImputationPatterns. The FastImputation\nfunction uses this
FastImputationPatterns object to impute (make\na good guess at) missing data in a
single line or a whole data frame\nof data. This approximates the process used by
Amelia\n[http:\/\/gking.harvard.edu\/amelia\/] but is much faster when\nfilling in
values for a single line of data.","Imports":"methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"FastImputation","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat","Title":"Learn from Training Data
then Quickly Fill in Missing Data","Version":"1.3"},"FastKM":{"Author":"Rachel
Marceau, Wenbin Lu, Michele M. Sale, Bradford B. Worrall, Stephen R. Williams,
Fang-Chi Hsu, Jung-Ying Tzeng, and Shannon T. Holloway","Depends":"rARPACK, stats,
methods","Description":"A computationally efficient and statistically rigorous fast
Kernel Machine method for multi-kernel analysis. The approach is based on a low-
rank approximation to the nuisance effect kernel matrices. The algorithm is
applicable to continuous, binary, and survival traits and is implemented using the
existing single-kernel analysis software 'SKAT' and 'coxKM'. 'coxKM' can be
obtained from http:\/\/www.hsph.harvard.edu\/xlin\/software.html.","License":"GPL-
2","NeedsCompilation":"no","Package":"FastKM","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"coxKM, SKAT, survival","Title":"A Fast Multiple-Kernel
Method Based on a Low-Rank Approximation","Version":"1.0"},"FastKNN":
{"Author":"Gaston Besanson","Description":"Compute labels for a test set according
to the k-Nearest Neighbors classification. This is a fast way to do k-Nearest
Neighbors classification because the distance matrix -between the features of the
observations- is an input to the function rather than being calculated in the
function itself every time.","Imports":"pdist, assertthat","License":"GPL-
3","NeedsCompilation":"no","Package":"FastKNN","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Fast k-Nearest Neighbors","Version":"0.0.1"},"FastPCS":
{"Author":"Kaveh Vakili [aut, cre]","Depends":"R (>= 3.1.1),
matrixStats","Description":"The FastPCS algorithm of Vakili and Schmitt (2014) for
robust estimation of multivariate location and scatter and multivariate outliers
detection.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"FastPCS","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"mvtnorm","Title":"FastPCS Robust Fit of Multivariate
Location and Scatter","Version":"0.1.2"},"FastRCS":{"Author":"Kaveh Vakili [aut,
cre]","Depends":"R (>= 3.1.1), matrixStats","Description":"The FastRCS algorithm of
Vakili and Schmitt (2014) for robust fit of the multivariable linear regression
model and outliers detection.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"FastRCS","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"mvtnorm","Title":"Fits the FastRCS Robust
Multivariable Linear Regression Model","Version":"0.0.7"},"FastRWeb":
{"Author":"Simon Urbanek <Simon.Urbanek@r-project.org>, Jeffrey Horner
<jeffrey.horner@gmail.com>","Depends":"R (>= 2.0.0)","Description":"Infrastrcture
for creating rich, dynamic web content using R scripts while maintaining very fast
response time.","Imports":"base64enc, grDevices, stats, utils,
Cairo","License":"GPL-
2","NeedsCompilation":"yes","Package":"FastRWeb","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"Rserve","Title":"Fast Interactive Framework for Web
Scripting Using R","URL":"http:\/\/www.rforge.net\/FastRWeb\/","Version":"1.1-
1"},"FatTailsR":{"Author":"Patrice Kiener","Depends":"R (>=
3.1.0)","Description":"Kiener distributions K1, K2, K3 and K4 to
characterize\ndistributions with left and right, symmetric or asymmetric fat tails
in market\nfinance, neuroscience and other disciplines. Two algorithms to estimate
with\na high accuracy distribution parameters, quantiles, value-at-risk and
expected\nshortfall. Also, power hyperbolas and power hyperbolic functions. v1.5-
5\ncorresponds to upgrade from 3.1.0 to R-3.2.3.","Imports":"minpack.lm,
timeSeries, parallel, stats","License":"GPL-
2","NeedsCompilation":"no","Package":"FatTailsR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"zoo, xts","Title":"Kiener Distributions and Fat Tails
in Finance","URL":"http:\/\/www.inmodelia.com\/fattailsr-en.html","Version":"1.6-
0"},"FeaLect":{"Author":"Habil Zare","Depends":"lars, rms","Description":"For each
feature, a score is computed that can be useful\nfor feature selection. Several
random subsets are sampled from\nthe input data and for each random subset, various
linear\nmodels are fitted using lars method. A score is assigned to\neach feature
based on the tendency of LASSO in including that\nfeature in the models.Finally,
the average score and the models\nare returned as the output. The features with
relatively low\nscores are recommended to be ignored because they can lead
to\noverfitting of the model to the training data. Moreover, for\neach random
subset, the best set of features in terms of global\nerror is returned. They are
useful for applying Bolasso, the\nalternative feature selection method that
recommends the\nintersection of features subsets.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"FeaLect","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Scores Features for Feature
Selection","Version":"1.10"},"FeatureHashing":{"Author":"Wush Wu [aut,
cre],\nMichael Benesty [aut, ctb]","Depends":"R (>= 3.1),
methods","Description":"Feature hashing, also called as the hashing trick, is a
method to transform\nfeatures of a instance to a vector. Thus, it is a method to
transform a real dataset to a matrix.\nWithout looking up the indices in an
associative array,\nit applies a hash function to the features and uses their hash
values as indices directly.\nThe method of feature hashing in this package was
proposed in Weinberger et al. (2009).\nThe hashing algorithm is the murmurhash3
from the digest package.\nPlease see the README in
https:\/\/github.com\/wush978\/FeatureHashing for more
information.","Imports":"Rcpp (>= 0.11), Matrix, digest(>= 0.6.8), magrittr (>=
1.5)","License":"GPL (>= 3) | file
LICENSE","NeedsCompilation":"yes","Package":"FeatureHashing","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Suggests":"RUnit, glmnet, knitr, xgboost,
rmarkdown","Title":"Creates a Model Matrix via Feature Hashing with a
Formula\nInterface","URL":"https:\/\/github.com\/wush978\/FeatureHashing","Version"
:"0.9.1.1"},"FedData":{"Author":"R. Kyle Bocinsky [aut, cre], Dylan Beaudette
[ctb], Scott Chamberlain [ctb]","Depends":"R (>= 3.2.0),
sp","Description":"Functions to automate downloading geospatial data available
from\nseveral federated data sources (mainly sources maintained by the US
Federal\ngovernment). Currently, the package allows for retrieval of five
datasets:\nThe National Elevation Dataset digital elevation models (1 and 1\/3 arc-
second;\nUSGS); The National Hydrography Dataset (USGS); The Soil Survey
Geographic\n(SSURGO) database from the
National Cooperative Soil Survey (NCSS), which is\nled by the Natural Resources
Conservation Service (NRCS) under the USDA; the\nGlobal Historical Climatology
Network (GHCN), coordinated by National Climatic\nData Center at NOAA; and the
International Tree Ring Data Bank. Additional\ndata sources are in the works,
including global DEM resources (ETOPO1, ETOPO5,\nETOPO30, SRTM), global soils
(HWSD), MODIS satellite data products, the National\nAtlas (US), Natural Earth,
PRISM, and WorldClim.","Imports":"data.table, devtools, soilDB, igraph, curl,
methods, rgdal (>=\n1.1), raster, Hmisc","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"FedData","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Functions to Automate Downloading Geospatial Data
Available from\nSeveral Federated Data Sources","Version":"2.0.8"},"FeedbackTS":
{"Author":"Samuel Soubeyrand, Cindy E. Morris, E. Keith Bigg","Depends":"R (>=
3.0.0), methods, maps, mapdata, proj4, geoR, sp","Description":"Analysis of
fragmented time directionality to investigate feedback in time series. Tools
provided by the package allow the analysis of feedback for a single time series and
the analysis of feedback for a set of time series collected across a spatial
domain.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"FeedbackTS","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Analysis of Feedback in Time
Series","Version":"1.3.1"},"Fgmutils":{"Author":"Clayton Vieira Fraga,\nAna Paula
Simiqueli,\nWagner Amorim da Silva Altoe","Depends":"sqldf, stringr, plyr, R (>=
3.0)","Description":"Growth models and forest production require existing
data\nmanipulation and the creation of new data, structured from basic
forest\ninventory data. The purpose of this package is provide functions to
support\nthese activities.","Imports":"data.table, tcltk, utils, stats, graphics,
devEMF, png,\ngrDevices","License":"GPL-
2","NeedsCompilation":"no","Package":"Fgmutils","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"testthat","Title":"Forest Growth Model
Utilities","Version":"0.4"},"FieldSim":{"Author":"Alexandre Brouste
<Alexandre.Brouste@univ-lemans.fr>,\nSophie Lambert-Lacroix
<Sophie.Lambert@imag.fr>.","Depends":"R (>= 2.0.0), methods, rgl,
RColorBrewer","Description":"Tools for random fields and bridges
simulations.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"FieldSim","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Random Fields (and Bridges)
Simulations","URL":"http:\/\/cran.r-
project.org\/web\/packages\/FieldSim\/","Version":"3.2.1"},"FinAsym":
{"Author":"Paolo Zagaglia","Description":"This package accomplishes two tasks: a)
it classifies\nimplicit trading activity from quotes in OTC markets using
the\nalgorithm of Lee and Ready (1991); b) based on information for\ntrade
initiation, the package computes the probability of\ninformed trading of Easley and
O'Hara (1987).","License":"GPL-
3","NeedsCompilation":"no","Package":"FinAsym","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Classifies implicit trading activity from market quotes
and\ncomputes the probability of informed trading","Version":"1.0"},"FinCal":
{"Author":"Felix Yanhui Fan <nolanfyh@gmail.com>","Description":"Package for time
value of money calculation, time series analysis and computational
finance.","Imports":"ggplot2, reshape2, RCurl","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"FinCal","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Time Value of Money, Time Series Analysis and
Computational\nFinance","URL":"http:\/\/felixfan.github.io\/FinCal\/","Version":"0.
6.2"},"FinCovRegularization":{"Author":"Yachen Yan [aut, cre]","Depends":"R (>=
2.10)","Description":"Estimation and regularization for covariance matrix of asset
returns. For covariance matrix estimation,\nthree major types of factor models are
included: macroeconomic factor model, fundamental factor model and
statistical\nfactor model. For covariance matrix regularization, four regularized
estimators are included: banding, tapering,\nhard-thresholding and soft-
thresholding. The tuning parameters of these regularized estimators are selected
via\ncross-validation.","Imports":"quadprog","License":"GPL-
2","NeedsCompilation":"no","Package":"FinCovRegularization","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Title":"Covariance Matrix Estimation and
Regularization for
Finance","URL":"http:\/\/github.com\/yanyachen\/FinCovRegularization","Version":"1.
0.0"},"FinTS":{"Author":"Spencer Graves","Depends":"R (>= 2.10), zoo,
graphics","Description":"R companion to Tsay (2005)\nAnalysis of Financial Time
Series, 2nd ed. (Wiley).\nIncludes data sets, functions and script files\nrequired
to work some of the examples. Version 0.3-x\nincludes R objects for all data files
used in the text\nand script files to recreate most of the analyses in\nchapters 1-
3 and 9 plus parts of chapters 4 and 11.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"FinTS","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"moments, distrEx, tseries, urca, lmtest, sandwich,
psych,\nGPArotation, chron, polynom, fUnitRoots, e1071","Title":"Companion to Tsay
(2005) Analysis of Financial Time
Series","URL":"http:\/\/faculty.chicagobooth.edu\/ruey.tsay\/teaching\/bs41202\/sp2
009","Version":"0.4-5"},"FinancialInstrument":{"Author":"Peter Carl, Brian G.
Peterson, Garrett See","Depends":"R (>= 2.12.0), quantmod (>= 0.4-3), zoo (>= 1.7-
5), xts","Description":"Infrastructure for defining meta-data and\nrelationships
for financial
instruments.","Imports":"TTR","License":"GPL","NeedsCompilation":"no","Package":"Fi
nancialInstrument","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"
foreach, XML (>= 3.96.1.1), testthat, its, timeSeries","Title":"Financial
Instrument Model Infrastructure for R","URL":"https:\/\/r-forge.r-
project.org\/projects\/blotter\/","Version":"1.2.0"},"FindAllRoots":
{"Author":"Bingpei Wu & Jiajun He & Sijie Chen & Yangyang Liu","Description":"Find
all root(s) of the equation,including complex\nroots;Find root(s) of the equation
by dichotomy.Besides,in\ndichotomy, more than one interval can be given at a
time.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"FindAllRoots","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Find all root(s) of the equation and Find root(s) of
the\nequation by dichotomy","Version":"1.0"},"FindIt":{"Author":"Naoki Egami
<naoki.egami5@gmail.com>, Marc Ratkovic <ratkovic@princeton.edu>, Kosuke Imai
<kimai@princeton.edu>,","Depends":"R (>= 2.15.0), glmnet, lars,
Matrix","Description":"The heterogeneous treatment effect estimation
procedure\nproposed by Imai and Ratkovic (2013).\nThe proposed method is
applicable, for\nexample, when selecting a small number of most (or
least)\nefficacious treatments from a large number of alternative\ntreatments as
well as when identifying subsets of the\npopulation who benefit (or are harmed by)
a treatment of\ninterest. The method adapts the Support Vector Machine\nclassifier
by placing separate LASSO constraints over the\npre-treatment parameters and causal
heterogeneity parameters of\ninterest. This allows for the qualitative distinction
between\ncausal and other parameters, thereby making the variable\nselection
suitable for the exploration of causal heterogeneity.\nThe package also contains
the function, INT, which estimates\nthe average marginal treatment effect, the
average treatment\ncombination effect, and the average marginal treatment
interaction\neffect proposed by Egami and Imai (2015).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"FindIt","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Finding Heterogeneous Treatment
Effects","Version":"0.5"},"FindMinIC":{"Author":"Nicholas Lange, Tom Fletcher,
Kristen Zygmunt","Description":"Creates models from all combinations of a list of
variables and sorts by minimum IC (information criterion).","Imports":"nlme,
sets","License":"LGPL (>=
3.0)","NeedsCompilation":"no","Package":"FindMinIC","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Find Models with Minimum
IC","Version":"1.6"},"FisHiCal":{"Author":"Yoli Shavit, Fiona Kathryn Hamey and
Pietro Lio'","Depends":"R (>= 3.0.2), igraph, RcppArmadillo (>=
0.4.100.2.1)","Description":"FisHiCal integrates Hi-C and FISH data, offering a
modular and easy-to-use tool for chromosomal spatial
analysis.","License":"GPL","NeedsCompilation":"yes","Package":"FisHiCal","Repositor
y":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"rgl","Title":"Iterative FISH-
based Calibration of Hi-C Data","Version":"1.1"},"FisherEM":{"Author":"Charles
Bouveyron and Camille Brunet","Depends":"MASS,elasticnet","Description":"The
FisherEM package provides an efficient algorithm for\nthe unsupervised
classification of high-dimensional data. This\nFisherEM algorithm models and
clusters the data in a\ndiscriminative and low-dimensional latent subspace. It
also\nprovides a low-dimensional representation of the clustered\ndata. A sparse
version of Fisher-EM algorithm is also provided.","License":"GPL-
2","NeedsCompilation":"no","Package":"FisherEM","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"The Fisher-EM algorithm","Version":"1.4"},"FitAR":
{"Author":"A.I. McLeod, Ying Zhang and Changjiang Xu","Depends":"R (>= 2.0.0),
lattice, leaps, ltsa, bestglm","Description":"Comprehensive model building function
for identification,\nestimation and diagnostic checking for AR and subset AR
models.\nTwo types of subset AR models are supported. One family of\nsubset AR
models, denoted by ARp, is formed by taking subet of\nthe original AR coefficients
and in the other, denoted by ARz,\nsubsets of the partial autocorrelations are
used. The main\nadvantage of the ARz model is its applicability to very
large\norder models.","Imports":"lattice,
leaps, ltsa","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"FitAR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Subset AR Model
Fitting","URL":"http:\/\/www.stats.uwo.ca\/faculty\/aim","Version":"1.94"},"FitARMA
":{"Author":"A.I. McLeod","Depends":"R (>= 2.1.0), FitAR","Description":"Implements
fast maximum likelihood algorithm for fitting ARMA time series. Uses S3 methods
print, summary, fitted, residuals. Fast exact Gaussian ARMA
simulation.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"FitARMA","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"FitARMA: Fit ARMA or ARIMA using fast MLE
algorithm","URL":"http:\/\/www.stats.uwo.ca\/faculty\/aim","Version":"1.6"},"FlexPa
ramCurve":{"Author":"Stephen Oswald [aut,
cre]","Depends":"nlme","Description":"Model selection tools and 'selfStart'
functions to fit parametric curves in 'nls', 'nlsList' and 'nlme'
frameworks.","Imports":"stats, utils","License":"GPL-
2","NeedsCompilation":"no","Package":"FlexParamCurve","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Tools to Fit Flexible Parametric
Curves","URL":"http:\/\/pennstate.academia.edu\/SteveOswald","Version":"1.5-
3"},"FlowScreen":{"Author":"Jennifer Dierauer [aut, cre],\nPaul Whitfield
[aut]","Depends":"R (>= 3.0)","Description":"Screens daily streamflow time series
for temporal trends and\nchange-points. This package has been primarily developed
for assessing\nthe quality of daily streamflow time series. It also contains tools
for\nplotting and calculating many different streamflow metrics. The package can
be\nused to produce summary screening plots showing change-points and
significant\ntemporal trends for high flow, low flow, and\/or baseflow statistics,
or it can\nbe used to perform more detailed hydrological time series analyses.
The\npackage was designed for screening daily streamflow time series from
Water\nSurvey Canada and the United States Geological Survey but will also
work\nwith streamflow time series from many other agencies.","Imports":"zyp,
changepoint, evir, graphics, grDevices, stats, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"FlowScreen","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Daily Streamflow Trend and Change Point
Screening","Version":"1.0"},"Flury":{"Author":"Bernard
Flury","Description":"Contains data sets from Bernard Flury (1997) A First\nCourse
in Multivariate Statistics, Springer NY","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Flury","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Data Sets from Flury, 1997","Version":"0.1-3"},"ForIT":
{"Author":"Nicola Puletti, Marco Mura, Cristiano Castaldi, Maurizio Marchi,
Ugo\nChiavetta, Roberto Scotti","Description":"This package provides estimates of
tree volume and biomass from\nItalian NFI models","License":"GPL-
3","NeedsCompilation":"no","Package":"ForIT","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Functions from the 2nd Italian Forest Inventory
(INFC)","Version":"1.0"},"ForImp":{"Author":"Alessandro Barbiero, Pier Alda
Ferrari, Giancarlo Manzi","Depends":"homals, sampling,
mvtnorm","Description":"Imputation of missing values in datasets of ordinal
variables through a forward imputation
algorithm","License":"GPL","NeedsCompilation":"no","Package":"ForImp","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Title":"Imputation of Missing Values
Through a Forward Imputation\nAlgorithm","Version":"1.0.3"},"ForeCA":
{"Author":"Georg M. Goerg <im@gmge.org>","Depends":"R (>= 3.0.0), ifultools (>=
2.0.0)","Description":"Implementation of Forecastable Component Analysis
('ForeCA'),\nincluding main algorithms and auxiliary function (summary, plotting,
etc.) to\napply 'ForeCA' to multivariate time series data. 'ForeCA' is a novel
dimension\nreduction (DR) technique for temporally dependent signals. Contrary to
other\npopular DR methods, such as 'PCA' or 'ICA', 'ForeCA' takes time
dependency\nexplicitly into account and searches for the most ''forecastable''
signal.\nThe measure of forecastability is based on the Shannon entropy of the
spectral\ndensity of the transformed signal.","Imports":"MASS, sapa, graphics,
reshape2, utils","License":"GPL-
2","NeedsCompilation":"no","Package":"ForeCA","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"astsa, mgcv, nlme (>= 3.1-64), testthat (>= 0.9.0),
rSFA,","Title":"Forecastable Component
Analysis","URL":"http:\/\/www.gmge.org","Version":"0.2.4"},"ForecastCombinations":
{"Author":"Eran Raviv","Depends":"quantreg, quadprog, utils","Description":"Aim:
Supports the most frequently used methods to combine forecasts. Among others:
Simple average, Ordinary Least Squares, Least Absolute Deviation, Constrained Least
Squares, Variance-based, Best Individual model, Complete subset regressions and
Information-theoretic (information criteria based).","License":"GPL-
2","NeedsCompilation":"no","Package":"ForecastCombinations","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Suggests":"MASS","Title":"Forecast
Combinations","Version":"1.1"},"FormalSeries":{"Author":"Tomasz
Zmorzynski","Depends":"methods","Description":"Implemented, addition, subtracking,
multiplication,\ndivision in formal series rings of any number of
variables\n(except division is only to 3 variables). Also are
available\n\"[\" \"[<-\" operators.","License":"GPL-
2","NeedsCompilation":"no","Package":"FormalSeries","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Elementary arithemtic in formal series
rings","Version":"1.0"},"Formula":{"Author":"Achim Zeileis [aut, cre],\nYves
Croissant [aut]","Depends":"R (>= 2.0.0), stats","Description":"Infrastructure for
extended formulas with multiple parts on the\nright-hand side and\/or multiple
responses on the left-hand side.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"Formula","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Extended Model Formulas","Version":"1.2-
1"},"ForwardSearch":{"Author":"Bent
Nielsen","Depends":"robustbase","Description":"Forward Search analysis of time
series regressions. Implements the asymptotic theory developed in Johansen and
Nielsen (2013, 2014).","License":"GPL-
3","NeedsCompilation":"no","Package":"ForwardSearch","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Forward Search using asymptotic
theory","URL":"http:\/\/users.ox.ac.uk\/~nuff0078\/","Version":"1.0"},"FourScores":
{"Author":"Matthias Speidel","Description":"A game for two players: Who gets first
four in a row\n(horizontal, vertical or diagonal) wins. Published by
Milton\nBradley, designed by Howard Wexler and Ned Strongin.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"FourScores","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"FourScores - A game for two
players","Version":"1.0"},"FrF2":{"Author":"Ulrike Groemping","Depends":"R(>=
2.13.0), DoE.base(>= 0.25)","Description":"This package creates regular and non-
regular Fractional\nFactorial designs. Furthermore, analysis tools for
Fractional\nFactorial designs with 2-level factors are offered (main\neffects and
interaction plots for all factors simultaneously,\ncube plot for looking at the
simultaneous effects of three\nfactors, full or half normal plot, alias structure
in a more\nreadable format than with the built-in function alias). The\npackage is
still under development. While much of the intended\nfunctionality is already
available, some changes and\nimprovements are still to be expected. Suggestions are
welcome.","Imports":"sfsmisc(>= 1.0-26), BsMD, utils, scatterplot3d, igraph(>=
2)","NeedsCompilation":"no","Package":"FrF2","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"FrF2.catlg128","Title":"Fractional Factorial designs with
2-level factors","URL":"http:\/\/prof.beuth-
hochschule.de\/groemping\/","Version":"1.7-1"},"FrF2.catlg128":{"Author":"Ulrike
Groemping","Depends":"R(>= 2.13.0), FrF2(>= 1.4)","Description":"This package
provides catalogues of resolution IV regular\nfractional factorial designs in 128
runs for up to 33 2-level\nfactors. The catalogues are complete, excluding
resolution IV\ndesigns without 5-letter words, because these do not add value\nfor
a search for clear designs. The previous package version\n1.0 with complete
catalogues up to 24 runs (24 runs and a\nnamespace added later) can be downloaded
from the authors\nwebsite.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"FrF2.catlg128","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Catalogues of resolution IV 128 run 2-level
fractional\nfactorials up to 33 factors that do have 5-letter
words","URL":"http:\/\/prof.beuth-
hochschule.de\/groemping\/","Version":"1.2-1"},"FractalParameterEstimation":
{"Author":"Philipp Hermann","Description":"The parameters p and q are estimated
with the aid of randomized Sierpinski Carpet which is built on [p-p-p-q]-model.
Thereby, for three times simulation with p-value and once with q-value is assumed.
Hence these parameters are estimated and displayed.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"FractalParameterEstimation","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"Estimation of Parameters p and q for
Randomized Sierpinski\nCarpet for [p-p-p-q]-Model","Version":"1.0"},"Fragman":
{"Author":"Giovanny Covarrubias-Pazaran, Luis Diaz-Garcia, Brandon Schlautman,
Walter Salazar, Juan Zalapa.","Depends":"R (>= 2.10)","Description":"Performs
fragment analysis using genetic data coming from capillary electrophoresis
machines. These are files with FSA extension which stands for FASTA-type file and
contains DNA fragment intensities read by machinery. In addition to visualization,
it performs automatic scoring of SSRs (Sample Sequence Repeats; a
type of genetic marker very common across the genome) and other type of PCR
markers (standing for Polymerase Chain Reaction) in biparental populations such as
F1, F2, BC (backcross), and diversity panels (collection of genetic
diversity).","License":"GPL-
3","NeedsCompilation":"no","Package":"Fragman","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Fragment Analysis in
R","URL":"http:\/\/www.wisc.edu","Version":"1.0.3"},"Frames2":{"Author":"Antonio
Arcos <arcos@ugr.es>, Maria del Mar Rueda <mrueda@ugr.es>,\nMaria Giovanna Ranalli
<giovanna.ranalli@stat.unipg.it> and David
Molina\n<dmolinam@ugr.es>","Description":"Point and interval estimation in dual
frame surveys. In contrast\nto classic sampling theory, where only one sampling
frame is considered,\ndual frame methodology assumes that there are two frames
available for\nsampling and that, overall, they cover the entire target population.
Then,\ntwo probability samples (one from each frame) are drawn and
information\ncollected is suitably combined to get estimators of the parameter
of\ninterest.","Imports":"sampling, MASS, nnet","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Frames2","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Estimation in Dual Frame
Surveys","Version":"0.2.1"},"FreeSortR":{"Author":"Philippe Courcoux","Depends":"R
(>= 3.1), methods, smacof, vegan, ellipse","Description":"The package FreeSortR
provides tools for describing and analysing free sorting data. Main methods are
computation of consensus partition and factorial analysis of the dissimilarity
matrix between stimuli (using multidimensional scaling approach).","License":"GPL-
2","NeedsCompilation":"no","Package":"FreeSortR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Free Sorting data analysis","Version":"1.1"},"FreqProf":
{"Author":"Robert Epstein [aut],\nThomas Boulier [aut],\nRonald E. Robertson [cre,
aut],\nJonathan Mejia [ctb],\nAIBRT [cph]","Depends":"R (>=
3.2.2)","Description":"Tools for generating an informative type of line graph, the
frequency profile,\nwhich allows single behaviors, multiple behaviors, or the
specific behavioral patterns\nof individual subjects to be graphed from
occurrence\/nonoccurrence behavioral data.","Imports":"reshape2, ggplot2,
shiny","License":"GPL-
3","NeedsCompilation":"no","Package":"FreqProf","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Frequency Profiles Computing and
Plotting","URL":"https:\/\/github.com\/AIBRT\/FreqProf","Version":"0.0.1"},"FunChis
q":{"Author":"Yang Zhang, Hua Zhong, and Joe Song","Depends":"R (>=
3.0.0)","Description":"Statistical hypothesis testing methods for non-parametric
functional dependencies using asymptotic chi-square or exact statistics. These
tests were motivated to reveal evidence for causality based on functional
dependencies. They include asymptotic functional chi-square tests, an exact
functional test, a comparative functional chi-square test, and also a comparative
chi-square test. The normalized non-constant functional chi-square test was used by
Best Performer NMSUSongLab in HPN-DREAM (DREAM8) Breast Cancer Network Inference
Challenges. These tests offer an advantage over regression analysis when a
parametric functional form cannot be assumed.","Imports":"Rcpp,
stats","License":"LGPL (>=
3)","NeedsCompilation":"yes","Package":"FunChisq","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"Ckmeans.1d.dp, testthat","Title":"Chi-Square and
Exact Tests for Non-Parametric
Functional\nDependencies","URL":"http:\/\/www.cs.nmsu.edu\/~joemsong\/software,\nht
tp:\/\/www.cs.nmsu.edu\/~joemsong\/publications","Version":"2.2.3"},"FunCluster":
{"Author":"Corneliu Henegar <corneliu@henegar.info>","Depends":"R (>= 2.10), Hmisc,
cluster","Description":"FunCluster performs a functional analysis of
microarray\nexpression data based on Gene Ontology & KEGG functional\nannotations.
From expression data and functional annotations\nFunCluster builds classes of
putatively co-regulated biological\nprocesses through a specially designed
clustering procedure.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"FunCluster","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Functional Profiling of Microarray Expression
Data","URL":"http:\/\/corneliu.henegar.info\/FunCluster.htm","Version":"1.09"},"Fun
cMap":{"Author":"Bryan A. Hanson DePauw University, Greencastle Indiana
USA","Description":"Analyzes the function calls in an R package and creates a hive
plot of the calls, dividing them among functions that only make outgoing calls
(sources), functions that have only incoming calls (sinks), and those that have
both incoming calls and make outgoing calls (managers). Function calls can be
mapped by their absolute numbers, their normalized absolute numbers, or their rank.
FuncMap should be useful for comparing packages at a high level for their overall
design. Plus, it's just plain fun. The hive plot concept was developed by Martin
Krzywinski (www.hiveplot.com) and inspired this package. Note: this package is
maintained for historical reasons. HiveR is a full package for creating hive
plots.","Imports":"grid, stats, mvbutils","License":"GPL-
3","NeedsCompilation":"no","Package":"FuncMap","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"lattice","Title":"Hive Plots of R Package Function
Calls","Version":"1.0.8"},"Funclustering":{"Author":"Mohamed Soueidatt
<mohamed.soueidatt@inria.fr>, <msoueidatt@gmail.com>*.","Depends":"fda (>= 2.2.6),
R (>= 2.15.1), methods","Description":"This packages proposes a model-based
clustering algorithm for\nmultivariate functional data. The parametric mixture
model, based on the\nassumption of normality of the principal components resulting
from a\nmultivariate functional PCA, is estimated by an EM-like algorithm. The
main\nadvantage of the proposed algorithm is its ability to take into account
the\ndependence among curves.","Imports":"Rcpp (>= 0.10.3)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"Funclustering","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"A package for functional data
clustering","Version":"1.0.1"},"FunctionalNetworks":{"Author":"Alejandro Quiroz-
Zarate","Depends":"R (>= 2.10), breastCancerVDX, Biobase","Description":"R package
providing functions to perform gene and gene set network
inference.","License":"Artistic-
2.0","NeedsCompilation":"yes","Package":"FunctionalNetworks","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Title":"An algorithm for gene and gene set network
inference","URL":"http:\/\/compbio.dfci.harvard.edu\/","Version":"1.0.0"},"FusedPCA
":{"Author":"Yang Feng, Richard J. Samworth and Yi Yu","Depends":"R (>= 2.15.1),
genlasso","Description":"Efficient procedures for community detection in network
studies, especially for sparse networks. The algorithms impose penalties on the
differences of the coordinates which represent the community labels of the
nodes.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"FusedPCA","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Community Detection via Fused Principal Component
Analysis","Version":"0.2"},"FuzzyAHP":{"Author":"Jan Caha [aut, cre],\nAneta
DrÃ¡Å¾nÃ¡ [ctb, com]","Depends":"R (>= 3.0.0), methods","Description":"Calculation
of AHP (Analytic Hierarchy Process -
<http:\/\/en.wikipedia.org\/wiki\/Analytic_hierarchy_process>)\nwith classic and
fuzzy weights based on Saaty's pairwise comparison method for determination of
weights.","License":"LGPL (>=
3)","NeedsCompilation":"no","Package":"FuzzyAHP","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr","Title":"(Fuzzy) AHP
Calculation","URL":"http:\/\/github.com\/JanCaha\/FuzzyAHP\/","Version":"0.6.1"},"F
uzzyLP":{"Author":"Carlos A. Rabelo [aut, cre],\nPablo J. Villacorta
[ctb]","Depends":"FuzzyNumbers","Description":"Methods to solve Fuzzy Linear
Programming Problems with\nfuzzy constraints (by Verdegay, Zimmermann, Werner,
Tanaka),\nfuzzy costs (multiobjective, interval arithmetic, stratified piecewise
reduction,\ndefuzzification-based), and fuzzy technological
matrix.","Imports":"ROI, ROI.plugin.glpk","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"FuzzyLP","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"R.rsp","Title":"Fuzzy Linear
Programming","URL":"http:\/\/decsai.ugr.es\/~pjvi","Version":"0.1-
3"},"FuzzyNumbers":{"Author":"Marek Gagolewski [aut, cre],\nJan Caha
[ctb]","Depends":"R (>= 3.0.0), methods, grDevices, graphics,
stats","Description":"S4 classes and methods\nto deal with fuzzy numbers. With them
you can compute any arithmetic\noperations (e.g. by using the Zadeh extension
principle),\nperform approximation of arbitrary FNs by trapezoidal and
piecewise\nlinear FNs, prepare plots of FNs for publications,
calculate\npossibility and necessity values for comparisons, etc.","License":"LGPL
(>=
3)","NeedsCompilation":"no","Package":"FuzzyNumbers","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"knitr","Title":"Tools to Deal with Fuzzy
Numbers","URL":"http:\/\/FuzzyNumbers.rexamine.com","Version":"0.4-
1"},"FuzzyStatProb":{"Author":"Author: Pablo J. Villacorta
<pjvi@decsai.ugr.es>","Description":"An implementation of a method for computing
fuzzy numbers representing stationary probabilities of an unknown Markov
chain,\nfrom which a sequence of observations along time has been obtained. The
algorithm is based on the proposal presented by James Buckley\nin his book on Fuzzy
probabilities (Springer, 2005), chapter 6. Package FuzzyNumbers is used to
represent the output probabilities.","Imports":"MultinomialCI, parallel,
FuzzyNumbers, DEoptim","License":"LGPL (>=
3)","NeedsCompilation":"no","Package":"FuzzyStatProb","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"markovchain, R.rsp","Title":"Fuzzy Stationary
Probabilities from a Sequence of Observations\nof
an Unknown Markov Chain","URL":"http:\/\/decsai.ugr.es\/~pjvi\/r-
packages.html","Version":"2.0.1"},"FuzzyToolkitUoN":{"Author":"Craig Knott, Luke
Hovell, Nathan Karimian with supervision from\nDr. Jon Garibaldi","Depends":"R (>=
2.15.1), splines","Description":"A custom framework for working with Type 1 Fuzzy
Logic,\nproduced by the University of Nottingham IMA Group.","License":"GPL (>=
2)","NeedsCompilation":"No","Package":"FuzzyToolkitUoN","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Type 1 Fuzzy Logic
Toolkit","URL":"http:\/\/ima.ac.uk","Version":"1.0"},"G1DBN":{"Author":"Sophie
Lebre <sophie.lebre@icube.unistra.fr>, original\nversion 1.0 by Sophie
Lebre\n<sophie.lebre@icube.unistra.fr>, contribution of Julien\nChiquet
<julien.chiquet@genopole.cnrs.fr> to version 2.0","Depends":"R (>= 2.11.1), MASS,
igraph","Description":"G1DBN performs DBN inference using 1st order
conditional\ndependencies.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"G1DBN","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"A package performing Dynamic Bayesian Network
inference","Version":"3.1.1"},"G2Sd":{"Author":"Regis K. Gallon (MNHN), Jerome
Fournier (CNRS|MNHN)","Depends":"R (>= 3.0.2)","Description":"Full descriptive
statistics, physical description of sediment,\nmetric or phi
sieves.","Imports":"shiny, xlsx, rJava, xlsxjars, reshape2, ggplot2,
stats,\ngraphics, grDevices","License":"GPL-
3","NeedsCompilation":"no","Package":"G2Sd","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Grain-Size Statistics and Description of
Sediment","URL":"https:\/\/cran.r-
project.org\/package=G2Sd,\nhttp:\/\/regisgallon.wordpress.com\/r-
software\/","Version":"2.1.5"},"GA":{"Author":"Luca Scrucca
<luca@stat.unipg.it>","Depends":"R (>= 2.15), methods, foreach,
iterators","Description":"An R package for optimization using genetic algorithms.
The package provides a flexible general-purpose set of tools for implementing
genetic algorithms search in both the continuous and discrete case, whether
constrained or not. Users can easily define their own objective function depending
on the problem at hand. Several genetic operators are available and can be combined
to explore the best settings for the current task. Furthermore, users can define
new genetic operators and easily evaluate their performances. GAs can be run
sequentially or in parallel.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GA","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"parallel, doParallel","Title":"Genetic
Algorithms","Version":"2.2"},"GA4Stratification":{"Author":"Sebnem Er, Timur
Keskinturk, Charlie Daly","Description":"This is a Genetic Algorithm package for
the determination\nof the stratum boundaries and sample sizes of each stratum
in\nstratified sampling","License":"GPL-
2","NeedsCompilation":"no","Package":"GA4Stratification","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"A genetic algorithm approach to determine
stratum boundaries and\nsample sizes of each stratum in stratified
sampling","Version":"1.0"},"GABi":{"Author":"Ed Curry","Depends":"R (>= 2.15.0),
hash","Description":"Generalized subspace pattern mining in data arrays, using a
genetic algorithm framework.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GABi","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"ArrayBin","Title":"Framework for Generalized Subspace
Pattern Mining","URL":"http:\/\/www.r-
"0.1"},"GAD":{"Author":"Leonardo Sandrini-Neto & Mauricio G. Camargo","Depends":"R
(>= 2.7.0), stats, matrixStats, R.methodsS3","Description":"This package analyses
complex ANOVA models with any\ncombination of orthogonal\/nested and fixed\/random
factors, as\ndescribed by Underwood (1997). There are two restrictions: (i)\ndata
must be balanced; (ii) fixed nested factors are not\nallowed. Homogeneity of
variances is checked using Cochran's C\ntest and 'a posteriori' comparisons of
means are done using\nStudent-Newman-Keuls (SNK) procedure.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"GAD","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"GAD: Analysis of variance from general
principles","Version":"1.1.1"},"GAIPE":{"Author":"Tzu-Yao Lin","Depends":"R (>=
2.15.3)","Description":"GAIPE implements graphical representation of accuracy
in\nparameter estimation (AIPE) on RMSEA for sample size planning\nin structural
equation modeling. Sample sizes suggested by\nRMSEA with AIPE method and power
analysis approach can also be\nobtained separately using the provided
functions.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GAIPE","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Graphical Extension with Accuracy in Parameter
Estimation\n(GAIPE)","URL":"http:\/\/www.r-
project.org,","Version":"1.0"},"GAMBoost":{"Author":"Harald Binder <binderh@uni-
mainz.de>","Depends":"R (>= 2.14.0), Matrix","Description":"This package provides
routines for fitting generalized\nlinear and and generalized additive models by
likelihood based\nboosting, using penalized B-splines","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"GAMBoost","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"parallel, snowfall","Title":"Generalized linear and
additive models by likelihood based\nboosting","Version":"1.2-3"},"GAMens":
{"Author":"Koen W. De Bock, Kristof Coussement and Dirk Van den Poel","Depends":"R
(>= 2.4.0), splines, gam, mlbench, caTools","Description":"Ensemble classifiers
based upon generalized additive models for binary\nclassification (De Bock et al.
(2010) <DOI:10.1016\/j.csda.2009.12.013>). The ensembles\nimplement Bagging
(Breiman (1996) <DOI:10.1023\/A:1018054314350>), the Random Subspace Method (Ho
(1998) <DOI:10.1109\/34.709601>), or\nboth, and use Hastie and Tibshirani's (1990)
generalized additive models (GAMs)\nas base classifiers. Once an ensemble
classifier has been trained, it can\nbe used for predictions on new data. A
function for cross validation is also\nincluded.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GAMens","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Applies GAMbag, GAMrsm and GAMens Ensemble Classifiers
for\nBinary Classification","Version":"1.2"},"GANPA":{"Author":"Zhaoyuan Fang,
Weidong Tian and Hongbin Ji","Depends":"GANPAdata","Description":"This package
implements a network-based gene weighting\nalgorithm for pathways, as well as a
gene-weighted gene set\nanalysis approach for microarray data pathway
analysis.","Imports":"graphics, stats, grDevices, utils","License":"GPL-
2","NeedsCompilation":"no","Package":"GANPA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Gene Association Network-based Pathway
Analysis","Version":"1.0"},"GANPAdata":{"Author":"Zhaoyuan Fang, Weidong Tian and
Hongbin Ji","Depends":"R (>= 2.10)","Description":"This is a dataset package for
GANPA, which implements a\nnetwork-based gene weighting approach to pathway
analysis. This\npackage includes data useful for GANPA, such as a
functional\nassociation network, pathways, an expression dataset and\nmulti-subunit
proteins.","License":"GPL-
2","NeedsCompilation":"no","Package":"GANPAdata","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"GANPA","Title":"The GANPA Datasets
Package","Version":"1.0"},"GAR":{"Author":"Andrew Geisler","Depends":"httr,
jsonlite","Description":"The functions included are used to obtain initial
authentication with Google Analytics as well as simple and organized data retrieval
from the API. Allows for retrieval from multiple profiles at once.","License":"GPL-
2","NeedsCompilation":"no","Package":"GAR","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Authorize and Request Google Analytics
Data","Version":"1.1"},"GAabbreviate":{"Author":"Luca Scrucca [aut],\nBaljinder K.
Sahdra [aut, cre]","Depends":"R (>= 3.0), GA (>= 2.0), psych (>=
1.4.3)","Description":"The GAabbreviate package uses Genetic Algorithms as an
optimization tool for scale abbreviation or subset selection that maximally
captures the variance in the original data.","Imports":"stats, graphics, grDevices,
2)","NeedsCompilation":"no","Package":"GAabbreviate","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Abbreviating Items Measures using Genetic
Algorithms","Version":"1.2"},"GB2":{"Author":"Monique Graf
<monique.p.n.graf@bluewin.ch>, Desislava Nedyalkova
<desislava.nedyalkova@gmail.com>.","Depends":"R (>= 3.1.0)","Description":"Package
GB2 explores the Generalized Beta distribution of the second kind. Density,
cumulative distribution function, quantiles and moments of the distributions are
given. Functions for the full log-likelihood, the profile log-likelihood and the
scores are provided. Formulas for various indicators of inequality and poverty
under the GB2 are implemented. The GB2 is fitted by the methods of maximum pseudo-
likelihood estimation using the full and profile log-likelihood, and non-linear
least squares estimation of the model parameters. Various plots for the
visualization and analysis of the results are provided. Variance estimation of the
parameters is provided for the method of maximum pseudo-likelihood estimation. A
mixture distribution based on the compounding property of the GB2 is presented
(denoted as \"compound\" in the documentation). This mixture distribution is based
on the discretization of the distribution of the underlying random scale parameter.
The discretization can be left or right tail. Density, cumulative distribution
function, moments and quantiles for the mixture distribution are provided. The
compound mixture distribution is fitted using the method of maximum pseudo-
likelihood estimation. The fit can also incorporate the use of auxiliary
information. In
this new version of the package, the mixture case is complemented with new
functions for variance estimation by linearization and comparative density
plots.","Imports":"cubature, hypergeo, laeken, numDeriv, stats,
survey","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GB2","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"simFrame","Title":"Generalized Beta Distribution of the
Second Kind: Properties,\nLikelihood, Estimation","Version":"2.1"},"GCAI.bias":
{"Author":"Guoshuai Cai","Depends":"R (>= 2.10)","Description":"Many inherited
biases and effects exists in RNA-seq due to both biological and technical effects.
We observed the biological variance of testing target transcripts can influence the
yield of sequencing reads, which might indicate a resource competition existing in
RNA-seq. We developed this package to capture the bias depending on local sequence
and perform the correction of this type of bias by borrowing information from
spike-in measurement.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GCAI.bias","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Guided Correction Approach for Inherited bias
(GCAI.bias)","Version":"1.0"},"GCD":{"Author":"Global Paleofire Working Group
<paleofire@univ-fcomte.fr>","Depends":"R(>= 2.10.0)","Description":"Contains the
Global Charcoal database data. Data include charcoal\nseries (age, depth, charcoal
quantity, associated units and methods) and\ninformations on sedimentary sites
(localisation, depositional environment, biome, etc.).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GCD","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"paleofire","Title":"Global Charcoal
Database","URL":"http:\/\/gpwg.org","Version":"3.0.5"},"GCPM":{"Author":"Kevin
Jakob","Description":"Analyze the default risk of credit portfolios. Commonly known
models,\nlike CreditRisk+ or the CreditMetrics model are implemented in their very
basic settings.\nThe portfolio loss distribution can be achieved either by
simulation or analytically\nin case of the classic CreditRisk+ model. Models are
only implemented to respect losses\ncaused by defaults, i.e. migration risk is not
included. The package structure is kept\nflexible especially with respect to
distributional assumptions in order to quantify the\nsensitivity of risk figures
with respect to several assumptions. Therefore the package\ncan be used to
determine the credit risk of a given portfolio as well as to quantify\nmodel
sensitivities.","Imports":"Rcpp (>= 0.11.2), methods, RcppProgress(>= 0.1),
parallel","License":"GPL-
2","NeedsCompilation":"yes","Package":"GCPM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Generalized Credit Portfolio
Model","Version":"1.2"},"GDAdata":{"Author":"Antony Unwin","Depends":"R (>=
2.10)","Description":"Datasets used in the book 'Graphical Data Analysis with R'
(Antony Unwin, CRC Press 2015).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GDAdata","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"ggplot2","Title":"Datasets for the Book Graphical Data
Analysis with R","Version":"0.93"},"GDAtools":{"Author":"Nicolas
Robette","Description":"This package contains functions for 'specific' MCA
(Multiple Correspondence Analysis),\n'class specific' MCA, computing and plotting
structuring factors and concentration ellipses,\n'standardized' MCA, inductive
tests and others tools for Geometric Data Analysis. It also provides functions\nfor
the translation of logit models coefficients into percentages (forthcoming),
weighted contingency tables and an association\nmeasure - i.e. Percentages of
Maximum Deviation from Independence (PEM).","Imports":"FactoMineR","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"GDAtools","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"cluster, WeightedCluster","Title":"A toolbox for the
analysis of categorical data in social\nsciences, and especially Geometric Data
Analysis","URL":"http:\/\/nicolas.robette.free.fr\/outils_eng.html","Version":"1.3"
},"GDELTtools":{"Author":"Stephen R. Haptonstahl, Thomas Scherer, Timo Thoms, and
Patrick Wheatley","Depends":"R (>= 2.10), tools","Description":"The GDELT data set
is over 60 GB now and growing 100 MB a month.\nThe number of source articles has
increased over time and unevenly across\ncountries. This package makes it easy to
download a subset of that data,\nthen normalize that data to facilitate valid time
series analysis.","Imports":"plyr, TimeWarp","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"GDELTtools","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Download, slice, and
normalize GDELT data","Version":"1.2"},"GENEAread":{"Author":"Zhou Fang
<zhou@activinsights.co.uk>","Depends":"bitops","Description":"Functions and
analytics for GENEA-compatible accelerometer\ndata into R objects. See topic
'GENEAread' for an introduction\nto the
package.","License":"GPL","NeedsCompilation":"no","Package":"GENEAread","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"mmap, MASS","Title":"Package
For Reading Binary files","Version":"1.1.1"},"GENLIB":{"Author":"Louis Houde
[aut],\nJean-Francois Lefebvre [aut],\nValery Roy-Lagace [aut],\nSebastien Lemieux
[aut],\nMichael J. Fromberger [ctb],\nMarie-Helene Roy-Gagnon [cre]","Depends":"R
(>= 3.1.0), Rcpp (>= 0.9.10)","Description":"Genealogical data analysis including
descriptive statistics (e.g., kinship and inbreeding coefficients) and gene-
dropping simulations.","Imports":"kinship2, methods, bootstrap, Matrix, lattice,
quadprog,\nforeach, parallel, doParallel","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"GENLIB","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Genealogical Data Analysis","Version":"1.0.4"},"GEOmap":
{"Author":"Jonathan M. Lees","Depends":"R (>= 3.0)","Description":"Set of routines
for making Map Projections (forward and inverse), Topographic Maps, Perspective
plots, Geological Maps, geological map symbols, geological databases, interactive
plotting and selection of focus regions.","Imports":"RPMG, splancs, fields,
MBA","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"GEOmap","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"geomapdata, maps, RFOC","Title":"Topographic and
Geologic Mapping","Version":"2.3-8"},"GERGM":{"Author":"Matthew J. Denny
<mdenny@psu.edu>, James D. Wilson\n<jdwilson1212@gmail.com>, Skyler Cranmer
<cranmer.12@osu.edu >, Bruce A.\nDesmarais <bdesmarais@psu.edu>, Shankar Bhamidi
<bhamidi@email.unc.edu>","Depends":"R (>= 3.2.1)","Description":"Estimation and
diagnosis of the convergence of Generalized\nExponential Random Graph Models via
Gibbs sampling or Metropolis\nHastings with exponential down
weighting.","Imports":"Rcpp, ggplot2, methods, stringr, igraph, plyr, parallel,
coda","License":"GPL-
3","NeedsCompilation":"yes","Package":"GERGM","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat","Title":"Estimation and Fit Diagnostics for
Generalized Exponential\nRandom Graph
Models","URL":"https:\/\/github.com\/matthewjdenny\/GERGM","Version":"0.7.4"},"GEST
r":{"Author":"Ed Curry","Depends":"R (>= 2.15.0), mclust,
gtools","Description":"The Gene Expression State Transformation (GESTr) models\nthe
states of expression of genes across a compendium of\nsamples in order to provide a
universal scale of gene\nexpression for all genes. TranSAM is a modification of the
SAM\napproach designed to utilise GESTr-transformed gene
expression\ndata.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GESTr","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Gene Expression State
Transformation","URL":"http:\/\/www.r-
"0.1"},"GEVStableGarch":{"Author":"Thiago Sousa [aut, cre],\nCira Otiniano
[ctb],\nSilvia Lopes [ctb],\nDiethelm Wuertz [ctb, cph]","Depends":"R(>=
2.15.0),Rsolnp,methods,skewt","Description":"Package for simulation and estimation
of ARMA-GARCH\/APARCH models with GEV and stable
distributions.","Enhances":"stable","Imports":"fGarch,fExtremes,stabledist,timeDate
,timeSeries","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GEVStableGarch","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"ARMA-GARCH\/APARCH Models with GEV and Stable
Distributions","Version":"1.1"},"GEVcdn":{"Author":"Alex J.
Cannon","Depends":"VGAM","Description":"Implements a flexible nonlinear modelling
framework for nonstationary\ngeneralized extreme value analysis in
hydroclimatology.","License":"GPL-
2","NeedsCompilation":"no","Package":"GEVcdn","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"boot","Title":"GEV Conditional Density Estimation
Network","Version":"1.1.4"},"GExMap":{"Author":"Nicolas Cagnard","Depends":"R (>=
2.10), Biobase, multtest","Description":"Perform statistical tests to unveil
genomic clusters,\nproduces garphical interpretations of the statistical
results\nin pdf files, perform a Gene Ontology analysis and produces\ngraphic
results in pdf
files","License":"GPL","NeedsCompilation":"no","Package":"GExMap","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Title":"A visual, intuitive, easy to use
software giving access to a new\ntype of information buried into your microarray
data","Version":"1.1.3"},"GFD":{"Author":"Sarah Friedrich, Frank Konietschke,
Markus Pauly","Depends":"R (>= 3.2.2), RGtk2 (>=
2.20.31)","Description":"Implemented are the Wald-type statistic,\na permuted
version thereof as well as the ANOVA-type statistic\nfor general factorial designs,
even with non-normal error terms\nand\/or heteroscedastic variances, for crossed
designs with an\narbitrary number of factors and nested designs with up to three
factors.","Imports":"plyr (>= 1.8.3), MASS (>= 7.3-43), Matrix (>= 1.2-2),
magic\n(>= 1.5-6), plotrix (>= 3.5-12)","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"GFD","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"HSAUR","Title":"Tests for General Factorial
Designs","Version":"0.1.4"},"GGEBiplotGUI":{"Author":"Elisa Frutos Bernal
<efb@usal.es>, Purificacion Galindo Villardon <pgalindo@usal.es>","Depends":"R (>=
3.2.2), rgl (>= 0.95.1441), tcltk (>= 3.2.2), tkrplot\n(>= 0.0-
23)","Description":"Description: A GUI with which to construct and interact with
GGE biplots.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GGEBiplotGUI","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Interactive GGE Biplots in R","Version":"1.0-
9"},"GGIR":{"Author":"Vincent T van Hees [aut, cre],\nZhou Fang [ctb],\nJing Hua
Zhao [ctb],\nSeverine Sabia [ctb]","Depends":"stats, utils, R (>=
2.10)","Description":"A tool to process and analyse data collected with wearable
raw acceleration sensors. The package has been developed and tested for binary data
from GENEActiv and GENEA devices and .csv-export data from Actigraph devices.
These devices are currently widely used in research on human daily physical
activity.","License":"LGPL (>= 2.0, <
3)","NeedsCompilation":"no","Package":"GGIR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"MASS, signal, zoo, mmap, bitops, matlab,
GENEAread","Title":"Raw Accelerometer Data Analysis","Version":"1.2-2"},"GGMridge":
{"Author":"Min Jin Ha [aut, cre], Shannon Holloway [ctb]","Depends":"mvtnorm, MASS,
stats, graphics, methods","Description":"Estimation of partial correlation matrix
using ridge penalty followed by thresholding and reestimation. Under multivariate
Gaussian assumption, the matrix constitutes an Gaussian graphical model
(GGM).","License":"GPL-
2","NeedsCompilation":"no","Package":"GGMridge","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Gaussian Graphical Models Using Ridge Penalty Followed
by\nThresholding and Reestimation","Version":"1.1"},"GGMselect":{"Author":"Annie
Bouvier, Christophe Giraud, Sylvie Huet, Verzelen
N.","Depends":"mvtnorm","Description":"Graph estimation in Gaussian Graphical
Models. The main functions return the adjacency matrix of an undirected graph
estimated from a data matrix.","Imports":"lars, gtools, stats","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"GGMselect","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"network, glasso","Title":"Gaussian Graphs Models
Selection","URL":"http:\/\/www.inra.fr\/miaj\/public\/logiciels\/GGMselect","Versio
n":"0.1-10"},"GGally":{"Author":"Barret Schloerke [aut, cre] (author for ggpairs
and ggally_*.\ncontributor for all functions.),\nJason Crowley [aut]
(ggparcoord),\nDi Cook [aut, ths] (ggscatmat, gglyph),\nHeike Hofmann
[ths],\nHadley Wickham [ths],\nFrancois Briatte [aut] (ggcorr, ggnet,
ggnet2),\nMoritz Marbach [aut] (ggnet, ggnet2),\nEdwin Thoen [aut] (ggsurv),\nAmos
Elberg [aut] (ggnetworkmap)","Depends":"R (>= 2.14)","Description":"The R package
'\\href{http:\/\/docs.ggplot2.org\/current\/}{ggplot2}'\nis a plotting system based
on the grammar of graphics. '\\href{https:\/\/\nggobi.github.io\/ggally}{GGally}'
extends 'ggplot2' by adding several functions to\nreduce the complexity of
combining geoms with transformed data. Some of these\nfunctions include a pairwise
plot matrix, a scatterplot plot matrix, a parallel\ncoordinates plot, a survival
plot, and several functions to plot networks.","Imports":"ggplot2 (>= 2.0.0), grid
(>= 3.0.0), gtable (>= 0.1.2), plyr\n(>= 1.8), reshape (>= 0.8.4)","License":"GPL
(>=
2.0)","NeedsCompilation":"no","Package":"GGally","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"arm (>= 1.7), geosphere (>= 1.3-11), ggmap (>= 2.3),
igraph\n(>= 1.0.0), intergraph (>= 2.0-0), maps (>= 2.3-9), network (>=\n1.7.2),
RColorBrewer (>= 1.0-5), scagnostics (>= 0.2-4), scales\n(>= 0.2.3), sna (>= 2.3-
1), survival (>= 2.37-4), tnet (>=\n3.0), knitr (>= 1.12), rmarkdown (>= 0.9.2),
roxygen2 (>=\n5.0.0), testthat","Title":"Extension to
ggplot2","URL":"https:\/\/ggobi.github.io\/ggally,
https:\/\/github.com\/ggobi\/ggally","Version":"1.0.1"},"GHQp":{"Author":"Freddy
Hernandez Barajas","Depends":"R (>= 2.10), statmod","Description":"The GHQ function
can be used to obtain the quadrature points and weights to approximate an integral
in two or more dimensions. This function uses the pruning approach to eliminate
that points that do not contribute to the approximation of the integral and
increases computational cost. The advantage to conducting this elimination of
points is the decrease in the number of times that the function of interest is
evaluated. This advantage is crucial in mixed models in which we must address
several integrations within an iterative process to obtain model
parameters.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GHQp","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"scatterplot3d","Title":"Gauss Hermite Quadrature with
pruning","Version":"1.0"},"GIGrvg":{"Author":"Josef Leydold and Wolfgang
Hormann","Description":"\nGenerator and density function for the\nGeneralized
Inverse Gaussian (GIG) distribution.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"GIGrvg","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Random Variate Generator for the GIG
Distribution","Version":"0.4"},"GISTools":{"Author":"Chris Brunsdon and Hongyan
Chen","Depends":"R (>= 2.15.0), maptools, sp, RColorBrewer, MASS,
rgeos","Description":"Some mapping and spatial data manipulation tools - in
particular\ndrawing choropleth maps with nice looking legends, and aggregation of
point\ndata to polygons.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GISTools","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Some further GIS capabilities for R","Version":"0.7-
4"},"GLDEX":{"Author":"Steve Su, with contributions from: Diethelm Wuertz, Martin
Maechler and Rmetrics core team members for low discrepancy algorithm, Juha
Karvanen for L moments codes, Robert King for gld C codes and starship codes,
Benjamin Dean for corrections and input in ks.gof code and R core team for histsu
function.","Depends":"cluster, grDevices, graphics, stats","Description":"The
fitting algorithms considered in this package have two major objectives. One is to
provide a smoothing device to fit distributions to data using the weight and
unweighted discretised approach based on the bin width of the histogram. The other
is to provide a definitive fit to the data set using the maximum likelihood and
quantile matching estimation. Other methods such as moment matching, starship
method, L moment matching are also provided. Diagnostics on goodness of fit can be
done via qqplots, KS-resample tests and comparing mean, variance, skewness and
kurtosis of the data with the fitted distribution.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"GLDEX","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Fitting Single and Mixture of Generalised Lambda
Distributions\n(RS and FMKL) using Various Methods","Version":"2.0.0.3"},"GLDreg":
{"Author":"Steve Su, with contributions from: R core team for qqgld.default
function.","Depends":"GLDEX (>= 2.0.0.1), grDevices, graphics,
stats","Description":"Owing to the rich shapes of GLDs, GLD standard\/quantile
regression is a competitive flexible model compared to standard\/quantile
regression. The proposed method has some major advantages: 1) it provides a
reference line which is very robust to outliers with the attractive property of
zero mean residuals and 2) it gives a unified, elegant quantile regression model
from the reference line with smooth regression coefficients across different
quantiles. The goodness of fit of the proposed model can be assessed via QQ plots
and the Kolmogorov-Smirnov test, to ensure the appropriateness of the statistical
inference under consideration. Statistical distributions of coefficients of the GLD
regression line are obtained using simulation, and interval estimates are obtained
directly from simulated data.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"GLDreg","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"MASS, quantreg","Title":"Fit GLD Regression Model and
GLD Quantile Regression Model to\nEmpirical Data","Version":"1.0.3"},"GLMMGibbs":
{"Depends":"R (>= 2.10)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"GLMMGibbs","Repository":"http:\/\/www.stats
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Paul Fox [aut], Konrad Klotzke [aut], Duco Veen [aut]","Depends":"lme4,
methods","Description":"Generalized Linear Mixed Model (GLMM) for Binary Randomized
Response Data.\nIncludes Cauchit, Log-Log, Logistic, and Probit link functions for
Bernoulli distributed RR data.","Imports":"stats","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"GLMMRR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Generalized Linear Mixed Model (GLMM) for Binary
Randomized\nResponse Data","Version":"0.1.2"},"GLSME":{"Author":"Krzysztof
Bartoszek <bartoszekkj@gmail.com>","Depends":"R(>= 2.9.1), mvtnorm,
corpcor","Description":"Performs linear regression with correlated predictors,
responses and correlated measurement errors in predictors and responses, correcting
for biased caused by these.","License":"GPL (>= 2) | file
LICENCE","NeedsCompilation":"no","Package":"GLSME","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"ape, mvSLOUCH, ouch","Title":"Generalized Least
Squares with Measurement Error","Version":"1.0.3"},"GMCM":{"Author":"Anders Ellern
Bilgrau, Martin Boegsted, Poul Svante Eriksen","Description":"Unsupervised
Clustering and Meta-analysis using Gaussian Mixture\nCopula
Models.","Imports":"Rcpp (>= 0.10.6)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"GMCM","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"idr,
Hmisc, RColorBrewer, foreach, jpeg, testthat (>= 0.3),\nknitr","Title":"Fast
Estimation of Gaussian Mixture Copula
Models","URL":"https:\/\/github.com\/AEBilgrau\/GMCM","Version":"1.2.3"},"GMD":
{"Author":"Xiaobei Zhao [aut, cre, cph],\nAlbin Sandelin [aut]","Depends":"R (>=
3.1.0)","Description":"GMD is a package for non-parametric distance measurement
between\ntwo discrete frequency distributions.","Imports":"stats, grDevices,
2)","NeedsCompilation":"no","Package":"GMD","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"datasets, MASS, cluster","Title":"Generalized Minimum
Distance of distributions","URL":"http:\/\/CRAN.R-
project.org\/package=GMD","Version":"0.3.3"},"GMDH":{"Author":"Osman Dag, Ceylan
Yozgatligil","Depends":"R (>= 3.1.1)","Description":"Group method of data handling
(GMDH) - type neural network algorithm is the heuristic self-organization method
for modelling the complex systems. In this package, GMDH-type neural network
algorithms are applied to make short term forecasting for a univariate time
series.","Imports":"MASS, graphics, stats, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GMDH","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Short Term Forecasting via GMDH-Type Neural Network
Algorithms","Version":"1.3"},"GMMBoost":{"Author":"Andreas
Groll","Description":"Likelihood-based Boosting for Generalized mixed
models","Imports":"minqa, magic","License":"GPL-
2","NeedsCompilation":"no","Package":"GMMBoost","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Likelihood-based Boosting for Generalized mixed
models","Version":"1.1.2"},"GNE":{"Author":"Christophe Dutang","Depends":"R (>=
2.6.0), alabama, nleqslv, BB, SQUAREM","Description":"Provide functions to compute
standard and generalized Nash Equilibria. Optimization methods are available
nonsmooth reformulation, fixed-point formulation, minimization problem and
constrained-equation reformulation.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"GNE","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"sensitivity","Title":"Computation of Generalized Nash
Equilibria","URL":"http:\/\/optimizer.r-forge.r-project.org\/","Version":"0.99-
1"},"GOGANPA":{"Author":"Billy Chang","Depends":"R (>= 2.10), GANPA,
WGCNA","Description":"Accounting for genes' functional-non-equivalence within
pathways in classical Gene-set-analysis.","License":"GPL-
2","NeedsCompilation":"no","Package":"GOGANPA","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"GANPA, WGCNA, GANPAdata","Title":"GO-Functional-
Network-based Gene-Set-Analysis","Version":"1.0"},"GORCure":{"Author":"Jie Zhou,
Jiajia Zhang, Wenbin Lu","Depends":"R (>=
2.15.0),stats,graphics,survival,ICsurv,pracma,MASS","Description":"Generalized Odds
Rate Mixture Cure (GORMC) model is a flexible model of fitting survival data with a
cure fraction, including the Proportional Hazards Mixture Cure (PHMC) model and the
Proportional Odds Mixture Cure Model as special cases. This package fit the GORMC
model with interval censored data.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GORCure","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Fit Generalized Odds Rate Mixture Cure Model with
Interval\nCensored Data","Version":"1.0"},"GOplot":{"Author":"Wencke Walter [aut,
cre],\nFatima Sanchez-Cabo [aut]","Depends":"ggplot2 (>= 2.0.0), ggdendro (>= 0.1-
17), gridExtra (>=\n2.0.0), RColorBrewer (>= 1.1.2), R (>=
3.2.3)","Description":"Implementation of multilayered visualizations for
enhanced\ngraphical representation of functional analysis data. It combines and
integrates\nomics data derived from expression and functional annotation
enrichment\nanalyses. Its plotting functions have been developed with an
hierarchical\nstructure in mind: starting from a general overview to identify the
most\nenriched categories (modified bar plot, bubble plot) to a more detailed
one\ndisplaying different types of relevant information for the molecules in a
given\nset of categories (circle plot, chord plot, cluster plot, Venn diagram,
heatmap).","License":"GPL-
2","NeedsCompilation":"no","Package":"GOplot","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"knitr, rmarkdown","Title":"Visualization of Functional
Analysis
Data","URL":"https:\/\/github.com\/wencke\/wencke.github.io","Version":"1.0.2"},"GP
Arotation":{"Author":"Coen Bernaards and Robert Jennrich","Depends":"R (>=
2.0.0)","Description":"Gradient Projection Algorithm Rotation for Factor Analysis.
See ?GPArotation.Intro for more details.","License":"GPL (>= 2) | file
LICENSE","NeedsCompilation":"no","Package":"GPArotation","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"GPA Factor
Rotation","URL":"http:\/\/www.stat.ucla.edu\/research\/gpa","Version":"2014.11-
1"},"GPC":{"Author":"Miguel Munoz Zuniga and Jordan Ko","Depends":"R (>= 2.7.0),
randtoolbox, orthopolynom, ks, lars","Description":"A generalized polynomial chaos
expansion of a model taking as input independent random variables is achieved. A
statistical and a global sensitivity analysis of the model are also carried
out.","License":"GPL-
3","NeedsCompilation":"no","Package":"GPC","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Generalized Polynomial Chaos","Version":"0.1"},"GPCSIV":
{"Author":"Brahim Brahim and Sun Makosso-Kallyth <sun.makosso-
kallyth@crchuq.ulaval.ca>","Depends":"scatterplot3d, sqldf","Description":"This
package implements an extension of principal component analysis (PCA) tailored to
handle multiple data tables. It can handle Big Data in the sense that the variation
in massive data can be described by intervals [a, b] and multiple
tables.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GPCSIV","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"GPCSIV, Generalized Principal Component of Symbolic
Interval\nvariables","Version":"0.1.0"},"GPFDA":{"Author":"Jian Qing Shi, Yafeng
Cheng","Depends":"R (>= 3.1),fda.usc,spam, fda","Description":"Use functional
regression as the mean structure and Gaussian Process as the covariance
structure.","Imports":"MASS","License":"GPL-
3","NeedsCompilation":"no","Package":"GPFDA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Apply Gaussian Process in Functional data
analysis","Version":"2.2"},"GPLTR":{"Author":"Cyprien Mbogning
<cyprien.mbogning@inserm.fr> and Wilson Toussile","Depends":"rpart ,
parallel","Description":"Combining a generalized linear model with an additional
tree part\non the same scale. A four-step procedure is proposed to fit the model
and test\nthe joint effect of the selected tree part while adjusting on confounding
factors.\nWe also proposed an ensemble procedure based on the bagging to improve
prediction\naccuracy and computed several scores of importance for variable
2.0)","NeedsCompilation":"no","Package":"GPLTR","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Generalized Partially Linear Tree-Based Regression
Model","Version":"1.2"},"GPareto":{"Author":"Mickael Binois, Victor
Picheny","Depends":"DiceKriging (>= 1.5.3), emoa, methods","Description":"Gaussian
process regression models, a.k.a. kriging models, are\napplied to global
multiobjective optimization of black-box functions.\nMultiobjective Expected
Improvement and Step-wise Uncertainty Reduction\nsequential infill criteria are
available. A quantification of uncertainty\non Pareto fronts is provided using
conditional simulations.","Imports":"Rcpp (>= 0.11.1), rgenoud, pbivnorm, pso,
randtoolbox,\nKrigInv, MASS, DiceDesign (>= 1.4), ks","License":"GPL-
3","NeedsCompilation":"yes","Package":"GPareto","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr","Title":"Gaussian Processes for Pareto Front
Estimation and Optimization","Version":"1.0.2"},"GPfit":{"Author":"Blake MacDoanld,
Hugh Chipman, Pritam Ranjan","Description":"A computationally stable approach of
fitting a Gaussian Process (GP) model to a deterministic simulator.","Imports":"lhs
(>= 0.5), lattice (>= 0.18-8)","License":"GPL-
2","NeedsCompilation":"no","Package":"GPfit","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Gaussian Processes Modeling","Version":"1.0-0"},"GPseq":
{"Author":"Sudeep Srivastava, Liang Chen","Depends":"R (>=
2.10.1)","Description":"Some functions for modeling sequence read counts as
a\ngeneralized poisson model and to use this model for detecting\ndifferentially
expressed genes in different conditions and\ndifferentially spliced
exons.","License":"GPL-
2","NeedsCompilation":"no","Package":"GPseq","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"gpseq: Using the generalized Poisson distribution to
model\nsequence read counts from high throughput
sequencing\nexperiments","Version":"0.5"},"GPvam":{"Author":"Andrew Karl, Yan Yang,
and Sharon Lohr","Depends":"R (>= 3.0.0), Matrix","Description":"Maximum likelihood
estimators are obtained via an EM algorithm.","Imports":"numDeriv, Rcpp (>=
0.11.2), graphics, grDevices, methods,\nstats, utils","License":"GPL-
2","NeedsCompilation":"yes","Package":"GPvam","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Maximum Likelihood Estimation of Multiple Membership
Mixed\nModels Used in Value-Added Modeling","Version":"3.0-3"},"GRTo":
{"Author":"Daniel Amorese, Paul A. Rydelek and Jean-Robert Grasso","Depends":"R (>=
2.2.0)","Description":"Offers functions for the comparison of Gutenberg-Richter\nb-
values. Several functions in GRTo are helpful for the assessment of the\nquality of
seismicity catalogs.","Imports":"bootstrap, grDevices, graphics, stats,
utils","License":"GPL","NeedsCompilation":"no","Package":"GRTo","Repository":"http:
\/\/cran.csiro.au\/src\/contrib","Title":"Tools for the Analysis of Gutenberg-
Richter Distributions of\nEarthquake Magnitudes","Version":"1.3"},"GRaF":
{"Author":"Nick
Golding","Depends":"dismo","Description":"Functions to fit, visualise and compare
Gaussian random field species distribution models.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GRaF","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Species distribution modelling using latent Gaussian
random\nfields","Version":"0.1-12"},"GSA":{"Author":"Brad Efron and R.
Tibshirani","Description":"Gene set
analysis","License":"LGPL","NeedsCompilation":"no","Package":"GSA","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Suggests":"impute","Title":"Gene set
analysis","URL":"http:\/\/www-
stat.stanford.edu\/~tibs\/GSA","Version":"1.03"},"GSAgm":{"Author":"Rama Raghavan,
Alice Wang","Depends":"survival, edgeR","Description":"GSAgm is an R package that
completes a self-contained gene set analysis (GSA) for RNA-seq and SNP data using
the Gamma Method.","License":"GPL-
2","NeedsCompilation":"no","Package":"GSAgm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Gene Set Analysis using the Gamma
Method","Version":"1.0"},"GSE":{"Author":"Andy Leung, Mike Danilov, Victor Yohai,
Ruben Zamar","Depends":"R (>= 3.0.0), Rcpp (>= 0.10.0), MASS, methods,
ggplot2","Description":"Robust Estimation of Multivariate Location and Scatter in
the\nPresence of Cellwise and Casewise Contamination and Missing
Data.","Imports":"rrcov","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"GSE","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Robust Estimation in the Presence of Cellwise and
Casewise\nContamination and Missing Data","Version":"3.3"},"GSIF":
{"Author":"Tomislav Hengl [cre, aut],\nBas Kempen [ctb],\nGerard Heuvelink
[ctb],\nBrendan Malone [ctb]","Depends":"R (>= 2.15.0)","Description":"Global Soil
Information Facilities - tools (standards and functions) and sample datasets for
global soil mapping.","Imports":"methods, sp (>= 1.0-8), RSAGA, dismo, rgdal,
raster, aqp,\nplotKML, gstat, stats, plyr, grDevices,
graphics","License":"GPL","NeedsCompilation":"no","Package":"GSIF","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Suggests":"rjson, RCurl, soiltexture,
spatstat, stringr, XML, boot,\nsplines, mda, psych, nortest, rpart,
quantregForest,\nrandomForest, nlme, reshape, fossil, AICcmodavg, maptools,\nnnet,
SDMTools, rJava (>= 0.5-0), spacetime, gdalUtils, tools,\nmaxlike,
Hmisc","Title":"Global Soil Information Facilities","URL":"http:\/\/gsif.r-forge.r-
project.org\/","Version":"0.4-7"},"GSM":{"Author":"Sergio
Venturini","Depends":"gtools, methods, utils","Description":"Implementation of a
Bayesian approach for estimating a mixture of gamma distributions in which the
mixing occurs over the shape parameter. This family provides a flexible and novel
approach for modeling heavy-tailed distributions, it is computationally efficient,
and it only requires to specify a prior distribution for a single
parameter.","Imports":"graphics, grDevices, stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GSM","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Gamma Shape
Mixture","URL":"http:\/\/projecteuclid.org\/euclid.aoas\/1215118537","Version":"1.3
.2"},"GSSE":{"Author":"Baosheng Liang, Yuanjia Wang and Donglin
Zeng","Depends":"R(>= 3.0.1)","Description":"We propose a fully efficient sieve
maximum likelihood method to estimate genotype-specific distribution of time-to-
event outcomes under a nonparametric model. We can handle missing genotypes in
pedigrees. We estimate the time-dependent hazard ratio between two genetic
mutation groups using B-splines, while applying nonparametric maximum likelihood
estimation to the reference baseline hazard function. The estimators are
calculated via an expectation-maximization algorithm.","Imports":"Iso (>= 0.0-17),
splines, stats, zoo (>= 1.7-12)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GSSE","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"MASS","Title":"Genotype-Specific Survival
Estimation","Version":"0.1"},"GUIDE":{"Author":"S Subramanian
<ssubramanian@sssihl.edu.in>","Depends":"R (>= 2.14), rpanel,
tkrplot","Description":"GUI for DErivatives in R","License":"GPL-
2","NeedsCompilation":"no","Package":"GUIDE","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"GUI for DErivatives in R","Version":"1.0.9"},"GUILDS":
{"Author":"Thijs Janzen","Depends":"R (>= 3.0.2)","Description":"The GUILDS package
combines a range of sampling formulas for the unified neutral model of biogeography
and biodiversity. Alongside the sampling formulas, it includes methods to perform
maximum likelihood optimization of the sampling formulas, methods to generate data
given the neutral model, and methods to estimate the expected species abundance
distribution. Sampling formulas included in the GUILDS package are the Etienne
Sampling Formula (Etienne 2005), the guild sampling formula, where guilds are
assumed to differ in dispersal ability (Janzen et al. 2015), and the guilds
sampling formula conditioned on guild size (Janzen et al. 2015).","Imports":"Rcpp
(>= 0.11.0), pracma, subplex","License":"GPL-
2","NeedsCompilation":"yes","Package":"GUILDS","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Implementation of Sampling Formulas for the Unified
Neutral\nModel of Biodiversity and Biogeography, with or without
Guild\nStructure","Version":"1.2.1"},"GUIProfiler":{"Author":"Fernando de
Villar<fdevillar@gmail.com> and Angel Rubio <arubio@ceit.es>","Depends":"Nozzle.R1,
MASS, proftools, Rgraphviz, graph","Description":"Show graphically the results of
profiling R functions by tracking their execution time.","Imports":"methods, utils,
rstudioapi,grDevices","License":"GPL","NeedsCompilation":"no","Package":"GUIProfile
r","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Graphical User
Interface for Rprof()","Version":"2.0.1"},"GUTS":{"Author":"Carlo Albert
<carlo.albert@eawag.ch> and SÃ¶ren Vogel <soeren.vogel@posteo.ch>","Depends":"R (>=
3.1.0), methods, Rcpp (>= 0.11.5)","Description":"Given exposure and survival time
series as well as parameter values, GUTS allows for the fast calculation of the
survival probabilities as well as the logarithm of the corresponding
likelihood.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"GUTS","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"adaptMCMC (>= 1.1)","Title":"Fast Calculation of the
Likelihood of a Stochastic Survival\nModel","Version":"1.0.0"},"GUniFrac":
{"Author":"Jun Chen","Depends":"vegan, ape","Description":"Generalized UniFrac
distance for comparing microbial\ncommunities. Permutational multivariate analysis
of variance\nusing multiple distance matrices.","License":"GPL-
2","NeedsCompilation":"no","Package":"GUniFrac","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"ade4","Title":"Generalized UniFrac
distances","Version":"1.0"},"GWAF":{"Author":"Ming-Huei Chen <mhchen@bu.edu> and
Qiong Yang <qyang@bu.edu>","Depends":"R(>= 2.15.1), geepack, coxme,
lme4","Description":"Functions for genome-wide association\/interaction analysis
and rare variant analysis on a continuous\/dichotomous trait using family data, and
for making genome-wide p-value plot and QQ plot.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GWAF","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Genome-Wide Association\/Interaction Analysis and Rare
Variant\nAnalysis with Family Data","Version":"2.2"},"GWASExactHW":{"Author":"Ian
Painter, University of Washington","Description":"This package contains a function
to do exact\nHardy-Weinburg testing (using Fisher's test) for SNP genotypes\nas
typically obtained in a Genome Wide Association Study\n(GWAS).","License":"GPL-
3","NeedsCompilation":"yes","Package":"GWASExactHW","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Exact Hardy-Weinburg testing for Genome Wide
Association Studies","Version":"1.01"},"GWG":{"Author":"Christina
Riedel","Description":"Based on calculations of 758 women this package
calculates\npositive predictive values (PPV) and negative predictive values\n(NPV)
for inadequate and excessive gestational weight gain\n(GWG) for different
prevalences for different BMI categories.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GWG","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Calculation of probabilities for inadequate and
excessive\ngestational weight gain","Version":"1.0"},"GWLelast":{"Author":"Daisuke
Yoneoka, Eiko Saito","Description":"Fit a geographically weighted logistic elastic
net
regression.","Imports":"doParallel,geosphere,sp,spgwr,glmnet,foreach","License":"GP
L-
2","NeedsCompilation":"no","Package":"GWLelast","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"testthat","Title":"Geographically Weighted Logistic
Elastic Net Regression","Version":"1.1"},"GWRM":{"Author":"Antonio Jose Saez-
Castillo [aut, cre],\nSilverio Vilchez-Lopez [aut],\nMaria Jose Olmo-Jimenez
[aut],\nJose Rodriguez-Avi [aut],\nAntonio Conde-Sanchez [aut],\nAna Maria
Martinez-Rodriguez [aut]","Depends":"R (>= 3.0.0)","Description":"Statistical
functions to fit, validate and describe a Generalized\nWaring Regression Model
(GWRM).","Imports":"foreach, doParallel, stats, parallel","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"GWRM","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Generalized Waring Regression Model for Count
Data","Version":"2.1.0.1"},"GWmodel":{"Author":"Binbin Lu[aut], Paul Harris[aut],
Martin Charlton[aut], Chris Brunsdon[aut], Tomoki Nakaya[aut], Isabella
Gollini[ctb]","Depends":"R (>= 3.0.0),maptools (>= 0.5-2),
robustbase,sp","Description":"In GWmodel, we introduce techniques from a particular
branch of spatial statistics,termed geographically-weighted (GW) models. GW models
suit situations when data are not described well by some global model, but where
there are spatial regions where a suitably
localised calibration provides a better description. GWmodel includes functions to
calibrate: GW summary statistics, GW principal components analysis, GW discriminant
analysis and various forms of GW regression; some of which are provided in basic
and robust (outlier resistant) forms.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GWmodel","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"mvoutlier, RColorBrewer,
gstat","Title":"Geographically-Weighted
Models","URL":"http:\/\/gwr.nuim.ie\/","Version":"1.2-5"},"GWsignif":
{"Author":"ChangJiang Xu and Celia M.T. Greenwood","Description":"Estimate genome-
wide significance using extrapolation approach","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GWsignif","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Genome-wide significance for whole genome sequencing
studies","Version":"1.0"},"GaDiFPT":{"Author":"A. Buonocore, M.F.
Carfora","Description":"In this package we consider Gaussian Diffusion processes
and smooth thresholds. After evaluating the mean of the process to check the
subthreshold regimen hypothesis, the FPT density function is reconstructed via the
numerical quadrature of the integral equation in (Buonocore 1987); first passage
times are also generated by the method in (Buonocore 2014) and results are
compared. The timestep of the simulations can iteratively be refined. User should
provide the functional form for the drift and the infinitesimal variance in the
script 'userfunc.R' and for the threshold in the script 'userthresh.R'. All the
parameters required by the implementation are to be set in the script
'userparam.R'. Example scripts for common drifts and thresholds are
given.","License":"GPL-
2","NeedsCompilation":"no","Package":"GaDiFPT","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"First Passage Time Simulation for Gaussian Diffusion
Processes","Version":"1.0"},"GameTheory":{"Author":"Sebastian Cano-
Berlanga","Depends":"lpSolveAPI, combinat, gtools, ineq,
kappalab","Description":"Implementation of a common set of punctual solutions for
Cooperative Game Theory.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GameTheory","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"R.rsp","Title":"Cooperative Game
Theory","URL":"http:\/\/canoberlanga.com","Version":"2.0"},"Gammareg":
{"Author":"Martha Corrales and Edilberto Cepeda-Cuervo, with the colaboration of
Maria Fernanda Zarate,Ricardo Duplat and Campo Elias Pardo.","Depends":"R (>=
2.12.1)","Description":"This package performs gamma regression, where both mean and
shape parameters follows lineal regression structures.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Gammareg","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"classic gamma regression: joint modeling of mean and
shape\nparameters","Version":"1.0"},"GeNetIt":{"Author":"Jeffrey S. Evans [aut,
cre],\nMelanie Murphy [aut]","Depends":"R (>= 3.1.0)","Description":"Implementation
of spatial graph-theoretic genetic gravity models.\nThe model framework is
applicable for other types of spatial flow questions.\nIncludes functions for
constructing spatial graphs, sampling and summarizing\nassociated raster variables
and building unconstrained and singly constrained\ngravity
models.","Imports":"nlme, sp, spdep, spatialEco, raster, rgeos","License":"GPL-
3","NeedsCompilation":"no","Package":"GeNetIt","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Spatial Graph-Theoretic Genetic Gravity
Modelling","Version":"0.1-0"},"GenABEL":{"Author":"GenABEL project
developers","Depends":"R (>= 2.15.0), methods, MASS, utils,
GenABEL.data","Description":"a package for genome-wide association analysis
between\nquantitative or binary traits and single-nucleotide\npolymorphisms
(SNPs).","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"GenABEL","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"qvalue, genetics, haplo.stats, DatABEL (>= 0.9-0),
hglm,\nMetABEL, PredictABEL, VariABEL, bigRR","Title":"genome-wide SNP association
analysis","URL":"http:\/\/www.genabel.org,
http:\/\/forum.genabel.org,\nhttp:\/\/genabel.r-forge.r-
project.org\/","Version":"1.8-0"},"GenABEL.data":{"Author":"Maksim Struchalin
<m.v.struchalin@mail.ru> and GenABEL project developers
<genabel.project@gmail.com>","Depends":"R (>= 2.15.0)","Description":"GenABEL.data
package consists of a data set used by GenABEL functions","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GenABEL.data","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Package contains data which is used by GenABEL
example and test\nfunctions","URL":"http:\/\/www.genabel.org,
http:\/\/forum.genabel.org,\nhttp:\/\/genabel.r-forge.r-
project.org\/","Version":"1.0.0"},"GenBinomApps":{"Author":"Horst Lewitschnig,
David Lenzi","Depends":"stats","Description":"Density, distribution function,
quantile function and random generation for the Generalized Binomial Distribution.
Functions to compute the Clopper-Pearson Confidence Interval and the required
sample size. Enhanced model for burn-in studies, where failures are tackled by
countermeasures.","License":"GPL-
3","NeedsCompilation":"no","Package":"GenBinomApps","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Clopper-Pearson Confidence Interval and Generalized
Binomial\nDistribution","Version":"1.0-2"},"GenCAT":{"Author":"Eric Reed, Sara
Nunez, Jing Qian, Andrea Foulkes","Depends":"R (>= 2.10), stats, dplyr, doParallel,
ggplot2, foreach,\nparallel, methods","Description":"Implementation of the genetic
class level association testing (GenCAT) method from SNP level association data.
Refer to: \"Qian, J., Reed, E., Nunez, S., Qu, L., Reilly, M., Foulkes, A. (2016)
Testing class-level genetic associations using single-element summary statistics.
(Under review).\".","License":"GPL-
2","NeedsCompilation":"no","Package":"GenCAT","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"snpStats, knitr","Title":"Genetic Class Association
Testing","Version":"1.0.2"},"GenForImp":{"Author":"Nadia Solaro, Alessandro
Barbiero, Giancarlo Manzi, Pier Alda Ferrari","Depends":"mvtnorm,
sn","Description":"Two methods based on the Forward Imputation approach are
implemented for the imputation of quantitative missing data. One method alternates
Nearest Neighbour Imputation and Principal Component Analysis (function
'ForImp.PCA'), the other uses Nearest Neighbour Imputation with the Mahalanobis
distance (function 'ForImp.Mahala').","License":"GPL-
3","NeedsCompilation":"no","Package":"GenForImp","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"The Forward Imputation: A Sequential Distance-Based
Approach for\nImputing Missing Data","Version":"1.0"},"GenKern":{"Author":"David
Lucy <d.lucy@lancaster.ac.uk> and Robert Aykroyd
<r.g.aykroyd@leeds.ac.uk>","Depends":"KernSmooth, utils","Description":"Computes
generalised KDEs","License":"GPL-
2","NeedsCompilation":"yes","Package":"GenKern","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Functions for generating and manipulating binned kernel
density\nestimates","Version":"1.2-60"},"GenOrd":{"Author":"Alessandro Barbiero,
Pier Alda Ferrari","Depends":"mvtnorm, Matrix, MASS, stats","Description":"A
gaussian copula based procedure for generating samples from discrete random
variables with prescribed correlation matrix and marginal
distributions.","License":"GPL","NeedsCompilation":"no","Package":"GenOrd","Reposit
ory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Simulation of Discrete Random
Variables with Given Correlation\nMatrix and Marginal
Distributions","Version":"1.4.0"},"GenSA":{"Author":"Sylvain Gubian, Yang Xiang,
Brian Suomela, Julia Hoeng, PMP SA.","Depends":"R (>=
2.12.0)","Description":"Performs search for global minimum of a very complex non-
linear objective function with a very large number of optima.","License":"GPL-
2","NeedsCompilation":"yes","Package":"GenSA","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"R Functions for Generalized Simulated
Annealing","Version":"1.1.6"},"GenWin":{"Author":"Timothy M. Beissinger
<beissinger@ucdavis.edu>","Depends":"R (>= 3.1.1)","Description":"Defines window or
bin boundaries for the analysis of genomic data.\nBoundaries are based on the
inflection points of a cubic smoothing spline\nfitted to the raw data. Along with
defining boundaries, a technique to\nevaluate results obtained from unequally-sized
windows is provided.\nApplications are particularly pertinent for, though not
limited to, genome\nscans for selection based on variability between populations
(e.g. using\nWright's fixations index, Fst, which measures variability in
subpopulations\nrelative to the total
population).","Imports":"pspline","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"GenWin","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Spline Based Window Boundaries for Genomic
Analyses","Version":"0.1"},"GeneCycle":{"Author":"Miika Ahdesmaki, Konstantinos
Fokianos, and Korbinian Strimmer.","Depends":"R (>= 2.7.0), MASS, longitudinal (>=
1.1.3), fdrtool (>=\n1.2.5)","Description":"The GeneCycle package implements the
approaches of Wichert\net al. (2004), Ahdesmaki et al. (2005) and Ahdesmaki et
al.\n(2007) for detecting periodically expressed genes from gene\nexpression time
series data.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"GeneCycle","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Identification of Periodically Expressed
Genes","URL":"http:\/\/www.cs.tut.fi\/~ahdesmak\/robustperiodic\/index.html","Versi
on":"1.1.2"},"GeneF":{"Author":"Yinglei Lai <ylai@gwu.edu>","Description":"This
package implements several generalized F-statistics.\nThe current version includes
a generalized F-statistic based on\nthe flexible isotonic\/monotonic regression or
order restricted\nhypothesis testing.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"GeneF","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Package for Generalized F-
statistics","Version":"1.0"},"GeneFeST":{"Author":"Bastian Pfeifer","Depends":"R
(>= 2.14.2), BASIX","Description":"GeneFeST is a genome scan method to detect
outlier loci (genes) which are under balancing or directional
selection.","Imports":"methods","License":"GPL-
2","NeedsCompilation":"yes","Package":"GeneFeST","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"PopGenome, coda","Title":"Bayesian calculation of
gene-specific FST from genomic SNP data","Version":"1.0.1"},"GeneNet":
{"Author":"Juliane Schaefer, Rainer Opgen-Rhein, and\nKorbinian
Strimmer.","Depends":"R (>= 3.0.2), corpcor (>= 1.6.8), longitudinal (>=
1.1.12),\nfdrtool (>= 1.2.15)","Description":"Analyzes gene expression\n(time
series) data with focus on the inference of gene networks.\nIn particular, GeneNet
implements the methods of Schaefer and\nStrimmer (2005a,b,c) and Opgen-Rhein and
Strimmer (2006, 2007)\nfor learning large-scale gene association networks
(including\nassignment of putative directions).","Imports":"stats,
grDevices","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"GeneNet","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"graph, Rgraphviz","Title":"Modeling and Inferring Gene
Networks","URL":"http:\/\/strimmerlab.org\/software\/genenet\/","Version":"1.2.13"}
,"GeneReg":{"Author":"Tao Huang","Depends":"splines, igraph","Description":"GeneReg
is an R package for inferring time delay gene\nregulatory network using time course
gene expression profiles.\nThe main idea of time delay linear model is to fit a
linear\nregression model using a set of putative regulators to estimate\nthe
transcription pattern of a specific target
gene.","License":"LGPL","NeedsCompilation":"no","Package":"GeneReg","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Title":"Construct time delay gene regulatory
network","URL":"http:\/\/www.biomedcentral.com\/1756-
0500\/3\/142","Version":"1.1.2"},"Geneland":{"Author":"Gilles Guillot, Filipe
Santos, Arnaud
Estoup","Depends":"RandomFields,fields,tcltk","Description":"Stochastic simulation
and MCMC inference of structure from genetic
data.","License":"GPL","NeedsCompilation":"yes","Package":"Geneland","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Suggests":"mapproj,maps","Title":"Detection
of structure from multilocus genetic
data","URL":"http:\/\/www2.imm.dtu.dk\/~gigu\/Geneland\/","Version":"4.0.5"},"Gener
alOaxaca":{"Author":"Aurelien Nicosia and Simon Baillargeon-
Ladouceur","Description":"Perform the Blinder-Oaxaca decomposition for generalized
linear\nmodel with bootstrapped standard errors. The twofold and
threefold\ndecomposition are given, even the generalized linear model output in
each group.","Imports":"boot, stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GeneralOaxaca","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"MASS","Title":"Blinder-Oaxaca Decomposition for
Generalized Linear Model","Version":"1.0"},"GeneralizedHyperbolic":{"Author":"David
Scott <d.scott@auckland.ac.nz>","Depends":"R (>= 2.10.0), DistributionUtils,
RUnit","Description":"This package provides functions for the hyperbolic
and\nrelated distributions. Density, distribution and quantile\nfunctions and
random number generation are provided for the\nhyperbolic distribution, the
generalized hyperbolic\ndistribution, the generalized inverse Gaussian distribution
and\nthe skew-Laplace distribution. Additional functionality is\nprovided for the
hyperbolic distribution, normal inverse\nGaussian distribution and generalized
inverse Gaussian\ndistribution, including fitting of these distributions to
data.\nLinear models with hyperbolic errors may be fitted
using\nhyperblmFit.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GeneralizedHyperbolic","Repository":"http:\/
\/cran.csiro.au\/src\/contrib","Suggests":"VarianceGamma, actuar, SkewHyperbolic,
MASS","Title":"The Generalized Hyperbolic Distribution","URL":"http:\/\/www.r-
project.org","Version":"0.8-1"},"GeneticSubsetter":{"Author":"Ryan C. Graebner and
Alfonso Cuesta-Marcos","Depends":"rrBLUP","Description":"Finds subsets of sets of
genotypes with a high Heterozygosity, and Mean of Transformed Kinships (MTK),
measures that can indicate a subset would be beneficial for rare-trait discovery
and genome-wide association scanning, respectively.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GeneticSubsetter","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Identify Favorable Subsets of Germplasm
Collections","Version":"0.7"},"GeneticTools":{"Author":"Daniel
Fischer","Depends":"R (>= 3.0.2), gMWT (>= 0.3), snpStats, Rcpp (>=
0.9.13),\nplotrix","Description":"A loose collection of tools for the analysis of
gene expression and genotype data, currently with main focus on eQTL and MDR
analysis.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"GeneticTools","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Collection of Genetic Data Analysis
Tools","Version":"0.3.1"},"GeoBoxplot":{"Author":"Ao Li","Description":"Make
geographic box plot as detailed in Willmott et al. (2007).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GeoBoxplot","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Geographic Box Plot","Version":"1.0"},"GeoDE":
{"Author":"Neil R. Clark and Avi Ma'ayan","Depends":"R (>= 2.10), Matrix,
MASS","Description":"Given expression data this package calculate a
multivariate\ngeometrical characterization of the differential expression and can
also\nperform gene-set enrichment.","License":"GPL-
2","NeedsCompilation":"no","Package":"GeoDE","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"A geometrical Approach to Differential expression and gene-
set\nenrichment","Version":"1.0"},"GeoGenetix":{"Author":"Filippo Botta, Gilles
Guillot","Depends":"RandomFields","Description":"Quantification of the effect of
geographic versus environmental isolation on genetic
differentiation","License":"GPL","NeedsCompilation":"yes","Package":"GeoGenetix","R
epository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Quantification of the
effect of geographic versus environmental\nisolation on genetic
differentiation","URL":"http:\/\/www2.imm.dtu.dk\/~gigu\/Tangle","Version":"0.0.2"}
,"GeoLight":{"Author":"Simeon Lisovski, Simon Wotherspoon, Michael Sumner, Silke
Bauer, Tamara Emmenegger","Depends":"R (>= 2.10), maps","Description":"Provides
basic functions for global\npositioning based on light intensity measurements over
time.\nPositioning process includes the determination of sun events,
a\ndiscrimination of residency and movement periods, the\ncalibration of period-
specific data and, finally, the\ncalculation of positions.","Imports":"changepoint,
fields, MASS,","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GeoLight","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr","Title":"Analysis of Light Based Geolocator
Data","Version":"2.0.0"},"GeoXp":{"Author":"Yves Aragon, Thibault Laurent, Lauriane
Robidou, Anne\nRuiz-Gazen, Christine Thomas-Agnan","Depends":"R (>= 2.14.0),
quantreg, rgl, spdep","Description":"GeoXp is a tool for researchers in spatial
statistics,\nspatial econometrics, geography, ecology etc allowing to
link\ndynamically statistical plots with elementary maps. This\ncoupling consists
in the fact that the selection of a zone on\nthe map results in the automatic
highlighting of the\ncorresponding points on the statistical graph or reversely
the\nselection of a portion of the graph results in the automatic\nhighlighting of
the corresponding points on the map. GeoXp\nincludes tools from different areas of
spatial statistics\nincluding geostatistics as well as spatial econometrics
and\npoint processes. Besides elementary plots like boxplots,\nhistograms or simple
scatterplot, GeoXp also couples with maps\nMoran scatterplots, variogram cloud,
Lorentz Curves,...In order\nto make the most of the multidimensionality of the
data, GeoXp\nincludes some dimension reduction techniques such as
PCA.","Imports":"KernSmooth, rgeos, robustbase, splancs, stats,
tcltk","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GeoXp","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"maptools, MatrixModels, RANN","Title":"Interactive
exploratory spatial data
analysis","URL":"http:\/\/www.jstatsoft.org\/v47\/i02\/paper","Version":"1.6.2"},"G
etR":{"Author":"Johannes Beller, Soeren Kliem","Depends":"party","Description":"The
GetR package calculates Guttman error trees, which can\nbe used to find homogeneous
subgroups regarding Guttman errors.","License":"GPL-
3","NeedsCompilation":"no","Package":"GetR","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"GetR: Calculate Guttman error trees in
R","Version":"0.1"},"GetTDData":{"Author":"Marcelo Perlin [aut, cre]","Depends":"R
(>= 3.2.3)","Description":"Downloads and aggregates data for Brazilian government
issued bonds directly from the website of Tesouro Direto
<http:\/\/www.tesouro.fazenda.gov.br\/tesouro-direto-balanco-e-
estatisticas>.","Imports":"stringr,xlsx,utils,stats","License":"GPL-
2","NeedsCompilation":"no","Package":"GetTDData","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr, rmarkdown, testthat, ggplot2","Title":"Get
Data for Brazilian Bonds (Tesouro Direto)","Version":"1.0"},"GetoptLong":
{"Author":"Zuguang Gu","Depends":"R (>= 2.10.0), methods","Description":"This is
yet another command-line argument parser which wraps the\npowerful Perl module
Getopt::Long and with some adaptation for easier use\nin R. It also provides a
simple way for variable interpolation in R.","Imports":"rjson, GlobalOptions (>=
0.0.9)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GetoptLong","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat
(>= 0.3), knitr","Title":"Parsing Command-Line Arguments and Variable
Interpolation","URL":"https:\/\/github.com\/jokergoo\/GetoptLong","Version":"0.1.2"
},"GiANT":{"Author":"Florian Schmid, Christoph MÃ¼ssel, Johann M. Kraus, Hans A.
Kestler","Description":"Toolbox for various enrichment analysis methods and
quantification of uncertainty of gene sets.","Imports":"parallel, graphics,
grDevices, methods, stats, utils","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"GiANT","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"GlobalAncova, globaltest, fdrtool, st, limma,
DESeq","Title":"Gene Set Uncertainty in Enrichment
Analysis","Version":"1.2"},"GiNA":{"Author":"Luis Diaz-Garcia and Giovanny
Covarrubias-Pazaran, with collaborations of Brandon Schlautman, Walter Salazar and
Juan Zalapa.","Depends":"R (>= 3.2.1), methods, stats, EBImage, png,
parallel,\ndoParallel, foreach","Description":"Performs image segmentation in fruit
or seeds pictures in order to measure physical features in a high-throughput manner
for genome-wide association (GWAS) and genomic selection programs.","License":"GPL-
3","NeedsCompilation":"no","Package":"GiNA","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"High Throughput
Phenotyping","URL":"http:\/\/www.wisc.edu","Version":"1.0.1"},"GiRaF":
{"Author":"Julien Stoehr, Pierre Pudlo and Nial Friel","Description":"Allows
calculation on, and\nsampling from Gibbs Random Fields, and more precisely
general\nhomogeneous Potts model. The primary tool is the exact computation of\nthe
intractable normalising constant for small rectangular lattices.\nBeside the latter
function, it contains method that give exact sample from the likelihood\nfor small
enough rectangular lattices or approximate sample from the\nlikelihood using MCMC
samplers for large lattices.","Imports":"methods, Rcpp (>= 0.12.3)","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"GiRaF","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr","Title":"Gibbs Random Fields
Analysis","Version":"1.0"},"GibbsACOV":{"Author":"Emily Goren and Quan
Zhang","Depends":"MASS","Description":"Gibbs sampler for one-way linear mixed-
effects models\n(ANOVA, ANCOVA) with homoscedasticity of errors and
uniform\npriors.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GibbsACOV","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Gibbs Sampler for One-Way Mixed-Effects ANOVA and
ANCOVA Models","Version":"1.1"},"GillespieSSA":{"Author":"Mario Pineda-Krch
<mpineda@math.ualbeta.ca>","Depends":"R (>= 2.0.0)","Description":"GillespieSSA
provides a simple to use, intuitive, and\nextensible interface to several
stochastic simulation\nalgorithms for generating simulated trajectories of
finite\npopulation continuous-time model. Currently it implements\nGillespie's
exact stochastic simulation algorithm (Direct\nmethod) and several approximate
methods (Explicit tau-leap,\nBinomial tau-leap, and Optimized tau-leap). The
package also\ncontains a library of template models that can be run as demo\nmodels
and can easily be customized and extended. Currently the\nfollowing models are
included, decaying-dimerization reaction\nset, linear chain system, logistic growth
model, Lotka\npredator-prey model, Rosenzweig-MacArthur predator-prey
model,\nKermack-McKendrick SIR model, and a metapopulation SIRS
model.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"GillespieSSA","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Gillespie's Stochastic Simulation Algorithm
(SSA)","URL":"http:\/\/pineda-krch.com\/gillespiessa","Version":"0.5-
4"},"GiniWegNeg":{"Author":"Emanuela Raffinetti, Fabio
Aimar","Description":"Computation of the Gini coefficient in the presence of
weighted and\/or negative attributes. Two different approaches are considered in
order to fulfill, in the case of negative attributes, the normalization principle,
that is a value of the Gini coefficient bounded into the close range [0,1]. The
first approach is based on the proposal by Chen, Tsaur and Rhai (1982) and Berebbi
and Silber (1985), while the second approach is based on a recent proposal by
Raffinetti, Siletti and Vernizzi (2015). The plot of the curve of maximum
inequality, defined in the contribution of Raffinetti, Siletti and Vernizzi (2015),
is provided.","Imports":"graphics","License":"GPL-
3","NeedsCompilation":"no","Package":"GiniWegNeg","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Computing the Gini Coefficient for Weighted and
Negative\nAttributes","Version":"1.0"},"Giza":{"Author":"Erich
Striessnig","Depends":"R (>= 2.10.0), reshape, lattice","Description":"`Giza'
offers a simple way of creating multiple pyramid\nplots in one graphics window,
exploiting the power of the\nlattice package. It is a handy way of visualizing
longitudinal\ngrouped (i.e.: age- and education-structured)
data.","Imports":"lattice","License":"GPL-
2","NeedsCompilation":"no","Package":"Giza","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Constructing panels of population pyramid plots based on
lattice","Version":"1.0"},"GlobalDeviance":{"Author":"Frederike
Fuhlbrueck","Depends":"snowfall","Description":"permutation based global test with
deviance as test statistic","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GlobalDeviance","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Global Deviance Permutation
Tests","Version":"0.4"},"GlobalFit":{"Author":"Daniel Hartleb","Depends":"R (>=
2.12.0), sybil (>= 1.1.7), methods","Description":"Initial metabolic networks often
inaccurately predict in-silico growth or non-growth if compared to in-vivo data.
This package refines metabolic network models by making networks changes (i.e.,
removing, adding, changing reversibility of reactions; adding and removing biomass
metabolites) and simultaneously matching sets of experimental growth and non-growth
data (e.g., KO-mutants, mutants grown under different media
conditions,...)","License":"GPL-
3","NeedsCompilation":"no","Package":"GlobalFit","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"cplexAPI (>= 1.2.1)","Title":"Bi-Level Optimization
of Metabolic Network Models","Version":"1.1"},"GlobalOptions":{"Author":"Zuguang
Gu","Depends":"R (>= 2.10.0), methods","Description":"It provides more controls on
the option values such as validation\nand filtering on the values, making options
invisible or private.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GlobalOptions","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat (>= 0.3), knitr,
markdown","Title":"Generate Functions to Get or Set Global
Options","URL":"https:\/\/github.com\/jokergoo\/GlobalOptions","Version":"0.0.9"},"
Gmedian":{"Author":"Herve Cardot","Depends":"R (>= 3.0.2),
RSpectra","Description":"Fast algorithms based on averaged stochastic gradient for
robust estimation with large samples. Estimation of the geometric median, robust k-
Gmedian clustering, and robust PCA based on the Gmedian covariation
matrix.","Imports":"Rcpp (>= 0.12.3)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"Gmedian","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Geometric Median, k-Median Clustering and Robust Median
PCA","Version":"1.1"},"Gmisc":{"Author":"Max Gordon <max@gforge.se>","Depends":"R
(>= 3.2.0), Rcpp(>= 0.11.4), htmlTable (>= 1.1)","Description":"Tools for making
the descriptive \"Table 1\" used in medical\narticles, a transition plot for
showing changes between categories, a method for\nvariable selection based on the
SVD, BÃ©zier lines with arrows complementing the\nones in the 'grid' package, and
more.","Imports":"grid, grDevices, graphics, lattice, Hmisc, forestplot,
abind,\nmethods, knitr, magrittr, rmarkdown, XML, utils, stats","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"Gmisc","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat","Title":"Descriptive Statistics, Transition
Plots, and More","URL":"http:\/\/gforge.se","Version":"1.3.1"},"GoFKernel":
{"Author":"Jose M. Pavia","Depends":"stats, KernSmooth","Description":"Tests of
goodness-of-fit based on a kernel smoothing of the
data.","License":"GPL","NeedsCompilation":"no","Package":"GoFKernel","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Title":"Testing Goodness-of-Fit with the
Kernel Density Estimator","Version":"2.1-0"},"GoodmanKruskal":{"Author":"Ron
Pearson [aut, cre]","Depends":"R (>= 3.2.3)","Description":"Association analysis
between categorical\nvariables using the Goodman and Kruskal tau measure. This
asymmetric association\nmeasure allows the detection of asymmetric relations
between categorical\nvariables (e.g., one variable obtained by re-grouping
another).","Imports":"classInt, corrplot","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"GoodmanKruskal","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Suggests":"knitr, MASS, testthat, car,
rmarkdown","Title":"Association Analysis for Categorical
Variables","Version":"0.0.1"},"Grace":{"Author":"Sen Zhao","Depends":"glmnet,
scalreg","Description":"Use the graph-constrained estimation (Grace) procedure to
estimate graph-guided linear regression coefficients and use the
Grace\/GraceI\/GraceR tests to perform graph-guided hypothesis tests on the
association between the response and the predictors.","License":"GPL-
3","NeedsCompilation":"no","Package":"Grace","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"penalized","Title":"Graph-Constrained Estimation and
Hypothesis Tests","Version":"0.2"},"GrammR":{"Author":"Deepak Nag Ayyala [aut,
cre],\nShili Lin [aut]","Depends":"R (>= 3.1.0),","Description":"Represents
metagenomic samples on the Euclidean space to examine similarity amongst samples by
studying clusters in the model. Given the matrix of metagenomic counts for samples,
this package (1) quantifies
dissimilarity between samples using Kendall's tau-distance, (2) constructs
multidimensional models of different dimension, and (3) plots the models for
visualization and comparison.","Imports":"gWidgets, RGtk2, gWidgetsRGtk2, MASS,
cluster, rgl, GUniFrac,\nape","License":"LGPL-
3","NeedsCompilation":"yes","Package":"GrammR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"rglwidget","Title":"Graphical Representation and
Modeling of Metagenomic Reads","URL":"https:\/\/www.r-
project.org,\nhttp:\/\/www.stat.osu.edu\/~statgen\/SOFTWARE\/GrammR\/","Version":"1
.1.0"},"GrapheR":{"Author":"Maxime Hervé","Depends":"R (>= 2.13.0),
tcltk","Description":"A multi-platform user interface for drawing highly
customizable graphs in R. It aims to be a valuable help to quickly draw publishable
graphs without any knowledge of R commands. Six kinds of graph are available:
histogram, box-and-whisker plot, bar plot, pie chart, curve and scatter
plot.","License":"GPL-
2","NeedsCompilation":"no","Package":"GrapheR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"A Multi-Platform GUI for Drawing Customizable Graphs in
R","Version":"1.9-85"},"GrassmannOptim":{"Author":"Kofi Placid Adragni and Seongho
Wu","Depends":"Matrix","Description":"Optimizing a function F(U), where U is a
semi-orthogonal matrix and F is invariant under an orthogonal transformation of
U","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GrassmannOptim","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Grassmann Manifold
Optimization","URL":"http:\/\/www.math.umbc.edu\/~kofi\/GrassmannOptim","Version":"
2.0"},"Greg":{"Author":"Max Gordon [aut, cre],\nReinhard Seifert [aut] (Author of
original plotHR)","Depends":"forestplot, Gmisc (>= 1.0.3)","Description":"Methods
for manipulating regression models and for describing these in a style adapted for
medical journals.\nContains functions for generating an HTML table with crude and
adjusted estimates, plotting hazard ratio, plotting model\nestimates and confidence
intervals using forest plots, extending this to comparing multiple models in a
single forest plots.\nIn addition to the descriptives methods, there are addons for
the robust covariance matrix provided by the sandwich\npackage, a function for
adding non-linearities to a model, and a wrapper around the Epi package's Lexis
functions for\ntime-spliting a dataset when modeling non-proportional hazards in
Cox regressions.","Imports":"Hmisc, stringr, rms, sandwich, stats, nlme,
methods,\nhtmlTable, magrittr, knitr, Epi, utils, graphics,
3)","NeedsCompilation":"no","Package":"Greg","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"boot, testthat, cmprsk, survival, dplyr,
ggplot2","Title":"Regression Helper
Functions","URL":"http:\/\/gforge.se","Version":"1.2"},"Grid2Polygons":
{"Author":"Jason C. Fisher","Depends":"R (>= 2.15.0), sp,
rgeos","Description":"Converts a spatial object from class SpatialGridDataFrame
to\nSpatialPolygonsDataFrame.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"Grid2Polygons","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"rgdal","Title":"Convert Spatial Grids to
Polygons","URL":"https:\/\/github.com\/jfisher-usgs\/Grid2Polygons","Version":"0.1-
5"},"GriegSmith":{"Author":"Brian McGuire","Depends":"spatstat","Description":"The
function GriegSmith accepts either quadrat count data,\na point process object(ppp)
or a matrix of x and y coordinates.\nThe function calculates a nested analysis of
variance and\nsimulation envelopes.","License":"GPL-
2","NeedsCompilation":"no","Package":"GriegSmith","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Uses Grieg-Smith method on 2 dimentional spatial
data","Version":"1.0"},"GroupSeq":{"Author":"Roman Pahl","Description":"A graphical
user interface to compute group sequential designs\nbased on normally distributed
test statistics, particularly critical\nboundaries, power, drift, and confidence
intervals of such designs. All\ncomputations are based on the alpha spending
approach by Lan-DeMets with\nvarious alpha spending functions being available to
choose among.","Imports":"tcltk","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GroupSeq","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"A GUI-Based Program to Compute Probabilities Regarding
Group\nSequential Designs","Version":"1.3.3"},"GroupTest":{"Author":"Zhigen
Zhao","Description":"Contains functions for a two-stage multiple testing procedure
for grouped hypothesis, aiming at controlling both the total posterior false
discovery rate and within-group false discovery rate.","License":"GPL-
3","NeedsCompilation":"no","Package":"GroupTest","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Multiple Testing Procedure for Grouped
Hypotheses","Version":"1.0.1"},"GsymPoint":{"Author":"Mónica López-Ratón, Carmen
Cadarso-Suárez, Elisa M. Molanes-López, Emilio Letón","Depends":"truncnorm,
Rsolnp","Description":"Estimation of the cutpoint defined by the Generalized
Symmetry point in a binary classification setting based on a continuous diagnostic
test or marker. Two methods have been implemented to construct confidence intervals
for this optimal cutpoint, one based on the Generalized Pivotal Quantity and the
other based on Empirical Likelihood. Numerical and graphical outputs for these two
methods are easily
obtained.","License":"GPL","NeedsCompilation":"no","Package":"GsymPoint","Repositor
y":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Estimation of the Generalized
Symmetry Point, an Optimal\nCutpoint in Continuous Diagnostic
Tests","Version":"1.0"},"GuardianR":{"Author":"Marco T. Bastos & Cornelius
Puschmann","Description":"Provides an interface to the Open Platform's Content API
of the Guardian Media Group. It retrieves content from news outlets The Observer,
The Guardian, and guardian.co.uk from 1999 to current day.","Imports":"RCurl,
RJSONIO","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"GuardianR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"The Guardian API Wrapper","Version":"0.6"},"Guerry":
{"Author":"Michael Friendly [aut, cre], Stephane Dray [aut]","Depends":"R (>=
2.10)","Description":"This package comprises maps of France in 1830, multivariate
data from A.-M. Guerry and others, and statistical and\ngraphic methods related to
Guerry's \"Moral Statistics of France\". The goal is to facilitate the exploration
and\ndevelopment of statistical and graphic methods for multivariate data in a geo-
spatial context of historical
interest.","License":"GPL","NeedsCompilation":"no","Package":"Guerry","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"sp, shapefiles, spdep, ade4,
maptools","Title":"Maps, data and methods related to Guerry
(1833) \"Moral\nStatistics of France\"","URL":"http:\/\/guerry.r-forge.r-
project.org\/","Version":"1.6-1"},"GxM":{"Author":"Hao Zheng and Paul
Rathouz","Description":"Quantifying and testing gene-by-measured-environment
interaction in behavior genetic designs.","Imports":"methods, Rcpp, minqa, nlme,
2","NeedsCompilation":"no","Package":"GxM","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Maximum Likelihood Estimation for Gene-by-Measured
Environment\nInteraction Models","Version":"1.1"},"HAC":{"Author":"Ostap Okhrin
<ostap.okhrin@tu-dresden.de> and Alexander Ristig
<alexander.ristig@univie.ac.at>","Depends":"R (>= 2.15.2),
copula","Description":"Package provides the estimation of the structure and the
parameters, sampling methods and structural plots of Hierarchical Archimedean
Copulae (HAC).","Imports":"graphics, numDeriv, stats","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"HAC","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Estimation, Simulation and Visualization of
Hierarchical\nArchimedean Copulae (HAC)","URL":"\nhttp:\/\/tu-
dresden.de\/die_tu_dresden\/fakultaeten\/vkw\/iwv\/osv\/mitarbeiter\/ostap.okhrin\/
index_html","Version":"1.0-4"},"HAP.ROR":{"Author":"Lue Ping Zhao and Xin
Huang","Depends":"R (>= 2.15.2), hash, ape","Description":"Functions to perform ROR
for sequence-based association\nanalysis","License":"GPL-
2","NeedsCompilation":"no","Package":"HAP.ROR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Recursive Organizer (ROR)","Version":"1.0"},"HAPim":
{"Author":"S. Dejean, N. Oumouhou, D. Estivals, B. Mangin","Description":"The
package provides a set of functions whose aim is to\npropose 4 methods of QTL
detection. HAPimLD is an\ninterval-mapping method designed for unrelated
individuals with\nno family information that makes use of linkage
disequilibrium.\nHAPimLDL is an interval-mapping method for design of half-
sib\nfamilies. It combines linkage analysis and linkage\ndisequilibrium. HaploMax
is based on an analysis of variance\nwith a dose haplotype effect. HaploMaxHS is
based on an\nanalysis of variance with a sire effect and a dose haplotype\neffect
in half-sib family design. Fundings for the package\ndevelopment were provided to
the LDLmapQTL project by the ANR\nGENANIMAL program and APIS-
GENE.","License":"GPL","NeedsCompilation":"no","Package":"HAPim","Repository":"http
:\/\/cran.csiro.au\/src\/contrib","Title":"HapIM","Version":"1.3"},"HBSTM":
{"Author":"Pilar Munyoz, Alberto Lopez Moreno","Depends":"methods, MASS, fBasics,
maps","Description":"This package fits Hierarchical Bayesian space-Time models for
Gaussian data. Furthermore, its functions have been implemented for analysing the
fitting qualities of those models.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"HBSTM","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Hierarchical Bayesian Space-Time models for Gaussian
space-time\ndata","Version":"1.0.1"},"HBglm":{"Author":"Asad Hasan, Alireza S.
Mahani","Depends":"R (>= 2.10)","Description":"Convenient and efficient
functions for performing 2-level hierarchical Bayesian regression analysis for
multi-group data. The lowest level may belong to the generalized linear model (GLM)
family while the prior level, which effects pooling, allows for linear regression
on lower level covariates. Constraints on all or part of the parameter set maybe
specified with ease. A rich set of methods is included to visualize and analyze
results.","Imports":"Formula, bayesm, sns, MfUSampler, stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"HBglm","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Hierarchical Bayesian Regression for
GLMs","Version":"0.1"},"HDGLM":{"Author":"Bin Guo","Depends":"R (>=
3.1.1)","Description":"Test the significance of coefficients in high dimensional
generalized linear models.","License":"GPL-
2","NeedsCompilation":"yes","Package":"HDGLM","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Tests for High Dimensional Generalized Linear
Models","Version":"0.1"},"HDInterval":{"Author":"Mike Meredith and John
Kruschke","Description":"A generic function and a set of methods to calculate
highest density intervals for a variety of classes of objects which can specify a
probability density distribution, including MCMC output, fitted density objects,
and functions.","License":"GPL-
3","NeedsCompilation":"no","Package":"HDInterval","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"coda","Title":"Highest (Posterior) Density
Intervals","Version":"0.1.2"},"HDMD":{"Author":"Lisa McFerrin","Depends":"psych,
MASS","Description":"High Dimensional Molecular Data (HDMD) typically have
many\nmore variables or dimensions than observations or replicates\n(D>>N). This
can cause many statistical procedures to fail,\nbecome intractable, or produce
misleading results. This\npackage provides several tools to reduce dimensionality
and\nanalyze biological data for meaningful interpretation of\nresults. Factor
Analysis (FA), Principal Components Analysis\n(PCA) and Discriminant Analysis (DA)
are frequently used\nmultivariate techniques. However, PCA methods prcomp
and\nprincomp do not reflect the proportion of total variation of\neach principal
component. Loadings.variation displays the\nrelative and cumulative contribution
of variation for each\ncomponent by accounting for all variability in data. When
D>>N,\nthe maximum likelihood method cannot be applied in FA and the\nthe principal
axes method must be used instead, as in factor.pa\nof the psych package. The
factor.pa.ginv function in this\npackage further allows for a singular covariance
matrix by\napplying a general inverse method to estimate factor scores.\nMoreover,
factor.pa.ginv removes and warns of any variables\nthat are constant, which would
otherwise create an invalid\ncovariance matrix. Promax.only further allows users to
define\nrotation parameters during factor estimation. Similar to the\nEuclidean
distance, the Mahalanobis distance estimates the\nrelationship among groups.
pairwise.mahalanobis computes all\nsuch pairwise Mahalanobis distances among groups
and is useful\nfor quantifying the separation of groups in DA. Genetic\nsequences
are composed of discrete alphabetic characters, which\nmakes estimates of
variability difficult. MolecularEntropy and\nMolecularMI calculate the entropy and
mutual information to\nestimate variability and covariability, respectively, of DNA
or\nAmino Acid sequences. Functional grouping of amino acids\n(Atchley et al 1999)
is also available for entropy and mutual\ninformation estimation. Mutual
information values can be\nnormalized by NMI to account for the background
distribution\narising from the stochastic pairing of independent, random\nsites.
Alternatively, discrete alphabetic sequences can be\ntransformed into biologically
informative metrics to be used in\nvarious multivariate procedures.
FactorTransform converts\namino acid sequences using the amino acid indices
determined by\nAtchley et al 2005.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"HDMD","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"scatterplot3d","Title":"Statistical Analysis Tools for
High Dimension Molecular Data\n(HDMD)","Version":"1.2"},"HDPenReg":
{"Author":"Quentin Grimonprez [aut, cre],\nSerge Iovleff [aut]","Depends":"R (>=
3.0.2), rtkore (>= 0.9.2)","Description":"Algorithms for lasso and fused-lasso
problems: implementation of\nthe lars algorithm for lasso and fusion penalization
and EM-based\nalgorithms for (logistic) lasso and fused-lasso
penalization.","Imports":"methods, Matrix","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"HDPenReg","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"High-Dimensional Penalized
Regression","Version":"0.93.1"},"HDclassif":{"Author":"Laurent Berge, Charles
Bouveyron and Stephane Girard","Depends":"grDevices, utils, graphics, stats,
MASS","Description":"Discriminant analysis and data clustering methods for high
dimensional data, based on the assumption that high-dimensional data live in
different subspaces with low dimensionality proposing a new parametrization of the
Gaussian mixture model which combines the ideas of dimension reduction and
constraints on the model.","License":"GPL-
2","NeedsCompilation":"no","Package":"HDclassif","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"High Dimensional Supervised Classification and
Clustering","Version":"1.3"},"HDtweedie":{"Author":"Wei Qian
<weiqian@stat.umn.edu>, Yi Yang <yiyang@umn.edu>, Hui Zou
<hzou@stat.umn.edu>","Description":"This package implements a iteratively reweighed
least square (IRLS) strategy that incorporates a blockwise majorization decent
(BMD) method, for efficiently computing the solution paths of the (grouped) lasso
and the (grouped) elastic net for the Tweedie model.","License":"GPL-
2","NeedsCompilation":"yes","Package":"HDtweedie","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"The Lasso for the Tweedie's Compound Poisson Model
Using an\nIRLS-BMD Algorithm","Version":"1.1"},"HEAT":{"Author":"Youn-Hee Lim, Il-
Sang Ohn, and Ho Kim","Depends":"R (>= 2.10), splines","Description":"Timeseries
analysis is conducted using Korean mortality and environmental
variables","License":"GPL-
2","NeedsCompilation":"no","Package":"HEAT","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Health Effects of Air Pollution and Temperature
(HEAT)","Version":"1.2"},"HGNChelper":{"Author":"Levi Waldron and Markus
Riester","Depends":"R (>= 2.10)","Description":"Contains functions for\nidentifying
and correcting HGNC gene symbols which have been converted\nto date format by
Excel, for reversibly converting between HGNC\nsymbols and valid R names,
identifying invalid HGNC symbols and\ncorrecting synonyms and outdated symbols
which can be mapped to an\nofficial symbol.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"HGNChelper","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Handy Functions for Working With HGNC Gene Symbols
and\nAffymetrix Probeset
Identifiers","URL":"https:\/\/bitbucket.org\/lwaldron\/hgnchelper","Version":"0.3.1
"},"HH":{"Author":"Richard M. Heiberger","Depends":"R (>= 3.0.2), lattice, stats,
grid, latticeExtra, multcomp,\ngridExtra (>= 2.0.0),
graphics","Description":"Support software for Statistical Analysis and Data Display
(Second Edition, Springer, ISBN 978-1-4939-2121-8, 2015) and (First Edition,
Springer, ISBN 0-387-40270-5, 2004) by Richard M. Heiberger and Burt Holland. This
contemporary presentation of statistical methods features extensive use of
graphical displays for exploring data and for displaying the analysis. The second
edition includes redesigned graphics and additional chapters. The authors emphasize
how to construct and interpret graphs, discuss principles of graphical design, and
show how accompanying traditional tabular results are used to confirm the visual
impressions derived directly from the graphs. Many of the graphical formats are
novel and appear here for the first time in print. All chapters have exercises.
All functions introduced in the book are in the package. R code for all examples,
both graphs and tables, in the book is included in the scripts directory of the
package.","Imports":"reshape2, leaps, vcd, colorspace, RColorBrewer, shiny
(>=\n0.13.1), Hmisc, abind, Rmpfr (>= 0.6.0), grDevices, methods","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"HH","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"mvtnorm, car, Rcmdr, RcmdrPlugin.HH,
TeachingDemos","Title":"Statistical Analysis and Data Display: Heiberger and
Holland","Version":"3.1-31"},"HHG":{"Author":"Barak Brill & Shachar Kaufman, based
in part on an earlier implementation by Ruth Heller and Yair Heller.","Depends":"R
(>= 3.1.0)","Description":"Heller-Heller-Gorfine (HHG) tests are a set of powerful
statistical tests of multivariate k-sample homogeneity and independence. For the
univariate case, the package also offers implementations of the MinP DDP and MinP
ADP tests, which are consistent against all continuous alternatives but are
distribution-free, and are thus much faster to apply.","License":"GPL-
2","NeedsCompilation":"yes","Package":"HHG","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"MASS,knitr","Title":"Heller-Heller-Gorfine Tests of
Independence and Equality of\nDistributions","Version":"1.5.1"},"HI":
{"Author":"Giovanni Petris <GPetris@Uark.edu> and Luca
Tardella\n<luca.tardella@@uniroma1.it>; original C code for ARMS by
Wally\nGilks.","Depends":"R (>= 1.7.0)","Description":"Simulation from
distributions supported by nested\nhyperplanes, using the algorithm described in
Petris &\nTardella, \"A geometric approach to transdimensional Markov\nchain Monte
Carlo\", Canadian Journal of Statistics, v.31, n.4,\n(2003). Also random direction
multivariate Adaptive Rejection\nMetropolis
Sampling.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"HI","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Simulation from distributions supported by nested
hyperplanes","Version":"0.4"},"HIV.LifeTables":{"Author":"David J
Sharrow","Depends":"R (>= 2.10)","Description":"The functions in this package
produce a complete set of mortality rates as a function of a combination of HIV
prevalence and either life expectancy at birth (e0), child mortality (5q0), or
child mortality with adult mortality
(45q15)","License":"Unlimited","NeedsCompilation":"no","Package":"HIV.LifeTables","
Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"HIV calibrated model
life tables for countries with generalized\nHIV
epidemics","Version":"0.1"},"HIest":{"Author":"Ben Fitzpatrick","Depends":"nnet,
stats","Description":"Uses likelihood to estimate ancestry and
heterozygosity.\nEvaluates simple hybrid classifications (parentals, F1,
F2,\nbackcrosses). Estimates genomic clines.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"HIest","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Hybrid index estimation","Version":"2.0"},"HK80":
{"Author":"Jinlong Zhang","Description":"Conversion and Reverse Conversion between
WGS84UTM, WGS84GEO, HK80UTM, HK80GEO and HK1980GRID Coordinate Systems. Algorithms
follow Survey and Mapping Office Lands Department, Hong Kong Government
(1995)","License":"GPL-
2","NeedsCompilation":"no","Package":"HK80","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Conversion Tools for HK80 Geographical Coordinate
System","Version":"0.0.1"},"HKprocess":{"Author":"Hristos Tyralis","Depends":"R (>=
3.2.3)","Description":"Methods to make inference about the Hurst-Kolmogorov and the
AR(1) process.","Imports":"MCMCpack (>= 1.3-3), gtools(>= 3.5.0)","License":"GPL-
3","NeedsCompilation":"yes","Package":"HKprocess","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"ltsa (>= 1.4.6), FGN (>= 2.0-12)","Title":"Hurst-
Kolmogorov Process","URL":"www.itia.ntua.gr\/en\/softinfo\/31\/","Version":"0.0-
2"},"HLMdiag":{"Author":"Adam Loy <loyad01@gmail.com>","Depends":"R (>=
2.15.0)","Description":"A suite of diagnostic tools for hierarchical\n(multilevel)
linear models. The tools include\nnot only leverage and traditional deletion
diagnostics (Cook's\ndistance, covratio, covtrace, and MDFFITS) but
also\nconvenience functions and graphics for residual analysis. Models\ncan be fit
using either lmer in the 'lme4' package or lme in the 'nlme' package,\nbut only
two-level models fit using lme are currently supported.","Imports":"ggplot2 (>=
0.9.2), stats, methods, plyr, reshape2, MASS,\nMatrix, RLRsim,
mgcv","License":"GPL-
2","NeedsCompilation":"yes","Package":"HLMdiag","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"mlmRev, WWGbook, lme4 (>= 1.0),
nlme","Title":"Diagnostic Tools for Hierarchical (Multilevel) Linear
Models","URL":"https:\/\/github.com\/aloy\/HLMdiag","Version":"0.3.1"},"HLSM":
{"Author":"Samrachana Adhikari, Brian Junker, Tracy Sweet, Andrew C.
Thomas","Depends":"R (>= 3.0.0)","Description":"Hierarchical latent space network
model for fitting ensemble of networks.","Imports":"MASS, coda, grDevices,
graphics, stats","License":"GPL (>
3)","NeedsCompilation":"yes","Package":"HLSM","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Hierarchical Latent Space Network Model
(HLSM)","Version":"0.5"},"HMDHFDplus":{"Author":"Tim Riffe, Carl Boe, Josh
Goldstein","Depends":"R (>= 3.1.2),","Description":"Utilities for reading data from
the Human Mortality Database (<www.mortality.org>), Human Fertility Database
(<www.humanfertility.org>), and similar databases from the web or locally into an R
session as data.frame objects. These are the two most widely used sources of
demographic data to study basic demographic change, trends, and develop new
demographic methods. Other supported databases at this time include the Human
Fertility Collection (<http:\/\/www.fertilitydata.org\/>), The Japanese Mortality
Database (<http:\/\/www.ipss.go.jp\/p-toukei\/JMD>), and the Canadian Human
Mortality Database (<http:\/\/www.bdlc.umontreal.ca\/chmd\/>). Arguments and data
are standardized.","Imports":"RCurl, XML","License":"GPL-
2","NeedsCompilation":"no","Package":"HMDHFDplus","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Read HMD and HFD Data from the
Web","URL":"https:\/\/github.com\/timriffe\/TR1","Version":"1.1.8"},"HMM":
{"Author":"Scientific Software Development - Dr. Lin
Himmelmann,\nwww.linhi.com","Depends":"R (>= 2.0.0)","Description":"Easy to use
library to setup, apply and make inference\nwith discrete time and discrete space
Hidden Markov Models","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"HMM","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"HMM - Hidden Markov Models","Version":"1.0"},"HMMCont":
{"Author":"Mikhail A. Beketov","Description":"The package includes the functions
designed to analyse continuous observations processes with the Hidden Markov Model
approach. They include Baum-Welch and Viterbi algorithms and additional
visualisation functions. The observations are assumed to have Gaussian distribution
and to be weakly stationary processes. The package was created for analyses of
financial time series, but can also be applied to any continuous observations
processes.","License":"GPL-
3","NeedsCompilation":"no","Package":"HMMCont","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Hidden Markov Model for Continuous Observations
Processes","Version":"1.0"},"HMMpa":{"Author":"Vitali Witowski, Dr. Ronja
Foraita","Depends":"R (>= 2.10.0)","Description":"Analysing time-series
accelerometer data to quantify length and intensity of physical
activity.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"HMMpa","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Analysing accelerometer data using hidden Markov
models","Version":"1.0"},"HMP":{"Author":"Patricio S. La Rosa, Elena Deych, Berkley
Shands, William D. Shannon","Depends":"R (>= 3.1.0), dirmult","Description":"Using
Dirichlet-Multinomial distribution to provide several functions for formal
hypothesis testing, power and sample size calculations for human microbiome
experiments.","Imports":"MASS, gplots, doParallel, foreach,
parallel","License":"Apache License (==
2.0)","NeedsCompilation":"no","Package":"HMP","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Hypothesis Testing and Power Calculations for
Comparing\nMetagenomic Samples from HMP","Version":"1.4.3"},"HMPTrees":
{"Author":"Patricio S. La Rosa, Elena Deych, Berkley Shands, William D.
Shannon","Depends":"R (>= 3.0.0)","Description":"Tools to model, compare, and
visualize populations of taxonomic tree objects.","Imports":"ape, HMP, dirmult,
doParallel, foreach, parallel","License":"Apache License (==
2.0)","NeedsCompilation":"no","Package":"HMPTrees","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Statistical Object Oriented Data Analysis of RDP-Based
Taxonomic\nTrees from Human Microbiome Data","Version":"1.3"},"HMR":
{"Author":"Asger R. Pedersen <asger@clin.au.dk>","Description":"Statistical
analysis of static chamber concentration data for trace gas flux
estimation.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"HMR","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Flux Estimation with Static Chamber
Data","Version":"0.4.1"},"HPbayes":{"Author":"David J Sharrow","Depends":"MASS,
mvtnorm, corpcor, numDeriv, stats, boot","Description":"This package provides all
the functions necessary to\nestimate the 8 parameters of the Heligman Pollard
mortality\nmodel using a Bayesian Melding procedure with IMIS as well as\nto
convert those parameters into age-specifc probabilities of\ndeath and a
corresponding life
table","License":"Unlimited","NeedsCompilation":"no","Package":"HPbayes","Repositor
y":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Heligman Pollard mortality model
parameter estimation using\nBayesian Melding with Incremental Mixture Importance
Sampling","Version":"0.1"},"HRM":{"Author":"Martin Happ [aut, cre], Harrar W.
Solomon [aut], Arne C. Bathke [aut]","Depends":"R (>= 1.8.0), MASS,
matrixcalc","Description":"Tests for main and simple treatment effects, time
effects, as well as treatment by time interactions in possibly high-dimensional
multi-group repeated measures designs.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"HRM","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"High-Dimensional Repeated Measures","Version":"0.1"},"HSAR":
{"Author":"Guanpeng Dong, Richard Harris, Angelos Mimis","Depends":"R (>=
2.7.0)","Description":"A library of the Hierarchical Spatial Autoregressive Model
(HSAR), based on a Bayesian Markov Chain Monte Carlo (MCMC)
algorithm.","Imports":"spdep, Rcpp","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"HSAR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Hierarchical Spatial Autoregressive Model
(HSAR)","Version":"0.3.6"},"HSAUR":{"Author":"Brian S. Everitt and Torsten
Hothorn","Depends":"R (>= 2.2.0), tools","Description":"Functions, data sets,
analyses and examples from the book\nÀ Handbook of Statistical Analyses Using R'
(Brian S. Everitt and Torsten\nHothorn, Chapman & Hall\/CRC, 2006). The first
chapter\nof the book, which is entitled Àn Introduction to R',\nis completely
included in this package, for all other chapters,\na vignette containing all data
analyses is
available.","License":"GPL","NeedsCompilation":"no","Package":"HSAUR","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"lattice, MASS, scatterplot3d (>=
0.3-23), ape (>= 1.6), coin\n(>= 0.3-3), flexmix (>= 1.1-0), gee (>= 4.13-10), lme4
(>=\n0.98-1), mclust (>= 3.0-0), party (>= 0.2-8), randomForest (>=\n4.5-12), rmeta
(>= 2.12), vcd (>= 0.9-3), survival, KernSmooth,\nrpart,
mvtnorm, Matrix, boot, TH.data","Title":"A Handbook of Statistical Analyses Using
R (1st Edition)","Version":"1.3-7"},"HSAUR2":{"Author":"Brian S. Everitt and
Torsten Hothorn","Depends":"R (>= 2.2.0), tools","Description":"Functions, data
sets, analyses and examples from the\nsecond edition of the book\nÀ Handbook of
Statistical Analyses Using R' (Brian S. Everitt and Torsten\nHothorn, Chapman &
Hall\/CRC, 2008). The first chapter\nof the book, which is entitled Àn
Introduction to R',\nis completely included in this package, for all other
chapters,\na vignette containing all data analyses is available. In addition,\nthe
package contains Sweave code for producing slides for selected\nchapters (see
HSAUR2\/inst\/slides).","License":"GPL-
2","NeedsCompilation":"no","Package":"HSAUR2","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"lattice, MASS, scatterplot3d (>= 0.3-23), alr3, ape (>=
1.6),\ncoin (>= 0.3-3), flexmix (>= 1.1-0), gee (>= 4.13-10), lme4 (>=\n0.98-1),
mclust (>= 3.0-0), party (>= 0.2-8), randomForest (>=\n4.5-12), rmeta (>= 2.12),
vcd (>= 0.9-3), survival, rpart,\ngamair, multcomp (>= 1.0-3), sandwich, mboost,
KernSmooth,\nMatrix, boot, mgcv, mvtnorm, partykit, tm, wordcloud,
TH.data","Title":"A Handbook of Statistical Analyses Using R (2nd
Edition)","Version":"1.1-14"},"HSAUR3":{"Author":"Torsten Hothorn and Brian S.
Everitt","Depends":"R (>= 3.0.0), tools","Description":"Functions, data sets,
analyses and examples from the\nthird edition of the book\nÀ Handbook of
Statistical Analyses Using R' (Torsten Hothorn and Brian S.\nEveritt, Chapman &
Hall\/CRC, 2014). The first chapter\nof the book, which is entitled Àn
Introduction to R',\nis completely included in this package, for all other
chapters,\na vignette containing all data analyses is available. In
addition,\nSweave source code for slides of selected chapters is included in\nthis
package (see HSAUR3\/inst\/slides).","License":"GPL-
2","NeedsCompilation":"no","Package":"HSAUR3","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"boot (>= 1.3-9), lattice (>= 0.20-23), MASS (>= 7.3-29),
mgcv\n(>= 1.7-27), rpart (>= 4.1-4), survival (>= 2.37-4), alr3 (>=\n2.0.5), ape
(>= 3.0-11), coin (>= 1.0-23), flexmix (>= 2.3-11),\nFormula (>= 1.1-1), gamair (>=
0.0.8), gamlss.data (>= 4.2.6),\ngee (>= 4.13-18), KernSmooth (>= 2.23-10), lme4
(>= 1.0-5),\nmaps (>= 2.3-6), maptools (>= 0.8-27), mboost (>= 2.2-3),\nmclust (>=
4.2), mlbench (>= 2.1-1), mice (>= 2.18), multcomp\n(>= 1.3-1), mvtnorm (>= 0.9-
9996), partykit (>= 0.8-0),\nquantreg (>= 5.05), randomForest (>= 4.6-7), rmeta (>=
2.16),\nsandwich (>= 2.3-0), scatterplot3d (>= 0.3-34), sp (>= 1.0-14),\nTH.data
(>= 1.0-2), tm (>= 0.5-9.1), vcd (>= 1.3-1), wordcloud\n(>= 2.4)","Title":"A
Handbook of Statistical Analyses Using R (3rd Edition)","URL":"The publishers web
page is\nhttp:\/\/www.crcpress.com\/product\/isbn\/9781482204582","Version":"1.0-
5"},"HSROC":{"Author":"Ian Schiller and Nandini Dendukuri","Depends":"R (>= 3.1.2),
lattice, coda, MASS, MCMCpack","Description":"Implements a model for joint meta-
analysis of sensitivity and specificity of the diagnostic test under evaluation,
while taking into account the possibly imperfect sensitivity and specificity of the
reference test. This hierarchical model accounts for both within and between study
variability. Estimation is carried out using a Bayesian approach, implemented via a
Gibbs sampler. The model can be applied in situations where more than one reference
test is used in the selected studies.","License":"GPL-
2","NeedsCompilation":"yes","Package":"HSROC","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Meta-Analysis of Diagnostic Test Accuracy when Reference
Test
is\nImperfect","URL":"http:\/\/www.nandinidendukuri.com\/","Version":"2.1.8"},"HSSV
D":{"Author":"Guanhua Chen [aut, cre],\nMichael Kosorok [aut],\nShannon Holloway
[ctb]","Depends":"R (>= 2.10), bcv","Description":"A data mining tool for
discovering subgroups of patients and genes that simultaneously display unusual
levels of variability compared to other genes and patients. Based on sparse
singular value decomposition (SSVD), the method can detect both mean and variance
biclusters in the presence of heterogeneous residual variance.","License":"GPL-
2","NeedsCompilation":"no","Package":"HSSVD","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Biclustering with Heterogeneous
Variance","Version":"1.2"},"HTMLUtils":{"Author":"\"Markus Loecher, Berlin School
of Economics and Law (BSEL)\"
<markus.loecher@gmail.com>","Depends":"R2HTML","Description":"Facilitates automated
HTML report creation, in particular\nframed HTML pages and dynamically sortable
tables.","License":"GPL","NeedsCompilation":"no","Package":"HTMLUtils","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Title":"Facilitates Automated HTML Report
Creation","Version":"0.1.7"},"HTSCluster":{"Author":"Andrea Rau, Gilles Celeux,
Marie-Laure Martin-Magniette, Cathy Maugis-Rabusseau","Depends":"R (>= 2.10.0),
capushe","Description":"This package implements a Poisson mixture model to cluster
observations (e.g., genes) in high throughput sequencing data. Parameter estimation
is performed using either the EM or CEM algorithm, and the slope heuristics are
used for model selection (i.e., to choose the number of
clusters).","Imports":"edgeR, poisson.glm.mix, plotrix","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"HTSCluster","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"HTSFilter, Biobase","Title":"Clustering high
throughput sequencing (HTS) data","Version":"2.0.4"},"HUM":{"Author":"Natalia
Novoselova,Junxi Wang,Jialiang Li, Frank Pessler,Frank Klawonn","Depends":"R (>=
2.10),gtools, Rcpp (>= 0.10.5)","Description":"Tools for computing HUM (Hypervolume
Under the Manifold) value to estimate features ability\nto discriminate the class
labels, visualizing the ROC curve for two or three class
labels.","Imports":"rgl","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"HUM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"compute HUM value and visualize ROC
curves","URL":"http:\/\/public.ostfalia.de\/~klawonn\/HUM.htm","Version":"1.0"},"HW
.pval":{"Author":"Shubhodeep Mukherji
<deep.mukherji@utexas.edu>","Description":"HW.pval calculates plain and fully
conditional\nroot-mean-square, chi-square, and log likelihood-ratio P-values\nfor
the user-provided genotypic counts to be consistent with\nthe Hardy-Weinberg
equilibrium model. For further information\non the Hardy-Weinberg equilibrium
model and the pseudocode,\nrefer to the paper \"Testing Hardy-Weinberg equilibrium
with a\nsimple root-mean-square statistic\" by Rachel Ward.","License":"GPL-
3","NeedsCompilation":"no","Package":"HW.pval","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Testing Hardy-Weinberg Equilibrium for Multiallelic
Genes","Version":"1.0"},"HWEBayes":{"Author":"Jon Wakefield [aut, cre],\nMartyn
Plummer [ctb]","Description":"Estimation and testing of HWE using Bayesian
methods.\nThree models are currently considered: HWE, a model\nparameterized in
terms of the allele frequencies and a single\ninbreeding coefficient f, and the
saturated model. Testing is\nbased on Bayes factors.","Imports":"MCMCpack,
mvtnorm","License":"GPL-
2","NeedsCompilation":"no","Package":"HWEBayes","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Bayesian investigation of Hardy-Weinberg Equilibrium
via\nestimation and testing","Version":"1.4"},"HWEintrinsic":{"Author":"Sergio
Venturini","Depends":"methods, utils","Description":"General (multi-allelic) Hardy-
Weinberg equilibrium problem from an objective Bayesian testing standpoint. This
aim is achieved through the identification of a class of priors specifically
designed for this testing problem. A class of intrinsic priors under the full model
is considered. This class is indexed by a tuning quantity, the training sample
size, as discussed in Consonni, Moreno and Venturini (2010). These priors are
objective, satisfy Savage's continuity condition and have proved to behave
extremely well for many statistical testing problems.","Imports":"graphics,
grDevices, stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"HWEintrinsic","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Objective Bayesian Testing for the Hardy-Weinberg
Equilibrium\nProblem","URL":"http:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/sim.40
84\/abstract","Version":"1.2.2"},"HWxtest":{"Author":"Bill Engels
<wrengels@wisc.edu>","Depends":"R (>= 2.14)","Description":"Tests whether a set of
genotype counts fits the HW expectations.\nExact tests performed by an efficient
algorithm. Included test statistics\nare likelihood ratio, probability, U-score and
Pearson's
X2.","License":"GPL","NeedsCompilation":"yes","Package":"HWxtest","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Suggests":"ggplot2, rmarkdown, knitr,
RefManageR, adegenet, genetics,\nparallel","Title":"Exact Tests for Hardy-Weinberg
Proportions","Version":"1.1.7"},"HadoopStreaming":{"Author":"David S. Rosenberg
<drosen@sensenetworks.com>","Depends":"getopt","Description":"Provides a framework
for writing map\/reduce scripts for\nuse in Hadoop Streaming. Also facilitates
operating on data in\na streaming fashion, without
Hadoop.","License":"GPL","NeedsCompilation":"no","Package":"HadoopStreaming","Repos
itory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Utilities for using R
scripts in Hadoop streaming","Version":"0.2"},"HandTill2001":{"Author":"Andreas
Dominik Cullmann [aut, cre],\nEdgar Kublin [ctb]","Depends":"R (>= 2.14), methods,
utils","Description":"An S4 implementation of Eq. (3) and Eq. (7)\nby David J. Hand
and Robert J. Till (2001). A Simple Generalisation of\nthe Area Under the ROC Curve
for Multiple Class Classification Problems.\nMachine Learning, 45 (2), p. 171--186.
DOI:10.1023\/A:1010920819831.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"HandTill2001","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"MASS, rpart, mda, nnet","Title":"Multiple Class
Area under ROC
Curve","URL":"https:\/\/github.com\/fvafrCU\/HandTill2001","Version":"0.2-
11"},"Hankel":{"Author":"Daniel Kolbe <Daniel-
Kolbe@web.de>","Description":"Provides an R routine for a Cramer-von Mises type two
sample test which is based on empirical Hankel transforms of the non-negative
sample variables. The test is non-parametric and not distribution free. The exact
value of the test statistic for univariate data as well as the p-value and the
critical value are computed.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"Hankel","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Univariate non-parametric two-sample test based on
empirical\nHankel transforms","Version":"0.0-1"},"HapEstXXR":{"Author":"Sven
Knueppel and Klaus Rohde","Depends":"survival","Description":"The multi-locus
stepwise regression (MSR) combines the advantages of stepwise regression and
haplotype-based analysis. The MSR can be used to identify informative combinations
of single nucleotide polymorphisms (SNPs) from unlinked SNPs (allele combinations)
or SNPs within a chromosomal region (haplotypes).","License":"LGPL (>=
2.1)","NeedsCompilation":"yes","Package":"HapEstXXR","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Multi-Locus Stepwise Regression","Version":"0.1-
8"},"Haplin":{"Author":"Hakon K. Gjessing","Depends":"GenABEL,
DatABEL","Description":"Performs genetic association analyses of case-parent triad
(trio) data with multiple markers. It can also incorporate complete or incomplete
control triads, for instance independent control children. Estimation is based on
haplotypes, for instance SNP haplotypes, even though phase is not known from the
genetic data. Haplin estimates relative risk (RR + conf.int.) and p-value
associated with each haplotype. It uses maximum likelihood estimation to make
optimal use of data from triads with missing genotypic data, for instance if some
SNPs has not been typed for some individuals. Haplin also allows estimation of
effects of maternal haplotypes and parent-of-origin effects, particularly
appropriate in perinatal epidemiology. Haplin allows special models, like X-
inactivation, to be fitted on the X-chromosome.","Imports":"parallel, tools, mgcv,
MASS, SuppDists, snow","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Haplin","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Analyzing Case-Parent Triad and\/or Case-Control Data with
SNP\nHaplotypes","URL":"http:\/\/www.uib.no\/smis\/gjessing\/genetics\/software\/ha
plin\/","Version":"5.5"},"HaploSim":{"Author":"Albart Coster [aut, cre],\nJohn
Bastiaansen [aut]","Depends":"methods,utils, R (>= 2.6.0)","Description":"Simulate
haplotypes through meioses. Allows specification\nof population
2)","NeedsCompilation":"no","Package":"HaploSim","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"pedigree (>= 1.3.1)","Title":"Functions to simulate
haplotypes","Version":"1.8.4"},"HardyWeinberg":{"Author":"Jan Graffelman
<jan.graffelman@upc.edu>","Depends":"R (>= 1.8.0), mice","Description":"Contains
tools for exploring Hardy-Weinberg equilibrium for\ndiallelic genetic marker data.
All classical tests (chi-square, exact,\nlikelihood-ratio and permutation tests)
for Hardy-Weinberg equilibrium\nare included in the package, as well as functions
for power computation and\nfor the simulation of marker data under equilibrium and
disequilibrium.\nRoutines for dealing with markers on the X-chromosome are
included.\nFunctions for testing equilibrium in the presence of missing data
by\nusing multiple imputation are also provided. Implements several graphics\nfor
exploring the equilibrium status of a large set of diallelic markers:\nternary
plots with acceptance regions, log-ratio plots and Q-Q plots.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"HardyWeinberg","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Statistical Tests and Graphics for Hardy-Weinberg
Equilibrium","URL":"http:\/\/www.r-project.org, http:\/\/www-
eio.upc.edu\/~jan","Version":"1.5.6"},"HarmonicRegression":{"Author":"Paal O.
Westermark","Depends":"R (>= 2.10)","Description":"Fits the first harmonics in a
Fourier expansion to one or more time series. Trend elimination can be performed.
Computed values include estimates of amplitudes and phases, as well as confidence
intervals and p-values for the null hypothesis of Gaussian noise.","License":"MIT +
file
LICENSE","NeedsCompilation":"no","Package":"HarmonicRegression","Repository":"http:
\/\/cran.csiro.au\/src\/contrib","Suggests":"knitr","Title":"Harmonic Regression to
One or more Time Series","Version":"1.0"},"Harvest.Tree":{"Author":"Bingyuan
Liu\/Yan Yuan\/Qian Shi","Depends":"R (>= 3.0.1)","Description":"Aimed at applying
the Harvest classification tree algorithm, modified algorithm of classic
classification tree.The harvested tree has advantage of deleting redundant rules in
trees, leading to a simplify and more efficient tree model.It was firstly used in
drug discovery field, but it also performs well in other kinds of data, especially
when the region of a class is disconnected. This package also improves the basic
harvest classification tree algorithm by extending the field of data of algorithm
to both continuous and categorical variables. To learn more about the harvest
classification tree algorithm, you can go to
http:\/\/www.stat.ubc.ca\/Research\/TechReports\/techreports\/220.pdf for more
information.","Imports":"rpart,stats","License":"GPL-
2","NeedsCompilation":"no","Package":"Harvest.Tree","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Harvest the Classification
Tree","Version":"1.1"},"HelpersMG":{"Author":"Marc Girondot","Depends":"coda, R (>=
2.14.0)","Description":"Contains many functions useful for managing 'NetCDF' files
(see http:\/\/en.wikipedia.org\/wiki\/NetCDF), get tide levels on any point of the
globe, get moon phase and time for sun rise and fall, analyse and reconstruct
periodic time series of temperature with irregular sinusoidal pattern, show scales
and wind rose in plot with change of color of text, Metropolis-Hastings algorithm
for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in
disk by there names or their content, read the contents of all files from a folder
at one time.","License":"GPL-
2","NeedsCompilation":"no","Package":"HelpersMG","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"RNetCDF, ncdf4, maps, XML","Title":"Tools for Earth
Meteorological Analysis","Version":"1.4"},"HiCfeat":{"Author":"Raphael
Mourad","Depends":"R (>= 3.2.0), GenomicRanges, Matrix, glmnet,
rtracklayer","Description":"We propose a multiple logistic regression model to
assess the influences of genomic features such as DNA-binding proteins and
functional elements on topological domain borders.","Imports":"IRanges,
GenomeInfoDb","License":"GPL-
2","NeedsCompilation":"no","Package":"HiCfeat","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Multiple Logistic Regression for 3D Chromatin Domain
Border\nAnalysis","Version":"1.0"},"HiClimR":{"Author":"Hamada S. Badr [aut, cre],
Benjamin F. Zaitchik [aut], Amin K. Dezfuli [aut]","Depends":"R (>=
2.10)","Description":"A tool for Hierarchical Climate Regionalization applicable to
any correlation-based clustering.\nIt adds several features and a new clustering
method (called, 'regional' linkage) to hierarchical\nclustering in R ('hclust'
function in 'stats' library): data regridding, coarsening spatial
resolution,\ngeographic masking (by continents, regions, or countries), data
filtering by mean and\/or variance\nthresholds, data preprocessing (detrending,
standardization, and PCA), faster correlation function\nwith preliminary big data
support, different clustering methods, hybrid hierarchical clustering,\nmulti-
variate clustering (MVC), cluster validation, and visualization of region
maps.","Imports":"graphics, grDevices, stats, utils","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"HiClimR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Hierarchical Climate
Regionalization","URL":"https:\/\/github.com\/hsbadr\/HiClimR","Version":"1.2.3"},"
HiCseg":{"Author":"Celine Levy-Leduc","Depends":"R (>= 2.10)","Description":"This
package allows you to detect domains in HiC data by rephrasing this problem as a
two-dimensional segmentation issue.","License":"GPL-
2","NeedsCompilation":"yes","Package":"HiCseg","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Detection of domains in HiC
data","Version":"1.1"},"HiDimDA":{"Author":"Antonio Pedro Duarte Silva
<psilva@porto.ucp.pt>","Depends":"R (>= 2.10.0)","Description":"Performs linear
discriminant analysis in high dimensional\nproblems based on reliable covariance
estimators for problems\nwith (many) more variables than observations. Includes
routines\nfor classifier training, prediction, cross-validation and\nvariable
selection.","Imports":"splines","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"HiDimDA","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"MASS","Title":"High Dimensional Discriminant
Analysis","URL":"http:\/\/www.r-project.org","Version":"0.2-4"},"HiDimMaxStable":
{"Author":"Alexis BienvenÃ¼e [aut, cre],\nChristian Robert [aut]","Depends":"R (>=
2.2.0), methods, copula","Description":"Inference of high dimensional max-
stable\ndistributions, from the paper \"Likelihood based inference for\nhigh-
dimensional extreme value distributions\", by A. BienvenÃ¼e\nand C. Robert,
arXiv:1403.0065 [stat.AP].","Imports":"mnormt, partitions, maxLik, mnormpow,
VGAM","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"HiDimMaxStable","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"rgl,
snowfall, MASS, SpatialExtremes","Title":"Inference on High Dimensional Max-Stable
Distributions","URL":"http:\/\/arxiv.org\/abs\/1403.0065","Version":"0.1.1"},"HiLMM
":{"Author":"Anna Bonnet","Description":"Estimation of heritability with confidence
intervals in linear mixed models.","License":"GPL-
2","NeedsCompilation":"no","Package":"HiLMM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Estimation of Heritability in Linear Mixed
Models","Version":"1.1"},"HiddenMarkov":{"Author":"David
Harte","Description":"Contains functions for the analysis of Discrete Time Hidden
Markov Models, Markov Modulated GLMs and the Markov Modulated Poisson Process. It
includes functions for simulation, parameter estimation, and the Viterbi algorithm.
See the topic \"HiddenMarkov\" for an introduction to the package, and \"Change
Log\" for a list of recent changes. The algorithms are based of those of Walter
Zucchini.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"HiddenMarkov","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"parallel","Title":"Hidden Markov
Models","URL":"http:\/\/homepages.maxnet.co.nz\/davidharte\/SSLib\/","Version":"1.8
-4"},"HierO":{"Author":"Kari Tokola","Depends":"methods,
rneos","Description":"HierO is a graphical user interface (GUI) tool for
calculating optimal statistical power and sample size for hierarchical data
structure. HierO constructs a user defined sample size optimization problem to GAMS
(General Algebraic Modeling System)form and uses Rneos package to send the problem
to NEOS server for solving.","Imports":"RCurl, bitops, XML, tcltk,
tcltk2","License":"GPL-
2","NeedsCompilation":"no","Package":"HierO","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"XMLRPC","Title":"A graphical user interface for
calculating power and sample size\nfor hierarchical
data","Version":"0.2"},"HighDimOut":{"Author":"Cheng Fan
<raja8885@hotmail.com>","Depends":"R (>= 3.0.1)","Description":"Three high-
dimensional outlier detection algorithms and a outlier unification scheme are
implemented in this package. The angle-based outlier detection (ABOD) algorithm is
based on the work of Kriegel, Schubert, and Zimek [2008]. The subspace outlier
detection (SOD) algorithm is based on the work of Kriegel, Kroger, Schubert, and
Zimek [2009]. The feature bagging-based outlier detection (FBOD) algorithm is based
on the work of Lazarevic and Kumar [2005]. The outlier unification scheme is based
on the work of Kriegel, Kroger, Schubert, and Zimek [2011].","Imports":"foreach,
DMwR, plyr, proxy, FNN, ggplot2","License":"GPL-
3","NeedsCompilation":"no","Package":"HighDimOut","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr","Title":"Outlier Detection Algorithms for
High-Dimensional Data","Version":"1.0.0"},"HistDAWass":{"Author":"Antonio Irpino
[aut, cre]","Depends":"R(>= 3.1), methods","Description":"In the framework of
Symbolic Data Analysis, a relatively new\napproach to the statistical analysis of
multi-valued data, we consider\nhistogram-valued data, i.e., data described by
univariate histograms. The\nmethods and the basic statistics for histogram-valued
data are mainly based\non the L2 Wasserstein metric between distributions, i.e., a
Euclidean metric\nbetween quantile functions. The package contains unsupervised
classification\ntechniques, least square regression and tools for histogram-valued
data and for\nhistogram time series.","Imports":"graphics, class, FactoMineR,
ggplot2, grid, histogram,\ngrDevices, stats, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"HistDAWass","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Histogram-Valued Data
Analysis","Version":"0.1.4"},"HistData":{"Author":"Michael Friendly [aut,
cre],\nStephane Dray [ctb],\nHadley Wickham [ctb],\nJames Hanley [ctb],\nDennis
Murphy [ctb]","Depends":"R (>= 2.10)","Description":"The HistData package provides
a collection of small data sets\nthat are interesting and important in the history
of statistics and data visualization.\nThe goal of the package is to make these
available, both for instructional use\nand for historical research. Some of these
present interesting challenges for graphics\nor analysis in
R.","License":"GPL","NeedsCompilation":"no","Package":"HistData","Repository":"http
:\/\/cran.csiro.au\/src\/contrib","Suggests":"gtools, KernSmooth, maps, ggplot2,
proto, grid, reshape,\nplyr, lattice, jpeg, car, gplots, sp, heplots","Title":"Data
Sets from the History of Statistics and Data Visualization","Version":"0.7-
6"},"HistogramTools":{"Author":"Murray Stokely [aut, cre],\nTim Hesterberg
[ctb]","Description":"Provides a number of utility functions useful for
manipulating large histograms. This includes methods to trim, subset, merge
buckets, merge histograms, convert to CDF, and calculate information loss due to
binning. It also provides a protocol buffer representations of the default R
histogram class to allow histograms over large data sets to be computed and
manipulated in a MapReduce environment.","Enhances":"RProtoBuf","Imports":"Hmisc,
ash, stringr","License":"Apache License
2.0","NeedsCompilation":"no","Package":"HistogramTools","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"RUnit, emdist, gdata","Title":"Utility
Functions for R Histograms","URL":"https:\/\/r-forge.r-
project.org\/projects\/histogramtools\/","Version":"0.3.2"},"HiveR":
{"Author":"Bryan A. Hanson [aut, cre],\nVesna Memisevic [ctb],\nJonathan Chung
[ctb]","Depends":"R (>= 3.0)","Description":"Creates and plots 2D and 3D hive
plots. Hive plots are a unique method of displaying networks of many types in which
node properties are mapped to axes using meaningful properties rather than being
arbitrarily positioned. The hive plot concept was invented by Martin Krzywinski at
the Genome Science Center (www.hiveplot.net\/). Keywords: networks, food webs,
linnet, systems biology, bioinformatics.","Imports":"grid, plyr, jpeg, png,
RColorBrewer, utils, stats","License":"GPL-
3","NeedsCompilation":"no","Package":"HiveR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"mvbutils, FuncMap, lattice, reshape, ggplot2,
knitr,\nbipartite, sna, tcltk, rgl, xtable, tkrgl","Title":"2D and 3D Hive Plots
for
R","URL":"http:\/\/academic.depauw.edu\/~hanson\/HiveR\/HiveR.html","Version":"0.2.
55"},"Hmisc":{"Author":"Frank E Harrell Jr <f.harrell@vanderbilt.edu>,
with\ncontributions from Charles Dupont and many others.","Depends":"lattice,
survival (>= 2.37-6), Formula, ggplot2 (>= 2.0)","Description":"Contains many
functions useful for data\nanalysis, high-level graphics, utility operations,
functions for\ncomputing sample size and power, importing and annotating
datasets,\nimputing missing values, advanced table making, variable
clustering,\ncharacter string manipulation, conversion of R objects to LaTeX
code,\nand recoding variables.","Imports":"methods, latticeExtra, cluster, rpart,
nnet, acepack, foreign,\ngtable, grid, gridExtra","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"Hmisc","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"chron, rms, mice, tables, knitr, ff, ffbase,
htmltools","Title":"Harrell
Miscellaneous","URL":"http:\/\/biostat.mc.vanderbilt.edu\/Hmisc,\nhttps:\/\/github.
com\/harrelfe\/Hmisc","Version":"3.17-3"},"Holidays":{"Author":"Jeffery Horner,
Lars Hansen, Tony Plate","Depends":"R (>= 2.6), TimeWarp","Description":"Contains
trading holiday and half-day data that is automatically registered when
loaded.","License":"GPL","NeedsCompilation":"no","Package":"Holidays","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"scriptests","Title":"Holiday and
Half-Day Data, for Use with the 'TimeWarp' Package","Version":"1.0-
6"},"HomoPolymer":{"Author":"Gianmarco Polotti","Depends":"R (>= 3.0.0), RGtk2,
MenuCollection","Description":"A theoretical model to simulate radical
polymerization. Material, energy and population balances are integrated for batch,
semi batch and continuous process in a ideally mixed reactor. Limitations: single
monomer (i.e.homo polymer), one phase (organic, aqueous). Datasets with chemical-
physical data for the most common monomers is included. Some background in polymer
science is suggested for its use. Graphical interface for a quick and friendly use
is available.","Imports":"deSolve","License":"GPL-
2","NeedsCompilation":"no","Package":"HomoPolymer","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Theoretical Model to Simulate Radical
Polymerization","Version":"1.0"},"HotDeckImputation":{"Author":"Dieter William
Joenssen [aut, cre, cph]","Depends":"R (>= 3.0.0), stats","Description":"Hot deck
imputation methods to resolve missing data.","Imports":"Rglpk","License":"GPL-
3","NeedsCompilation":"yes","Package":"HotDeckImputation","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Hot Deck Imputation Methods for Missing
Data","URL":"https:\/\/cran.r-
project.org\/package=HotDeckImputation,\nhttps:\/\/www.researchgate.net\/profile\/D
ieter_Joenssen","Version":"1.1.0"},"Hotelling":{"Author":"James M. Curran
<j.curran@auckland.ac.nz>","Depends":"corpcor","Description":"A set of R functions
and data sets which implements Hotelling's T^2 test, and some variants of it.
Functions are also included for Aitchison's additive log ratio and centred log
ratio transformations","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Hotelling","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Hotelling's T-squared test and
variants","URL":"\nhttp:\/\/www.stat.auckland.ac.nz\/showperson?
firstname=James&surname=Curran","Version":"1.0-2"},"HyPhy":{"Author":"Nathaniel
Malachi Hallinan","Depends":"ape, R.utils","Description":"A Bay Area high level
phylogenetic analysis package mostly\nusing the birth-death process. Analysis of
species tree\nbranching times and simulation of species trees under
a number\nof different time variable birth-death processes. Analysis of\ngene
tree species tree reconciliations and simulations of gene\ntrees in species
trees.","License":"GPL-
2","NeedsCompilation":"no","Package":"HyPhy","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Macroevolutionary phylogentic analysis of species trees and
gene\ntrees","Version":"1.0"},"HybridMC":{"Author":"Richard D.
Morey","Depends":"utils, coda","Description":"This package is an R implementation
of the Hybrid Monte\nCarlo and Multipoint Hybrid Monte Carlo sampling
techniques\ndescribed in Liu (2001): \"Monte Carlo Strategies in
Computing\".","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"HybridMC","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Implementation of the Hybrid Monte Carlo and Multipoint
Hybrid\nMonte Carlo sampling techniques","URL":"http:\/\/www.r-
project.org","Version":"0.2"},"HydeNet":{"Author":"Jarrod E. Dalton
<daltonj@ccf.org> and Benjamin Nutter <benjamin.nutter@gmail.com>","Depends":"R (>=
3.0.0), nnet, rjags","Description":"Facilities for easy implementation of hybrid
Bayesian networks\nusing R. Bayesian networks are directed acyclic graphs
representing joint\nprobability distributions, where each node represents a random
variable and\neach edge represents conditionality. The full joint distribution
is\ntherefore factorized as a product of conditional densities, where each node\nis
assumed to be independent of its non-descendents given information on its\nparent
nodes. Since exact, closed-form algorithms are computationally\nburdensome for
inference within hybrid networks that contain a combination\nof continuous and
discrete nodes, particle-based approximation techniques\nlike Markov Chain Monte
Carlo are popular. We provide a user-friendly\ninterface to constructing these
networks and running inference using the 'rjags' package.\nEconometric analyses
(maximum expected utility under competing policies,\nvalue of information)
involving decision and utility nodes are
also\nsupported.","Imports":"ArgumentCheck, DiagrammeR (>= 0.8), plyr, dplyr,
graph,\ngRbase, magrittr, pixiedust (>= 0.6.1), stats, stringr,
utils","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"HydeNet","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"knitr, survival, testthat","Title":"Hybrid
Bayesian Networks Using R and
JAGS","URL":"https:\/\/github.com\/nutterb\/HydeNet,","Version":"0.10.3"},"HydroMe"
:{"Author":"Christian Thine Omuto","Depends":"R (>= 2.10), nlme,
minpack.lm","Description":"This package is version 2 of HydroMe v.1 package.
It\nestimates the parameters in infiltration and water retention\nmodels by curve-
fitting method. The models considered are those\nthat are commonly used in soil
science. It has new models for\nwater retention characteristic curve and debugging
of errors in\nHydroMe v.1","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"HydroMe","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"R codes for estimating water retention and infiltration
model\nparameters using experimental data","URL":"http:\/\/www.r-
project.org,\nhttp:\/\/archive.uonbi.ac.ke\/profiles\/research_description.php?
height=250&width=400&id=%206000023%20title=","Version":"2.0"},"HyperbolicDist":
{"Author":"David Scott <d.scott@auckland.ac.nz>","Depends":"R (>=
2.3.0)","Description":"This package provides functions for the hyperbolic
and\nrelated distributions. Density, distribution and quantile\nfunctions and
random number generation are provided for the\nhyperbolic distribution, the
generalized hyperbolic\ndistribution, the generalized inverse Gaussian distribution
and\nthe skew-Laplace distribution. Additional functionality is\nprovided for the
hyperbolic distribution, including fitting of\nthe hyperbolic to
2)","NeedsCompilation":"no","Package":"HyperbolicDist","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"VarianceGamma, actuar","Title":"The hyperbolic
distribution","URL":"http:\/\/www.r-project.org","Version":"0.6-2"},"IASD":
{"Author":"Satoshi Takahashi","Depends":"stats4","Description":"Calculate AIC's and
AICc's of unimodal model (one normal distribution) and bimodal model(a mixture of
two normal distributions) which fit the distribution of indices of asymmetry (IAS),
and plot their density, to help determine IAS distribution is unimodal or
bimodal.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"IASD","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Model Selection for Index of Asymmetry
Distribution","Version":"1.1"},"IAT":{"Author":"Dan Martin
<dpmartin42@gmail.com>","Depends":"R (>= 2.15.3)","Description":"Contains a
function to implement the standard D-Scoring algorithm\n(Greenwald, Banaji, &
Nosek, 2003) for Implicit Association Test (IAT)\ndata, as well as various other
functions to produce plots of IAT data.","Imports":"data.table,
ggplot2","License":"Apache License
2.0","NeedsCompilation":"no","Package":"IAT","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Functions to use with data from the Implicit Association
Test","Version":"0.2"},"IATscores":{"Author":"Giulio Costantini","Depends":"R (>=
3.2.0)","Description":"Compute several variations of the Implicit Association Test
(IAT) scores, including the D scores (Greenwald, Nosek, Banaji, 2003) and the new
scores that were developed using robust statistics (Richetin, Costantini, Perugini,
and Schonbrodt, 2015).","Imports":"stringr (>= 0.6.2), dplyr (>= 0.2), reshape2 (>=
1.4), nem (>=\n2.38.0), qgraph (>= 1.2.5)","License":"GPL-
2","NeedsCompilation":"no","Package":"IATscores","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"nparcomp (>= 2.0)","Title":"Implicit Association Test
Scores Using Robust Statistics","Version":"0.1-2"},"IBDLabels":{"Author":"Fiona
Grimson","Description":"Convert \"label\", \"lexicographic\", \"jacquard\"
and \"vec\", full state description vector. All conversions are done to and
from \"label\", as used in IBD_Haplo. More information regarding IBD_Haplo can be
found at
http:\/\/www.stat.washington.edu\/thompson\/Genepi\/pangaea.shtml.","License":"GPL-
3","NeedsCompilation":"no","Package":"IBDLabels","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Convert Between Different IBD-State Labelling
Schemes","Version":"1.1"},"IBDhaploRtools":{"Author":"Marshall Brown, Fiona
Grimson","Depends":"R (>= 2.10)","Description":"Functions to analyze, plot, and
store the output of running IBD_Haplo software package. More information regarding
IBD_Haplo can be found at
http:\/\/www.stat.washington.edu\/thompson\/Genepi\/pangaea.shtml.","License":"GPL-
3","NeedsCompilation":"no","Package":"IBDhaploRtools","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Functions for the Analysis of IBD Haplo
Output","Version":"1.8"},"IBDsim":{"Author":"Magnus Dehli Vigeland","Depends":"R
(>= 3.2), paramlink (>= 0.9)","Description":"R package for simulation of IBD
sharing among family members. Using sex specific recombination rates from the
Decode map (2010) of the human genome, phased chromosomes are simulated for all
pedigree members, either by unconditional 'gene dropping' or conditional on a
specified IBD pattern. Regions compatible with the query IBD pattern (possibly
different from the conditional pattern) are subsequently detected and
summarized.","Imports":"stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"IBDsim","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Simulation of Chromosomal Regions Shared by Family
Members","Version":"0.9-5"},"IBHM":{"Author":"Pawel Zawistowski","Depends":"R(>=
2.15.2), compiler, DEoptim (>= 2.2-1), cmaes (>= 1.0-11),\nRcpp (>= 0.10.3),
methods (>= 3.0.1)","Description":"Implementation of an incremental model
construction method called IBHM which\nstands for Incrementally Built Heterogeneous
Model. The method is designed for solving\nreal number approximation problems in a
highly automated fashion.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"IBHM","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Approximation using the IBHM method","Version":"1.1-
11"},"IBrokers":{"Author":"Jeffrey A. Ryan","Depends":"xts,
zoo","Description":"Provides native R access to Interactive Brokers Trader
Workstation API.","License":"GPL-
3","NeedsCompilation":"no","Package":"IBrokers","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"R API to Interactive Brokers Trader
Workstation","Version":"0.9-12"},"IC2":{"Author":"Didier
Plat","Description":"Lorenz and concentration curves; Atkinson,
Generalized\nentropy and SGini indices (with decomposition)","License":"GPL-
2","NeedsCompilation":"no","Package":"IC2","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Inequality and Concentration Indices and
Curves","Version":"1.0-1"},"ICAFF":{"Author":"Farimah Houshmand, Farzad Eskandari
Ph.D. <Askandari@atu.ac.ir>","Depends":"R (>= 3.0.0), graphics,
stats","Description":"Imperialist Competitive Algorithm
(ICA)\n<http:\/\/en.wikipedia.org\/wiki\/Imperialist_competitive_algorithm>\nis a
computational method that is used to solve optimization\nproblems of different
types and it is the mathematical model\nand the computer simulation of human social
evolution.\nThe package provides a minimum value for the cost function\nand the
best value for the optimization variables by\nImperialist Competitive
Algorithm.\nUsers can easily define their own objective function\ndepending on the
problem at hand.\nThis version has been successfully applied to solve\noptimization
problems, for continuous functions.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ICAFF","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Imperialist Competitive
Algorithm","Version":"1.0.1"},"ICBayes":{"Author":"Chun Pan, Bo Cai, Lianming Wang,
and
Xiaoyan Lin","Depends":"HI, survival","Description":"Contains functions to fit
Bayesian semiparametric regression survival models (proportional hazards model,
proportional odds model, and probit model) to interval-censored time-to-event
2)","NeedsCompilation":"no","Package":"ICBayes","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Bayesian Semiparametric Models for Interval-Censored
Data","Version":"1.0"},"ICC":{"Author":"Matthew Wolak [cre,
aut]","Description":"Assist in the estimation of the Intraclass Correlation
Coefficient (ICC) from variance components of a one-way analysis of variance and
also estimate the number of individuals or groups necessary to obtain an ICC
estimate with a desired confidence interval width.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ICC","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Facilitating Estimation of the Intraclass
Correlation\nCoefficient","URL":"http:\/\/github.com\/matthewwolak\/ICC","Version":
"2.3.0"},"ICC.Sample.Size":{"Author":"Alasdair Rathbone [aut,cre], Saurabh Shaw
[aut], Dinesh Kumbhare [aut]","Description":"Provides functions to calculate the
requisite sample size for studies where ICC is\nthe primary outcome. Can also be
used for calculation of power. In both cases it\nallows the user to test the impact
of changing input variables by calculating the outcome\nfor several different
values of input variables. Based off the work of Zou.\nZou, G. Y. (2012). Sample
size formulas for estimating intraclass correlation coefficients with\nprecision
and assurance. Statistics in medicine, 31(29), 3972-
3981.","Imports":"stats","License":"GPL-
3","NeedsCompilation":"no","Package":"ICC.Sample.Size","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Calculation of Sample Size and Power for
ICC","Version":"1.0"},"ICE":{"Author":"W. John Braun","Depends":"R (>= 2.0.1),
KernSmooth, stats","Description":"Kernel Estimators for Interval-Censored
Data","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ICE","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Iterated Conditional
Expectation","Version":"0.69"},"ICEbox":{"Author":"Alex Goldstein, Adam Kapelner,
Justin Bleich","Depends":"sfsmisc","Description":"This package implements
Individual Conditional Expectation (ICE) plots, a tool for visualizing the model
estimated by any supervised learning algorithm. ICE plots refine Friedman's partial
dependence plot by graphing the functional relationship between the predicted
response and a covariate of interest for individual observations. Specifically, ICE
plots highlight the variation in the fitted values across the range of a covariate
of interest, suggesting where and to what extent they may exist.","License":"GPL-2
| GPL-
3","NeedsCompilation":"no","Package":"ICEbox","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"randomForest, MASS","Title":"Individual Conditional
Expectation Plot Toolbox","Version":"1.0"},"ICEinfer":{"Author":"Bob Obenchain
<wizbob@att.net>","Depends":"R (>= 2.5.0), lattice","Description":"Given two
unbiased samples of patient level data on cost and effectiveness\nfor a pair of
treatments, make head-to-head treatment comparisons by (i) generating
the\nbivariate bootstrap resampling distribution of ICE uncertainty for a specified
value of\nthe shadow price of health, lambda, (ii) form the wedge-shaped ICE
confidence region with\nspecified confidence fraction within [0.50, 0.99] that is
equivariant with respect to\nchanges in lambda, (iii) color the bootstrap outcomes
within the above confidence wedge\nwith economic preferences from an ICE map with
specified values of lambda, beta and gamma\nparameters, (iv) display VAGR and ALICE
acceptability curves, and (v) illustrate variation\nin ICE preferences by
displaying potentially non-linear indifference(iso-preference) curves\nfrom an ICE
map with specified values of lambda, beta and gamma or eta
2)","NeedsCompilation":"no","Package":"ICEinfer","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Incremental Cost-Effectiveness (ICE) Statistical
Inference from\nTwo Unbiased Samples","URL":"http:\/\/www.r-project.org,
http:\/\/members.iquest.net\/~softrx\/","Version":"1.0-1"},"ICGE":{"Author":"Itziar
Irigoien [aut, cre],\nConcepcion Arenas [aut]","Depends":"R (>= 2.0.1), utils,
stats, MASS, cluster","Description":"ICGE is a package that helps to estimate the
number of real clusters in data as well as to identify atypical units. The
underlying methods are based on distances rather than on unit x
2)","NeedsCompilation":"no","Package":"ICGE","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Estimation of number of clusters and identification of
atypical\nunits","Version":"0.3"},"ICGOR":{"Author":"Jie Zhou, Jiajia Zhang, Wenbin
Lu","Depends":"R (>=
2.15.0),stats,graphics,survival,ICsurv,pracma,MASS","Description":"Generalized Odds
Rate Hazards (GORH) model is a flexible model of fitting survival data, including
the Proportional Hazards (PH) model and the Proportional Odds (PO) Model as special
cases. This package fit the GORH model with interval censored data.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"ICGOR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Fit Generalized Odds Rate Hazards Model with Interval
Censored\nData","Version":"1.0"},"ICS":{"Author":"Klaus Nordhausen, Hannu Oja,
David E. Tyler","Depends":"R (>= 2.5.0), methods,
mvtnorm","Description":"Implementation of Tyler et al.'s and Oja et al.'s method of
two different scatter\nmatrices to obtain an invariant coordinate system or
independent\ncomponents, depending on the underlying
assumptions.","Imports":"survey, graphics","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ICS","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"pixmap, robustbase, MASS, ICSNP","Title":"Tools for
Exploring Multivariate Data via ICS\/ICA","Version":"1.2-5"},"ICSNP":
{"Author":"Klaus Nordhausen, Seija Sirkia, Hannu Oja, David E. Tyler","Depends":"R
(>= 2.4.0), mvtnorm, ICS","Description":"Tools for multivariate nonparametrics, as
location tests based on marginal ranks, spatial median and spatial signs
computation, Hotelling's T-test, estimates of shape are
implemented.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ICSNP","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Tools for Multivariate Nonparametrics","Version":"1.1-
0"},"ICsurv":{"Author":"Christopher S. McMahan and Lianming
Wang","Description":"Currently using the proportional hazards (PH) model. More
methods under other semiparametric regression models will be included in later
versions.","Imports":"MASS (>= 7.3-33), matrixcalc (>= 1.0-3)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ICsurv","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"A package for semiparametric regression analysis
of\ninterval-censored data","Version":"1.0"},"IDPSurvival":{"Author":"Francesca
Mangili <francesca@idsia.ch>,\nAlessio Benavoli <alessio@idsia.ch>,\nCassio P. de
Campos <cassiopc@acm.org>,\nMarco Zaffalon <zaffalon@idsia.ch>","Depends":"R (>=
3.0.2), Rsolnp, gtools, survival","Description":"This package contains functions to
perform robust\nnonparametric survival analysis with right censored\ndata using a
prior near-ignorant Dirichlet Process.","License":"GPL (>= 3) | file
LICENSE","NeedsCompilation":"no","Package":"IDPSurvival","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Imprecise Dirichlet Process for Survival
Analysis","URL":"http:\/\/ipg.idsia.ch\/software\/","Version":"1.0"},"IDPmisc":
{"Author":"Rene Locher, Andreas Ruckstuhl et al.","Depends":"R(>= 2.15.2), methods,
grid(>= 2.13.1), lattice(>= 0.19-26),","Description":"The IDPmisc package contains
different high-level graphics\nfunctions for displaying large datasets, displaying
circular\ndata in a very flexible way, finding local maxima, brewing\ncolor ramps,
drawing nice arrows, zooming 2D-plots, creating\nfigures with differently colored
margin and plot region. In\naddition, the package contains auxiliary functions for
data\nmanipulation like omitting observations with irregular values\nor selecting
data by logical vectors, which include NAs. Other\nfunctions are especially useful
in spectroscopy and analyses of\nenvironmental data: robust baseline fitting,
finding peaks in\nspectra.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"IDPmisc","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"SwissAir(>= 1.1.3), PROcess","Title":"Utilities of
Institute of Data Analyses and Process
Design\n(www.idp.zhaw.ch)","Version":"1.1.17"},"IDTurtle":{"Author":"Aitor
Valdeon","Description":"It is a method to identify individually turtles using the
plastral biometries. It is also useful to detect errors on the identification of
turtles as is explained in Valdeon & Longares 2015.","Imports":"stats, graphics,
2)","NeedsCompilation":"no","Package":"IDTurtle","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Identify Turtles by their Plastral
Biometries","Version":"1.2"},"IFP":{"Author":"Leeyoung Park","Depends":"R (>=
2.11.1)","Description":"A suite for identifying causal models using relative
concordances and identifying causal polymorphisms in case-control genetic
association data, especially with large controls re-sequenced
data.","Imports":"haplo.stats,coda","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"IFP","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Identifying Functional Polymorphisms","URL":"http:\/\/www.r-
project.org","Version":"0.2.1"},"IGM.MEA":{"Author":"Quanli Wang, Sahar Gelfman,
Diana Hall, Ryan Dhindsa","Depends":"R (>= 3.2.2)","Description":"Software tools
for the characterization of neuronal
networks as recorded on multi-electrode
arrays.","Imports":"lattice,tcltk,emdist,ggplot2 (>=
2.0.0),\ngridExtra,reshape2,plyr, gtools","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"IGM.MEA","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"IGM MEA Analysis","Version":"0.3.1"},"IM":
{"Author":"Bartek Rajwa, Murat Dundar, Allison Irvine, Tan Dang","Depends":"R (>=
2.10.0),png (>= 0.1-4),jpeg (>= 0.1-2),bmp (>=
0.1),\nmethods","Description":"Compute moments of images and perform reconstruction
from\nmoments.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"IM","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Orthogonal Moment Analysis","Version":"1.0"},"IMIS":
{"Author":"Adrian Raftery, Le Bao","Depends":"mvtnorm","Description":"IMIS
algorithm draws samples from the posterior\ndistribution. The user has to define
the following R functions\nin advance: prior(x) calculates prior density of
x,\nlikelihood(x) calculates the likelihood of x, and\nsample.prior(n) draws n
samples from the prior distribution.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"IMIS","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Increamental Mixture Importance
Sampling","URL":"http:\/\/www.stat.washington.edu\/research\/reports\/2009\/tr560.p
df","Version":"0.1"},"IMP":{"Author":"Anup Nair [aut, cre]","Description":"Contains
functions for evaluating & comparing the performance of Binary classification
models. Functions can be called either statically or interactively (as Shiny
Apps).","Imports":"dplyr, ggplot2, stats, tidyr,
shiny","License":"GPL","NeedsCompilation":"no","Package":"IMP","Repository":"http:\
/\/cran.csiro.au\/src\/contrib","Title":"Interactive Model Performance
Evaluation","URL":"https:\/\/github.com\/anup50695\/IMPPackage","Version":"1.1"},"I
Mak":{"Author":"Diego Blum [aut, cre]","Description":"This is an Automatic Item
Generator for Psychological Testing. It is recommended for research purposes
only.","Imports":"grDevices, graphics, utils","License":"GPL-
3","NeedsCompilation":"no","Package":"IMak","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Item Maker","Version":"1.1.1"},"INLABMA":{"Author":"Virgilio
Gómez-Rubio <virgilio.gomez@uclm.es>, Roger Bivand
<Roger.Bivand@nhh.no>","Depends":"R(>= 2.15.0), parallel,
sp","Description":"Spatial Econometrics models using Bayesian Model Averaging\non
models fitted with INLA. The INLA package can be obtained from\nhttp:\/\/www.r-
inla.org . We recommend the testing version, which can be\ndownloaded by
running:\nsource(\"http:\/\/www.math.ntnu.no\/inla\/givemeINLA-
testing.R\")","Imports":"Matrix, spdep","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"INLABMA","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"INLA","Title":"Bayesian Model Averaging with
INLA","Version":"0.1-6"},"IPMpack":{"Author":"CJE Metcalf, SM McMahon, R Salguero-
Gomez, E Jongejans, C Merow","Depends":"Matrix, MASS, nlme","Description":"IPMpack
takes demographic vital rates and (optionally) environmental data to build integral
projection models. A number of functional forms for growth and survival can be
incorporated, as well as a range of reproductive strategies. The package also
includes a suite of diagnostic routines, provides classic matrix model output
(e.g., lambda, elasticities, sensitivities), and produces post-hoc metrics (e.g.,
passage time and life
expectancy).","License":"GPL","NeedsCompilation":"no","Package":"IPMpack","Reposito
ry":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"MCMCglmm, truncnorm,
mvtnorm, methods, MCMCpack, fields","Title":"Builds and analyses Integral
Projection Models (IPMs)","Version":"2.1"},"IPSUR":{"Author":"G. Jay
Kerns","Depends":"R (>= 2.10)","Description":"This package contains the Sweave
source code used to\ngenerate IPSUR, an introductory probability and
statistics\ntextbook, alongside other supplementary materials such as the\nparsed R
code for the book and data for the examples and\nexercises. The book is released
under the GNU Free\nDocumentation License.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"IPSUR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"actuar, aplpack, boot, coin, combinat, DAAG, diagram,
distr,\ndistrEx, distrTeach, e1071, HH (>= 2.1-32), Hmisc, lattice,\nlmtest,
mvtnorm, odfWeave, prob, qcc, RcmdrPlugin.IPSUR (>=\n0.1-6), Rcmdr, reshape,
scatterplot3d, TeachingDemos (>= 2.5),\nvcd","Title":"Introduction to Probability
and Statistics Using R","Version":"1.5"},"IQCC":{"Author":"Emanuel P.
Barbosa,\nFlavio M. M. Barros <flaviomargarito@gmail.com>,\nElias de Jesus
Goncalves <eliasjg@gmail.com>,\nDaniela R. Recchia
<daniela_recchia@yahoo.com.br>","Depends":"qcc, MASS, micEcon,
miscTools","Description":"Builds statistical control charts with exact limits
for\nunivariate and multivariate cases.","License":"GPL-
2","NeedsCompilation":"no","Package":"IQCC","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Improved Quality Control
Charts","Version":"0.6"},"IRISMustangMetrics":{"Author":"Jonathan Callahan [aut,
cre],\nRob Casey [aut],\nMary Templeton [aut]","Depends":"R (>= 3.1.0), IRISSeismic
(>= 1.0.5)","Description":"Classes and functions for metrics calculation as part of
the\n'IRIS DMC MUSTANG' project. The functionality in this package\nbuilds upon the
base classes of the 'IrisSeismic' package.\nMetrics include basic statistics as
well as higher level\n'health' metrics that can help identify problematic
seismometers.","Imports":"methods, pracma, RCurl, seismicRoll (>= 1.0.1),
signal,\nstringr, XML","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"IRISMustangMetrics","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Title":"Statistics and Metrics for Seismic
Data","Version":"1.0.1"},"IRISSeismic":{"Author":"Jonathan Callahan [aut,
cre],\nRob Casey [aut],\nMary Templeton [aut]","Depends":"R (>=
3.1.0)","Description":"Provides classes and methods for seismic data analysis.
The\nbase classes and methods are inspired by the python code found in\nthe 'ObsPy'
python toolbox <http:\/\/github.com\/obsypy\/obspy>. Additional classes
and\nmethods support data returned by web services provided by the 'IRIS
DMC'\n<http:\/\/service.iris.edu\/>.","Imports":"methods, pracma, RCurl,
seismicRoll (>= 1.0.1), signal,\nstringr, XML","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"IRISSeismic","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"mapdata, maps","Title":"Classes and Methods for
Seismic Data Analysis","Version":"1.0.7"},"IRTShiny":{"Author":"William Kyle
Hamilton <kyle.hamilton@gmail.com>, Atsushi
Mizumoto\n<atsushi@mizumot.com>","Depends":"R (>=
3.0.3)","Description":"Interactive shiny application for running Item Response
Theory\nanalysis.","Imports":"shiny, shinyAce, beeswarm, CTT, ltm, parallel,
psych","License":"GPL-
3","NeedsCompilation":"no","Package":"IRTShiny","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Item Response Theory via Shiny","Version":"1.1"},"ISBF":
{"Author":"Pierre Alquier","Description":"Selection of features for sparse
regression estimation (like the LASSO). Selection of blocks of features when the
regression parameter is sparse and constant by blocks (like the Fused-LASSO).
Application to cgh
arrays.","License":"GPL","NeedsCompilation":"yes","Package":"ISBF","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"Iterative Selection of Blocks of
Features - ISBF","Version":"0.2.1"},"ISDA.R":{"Author":"Ricardo Jorge de Almeida
Queiroz Filho <rjaqfcin@gmail.com>,\nRoberta Andrade de Araujo Fagundes
<raaf@cin.ufpe.br>","Depends":"R(>= 2.7.0), scatterplot3d","Description":"describes
a set of operations for symbolic data type based\non interval-valued. The
operations are processing of punctuals\nvariables to interval variables,
construction of a 3D graphic\ninterval, linear regression interval and interval
descriptive\nstatistics such as mean, median, variance, standard deviation\nand
mode.","License":"GPL-
2","NeedsCompilation":"no","Package":"ISDA.R","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"interval symbolic data analysis for
R","Version":"1.0"},"ISLR":{"Author":"Gareth James, Daniela Witten, Trevor Hastie
and Rob Tibshirani","Depends":"R (>= 2.10)","Description":"The collection of
datasets used in the book \"An\nIntroduction to Statistical Learning with
Applications in R\"","License":"GPL-
2","NeedsCompilation":"no","Package":"ISLR","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"MASS","Title":"Data for An Introduction to Statistical
Learning with\nApplications in
R","URL":"http:\/\/www.StatLearning.com","Version":"1.0"},"ISOcodes":
{"Author":"Christian Buchta [aut],\nKurt Hornik [aut, cre]","Depends":"R (>=
2.10)","Description":"ISO language, territory, currency, script and character
codes.\nProvides ISO 639 language codes, ISO 3166 territory codes, ISO
4217\ncurrency codes, ISO 15924 script codes, and the ISO 8859 character codes\nas
well as the UN M.49 area codes.","License":"GPL-
2","NeedsCompilation":"no","Package":"ISOcodes","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Selected ISO Codes","Version":"2016.03.15"},"ISOpureR":
{"Author":"Gerald Quon [aut], Catalina V Anghel [aut, trl], Syed Haider [aut],
Francis Nguyen [aut], Amit G Deshwar [aut], Quaid D\nMorris [aut], Paul C Boutros
[aut, cre]","Depends":"R (>= 3.1.1)","Description":"Deconvolution of mixed tumour
profiles into normal and cancer for each patient, using\nthe ISOpure algorithm in
Quon et al. Genome Medicine, 2013 5:29. Deconvolution requires\nmixed tumour
profiles and a set of unmatched \"basis\" normal profiles.","Imports":"Rcpp (>=
0.11.3), stats, futile.logger","License":"GPL-
2","NeedsCompilation":"yes","Package":"ISOpureR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr","Title":"Deconvolution of Tumour
Profiles","Version":"1.0.18"},"ISOweek":{"Author":"Uwe Block
<u.block.mz@googlemail.com>, using an algorithm by\nHatto von Hatzfeld
<hatto@salesianer.de>","Description":"This is an substitute for the %V and %u
formats which are\nnot implemented on Windows. In addition, the package
offers\nfunctions to convert from standard calender format yyyy-mm-dd\nto and from
ISO 8601 week format yyyy-Www-d.","Imports":"stringr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ISOweek","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"testthat","Title":"Week of the year and weekday
according to ISO 8601","Version":"0.6-2"},"ISwR":{"Author":"Peter
Dalgaard","Depends":"R (>= 2.6.0)","Description":"Data sets and scripts for text
examples and exercises in\nP. Dalgaard (2008), Ìntroductory Statistics with R',
2nd ed., Springer Verlag, ISBN 978-0387790534.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ISwR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"survival,MASS","Title":"Introductory Statistics with
R","Version":"2.0-7"},"ITEMAN":{"Author":"Cengiz Zopluoglu","Depends":"ggplot2,
polycor, car","Description":"Runs classical item analysis for multiple-choice test
items and polytomous items (e.g., rating scales).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ITEMAN","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Classical Item
Analysis","URL":"http:\/\/sites.education.miami.edu\/zopluoglu\/","Version":"1.0"},
"IUPS":{"Author":"Weihua An, Huizi Xu, and Zhida Zheng, Indiana
University\nBloomington","Depends":"R (>= 2.14), R2jags, Matching,
boot","Description":"This package includes functions to incorporate\nuncertainties
in estimated propensity scores and provide\nadjusted standard errors for making
valid causal inference.","License":"GPL-
3","NeedsCompilation":"no","Package":"IUPS","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Incorporating Uncertainties in Propensity
Scores","Version":"1.0"},"IalsaSynthesis":{"Author":"Will Beasley [aut,
cre],\nAndrey Koval [aut],\nIntegrative Analysis of Longitudinal Studies of Aging
(IALSA) [cph]","Depends":"R(>= 3.0.0), stats","Description":"Synthesizes
information across collaborating research. Created specifically for Integrative
Analysis of Longitudinal Studies of Aging
(IALSA).","Imports":"testit","License":"GPL-
2","NeedsCompilation":"no","Package":"IalsaSynthesis","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"devtools, knitr, readr, testthat (>=
0.9)","Title":"Synthesizing Information Across Collaborating
Research","URL":"https:\/\/github.com\/IALSA\/IalsaSynthesis,
http:\/\/www.ialsa.org\/","Version":"0.1.6"},"Iboot":{"Author":"Nicola Lunardon
<nicola.lunardon@econ.units.it>","Description":"The package implements a general
algorithm to obtain\niterated bootstrap tests and confidence sets for a\np-
dimensional parameter based on the unstudentized version of\nthe Rao
statistic.","License":"GPL-
2","NeedsCompilation":"yes","Package":"Iboot","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Iboot: iterated bootstrap tests and confidence
sets","Version":"0.1-1"},"IgorR":{"Author":"Greg Jefferis with contributions from
Thomas Braun","Description":"Provides function to read data from the 'Igor Pro'
data analysis\nprogram by Wavemetrics. The data formats supported are 'Igor'
packed\nexperiment format (pxp) and 'Igor' binary wave (ibw).
See:\nhttp:\/\/www.wavemetrics.com\/ for details. Also includes functions to
load\nspecial pxp files produced by the 'Igor Pro' 'Neuromatic' and
'Nclamp'\npackages for recording and analysing neuronal data.
See\nhttp:\/\/www.neuromatic.thinkrandom.com\/ for details.","Imports":"bitops,
tools","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"IgorR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat","Title":"Read Binary Files Saved by 'Igor Pro'
(Including 'Neuromatic'\nData)","Version":"0.8"},"Imap":{"Author":"John R. Wallace
<Imap.for.R@gmail.com>","Depends":"R (>= 2.10.0)","Description":"Zoom in and out of
maps or any supplied lines or points,\nwith control for color, poly fill, and
aspect.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Imap","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Interactive Mapping","Version":"1.32"},"ImpactIV":
{"Author":"Peng Ding <dingyunyiqiu@163.com>","Depends":"nnet","Description":"In
this package, you can find two functions proposed in\nDing, Geng and Zhou (2011) to
estimate direct and indirect\ncausal effects with randomization and multiple-
component\nintervention using instrumental variable method.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ImpactIV","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Identifying Causal Effect for Multi-Component
Intervention Using\nInstrumental Variable Method","Version":"1.0"},"ImportExport":
{"Author":"Roger Pros, Isaac Subirana, Joan
Vila.","Depends":"xlsx,gdata,Hmisc,chron,RODBC","Description":"Import and export
data from the most common statistical formats by using\nR functions that guarantee
the least loss of the data information, giving special\nattention to the date
variables and the labelled ones.","Imports":"haven,utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ImportExport","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"shiny,shinyBS,shinythemes,compareGroups,foreign",
"Title":"Import and Export Data","Version":"1.1"},"InPosition":{"Author":"Derek
Beaton, Joseph Dunlop, Herve Abdi","Depends":"prettyGraphs (>= 2.1.4), ExPosition
(>= 2.0.0)","Description":"Non-parametric resampling-based inference tests for
ExPosition.","License":"GPL-
2","NeedsCompilation":"no","Package":"InPosition","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Inference Tests for
ExPosition","Version":"0.12.7"},"InSilicoVA":{"Author":"Zehang Li, Tyler McCormick,
Sam Clark","Depends":"R (>= 2.15.0), rJava, coda, ggplot2","Description":"Computes
individual causes of death and population cause-specific mortality fractions using
the 'InSilicoVA' algorithm. It uses data derived from verbal autopsy (VA)
interviews, in a format similar to the input of the widely used 'InterVA4' method.
This package provides general model fitting and customization for 'InSilicoVA'
algorithm and basic graphical visualization of the output.","License":"GPL-
2","NeedsCompilation":"no","Package":"InSilicoVA","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Probabilistic Verbal Autopsy Coding with 'InSilicoVA'
Algorithm","Version":"1.1.2"},"IndependenceTests":{"Author":"P Lafaye de Micheaux
<lafaye@dms.umontreal.ca>, M Bilodeau\n<bilodeau@dms.umontreal.ca>","Depends":"R
(>= 2.3.0), xtable","Description":"Functions for testing mutual independence
between many\nnumerical random vectors or serial independence of a\nmultivariate
stationary sequence. The proposed test works when\nsome or all of the marginal
distributions are singular with\nrespect to Lebesgue measure.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"IndependenceTests","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Suggests":"snow, rsprng, Rmpi","Title":"Nonparametric
tests of independence between random vectors","Version":"0.2"},"InfDim":
{"Author":"Anna Kuparinen, Mats Bjorklund","Description":"This package contains
functions to perform calculations of\nthe infine-dimensional model (IDM) and to
produce 95%\nconfidence intervals around the model elements
through\nbootstrapping.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"InfDim","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Infine-dimensional model (IDM) to analyse phenotypic
variation\nin growth trajectories","Version":"1.0"},"InferenceSMR":{"Author":"Denis
Talbot, Thierry Duchesne, Jacques Brisson,
Nathalie\nVandal","Depends":"survival","Description":"The InferenceSMR package
provides functions to make\ninference about the standardized mortality ratio (SMR)
when\nevaluating the effect of a screening program. The package is\nbased on
methods described in Sasieni (2003) and Talbot et al.\n(2011).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"InferenceSMR","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Inference about the standardized mortality ratio
when evaluating\nthe effect of a screening program on
survival","Version":"1.0"},"Information":{"Author":"Larsen Kim [aut,
cre]","Depends":"R (>= 3.1.2)","Description":"Performs exploratory data analysis
and variable screening for\nbinary classification models using weight-of-evidence
(WOE) and information\nvalue (IV). In order to make the package as efficient as
possible, aggregations\nare done in data.table and creation of WOE vectors can be
distributed across\nmultiple cores. The package also supports exploration for
uplift models (NWOE\nand NIV).","Imports":"data.table, ggplot2, grid, plyr, utils,
iterators, doParallel,\nparallel, foreach","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"Information","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"knitr, reshape2, ClustOfVar,
rmarkdown","Title":"Data Exploration with Information Theory (Weight-of-Evidence
and\nInformation Value)","Version":"0.0.9"},"InformationValue":{"Author":"Selva
Prabhakaran","Depends":"R (>= 3.0.0)","Description":"Provides companion function
for analysing the performance of classification models. Also, provides function to
optimise probability cut-off score based on used specified objectives, Plot 'ROC'
Curve in 'ggplot2', 'AUROC', 'IV', 'WOE' Calculation, 'KS Statistic' etc to aid
accuracy improvement in binary classification
models.","Imports":"ggplot2","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"InformationValue","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"knitr","Title":"Performance Analysis and
Companion Functions for Binary\nClassification
Models","URL":"http:\/\/r-statistics.co\/Information-Value-With-
R.html","Version":"1.2.1"},"IntClust":{"Author":"Marijke Van Moerbeke","Depends":"R
(>= 2.10)","Description":"Several integrative data methods in which information of
objects from different data sources can be combined are included in the IntClust
package. As a single data source is limited in its point of view, this provides
more insight and the opportunity to investigate how the variables are
interconnected. Clustering techniques are to be applied to the combined
information. For now, only agglomerative hierarchical clustering is implemented.
Further, differential gene expression and pathway analysis can be conducted on the
clusters. Plotting functions are available to visualize and compare results of the
different methods.","Imports":"ade4,a4Core, Biobase, cluster, plotrix, plyr,
gplots,\ngridExtra, limma,
prodlim,\ngtools,e1071,pls,stats,utils,graphics,FactoMineR,analogue,lsa,\nSNFtool,g
rDevices,ggplot2","License":"GPL-
3","NeedsCompilation":"no","Package":"IntClust","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"MLP, biomaRt, org.Hs.eg.db,
a4Base","Title":"Integrated Data Analysis via
Clustering","Version":"0.0.2"},"IntLik":{"Author":"Zhenyu
Zhao","Depends":"maxLik","Description":"This package calculates the integrated
likelihood numerically. Given the Likelihood function and the prior function, this
package integrates out the nuisance parameters by Metropolis-Hastings (MCMC)
Algorithm.","License":"GPL-
2","NeedsCompilation":"no","Package":"IntLik","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Numerical Integration for Integrated
Likelihood","Version":"1.0"},"IntegratedJM":{"Author":"Rudradev Sengupta, Nolen Joy
Perualila","Depends":"R (>= 3.0.0), grid","Description":"Offers modelling the
association between gene-expression and bioassay data, taking care of the effect
due to a fingerprint feature and helps with several plots to better understand the
analysis.","Imports":"ggplot2, nlme, Biobase","License":"GPL-
3","NeedsCompilation":"no","Package":"IntegratedJM","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Joint Modelling of the Gene-Expression and Bioassay
Data, Taking\nCare of the Effect Due to a Fingerprint
Feature","Version":"1.4"},"InterSIM":{"Author":"Prabhakar Chalise, Rama Raghavan,
Brooke Fridley","Depends":"R (>= 2.14), MASS, NMF, tools","Description":"Generates
three inter-related genomic datasets : methylation, gene expression and protein
expression.","License":"GPL","NeedsCompilation":"no","Package":"InterSIM","Reposito
ry":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Simulation of Inter-Related
Genomic Datasets","Version":"2.0"},"InterVA4":{"Author":"Zehang Li, Tyler
McCormick, Sam Clark","Description":"Provides an R version of the InterVA4 software
for\ncoding cause of death from verbal autopsies. It also provides
simple\ngraphical representation of individual and population level
statistics.","License":"GPL-
2","NeedsCompilation":"no","Package":"InterVA4","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Replicate and Analyse
InterVA4","Version":"1.7.1"},"Interact":{"Author":"Noah Simon and Robert
Tibshirani","Description":"This package searches for marginal interactions in
a\nbinary response model. Interact uses permutation methods to\nestimate false
discovery rates for these marginal interactions\nand has some, limited
visualization capabilities","License":"GPL-
3","NeedsCompilation":"yes","Package":"Interact","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Tests for marginal interactions in a 2 class response
model","Version":"1.1"},"InteractiveIGraph":{"Author":"Vygantas
Butkus","Depends":"igraph, grDevices","Description":"An extension of the package
'igraph'. This package create\npossibly to work with 'igraph' objects
interactively.","License":"GPL-
2","NeedsCompilation":"no","Package":"InteractiveIGraph","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"interactive network analysis and
visualization","Version":"1.0.6.1"},"Interatrix":{"Author":"AurÃ©lie Siberchicot,
ElÃ©onore Hellard, Dominique Pontier, David Fouchet and Franck
Sauvage","Depends":"R (>= 2.14)","Description":"Chi-square tests are computed with
corrections.","Imports":"graphics, grDevices, MASS, stats, tcltk, tkrplot, tools,
2)","NeedsCompilation":"no","Package":"Interatrix","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"doParallel, foreach","Title":"Compute Chi-Square
Measures with Corrections","Version":"1.1.1"},"Interpol":{"Author":"Dominik Heider,
PhD, University of Duisburg-Essen, Germany","Depends":"R (>=
2.10.0)","Description":"A package for numerical encoding as well as for linear
and\nnon-linear interpolation of amino acid sequences.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Interpol","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Interpolation of amino acid
sequences","Version":"1.3.1"},"Interpol.T":{"Author":"Emanuele Eccel & Emanuele
Cordano","Depends":"R (>= 2.10), date, chron","Description":"Hourly interpolation
of daily minimum and maximum temperature\nseries. Carries out interpolation on
multiple series ad once. Requires some\nhourly series for calibration
(alternatively can use default calibration\ntable).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Interpol.T","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Hourly interpolation of multiple temperature daily
series","Version":"2.1.1"},"InvariantCausalPrediction":{"Author":"Nicolai
Meinshausen","Depends":"glmnet, mboost","Description":"Confidence intervals for
causal effects, using data collected in different experimental or environmental
conditions. Hidden variables can be included in the model with a more experimental
version.","License":"GPL","NeedsCompilation":"no","Package":"InvariantCausalPredict
ion","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Invariant Causal
Prediction","Version":"0.5-0"},"InventorymodelPackage":{"Author":"Alejandro
Saavedra Nieves","Depends":"R(>= 2.15.0),e1071","Description":"This package
describes the associated cost games to inventory situations.","License":"GPL-
2","NeedsCompilation":"no","Package":"InventorymodelPackage","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Title":"Inventorymodel","Version":"1.0.2"},"IsingFit
":{"Author":"Claudia van Borkulo, Sacha Epskamp, with contributions from Alexander
Robitzsch","Depends":"R (>= 3.0.0)","Description":"This network estimation
procedure eLasso, which is based on the Ising model, combines l1-regularized
logistic regression with model selection based on the Extended Bayesian Information
Criterion (EBIC). EBIC is a fit measure that identifies relevant relationships
between variables. The resulting network consists of variables as nodes and
relevant relationships as edges. Can deal with binary data.","Imports":"qgraph,
Matrix, glmnet","License":"GPL-
2","NeedsCompilation":"no","Package":"IsingFit","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"IsingSampler","Title":"Fitting Ising models using the
eLasso method","Version":"0.3.0"},"IsingSampler":{"Author":"Sacha
Epskamp","Depends":"Rcpp (>= 0.10.4), R (>= 3.0.0)","Description":"Sample states
from the Ising model and compute the probability of states. Sampling can be done
for any number of nodes, but due to the intractibility of the Ising model the
distribution can only be computed up to ~10 nodes.","Imports":"plyr, magrittr,
nnet","License":"GPL-
2","NeedsCompilation":"yes","Package":"IsingSampler","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Sampling Methods and Distribution Functions for the
Ising Model","URL":"github.com\/SachaEpskamp\/IsingSampler","Version":"0.2"},"Iso":
{"Author":"Rolf Turner <r.turner@auckland.ac.nz>","Depends":"R (>=
1.7.0)","Description":"Linear order and unimodal order (univariate)\nisotonic
regression; bivariate isotonic regression\nwith linear order on both
2)","NeedsCompilation":"yes","Package":"Iso","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Functions to Perform Isotonic
Regression","URL":"http:\/\/www.stat.auckland.ac.nz\/~rolf\/","Version":"0.0-
17"},"IsoCI":{"Author":"Byeong Yeob Choi, Jason P. Fine and M. Alan
Brookhart","Depends":"R(>= 2.13.1), KernSmooth","Description":"Some functions for
confidence intervals for current status data based on transformations and
bootstrap.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"IsoCI","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Confidence intervals for current status data based
on\ntransformations and bootstrap","Version":"1.1"},"IsoGene":{"Author":"Dan Lin,
Setia Pramana, Tobias Verbeke and Ziv Shkedy","Depends":"R (>= 2.10),
Iso","Description":"Offers framework for testing for monotonic relationship between
gene expression and doses in a microarray experiment. Several testing procedures
including the global likelihood-ratio test (Bartholomew, 1961), Williams (1971,
1972), Marcus (1976), M (Hu et al. 2005) and the modified M (Lin et al. 2007) are
used to test for the monotonic trend in gene expression with respect to doses. BH
(Benjamini and Hochberg 1995) and BY (Benjamini and Yekutieli 2004) FDR controlling
procedures are applied to adjust the raw p-values obtained from the
permutations.","Imports":"xtable, Biobase, affy, ff(>= 2.0.0),
tcltk","License":"GPL-
3","NeedsCompilation":"no","Package":"IsoGene","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Order-Restricted Inference for Microarray
Experiments","Version":"1.0-24"},"IsotopeR":{"Author":"Jake Ferguson and Jack
Hopkins","Description":"Estimates diet contributions from isotopic sources using
JAGS.\nIncludes estimation of concentration dependence and measurement
error.","Imports":"fgui, runjags, colorspace, ellipse, plotrix","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"IsotopeR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"rgl","Title":"Stable Isotope Mixing
Model","Version":"0.5.2"},"JADE":{"Author":"Klaus Nordhausen, Jean-Francois
Cardoso, Jari Miettinen, Hannu Oja, Esa Ollila, Sara
Taskinen","Description":"Cardoso's JADE algorithm as well as his functions for
joint diagonalization are ported to R. Also several other blind source separation
(BSS) methods, like AMUSE and SOBI, and some criteria for performance evaluation of
BSS algorithms, are given.","Imports":"clue, graphics","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"JADE","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"ICS, ICSNP","Title":"Blind Source Separation Methods
Based on Joint Diagonalization\nand Some BSS Performance Criteria","Version":"1.9-
93"},"JAGUAR":{"Author":"Chaitanya R. Acharya and Andrew S. Allen","Depends":"R (>=
3.0.0), Rcpp, plyr, lme4, reshape2","Description":"Implements a novel score test
that measures 1) the overall shift in the gene expression due to genotype (additive
genetic effect), and 2) group-specific changes in gene expression due to genotype
(interaction effect) in a mixed-effects model framework.","License":"GPL-
2","NeedsCompilation":"yes","Package":"JAGUAR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Joint Analysis of Genotype and Group-Specific Variability
Using\na Novel Score Test Approach to Map Expression Quantitative\nTrait Loci
(eQTL)","URL":"https:\/\/groups.google.com\/d\/forum\/jaguar-r-
package","Version":"3.0.0"},"JASPAR":{"Author":"Xiaobei Zhao
<xiaobei@binf.ku.dk>","Depends":"R (>= 2.9.0), gtools","Description":"R modules for
JASPAR data processing and visualization","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"JASPAR","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"R modules for JASPAR databases: a collection of
transcription\nfactor DNA-binding preferences, modeled as
matrices","Version":"0.0.1"},"JBTools":{"Author":"Jannis v. Buttlar","Depends":"R
(>= 2.14.0)","Description":"Collection of several tools and helper functions used
across the other packages of J. Buttlar ('ncdf.tools' and
'spectral.methods').","Imports":"foreach, parallel, gplots, colorspace,
2","NeedsCompilation":"no","Package":"JBTools","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"doMC","Title":"Misc Small Tools and Helper Functions
for Other Code of J.\nButtlar","Version":"0.7.2.9"},"JGEE":{"Author":"Gul
Inan","Depends":"gee, MASS","Description":"Fits two different joint generalized
estimating equation models to multivariate longitudinal data.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"JGEE","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Joint Generalized Estimating Equation
Solver","Version":"1.1"},"JGL":{"Author":"Patrick
Danaher","Depends":"igraph","Description":"The Joint Graphical Lasso is a
generalized method for\nestimating Gaussian graphical models\/ sparse inverse
covariance\nmatrices\/ biological networks on multiple classes of data. We\nsolve
JGL under two penalty functions: The Fused Graphical\nLasso (FGL), which employs a
fused penalty to encourage inverse\ncovariance matrices to be similar across
classes, and the Group\nGraphical Lasso (GGL), which encourages similar
network\nstructure between classes. FGL is recommended over GGL for\nmost
applications.","License":"GPL-
2","NeedsCompilation":"no","Package":"JGL","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Performs the Joint Graphical Lasso for sparse inverse
covariance\nestimation on multiple classes","Version":"2.3"},"JGR":
{"Author":"Markus Helbig <info@markushelbig.de>, Simon Urbanek, Ian
Fellows","Depends":"R (>= 2.10), rJava (>= 0.9-5), JavaGD (>= 0.6), iplots
(>=\n1.1-7)","Description":"Java GUI for R - cross-platform, universal and unified
Graphical User Interface for R. For full functionality on Windows and Mac OS X JGR
requires a start application which depends on your OS. This can be downloaded from
JGR website: http:\/\/rforge.net\/JGR\/","License":"GPL-
2","NeedsCompilation":"no","Package":"JGR","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"XLConnect","Title":"JGR - Java GUI for
R","URL":"http:\/\/rforge.net\/JGR\/","Version":"1.7-16"},"JM":{"Author":"Dimitris
Rizopoulos <d.rizopoulos@erasmusmc.nl>","Depends":"R (>= 3.0.0), MASS, nlme,
splines, survival","Description":"Shared parameter models for the joint modeling of
longitudinal and time-to-event data.","Enhances":"xtable","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"JM","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Joint Modeling of Longitudinal and Survival
Data","URL":"http:\/\/jmr.r-forge.r-project.org\/","Version":"1.4-4"},"JMbayes":
{"Author":"Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>","Depends":"R (>=
3.1.2), MASS, nlme, splines, survival","Description":"Shared parameter models for
the joint modeling of longitudinal and time-to-event data using
MCMC.","Enhances":"xtable, shiny","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"JMbayes","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Joint Modeling of Longitudinal and Time-to-Event Data
under a\nBayesian Approach","Version":"0.7-9"},"JMdesign":{"Author":"Emil A.
Cornea, Liddy M. Chen, Bahjat F. Qaqish, Haitao Chu, and Joseph G.
Ibrahim","Depends":"methods","Description":"Performs power calculations for joint
modeling of longitudinal and survival data with k-th order trajectories when the
variance-covariance matrix, Sigma_theta, is unknown.","License":"GPL-
2","NeedsCompilation":"no","Package":"JMdesign","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Joint Modeling of Longitudinal and Survival Data -
Power\nCalculation","Version":"1.1"},"JOP":{"Author":"Sonja Kuhnt and Nikolaus
Rudak","Depends":"Rsolnp, dglm","Description":"JOP is a tool for simultaneous
optimization of multiple\nresponses and visualization of the results. The
visualization\nis done by the joint optimization plot introduced by Kuhnt
and\nErdbruegge (2004).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"JOP","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Joint Optimization Plot","Version":"3.6"},"JPEN":
{"Author":"Ashwini Maurya","Depends":"mvtnorm(>= 1.0-2), stats(>=
2.15.0),","Description":"A Joint PENalty Estimation of Covariance and Inverse
Covariance Matrices.","License":"GPL-
2","NeedsCompilation":"no","Package":"JPEN","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Covariance and Inverse Covariance Matrix Estimation Using
Joint\nPenalty","Version":"1.0"},"JPSurv":{"Author":"Yongwu Shao
<ywshao@gmail.com>,","Description":"Functions, methods, and datasets for cancer
survival\nanalysis, including the proportional hazard relative survival\nmodel, the
join point relative survival model.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"JPSurv","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Methods for population-based cancer survival
analysis","URL":"http:\/\/www.r-project.org","Version":"1.0.1"},"JRF":
{"Author":"Francesca Petralia Developer [aut, cre],\nPei Wang Developer
[aut],\nZhidong Tu Developer [aut],\nWon-min Song Developer [aut],\nAdele Cutler
Developer [ctb],\nLeo Breiman Developer [ctb],\nAndy Liaw Developer [ctb],\nMatthew
Wiener Developer [ctb]","Depends":"R (>= 3.0.0)","Description":"Simultaneous
estimation of multiple related networks.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"JRF","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"MASS","Title":"Joint Random Forest (JRF) for the
Simultaneous Estimation of\nMultiple Related Networks","URL":"https:\/\/www.r-
project.org","Version":"0.1-3"},"JacobiEigen":{"Author":"Bill
Venables","Description":"Implements the classical Jacobi (1846) algorithm for
the\neigenvalues and eigenvectors of a real symmetric matrix, both in\npure R and
in C++ using Rcpp. Mainly as a programming example\nfor teaching
purposes.","Imports":"Rcpp","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"JacobiEigen","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"stats, knitr, dplyr, tidyr, ggplot2,
microbenchmark","Title":"Classical Jacobi Eigensolution Algorithm","Version":"0.2-
2"},"JavaGD":{"Author":"Simon Urbanek <Simon.Urbanek@R-project.org>","Depends":"R
(>= 2.4.0)","Description":"Graphics device routing all graphics commands to a
Java\nprogram. The actual functionality of the JavaGD depends on the\nJava-side
implementation. Simple AWT and Swing implementations\nare
included.","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"JavaGD","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"rJava (>= 0.5-0)","Title":"Java Graphics
Device","URL":"http:\/\/www.rforge.net\/JavaGD\/","Version":"0.6-1"},"Jmisc":
{"Author":"TszKin Julian Chan <ctszkin@gmail.com>","Description":"Some handy
function in R","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Jmisc","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat","Title":"Julian Miscellaneous
Function","Version":"0.3.1"},"JoSAE":{"Author":"Johannes
Breidenbach","Depends":"nlme","Description":"Implementation of some unit level
EBLUP and GREG estimators as well as the estimate of their variances to further
document the publication of Breidenbach and Astrup (2011). The vignette further
explains the use of the implemented functions.","License":"GPL-
2","NeedsCompilation":"no","Package":"JoSAE","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"lattice,xtable","Title":"Functions for some Unit-Level
Small Area Estimators and their\nVariances","Version":"0.2.3"},"Johnson":
{"Author":"Edgar Santos Fernandez","Description":"RE.Johnson performs the Johnson
Transformation to increase the normality.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Johnson","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Johnson
Transformation","Version":"1.4"},"JohnsonDistribution":{"Author":"A.I. McLeod and
Leanna King","Depends":"R (>= 2.1.0)","Description":"Johnson curve distributions.
Implementation of AS100 and\nAS99.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"JohnsonDistribution","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Title":"Johnson
Distribution","URL":"http:\/\/www.stats.uwo.ca\/faculty\/aim","Version":"0.24"},"Jo
intRegBC":{"Author":"Ehsan Bahrami Samani and Zhale Tahmasebinejad","Depends":"R
(>= 2.14.0),nlme,MASS,survival","Description":"A joint regression model for mixed
correlated binary and\ncontinuous responses is presented. In this model
binary\nresponse can be dependent on the continuous response. With this\nmodel, the
dependence between responses can be taken into\naccount by the correlation between
errors in the models for\nbinary and continuous responses.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"JointRegBC","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Joint Modelling of Mixed Correlated Binary and
Continuous\nResponses : A Latent Variable Approach","Version":"0.1.1"},"Julia":
{"Author":"Mehmet Suzen [aut, main]","Description":"Generates image data for
fractals (Julia and Mandelbrot\nsets) on the complex plane in the given region and
resolution.","License":"GPL-
3","NeedsCompilation":"no","Package":"Julia","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Fractal Image Data Generator","Version":"1.1"},"KANT":
{"Author":"Noemie Robil","Depends":"affy,Biobase","Description":"Identify and sort
genes overexpressed and associated to transmembrane protein in Affymetrix
expression set or any other results of microarray
experiment.","License":"GPL","NeedsCompilation":"no","Package":"KANT","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Title":"Package to identify and sort genes
overexpressed","Version":"2.0"},"KATforDCEMRI":{"Author":"Gregory Z. Ferl, Georges
Hankov","Depends":"R (>= 2.11.0)","Description":"Package for kinetic analysis of
longitudinal voxel-wise Dynamic Contrast Enhanced MRI data. Includes tools for
visualization and exploration of voxel-wise parametric maps.","Imports":"locfit,
R.matlab, matlab","License":"LGPL-
3","NeedsCompilation":"no","Package":"KATforDCEMRI","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Kinetic analysis and visualization of DCE-MRI
data","Version":"0.740"},"KERE":{"Author":"Yi Yang, Teng Zhang, Hui
Zou","Depends":"methods","Description":"An efficient algorithm inspired by
majorization-minimization principle for solving the entire solution path of a
flexible nonparametric expectile regression estimator constructed in a reproducing
kernel Hilbert space.","License":"GPL-
2","NeedsCompilation":"yes","Package":"KERE","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Expectile Regression in Reproducing Kernel Hilbert
Space","Version":"1.0.0"},"KFAS":{"Author":"Jouni Helske
<jouni.helske@jyu.fi>","Depends":"R (>= 3.1.0)","Description":"Functions for Kalman
filtering, smoothing,\nforecasting and simulation of multivariate exponential
family state space\nmodels with exact diffuse initialization and sequential
processing.","Imports":"stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"KFAS","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"MASS, testthat, knitr, lme4","Title":"Kalman Filter and
Smoother for Exponential Family State Space\nModels","Version":"1.2.2"},"KFKSDS":
{"Author":"Javier LÃ³pez-de-Lacalle","Depends":"R (>= 3.0.0),
stats","Description":"Naive implementation of the Kalman filter, smoother and
disturbance\nsmoother for state space models.","License":"GPL-
2","NeedsCompilation":"yes","Package":"KFKSDS","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"dlm, dse, FKF, KFAS, numDeriv, stsm","Title":"Kalman
Filter, Smoother and Disturbance
Smoother","URL":"http:\/\/jalobe.com","Version":"1.6"},"KMDA":{"Author":"Xiang Zhan
and Debashis Ghosh","Depends":"R (>= 2.10)","Description":"Compute p-values of
metabolite differential expression analysis using the kernel-based
approach.","License":"GNU General Public
License","NeedsCompilation":"no","Package":"KMDA","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Kernel-Based Metabolite Differential
Analysis","Version":"1.0"},"KMsurv":{"Author":"Original by Klein and Moeschberger,
modifications by Jun Yan\n<jun.yan@uconn.edu>","Description":"Data sets and
functions for Klein and Moeschberger (1997),\n\"Survival Analysis, Techniques for
Censored and Truncated\nData\", Springer.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"KMsurv","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Data sets from Klein and Moeschberger (1997), Survival
Analysis","Version":"0.1-5"},"KODAMA":{"Author":"Stefano Cacciatore, Claudio
Luchinat, Leonardo Tenori","Depends":"R (>=
2.10.0),e1071,plsgenomics,class","Description":"KODAMA (KnOwledge Discovery by
Accuracy MAximization) is an unsupervised and semisupervised learning algorithm
that performs feature extraction from noisy and high-dimensional
2)","NeedsCompilation":"no","Package":"KODAMA","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"rgl,","Title":"Knowledge discovery by accuracy
maximization","Version":"0.0.1"},"KOGMWU":{"Author":"Mikhail V. Matz","Depends":"R
(>= 2.10), pheatmap","Description":"Rank-based tests for enrichment of KOG
(euKaryotic Orthologous Groups) classes with up- or down-regulated genes based on a
continuous measure. The meta-analysis is based on correlation of KOG delta-ranks
across datasets (delta-rank is the difference between mean rank of genes belonging
to a KOG class and mean rank of all other genes). With binary measure (1 or 0 to
indicate significant and non-significant genes), one-tailed Fisher's exact test for
over-representation of each KOG class among significant genes will be
performed.","License":"GPL-
3","NeedsCompilation":"no","Package":"KOGMWU","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Functional Summary and Meta-Analysis of Gene Expression
Data","Version":"1.0"},"KRLS":{"Author":"Jens Hainmueller (Stanford) Chad Hazlett
(UCLA)","Description":"Package implements Kernel-based Regularized Least Squares
(KRLS), a machine learning method to fit multidimensional functions y=f(x) for
regression and classification problems without relying on linearity or additivity
assumptions. KRLS finds the best fitting function by minimizing the squared loss of
a Tikhonov regularization problem, using Gaussian kernels as radial basis
functions. For further details see Hainmueller and Hazlett (2014).","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"KRLS","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"lattice","Title":"Kernel-based Regularized Least squares
(KRLS)","URL":"http:\/\/www.r-project.org,
http:\/\/www.stanford.edu\/~jhain\/","Version":"0.3-7"},"KScorrect":{"Author":"Phil
Novack-Gottshall, Steve C. Wang","Depends":"R (>= 3.1.0)","Description":"Implements
the Lilliefors-corrected Kolmogorov-Smirnoff test for use\nin goodness-of-fit
tests, suitable when population parameters are unknown and\nmust be estimated by
sample statistics. P-values are estimated by simulation.\nCan be used with a
variety of continuous distributions, including normal,\nlognormal, univariate
mixtures of normals, uniform, loguniform, exponential,\ngamma, and Weibull
distributions. Functions to generate random numbers and\ncalculate density,
distribution, and quantile functions are provided for use\nwith the log uniform and
mixture distributions.","Imports":"MASS (>= 7.3-44), mclust (>=
5.1)","License":"CC0","NeedsCompilation":"no","Package":"KScorrect","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Title":"Lilliefors-Corrected Kolmogorov-
Smirnoff Goodness-of-Fit Tests","URL":"https:\/\/github.com\/pnovack-
gottshall\/KScorrect","Version":"1.2.0"},"KappaGUI":{"Author":"Frederic
Santos","Depends":"R (>= 3.1.2), tcltk, irr","Description":"Offers a complete and
interactive GUI to work out Cohen's and Fleiss' Kappa.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"KappaGUI","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"GUI for Cohen's and Fleiss'
Kappa","Version":"1.2"},"KappaV":{"Author":"Vincent
Bonhomme","Depends":"PresenceAbsence, maptools, rgeos, sp","Description":"this
package allows to quantify the congruence between two patchy\nmosaics or
landscapes. This \"vectorial Kappa\" approach extends the\nprinciple of Cohen's
Kappa index by calculating areas of intersected\npatches between two mosaics rather
than agreement between pixels. It\nprovides an exact alternative for patchy mosaics
when a Kappa index is\nneeded.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"KappaV","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Calculates \"vectorial Kappa\", an index of congruence
between\npatchy
mosaics","URL":"http:\/\/www.vincentbonhomme.fr\/KappaV","Version":"0.3"},"Kendall"
:{"Author":"A.I. McLeod","Depends":"R (>= 2.1.0)","Description":"Computes the
Kendall rank correlation and Mann-Kendall\ntrend test. See documentation for use of
block bootstrap when\nthere is autocorrelation.","Imports":"boot","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"Kendall","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Kendall rank correlation and Mann-Kendall trend
test","URL":"http:\/\/www.stats.uwo.ca\/faculty\/aim","Version":"2.2"},"KernSmooth"
:{"Author":"Matt Wand [aut],\nBrian Ripley [trl, cre, ctb] (R port and
updates)","Depends":"R (>= 2.5.0), stats","Description":"Functions for kernel
smoothing (and density estimation)\ncorresponding to the book:\nWand, M.P. and
Jones, M.C. (1995) \"Kernel
Smoothing\".","License":"Unlimited","NeedsCompilation":"yes","Package":"KernSmooth"
,"Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"MASS","Title":"Fun
ctions for Kernel Smoothing Supporting Wand & Jones (1995)","Version":"2.23-
15"},"KernSmoothIRT":{"Author":"Angelo Mazza, Antonio Punzo, Brian
McGuire","Description":"This package fits nonparametric item and option
characteristic curves using kernel smoothing. It allows for optimal selection of
the smoothing bandwidth using cross-validation and a variety of exploratory
plotting tools.","Imports":"Rcpp, plotrix, rgl","License":"GPL-
2","NeedsCompilation":"yes","Package":"KernSmoothIRT","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Nonparametric Item Response
Theory","Version":"6.1"},"Kernelheaping":{"Author":"Marcus Gross","Depends":"R (>=
2.15.0), evmix, MASS, ks, sparr","Description":"In self-reported or anonymised data
the user often encounters\nheaped data, i.e. data which are rounded (to a possibly
different degree\nof coarseness). While this is mostly a minor problem in
parametric density\nestimation the bias can be very large for non-parametric
methods such as kernel\ndensity estimation. This package implements a partly
Bayesian algorithm treating\nthe true unknown values as additional parameters and
estimates the rounding\nparameters to give a corrected kernel density estimate. It
supports various\nstandard bandwidth selection methods. Varying rounding
probabilities (depending\non the true value) and asymmetric rounding is estimable
as well. Additionally,\nbivariate non-parametric density estimation for rounded
data is supported.","Imports":"sp","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"Kernelheaping","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Kernel Density Estimation for Heaped and Rounded
Data","Version":"1.5"},"Kmisc":{"Author":"Kevin Ushey","Description":"This package
contains a collection of functions for common data\nextraction and reshaping
operations, string manipulation, and\nfunctions for table and plot generation for R
Markdown documents.","Imports":"Rcpp (>= 0.10.5), data.table, lattice, grid, knitr,
markdown","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"Kmisc","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"ggplot2, plyr, reshape2, googleVis, testthat,
microbenchmark","Title":"Kevin
Miscellaneous","URL":"https:\/\/github.com\/kevinushey\/Kmisc","Version":"0.5.0"},"
KoNLP":{"Author":"Heewon Jeon","Depends":"R (>= 2.15.0), rJava (>= 0.9-0), utils
(>= 2.14.0), stringr\n(>= 0.6.2), hash (>= 2.2.6), tau (>= 0.0-15), Sejong (>=
0.01)","Description":"Korean language processing package. Morphological\nanalyzer,
POS tagger, Keystroke converter, Hangul automata,\nConcordance, Mutual
Information..","License":"GPL-
3","NeedsCompilation":"no","Package":"KoNLP","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Korean NLP Package","URL":"https:\/\/github.com\/haven-
jeon\/KoNLP","Version":"0.76.9"},"KoulMde":{"Author":"Jiwoong Kim [aut,
cre]","Depends":"R (>= 3.2.2)","Description":"Consider linear regression model and
autoregressive model of order p where errors in the linear regression model and
innovations in the autoregression model are independent and symmetrically
distributed. Hira L. Koul proposed a nonparametric minimum distance estimation
method by minimizing L2-type distance between certain weighted residual empirical
distribution functions. He also proposed a simpler version of the loss function by
using symmetry of the integrating measure in the distance. This package contains
two functions: KoulLrMde() and KoulArMde(). KoulLrMde() and KoulArMde() provide
minimum distance estimators for linear regression model and autoregression model,
respectively, where both are based on Koul's method. These two functions take much
less time for the computation than those based on parametric minimum distance
estimation methods.","License":"GPL-
2","NeedsCompilation":"no","Package":"KoulMde","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Koul's Minimum Distance Estimation in Linear Regression
and\nAutoregression Model","Version":"1.0"},"Kpart":{"Author":"Eric
Golinko","Depends":"leaps","Description":"Kpart spline fitting","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Kpart","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Spline Fitting","Version":"1.1"},"KrigInv":
{"Author":"Clement Chevalier, Victor Picheny and David
Ginsbourger","Depends":"DiceKriging, pbivnorm, rgenoud,
randtoolbox","Description":"Criteria and algorithms for sequentially estimating
level sets of a multivariate numerical function, possibly observed with
noise.","License":"GPL-
3","NeedsCompilation":"no","Package":"KrigInv","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Kriging-based Inversion for Deterministic and Noisy
Computer\nExperiments","URL":"\nhttp:\/\/www.sciencedirect.com\/science\/article\/p
ii\/S0167947313001060,\nhttp:\/\/www.clementchevalier.com","Version":"1.3.1"},"L1pa
ck":{"Author":"Felipe Osorio","Description":"L1 estimation for linear regression
and random number generation for\nthe multivariate Laplace
2)","NeedsCompilation":"yes","Package":"L1pack","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Routines for L1
Estimation","URL":"http:\/\/www.ies.ucv.cl\/l1pack\/","Version":"0.3"},"LANDD":
{"Author":"Shangzhao Qiu, Yan Yan, Tianwei Yu","Description":"Using Liquid
Association for Network Dynamics Detection.","Imports":"igraph, fdrtool, foreach,
doParallel, GOstats, GOSemSim,\nGGally, intergraph, ggplot2, modeest, Matrix,
2)","NeedsCompilation":"yes","Package":"LANDD","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Liquid Association for Network Dynamics
Detection","Version":"1.0.0"},"LARF":{"Author":"Weihua An and Xuefu Wang, Indiana
University Bloomington","Description":"Provides instrumental variable estimation of
treatment effects when both the endogenous treatment and its instrument are binary.
Applicable to both binary and continuous outcomes.","License":"GPL-
3","NeedsCompilation":"no","Package":"LARF","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Local Average Response Functions for Instrumental
Variable\nEstimation of Treatment Effects","Version":"1.3"},"LCA":{"Author":"Ed
Curry","Depends":"R (>= 2.15.0)","Description":"Performs model fitting and
significance estimation for Localised Co-Dependency between pairs of features of a
numeric dataset.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"LCA","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Localised Co-Dependency Analysis","URL":"http:\/\/www.r-
"0.1"},"LCAextend":{"Author":"Arafat TAYEB <arafat.tayeb@ircm.qc.ca>, Alexandre
BUREAU\n<alexandre.bureau@msp.ulaval.ca> and Aurelie
Labbe\n<aurelie.labbe@mcgill.ca>","Depends":"boot, mvtnorm, rms,
kinship2","Description":"This package performs a Latent Class Analysis
of\nphenotypic measurements in pedigrees and a model selection\nbased on one of two
methods: likelihood-based cross-validation\nand Bayesian Information Criterion. It
computes also individual\nand triplet child-parents weights in a pedigree using
an\nupward-downward algorithm. It takes into account the familial\ndependence
defined by the pedigree structure by considering\nthat a class of a child depends
on his parents classes via\ntriplet-transition probabilities of the classes. The
package\nhandles the case where measurements are available on all\nsubjects and the
case where measurements are available only on\nsymptomatic (i.e. affected)
subjects. Distributions for\ndiscrete (or ordinal) and continuous data are
currently\nimplemented. The package can deal with missing
data.","License":"GPL","NeedsCompilation":"no","Package":"LCAextend","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Title":"Latent Class Analysis (LCA) with
familial dependence in extended\npedigrees","URL":"http:\/\/www.r-
project.org,\nhttp:\/\/www.crulrg.ulaval.ca\/pages_perso_chercheurs\/bureau_a\/","V
ersion":"1.2"},"LCFdata":{"Author":"Antoine Tremblay, Department of Psychology,
Dalhousie University","Depends":"R (>= 3.0.0)","Description":"This package contains
(1) event-related brain potential data recorded from 10 participants at electrodes
Fz, Cz, Pz, and Oz (0--300 ms) in the context of Antoine Tremblay's PhD thesis
(Tremblay, 2009); (2) ERP amplitudes at electrode Fz restricted to the 100 to 175
millisecond time window; and (3) plotting data generated from a linear mixed-
effects model.","License":"GPL-
2","NeedsCompilation":"no","Package":"LCFdata","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Data sets for package
``LMERConvenienceFunctions''","Version":"2.0"},"LCMCR":{"Author":"Daniel Manrique-
Vallier","Depends":"R (>= 3.0.1)","Description":"Bayesian population size
estimation using non parametric latent-class
models.","Imports":"methods","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"LCMCR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Bayesian Nonparametric Latent-Class Capture-
Recapture","Version":"0.4.1"},"LDAvis":{"Author":"Carson Sievert [aut, cre],\nKenny
Shirley [aut]","Depends":"R (>= 2.10)","Description":"Tools to create an
interactive web-based visualization of a\ntopic model that has been fit to a corpus
of text data using\nLatent Dirichlet Allocation (LDA). Given the estimated
parameters of\nthe topic model, it computes various summary statistics as input
to\nan interactive visualization built with D3.js that is accessed via\na browser.
The goal is to help users interpret the topics in their\nLDA topic
model.","Imports":"proxy, RJSONIO, parallel","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"LDAvis","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"mallet,
lda, topicmodels, gistr (>= 0.0.8.99), servr, shiny,\nknitr, rmarkdown, digest,
htmltools","Title":"Interactive Visualization of Topic
Models","URL":"https:\/\/github.com\/cpsievert\/LDAvis","Version":"0.3.2"},"LDOD":
{"Author":"Ehsan Masoudi, Majid Sarmad and Hooshang Talebi","Depends":"R (>=
2.10.0), Rsolnp, Rmpfr","Description":"this package provides functions for Finding
Locally\nD-optimal designs for Logistic, Negative Binomial, Poisson,\nMichaelis-
Menten, Exponential, Log-Linear, Emax, Richards,\nWeibull and Inverse Quadratic
regression models and also\nfunctions for auto-constructing Fisher information
matrix and\nFrechet derivative based on some input variables and without\nuser-
interfere.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"LDOD","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Finding Locally D-optimal optimal designs for some nonlinear
and\ngeneralized linear models","Version":"1.0"},"LDPD":{"Author":"Denis
Surzhko","Description":"Implementation of most popular approaches to PD
(probability of default) calibration: Quasi Moment Matching algorithm (D. Tasche),
algorithm proposed by M. van der Burgt, K. Pluto and D. Tasche's most prudent
estimation methodology.","Imports":"MASS, nleqslv","License":"GPL-
2","NeedsCompilation":"no","Package":"LDPD","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Probability of Default
Calibration","Version":"1.1.2"},"LDRTools":{"Author":"Eero Liski [aut], Klaus
Nordhausen [aut, cre], Hannu Oja [aut], Anne Ruiz-Gazen [aut]","Depends":"R (>=
3.2.2)","Description":"Linear dimension reduction subspaces can be uniquely defined
using orthogonal projection matrices. This package provides tools to compute
distances between such subspaces and to compute the average
subspace.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"LDRTools","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"dr","Title":"Tools for Linear Dimension
Reduction","Version":"0.2"},"LDcorSV":{"Author":"David Desrousseaux, Florian
Sandron, Aurelie Siberchicot,\nChristine Cierco-Ayrolles and Brigitte
Mangin","Depends":"parallel, MASS","Description":"The package provides a set of
functions which aim is to\npropose four measures of linkage disequilibrium: the
usual r^2\nmeasure, the r^2_S measure (r^2 corrected by the structure\nsample), the
r^2_V (r^2 corrected by the relatedness of\ngenotyped individuals), the r^2_VS
measure (r^2 corrected by\nboth the relatedness of genotyped individuals and the
structure\nof the sample).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"LDcorSV","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Linkage disequilibrium corrected by the structure and
the\nrelatedness","Version":"1.3.1"},"LDheatmap":{"Author":"Ji-Hyung Shin
<shin@sfu.ca>, Sigal Blay <sblay@sfu.ca>,\nNicholas Lewin-Koh <nikko@hailmail.net>,
Brad McNeney\n<mcneney@sfu.ca>, Jinko Graham <jgraham@sfu.ca>","Depends":"R (>=
2.14.0), grid","Description":"Produces a graphical display, as a heat map, of
measures\nof pairwise linkage disequilibria between SNPs. Users may\noptionally
include the physical locations or genetic map\ndistances of each SNP on the
plot.","Imports":"genetics","License":"GPL-
3","NeedsCompilation":"no","Package":"LDheatmap","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"rtracklayer, GenomicRanges, chopsticks (>= 1.18.0),
lattice,\nggplot2","Title":"Graphical display of pairwise linkage disequilibria
between
SNPs","URL":"http:\/\/stat.sfu.ca\/statgen\/research\/ldheatmap.html","Version":"0.
99-1"},"LDtests":{"Author":"Alex Lewin","Description":"Exact tests for Linkage
Disequilibrium (LD) and Hardy-Weinberg Equilibrium (HWE). - 2-sided LD tests based
on different measures of LD (Kulinskaya and Lewin 2008) - 1-sided Fisher's exact
test for LD - 2-sided Haldane test for HWE (Wiggington 2005) - 1-sided test for
inbreeding - conditional p-values proposed in Kulinskaya (2008) to overcome the
problems of asymetric distributions (for both LD and
HWE)","License":"GPL","NeedsCompilation":"no","Package":"LDtests","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Title":"Exact tests for Linkage Disequilibrium
and Hardy-Weinberg\nEquilibrium","Version":"1.0"},"LEAPFrOG":{"Author":"Daniel JM
Crouch & Michael E Weale","Depends":"alabama, MASS","Description":"Contains
LEAPFrOG Gradient Optimisation and Expectation Maximisation functions for inferring
parental admixture proportions from an offspring with SNP
genotypes.","License":"GPL","NeedsCompilation":"no","Package":"LEAPFrOG","Repositor
y":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"rjags","Title":"Likelihood
Estimation of Admixture in Parents From
Offspring\nGenotypes","URL":"http:\/\/sites.google.com\/site\/mikeweale","Version":
"1.0.7"},"LFDR.MLE":{"Author":"Ye Yang, Marta Padilla, Alaa Ali, Kyle Leckett,
Zhenyu Yang, Zuojing Li, Corey M. Yanofsky and David R. Bickel","Depends":"stats,
methods","Description":"Suite of R functions for the estimation of the local false
discovery rate (LFDR) using Type II maximum likelihood estimation
(MLE).","License":"GPL-
3","NeedsCompilation":"no","Package":"LFDR.MLE","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Estimation of the Local False Discovery Rates by Type II
Maximum\nLikelihood Estimation","URL":"http:\/\/www.cran.r-project.org,
http:\/\/www.statomics.com","Version":"1.0"},"LGEWIS":{"Author":"Zihuai He,
Seunggeun Lee, Bhramar Mukherjee, Min Zhang","Depends":"CompQuadForm, SKAT, geeM,
pls, splines","Description":"Functions for testing the genetic association\/gene-
environment interaction in longitudinal gene-environment-wide interaction studies.
Generalized score type tests are used for set based analyses. Then GEE based score
tests are applied to all single variants within the defined set.","License":"GPL-
3","NeedsCompilation":"no","Package":"LGEWIS","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Tests for Genetic Association\/Gene-Environment Interaction
in\nLongitudinal Gene-Environment-Wide Interaction
Studies","Version":"0.2"},"LGRF":{"Author":"Zihuai He","Depends":"CompQuadForm,
SKAT, geepack","Description":"Functions for the longitudinal genetic random field
method (He et al., 2015, <doi:10.1111\/biom.12310>) to test the association between
a longitudinally measured quantitative outcome and a set of genetic variants in a
gene\/region.","License":"GPL-
3","NeedsCompilation":"no","Package":"LGRF","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Set-Based Tests for Genetic Association in Longitudinal
Studies","Version":"1.0"},"LICORS":{"Author":"Georg M. Goerg
<gmg@stat.cmu.edu>","Depends":"R (>= 2.12.1)","Description":"Estimates predictive
states from spatio-temporal data and\nconsequently can provide provably optimal
forecasts.\nCurrently this implementation\nsupports an N-dimensional spatial grid
observed over equally spaced time\nintervals. E.g. a video is a 2D spatial systems
observed over time. This\npackage implements mixed LICORS, has plotting tools (for
(1+1)D and (2+1)D\nsystems), and methods for optimal forecasting. Due to memory
limitations\nit is recommend to only analyze (1+1)D
systems.","Imports":"RColorBrewer, mvtnorm, zoo, FNN, fields, locfit,
Matrix","License":"GPL-
2","NeedsCompilation":"no","Package":"LICORS","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"huge, RANN, yaImpute, itertools","Title":"Light Cone
Reconstruction of States - Predictive State\nEstimation From Spatio-Temporal
Data","URL":"http:\/\/www.stat.cmu.edu\/~gmg","Version":"0.2.0"},"LICurvature":
{"Author":"Ehsan Bahrami Samani and Parisa ParsaMaram","Depends":"R (>= 2.14.0),
MASS,stats","Description":"This package presents a general method for assessing
the\nlocal influence of minor perturbations of case weight for the\nlinear
regression models.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"LICurvature","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Sensitivity Analysis for Case Weight in Normal Linear
Regression","Version":"0.1.1"},"LIHNPSD":{"Author":"Stephen Horng-Twu Lihn
<stevelihn@gmail.com>","Depends":"R (>= 2.14.1), sn, moments, BB, Bolstad2, optimx,
Rmpfr","Description":"A Poisson Subordinated Distribution to capture
major\nleptokurtic features in log-return time series of
financial\ndata.","License":"GPL-
2","NeedsCompilation":"no","Package":"LIHNPSD","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Poisson Subordinated
Distribution","URL":"http:\/\/papers.ssrn.com\/sol3\/papers.cfm?
abstract_id=2032762","Version":"0.2.1"},"LIM":{"Author":"Karline Soetaert
<karline.soetaert@nioz.nl>,\nDick van
Oevelen<dick.vanoevelen@nioz.nl>","Depends":"R (>= 2.10), limSolve,
diagram","Description":"Functions that read and solve linear inverse problems (food
web problems, linear programming problems).\nThese problems find solutions to
linear or quadratic functions:\nmin or max (f(x)), where f(x) = ||Ax-b||^2 or f(x)
= sum(ai*xi)\nsubject to equality constraints Ex=f and inequality constraints
Gx>=h. Uses package limSolve.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"LIM","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Linear Inverse Model examples and solution
methods","Version":"1.4.6"},"LINselect":{"Author":"Yannick Baraud, Christophe
Giraud, Sylvie Huet","Description":"Estimate the mean of a Gaussian vector, by
choosing among a large collection of estimators. In particular it solves the
problem of variable selection by choosing the best predictor among predictors
emanating from different methods as lasso, elastic-net, adaptive lasso, pls,
randomForest. Moreover, it can be applied for choosing the tuning parameter in a
Gauss-lasso procedure.","Imports":"mvtnorm, elasticnet, MASS, randomForest, pls,
gtools, stats","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"LINselect","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Selection
of Linear Estimators","Version":"0.0-2"},"LIStest":{"Author":"J. E. Garcia and V.
A. Gonzalez-Lopez","Depends":"R (>= 2.10)","Description":"Tests for independence
between X and Y computed from a paired sample (x1,y1),...(xn,yn) of (X,Y), using
one of the following statistics (a) the Longest Increasing Subsequence (Ln), (b)
JLn, a Jackknife version of Ln or (c) JLMn, a Jackknife version of the longest
monotonic subsequence. This family of tests can be applied under the assumption of
continuity of X and Y.","License":"GPL-
2","NeedsCompilation":"no","Package":"LIStest","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Tests of independence based on the Longest
Increasing\nSubsequence","Version":"2.1"},"LLSR":{"Author":"Diego F Coelho
<diegofcoelho@gmail.com>","Depends":"R (>= 2.10), rootSolve, XLConnect, digest,
svDialogs, ggtern","Description":"Analyses experimental data from liquid-liquid
phase diagrams and\nprovide a simple way to obtain its parameters and a simplified
report. Designed\ninitially to analyse Aqueous Two-Phases Systems, the package will
include (every\nother update) new functions in order to comprise useful tools in
liquid-liquid\nanalysis.","License":"GPL-
3","NeedsCompilation":"no","Package":"LLSR","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"testthat","Title":"Data Analysis of Liquid-Liquid
Systems","URL":"http:\/\/hutchr.github.io\/LLSR\/","Version":"0.0.2.0"},"LMERConven
ienceFunctions":{"Author":"Antoine Tremblay, Dalhousie University, and Johannes
Ransijn, University of Copenhagen","Description":"The main function of the package
is to perform backward selection of fixed effects, forward fitting of the random
effects, and post-hoc analysis using parallel capabilities. Other functionality
includes the computation of ANOVAs with upper- or lower-bound p-values and R-
squared values for each model term, model criticism plots, data trimming on model
residuals, and data visualization. The data to run examples is contained in package
LCF_data.","Imports":"Matrix, lme4, LCFdata, rgl, fields, mgcv,
2","NeedsCompilation":"no","Package":"LMERConvenienceFunctions","Repository":"http:
\/\/cran.csiro.au\/src\/contrib","Title":"Model Selection and Post-hoc Analysis for
(G)LMER Models","Version":"2.10"},"LMest":{"Author":"Francesco Bartolucci, Silvia
Pandolfi - University of Perugia (IT)","Depends":"R (>= 2.0.0), MASS, MultiLCIRT,
stats","Description":"Fit certain versions of the Latent Markov model for
longitudinal categorical data.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"LMest","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Latent Markov Models with and without
Covariates","Version":"2.2"},"LOGICOIL":{"Author":"Thomas L. Vincent
<tlfvincent@gmail.com>, Peter J. Green and Derek N. Woolfson
<D.N.Woolfson@bristol.ac.uk>","Depends":"R (>= 2.12), nnet","Description":"This
package contains the functions necessary to run the LOGICOIL algorithm. LOGICOIL
can be used to differentiate between antiparallel dimers, parallel dimers, trimers
and higher-order coiled-coil sequence. By covering >90 percent of the known coiled-
coil structures, LOGICOIL is a net improvement compared with other existing
methods, which achieve a predictive coverage of around 31 percent of this
population. As such, LOGICOIL is particularly useful for researchers looking to
characterize novel coiled-coil sequences or studying coiled-coil containing protein
assemblies. It may also be used to assist in the structural characterization of
synthetic coiled-coil sequences.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"LOGICOIL","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"LOGICOIL: multi-state prediction of coiled-coil
oligomeric\nstate","URL":"http:\/\/coiledcoils.chm.bris.ac.uk\/LOGICOIL","Version":
"0.99.0"},"LOGIT":{"Author":"Joseph M Hilbe <hilbe@asu.edu>, Rafael S. de Souza
<rafael.2706@gmail.com>","Depends":"R (>= 3.0)","Description":"Functions, data and
code for Hilbe, J.M. 2015. Practical Guide to Logistic Regression, by Chapman and
Hall\/CRC.","Imports":"caret, pROC, ggplot2, reshape, e1071, MASS","License":"GPL
(>=
3)","NeedsCompilation":"no","Package":"LOGIT","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Functions, Data and Code for Binary and Binomial
Data","Version":"1.3"},"LOST":{"Author":"J. Arbour and C.
Brown","Description":"LOST includes functions for simulating missing
morphometric\ndata randomly, with taxonomic bias and with anatomical bias. LOST
also\nincludes functions for estimating linear and geometric morphometric
data.","Imports":"gdata, shapes, e1071, pcaMethods, MASS, miscTools","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"LOST","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Missing morphometric data simulation and
estimation","Version":"1.1"},"LPCM":{"Author":"Jochen Einbeck and Ludger
Evers","Depends":"R (>= 2.10)","Description":"Fitting multivariate data patterns
with local principal curves; including simple tools for data compression
(projection), bandwidth selection, and measuring goodness-of-fit.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"LPCM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"scatterplot3d, lattice, dr","Title":"Local Principal
Curve Methods","Version":"0.45-0"},"LPM":{"Author":"Corrado Tallerini [aut,
cre],\nSalvatore Grimaldi [aut]","Description":"Apply Univariate Long Memory
Models,\nMultivariate Short Memory Models To Hydrological
Dataset.","Imports":"stats, graphics, grDevices, fracdiff, MASS,
QRM","License":"GPL-
2","NeedsCompilation":"no","Package":"LPM","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Linear Parametric Models Applied to Hydrological
Series","URL":"http:\/\/www.corradotallerini.altervista.org\/lpm.html","Version":"2
.6"},"LPR":{"Author":"Hanzhong Liu, Xin Xu, Jingyi Jessica Li, Bin
Yu*","Description":"Contains a function called \"LPR\" to estimate coefficients
using Lasso and Partial Ridge method and to calculate confidence intervals through
bootstrap.","Imports":"\nglmnet,slam,parallel,foreach,iterators,doParallel,lattice,
Matrix","License":"GNU General Public License version
2","NeedsCompilation":"no","Package":"LPR","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Lasso and Partial Ridge","Version":"1.0"},"LPS":
{"Author":"Sylvain Mareschal","Depends":"stats, R (>= 2.10)","Description":"An
implementation of the Linear Predictor Score approach, as initiated by Radmacher et
al. (J Comput Biol 2001) and enhanced by Wright et al. (PNAS 2003) for gene
expression signatures. Several tools for unsupervised clustering of gene expression
data are also provided.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"LPS","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"limma","Title":"Linear Predictor Score, for Binary
Inference from Multiple\nContinuous
Variables","URL":"http:\/\/bioinformatics.ovsa.fr\/LPS","Version":"1.0.10"},"LPStim
eSeries":{"Author":"Learned Pattern Similarity (LPS) for time series by Mustafa
Gokce Baydogan","Depends":"R (>= 2.5.0)","Description":"Learned Pattern Similarity
(LPS) for time series.\nImplements a novel approach to model the dependency
structure\nin time series that generalizes the concept of autoregression to
local\nauto-patterns. Generates a pattern-based representation of time
series\nalong with a similarity measure called Learned Pattern Similarity
(LPS).\nIntroduces a generalized autoregressive kernel.This package is based on
the\n'randomForest' package by Andy Liaw.","Imports":"RColorBrewer","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"LPStimeSeries","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Learned Pattern Similarity and Representation for
Time Series","URL":"http:\/\/www.mustafabaydogan.com\/learned-pattern-similarity-
lps.html","Version":"1.0-5"},"LPTime":{"Author":"Subhadeep Mukhopadhyay, Shinjini
Nandi","Depends":"orthopolynom","Description":"Specially designed rank transform
based Legendre Polynomial-like (LP) orthonormal transformations are implemented for
non-linear signal processing.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"LPTime","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"lattice","Title":"LP Nonparametric Approach to Non-
Gaussian Non-Linear Time
Series\nModelling","URL":"http:\/\/sites.temple.edu\/deepstat\/d-
products\/","Version":"1.0-2"},"LPmerge":{"Author":"Jeffrey
Endelman","Depends":"Rglpk, Matrix","Description":"LPmerge creates a consensus
genetic map by merging linkage maps from different populations. The software uses
linear programming (LP) to efficiently minimize the mean absolute error between the
consensus map and the linkage maps. This minimization is performed subject to
linear inequality constraints that ensure the ordering of the markers in the
linkage maps is preserved. When marker order is inconsistent between linkage maps,
a minimum set of ordinal constraints is deleted to resolve the
conflicts.","License":"GPL-
3","NeedsCompilation":"no","Package":"LPmerge","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Merging linkage maps by linear
programming","URL":"http:\/\/potatobreeding.cals.wisc.edu\/software","Version":"1.6
"},"LRTH":{"Author":"Zhiyuan (Jason) Xu and Wei Pan","Description":"R code of a
likelihood ratio test for genome-wide association under
genetic\nheterogeneity.","License":"GPL-
3","NeedsCompilation":"no","Package":"LRTH","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"A Likelihood Ratio Test Accounting for Genetic
Heterogeneity","Version":"1.3"},"LRcontrast":{"Author":"Kevin Kokot","Depends":"R
(>= 3.1.2)","Description":"Provides functions for calculating test statistics,
simulating quantiles\nand simulating p-values of likelihood ratio contrast tests in
regression models\nwith a lack
of identifiability.","Imports":"DoseFinding","License":"GPL-
3","NeedsCompilation":"yes","Package":"LRcontrast","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Dose Response Signal Detection under Model
Uncertainty","Version":"1.0"},"LS2W":{"Author":"Idris Eckley and Guy Nason, with
contributions from Sarah Taylor and Matthew Nunes","Depends":"R (>= 3.0),
wavethresh (>= 4.5)","Description":"Estimates two-dimensional local wavelet
spectra","License":"GPL-
2","NeedsCompilation":"yes","Package":"LS2W","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Locally stationary two-dimensional wavelet process
estimation\nscheme","Version":"1.3-3"},"LS2Wstat":{"Author":"Sarah Taylor [aut],
Matt Nunes [aut, cre], Idris Eckley [ctb, ths]","Depends":"LS2W(>= 1.3-1),
matrixStats, geoR, RandomFields, spdep","Description":"Wavelet-based methods for
testing stationarity and quadtree segmenting of images","License":"GPL-
2","NeedsCompilation":"no","Package":"LS2Wstat","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"A Multiscale Test of Spatial Stationarity for LS2W
processes","Version":"2.0-3"},"LSAfun":{"Author":"Fritz Guenther [aut,
cre]","Depends":"R (>= 3.1.0), lsa, rgl","Description":"Provides functions that
allow for convenient working\nwith Latent Semantic Analysis. For actually building
an LSA space, use the\npackage 'lsa' or other specialized software.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"LSAfun","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Applied Latent Semantic Analysis (LSA)
Functions","Version":"0.5"},"LSC":{"Author":"Georg M. Goerg
<gmg@stat.cmu.edu>","Depends":"R (>= 2.12.1), LICORS, RColorBrewer, fields, gam,
Matrix","Description":"Estimators and visualization for local statistical
complexity of\n(N+1)D fields. In particular for 0, 1 and 2 dimensional space this
package\nprovides useful visualization.","License":"GPL-
2","NeedsCompilation":"no","Package":"LSC","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Local Statistical Complexity - Automatic Pattern Discovery
in\nSpatio-Temporal Data","URL":"http:\/\/www.gmge.org","Version":"0.1.5"},"LSD":
{"Author":"Bjoern Schwalb, Achim Tresch, Phillipp Torkler, Sebastian Duemcke,
Carina Demel","Description":"Create lots of colorful plots in a plethora of
variations (try the LSD
demotour() )","License":"Unlimited","NeedsCompilation":"no","Package":"LSD","Reposi
tory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Lots of Superior
Depictions","Version":"3.0"},"LSDinterface":{"Author":"Marcelo C.
Pereira","Depends":"abind, utils, stats","Description":"Interfaces R with LSD.
Reads object-oriented data in results files (.res) produced by LSD and creates
appropriate multi-dimensional arrays in R. Also provides functions to extract basic
information and statistics from those files. LSD (Laboratory for Simulation
Development) is free software developed by Marco Valente (documentation and
downloads available at <http:\/\/labsimdev.org>).","License":"GPL-
3","NeedsCompilation":"no","Package":"LSDinterface","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Reading LSD Results (.res)
Files","Version":"0.2.1"},"LSMonteCarlo":{"Author":"Mikhail A.
Beketov","Depends":"mvtnorm, fBasics, stats, utils, graphics,
grDevices","Description":"The package compiles functions for calculating prices of
American put options with Least Squares Monte Carlo method. The option types are
plain vanilla American put, Asian American put, and Quanto American put. The
pricing algorithms include variance reduction techniques such as Antithetic
Variates and Control Variates. Additional functions are given to derive \"price
surfaces\" at different volatilities and strikes, create 3-D plots, quickly
generate Geometric Brownian motion, and calculate prices of European options with
Black & Scholes analytical solution.","License":"GPL-
3","NeedsCompilation":"no","Package":"LSMonteCarlo","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"American options pricing with Least Squares Monte
Carlo method","Version":"1.0"},"LSTS":{"Author":"Ricardo Olea <raolea@uc.cl>,
Wilfredo Palma <wilfredo@mat.puc.cl>, Pilar Rubio
<parubio@uc.cl>","Description":"Has a set of functions that allows stationary
analysis and locally stationary time series analysis.","Imports":"grDevices,
2","NeedsCompilation":"no","Package":"LSTS","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"rdatamarket","Title":"Locally Stationary Time
Series","Version":"1.0"},"LTPDvar":{"Author":"Nikola
Kasprikova","Depends":"methods","Description":"Calculation of rectifying LTPD and
AOQL plans for sampling inspection by variables which minimize mean inspection cost
per lot of process average quality.","Imports":"graphics","License":"GPL-
2","NeedsCompilation":"no","Package":"LTPDvar","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"LTPD and AOQL Plans for Acceptance Sampling Inspection
by\nVariables","URL":"http:\/\/samplingplans.tulipany.cz","Version":"1.2"},"LTR":
{"Author":"Paul C. Boutros","Depends":"R (>= 2.9.1)","Description":"A set of
functions to execute the linear-transformation of\nreplicate (LTR) algorithm for
preprocessing of microarray data","License":"GPL-
2","NeedsCompilation":"no","Package":"LTR","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Perform LTR analysis on microarray
data","Version":"1.0.0"},"LVMMCOR":{"Author":"Ehsan Bahrami Samani and Nourallah
Tazikeh Miyandarreh","Depends":"R (>= 2.14.0),nlme,MASS","Description":"A model for
mixed ordinal and continuous responses is\npresented where the heteroscedasticity
of the variance of the\ncontinuous response is also modeled. In this model
ordinal\nresponse can be dependent on the continuous response. The aim\nis to use
an approach similar to that of Heckman (1978) for the\njoint modelling of the
ordinal and continuous responses. With\nthis model, the dependence between
responses can be taken into\naccount by the correlation between errors in the
models for\ncontinuous and ordinal responses","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"LVMMCOR","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"A Latent Variable Model for Mixed Continuous and
Ordinal\nResponses","Version":"0.01.1"},"LW1949":{"Author":"Jean V. Adams [aut,
cre]","Depends":"R (>= 3.2.2)","Description":"The manual approach of Litchfield and
Wilcoxon
(1949)\n<http:\/\/jpet.aspetjournals.org\/content\/96\/2\/99.abstract>\nfor
evaluating dose-effect experiments\nis automated so that the computer can do the
work.","Imports":"MASS, mgcv, plotrix, tcltk, grDevices, graphics, stats,
utils","License":"GPL","NeedsCompilation":"no","Package":"LW1949","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Suggests":"magrittr, testthat,
knitr","Title":"An Automated Approach to Evaluating Dose-Effect
Experiments\nFollowing Litchfield and Wilcoxon
(1949)","URL":"https:\/\/github.com\/JVAdams\/LW1949","Version":"1.0.0"},"LaF":
{"Author":"Jan van der Laan","Depends":"methods","Description":"Methods for fast
access to large ASCII files. Currently the\nfollowing file formats are supported:
comma separated format (csv) and fixed\nwidth format. It is assumed that the files
are too large to fit into memory,\nalthough the package can also be used to
efficiently access files that do\nfit into memory. Methods are provided to access
and process files blockwise.\nFurthermore, an opened file can be accessed as one
would an ordinary\ndata.frame. The LaF vignette gives an overview of the
functionality\nprovided.","Imports":"Rcpp (>= 0.11.1)","License":"GPL-
3","NeedsCompilation":"yes","Package":"LaF","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"testthat, yaml","Title":"Fast access to large ASCII
files","URL":"https:\/\/github.com\/djvanderlaan\/LaF","Version":"0.6.2"},"Lahman":
{"Author":"Michael Friendly [aut], Dennis Murphy [ctb], Martin Monkman [ctb],
Chris Dalzell [cre, ctb]","Depends":"R (>= 2.10)","Description":"Provides the
tables from Sean Lahman's Baseball Database as a set of R data.frames.\nIt uses the
data on pitching, hitting and fielding performance and other tables\nfrom 1871
through 2014, as recorded in the 2015 version of the
database.","License":"GPL","NeedsCompilation":"no","Package":"Lahman","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"lattice, ggplot2, googleVis,
data.table, vcd, plyr, reshape2,\nzipcode","Title":"Sean Lahman's Baseball
Database","URL":"http:\/\/lahman.r-forge.r-project.org\/","Version":"4.0-
1"},"LakeMetabolizer":{"Author":"Luke Winslow, Jake Zwart, Ryan Batt, Jessica
Corman, Hilary Dugan, Paul\nHanson, Aline Jaimes, Jordan Read, Richard
Woolway","Depends":"R (>= 2.15.0), rLakeAnalyzer (>= 1.4)","Description":"A
collection of tools for the calculation of freewater metabolism.","Imports":"plyr,
2)","NeedsCompilation":"yes","Package":"LakeMetabolizer","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"R2jags","Title":"Tools for the Analysis of
Ecosystem Metabolism","Version":"1.4.1"},"Lambda4":{"Author":"Tyler Hunt
<tyler@psychoanalytix.com>","Description":"Currently the package includes 14
methods for calculating internal\nconsistency reliability but is still growing.
The package allows users\naccess to whichever reliability estimator is deemed most
appropriate for\ntheir situation.","License":"GPL-
2","NeedsCompilation":"no","Package":"Lambda4","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"mice, GPArotation, testthat","Title":"Collection of
Internal Consistency Reliability Coefficients","Version":"3.0"},"LambertW":
{"Author":"Georg M. Goerg <im@gmge.org>","Depends":"MASS,
ggplot2,","Description":"Lambert W x F distributions are a generalized framework to
analyze\nskewed, heavy-tailed data. It is based on an input\/output system, where
the\noutput
random variable (RV) Y is a non-linearly transformed version of an input\nRV X ~ F
with similar properties as X, but slightly skewed (heavy-tailed).\nThe transformed
RV Y has a Lambert W x F distribution. This package contains\nfunctions to model
and analyze skewed, heavy-tailed data the Lambert Way:\nsimulate random samples,
estimate parameters, compute quantiles, and plot\/\nprint results nicely. Probably
the most important function is 'Gaussianize',\nwhich works similarly to 'scale',
but actually makes the data Gaussian.\nA do-it-yourself toolkit allows users to
define their own Lambert W x\n'MyFavoriteDistribution' and use it in their analysis
right away.","Imports":"lamW (>= 1.0.0), stats, graphics, grDevices,
RColorBrewer,\nreshape2, Rcpp","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"LambertW","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"boot, Rsolnp, nortest, numDeriv, testthat,
moments,","Title":"Probabilistic Models to Analyze and Gaussianize Heavy-
Tailed,\nSkewed Data","URL":"http:\/\/www.gmge.org
http:\/\/arxiv.org\/abs\/0912.4554\nhttp:\/\/arxiv.org\/abs\/1010.2265
http:\/\/arxiv.org\/abs\/1602.02200","Version":"0.6.4"},"Langevin":
{"Author":"Philip Rinn [aut, cre],\nPedro G. Lind [aut],\nDavid Bastine
[ctb]","Depends":"R (>= 3.0.2)","Description":"Estimate drift and diffusion
functions from time series and\ngenerate synthetic time series from given drift and
diffusion coefficients.","Imports":"Rcpp (>= 0.11.0)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"Langevin","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Langevin Analysis in One and Two
Dimensions","Version":"1.1.1"},"LaplaceDeconv":{"Author":"Yves Rozenholc
(University Paris Descartes), Marianna Pensky (University\nof Central
Florida)","Depends":"parallel, polynom, orthopolynom","Description":"Solves the
problem of Laplace deconvolution with noisy discrete\nnon-equally spaced
observations on a finite time interval based on expansions\nof the convolution
kernel, the unknown function and the observed signal over\nLaguerre functions
basis. It implements the methodology proposed in the paper\n\"Laplace deconvolution
on the basis of time domain data and its application to\nDynamic Contrast Enhanced
imaging\" by F. Comte, C-A. Cuenod, M. Pensky and Y.\nRozenholc in ArXiv
(http:\/\/arxiv.org\/abs\/1405.7107).","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"LaplaceDeconv","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Title":"Laplace Deconvolution with Noisy Discrete Non-
Equally Spaced\nObservations on a Finite Time
Interval","Version":"1.0.4"},"Laterality":{"Author":"Borel A., Pouydebat E., Reghem
E.","Description":"Calculates and plots Handedness index (HI), absolute HI, mean HI
and z-score which are commonly used indexes for the study of hand preference
(laterality) in non-human primates.","Imports":"ade4","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"Laterality","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Functions to Calculate Common Laterality Statistics
in\nPrimatology","Version":"0.9.3"},"LatticeKrig":{"Author":"Douglas Nychka [aut,
cre], Dorit Hammerling [aut], Stephan Sain [aut], Nathan Lenssen
[aut]","Depends":"R (>= 3.0.1), methods, spam, fields (>=
6.9.1)","Description":"Functions for the interpolation of large spatial\ndatasets.
This package follows a \"fixed rank Kriging\" approach using\na large number of
basis functions and provides spatial estimates\nthat are comparable to standard
families of covariance functions.\nUsing a large number of basis functions allows
for estimates that\ncan come close to interpolating the observations (a spatial
model\nwith a small nugget variance.) Moreover, the covariance model for this
method\ncan approximate the Matern covariance family but also allows for a\nmulti-
resolution model and supports efficient computation of the\nprofile likelihood for
estimating covariance parameters. This is\naccomplished through compactly supported
basis functions and a\nMarkov random field model for the basis coefficients. These
features\nlead to sparse matrices for the computations. An extension of
this\nversion over previous ones ( < 5.4 ) is the support for different\ngeometries
besides a rectangular domain.\nOne benefit of the LatticeKrig model\/approach\nis
the facility to do unconditional and conditional\nsimulation of the field for large
numbers of arbitrary points. There\nis also the flexibility for estimating non-
stationary covariances. Included are\ngeneric methods for prediction, standard
errors for prediction,\nplotting of the estimated surface and conditional and
unconditional\nsimulation.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"LatticeKrig","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Multiresolution Kriging Based on Markov Random
Fields","URL":"http:\/\/www.r-project.org","Version":"5.4-1"},"LeLogicielR":
{"Author":"Lafaye de Micheaux Pierre, Drouilhet Remy, Liquet
Benoit","Depends":"xtable, RColorBrewer, gdata,
IndependenceTests","Description":"This package provides functions and datasets for
the\nreader of the book \"Le logiciel R: Maitriser le langage,\nEffectuer des
analyse statistiques\". The documentation and help\npages are written in
french.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"LeLogicielR","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Functions and datasets to accompany the book \"Le
logiciel R:\nMaitriser le langage, Effectuer des analyses
statistiques\"\n(french)","Version":"1.2"},"LeafAngle":{"Author":"Remko
Duursma","Description":"A leaf angle distribution is a special distribution that is
defined between 0 and 90 degrees, and a number of distributions are used to
characterize the leaf angle distribution in real plant canopies. This package
includes methods to fit distributions to data, visualize the fit, and compare fits
of nine different
distributions.","License":"GPL","NeedsCompilation":"no","Package":"LeafAngle","Repo
sitory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Analysis and Visualization
of Plant Leaf Angle Distributions","Version":"1.2-1"},"LeafArea":
{"Author":"Masatoshi Katabuchi <mattocci27@gmail.com>","Depends":"R (>=
3.0.0)","Description":"An interface for the image processing program ImageJ, which
allows a rapid digital image analysis for particle sizes. This package includes
function to write an ImageJ macro which is optimized for a leaf area analysis by
default.","Imports":"stats, utils","License":"GPL-
2","NeedsCompilation":"no","Package":"LeafArea","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Rapid Digital Image Analysis of Leaf
Area","Version":"0.1.1"},"LearnBayes":{"Author":"Jim
Albert","Description":"LearnBayes contains a collection of functions helpful in
learning the basic tenets of Bayesian statistical inference. It contains functions
for summarizing basic one and two parameter posterior distributions and predictive
distributions. It contains MCMC algorithms for summarizing posterior distributions
defined by the user. It also contains functions for regression models,
hierarchical models, Bayesian tests, and illustrations of Gibbs
sampling.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"LearnBayes","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Functions for Learning Bayesian
Inference","Version":"2.15"},"LexisPlotR":{"Author":"Philipp Ottolinger [aut, cre],
Marieke Smilde-Becker [ctb]","Depends":"R (>= 3.0.0), ggplot2 (>=
1.0.1)","Description":"Functions to plot Lexis Diagrams for Demographic
purposes.","License":"GPL-
2","NeedsCompilation":"no","Package":"LexisPlotR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr","Title":"Plot Lexis Diagrams for Demographic
Purposes","URL":"https:\/\/github.com\/ottlngr\/LexisPlotR","Version":"0.3"},"Libli
neaR":{"Author":"Thibault Helleputte <thibault.helleputte@dnalytics.com>; Pierre
Gramme\n<pierre.gramme@dnalytics.com>","Description":"A wrapper around the
LIBLINEAR C\/C++ library for\nmachine learning (available at
http:\/\/www.csie.ntu.edu.tw\/~cjlin\/liblinear).\nLIBLINEAR is a simple library
for solving large-scale regularized linear\nclassification and regression. It
currently supports L2-regularized\nclassification (such as logistic regression, L2-
loss linear SVM and L1-loss\nlinear SVM) as well as L1-regularized classification
(such as L2-loss linear\nSVM and logistic regression) and L2-regularized support
vector regression\n(with L1- or L2-loss). The main features of LiblineaR include
multi-class\nclassification (one-vs-the rest, and Crammer & Singer method),
cross\nvalidation for model selection, probability estimates (logistic
regression\nonly) or weights for unbalanced data. The estimation of the models
is\nparticularly fast as compared to other libraries.","License":"GPL-
2","NeedsCompilation":"yes","Package":"LiblineaR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"SparseM","Title":"Linear Predictive Models Based on
the LIBLINEAR C\/C++
Library","URL":"http:\/\/dnalytics.com\/liblinear\/","Version":"1.94-
2"},"LiblineaR.ACF":{"Author":"Aydin Demircioglu
<aydin.demircioglu@ini.rub.de>;\nTobias Glasmachers
<tobias.glasmachers@ini.rub.de>;\nUrun Dogan
<urundogan@gmail.com>","Description":"Solving the linear SVM problem with
coordinate descent\nis very efficient and is implemented in one of the most often
used packages,\n'LIBLINEAR' (available at
http:\/\/www.csie.ntu.edu.tw\/~cjlin\/liblinear).\nIt has been shown that the
uniform selection of coordinates can be\naccelerated by using an online adaptation
of coordinate frequencies (ACF).\nThis package implements ACF and is based on
'LIBLINEAR' as well as\nthe 'LiblineaR' package (<https:\/\/cran.r-
project.org\/package=LiblineaR>).\nIt currently supports L2-regularized L1-loss as
well as L2-loss linear
SVM.\nSimilar to 'LIBLINEAR' multi-class classification (one-vs-the rest,
and\nCrammer & Singer method) and cross validation for model selection
is\nsupported. The training of the models based on ACF is much faster
than\nstandard 'LIBLINEAR' on many problems.","License":"GPL-
2","NeedsCompilation":"yes","Package":"LiblineaR.ACF","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"SparseM, testthat","Title":"Linear
Classification with Online Adaptation of
Coordinate\nFrequencies","URL":"http:\/\/github.com\/aydindemircioglu\/liblineaR.AC
F\/","Version":"1.94-2"},"Libra":{"Author":"Feng Ruan, Jiechao Xiong and Yuan
Yao","Depends":"R (>= 3.0), nnls","Description":"Efficient procedures for fitting
the regularization path\nfor linear, binomial, multinomial, Ising and Potts models
with lasso,\ngroup lasso or column lasso(only for multinomial) penalty.\nThe
package uses Linearized Bregman Algorithm to solve the\nregularization path through
iterations. Bregman Inverse Scale Space Differential\nInclusion solver is also
provided for linear model with lasso penalty.","License":"GPL-
2","NeedsCompilation":"yes","Package":"Libra","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"lars, MASS, igraph","Title":"Linearized Bregman
Algorithms for Generalized Linear
Models","URL":"http:\/\/arxiv.org\/abs\/1406.7728","Version":"1.5"},"LifeHist":
{"Author":"Ruben H. Roa-Ureta","Depends":"R (>= 3.0.0),
Hmisc","Description":"Likelihood-based estimation of individual growth and sexual
maturity models for organisms, usually fish and invertebrates. It includes methods
for data organization, plotting standard exploratory and analytical plots,
predictions.","Imports":"optimx (>= 2013.8.6), BB","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"LifeHist","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Life History Models of Individuals","Version":"1.0-
1"},"LifeTables":{"Author":"David J. Sharrow, GUI by Hana Sevcikova","Depends":"R
(>= 2.10), mclust","Description":"Functions supplied in this package will
implement\ndiscriminant analysis to select an appropriate life table\nfamily,
select an appropriate alpha level based on a desired\nlife expectancy at birth,
produce a model mortality pattern\nbased on family and level as well as plot the
results.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"LifeTables","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"gWidgets, gWidgetsRGtk2, RGtk2","Title":"Two-
Parameter HMD Model Life Table System","Version":"1.0"},"LightningR":
{"Author":"Ermlab","Depends":"RJSONIO, RCurl, R6, httr","Description":"The purpose
of this package is to enable usage of lightningviz server to be accessible from R.
The\nserver itself can be found at http:\/\/lightning-viz.org\/ and is required to
work with this package. Package\nby itself cannot and will not create any
visualizations.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"LightningR","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Tools for Communication with Lightning-Viz
Server","URL":"https:\/\/github.com\/Ermlab\/lightining-
rstat\/","Version":"1.0.2"},"LinCal":{"Author":"Derick L. Rivers <riversdl@vcu.edu>
and Edward L. Boone","Depends":"R (>= 3.0.2)","Description":"Estimate and
confidence\/credible intervals for an unknown\nregressor x0 given an observed
y0.","License":"GPL-
2","NeedsCompilation":"no","Package":"LinCal","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Static Univariate Frequentist and Bayesian Linear
Calibration","Version":"1.0"},"LinRegInteractive":{"Author":"Martin
Meermeyer","Depends":"R (>= 3.0.0), rpanel (>= 1.1-3),
xtable","Description":"Interactive visualization of effects, response
functions\nand marginal effects for different kinds of regression models. In this
version\nlinear regression models, generalized linear models, generalized
additive\nmodels and linear mixed-effects models are supported.\nMajor features are
the interactive approach and the handling of the effects of categorical
covariates:\nif two or more factors are used as covariates every combination of the
levels of each\nfactor is treated separately. The automatic calculation
of\nmarginal effects and a number of possibilities to customize the graphical
output\nare useful features as well.","License":"GPL-
2","NeedsCompilation":"no","Package":"LinRegInteractive","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"AER, gam, mgcv, nlme","Title":"Interactive
Interpretation of Linear Regression Models","Version":"0.3-1"},"LindenmayeR":
{"Author":"Bryan Hanson [aut, cre]","Depends":"stringr, grid","Description":"L-
systems or Lindenmayer systems are parallel rewriting systems which can\nbe used to
simulate biological forms and certain kinds of fractals.\nBriefly, in an L-system a
series of symbols in a string are replaced\niteratively according to rules to give
a more complex string. Eventually,\nthe symbols are translated into turtle graphics
for plotting. Wikipedia has\na very good introduction: en.wikipedia.org\/wiki\/L-
system This package\nprovides basic functions for exploring L-
systems.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"LindenmayeR","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Functions to Explore L-Systems (Lindenmayer
Systems)","Version":"0.1.6"},"LinearRegressionMDE":{"Author":"Jiwoong Kim [aut,
cre]","Depends":"R (>= 3.2.2)","Description":"Consider linear regression model Y =
Xb + error where the distribution function of errors is unknown, but errors are
independent and symmetrically distributed. The package contains a function named
LRMDE which takes Y and X as input and returns minimum distance estimator of
parameter b in the model.","License":"GPL-
2","NeedsCompilation":"no","Package":"LinearRegressionMDE","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Title":"Minimum Distance Estimation in Linear
Regression Model","Version":"1.0"},"LinearizedSVR":{"Author":"Sriharsha
Veeramachaneni and Ken Williams","Description":"Train and predict using fast
prototype-based Linearized\nSupport-Vector Regression methods.","Imports":"kernlab,
LiblineaR, expectreg","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"LinearizedSVR","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Linearized Support
Vector Regression","Version":"1.3"},"LinkedMatrix":{"Author":"Gustavo de los Campos
[aut],\nAlexander Grueneberg [aut, cre]","Description":"Matrices implemented as
collections of matrix-like nodes, linked by\ncolumns or
rows.","Imports":"methods","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"LinkedMatrix","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"testthat, ff","Title":"Column-Linked and
Row-Linked
Matrices","URL":"https:\/\/github.com\/QuantGen\/LinkedMatrix","Version":"1.1.0"},"
Lmoments":{"Author":"Juha Karvanen","Description":"Contains functions to
estimate\nL-moments and trimmed L-moments from the data. Also\ncontains functions
to estimate the parameters of the normal\npolynomial quantile mixture and the
Cauchy polynomial quantile\nmixture from L-moments and trimmed L-
moments.","Imports":"stats","License":"GPL-
2","NeedsCompilation":"no","Package":"Lmoments","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"L-Moments and Quantile
Mixtures","URL":"http:\/\/www.tilastotiede.fi\/juha_karvanen.html","Version":"1.2-
3"},"LncMod":{"Author":"Yongsheng Li,Zishan Wang,Juan Xu*,Xia Li*","Depends":"R (>=
2.15.2),survival,pheatmap,parallel","Description":"Predict modulators regulating
the ability of effectors to regulate their targets and produce\nmodulator-effector-
target triplets followed by goterm functional enrichment and survival
analysis.This\nis mainly applied to long non-coding RNAs (lncRNAs) as candidate
modulators regulating the ability of\ntranscription factors (TFs) to regulate their
corresponding targets.","License":"GPL-
2","NeedsCompilation":"no","Package":"LncMod","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Predicting Modulator and Functional\/Survival
Analysis","Version":"1.1"},"LocFDRPois":{"Author":"Kris Sankaran [aut,
cre]","Depends":"R (>= 3.1.2)","Description":"The main idea of the Local FDR
algorithm is to estimate both proportion of null observations and the ratio of null
and alternative densities. In the case that there are many null observations, this
can be done reliably, through maximum likelihood or generalized linear models. This
package implements this in the case that the null and alternative densities are
Poisson.","Imports":"dplyr, ggplot2","License":"GPL-
2","NeedsCompilation":"no","Package":"LocFDRPois","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr","Title":"Functions for Performing Local FDR
Estimation when Null and\nAlternative are Poisson","Version":"1.0.0"},"Lock5Data":
{"Author":"Robin Lock","Depends":"R (>= 2.10)","Description":"Datasets
for \"Statistics:Unlocking the Power of Data\" by\nLock, Lock, Lock, Lock and
Lock","License":"GPL-
2","NeedsCompilation":"no","Package":"Lock5Data","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Datasets for \"Statistics: UnLocking the Power of
Data\"","Version":"2.6"},"Lock5withR":{"Author":"Randall Pruim","Depends":"R (>=
2.10)","Description":"Data sets and other utilities for\n'Statistics: Unlocking the
Power of Data'\nby Lock, Lock, Lock, Lock and Lock\n(ISBN : 978-0-470-60187-7,
http:\/\/lock5stat.com\/).","License":"GPL-
2","NeedsCompilation":"no","Package":"Lock5withR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"lubridate, lattice, mosaic","Title":"Datasets for
'Statistics: Unlocking the Power of Data'","Version":"1.2.2"},"LogConcDEAD":
{"Author":"Madeleine Cule, Robert Gramacy, Richard Samworth, Yining
Chen","Depends":"R (>= 3.0), MASS, mvtnorm","Description":"Computes a log-concave
(maximum likelihood) estimator for\ni.i.d. data in any number of
dimensions.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"LogConcDEAD","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"logcondens, rgl, mclust, tkrplot","Title":"Log-
concave Density Estimation in Arbitrary Dimensions","Version":"1.5-
9"},"LogicForest":{"Author":"Bethany Wolf","Depends":"R (>= 2.10), LogicReg,
CircStats","Description":"Two classification ensemble methods based on logic
regression models. LogForest uses a bagging approach to construct an ensemble of
logic regression models. LBoost uses a combination of boosting and cross-
validation to construct an ensemble of logic regression models. Both methods are
used for classification of binary responses based on binary predictors and for
identification of important variables and variable interactions predictive of a
binary outcome.","Imports":"gtools, plotrix","License":"GPL-
2","NeedsCompilation":"no","Package":"LogicForest","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Logic Forest","Version":"2.1.0"},"LogicReg":
{"Author":"Charles Kooperberg <clk@fredhutch.org> and Ingo Ruczinski
<ingo@jhu.edu>","Depends":"R (>= 2.10), survival","Description":"Routines for
fitting Logic Regression models.","Imports":"stats, graphics, utils,
2)","NeedsCompilation":"yes","Package":"LogicReg","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Logic Regression","Version":"1.5.8"},"LogisticDx":
{"Author":"Chris Dardis","Depends":"R (>= 3.0.0)","Description":"Diagnostic tests
and plots for GLMs (generalized linear models)\nwith binomial\/ binary outcomes,
particularly logistic regression.","Imports":"rms, stats, statmod, graphics,
speedglm, RColorBrewer,\ndata.table, pROC, aod","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"LogisticDx","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr","Title":"Diagnostic Tests for Models with a
Binomial Response","Version":"0.2"},"LogitNet":{"Author":"Pei Wang
<pwang@fhcrc.org>, Dennis Chao <dchao@fhcrc.org>, Li\nHsu
<lih@fhcrc.org>","Description":"LogitNet is developed for inferring network of
binary\nvariables under the high-dimension-low-sample-size setting","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"LogitNet","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Infer network based on binary arrays using regularized
logistic\nregression","Version":"0.1-1"},"LogrankA":{"Author":"Jonas Richter-Dumke
and Roland Rau","Description":"LogrankA provides a logrank test across unlimited
groups with the\npossibility to input aggregated survival data.","License":"GPL-
2","NeedsCompilation":"no","Package":"LogrankA","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"MASS, survival","Title":"Logrank Test for Aggregated
Survival Data","Version":"1.0"},"LoopAnalyst":{"Author":"Alexis Dinno
<alexis.dinno@pdx.edu>","Depends":"R (>= 1.8.0), nlme","Description":"Loop analysis
makes qualitative predictions of variable change in a system of causally
interdependent variables, where \"qualitative\" means sign only (i.e. increases,
decreases, non change, and ambiguous). This implementation includes output support
for graphs in .dot file format for use with visualization software such as graphviz
(graphviz.org). 'LoopAnalyst' provides tools for the construction and output of
community matrices, computation and output of community effect matrices, tables of
correlations, adjoint, absolute feedback, weighted feedback and weighted prediction
matrices, change in life expectancy matrices, and feedback, path and loop
enumeration tools.","License":"GPL-
2","NeedsCompilation":"no","Package":"LoopAnalyst","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"A Collection of Tools to Conduct Levins' Loop
Analysis","URL":"http:\/\/www.doyenne.com\/LoopAnalyst","Version":"1.2-
4"},"LotkasLaw":{"Author":"Kenneth Buker [aut, cre],\nDr. Alon Friedman
[ctb]","Depends":"R (>= 3.1.1)","Description":"Running Lotka's Law following Pao
(1985)(DOI: 10.1016\/0306-4573(85)90055-X). The Law is based around the proof that
the number of authors making n contributions is about 1\/n^{a} of those making one
contribution.","License":"GPL","NeedsCompilation":"no","Package":"LotkasLaw","Repos
itory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Runs Lotka's Law which is
One of the Special Applications of\nZipf's Law","Version":"0.0.1.0"},"LowRankQP":
{"Author":"John T. Ormerod <jormerod@sydney.edu.au>, M. P.
Wand\n<matt@maths.unsw.edua.au>","Description":"This package contains routines and
documentation for\nsolving quadratic programming problems where the hessian
is\nrepresented as the product of two matrices.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"LowRankQP","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Low Rank Quadratic
Programming","Version":"1.0.2"},"Luminescence":{"Author":"Sebastian Kreutzer [aut,
trl, cre],\nMichael Dietze [aut],\nChristoph Burow [aut],\nMargret C. Fuchs
[aut],\nChristoph Schmidt [aut],\nManfred Fischer [aut, trl],\nRachel K. Smedley
[aut],\nMarkus Fuchs [ths]","Depends":"R (>= 3.2.2), utils","Description":"A
collection of various R functions for the purpose of Luminescence\ndating data
analysis. This includes, amongst others, data import, export,\napplication of age
models, curve deconvolution, sequence analysis and\nplotting of equivalent dose
distributions.","Imports":"bbmle (>= 1.0.17), data.table (>= 1.9.6), digest (>=
0.6.8),\nhttr (>= 1.0.0), matrixStats (>= 0.15.0), methods, Rcpp (>=\n0.12.2),
minpack.lm (>= 1.2-0), raster (>= 2.4-18), readxl (>=\n0.1.0), shape (>= 1.4.2),
parallel, XML (>= 3.98-1.3), zoo (>=\n1.7-12)","License":"GPL-
3","NeedsCompilation":"yes","Package":"Luminescence","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"rgl (>= 0.95.1201)","Title":"Comprehensive
Luminescence Dating Data Analysis","URL":"http:\/\/CRAN.R-
project.org\/package=Luminescence","Version":"0.5.1"},"M3":{"Author":"Jenise Swall
<jswall@vcu.edu>","Depends":"ncdf4,rgdal,maps,mapdata","Description":"This package
contains functions to read in and manipulate\nair quality model output from
Models3-formatted files. This\nformat is used by the Community Multiscale Air
Quaility
(CMAQ)\nmodel.","License":"Unlimited","NeedsCompilation":"no","Package":"M3","Repos
itory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Reading M3
files","Version":"0.3"},"M4comp":{"Author":"Souhaib BenTaieb [aut,
cre]","Depends":"R (>= 3.2.1)","Description":"The 10.000 time series from the M4
time series forecasting\ncompetition, including print and plot
functions.","License":"GPL-
2","NeedsCompilation":"no","Package":"M4comp","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Data from the M4 Time Series Forecasting
Competition","URL":"https:\/\/github.com\/bsouhaib\/M4comp","Version":"0.0.1"},"MAI
NT.Data":{"Author":"Pedro Duarte Silva <psilva@porto.ucp.pt>, Paula Brito
<mpbrito.fep.up.pt>","Depends":"R (>= 2.8.0)","Description":"Implements
methodologies for modelling interval data, considering appropriate
parameterizations of the variance-covariance matrix that take into account the
intrinsic nature of interval data, and lead to five different possible
configuration structures.","Imports":"methods, miscTools, MASS","License":"GPL-
2","NeedsCompilation":"no","Package":"MAINT.Data","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Model and Analyse Interval
Data","Version":"0.5.1"},"MALDIquant":{"Author":"Sebastian Gibb [aut,
cre],\nKorbinian Strimmer [ths]","Depends":"R (>= 3.2.0), methods","Description":"A
complete analysis pipeline for matrix-assisted laser\ndesorption\/ionization-time-
of-flight (MALDI-TOF) and other\ntwo-dimensional mass spectrometry data. In
addition to commonly\nused plotting and processing methods it includes
distinctive\nfeatures, namely baseline subtraction methods such as\nmorphological
filters (TopHat) or the statistics-sensitive\nnon-linear iterative peak-clipping
algorithm (SNIP), peak\nalignment using warping functions, handling of
replicated\nmeasurements as well as allowing spectra with
different\nresolutions.","Imports":"parallel","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"MALDIquant","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"knitr, testthat (>= 0.8)","Title":"Quantitative
Analysis of Mass Spectrometry
Data","URL":"http:\/\/strimmerlab.org\/software\/maldiquant\/\nhttps:\/\/github.com
\/sgibb\/MALDIquant\/","Version":"1.14"},"MALDIquantForeign":{"Author":"Sebastian
Gibb [aut, cre],\nPietro Franceschi [ctb]","Depends":"R (>= 3.2.2), methods,
MALDIquant (>= 1.11.7)","Description":"Functions for reading (tab, csv, Bruker fid,
Ciphergen\nXML, mzXML, mzML, imzML, Analyze 7.5, CDF, mMass MSD) and\nwriting (tab,
csv, mMass MSD, mzML, imzML) different file\nformats of mass spectrometry data
into\/from MALDIquant objects.","Imports":"base64enc, digest, readBrukerFlexData
(>= 1.7), readMzXmlData\n(>= 2.7), XML","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"MALDIquantForeign","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"knitr, testthat (>= 0.8), RNetCDF (>=
1.6.1)","Title":"Import\/Export Routines for
MALDIquant","URL":"http:\/\/strimmerlab.org\/software\/maldiquant\/\nhttps:\/\/gith
ub.com\/sgibb\/MALDIquantForeign\/","Version":"0.10"},"MAMA":{"Author":"Ivana
Ihnatova <184415@mail.muni.cz>.","Depends":"R (>= 2.15.1), methods, genefilter,
metaMA, xtable, multtest,\ngtools, grid, GeneMeta","Description":"Implementation of
methods for microarray meta-analysis.","Imports":"MergeMaid, GeneMeta, xtable,
methods, metaArray","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MAMA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"gplots, RankProd","Title":"Meta-Analysis of
MicroArray","Version":"2.2.1"},"MAMS":{"Author":"Thomas
Jaki <jaki.thomas@gmail.com>, Dominic Magirr <d.magirr@gmail.com>, Philip Pallmann
<p.pallmann@lancaster.ac.uk>","Depends":"mvtnorm","Description":"Designing multi-
arm multi-stage studies with normal endpoints and known variance.","License":"GPL-
2","NeedsCompilation":"no","Package":"MAMS","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Designing Multi-Arm Multi-Stage
Studies","Version":"0.7"},"MAMSE":{"Author":"Jean-Francois Plante
<jfplante@hec.ca>","Depends":"R (>= 2.4.0)","Description":"This package calculates
the nonparametric adaptive MAMSE\nweights for univariate, right-censored or
multivariate data.\nThe MAMSE weights can be used in a weighted likelihood or
to\ndefine a mixture of empirical distribution functions.","License":"GPL-
2","NeedsCompilation":"yes","Package":"MAMSE","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Calculation of Minimum Averaged Mean Squared Error
(MAMSE)\nweights","Version":"0.1-3"},"MANCIE":{"Author":"Tao Wang, Chongzhi
Zang","Depends":"R (>= 2.15.0)","Description":"High-dimensional data integration is
a critical but difficult problem in genomics research because of potential biases
from high-throughput experiments. We present MANCIE, a computational method for
integrating two genomic data sets with homogenous dimensions from different sources
based on a PCA procedure as an approximation to a Bayesian
approach.","License":"GPL-
2","NeedsCompilation":"no","Package":"MANCIE","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Matrix Analysis and Normalization by Concordant
Information\nEnhancement","Version":"1.4"},"MAPA":{"Author":"Nikolaos Kourentzes
and Fotios Petropoulos","Depends":"forecast (>= 5.3), parallel","Description":"This
package contains functions and wrappers for using the Multiple Aggregation
Prediction Algorithm (MAPA) for time series forecasting. MAPA models and forecasts
time series at multiple temporal aggregation levels, thus strengthening and
attenuating the various time series components for better holistic estimation of
its structure.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MAPA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Multiple Aggregation Prediction
Algorithm","URL":"\nhttp:\/\/kourentzes.com\/forecasting\/2014\/04\/19\/multiple-
aggregation-prediction-algorithm-mapa\/","Version":"1.9"},"MAPLES":
{"Author":"Roberto Impicciatore","Depends":"mgcv","Description":"MAPLES is a
general method for the estimation of age\nprofiles that uses standard micro-level
demographic survey\ndata. The aim is to estimate smoothed age profiles and
relative\nrisks for time-fixed and time-varying covariates.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MAPLES","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Smoothed age profile estimation","Version":"1.0"},"MAR1":
{"Author":"Lindsay P. Scheef","Depends":"R (>= 2.15.1), tcltk, leaps,
bestglm","Description":"The MAR1 package provides basic tools for
preparing\necological community time-series data for MAR modeling,\nbuilding MAR-1
models via model selection and bootstrapping,\nand visualizing and exporting model
results. It is intended to\nmake MAR analysis (sensu Ives et al. (2003) Analysis
of\ncommunity stability and ecological interactions from\ntime-series data) a more
accessible tool for anyone studying\ncommunity dynamics. The user need not
necessarily be familiar\nwith time-series modeling or command-based statistics
programs\nsuch as R.","License":"GPL-
2","NeedsCompilation":"no","Package":"MAR1","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"MARSS (>= 3.2)","Title":"Multivariate Autoregressive
Modeling for Analysis of Community\nTime-Series Data","Version":"1.0"},"MARSS":
{"Author":"Eli Holmes, Eric Ward, and Kellie Wills, NOAA, Seattle,
USA","Depends":"R (>= 2.15.0)","Description":"The MARSS package provides maximum-
likelihood parameter estimation for constrained and unconstrained linear
multivariate autoregressive state-space (MARSS) models fit to multivariate time-
series data. Fitting is primarily via an Expectation-Maximization (EM) algorithm,
although fitting via the BFGS algorithm (using the optim function) is also
provided. MARSS models are a class of dynamic linear model (DLM) and vector
autoregressive model (VAR) model. Functions are provided for parametric and
innovations bootstrapping, Kalman filtering and smoothing, bootstrap model
selection criteria (AICb), confidences intervals via the Hessian approximation and
via bootstrapping and calculation of auxiliary residuals for detecting outliers and
shocks. The user guide shows examples of using MARSS for parameter estimation for
a variety of applications, model selection, dynamic factor analysis, outlier and
shock detection, and addition of covariates. Type RShowDoc(\"UserGuide\",
package=\"MARSS\") at the R command line to open the MARSS user guide. Online
workshops (lectures and computer labs) at
http:\/\/faculty.washington.edu\/eeholmes\/workshops.shtml See the NEWS file for
update information.","Imports":"nlme, mvtnorm, KFAS (>= 1.0.1), stats, utils,
graphics","License":"GPL-
2","NeedsCompilation":"no","Package":"MARSS","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"Hmisc, maps, xtable, stringr","Title":"Multivariate
Autoregressive State-Space Modeling","Version":"3.9"},"MASS":{"Author":"Brian
Ripley [aut, cre, cph],\nBill Venables [ctb],\nDouglas M. Bates [ctb],\nKurt Hornik
[trl] (partial port ca 1998),\nAlbrecht Gebhardt [trl] (partial port ca
1998),\nDavid Firth [ctb]","Depends":"R (>= 3.1.0), grDevices, graphics, stats,
utils","Description":"Functions and datasets to support Venables and
Ripley,\n\"Modern Applied Statistics with S\" (4th edition,
2002).","Imports":"methods","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"MASS","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"lattice, nlme, nnet, survival","Title":"Support Functions
and Datasets for Venables and Ripley's
MASS","URL":"http:\/\/www.stats.ox.ac.uk\/pub\/MASS4\/","Version":"7.3-
45"},"MASSTIMATE":{"Author":"Nicolas E. Campione","Depends":"R (>=
2.10.0)","Description":"Estimation equations are from a variety of sources but are,
in general, based on regressions between skeletal measurements (e.g., femoral
circumference) and body mass in living taxa.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MASSTIMATE","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Body Mass Estimation Equations for
Vertebrates","Version":"1.3"},"MAT":{"Author":"Seung W. Choi and David R.
King","Description":"Simulate Multidimensional Adaptive Testing","Imports":"Rcpp
(>= 0.11.2)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"MAT","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Multidimensional Adaptive Testing","Version":"2.2"},"MATA":
{"Author":"Daniel Turek [aut, cre]","Depends":"R (>=
3.1.3)","Description":"Calculates Model-Averaged Tail Area Wald (MATA-Wald)
confidence\nintervals, which are constructed using single-model estimators and
model\nweights.","License":"GPL-
2","NeedsCompilation":"no","Package":"MATA","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Model-Averaged Tail Area Wald (MATA-Wald) Confidence
Interval","Version":"0.3"},"MATTOOLS":{"Author":"Dr. M. Sawada.","Depends":"R (>=
2.15.0)","Description":"This package in includes functions for receiver
operating\ncharacteristic (ROC) analyses as well as Monte Carlo\nsimulation. It
includes specific graphical functions for\ninterpreting the output of these
techniques.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MATTOOLS","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Modern Calibration Functions for the Modern Analog
Technique\n(MAT)","Version":"1.1"},"MAVIS":{"Author":"William Kyle Hamilton [aut,
cre],\nAtsushi Mizumoto [aut],\nBurak Aydin [ctb, trl],\nKathleen Coburn
[ctb]","Depends":"R (>= 3.0.3)","Description":"Interactive shiny application for
running a meta-analysis,\nprovides support for both random effects and fixed
effects models with the 'metafor' package.\nAdditional support is included for
calculating effect sizes plus\nsupport for single case designs, graphical output,
and detecting publication bias.","Imports":"shiny, shinyAce, metafor, MAc, MAd,
quantreg, ggplot2,\ncompute.es, SCMA, SCRT, shinyBS","License":"GPL-
3","NeedsCompilation":"no","Package":"MAVIS","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Meta Analysis via Shiny","Version":"1.1.1"},"MAVTgsa":
{"Author":"Chih-Yi Chien, Chen-An Tsai, Ching-Wei Chang, and James J.
Chen","Depends":"R (>= 2.13.2), corpcor, foreach, multcomp, randomForest,
MASS","Description":"This package is a gene set analysis function for one-sided
test (OLS), two-sided test (multivariate analysis of variance).\nIf the
experimental conditions are equal to 2, the p-value for Hotelling's t^2 test is
calculated.\nIf the experimental conditions are great than 2, the p-value for
Wilks' Lambda is determined and post-hoc test is reported too.\nThree multiple
comparison procedures, Dunnett, Tukey, and sequential pairwise comparison, are
implemented.\nThe program computes the p-values and FDR (false discovery rate) q-
values for all gene sets.\nThe p-values for individual genes in a significant gene
set are also listed.\nMAVTgsa generates two visualization output: a p-value plot of
gene sets (GSA plot) and a GST-plot of the empirical distribution function of the
ranked test statistics of a given gene set.\nA Random Forests-based procedure is to
identify gene sets that can accurately predict samples from different experimental
conditions or are associated with the continuous phenotypes.","License":"GPL-
2","NeedsCompilation":"no","Package":"MAVTgsa","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Three methods to identify differentially expressed gene
sets,\nordinary least square test, Multivariate Analysis Of Variance\ntest with n
contrasts and Random forest","Version":"1.3"},"MAc":{"Author":"AC Del Re & William
T. Hoyt","Depends":"R (>= 2.10.1)","Description":"This is an integrated meta-
analysis package for conducting\na correlational research synthesis. One of the
unique features\nof this package is in its integration of user-friendly\nfunctions
to facilitate statistical analyses at each stage in a\nmeta-analysis with
correlations. It uses recommended procedures\nas described in The Handbook of
Research Synthesis and\nMeta-Analysis (Cooper, Hedges, & Valentine,
2009).","Enhances":"compute.es, irr","License":"GPL-
2","NeedsCompilation":"no","Package":"MAc","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"ggplot2, R2wd, metafor","Title":"Meta-Analysis with
Correlations","URL":"\nhttp:\/\/rwiki.sciviews.org\/doku.php?
id=packages:cran:ma_meta-analysis","Version":"1.1"},"MAclinical":{"Author":"Anne-
Laure Boulesteix <boulesteix@ibe.med.uni-muenchen.de>.","Depends":"R (>= 2.4.1),
party, plsgenomics, st, e1071","Description":"'Maclinical' implements class
prediction using both\nmicroarray data and clinical parameters. It addresses
the\nquestion of the additional predictive value of microarray data.\nClass
prediction is performed using a two-step method combining\n(pre-validated) PLS
dimension reduction and random forests.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MAclinical","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Class prediction based on microarray data and
clinical\nparameters","URL":"http:\/\/cran.r-
project.org\/web\/packages\/MAclinical\/index.html","Version":"1.0-5"},"MAd":
{"Author":"AC Del Re & William T. Hoyt","Depends":"R (>= 2.10.1)","Description":"A
collection of functions for conducting a meta-analysis with mean differences data.
It uses recommended procedures as\tdescribed in The \tHandbook of Research
Synthesis and Meta-Analysis\t(Cooper, Hedges, & Valentine,
2009).","Enhances":"compute.es, irr","License":"GPL-
2","NeedsCompilation":"no","Package":"MAd","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"metafor, R2wd, ggplot2","Title":"Meta-Analysis with Mean
Differences","URL":"http:\/\/acdelre.weebly.com","Version":"0.8-2"},"MBA":
{"Author":"Andrew O. Finley <finleya@msu.edu>, Sudipto
Banerjee\n<sudiptob@biostat.umn.edu>","Depends":"R (>= 2.8.0),
sp","Description":"Scattered data interpolation with Multilevel B-
Splines","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"MBA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Multilevel B-spline Approximation","Version":"0.0-
8"},"MBCluster.Seq":{"Author":"Yaqing Si","Description":"Cluster genes based on
Poisson or Negative-Binomial model\nfor RNA-Seq or other digital gene expression
(DGE) data","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"MBCluster.Seq","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Model-Based Clustering for RNA-seq
Data","Version":"1.0"},"MBESS":{"Author":"Ken Kelley [aut, cre]","Depends":"R (>=
3.2.0), stats","Description":"Implements methods that useful in designing research
and analyzing data, with\nparticular emphasis on methods that are developed for or
used within the behavioral,\neducational, and social sciences (broadly defined).
That being said, many of the methods\nimplemented within MBESS are applicable to a
wide variety of disciplines. MBESS has a\nsuite of functions for a variety of
related topics, such as effect sizes, confidence intervals\nfor effect sizes
(including standardized effect sizes and noncentral effect sizes), sample
size\nplanning (from the accuracy in parameter estimation [AIPE], power analytic,
equivalence, and\nminimum-risk point estimation perspectives), mediation analysis,
various properties of\ndistributions, and a variety of utility functions. MBESS
(pronounced `èm-bes'') was originally\nan acronym for \"Methods for the
Behavioral, Educational, and Social Sciences,\" but at this\npoint MBESS contains
methods applicable and used in a wide variety of fields and is an\norphan acronym,
in the sense that what was an acronym is now literally its name. MBESS has\ngreatly
benefited from others, see <http:\/\/nd.edu\/~kkelley\/site\/MBESS.html> for a
detailed\nlist of those that have contributed and other details.","Imports":"boot,
gsl, lavaan, MASS, methods, mnormt, nlme, OpenMx,\nparallel, sem,
semTools","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"MBESS","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"The MBESS R
Package","URL":"http:\/\/nd.edu\/~kkelley\/site\/MBESS.html","Version":"4.0.0"},"MB
I":{"Author":"Youhua Chen","Description":"Over 20 multiple-site diversity indices
can be calculated.\nLater versions will include phylogenetic
diversity","License":"GPL-
2","NeedsCompilation":"no","Package":"MBI","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"(M)ultiple-site (B)iodiversity (I)ndices
Calculator","Version":"1.0"},"MBTAr":{"Author":"Justin de Benedictis-Kessner [aut,
cre]","Depends":"R (>= 3.1.2)","Description":"Access to the MBTA API for R. Creates
an easy-to-use bundle of\nfunctions to work with all the built-in calls to the MBTA
API. Allows users\nto download realtime tracking data in dataframe format that is
manipulable\nin standard R analytics
functions.","Imports":"jsonlite","License":"GPL-
3","NeedsCompilation":"no","Package":"MBTAr","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Access Data from the Massachusetts Bay Transit Authority
(MBTA)\nWeb API","Version":"1.0.1"},"MBmca":{"Author":"Stefan Roediger [aut,
cre],\nMichal Burdukiewicz [ctb]","Depends":"R (>= 3.0.0), robustbase (>= 0.9),
chipPCR (>= 0.0.7)","Description":"The MBmca package provides data sets and
lightweight utilities for\nnucleic acid melting curve analysis and presentation on
microbead surfaces\nbut also for reactions in solution (e.g.,
qPCR).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MBmca","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Nucleic Acid Melting Curve Analysis on Microbead Surfaces
with R","URL":"https:\/\/github.com\/michbur\/MBmca\/","Version":"0.0.3-
5"},"MC2toPath":{"Author":"Dave Conklin and Emilie Henderson","Description":"Post
processes MC2 output, especially for use by Path or ST-Sim. MC2 (short for \"MC1
version 2\") is a dynamic global vegetation model (en.wikipedia.org\/wiki\/DGVM).
Path (essa.com\/tools\/path) and ST-Sim (www.apexrms.com) are state-and-transition
model (STM) engines. MC2 has a user website at
sites.google.com\/site\/mc1dgvmusers. Since 2001, MC1 has been used to simulate
changes in natural vegetation due to climate change at scales from regional to
global. In 2012, MC1 was reimplemented in C++ to make it faster and to reduce
storage requirements. This newer version is referred to as MC2, an abbreviation of
\"MC1 version 2\". Beginning in 2011, output from MC1 and MC2 has been used to
inform regional state-and-transition model simulations by the U.S. Forest Service
and the Washington State Department of Natural Resources. Projects to date have
involved study areas in central Oregon, the Olympic Peninsula, the Blue Mountains
ecoregion, southwestern Oregon, and southeastern Oregon. In the first of this
series of projects, the netCDF output files from MC2 were manually post-processed,
mostly in Excel, to produce input .csv files for the STM engines. Beginning with
the second project, R scripts were used to automate the post-processing work.
These R scripts have been collected into the MC2toPath R-
package.","Imports":"RNetCDF","License":"GPL-
2","NeedsCompilation":"no","Package":"MC2toPath","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Translates information from netcdf files with MC2 output
into\ninter-PVT transitions","Version":"0.0.16"},"MCAPS":{"Author":"Roger D. Peng
<rpeng@jhsph.edu>","Depends":"R (>= 2.14.0)","Description":"Weather and air
pollution data, risk estimates, and other\ninformation from the Medicare Air
Pollution Study (MCAPS) of\n204 U.S. counties, 1999--
2002","Imports":"stashR","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MCAPS","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"MCAPS data and
results","URL":"http:\/\/www.biostat.jhsph.edu\/MCAPS\/","Version":"0.3-2"},"MCDA":
{"Author":"Patrick Meyer, SÃ©bastien Bigaret, Richard Hodgett, Alexandru-Liviu
Olteanu","Description":"Functions which can be useful to support the analyst in the
Multicriteria Decision Aiding (MCDA) process involving multiple, conflicting
criteria.","Imports":"Rglpk, glpkAPI, methods","License":"CeCILL-
2","NeedsCompilation":"no","Package":"MCDA","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"Rgraphviz","Title":"Functions to Support the Multicriteria
Decision Aiding
Process","URL":"https:\/\/github.com\/paterijk\/MCDA","Version":"0.0.12"},"MCDM":
{"Author":"Blanca A. Ceballos Martin <bceballos@decsai.ugr.es>","Description":"An R
implementation of Four Multi-Criteria Decision Making (MCDM) Methods: Technique for
Order of Preference by Similarity to Ideal Solution (TOPSIS), \"VIseKriterijumska
Optimizacija I Kompromisno Resenje\" (VIKOR), both Multi-Objective Optimization by
Ratio Analysis and Full Multiplicative Form (Multi-MOORA) and Weighted Aggregated
Sum Product ASsessment (WASPAS). In addition, this package provides a MetaRanking
function which combines the output of the previous methods.","License":"LGPL (>=
3)","NeedsCompilation":"no","Package":"MCDM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Multi-Criteria Decision Making
Methods","URL":"http:\/\/decsai.ugr.es\/index.php?
p=miembros&id=19909","Version":"1.0"},"MCI":{"Author":"Thomas
Wieland","Description":"The Multiplicative Competitive Interaction (MCI) Model by
Nakanishi & Cooper (1974) <DOI:10.2307\/3151146> is an
econometric model for analyzing market shares and\/or market areas. The functions
in this package include fitting the MCI model, the log-centering transformation of
MCI datasets and tools for data preparation.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MCI","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Multiplicative Competitive Interaction (MCI)
Model","Version":"1.0.0"},"MCL":{"Author":"Martin L. JÃ¤ger","Depends":"R (>=
2.10.0)","Description":"Contains the Markov cluster algorithm (MCL) for identifying
clusters in networks and graphs. The algorithm simulates random walks on a (n x n)
matrix as the adjacency matrix of a graph. It alternates an expansion step and an
inflation step until an equilibrium state is
reached.","Imports":"expm","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MCL","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Markov Cluster Algorithm","Version":"1.0"},"MCMC.OTU":
{"Author":"Mikhail V.
Matz","Depends":"MCMCglmm,ggplot2,coda","Description":"Poisson-lognormal
generalized linear mixed model analysis of multivariate counts data using MCMC,
aiming to infer the changes in relative proportions of individual variables. The
package was originally designed for sequence-based analysis of microbial
communities (\"metabarcoding\", variables = operational taxonomic units, OTUs), but
can be used for other types of multivariate counts, such as in ecological
applications (variables = species). The results are summarized and plotted using
'ggplot2' functions. Includes functions to remove sample and variable outliers and
reformat counts into normalized log-transformed values for correlation and
principal component\/coordinate analysis. Walkthrough and examples:
http:\/\/www.bio.utexas.edu\/research\/matz_lab\/matzlab\/Methods_files\/walkthroug
hExample_mcmcOTU_R.txt.","License":"GPL-
3","NeedsCompilation":"no","Package":"MCMC.OTU","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Bayesian Analysis of Multivariate Counts Data in
DNA\nMetabarcoding and Ecology","Version":"1.0.10"},"MCMC.qpcr":{"Author":"Mikhail
V. Matz","Depends":"MCMCglmm,ggplot2,coda","Description":"Quantitative RT-PCR data
are analyzed using generalized linear mixed models based on lognormal-Poisson error
distribution, fitted using MCMC. Control genes are not required but can be
incorporated as Bayesian priors or, when template abundances correlate with
conditions, as trackers of global effects (common to all genes). The package also
implements a lognormal model for higher-abundance data and a \"classic\" model
involving multi-gene normalization on a by-sample basis. Several plotting functions
are included to extract and visualize results. The detailed tutorial is available
here: http:\/\/bit.ly\/1Nwo4CB.","License":"GPL-
3","NeedsCompilation":"no","Package":"MCMC.qpcr","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Bayesian Analysis of qRT-PCR
Data","Version":"1.2.2"},"MCMC4Extremes":{"Author":"Fernando Ferraz do Nascimento
[aut, cre], Wyara Vanesa Moura e Silva [aut, ctb]","Depends":"R (>= 3.0),
evir","Description":"Provides some function to perform posterior estimation for
some distribution, with emphasis to extreme value distributions.It contains some
extreme datasets, and functions that perform the runs of posterior points of the
GPD and GEV distribution. The package calculate some important extreme measures
like return level for each t periods of time, and some plots as the predictive
distribution, and return level plots.","License":"GPL-
2","NeedsCompilation":"no","Package":"MCMC4Extremes","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Posterior Distribution of Extreme Value Models in
R","Version":"1.0"},"MCMCglmm":{"Author":"Jarrod Hadfield","Depends":"Matrix, coda,
ape","Description":"MCMC Generalised Linear Mixed Models.","Imports":"corpcor,
tensorA, cubature, methods","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"MCMCglmm","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"rgl, combinat, mvtnorm, orthopolynom","Title":"MCMC
Generalised Linear Mixed Models","Version":"2.22.1"},"MCMCpack":{"Author":"Andrew
D. Martin, Kevin M. Quinn, and Jong Hee Park","Depends":"R (>= 2.10.0), coda (>=
0.11-3), MASS, stats","Description":"Contains functions to perform
Bayesian\ninference using posterior simulation for a number of\nstatistical models.
Most simulation is done in compiled C++\nwritten in the Scythe Statistical Library
Version 1.0.3. All\nmodels return coda mcmc objects that can then be
summarized\nusing the coda package. Some useful\nutility functions such as density
functions,\npseudo-random number generators for statistical\ndistributions, a
general purpose Metropolis sampling algorithm,\nand tools for visualization are
provided.","Imports":"graph, graphics, grDevices, lattice, methods,
Rgraphviz,\nutils, mcmc, quantreg","License":"GPL-
3","NeedsCompilation":"yes","Package":"MCMCpack","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Markov Chain Monte Carlo (MCMC)
Package","URL":"http:\/\/mcmcpack.berkeley.edu","Version":"1.3-5"},"MCPAN":
{"Author":"Frank Schaarschmidt [aut, cre], Daniel Gerhard [aut], Martin Sill
[aut]","Description":"Multiple contrast tests and simultaneous
confidence\nintervals based on normal approximation. With implementations
for\nbinomial proportions in a 2xk setting (risk difference and odds ratio),\npoly-
3-adjusted tumour rates, biodiversity indices (multinomial data)\nand expected
values under lognormal assumption. Approximative power\ncalculation for multiple
contrast tests of binomial and Gaussian data.","Imports":"mvtnorm, multcomp,
graphics, stats, magic, MCMCpack, plyr","License":"GPL-
2","NeedsCompilation":"no","Package":"MCPAN","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Multiple Comparisons Using Normal
Approximation","Version":"1.1-20"},"MCPMod":{"Author":"Bjoern Bornkamp, Jose
Pinheiro and Frank Bretz","Depends":"mvtnorm, lattice, R (>=
2.4.1)","Description":"This package implements a methodology for the design and
analysis of\ndose-response studies that combines aspects of multiple comparison
procedures\nand modeling approaches (Bretz, Pinheiro and Branson, 2005, Biometrics
61, 738-748).\nThe package provides tools for the analysis of dose finding trials
as well as a variety\nof tools necessary to plan a trial to be conducted with the
MCPMod methodology.\n***NOTE*** The MCPMod package will not be further developed,
all future development of\nthe MCP-Mod methodology will be done in the DoseFinding
R-package. ***NOTE***","License":"GPL-
3","NeedsCompilation":"no","Package":"MCPMod","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Design and Analysis of Dose-Finding Studies (see
also\nDoseFinding package)","Version":"1.0-8"},"MCPerm":{"Author":"Lanying Zhang
and Yongshuai Jiang","Depends":"metafor, graphics","Description":"A Monte Carlo
permutation method for multiple test\ncorrelation.","License":"GPL-
2","NeedsCompilation":"no","Package":"MCPerm","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"stats","Title":"A Monte Carlo permutation method for
multiple test correlation","Version":"1.1.4"},"MCS":{"Author":"Leopoldo Catania &
Mauro Bernardi","Depends":"R(>= 3.0.1)","Description":"Perform the model confidence
set procedure of Hansen et al (2011).","Imports":"methods","License":"GPL-
2","NeedsCompilation":"no","Package":"MCS","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Model Confidence Set Procedure","Version":"0.1.1"},"MCTM":
{"Author":"Alessandro Bessi","Depends":"R (>= 3.1.1)","Description":"Transition
matrices (probabilities or counts) estimation for discrete Markov Chains of order n
(1 <= n <= 5).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MCTM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Markov Chains Transition
Matrices","Version":"1.0"},"MChtest":{"Author":"M.P.
Fay","Depends":"stats","Description":"The package performs Monte Carlo hypothesis
tests. It\nallows a couple of different sequential stopping boundaries
(a\ntruncated sequential probability ratio test boundary and a\nboundary proposed
by Besag and Clifford, 1991). Gives valid\np-values and confidence intervals on p-
values.","License":"GPL","NeedsCompilation":"no","Package":"MChtest","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Title":"Monte Carlo hypothesis tests with
Sequential
Stopping","URL":"\nhttp:\/\/www3.niaid.nih.gov\/about\/organization\/dcr\/BRB\/staf
f\/michael.htm","Version":"1.0-2"},"MConjoint":{"Author":"William
Hughes","Description":"The package aids in creating a Conjoint Analysis
design\nwith extra cards. Unlike traditional \"holdout\" cards these\ncards are
used to create a set of \"good\" (balanced and low\ncorrelation) designs. Each of
these designs is analyzed and the\naverage calculated.","License":"GPL-
3","NeedsCompilation":"no","Package":"MConjoint","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Conjoint Analysis through Averaging of Multiple
Analyses","Version":"0.1"},"MDM":{"Author":"Glenn De'ath <g.death@aims.gov.au>;
Code for mdm was adapted from multinom in the nnet package (Brian Ripley
<ripley@stats.ox.ac.uk> and Bill Venables <Bill.Venables@csiro.au>)","Depends":"R
(>= 2.9.0), nnet","Description":"The multinomial diversity model is a toolbox for
relating diversity to complex predictors. It is based on (1) Shannon diversity; (2)
the multinomial logit model, and (3) the link between Shannon diversity and the
log-likelihood of the MLM.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"MDM","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Multinomial Diversity Model","Version":"1.3"},"MDMR":
{"Author":"Daniel B. McArtor (dmcartor@nd.edu) [aut, cre]","Depends":"R (>=
3.0.0),","Description":"Allows a user to conduct multivariate distance matrix
regression
using analytic p-values and compute measures of effect
size.","Imports":"CompQuadForm, parallel","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MDMR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr, rmarkdown","Title":"Multivariate Distance Matrix
Regression","URL":"http:\/\/github.com\/dmcartor\/mdmr","Version":"0.4.0"},"MDPtool
box":{"Author":"Iadine Chades, Guillaume Chapron, Marie-Josee Cros, Frederick
Garcia, Regis Sabbadin","Depends":"Matrix, linprog","Description":"The Markov
Decision Processes (MDP) toolbox proposes functions related to the resolution of
discrete-time Markov Decision Processes: finite horizon, value iteration, policy
iteration, linear programming algorithms with some variants and also proposes some
functions related to Reinforcement Learning.","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"MDPtoolbox","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Markov Decision Processes
toolbox","Version":"4.0.2"},"MDR":{"Author":"Stacey
Winham","Depends":"lattice","Description":"Performs multifactor dimensionality
reduction (MDR) to\ndetect potential gene-gene interactions in case-
control\nstudies.","License":"GPL-
2","NeedsCompilation":"no","Package":"MDR","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Detect gene-gene interactions using multifactor
dimensionality\nreduction","Version":"1.2"},"MDSGUI":{"Author":"Andrew Timm and
Sugnet Gardner-Lubbe","Depends":"MASS, boot, RColorBrewer, scatterplot3d, tcltk,
tcltk2,\ntkrplot, rpanel, graphics, rgl","Description":"A graphical user interface
(GUI) for performing Multidimensional Scaling applications and interactively
analysing the results all within the GUI environment. The MDS-GUI provides means of
performing Classical Scaling, Least Squares Scaling, Metric SMACOF, Non-Metric
SMACOF, Kruskal's Analysis and Sammon Mapping with animated
optimisation.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"MDSGUI","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"A GUI for interactive MDS in
R","Version":"0.1.6"},"MDimNormn":{"Author":"Mun-Gwan Hong","Depends":"R (>=
3.2.0)","Description":"Normalize data to minimize the difference between sample
plates\n(batch effects). For given data in a matrix and grouping variable
(or\nplate), the function 'normn_MA' normalizes the data on MA coordinates.\nMore
details are in the citation. The primary method is 'Multi-MA'. Other\nfitting
functions on MA coordinates can also be employed e.g. loess.","License":"GPL-
3","NeedsCompilation":"no","Package":"MDimNormn","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Multi-Dimensional MA Normalization for Plate
Effect","Version":"0.8.0"},"MDplot":{"Author":"Christian Margreitter [aut,
cre]","Depends":"R (>= 3.0.0), methods, MASS, RColorBrewer, gplots,
gtools","Description":"Provides automatization for plot generation succeeding
common molecular dynamics analyses.\nThis includes straightforward plots, such as
RMSD (Root-Mean-Square-Deviation) and\nRMSF (Root-Mean-Square-Fluctuation) but also
more sophisticated ones such as\ndihedral angle maps, hydrogen bonds, cluster bar
plots and\nDSSP (Definition of Secondary Structure of Proteins)
3","NeedsCompilation":"no","Package":"MDplot","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Visualizing Molecular Dynamics
Analyses","URL":"https:\/\/github.com\/MDplot\/MDplot","Version":"0.3"},"MEET":
{"Author":"Joan Maynou and Erola Pairo.","Depends":"R (>= 2.15.0), seqinr,
pcaMethods, Matrix,\nROCR,Hmisc,KernSmooth, methods, seqLogo","Description":"MEET
(Motif Elements Estimation Toolkit) is a R-package\nthat integrates a set of
computational algorithms for the\ndetection of Transcription Factor Binding Sites
(TFBS).","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"MEET","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"MEET: Motif Elements Estimation
Toolkit","Version":"5.1.1"},"MEMSS":{"Author":"Douglas Bates
<bates@stat.wisc.edu>,\nMartin Maechler <maechler@R-project.org> and\nBen Bolker
<bbolker@gmail.com>","Depends":"R(>= 2.12.0), lme4 (>= 0.999375-
36)","Description":"Data sets and sample analyses from Pinheiro and
Bates,\n\"Mixed-effects Models in S and S-PLUS\" (Springer, 2000).","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"MEMSS","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"lattice","Title":"Data sets from Mixed-effects Models in
S","Version":"0.9-2"},"MESS":{"Author":"Claus Ekstrom
<claus@rprimer.dk>","Depends":"geepack, glmnet, Matrix","Description":"A mixed
collection of useful and semi-useful functions, some of\nwhich may even be
referenced in The R Primer book.","Imports":"kinship2, parallel,
2","NeedsCompilation":"no","Package":"MESS","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"MASS, lme4","Title":"Miscellaneous Esoteric Statistical
Scripts","Version":"0.3-2"},"MExPosition":{"Author":"Cherise R. Chin Fatt, Derek
Beaton, Herve Abdi.","Depends":"prettyGraphs (>= 2.0.0), ExPosition (>=
2.0.0)","Description":"MExPosition is for descriptive (i.e., fixed-effects)\nmulti-
table multivariate analysis the singular value\ndecomposition.","License":"GPL-
2","NeedsCompilation":"no","Package":"MExPosition","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Multi-table ExPosition","Version":"2.0.3"},"MF":
{"Author":"David Siev","Depends":"R (>= 2.15.0), methods","Description":"Calculate
MF (mitigated fraction) with clustering and bootstrap options. See
http:\/\/goo.gl\/pcXYVr for definition of MF.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"MF","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Mitigated Fraction","Version":"4.3.2"},"MFAg":
{"Author":"Paulo Cesar Ossani <ossanipc@hotmail.com>\nMarcelo Angelo Cirillo
<macufla@dex.ufla.br>","Description":"Performs Multiple Factor Analysis method for
quantitative, categorical, frequency and mixed data, in addition to generating a
lot of graphics, also has other useful functions.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MFAg","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Multiple Factor Analysis (MFA)","Version":"1.3"},"MFHD":
{"Author":"M. Hubert, K. Vakili.","Depends":"fda.usc","Description":"Multivariate
functional halfspace depth and median for two-dimensional functional
data.","Imports":"deldir, depth, depthTools, matrixStats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MFHD","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Multivariate Functional Halfspace
Depth","Version":"0.0.1"},"MGGM":{"Author":"Yunzhang Zhu, Xiaotong Shen, Wei Pan,
Yiwen Sun","Description":"Implement algorithms to recover multiple networks by
pursuit of both sparseness and cluster.","License":"GPL-
2","NeedsCompilation":"yes","Package":"MGGM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"MASS","Title":"Structural Pursuit Over Multiple
Undirected Graphs","Version":"1.0"},"MGLM":{"Author":"Yiwen Zhang
<yzhang31@ncsu.edu> and Hua Zhou <hua_zhou@ncsu.edu>","Depends":"R (>=
3.0.0)","Description":"Provides functions that (1) fit multivariate discrete
distributions, (2) generate random numbers from multivariate discrete
distributions, and (3) run regression and penalized regression on the multivariate
categorical response data. Implemented models include: multinomial logit model,
Dirichlet multinomial model, generalized Dirichlet multinomial model, and negative
multinomial model. Making the best of the minorization-maximization (MM) algorithm
and Newton-Raphson method, we derive and implement stable and efficient algorithms
to find the maximum likelihood estimates. On a multi-core machine, multi-threading
is supported.","Imports":"methods, stats, parallel","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MGLM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"ggplot2, plyr, reshape2","Title":"Multivariate Response
Generalized Linear Models","Version":"0.0.7"},"MGRASTer":{"Author":"Daniel T.
Braithwaite [aut, cre]","Depends":"R (>= 3.0), utils","Description":"Convenience
Functions for R Language Access to the v.1 API of the MG-RAST Metagenome Annotation
Server, part of the US Department of Energy (DOE) Systems Biology Knowledge Base
(KBase).","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"MGRASTer","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"RJSONIO","Title":"API Client for the MG-RAST
Server of the US DOE
KBase","URL":"https:\/\/github.com\/braithwaite\/MGRASTer\/","Version":"0.9"},"MGSD
A":{"Author":"Irina Gaynanova","Description":"Implements Multi-Group Sparse
Discriminant Analysis proposal of 'I.Gaynanova, J.Booth and M.Wells (2015),
Simultaneous sparse estimation of canonical vectors in the p>>N
setting'.","Imports":"MASS, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"MGSDA","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Multi-Group Sparse Discriminant
Analysis","Version":"1.2"},"MHTrajectoryR":{"Author":"Matthieu Marbac and Mohammed
Sedki","Depends":"R (>= 2.10)","Description":"Spontaneous adverse event reports
have a high potential for detecting adverse drug reactions. However, due to their
dimension, the analysis of such databases requires statistical methods. We propose
to use a logistic regression whose sparsity is viewed as a model selection
challenge. Since the model space is huge, a Metropolis-Hastings algorithm carries
out the model selection by maximizing the BIC criterion.","Imports":"parallel,
mgcv","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MHTrajectoryR","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Bayesian Model Selection in Logistic Regression for
the\nDetection of Adverse Drug Reactions","Version":"1.0.1"},"MHadaptive":
{"Author":"Corey
Chivers","Depends":"MASS, R (>= 2.14.0)","Description":"Performs general
Metropolis-Hastings Markov Chain Monte\nCarlo sampling of a user defined function
which returns the\nun-normalized value (likelihood times prior) of a
Bayesian\nmodel. The proposal variance-covariance structure is updated\nadaptively
for efficient mixing when the structure of the\ntarget distribution is unknown.
The package also provides some\nfunctions for Bayesian inference including Bayesian
Credible\nIntervals (BCI) and Deviance Information Criterion
(DIC)\ncalculation.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"MHadaptive","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"General Markov Chain Monte Carlo for Bayesian
Inference using\nadaptive Metropolis-Hastings sampling","Version":"1.1-8"},"MIICD":
{"Author":"Marc Delord [aut, cre]","Depends":"R (>=
2.13.0)","Description":"Implements multiple imputation for proportional hazards
regression\nwith interval censored data or proportional sub-distribution
hazards\nregression for interval censored competing risks data. The main
functions\nallow to estimate survival function, cumulative incidence function,
Cox\nand Fine & Gray regression coefficients and associated variance-
covariance\nmatrix. 'MIICD' functions call 'Surv', 'survfit' and 'coxph' from
the\n'survival' package, 'crprep' from the 'mstate' package, and 'mvrnorm'
from\nthe 'MASS' package.","Imports":"survival, MASS, mstate","License":"GPL-
3","NeedsCompilation":"no","Package":"MIICD","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Multiple Imputation for Interval Censored
Data","Version":"2.2"},"MIIVsem":{"Author":"Zachary Fisher, Ken Bollen, Kathleen
Gates, and Mikko RÃ¶nkkÃ¶.","Depends":"R (>= 3.1.2), lavaan,
Matrix","Description":"Functions for estimating structural equation models using
model-\nimplied instrumental variables.","Imports":"methods","License":"GPL-
2","NeedsCompilation":"no","Package":"MIIVsem","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat","Title":"Model Implied Instrumental Variable
(MIIV) Estimation of\nStructural Equation Models","Version":"0.4.7"},"MILC":
{"Author":"Stavroula A. Chrysanthopoulou","Description":"The MILC package is
designed to predict individual trajectories using the continuous time
microsimulation model MILC, that describes the natural history of lung
cancer.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MILC","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"MIcrosimulation Lung Cancer (MILC)
model","Version":"1.0"},"MIPHENO":{"Author":"Shannon M. Bell
<bell.shannonm@gmail.com>, Lyle D. Burgoon\n<burgoon.lyle@epa.gov>","Depends":"R
(>= 2.12.1)","Description":"This package contains functions to carry out processing
of\nhigh throughput data analysis and detection of putative\nhits\/mutants.
Contents include a function for post-hoc quality\ncontrol for removal of outlier
sample sets, a median-based\nnormalization method for use in datasets where there
are no\nexplicit controls and where most of the responses are of the\nwildtype\/no
response class (see accompanying paper). The\npackage also includes a way to
prioritize individuals of\ninterest using am empirical cumulative distribution
function.\nMethods for generating synthetic data as well as data from
the\nChloroplast 2010 project are included.","Imports":"doBy, gdata","License":"GPL
(>=
3)","NeedsCompilation":"no","Package":"MIPHENO","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Mutant Identification through Probabilistic High
throughput\nEnabled NOrmalization","Version":"1.2"},"MIXFIM":{"Author":"Marie-
Karelle Riviere-Jourdan and France Mentre <france.mentre@inserm.fr>","Depends":"R
(>= 3.0.2), rstan (>= 2.7.0-1), mvtnorm (>= 1.0-2), ggplot2\n(>=
1.0.1)","Description":"Evaluation and optimization of the Fisher Information Matrix
in NonLinear Mixed Effect Models using Markov Chains Monte Carlo for continuous and
discrete data.","License":"GPL-
3","NeedsCompilation":"no","Package":"MIXFIM","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Evaluation of the FIM in NLMEMs using
MCMC","Version":"1.0"},"MImix":{"Author":"Russell Steele, Naisyin Wang, and Adrian
Raftery","Description":"Tools to combine results for multiply-imputed data
using\nmixture approximations","License":"GPL-
2","NeedsCompilation":"no","Package":"MImix","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"mitools","Title":"Mixture summary method for multiple
imputation","Version":"1.0"},"MInt":{"Author":"Surojit Biswas, Meredith McDonald,
Derek S. Lundberg, Jeffery L. Dangl,\nVladimir Jojic","Depends":"R (>= 3.1.2),
glasso (>= 1.8), trust (>= 0.1-6), MASS (>=\n7.3-35), testthat (>=
0.9.1)","Description":"Learns direct microbe-microbe interaction networks using a
Poisson\nmultivariate-normal hierarchical model with an L1 penalized
precision\nmatrix. Optimization is carried out using an iterative conditional
modes\nalgorithm.","License":"GPL-
2","NeedsCompilation":"no","Package":"MInt","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"knitr","Title":"Learn Direct Interaction
Networks","Version":"1.0.1"},"MKLE":{"Author":"Thomas Jaki","Description":"Package
for fast computation of the maximum kernel\nlikelihood estimator
(mkle)","License":"GPL","NeedsCompilation":"no","Package":"MKLE","Repository":"http
:\/\/cran.csiro.au\/src\/contrib","Title":"Maximum kernel likelihood
estimation","Version":"0.05"},"MKmisc":{"Author":"Matthias Kohl [aut,
cre]","Depends":"R(>= 2.14.0)","Description":"Contains several functions for
statistical data analysis; e.g. for sample size and power calculations, computation
of confidence intervals, and generation of similarity matrices.","Imports":"stats,
graphics, grDevices, RColorBrewer, robustbase","License":"LGPL-
3","NeedsCompilation":"no","Package":"MKmisc","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"gplots, Amelia","Title":"Miscellaneous Functions from M.
Kohl","URL":"http:\/\/www.stamats.de\/","Version":"0.991"},"MLCIRTwithin":
{"Author":"Francesco Bartolucci, Silvia Bacci - University of Perugia
(IT)","Depends":"R (>= 2.0.0), MASS, limSolve, MultiLCIRT","Description":"Framework
for the Item Response Theory analysis of dichotomous and ordinal polytomous
outcomes under the assumption of within-item multidimensionality and discreteness
of the latent traits. The fitting algorithms allow for missing responses and for
different item parametrizations and are based on the Expectation-Maximization
paradigm. Individual covariates affecting the class weights may be included in the
new version.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MLCIRTwithin","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Latent Class Item Response Theory (LC-IRT) Models
under\nWithin-Item Multidimensionality","Version":"1.1"},"MLCM":{"Author":"Ken
Knoblauch [aut, cre],\nLaurence T. Maloney [aut]","Depends":"R (>= 3.0), graphics,
stats, utils, base","Description":"Conjoint measurement is a psychophysical
procedure in which stimulus pairs are presented that vary along 2 or more
dimensions and the observer is required to compare the stimuli along one of them.
This package contains functions to estimate the contribution of the n scales to the
judgment by a maximum likelihood method under several hypotheses of how the
perceptual dimensions interact.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MLCM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Maximum Likelihood Conjoint
Measurement","Version":"0.4.1"},"MLDS":{"Author":"Kenneth Knoblauch and Laurence T.
Maloney,\nbased in part on C code written by Laurence T. Maloney\nand J. N.
Yang","Depends":"R (>= 3.0), graphics, stats, utils,
base","Description":"Difference scaling is a method for scaling perceived\nsupra-
threshold differences. The package contains functions that\nallow the user to
design and run a difference scaling experiment,\nto fit the resulting data by
maximum likelihood and test the\ninternal validity of the estimated
scale.","Imports":"MASS","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MLDS","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Maximum Likelihood Difference
Scaling","Version":"0.4.5"},"MLEcens":{"Author":"Marloes Maathuis
<maathuis@stat.math.ethz.ch>","Description":"This package contains functions to
compute the\nnonparametric maximum likelihood estimator (MLE) for the\nbivariate
distribution of (X,Y), when realizations of (X,Y)\ncannot be observed directly. To
be more precise, we consider\nthe situation where we observe a set of rectangles
that are\nknown to contain the unobservable realizations of (X,Y). We\ncompute the
MLE based on such a set of rectangles. The methods\ncan also be used for
univariate censored data (see data set\n'cosmesis'), and for censored data with
competing risks (see\ndata set 'menopause'). We also provide functions to
visualize\nthe observed data and the MLE.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"MLEcens","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Computation of the MLE for bivariate (interval) censored
data","URL":"http:\/\/stat.ethz.ch\/~maathuis\/","Version":"0.1-4"},"MLRMPA":
{"Author":"Meihong Xie and Xiaoyun Zhang","Depends":"R(>=
3.0.1),ClustOfVar","Description":"This package provides Multilinear Regression
Model Population\nAnalysis to build a pool of models between quantitative activity
and chemical\ndescriptors. Also some useful model validation functions. Contains
all\nmolecular descriptors of 101 organic compounds and acticity
dataset.","License":"GPL-
2","NeedsCompilation":"no","Package":"MLRMPA","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"A package for Multilinear Regression Model Population
Analysis","Version":"1.0"},"MLmetrics":{"Author":"Yachen Yan [aut,
cre]","Depends":"R
(>= 2.10)","Description":"A collection of evaluation metrics, including loss,
score and utility functions,\nthat measure regression and classification
performance.","License":"GPL-
2","NeedsCompilation":"no","Package":"MLmetrics","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"e1071","Title":"Machine Learning Evaluation
Metrics","URL":"http:\/\/github.com\/yanyachen\/MLmetrics","Version":"1.0.0"},"MM":
{"Author":"Robin K. S. Hankin and P. M. E. Altham","Depends":"R (>= 2.10.0),
methods, magic, partitions, emulator, Oarray\n(>= 1.4-
5)","Description":"Description: Various utilities for the
Multiplicative\nMultinomial distribution","License":"GPL-
2","NeedsCompilation":"no","Package":"MM","Repository":"http:\/\/cran.csiro.au\/src
\/contrib","Title":"The multiplicative multinomial distribution","Version":"1.6-
2"},"MM2S":{"Author":"Deena M.A. Gendoo <deena.gendoo@utoronto.ca>, Benjamin
Haibe-Kains <benjamin.haibe.kains@utoronto.ca>","Depends":"GSVA (>= 1.13.1), kknn
(>= 1.2-5), parallel, lattice,\npheatmap, R (>= 2.10)","Description":"Description:
A single-sample classifier that generates Medulloblastoma (MB) subtype predictions
for single-samples of human MB patients and model systems, including cell lines and
mouse-models. The MM2S algorithm uses a systems-based methodology that facilitates
application of the algorithm on samples irrespective of their platform or source of
origin. MM2S demonstrates > 96% accuracy for patients of well-characterized normal
cerebellum, Wingless (WNT), or Sonic hedgehog (SHH) subtypes, and the less-
characterized Group4 (86%) and Group3 (78.2%). MM2S also enables classification of
MB cell lines and mouse models into their human counterparts.This package contains
function for implementing the classifier onto human data and mouse data, as well as
graphical rendering of the results as PCA plots and heatmaps.","Imports":"datasets,
grDevices, graphics, stats, utils","License":"GPL-
3","NeedsCompilation":"no","Package":"MM2S","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"knitr, MM2Sdata","Title":"Single-Sample Classifier of
Medulloblastoma Subtypes for\nMedulloblastoma Patient Samples, Mouse Models, and
Cell
Lines","URL":"\nhttp:\/\/www.sciencedirect.com\/science\/article\/pii\/S08887543150
00774,\nhttp:\/\/www.pmgenomics.ca\/bhklab\/software\/mm2s","Version":"1.0.5"},"MM2
Sdata":{"Author":"Deena M.A. Gendoo <deena.gendoo@utoronto.ca>, Benjamin Haibe-
Kains <benjamin.haibe.kains@utoronto.ca>","Depends":"R (>= 2.10),
Biobase","Description":"Gene Expression datasets for the 'MM2S' package. Contains
normalized expression data for Human Medulloblastoma ('GSE37418') as well as Mouse
Medulloblastoma models ('GSE36594').","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"MM2Sdata","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr","Title":"Gene Expression Datasets for the
'MM2S'
Package","URL":"http:\/\/www.sciencedirect.com\/science\/article\/pii\/S08887543150
00774","Version":"1.0.1"},"MMMS":{"Author":"Lin Li, Tobias Guennel,Scott Marshall,
Leo Wang-Kit Cheung","Depends":"survival, glmnet","Description":"The package
implements a multi-marker molecular signature (MMMS) approach\nfor treatment-
specific subgroup identification.","License":"GPL-
3","NeedsCompilation":"no","Package":"MMMS","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Multi-Marker Molecular Signature for Treatment-specific
Subgroup\nIdentification","Version":"0.1"},"MMS":
{"Author":"F.Rohart","Depends":"glmnet,Matrix, mht (>= 3.00)","Description":"Fixed
effects Selection in Linear Mixed Models","License":"GPL-
3","NeedsCompilation":"no","Package":"MMS","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Fixed effects Selection in Linear Mixed
Models","Version":"3.00"},"MMWRweek":{"Author":"Jarad Niemi
<niemi@iastate.edu>","Description":"The first day of any MMWR week is Sunday.\nMMWR
week numbering is sequential beginning with 1\nand incrementing with each week to a
maximum of 52\nor 53. MMWR week #1 of an MMWR year is the first week\nof the year
that has at least four days in the calendar\nyear. This package provides
functionality to convert\nDates to MMWR day, week, and year and the
reverse.","License":"GPL (>= 2) | file
LICENSE","NeedsCompilation":"no","Package":"MMWRweek","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat","Title":"Convert Dates to MMWR Day,
Week, and
Year","URL":"http:\/\/wwwn.cdc.gov\/nndss\/document\/MMWR_Week_overview.pdf","Versi
on":"0.1.1"},"MNM":{"Author":"Klaus Nordhausen, Jyrki Mottonen, Hannu
Oja","Depends":"R (>= 2.9.2), ICSNP, SpatialNP","Description":"The package provides
multivariate tests, estimates and methods based on the identity score, spatial sign
score and spatial rank score. The methods include one and c-sample problems, shape
estimation and testing, linear regression and principal
components.","Imports":"ellipse, ICS","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MNM","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"Flury, gamlss, mvtnorm","Title":"Multivariate
Nonparametric Methods. An Approach Based on Spatial\nSigns and
Ranks","Version":"1.0-1"},"MNP":{"Author":"Kosuke Imai <kimai@princeton.edu>, David
A. van Dyk\n<dvd@uci.edu>.","Depends":"R (>= 2.1), MASS, utils","Description":"MNP
is a publicly available R package that fits the\nBayesian multinomial probit model
via Markov chain Monte Carlo.\nThe multinomial probit model is often used to
analyze the\ndiscrete choices made by individuals recorded in survey
data.\nExamples where the multinomial probit model may be useful\ninclude the
analysis of product choice by consumers in market\nresearch and the analysis of
candidate or party choice by\nvoters in electoral studies. The MNP software can
also fit the\nmodel with different choice sets for each individual, and\ncomplete
or partial individual choice orderings of the\navailable alternatives from the
choice set. The estimation is\nbased on the efficient marginal data augmentation
algorithm\nthat is developed by Imai and van Dyk (2005). `À Bayesian\nAnalysis of
the Multinomial Probit Model Using the Data\nAugmentation,'' Journal of
Econometrics, Vol. 124, No. 2\n(February), pp. 311-334. Detailed examples are given
in Imai\nand van Dyk (2005). ``MNP: R Package for Fitting the\nMultinomial Probit
Model.'' Journal of Statistical Software,\nVol. 14, No. 3 (May), pp. 1-
2)","NeedsCompilation":"yes","Package":"MNP","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"R Package for Fitting the Multinomial Probit
Model","URL":"http:\/\/imai.princeton.edu\/software\/MNP.html","Version":"2.6-
4"},"MNS":{"Author":"Ricardo Pio Monti, Christoforos Anagnostopoulos and Giovanni
Montana","Depends":"igraph, MASS, glmnet, mvtnorm, parallel, R (>=
2.10.1)","Description":"An implementation of the mixed neighbourhood selection
(MNS) algorithm. The MNS algorithm can be used to estimate multiple related
precision matrices. In particular, the motivation behind this work was driven by
the need to understand functional connectivity networks across multiple subjects.
This package also contains an implementation of a novel algorithm through which to
simulate multiple related precision matrices which exhibit properties frequently
reported in neuroimaging analysis.","Imports":"doParallel","License":"GPL-
2","NeedsCompilation":"no","Package":"MNS","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Mixed Neighbourhood Selection","Version":"1.0"},"MOCCA":
{"Author":"Johann Kraus <johann.kraus@uni-ulm.de>","Depends":"R (>= 2.0.0), cclust,
clv","Description":"This package provides methods to analyze cluster\nalternatives
based on multi-objective optimization of cluster\nvalidation
indices.","License":"Artistic License
2.0","NeedsCompilation":"no","Package":"MOCCA","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Multi-objective optimization for collecting cluster
alternatives","Version":"1.2"},"MODISTools":{"Author":"Sean Tuck, Helen
Phillips","Description":"Provides several functions for downloading, storing and
processing\nsubsets of MODIS Land Processes data as a batch
process.","Imports":"RCurl, XML","License":"GPL-
3","NeedsCompilation":"no","Package":"MODISTools","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"MODIS Subsetting
Tools","URL":"https:\/\/github.com\/seantuck12\/MODISTools\/","Version":"0.94.6"},"
MOJOV":{"Author":"Ke-Hao
Wu","Depends":"methods,aod,survey,saws,lattice","Description":"A package for
analysis between rare variants and\nquantitative traits by CMC (the combined
multivariate and\ncollapsing method).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MOJOV","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Mojo Variants: Rare Variants
analysis","Version":"1.0.1"},"MOrder":{"Author":"Akshay Chougule
<akshaychougule@email.arizona.edu>, Dr Robert
Canales\n<rcanales@email.arizona.edu>","Description":"MOrder provide functions to
check time homogeneity and order\nof markov chain by using chi-squared test, AIC
value and BIC value.","License":"GPL-
2","NeedsCompilation":"no","Package":"MOrder","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Check Time Homogeneity and Markov Chain
Order","Version":"0.1"},"MPAgenomics":{"Author":"Quentin Grimonprez with
contributions from Guillemette Marot and Samuel\nBlanck. Some functions use code
created by Sjoerd Vosse, Mark van de Wiel,\nPierre Neuvial, Henrik
Bengtsson.","Description":"Preprocess and analysis of genomic data.
MPAgenomics\nprovides wrappers from commonly used packages to streamline their
repeated\nmanipulation, offering an easy-to-use pipeline. The segmentation
of\nsuccessive multiple profiles is performed with an automatic choice
of\nparameters involved in the wrapped packages. Considering multiple profiles\nin
the same time, MPAgenomics
wraps efficient penalized regression methods\nto select relevant markers
associated with a given outcome.","Imports":"R.utils,changepoint(>=
1.1),glmnet,cghseg,HDPenReg(>=\n0.90),spikeslab","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MPAgenomics","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"\nCGHcall,aroma.affymetrix,aroma.cn,aroma.core,aro
ma.light,snowfall,R.devices,R.filesets,R.methodsS3,R.oo,matrixStats","Title":"Multi
-Patient Analysis of Genomic Markers","Version":"1.1.2"},"MPCI":{"Author":"Edgar
Santos-Fernandez, Michele Scagliarini.","Depends":"R (>= 3.1.0), graphics, stats,
utils","Description":"It performs the followings Multivariate Process Capability
Indices: Shahriari et al. (1995) Multivariate Capability Vector, Taam et al. (1993)
Multivariate Capability Index (MCpm), Pan and Lee (2010) proposal (NMCpm) and the
followings based on Principal Component Analysis (PCA):Wang and Chen (1998),
Xekalaki and Perakis (2002) and Wang (2005). Two datasets are
2","NeedsCompilation":"no","Package":"MPCI","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Multivariate Process Capability Indices
(MPCI)","Version":"1.0.7"},"MPDiR":{"Author":"Kenneth Knoblauch and Laurence T.
Maloney","Depends":"R (>= 3.0.0), stats, graphics","Description":"Data sets and
scripts for Modeling Psychophysical Data in R (Springer).","License":"GPL-
2","NeedsCompilation":"no","Package":"MPDiR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"lattice","Title":"Data sets and scripts for Modeling
Psychophysical Data in R","Version":"0.1-16"},"MPINet":{"Author":"Yanjun Xu,
Chunquan Li and Xia Li","Depends":"R (>= 2.15.2),BiasedUrn,mgcv","Description":"(1)
Our system provides a network-based strategies for metabolite pathway
identification.(2) The MPINet can support the identification of pathways using
Hypergeometric test based on metabolite set. (3)MPINet can support pathways from
multiple databases.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MPINet","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"The package can implement the network-based metabolite
pathway\nidentification of pathways","Version":"1.0"},"MPLikelihoodWB":
{"Author":"Mazharul Islam and Hasinur Rahaman Khan","Depends":"survival, MASS, R
(>= 3.0.2)","Description":"Computing modified profile likelihood estimates for
Weibull Shape and Regression Parameters. Modified likelihood estimates are
provided.","License":"GPL-
2","NeedsCompilation":"no","Package":"MPLikelihoodWB","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Modified Profile Likelihood Estimation for Weibull
Shape and\nRegression Parameters","Version":"1.0"},"MPSEM":{"Author":"Guillaume
Guenard, with contribution from Pierre Legendre","Depends":"R (>= 3.0.0), ape,
MASS","Description":"Computational tools to represent phylogenetic signals using
adapted eigenvector maps.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"MPSEM","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr, caper, xtable","Title":"Modeling Phylogenetic
Signals using Eigenvector Maps","Version":"0.3-1"},"MPTinR":{"Author":"Henrik
Singmann [aut, cre],\nDavid Kellen [aut],\nQuentin Gronau [aut],\nChristian Mueller
[ctb],\nAkhil S Bhel [ctb]","Depends":"R (>= 2.15.1)","Description":"Provides a
user-friendly way for the analysis of multinomial processing tree (MPT) models
(e.g., Riefer, D. M., and Batchelder, W. H. [1988]. Multinomial modeling and the
measurement of cognitive processes. Psychological Review, 95, 318-339) for single
and multiple datasets. The main functions perform model fitting and model
selection. Model selection can be done using AIC, BIC, or the Fisher Information
Approximation (FIA) a measure based on the Minimum Description Length (MDL)
framework. The model and restrictions can be specified in external files or within
an R script in an intuitive syntax or using the context-free language for MPTs. The
'classical' .EQN file format for model files is also supported. Besides MPTs, this
package can fit a wide variety of other cognitive models such as SDT models (see
fit.model). It also supports multicore fitting and FIA calculation (using the
snowfall package), can generate or bootstrap data for simulations, and plot
predicted versus observed data.","Imports":"numDeriv, Brobdingnag, Rcpp, stats,
2)","NeedsCompilation":"yes","Package":"MPTinR","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"snowfall (>= 1.84), knitr","Title":"Analyze
Multinomial Processing Tree Models","Version":"1.10.3"},"MPV":{"Author":"W.J.
Braun","Depends":"R (>= 2.0.1)","Description":"Most of this package consists of
data sets from the\ntextbook Introduction\nto Linear Regression Analysis (3rd ed),
by Montgomery et al.\nSome additional data sets and functions useful in
an\nundergraduate regression course are
included.","License":"Unlimited","NeedsCompilation":"no","Package":"MPV","Repositor
y":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Data Sets from Montgomery, Peck
and Vining's Book","Version":"1.38"},"MRCE":{"Author":"Adam J.
Rothman","Depends":"R (>= 2.10.1), QUIC","Description":"Multivariate regression
with covariance estimation","License":"GPL-
2","NeedsCompilation":"yes","Package":"MRCE","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Multivariate regression with covariance
estimation","Version":"2.0"},"MRCV":{"Author":"Natalie Koziol and Chris
Bilder","Depends":"R (>= 3.1.1)","Description":"The MRCV package provides functions
for analyzing the association between\none single response categorical variable
(SRCV) and one multiple response\ncategorical variable (MRCV), or between two or
three MRCVs. A modified Pearson\nchi-square statistic can be used to test for
marginal independence for the one or\ntwo MRCV case, or a more general loglinear
modeling approach can be used to examine\nvarious other structures of association
for the two or three MRCV case. Bootstrap-\nand asymptotic-based standardized
residuals and model-predicted odds ratios are\navailable, in addition to other
descriptive information.","Imports":"tables","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"MRCV","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"geepack","Title":"Methods for Analyzing Multiple Response
Categorical Variables\n(MRCVs)","Version":"0.3-3"},"MRH":{"Author":"Yolanda Hagar,
Yuanting Chen, Vanja Dukic","Depends":"survival, KMsurv","Description":"Used on
survival data to jointly estimate the hazard rate and the effects of covariates on
failure times. Can accommodate covariates under the proportional and non-
proportional hazards setting, and is ideal for analysis of survival data with long-
term follow-up.","Imports":"coda","License":"GPL-
2","NeedsCompilation":"yes","Package":"MRH","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"R.rsp","Title":"Multi-Resolution Estimation of the Hazard
Rate","Version":"2.2"},"MRIaggr":{"Author":"Brice Ozenne","Depends":"R (>= 2.10),
Rcpp","Description":"Provide a compact storage for medical imaging data with access
and display possibilities. Basic tools for processing brain imaging data are
proposed like extraction of brain voxels, morphological image segmentation, and
filtering \/ normalization of contrast parameters. Specific tools are also provided
for blood perfusion imaging to calculate hypoperfusion and reperfusion
volumes.","Imports":"graphics, grDevices, Matrix, methods, oro.dicom,
oro.nifti,\nRANN, ROCR, spam, stats, stats4, utils","License":"GPL-
3","NeedsCompilation":"yes","Package":"MRIaggr","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"coda, fields, mritc, nnet, parallel, pracma, rgl,
snowfall","Title":"Management, Display, and Processing of Medical Imaging
Data","Version":"1.1.5"},"MRMR":{"Author":"Brian A. Fannin","Depends":"reshape2,
ggplot2, lubridate, stats, lmtest, methods, plyr","Description":"Tools to analyze
non-life loss reserves","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MRMR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat","Title":"Multivariate Regression Models for
Reserving","Version":"0.1.3"},"MRQoL":{"Author":"Ahmad Ousmen","Description":"We
can calculate directly used this package the Minimal Clinically Important
Difference by applying the Anchor-based method and the Response shift effect by
applying the Then-Test method.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"MRQoL","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Minimal Clinically Important Difference and Response
Shift\nEffect for Health-Related Quality of Life","Version":"1.0"},"MRS":
{"Author":"Jacopo Soriano and Li Ma","Description":"An implementation of the MRS
algorithm for comparison across distributions.\nThe model is based on a
nonparametric process taking the form of a Markov model\nthat transitions between a
\"null\" and an \"alternative\" state\non a multi-resolution partition tree of the
sample space.\nMRS effectively detects and characterizes a variety of underlying
differences.\nThese differences can be visualized using several plotting
functions.","Imports":"Rcpp (>= 0.11.0), igraph, optimx","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"MRS","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"KernSmooth","Title":"Multi-Resolution Scanning for Cross-
Sample Differences","Version":"1.1"},"MRSP":{"Author":"Wolfgang
Poessnecker","Depends":"methods, parallel, compiler, matrixcalc, Formula, R
(>=\n2.14.1)","Description":"Fits regularized multinomial response models using
penalized loglikelihood methods with structured penalty
terms.","Imports":"base","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"MRSP","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Multinomial Response
Models with Structured Penalties","Version":"0.4.3"},"MRsurv":{"Author":"Y.
Foucher <Yohann.Foucher@univ-nantes.fr>, K. Trebern-Launay
<katygre@yahoo.fr>","Depends":"survival, mvtnorm","Description":"This package
contains functions, data and examples to compute a multiplicative-regression model
for relative survival.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MRsurv","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"A multiplicative-regression model for relative
survival","URL":"www.r-project.org, www.divat.fr","Version":"0.2"},"MRwarping":
{"Author":"L. Slaets, G. Claeskens, B.W. Silverman","Depends":"boa,
SemiPar","Description":"The Bayesian procedure starts with one warplet in the model
and uses the posterior distributions as priors for a more extended model with one
more warplet. The model is built with adding one warplet at a time and allows for
amplitude variations.","License":"GPL-
2","NeedsCompilation":"yes","Package":"MRwarping","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Multiresolution time warping for functional
data","Version":"1.0"},"MSBVAR":{"Author":"Patrick Brandt [aut, cre],\nW. Ryan
Davis [ctb]","Description":"Provides methods for estimating frequentist
and\nBayesian Vector Autoregression (VAR) models and Markov-switching\nBayesian VAR
(MSBVAR). Functions for reduced\nform and structural VAR models are also
available. Includes\nmethods for the generating posterior inferences for these
models,\nforecasts, impulse responses (using likelihood-based error bands),\nand
forecast error decompositions. Also includes utility functions\nfor plotting
forecasts and impulse responses, and generating draws\nfrom Wishart and singular
multivariate normal densities. Current\nversion includes functionality to build
and evaluate models with\nMarkov switching.","Imports":"KernSmooth, xtable, coda,
bit, mvtnorm, lattice","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"MSBVAR","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Markov-Switching, Bayesian, Vector Autoregression
Models","Version":"0.9-2"},"MSG":{"Author":"Yihui Xie","Description":"A companion
to the Chinese book ``Modern Statistical
Graphics''.","Imports":"RColorBrewer","License":"GPL","NeedsCompilation":"no","Pack
age":"MSG","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"animatio
n, KernSmooth, rgl, plotrix, ggplot2 (>= 0.9), sna","Title":"Data and Functions for
the Book Modern Statistical
Graphics","URL":"http:\/\/yihui.name\/cn\/publication","Version":"0.3"},"MSIseq":
{"Author":"Mini Huang","Depends":"IRanges, RWeka, rJava, R.utils, R (>=
3.2.0)","Description":"A decision tree classifier for detecting microsatellite
instability (MSI) in somatic mutation data from whole exome sequencing. MSI is
detected based on different mutation rates in all sites as well as in simple
sequence repeats. This mechanism can also be applied to sequence data of targeted
gene panels with shorter sequence length.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MSIseq","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Assess Tumor Microsatellite Instability with a Decision
Tree\nClassifier from Exome Somatic Mutations","Version":"1.0.0"},"MSQC":
{"Author":"Edgar Santos-Fernandez","Depends":"rgl","Description":"This package is a
toolkit for multivariate process monitoring. It contains the main alternatives of
multivariate control chart such as: Hotelling, Chi squared, MEWMA, MCUSUM and
Generelized Variance control chart. Also, it includes some tools for assessing
multivariate normality like: Mardia, Royston and Henze Zirkler test and the
univariate D'Agostino test. Moreover, it possess ten didactic
datasets.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MSQC","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Multivariate Statistical Quality
Control","Version":"1.0.1"},"MST":{"Author":"Xiaogang Su [aut],\nPeter Calhoun
[aut, cre],\nJuanjuan Fan [aut]","Description":"Constructs trees for multivariate
survival data using marginal and frailty models.","Imports":"graphics, grDevices,
MASS, stats, survival","License":"GPL-
2","NeedsCompilation":"no","Package":"MST","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Multivariate Survival Trees","Version":"1.2"},"MScombine":
{"Author":"Monica Calderon-Santiago","Depends":"R(>= 3.1.3),
plyr","Description":"Find common entities detected in both positive and
negative\nionization mode, delete this entity in the less sensible mode and combine
both\nmatrices.","License":"GPL-
2","NeedsCompilation":"no","Package":"MScombine","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat","Title":"Combine Data from Positive and
Negative Ionization Mode Finding\nCommon Entities","Version":"1.1"},"MSeasy":
{"Author":"Elodie Courtois <courtoiselodie@gmail.com>, Yann
Guitton\n<yann.guitton@gmail.com>, Florence Nicole\n<florence.nicole@univ-st-
etienne.fr>","Depends":"amap, clValid, cluster, fpc, mzR,
xcms","Description":"Package for the detection of molecules in complex mixtures\nof
compounds. It creates an initial_DATA matrix from several\nGC-MS analyses by
collecting and assembling the information\nfrom chromatograms and mass spectra
(MS.DataCreation), It can\nread several format (ASCII, CDF, mzML, mzXML or
mzData).It\ntests for the best unsupervised clustering method to group\nsimilar
mass spectra into molecules (MS.test.clust).It runs the\noptimal unsupervised
clustering method on the initial_DATA\nmatrix, identifies the optimal number of
clusters, produces\ndifferent files for facilitating the quality control
and\nidentification of putative molecules, and returns\nfingerprinting or profiling
matrices (MS.clust).It converts\noutput files from MS.clust for NIST mass spectral
library\nsearch and ARISTO webtool search","License":"GPL-
2","NeedsCompilation":"no","Package":"MSeasy","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"tcltk","Title":"Preprocessing of Gas Chromatography-Mass
Spectrometry (GC-
MS)\ndata","URL":"http:\/\/sites.google.com\/site\/rpackagemseasy\/","Version":"5.3
.3"},"MSeasyTkGUI":{"Author":"Yann Guitton <yann.guitton@gmail.com> Cyrille
Conord\n<conord@emse.fr>","Depends":"R (>= 2.12.0), MSeasy(>= 5.3),
tcltk","Description":"A Tcl\/Tk GUI for some basic functions in the
MSeasy\npackage","License":"GPL-
2","NeedsCompilation":"no","Package":"MSeasyTkGUI","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"xcms","Title":"MSeasy Tcl\/Tk Graphical User
Interface","URL":"http:\/\/sites.google.com\/site\/rpackagemseasy\/","Version":"5.3
.3"},"MSwM":{"Author":"Josep A. Sanchez-Espigares, Alberto Lopez-
Moreno","Depends":"methods, nlme, graphics, parallel","Description":"Univariate
Autoregressive Markov Switching Models for Linear and Generalized
Models","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"MSwM","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Fitting Markov Switching Models","Version":"1.2"},"MTS":
{"Author":"Ruey S. Tsay","Description":"Multivariate Time Series (MTS) is a general
package for analyzing multivariate linear time series and estimating multivariate
volatility models. It also handles factor models, constrained factor models,
asymptotic principal component analysis commonly used in finance and econometrics,
and principal volatility component analysis. (a) For the multivariate linear time
series analysis, the package performs model specification, estimation, model
checking, and prediction for many widely used models, including vector AR models,
vector MA models, vector ARMA models, seasonal vector ARMA models, VAR models with
exogenous variables, multivariate regression models with time series errors,
augmented VAR models, and Error-correction VAR models for co-integrated time
series. For model specification, the package performs structural specification to
overcome the difficulties of identifiability of VARMA models. The methods used for
structural specification include Kronecker indices and Scalar Component Models.
(b) For multivariate volatility modeling, the MTS package handles several commonly
used models, including multivariate exponentially weighted moving-average
volatility, Cholesky decomposition volatility models, dynamic conditional
correlation (DCC) models, copula-based volatility models, and low-dimensional BEKK
models. The package also considers multiple tests for conditional
heteroscedasticity, including rank-based statistics. (c) Finally, the MTS package
also performs forecasting using diffusion index, transfer function analysis,
Bayesian estimation of VAR models, and multivariate time series analysis with
missing values.Users can also use the package to simulate VARMA models, to compute
impulse response functions of a fitted VARMA model, and to calculate theoretical
cross-covariance matrices of a given VARMA model.","Imports":"Rcpp, fGarch,
mvtnorm","License":"Artistic License
2.0","NeedsCompilation":"yes","Package":"MTS","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"All-Purpose Toolkit for Analyzing Multivariate Time Series
(MTS)\nand Estimating Multivariate Volatility Models","Version":"0.33"},"MTurkR":
{"Author":"Thomas J. Leeper [aut, cre],\nSolomon Messing [ctb],\nSean Murphy
[ctb],\nJonathan Chang [ctb]","Description":"Provides programmatic access to the
Amazon Mechanical Turk (MTurk) Requester API.","Imports":"utils, stats, curl,
digest, base64enc, XML","License":"GPL-
2","NeedsCompilation":"no","Package":"MTurkR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat","Title":"R Client for the MTurk Requester
API","URL":"https:\/\/github.com\/leeper\/MTurkR","Version":"0.7.0"},"MTurkRGUI":
{"Author":"Thomas J. Leeper [aut, cre]","Description":"A graphical user interface
(GUI) for the MTurkR package.","Imports":"MTurkR, tcltk, grDevices, utils, XML,
curl","License":"GPL-
2","NeedsCompilation":"no","Package":"MTurkRGUI","Repository":"http:\/\/cran.csiro.
au\/s
rc\/contrib","Title":"A Graphical User Interface for
MTurkR","URL":"https:\/\/github.com\/leeper\/MTurkRGUI","Version":"0.1.5"},"MUCflig
hts":{"Author":"The students of the Àdvanced R Programming Course' Basil Abou\nEl-
Komboz, Andreas Bender, Abdelilah El Hadad, Laura Goeres,\nRoman Hornung, Max
Hughes-Brandl, Christian Lindenlaub,\nChristina Riedel, Ariane Straub, Florian
Wickler under the\nsupervision of Manuel Eugster and Torsten
Hothorn","Depends":"XML, geosphere (>= 1.2-15), sp, RSQLite,
NightDay","Description":"Functions for downloading flight data
from\nhttp:\/\/www.munich-airport.de and for analyzing flight
patterns.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MUCflights","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Munich Franz-Josef-Strauss Airport Pattern
Analysis","URL":"http:\/\/www.youtube.com\/watch?v=y3RW_N-TPb4","Version":"0.0-
3"},"MVA":{"Author":"Brian S. Everitt and Torsten
Hothorn","Depends":"HSAUR2","Description":"Functions, data sets, analyses and
examples from the book\nÀn Introduction to Applied Multivariate Analysis with
R'\n(Brian S. Everitt and Torsten Hothorn, Springer, 2011).","License":"GPL-
2","NeedsCompilation":"no","Package":"MVA","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"mvtnorm, mclust, lattice, flexclust, nlme, RLRsim,
multcomp,\nape, MASS, sem, KernSmooth, scatterplot3d","Title":"An Introduction to
Applied Multivariate Analysis with R","URL":"http:\/\/dx.doi.org\/10.1007\/978-1-
4419-9650-3","Version":"1.0-6"},"MVB":{"Author":"Bin Dai","Depends":"Rcpp (>=
0.9.9), RcppArmadillo (>= 0.2.34)","Description":"Fit log-linear model for
multivariate Bernoulli\ndistribution with mixed effect models and
LASSO","License":"GPL (>=
2.0)","NeedsCompilation":"yes","Package":"MVB","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Mutivariate Bernoulli log-linear
model","Version":"1.1"},"MVN":{"Author":"Selcuk Korkmaz [aut, cre], Dincer Goksuluk
[aut], Gokmen Zararsiz [aut]","Depends":"R (>= 2.15.0)","Description":"Performs
multivariate normality tests and graphical approaches and implements multivariate
outlier detection and univariate normality of marginal distributions through plots
and tests.","Imports":"methods, nortest, moments, MASS, robustbase, mvoutlier,
plyr,\npsych","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MVN","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"knitr","Title":"Multivariate Normality
Tests","URL":"http:\/\/www.biosoft.hacettepe.edu.tr\/MVN\/","Version":"4.0"},"MVR":
{"Author":"Jean-Eudes Dazard [aut, cre], Hua Xu [ctb], Alberto Santana
[ctb]","Depends":"R (>= 3.0.2), parallel, statmod","Description":"This is a non-
parametric method for joint adaptive mean-variance regularization and variance
stabilization of high-dimensional data. It is suited for handling difficult
problems posed by high-dimensional multivariate datasets (p >> n paradigm). Among
those are that the variance is often a function of the mean, variable-specific
estimators of variances are not reliable, and tests statistics have low powers due
to a lack of degrees of freedom. Key features include:\n(i) Normalization and\/or
variance stabilization of the data,\n(ii) Computation of mean-variance-regularized
t-statistics (F-statistics to follow),\n(iii) Generation of diverse diagnostic
plots,\n(iv) Computationally efficient implementation using C\/C++ interfacing and
an option for parallel computing to enjoy a faster and easier experience in the R
environment.","Imports":"graphics, grDevices, methods, stats","License":"GPL (>= 3)
| file
LICENSE","NeedsCompilation":"yes","Package":"MVR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Mean-Variance
Regularization","URL":"https:\/\/github.com\/jedazard\/MVR","Version":"1.30.3"},"MV
T":{"Author":"Felipe Osorio","Description":"Routines to perform estimation and
inference under the multivariate t-distribution.\nCurrently, the following
methodologies are implemented: multivariate mean and covariance\nestimation,
hypothesis testing about the mean, equicorrelation and homogeneity of
variances,\nthe Wilson-Hilferty transformation, QQ-plots with envelopes and random
variate\ngeneration. Some auxiliary functions are also provided.","Imports":"stats,
utils, graphics","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"MVT","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"heavy","Title":"Estimation and Testing for the
Multivariate t-
Distribution","URL":"http:\/\/www.ies.ucv.cl\/mvt\/","Version":"0.3"},"MVar.pt":
{"Author":"Paulo Cesar Ossani <ossanipc@hotmail.com>\nMarcelo Angelo Cirillo
<macufla@dex.ufla.br>","Description":"Pacote para analise multivariada, que possui
funcoes que executam analise de correspondencia simples (CA) e multipla (MCA),
analise de componentes principais (PCA), analise de multiplos fatores (MFA) para
dados quantitativos, qualitativos, de frequencia (MFACT) e dados mistos. Tambem
possui outras funcoes uteis para a analise multivariada.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MVar.pt","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Analise multivariada (brazilian
portuguese)","Version":"1.6"},"MXM":{"Author":"Ioannis Tsamardinos, Vincenzo
Lagani, Giorgos Athineou, Michail Tsagris, Giorgos
Borboudakis","Description":"Feature selection methods for identifying minimal,
statistically-equivalent and equally-predictive feature subsets.\nThe package name
'MXM' stands for \"Mens eX Machina\", meaning \"Mind from the Machine\" in
Latin.","Imports":"methods, stats, utils, survival, MASS, TunePareto, ROCR,\nHmisc,
graphics, ordinal, nnet, betareg, quantreg, pscl, lme4,\nforeach, doParallel,
parallel, speedglm","License":"GPL-
2","NeedsCompilation":"yes","Package":"MXM","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"gRbase, Biobase, hash, Rgraphviz","Title":"Discovering
Multiple, Statistically-Equivalent
Signatures","URL":"http:\/\/mensxmachina.org","Version":"0.8"},"MaXact":
{"Author":"Jianan Tian <jiant17@gmail.com>, Chenliang
Xu\n<lucky.random@gmail.com>","Depends":"R (>= 2.2.0),
mnormt","Description":"Perform exact MAX3 or MAX2 test for one-locus
genetic\nassociation analysis and trend test for dominant, recessive and\nadditive
models. It can also calculate approximated p-value\nwith the normal approximation
2","NeedsCompilation":"yes","Package":"MaXact","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Exact max-type Cochran-Armitage trend
test(CATT)","Version":"0.2.1"},"Maeswrap":{"Author":"Remko
Duursma","Depends":"rgl,lattice,geometry,stringr,tools","Description":"A bundle of
functions for modifying MAESTRA\/MAESPA input files,reading output files, and
visualizing the stand in 3D. Handy for running sensitivity analyses, scenario
analyses,
etc.","License":"GPL","NeedsCompilation":"no","Package":"Maeswrap","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"Wrapper Functions for
MAESTRA\/MAESPA","Version":"1.7"},"MakefileR":{"Author":"Kirill MÃ¼ller [aut,
cre]","Description":"A user-friendly interface for the construction
of\n'Makefiles'.","Imports":"magrittr","License":"GPL-
3","NeedsCompilation":"no","Package":"MakefileR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat, knitr, rmarkdown","Title":"Create
'Makefiles' Using
R","URL":"http:\/\/krlmlr.github.io\/MakefileR","Version":"1.0"},"ManlyMix":
{"Author":"Xuwen Zhu [aut, cre],\nVolodymyr Melnykov [aut],\nMichael Hutt [ctb,
cph] (NM optimization in c),\nStephen Moshier [ctb, cph] (eigen calculations in
c),\nRouben Rostamian [ctb, cph] (memory allocation in c)","Depends":"R (>=
3.0.0)","Description":"The utility of this package includes finite mixture modeling
and model-based clustering through Manly mixture models. It also provides
capabilities for forward and backward model selection procedures.","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"ManlyMix","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Manly Mixture Modeling and Model-Based
Clustering","Version":"0.1.2"},"ManyTests":{"Author":"Christiana
Kartsonaki","Description":"Performs the multiple testing procedures of Cox (2011)
and Wang and Cox (2007).","License":"GPL-
2","NeedsCompilation":"no","Package":"ManyTests","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Multiple testing procedures of Cox (2011) and Wang and
Cox\n(2007)","Version":"1.1"},"Map2NCBI":{"Author":"Lauren L. Hulsman Hanna and
David G. Riley","Depends":"R (>= 2.15.3)","Description":"Allows the user to
generate a list of features (gene, pseudo, RNA,\nCDS, and\/or UTR) directly from
NCBI database for any species with a current\nbuild available. Option to save
downloaded and formatted files is available,\nand the user can prioritize the
feature list based on type and assembly builds\npresent in the current build used.
The user can then use the list of features\ngenerated or provide a list to map a
set of markers (designed for SNP markers\nwith a single base pair position
available) to the closest feature based on\nthe map build. This function does
require map positions of the markers to be\nprovided and the positions should be
based on the build being queried through\nNCBI.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Map2NCBI","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Mapping Markers to the Nearest Genomic
Feature","Version":"1.1"},"MapGAM":{"Author":"Veronica Vieira, Scott Bartell, and
Robin Bliss","Depends":"R (>= 2.10.0), sp, gam","Description":"Contains functions
for mapping odds ratios or other effect estimates using individual-level data such
as case-control study data, using generalized additive models (GAMs) for smoothing
with a two-dimensional predictor (e.g., geolocation or exposure to chemical
mixtures) while adjusting for confounding variables, using methods described
by Kelsall and Diggle (1998) and Webster at al. (2006). Includes convenient
functions for mapping, efficient control sampling, and permutation tests for the
null hypothesis that the two-dimensional predictor is not associated with the
outcome variable (adjusting for confounders).","Imports":"maptools","License":"GPL-
3","NeedsCompilation":"no","Package":"MapGAM","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"maps, mapproj, PBSmapping","Title":"Mapping Smoothed
Effect Estimates from Individual-Level Data","Version":"0.7-5"},"MareyMap":
{"Author":"Aurelie Siberchicot, Clement Rezvoy, Delphine Charif, Laurent Gueguen
and Gabriel Marais","Depends":"R (>= 2.10)","Description":"Local recombination
rates are graphically estimated across a genome using marey
maps.","Imports":"graphics, grDevices, methods, stats, tcltk, tkrplot,
tools,\nutils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MareyMap","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Estimation of Meiotic Recombination Rates Using Marey
Maps","URL":"http:\/\/pbil.univ-
lyon1.fr\/software\/mareymap","Version":"1.3.1"},"MarkowitzR":{"Author":"Steven E.
Pav [aut, cre]","Depends":"R (>= 3.0.2)","Description":"a collection of tools for
analyzing significance of\nMarkowitz portfolios.","Imports":"matrixcalc, sandwich,
gtools","License":"LGPL-
3","NeedsCompilation":"no","Package":"MarkowitzR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"SharpeR, testthat, knitr","Title":"Statistical
Significance of the Markowitz
Portfolio","URL":"https:\/\/github.com\/shabbychef\/MarkowitzR","Version":"0.1502"}
,"MasterBayes":{"Author":"Jarrod Hadfield","Depends":"coda, genetics, gtools,
kinship2","Description":"The primary aim of MasterBayes is to use MCMC techniques
to integrate over uncertainty in pedigree configurations estimated from molecular
markers and phenotypic data. Emphasis is put on the marginal distribution of
parameters that relate the phenotypic data to the pedigree. All simulation is done
in compiled C++ for efficiency.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"MasterBayes","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"ML and MCMC Methods for Pedigree Reconstruction and
Analysis","Version":"2.52"},"MatchIt":{"Author":"Daniel Ho <daniel.e.ho@gmail.com>,
Kosuke Imai\n<kimai@Princeton.Edu>, Gary King <king@harvard.edu>, Elizabeth\nStuart
<stuart@stat.harvard.edu>","Depends":"R (>= 2.6), MASS","Description":"MatchIt
selects matched samples of the the original\ntreated and control groups with
similar covariate distributions\n-- can be used to match exactly on covariates, to
match on\npropensity scores, or perform a variety of other
matching\nprocedures.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MatchIt","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"cem, optmatch, Matching, nnet, rpart, mgcv,
WhatIf","Title":"MatchIt: Nonparametric Preprocessing for Parametric
Casual\nInference","URL":"http:\/\/gking.harvard.edu\/matchit","Version":"2.4-
21"},"MatchLinReg":{"Author":"Alireza S. Mahani, Mansour T.A.
Sharabiani","Depends":"R (>= 3.1.0)","Description":"Core functions as well as
diagnostic and calibration tools for combining matching and linear regression for
causal inference in observational studies.","Imports":"Hmisc, Matching, graphics,
2)","NeedsCompilation":"no","Package":"MatchLinReg","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Combining Matching and Linear Regression for Causal
Inference","Version":"0.7.0"},"Matching":{"Author":"Jasjeet Singh Sekhon
<sekhon@berkeley.edu>","Depends":"R (>= 2.6.0), MASS (>= 7.2-1), graphics,
grDevices, stats","Description":"Provides functions for multivariate and propensity
score matching\nand for finding optimal balance based on a genetic search
algorithm.\nA variety of univariate and multivariate metrics to\ndetermine if
balance has been obtained are also provided.","License":"GPL-
3","NeedsCompilation":"yes","Package":"Matching","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"parallel, rgenoud (>= 2.12),
rbounds","Title":"Multivariate and Propensity Score Matching with
Balance\nOptimization","URL":"http:\/\/sekhon.berkeley.edu\/matching","Version":"4.
9-2"},"MatchingFrontier":{"Author":"Gary King, Christopher Lucas, and Richard
Nielsen","Description":"Returns the subset of the data with the minimum imbalance
for\nevery possible subset size (N - 1, N - 2, ...), down to the data set with
the\nminimum possible imbalance. Also includes tools for the estimation\nof causal
effects for each subset size, functions for visualization\nand data export, and
functions for calculating\nmodel dependence as proposed by Athey and
Imbens.","Imports":"MASS, igraph, segmented","License":"GPL-
3","NeedsCompilation":"no","Package":"MatchingFrontier","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"stargazer","Title":"Computation of the Balance
- Sample Size Frontier in Matching\nMethods for Causal
Inference","URL":"http:\/\/projects.iq.harvard.edu\/frontier","Version":"1.0.0"},"M
atrix":{"Author":"Douglas Bates <bates@stat.wisc.edu> and Martin
Maechler","Depends":"R (>= 3.0.1)","Description":"Classes and methods for dense and
sparse matrices and\noperations on them using 'LAPACK' and
'SuiteSparse'.","Enhances":"MatrixModels, graph, SparseM,
sfsmisc","Imports":"methods, graphics, grid, stats, utils, lattice","License":"GPL
(>= 2) | file
LICENCE","NeedsCompilation":"yes","Package":"Matrix","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"expm, MASS","Title":"Sparse and Dense Matrix
Classes and Methods","URL":"http:\/\/Matrix.R-forge.R-
project.org\/","Version":"1.2-4"},"Matrix.utils":{"Author":"Craig Varrichio
<canthony427@gmail.com>","Depends":"R (>= 3.0.0), Matrix","Description":"Implements
data manipulation methods such as cast, aggregate, and merge\/join for Matrix and
matrix-like objects.","Imports":"grr, methods, stats","License":"GPL-
3","NeedsCompilation":"no","Package":"Matrix.utils","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"reshape2, data.table, dplyr","Title":"Data.frame-
Like Operations on Sparse and Dense Matrix
Objects","Version":"0.9.0"},"MatrixCorrelation":{"Author":"Kristian Hovde Liland
[aut, cre],\nTormod Næs [ctb],\nUlf Geir Indahl [ctb]","Depends":"R (>=
3.0.1)","Description":"Computation and visualization of matrix correlation
coefficients.\nThe main method is the Similarity of Matrices Index, while various
related\nmeasures like r1, r2, r3, r4, Yanai's GCD, RV, RV2 and adjusted RV are
included\nfor comparison.","Imports":"Rcpp, plotrix, pracma, progress,
rARPACK","License":"GPL-
2","NeedsCompilation":"yes","Package":"MatrixCorrelation","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Matrix Correlation
Coefficients","Version":"0.8.0"},"MatrixEQTL":{"Author":"Andrey
Shabalin","Depends":"R (>= 2.12.0), methods","Description":"Matrix eQTL is designed
for fast eQTL analysis on large datasets.\nMatrix eQTL can test for association
between genotype and gene expression using linear regression\nwith either additive
or ANOVA genotype effects.\nThe models can include covariates to account for
factors\nas population stratification, gender, and clinical variables.\nIt also
supports models with heteroscedastic and\/or correlated errors,\nfalse discovery
rate estimation and separate treatment of local (cis) and distant (trans)
eQTLs.","License":"LGPL-
3","NeedsCompilation":"no","Package":"MatrixEQTL","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Matrix eQTL: Ultra fast eQTL analysis via large
matrix\noperations","URL":"http:\/\/www.bios.unc.edu\/research\/genomic_software\/M
atrix_eQTL\/","Version":"2.1.1"},"MatrixModels":{"Author":"Douglas Bates
<bates@stat.wisc.edu> and Martin Maechler
<maechler@stat.math.ethz.ch>","Depends":"R (>= 3.0.1)","Description":"Modelling
with sparse and dense 'Matrix' matrices, using\nmodular prediction and response
module classes.","Imports":"stats, methods, Matrix (>= 1.1-5)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MatrixModels","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Modelling with Sparse And Dense
Matrices","URL":"http:\/\/Matrix.R-forge.R-project.org\/","Version":"0.4-
1"},"MaxPro":{"Author":"Shan Ba and V. Roshan
Joseph","Depends":"nloptr","Description":"Generate a maximum projection (MaxPro)
design, a MaxPro Latin hypercube design or improve an initial design based on the
MaxPro criterion. Details of the MaxPro criterion can be found in: Joseph, V. R.,
Gul, E., and Ba, S. (2015) \"Maximum Projection Designs for Computer Experiments\",
Biometrika.","License":"LGPL-
2.1","NeedsCompilation":"yes","Package":"MaxPro","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Maximum Projection Designs","Version":"3.1-
2"},"MaxentVariableSelection":{"Author":"Alexander Jueterbock","Depends":"R (>=
3.1.2)","Description":"Complex niche models show low performance in
identifying\nthe most important range-limiting environmental variables and
in\ntransferring habitat suitability to novel environmental conditions\n(Warren and
Seifert, 2011; Warren et al., 2014). This package helps to\nidentify the most
important set of uncorrelated variables and to\nfine-tune Maxent's regularization
multiplier. In combination, this\nallows to constrain complexity and increase
performance of Maxent niche\nmodels (assessed by information criteria, such as AICc
(Akaike, 1974) ,\nand by the area under the receiver operating characteristic
(AUC)\n(Fielding and Bell, 1997). Users of this package should be familiar
with\nMaxent niche modelling.","Imports":"ggplot2, raster","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MaxentVariableSelection","Repository":"http:
\/\/cran.csiro.au\/src\/contrib","Suggests":"knitr, rmarkdown","Title":"Selecting
the Best
Set of Relevant Environmental Variables along\nwith the Optimal Regularization
Multiplier for Maxent Niche\nModeling","Version":"1.0-2"},"MazamaSpatialUtils":
{"Author":"Jonathan Callahan [aut, cre],\nWill Leahy [aut],\nHenry Nguyen
[aut],\nRobin Winstanley [aut],\nRuby Fore [aut]","Depends":"R (>=
3.1.0)","Description":"A suite of conversion scripts to create internally
standardized\nspatial polygons dataframes. Utility scripts use these datasets to
return\nvalues such as country, state, timezone, watershed, etc. associated with
a\nset of longitude\/latitude pairs. (They also make cool maps.)","Imports":"dplyr,
rgdal, rgeos, rvest, sp, stringr, utils","License":"GPL-
2","NeedsCompilation":"no","Package":"MazamaSpatialUtils","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"knitr, maps, testthat","Title":"Mazama
Science Spatial Data Download and Utility
Functions","Version":"0.4.3"},"McSpatial":{"Author":"Daniel
McMillen","Depends":"lattice, locfit, maptools, quantreg, RANN,
SparseM","Description":"Locally weighted regression, semiparametric
and\nconditionally parametric regression, fourier and cubic spline\nfunctions, GMM
and linearized spatial logit and probit,\nk-density functions and counterfactuals,
nonparametric quantile\nregression and conditional density functions, Machado-
Mata\ndecomposition for quantile regressions, spatial AR model,\nrepeat sales
models, conditionally parametric logit and
probit","License":"GPL","NeedsCompilation":"no","Package":"McSpatial","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"car, classInt, mlogit,
RColorBrewer, spatstat, spdep","Title":"Nonparametric spatial data
analysis","Version":"2.0"},"Mcomp":{"Author":"Rob J Hyndman with assistance from
Muhammad Akram and Christoph\nBergmeir.","Depends":"R (>= 2.10), graphics, stats,
tseries, forecast","Description":"The 1001 time series from the M-competition
(Makridakis et\nal. 1982) and the 3003 time series from the IJF-M3
competition\n(Makridakis and Hibon, 2000).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Mcomp","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Data from the M-
competitions","URL":"http:\/\/robjhyndman.com\/software\/mcomp\/","Version":"2.05"}
,"MeanShift":{"Author":"Mattia Ciollaro and Daren
Wang","Depends":"parallel","Description":"Clustering using the mean shift algorithm
(multi-core processing is supported) or its blurring version.","License":"GPL-
3","NeedsCompilation":"no","Package":"MeanShift","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Clustering via the Mean Shift Algorithm","Version":"1.0-
2"},"MedOr":{"Author":"Adriano Polpo <polpo@ufscar.br>, Carlos Alberto de
Braganca\nPereira <cpereira@ime.usp.br>","Depends":"R (>=
2.15.0)","Description":"This package contains the functions used to perform
some\nconfidence statistics based in population median.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"MedOr","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Median Ordering Statistical R
package","URL":"http:\/\/code.google.com\/p\/medor\/","Version":"0.1"},"MediaK":
{"Author":"Zizhuo Ren, Hesen Peng, Tianwei Yu","Description":"Calculates MeDiA_K
(means Mean Distance Association by K-nearest neighbor) in order to detect
nonlinear associations.","Imports":"Rcpp (>=
0.11.3)","License":"GPL","NeedsCompilation":"yes","Package":"MediaK","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Title":"Calculate MeDiA_K
Distance","Version":"1.0"},"Mediana":{"Author":"Gautier Paux, Alex
Dmitrienko.","Description":"Provides a general framework for clinical trial
simulations based\non the Clinical Scenario Evaluation (CSE) approach. The package
supports a\nbroad class of data models (including clinical trials with continuous,
binary,\nsurvival-type and count-type endpoints as well as multivariate outcomes
that are\nbased on combinations of different endpoints), analysis strategies and
commonly\nused evaluation criteria.","Imports":"doParallel, doRNG, foreach, MASS,
mvtnorm, ReporteRs, stats,\nsurvival, utils","License":"GPL-
2","NeedsCompilation":"no","Package":"Mediana","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Clinical Trial
Simulations","URL":"http:\/\/gpaux.github.io\/Mediana\/","Version":"1.0.2"},"MenuCo
llection":{"Author":"Gianmarco Polotti","Depends":"R (>= 3.0.0), RGtk2,
RGtk2Extras","Description":"Set of configurable menus built with GTK+ to
graphically interface new functions.","Imports":"gplots, grDevices,
2","NeedsCompilation":"no","Package":"MenuCollection","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Collection of Configurable GTK+
Menus","Version":"1.2"},"MergeGUI":{"Author":"Xiaoyue Cheng, Dianne Cook, Heike
Hofmann","Depends":"gWidgetsRGtk2, ggplot2","Description":"A GUI for merging
datasets in R using gWidgets.","Imports":"cairoDevice, rpart","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"MergeGUI","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"A GUI for Merging Datasets in R","Version":"0.2-
1"},"MetABEL":{"Author":"Maksim Struchalin, Yurii Aulchenko","Depends":"R (>=
2.5.1)","Description":"A package for meta-analysis of genome-wide
association\nscans between quantitative or binary traits and SNPs","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"MetABEL","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"GenABEL","Title":"Meta-analysis of genome-wide SNP
association results","Version":"0.2-0"},"MetFns":{"Author":"Kristina
Veljkovic","Depends":"astroFns, fBasics, lubridate, plotrix, spatial, R (>=
3.2.3)","Description":"Functions for selection of visual meteor data, calculations
of Zenithal Hourly Rate (ZHR) and population index, graphics of population index,
ZHR and magnitude distribution.","Imports":"graphics, stats, utils","License":"GPL-
2 | GPL-
3","NeedsCompilation":"no","Package":"MetFns","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Analysis of Visual Meteor Data","Version":"2.0"},"MetNorm":
{"Author":"Alysha M De Livera","Description":"Metabolomics data are inevitably
subject to a component of unwanted variation, due to factors such as batch effects,
matrix effects, and confounding biological variation. This package contains a
collection of R functions which can be used to remove unwanted variation and obtain
normalized metabolomics data.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"MetNorm","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Statistical Methods for Normalizing Metabolomics
Data","Version":"0.1"},"MetSizeR":{"Author":"Gift Nyamundanda, Isobel Claire
Gormley, Yue Fan, William M Gallagher, Lorraine
Brennan","Depends":"mvtnorm,MetabolAnalyze,cairoDevice, gWidgets,
gWidgetsRGtk2","Description":"An easy to use Graphical User Interface for
estimating sample sizes required for metabolomic experiments even when experimental
pilot data is not available.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MetSizeR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"GUI Tool for Estimating Sample Sizes for Metabolomic
Experiments","Version":"1.1"},"MetStaT":{"Author":"Tim Dorscheidt","Depends":"MASS,
abind, pls","Description":"A diverse collection of metabolomics related statistical
tools.","License":"Apache License (==
2.0)","NeedsCompilation":"no","Package":"MetStaT","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Statistical metabolomics
tools","Version":"1.0"},"MetaCycle":{"Author":"Gang Wu [aut, cre],\nRon Anafi [aut,
ctb],\nJohn Hogenesch [aut, ctb],\nMichael Hughes [aut, ctb],\nKarl Kornacker [aut,
ctb]","Depends":"R (>= 3.0.2)","Description":"Provides two functions-meta2d and
meta3d for detecting\nrhythmic signals from time-series datasets. For
analyzing\ntime-series datasets without individual information, 'meta2d'
is\nsuggested, which could incorporates multiple methods from ARSER,\nJTK_CYCLE and
Lomb-Scargle in the detection of interested rhythms. For\nanalyzing time-series
datasets with individual information, 'meta3d' is\nsuggested, which takes use of
any one of these three methods to analyze\ntime-series data individual by
individual and gives out integrated values\nbased on analysis result of each
individual.","Imports":"gnm","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MetaCycle","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr, rmarkdown, diagram, shape","Title":"Evaluate
Periodicity in Large Scale Data","Version":"1.1.0"},"MetaDE":{"Author":"Xingbin
Wang, Jia Li and George C Tseng","Depends":"survival,
impute,Biobase,combinat,tools","Description":"MetaDE package implements 12 major
meta-analysis methods\nfor differential expression analysis.","License":"GPL-
2","NeedsCompilation":"no","Package":"MetaDE","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"MetaDE: Microarray meta-analysis for differentially
expressed\ngene detection","Version":"1.0.5"},"MetaLandSim":{"Author":"Frederico
Mestre, Fernando Canovas, Ricardo Pita, Antonio Mira, Pedro\nBeja.","Depends":"R
(>= 2.10), tcltk","Description":"Tools to generate random landscape graphs,
evaluate species\noccurrence in dynamic landscapes, simulate future landscape
occupation and\nevaluate range expansion when new empty patches are available (e.g.
as a\nresult of climate change).","Imports":"Biobase, e1071, fgui, grDevices,
graphics, googleVis,\nmaptools, rgeos, rgrass7, raster, spatstat, stats,
sp,\nminpack.lm","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MetaLandSim","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"rasterVis","Title":"Landscape and Range Expansion
Simulation","Version":"0.5"},"MetaPCA":{"Author":"Don Kang <donkang75@gmail.com>
and George Tseng\n<ctseng@pitt.edu>","Depends":"R (>= 2.10.0),
foreach","Description":"MetaPCA implements simultaneous dimension reduction
using\nPCA
when multiple studies are combined. We propose two basic\nideas to find a common
PC subspace by eigenvalue maximization\napproach and angle minimization approach,
and we extend the\nconcept to incorporate Robust PCA and Sparse PCA in the\nmeta-
analysis realm.","License":"GPL-
2","NeedsCompilation":"no","Package":"MetaPCA","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"MASS, GEOquery, pcaPP, affy, hgu133plus2.db, doMC,
doSMP,\nellipse, impute","Title":"MetaPCA: Meta-analysis in the Dimension Reduction
of
Genomic\ndata","URL":"https:\/\/github.com\/donkang75\/MetaPCA","Version":"0.1.4"},
"MetaPath":{"Author":"Kui Shen and Geroge Tseng","Depends":"R (>=
3.0.0),Biobase,GSEABase,genefilter,impute","Description":"Perform the Meta-analysis
for Pathway Enrichment (MAPE)\nmethods introduced by Shen and Tseng (2010). It
includes functions to\nautomatically perform MAPE_G (integrating multiple studies
at\ngene level), MAPE_P (integrating multiple studies at pathway\nlevel) and MAPE_I
(a hybrid method integrating MAEP_G and\nMAPE_P methods). In the simulation and
real data analyses in\nthe paper, MAPE_G and MAPE_P have complementary advantages
and\ndetection power depending on the data structure. In general,\nthe integrative
form of MAPE_I is recommended to use. In the\ncase that MAPE_G (or MAPE_P) detects
almost none pathway, the\nintegrative MAPE_I does not improve performance and
MAPE_P (or\nMAPE_G) should be used. Reference: Shen, Kui, and George C\nTseng.
Meta-analysis for pathway enrichment analysis when\ncombining multiple microarray
studies.Bioinformatics (Oxford,\nEngland) 26, no. 10 (April 2010): 1316-
1323.\ndoi:10.1093\/bioinformatics\/btq148.\nhttp:\/\/www.ncbi.nlm.nih.gov\/pubmed\
/20410053.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"MetaPath","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Perform the Meta-Analysis for Pathway Enrichment
Analysis (MAPE)","Version":"1.0"},"MetaQC":{"Author":"Don Kang
<donkang75@gmail.com> and George Tseng\n<ctseng@pitt.edu>","Depends":"R (>=
2.10.0), proto, foreach, iterators","Description":"MetaQC implements our proposed
quantitative quality\ncontrol measures: (1) internal homogeneity of co-
expression\nstructure among studies (internal quality control; IQC); (2)\nexternal
consistency of co-expression structure correlating\nwith pathway database (external
quality control; EQC); (3)\naccuracy of differentially expressed gene detection
(accuracy\nquality control; AQCg) or pathway identification (AQCp);
(4)\nconsistency of differential expression ranking in genes\n(consistency quality
control; CQCg) or pathways (CQCp). (See\nthe reference for detailed explanation.)
For each quality\ncontrol index, the p-values from statistical hypothesis
testing\nare minus log transformed and PCA biplots were applied to\nassist
visualization and decision. Results generate systematic\nsuggestions to exclude
problematic studies in microarray\nmeta-analysis and potentially can be extended to
GWAS or other\ntypes of genomic meta-analysis. The identified problematic\nstudies
can be scrutinized to identify technical and biological\ncauses (e.g. sample size,
platform, tissue collection,\npreprocessing etc) of their bad quality or
irreproducibility\nfor final inclusion\/exclusion decision.","License":"GPL-
2","NeedsCompilation":"no","Package":"MetaQC","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"doMC, doSNOW, FactoMineR, matrixStats, gdata,
gtools,\nsurvival","Title":"MetaQC: Objective Quality Control and
Inclusion\/Exclusion\nCriteria for Genomic Meta-
Analysis","URL":"https:\/\/github.com\/donkang75\/MetaQC","Version":"0.1.13"},"Meta
SKAT":{"Author":"Seunggeun (Shawn) Lee","Depends":"R (>=
2.13.0)","Description":"Functions for Meta-analysis Burden test, SKAT and SKAT-O.
These methods use summary-level score statistics to carry out gene-based meta-
analysis for rare variants.","Imports":"SKAT","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"MetaSKAT","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Meta Analysis for SNP-Set (Sequence) Kernel Association
Test","Version":"0.60"},"MetabolAnalyze":{"Author":"Nyamundanda Gift, Isobel Claire
Gormley and Lorraine Brennan.","Depends":"mclust, mvtnorm, ellipse, gtools,
gplots","Description":"Fits probabilistic principal components
analysis,\nprobabilistic principal components and covariates analysis and\nmixtures
of probabilistic principal components models to\nmetabolomic spectral
data.","License":"GPL-
2","NeedsCompilation":"no","Package":"MetabolAnalyze","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Probabilistic latent variable models for
metabolomic data","Version":"1.3"},"Metatron":{"Author":"Huiling
Huang","Depends":"R (>= 2.15.0), lme4, mpt, Matrix","Description":"This package
allows doing meta-analysis for primary studies with classification outcomes in
order to evaluate systematically the accuracies of classifiers, namely, the
diagnostic tests. It provides functions to fit the bivariate model of Reitsma et
al.(2005). Moreover, if the reference employed in the classification process isn't
a gold standard, its deficit can be detected and its influence to the
underestimation of the diagnostic test's accuracy can be corrected, as described in
Botella et al.(2013).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Metatron","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Meta-analysis for Classification Data and Correction
to\nImperfect Reference","Version":"0.1-1"},"Meth27QC":{"Author":"Ling Teng, Chao
Chen, Chunyu Liu","Depends":"gplots,tcltk","Description":"Meth27QC is a tool for
analyzing Illumina Infinium\nHumanMethylation27 BeadChip Data and generating QC
reports.\nThis package allows users quickly assess data quality of the\nAssay.
Users can evaluate the data quality in the way that\nIllumina
GenomeStudio\/BeadStudio recommended based on the\ncontrol probes. The package
reads files exported from\nGenomeStudio\/BeadStudio software, generating intensity
and\nstandard deviation plots grouped by the types of the control\nprobes. Meth27
carries 40 control probes for staining,\nhybridization, target removal, extension,
bisulfite conversion,\nspecificity, negative and non-polymorphic controls. Details
of\nthose control probes can be found in the Infinium Assay for\nMethylation
Protocol Guide from Illumina.We also used the other\nnon-control probes to plot
intensity of detected genes, signal\naverage for green and red. Outliers can be
identified.","License":"GPL-
2","NeedsCompilation":"no","Package":"Meth27QC","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Meth27QC: sample quality analysis, and sample control
analysis","Version":"1.1"},"MethComp":{"Author":"Bendix Carstensen, Lyle Gurrin,
Claus Ekstrom, Michal Figurski","Depends":"R (>= 3.0.0),
nlme","Description":"Methods (standard and advanced) for analysis of
agreement\nbetween measurement methods.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MethComp","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"R2WinBUGS, BRugs, rjags, coda, lattice,
lme4","Title":"Functions for Analysis of Agreement in Method Comparison
Studies","URL":"http:\/\/BendixCarstensen.com\/MethComp\/","Version":"1.22.2"},"Met
hplot":{"Author":"Xin Yang","Description":"It plots the output from Methpup
(https:\/\/github.com\/XinYang6699\/Methpup)","Imports":"ggplot2, grid,
reshape","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Methplot","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Visualize the methylation
patterns","Version":"1.0"},"MethylCapSig":{"Author":"Deepak N. Ayyala, David E.
Frankhouser, Javkhlan-Ochir Ganbat, Guido Marcucci, Ralf Bundschuh, Pearlly Yan and
Shili Lin.","Depends":"R (>= 3.0.0)","Description":"Provides a univariate and
several high dimensional multivariate test statistics for detecting differentially
methylated regions based on MethylCap-seq
data.","Imports":"geepack","License":"LGPL-
3","NeedsCompilation":"no","Package":"MethylCapSig","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Detection of Differentially Methylated Regions
using\nMethylCap-Seq Data","Version":"1.0.1"},"Metrics":{"Author":"Ben Hamner
<ben@benhamner.com>","Description":"Metrics is a set of evaluation metrics that is
commonly\nused in supervised machine
learning.","License":"BSD","NeedsCompilation":"no","Package":"Metrics","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Title":"Evaluation metrics for machine
learning","URL":"https:\/\/github.com\/benhamner\/Metrics\/tree\/master\/R","Versio
n":"0.1.1"},"MfUSampler":{"Author":"Alireza S. Mahani, Mansour T.A.
Sharabiani","Description":"Convenience functions for multivariate MCMC using
univariate samplers including:\nslice sampler with stepout and shrinkage (Neal,
2003),\nadaptive rejection sampler (Gilks and Wild, 1992),\nadaptive rejection
Metropolis (Gilks et al 1995), and\nunivariate Metropolis with Gaussian
proposal.","Imports":"ars, HI, coda","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MfUSampler","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"sns, RcppArmadillo, inline,
mvtnorm","Title":"Multivariate-from-Univariate (MfU) MCMC
Sampler","Version":"1.0.0"},"MiRSEA":{"Author":"Junwei Han, Siyao Liu","Depends":"R
(>= 2.15.1)","Description":"The tools for 'MicroRNA Set Enrichment Analysis' can
identify risk pathways(or prior gene sets) regulated by microRNA set in the context
of microRNA expression data. (1) This package constructs a correlation profile of
microRNA and pathways by the hypergeometric statistic test. The gene sets of
pathways derived from the three public databases (Kyoto Encyclopedia of Genes and
Genomes ('KEGG'); 'Reactome'; 'Biocarta') and the target gene sets of microRNA are
provided by four databases('TarBaseV6.0'; 'mir2Disease'; 'miRecords';
'miRTarBase';).
(2) This package can quantify the change of correlation between microRNA for each
pathway(or prior gene set) based on a microRNA expression data with cases and
controls. (3) This package uses the weighted Kolmogorov-Smirnov statistic to
calculate an enrichment score (ES) of a microRNA set that co-regulate to a
pathway , which reflects the degree to which a given pathway is associated with the
specific phenotype. (4) This package can provide the visualization of the
2)","NeedsCompilation":"no","Package":"MiRSEA","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"stats,graphics,grDevices","Title":"'MicroRNA' Set
Enrichment Analysis","Version":"1.1"},"MiSPU":{"Author":"Chong Wu, Wei
Pan","Depends":"R (>= 3.2.3), vegan, ape, aSPU,cluster","Description":"There is an
increasing interest in investigating how the compositions of microbial communities
are associated with human health and disease. In this package, we present a novel
global testing method called aMiSPU, that is highly adaptive and thus high powered
across various scenarios, alleviating the issue with the choice of a phylogenetic
distance. Our simulations and real data analysis demonstrated that aMiSPU test was
often more powerful than several competing methods while correctly controlling type
I error rates.","Imports":"Rcpp (>= 0.12.1)","License":"GPL-
2","NeedsCompilation":"yes","Package":"MiSPU","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"ade4","Title":"Microbiome Based Sum of Powered Score
(MiSPU) Tests","Version":"1.0"},"MiST":{"Author":"Jianping Sun, Yingye Zheng, and
Li Hsu","Depends":"CompQuadForm","Description":"Test for association between a set
of SNPS\/genes and\ncontinuous or binary outcomes by including
variant\ncharacteristic information and using (weighted)
score\nstatistics.","License":"LGPL (>=
2.0)","NeedsCompilation":"no","Package":"MiST","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Mixed effects Score Test for continuous
outcomes","Version":"1.0"},"MicSim":{"Author":"Sabine Zinn","Depends":"R (>=
3.0.1), chron, snowfall, rlecuyer","Description":"This entry-level toolkit allows
performing continuous-time microsimulation for a wide range of demographic
applications. Individual life-courses are specified by a continuous-time multi-
state model.","License":"GPL-
2","NeedsCompilation":"no","Package":"MicSim","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Performing Continuous-Time
Microsimulation","Version":"1.0.11"},"MicroDatosEs":{"Author":"Carlos J. Gil
Bellosta [aut, cre],\nCarlos Neira [ctb],\nDiego Paniagua SÃ¡nchez [ctb],\nJosÃ©
Luis CaÃ±adas Reche [ctb]","Depends":"memisc, Hmisc","Description":"The
MicroDatosEs package provides utilities for reading and processing microdata from
Spanish official statistics with R.","License":"GPL-
3","NeedsCompilation":"no","Package":"MicroDatosEs","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Utilities for Official Spanish
Microdata","URL":"\nhttp:\/\/www.datanalytics.com\/2012\/08\/06\/un-paseo-por-el-
paquete-microdatoses-y-la-epa-de-nuevo\/","Version":"0.7.1"},"MicroStrategyR":
{"Author":"Rick Pechter <rpechter@microstrategy.com>","Depends":"R (>= 3.0.0),
gWidgetsRGtk2","Description":"Deploys your R Analytic to
MicroStrategy","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"MicroStrategyR","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"MicroStrategyR
Package","URL":"http:\/\/RIntegrationPack.codeplex.com","Version":"1.0-
1"},"MigClim":{"Author":"Robin Engler <robin.engler@gmail.com> and\nWim Hordijk
<wim@WorldWideWanderings.net> and\nLoic Pellissier
<loic.pellissier@unil.ch>","Depends":"SDMTools, raster","Description":"Functions
for implementing species dispersal into projections\nof species distribution models
(e.g. under climate change
scenarios).","License":"GPL","NeedsCompilation":"yes","Package":"MigClim","Reposito
ry":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Implementing dispersal into
species distribution models","Version":"1.6"},"MindOnStats":{"Author":"A. Jonathan
R. Godfrey [aut, cre]","Depends":"R (>= 2.14.0)","Description":"66 data sets that
were imported using read.table() where appropriate but more commonly after
converting to a csv file for importing via
read.csv().","License":"GPL","NeedsCompilation":"no","Package":"MindOnStats","Repos
itory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Data sets included in Utts
and Heckard's Mind on Statistics","Version":"0.11"},"Miney":{"Author":"Roland
Rau","Description":"This package implements the core idea of games known
as\n'Minesweeper' on Microsoft Windows or 'KMines' for KDE on\nUnix-like operating
systems.","License":"GPL-
2","NeedsCompilation":"no","Package":"Miney","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Implementation of the Well-Known Game to Clear Bombs from
a\nGiven Field (Matrix)","Version":"0.1"},"MissMech":{"Author":"Mortaza Jamshidian,
Siavash Jalal, and Camden Jansen","Description":"To test whether the missing data
mechanism, in a set of incompletely observed data, is one of missing completely at
random (MCAR).\nFor detailed description see Jamshidian, M. Jalal, S., and Jansen,
C. (2014). \"MissMech: An R Package for Testing Homoscedasticity, Multivariate
Normality, and Missing Completely at Random (MCAR),\" Journal of Statistical
Software, 56(6), 1-31. URL
http:\/\/www.jstatsoft.org\/v56\/i06\/.","Imports":"graphics","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MissMech","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Testing Homoscedasticity, Multivariate Normality, and
Missing\nCompletely at Random","Version":"1.0.2"},"MissingDataGUI":
{"Author":"Xiaoyue Cheng, Dianne Cook, Heike Hofmann","Depends":"gWidgetsRGtk2,
ggplot2","Description":"Provides numeric and graphical\nsummaries for the missing
values from both categorical\nand quantitative variables. A variety of
imputation\nmethods are applied, including the univariate imputations\nlike fixed
or random values, multivariate imputations\nlike the nearest neighbors and multiple
imputations,\nand imputations conditioned on a categorical
variable.","Imports":"GGally, cairoDevice (>= 2.23), grid, reshape","License":"GPL
(>=
2.0)","NeedsCompilation":"no","Package":"MissingDataGUI","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"Hmisc, norm, mice, mi (>= 1.0)","Title":"A
GUI for Missing Data Exploration","Version":"0.2-4"},"MitISEM":{"Author":"N.
Basturk, L.F. Hoogerheide, A. Opschoor, H.K. van
Dijk","Depends":"mvtnorm","Description":"Flexible multivariate function
approximation using adapted\nMixture of Student t Distributions. Mixture of t
distribution\nis obtained using Importance Sampling weighted
Expectation\nMaximization algorithm.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"MitISEM","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"AdMit","Title":"Mixture of Student t Distributions
using Importance Sampling and\nExpectation
Maximization","URL":"http:\/\/people.few.eur.nl\/basturk\/","Version":"1.0"},"MixAl
l":{"Author":"Serge Iovleff [aut, cre]","Depends":"R (>= 3.0.2), rtkpp (>=
0.9.2),","Description":"Algorithms and methods for estimating parametric mixture
models with missing data.","Imports":"methods","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"MixAll","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Clustering using Mixture
Models","Version":"1.1.1"},"MixGHD":{"Author":"Cristina Tortora, Ryan P. Browne,
Brian C. Franczak, and Paul D. McNicholas.","Depends":"MASS, R (>=
3.1.3)","Description":"Carries out model-based clustering, classification and
discriminant analysis using five different models. The models are all based on the
generalized hyperbolic distribution.The first model 'MGHD' is the classical mixture
of generalized hyperbolic distributions. The 'MGHFA' is the mixture of generalized
hyperbolic factor analyzers for high dimensional data sets. The 'MSGHD', mixture of
multiple scaled generalized hyperbolic distributions. The 'cMSGHD' is a 'MSGHD'
with convex contour plots. The 'MCGHD', mixture of coalesced generalized
hyperbolic distributions is a new more flexible model.","Imports":"Bessel,stats,
mvtnorm, ghyp, numDeriv, mixture, e1071,cluster","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MixGHD","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Model Based Clustering, Classification and Discriminant
Analysis\nUsing the Mixture of Generalized Hyperbolic
Distributions","Version":"1.8"},"MixMAP":{"Author":"Gregory J.
Matthews","Depends":"R (>= 2.15.1)","Description":"A collection of functions to
implement the MixMAP algorithm, which performs gene\nlevel tests of association
using data from a previous GWAS or data from a\nmeta-analysis of several GWAS.
Conceptually, genes are detected as\nsignificant if the collection of p-values
within a gene are determined to\nbe collectively smaller than would be observed by
chance.","Imports":"methods, graphics, stats, utils, lme4","License":"GPL-
3","NeedsCompilation":"no","Package":"MixMAP","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Implements the MixMAP
Algorithm","Version":"1.3.4"},"MixRF":{"Author":"Jiebiao Wang and Lin S.
Chen","Depends":"doParallel, randomForest, lme4, foreach","Description":"It offers
random-forest-based functions to impute clustered\nincomplete data. The package is
tailored for but not limited to imputing\nmultitissue expression data, in which a
gene's expression is measured on the\ncollected tissues of an individual but
missing on the uncollected
tissues.","License":"GPL","NeedsCompilation":"no","Package":"MixRF","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Title":"A Random-Forest-Based Approach for
Imputing Clustered
Incomplete\nData","URL":"https:\/\/github.com\/randel\/MixRF","Version":"1.0"},"Mix
Sim":{"Author":"Volodymyr
Melnykov [aut],\nWei-Chen Chen [aut, cre],\nRanjan Maitra [aut],\nRobert Davies
[ctb] (quadratic form probabilities),\nStephen Moshier [ctb] (eigenvalue
calculations),\nRouben Rostamian [ctb] (memory allocation)","Depends":"R (>=
3.0.0), MASS","Description":"The utility of this package is in simulating mixtures
of Gaussian\ndistributions with different levels of overlap between
mixture\ncomponents. Pairwise overlap, defined as a sum of two\nmisclassification
probabilities, measures the degree of\ninteraction between components and can be
readily employed to\ncontrol the clustering complexity of datasets simulated
from\nmixtures. These datasets can then be used for systematic\nperformance
investigation of clustering and finite mixture\nmodeling algorithms. Among other
capabilities of 'MixSim', there\nare computing the exact overlap for Gaussian
mixtures,\nsimulating Gaussian and non-Gaussian data, simulating outliers\nand
noise variables, calculating various measures of agreement\nbetween two
partitionings, and constructing parallel\ndistribution plots for the graphical
display of finite mixture\nmodels.","Enhances":"mclust, cluster","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"MixSim","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Simulating Data to Study Performance of Clustering
Algorithms","Version":"1.1-2"},"MixedDataImpute":{"Author":"Jared S.
Murray","Depends":"gdata, Rcpp (>= 0.11), R (>= 3.1.0)","Description":"Missing data
imputation for continuous and categorical data, using nonparametric Bayesian joint
models (specifically the hierarchically coupled mixture model with local dependence
described in Murray and Reiter (2015); see 'citation(\"MixedDataImpute\")' or
http:\/\/arxiv.org\/abs\/1410.0438). See '?hcmm_impute' for example
usage.","Imports":"methods","License":"GPL-
3","NeedsCompilation":"yes","Package":"MixedDataImpute","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Missing Data Imputation for Continuous and
Categorical Data\nusing Nonparametric Bayesian Joint
Models","Version":"0.1"},"MixedPoisson":{"Author":"Alicja Wolny-Dominiak and Michal
Trzesiok","Depends":"gaussquad, MASS","Description":"The estimation of the
parameters in Mixed Poisson models.","License":"GPL-
2","NeedsCompilation":"no","Package":"MixedPoisson","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Mixed Poisson Models","Version":"1.0"},"MixedTS":
{"Author":"Lorenzo Mercuri, Edit Rroji","Depends":"methods, stats, graphics,
stats4, MASS","Description":"We provide detailed functions for univariate Mixed
Tempered Stable distribution.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MixedTS","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Mixed Tempered Stable
Distribution","Version":"1.0.4"},"MixtureInf":{"Author":"Shaoting Li, Jiahua Chen
and Pengfei Li.","Description":"Functions for computing the penalized maximum
likelihood estimate (PMLE) or maximum likelihood estimate (MLE), testing the order
of a finite mixture model using EM-test, drawing histogram of observations and the
fitted density or probability mass function of the mixture
model.","Imports":"quadprog","License":"AGPL (>=
3)","NeedsCompilation":"no","Package":"MixtureInf","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Inference for Finite Mixture
project.org\/package=MixtureInf","Version":"1.1"},"MoTBFs":{"Author":"Inmaculada
PÃ©rez-BernabÃ©, Antonio SalmerÃ³n","Depends":"R (>=
3.2.0)","Description":"Learning, manipulation and evaluation of mixtures of
truncated basis functions\n(MoTBFs), which include mixtures of polynomials
(MOPs) and mixtures of truncated\nexponentials (MTEs). MoTBFs are a flexible
framework for modelling hybrid Bayesian\nnetworks. The package provides
functionality for learning univariate, multivariate and\nconditional densities,
with the possibility of incorporating prior knowledge. Structural\nlearning of
hybrid Bayesian networks is also provided. A set of useful tools is
provided,\nincluding plotting, printing and likelihood evaluation. This package
makes use of S3\nobjects, with two new classes called 'motbf' and
'jointmotbf'.","Imports":"quadprog, lpSolve, bnlearn, methods","License":"LGPL-
3","NeedsCompilation":"yes","Package":"MoTBFs","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"mnormt","Title":"Learning Hybrid Bayesian Networks
using Mixtures of Truncated\nBasis Functions","Version":"1.0"},"Mobilize":
{"Author":"Jeroen Ooms","Depends":"R (>= 2.14), stats, methods,
Ohmage","Description":"Some canned plots and functions designed for the mobilize
project.\nDesigned to be called remotely.","Imports":"ggplot2, wordcloud,
reshape2","License":"GPL","NeedsCompilation":"no","Package":"Mobilize","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"XML, maps","Title":"Mobilize
plots and functions","Version":"2.16-4"},"Modalclust":{"Author":"Surajit Ray and
Yansong Cheng","Depends":"R (>= 2.14.0), mvtnorm, zoo,
class","Description":"Performs Modal Clustering (MAC) including Hierarchical Modal
Clustering (HMAC) along with their parallel implementation (PHMAC) over several
processors. These model-based non-parametric clustering techniques can extract
clusters in very high dimensions with arbitrary density shapes. By default
clustering is performed over several resolutions and the results are summarised as
a hierarchical tree. Associated plot functions are also provided. There is a
package vignette that provides many examples. This version adheres to CRAN policy
of not spanning more than two child processes by default.","License":"GPL-
2","NeedsCompilation":"no","Package":"Modalclust","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"parallel, MASS","Title":"Hierarchical Modal
Clustering","Version":"0.6"},"ModelGood":{"Author":"Thomas A.
Gerds","Description":"Bootstrap cross-validation for ROC, AUC and Brier score to
assess\nand compare predictions of binary status responses.","Imports":"prodlim,
2)","NeedsCompilation":"yes","Package":"ModelGood","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"party, rpart, glmnet, rms, randomForest,
randomForestSRC","Title":"Validation of risk prediction
models","Version":"1.0.9"},"ModelMap":{"Author":"Elizabeth Freeman, Tracey
Frescino","Depends":"R (>= 2.13.0), randomForest, raster,
rgdal","Description":"Creates sophisticated models of training data and validates
the models with an independent test set, cross validation, or in the case of Random
Forest Models, with Out Of Bag (OOB) predictions on the training data. Create
graphs and tables of the model validation results. Applies these models to GIS .img
files of predictors to create detailed prediction surfaces. Handles large predictor
files for map making, by reading in the .img files in chunks, and output to the
.txt file the prediction for each data chunk, before reading the next chunk of
data.","Imports":"\ngraphics,grDevices,stats,utils,mgcv,corrplot,fields,HandTill200
1,PresenceAbsence","License":"Unlimited","NeedsCompilation":"no","Package":"ModelMa
p","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"party,
quantregForest, gbm","Title":"Modeling and Map Production using Random Forest and
Stochastic\nGradient Boosting","Version":"3.3.2"},"Momocs":{"Author":"Vincent
Bonhomme [aut, cre],\nJulien Claude [aut]","Depends":"R(>= 3.2)","Description":"A
complete toolkit for morphometrics, from data extraction to multivariate
analyses.\nMost common 2D morphometrics approaches are included:\noutlines, open
outlines, configurations of landmarks, traditional morphometrics,\nand facilities
for data preparation, manipulation and visualization\nwith a consistent grammar
throughout.\nMomocs allows reproducible, complex morphometric analyses,\npaves the
way for a pure open-source workflow in R,\nand other morphometrics approaches
should be easy to plug in,\nor develop from, on top of this
canvas.","Imports":"ape, dplyr, magrittr, graphics, geometry, geomorph,
ggplot2,\njpeg, MASS, plyr, reshape2, sp, utils","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"Momocs","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"devtools, knitr, rmarkdown, testthat,
covr","Title":"Morphometrics using
R","URL":"https:\/\/github.com\/vbonhomme\/Momocs\/","Version":"1.0.0"},"Mondrian":
{"Author":"AurÃ©lie Siberchicot, Delphine Charif, Gabriel Terraz and Fabrice
Vavre","Description":"The unique function of this package allows representing in a
single graph the relative occurrence and co-occurrence of events measured in a
sample.\nAs examples, the package was applied to describe the occurrence and co-
occurrence of different species of bacterial or viral symbionts infecting
arthropods at the individual level. The graphics allows determining the prevalence
of each symbiont and the patterns of multiple infections (i.e. how different
symbionts share or not the same individual hosts).\nWe named the package after the
famous painter as the graphical output recalls Mondrianâ€™s
paintings.","Imports":"RColorBrewer","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"Mondrian","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"A Simple Graphical Representation of the Relative
Occurrence and\nCo-Occurrence of
Events","URL":"https:\/\/github.com\/aursiber\/Mondrian","Version":"1.0-
0"},"MonetDB.R":{"Author":"Hannes Muehleisen [aut, cre], Anthony Damico [aut],
Thomas Lumley [ctb]","Description":"Allows to pull data from MonetDB into R.
Includes a DBI implementation and a dplyr backend.","Enhances":"dplyr (>= 0.3.0),
MonetDBLite","Imports":"DBI (>= 0.3.1), digest (>= 0.6.4), methods,
codetools","License":"MPL (==
2.0)","NeedsCompilation":"yes","Package":"MonetDB.R","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Connect MonetDB
to R","URL":"http:\/\/www.monetdb.org","Version":"1.0.1"},"MonetDBLite":
{"Author":"Hannes Muehleisen [aut, cre], MonetDB Development Team
[ctb]","Description":"An in-process version of MonetDB, a relational database
focused on analytical tasks. Similar to SQLite, the database runs entirely inside
the R shell, with the main difference that queries complete much faster thanks to
MonetDB's columnar architecture.","License":"MPL (==
1.1)","NeedsCompilation":"yes","Package":"MonetDBLite","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"In-Process Version of MonetDB for
R","URL":"http:\/\/www.monetdb.org","Version":"0.2.0"},"MonoPhy":{"Author":"Orlando
Schwery","Depends":"ape, phytools, phangorn, RColorBrewer,
taxize","Description":"Requires rooted resolved phylogeny as input and creates a
table of genera, their monophyly-status, which taxa cause problems in monophyly
etc. Different information can be extracted from the output and a plot function
allows visualization of the results in a number of ways.","License":"GPL-
3","NeedsCompilation":"no","Package":"MonoPhy","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr, testthat, spacodiR, rmarkdown","Title":"Allows
to Explore Monophyly (or Lack of it) of Taxonomic Groups\nin a
Phylogeny","Version":"1.1"},"MonoPoly":{"Author":"Berwin A. Turlach [aut,
cre],\nKevin Murray [ctb]","Depends":"R (>= 3.1.0),
quadprog","Description":"Functions for fitting monotone polynomials to
2)","NeedsCompilation":"yes","Package":"MonoPoly","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Functions to Fit Monotone Polynomials","Version":"0.3-
8"},"Morpho":{"Author":"Stefan Schlager [aut, cre, cph],\nGregory Jefferis
[ctb]","Depends":"R (>= 3.0.2)","Description":"A toolset for Geometric
Morphometrics and mesh processing. This\nincludes (among other stuff) mesh
deformations based on reference points,\npermutation tests, detection of outliers,
processing of sliding\nsemi-landmarks and semi-automated surface landmark
placement.","Imports":"Rvcg (>= 0.7), rgl (>= 0.93.963), foreach (>= 1.4.0),
Matrix\n(>= 1.0-1), parallel, yaImpute, doParallel (>= 1.0.6),\ncolorRamps, Rcpp,
graphics, grDevices, methods, stats, utils","License":"GPL-
2","NeedsCompilation":"yes","Package":"Morpho","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"car, lattice, MASS, shapes,
testthat","Title":"Calculations and Visualisations Related to
Geometric\nMorphometrics","URL":"https:\/\/github.com\/zarquon42b\/Morpho","Version
":"2.3.1.1"},"MorseGen":{"Author":"Brendan Morse","Description":"MorseGen is a
program for generating raw data based on\nuser-specified summary (descriptive)
statistics. Samples based\non the supplied statistics are drawn from a normal
distribution\n(or, in some cases, an exponential distribution) and scaled to\nmatch
the desired descriptive statistics. Intended uses include\ncreating raw data that
fits desired characteristics or to\nreplicate the results in a published
study.","License":"GPL-
2","NeedsCompilation":"no","Package":"MorseGen","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Simple raw data generator based on user-specified
summary\nstatistics","Version":"1.2"},"MortalitySmooth":{"Author":"Carlo G
Camarda","Depends":"R (>= 3.0.2), svcm, lattice","Description":"Smoothing one- and
two-dimensional Poisson counts with\nP-splines specifically tailored to mortality
data.\nExtra-Poisson variation can be accounted as well as forecasting.\nCollection
of mortality data and a specific function for\nselecting those data by country,
sex, age and years.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MortalitySmooth","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"knitr","Title":"Smoothing and Forecasting
Poisson Counts with P-Splines","Version":"2.3.4"},"MotilityLab":
{"Author":"Katharina Dannenberg, Jeffrey Berry, Johannes Textor","Depends":"R (>=
3.0.0)","Description":"Statistics to quantify tracks of moving things (x-y-z-t
data),\nsuch as cells, bacteria or animals. Available measures include mean
square\ndisplacement, confinement ratio, autocorrelation, straightness, turning
angle,\nand fractal dimension.","Imports":"stats, grDevices, graphics, utils,
ellipse","License":"GPL-
2","NeedsCompilation":"no","Package":"MotilityLab","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"pracma, scatterplot3d, fractaldim,
testthat","Title":"Quantitative Analysis of
Motion","URL":"http:\/\/www.motilitylab.net","Version":"0.2-4"},"MplusAutomation":
{"Author":"Michael Hallquist [aut, cre],\nJoshua Wiley [aut]","Depends":"R (>=
2.15.0), methods","Description":"The MplusAutomation package leverages the
flexibility of the R\nlanguage to automate latent variable model estimation and
interpretation\nusing Mplus, a powerful latent variable modeling program developed
by\nMuthen and Muthen (www.statmodel.com). Specifically, MplusAutomation\nprovides
routines for creating related groups of models, running batches of\nmodels, and
extracting and tabulating model parameters and fit statistics.","Imports":"boot,
plyr, gsubfn, coda, xtable, lattice, texreg","License":"LGPL-
3","NeedsCompilation":"no","Package":"MplusAutomation","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"rhdf5, tcltk, relimp,
testthat","Title":"Automating Mplus Model Estimation and
Interpretation","URL":"https:\/\/github.com\/michaelhallquist\/MplusAutomation","Ve
rsion":"0.6-3"},"Mposterior":{"Author":"Sanvesh Srivastava
<sanvesh@gmail.com>","Depends":"R (>= 3.0.2), Rcpp (>=
0.11.0)","Description":"Mposterior package provides a general framework for
estimating a\nmedian of subset posterior measures (M-posterior). Each subset
posterior measure\nis represented as a matrix of posterior samples; rows represent
the atoms and\ncolumns index the dimensions. All subset measures are represented as
list of\nmatrices; length of the list equals the number of subsets (or machines).
The\ndistance between subset posterior measures and M-posterior is measured using
the RBF kernel.\nM-posterior is represented as a weighted combination of empirical
measures based on\nsubsets measures. These weights are estimated using Weiszfeld
algorithm implemented\nin this package.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"Mposterior","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Mposterior: R package for Robust and Scalable Bayes
via a Median\nof Subset Posterior
Measures","URL":"http:\/\/www.stat.duke.edu\/~ss602\/Mposterior\/Mposterior.html","
Version":"0.1.2"},"MuFiCokriging":{"Author":"Loic Le
Gratiet","Depends":"DiceKriging, methods","Description":"This package builds multi-
fidelity cokriging models from\nresponses with different levels of fidelity.
Important\nfunctions : MuFicokm, predict.MuFicokm,
summary.MuFicokm.","License":"GPL-
3","NeedsCompilation":"no","Package":"MuFiCokriging","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"rgenoud","Title":"Multi-Fidelity Cokriging
models","URL":"http:\/\/www.redice-project.org","Version":"1.2"},"MuMIn":
{"Author":"Kamil BartoÅ„","Depends":"R (>= 3.0.0)","Description":"Model selection
and model averaging based on information criteria\n(AICc and
alike).","Enhances":"aod, aods3, betareg, caper, coxme, cplm, gee,
glmmML,\nlogistf, MCMCglmm, ordinal, pscl, spdep, splm, unmarked, geeM\n(>=
0.7.5)","Imports":"graphics, methods, Matrix, stats, stats4","License":"GPL-
2","NeedsCompilation":"no","Package":"MuMIn","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"lme4 (>= 1.1.0), nlme, mgcv (>= 1.7.5), gamm4, MASS,
nnet,\nsurvival, geepack","Title":"Multi-Model
Inference","Version":"1.15.6"},"MuViCP":{"Author":"Mohit Dayal","Depends":"R (>=
2.10)","Description":"An ensemble classifier for multiclass classification. This is
a novel classifier that natively works as an ensemble. It projects data on a large
number of matrices, and uses very simple classifiers on each of these projections.
The results are then combined, ideally via Dempster-Shafer
Calculus.","Imports":"sm, MASS, gtools, parallel","License":"GPL-
3","NeedsCompilation":"no","Package":"MuViCP","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"MultiClass Visualizable Classification using Combination
of\nProjections","Version":"1.3.2"},"MultAlloc":{"Author":"Jose Brito, Pedro Silva,
Nelson Maculan and Gustavo Semaan","Description":"Integer Programming Formulations
Applied to Univariate and Multivariate Allocation
Problems.","Imports":"Rglpk","License":"GPL-
2","NeedsCompilation":"no","Package":"MultAlloc","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Optimal Allocation in Stratified
Sampling","Version":"1.2"},"MultEq":{"Author":"Mario Hasler","Depends":"R (>=
2.10.0)","Description":"Equivalence tests and related confidence intervals for
the\ncomparison of two treatments, simultaneously for one or many\nnormally
distributed, primary response variables (endpoints).\nThe step-up procedure of Quan
et al. (2001) is both applied for\ndifferences and extended to ratios of means. A
related\nsingle-step procedure is also
available.","License":"GPL","NeedsCompilation":"no","Package":"MultEq","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"SimComp","Title":"Multiple
Equivalence Tests and Simultaneous Confidence
Intervals","Version":"2.3"},"MultNonParam":{"Author":"John E. Kolassa & Stephane
Jankowski","Description":"A collection of multivariate nonparametric methods,
selected in part to support an MS level course in nonparametric statistical
methods. Methods include adjustments for multiple comparisons, implementation of
multivariate Mann-Whitney-Wilcoxon testing, inversion of these tests to produce a
confidence region, some permutation tests for linear models, and some algorithms
for calculating exact probabilities associated with one- and two- stage testing
involving
Mann-Whitney-Wilcoxon statistics.","License":"GPL-
2","NeedsCompilation":"yes","Package":"MultNonParam","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Multivariate Nonparametric
Methods","Version":"1.2.1"},"MultiCNVDetect":{"Author":"Hao Lin, Qiang
Kou","Description":"This package provides a tool for analysis of multiple
CNV.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"MultiCNVDetect","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Multiple Copy Number Variation
Detection","Version":"0.1-1"},"MultiGHQuad":{"Author":"Karel Kroeze","Depends":"R
(>= 3.2.2)","Description":"Uses a transformed, rotated and optionally adapted n-
dimensional grid of quadrature\npoints to calculate the numerical integral of n
multivariate normal\ndistributed parameters.","Imports":"fastGHQuad (>=
3","NeedsCompilation":"no","Package":"MultiGHQuad","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat","Title":"Multidimensional Gauss-Hermite
Quadrature","Version":"1.0"},"MultiLCIRT":{"Author":"Francesco Bartolucci, Silvia
Bacci, Michela Gnaldi - University of Perugia (IT)","Depends":"R (>= 2.0.0), MASS,
limSolve","Description":"Framework for the Item Response Theory analysis of
dichotomous and ordinal polytomous outcomes under the assumption of
multidimensionality and discreteness of the latent traits. The fitting algorithms
allow for missing responses and for different item parameterizations and are based
on the Expectation-Maximization paradigm. Individual covariates affecting the class
weights may be included in the new version (since 2.1).","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"MultiLCIRT","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Multidimensional Latent Class Item Response Theory
Models","Version":"2.9"},"MultiMeta":{"Author":"Dragana
Vuckovic","Depends":"gtable,grid","Description":"Allows running a meta-analysis of
multivariate Genome Wide\nAssociation Studies (GWAS) and easily visualizing results
through custom\nplotting functions. The multivariate setting implies that results
for each\nsingle nucleotide polymorphism (SNP) include several effect sizes
(also\nknown as \"beta coefficients\", one for each trait), as well as
related\nvariance values, but also covariance between the betas. The main goal
of\nthe package is to provide combined beta coefficients across different\ncohorts,
together with the combined variance\/covariance matrix. The method\nis inverse-
variance based, thus each beta is weighted by the inverse of its\nvariance-
covariance matrix, before taking the average across all betas. The\ndefault options
of the main function \\code{multi_meta} will work with files\nobtained from GEMMA
multivariate option for GWAS (Zhou & Stephens, 2014).\nIt will work with any other
output, as soon as columns are formatted to\nhave the according names. The package
also provides several plotting\nfunctions for QQ-plots, Manhattan Plots and custom
summary plots.","Imports":"mvtnorm,expm,ggplot2,reshape2","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MultiMeta","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Meta-analysis of Multivariate Genome Wide Association
Studies","Version":"0.1"},"MultiOrd":{"Author":"Anup Amatya and Hakan
Demirtas","Depends":"mvtnorm, corpcor, Matrix, psych","Description":"A method for
multivariate ordinal data generation given marginal distributions and correlation
matrix based on the methodology proposed by Demirtas (2006).","License":"GPL-
2","NeedsCompilation":"no","Package":"MultiOrd","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Generation of multivariate ordinal
variates","Version":"2.1"},"MultiPhen":{"Author":"Lachlan Coin, Paul O'Reilly,
Yotsawat Pompyen, Clive Hoggart\nand Federico Calboli","Depends":"MASS, abind,
epitools, meta","Description":"Performs genetic association tests between
SNPs\n(one-at-a-time) and multiple phenotypes (separately or in
joint\nmodel).","Imports":"HardyWeinberg, RColorBrewer, gplots","License":"GPL-
2","NeedsCompilation":"no","Package":"MultiPhen","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"A Package to Test for Pleiotropic
Effects","Version":"2.0.1"},"MultiRR":{"Author":"Yimen G. Araya-
Ajoy","Description":"Calculates bias, precision, and power for multi-level random
regressions. Random regressions are types of hierarchical models in which data are
structured in groups and (regression) coefficients can vary by groups. Tools to
estimate model performance are designed mostly for scenarios where (regression)
coefficients vary at just one level. 'MultiRR' provides simulation and analytical
tools (based on 'lme4') to study model performance for random regressions that vary
at more than one level (multi-level random regressions), allowing researchers to
determine optimal sampling designs.","Imports":"MASS, lme4","License":"GPL-
2","NeedsCompilation":"no","Package":"MultiRR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Bias, Precision, and Power for Multi-Level Random
Regressions","Version":"1.1"},"MultiSV":{"Author":"Khurram Maqbool","Depends":"R
(>= 2.10)","Description":"MultiSV is an R package for identification of
structural\nvariations in multiple populations based on whole genome resequencing.
It\nfits linear mixed model and identifies structural variations in
multiple\npopulations using whole genome sequencing data. It could also
be\nmanipulated to use on RNA-seq data for differential gene
expression\n(implementation in future releases). Main steps for analysis
include\ngenerating read depth in bins using ComputeBinCounts. conversion of bins
to\nMultiSV format using Bin2MultiSV. Finally, identification of
structural\nvariations using CallMultiSV.","Imports":"nlme,reshape","License":"LGPL
(>=
3)","NeedsCompilation":"no","Package":"MultiSV","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"MultiSV: an R package for identification of
structural\nvariations in multiple populations based on whole
genome\nresequencing","Version":"0.0-67"},"MultinomialCI":{"Author":"Pablo J.
Villacorta <pjvi@decsai.ugr.es>","Depends":"R (>= 2.15.0)","Description":"An
implementation of a method for building simultaneous\nconfidence intervals for the
probabilities of a multinomial\ndistribution given a set of observations, proposed
by Sison and\nGlaz in their paper Sison, C.P and J. Glaz. Simultaneous\nconfidence
intervals and sample size determination for\nmultinomial proportions. Journal of
the American Statistical\nAssociation, 90:366-369 (1995). The method is an R
translation\nof the SAS code implemented by May and Johnson in their paper:\nMay,
W.L. and W.D. Johnson. Constructing two-sided simultaneous\nconfidence intervals
for multinomial proportions for small\ncounts in a large number of cells. Journal
of Statistical\nSoftware 5(6) (2000). Paper and code available
at\nhttp:\/\/www.jstatsoft.org\/v05\/i06","License":"LGPL (>=
3)","NeedsCompilation":"no","Package":"MultinomialCI","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Simultaneous confidence intervals for multinomial
proportions\naccording to the method by Sison and
Glaz","URL":"http:\/\/decsai.ugr.es\/~pjvi","Version":"1.0"},"MultivariateRandomFor
est":{"Author":"Raziur Rahman <razeeebuet@gmail.com>","Description":"In Random
Forest, prediction has been done for single\noutput feature, while linear relation
between the\noutput features has not been considered in other\npackages. In this
package, using linear relation of\nthe output features, a multivariate random
forest\nprediction has been done, which can predict all the\noutput features with
one Random forest. If there is\nhigh correlation among the features, this
MRF\nprediction gives better result than the
individual\nRFs.","Imports":"bootstrap, stats","License":"GPL-
3","NeedsCompilation":"no","Package":"MultivariateRandomForest","Repository":"http:
\/\/cran.csiro.au\/src\/contrib","Title":"Multivariate Random Forest for Linearly
Related Output Features","Version":"1.1"},"MvBinary":{"Author":"Matthieu Marbac and
Mohammed Sedki","Depends":"R (>= 3.0.2)","Description":"Modelling Multivariate
Binary Data with Blocks of Specific One-Factor Distribution. Variables are grouped
into independent blocks. Each variable is described by two continuous parameters
(its marginal probability and its dependency strength with the other block
variables), and one binary parameter (positive or negative dependency). Model
selection consists in the estimation of the repartition of the variables into
blocks. It is carried out by the maximization of the BIC criterion by a
deterministic (faster) algorithm or by a stochastic (more time consuming but
optimal) algorithm. Tool functions facilitate the model
interpretation.","Imports":"methods, mgcv, parallel","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"MvBinary","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Modelling Multivariate Binary Data with Blocks of
Specific\nOne-Factor Distribution","Version":"1.0"},"Myrrix":{"Author":"Jan
Wijffels [aut, cre]","Depends":"R (>= 2.6.0),
Myrrixjars","Description":"Recommendation engine based on Myrrix. Myrrix is a
complete,\nreal-time, scalable clustering and recommender system, evolved from
Apache\nMahout. It uses Alternating Least Squares to build a recommendation
engine.","Imports":"methods, rJava (>= 0.6-3)","License":"Apache License (==
2.0)","NeedsCompilation":"no","Package":"Myrrix","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Interface to Myrrix. Myrrix is a complete, real-time,
scalable\nclustering and recommender system, evolved from Apache
Mahout","URL":"http:\/\/www.bnosac.be, myrrix.com","Version":"1.1"},"Myrrixjars":
{"Author":"Jan Wijffels [aut, cre]","Depends":"R (>=
2.6.0)","Description":"External jars required for package Myrrix. Myrrix is
a\nrecommendation
engine","Imports":"rJava (>= 0.6-3)","License":"Apache License (==
2.0)","NeedsCompilation":"no","Package":"Myrrixjars","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"External jars required for package
Myrrix","URL":"http:\/\/www.bnosac.be, myrrix.com","Version":"1.0-1"},"NADA":
{"Author":"Lopaka Lee","Depends":"methods,survival","Description":"Contains methods
described by Dennis R. Helsel in\nhis book \"Nondetects And Data Analysis:
Statistics\nfor Censored Environmental Data\"","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"NADA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Nondetects And Data Analysis for environmental
data","Version":"1.5-6"},"NAM":{"Author":"Alencar Xavier, William Muir, Katy
Rainey, Shizhong Xu.","Depends":"R (>= 3.0.2)","Description":"Designed for
association studies in nested association mapping (NAM) panels, also handling
biparental and random panels. It includes functions for genome-wide associations
mapping of multiple populations, marker quality control, solving mixed models and
finding variance components through REML and Gibbs sampling.","Imports":"Rcpp,
randomForest","License":"GPL-
3","NeedsCompilation":"yes","Package":"NAM","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"knitr, rmarkdown","Title":"Nested Association Mapping
Analysis","Version":"1.4.4"},"NAPPA":{"Author":"Chris Harbron, Mark
Wappett","Depends":"R (>= 3.0.1), plyr (>= 1.8), NanoStringNorm (>=
1.1)","Description":"Enables the processing and normalisation of the standard mRNA
data output from the Nanostring nCounter software.","License":"GPL-
2","NeedsCompilation":"no","Package":"NAPPA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Performs the Processing and Normalisation of Nanostring
miRNA\nand mRNA Data","Version":"2.0.1"},"NB":{"Author":"Tin-Yu Hui @ Imperial
College London","Description":"Estimate the effective population size of a closed
population using genetic data collected from two or more data
points.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"NB","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Maximum Likelihood method in estimating effective
population\nsize from genetic data","Version":"0.9"},"NBDdirichlet":
{"Author":"Feiming Chen","Description":"The Dirichlet (aka NBD-Dirichlet) model
describes the\npurchase incidence and brand choice of consumer products.
We\nestimate the model and summarize various theoretical quantities\nof interest to
marketing researchers. Also provides functions\nfor making tables that compare
observed and theoretical\nstatistics.","License":"GPL-
3","NeedsCompilation":"no","Package":"NBDdirichlet","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"NBD-Dirichlet Model of Consumer Buying Behavior for
Marketing\nResearch","URL":"\nhttp:\/\/stat.fsu.edu\/~fchen\/R-package-
NBDdirichlet\/how-to-use-Dirichlet-marketing-model.html","Version":"1.3"},"NBPSeq":
{"Author":"Yanming Di <diy@stat.oregonstate.edu>, Daniel W
Schafer\n<schafer@stat.oregonstate.edu>, with contributions from Jason S
Cumbie\n<cumbiej@onid.orst.edu> and Jeff H Chang
<changj@cgrb.oregonstate.edu>.","Depends":"R (>= 3.00)","Description":"Negative
Binomial (NB) models for two-group comparisons and\nregression inferences from RNA-
Sequencing Data.","Imports":"splines, qvalue","License":"GPL-
2","NeedsCompilation":"yes","Package":"NBPSeq","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Negative Binomial Models for RNA-Sequencing
Data","Version":"0.3.0"},"NCA":{"Author":"Jan Dul
<jdul@rsm.nl>","Description":"Performs a Necessary Condition Analysis (NCA). (Dul,
J. 2015. Necessary Condition Analysis (NCA). ''Logic and Methodology of 'Necessary
but not Sufficient' causality.\" Organizational Research Methods)\nNCA identifies
necessary (but not sufficient) conditions in datasets. Instead of drawing a
regression line ''through the middle of the data'' in an xy-plot, NCA draws the
ceiling line. The ceiling line y = f(x) separates the area with observations from
the area without observations.\n(Nearly) all observations are below the ceiling
line: y <= f(x). The empty zone is in the upper left hand corner of the xy-plot
(with the convention that the x-axis is ''horizontal'' and the y-axis is
''vertical'' and that values increase ''upwards'' and ''to the right''). The
ceiling line is a (piecewise) linear non-decreasing line: a linear step function or
a straight line. It indicates which level of x (e.g. an effort or input) is
necessary but not sufficient for a (desired) level of y (e.g. good performance or
output).","Imports":"gplots, quantreg, Benchmarking, sfa","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"NCA","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"testthat","Title":"Necessary Condition
Analysis","Version":"1.1"},"NCmisc":{"Author":"Nicholas Cooper","Depends":"R (>=
2.10), grDevices, graphics, stats, utils","Description":"A set of handy functions.
Includes a versatile one line progress bar, one\nline function timer with detailed
output, time delay function, text histogram, object\npreview, CRAN package search,
simpler package installer, Linux command install check,\na flexible Mode function,
top function, simulation of correlated data, and more.","Imports":"tools,
proftools, dplyr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"NCmisc","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"KernSmooth, BiocInstaller,
Matrix","Title":"Miscellaneous Functions for Creating Adaptive Functions
and\nScripts","Version":"1.1.4"},"NEff":{"Author":"Annegret Grimm, Bernd Gruber &
Klaus Henle","Depends":"msm, bit","Description":"Effective population sizes (often
abbreviated as \"Neff\") are essential in biodiversity monitoring and conservation.
For the first time, calculating effective sizes with data obtained within less than
a generation but considering demographic parameters is possible. This individual
based model uses demographic parameters of a population to calculate annual
effective sizes and effective population sizes (per generation). A defined number
of alleles and loci will be used to simulate the genotypes of the individuals.
Stepwise mutation rates can be included. Variations in life history parameters (sex
ratio, sex-specific survival, recruitment rate, reproductive skew) are possible.
These results will help managers to define existing populations as viable or
not.","License":"GPL-
2","NeedsCompilation":"no","Package":"NEff","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Calculating Effective Sizes Based on Known
Demographic\nParameters of a Population","Version":"1.1"},"NEpiC":
{"Author":"Peifeng Ruan","Depends":"igraph, PairedData","Description":"Package for
a Network assisted algorithm for Epigenetic studies using mean and variance
Combined signals: NEpiC. NEpiC combines both signals in mean and variance
differences in methylation level between case and control groups searching for
differentially methylated sub-networks (modules) using the protein-protein
interaction network.","License":"GPL-
2","NeedsCompilation":"no","Package":"NEpiC","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Network Assisted Algorithm for Epigenetic Studies Using Mean
and\nVariance Combined Signals","Version":"1.0.1"},"NHANES":{"Author":"Randall
Pruim <rpruim@calvin.edu>","Depends":"R (>= 3.0)","Description":"Body Shape and
related measurements from the US National Health\nand Nutrition Examination Survey
(NHANES, 1999-2004). See\nhttp:\/\/www.cdc.gov\/nchs\/nhanes.htm for
details.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"NHANES","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"mosaic","Title":"Data from the US National Health and
Nutrition Examination Study","Version":"2.1.0"},"NHEMOtree":{"Author":"Swaantje
Casjens","Depends":"partykit, emoa, sets, rpart","Description":"NHEMOtree performs
cost-sensitive classification by\nsolving the two-objective optimization problem of
minimizing\nmisclassification rate and minimizing total costs for\nclassification.
The three methods comprised in NHEMOtree are\nbased on EMOAs with either tree
representation or bitstring\nrepresentation with an enclosed classification tree
algorithm.","License":"GPL-
3","NeedsCompilation":"no","Package":"NHEMOtree","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Non-hierarchical evolutionary multi-objective tree
learner to\nperform cost-sensitive classification","Version":"1.0"},"NHMM":
{"Author":"Tracy Holsclaw","Depends":"BayesLogit, msm, MCMCpack,
MASS","Description":"Bayesian NHMM modeling for multiple time series. The emission
distribution can be mixtures of Gammas, Poissons, Normals and zero inflation is
possible.","Imports":"Rcpp (>= 0.11.0)","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"NHMM","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Bayesian NHMM Modeling (Multiple Time
Series)","URL":"http:\/\/iamrandom.com\/nhmm-package","Version":"3.5"},"NHMSAR":
{"Author":"Valerie Monbet","Depends":"R (>= 2.10)","Description":"Calibration,
simulation, validation of (non-)homogeneous Markov switching autoregressive models
with Gaussian or von Mises innovations. Penalization methods are implemented for
Markov Switching Vector Autoregressive Models of order 1 only.","Imports":"ucminf,
lars, SIS, caTools,
glasso","License":"GPL","NeedsCompilation":"no","Package":"NHMSAR","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"Non-Homogeneous Markov Switching
Autoregressive Models","Version":"1.1"},"NHPoisson":{"Author":"Ana C. Cebrian
<acebrian@unizar.es>","Depends":"methods, stats4","Description":"Tools for
modelling, ML estimation, validation analysis and simulation of non homogeneous
Poisson processes in time.","Imports":"car, parallel","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"NHPoisson","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Modelling
and Validation of Non Homogeneous Poisson Processes","Version":"3.1"},"NIPTeR":
{"Author":"Dirk de Weerd, Lennart Johansson","Depends":"R (>=
3.1.0),","Description":"Fast and Accurate Trisomy Prediction in Non-Invasive
Prenatal\nTesting.","Imports":"stats, Rsamtools, sets, S4Vectors","License":"GNU
Lesser General Public
License","NeedsCompilation":"no","Package":"NIPTeR","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"knitr, pander","Title":"Fast and Accurate Trisomy
Prediction in Non-Invasive Prenatal\nTesting","Version":"1.0.2"},"NISTnls":
{"Author":"original from National Institutes for Standards and Technology\n(NIST)
http:\/\/www.itl.nist.gov\/div898\/strd\/nls\/nls_main.shtml R\nport by Douglas
Bates <bates@stat.wisc.edu>","Depends":"stats, R (>=
2.14.0)","Description":"Datasets for testing nonlinear regression
routines.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"NISTnls","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Nonlinear least squares examples from
NIST","Version":"0.9-13"},"NISTunits":{"Author":"Jose Gama [aut, cre]","Depends":"R
(>= 2.7.0)","Description":"Fundamental physical constants (Quantity, Value,
Uncertainty, Unit) for\nSI (International System of Units) and non-SI, plus unit
conversions\nBased on the data from NIST (National Institute of Standards and
Technology)","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"NISTunits","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Fundamental Physical Constants and Unit Conversions
from NIST","Version":"1.0.0"},"NLP":{"Author":"Kurt Hornik [aut, cre]","Depends":"R
(>= 2.10)","Description":"Basic classes and methods for Natural Language
Processing.","Imports":"utils","License":"GPL-
3","NeedsCompilation":"no","Package":"NLP","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Natural Language Processing Infrastructure","Version":"0.1-
9"},"NLPutils":{"Author":"Kurt Hornik [aut, cre]","Description":"Utilities for
Natural Language Processing.","Imports":"NLP (>= 0.1-6.3), SnowballC, qdap,
2","NeedsCompilation":"no","Package":"NLPutils","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Natural Language Processing Utilities","Version":"0.0-
3"},"NLRoot":{"Author":"Zheng Sengui,Lu Xufen,Hou Qiongchen,Zheng
Jianhui","Description":"This is a package which can help you search for the
root\nof a equation.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"NLRoot","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"searching for the root of
equation","Version":"1.0"},"NMF":{"Author":"Renaud Gaujoux, Cathal
Seoighe","Depends":"R (>= 3.0.0), methods, utils, pkgmaker (>= 0.20),
registry,\nrngtools (>= 1.2.3), cluster","Description":"Provides a framework to
perform Non-negative Matrix\nFactorization (NMF). The package implements a set of
already published algorithms\nand seeding methods, and provides a framework to
test, develop and plug\nnew\/custom algorithms. Most of the built-in algorithms
have been optimized\nin C++, and the main interface function provides an easy way
of performing\nparallel computations on multicore machines.","Imports":"graphics,
stats, stringr (>= 1.0.0), digest, grid, grDevices,\ngridBase, colorspace,
RColorBrewer, foreach, doParallel,\nggplot2, reshape2","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"NMF","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"RcppOctave (>= 0.11), fastICA, doMPI, bigmemory (>=
4.2),\nsynchronicity, corpcor, xtable, devtools, knitr, bibtex, RUnit,\nmail,
Biobase","Title":"Algorithms and Framework for Nonnegative Matrix
Factorization\n(NMF)","URL":"http:\/\/renozao.github.io\/NMF","Version":"0.20.6"},"
NMFN":{"Author":"Suhai (Timothy) Liu","Description":"Non-negative Matrix
Factorization","License":"GPL","NeedsCompilation":"no","Package":"NMFN","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Non-negative Matrix
Factorization","Version":"2.0"},"NMOF":{"Author":"Enrico Schumann [aut,
cre]","Depends":"R (>= 2.14)","Description":"Functions, examples and data from
the book\n'Numerical Methods and Optimization in Finance' by M.\nGilli, D.
Maringer and E. Schumann. The package provides\nimplementations of several
optimisation heuristics, such as\nDifferential Evolution, Genetic Algorithms and
Threshold\nAccepting. There are also functions for the valuation of\nfinancial
instruments, such as bonds and options, and\nfunctions that help with
stochastic simulations.","Imports":"grDevices, graphics, parallel, stats,
3","NeedsCompilation":"no","Package":"NMOF","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"MASS, RUnit, quadprog","Title":"Numerical Methods and
Optimization in Finance","URL":"http:\/\/nmof.net,
http:\/\/enricoschumann.net\/NMOF.htm","Version":"0.36-2"},"NNLM":{"Author":"Xihui
Lin [aut, cre],\nPaul C Boutros [aut]","Depends":"R (>= 3.0.1)","Description":"This
is a package for Non-Negative Linear Models (NNLM). It implements\nfast sequential
coordinate descent algorithms for non-negative linear regression\nand non-negative
matrix factorization (NMF). It supports mean square error and Kullback-Leibler
divergence loss.\nMany other features are also implemented, including missing value
imputation, domain knowledge integration,\ndesignable W and H matrices and multiple
forms of regularizations.","Imports":"Rcpp (>= 0.11.0), stats,
utils","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"yes","Package":"NNLM","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat, knitr, rmarkdown, mice, missForest,
ISOpureR","Title":"Fast and Versatile Non-Negative Matrix
Factorization","URL":"https:\/\/github.com\/linxihui\/NNLM","Version":"0.4.1"},"NNS
":{"Author":"Fred Viole","Description":"Nonlinear nonparametric statistics using
partial moments.","License":"GPL-
3","NeedsCompilation":"no","Package":"NNS","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Nonlinear Nonparametric
Statistics","Version":"0.1.1"},"NNTbiomarker":{"Author":"Roger
Day","Description":"Helps a clinical trial team discuss\nthe clinical goals of a
well-defined biomarker with a diagnostic,\nstaging, prognostic, or predictive
purpose. From this discussion will\ncome a statistical plan for a (non-randomized)
validation trial.\nBoth prospective and retrospective trials are supported. In a
specific\nfocused discussion, investigators should determine the range
of\n\"discomfort\" for the NNT, number needed to treat. The meaning of\nthe
discomfort range, [NNTlower, NNTupper], is that within this range\nmost physicians
would feel discomfort either in treating or withholding\ntreatment. A pair of NNT
values bracketing that range, NNTpos and NNTneg,\nbecome the targets of the study's
design. If the trial can demonstrate\nthat a positive biomarker test yields an NNT
less than NNTlower,\nand that a negative biomarker test yields an NNT less than
NNTlower,\nthen the biomarker may be useful for patients. A highlight of the
package\nis visualization of a \"contra-Bayes\" theorem, which produces criteria
for\nretrospective case-controls studies.","Imports":"shiny, xtable, stringr,
magrittr, mvbutils","License":"GPL-
3","NeedsCompilation":"no","Package":"NNTbiomarker","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat (>= 0.8.1), knitr (>= 1.6), rmarkdown,
ggplot2, plyr","Title":"Calculate Design Parameters for Biomarker Validation
Studies","Version":"0.29.11"},"NORMT3":{"Author":"Guy Nason
<g.p.nason@bristol.ac.uk>","Depends":"R (>= 2.0)","Description":"Evaluates the
probability density function of the sum of\nthe Gaussian and Student's t density on
3 degrees of freedom.\nEvaluates the p.d.f. of the sphered Student's t
density\nfunction. Also evaluates the erf, and erfc functions on\ncomplex-valued
arguments. Thanks to Krishna Myneni the function\nis calculates the Faddeeva
function also!","License":"GPL-
2","NeedsCompilation":"yes","Package":"NORMT3","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Evaluates complex erf, erfc, Faddeeva, and density of sum
of\nGaussian and Student's t","Version":"1.0-3"},"NORRRM":{"Author":"Renee Gonzalez
Guzman","Depends":"R (>= 3.1.1)","Description":"CIPW Norm (acronym from the
surnames of the authors: Cross, Iddings, Pirrson and Washington)\nis the most
commonly used calculation algorithm to estimate the standard mineral
assemblages\nfor igneous rocks from its geochemical composition. NORRRM (acronym
from noRm, R language and\nRenee) is the highly consistent program to calculate the
CIPW Norm.","Imports":"ggplot2,SDMTools","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"NORRRM","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Geochemical Toolkit for R","Version":"1.0.0"},"NORTARA":
{"Author":"Po Su [aut, cre]","Depends":"R (>= 3.1.2)","Description":"An
implementation of a specific method for generating\nn-dimensional random vectors
with given marginal distributions and\ncorrelation matrix. The method uses the
NORTA (NORmal To Anything)\napproach which generates a standard normal random
vector and then\ntransforms it into a random vector with specified marginal
distributions\nand the RA (Retrospective Approximation) algorithm which is a
generic\nstochastic root-finding algorithm. The marginals can be continuous
or\ndiscrete. See the vignette of package for more details.","Imports":"corpcor(>=
1.6.7), Matrix(>= 1.1-4)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"NORTARA","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"knitr","Title":"Generation of Multivariate Data
with Arbitrary
Marginals","URL":"https:\/\/github.com\/superdesolator\/NORTARA","Version":"1.0.0"}
,"NPBayesImpute":{"Author":"Quanli Wang, Daniel Manrique-Vallier, Jerome P. Reiter
and Jingchen Hu","Depends":"methods, Rcpp (>=
0.10.2)","Description":"These routines create multiple imputations of missing at
random categorical data, with or without structural zeros. Imputations are based on
Dirichlet process mixtures of multinomial distributions, which is a non-parametric
Bayesian modeling approach that allows for flexible joint modeling.","License":"GPL
(>=
3)","NeedsCompilation":"yes","Package":"NPBayesImpute","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Non-Parametric Bayesian Multiple Imputation for
Categorical Data","Version":"0.6"},"NPC":{"Author":"Devin Caughey [aut,
cre]","Depends":"R (>= 3.2.0)","Description":"An implementation of nonparametric
combination of hypothesis tests.\nThis package performs nonparametric combination
(Pesarin and Salmaso 2010),\na permutation-based procedure for jointly testing
multiple hypotheses. The\ntests are conducted under the global \"sharp\" null
hypothesis of no effects,\nand the component tests are combined on the metric of
their p-values. A\nkey feature of nonparametric combination is that it accounts for
the\ndependence among tests under the null hypothesis. In addition to the\n\"NPC\"
function, which performs nonparametric combination itself, the\npackage also
contains a number of helper functions, many of which calculate\na test statistic
given an input of data.","Imports":"permute, dplyr, coin, matlab","License":"GPL-
3","NeedsCompilation":"no","Package":"NPC","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"car, mvtnorm, plyr, xtable","Title":"Nonparametric
Combination of Hypothesis Tests","Version":"1.1.0"},"NPCD":{"Author":"Yi Zheng
[aut, cre],\nChia-Yi Chiu [aut],\nJeffrey A. Douglas [ctb]","Depends":"R (>=
2.14.2), BB, R.oo","Description":"An array of nonparametric and parametric
estimation methods for cognitive diagnostic models, including nonparametric
classification of examinee attribute profiles, joint maximum likelihood estimation
(JMLE) of examinee attribute profiles and item parameters, and nonparametric
refinement of the Q-matrix, as well as conditional maximum likelihood estimation
(CMLE) of examinee attribute profiles given item parameters and CMLE of item
parameters given examinee attribute profiles. Currently the nonparametric methods
in the package support both conjunctive and disjunctive models, and the parametric
methods in the package support the DINA model, the DINO model, the NIDA model, the
G-NIDA model, and the R-RUM model.","Imports":"R.methodsS3","License":"LGPL (>=
2.1)","NeedsCompilation":"no","Package":"NPCD","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Nonparametric Methods for Cognitive
Diagnosis","Version":"1.0-9"},"NPCirc":{"Author":"María Oliveira, Rosa M. Crujeiras
and Alberto Rodríguez-Casal","Depends":"R(>= 2.15.0), circular","Description":"This
package implements nonparametric smoothing methods for circular
data.","Imports":"misc3d, movMF, plotrix, rgl, shape","License":"GPL-
2","NeedsCompilation":"no","Package":"NPCirc","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Nonparametric Circular
Methods","URL":"http:\/\/www.jstatsoft.org\/v61\/i09\/","Version":"2.0.1"},"NPHMC":
{"Author":"Chao Cai, Songfeng Wang, Wenbin Lu, Jiajia Zhang","Depends":"survival,
smcure","Description":"An R-package for calculating sample size of a survival trial
with or without cure fractions","License":"GPL-
2","NeedsCompilation":"no","Package":"NPHMC","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Sample Size Calculation for the Proportional Hazards
Mixture\nCure Model","Version":"2.2"},"NPMLEcmprsk":{"Author":"Chung-Hsing Chen, I-
Shou Chang and Chao A. Hsiung","Description":"Given a failure type, the function
computes covariate-specific probability of failure over time and covariate-specific
conditional hazard rate based on possibly right-censored competing risk data.
Specifically, it computes the non-parametric maximum-likelihood estimates of these
quantities and their asymptotic variances in a semi-parametric mixture model for
competing-risks data, as described in Chang et al. (2007a).","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"NPMLEcmprsk","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Type-Specific Failure Rate and Hazard Rate on
Competing Risks\nData","Version":"2.1"},"NPMPM":{"Author":"Nadine
Schoene","Depends":"R (>= 2.11.0)","Description":"The main method npmpm calculates
bacterial concentrations\nduring food manufacture after a contamination.
Variability and\nuncertainty are included by use of probability distributions\nand
Monte Carlo Simulation. The model aims at predicting\npossible bacterial
concentrations at one certain point in time\ns, e.g. at the end of a process chain.
The process steps of\nthis process chain are run through in linear
order.\nExperimental data that match current process step conditions\nare gathered,
and one deterministic primary model is fitted to\nevery series of measured values.
From every fitted curve one\nconcentration of bacteria at time s is computed,
yielding a set\nof concentrations. This sample of possible contamination sizes\nis
assumed to follow a certain probability distribution. After\ncalculation of
distribution parameters, one value is randomly\ndrawn from this probability
distribution. This value may be\nmodified, and then serves as contamination for the
next process\nstep.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"NPMPM","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"SweaveListingUtils, graphics","Title":"tertiary
probabilistic model in predictive microbiology for use\nin food
manufacture","Version":"1.0"},"NPMVCP":{"Author":"Mark D.
Holland","Description":"Nonparametric Multivariate Change Point
Model","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"NPMVCP","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Nonparametric Multivariate Change Point
Model","Version":"1.1"},"NPS":{"Author":"Brendan Rocks","Description":"Small
functions to make working with survey data in the context of\na Net Promoter
programme easier. Specifically, data transformation methods,\nsome methods for
examining the statistical properties of the NPS, such as\nits variance and standard
errors, and some simple inferential testing\nprocedures. Net Promoter and NPS are
registered trademarks of Bain &\nCompany, Satmetrix Systems and Fred
Reichheld.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"NPS","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Convenience Functions and Tests for Working With the
Net\nPromoter Score (NPS)","Version":"1.1"},"NPsimex":{"Author":"Xiao-Feng
Wang","Description":"This package contains a collection of functions to to perform
nonparametric deconvolution using simulation extrapolation (SIMEX). We propose an
estimator that adopts the SIMEX idea but bypasses the simulation step in the
original SIMEX algorithm. There is no bandwidth parameter and the estimate is
determined by appropriately selecting \"design points\". See details in: Wang,
X.F., Sun, J. and Fan, Z. (2011). Deconvolution density estimation with
heteroscedastic errors using SIMEX.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"NPsimex","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Nonparametric Smoothing for contaminated data
using\nSimulation-Extrapolation","Version":"0.2-1"},"NSA":{"Author":"Maria Ortiz-
Estevez <mortizest@gmail.com>, Ander Aranburu\n<aaranburu@ceit.es>, Angel Rubio
<arubio@ceit.es>","Depends":"R (>= 2.11.1), R.methodsS3 (>= 1.2.0), MASS,
matrixStats (>=\n0.2.1), R.oo (>= 1.7.3), R.utils (>= 1.4.2), aroma.core
(>=\n1.6.0), aroma.affymetrix, DNAcopy","Description":"Post-normalization of total
copy-number estimates.","License":"LGPL (>=
2.1)","NeedsCompilation":"no","Package":"NSA","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Post-normalization of total copy
numbers","URL":"http:\/\/r-forge.r-
project.org\/projects\/snpsprocessing\/","Version":"0.0.32"},"NSM3":
{"Author":"Grant Schneider, Eric Chicken, Rachel Becvarik","Depends":"R (>= 2.10),
combinat, MASS, partitions, stats, survival","Description":"Designed to replace the
tables which were in the back of the first two editions of Hollander and Wolfe -
Nonparametric Statistical Methods. Exact procedures are performed when
computationally possible. Monte Carlo and Asymptotic procedures are performed
otherwise. For those procedures included in the base packages, our code simply
provides a wrapper to standardize the output with the other procedures in the
package.","Imports":"agricolae, ash, binom, BSDA, coin, epitools, fANCOVA,
gtools,\nHmisc, km.ci, metafor, nortest, np, quantreg, Rfit, SemiPar,\nSuppDists,
waveslim","License":"GPL-
2","NeedsCompilation":"yes","Package":"NSM3","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Functions and Datasets to Accompany Hollander, Wolfe,
and\nChicken - Nonparametric Statistical Methods, Third
Edition","Version":"1.3"},"NSUM":{"Author":"Rachael Maltiel and Aaron J.
Baraff","Description":"A Bayesian framework for population group size estimation
using the Network Scale Up Method (NSUM). Size estimates are based on a random
degree model and include options to adjust for barrier and transmission
effects.","Imports":"MASS, MCMCpack","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"NSUM","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Network Scale Up Method","Version":"1.0"},"NScluster":
{"Author":"The Institute of Statistical Mathematics, based on the program by Ushio
Tanaka","Depends":"R (>= 2.14.0), graphics","Description":"This package simulates
and estimates spatial clustered point patterns of the Neyman-Scott model and their
extensions.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"NScluster","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Simulation and Estimation of the Neyman-Scott
Type Spatial\nCluster Models","Version":"1.0.2"},"NanoStringNorm":{"Author":"Daryl
M. Waggott","Depends":"R (>= 2.14.0), gdata (>= 2.8.2), vsn (>=
3.22.0)","Description":"A set of tools for normalizing, diagnostics and
visualization of NanoString nCounter data.","Imports":"methods","License":"GPL-
2","NeedsCompilation":"no","Package":"NanoStringNorm","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"googleVis (>= 0.2.14), lme4, RUnit (>=
0.4.26)","Title":"Normalize NanoString miRNA and mRNA
Data","Version":"1.1.21"},"NbClust":{"Author":"Malika Charrad and Nadia Ghazzali
and Veronique Boiteau and Azam Niknafs","Depends":"R (>= 3.1.0)","Description":"It
provides 30 indexes for determining the optimal number of clusters in a data set
and offers the best clustering scheme from different results to the
user.","License":"GPL-
2","NeedsCompilation":"no","Package":"NbClust","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Determining the Best Number of Clusters in a Data
Set","URL":"\nhttps:\/\/sites.google.com\/site\/malikacharrad\/research\/nbclust-
package","Version":"3.0"},"NeatMap":{"Author":"Satwik Rajaram and Yoshi
Oono","Depends":"ggplot2, rgl","Description":"NeatMap is a package to create
heatmap like plots in 2 and\n3 dimensions, without the need for cluster analysis.
Like the\nheatmap, the plots created by NeatMap display both a\ndimensionally
reduced representation of the data as well as the\ndata itself. They are intended
to be used in conjunction with\ndimensional reduction techniques such as
PCA.","License":"GPL-
3","NeedsCompilation":"yes","Package":"NeatMap","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Non-clustered heatmap
alternatives","Version":"0.3.6.2"},"NestedCohort":{"Author":"Hormuzd A. Katki
<katkih@mail.nih.gov>","Depends":"R (>= 2.15.2), survival,
MASS","Description":"Estimate hazard ratios, survival curves and
attributable\nrisks for cohorts with missing covariates, using Cox models
or\nKaplan-Meier estimated for strata. This handles studies nested\nwithin
cohorts, such as case-cohort studies with stratified\nsampling.
See\nhttp:\/\/www.r-project.org\/doc\/Rnews\/Rnews_2008-1.pdf","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"NestedCohort","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Survival Analysis for Cohorts with Missing Covariate
Information","URL":"http:\/\/dceg.cancer.gov\/about\/staff-bios\/katki-
hormuzd","Version":"1.1-3"},"NetCluster":{"Author":"Mike Nowak
<michael.nowak@gmail.com>, Solomon Messing\n<solomon.messing@gmail.com>, Sean J
Westwood\n<seanjw@stanford.edu>, and Dan
McFarland\n<dmcfarla@stanford.edu>","Depends":"stats,
sna","Description":"Facilitates network clustering and evaluation of
cluster\nconfigurations.","License":"GPL-
2","NeedsCompilation":"no","Package":"NetCluster","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Clustering for networks","Version":"0.2"},"NetComp":
{"Author":"Shannon M. Bell <bell.shannonm@gmail.com>, Lyle D.
Burgoon\n<burgoon.lyle@gmail.com>","Depends":"R (>= 2.12.1)","Description":"This
package contains functions to carry out high\nthroughput data analysis and to
conduct data set comparisons.\nSimilarity matrices from high throughput phenotypic
data\ncontaining uninformative (e.g. wild type) or missing data can\nbe calculated
to report similarity of response. A suite of\ngraph comparisons using an adjacency
or correlation matrix\nformat are included to facilitate quick network
analysis.","Imports":"gdata","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"NetComp","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Network Generation and
Comparison","Version":"1.6"},"NetData":{"Author":"Mike Nowak
<michael.nowak@gmail.com>, Sean J Westwood\n<seanjw@stanford.edu>, Solomon
Messing\n<solomon.messing@gmail.com>, and Dan
McFarland\n<dmcfarla@stanford.edu>","Description":"This package contains all data
needed for Dan McFarland's\nSNA R labs.","License":"GPL-
2","NeedsCompilation":"no","Package":"NetData","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Network Data for McFarland's SNA R
labs","Version":"0.3"},"NetIndices":{"Author":"Karline Soetaert
<karline.soetaert@nioz.nl>,\nJulius Kipyegon Kones <jkones@uonbi.ac.ke>,\nDick van
Oevelen <dick.vanoevelen@nioz.nl>","Depends":"R (>= 2.01),
MASS","Description":"Given a network (e.g. a food web), estimates several network
indices. These include: Ascendency network indices, Direct and indirect
dependencies, Effective measures, Environ network indices, General network indices,
Pathway analysis, Network uncertainty indices and constraint efficiencies and the
trophic level and omnivory indices of food webs.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"NetIndices","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"LIM","Title":"Estimating network indices, including
trophic structure of\nfoodwebs in R","Version":"1.4.4"},"NetPreProc":
{"Author":"Giorgio Valentini, Matteo Re -- Universita' degli Studi di
Milano","Depends":"methods","Description":"Package for the pre-processing and
normalization of graphs.","Imports":"graph","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"NetPreProc","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"bionetdata","Title":"Network Pre-Processing and
Normalization","Version":"1.1"},"NetSim":{"Author":"Christoph
Stadtfeld","Depends":"Rcpp (>= 0.9.15)","Description":"NetSim allows to combine and
simulate a variety of micro-models to research their impact on the macro-features
of social networks.","License":"GPL-
2","NeedsCompilation":"yes","Package":"NetSim","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"igraph","Title":"A Social Networks Simulation Tool in
R","Version":"0.9"},"NetSwan":{"Author":"Serge
Lhomme","Depends":"igraph","Description":"A set of functions for studying network
robustness, resilience and vulnerability.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"NetSwan","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Network Strengths and Weaknesses
Analysis","Version":"0.1"},"NeuralNetTools":{"Author":"Marcus W. Beck [aut,
cre]","Depends":"R (>= 3.1.1)","Description":"Visualization and analysis tools to
aid in the interpretation of\nneural network models. Functions are available for
plotting,\nquantifying variable importance, conducting a sensitivity analysis,
and\nobtaining a simple list of model weights.","Imports":"ggplot2, nnet, reshape2,
scales,
tidyr","License":"CC0","NeedsCompilation":"no","Package":"NeuralNetTools","Reposito
ry":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"caret, neuralnet,
RSNNS","Title":"Visualization and Analysis Tools for Neural
Networks","Version":"1.4.0"},"Newdistns":{"Author":"Saralees Nadarajah, Ricardo
Rocha","Depends":"AdequacyModel","Description":"Computes the probability density
function, cumulative distribution function, quantile function, random numbers and
measures of inference for the following general families of distributions (each
family defined in terms of an arbitrary cdf G): Marshall Olkin G distributions,
exponentiated G distributions, beta G distributions, gamma G distributions,
Kumaraswamy G distributions, generalized beta G distributions, beta extended G
distributions, gamma G distributions, gamma uniform G distributions, beta
exponential G distributions, Weibull G distributions, log gamma G I distributions,
log gamma G II distributions, exponentiated generalized G distributions,
exponentiated Kumaraswamy G distributions, geometric exponential Poisson G
distributions, truncated-exponential skew-symmetric G distributions, modified beta
G distributions, and exponentiated exponential Poisson G
distributions.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Newdistns","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Computes Pdf, Cdf, Quantile and Random Numbers,
Measures of\nInference for 19 General Families of
Distributions","Version":"2.1"},"NightDay":{"Author":"Max Hughes-
Brandl","Depends":"R(>= 2.9.9), maps","Description":"Computes and plots the
boundary between night and
day.","License":"GPL","NeedsCompilation":"no","Package":"NightDay","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"Night and Day Boundary Plot
Funtion","Version":"1.0.1"},"Nippon":{"Author":"Susumu Tanimura
<aruminat@gmail.com> [aut, cre],\nHironobu Takahashi [cph],\nHajime Baba
[cph],\nTakatsugu Nokubi [cph]","Depends":"maptools, sp","Description":"Japan-
specific data is sometimes too unhandy for R users to manage. The utility functions
and data in this package disencumber us from such an unnecessary
burden.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"Nippon","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"RColorBrewer, foreign","Title":"Japanese Utility
Functions and Data","Version":"0.6.3"},"NlcOptim":{"Author":"Xianyan Chen
<xychen@uga.edu>, Xiangrong Yin <yinxiangrong@uky.edu>","Depends":"MASS, R (>=
2.15.1)","Description":"Optimization for nonlinear objective and constraint
functions. Linear or nonlinear equality and inequality constraints are allowed.
It accepts the input parameters as a constrained matrix.","License":"GPL-
3","NeedsCompilation":"no","Package":"NlcOptim","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Solve Nonlinear Optimization with Nonlinear
Constraints","Version":"0.4"},"NlsyLinks":{"Author":"Will Beasley, Joe Rodgers,
David Bard, Michael Hunter, S. Mason Garrison, and Kelly\nMeredith","Depends":"R
(>= 3.0.0), stats","Description":"Utilities and kinship information for behavior
genetics and\ndevelopmental research using the National Longitudinal Survey of
Youth\n(NLSY; <http:\/\/www.bls.gov\/nls\/>).","Imports":"lavaan,
methods","License":"GPL","NeedsCompilation":"no","Package":"NlsyLinks","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"devtools,
ggplot2, knitr, plyr, scales, testit, testthat,\nxtable","Title":"Utilities and
Kinship Information for Research with the
NLSY","URL":"http:\/\/liveoak.github.io\/NlsyLinks,\nhttps:\/\/github.com\/LiveOak\
/NlsyLinks,\nhttps:\/\/r-forge.r-
project.org\/projects\/nlsylinks","Version":"2.0.1"},"NominalLogisticBiplot":
{"Author":"Julio Cesar Hernandez Sanchez, Jose Luis Vicente-Villardon","Depends":"R
(>= 2.15.1),mirt,gmodels,MASS","Description":"Analysis of a matrix of polytomous
items using Nominal Logistic Biplots (NLB)\naccording to Hernandez-Sanchez and
Vicente-Villardon (2013).\nThe NLB procedure extends the binary logistic biplot to
nominal (polytomous) data.\nThe individuals are represented as points on a plane
and the variables are represented\nas convex prediction regions rather than
vectors as in a classical or binary biplot.\nUsing the methods from Computational
Geometry, the set of prediction regions is converted to a set of points\nin such a
way that the prediction for each individual is established by its
closest\n\"category point\". Then interpretation is based on distances rather than
on projections.\nIn this package we implement the geometry of such a representation
and construct computational algorithms\nfor the estimation of parameters and the
calculation of prediction regions.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"NominalLogisticBiplot","Repository":"http:\/
\/cran.csiro.au\/src\/contrib","Title":"Biplot representations of categorical
data","Version":"0.2"},"NonpModelCheck":{"Author":"Adriano Zanin
Zambom","Depends":"R (>= 3.2.0), graphics","Description":"Provides tests of
significance for covariates (or groups of covariates) in a fully nonparametric
regression model and a variable (or group) selection procedure based on False
Discovery Rate. In addition, it provides a function for local polynomial regression
for any number of dimensions, using a bandwidth specified by the user or
automatically chosen by cross validation or an adaptive
procedure.","Imports":"dr","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"NonpModelCheck","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Model Checking and Variable Selection in
Nonparametric\nRegression","Version":"2.0"},"NormPsy":{"Author":"Cecile Proust-
Lima, Viviane Philipps","Depends":"R (>= 2.14.0)","Description":"Functions for
normalizing psychometric test scores. The normalization aims at correcting the
metrological properties of the psychometric tests such as the ceiling and floor
effects and the curvilinearity (unequal interval scaling). Functions to compute and
plot predictions in the natural scale of the psychometric test from the estimates
of a linear mixed model estimated on the normalized scores are also
provided.","Imports":"lcmm (>=
1.7.1)","License":"GPL","NeedsCompilation":"yes","Package":"NormPsy","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Title":"Normalisation of Psychometric
Tests","Version":"1.0.3"},"NormalGamma":{"Author":"S. Plancade and Y.
Rozenholc","Depends":"optimx , histogram","Description":"The functions proposed in
this package compute the density of the sum of a Gaussian and a gamma random
variables, estimate the parameters and correct the noise effect in a gamma-signal
and Gaussian-noise model. This package has been used to implement the background
correction method for Illumina microarray data presented in Plancade S., Rozenholc
Y. and Lund E. \"Generalization of the normal-exponential model : exploration of a
more accurate parameterization for the signal distribution on Illumina
BeadArrays\", BMC Bioinfo 2012, 13(329).","License":"GPL-
2","NeedsCompilation":"no","Package":"NormalGamma","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Normal-gamma convolution
model","Version":"1.1"},"NormalLaplace":{"Author":"David Scott
<d.scott@auckland.ac.nz>, Jason Shicong Fu and\nSimon Potter","Depends":"R (>=
2.3.0), DistributionUtils, GeneralizedHyperbolic","Description":"This package
provides functions for the normal Laplace\ndistribution. It is currently under
development and provides\nonly limited functionality. Density, distribution and
quantile\nfunctions, random number generation, and moments are
provided.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"NormalLaplace","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"RUnit","Title":"The Normal Laplace
Distribution","Version":"0.2-0"},"NostalgiR":{"Author":"Hien D.
Nguyen","Depends":"txtplot","Description":"Provides functions to produce advanced
ascii graphics, directly to the terminal window. This package utilizes the
txtplot() function from the 'txtplot' package, to produce text-based histograms,
empirical cumulative distribution function plots, scatterplots with fitted and
regression lines, quantile plots, density plots, image plots, and contour
plots.","License":"LGPL-
3","NeedsCompilation":"no","Package":"NostalgiR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Advanced Text-Based
Plots","Version":"1.0.2"},"Nozzle.R1":{"Author":"Nils Gehlenborg
<nils@hms.harvard.edu>","Description":"The Nozzle package provides an API to
generate HTML\nreports with dynamic user interface elements based on\nJavaScript
and CSS (Cascading Style Sheets). Nozzle was\ndesigned to facilitate summarization
and rapid browsing of\ncomplex results in data analysis pipelines where
multiple\nanalyses are performed frequently on big data sets. The package\ncan be
applied to any project where user-friendly reports need\nto be
created.","License":"LGPL-
2","NeedsCompilation":"no","Package":"Nozzle.R1","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Nozzle
Reports","URL":"http:\/\/github.com\/parklab\/nozzle,\nhttp:\/\/gdac.broadinstitute
.org\/nozzle","Version":"1.1-1"},"OAIHarvester":{"Author":"Kurt Hornik [aut,
cre]","Description":"\nHarvest metadata using the Open Archives Initiative Protocol
for Metadata\nHarvesting (OAI-PMH) version 2.0.","Imports":"XML, curl,
2","NeedsCompilation":"no","Package":"OAIHarvester","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Harvest Metadata Using OAI-PMH v2.0","Version":"0.2-
0"},"OBsMD":{"Author":"Marta Nai Ruscone based on Laura Deldossi's
code.","Depends":"R(>= 3.02.02)","Description":"Implements the objective Bayesian
methodology proposed in Consonni and Deldossi in order to choose the optimal
experiment that better discriminate between competing models.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"OBsMD","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Objective Bayesian Model Discrimination in Follow-Up
Designs","Version":"0.1-0.4"},"ODB":{"Author":"Sylvain
Mareschal","Depends":"methods, DBI, RJDBC","Description":"This package provides
functions to create, connect, update\nand query HSQL databases embedded in Open
Document Databases\n(.odb) files, as OpenOffice and LibreOffice do.","License":"GPL
(>=
3)","NeedsCompilation":"no","Package":"ODB","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Open Document Databases (.odb)
management","URL":"http:\/\/bioinformatics.ovsa.fr\/R","Version":"1.1.1"},"ODMconve
rter":{"Author":"Martin Dugas","Depends":"R (>=
2.13.1)","Description":"Transformation of 'ODM' (see http:\/\/www.cdisc.org\/odm)
files into R format, Microsoft Office format, 'CDA' format and vice versa. 'ODM'
format is commonly used in clinical trials. Semantic annotation (such as 'UMLS',
'SNOMED' or 'LOINC' codes) are transformed accordingly.","Imports":"XML,
xlsx","License":"GPL","NeedsCompilation":"no","Package":"ODMconverter","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Title":"Tools to Convert ODM
Files","Version":"2.1"},"OData":{"Author":"Patrick Beaucamp, Kevin Monnery,
Sebastien Vigroux, BPM-Conseil","Description":"Helper methods for accessing data
from web service based on OData Protocol.\nIt provides several helper methods to
access the service metadata, the data from datasets and to download some file
resources (it only support CSV for now).\nFor more information about OData go to
http:\/\/www.odata.org\/documentation\/.","Imports":"XML, RJSONIO,
2","NeedsCompilation":"no","Package":"OData","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"R Helper for OData Web Services","Version":"0.3"},"OECD":
{"Author":"Eric Persson [aut, cre]","Description":"Search and extract data from the
OECD.","Imports":"httr (>= 0.6.1), rsdmx (>= 0.4-7), methods (>= 3.2.2), xml2\n(>=
0.1.2)","License":"CC0","NeedsCompilation":"no","Package":"OECD","Repository":"http
:\/\/cran.csiro.au\/src\/contrib","Suggests":"knitr, ggplot2,
testthat","Title":"Search and Extract Data from the
OECD","URL":"https:\/\/www.github.com\/expersso\/OECD","Version":"0.2.2"},"OIdata":
{"Author":"Andrew P Bray and David M Diez","Depends":"RCurl, maps, R (>=
2.10)","Description":"A collection of data sets from several sources that may
be\nuseful for teaching, practice, or other purposes. Functions\nhave also been
included to assist in the retrieval of table\ndata from websites or in visualizing
sample data.","Imports":"RCurl, maps","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"OIdata","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Data sets and supplements
(OpenIntro)","URL":"http:\/\/www.openintro.org","Version":"1.0"},"OIsurv":
{"Author":"David M Diez","Depends":"stats, survival,
KMsurv","Description":"Supplemental functions and data for the OpenIntro guide to
the survival package in R.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"OIsurv","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Survival analysis supplement to OpenIntro
guide","URL":"http:\/\/www.openintro.org\/stat\/surv.php","Version":"0.2"},"OLScurv
e":{"Author":"Phil Chalmers [cre, aut],\nCarrie Smith [ctb],\nMatthew Sigal
[ctb]","Depends":"lattice","Description":"Provides
tools for more easily organizing and\nplotting individual ordinary least square
(OLS) growth curve\ntrajectories.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"OLScurve","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat, knitr, lavaan","Title":"OLS growth curve
trajectories","URL":"https:\/\/github.com\/philchalmers\/OLScurve","Version":"0.2.0
"},"ONETr":{"Author":"Eric Knudsen","Depends":"XML, RCurl,
plyr","Description":"Provides a series of functions designed to enable users to
easily search and interact with occupational data from the O*NET API
<www.onetonline.org>. The package produces parsed and listed XML data for custom
interactions, or pre-packaged functions for easy extraction of specific data (e.g.,
Knowledge, Skills, Abilities, Work Styles, etc.).","License":"GPL-
3","NeedsCompilation":"no","Package":"ONETr","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Efficient Authenticated Interaction with the O*NET
API","Version":"1.0.3"},"OOmisc":{"Author":"Ozgur Asar, Ozlem
Ilk","Description":"Includes miscellaneous functions.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"OOmisc","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Ozgur-Ozlem Miscellaneous","Version":"1.2"},"OPDOE":
{"Author":"Petr Simecek <simecek@gmail.com>,\nJuergen Pilz <juergen.pilz@uni-
klu.ac.at>,\nMingui Wang <mail.mwang@gmail.com>,\nAlbrecht Gebhardt
<albrecht.gebhardt@uni-klu.ac.at>.","Depends":"gmp","Description":"Experimental
Design","Imports":"mvtnorm, orthopolynom, nlme, crossdes, polynom","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"OPDOE","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"OPtimal Design Of Experiments","Version":"1.0-9"},"OPI":
{"Author":"Andrew Turpin, David Lawson, Matthias
Muller","Depends":"methods","Description":"Implementation of the Open Perimetry
Interface (OPI) for simulating and controlling visual field machines using R. The
OPI is a standard for interfacing with visual field testing machines (perimeters).
It specifies basic functions that allow many visual field tests to be constructed.
As of February 2015 it is fully implemented on the Octopus 600 and Octopus 900 and
partially on the Heidelberg Edge Perimeter and the Kowa AP 7000. It also has a
cousin: the R package visualFields, which has tools for analysing and manipulating
visual field data.","License":"GPL-
3","NeedsCompilation":"no","Package":"OPI","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Open Perimetry
Interface","URL":"http:\/\/perimetry.org\/OPI","Version":"2.3"},"ORCI":
{"Author":"Libo Sun","Description":"Computes various confidence intervals for the
odds ratio of two independent binomial proportions.","Imports":"BiasedUrn,
BlakerCI, PropCIs","License":"GPL-
2","NeedsCompilation":"no","Package":"ORCI","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Several confidence intervals for the odds
ratio","Version":"1.1"},"ORCME":{"Author":"Adetayo Kasim, Martin Otava, Tobias
Verbeke","Depends":"R (>= 2.10)","Description":"Provides clustering of genes with
similar\ndose response (or time course) profiles. It implements the
method\ndescribed by Lin et al. (2012).","Imports":"Iso","License":"GPL-
3","NeedsCompilation":"no","Package":"ORCME","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Order Restricted Clustering for Microarray
Experiments","Version":"2.0.2"},"ORDER2PARENT":{"Author":"Cheng
Chou","Depends":"splines, Matrix","Description":"This package uses B-spline based
nonparametric smooth\nestimators to estimate parent distributions given
observations\non multiple order statistics.","License":"GPL-
2","NeedsCompilation":"no","Package":"ORDER2PARENT","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Estimate parent distributions with data of several
order\nstatistics","Version":"1.0"},"ORIClust":{"Author":"Tianqing Liu, Nan Lin,
Ningzhong Shi and Baoxue Zhang","Description":"ORIClust is a user-friendly R-based
software package for\ngene clustering. Clusters are given by genes matched
to\nprespecified profiles across various ordered treatment groups.\nIt is
particularly useful for analyzing data obtained from\nshort time-course or dose-
response microarray experiments.","License":"GPL-
2","NeedsCompilation":"no","Package":"ORIClust","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Order-restricted Information Criterion-based
Clustering\nAlgorithm","Version":"1.0-1"},"ORMDR":{"Author":"Eun-Kyung Lee, Sung
Gon Yi, Yoojin Jung, Junghyun Namkung,\nTaesung Park","Description":"Odds ratio
based multifactor-dimensionality reduction\nmethod for detecting gene-gene
interactions","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ORMDR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"ORMDR","Version":"1.3-2"},"OTE":{"Author":"Zardad Khan,
Asma Gul, Aris Perperoglou, Osama Mahmoud, Werner Adler, Miftahuddin and Berthold
Lausen","Description":"Functions for creating ensembles of optimal trees for
regression, classification and class membership probability estimation are given. A
few trees are selected from an initial set of trees grown by random forest for the
ensemble on the basis of their individual and collective performance. Trees are
assessed on out-of-bag data and on an independent training data set for individual
and collective performance respectively. The prediction functions return estimates
of the test responses and their class membership probabilities. Unexplained
variations, error rates, confusion matrix, Brier scores, etc. are also returned for
the test data.","Imports":"randomForest,stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"OTE","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Optimal Trees Ensembles for Regression, Classification and
Class\nMembership Probability Estimation","Version":"1.0"},"OTRselect":
{"Author":"Wenbin Lu, Hao Helen Zhang, Donglin Zeng, Yuan Geng, and Shannon
Holloway","Depends":"stats, lars, survival, methods","Description":"A penalized
regression framework that can simultaneously estimate the optimal treatment
strategy and identify important variables. Appropriate for either censored or
uncensored continuous response.","License":"GPL-
2","NeedsCompilation":"no","Package":"OTRselect","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Variable Selection for Optimal Treatment
Decision","Version":"1.0"},"OTUtable":{"Author":"Alexandra Linz","Depends":"R (>=
2.10)","Description":"Analyses of OTU tables produced by 16S sequencing, as well as
example data. It contains the data and scripts used in the paper Linz, et al.
(2016) \"Seasonal mixing as a barrier to the development of stable bacterial
communities in bog lakes\" (Manuscript in prep).","License":"GPL-
3","NeedsCompilation":"no","Package":"OTUtable","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"North Temperate Lakes - Microbial Observatory 16S Time
Series\nData and Functions","Version":"1.0.0"},"OUwie":{"Author":"Jeremy M.
Beaulieu <jbeaulieu@nimbios.org>, Brian O'Meara <bomeara@utk.edu>","Depends":"R (>=
3.2.0), ape, nloptr","Description":"Calculates and compares rate differences of
continuous character evolution under Brownian motion and a new set of Ornstein-
Uhlenbeck-based Hansen models that allow the strength of selection and stochastic
motion to vary across selective regimes.","Imports":"numDeriv, corpcor, lattice,
grDevices, phytools, phangorn,\nstats, expm, corHMM, Rmpfr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"OUwie","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Analysis of Evolutionary Rates in an OU
Framework","Version":"1.49"},"Oarray":{"Author":"Jonathan Rougier
<j.c.rougier@bristol.ac.uk>","Depends":"methods","Description":"Generalise the
starting point of the array
index","License":"GPL","NeedsCompilation":"no","Package":"Oarray","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Title":"Arrays with arbitrary
offsets","Version":"1.4-5"},"OasisR":{"Author":"Mihai Tivadar
<mihai.tivadar@irstea.fr>","Depends":"R (>= 3.1.2)","Description":"A set of indexes
and tests for the analysis of social segregation.","Imports":"rgdal (>= 0.9-1),
rgeos (>= 0.3-8), spdep (>= 0.5-83)","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"OasisR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat, knitr","Title":"Outright Tool for the Analysis
of Spatial Inequalities and\nSegregation","Version":"1.0.0"},"OceanView":
{"Author":"Karline Soetaert <karline.soetaert@nioz.nl>","Depends":"plot3D,
plot3Drgl, R (>= 3.2)","Description":"Functions for transforming and viewing 2-D
and 3-D (oceanographic) data and model output.","Imports":"methods, graphics,
grDevices, stats, rgl, shape","License":"GPL (>=
3.0)","NeedsCompilation":"yes","Package":"OceanView","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Visualisation of Oceanographic Data and Model
Output","Version":"1.0.4"},"Ohmage":{"Author":"Jeroen Ooms","Depends":"R (>= 2.14),
stats, methods","Description":"R Client for Ohmage 2 server. Implements basic
R\nfunctions to retrieve and process data.","Imports":"RCurl,
RJSONIO","License":"GPL","NeedsCompilation":"no","Package":"Ohmage","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Suggests":"XML","Title":"R Client for Ohmage
2 server","Version":"2.11-4"},"OjaNP":{"Author":"Daniel Fischer, Jyrki Möttönen,
Klaus Nordhausen, Daniel Vogel","Depends":"R (>= 2.9.0), ICS,
ICSNP","Description":"The package provides functions for the Oja median, Oja\nsigns
and ranks and methods based upon them.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"OjaNP","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Multivariate Methods Based on the Oja Median and
Related\nConcepts","Version":"0.9-8"},"OligoSpecificitySystem":{"Author":"Rory
Michelland <rory.michelland@gmail.com>,Laurent
Cauquil\n<laurent.cauquil@toulouse.inra.fr>","Depends":"tcltk,tkrplot","Description
":"Calculate the theorical specificity of a system of\nmultiple primers used for
PCR, qPCR primers or degenerated\nprimer design","License":"GPL-
2","NeedsCompilation":"no","Package":"OligoSpecificitySystem","Repository":"http:\/
\/cran.csiro.au\/src\/contrib","Title":"Oligo Specificity
System","Version":"1.3"},"OmicKriging":{"Author":"Hae Kyung Im, Heather E. Wheeler,
Keston Aquino Michaels, Vassily\nTrubetskoy","Depends":"R(>= 2.15.1),
doParallel","Description":"It provides functions to generate a correlation
matrix\nfrom a genetic dataset and to use this matrix to predict the phenotype of
an\nindividual by using the phenotypes of the remaining individuals
through\nkriging. Kriging is a geostatistical method for optimal prediction or
best\nunbiased linear prediction. It consists of predicting the value of
a\nvariable at an unobserved location as a weighted sum of the variable
at\nobserved locations. Intuitively, it works as a reverse linear
regression:\ninstead of computing correlation (univariate regression coefficients
are\nsimply scaled correlation) between a dependent variable Y and
independent\nvariables X, it uses known correlation between X and Y to predict
Y.","Imports":"ROCR, irlba, parallel, foreach","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"OmicKriging","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Poly-Omic Prediction of Complex
TRaits","Version":"1.4.0"},"Oncotree":{"Author":"Aniko Szabo, Lisa
Pappas","Depends":"R (>= 2.10), boot","Description":"Contains functions to
construct and evaluate directed tree structures that\nmodel the process of
occurrence of genetic alterations during carcinogenesis.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Oncotree","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"lattice","Title":"Estimating oncogenetic
trees","Version":"0.3.3"},"OneArmPhaseTwoStudy":{"Author":"Marius
Wirths","Depends":"methods, Rcpp (>= 0.9.11), R (>= 3.1.0)","Description":"Purpose
of this package is it to plan, monitor and evaluate oncological phase II studies.
In general this kind of studies are single-arm trials with planned interim analysis
and binary endpoint. To meet the resulting requirements, the package provides
functions to calculate and evaluate 'Simon's two-stage designs' and 'so-called'
'subset designs'. If you are unfamiliar with this package a good starting point is
to take a closer look at the functions getSolutions() and
getSolutionsSub1().","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"OneArmPhaseTwoStudy","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Title":"Planing, Monitoring and Evaluating
Oncological Phase 2 Studies","Version":"0.1.4"},"OneTwoSamples":{"Author":"Ying-
Ying Zhang (Robert)","Description":"In this package, we introduce an R
function\none_two_sample() which can deal with one and two (normal)\nsamples. For
one normal sample x, the function reports\ndescriptive statistics, plot, interval
estimation and test of\nhypothesis of x. For two normal samples x and y, the
function\nreports descriptive statistics, plot, interval estimation and\ntest of
hypothesis of x and y, respectively. It also reports\ninterval estimation and test
of hypothesis of mu1-mu2 (the\ndifference of the means of x and y) and sigma1^2 \/
sigma2^2\n(the ratio of the variances of x and y), tests whether x and y\nare from
the same population, finds the correlation coefficient\nof x and y if x and y have
the same length.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"OneTwoSamples","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Deal with one and two (normal)
samples","Version":"1.0-3"},"OpasnetUtils":{"Author":"Teemu Rintala, Einari
Happonen, Jouni Tuomisto","Description":"Contains tools for open assessment and
modelling in Opasnet,\na wiki-based web site and workspace for societal decision
making\n(see <http:\/\/en.opasnet.org\/w\/Main_Page> for more information).\nThe
core principle of the workspace is maximal openness and modularity.\nVariables are
defined on public wiki pages using wiki inputs\/tables,\ndatabases and R code. This
package provides the functionality to download and use these\nvariables. It also
contains health impact assessment tools such as\nspatial methods for exposure
modelling.","Imports":"methods, rjson, RCurl, reshape2, triangle,
httpRequest,\ndigest, xtable, ggplot2, rgdal, sp, plyr","License":"GPL-
3","NeedsCompilation":"no","Package":"OpasnetUtils","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Opasnet Modelling Environment Utility
Functions","URL":"http:\/\/en.opasnet.org\/w\/Main_Page
,\nhttp:\/\/en.opasnet.org\/w\/Modelling_in_Opasnet
,\nhttp:\/\/en.opasnet.org\/w\/OpasnetUtils","Version":"1.2.0"},"OpenCL":
{"Author":"Simon Urbanek <Simon.Urbanek@r-project.org>","Depends":"R (>=
2.0.0)","Description":"This package provides an interface to OpenCL, allowing R\nto
leverage computing power of GPUs and other HPC
accelerator\ndevices.","License":"BSD","NeedsCompilation":"yes","Package":"OpenCL",
"Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Interface allowing R
to use OpenCL","URL":"http:\/\/www.rforge.net\/OpenCL\/","Version":"0.1-
3"},"OpenMPController":{"Author":"Simon Guest
<simon.guest@agresearch.co.nz>","Description":"The OpenMPController package
provides a function\n'omp_set_num_threads()' to set the number of OpenMP threads
to\nbe used. This may be useful, for example, when linking against\na vendor
optimised BLAS\/LAPACK library (e.g. the AMD Core Math\nLibrary), since the
defaults used by those libraries may not be\nhighly performant.","License":"GPL-
2","NeedsCompilation":"yes","Package":"OpenMPController","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Control number of OpenMP threads
dynamically","Version":"0.1-2"},"OpenMx":{"Author":"Steven M. Boker [aut],\nMichael
C. Neale [aut],\nHermine H. Maes [aut],\nMichael J. Wilde [ctb],\nMichael Spiegel
[aut],\nTimothy R. Brick [aut],\nRyne Estabrook [aut],\nTimothy C. Bates
[aut],\nParas Mehta [ctb],\nTimo von Oertzen [ctb],\nRoss J. Gore [aut],\nMichael
D. Hunter [aut],\nDaniel C. Hackett [ctb],\nJulian Karch [ctb],\nAndreas M.
Brandmaier [ctb],\nJoshua N. Pritikin [aut, cre],\nMahsa Zahery [aut],\nRobert M.
Kirkpatrick [aut],\nYang Wang [ctb],\nCharles Driver [ctb]","Depends":"R (>=
3.0.2), digest, MASS, methods, Matrix, Rcpp, parallel","Description":"Facilitates
treatment of statistical model specifications as things\nthat can be generated and
manipulated programmatically. Structural equation\nmodels may be specified with
reticular action model matrices or paths, linear\nstructural relations matrices or
paths, or directly in matrix algebra. Fit\nfunctions include full information
maximum likelihood, maximum likelihood, and\nweighted least squares. Example models
include confirmatory factor, multiple\ngroup, mixture distribution, categorical
threshold, modern test theory,\ndifferential equations, state space, and many
others.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"OpenMx","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"mvtnorm, numDeriv, roxygen2 (>= 3.1), Rmpi, rpf (>=
0.45),\nsnowfall, lme4","Title":"Extended Structural Equation
Modelling","URL":"http:\/\/openmx.psyc.virginia.edu,
https:\/\/github.com\/OpenMx\/OpenMx","Version":"2.5.2"},"OpenRepGrid":
{"Author":"Mark Heckmann [aut, cre]","Depends":"pvclust","Description":"Tools to
analyse repertory grid data","Imports":"methods, grid, colorspace, plyr, stringr,
abind, rgl,\nGPArotation, psych, XML, tcltk","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"OpenRepGrid","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"xlsx","Title":"Tools to analyse repertory grid
data","Version":"0.1.9"},"OpenStreetMap":{"Author":"Ian Fellows, using the
JMapViewer library by Jan Peter Stotz","Depends":"methods, R (>=
2.10.0)","Description":"Accesses high resolution raster maps using the
OpenStreetMap protocol. Dozens of road, satellite,\nand topographic map servers are
directly supported, including CloudMade,\nMapnik, Bing, stamen, and MapQuest. Maps
can be plotted using either base\ngraphics, or ggplot2. This package is not
affiliated with the OpenStreetMap.org mapping project.","Imports":"ggplot2 (>=
0.9.0), rJava, raster, rgdal, sp","License":"GPL-2 | file
LICENCE","NeedsCompilation":"no","Package":"OpenStreetMap","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Suggests":"colorspace, maptools","Title":"Access to
Open Street Map Raster Images","URL":"http:\/\/www.fellstat.com
http:\/\/blog.fellstat.com\/?
cat=15\nhttp:\/\/research.cens.ucla.edu\/","Version":"0.3.2"},"OptGS":
{"Author":"James Wason [aut, cre],\nJohn Burkardt [ctb]","Description":"Functions
to find near-optimal multi-stage designs for continuous outcomes.","License":"GPL-
2","NeedsCompilation":"yes","Package":"OptGS","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Near-Optimal and Balanced Group-Sequential Designs for
Clinical\nTrials with Continuous Outcomes","Version":"1.1.1"},"OptHedging":
{"Author":"Bruno Remillard","Description":"Estimation of value and hedging strategy
of call and put options, based on optimal hedging and Monte Carlo method, from
Chapter 3 of 'Statistical Methods for Financial Engineering', by Bruno Remillard,
CRC Press, (2013).","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"OptHedging","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Estimation of value and hedging strategy of call and
put\noptions","URL":"http:\/\/www.r-project.org,
http:\/\/www.brunoremillard.com","Version":"1.0"},"OptInterim":{"Author":"Bo Huang
<bo.huang@pfizer.com> and Neal
Thomas\n<neal.thomas@pfizer.com>","Depends":"mvtnorm, clinfun, stats, graphics, R
(>= 2.14.1)","Description":"Optimal two and three
stage designs monitoring\ntime-to-event endpoints at a specified
timepoint","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"OptInterim","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Optimal Two and Three Stage Designs for Single-Arm and
Two-Arm\nRandomized Controlled Trials with a Long-Term Binary
Endpoint","Version":"3.0.1"},"OptiQuantR":{"Author":"Joao Pinelo Silva [aut,
cre]","Depends":"R (>= 3.2.2)","Description":"Greatly simplifies the process to
read, analyze and report log data\ncollated by OptiQuant (optiquant.opti55.com) in
R. It automates efficient\nimport of databases while preparing them for analysis
and for semi-automated\nreporting.","Imports":"data.table (>= 1.9.4), lubridate (>=
3","NeedsCompilation":"no","Package":"OptiQuantR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat","Title":"Simplifies and Automates
Analyzing and Reporting OptiQuant's log\nData","Version":"0.0.1"},"OptimaRegion":
{"Author":"Enrique del Castillo, John Hunt, and James Rapkin","Depends":"R (>=
3.2.3)","Description":"Computes confidence regions on the location of\nresponse
surface optima.","Imports":"fields,rsm,nloptr,DepthProc","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"OptimaRegion","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Confidence Regions for
Optima","Version":"0.1.0"},"OptimalCutpoints":{"Author":"Monica Lopez-Raton, Maria
Xose Rodriguez-Alvarez","Description":"This package enables users to compute one or
more optimal cutpoints for diagnostic tests or continuous markers. Various
approaches for selecting optimal cutoffs have been implemented, including methods
based on cost-benefit analysis and diagnostic test accuracy measures
(Sensitivity\/Specificity, Predictive Values and Diagnostic Likelihood Ratios).
Numerical and graphical output for all methods is easily
obtained.","License":"GPL","NeedsCompilation":"no","Package":"OptimalCutpoints","Re
pository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Computing optimal
cutpoints in diagnostic tests","Version":"1.1-3"},"OptionPricing":{"Author":"Kemal
Dingec, Wolfgang Hormann","Description":"Efficient Monte Carlo Algorithms for the
price and the sensitivities of Asian and European Options under Geometric Brownian
Motion.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"OptionPricing","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Option Pricing with Efficient Simulation
Algorithms","Version":"0.1"},"OrdFacReg":{"Author":"Kaspar
Rufibach","Depends":"survival, eha, MASS","Description":"In biomedical studies,
researchers are often interested in assessing the association between one or more
ordinal explanatory variables and an outcome variable, at the same time adjusting
for covariates of any type. The outcome variable may be continuous, binary, or
represent censored survival times. In the absence of a precise knowledge of the
response function, using monotonicity constraints on the ordinal variables improves
efficiency in estimating parameters, especially when sample sizes are small. This
package implements an active set algorithm that efficiently computes such
estimators.","Imports":"stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"OrdFacReg","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Least Squares, Logistic, and Cox-Regression with
Ordered\nPredictors","URL":"http:\/\/www.kasparrufibach.ch","Version":"1.0.6"},"Ord
LogReg":{"Author":"Bethany Wolf","Depends":"LogicReg","Description":"Method for
develops a classification model for ordinal responses based on logic
regression.","License":"GPL-
2","NeedsCompilation":"no","Package":"OrdLogReg","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Ordinal Logic Regression","Version":"1.1"},"OrdMonReg":
{"Author":"Fadoua Balabdaoui, Kaspar Rufibach, Filippo
Santambrogio","Description":"We consider the problem of estimating two isotonic
regression curves g1* and g2* under the constraint that they are ordered, i.e. g1*
<= g2*. Given two sets of n data points y_1, ..., y_n and z_1, ..., z_n that are
observed at (the same) deterministic design points x_1, ..., x_n, the estimates are
obtained by minimizing the Least Squares criterion L(a, b) = sum_{i=1}^n (y_i -
a_i)^2 w1(x_i) + sum_{i=1}^n (z_i - b_i)^2 w2(x_i) over the class of pairs of
vectors (a, b) such that a and b are isotonic and a_i <= b_i for all i = 1, ..., n.
We offer two different approaches to compute the estimates: a projected subgradient
algorithm where the projection is calculated using a PAVA as well as Dykstra's
cyclical projection algorithm.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"OrdMonReg","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Compute least squares estimates of one bounded or two
ordered\nisotonic regression
curves","URL":"http:\/\/www.ceremade.dauphine.fr\/~fadoua,\nhttp:\/\/www.kasparrufi
bach.ch,\nhttp:\/\/www.math.u-psud.fr\/~santambr\/","Version":"1.0.3"},"OrdNor":
{"Author":"Anup Amatya and Hakan Demirtas","Depends":"mvtnorm, corpcor, Matrix,
GenOrd","Description":"Implementation of a procedure for generating samples from a
mixed distribution of ordinal and normal random variables with pre-specified
correlation matrix and marginal
distributions.","Imports":"stats","License":"GPL","NeedsCompilation":"no","Package"
:"OrdNor","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Concurrent
Generation of Ordinal and Normal Data with Given\nCorrelation Matrix and Marginal
Distributions","Version":"2.0"},"OrdinalLogisticBiplot":{"Author":"Julio Cesar
Hernandez Sanchez, Jose Luis Vicente-Villardon","Depends":"R (>=
2.15.1),mirt,MASS,NominalLogisticBiplot","Description":"Analysis of a matrix of
polytomous items using Ordinal Logistic Biplots (OLB)\nThe OLB procedure extends
the binary logistic biplot to ordinal (polytomous) data.\nThe individuals are
represented as points on a plane and the variables are represented\nas lines rather
than vectors as in a classical or binary biplot, specifying the points\nfor each of
the categories of the variable.\nThe set of prediction regions is established by
stripes perpendicular to the line\nbetween the category points, in such a way that
the prediction for each individual is given\nby its projection into the line of the
variable.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"OrdinalLogisticBiplot","Repository":"http:\/
\/cran.csiro.au\/src\/contrib","Title":"Biplot representations of ordinal
variables","Version":"0.4"},"OrgMassSpecR":{"Author":"Nathan G. Dodder, with code
contributions from Katharine M. Mullen.","Depends":"R (>=
3.0.0)","Description":"Organic\/biological mass spectrometry data
analysis.","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"OrgMassSpecR","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"lattice, knitr","Title":"Organic Mass
Spectrometry","URL":"http:\/\/OrgMassSpec.github.io\/","Version":"0.4-4"},"OriGen":
{"Author":"John Michael O Ranola, John Novembre, and Kenneth
Lange","Depends":"maps, ggplot2","Description":"Used primarily for estimates of
allele frequency surfaces from point estimates.\nIt can also place individuals of
unknown origin back onto the geographic map with great accuracy.\nAdditionally, it
can place admixed individuals by estimating contributing fractions at
each\nlocation on a map. Lastly, it can rank SNPs by their ability to differentiate
populations.\nSee \"Fast Spatial Ancestry via Flexible Allele Frequency Surfaces\"
(John Michael Ranola, John\nNovembre, Kenneth Lange) in Bioinformatics 2014 for
more info.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"OriGen","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Fast Spatial Ancestry via Flexible Allele Frequency
Surfaces","Version":"1.4.3"},"OrthoPanels":{"Author":"Davor Cubranic [aut,
cre],\nMark Pickup [aut],\nPaul Gustafson [aut],\nGeoffrey Evans
[aut]","Depends":"R (>= 3.1.0)","Description":"Implements the orthogonal
reparameterization\napproach recommended by Lancaster (2002) to estimate dynamic
panel\nmodels with fixed effects (and optionally: panel specific\nintercepts). The
approach uses a likelihood-based estimator and\nproduces estimates that are
asymptotically unbiased as N goes to\ninfinity, with a T as low as
2.","Imports":"MASS","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"OrthoPanels","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat, knitr","Title":"Dynamic Panel Models
with Orthogonal Reparameterization of Fixed\nEffects","Version":"0.9-
1"},"OutbreakTools":{"Author":"The Hackout team (In alphabetic order: David
Aanensen, Marc Baguelin, Paul Birrell, Simon Cauchemez, Anton Camacho, Caroline
Colijn, Anne Cori, Xavier Didelot, Ken Eames, Christophe Fraser, Simon Frost, Niel
Hens, Joseph Hugues, Thibaut Jombart, Lulla Opatowski, Oliver Ratmann, Samuel
Soubeyrand, Marc Suchard, Jacco Wallinga, Rolf Ypma)","Depends":"R (>= 3.0.0),
methods, ggplot2, network, knitr","Description":"Implements basic tools for
storing, handling and visualizing disease outbreak data, as well as simple analysis
tools. OutbreakTools defines the new formal class obkData which can be used to
store any case-base outbreak data, and provides summaries for these objects,
alongside a range of functions for subsetting and data manipulation. It implements
a range of graphics for visualising timelines, maps, contact networks and genetic
analyses. It also includes a simple case-base outbreak simulation
tool.","Imports":"utils, RColorBrewer, ape, reshape2, sna, plyr, ggmap,
scales,\nrjson, networkDynamic, RCurl","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"OutbreakTools","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"EpiEstim","Title":"Basic Tools for the Analysis
of Disease Outbreaks","URL":"http:\/\/sites.google.com\/site\/therepiproject\/r-
pac\/about","Version":"0.1-14"},"OutlierDC":{"Author":"
Soo-Heang Eo [aut, cre],\nHuixia Judy Wang [ctb],\nLan Wang [ctb],\nHyungJun Cho
[aut]","Depends":"R (>= 3.0.0), methods, survival, quantreg,
Formula","Description":"This package provides three algorithms to detect outlying
observations for censored survival data.","License":"GPL-
3","NeedsCompilation":"no","Package":"OutlierDC","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Outlier Detection using quantile regression for Censored
Data","Version":"0.3-0"},"OutlierDM":{"Author":"Soo-Heang Eo [aut, cre],\nHyungJun
Cho [aut]","Depends":"R (>= 3.1.0)","Description":"Detecting outlying values such
as genes, peptides or samples for multi-replicated high-throughput high-dimensional
data","Imports":"quantreg, MatrixModels, outliers, pcaPP, methods,
3","NeedsCompilation":"no","Package":"OutlierDM","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Outlier Detection for Multi-replicated High-throughput
Data","Version":"1.1.1"},"OutrankingTools":{"Author":"Michel Prombo
<michel.prombo@statec.etat.lu> or
<michel.prombo@gmail.com>","Depends":"igraph","Description":"Functions to process
''outranking'' ELECTRE methods existing in the literature. See,
e.g.,\n<http:\/\/en.wikipedia.org\/wiki\/ELECTRE> about the outranking approach and
the foundations of ELECTRE methods.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"OutrankingTools","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Functions for Solving Multiple-criteria Decision-
making Problems","Version":"1.0"},"OxyBS":{"Author":"E. Andres Houseman, Sc.D. and
Kevin C. Johnson","Depends":"R (>= 3.2.2)","Description":"\nProvides utilities for
processing of Oxy-Bisulfite microarray data\n(e.g. via the Illumina Infinium
platform) with tandem arrays, one using conventional\nbisulfite sequencing, the
other using oxy-bisulfite sequencing.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"OxyBS","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Processing of Oxy-Bisulfite Microarray
Data","Version":"1.0"},"PAC":{"Author":"Dangna Li, Henry
Li","Description":"Implements Partition-Assisted Clustering, which utilizes a
collection of partition based nonparametric density estimation techniques to
improve the robustness and accuracy of downstream clustering.\nThe package also
provides functions for effectively visualizing the clustering results.\nIt is
particularly useful for finding and visualizing subpopulations in single-cell data
analysis.","Imports":"Rcpp (>=
0.12.2),NMF,RJSONIO,data.table,dplyr","License":"GPL-
3","NeedsCompilation":"yes","Package":"PAC","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"knitr","Title":"Partition-Assisted
Clustering","Version":"1.0.5"},"PACVB":{"Author":"James Ridgway","Depends":"Rcpp,
MASS","Description":"Variational Bayesian approximations of Gibbs measures with
hinge losses for classification and ranking.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"PACVB","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Variational Bayes (VB) Approximation of Gibbs Posteriors
with\nHinge Losses","Version":"1.1"},"PAFit":{"Author":"Thong Pham, Paul Sheridan,
Hidetoshi Shimodaira","Depends":"R(>= 2.10.0)","Description":"A statistically sound
method for estimating jointly the attachment function and node fitness in a
temporal complex network by maximizing a suitable penalized log-likelihood function
is implemented in this package. Tutorial can be found in the accompanying vignette.
More details about the method can be found at
http:\/\/dx.doi.org\/10.1371\/journal.pone.0137796. To cite this package in your
projects, please run the command: citation(\"PAFit\") for a list of references you
should cite.","Imports":"Rcpp (>= 0.11.3) , grDevices, graphics,
3","NeedsCompilation":"yes","Package":"PAFit","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"R.rsp","Title":"Nonparametric Estimation of Preferential
Attachment and Node\nFitness in Temporal Complex
Networks","URL":"http:\/\/www.thongpham.net,\nhttp:\/\/dx.doi.org\/10.1371\/journal
.pone.0137796","Version":"0.7.5"},"PAGI":{"Author":"Junwei Han,Yanjun Xu,Haixiu
Yang,Chunquan Li and Xia Li","Depends":"R (>= 2.15.1),igraph","Description":"The
package can identify the dysregulated KEGG pathways\nbased on global influence from
the internal effect of pathways\nand crosstalk between pathways. (1) The PAGI
package can\nprioritize the pathways associated with two biological states\nby
statistical significance or FDR. (2) The PAGI package can\nevaluated the global
influence factor (GIF) score in the global\ngene-gene network constructed based on
the relationships of\ngenes extracted from each pathway in KEGG database and
the\noverlapped genes between pathways.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"PAGI","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"Matrix","Title":"The package can identify the
dysregulated KEGG pathways based on\nglobal influence from the internal effect of
pathways and\ncrosstalk between pathways","Version":"1.0"},"PAGWAS":
{"Author":"Marina Evangelou","Depends":"lars, foreach,
mnormt","Description":"Bayesian hierarchical methods for pathway analysis of
genomewide association data: Normal\/Bayes factors and Sparse Normal\/Adaptive
lasso. The Frequentist Fisher's product method is included as well.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"PAGWAS","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Pathway Analysis Methods for Genomewide Association
Data","Version":"2.0"},"PANDA":{"Author":"Hua Li and Pan Tong","Description":"PANDA
(Preferential Attachment based common Neighbor Distribution derived Associations)
is designed to perform the following tasks in PPI networks: (1) identify
significantly functionally associated protein pairs, (2) predict GO terms and KEGG
pathways for proteins, (3) make a cluster of proteins based on the significant
protein pairs, (4) identify subclusters whose members are enriched in KEGG
pathways. For other types of biological networks, (1) and (3) can still be
performed.","Imports":"GO.db, cluster","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"PANDA","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Preferential Attachment Based Common Neighbor
Distribution\nDerived Functional Associations","Version":"0.9.9"},"PANICr":
{"Author":"Steve Bronder <sbronder@stevebronder.com>","Depends":"R(>=
2.10.0)","Description":"This package contains a methodology that makes use of the
factor\nstructure of large dimensional panels to understand the nature
of\nnonstationarity inherent in data. This is referred to as PANIC -
Panel\nAnalysis of Nonstationarity in Idiosyncratic and Common Components.
PANIC\n(2004) includes valid pooling methods that allow panel unit root
tests\ntests to be constructed. PANIC (2004) can detect whether
the\nnonstationarity in a series is pervasive, or variable specific, or
both.\nPANIC (2010) includes the Panel Modified Sargan-Bhargava test, three
models\nfor a Moon and Perron style test, and a bias correction for
the\nidiosyncratic unit root test of PANIC (2004). The PANIC model
approximates\nthe number of factors based on Bai and Ng
(2002).","Imports":"MCMCpack","License":"GPL-
3","NeedsCompilation":"no","Package":"PANICr","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"knitr","Title":"PANIC Tests of
Nonstationarity","URL":"stevebronder.com","Version":"0.0.0.5"},"PAS":
{"Author":"Zhiqiu Hu; Shizhong Xu; Zhiquan Wang; Rongcai Yang","Depends":"R (>=
2.10), glmnet","Description":"An R package for polygenic trait
analysis","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"PAS","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Polygenic Analysis System
(PAS)","URL":"http:\/\/statgen.ucr.edu,
http:\/\/www.ualberta.ca\/~zhiqiu1","Version":"1.2"},"PASWR":{"Author":"Alan T.
Arnholt","Depends":"e1071, MASS, lattice","Description":"Data and functions for the
book PROBABILITY and STATISTICS\nWITH R.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"PASWR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"PROBABILITY and STATISTICS WITH
R","URL":"http:\/\/www1.appstate.edu\/~arnholta\/PASWR\/","Version":"1.1"},"PASWR2"
:{"Author":"Alan T. Arnholt","Depends":"R (>= 2.10), lattice,
ggplot2","Description":"Functions and data sets for the text Probability and
Statistics\nwith R, Second Edition.","Imports":"e1071","License":"GPL-
2","NeedsCompilation":"no","Package":"PASWR2","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Probability and Statistics with R, Second
Edition","Version":"1.0.2"},"PAWL":{"Author":"Luke Bornn, Pierre E.
Jacob","Depends":"methods, mvtnorm, foreach, reshape,
ggplot2","Description":"Implementation of the Parallel Adaptive Wang-
Landau\nalgorithm. Also implemented for comparison: parallel adaptive\nMetropolis-
Hastings,SMC sampler.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"PAWL","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Implementation of the PAWL
algorithm","Version":"0.5"},"PAactivPAL":{"Author":"Yukun Zhang [aut,cre], Haocheng
Li [aut], Sarah Keadle [ctb], Charles Matthews [ctb], Raymond Carroll
[ctb]","Description":"Summarize physical activity (Mets, Proportion, Total, etc.)
in the given time period from accelerometer data. This package has been tested by
data exported from 'activPAL'. 'activPAL' is a wearable device for medical and
healthcare research application developed by PAL Technologies, Glasgow, Scotland. A
simulated accelerometer sample dataset is provided in this package. See
https:\/\/github.com\/YukunZhang\/PAactivPAL1.0 for more
information.","Imports":"stats","License":"GPL-
2","NeedsCompilation":"no","Package":"PAactivPAL","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Summarize Daily Physical
Activity from 'activPAL' Accelerometer\nData","Version":"1.0"},"PBD":
{"Author":"Rampal S. Etienne","Depends":"R (>= 3.0)","Description":"Conducts
maximum likelihood analysis and simulation of the protracted speciation
model.","Imports":"deSolve, ade4, ape, DDD, phytools, graphics, stats,
2","NeedsCompilation":"no","Package":"PBD","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Protracted Birth-Death Model of
Diversification","Version":"1.2"},"PBImisc":{"Author":"Przemyslaw Biecek
<przemyslaw.biecek@gmail.com>","Depends":"R (>= 2.8.0)","Description":"A set of
datasets and functions used in the book\n'Modele liniowe i mieszane w R, wraz z
przykladami w analizie danych'.\nDatasets either come from real studies or are
created to be as similar\nas possible to real studies.","Imports":"lme4,
Matrix","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"PBImisc","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"ggplot2, ca, lattice","Title":"A Set of Datasets Used
in My Classes or in the Book 'Modele\nLiniowe i Mieszane w R, Wraz z Przykladami w
Analizie Danych'","URL":"http:\/\/www.biecek.pl\/R\/","Version":"1.0"},"PBSadmb":
{"Author":"Jon T. Schnute <schnutej-dfo@shaw.ca>,\nRowan Haigh <rowan.haigh@dfo-
mpo.gc.ca>,\nAlex Couture-Beil <alex@mofo.ca>","Depends":"R (>= 2.15.0),
PBSmodelling (>= 2.65)","Description":"R Support for ADMB (Automatic
Differentiation Model Builder)","Imports":"methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"PBSadmb","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"ADMB for R Using Scripts or
GUI","URL":"http:\/\/code.google.com\/p\/pbs-
admb\/","Version":"0.68.104"},"PBSddesolve":{"Author":"Alex Couture-Beil
<alex@mofo.ca>,\nJon T. Schnute <schnutej-dfo@shaw.ca>,\nRowan Haigh
<rowan.haigh@dfo-mpo.gc.ca>,\nNicholas Boers <boersn@macewan.ca>,\nSimon N. Wood,
Ben J. Cairns","Depends":"R (>= 2.15.0)","Description":"This package solves systems
of delay differential equations.\nby interfacing numerical routines written by
Simon N. Wood , with\ncontributions by Benjamin J. Cairns. These numerical routines
first\nappeared in Simon Wood's solv95 program.\nThis package includes a vignette
and a complete user's guide.\n'PBSddesolve' originally appeared on CRAN under the
name 'ddesolve'.\nThat version is no longer supported. The current name emphasizes
a close\nassociation with other PBS packages, particularly
'PBSmodelling'.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"PBSddesolve","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"PBSmodelling","Title":"Solver for Delay
Differential Equations","Version":"1.11.29"},"PBSmapping":{"Author":"Jon T. Schnute
[aut], Nicholas Boers [aut], Rowan Haigh [aut, cre],\nAlex Couture-Beil [ctb],
Denis Chabot [ctb], Chris Grandin [ctb],\nAngus Johnson [ctb], Paul Wessel [ctb],
Franklin Antonio [ctb],\nNicholas J. Lewin-Koh [ctb], Roger Bivand
[ctb]","Depends":"R (>= 2.15.0)","Description":"This software has evolved from
fisheries research conducted at the\nPacific Biological Station (PBS) in `Nanaimo',
British Columbia, Canada. It\nextends the R language to include two-dimensional
plotting features similar\nto those commonly available in a Geographic Information
System (GIS).\nEmbedded C code speeds algorithms from computational geometry, such
as\nfinding polygons that contain specified point events or converting
between\nlongitude-latitude and Universal Transverse Mercator (UTM)
coordinates.\nAdditionally, we include `C++' code developed by Angus Johnson for
the `Clipper'\nlibrary. Also included are data for a global shoreline and
other\ndata sets in the public domain. The R directory
`...\/library\/PBSmapping\/doc'\noffers a complete user's guide, which should be
consulted to use package\nfunctions effectively.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"PBSmapping","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"foreign, maptools, deldir","Title":"Mapping
Fisheries Data and Spatial Analysis Tools","URL":"http:\/\/code.google.com\/p\/pbs-
mapping\/,\nhttp:\/\/code.google.com\/p\/pbs-
mapx\/,\nhttp:\/\/www.angusj.com\/delphi\/clipper.php","Version":"2.69.76"},"PBSmod
elling":{"Author":"Jon T. Schnute <schnutej-dfo@shaw.ca>,\nAlex Couture-Beil
<alex@mofo.ca>,\nRowan Haigh <rowan.haigh@dfo-mpo.gc.ca>,\nA.R. (Rob) Kronlund
<allen.kronlund@dfo-mpo.gc.ca>, and\nNicholas Boers
<boersn@macewan.ca>","Depends":"R (>= 2.15.0)","Description":"Provides software to
facilitate the design, testing, and operation\nof computer models. It focuses
particularly on tools that make it easy to\nconstruct and edit a customized
graphical user interface (GUI). Although our\nsimplified GUI language depends
heavily on the R interface to the Tcl\/Tk\npackage, a user does not need to know
Tcl\/Tk. Examples illustrate models\nbuilt with other R packages, including
PBSmapping, PBSddesolve, and BRugs.\nA complete user's guide `PBSmodelling-UG.pdf'
shows how to use this package\neffectively.","Imports":"methods, tcltk,
XML","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"PBSmodelling","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"PBSmapping, deSolve, KernSmooth","Title":"GUI
Tools Made Easy: Interact with Models and Explore
Data","URL":"http:\/\/code.google.com\/p\/pbs-
modelling\/,\nhttp:\/\/code.google.com\/p\/pbs-
tools\/","Version":"2.67.266"},"PCA4TS":{"Author":"Jinyuan Chang, Bin Guo and Qiwei
Yao","Depends":"R (>= 3.1.1)","Description":"To seek for a contemporaneous linear
transformation for\na multivariate time series such that the transformed series is
segmented\ninto several lower-dimensional subseries, and those subseries
are\nuncorrelated with each other both contemporaneously and
serially.","Imports":"tseries","License":"GPL-
2","NeedsCompilation":"yes","Package":"PCA4TS","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Segmenting Multiple Time Series by Contemporaneous
Linear\nTransformation","Version":"0.1"},"PCAmixdata":{"Author":"Marie Chavent and
Vanessa Kuentz and Amaury Labenne and Benoit Liquet and Jerome
Saracco.","Description":"Principal Component Analysis, orthogonal rotation and
multiple factor analysis for a mixture of quantitative and qualitative
2.0)","NeedsCompilation":"no","Package":"PCAmixdata","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Multivariate Analysis of Mixed
Data","Version":"2.2"},"PCDSpline":{"Author":"Bin Yao <yaob@email.sc.edu> and
Lianming Wang <wangl@stat.sc.edu>","Description":"Semiparametric regression
analysis of panel count data under the non-homogeneous Poisson\nprocess model with
and without Gamma frailty using monotone splines.","Imports":"nleqslv (>= 2.2),
matrixcalc (>= 1.0-3)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"PCDSpline","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Semiparametric regression analysis of panel count data
using\nmonotone splines","Version":"1.0"},"PCGSE":{"Author":"H. Robert
Frost","Depends":"R (>= 2.15.0), safe (>= 3.0.0), RMTstat,
MASS","Description":"Contains logic for computing the statistical association of
variable groups, i.e., gene sets, with respect to the principal components of
genomic data.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"PCGSE","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Principal Component Gene Set
Enrichment","Version":"0.2"},"PCICt":{"Author":"David Bronaugh <bronaugh@uvic.ca>
for the Pacific Climate\nImpacts Consortium (PCIC); portions based on code written
by\nthe R-Core team and Ulrich Drepper.","Depends":"R (>= 2.12.0), methods,
graphics","Description":"This package implements a work-alike to R's POSIXct
class\nwhich implements 360- and 365-day calendars in addition to the\ngregorian
calendar.","License":"GPL-
2","NeedsCompilation":"yes","Package":"PCICt","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"RUnit","Title":"Implementation of POSIXct work-alike for
365 and 360 day\ncalendars","URL":"http:\/\/www.r-project.org","Version":"0.5-
4"},"PCIT":{"Author":"Nathan S. Watson-Haigh","Depends":"R (>=
2.10)","Description":"Apply Partial Correlation coefficient with
Information\nTheory (PCIT) to a correlation matrix.\nThe PCIT algorithm identifies
meaningful correlations to define\nedges in a weighted network. The algorithm can
be applied to\nany correlation-based network including but not limited to gene\nco-
expression networks.\nTo reduce compute time by making use of multiple compute
cores,\nsimply run PCIT on a computer with has multiple cores and also\nhas the
Rmpi package installed. PCIT will then auto-detect the\nmulticore environment and
run in parallel mode without the need\nto rewrite your scripts. This makes scripts,
using PCIT, portable\nacross single core (or no Rmpi package installed)
computers\nwhich will run in serial mode and multicore (with Rmpi
package\ninstalled) computers which will run in parallel mode.","License":"GPL-
3","NeedsCompilation":"yes","Package":"PCIT","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"Rmpi","Title":"Partial Correlation Coefficient with
Information
Theory","URL":"http:\/\/dx.doi.org\/10.1093\/bioinformatics\/btn482\nhttp:\/\/bioin
formatics.oxfordjournals.org\/cgi\/content\/abstract\/26\/3\/411","Version":"1.5-
3"},"PCPS":{"Author":"Vanderlei Julio
Debastiani","Depends":"SYNCSA","Description":"Set of functions for analysis of
Principal Coordinates of\nPhylogenetic Structure (PCPS).","Imports":"ape, picante,
phylobase, vegan","License":"GPL-
2","NeedsCompilation":"no","Package":"PCPS","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Principal Coordinates of Phylogenetic
Structure","Version":"1.0.3"},"PCS":{"Author":"Jason Wilson","Depends":"statmod,
multtest","Description":"Given k populations (can be in thousands), what is the
probability
that a given subset of size t contains the true top t populations? This package
finds this probability and offers three tuning parameters (G, d, L) to relax the
definition.","License":"GPL-
3","NeedsCompilation":"no","Package":"PCS","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Calculate the probability of correct selection
(PCS)","Version":"1.2"},"PCovR":{"Author":"Marlies Vervloet [aut, cre],\nHenk Kiers
[aut],\nEva Ceulemans [ctb]","Depends":"GPArotation, ThreeWay, MASS,
Matrix","Description":"Analyzing regression data with many and\/or highly collinear
predictor variables, by simultaneously reducing the predictor variables to a
limited number of components and regressing the criterion variables on these
components. Several rotation options are provided in this package, as well as model
selection options.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"PCovR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Principal Covariates
Regression","Version":"2.6"},"PDQutils":{"Author":"Steven E. Pav [aut,
cre]","Depends":"R (>= 3.0.2)","Description":"A collection of tools for
approximating the 'PDQ' functions (respectively, the\ncumulative distribution,
density, and quantile) of probability distributions via classical\nexpansions
involving moments and cumulants.","Imports":"orthopolynom,
moments","License":"LGPL-
3","NeedsCompilation":"no","Package":"PDQutils","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"ggplot2, reshape2, testthat, knitr","Title":"PDQ
Functions via Gram Charlier, Edgeworth, and Cornish
Fisher\nApproximations","URL":"https:\/\/github.com\/shabbychef\/PDQutils","Version
":"0.1.4"},"PDSCE":{"Author":"Adam J. Rothman","Depends":"R (>=
2.10)","Description":"A package to compute and tune some positive definite
and\nsparse covariance estimators","License":"GPL-
2","NeedsCompilation":"yes","Package":"PDSCE","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Positive definite sparse covariance
estimators","Version":"1.2"},"PEIP":{"Author":"Jonathan M. Lees","Depends":"R (>=
2.12)","Description":"Several functions introduced in Aster et al.'s book on
inverse theory. The functions are often translations of MATLAB code developed by
the authors to illustrate concepts of inverse theory as applied to geophysics.
Generalized inversion, tomographic inversion algorithms (conjugate gradients, 'ART'
and 'SIRT'), non-linear least squares, first and second order Tikhonov
regularization, roughness constraints, and procedures for estimating smoothing
parameters are included. Includes a wrapper for the FORTRAN based 'LSQR' (Paige and
Saunders) routine.","Imports":"bvls, Matrix, RSEIS, pracma","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"PEIP","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Geophysical Inverse Theory and
Optimization","Version":"2.0-1"},"PEMM":{"Author":"Lin Chen
<lchen@health.bsd.uchicago.edu> and Pei Wang <pwang@fhcrc.org>","Description":"This
package provides functions to perform multivariate Gaussian parameter estimation
based on data with abundance-dependent missingness. It implements a penalized
Expectation-Maximization (EM) algorithm. The package is tailored for but not
limited to proteomics data applications, in which a large proportion of the data
are often missing-not-at-random with lower values (or absolute values) more likely
to be
missing.","License":"GPL","NeedsCompilation":"no","Package":"PEMM","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"A Penalized EM algorithm incorporating
missing-data mechanism","Version":"1.0"},"PET":{"Author":"Joern Schulz
<jschulz78@web.de> Peter Toft <pto@imm.dtu.dk>\nJesper James Jensen <jjj@oedan.dk>
Peter Philipsen\n<pap@imm.dtu.dk>","Depends":"adimpro (>=
0.4.2)","Description":"This package implements different analytic\/direct
and\niterative reconstruction methods of Peter Toft. It also offer\nthe possibility
to simulate PET data.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"PET","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Simulation and Reconstruction of PET
Images","Version":"0.4.9"},"PGEE":{"Author":"Gul Inan (Visiting scholar, University
of Minnesota), Jianhui Zhou (Associate Professor, University of Virginia) and Lan
Wang (Professor, University of Minnesota)","Depends":"MASS,
mvtnorm","Description":"Fits penalized generalized estimating equations to
longitudinal data with high-dimensional covariates.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"PGEE","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Penalized Generalized Estimating Equations in High-
Dimension","Version":"1.0"},"PGICA":{"Author":"Shaojie Chen; Lei Huang; Huitong
Qiu; Ani Eloyan; Brian Caffo; Ciprian Crainiceanu","Description":"A Group ICA
Algorithm that can run in parallel on an SGE platform or multi-core
PCs","Imports":"parallel, fastICA","License":"GPL-
2","NeedsCompilation":"no","Package":"PGICA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Parallel Group ICA Algorithm","Version":"1.0"},"PGM2":
{"Author":"Mohamed LAIB, Abla BOUDRAA and Zoubida Gheribi-
Aoulmi","Description":"Construction of balanced incomplete binary blocks designs
(BIB) from a projective geometry defined on a Galois fields order 2, using to
extract the RBIBD & the uniforms designs associated.","License":"GPL-
3","NeedsCompilation":"no","Package":"PGM2","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Recursive method for construction of nested resolvable
designs\nand uniform designs associated","Version":"1.0"},"PGRdup":{"Author":"J.
Aravind [aut, cre],\nJ. Radhamani [aut],\nKalyani Srinivasan [aut],\nB. Ananda
Subhash [aut],\nR. K. Tyagi [aut]","Depends":"R (>= 3.0.2)","Description":"Provides
functions to aid the identification of probable\/possible\nduplicates in Plant
Genetic Resources (PGR) collections using\n'passport databases' comprising of
information records of each constituent\nsample. These include methods for cleaning
the data, creation of a\nsearchable Key Word in Context (KWIC) index of keywords
associated with\nsample records and the identification of nearly identical records
with\nsimilar information by fuzzy, phonetic and semantic matching of
keywords.","Imports":"data.table (>= 1.9.3), igraph, stringdist (>= 0.9.4),
stringi,\nggplot2, grid, gridExtra, methods, utils, stats","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"PGRdup","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"diagram, wordcloud, microbenchmark,
knitr","Title":"Discover Probable Duplicates in Plant Genetic
Resources\nCollections","Version":"0.2.2.1"},"PHENIX":{"Author":"R. Torices, A. J.
MuÃ±oz-Pajares","Description":"Provides functions to estimate the size-controlled
phenotypic integration index, a novel method by Torices & MÃ©ndez (2014) to solve
problems due to individual size when estimating integration (namely, larger
individuals have larger components, which will drive a correlation between
components only due to resource availability that might obscure the observed
measures of integration). In addition, the package also provides the classical
estimation by Wagner (1984), bootstrapping and jackknife methods to calculate
confidence intervals and a significance test for both integration
indices.","Imports":"ppcor, SuppDists","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"PHENIX","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Phenotypic Integration
Index","Version":"1.2.2"},"PHYLOGR":{"Author":"Ramon Diaz-Uriarte <rdiaz@cnio.es>
and Theodore Garland, Jr\n<theodore.garland@ucr.edu>","Depends":"R(>=
1.8.1)","Description":"Manipulation and analysis of phylogenetically
simulated\ndata sets and phylogenetically based analyses using GLS.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"PHYLOGR","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Functions for Phylogenetically Based Statistical
Analyses","URL":"http:\/\/ligarto.org\/rdiaz","Version":"1.0.8"},"PHeval":
{"Author":"Cecile Chauvel","Depends":"R (>= 1.8.0), survival, graphics,
splines","Description":"Provides tools for the evaluation of the goodness of fit
and the predictive capacity of the proportional hazards model.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"PHeval","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Evaluation of the Proportional Hazards Assumption with
a\nStandardized Score Process","URL":"http:\/\/www.r-
project.org","Version":"0.5.3"},"PIGE":{"Author":"Benoit Liquet, Therese
Truong","Depends":"snowfall,ARTP,xtable,survival","Description":"Extension of the
ARTP package for gene- and pathway-environment\ninteraction","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"PIGE","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Self contained gene set analysis for gene- and\npathway-
environment interaction analysis","Version":"0.9"},"PIGShift":{"Author":"Joshua G.
Schraiber <schraib@uw.edu>","Depends":"R (>= 2.10)","Description":"Fits models of
gene expression evolution to expression data from\ncoregulated groups of genes,
assuming inverse gamma distributed rate\nvariation.","Imports":"ape,
3","NeedsCompilation":"no","Package":"PIGShift","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Polygenic Inverse Gamma
Shifts","Version":"1.0.1"},"PIPS":{"Author":"Daniel G. Muenz, Ray Griner
<rgriner@sdac.harvard.edu>, Huichao\nChen, Lijuan Deng, Sachiko Miyahara, and Scott
R. Evans\n<evans@sdac.harvard.edu>, with contributions from Lingling Li,\nHajime
Uno, and Laura M. Smeaton.","Depends":"R (>= 2.12.1)","Description":"Generate
Predicted Interval Plots. Simulate and plot\nconfidence intervals of an effect
estimate given observed data\nand a hypothesis about the distribution of future
2","NeedsCompilation":"no","Package":"PIPS","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Predicted
Interval Plots","Version":"1.0.1"},"PK":{"Author":"Thomas Jaki
<jaki.thomas@gmail.com> and Martin J.
Wolfsegger\n<wolfseggerm@gmx.at>","Depends":"R (>= 2.2.1),
utils","Description":"Estimation of pharmacokinetic parameters using non-
compartmental theory.","License":"GPL-
2","NeedsCompilation":"no","Package":"PK","Repository":"http:\/\/cran.csiro.au\/src
\/contrib","Title":"Basic Non-Compartmental Pharmacokinetics","Version":"1.3-
3"},"PKI":{"Author":"Simon Urbanek <Simon.Urbanek@r-project.org>","Depends":"R (>=
2.9.0), base64enc","Description":"PKI functions such as verifying certificates, RSA
encription and signing which can be used to build PKI infrastructure and perform
cryptographic tasks.","Enhances":"gmp","License":"GPL-2 | GPL-3 | file
LICENSE","NeedsCompilation":"yes","Package":"PKI","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Public Key Infrastucture for R Based on the X.509
Standard","URL":"http:\/\/www.rforge.net\/PKI","Version":"0.1-3"},"PKNCA":
{"Author":"Bill Denney [aut, cre],\nClare Buckeridge [aut]","Description":"Compute
standard Non-Compartmental Analysis (NCA)\nparameters and summarize them. In
addition to this core work, it\nalso provides standardized plotting routines, basic
assessments\nfor biocomparison or drug interaction, and model-based
estimation\nroutines for calculating doses to reach specific values of AUC
or\nCmax.","Imports":"digest, doBy, plyr, nlme, parallel, lattice, stats,
utils","License":"AGPL-
3","NeedsCompilation":"no","Package":"PKNCA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr, testthat","Title":"Perform Pharmacokinetic Non-
Compartmental
Analysis","URL":"https:\/\/github.com\/billdenney\/pknca","Version":"0.7"},"PKPDmod
els":{"Author":"Anne Dubois, Julie Bertand, France Mentre and Douglas
Bates","Depends":"R(>= 2.13.0)","Description":"Provides functions to evaluate
common\npharmacokinetic\/pharmacodynamic models and their
gradients.","Imports":"compiler","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"PKPDmodels","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"lattice","Title":"Pharmacokinetic\/pharmacodynamic
models","URL":"http:\/\/PKPD.R-forge.R-project.org","Version":"0.3.2"},"PKgraph":
{"Author":"Xiaoyong Sun","Depends":"R (>= 2.10.0), RGtk2, gWidgetsRGtk2,
cairoDevice, lattice,\nrggobi, ggplot2, proto","Description":"PKgraph provides a
graphical user interface for population\npharmacokinetic model diagnosis. It also
provides an integrated\nand comprehensive platform for the analysis of
pharmacokinetic\ndata including exploratory data analysis, goodness of model\nfit,
model validation and model comparison. Results from a\nvariety of modeling fitting
software, including NONMEM,\nMonolix, SAS and R, can be used. PKgraph is programmed
in R,\nand uses the R packages lattice, ggplot2 for static graphics,\nand rggobi
for interactive graphics.","Imports":"RGtk2, gWidgetsRGtk2","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"PKgraph","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Model diagnostics for population pharmacokinetic
models","Version":"1.7"},"PKreport":{"Author":"Xiaoyong Sun","Depends":"R (>=
2.7.0), methods, lattice, ggplot2","Description":"PKreport aims to 1) provide
automatic pipeline for users\nto visualize data and models. It creates a flexible R
framework\nwith automatically generated R scripts to save time and cost\nfor later
usage; 2) implement an archive-oriented management\ntool for users to store,
retrieve and modify figures. 3) offer\npowerful and convenient service to generate
high-quality graphs\nbased on two R packages: lattice and ggplot2.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"PKreport","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"A reporting pipeline for checking population
pharmacokinetic\nmodel assumption","Version":"1.5"},"PLIS":{"Author":"Zhi Wei &
Wenguang Sun","Description":"PLIS is a multiple testing procedure for testing
several\ngroups of hypotheses. Linear dependency is expected from the\nhypotheses
within the same group and is modeled by hidden\nMarkov Models. It is noted that,
for PLIS, a smaller p value\ndoes not necessarily imply more significance because
of\ndependency among the hypotheses. A typical application of PLIS\nis to analyze
genome wide association studies datasets, where\nSNPs from the same chromosome are
treated as a group and\nexhibit strong linear genomic dependency.","License":"GPL-
3","NeedsCompilation":"no","Package":"PLIS","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Multiplicity control using Pooled LIS
statistic","Version":"1.1"},"PLRModels":{"Author":"German Aneiros Perez and Ana
Lopez Cheda","Description":"This package provides statistical inference tools
applied to Partial Linear Regression (PLR)\nmodels. Specifically, point estimation,
confidence intervals estimation, bandwidth selection, goodness-of-fit tests and
analysis of\ncovariance are considered.\nKernel-based methods, combined with
ordinary least squares estimation, are used and time series\nerrors are allowed. In
addition, these techniques are also implemented for both parametric (linear)\nand
nonparametric regression
models.","License":"GPL","NeedsCompilation":"no","Package":"PLRModels","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Title":"Statistical inference in partial
linear regression models","Version":"1.1"},"PLSbiplot1":{"Author":"Opeoluwa F.
Oyedele [aut, cre],\nSugnet Gardner-Lubbe [aut]","Depends":"R (>=
3.0.0)","Description":"Principal Component Analysis (PCA) biplots, Covariance
monoplots\nand biplots, Partial Least Squares (PLS) biplots, Partial Least Squares
for\nGeneralized Linear Model (PLS-GLM) biplots, Sparse Partial Least
Squares\n(SPLS) biplots and Sparse Partial Least Squares for Generalized
Linear\nModel (SPLS-GLM) biplots.","License":"GPL-
2","NeedsCompilation":"no","Package":"PLSbiplot1","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"chemometrics, MASS, mixOmics, mvabund, pls,
plsgenomics,\nrobustbase, SensoMineR","Title":"The Partial Least Squares (PLS)
Biplot","URL":"\nhttps:\/\/www.dropbox.com\/sh\/wr66u07t1vjm9da\/AACg_E4h8MvgOHuCXk
69yDIya","Version":"0.1"},"PLordprob":{"Author":"Euloge Clovis Kenne Pagui
[aut,cre], Antonio Canale [aut], Alan Genz [ctb], Adelchi Azzalini
[ctb]","Depends":"mnormt","Description":"Multivariate ordered probit model, i.e.
the extension of the scalar ordered probit model where the observed variables have
dimension greater than one. Estimation of the parameters is done via maximization
of the pairwise likelihood, a special case of the composite likehood obtained as
product of bivariate marginal distributions. The package uses the Fortran 77
subroutine SADMVN by Alan Genz, with minor adaptations made by Adelchi Azzalini in
his \"mvnormt\" package for evaluating the two-dimensional Gaussian integrals
involved in the pairwise log-likelihood. Optimization of the latter objective
function is performed via quasi-Newton box-constrained optimization algorithm, as
implemented in nlminb.","License":"GPL-
2","NeedsCompilation":"yes","Package":"PLordprob","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Multivariate Ordered Probit Model via Pairwise
Likelihood","Version":"1.0"},"PMA":{"Author":"Daniela Witten and Rob Tibshirani and
Sam Gross and\nBalasubramanian Narasimhan","Depends":"R (>= 2.10), plyr,
impute","Description":"Performs Penalized Multivariate Analysis: a
penalized\nmatrix decomposition, sparse principal components analysis, and\nsparse
canonical correlation analysis, described in the\nfollowing papers: (1) Witten,
Tibshirani and Hastie (2009) A\npenalized matrix decomposition, with applications
to sparse\nprincipal components and canonical correlation analysis.\nBiostatistics
10(3):515-534. (2) Witten and Tibshirani (2009)\nExtensions of sparse canonical
correlation analysis, with\napplications to genomic data. Statistical Applications
in\nGenetics and Molecular Biology 8(1): Article 28.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"PMA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Penalized Multivariate Analysis","Version":"1.0.9"},"PMCMR":
{"Author":"Thorsten Pohlert","Depends":"R (>= 3.0.0), stats,
base","Description":"The Kruskal and Wallis one-way analysis of variance by
ranks\nor van der Waerden's normal score test can be employed,\nif the data do not
meet the assumptions\nfor one-way ANOVA. Provided that significant
differences\nwere detected by the omnibus test, one may be interested\nin applying
post-hoc tests for pairwise multiple comparisons\n(such as Nemenyi's test, Dunn's
test, Conover's test,\nvan der Waerden's test). Similarly, one-way ANOVA with
repeated\nmeasures that is also referred to as ANOVA with unreplicated\nblock
design can also be conducted via the Friedman-Test\nor the Quade-test. The
consequent post-hoc pairwise\nmultiple comparison tests according to Nemenyi,
Conover and Quade\nare also provided in this package. Finally Durbin's test for\na
two-way balanced incomplete block design (BIBD) is also given\nin this
package.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"PMCMR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"multcompView, xtable, graphics","Title":"Calculate
Pairwise Multiple Comparisons of Mean Rank Sums","Version":"4.1"},"PP":
{"Author":"Manuel Reif <manuel.reif@gmail.com>","Depends":"R (>=
3.0)","Description":"The PP package includes estimation of (MLE, WLE, MAP, EAP,
ROBUST)\nperson parameters for the 1,2,3,4-PL model and the GPCM
(generalized\npartial credit model). The parameters are estimated under the
assumption\nthat the item parameters are known and fixed. The package is useful
e.g. in\nthe case that items from an item pool \/ item bank with known item
parameters\nare administered to a new population of test-takers
and an ability\nestimation for every test-taker is needed.","Imports":"Rcpp (>=
3","NeedsCompilation":"yes","Package":"PP","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"testthat, roxygen2, knitr","Title":"Person Parameter
estimation","URL":"https:\/\/github.com\/manuelreif\/PP","Version":"0.5.3"},"PPtree
":{"Author":"Eun-Kyung Lee, Yoondong Lee","Description":"Projection pursuit
classification tree using LDA, Lr or PDA projection pursuit index","Imports":"MASS
(>= 3.1-20), penalizedLDA (>= 1.0)","License":"LGPL-
2.1","NeedsCompilation":"yes","Package":"PPtree","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Projection pursuit classification
tree","Version":"2.3.0"},"PPtreeViz":{"Author":"Eun-Kyung Lee","Depends":"R (>=
2.10),gridExtra, ggplot2","Description":"Tools for exploring projection pursuit
classification tree using\nvarious projection pursuit
indices.","Imports":"Rcpp","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"PPtreeViz","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"MASS (>= 3.1-20),stats","Title":"Projection Pursuit
Classification Tree Visualization","Version":"1.3.0"},"PRIMsrc":{"Author":"Jean-
Eudes Dazard [aut, cre], Michael Choe [ctb], Michael LeBlanc [ctb], Alberto Santana
[ctb]","Depends":"R (>= 3.0.2), parallel, survival, Hmisc, glmnet,
MASS","Description":"Performs a unified treatment of Bump Hunting by Patient Rule
Induction Method (PRIM) in Survival, Regression and Classification settings (SRC).
The current version is a development release that only implements the case of a
survival response. New features will be added soon as they are
available.","Imports":"graphics, grDevices, stats","License":"GPL (>= 3) | file
LICENSE","NeedsCompilation":"no","Package":"PRIMsrc","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"PRIM Survival Regression
Classification","URL":"https:\/\/github.com\/jedazard\/PRIMsrc","Version":"0.6.3"},
"PRISMA":{"Author":"Tammo Krueger, Nicole Kraemer","Depends":"R (>= 2.10), Matrix,
gplots, ggplot2","Description":"The PRISMA package is capable of loading and
processing huge text\ncorpora processed with the sally toolbox
(http:\/\/www.mlsec.org\/sally\/).\nsally acts as a very fast preprocessor which
splits the text files into\ntokens or n-grams. These output files can then be read
with the PRISMA\npackage which applies testing-based token selection and has
some\nreplicate-aware, highly tuned non-negative matrix factorization
and\nprincipal component analysis implementation which allows the processing
of\nvery big data sets even on desktop machines.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"PRISMA","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"tm (>= 0.6)","Title":"Protocol Inspection and State
Machine Analysis","Version":"0.2-5"},"PROFANCY":{"Author":"Qianlan Yao, Desi Shang,
Chunquan Li","Depends":"R (>= 2.15.2),Matrix,lattice,igraph","Description":"The
package can prioritize the candidate disease metabolites based on the
assumption\nthat functionally related metabolites tend to associate with the same
or similar\ndiseases in the context of metabolic pathway. The PROFANCY package (1)
prioritizes the\ndisease metabolites from global functional similarity and local
modularity of the\nmetabolic network; (2) allows users to select default
metabolites or input their\ninterested metabolites as seed nodes or candidate nodes
(3) can prioritize the candidate\nmetabolites in KEGG or EHMN metabolic
network.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"PROFANCY","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"The package can prioritize candidate disease metabolites
based\non global functional relationships between metabolites in the\ncontext of
metabolic pathways","Version":"1.0"},"PROTOLIDAR":{"Author":"Monica Fernanda
Rinaldi","Description":"PROTOLIDAR package contains functions for analyze
the\nLIDAR scan of plants (grapevine) and make 3D maps in GRASS
GIS.","License":"GPL","NeedsCompilation":"no","Package":"PROTOLIDAR","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Title":"PRocess TOol LIdar DAta in
R","Version":"0.1"},"PRROC":{"Author":"Jan Grau and Jens
Keilwagen","Description":"Computes the areas under the precision-recall (PR) and
ROC curve for weighted (e.g., soft-labeled) and unweighted data. In contrast to
other implementations, the interpolation between points of the PR curve is done by
a non-linear piecewise function. In addition to the areas under the curves, the
curves themselves can also be computed and plotted by a specific S3-
3","NeedsCompilation":"no","Package":"PRROC","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat, ggplot2","Title":"Precision-Recall and ROC
Curves for Weighted and Unweighted Data","Version":"1.1"},"PReMiuM":
{"Author":"David I. Hastie <david.hastie@rsimony.com>, Silvia Liverani
<liveranis@gmail.com> and Sylvia Richardson <sylvia.richardson@mrc-bsu.cam.ac.uk>
with contributions from Aurore J. Lavigne, Lucy Leigh, Lamiae Azizi","Depends":"R
(>= 3.0.2)","Description":"Bayesian clustering using a Dirichlet process mixture
model. This model is an alternative to regression models, non-parametrically
linking a response vector to covariate data through cluster membership. The package
allows Bernoulli, Binomial, Poisson, Normal, survival and categorical response, as
well as Normal and discrete covariates. It also allows for fixed effects in the
response model, where a spatial CAR (conditional autoregressive) term can be also
included. Additionally, predictions may be made for the response, and missing
values for the covariates are handled. Several samplers and label switching moves
are implemented along with diagnostic tools to assess convergence. A number of R
functions for post-processing of the output are also provided. In addition to
fitting mixtures, it may additionally be of interest to determine which covariates
actively drive the mixture components. This is implemented in the package as
variable selection.","Imports":"Rcpp (>= 0.11), ggplot2 (>= 0.9.2.1), cluster,
plotrix (>=\n3.5), gamlss.dist (>= 4.3-1)","License":"GPL-
2","NeedsCompilation":"yes","Package":"PReMiuM","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Dirichlet Process Bayesian Clustering, Profile
Regression","URL":"http:\/\/www.silvialiverani.com\/software\/","Version":"3.1.3"},
"PSAboot":{"Author":"Jason Bryer <jason@bryer.org>","Depends":"R (>=
3.0),graphics,ggplot2,PSAgraphics","Description":"Bootstrapping for propensity
score analysis and
matching.","Imports":"\nutils,Matching,MatchIt,modeltools,parallel,party,psych,resh
ape2,rpart,TriMatch,ggthemes,stats","License":"GPL","NeedsCompilation":"no","Packag
e":"PSAboot","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"devtoo
ls,knitr,multilevelPSA","Title":"Bootstrapping for Propensity Score
Analysis","URL":"http:\/\/jason.bryer.org\/PSAboot,
http:\/\/github.com\/jbryer\/PSAboot","Version":"1.1.4"},"PSAgraphics":
{"Author":"James E. Helmreich <James.Helmreich@Marist.edu> and Robert M.\nPruzek
<RMPruzek@yahoo.com>. We are grateful to KuangNan Xiong\nfor significant work on
the functions new to version 2.0:\ncstrata.psa, cv.bal.psa, and
cv.trans.psa.","Depends":"R (>= 2.14.0), rpart","Description":"A collection of
functions that primarily produce graphics\nto aid in a Propensity Score Analysis
(PSA). Functions\ninclude: cat.psa and box.psa to test balance within strata
of\ncategorical and quantitative covariates, circ.psa for a\nrepresentation of the
estimated effect size by stratum,\nloess.psa that provides a graphic and loess
based effect size\nestimate, and various balance functions that provide
measures\nof the balance achieved via a PSA in a categorical
covariate.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"PSAgraphics","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Propensity Score Analysis
Graphics","Version":"2.1.1"},"PSCBS":{"Author":"Henrik Bengtsson [aut, cre,
cph],\nPierre Neuvial [aut],\nVenkatraman E. Seshan [aut],\nAdam B. Olshen
[aut],\nPaul T. Spellman [aut],\nRichard A. Olshen [aut]","Depends":"R (>= 3.1.2),
utils","Description":"Segmentation of allele-specific DNA copy number data and
detection of regions with abnormal copy number within each parental chromosome.
Both tumor-normal paired and tumor-only analyses are
supported.","Imports":"R.methodsS3 (>= 1.7.0), R.oo (>= 1.19.0), R.utils (>=
2.2.0),\nR.cache (>= 0.12.0), matrixStats (>= 0.50.1), DNAcopy (>=\n1.40.0),
listenv (>= 0.6.0), future (>= 0.11.0), parallel","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"PSCBS","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"Hmisc (>= 3.16-0), R.rsp (>= 0.21.0), R.devices (>=
2.13.2),\nggplot2 (>= 1.0.1), aroma.light (>= 2.2.1)","Title":"Analysis of Parent-
Specific DNA Copy
Numbers","URL":"https:\/\/github.com\/HenrikBengtsson\/PSCBS","Version":"0.61.0"},"
PSF":{"Author":"Neeraj Bokde","Description":"Various functions in Pattern Sequence
Based Forecasting (PSF) takes\ntime series data as input and assist to forecast the
future value with\nthe help of Algorithm PSF. This algorithm forecasts the behavior
of time series\nbased on similarity of pattern sequences. Initially, clustering is
done with the\nlabeling of samples from database. The labels associated with
samples are then\nused for forecasting the future behaviour of time series data.
The further\ntechnical details and references regarding PSF are discussed in
Vignette.","Imports":"cluster","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"PSF","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"knitr, rmarkdown","Title":"Algorithm for Pattern Sequence
Based Forecasting","Version":"0.1"},"PSM":{"Author":"Stig Bousgaard Mortensen
<stigbm@gmail.com> and Søren Klim\n<soren@klimens.dk>","Depends":"MASS,
numDeriv, deSolve, ucminf","Description":"This package provides functions for
estimation of linear\nand non-linear mixed-effects models using
stochastic\ndifferential equations. Moreover it provides functions for\nfinding
smoothed estimates of model states and for simulation.\nThe package allows for any
multivariate non-linear time-variant\nmodel to be specified, and it also handles
multidimensional\ninput, co-variates, missing observations and specification
of\ndosage regimen.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"PSM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Non-Linear Mixed-Effects modelling using Stochastic
Differential\nEquations","URL":"http:\/\/www.imm.dtu.dk\/psm","Version":"0.8-
10"},"PST":{"Author":"Alexis Gabadinho [aut, cre, cph]","Depends":"R (>= 2.10),
TraMineR, RColorBrewer","Description":"Provides a framework for analysing state
sequences with probabilistic suffix trees (PST), the construction that stores
variable length Markov chains (VLMC). Besides functions for learning and optimizing
VLMC models, the PST library includes many additional tools to analyse sequence
data with these models: visualization tools, functions for sequence prediction and
artificial sequences generation, as well as for context and pattern mining. The
package is specifically adapted to the field of social sciences by allowing to
learn VLMC models from sets of individual sequences possibly containing missing
values, and by accounting for case weights. The library also allows to compute
probabilistic divergence between two models, and to fit segmented VLMC, where sub-
models fitted to distinct strata of the learning sample are stored in a single PST.
This software results from research work executed within the framework of the Swiss
National Centre of Competence in Research LIVES, which is financed by the Swiss
National Science Foundation. The authors are grateful to the Swiss National Science
Foundation for its financial support.","Imports":"methods, stats4","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"PST","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Probabilistic Suffix Trees and Variable Length Markov
Chains","URL":"http:\/\/r-forge.r-
project.org\/projects\/pst","Version":"0.86"},"PTAk":{"Author":"Didier G. Leibovici
<didier.leibovici@nottingham.ac.uk>","Depends":"tensor","Description":"A multiway
method to decompose a tensor (array) of any order, as a generalisation of SVD also
supporting non-identity metrics and penalisations. 2-way SVD with these extensions
is also available. The package includes also some other multiway methods: PCAn
(Tucker-n) and PARAFAC\/CANDECOMP with these extensions.","Imports":"graphics,
2)","NeedsCompilation":"no","Package":"PTAk","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Principal Tensor Analysis on k
Modes","URL":"http:\/\/c3s2i.free.fr\/","Version":"1.2-12"},"PTE":{"Author":"Adam
Kapelner, Justin Bleich","Depends":"R (>= 3.0), doParallel","Description":"A tool
to draw inference in personalized medicine regimes","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"PTE","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Personalized Treatment
Evaluator","Version":"1.0"},"PVAClone":{"Author":"Khurram Nadeem, Peter
Solymos","Depends":"R (>= 2.15.0), dcmle (>= 0.3-0), dclone,
stats4","Description":"Likelihood based population viability analysis in
the\npresence of observation error and missing data.\nThe package can be used to
fit, compare, predict,\nand forecast various growth model types using data
cloning.","Imports":"methods, coda","License":"GPL-
2","NeedsCompilation":"no","Package":"PVAClone","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"parallel","Title":"Population Viability Analysis with
Data Cloning","URL":"https:\/\/github.com\/psolymos\/PVAClone","Version":"0.1-
6"},"PVR":{"Author":"Thiago Santos, Jose Alexandre Diniz-Filho, Thiago Rangel e
Luis\nMauricio Bini","Depends":"R (>= 2.14.0), ape, splancs,
methods","Description":"Computes PVR and PSR.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"PVR","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"picante, geiger","Title":"Computes phylogenetic
eigenvectors regression (PVR) and\nphylogenetic signal-representation curve (PSR)
(with null and\nBrownian expectations)","Version":"0.2.1"},"PWD":{"Author":"Daniel
McCarthy [aut, cre, ctb]","Description":"Contains functions which allow the user to
perform time series regression quickly using the Power Weighted Densities (PWD)
approach. alphahat_LR_one_Rcpp() is the main workhorse function within this
package.","Imports":"Rcpp (>= 0.11.5), stats, graphics","License":"GPL-
3","NeedsCompilation":"yes","Package":"PWD","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Time Series Regression Using the Power Weighted Densities
(PWD)\nApproach","URL":"http:\/\/www-
stat.wharton.upenn.edu\/~danielmc\/","Version":"1.0"},"PabonLasso":
{"Author":"Nezami,H (nezamih921@mums.ac.ir; HosseinNezami1370@yahoo.com) and
Tabesh,H (tabeshh@mums.ac.ir) and Azarian,AA
(azarianaa1@mums.ac.ir)","Description":"Pabon Lasso is a graphical method for
monitoring the efficiency of different wards of a hospital or different
hospitals.Pabon Lasso graph is divided into 4 parts which are created after drawing
the average of BTR and BOR. The part in the left-down side is Zone I, left-up side
is Zone II, Right-up side part is Zone III and the last part is Zone
IV.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"PabonLasso","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Pabon Lasso Graphs and Comparing Situations of a Unit
in Two\nDifferent Times","Version":"1.0"},"Pade":{"Author":"Avraham Adler [aut,
cph, cre]","Description":"Given a vector of Taylor series coefficients of
sufficient length as input, the function returns the numerator and denominator
coefficients for the PadÃ© approximant of appropriate
order.","Imports":"utils","License":"GPL (>= 2) | BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"Pade","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat","Title":"PadÃ© Approximant
Coefficients","URL":"https:\/\/bitbucket.org\/aadler\/pade","Version":"0.1-
4"},"PairViz":{"Author":"C.B. Hurley and R.W. Oldford","Depends":"TSP,
gtools,graph,methods","Description":"Eulerian tours and Hamiltonian decompositions
of complete graphs are used to ameliorate order effects in statistical
graphics.","License":"GPL-
2","NeedsCompilation":"no","Package":"PairViz","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Visualization using Eulerian tours and
Hamiltonian\ndecompositions","Version":"1.2.1"},"PairedData":{"Author":"Stephane
Champely <champely@univ-
lyon1.fr>","Depends":"methods,graphics,MASS,gld,mvtnorm,lattice,ggplot2","Descripti
on":"This package provides many datasets and a set of graphics\n(based on ggplot2),
statistics, effect sizes and hypothesis\ntests for analysing paired data with S4
class.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"PairedData","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Paired Data Analysis","Version":"1.0.1"},"PanelCount":
{"Author":"Jing Peng","Depends":"R (>= 3.0.0)","Description":"A high performance
package implementing random effects and\/or sample selection models for panel count
data.","Imports":"Rcpp, statmod","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"PanelCount","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Random Effects and\/or Sample Selection Models for
Panel Count\nData","Version":"1.0.9"},"Paneldata":{"Author":"Zaghdoudi
Taha","Description":"Linear models for panel data: the fixed effect model and
the\nrandom effect model","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"Paneldata","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Linear models for panel
data","Version":"1.0"},"ParDNAcopy":{"Author":"Alex Krasnitz, Guoli
Sun","Depends":"DNAcopy, parallel","Description":"Parallelized version of
the \"segment\" function from Bioconductor package \"DNAcopy\", utilizing multi-
core computation on host CPU","License":"GPL-
2","NeedsCompilation":"no","Package":"ParDNAcopy","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Parallel implementation of the \"segment\" function of
package\n\"DNAcopy\"","Version":"2.0"},"ParallelForest":{"Author":"Bertram Ieong
[aut, cre, cph]","Depends":"R (>= 2.10), methods","Description":"R package
implementing random forest classification using parallel computing, built with
Fortran and OpenMP in the backend.","License":"AGPL-
3","NeedsCompilation":"yes","Package":"ParallelForest","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"knitr","Title":"Random Forest Classification
with Parallel
Computing","URL":"https:\/\/github.com\/bert9bert\/ParallelForest","Version":"1.1.0
"},"ParallelPC":{"Author":"Thuc Duy Le, Tao Hoang, Shu Hu, and Liang
Zhang","Description":"Parallelise constraint based causality discovery and causal
inference methods. The parallelised algorithms in the package will generate the
same results as that of the 'pcalg' package but will be much more
efficient.","Imports":"methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ParallelPC","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"bnlearn, pcalg, parallel,
Rgraphviz","Title":"Paralellised Versions of Constraint Based Causal
Discovery\nAlgorithms","Version":"1.2"},"ParamHelpers":{"Author":"Bernd Bischl
[aut, cre],\nMichel Lang [aut],\nJakob Bossek [aut],\nDaniel Horn [aut],\nKarin
Schork [aut]","Description":"Functions for parameter descriptions and operations in
black-box\noptimization, tuning and machine learning. Parameters can be
described\n(type, constraints, defaults, etc.), combined to parameter sets and can
in\ngeneral be programmed on. A useful OptPath object (archive) to log
function\nevaluations is also provided.","Imports":"BBmisc (>= 1.9), checkmate (>=
1.6.1), methods","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"yes","Package":"ParamHelpers","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Suggests":"akima, eaf, emoa, GGally, ggplot2,
gridExtra, irace (>=\n1.0.7), lhs, plyr, reshape2, soobench,
testthat","Title":"Helpers for Parameters in Black-Box Optimization, Tuning
and\nMachine
Learning","URL":"https:\/\/github.com\/berndbischl\/ParamHelpers","Version":"1.7"},
"ParentOffspring":{"Author":"Pengsheng Ji, Hussein Abdel-Haleem, H. Roger Boerma
and Zenglu Li","Description":"Conduct the Parent-Offspring Test Using Monomorphic
SNP Markers. The similarity to the parents is computed for each offspring, and a
plot of similarity for all offspring is produced. One can keep the offspring above
some threshold for the similarity for further studies.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ParentOffspring","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Conduct the Parent-Offspring Test Using
Monomorphic SNP Markers","Version":"1.0"},"ParetoPosStable":{"Author":"Antonio Jose
Saez-Castillo [aut, cre],\nFaustino Prieto [aut],\nJose Maria Sarabia
[aut]","Depends":"R (>= 3.0.0)","Description":"Statistical functions to describe a
Pareto Positive Stable (PPS)\ndistribution and fit it to real data. Graphical and
statistical tools to\nvalidate the fits are included.","Imports":"graphics,
grDevices, stats, ADGofTest, lmom, foreach,\ndoParallel, parallel","License":"GPL-2
| GPL-
3","NeedsCompilation":"no","Package":"ParetoPosStable","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Computing, Fitting and Validating the PPS
Distribution","Version":"1.1"},"Pasha":{"Author":"Romain Fenouil, Nicolas
Descostes, Lionel Spinelli, Frederic Koch, Muhammad Ahmad Maqbool, Touati
Benoukraf, Pierre Cauchy, Charlene Innocenti, Pierre Ferrier, Jean-Christophe
Andrau","Depends":"R (>= 3.2.0), parallel,
GenomicAlignments","Description":"Pipeline and additional tools designed to handle
aligned data from chromatin NGS experiments (less adapted for typical RNAseq
applications). Specifically, starting from aligned reads after sequencing, the
pipeline function aims at removing artefacts from datasets, estimate in-silico the
fragments size, and generate WIG files with corrected values. The package also
provides several tools for WIG files manipulations, scaling, merging and subtract
(e.g. input).","Imports":"bitops, tools, methods, S4Vectors, IRanges,
GenomicRanges,\nShortRead, Rsamtools, Biostrings, gtools,
rtracklayer,\nGenomeInfoDb","License":"GPL-
3","NeedsCompilation":"yes","Package":"Pasha","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Preprocessing of Aligned Sequences from HTS
Analyses","Version":"0.99.21"},"PatternClass":{"Author":"Tarmo K. Remmel, (Marie-
Josee Fortin, Ferenc Csillag, Sandor Kabos)","Depends":"R (>= 2.14),
SDMTools","Description":"This library provides tools for estimating composition and
configuration parameters from a categorical (binary) landscape map (grid) and then
simulates a selected number of statistically similar landscapes. Class-focused
pattern metrics are computed for each simulated map to produce empirical
distributions against which statistical comparisons can be made. The code permits
the analysis of single maps or pairs of maps.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"PatternClass","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Class-focused pattern metric comparisons using
simulation","Version":"1.5"},"Peaks":{"Author":"Miroslav Morhac","Depends":"R (>=
2.5)","Description":"Spectrum manipulation: background estimation,
Markov\nsmoothing, deconvolution and peaks search functions. Ported\nfrom
ROOT\/TSpectrum
class.","License":"LGPL","NeedsCompilation":"yes","Package":"Peaks","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Title":"Peaks","Version":"0.2"},"PearsonDS":
{"Author":"Martin Becker and Stefan Klößner","Description":"Implementation of the
Pearson distribution system, including full\nsupport for the (d,p,q,r)-family of
functions for probability distributions\nand fitting via method of moments and
maximum likelihood method.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"PearsonDS","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"gsl","Title":"Pearson Distribution
System","Version":"0.97"},"PearsonICA":{"Author":"Juha Karvanen","Description":"The
Pearson-ICA algorithm is a mutual information-based\nmethod for blind separation of
statistically independent source\nsignals. It has been shown that the minimization
of mutual\ninformation leads to iterative use of score functions, i.e.\nderivatives
of log densities. The Pearson system allows\nadaptive modeling of score functions.
The flexibility of the\nPearson system makes it possible to model a wide range
of\nsource distributions including asymmetric distributions. The\nalgorithm is
designed especially for problems with asymmetric\nsources but it works for
symmetric sources as well.","License":"GPL-
2","NeedsCompilation":"no","Package":"PearsonICA","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Independent component analysis using score functions
from the\nPearson system","Version":"1.2-4"},"PedCNV":{"Author":"Meiling Liu,
Sungho Won and Weicheng Zhu","Depends":"Rcpp (>= 0.10.4), RcppArmadillo (>=
0.3.900.0), ggplot2","Description":"An implementation for association analysis with
CNV data in R. It\nprovides two methods for association study: first, the observed
probe\nintensity measurement can be directly used to detect the association of
CNV\nwith phenotypes of interest. Second, the most probable copy number
is\nestimated with the proposed likelihood and the association of the
most\nprobable copy number with phenotype is tested. This method can be applied\nto
both the independent and correlated population.","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"PedCNV","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"An implementation for association analysis with CNV
data","URL":"https:\/\/github.com\/rksyouyou\/PedCNV","Version":"0.1"},"PenCoxFrail
":{"Author":"Andreas Groll","Depends":"survival","Description":"A regularization
approach for Cox Frailty Models by penalization methods is
provided.","Imports":"Rcpp (>= 0.11.6), Matrix","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"PenCoxFrail","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Regularization in Cox Frailty
Models","Version":"1.0.0"},"PepPrep":{"Author":"Rafael Dellen","Depends":"biomaRt,
stringr","Description":"Amino acid exchange based on single nucleotide variant
(SNV) information and tryptic digestion on peptide sequence. Searching for
homologous by comparison of tryptic digested peptide sequences.","License":"GPL-
3","NeedsCompilation":"no","Package":"PepPrep","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Insilico peptide mutation, digestion and homologous
comparison","Version":"1.1.0"},"Peptides":{"Author":"Daniel Osorio, Paola Rondon-
Villarreal and Rodrigo Torres.","Description":"Calculate physicochemical properties
and indices from amino-acid sequences of peptides and proteins. Include also the
option to read and plot output files from the 'GROMACS' molecular dynamics
package.","License":"GPL-
2","NeedsCompilation":"no","Package":"Peptides","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"RUnit","Title":"Calculate Indices and Theoretical
Properties of
Protein\nSequences","URL":"https:\/\/github.com\/dosorio\/Peptides\/","Version":"1.
1.1"},"PerFit":{"Author":"Jorge N. Tendeiro","Depends":"ltm,
mirt","Description":"Several person-fit statistics (PFSs) are offered. These
statistics allow assessing whether\nindividual response patterns to tests or
questionnaires are (im)plausible given\nthe other respondents in the sample or
given a specified item response theory model. Some PFSs apply to\ndichotomous data,
such as the likelihood-based PFSs (lz, lz*) and the group-based PFSs\n(personal
biserial correlation, caution index, (normed) number of Guttman
errors,\nagreement\/disagreement\/dependability statistics, U3, ZU3, NCI, Ht). PFSs
suitable to polytomous data include\nextensions of lz, U3, and (normed) number of
Guttman errors.","Imports":"stats, graphics, fda, Hmisc, irtoys, MASS,
2)","NeedsCompilation":"no","Package":"PerFit","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Person Fit","Version":"1.4"},"PerMallows":
{"Author":"Ekhine Irurozki <ekhine.irurozqui@ehu.eus>, Borja Calvo
<borja.calvo@ehu.eus>, Jose A. Lozano <ja.lozano@ehu.eus>","Depends":"Rcpp (>=
0.10.3)","Description":"Includes functions to work with the Mallows and Generalized
Mallows Models. The considered distances are Kendall's-tau, Cayley, Hamming and
Ulam and it includes functions for making inference, sampling and learning such
distributions, some of which are novel in the literature. As a by-product,
PerMallows also includes operations for permutations, paying special attention to
those related with the Kendall's-tau, Cayley, Ulam and Hamming distances. It is
also possible to generate random permutations at a given distance, or with a given
number of inversions, or cycles, or fixed points or even with a given length on LIS
(longest increasing subsequence).","Imports":"utils","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"PerMallows","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Permutations and Mallows
Distributions","Version":"1.10"},"Perc":{"Author":"Kevin Fujii [aut],\nJian Jin
[aut, cre],\nAaron Shev [aut],\nBrianne Beisner [aut],\nBrenda McCowan [aut,
cph],\nHsieh Fushing [aut, cph]","Depends":"R (>= 2.14.0)","Description":"To
find the certainty of dominance interactions with indirect interactions being
considered.","Imports":"stats, grDevices","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Perc","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat, knitr, devtools, reshape2,
lattice","Title":"Using Percolation and Conductance to Find Information
Flow\nCertainty in a Direct Network","Version":"0.1.1"},"PerfMeas":
{"Author":"Giorgio Valentini, Matteo Re -- Universita' degli Studi di
Milano","Depends":"limma, graph, RBGL","Description":"Package that implements
different performance measures for classification and ranking tasks. AUC, precision
at a given recall, F-score for single and multiple classes are
available.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"PerfMeas","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"PerfMeas: Performance Measures for ranking and
classification\ntasks","Version":"1.2.1"},"PerformanceAnalytics":{"Author":"Brian
G. Peterson [cre, aut, cph],\nPeter Carl [aut, cph],\nKris Boudt [ctb, cph],\nRoss
Bennett [ctb],\nJoshua Ulrich [ctb],\nEric Zivot [ctb],\nMatthieu Lestel
[ctb],\nKyle Balkissoon [ctb],\nDiethelm Wuertz [ctb]","Depends":"R (>= 3.0.0), xts
(>= 0.9)","Description":"Collection of econometric functions for\nperformance and
risk analysis. This package aims to aid\npractitioners and researchers in utilizing
the latest\nresearch in analysis of non-normal return streams. In\ngeneral, it is
most tested on return (rather than\nprice) data on a regular scale, but most
functions will\nwork with irregular return data as well, and increasing\nnumbers of
functions will work with P&L or price data\nwhere
possible.","Imports":"zoo","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"PerformanceAnalytics","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Suggests":"Hmisc, MASS, quantmod, gamlss,
gamlss.dist, robustbase,\nquantreg, gplots","Title":"Econometric tools for
performance and risk analysis","URL":"http:\/\/r-forge.r-
project.org\/projects\/returnanalytics\/","Version":"1.4.3541"},"PermAlgo":
{"Author":"Marie-Pierre Sylvestre, Thad Edens, Todd MacKenzie,
Michal\nAbrahamowicz","Description":"This version of the permutational algorithm
generates a\ndataset in which event and censoring times are conditional on\nan
user-specified list of covariates, some or all of which are\ntime-
dependent.","License":"GPL-
2","NeedsCompilation":"no","Package":"PermAlgo","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Permutational Algorithm to Simulate Survival
Data","Version":"1.1"},"PhViD":{"Author":"IsmaÃ¯l Ahmed & Antoine
Poncet","Depends":"R (>= 2.10), LBE, MCMCpack","Description":"PhViD contains
several pharmacovigilance signal detection\nmethods extended to the multiple
comparison setting.","License":"GPL-
2","NeedsCompilation":"no","Package":"PhViD","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"PhViD: an R package for PharmacoVigilance signal
Detection","Version":"1.0.6"},"PharmPow":{"Author":"Frank Kloprogge & Joel
Tarning","Description":"This package contains functions performing power
calculations for mixed (sparse\/dense sampled) pharmacokinetic study designs. The
input data for these functions is tailored for NONMEM .phi
files.","Imports":"scatterplot3d","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"PharmPow","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Pharmacometric Power calculations for mixed study
designs","Version":"1.0"},"PharmacoGx":{"Author":"Petr Smirnov, Zhaleh Safikhani,
Benjamin Haibe-Kains","Depends":"R (>= 3.2)","Description":"Contains a set of
functions to perform large-scale analysis of pharmacogenomic
data.","Imports":"Biobase, piano, magicaxis, RColorBrewer, parallel,
caTools,\nmethods, downloader, stats, utils, graphics,
grDevices","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"PharmacoGx","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"xtable","Title":"Analysis of Large-Scale
Pharmacogenomic Data","Version":"1.1.4"},"PhaseType":{"Author":"Louis Aslett
<louis@maths.tcd.ie>","Depends":"coda, ggplot2, reshape","Description":"Functions
to perform Bayesian inference on absorption time\ndata for Phase-type
distributions. Plans to expand this to\ninclude frequentist inference and
simulation tools.","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"PhaseType","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"actuar","Title":"Inference for Phase-type
Distributions","URL":"http:\/\/www.louisaslett.com\/PhaseType\/","Version":"0.1.3"}
,"Phxnlme":{"Author":"Chay Ngee Lim [aut,cre],\nShuang Liang [aut],\nKevin Feng
[aut,cre],\nGrygoriy Vasilinin [aut],\nAngela Birnbaum [aut,ths],\nJason Chittenden
[aut],\nBob Leary [ctb],\nAna Henry [ctb],\nMike Dunlavey [ctb],\nSamer
Mouksassi[com]","Depends":"R (>= 2.10)","Description":"Calls 'Phoenix NLME' (non-
linear mixed effects), a population\nmodeling and simulation software, for
pharmacokinetics and pharmacodynamics\nanalyses and conducts post-processing of the
results. This includes creation of\nvarious diagnostic plots, bootstrap and visual
predictive checks. See <http:\/\/\nwww.certara.com\/software\/pkpd-modeling-and-
simulation\/phoenix-nlme\/> for more\ninformation about 'Phoenix
NLME'.","Imports":"ggplot2, gridExtra, manipulate, grid, lattice,
testthat","License":"GPL-
2","NeedsCompilation":"no","Package":"Phxnlme","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Run Phoenix NLME and Perform Post-
Processing","Version":"1.0.0"},"PhyActBedRest":{"Author":"J. Dustin Tracy, Zhiyi
Xu, Leena Choi, Sari Acra, Kong Y. Chen, Maciej S.
Buchowski","Description":"Applies an automated algorithm to mark Actigraph
accelerometer data as either bedrest or active. There are separate functions for
waist and wrist data. Its input is a dataframe with a timestamp column and one of
counts. The output is the same dataframe with an additional column, bedrest.
Bedrest will have \"a\" active or \"br\" for each line. Options also allow
for \"n\" nap which only differ than \"s\" in being for a shorter (specifiable)
time period. Designed to be used after wearmarking function in Physical Activity
3)","NeedsCompilation":"no","Package":"PhyActBedRest","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Marks periods of sleep in Actigraph accelerometer
data","Version":"1.0"},"PhySortR":{"Author":"Timothy Stephens [aut, cre, trl] (R
port),\nDebashish Bhattacharya [aut],\nMark Ragan [aut],\nCheong Xin Chan [aut,
cph] (Original Perl implementation)","Depends":"R (>=
3.0.0)","Description":"Screens and sorts phylogenetic trees in both traditional
and\nextended Newick format. Allows for the fast and flexible screening (within\na
tree) of Exclusive clades that comprise only the target taxa and\/or
Non-\nExclusive clades that includes a defined portion of non-target
taxa.","Imports":"phytools, ape","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"PhySortR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"A Fast, Flexible Tool for Sorting Phylogenetic
Trees","Version":"1.0.6"},"PhyloMeasures":{"Author":"Constantinos Tsirogiannis
[aut, cre], Brody Sandel [aut]","Description":"Given a phylogenetic tree T and a
sample S of species represented as\na subset of tips in T, we want to compute a
measure of the diversity\nof the species in S with respect to T. The current
package offers the\nimplementations of efficient algorithms for several such
measures.\nMost importantly, the package includes algorithms for computing exactly
and\nefficiently the expectation and the variance of these measures, which
are\nessential for null model comparisons. Efficient computation of\nrichness-
standardized versions of these metrics, such as the net\nrelatedness index (NRI),
nearest taxon index (NTI), phylogenetic\ndiversity index (PDI), and the
corresponding indices of two-sample measures\nare also available in this package.
The package also introduces a new\nsingle-sample measure, the Core Ancestor Cost
(CAC); the package provides\nfunctions for computing the value and the standardised
index of the CAC and,\nmore than that, there is an extra function available that
can compute exactly\nany statistical moment of the
measure.","Imports":"ape","License":"GPL-
3","NeedsCompilation":"yes","Package":"PhyloMeasures","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Fast and Exact Algorithms for Computing
Phylogenetic\nBiodiversity Measures","Version":"1.1"},"PhysActBedRest":
{"Author":"J. Dustin Tracy, Zhiyi Xu, Sari Acra, Kong Y. Chen, Maciej S.
Buchowski","Depends":"R (>= 2.10), chron, stringr","Description":"Contains a
function to categorize accelerometer readings collected in free-living (e.g., for
24 hours\/day for 7 days), preprocessed and compressed as counts (unit-less value)
in a specified time period termed epoch (e.g., 1 minute) as either bedrest (sleep)
or active. The input is a matrix with a timestamp column and a column with number
of counts per epoch. The output is the same dataframe with an additional column
termed bedrest. In the bedrest column each line (epoch) contains a function-
generated classification 'br' or 'a' denoting bedrest\/sleep and activity,
respectively. The package is designed to be used after wear\/nonwear marking
function in the 'PhysicalActivity' package.","Imports":"lubridate","License":"GPL
(>=
3)","NeedsCompilation":"no","Package":"PhysActBedRest","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Marks Periods of 'Bedrest' in Actigraph
Accelerometer Data","Version":"1.0"},"PhysicalActivity":{"Author":"Leena Choi,
Zhouwen Liu, Charles E. Matthews, and Maciej S. Buchowski","Depends":"R (>=
2.10)","Description":"This package contains functions to classify monitor wear and
nonwear time intervals in accelerometer data
collected to assess physical activity in free-living condition. The package also
contains functions to make plot for accelerometer data, and to obtain the summary
of daily monitor wear time and the mean of monitor wear time during valid days. A
monitored day is considered valid if the total minutes of classified monitor wear
time per day is greater than a user defined cutoff.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"PhysicalActivity","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Process Physical Activity Accelerometer
Data","Version":"0.1-1"},"Pijavski":{"Author":"Gleb Beliakov [aut, cre],\nGita Das
[aut],\nJonathan Wells [ctb],\nHewlett-Packard Company [ctb],\nSilicon Graphics
Computer Systems Inc. [ctb]","Description":"Global univariate minimization of
Lipschitz functions is performed by using Pijavski method, which was published in
Pijavski (1972) <DOI:10.1016\/0041-5553(72)90115-2>.","Imports":"Rcpp (>=
0.12.3)","License":"LGPL-
3","NeedsCompilation":"yes","Package":"Pijavski","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Global Univariate
Minimization","Version":"1.0"},"PivotalR":{"Author":"Predictive Analytics Team at
Pivotal Inc. <user@madlib.net>,\nwith contributions from Data Scientist Team at
Pivotal Inc.","Depends":"R (>= 2.14.0), methods, Matrix","Description":"R interface
of Pivotal Data Fabrics running on PostgreSQL\nor Pivotal (Greenplum and HAWQ)
database with parallel and\ndistributed computation ability for big data
analytics.\nPivotalR is a package that enables users of R to interact with\nthe
Pivotal (Greenplum) Database as well as Pivotal HD\/HAWQ for\nBig Data analytics.
It does so by providing an interface to the\noperations on tables\/views in the
database. These operations\nare almost the same as those of data.frame. Thus the
users of R\ndo not need to learn SQL when they operate on the objects in\nthe
database. It also provides a wrapper for MADlib, which is\nan open-source library
for parallel and scalable in-database\nanalytics.","Enhances":"DBI, RPostgreSQL,
shiny, testthat, tools, rpart","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"PivotalR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"A Fast, Easy-to-use Tool for Manipulating Tables in
Databases\nand A Wrapper of MADlib","Version":"0.1.17.45"},"PlayerRatings":
{"Author":"Alec Stephenson and Jeff Sonas.","Description":"Implements schemes for
estimating player or\nteam skill based on dynamic updating. Implemented methods
include\nElo, Glicko and Stephenson. Contains pdf documentation of a\nreproducible
analysis using approximately two million chess\nmatches.","License":"GPL-
3","NeedsCompilation":"yes","Package":"PlayerRatings","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Dynamic Updating Methods for Player Ratings
Estimation","Version":"1.0-1"},"PlotPrjNetworks":{"Author":"Javier Celigueta
Mu<c3><b1>oz","Description":"Useful set of tools for plotting network diagrams in
any kind of project.","Imports":"reshape2, ggplot2, grid","License":"GPL-
3","NeedsCompilation":"no","Package":"PlotPrjNetworks","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Useful Networking Tools for Project
Management","Version":"1.0.0"},"PlotRegionHighlighter":{"Author":"Elliot
Noma","Description":"Creates an envelope around a set of plotted points.
The\nenvelope is compact with a boundary that is continuous, smooth\nand convex.
Each point is represented as a circle and the\ncircles and connecting lines are the
solution to the multiple\npulley problem. This method can be used to highlight
regions in\na two-dimensional space.","License":"GPL-
2","NeedsCompilation":"no","Package":"PlotRegionHighlighter","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Title":"Creates an envelope that surrounds a set of
points plotted in a\ntwo dimensional space","Version":"1.0"},"PogromcyDanych":
{"Author":"Przemyslaw Biecek","Depends":"R (>= 3.0), dplyr,
SmarterPoland","Description":"The data sets used in the online course
,,PogromcyDanych''. You can process data in many ways. The course Data Crunchers
will introduce you to this variety. For this reason we will work on datasets of
different size (from several to several hundred thousand rows), with various level
of complexity (from two to two thousand columns) and prepared in different formats
(text data, quantitative data and qualitative data). All of these data sets were
gathered in a single big package called PogromcyDanych to facilitate access to
them. It contains all sorts of data sets such as data about offer prices of cars,
results of opinion polls, information about changes in stock market indices, data
about names given to newborn babies, ski jumping results or information about
outcomes of breast cancer patients treatment.","License":"GPL-
3","NeedsCompilation":"no","Package":"PogromcyDanych","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"PogromcyDanych \/ DataCrunchers is the Masive
Online Open Course\nthat Brings R and Statistics to the
People","Version":"1.5"},"PoiClaClu":{"Author":"Daniela
Witten","Description":"Implements the methods described in the paper, Witten (2011)
Classification and Clustering of Sequencing Data using a Poisson Model, Annals of
Applied Statistics 5(4) 2493-2518.","License":"GPL-
2","NeedsCompilation":"no","Package":"PoiClaClu","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Classification and clustering of sequencing data based
on a\nPoisson model","Version":"1.0.2"},"PoisBinNonNor":{"Author":"Gul Inan, Hakan
Demirtas","Depends":"BB, corpcor, Matrix, mvtnorm","Description":"Generation of
multiple count, binary and continuous variables simultaneously\ngiven the marginal
characteristics and association structure. Throughout the package,\nthe word
'Poisson' is used to imply count data under the assumption of Poisson
2)","NeedsCompilation":"no","Package":"PoisBinNonNor","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Data Generation with Poisson, Binary and Continuous
Components","Version":"1.0"},"PoisBinOrd":{"Author":"Gul Inan, Hakan
Demirtas","Depends":"corpcor, GenOrd, Matrix, mvtnorm","Description":"Generation of
multiple count, binary and ordinal variables simultaneously\ngiven the marginal
characteristics and association structure. Throughout the package,\nthe word
'Poisson' is used to imply count data under the assumption of Poisson
2)","NeedsCompilation":"no","Package":"PoisBinOrd","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Data Generation with Poisson, Binary and Ordinal
Components","Version":"1.1"},"PoisBinOrdNonNor":{"Author":"Rachel Nordgren, Hakan
Demirtas","Depends":"Matrix, corpcor, MASS, GenOrd, BB","Description":"Generation
of a chosen number of count, binary, ordinal, and continuous (via Fleishman
polynomials) random variables, with specified correlations and marginal
properties.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"PoisBinOrdNonNor","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"moments","Title":"Generation of up to Four
Different Types of Variables","Version":"1.0"},"PoisBinOrdNor":{"Author":"Yiran Hu,
Hakan Demirtas","Depends":"Matrix,corpcor, mvtnorm, psych,
GenOrd","Description":"Generation of multiple count, binary, ordinal and normal
variables simultaneously given the marginal characteristics and association
structure.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"PoisBinOrdNor","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Data Generation with Poisson, Binary, Ordinal and
Normal\nComponents","Version":"1.1"},"PoisNonNor":{"Author":"Yaru Shi, Hakan
Demirtas","Depends":"graphics, grDevices, stats, utils, BB, corpcor, MASS,
Matrix","Description":"This package generates count (assuming Poisson distribution)
and continuous data (using Fleishman polynomials) simultaneously.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"PoisNonNor","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Simultaneous Generation of Count and Continuous
Data","Version":"1.0"},"PoisNor":{"Author":"Anup Amatya and Hakan
Demirtas","Depends":"mvtnorm, corpcor, Matrix","Description":"A package for
simulating multivariate data with count and continuous variables with a pre-
specified correlation matrix. The count and continuous variables are assumed to
have Poisson and normal marginals, respectively. The data generation mechanism is a
combination of the normal to anything principle and a connection between Poisson
and normal correlations in the mixture.","License":"GPL-
2","NeedsCompilation":"no","Package":"PoisNor","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Simultaneous generation of multivariate data with Poisson
and\nnormal marginals","Version":"1.0"},"PoissonSeq":{"Author":"Jun
Li","Depends":"R(>= 2.10),combinat,splines","Description":"This package implements
a method for normalization,\ntesting, and false discovery rate estimation for RNA-
sequencing\ndata. The description of the method is in Li J, Witten DM,\nJohnstone
I, Tibshirani R (2012). Normalization, testing, and\nfalse discovery rate
estimation for RNA-sequencing data.\nBiostatistics 13(3): 523-38. We estimate the
sequencing depths\nof experiments using a new method based on Poisson\ngoodness-of-
fit statistic, calculate a score statistic on the\nbasis of a Poisson log-linear
model, and then estimate the\nfalse discovery rate using a modified version of
permutation\nplug-in method. A more detailed instruction as well as sample\ndata is
available at\nhttp:\/\/www.stanford.edu\/~junli07\/research.html. In
this\nversion, we changed the way of calculating log foldchange for\ntwo-class
data. The FDR estimation part remains unchanged.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"PoissonSeq","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Significance
analysis of sequencing data based on a Poisson log\nlinear
model","Version":"1.1.2"},"PolyPatEx":{"Author":"Alexander
Zwart","Description":"Functions to perform paternity exclusion via
allele\nmatching, in autopolyploid species having ploidy 4, 6, or 8. The\nmarker
data used can be genotype data (copy numbers known) or\n'allelic phenotype data'
(copy numbers not known).","Imports":"gtools, utils","License":"GPL-3 + file
LICENSE","NeedsCompilation":"no","Package":"PolyPatEx","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Paternity Exclusion in Autopolyploid
Species","Version":"0.9.2"},"PolynomF":{"Author":"Bill
Venables","Description":"Implements univariate polynomial operations in
R","License":"GPL-
2","NeedsCompilation":"yes","Package":"PolynomF","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Polynomials in R","Version":"0.94"},"Pomic":
{"Author":"Author: Cyril Piou","Depends":"stats","Description":"This package
propose calculations of an information criterion to check the quality of
simulations results of ABM\/IBM or other non-linear rule-based models. The POMDEV
measure is based on the KL divergence and likelihood theory. It basically indicates
the deviance of simulation results from field observations. Once POMDEV scores and
metropolis-hasting sampling on different model versions are effectuated, POMIC
scores can be calculated. This method is still under development and further work
are needed for the incorporation of multiple patterns assessment.","License":"GPL-
2","NeedsCompilation":"no","Package":"Pomic","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Pomic","Version":"1.0.2"},"PopED":{"Author":"Andrew C.
Hooker [aut, cre, trl, cph],\nSebastian Ueckert [aut] (MATLAB version),\nMarco
Foracchia [aut] (O-Matrix version),\nJoakim Nyberg [aut] (MATLAB version),\nEric
Stroemberg [ctb] (MATLAB version)","Depends":"ggplot2","Description":"Optimal
experimental designs for both population and individual\nstudies based on nonlinear
mixed-effect models. Often this is based on a\ncomputation of the Fisher
Information Matrix (FIM). This package was developed\nfor pharmacometric problems,
and examples and predefined models are available\nfor these types of
systems.","Imports":"MASS, mvtnorm, nlme, dplyr, codetools, stats,
utils","License":"LGPL (>=
3)","NeedsCompilation":"no","Package":"PopED","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat, Hmisc, GA","Title":"Population (and
Individual) Optimal Experimental
Design","URL":"http:\/\/poped.sourceforge.net","Version":"0.3.0"},"PopGenKit":
{"Author":"Sebastien Rioux Paquette","Description":"There are two main purposes to
this package. The first is\nto allow batch conversion of Genepop (Rousset 2008)
input files\nfor use with Arlequin (Excoffier and Lischer 2010), which has
a\nsimple GUI to analyze batch files. Two commonly used simulation\nsoftware,
BottleSim (Kuo & Janzen 2003) and Easypop (Balloux\n2001) produce Genepop output
files that can be analyzed this\nway. There are also functions to convert to and
from BottleSim\nformat, to quickly produce allele frequency tables or to\nconvert a
file directly for use in ordination analyses (e.g.\nprincipal component analysis).
This package also includes\nfunctions to calculate allele rarefaction curves,
confidence\nintervals on heterozygosity and allelic richness with\nresampling
strategies (bootstrap and jackknife).","License":"GPL-
2","NeedsCompilation":"no","Package":"PopGenKit","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Useful functions for (batch) file conversion and data
resampling\nin microsatellite datasets","Version":"1.0"},"PopGenReport":
{"Author":"Bernd Gruber [aut, cre],\nAaron Adamack [aut]","Depends":"R (>= 3.0.0),
knitr, adegenet (>= 2.0.0), raster","Description":"Provides beginner friendly
framework to analyse population genetic data. It uses 'knitr' to create
comprehensive reports on spatial genetic data. For detailed information how to use
the package refer to the comprehensive tutorials or visit
www.popgenreport.org.","Imports":"lattice, RgoogleMaps, gap, calibrate, xtable,
plyr, dismo,\nreshape, ggplot2, R.utils, ade4, pegas, genetics, rgdal,\ngdistance,
vegan, sp, mmod, GGally, data.table, graphics,\ngrDevices, methods, stats,
utils","License":"GPL","NeedsCompilation":"no","Package":"PopGenReport","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Title":"A Simple Framework to Analyse
Population Genetic Data","URL":"https:\/\/github.com\/green-striped-
gecko\/PopGenReport","Version":"2.2"},"PopGenome":{"Author":"Bastian Pfeifer [aut,
cre], Ulrich Wittelsbuerger [ctb], Heng Li [ctb], Bob Handsaker [ctb]","Depends":"R
(>= 2.14.2),ff","Description":"Provides efficient tools for population genomics
data analysis,\nable to process individual loci, large sets of loci, or whole
genomes. PopGenome not only\nimplements a wide range of population genetics
statistics, but also facilitates the easy\nimplementation of new algorithms by
other researchers. PopGenome is optimized for speed via\nthe seamless integration
of C code.","Imports":"methods","License":"GPL-
3","NeedsCompilation":"yes","Package":"PopGenome","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"parallel, bigmemory, BASIX, WhopGenome","Title":"An
Efficient Swiss Army Knife for Population Genomic
Analyses","URL":"http:\/\/popgenome.weebly.com","Version":"2.1.6"},"PopVar":
{"Author":"Tyler Tiede [aut, cre], Mohsen Mohammadi [ctb], Kevin P. Smith
[ctb]","Depends":"R (>= 3.1.1)","Description":"The main attribute of 'PopVar' is
the prediction of genetic variance in bi-parental populations, from which the
package derives its name. 'PopVar' contains a set of functions that use phenotypic
and genotypic data from a set of candidate parents to 1) predict the mean, genetic
variance, and superior progeny value of all, or a defined set of pairwise bi-
parental crosses, and 2) perform cross-validation to estimate genome-wide
prediction accuracy of multiple statistical models. More details are available in
Mohammadi, Tiede, and Smith (2015). Crop Sci. doi:10.2135\/cropsci2015.01.0030. A
dataset 'think_barley.rda' is included for reference and
examples.","Imports":"BGLR, qtl, rrBLUP, stats, utils","License":"GPL-
3","NeedsCompilation":"no","Package":"PopVar","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Genomic Breeding Tools: Genetic Variance Prediction
and\nCross-Validation","Version":"1.2.1"},"PortRisk":{"Author":"Sourish Das [aut,
cre],\nTamal Kanti Panja [aut]","Depends":"R (>= 3.0.0)","Description":"Risk
Attribution of a portfolio with Volatility Risk Analysis.","Imports":"zoo,
MCMCpack, tseries, copula, MASS","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"PortRisk","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Portfolio Risk
Analysis","Version":"1.1.0"},"PortfolioAnalytics":{"Author":"Brian G. Peterson
[cre, aut, cph],\nPeter Carl [aut, cph],\nKris Boudt [ctb, cph],\nRoss Bennett
[ctb, cph],\nHezky Varon [ctb],\nGuy Yollin [ctb],\nR. Douglas Martin
[ctb]","Depends":"R (>= 2.14.0), zoo, xts (>= 0.8), foreach,\nPerformanceAnalytics
(>= 1.1.0)","Description":"Portfolio optimization and analysis routines and
graphics.","License":"GPL","NeedsCompilation":"yes","Package":"PortfolioAnalytics",
"Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"quantmod,
DEoptim(>= 2.2.1), iterators, fGarch, Rglpk,\nquadprog, ROI (>= 0.1.0),
ROI.plugin.glpk (>= 0.0.2),\nROI.plugin.quadprog (>= 0.0.2), ROI.plugin.symphony
(>= 0.0.2),\npso, GenSA, corpcor, testthat, nloptr (>= 1.0.0),
MASS,\nrobustbase","Title":"Portfolio Analysis, Including Numerical Methods for
Optimization\nof Portfolios","Version":"1.0.3636"},"PortfolioEffectEstim":
{"Author":"Andrey Kostin [aut, cre],\nAleksey Zemnitskiy [aut],\nOleg Nechaev
[aut]","Depends":"methods,PortfolioEffectHFT(>= 1.5)","Description":"R interface to
PortfolioEffect cloud service for estimating\nhigh frequency price variance,
quarticity, microstructure noise variance,\nand other metrics in both aggregate and
rolling window flavors.\nConstructed estimators could use client-side market data
or access\nHF intraday price history for all major US Equities.\nSee
https:\/\/www.portfolioeffect.com\/ for more information on the\nPortfolioEffect
high frequency portfolio analytics platform.","Imports":"rJava","License":"GPL-
3","NeedsCompilation":"no","Package":"PortfolioEffectEstim","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Title":"High Frequency Price Estimators by
PortfolioEffect","URL":"https:\/\/www.portfolioeffect.com\/","Version":"1.2"},"Port
folioEffectHFT":{"Author":"Aleksey Zemnitskiy [aut, cre],\nAndrey Kostin
[aut],\nOleg Nechaev [aut],\nCraig Otis and others [ctb, cph] (OpenFAST
library),\nDaniel Lemire, Muraoka Taro and others [ctb, cph]
(JavaFastPFOR\nlibrary),\nJoe Walnes, Jorg Schaible and others [ctb, cph] (XStream
library),\nDain Sundstrom [ctb, cph] (Snappy library),\nExtreme! Lab, Indiana
University [ctb, cph] (XPP3 library),\nThe Apache Software Foundation [ctb, cph]
(Apache Log4j and Commons\nLang libraries),\nGoogle, Inc. [ctb, cph] (GSON
library),\nFree Software Foundation [ctb, cph] (GNU Trove and GNU
Crypto\nlibraries)","Depends":"R (>= 2.13.2), ggplot2 (>= 2.0.0)","Description":"R
interface to PortfolioEffect cloud service for backtesting\nhigh frequency trading
(HFT) strategies, intraday portfolio analysis\nand optimization. Includes auto-
calibrating model pipeline for market\nmicrostructure noise, risk factors, price
jumps\/outliers, tail risk\n(high-order moments) and price fractality (long
memory). Constructed\nportfolios could use client-side market data or access HF
intraday price\nhistory for all major US Equities. See
https:\/\/www.portfolioeffect.com\/\nfor more information on the PortfolioEffect
high frequency portfolio\nanalytics platform.","Imports":"methods, rJava,
grid","License":"GPL-
3","NeedsCompilation":"no","Package":"PortfolioEffectHFT","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"High Frequency Portfolio Analytics by
PortfolioEffect","URL":"https:\/\/www.portfolioeffect.com\/","Version":"1.5"},"Pott
sUtils":{"Author":"Dai Feng [aut, cre], Luke Tierney [ctb]","Depends":"R (>=
3.0.2)","Description":"A package including several functions related to the Potts
models.","Imports":"miscF (>= 0.1-2)","License":"GPL-
2","NeedsCompilation":"yes","Package":"PottsUtils","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Utility Functions of the Potts Models","Version":"0.3-
2"},"PoweR":{"Author":"Pierre Lafaye de Micheaux <lafaye@dms.umontreal.ca>, Viet
Anh Tran <vietanhtran184@yahoo.com>","Depends":"R (>= 3.0), parallel,
Rcpp","Description":"Functions for the computation of power and level tables for
hypothesis tests, in LaTeX format, functions to build explanatory graphs for
studying power of test statistics.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"PoweR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Computation of Power and Level Tables for Hypothesis
Tests","Version":"1.0.5"},"Power2Stage":{"Author":"Detlew Labes [aut, cre],\nHelmut
Schuetz [ctb]","Description":"Functions to obtain the operational characteristics
of\nbioequivalence studies with 2-stage designs via simulations\n- Contains a
function to calculate power and sample-size distribution\nof 2-stage bioequivalence
(BE) studies with a 2x2 crossover design\naccording to Potvin et al. \/ Montague et
al. modified to include a\nfutility Nmax and modified to do the sample size
estimation step\nwith PE and mse of stage 1.\n- Contains further a function with
the modifications according to\nKaralis & Macheras which use both point estimate
(PE) and mse from stage 1\nalso for the power monitoring steps.\n- The third
function power.2stage.fC() calculates power and sample-size\ndistribution of 2-
stage BE studies with a futility criterion\nfor the PE or CI of T\/R from stage
1.\n- The fourth function power.2stage.GS() calculates power of non-adaptive\ngroup
sequential (2-stage) BE studies.\n- The fifth function power.2stage.p() calculates
power and sample size\ndistribution of 2-stage BE studies with 2 parallel
groups.\nThis function has a sibling power.2stage.pAF(), which performs exactly
as\ndescribed in A.Fuglsang 2014\n- Another function power.2stage.ssr() allows the
power calculation\nfor 2-stage studies with (blinded) interim sample size re-
estimation.","Imports":"PowerTOST, stats, mvtnorm","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Power2Stage","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"graphics","Title":"Power and Sample-Size
Distribution of 2-Stage Bioequivalence\nStudies","Version":"0.4-3"},"PowerTOST":
{"Author":"Detlew Labes [aut, cre],\nHelmut Schuetz [aut],\nBenjamin Lang
[aut]","Description":"Contains functions to calculate power and sample size
for\nvarious study designs used for bioequivalence studies.\nSee function
known.designs() for study designs covered.\nMoreover the package contains functions
for power and sample size\nbased on 'expected' power in case of uncertain
(estimated) variability.\n-----\nAdded are functions for the power and sample size
for the ratio of\ntwo means with normally distributed data on the original
scale\n(based on Fieller's confidence ('fiducial') interval).\n-----\nContains
further functions for power and sample size calculations based on\nnon-inferiority
t-test. This is not a TOST procedure but eventually useful\nif the question of
'non-superiority' must be evaluated.\nThe power and sample size calculations based
on non-inferiority test may\nalso performed via 'expected' power in case of
uncertain (estimated)\nvariability.\n-----\nContains functions power.scABEL() and
sampleN.scABEL() to calculate power\nand sample size for the BE decision via scaled
(widened) BE acceptance\nlimits (EMA recommended) based on simulations.\nContains
also functions scABEL.ad() and sampleN.scABEL.ad() to iteratively\nadjust alpha in
order to maintain the consumer risk in ABEL studies\nand adapt the sample size for
the loss in power.\nContains further functions power.RSABE() and sampleN.RSABE() to
calculate\npower and sample size for the BE decision via reference scaled ABE
criterion\naccording to the FDA procedure based on simulations.\nContains further
functions power.NTIDFDA() and sampleN.NTIDFDA() to calculate\npower and sample size
for the BE decision via the FDA procedure for NTID's\nbased on
simulations.\nContains further functions power.HVNTID() and sampleN.HVNTID() to
calculate\npower and sample size for the BE decision via the FDA procedure
for\nhighly variable NTID's (see FDA Dabigatran \/ rivaroxaban
guidances)\n-----\nContains functions for power analysis of a sample size plan for
ABE\n(pa.ABE()), scaled ABE (pa.scABE()) and scaled ABE for NTID's
(pa.NTIDFDA())\nanalysing power if deviating from assumptions of the
plan.\n-----\nContains further functions for power calculations \/ sample size
estimation\nfor dose proportionality studies using the Power
model.","Imports":"mvtnorm, stats, utils, graphics, grDevices","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"PowerTOST","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"crossdes","Title":"Power and Sample Size Based on
Two One-Sided t-Tests (TOST) for\n(Bio)Equivalence Studies","Version":"1.3-
4"},"PracTools":{"Author":"Richard Valliant, Jill A. Dever, Frauke
Kreuter","Depends":"R (>= 2.10)","Description":"Contains functions for sample size
calculation for survey samples using stratified or clustered one-, two-, and three-
stage sample designs. Other functions compute variance components for multistage
designs and sample sizes in two-phase designs. A number of example datasets are
included.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"PracTools","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"doBy, foreign, pps, reshape, sampling, samplingbook,
survey","Title":"Tools for Designing and Weighting Survey
Samples","Version":"0.3"},"PredictABEL":{"Author":"Suman Kundu, Yurii S. Aulchenko,
A. Cecile J.W. Janssens","Depends":"R (>= 2.12.0), Hmisc, ROCR, epitools,
PBSmodelling","Description":"PredictABEL includes functions to assess the
performance of\nrisk models. The package contains functions for the various
measures that are\nused in empirical studies, including univariate and multivariate
odds ratios\n(OR) of the predictors, the c-statistic (or area under the receiver
operating\ncharacteristic (ROC) curve (AUC)), Hosmer-Lemeshow goodness of fit
test,\nreclassification table, net reclassification improvement (NRI)
and\nintegrated discrimination improvement (IDI). Also included are functions\nto
create plots, such as risk distributions, ROC curves, calibration
plot,\ndiscrimination box plot and predictiveness curves. In addition to
functions\nto assess the performance of risk models, the package includes functions
to\nobtain weighted and unweighted risk scores as well as predicted risks
using\nlogistic regression analysis. These logistic regression functions
are\nspecifically written for models that include genetic variables, but they\ncan
also be applied to models that are based on non-genetic risk factors
only.\nFinally, the package includes function to construct a simulated dataset
with\ngenotypes, genetic risks, and disease status for a hypothetical population,
which\nis used for the evaluation of genetic risk models.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"PredictABEL","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"GenABEL","Title":"Assessment of Risk Prediction
Models","URL":"http:\/\/www.genabel.org\/packages\/PredictABEL","Version":"1.2-
2"},"PredictiveRegression":{"Author":"Vladimir Vovk <vovk@cs.rhul.ac.uk> and Ilia
Nouretdinov\n<ilia@cs.rhul.ac.uk>","Description":"Three prediction algorithms
described in the paper\n\"On-line predictive linear regression\" Annals of
Statistics 37,\n1566 - 1590 (2009)","License":"file
LICENSE","NeedsCompilation":"no","Package":"PredictiveRegression","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Title":"Prediction Intervals for Three Basic
Statistical Models","Version":"0.1-4"},"PresenceAbsence":{"Author":"Elizabeth
Freeman","Depends":"R (>= 2.2.0)","Description":"This package provides a set of
functions useful when\nevaluating the results of presence-absence models.
Package\nincludes functions for calculating threshold dependent measures\nsuch as
confusion matrices, pcc, sensitivity, specificity, and\nKappa, and produces plots
of each measure as the threshold is\nvaried. It will calculate optimal threshold
choice according to\na choice of optimization criteria. It also includes
functions\nto plot the threshold independent ROC curves along with the\nassociated
AUC (area under the
curve).","License":"Unlimited","NeedsCompilation":"no","Package":"PresenceAbsence",
"Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Presence-Absence Model
Evaluation","Version":"1.1.9"},"PrevMap":{"Author":"Emanuele Giorgi, Peter J.
Diggle","Depends":"geoR, maxLik, raster, pdist","Description":"It provides
functions for both likelihood-based\nand Bayesian analysis of spatially referenced
prevalence data, and is\nalso an extension of the 'geoR'
package.","Imports":"splancs, truncnorm, methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"PrevMap","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Geostatistical Modelling of Spatially Referenced
Prevalence Data","Version":"1.3.2"},"PrivateLR":{"Author":"Staal A. Vinterbo
<sav@ucsd.edu>","Description":"PrivateLR implements two differentially private
algorithms for\nestimating L2-regularized logistic regression coefficients. A
randomized\nalgorithm F is epsilon-differentially
private (C. Dwork, Differential\nPrivacy, ICALP 2006), if\n|log(P(F(D) in S)) -
log(P(F(D') in S))| <= epsilon\nfor any pair D, D' of datasets that differ in
exactly one element, any\nset S, and the randomness is taken over the choices F
makes.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"PrivateLR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Differentially Private Regularized Logistic
Regression","Version":"1.2-21"},"ProDenICA":{"Author":"Trevor Hastie, Rob
Tibshirani","Depends":"gam","Description":"A direct and flexible method for
estimating an ICA model.\nThis approach estimates the densities for each
component\ndirectly via a tilted gaussian. The tilt functions are\nestimated via a
GAM poisson model. Details can be found in\n\"Elements of Statistical Learning (2nd
Edition)\" Section 14.7.4","License":"GPL-
2","NeedsCompilation":"no","Package":"ProDenICA","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Product Density Estimation for ICA using tilted Gaussian
density\nestimates","URL":"http:\/\/www-
stat.stanford.edu\/~hastie\/Papers\/ESLII.pdf","Version":"1.0"},"ProNet":
{"Author":"Xiang-Yun Wu and Xia-Yu Xia","Depends":"R (>= 3.1.0), Rcpp (>= 0.10.4),
igraph (>= 0.5.5-2), MCL,\nlinkcomm","Description":"High-throughput experiments are
now widely used in biological researches, which improves both the quality and
quantity of omics data. Network-based presentation of these data has become a
popular way in data analyses. This package mainly provides functions for biological
network construction, visualization and analyses. Networks can be constructed
either from experimental data or from a set of proteins and integrated PPI
database. Based on them, users can perform traditional visualization, along with
the subcellular localization based ones for Homo sapiens and Arabidopsis thaliana.
Furthermore, analyses including topological statistics, functional module
clustering and go profiling can also be achieved.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ProNet","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Biological Network Construction, Visualization and
Analyses","Version":"1.0.0"},"ProTrackR":{"Author":"Pepijn de Vries [aut, cre,
dtc]","Depends":"lattice, tuneR (>= 1.0), audio,
signal","Description":"'ProTracker' is a popular music tracker to sequence\nmusic
on a Commodore Amiga machine. This package offers the\nopportunity to import,
export, manipulate an play 'ProTracker'\nmodule files. Even though the file format
could be considered\narchaic, it still remains popular to this date. This
package\nintends to contribute to this popularity and therewith\nkeeping the legacy
of 'ProTracker' and the Commodore Amiga\nalive.","Imports":"graphics, methods,
stats, utils","License":"GPL-
3","NeedsCompilation":"no","Package":"ProTrackR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Manipulate and Play 'ProTracker'
Modules","Version":"0.3.3"},"ProbForecastGOP":{"Author":"Veronica J. Berrocal
<veroberrocal@gmail.com>, Yulia Gel,\nAdrian E. Raftery, Tilmann
Gneiting","Depends":"R (>= 1.8.0), RandomFields, fields","Description":"The
ProbForecastGOP package contains a main function,\ncalled ProbForecastGOP and other
functions, to produce\nprobabilistic weather forecasts of weather fields using
the\nGeostatistical Output Perturbation (GOP) method of Gel,\nRaftery, and Gneiting
(JASA, 2004).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ProbForecastGOP","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Probabilistic weather forecast using the GOP
method","Version":"1.3.2"},"ProbYX":{"Author":"Giuliana Cortese","Depends":"R (>=
3.0-0), rootSolve","Description":"Confidence intervals and point estimation for R
under various parametric model assumptions; likelihood inference based on classical
first-order approximations and higher-order asymptotic
procedures.","Imports":"stats, graphics","License":"GPL-
2","NeedsCompilation":"no","Package":"ProbYX","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Inference for the Stress-Strength Model R =
P(Y<X)","Version":"1.1-0"},"ProbitSpatial":{"Author":"Davide Martinetti and
Ghislain Geniaux","Depends":"Matrix, methods, Rcpp,
speedglm","Description":"Binomial Spatial Probit models for big
data.","Imports":"numDeriv, RANN","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ProbitSpatial","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Probit with Spatial Dependence, SAR and SEM
Models","Version":"1.0"},"ProfessR":{"Author":"Jonathan M. Lees","Depends":"R (>=
2.12)","Description":"Programs to determine student grades and create\nexaminations
from Question banks. Programs will create numerous\nmultiple choice exams,
randomly shuffled, for different versions of same question
list.","Imports":"RPMG","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ProfessR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Grades Setting and Exam
Maker","Version":"2.3"},"ProfileLikelihood":{"Author":"Leena Choi","Depends":"nlme,
MASS","Description":"This package provides profile likelihoods for a parameter of
interest in commonly used statistical models. The models include linear models,
generalized linear models, proportional odds models, linear mixed-effects models,
and linear models for longitudinal responses fitted by generalized least squares.
The package also provides plots for normalized profile likelihoods as well as the
maximum profile likelihood estimates and the kth likelihood support
intervals.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"ProfileLikelihood","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Profile Likelihood for a Parameter in Commonly
Used Statistical\nModels","Version":"1.1"},"ProgGUIinR":{"Author":"Michael Lawrence
and John Verzani","Depends":"methods, utils, ggplot2, svMisc,
MASS","Description":"sample code, appendices and functions for the
text\nProgramming GUIs in R","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ProgGUIinR","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"qtbase, RGtk2, cairoDevice, gWidgetsRGtk2,
gWidgets, tcltk","Title":"support package for \"Programming Graphical User
Interfaces in R\"","URL":"NA","Version":"0.0-4"},"ProjectTemplate":
{"Author":"Aleksandar Blagotic [ctb],\nDiego Valle-Jones [ctb],\nJeffrey Breen
[ctb],\nJoakim Lundborg [ctb],\nJohn Myles White [aut, cph],\nJosh Bode
[ctb],\nKenton White [ctb],\nKirill Mueller [ctb, cre],\nMatteo Redaelli
[ctb],\nNoah Lorang [ctb],\nPatrick Schalk [ctb]","Depends":"R (>=
2.7)","Description":"ProjectTemplate provides functions to\nautomatically build a
directory structure for a new R\nproject. Using this structure,
ProjectTemplate\nautomates data loading, preprocessing, library\nimporting and unit
testing.","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"ProjectTemplate","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"foreign, reshape, plyr, stringr, ggplot2,
lubridate, log4r\n(>= 0.1-5), DBI, RMySQL, RSQLite, gdata, RODBC, RJDBC,
xlsx,\ntuneR, pixmap, data.table, RPostgreSQL, GetoptLong,
whisker,\ntestthat","Title":"Automates the creation of new statistical analysis
projects","URL":"http:\/\/projecttemplate.net","Version":"0.6"},"PropCIs":
{"Author":"Ralph Scherer","Description":"Computes two-sample confidence intervals
for single, paired and independent
proportions","License":"GPL","NeedsCompilation":"no","Package":"PropCIs","Repositor
y":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Various confidence interval
methods for
proportions","URL":"https:\/\/github.com\/shearer\/PropCIs","Version":"0.2-
5"},"PropClust":{"Author":"John Michael O Ranola, Kenneth Lange, Steve Horvath,
Peter Langfelder","Depends":"R (>= 2.10), flashClust,
dynamicTreeCut","Description":"This package implements propensity clustering
and\ndecomposition. Propensity decomposition can be viewed on the\none hand as a
generalization of the eigenvector-based\napproximation of correlation networks, and
on the other hand as\na generalization of random multigraph models and\nconformity-
based decompositions.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"PropClust","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Propensity Clustering and
Decomposition","Version":"1.4-2"},"PropScrRand":{"Author":"Travis M.
Loux","Description":"This package contains functions to run propensity-biased
allocation to balance covariate distributions in sequential trials and propensity-
constrained randomization to balance covariate distributions in trials with known
baseline covariates at time of randomization. Currently this package only supports
trials comparing two groups.","License":"GPL-
3","NeedsCompilation":"no","Package":"PropScrRand","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Propensity score methods for assigning treatment in
randomized\ntrials","Version":"1.1"},"ProteinDescriptors":{"Author":"Berat Kurar
[aut, cre],\nSami Abu Sneineh [aut],\nYaqoub Ashhab [aut]","Description":"An
implementation of protein descriptors in R. These descriptors\ncombine the
advantages of being fixed length and including partial sequential\neffect: Various
length of protein sequences are described with fixed length\nvectors that are
suitable for machine learning algorithms, and still includes\npartial sequential
effect.","License":"BSD 3-clause License + file
LICENSE","NeedsCompilation":"no","Package":"ProteinDescriptors","Repository":"http:
\/\/cran.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Generates Various
Protein Descriptors for Machine Learning\nAlgorithms","Version":"0.1.0"},"PsiHat":
{"Author":"Alaa Ali, Kyle Leckett, Marta Padilla, David R. Bickel (contributions
from Bradley Efron, Brit B. Turnbull, Balasubramanian Narasimhan from package
locfdr).","Depends":"methods, qvalue, splines","Description":"Suite
of R functions for the estimation of local false discovery rate (LFDR) using
several methods.","License":"GPL-
3","NeedsCompilation":"no","Package":"PsiHat","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Several Local False Discovery Rate
Estimators","URL":"http:\/\/www.r-project.org,
http:\/\/www.bioconductor.org,\nhttp:\/\/www.statomics.com","Version":"1.0"},"Psumt
Sim":{"Author":"Peter N. Steinmetz
<PeterNSteinmetz@steinmetz.org>","Depends":"EffectsRelBaseline,
boot","Description":"Functions to simulate Poisson or Normally distributed
responses relative to\na baseline and compute achieved significance level and
powers for tests on the\nsimulated responses.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"PsumtSim","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Simulations of grouped responses relative to
baseline","Version":"0.4"},"PtProcess":{"Author":"David Harte","Description":"Fits
and analyses time dependent marked point process models with an emphasis on
earthquake modelling. For a more detailed introduction to the package, see the
topic \"PtProcess\". A list of recent changes can be found in the topic \"Change
Log\".","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"PtProcess","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"parallel","Title":"Time Dependent Point Process
Modelling","URL":"http:\/\/homepages.maxnet.co.nz\/davidharte\/SSLib\/","Version":"
3.3-10"},"PubBias":{"Author":"Simon Thornley","Depends":"rmeta,
R.utils","Description":"I adapted a method designed by Ioannidis and Trikalinos,
which\ncompares the observed number of positive studies in a meta-analysis
with\nthe expected number, if the summary measure of effect, averaged over
the\nindividual studies, were assumed true. Excess in the observed number
of\npositive studies, compared to the expected, is taken as evidence
of\npublication bias. The observed number of positive studies, at a given
level\nfor statistical significance, is calculated by applying Fisher's exact
test\nto the reported 2x2 table data of each constituent study, doubling
the\nFisher one-sided P-value to make a two-sided test. The corresponding\nexpected
number of positive studies was obtained by summing the statistical\npowers of each
study. The statistical power depended on a given measure of\neffect which, here,
was the pooled odds ratio of the meta-analysis was\nused. By simulating each
constituent study, with the given odds ratio, and\nthe same number of treated and
non-treated as in the real study, the power\nof the study is estimated as the
proportion of simulated studies that are\npositive, again by a Fisher's exact test.
The simulated number of events in\nthe treated and untreated groups was done with
binomial sampling. In the\nuntreated group, the binomial proportion was the
percentage of actual\nevents reported in the study and, in the treated group, the
binomial\nsampling proportion was the untreated percentage multiplied by the
risk\nratio which was derived from the assumed common odds ratio. The
statistical\nsignificance for judging a positive study may be varied and
large\ndifferences between expected and observed number of positive studies
around\nthe level of 0.05 significance constitutes evidence of publication
bias.\nThe difference between the observed and expected is tested by chi-square.
A\nchi-square test P-value for the difference below 0.05 is suggestive
of\npublication bias, however, a less stringent level of 0.1 is often used
in\nstudies of publication bias as the number of published studies is
usually\nsmall.","License":"GPL-
3","NeedsCompilation":"no","Package":"PubBias","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Performs simulation study to look for publication bias,
using a\ntechnique described by Ioannidis and Trikalinos; Clin
Trials.\n2007;4(3):245-53","Version":"1.0"},"PubMedWordcloud":{"Author":"Felix
Yanhui Fan <nolanfyh@gmail.com>","Description":"create a word cloud using the
abstract of publications from PubMed","Imports":"XML, stringr, RCurl, wordcloud,
tm, RColorBrewer","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"PubMedWordcloud","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"PubMed Word
Clouds","URL":"http:\/\/felixfan.github.io\/PubMedWordcloud\/","Version":"0.3.2"},"
PurBayes":{"Author":"Nicholas B. Larson","Depends":"rjags","Description":"PurBayes
is an MCMC-based algorithm that uses\nnext-generation sequencing data to estimate
tumor purity and\nclonality for paired tumor-normal data.","License":"GPL-
2","NeedsCompilation":"no","Package":"PurBayes","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Bayesian Estimation of Tumor Purity and
Clonality","Version":"1.3"},"PwrGSD":{"Author":"Grant
Izmirlian","Depends":"survival","Description":"Tools the evaluation of interim
analysis plans for sequentially\nmonitored trials on a survival endpoint; tools to
construct efficacy and\nfutility boundaries, for deriving power of a sequential
design at a specified\nalternative, template for evaluating the performance of
candidate plans at a\nset of time varying alternatives.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"PwrGSD","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Power in a Group Sequential
Design","Version":"2.000"},"PythonInR":{"Author":"Florian Schwendinger [aut,
cre]","Depends":"R (>= 2.15)","Description":"Interact with Python from within
R.","Imports":"pack, methods, R6, stats","License":"GPL-
3","NeedsCompilation":"yes","Package":"PythonInR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Use Python from Within
R","URL":"https:\/\/bitbucket.org\/Floooo\/pythoninr\/","Version":"0.1-3"},"QCA":
{"Author":"Adrian Dusa [aut, cre, cph],\nAlrik Thiem [aut] (from version 1.0-0, up
to version 1.1-3)","Depends":"R (>= 3.0.0), QCAGUI (>=
2.1)","Description":"Starting with version 2.0, the package QCA acts as an
aggregator for the various packages dealing with Qualitative Comparative Analysis.
For the moment, it is a gateway to the QCAGUI package, but more related packages
are expected to be loaded at runtime.","Imports":"lpSolve, shiny, utils,
venn","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"QCA","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Qualitative Comparative Analysis","Version":"2.1"},"QCA3":
{"Author":"Ronggui HUANG","Description":"A set of functions for Qualitative
Comparative Analysis (QCA). It can be used for various types of QCA (csQCA, mvQCA
fsQCA and crip set TQCA and time-serious QCA). It has methods for simplifying
assumption, contradictory simplifying
assumption.","Imports":"lpSolveAPI","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"QCA3","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Yet another package for Qualitative Comparative
Analysis","URL":"http:\/\/asrr.r-forge.r-project.org\/","Version":"0.0-
7"},"QCAGUI":{"Author":"Adrian Dusa [aut, cre, cph],\njQuery Foundation [cph]
(jQuery library and jQuery UI library),\njQuery contributors [ctb, cph] (jQuery
library; authors listed in\ninst\/gui\/www\/shared\/jquery-AUTHORS.txt),\nVasil
Dinkov [ctb, cph] (jquery.smartmenus.js library),\nDmitry Baranovskiy [ctb, cph]
(raphael.js library),\nEmmanuel Quentin [ctb, cph] (raphael.inline_text_editing.js
library),\nJimmy Breck-McKye [ctb, cph] (raphael-paragraph.js library),\nAlrik
Thiem [ctb] (package QCA versions 1.0-0 to 1.1-3)","Depends":"R (>=
3.0.0)","Description":"An extensive set of functions to perform Qualitative
Comparative Analysis:\ncrisp sets ('csQCA'), temporal ('tQCA'), multi-value
('mvQCA') and fuzzy sets ('fsQCA'),\nusing a GUI - graphical user interface.\nQCA
is a methodology that bridges the qualitative and quantitative divide\nin social
science research. It uses a boolean algorithm that results in a minimal\ncausal
combination which explains a given phenomenon.","Imports":"lpSolve, shiny, utils,
venn","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"QCAGUI","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Modern Functions for Qualitative Comparative
Analysis","Version":"2.1"},"QCAfalsePositive":{"Author":"Bear Braumoeller
<braumoeller.1@osu.edu>","Depends":"R (>= 3.2.0)","Description":"Implements tests
for Type I error in Qualitative Comparative Analysis (QCA) that take into account
the multiple hypothesis tests inherent in the procedure. Tests can be carried out
on three variants of QCA: crisp-set QCA (csQCA), multi-value QCA (mvQCA) and fuzzy-
set QCA (fsQCA). For fsQCA, the fsQCApermTest() command implements a permutation
test that provides 95% confidence intervals for the number of counterexamples and
degree of consistency, respectively. The distributions of permuted values can be
plotted against the observed values. For csQCA and mvQCA, simple binomial tests are
implemented in csQCAbinTest() and mvQCAbinTest(), respectively.","License":"GPL-
3","NeedsCompilation":"no","Package":"QCAfalsePositive","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Tests for Type I Error in Qualitative Comparative
Analysis (QCA)","Version":"1.1.1"},"QCApro":{"Author":"Alrik Thiem [aut,
cre],\nMichael Baumgartner [ctb],\nAdrian Dusa [ctb] (co-author of package 'QCA'
(predecessor of 'QCApro',\nversions 1.0-0 to 1.1-4),\nReto Spoehel
[ctb]","Depends":"R (>= 3.2.2)","Description":"With numerous improvements on its
predecessor package 'QCA', the 'QCApro' package provides professional functionality
for performing configurational comparative research with Qualitative Comparative
Analysis (QCA), including crisp-set QCA, multi-value QCA, and fuzzy-set QCA. It
also offers advanced tools for methodological evaluations.","Imports":"lpSolve,
3","NeedsCompilation":"yes","Package":"QCApro","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"QCA3 (<= 0.0-7),
QCAGUI (<= 2.0), testthat (<= 0.11.0)","Title":"Professional Functionality for
Performing and Evaluating\nQualitative Comparative
Analysis","URL":"http:\/\/www.alrik-
thiem.net\/;\nhttps:\/\/www.researchgate.net\/profile\/Alrik_Thiem","Version":"1.0-
0"},"QCAtools":{"Author":"Jirka Lewandowski <jirka.lewandowski@wzb.eu> [aut,
cre]","Depends":"R (>= 3.1.0)","Description":"Helper functions for Qualitative
Comparative Analysis: evaluate and\nplot Boolean formulae on fuzzy set score data,
apply Boolean operations, compute\nconsistency and coverage
measures.","Imports":"stringr (>= 0.6.2), ggplot2 (>= 0.9.3.1), directlabels
(>=\n2013.6.15), graphics, QCAGUI (>= 2.0)","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"QCAtools","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Helper Functions for QCA in
R","Version":"0.2.1"},"QCGWAS":{"Author":"Peter J. van der Most and Ilja M.
Nolte","Depends":"R (>= 3.0.0)","Description":"Tools for (automated and manual)
quality control of\nthe results of Genome Wide Association Studies","License":"GPL
(>=
3)","NeedsCompilation":"no","Package":"QCGWAS","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Quality Control of Genome Wide Association Study
results","Version":"1.0-8"},"QCSIS":{"Author":"Xuejun Ma, Jingxiao Zhang, Jingke
Zhou","Description":"Quantile correlation-sure independence screening (QC-SIS) and
composite quantile correlation-sure independence screening (CQC-SIS) for ultrahigh-
dimensional data.","License":"GPL-
2","NeedsCompilation":"no","Package":"QCSIS","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Sure Independence Screening via Quantile Correlation
and\nComposite Quantile Correlation","URL":"http:\/\/www.r-
project.org","Version":"0.1"},"QFRM":{"Author":"Oleg Melnikov [aut, cre],\nMax Lee
[ctb],\nRobert Abramov [ctb],\nRichard Huang [ctb],\nLiu Tong [ctb],\nJake Kornblau
[ctb],\nXinnan Lu [ctb],\nKiryl Novikau [ctb],\nTongyue Luo [ctb],\nLe You
[ctb],\nJin Chen [ctb],\nChengwei Ge [ctb],\nJiayao Huang [ctb],\nKim Raath
[ctb]","Depends":"R (>= 2.14.0)","Description":"\nOption pricing (financial
derivatives) techniques mainly following textbook 'Options, Futures and Other
Derivatives', 9ed by John C.Hull, 2014. Prentice Hall. Implementations are via
binomial tree option model (BOPM), Black-Scholes model, Monte Carlo simulations,
etc.\nThis package is a result of Quantitative Financial Risk Management course
(STAT 449 and STAT 649) at Rice University, Houston, TX, USA, taught by Oleg
Melnikov, statistics PhD student, as of Spring
2015.","Imports":"stats,methods,graphics","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"QFRM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Pricing of Vanilla and Exotic Option
Contracts","URL":"http:\/\/Oleg.Rice.edu","Version":"1.0.1"},"QICD":{"Author":"Bo
Peng [aut, cre],\nRondall E. Jones [ctb],\nJohn A. Wisniewski [ctb]","Depends":"R
(>= 3.0.0)","Description":"Extremely fast algorithm \"QICD\", Iterative
Coordinate\nDescent Algorithm for High-dimensional Nonconvex Penalized
Quantile\nRegression. This algorithm combines the coordinate descent algorithm\nin
the inner iteration with the majorization minimization step\nin the outside step.
For each inner univariate minimization problem,\nwe only need to compute a one-
dimensional weighted median,\nwhich ensures fast computation. Tuning parameter
selection is based\non two different method: the cross validation and BIC
for\nquantile regression model. Details are described in the Peng,B and Wang,L.
(2015)\nlinked to via the URL below with
<DOI:10.1080\/10618600.2014.913516>.","Imports":"stats, parallel","License":"GPL-
2","NeedsCompilation":"yes","Package":"QICD","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"mvtnorm, knitr","Title":"Estimate the Coefficients for
Non-Convex Penalized Quantile\nRegression Model by using QICD
Algorithm","URL":"\nhttp:\/\/www.tandfonline.com\/doi\/abs\/10.1080\/10618600.2014.
913516#.VsoK-JMrJp8","Version":"1.0.1"},"QPot":{"Author":"Christopher Moore
[aut],\nChristopher Stieha [aut, cre],\nBen Nolting [aut],\nMaria Cameron
[aut],\nKaren Abbott [aut],\nJames Gregson [cph] (author of expression_parser
library:\nhttps:\/\/github.com\/jamesgregson\/expression_parser)","Depends":"R (>=
3.0.2)","Description":"Tools to 1) simulate and visualize stochastic
differential\nequations and 2) determine stability of equilibria using the ordered-
upwind\nmethod to compute the quasi-potential.","Imports":"MASS","License":"GPL-
2","NeedsCompilation":"yes","Package":"QPot","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Quasi-Potential Analysis for Stochastic Differential
Equations","URL":"http:\/\/www.r-project.org,
https:\/\/github.com\/bmarkslash7\/QPot","Version":"1.1"},"QRM":{"Author":"Bernhard
Pfaff [aut, cre],\nMarius Hofert [ctb],\nAlexander McNeil [aut] (S-Plus original
(QRMlib)),\nScott Ulmann [trl] (First R port as package QRMlib)","Depends":"R (>=
3.0.1), gsl, Matrix, mvtnorm, numDeriv, timeSeries","Description":"Accompanying
package to the book\nQuantitative Risk Management: Concepts, Techniques and Tools
by\nAlexander J. McNeil, RÃ¼diger Frey, and Paul Embrechts.","Imports":"Rcpp (>=
0.11.1), mgcv, methods, timeDate","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"QRM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Provides R-Language Code to Examine Quantitative Risk
Management\nConcepts","Version":"0.4-13"},"QSARdata":{"Author":"Max
Kuhn","Depends":"R (>= 2.10)","Description":"Molecular descriptors and outcomes for
several public domain data
sets","License":"GPL","NeedsCompilation":"no","Package":"QSARdata","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"Quantitative Structure Activity
Relationship (QSAR) Data Sets","URL":"http:\/\/qsardata.r-forge.r-
project.org\/","Version":"1.3"},"QTLRel":{"Author":"Riyan Cheng
<riyan.cheng@anu.edu.au>","Depends":"R (>= 2.10)","Description":"This software
provides tools for quantitative trait mapping in populations such as advanced
intercross lines where relatedness among individuals should not be ignored. It can
estimate background genetic variance components, impute missing genotypes, simulate
genotypes, perform a genome scan for putative quantitative trait loci (QTL), and
plot mapping results. It also has functions to calculate identity coefficients from
pedigrees, especially suitable for pedigrees that consist of a large number of
generations, or estimate identity coefficients from genotypic data in certain
circumstances.","Imports":"gdata, lattice, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"QTLRel","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"qtl","Title":"Tools for Mapping of Quantitative Traits
of Genetically Related\nIndividuals and Calculating Identity Coefficients
from\nPedigrees","Version":"0.2-15"},"QUIC":{"Author":"Cho-Jui Hsieh [aut], Matyas
A. Sustik [aut, cre], Inderjit S.\nDhillon [aut], Pradeep Ravikumar
[aut]","Depends":"R (>= 2.10)","Description":"Use Newton's method and coordinate
descent to solve the\nregularized inverse covariance matrix estimation
problem.\nPlease refer to: Sparse Inverse Covariance Matrix Estimation\nUsing
Quadratic Approximation, Cho-Jui Hsieh, Matyas A. Sustik,\nInderjit S. Dhillon,
Pradeep Ravikumar, Advances in Neural\nInformation Processing Systems 24, 2011, p.
2330--2338.","License":"GPL-
3","NeedsCompilation":"yes","Package":"QUIC","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Regularized sparse inverse covariance matrix
estimation","URL":"http:\/\/www.r-
project.org,\nhttp:\/\/www.cs.utexas.edu\/users\/sustik\/QUIC","Version":"1.1"},"QZ
":{"Author":"Wei-Chen Chen, partly adapted and using routines from
LAPACK.","Depends":"R (>= 2.15.0), methods","Description":"QZ package provides
generalized eigenvalues and QZ\ndecomposition (generalized Schur form) for an N-by-
N\nnon-symmetric matrix A or paired matrices (A,B) with\neigenvalues reordering
mechanism. The package is mainly based\ncomplex*16 and double precision of LAPACK
library (version\n3.4.2.)","Enhances":"fda","License":"Mozilla Public License
2.0","NeedsCompilation":"yes","Package":"QZ","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Generalized Eigenvalues and QZ
Decomposition","Version":"0.1-4"},"QoLR":{"Author":"Amelie Anota","Depends":"R (>=
2.10.0), survival, zoo","Description":"To generate the scores of the EORTC QLQ-C30
questionnaire and supplementary modules and to determine the time to health-related
quality of life score deterioration in longitudinal analysis.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"QoLR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr","Title":"Analysis of Health-Related Quality of
Life in Oncology","URL":"\nhttp:\/\/www.umqvc.org\/en\/tool\/the-r-package-qolr-
analysis-of-health-related-quality-of-life-in-oncology-
6.html","Version":"1.0.2"},"Qtools":{"Author":"Marco Geraci","Depends":"R (>=
3.0.0)","Description":"This is a collection of functions for unconditional and
conditional quantiles.","Imports":"utils, grDevices, graphics, stats, MASS,
quantreg, mice, boot","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"Qtools","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"survey, R.rsp","Title":"Utilities for
Quantiles","Version":"1.0"},"QuACN":{"Author":"Karl G. Kugler, Matthias Wieser,
Matthias Dehmer, Michael Schutte, Laurin A.J. Mueller","Depends":"graph, RBGL,
combinat","Description":"Quantitative Analysis of Complex Networks. This package
offers a set of topological network measures to analyze complex Networks
structurally.","Imports":"igraph","License":"LGPL","NeedsCompilation":"yes","Packag
e":"QuACN","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"Rmpfr","
Title":"QuACN: Quantitative Analysis of Complex
Networks","Version":"1.8.0"},"QualInt":{"Author":"Lixi
Yu, Eun-Young Suh, Guohua (James) Pan","Depends":"survival,
ggplot2","Description":"Used for testing for qualitative interactions
between\ntreatment effects and patient subgroups. Here the term treatment
effect\nmeans a comparison result of two treatments within each patient
subgroup.\nModels included in this package are Gaussian, binomial and Cox
models.\nMethods included here are interval based graphical approach and Gail
Simon\nLRT.","License":"GPL-
2","NeedsCompilation":"no","Package":"QualInt","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Test for Qualitative
Interactions","Version":"1.0.0"},"Quandl":{"Author":"Raymond McTaggart [aut,
cre],\nGergely Daroczi [aut],\nClement Leung [aut],\nQuandl Inc.
[cph]","Depends":"R (>= 2.15.0), xts","Description":"Functions for interacting
directly with the Quandl API to offer data in a number of formats usable in R,
downloading a zip with all data from a Quandl database, and the ability to search.
This R package uses the Quandl API. For more information go to
https:\/\/www.quandl.com\/docs\/api. For more help on the package itself go to
https:\/\/www.quandl.com\/help\/r.","Imports":"httr (>= 0.6.1), zoo, jsonlite (>=
0.9.14)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"Quandl","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat (>= 0.10.0), roxygen2,
timeSeries","Title":"API Wrapper for
Quandl.com","URL":"https:\/\/github.com\/quandl\/quandl-
r","Version":"2.7.0"},"QuantPsyc":{"Author":"Thomas D. Fletcher","Depends":"boot,
MASS","Description":"Contains functions useful for data screening,
testing\nmoderation, mediation and estimating power.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"QuantPsyc","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Quantitative Psychology
Tools","Version":"1.5"},"QuantifQuantile":{"Author":"Isabelle Charlier and Davy
Paindaveine and Jerome Saracco","Depends":"rgl, parallel","Description":"Estimation
of conditional quantiles using optimal quantization.\nConstruction of an optimal
grid of N quantizers, estimation of conditional\nquantiles and data driven
selection of the size N of the grid. Graphical\nillustrations for the selection of
N and of resulting estimated curves or\nsurfaces when the dimension of the
covariate is one or two.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"QuantifQuantile","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Estimation of Conditional Quantiles using
Optimal Quantization","Version":"2.2"},"QuantumClone":{"Author":"Paul Deveau [aut,
cre]","Depends":"R (>= 3.1.0), fpc,foreach,","Description":"Using HTS data,
clusters mutations in order to recreate putative clones from the data provided. It
requires genotype at the location of the variant as well as the depth of coverage
and number of reads supporting the mutation. Additional information may be
provided, such as the contamination in the tumor sample. This package also provides
a function QuantumCat() which simulates data obtained from tumor sequencing. Latest
version can be found at
github\/DeveauP\/QuantumClone .","Imports":"doParallel,parallel,gridExtra,rgl,","Li
cense":"GPL-
2","NeedsCompilation":"no","Package":"QuantumClone","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"ggplot2, knitr, rmarkdown","Title":"Clustering
Mutations using High Throughput Sequencing (HTS)
Data","Version":"0.15.11"},"QuasiSeq":{"Author":"Steve Lund [aut],\nLong Qu [aut,
cre, ctb],\nIan Marschner [aut] (The author of glm2::glm.fit2, which was
modified\nslightly leading to glm.fit3 in this package.),\nR Core Team [aut] (The
author of stats::glm.fit, which was modified\nslightly leading to glm.fit3 in this
package.)","Depends":"R (>= 3.1.2)","Description":"Identify differentially
expressed genes in RNA-seq count data using quasi-Poisson or quasi-negative
binomial models with 'QL', 'QLShrink' and 'QLSpline' methods (Lund, Nettleton,
McCarthy, and Smyth, 2012).","Imports":"edgeR, mgcv, pracma","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"QuasiSeq","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"BB, nleqslv","Title":"Analyzing RNA Sequencing Count
Tables Using Quasi-Likelihood","Version":"1.0-8"},"Quor":{"Author":"Adriano Polpo
<polpo@ufscar.br>,\nCarlos A. de B. Pereira <cpereira@ime.usp.br>,\nCassio P. de
Campos <cassiopc@acm.org>","Depends":"R (>= 3.1.2)","Description":"Functions to
compute confidence statistics\nfor ordering population
quantiles.","Imports":"combinat","License":"GPL (>= 3) | file
LICENSE","NeedsCompilation":"yes","Package":"Quor","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Quantile
Ordering","URL":"http:\/\/code.google.com\/p\/quor\/","Version":"0.1"},"R.cache":
{"Author":"Henrik Bengtsson [aut, cre, cph]","Depends":"R (>=
2.5.0)","Description":"Memoization can be used to speed up repetitive and
computational expensive function calls. The first time a function that implements
memoization is called the results are stored in a cache memory. The next time the
function is called with the same set of parameters, the results are momentarily
retrieved from the cache avoiding repeating the calculations. With this package,
any R object can be cached in a key-value storage where the key can be an arbitrary
set of R objects. The cache memory is persistent (on the file
system).","Imports":"utils, R.methodsS3 (>= 1.7.0), R.oo (>= 1.19.0), R.utils
(>=\n2.1.0), digest (>= 0.6.8)","License":"LGPL (>=
2.1)","NeedsCompilation":"no","Package":"R.cache","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Fast and Light-Weight Caching (Memoization) of Objects
and\nResults to Speed Up
Computations","URL":"https:\/\/github.com\/HenrikBengtsson\/R.cache","Version":"0.1
2.0"},"R.devices":{"Author":"Henrik Bengtsson [aut, cre, cph]","Depends":"R (>=
2.14.0)","Description":"Functions for creating plots and image files in a unified
way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.). Default
device options as well as scales and aspect ratios are controlled in a uniform way
across all device types. Switching output format requires minimal changes in code.
This package is ideal for large-scale batch processing, because it will never leave
open graphics devices or incomplete image files behind, even on errors or user
interrupts.","Imports":"grDevices, R.methodsS3 (>= 1.7.0), R.oo (>= 1.19.0),
R.utils\n(>= 2.2.0), base64enc (>= 0.1-2)","License":"LGPL (>=
2.1)","NeedsCompilation":"no","Package":"R.devices","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"digest (>= 0.6.8), Cairo (>= 1.5-6), R.rsp (>=
0.20.0)","Title":"Unified Handling of Graphics
Devices","URL":"https:\/\/github.com\/HenrikBengtsson\/R.devices","Version":"2.14.0
"},"R.filesets":{"Author":"Henrik Bengtsson [aut, cre, cph]","Depends":"R (>=
3.1.2), R.oo (>= 1.19.0)","Description":"A file set refers to a set of files
located in one or more directories on the file system. This package provides
classes and methods to locate, setup, subset, navigate and iterate such sets. The
API is designed such that these classes can be extended via inheritance to provide
a richer API for special file formats. Moreover, a specific name format is defined
such that filenames and directories can be considered to have full names which
consists of a name followed by comma-separated tags. This adds additional
flexibility to identify file sets and individual files. NOTE: This package's API
should be considered to be in an beta stage. Its main purpose is currently to
support the aroma.* packages, where it is one of the main core components; if you
decide to build on top of this package, please contact the author
first.","Imports":"digest (>= 0.6.8), future (>= 0.10.0), listenv (>=
0.6.0),\nR.methodsS3 (>= 1.7.0), R.utils (>= 2.2.0), R.cache (>=\n0.12.0),
stats","License":"LGPL (>=
2.1)","NeedsCompilation":"no","Package":"R.filesets","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"BatchJobs (>= 1.6), BiocParallel (>= 1.0.3),
gtools (>=\n3.5.0)","Title":"Easy Handling of and Access to Files Organized in
Structured\nDirectories","URL":"https:\/\/github.com\/HenrikBengtsson\/R.filesets,\
nhttp:\/\/www.aroma-project.org\/","Version":"2.10.0"},"R.huge":{"Author":"Henrik
Bengtsson [aut, cre, cph]","Depends":"R (>= 2.10.0)","Description":"DEPRECATED. Do
not start building new projects based on this package. Cross-platform alternatives
are the following packages: bigmemory (CRAN), ff (CRAN), BufferedMatrix
(Bioconductor). The main usage of it was inside the aroma.affymetrix package. (The
package currently provides a class representing a matrix where the actual data is
stored in a binary format on the local file system. This way the size limit of the
data is set by the file system and not the memory.)","Imports":"R.methodsS3 (>=
1.7.0), R.oo (>= 1.18.0), R.utils (>= 1.34.0)","License":"LGPL (>=
2.1)","NeedsCompilation":"no","Package":"R.huge","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Methods for Accessing Huge Amounts of Data
[deprecated]","URL":"https:\/\/github.com\/HenrikBengtsson\/R.huge","Version":"0.9.
0"},"R.matlab":{"Author":"Henrik Bengtsson [aut, cre, cph], Andy Jacobson [ctb]
(Internal MAT v4 reader), Jason Riedy [ctb] (Support for reading compressed files,
sparse matrices and UTF-encoded strings.)","Depends":"R (>=
2.14.0)","Description":"Methods readMat() and writeMat() for reading and writing
MAT files. For user with MATLAB v6 or newer installed (either locally or on a
remote host), the package also provides methods for controlling MATLAB (trademark)
via R and sending and retrieving data between R and MATLAB.","Imports":"methods,
utils, R.methodsS3 (>= 1.7.1), R.oo (>= 1.20.0),\nR.utils (>=
2.2.0)","License":"LGPL (>=
2.1)","NeedsCompilation":"no","Package":"R.matlab","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"Matrix,
SparseM","Title":"Read and Write MAT Files and Call MATLAB from Within
R","URL":"https:\/\/github.com\/HenrikBengtsson\/R.matlab","Version":"3.5.1"},"R.me
thodsS3":{"Author":"Henrik Bengtsson [aut, cre, cph]","Depends":"R (>=
2.13.0)","Description":"Methods that simplify the setup of S3 generic functions and
S3 methods. Major effort has been made in making definition of methods as simple
as possible with a minimum of maintenance for package developers. For example,
generic functions are created automatically, if missing, and naming conflict are
automatically solved, if possible. The method setMethodS3() is a good start for
those who in the future may want to migrate to S4. This is a cross-platform
package implemented in pure R that generates standard S3
methods.","Imports":"utils","License":"LGPL (>=
2.1)","NeedsCompilation":"no","Package":"R.methodsS3","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"S3 Methods Simplified","Version":"1.7.1"},"R.oo":
{"Author":"Henrik Bengtsson [aut, cre, cph]","Depends":"R (>= 2.13.0), R.methodsS3
(>= 1.7.0)","Description":"Methods and classes for object-oriented programming in R
with or without references. Large effort has been made on making definition of
methods as simple as possible with a minimum of maintenance for package developers.
The package has been developed since 2001 and is now considered very stable. This
is a cross-platform package implemented in pure R that defines standard S3 classes
without any tricks.","Imports":"methods, utils","License":"LGPL (>=
2.1)","NeedsCompilation":"no","Package":"R.oo","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"tools","Title":"R Object-Oriented Programming with or
without
References","URL":"https:\/\/github.com\/HenrikBengtsson\/R.oo","Version":"1.20.0"}
,"R.rsp":{"Author":"Henrik Bengtsson [aut, cre, cph]","Depends":"R (>=
2.14.0)","Description":"The RSP markup language makes any text-based document come
alive. RSP provides a powerful markup for controlling the content and output of
LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr documents (and more), e.g.
'Today's date is <%=Sys.Date()%>'. Contrary to many other literate programming
languages, with RSP it is straightforward to loop over mixtures of code and text
sections, e.g. in month-by-month summaries. RSP has also several preprocessing
directives for incorporating static and dynamic contents of external files (local
or online) among other things. Functions rstring() and rcat() make it easy to
process RSP strings, rsource() sources an RSP file as it was an R script, while
rfile() compiles it (even online) into its final output format, e.g.
rfile('report.tex.rsp') generates 'report.pdf' and rfile('report.md.rsp') generates
'report.html'. RSP is ideal for self-contained scientific reports and R package
vignettes. It's easy to use - if you know how to write an R script, you'll be up
and running within minutes.","Imports":"methods, stats, tools, utils, R.methodsS3
(>= 1.7.0), R.oo (>=\n1.19.0), R.utils, R.cache (>= 0.12.0)","License":"LGPL (>=
2.1)","NeedsCompilation":"no","Package":"R.rsp","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"tcltk, digest (>= 0.6.8), ascii (>= 2.1), markdown
(>=\n0.7.7), knitr (>= 1.11), R.devices (>= 2.13.2), base64enc (>=\n0.1-
2)","Title":"Dynamic Generation of Scientific
Reports","URL":"https:\/\/github.com\/HenrikBengtsson\/R.rsp","Version":"0.21.0"},"
R.utils":{"Author":"Henrik Bengtsson [aut, cre, cph]","Depends":"R (>= 2.5.0), R.oo
(>= 1.19.0)","Description":"Utility functions useful when programming and
developing R packages.","Imports":"methods, utils, tools, R.methodsS3 (>=
1.7.0)","License":"LGPL (>=
2.1)","NeedsCompilation":"no","Package":"R.utils","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"digest (>= 0.6.8)","Title":"Various Programming
Utilities","URL":"https:\/\/github.com\/HenrikBengtsson\/R.utils","Version":"2.2.0"
},"R0":{"Author":"Pierre-Yves Boelle, Thomas Obadia","Depends":"R (>= 2.13.0),
MASS","Description":"Estimation of reproduction numbers for disease outbreak, based
on\nincidence data. The R0 package implements several documented methods. It
is\ntherefore possible to compare estimations according to the methods
used.\nDepending on the methods requested by user, basic reproduction
number\n(commonly denoted as R0) or real-time reproduction number (referred to
as\nR(t)) is computed, along with a 95% Confidence Interval. Plotting outputs\nwill
give different graphs depending on the methods requested : basic\nreproductive
number estimations will only show the epidemic curve\n(collected data) and an
adjusted model, whereas real-time methods will also\nshow the R(t) variations
throughout the outbreak time period. Sensitivity\nanalysis tools are also provided,
and allow for investigating effects of\nvarying Generation Time distribution or
time window on estimates.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"R0","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Estimation of R0 and Real-Time Reproduction Number
from\nEpidemics","Version":"1.2-6"},"R1magic":{"Author":"Mehmet Suzen [aut,
cre]","Depends":"stats, utils","Description":"Utilities for sparse signal recovery
suitable for compressed sensing. L1, L2 and TV penalties, DFT basis matrix, simple
sparse signal generator, mutual cumulative coherence between two matrices and
examples, Lp complex norm, scaling back regression coefficients.","License":"GPL
(>=
3)","NeedsCompilation":"no","Package":"R1magic","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Compressive Sampling: Sparse Signal Recovery
Utilities","Version":"0.3.2"},"R2BayesX":{"Author":"Nikolaus Umlauf [aut,
cre],\nThomas Kneib [aut],\nStefan Lang [aut],\nAchim Zeileis [aut]","Depends":"R
(>= 2.13.0), BayesXsrc, colorspace, mgcv","Description":"An R interface to estimate
structured additive regression (STAR) models with BayesX.","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"R2BayesX","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"akima, coda, maps, maptools, MBA, parallel,
shapefiles, sp,\nspdep, splines","Title":"Estimate Structured Additive Regression
Models with BayesX","Version":"1.0-0"},"R2Cuba":{"Author":"The Cuba library has
been written by Thomas Hahn (http:\/\/wwwth.mppmu.mpg.de\/members\/hahn); Interface
to R was written by Annie Bouvier and KiÃªn KiÃªu","Description":"It is a wrapper
around the Cuba-1.6 library by Thomas Hahn available from the URL
http:\/\/www.feynarts.de\/cuba\/. Implement four general-purpose multidimensional
integration algorithms: Vegas, Suave, Divonne and Cuhre.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"R2Cuba","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"deldir, mvtnorm","Title":"Multidimensional Numerical
Integration","Version":"1.1-0"},"R2G2":{"Author":"Nils
Arrigo","Description":"Converting R CRAN outputs into Google
Earth.","License":"LGPL","NeedsCompilation":"no","Package":"R2G2","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Title":"Converting R CRAN outputs into Google
Earth","Version":"1.0-2"},"R2GUESS":{"Author":"Gianluca Campanella [cre],\nBenoit
Liquet [aut],\nMarc Chadeau-Hyam [aut],\nLeonardo Bottolo [ctb],\nSylvia Richardson
[ctb]","Depends":"R (>= 3.0.0), fields, MCMCpack, methods, mixOmics,
mvtnorm,\nsnowfall","Description":"Wrapper functions for GUESS, a GPU-enabled
sparse Bayesian variable\nselection method for linear regression based analysis of
possibly\nmultivariate\/correlated outcomes.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"R2GUESS","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Wrapper Functions for GUESS","Version":"1.7"},"R2HTML":
{"Author":"Eric Lecoutre [aut],\nMilan Bouchet-Valat [cre, ctb],\nThomas
Friedrichsmeier [ctb]","Depends":"R (>= 2.0)","Description":"Includes HTML function
and methods to write in an HTML\nfile. Thus, making HTML reports is easy. Includes
a function\nthat allows redirection on the fly, which appears to be very\nuseful
for teaching purpose, as the student can keep a copy of\nthe produced output to
keep all that he did during the course.\nPackage comes with a vignette describing
how to write HTML\nreports for statistical analysis. Finally, a driver for
Sweave\nallows to parse HTML flat files containing R code and to\nautomatically
write the corresponding outputs (tables and\ngraphs).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"R2HTML","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"boot, splines, survival, stats, cluster, nlme, rpart,
nnet,\nutils","Title":"HTML exportation for R
objects","URL":"https:\/\/github.com\/nalimilan\/R2HTML","Version":"2.3.1"},"R2MLwi
N":{"Author":"Zhengzheng Zhang [aut, cre],\nChris Charlton [aut],\nRichard Parker
[aut],\nGeorge Leckie [aut],\nWilliam Browne [aut]","Depends":"R (>= 2.15.0),
stats, stats4, methods, lattice, coda (>=\n0.16-1)","Description":"An R command
interface to the 'MLwiN' multilevel\nmodelling software
package.","Enhances":"reshape","Imports":"Matrix, foreign (>= 0.8-46), rbugs (>=
0.5-7), digest (>=\n0.6.5)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"R2MLwiN","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"doBy, car, lmtest","Title":"Running 'MLwiN' from
Within
R","URL":"\nhttp:\/\/www.bristol.ac.uk\/cmm\/software\/r2mlwin\/,https:\/\/r-
forge.r-
project.org\/projects\/r2mlwin\/,http:\/\/www.bristol.ac.uk\/cmm\/software\/mlwin\/
","Version":"0.8-1"},"R2OpenBUGS":{"Author":"originally written as R2WinBUGS by
Andrew Gelman <gelman@stat.columbia.edu>;\nchanges and packaged by Sibylle Sturtz
<sturtz@statistik.tu-dortmund.de>\nand Uwe Ligges <ligges@statistik.tu-
dortmund.de>.\nWith considerable contributions by Gregor Gorjanc
<gregor.gorjanc@bfro.uni-lj.si>\nand Jouni Kerman
<kerman@stat.columbia.edu>.\nAdapted
to R2OpenBUGS from R2WinBUGS by Neal Thomas.","Depends":"R (>=
2.13.0)","Description":"Using this package,\nit is possible to call a BUGS model,
summarize inferences and\nconvergence in a table and graph, and save the
simulations in arrays for easy access\nin R.","Imports":"coda (>= 0.11-0),
boot","License":"GPL-
2","NeedsCompilation":"no","Package":"R2OpenBUGS","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Running OpenBUGS from R","Version":"3.2-3.1"},"R2PPT":
{"Author":"Wayne Jones","Depends":"R (>= 2.3.0)","Description":"R2PPT provides a
simple set of wrappers to easily use rcom\nor RDCOMClient for generating Microsoft
PowerPoint\npresentations.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"R2PPT","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"rcom, RDCOMClient","Title":"Simple R Interface to
Microsoft PowerPoint using rcom or\nRDCOMClient","Version":"2.1"},"R2STATS":
{"Author":"Yvonnick Noel","Depends":"R (>= 2.14.0), proto,
Matrix","Description":"R2STATS is a gWidgetsRGtk2 GUI for fitting and comparing GLM
or GLMM (based on Douglas Bates' lme4 package) in R. It is designed to make
comparisons between numerous models easy, both numerically and graphically, which
may be useful for teaching. Relevant plots are automatically produced for each
model family. R2STATS is *not* a generic graphical interface for R, but a GUI for
statistical modelling in a model comparison approach.","Imports":"grDevices,
lattice, lme4, cairoDevice, gWidgets,\ngWidgetsRGtk2, RGtk2Extras, MASS, utils,
latticeExtra, statmod","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"R2STATS","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"A GTK GUI for fitting and comparing GLM and GLMM in
R","URL":"http:\/\/yvonnick.noel.free.fr\/r2stats","Version":"0.68-38"},"R2SWF":
{"Author":"Yixuan Qiu, Yihui Xie, Cameron Bracken and authors of
included\nsoftware. See file AUTHORS for details.","Description":"Using the Ming
library\n(http:\/\/www.libming.org\/) to create Flash animations.\nUsers can either
use the SWF device swf() to generate SWF file\ndirectly through plotting functions
like plot() and lines(),\nor convert images of other formats (SVG, PNG, JPEG) into
SWF.","Imports":"sysfonts, grDevices, utils","License":"GPL-
2","NeedsCompilation":"yes","Package":"R2SWF","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"XML, Cairo","Title":"Convert R Graphics to Flash
Animations","URL":"https:\/\/github.com\/yixuan\/R2SWF","Version":"0.9-
1"},"R2WinBUGS":{"Author":"originally written by Andrew Gelman
<gelman@stat.columbia.edu>;\nchanges and packaged by Sibylle Sturtz
<sturtz@statistik.tu-dortmund.de>\nand Uwe Ligges <ligges@statistik.tu-
dortmund.de>.\nWith considerable contributions by Gregor Gorjanc
<gregor.gorjanc@bfro.uni-lj.si>\nand Jouni Kerman
<kerman@stat.columbia.edu>.\nPorted to S-PLUS by Insightful Corp.","Depends":"R (>=
2.13.0), coda (>= 0.11-0), boot","Description":"Invoke a 'BUGS' model in 'OpenBUGS'
or 'WinBUGS', a class \"bugs\" for 'BUGS'\nresults and functions to work with that
class.\nFunction write.model() allows a 'BUGS' model file to be written.\nThe class
and auxiliary functions could be used with other MCMC programs, including
'JAGS'.","Imports":"utils, stats, graphics","License":"GPL-
2","NeedsCompilation":"no","Package":"R2WinBUGS","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"BRugs (>= 0.3-2)","Title":"Running 'WinBUGS' and
'OpenBUGS' from 'R' \/ 'S-PLUS'","Version":"2.1-21"},"R2admb":{"Author":"Ben
Bolker, Hans Skaug, Jeff Laake","Depends":"R (>= 3.0.1)","Description":"A series of
functions to call AD Model Builder (i.e.,\ncompile and run models) from within R,
read the results back\ninto R as 'admb' objects, and provide standard accessors
(i.e.\ncoef(), vcov(), etc.)","Imports":"coda,
lattice","License":"GPL","NeedsCompilation":"no","Package":"R2admb","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Suggests":"bbmle, lme4, ggplot2, testthat,
knitr","Title":"'ADMB' to R Interface Functions","Version":"0.7.13"},"R2jags":
{"Author":"Yu-Sung Su <suyusung@tsinghua.edu.cn>,\nMasanao Yajima
<yajima@stat.ucla.edu>,","Depends":"R (>= 2.14.0), rjags (>= 3-
3)","Description":"Providing wrapper functions to implement Bayesian analysis in
JAGS. Some major features include monitoring convergence of a MCMC model using
Rubin and Gelman Rhat statistics, automatically running a MCMC model till it
converges, and implementing parallel processing of a MCMC model for multiple
chains.","Imports":"abind, coda (>= 0.13), graphics, grDevices,
methods,\nR2WinBUGS, parallel, stats, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"R2jags","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Using R to Run 'JAGS'","Version":"0.5-7"},"R2wd":
{"Author":"Christian Ritter","Depends":"R (>= 2.10.0)","Description":"This package
uses either the statconnDCOM server (via the\nrcom package) or the RDCOMClient to
communicate with MS-Word\nvia the COM interface.","License":"GPL-
2","NeedsCompilation":"no","Package":"R2wd","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"rcom, RDCOMClient","Title":"Write MS-Word documents from
R","Version":"1.5"},"R330":{"Author":"Alan Lee, Blair Robertson","Depends":"s20x,
leaps, rgl, lattice","Description":"This is a collection of useful functions and
data for\nStats 330","License":"GPL-
2","NeedsCompilation":"no","Package":"R330","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"An R package for Stats 330","Version":"1.0"},"R4CouchDB":
{"Author":"Thomas Bock","Depends":"R (>= 2.7.0), bitops, RCurl (>= 1.95), RJSONIO
(>= 1.3)","Description":"Provides a collection of functions for basic\ndatabase and
document management operations such as add, get, list or\ndelete. Every
cdbFunction() gets and returns a list() containing the\nconnection setup.\nSuch a
list (in the documentation mostly called cdb) can be generated by\ncdb <- cdbIni().
Then, the list cdb provides some functions respectively\nfunctionality e.g
cdb$baseUrl() or cdb$getDocRev().","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"R4CouchDB","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"roxygen2 (>= 4.0), testthat (>=
0.8)","Title":"An R Convenience Layer for
CouchDB","URL":"https:\/\/github.com\/wactbprot\/R4CouchDB","Version":"0.7.1"},"R6"
:{"Author":"Winston Chang [aut, cre]","Depends":"R (>= 3.0)","Description":"The R6
package allows the creation of classes with reference\nsemantics, similar to R's
built-in reference classes. Compared to reference\nclasses, R6 classes are simpler
and lighter-weight, and they are not built\non S4 classes so they do not require
the methods package. These classes\nallow public and private members, and they
support inheritance, even when\nthe classes are defined in different
packages.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"R6","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr, microbenchmark, pryr, testthat, ggplot2,
scales","Title":"Classes with Reference
Semantics","URL":"https:\/\/github.com\/wch\/R6\/","Version":"2.1.2"},"RAD":
{"Author":"Piers K Dunstan and Scott D Foster","Depends":"R (>= 2.10), mvtnorm,
MASS","Description":"Fit a variety of models to Rank Abundance
Data","License":"GPL-
2","NeedsCompilation":"yes","Package":"RAD","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Fit RAD models to biological data","Version":"0.3"},"RADami":
{"Author":"Andrew L. Hipp
<ahipp@mortonarb.org>","Depends":"ape","Description":"This package implements
import, export, manipulation, visualization, and downstream\n(post-clustering)
analysis of RADseq data, integrating with the pyRAD package by Deren
Eaton.","Imports":"geiger, Biostrings, phangorn","License":"GPL-
3","NeedsCompilation":"no","Package":"RADami","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"R Package for Phylogenetic Analysis of RADseq
Data","Version":"1.0-3"},"RADanalysis":{"Author":"Mohmmadkarim Saeedghalati [aut,
cre],\nFarnoush Farahpour [aut],\nDaniel Hoffmann [aut]","Depends":"R (>=
2.10)","Description":"It has tools for normalization of rank
abundance\ndistributions (RAD) to a desired number of ranks using
MaxRank\nNormalization method.\nRADs are commonly used in biology\/ecology and
mathematically equivalent\nto complementary cumulative distributions (CCDFs) which
are used in\nphysics, linguistics and sociology and more generally in data
science.","Imports":"sfsmisc, scales, stats, graphics","License":"GPL-
3","NeedsCompilation":"no","Package":"RADanalysis","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr, rmarkdown","Title":"Normalization and Study
of Rank Abundance Distributions","Version":"0.5.5"},"RAHRS":{"Author":"Jose Gama
[aut, cre, trl],\nVlad Maximov [aut],\nSebastian O.H. Madgwick [aut],\nAlain
Barraud [ctb]","Depends":"R (>= 2.10), pracma, RSpincalc (>=
1.0.1)","Description":"Data fusion filters for Attitude Heading Reference System
(AHRS) based on\nVlad Maximov's GyroLib AHRS library (quaternion based
linearized\/extended\/unscented Kalman filter,\nEuler based LKF, gyro-free with
vector matching, SVD calibration and EKF calibration),\nSebastian O.H. Madgwick
AHRS algorithms and Sebastian O.H. Madgwick implementation of Mayhony et al AHRS
3)","NeedsCompilation":"yes","Package":"RAHRS","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Data Fusion Filters for Attitude Heading Reference System
(AHRS)\nwith Several Variants of the Kalman Filter and the Mahoney and\nMadgwick
Filters","Version":"1.0.2"},"RAM":{"Author":"Wen Chen, Joshua Simpson, C. Andre
Levesque","Depends":"vegan, ggplot2, stats","Description":"Characterizing
environmental microbiota diversity using amplicon-based next generation sequencing
(NGS) data. Functions are developed to manipulate operational taxonomic
unit (OTU) table, perform descriptive and inferential statistics, and generate
publication-quality plots.","Imports":"RColorBrewer, gplots, plyr, reshape2,
scales, labdsv, grid,\ngridExtra, ggmap, permute, VennDiagram, data.table, FD,
MASS,\nRgoogleMaps, lattice, reshape, ade4, phangorn, phytools, utils,\ngraphics,
grDevices, ape","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"RAM","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat, mapproj, gtable, indicspecies,
Heatplus","Title":"R for Amplicon-Sequencing-Based Microbial-
Ecology","URL":"http:\/\/cran.r-
project.org\/package=RAM,\nhttps:\/\/bitbucket.org\/Wen_Chen\/ram_releases\/src\/",
"Version":"1.2.1.3"},"RAMP":{"Author":"Yang Feng, Ning Hao and Hao Helen
Zhang","Description":"This package provides an efficient procedure for fitting the
entire solution path for high-dimensional regularized generalized linear models
with interactions effects under the strong heredity constraint.","License":"GPL-
2","NeedsCompilation":"yes","Package":"RAMP","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Regularized Generalized Linear Models with Interaction
Effects","Version":"1.0"},"RAMpath":{"Author":"Zhiyong Zhang, Jack McArdle, Aki
Hamagami, & Kevin Grimm","Depends":"R (>= 2.0), lavaan,
ellipse","Description":"RAMpath is a rewrite of RAMpath software developed by John
McArdle and Steven Boker. In addition to performing regular SEM analysis through
the R package lavaan, RAMpath has unique features. First, it can generate path
diagrams according to a given model. Second, it can display path tracing rules
through path diagrams and decompose total effects into their respective direct and
indirect effects as well as decompose variances and covariances into individual
bridges. Furthermore, RAMpath can fit dynamic system models automatically based on
latent change scores and generate vector field plots based upon results obtained
from a bivariate dynamic system.","License":"GPL-
2","NeedsCompilation":"no","Package":"RAMpath","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Structural Equation Modeling using the reticular action
model\n(RAM)
Notation","URL":"http:\/\/nd.psychstat.org","Version":"0.3.8"},"RANKS":
{"Author":"Giorgio Valentini -- AnacletoLab, Dipartimento di Informatica,
Universita' degli Studi di Milano","Description":"Implementation of Kernelized
score functions and other semi-supervised learning algorithms for node label
ranking in biomolecular networks. RANKS can be easily applied to a large set of
different relevant problems in computational biology, ranging from automatic
protein function prediction, to gene disease prioritization and drug repositioning,
and more in general to any bioinformatics problem that can be formalized as a node
label ranking problem in a graph. The modular nature of the implementation allows
to experiment with different score functions and kernels and to easily compare the
results with baseline network-based methods such as label propagation and random
walk algorithms, as well as to enlarge the algorithmic scheme by adding novel user-
defined score functions and kernels.","Imports":"methods, graph, RBGL, limma,
NetPreProc, PerfMeas","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"RANKS","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"bionetdata","Title":"Ranking of Nodes with Kernelized
Score Functions","Version":"1.0"},"RANN":{"Author":"Sunil Arya and David Mount (for
ANN), Samuel E. Kemp, Gregory Jefferis","Description":"Finds the k nearest
neighbours for every point in a given dataset\nin O(N log N) time using Arya and
Mount's ANN library (v1.1.3). There is\nsupport for approximate as well as exact
searches, fixed radius searches\nand bd as well as kd trees.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"RANN","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat","Title":"Fast Nearest Neighbour Search (Wraps
Arya and Mount's
ANN\nLibrary)","URL":"https:\/\/github.com\/jefferis\/RANN","Version":"2.5"},"RANN.
L1":{"Author":"Sunil Arya and David Mount (for ANN), Samuel E. Kemp, Gregory
Jefferis,\nKirill MÃ¼ller","Description":"Finds the k nearest neighbours for every
point in a given dataset\nin O(N log N) time using Arya and Mount's ANN library
(v1.1.3). There is\nsupport for approximate as well as exact searches, fixed radius
searches\nand 'bd' as well as 'kd' trees. The distance is computed using the
L1\n(Manhattan, taxicab) metric. Please see package 'RANN' for the
same\nfunctionality using the L2 (Euclidean) metric.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"RANN.L1","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat","Title":"Fast Nearest Neighbour Search
(Wraps ANN Library) Using
L1\nMetric","URL":"https:\/\/github.com\/jefferis\/RANN\/tree\/master-
L1","Version":"2.5"},"RAP":{"Author":"U.Sangeetha, M.Subbiah with considerable
contribution from\nM.R.Srinivasan","Description":"To find the reversal association
between variables.","License":"GPL-
2","NeedsCompilation":"no","Package":"RAP","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Reversal Association Pattern","Version":"1.1"},"RAPIDR":
{"Author":"Kitty Lo <kitty.lo@ucl.ac.uk>","Depends":"R (>=
3.1.1)","Description":"Package to perform non-invasive fetal testing for
aneuploidies\nusing sequencing count data from cell-free
DNA","Imports":"data.table, Biostrings, Rsamtools,
GenomicRanges,\nGenomicAlignments, PropCIs","License":"GPL-
3","NeedsCompilation":"no","Package":"RAPIDR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"BSgenome.Hsapiens.UCSC.hg19","Title":"Reliable Accurate
Prenatal non-Invasive Diagnosis R package","Version":"0.1.1"},"RAdwords":
{"Author":"Johannes Burkhardt <johannes.burkhardt@gmail.com>, Matthias
Bannert\n<matthias.bannert@gmail.com>","Depends":"R (>= 3.0.0)","Description":"Aims
at loading Google Adwords data into R. Adwords is an online\nadvertising service
that enables advertisers to display advertising copy to web users.\nTherefore the
package implements three main features. First, the package provides
an\nauthentication process for R with the Google Adwords API via OAUTH2. Second,
the\npackage offers an interface to apply the Adwords query language in R
and\nquery the Adwords API with ad-hoc reports. Third, the received data
are\ntransformed into suitable data formats for further data processing and
data\nanalysis.","Imports":"RCurl, rjson","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"RAdwords","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Loading Google Adwords Data into
R","URL":"https:\/\/github.com\/jburkhardt\/RAdwords,\nhttp:\/\/www.google.com\/adw
ords\/","Version":"0.1.6"},"RApiSerialize":{"Author":"Dirk Eddelbuettel, Junji
Nakano, Ei-ji Nakama, and R Core (original code)","Description":"This package
provides other packages with access to the internal\nR serialization code. Access
to this code is provided at the C function\nlevel by using the registration of
native function mechanism. Client\npackages simply include a single header file
RApiSerializeAPI.h provided by\nthis package.\n\nThis packages builds on the Rhpc
package by Junji Nakano and Ei-ji Nakama\nwhich also includes a (partial) copy of
the file src\/main\/serialize.c from R\nitself.\n\nThe R Core group is the original
author of the serialization code made\navailable by this package.","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"RApiSerialize","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"R API
Serialization","Version":"0.1.0"},"RArcInfo":{"Author":"Virgilio Gómez-Rubio
<virgilio.gomez@uv.es>","Depends":"R (>= 2.3.0), RColorBrewer","Description":"This
package uses the functions written by Daniel\nMorissette <danmo@videotron.ca> to
read geographical information in Arc\/Info\nV 7.x format and E00 files to import
the coverages into R variables.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"RArcInfo","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Functions to import data from Arc\/Info V7.x binary
coverages","URL":"\nhttp:\/\/sourceforge.net\/projects\/rarcinfo\/,http:\/\/avce00.
maptools.org\/docs\/v7_bin_cover.html","Version":"0.4-12"},"RAtmosphere":
{"Author":"Gionata Biavati","Description":"This package provide an easy way to
produce atmospheric profiles of Pressure,\nTemperature and Density according to the
standard atmosphere 1976.\nIt provides also profiles of molecular volume
backscatter coefficients for standard atmosphere,\nand approximated estimations of
sunset, sunrise and solar zenith
angle.","License":"GPL","NeedsCompilation":"no","Package":"RAtmosphere","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Standard Atmospheric
profiles","Version":"1.1"},"RBPcurve":{"Author":"Giuseppe Casalicchio, Bernd
Bischl","Depends":"R (>= 3.0.2), mlr (>= 2.5)","Description":"The RBP curve is a
visual tool to assess the\nperformance of prediction models.","Imports":"BBmisc (>=
1.9), checkmate (>= 1.6.2), shape, TeachingDemos","License":"GPL-
3","NeedsCompilation":"no","Package":"RBPcurve","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"testthat, mlbench, mboost","Title":"The Residual-Based
Predictiveness
Curve","URL":"https:\/\/github.com\/giuseppec\/RBPcurve","Version":"1.0-33"},"RCA":
{"Author":"Amir Goldberg, Sarah K. Stein","Depends":"igraph,
gplots","Description":"Relational Class Analysis (RCA) is a method for
detecting\nheterogeneity in attitudinal data (as described in Goldberg\nA., 2011,
Am. J. Soc, 116(5)).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RCA","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Relational Class Analysis","Version":"2.0"},"RCALI":
{"Author":"Annie Bouvier, Kien Kieu, Kasia Adamczyk, and Herve
Monod","Description":"Calculate the flow
of particles between polygons by two integration methods: integration by a
cubature method and integration on a grid of
points.","Imports":"splancs","License":"GPL-3 + file
LICENSE","NeedsCompilation":"yes","Package":"RCALI","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Calculation of the Integrated Flow of Particles
between
Polygons","URL":"http:\/\/www.inra.fr\/miaj\/public\/logiciels\/RCALI\/","Version":
"0.2-15"},"RCEIM":{"Author":"Alberto Krone-Martins","Description":"RCEIM is a
package implementing a stochastic heuristic method for performing multidimensional
function optimization. The method is inspired in the Cross-Entropy Method. It does
not relies on derivatives, neither imposes particularly strong requirements into
the function to be optimized. Additionally, it takes profit from multicore
processing to enable optimization of time-consuming functions.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RCEIM","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"parallel","Title":"RCEIM - R Cross Entropy Inspired
Method for Optimization","Version":"0.2"},"RCMIP5":{"Author":"Ben Bond-Lamberty
[aut],\nKathe Todd-Brown [aut, cre]","Depends":"R (>=
3.1.0)","Description":"Working with CMIP5 data can be tricky, forcing scientists to
write\ncustom scripts and programs. The `RCMIP5` package aims to ease
this\nprocess, providing a standard, robust, and high-performance set of
scripts\nto (i) explore what data have been downloaded, (ii) identify missing
data,\n(iii) average (or apply other mathematical operations) across
experimental\nensembles, (iv) produce both temporal and spatial statistical
summaries,\nand (v) produce easy-to-work-with graphical and data
summaries.","Imports":"abind (>= 1.4), dplyr (>= 0.3), reshape2 (>= 1.4),
digest","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"RCMIP5","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"ggplot2 (>= 0.9), ncdf4 (>= 1.9), ncdf (>= 1.6),
testthat (>=\n0.9), knitr","Title":"Tools for Manipulating and Summarizing CMIP5
Data","Version":"1.1"},"RCPmod":{"Author":"Scott D. Foster","Depends":"numDeriv,
gtools","Description":"Identifies regions of common (species) profiles (RCPs).
Within a region the probability of sampling all species remains approximately
constant. This is performed using mixtures-of-experts models. The package also
contains associated methods, such as diagnostics. Currently, the model and methods
are defined for species presence-absence data for a number of
sites.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"RCPmod","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"MASS","Title":"Regions of common profiles modelling
with mixtures-of-experts","Version":"1.4"},"RCassandra":{"Author":"Simon Urbanek
<simon.urbanek@r-project.org>","Description":"This packages provides a direct
interface (without the\nuse of Java) to the most basic functionality of
Apache\nCassanda such as login, updates and queries.","License":"GPL-
2","NeedsCompilation":"yes","Package":"RCassandra","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"R\/Cassandra
interface","URL":"http:\/\/www.rforge.net\/RCassandra","Version":"0.1-
3"},"RCircos":{"Author":"Hongen Zhang","Depends":"R (>= 2.10)","Description":"A
simple and flexible way to generate Circos 2D track plot images for genomic data
visualization is implemented in this package. The types of plots include: heatmap,
histogram, lines, scatterplot, tiles and plot items for further decorations include
connector, link (lines and ribbons), and text (gene) label. All functions require
only R graphics package that comes with R base installation.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RCircos","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Circos 2D Track
Plot","URL":"http:\/\/bitbucket.org\/henryhzhang\/rcircos","Version":"1.1.3"},"RCli
mMAWGEN":{"Author":"Emanuele Cordano, Annalisa Di Piazza","Depends":"R (>=
2.10),climdex.pcic,RMAWGEN","Description":"This package contains wrapper functions
and methods which allow to\nuse \"climdex.pcic\" and \"RMAWGEN\" packages. With
this simple approach it is\npossible to calculate climate change indices, suggested
by the WMO-CCL,\nCLIVAR, ETCCDMI(http:\/\/www.climdex.org),on stochastic
generations of\ntemperature and precipitation time series, obtained by the
application of\nRMAWGEN. Each index can be applied to both observed data and to
synthetic\ntime series produced by the Weather Generator, over a reference
period\n(e.g. 1981-2010, as in the example). It contains also functions and
methods\nto evaluate the generated time series of climate change indices
consistency\nby statistical tests.Bugs\/comments\/questions\/collaboration of any
kind are\nwarmly welcomed.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RClimMAWGEN","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"RClimMAWGEN (R Climate Index Multi-site Auto-
regressive Weather\nGENeretor): a package to generate time series of
climate\nindices from RMAWGEN
generations","URL":"http:\/\/presentations.copernicus.org\/EGU2012-
5404_presentation.pdf","Version":"1.1"},"RClone":{"Author":"Sophie Arnaud-Haond
[aut],\nDiane Bailleul [aut, cre],\nCLONIX [ctb]","Depends":"R (>= 3.2.0),
graphics, stats, grDevices, utils, datasets,\nmethods","Description":"R version of
'GenClone' (a computer program to analyse genotypic data, test for clonality and
describe spatial clonal organization, Arnaud-Haond & Belkhir 2007,
<http:\/\/wwz.ifremer.fr\/clonix\/content\/download\/68205\/903914\/file\/GenClone2
.0.setup.zip>), this package allows clone handling as 'GenClone' does, plus the
possibility to work with several populations, MultiLocus Lineages (MLL) custom
definition and use, and p-value calculation for psex statistic (probability of
originating from distinct sexual events) and psex_Fis statistic (taking account of
Hardy-Weinberg equilibrium departure) as 'MLGsim'\/'MLGsim2' (a program for
detecting clones using a simulation approach, Stenberg et al.
2003).","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"RClone","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr, pander","Title":"Partially Clonal Populations
Analysis","URL":"\nhttps:\/\/www.dropbox.com\/sh\/8vx9kty4ny5dn7j\/AABj8iqX-
TzKwheuDtgE7peGa?dl=0","Version":"1.0"},"RColorBrewer":{"Author":"Erich Neuwirth
[aut, cre]","Depends":"R (>= 2.0.0)","Description":"Provides color schemes for maps
(and other graphics)\ndesigned by Cynthia Brewer as described at
http:\/\/colorbrewer2.org","License":"Apache License
2.0","NeedsCompilation":"no","Package":"RColorBrewer","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"ColorBrewer Palettes","Version":"1.1-2"},"RConics":
{"Author":"Emanuel Huber","Description":"Solve some conic related problems
(intersection of conics with lines and conics, arc length of an ellipse, polar
lines, etc.).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RConics","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Computations on Conics","Version":"1.0"},"RCriteo":
{"Author":"Johannes Burkhardt <johannes.burkhardt@gmail.com>","Depends":"R (>=
3.1.1)","Description":"Aims at loading Criteo online advertising campaign data into
R. Criteo <http:\/\/www.criteo.com\/> is an online\nadvertising service that
enables advertisers to display advertising copy to web users. The\npackage provides
an authentication process for R with the Criteo API
<http:\/\/kb.criteo.com\/advertising\/content\/5\/27\/en\/api.html>.\nMoreover, the
package features an interface to query campaign data from the\nCriteo API. The data
can be downloaded and will be transformed into a R\ndata frame.","Imports":"RCurl,
XML, httr, plyr","License":"GPL (>= 2) | MIT + file
LICENSE","NeedsCompilation":"no","Package":"RCriteo","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Loading Criteo Data into
R","URL":"http:\/\/jburkhardt.github.io\/RCriteo\/,
http:\/\/www.criteo.com\/,\nhttp:\/\/kb.criteo.com\/advertising\/content\/5\/27\/en
\/api.html","Version":"1.0.1"},"RCryptsy":{"Author":"William Kyle Hamilton
<kyle.hamilton@gmail.com>","Depends":"R (>= 3.0.3)","Description":"Basic access to
market infomation from the public API for the Crypto-Currency exchange
Cryptsy.","Imports":"RJSONIO, RCurl","License":"GPL-
3","NeedsCompilation":"no","Package":"RCryptsy","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Access to Cryptsy Crypto-Currency Exchange Public
Information\nAPI via
R","URL":"https:\/\/github.com\/ropensci\/RCryptsy","Version":"0.4"},"RCurl":
{"Author":"Duncan Temple Lang and the CRAN team","Depends":"R (>= 3.0.0), methods,
bitops","Description":"A wrapper for 'libcurl'
<http:\/\/curl.haxx.se\/libcurl\/>\nProvides functions to allow one to compose
general HTTP requests\nand provides convenient functions to fetch URIs, get &
post\nforms, etc. and process the results returned by the Web server.\nThis
provides a great deal of control over the HTTP\/FTP\/...\nconnection and the form
of the request while providing a\nhigher-level interface than is available just
using R socket\nconnections. Additionally, the underlying implementation
is\nrobust and extensive, supporting FTP\/FTPS\/TFTP (uploads and\ndownloads),
SSL\/HTTPS, telnet, dict, ldap, and also supports\ncookies, redirects,
authentication,
etc.","License":"BSD","NeedsCompilation":"yes","Package":"RCurl","Repository":"http
:\/\/cran.csiro.au\/src\/contrib","Suggests":"Rcompression, XML","Title":"General
Network (HTTP\/FTP\/...) Client Interface for
R","URL":"http:\/\/www.omegahat.net\/RCurl","Version":"1.95-4.8"},"RDCOMClient":
{"Depends":"methods","License":"GPL-
2","NeedsCompilation":"yes","Package":"RDCOMClient","Repository":"http:\/\/www.stat
s.ox.ac.uk\/pub\/RWin\/src\/contrib","Suggests":"SWinTypeLibs","Version":"0.93-
0.2"},"RDIDQ":{"Author":"Rahul
Mehta","Description":"The package has many function that helps to perform\nvarious
quality check on the data.It basically provides many\nfunction that helps in
performing Extrapolative data analysis.","License":"GPL-
2","NeedsCompilation":"no","Package":"RDIDQ","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"descr","Title":"It perform Quality check on
data","Version":"1.0"},"RDML":{"Author":"Konstantin A. Blagodatskikh [cre,
aut],\nStefan Roediger [aut],\nMichal Burdukiewicz [aut]","Depends":"R (>
3.0.3)","Description":"Imports real-time thermo cycler (qPCR) data from Real-time
PCR\nData Markup Language (RDML) format files and transforms to the
appropriate\nformats of the 'qpcR' and 'chipPCR' packages. Contains a
dendrogram\nvisualization for the structure of RDML object.","Imports":"R6 (>=
2.0.1), assertthat (>= 0.1), XML (>= 3.98-1.1), plyr\n(>= 1.8.1), dplyr (>= 0.4.1),
tidyr (>= 0.2.0), rlist (>= 0.4)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RDML","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr, chipPCR, ggplot2","Title":"Importing Real-Time
Thermo Cycler (qPCR) Data from RDML
Format\nFiles","URL":"https:\/\/github.com\/kablag\/RDML","Version":"0.9-1"},"RDS":
{"Author":"Mark S. Handcock [aut, cre],\nKrista J. Gile [aut],\nIan E. Fellows
[aut],\nW. Whipple Neely [aut]","Depends":"R (>= 2.5.1),
methods","Description":"Provides functionality for carrying out estimation\nwith
data collected using Respondent-Driven Sampling. This includes\nHeckathorn's RDS-I
and RDS-II estimators as well as Gile's Sequential\nSampling estimator. The package
is part of the \"RDS Analyst\" suite of\npackages for the analysis of respondent-
driven sampling data.","Imports":"gridExtra, ggplot2 (>= 2.0.0), igraph, reshape2,
scales","License":"LGPL-
2.1","NeedsCompilation":"yes","Package":"RDS","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"isotone, network, survey, testthat","Title":"Respondent-
Driven Sampling","URL":"http:\/\/www.hpmrg.org","Version":"0.7-6"},"RDSTK":
{"Author":"Ryan Elmore and Andrew Heiss","Depends":"plyr, rjson,
RCurl","Description":"This package provides an R interface to Pete Warden's
Data\nScience Toolkit. See www.datasciencetoolkit.org for more\ninformation. The
source code for this package can be found at\ngithub.com\/rtelmore\/RDSTK Happy
hacking!","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"RDSTK","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"An R wrapper for the Data Science Toolkit
API","Version":"1.1"},"RDataCanvas":{"Author":"Xiaolin Zhang [aut,
cre]","Depends":"R (>= 3.0.0)","Description":"Provides basic functionalities for
writing a module\nfor http:\/\/datacanvas.io. The http:\/\/datacanvas.io is a big
data\nanalytics platform that helps data scientists to build, manage\nand share
data pipelines.","Imports":"jsonlite","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"RDataCanvas","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Basic Runtime Support for
Datacanvas.io","URL":"https:\/\/github.com\/DataCanvasIO\/RDataCanvas","Version":"0
.1"},"RDieHarder":{"Author":"Dirk Eddelbuettel <edd@debian.org>","Depends":"R (>=
2.5.0)","Description":"The RDieHarder packages provides an R interface to\nthe
dieharder suite of random number generators and tests that\nwas developed by Robert
G. Brown and David Bauer, extending\nearlier work by George Marsaglia and
2)","NeedsCompilation":"yes","Package":"RDieHarder","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"R interface to the dieharder RNG test
suite","URL":"http:\/\/code.google.com\/p\/rdieharder\/","Version":"0.1.3"},"RDota"
:{"Author":"Xiao Lei","Depends":"R(>= 3.1.2), XML","Description":"Data analysis
functions for Dota2. Dota2 is a popular online game (see, e.g.
<http:\/\/en.wikipedia.org\/wiki\/Dota_2> for more information) and there are more
and more websites doing data analysis for paid players.The data of the latest hero,
Winter Wyvern and the latest game version, 6.83c, are included. The package now
contains functions for calculating the best choice given specific lineup, showing
unconditional win rates and the global online population.","License":"GPL-
3","NeedsCompilation":"no","Package":"RDota","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Data Analysis Toolbox for Dota2","Version":"1.2"},"REBayes":
{"Author":"Roger Koenker [aut, cre],\nJiaying Gu [ctb],\nIvan Mizera
[ctb]","Depends":"R (>= 2.10), Matrix","Description":"Kiefer-Wolfowitz maximum
likelihood estimation for mixture models\nand some other density estimation and
regression methods based on convex\noptimization.","Imports":"Rmosek, methods,
reliaR","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"REBayes","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Empirical Bayes Estimation and Inference in
R","URL":"http:\/\/www.r-project.org","Version":"0.62"},"RECA":{"Author":"Nan Xiao
<road2stat@gmail.com>","Description":"Relevant Component Analysis (RCA) tries to
find a linear\ntransformation of the feature space such that the effect of
irrelevant\nvariability is reduced in the transformed space.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RECA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"MASS","Title":"Relevant Component Analysis for Supervised
Distance
Metric\nLearning","URL":"https:\/\/github.com\/road2stat\/RECA","Version":"1.1"},"R
EDCapR":{"Author":"Will Beasley [aut, cre],\nDavid Bard [ctb],\nThomas Wilson
[ctb],\nJohn J Aponte [ctb],\nRollie Parrish [ctb],\nBenjamin Nutter [ctb],\nAndrew
Peters [ctb]","Depends":"R(>= 3.0.0), stats","Description":"Encapsulates functions
to streamline calls from R to the REDCap\nAPI. REDCap (Research Electronic Data
CAPture) is a web application for\nbuilding and managing online surveys and
databases developed at Vanderbilt\nUniversity. The Application Programming
Interface (API) offers an avenue\nto access and modify data programmatically,
improving the capacity for\nliterate and reproducible
programming.","Imports":"httr(>= 1.0.0), methods, plyr","License":"GPL-
2","NeedsCompilation":"no","Package":"REDCapR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"devtools, knitr, rmarkdown, RODBC, testthat (>=
0.9)","Title":"Interaction Between R and
REDCap","URL":"https:\/\/github.com\/OuhscBbmc\/REDCapR,
http:\/\/ouhsc.edu\/bbmc\/,\nhttp:\/\/project-
redcap.org","Version":"0.9.3"},"REEMtree":{"Author":"Rebecca Sela and Jeffrey
Simonoff","Depends":"nlme, rpart, methods","Description":"This package estimates
regression trees with random\neffects as a way to use data mining techniques to
describe\nlongitudinal or panel
data.","License":"GPL","NeedsCompilation":"no","Package":"REEMtree","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Suggests":"AER","Title":"Regression Trees
with Random Effects for Longitudinal
(Panel)\nData","URL":"http:\/\/pages.stern.nyu.edu\/~jsimonof\/REEMtree\/","Version
":"0.90.3"},"REGENT":{"Author":"Daniel J.M. Crouch, Graham H.M. Goddard & Cathryn
M. Lewis","Depends":"R (>= 2.14.0)","Description":"Produces population distribution
of disease risk and statistical risk categories, and predicts risks for individuals
with genotype
information.","License":"GPL","NeedsCompilation":"no","Package":"REGENT","Repositor
y":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Risk Estimation for Genetic and
Environmental Traits","Version":"1.0.6"},"REPPlab":{"Author":"Daniel Fischer, Alain
Berro, Klaus Nordhausen, Anne Ruiz-Gazen","Depends":"R (>= 2.15.1), rJava, lattice,
LDRTools (>= 0.2), utils,\ngraphics","Description":"An R Interface to 'EPP-lab'
v1.0. 'EPP-lab' is a Java program for\nprojection pursuit using genetic algorithms
written by Alain Berro and S. Larabi\nMarie-Sainte and is included in the package.
The 'EPP-lab' sources are available\nunder https:\/\/github.com\/fischuu\/EPP-
lab.git.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"REPPlab","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"tourr, amap","Title":"R Interface to 'EPP-Lab', a Java
Program for Exploratory\nProjection Pursuit","Version":"0.9.3"},"REQS":
{"Author":"Patrick Mair, Eric Wu","Depends":"gtools","Description":"This package
contains the function run.eqs() which calls\nan EQS script file, executes the EQS
estimation, and, finally,\nimports the results as R objects. These two steps can
be\nperformed separately: call.eqs() calls and executes EQS,\nwhereas read.eqs()
imports existing EQS outputs as objects into\nR. It requires EQS 6.2 (build 98 or
higher).","License":"GPL","NeedsCompilation":"no","Package":"REQS","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"R\/EQS
Interface","URL":"http:\/\/www.mvsoft.com","Version":"0.8-12"},"RESS":
{"Author":"Ben Waxer","Description":"Contains three functions that query AuriQ
Systems' Essentia Database and return the results in R. 'essQuery' takes a single
Essentia command and captures the output in R, where you can save the output to a
dataframe or stream it directly into additional analysis. 'read.essentia' takes an
Essentia script and captures the output csv data into R, where you can save the
output to a dataframe or stream it directly into additional analysis.
'capture.essentia' takes a file containing any number of Essentia commands and
captures the output of the specified statements into R dataframes. Essentia can be
downloaded for free at
http:\/\/www.auriq.com\/documentation\/source\/install\/index.html.","Imports":"uti
ls","License":"LGPL-
3","NeedsCompilation":"no","Package":"RESS","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Integrates R and Essentia","Version":"1.3"},"REST":
{"Author":"De Troyer Ewoud","Description":"Contains easy scripts which can be used
to quickly create GUI windows
for 'Rcmdr' Plugins. No knowledge about Tcl\/Tk is required to make use of these
scripts (These scripts are a generalisation of the template scripts in the
'RcmdrPlugin.BiclustGUI' package).","Imports":"Rcmdr, tcltk","License":"GPL-
3","NeedsCompilation":"no","Package":"REST","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"knitr","Title":"RcmdrPlugin Easy Script
Templates","Version":"1.0.1"},"REdaS":{"Author":"Marco Johannes Maier [cre,
aut]","Depends":"R (>= 3.0.0), grid","Description":"Provides functions used in the
'R: EinfÃ¼hrung durch angewandte Statistik' (second
edition).","Imports":"stats","License":"GPL-
2","NeedsCompilation":"no","Package":"REdaS","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"car, cluster, foreign, GPArotation, MASS, mclust,
psych,\nUsingR, vcd","Title":"Companion Package to the Book 'R: EinfÃ¼hrung durch
angewandte\nStatistik'","Version":"0.9.3"},"REndo":{"Author":"Raluca Gui,\nMarkus
Meierer,\nRene Algesheimer","Description":"Fits linear models with endogenous
regressors using Internal\nInstrumental Variables (IIV) methods. These are
statistical techniques to\ncorrect for endogeneity when no strong, valid external
instrumental variables\nare available. The first version of the package offers two
methods, the Latent\nInstrumental Variables (Ebbes et al., 2005) and Lewbel's
higher moments approach\n(Lewbel, 1997). In a second version of the package, two
other methods will be\nadded, joint estimation using copulas (Park and Gupta, 2012)
and multilevel GMM\n(Kim and Frees,
2007).","Imports":"stats,optimx,mvtnorm,AER,e1071,utils,methods","License":"GPL-
3","NeedsCompilation":"no","Package":"REndo","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Fitting Linear Models with Endogenous Regressors when
No\nExternal Instruments are Available","Version":"1.0"},"RFGLS":{"Author":"Robert
M. Kirkpatrick <rkirkpatrick2@vcu.edu>, Xiang Li <lixxx554@umn.edu>, and Saonli
Basu <saonli@umn.edu>.","Depends":"stats, bdsmatrix, Matrix, R (>=
2.15.0)","Description":"RFGLS uses a generalized least-squares method to perform
single-marker association analysis,\nin datasets of nuclear families containing
parents, twins, and\/or adoptees","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RFGLS","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Rapid Feasible Generalized Least
Squares","Version":"1.1"},"RFLPtools":{"Author":"Fabienne Flessa, Alexandra Kehl,
Mohammed Aslam Imtiaz, Matthias Kohl","Depends":"R(>= 3.0.0), stats, utils,
graphics, grDevices, RColorBrewer","Description":"RFLPtools provides functions to
analyse DNA fragment samples\n(i.e. derived from RFLP-analysis) and standalone
BLAST report files\n(i.e. DNA sequence analysis).","License":"LGPL-
3","NeedsCompilation":"no","Package":"RFLPtools","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"lattice, MKmisc(>= 0.8)","Title":"Tools to analyse
RFLP data","Version":"1.6"},"RFOC":{"Author":"Jonathan M. Lees","Depends":"R (>=
2.12)","Description":"Graphics for statistics on a sphere, as applied to geological
fault data, crystallography, earthquake focal mechanisms, radiation patterns,
ternary plots and geographical\/geological maps. Non-double couple plotting of
focal spheres and source type maps are included for statistical analysis of moment
tensors.","Imports":"RPMG, GEOmap, RSEIS, MASS, splancs","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RFOC","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Graphics for Spherical Distributions and Earthquake
Focal\nMechanisms","Version":"3.3-3"},"RFgroove":{"Author":"Baptiste
Gregorutti","Depends":"randomForest, wmtsa, fda","Description":"Variable selection
tools for groups of variables and functional data based on a new grouped variable
importance with random forests.","License":"GPL (>=
2.0)","NeedsCompilation":"yes","Package":"RFgroove","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Importance Measure and Selection for Groups of
Variables with\nRandom Forests","Version":"1.1"},"RFinanceYJ":{"Author":"Yohei
Sato, Nobuaki Oshiro, Shinichi
Takayanagi","Depends":"XML,xts","Description":"Japanese stock market from Yahoo!-
finance-Japan","License":"BSD 3-clause
License","NeedsCompilation":"no","Package":"RFinanceYJ","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"RFinanceYJ","Version":"0.3.1"},"RFmarkerDetector"
:{"Author":"Piergiorgio Palla, Giuliano Armano","Depends":"AUCRF","Description":"A
collection of tools for multivariate analysis of metabolomics\ndata, which includes
several preprocessing methods (normalization, scaling)\nand various exploration and
data visualization techniques (Principal\nComponents Analysis and Multi Dimensional
Scaling). The core of the package\nis the Random Forest algorithm used for the
construction, optimization and\nvalidation of classification models with the aim of
identifying potentially\nrelevant biomarkers.","Imports":"randomForest, ggplot2,
UsingR, WilcoxCV, ROCR, methods","License":"GPL-
3","NeedsCompilation":"no","Package":"RFmarkerDetector","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Multivariate Analysis of Metabolomics Data using
Random Forests","Version":"1.0.1"},"RForcecom":{"Author":"Takekatsu Hiramura [aut,
cre],\nSteven Mortimer [ctb],\nAlexis Iglauer [ctb]","Depends":"R (>=
3.1.0)","Description":"Insert, update,\nretrieve, delete and bulk operate datasets
with a SaaS based CRM\nSalesforce.com and a PaaS based application platform
Force.com from R.","Imports":"methods, utils, XML, RCurl, httr,
plyr","License":"Apache License
2.0","NeedsCompilation":"no","Package":"RForcecom","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat","Title":"Data Integration Feature for
Force.com and
Salesforce.com","URL":"http:\/\/rforcecom.plavox.info\/","Version":"0.8"},"RFormatt
er":{"Author":"Benjamin Fischer [aut, cre]","Depends":"R (>=
3.2.2)","Description":"The R Formatter formats R source code. It is very much based
on\nformatR, but tries to improve it by heuristics. For example, spaces can
be\nforced around the division operator \"\/\".","Imports":"formatR (>=
3","NeedsCompilation":"no","Package":"RFormatter","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat","Title":"R Source Code
Formatter","URL":"https:\/\/github.com\/evolutics\/RFormatter","Version":"0.1.0"},"
RFreak":{"Author":"Robin Nunkesser <Robin.Nunkesser@hshl.de>","Description":"An R
interface to a modified version of the Free Evolutionary Algorithm Kit FrEAK. FrEAK
is a toolkit written in Java to design and analyze evolutionary algorithms. Both
the R interface and an extended version of FrEAK are contained in the RFreak
package. For more information on FrEAK see
http:\/\/sourceforge.net\/projects\/freak427\/.","Imports":"methods, rJava (>=
0.5.0)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RFreak","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"R\/FrEAK interface","Version":"0.3-0"},"RGA":
{"Author":"Artem Klevtsov [aut, cre],\nPhilipp Upravitelev [ctb],\nOlga Shramko
[ctb]","Depends":"R (>= 3.2.0)","Description":"Provides functions for accessing and
retrieving data from the\nGoogle Analytics APIs
(https:\/\/developers.google.com\/analytics\/). Supports\nOAuth 2.0 authorization.
Package provides access to the Management, Core\nReporting, Multi-Channel Funnels
Reporting, Real Time Reporting and\nMetadata APIs. Access to all the Google
Analytics accounts which the user\nhas access to. Auto-pagination to return more
than 10,000 rows of the\nresults by combining multiple data requests. Also package
provides\nshiny app to explore the core reporting API dimensions and
metrics.","Imports":"jsonlite, httr (>= 1.1.0), plyr, lubridate","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RGA","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"knitr, rmarkdown, testthat, shiny","Title":"A Google
Analytics API
Client","URL":"https:\/\/github.com\/artemklevtsov\/RGA","Version":"0.4.2"},"RGCCA"
:{"Author":"Arthur Tenenhaus and Vincent
Guillemot","Depends":"MASS","Description":"Multi-block data analysis concerns the
analysis of several sets of variables (blocks) observed on the same group of
individuals. The main aims of the RGCCA package are: (i) to study the relationships
between blocks and (ii) to identify subsets of variables of each block which are
active in their relationships with the other blocks.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RGCCA","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"RGCCA and Sparse GCCA for multi-block data
analysis","Version":"2.0"},"RGENERATE":{"Author":"Emanuele Cordano","Depends":"R
(>= 2.10),RMAWGEN","Description":"A method 'generate' is implemented in this
package for the random\ngeneration of vector time series according to models
obtained by 'RMAWGEN',\n'vars' or other packages. This package was created to
generalize the\nalgorithms of the RMAWGEN package for the analysis and generation
of any\nenvironmental vector time series.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RGENERATE","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Tools To Generate Vector Time
Series","URL":"https:\/\/github.com\/ecor\/RGENERATE","Version":"1.3"},"RGENERATEPR
EC":{"Author":"Emanuele Cordano","Depends":"R (>= 3.0), copula, RGENERATE,
blockmatrix, Matrix, stringr","Description":"The method 'generate' is extended for
spatial multi-site\nstochastic generation of daily precipitation. It generates
precipitation\noccurrence in several sites using logit regression (Generalized
Linear\nModels) and D.S. Wilks' approach (Journal of Hydrology,
1998).","Imports":"RMAWGEN","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RGENERATEPREC","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Tools To Generate
Daily-Precipitation Time
Series","URL":"https:\/\/github.com\/ecor\/RGENERATEPREC","Version":"1.0"},"RGIFT":
{"Author":"María José Haro-Delicado, Virgilio Gómez-Rubio and Francisco\nParreño-
Torres","Depends":"R (>= 2.10.0)","Description":"This package provides some
functions to create quizzes\nin the GIFT format. This format is used by several
Virtual Learning\nEnvironments such as Moodle.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RGIFT","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"foreign","Title":"Create quizzes in GIFT
Format","URL":"http:\/\/docs.moodle.org\/21\/en\/GIFT_format","Version":"0.1-
5"},"RGenetics":{"Author":"Felix Yanhui Fan <nolanfyh@gmail.com>","Description":"R
packages for genetics research","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RGenetics","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"R packages for genetics
research","Version":"0.1"},"RGoogleAnalytics":{"Author":"Michael Pearmain.
Contributions from Nick Mihailowski,\nVignesh Prajapati, Kushan Shah and Nicolas
Remy","Depends":"R(>= 3.0.2), lubridate, httr","Description":"Provides functions
for accessing and retrieving data from the\nGoogle Analytics API","License":"Apache
License
2.0","NeedsCompilation":"no","Package":"RGoogleAnalytics","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"testthat","Title":"R Wrapper for the Google
Analytics API","Version":"0.1.1"},"RGoogleAnalyticsPremium":{"Author":"Jalpa Joshi
Dave","Depends":"R(>= 3.2.2), httr, lubridate, jsonlite, utils","Description":"It
fires a query to the API to get the unsampled data in R for Google Analytics
Premium Accounts. It retrieves data from the Google drive document and stores it
into the local drive. The path to the excel file is returned by this package. The
user can read data from the excel file into R using read.csv()
function.","License":"Apache License
2.0","NeedsCompilation":"no","Package":"RGoogleAnalyticsPremium","Repository":"http
:\/\/cran.csiro.au\/src\/contrib","Title":"Unsampled Data in R for Google Analytics
Premium Accounts","Version":"0.1.1"},"RGraphics":{"Author":"Paul
Murrell","Depends":"R (>= 2.13.0), datasets, stats, grDevices, graphics,
methods,\ngrid","Description":"Data and Functions from the book R Graphics, Second
Edition. There is a function to produce each figure in the book, plus several
functions, classes, and methods defined in Chapter 8.","Imports":"lattice,
ggplot2","License":"GPL","NeedsCompilation":"no","Package":"RGraphics","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"agricolae, animation,
CircStats, circular, cluster,\ncolorspace, diagram, dichromat, gplots, graph,
gridBase,\ngridExtra, gridSVG, grImport, gWidgets, gWidgetsRGtk2, hexbin,\nHmisc,
hyperdraw, hypergraph, igraph, iplots, ipred,\nlatticeExtra, mapdata, maps,
maptools, MASS, misc3d, munsell,\nnetwork, openair, oz, party, pixmap, playwith,
plotrix, pmg,\npng, quantmod, raster, Rcmdr, RColorBrewer, rgdal, rggobi,
rgl,\nRGraphics, Rgraphviz, scatterplot3d, soiltexture, sp,\nSVGAnnotation,
symbols, TeachingDemos, tools, vcd, vcdExtra,\nvenneuler, vrmlgen,
XML","Title":"Data and Functions from the Book R Graphics, Second
Edition","URL":"https:\/\/www.stat.auckland.ac.nz\/~paul\/RG2e\/index.html","Versio
n":"2.0-14"},"RGtk2":{"Author":"Michael Lawrence <michafla@gene.com> and Duncan
Temple Lang <duncan@wald.ucdavis.edu>","Depends":"R (>=
2.5.0)","Description":"Facilities in the R language for programming\ngraphical
interfaces using Gtk, the Gimp Tool
Kit.","License":"GPL","NeedsCompilation":"yes","Package":"RGtk2","Repository":"http
:\/\/cran.csiro.au\/src\/contrib","Title":"R bindings for Gtk 2.8.0 and
above","URL":"http:\/\/www.ggobi.org\/rgtk2,
http:\/\/www.omegahat.org","Version":"2.20.31"},"RGtk2Extras":{"Author":"Tom
Taverner, with contributions from John Verzani, Iago Conde\nand Liviu
Andronic","Depends":"methods, RGtk2(>= 2.12.8)","Description":"Useful add-ons for
RGtk2","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"RGtk2Extras","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"gWidgetsRGtk2","Title":"Data frame editor and
dialog making wrapper for RGtk2","Version":"0.6.1"},"RH2":{"Author":"G.
Grothendieck. Author of h2 is Thomas Mueller.","Depends":"chron, methods, RJDBC,
rJava","Description":"DBI\/RJDBC interface to h2 database. h2 version 1.3.175 is
included.","License":"Mozilla Public License
1.1","NeedsCompilation":"no","Package":"RH2","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"DBI\/RJDBC interface to h2
Database","URL":"https:\/\/github.com\/dmkaplan2000\/RH2.git","Version":"0.2.3"},"R
HRV":{"Author":"A. Mendez, L. Rodriguez-Linares, A. Otero, C.A. Garcia, X. Vila, M.
Lado","Depends":"R (>= 3.0.0), tcltk(>= 2.4.1), tkrplot(>= 0.0-18),
waveslim(>=\n1.6.4), nonlinearTseries (>= 0.2)","Description":"Methods and tools
for performing Heart Rate Variability analysis\nof ECG records. RHRV allows to
import data files containing heartbeat positions\nin the most broadly used formats;
eliminating outliers or spurious points\npresent in the time series with
unacceptable physiological values; plotting HRV\ndata and performing time domain,
frequency domain and nonlinear HRV analysis.","License":"GPL-
2","NeedsCompilation":"yes","Package":"RHRV","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"highlight","Title":"Heart rate variability analysis of
ECG data","URL":"http:\/\/rhrv.r-forge.r-project.org\/","Version":"4.0"},"RHT":
{"Author":"Lin S. Chen and Pei Wang","Description":"This package offers functions
to perform regularized\nHotelling's T-square test for pathway or gene set analysis.
The\npackage is tailored for but not limited to proteomics data, in\nwhich sample
sizes are often small, a large proportion of the\ndata are missing and\/or
correlations may be
present.","License":"GPL","NeedsCompilation":"no","Package":"RHT","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Title":"Regularized Hotelling's T-square Test
for Pathway (Gene Set)\nAnalysis","Version":"1.0"},"RI2by2":{"Author":"Joseph
Rigdon","Depends":"compiler, gtools","Description":"Computes attributable effects
based confidence set, permutation test confidence set, and asymptotic confidence
interval for the average treatment effect on a binary outcome.","License":"GPL-
3","NeedsCompilation":"no","Package":"RI2by2","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Randomization inference for treatment effects on a
binary\noutcome","Version":"1.2"},"RIFS":{"Author":"Pavel V. Moskalev, Alexey G.
Bukhovets and Tatyana Ya.\nBiruchinskay","Depends":"R (>=
2.14.0)","Description":"RIFS package provides functionality for generating
&\nplotting prefractals in R^n with various protofractal sets and\npartition
coefficient for iterative segments","License":"GPL-
3","NeedsCompilation":"no","Package":"RIFS","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Random Iterated Function System
(RIFS)","URL":"http:\/\/www.r-project.org","Version":"0.1-5"},"RISmed":
{"Author":"Stephanie Kovalchik","Depends":"R (>= 2.8.0), methods","Description":"A
set of tools to extract bibliographic content from the National Center for
Biotechnology Information (NCBI) databases, including PubMed. The name RISmed is a
portmanteau of RIS (for Research Information Systems, a common tag format for
bibliographic data) and PubMed.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RISmed","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Download Content from NCBI
Databases","Version":"2.1.5"},"RImageJROI":{"Author":"David C Sterratt [aut, cph,
cre],\nMikko Vihtakari [aut, cph]","Depends":"R (>= 3.0.2)","Description":"Provides
functions to read 'ImageJ' (http:\/\/imagej.nih.gov\/ij\/)\nRegion of Interest
(ROI) files, to plot the ROIs and to convert them to\n'spatstat'
(http:\/\/spatstat.org\/) spatial patterns.","Imports":"spatstat","License":"GPL-
3","NeedsCompilation":"no","Package":"RImageJROI","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"png, testthat","Title":"Read 'ImageJ' Region of
Interest (ROI)
Files","URL":"https:\/\/github.com\/davidcsterratt\/RImageJROI","Version":"0.1.1"},
"RImagePalette":{"Author":"Joel Carlson","Depends":"R (>= 2.1.0)","Description":"A
pure R implementation of the median cut algorithm.\nExtracts the dominant colors
from an image, and turns them into\na scale for use in plots or for
fun!","Imports":"ggplot2","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"RImagePalette","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Suggests":"testthat, scales, jpeg,
png","Title":"Extract the Colors from Images","Version":"0.1.1"},"RImpala":
{"Author":"Vijay Raajaa, Austin Chungath Vincent, Sachin Sudarshana, Vikas
Raguttahalli","Depends":"R (>= 2.7.0), rJava (>= 0.5-0)","Description":"Cloudera
'Impala', which is a massively parallel processing (MPP) SQL query engine runs
natively in Apache Hadoop. 'RImpala' facilitates the connection and execution of
distributed queries through 'R'. 'Impala' supports JDBC integration which 'RImpala'
utilizes to establish the connection between 'R' and 'Impala'. Thanks to Mu Sigma
for their continued support throughout the development of the
3","NeedsCompilation":"no","Package":"RImpala","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Using Cloudera 'Impala' Through
'R'","Version":"0.1.6"},"RInSp":{"Author":"Dr. Nicola Zaccarelli, Dr. Giorgio
Mancinelli, and Prof. Dan Bolnick","Description":"Functions to calculate several
ecological indices of individual and population niche width\n(Araujo's E,
clustering and pairwise similarity among individuals, IS, Petraitis' W, and
Roughgarden's\nWIC\/TNW) to assess individual specialization based on data of
resource use. Resource use can be\nquantified by counts of categories, measures of
mass\/lenght or proportions.
Monte Carlo resampling\nprocedures are available for hypothesis testing against
multinomial null models.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"RInSp","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"R Individual Specialization
(RInSp)","Version":"1.2"},"RInside":{"Author":"Dirk Eddelbuettel and Romain
Francois","Depends":"R (>= 2.10.0)","Description":"C++ classes to embed R in C++
applications\nThe 'RInside' packages makes it easier to have \"R inside\" your C++
application\nby providing a C++ wrapper class providing the R interpreter.\n\nAs R
itself is embedded into your application, a shared library build of R\nis required.
This works on Linux, OS X and even on Windows provided you use\nthe same tools used
to build R itself.\n\nNumerous examples are provided in the eight subdirectories of
the examples\/\ndirectory of the installed package: standard, mpi (for parallel
computing)\nqt (showing how to embed 'RInside' inside a Qt GUI application), wt
(showing\nhow to build a \"web-application\" using the Wt toolkit), armadillo
(for\n'RInside' use with 'RcppArmadillo') and eigen (for 'RInside' use with
'RcppEigen').\nThe example use GNUmakefile(s) with GNU extensions, so a GNU make is
required\n(and will use the GNUmakefile automatically).\n\nDoxygen-generated
documentation of the C++ classes is available at the\n'RInside' website as
well.","Imports":"Rcpp (>= 0.11.0)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"RInside","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"C++ Classes to Embed R in C++
Applications","URL":"http:\/\/dirk.eddelbuettel.com\/code\/rinside.html","Version":
"0.2.13"},"RItools":{"Author":"Jake Bowers <jwbowers@illinois.edu>, Mark
Fredrickson\n<mark.m.fredrickson@gmail.com>, and Ben Hansen
<ben.hansen@umich.edu>","Depends":"R (>= 2.2.0), stats, methods, graphics,
utils","Description":"Tools for randomization
inference.","Enhances":"optmatch","Imports":"grDevices, SparseM, abind, xtable,
svd","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RItools","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"testthat, MASS, RSVGTipsDevice","Title":"Randomization
Inference Tools","URL":"http:\/\/CRAN.R-
project.org\/package=RItools,\nhttp:\/\/www.jakebowers.org\/
RItools.html","Version":"0.1-13"},"RJDBC":{"Author":"Simon Urbanek
<Simon.Urbanek@r-project.org>","Depends":"methods, DBI, rJava (>= 0.4-15), R (>=
2.4.0)","Description":"RJDBC is an implementation of R's DBI interface using JDBC
as a back-end. This allows R to connect to any DBMS that has a JDBC
driver.","License":"GPL-
2","NeedsCompilation":"no","Package":"RJDBC","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Provides access to databases through the JDBC
interface","URL":"http:\/\/www.rforge.net\/RJDBC\/","Version":"0.2-5"},"RJSDMX":
{"Author":"Attilio Mattiocco, Diana Nicoletti, Gianpaolo Lopez, Banca
d'Italia","Depends":"R (>= 2.12.0), rJava (>= 0.8-8), zoo (>= 1.6-
4)","Description":"Provides functions to retrieve data and metadata from
providers\nthat disseminate data by means of SDMX web services.\nSDMX (Statistical
Data and Metadata eXchange) is a standard that\nhas been developed with the aim of
simplifying the exchange of\nstatistical information.\nMore about the SDMX standard
and the SDMX Web Services\ncan be found at:
http:\/\/sdmx.org .","License":"EUPL","NeedsCompilation":"no","Package":"RJSDMX","R
epository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"R Interface to SDMX Web
Services","URL":"https:\/\/github.com\/amattioc\/SDMX\/","Version":"1.6-
1"},"RJSONIO":{"Author":"Duncan Temple Lang","Description":"This is a package that
allows conversion to and from\ndata in Javascript object notation (JSON)
format.\nThis allows R objects to be inserted into
Javascript\/ECMAScript\/ActionScript code\nand allows R programmers to read and
convert JSON content to R objects.\nThis is an alternative to rjson package.
Originally, that was too slow for converting large R objects to JSON\nand was not
extensible. rjson's performance is now similar to this package, and perhaps
slightly faster in some cases.\nThis package uses methods and is readily extensible
by defining methods for different classes,\nvectorized operations, and C code and
callbacks to R functions for deserializing JSON objects to R.\nThe two packages
intentionally share the same basic interface. This package (RJSONIO) has many
additional\noptions to allow customizing the generation and processing of JSON
content.\nThis package uses libjson rather than implementing yet another JSON
parser. The aim is to support\nother general projects by building on their work,
providing feedback and benefit from their ongoing
development.","Imports":"methods","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"yes","Package":"RJSONIO","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Serialize R objects to JSON, JavaScript Object
Notation","Version":"1.3-0"},"RJaCGH":{"Author":"Oscar Rueda <rueda.om@gmail.com>
and Ramon Diaz-Uriarte\n<rdiaz02@gmail.com>. zlib from Jean-loup Gailly and Mark
Adler;\nsee README. Function \"getHostname.System\" from package R.utils\nby Henrik
Bengtsson.","Depends":"R (>= 2.13)","Description":"Bayesian analysis of CGH
microarrays fitting Hidden Markov\nChain models. The selection of the number of
states is made via\ntheir posterior probability computed by Reversible Jump
Markov\nChain Monte Carlo Methods. Also returns probabilistic common\nregions for
gains\/losses.","License":"GPL-
3","NeedsCompilation":"yes","Package":"RJaCGH","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Reversible Jump MCMC for the Analysis of CGH
Arrays","URL":"http:\/\/www.r-project.org","Version":"2.0.4"},"RJafroc":
{"Author":"Xuetong Zhai [aut, cre],\nDev Chakraborty [aut, ths]","Depends":"tools,
xlsx, ggplot2, stringr, utils, stats, shiny","Description":"A common task in
medical imaging is assessing whether a new imaging system or device is an
improvement over an existing one. Observer performance methodology, such as
receiver operating characteristic analysis, is widely used for this purpose.
Receiver operating characteristic studies are often required for regulatory
approval of new devices. The purpose of this work is to software for the analysis
of data acquired using the receiver operating characteristic paradigm and its
location specific extensions. It is an enhanced implementation of existing Windows
software (http:\/\/www.devchakraborty.com). In this paradigm the radiologist rates
each image for confidence in presence of disease. The images are typically split
equally between actually non-diseased and diseased. A common figure of merit is the
area under the receiver operating characteristic curve, which has the physical
interpretation as the probability that a diseased image is rated higher than a non-
diseased one. In receiver operating characteristic studies a number of radiologists
(readers) rate images in two or more treatments, and the object of the analysis is
to determine the significance of the inter-treatment difference between reader-
averaged figures of merit. In the free-response paradigm the reader marks the
locations of suspicious regions and rates each region for confidence in presence of
disease, and credit for detection is only given if a true lesion is correctly
localized. In the region of interest paradigm each image is divided into a number
of regions and the reader rates each region. Each paradigm requires definition of a
valid figure of merit that rewards correct decisions and penalizes incorrect ones
and specialized significance testing procedures are applied. The package reads data
in all currently used data formats including Excel. Significance testing uses two
models in widespread use, a jackknife pseudo-value based model and an analysis of
variance model with correlated errors. Included are tools for (1) calculating a
variety of free-response figures of merit; (2) sample size estimation for planning
a future study based on pilot data; (3) viewing empirical operating characteristics
in receiver operating characteristic and free-response paradigms; (4) producing
formatted report files; and (5) saving a data file in appropriate format for
analysis with alternate software. In addition to open-source access to the
functions, the package includes a graphical interface for users already familiar
with the Windows software, who simply wish to run the program.","License":"GPL-
3","NeedsCompilation":"no","Package":"RJafroc","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr","Title":"Analysis of Data Acquired Using the
Receiver Operating\nCharacteristic Paradigm and Its
Extensions","URL":"http:\/\/www.devchakraborty.com","Version":"0.1.1"},"RKEA":
{"Author":"Ingo Feinerer [aut],\nKurt Hornik [aut, cre]","Description":"An R
interface to KEA (Version 5.0).\nKEA (for Keyphrase Extraction Algorithm) allows
for extracting\nkeyphrases from text documents. It can be either used for
free\nindexing or for indexing with a controlled vocabulary. For more\ninformation
see <http:\/\/www.nzdl.org\/Kea\/>.","Imports":"RKEAjars (>= 5.0-1), rJava (>= 0.6-
3), tm","License":"GPL-
2","NeedsCompilation":"no","Package":"RKEA","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"R\/KEA Interface","Version":"0.0-6"},"RKEAjars":
{"Author":"Kurt Hornik [aut, cre],\nEibe Frank [ctb, cph] (KEA Java
library),\nOlena Medelyan [ctb, cph] (KEA Java library),\nThe Apache Software
Foundation [ctb, cph] (Apache Commons Logging and\nApache Jena Java
libraries),\nInternational Business Machines Corporation and others [ctb,
cph]\n(International Components for Unicode for Java (ICU4J)),\nMartin Porter [ctb,
cph] (Snowball base),\nRichard Boulton [ctb, cph] (Snowball Java
library),\nUniversity of Waikato [ctb, cph] (Weka Java
library)","Description":"External jars required
for package RKEA.","Imports":"rJava (>= 0.6-3)","License":"GPL-
2","NeedsCompilation":"no","Package":"RKEAjars","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"R\/KEA Interface Jars","Version":"5.0-1"},"RKEEL":
{"Author":"Jose Moyano [aut, cre], Luciano Sanchez Ramos [aut]","Depends":"R (>=
3.0)","Description":"KEEL is a popular Java software for a large number of
different knowledge data discovery tasks.\nThis package takes the advantages of
KEEL and R, allowing to use KEEL algorithms in simple R code.\nThe implemented R
code layer between R and KEEL makes easy both using KEEL algorithms in R as
implementing new algorithms for 'RKEEL' in a very simple way.\nIt includes more
than 100 algorithms for classification, regression and preprocess, which allows a
more complete experimentation process.\nFor more information about KEEL, see
<http:\/\/www.keel.es\/>.","Imports":"R6, XML, doParallel, foreach, gdata,
RKEELjars (>= 1.0.10),\nRKEELdata (>=
1.0.2)","License":"GPL","NeedsCompilation":"no","Package":"RKEEL","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Title":"Using Keel in R
Code","Version":"1.1.6"},"RKEELdata":{"Author":"Jose Moyano [aut, cre], Luciano
Sanchez Ramos [aut]","Description":"KEEL is a popular Java software for a large
number of different knowledge data discovery tasks. Furthermore, RKEEL is a package
with a R code layer between R and KEEL, for using KEEL in R code. This package
includes the datasets from KEEL in .dat format for its use in RKEEL package. For
more information about KEEL, see
<http:\/\/www.keel.es\/>.","License":"GPL","NeedsCompilation":"no","Package":"RKEEL
data","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Datasets from
KEEL for it Use in RKEEL","Version":"1.0.2"},"RKEELjars":{"Author":"Jose Moyano
[aut, cre], Luciano Sanchez Ramos [aut]","Description":"KEEL is a popular Java
software for a large number of different knowledge data discovery tasks.
Furthermore, 'RKEEL' is a package with a R code layer between R and KEEL, for using
KEEL in R code. This package downloads and install the .jar files necessary for
'RKEEL' algorithms execution. For more information about KEEL, see
<http:\/\/www.keel.es\/>.","Imports":"downloader","License":"GPL-
3","NeedsCompilation":"no","Package":"RKEELjars","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Java Executable .jar Files for
'RKEEL'","Version":"1.0.11"},"RKlout":{"Author":"Binayak Goswami","Description":"An
interface of R to Klout API v2. It fetches Klout Score for a Twitter
Username\/handle in real time. Klout is a website and mobile app that uses social
media analytics to rank its users according to online social influence via
the \"Klout Score\", which is a numerical value between 1 and 100. In determining
the user score, Klout measures the size of a user's social media network and
correlates the content created to measure how other users interact with that
content.","Imports":"RCurl","License":"GPL-
2","NeedsCompilation":"no","Package":"RKlout","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Fetch Klout Scores for Twitter
Users","Version":"1.0"},"RLRsim":{"Author":"Fabian Scheipl [aut, cre],\nBen Bolker
[aut]","Depends":"R (>= 2.14.0)","Description":"Rapid, simulation-based exact
(restricted) likelihood ratio tests\nfor testing the presence of variance
components\/nonparametric terms for\nmodels fit with nlme::lme(),lme4::lmer(),
gamm4::gamm4(), mgcv::gamm()
and\nSemiPar::spm().","Enhances":"SemiPar","Imports":"Rcpp (>= 0.11.1), lme4 (>=
1.1), mgcv,
nlme","License":"GPL","NeedsCompilation":"yes","Package":"RLRsim","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Title":"Exact (Restricted) Likelihood Ratio
Tests for Mixed and Additive\nModels","URL":"https:\/\/github.com\/fabian-
s\/RLRsim","Version":"3.1-2"},"RLogicalOps":{"Author":"Sunny Kumar
<sunny.nitie14@gmail.com>","Description":"Processing logical operations such as
AND\/OR\/NOT operations\ndynamically. It also handles nesting in the
operations.","Imports":"stringr,
rstackdeque","License":"GPL","NeedsCompilation":"no","Package":"RLogicalOps","Repos
itory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Process Logical
Operations","Version":"0.1"},"RLumModel":{"Author":"Johannes Friedrich [aut, trl,
cre],\nSebastian Kreutzer [aut, ths],\nChristoph Schmidt [aut, ths]","Depends":"R
(>= 3.2.3), utils, Luminescence (>= 0.5.1)","Description":"A collection of function
to simulate luminescence signals in the\nmineral quartz based on published
models.","Imports":"deSolve (>= 1.12), methods","License":"GPL-
3","NeedsCompilation":"no","Package":"RLumModel","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat","Title":"Modelling Ordinary Differential
Equations Leading to\nLuminescence","Version":"0.1.0"},"RLumShiny":
{"Author":"Christoph Burow [aut, cre],\nJan Odvarko [cph] (jscolor.js in
www\/jscolor),\nAnalytixWare [cph] (ShinySky package)","Depends":"R (>=
3.1.2)","Description":"A collection of 'shiny' applications for the R package
'Luminescence'.\nThese mainly, but not exclusively, include applications for
plotting chronometric\ndata from e.g. luminescence or radiocarbon dating. It
further provides access to\nbootstraps tooltip and popover functionality and
contains the 'jscolor.js' library\nwith a custom 'shiny' output
binding.","Imports":"Luminescence (>= 0.4.2), shiny (>= 0.11.1), digest,
googleVis,\nRCurl","License":"GPL-
3","NeedsCompilation":"no","Package":"RLumShiny","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"'Shiny' Applications for the R Package
'Luminescence'","URL":"https:\/\/github.com\/tzerk\/RLumShiny","Version":"0.1.0"},"
RM2":{"Author":"Tudor Bodea <tudor.bodea@ihg.com> & Dev
Koushik\n<dev.koushik@ihg.com> & Mark
Ferguson\n<mark.ferguson@mgt.gatech.edu>.","Depends":"R (>= 2.7.1),
msm","Description":"RM2 is a simple package that implements functions used
in\nrevenue management and pricing environments.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"RM2","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Revenue Management and Pricing
Package","Version":"0.0"},"RMAWGEN":{"Author":"Emanuele Cordano, Emanuele
Eccel","Depends":"R (>= 2.10),chron,date,vars,methods","Description":"S3 and S4
functions are implemented for spatial multi-site\nstochastic generation of daily
time series of temperature and\nprecipitation. These tools make use of Vector
AutoRegressive models (VARs).\nThe weather generator model is then saved as an
object and is calibrated by\ndaily instrumental \"Gaussianized\" time series
through the 'vars' package\ntools. Once obtained this model, it can it can be used
for weather\ngenerations and be adapted to work with several climatic monthly
time\nseries.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RMAWGEN","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"RgoogleMaps","Title":"Multi-site Auto-regressive
Weather
GENerator","URL":"https:\/\/github.com\/ecor\/RMAWGEN,\nhttps:\/\/docs.google.com\/
file\/d\/0B66otCUk3Bv6V3RPbm1mUG4zVHc\/edit,\nhttp:\/\/presentations.copernicus.org
\/EGU2012-14026_presentation.pdf,\nhttp:\/\/presentations.copernicus.org\/EGU2012-
5404_presentation.pdf","Version":"1.3.0"},"RMC":{"Author":"Scott D.
Foster","Description":"Functions for fitting, diagnosing and predicting from
a\nclass of Markov models.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"RMC","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Functions for fitting Markov
models","Version":"0.2"},"RMKdiscrete":{"Author":"Robert M. Kirkpatrick
<rkirkpatrick2@vcu.edu>","Depends":"stats, R (>= 2.15.0)","Description":"Sundry
discrete probability distributions and helper functions.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"RMKdiscrete","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Sundry Discrete Probability
Distributions","Version":"0.1"},"RMOA":{"Author":"Jan Wijffels [aut, cre],\nBNOSAC
[cph]","Depends":"RMOAjars (>= 1.0), rJava (>= 0.6-3),
methods","Description":"Connect R with MOA (Massive Online Analysis
-\nhttp:\/\/moa.cms.waikato.ac.nz) to build classification models and\nregression
models on streaming data or out-of-RAM data","License":"GPL-
3","NeedsCompilation":"no","Package":"RMOA","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"ff","Title":"Connect R with MOA for Massive Online
Analysis","URL":"http:\/\/www.bnosac.be,
https:\/\/github.com\/jwijffels\/RMOA,\nhttp:\/\/moa.cms.waikato.ac.nz\/","Version"
:"1.0"},"RMOAjars":{"Author":"See file AUTHORS","Depends":"R (>=
2.6.0)","Description":"External jars required for package RMOA. RMOA is a framework
to\nbuild data stream models on top of MOA (Massive Online Analysis
-\nhttp:\/\/moa.cms.waikato.ac.nz)","Imports":"rJava (>= 0.6-3)","License":"GPL-
3","NeedsCompilation":"no","Package":"RMOAjars","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"External jars required for package
RMOA","URL":"http:\/\/moa.cms.waikato.ac.nz\/,
https:\/\/github.com\/jwijffels\/RMOA","Version":"1.0"},"RMRAINGEN":
{"Author":"Emanuele Cordano","Depends":"R (>= 3.0), copula,
RGENERATE,RMAWGEN,blockmatrix,Matrix","Description":"This package contains
functions and S3 methods for spatial\nmulti-site stochastic generation of daily
precipitation. It generates\nprecipitation occurrence in several sites using Wilks'
Approach (1998).\nBugs\/comments\/questions\/collaboration of any kind are warmly
welcomed.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RMRAINGEN","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"RMRAINGEN (R Multi-site RAINfall GENeretor): a package
to\ngenerate daily time series of rainfall from monthly mean
values","URL":"https:\/\/github.com\/ecor\/RMRAINGEN","Version":"1.0"},"RMTstat":
{"Author":"Iain M. Johnstone, Zongming Ma, Patrick O. Perry and Morteza
Shahram.","Description":"\nFunctions for working
with the Tracy-Widom laws and other distributions\nrelated to the eigenvalues of
large Wishart matrices.\nThe tables for computing the Tracy-Widom densities and
distribution\nfunctions were computed by Momar Dieng's MATLAB
package \"RMLab\"\n(formerly available on his homepage
at\nhttp:\/\/math.arizona.edu\/~momar\/research.htm ).\nThis package is part of a
collaboration between Iain Johnstone,\nZongming Ma, Patrick Perry, and Morteza
Shahram. It will soon be\nreplaced by a package with more accuracy and built-in
support for\nrelevant statistical tests.","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"RMTstat","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Distributions, Statistics and Tests derived from
Random Matrix\nTheory","Version":"0.3"},"RMallow":{"Author":"Erik
Gregory","Depends":"combinat","Description":"An EM algorithm to fit Mallows' Models
to full or partial\nrankings, with or without ties.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RMallow","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Fit Multi-Modal Mallows' Models to ranking
data","Version":"1.0"},"RMark":{"Author":"Jeff Laake <jeff.laake@noaa.gov> with
code contributions from Eldar\nRakhimberdiev, Ben Augustine and Daniel Turek, and
example data and\nanalysis from Bret Collier, Jay Rotella, David Pavlacky,Andrew
Paul and Luke Eberhart-Phillips.","Depends":"R (>= 2.13.0),
snowfall","Description":"An interface to the software package MARK that constructs
input\nfiles for MARK and extracts the output. MARK was developed by Gary
White\nand is freely available at
(http:\/\/www.phidot.org\/software\/mark\/downloads\/)\nbut is not open
source.","Imports":"parallel, matrixcalc, msm, coda","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RMark","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"lattice, splines, nlme, plotrix","Title":"R Code for
Mark Analysis","Version":"2.1.14"},"RMediation":{"Author":"Davood Tofighi
<dtofighi@unm.com> and David P. MacKinnon\n<davidpm@asu.edu>","Depends":"R (>=
2.11.0), base, MASS, lavaan, e1071","Description":"We provide functions to compute
confidence\nintervals (CIs) for a well-defined nonlinear function of the
model\nparameters (e.g., product of k coefficients) in single--level
and\nmultilevel structural equation models.","License":"GPL-
2","NeedsCompilation":"no","Package":"RMediation","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Mediation Analysis Confidence
Intervals","URL":"http:\/\/amp.gatech.edu\/RMediation
http:\/\/amp.gatech.edu\/MonteCarlo\nhttp:\/\/www.public.asu.edu\/~davidpm\/ripl\/P
rodclin","Version":"1.1.4"},"RMixpanel":{"Author":"Meinhard Ploner","Depends":"R
(>= 3.2.0)","Description":"Provides an interface to many endpoints of Mixpanel's
Data Export and Engage API. The R functions allow for event and profile data export
as well as for segmentation, retention and addiction analysis. Results are always
parsed into convenient R objects. Furthermore it is possible to load and update
profiles.","Imports":"digest, jsonlite, uuid, RCurl","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"RMixpanel","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"R API for Mixpanel","URL":"https:\/\/www.r-
project.org, https:\/\/github.com\/7factory\/RMixpanel","Version":"0.2-
1"},"RMongo":{"Author":"Tommy Chheng","Depends":"R(>= 2.14.1), rJava,
methods","Description":"MongoDB Database interface for R. The interface is provided
via Java calls to the mongo-java-driver.","License":"GPL-
3","NeedsCompilation":"no","Package":"RMongo","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"RUnit","Title":"MongoDB Client for
R","URL":"http:\/\/github.com\/tc\/RMongo","Version":"0.0.25"},"RMySQL":
{"Author":"Jeroen Ooms [aut, cre],\nDavid James [aut],\nSaikat DebRoy
[aut],\nHadley Wickham [aut],\nJeffrey Horner [aut],\nRStudio [cph]","Depends":"R
(>= 2.8.0), DBI (>= 0.3.1)","Description":"Implements 'DBI' Interface to 'MySQL'
and 'MariaDB' Databases.","Imports":"methods","License":"GPL-
2","NeedsCompilation":"yes","Package":"RMySQL","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat","Title":"Database Interface and 'MySQL'
Driver for R","URL":"https:\/\/github.com\/rstats-
db\/rmysql,\nhttps:\/\/downloads.mariadb.org\/connector-
c\/","Version":"0.10.8"},"RNCBIEUtilsLibs":{"Author":"Martin Schumann","Depends":"R
(>= 2.9.0), rJava (>= 0.8)","Description":"Provides the libraries of the EUtils
operations for the\nRNCBI package.","Imports":"methods","License":"GPL-
3","NeedsCompilation":"no","Package":"RNCBIEUtilsLibs","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"EUtils libraries for use in the R
environment","URL":"https:\/\/code.google.com\/p\/rncbi\/","Version":"0.9"},"RNCEP"
:{"Author":"Michael U. Kemp <mukemp+RNCEP@gmail.com> with contributions from E.
Emiel van Loon, Judy Shamoun-Baranes, and Willem Bouten","Depends":"R (>= 2.10),
maps","Description":"This package contains functions to retrieve, organize, and
visualize weather data from the NCEP\/NCAR Reanalysis
(http:\/\/www.esrl.noaa.gov\/psd\/data\/gridded\/data.ncep.reanalysis.html) and
NCEP\/DOE Reanalysis II
(http:\/\/www.esrl.noaa.gov\/psd\/data\/gridded\/data.ncep.reanalysis2.html)
datasets. Data are queried via the Internet and may be obtained for a specified
spatial and temporal extent or interpolated to a point in space and time. We also
provide functions to visualize these weather data on a map. There are also
functions to simulate flight trajectories according to specified behavior using
either NCEP wind data or data specified by the user.","Imports":"RColorBrewer,
abind, fields, fossil, tgp, tcltk, graphics, sp","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RNCEP","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Obtain, Organize, and Visualize NCEP Weather
Data","URL":"http:\/\/www.esrl.noaa.gov\/psd\/data\/gridded\/reanalysis\/\nhttp:\/\
/sites.google.com\/site\/michaelukemp\/rncep","Version":"1.0.7"},"RND":
{"Author":"Kam Hamidieh <kh@zoolytics.com>","Depends":"R (>=
3.0.1)","Description":"This package is a collection of various functions to extract
the implied risk neutral density from option.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RND","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Risk Neutral Density Extraction
Package","Version":"1.1"},"RNaviCell":{"Author":"Eric Bonnet [aut, cre],\nPaul
Deveau [aut]","Depends":"R (>= 2.14.0), RCurl, RJSONIO","Description":"Provides a
set of functions to access a data visualization web service. For more information
and a tutorial on how to use it, see
https:\/\/navicell.curie.fr\/pages\/nav_web_service.html and
https:\/\/github.com\/sysbio-
curie\/RNaviCell.","Imports":"methods","License":"LGPL-2.1 | file
LICENSE","NeedsCompilation":"no","Package":"RNaviCell","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Visualization of High-Throughput Data on Large-
Scale Biological\nNetworks","Version":"0.2"},"RNeXML":{"Author":"Carl Boettiger
[cre, aut],\nScott Chamberlain [aut],\nHilmar Lapp [aut],\nKseniia Shumelchyk
[aut],\nRutger Vos [aut]","Depends":"R (>= 3.0.0), ape (>= 3.1), methods (>=
3.0.0)","Description":"Provides access to phyloinformatic data in 'NeXML' format.
The\npackage should add new functionality to R such as the possibility
to\nmanipulate 'NeXML' objects in more various and refined way and
compatibility\nwith 'ape' objects.","Imports":"XML (>= 3.95), plyr (>= 1.8), taxize
(>= 0.2.2), reshape2 (>=\n1.2.2), httr (>= 0.3), uuid (>= 0.1-1), dplyr (>=
0.4.0),\nlazyeval (>= 0.1.0), tidyr (>= 0.3.1), stringr (>=
1.0)","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"RNeXML","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"rrdf (>= 2.0.2), geiger (>= 2.0), phytools (>=
0.3.93), knitr\n(>= 1.5), rfigshare (>= 0.3.0), knitcitations (>= 1.0.1),\ntestthat
(>= 0.10.0), phylobase (>= 0.6.8), rmarkdown (>=\n0.3.3), Sxslt (>=
0.91)","Title":"Semantically Rich I\/O for the 'NeXML'
Format","URL":"https:\/\/github.com\/ropensci\/RNeXML","Version":"2.0.6"},"RNeo4j":
{"Author":"Nicole White","Description":"Neo4j, a graph database, allows users to
store their data as a property graph. A graph consists of nodes that are connected
by relationships; both nodes and relationships can have properties, or key-value
pairs. RNeo4j is Neo4j's R driver. It allows users to read and write data from and
to Neo4j directly from their R environment by exposing an interface for interacting
with nodes, relationships, paths, and more. Most notably, it allows users to
retrieve Cypher query results as R data frames, where Cypher is Neo4j's graph query
language. Visit <http:\/\/www.neo4j.com> to learn more about
Neo4j.","Imports":"httr (>= 1.1.0), jsonlite, rstudioapi","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"RNeo4j","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat","Title":"Neo4j Driver for
R","URL":"http:\/\/github.com\/nicolewhite\/RNeo4j","Version":"1.6.4"},"RNetCDF":
{"Author":"Pavel Michna, with contributions from Milton Woods","Depends":"R (>=
2.5.0)","Description":"An interface to the NetCDF file format designed by
Unidata\nfor efficient storage of array-oriented scientific data and
descriptions.\nThe R interface is closely based on the C API of the NetCDF
library,\nand it includes calendar conversions from the Unidata UDUNITS
library.\nThe current implementation supports all operations on NetCDF datasets\nin
classic and 64-bit offset file formats, and NetCDF4-classic format\nis supported
for reading and modification of existing files.","License":"GPL (>= 2) | file
LICENSE","NeedsCompilation":"yes","Package":"RNetCDF","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Interface to NetCDF
Datasets","URL":"http:\/\/rnetcdf.r-forge.r-
project.org\nhttp:\/\/www.unidata.ucar.edu\/software\/netcdf\/\nhttp:\/\/www.uni
data.ucar.edu\/software\/udunits\/","Version":"1.8-2"},"RNetLogo":{"Author":"Jan C.
Thiele","Depends":"R (>= 3.2.2), rJava (>= 0.9-8), igraph","Description":"Interface
to use and access Wilensky's NetLogo (Wilensky 1999) from R using either headless
(no GUI) or interactive GUI mode. Provides functions to load models, execute
commands, and get values from reporters. Mostly analogous to the NetLogo
Mathematica Link https:\/\/github.com\/NetLogo\/Mathematica-Link.","License":"GPL-
2","NeedsCompilation":"no","Package":"RNetLogo","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"parallel","Title":"Provides an Interface to the Agent-
Based Modelling Platform\nNetLogo","URL":"http:\/\/rnetlogo.r-forge.r-
project.org\/","Version":"1.0-2"},"RNewsflow":{"Author":"Kasper Welbers & Wouter
van Atteveldt","Depends":"R (>= 3.2.0), tm, igraph, Matrix","Description":"A
collection of tools for measuring the similarity of news content and tracing the
flow of (news) messages over\ntime and across media.","Imports":"plyr, slam,
scales, wordcloud, data.table, methods","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"RNewsflow","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"knitr, rmarkdown, RTextTools","Title":"Tools
for Analyzing Content Homogeneity and News Diffusion using\nComputational Text
Analysis","Version":"1.0.1"},"RNiftyReg":{"Author":"Jon Clayden, based on original
code by Marc Modat, Pankaj Daga and\nothers","Description":"Provides an R interface
to the NiftyReg image registration
tools\n<http:\/\/sourceforge.net\/projects\/niftyreg\/>. Linear and nonlinear
registration\nare supported, in two and three
dimensions.","Enhances":"oro.nifti","Imports":"Rcpp (>= 0.11.0), ore, splines,
2","NeedsCompilation":"yes","Package":"RNiftyReg","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"jpeg, png, mmand, testthat (>=
0.11.0)","Title":"Image Registration Using the NiftyReg
Library","URL":"https:\/\/github.com\/jonclayden\/RNiftyReg","Version":"2.2.0"},"RO
Auth":{"Author":"Jeff Gentry <geoffjentry@gmail.com>, Duncan Temple
Lang\n<duncan@r-project.org>","Depends":"R (>= 2.12.0)","Description":"Provides an
interface to the OAuth 1.0 specification\nallowing users to authenticate via OAuth
to the\nserver of their choice.","Imports":"RCurl, digest,
methods","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"ROAuth","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"R Interface For OAuth","Version":"0.9.6"},"ROC632":
{"Author":"Y. Foucher <Yohann.Foucher@univ-nantes.fr>","Depends":"R (>= 2.10),
splines, survival, penalized, survivalROC","Description":"This package computes
traditional ROC curves and time-dependent ROC curves using the cross-validation,
the 0.632 and the 0.632+ estimators. The 0.632+ estimator of time-dependent ROC
curve is useful to estimate the predictive accuracy of prognostic signature based
on high-dimensional data. For instance, it outperforms the other approaches,
especially the cross-validation solution which is often used. The 0.632+ estimators
correct the area under the curve in order to adequately estimate the prognostic
capacities regardless of the overfitting level. This package also allows for the
construction of diagnostic or prognostic scoring systems (penalized regressions).
The methodology is adapted to complete data (penalized logistic regression
associated with ROC curve) or incomplete time-to-event data (penalized Cox model
associated with time-dependent ROC curve).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ROC632","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Construction of diagnostic or prognostic scoring system
and\ninternal validation of its discriminative capacities based on\nROC curve and
0.633+ boostrap resampling","URL":"www.r-project.org,
www.divat.fr","Version":"0.6"},"ROCR":{"Author":"Tobias Sing, Oliver Sander, Niko
Beerenwinkel, Thomas Lengauer","Depends":"gplots, methods","Description":"ROC
graphs, sensitivity\/specificity curves, lift charts,\nand precision\/recall plots
are popular examples of trade-off\nvisualizations for specific pairs of performance
measures. ROCR is a\nflexible tool for creating cutoff-parameterized 2D performance
curves\nby freely combining two from over 25 performance measures (new\nperformance
measures can be added using a standard interface).\nCurves from different cross-
validation or bootstrapping runs can be\naveraged by different methods, and
standard deviations, standard\nerrors or box plots can be used to visualize the
variability across\nthe runs. The parameterization can be visualized by printing
cutoff\nvalues at the corresponding curve positions, or by coloring the\ncurve
according to cutoff. All components of a performance plot can\nbe quickly adjusted
using a flexible parameter dispatching\nmechanism. Despite its flexibility, ROCR is
easy to use, with only\nthree commands and reasonable default values for all
optional\nparameters.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ROCR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Visualizing the Performance of Scoring
Classifiers","URL":"http:\/\/rocr.bioinf.mpi-sb.mpg.de\/","Version":"1.0-
7"},"ROCS":{"Author":"Tianwei Yu","Depends":"rgl","Description":"Plots the Receiver
Operating Characteristics Surface for high-throughput class-skewed data, calculates
the Volume under the Surface (VUS) and the FDR-Controlled Area Under the Curve
(FCAUC), and conducts tests to compare two ROC surfaces.","License":"GPL-
2","NeedsCompilation":"no","Package":"ROCS","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Receiver Operating Characteristics
Surface","Version":"1.2"},"ROCt":{"Author":"Y. Foucher, E. Dantan, P. Tessier, F.
Le Borgne, and M. Lorent","Depends":"R (>= 2.10), splines, date, survival, relsurv,
timereg","Description":"Contains functions in order to estimate diagnostic and
prognostic capacities of continuous markers. More precisely, one function concerns
the estimation of time-dependent ROC (ROCt) curve, as proposed by Heagerty et al.
(2000) <DOI: 10.1111\/j.0006-341X.2000.00337.x>. One function concerns the
adaptation of the ROCt theory for studying the capacity of a marker to predict the
excess of mortality of a specific population compared to the general population.
This last part is based on additive relative survival models and the work of Pohar-
Perme et al. (2012) <DOI: 10.1111\/j.1541-0420.2011.01640.x>. We also propose two
functions for cut-off estimation in medical decision making by maximizing time-
dependent expected utility function. Finally, we propose confounder-adjusted
estimators of ROC and ROCt curves by using the Inverse Probability Weighting (IPW)
approach. For the confounder-adjusted ROC curve (without censoring), we also
proposed the implementation of the estimator based on placement values proposed by
Pepe and Cai (2004) <DOI: 10.1111\/j.0006-341X.2004.00200.x>.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ROCt","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Time-Dependent ROC Curve Estimators and Expected
Utility\nFunctions","URL":"www.r-project.org,
www.divat.fr","Version":"0.9.4"},"ROCwoGS":{"Author":"Chong Wang
<chwang@iastate.edu>","Description":"Function to estimate the ROC Curve of a
continuous-scaled\ndiagnostic test with the help of a second imperfect
diagnostic\ntest with binary responses.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ROCwoGS","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Non-parametric estimation of ROC curves without Gold
Standard\nTest","Version":"1.0"},"RODBC":{"Author":"Brian Ripley [aut,
cre],\nMichael Lapsley [aut] (1999 to Oct 2002)","Depends":"R (>=
3.0.0)","Description":"An ODBC database
interface.","Imports":"stats","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"RODBC","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"ODBC Database Access","Version":"1.3-12"},"RODBCDBI":
{"Author":"Nagi Teramo [aut, cre],\nShinichi Takayanagi [aut]","Description":"An
implementation of R's DBI interface using ODBC package as a\nback-end. This allows
R to connect to any DBMS that has a ODBC driver.","Imports":"methods, DBI,
RODBC","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"RODBCDBI","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat","Title":"Provides Access to Databases
Through the ODBC Interface","Version":"0.1.1"},"RODBCext":{"Author":"Mateusz Zoltak
[aut, cre],\nBrian Ripley [aut],\nMichael Lapsley [aut]","Depends":"R (>= 3.0.0),
RODBC (>= 1.3.0)","Description":"An extension for RODBC package adding support for
parameterized\nqueries.","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"RODBCext","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr","Title":"Parameterized Queries Extension for
RODBC","Version":"0.2.5"},"RODM":{"Author":"Pablo Tamayo <pablo.tamayo@oracle.com>
and Ari Mozes\n<ari.mozes@oracle.com>","Depends":"R (>= 2.10.1),
RODBC","Description":"This package implements an interface to Oracle Data
Mining\n(ODM). It provides an ideal environment for rapid development\nof demos and
proof of concept data mining studies. It\nfacilitates the prototyping of vertical
applications and makes\nODM and the RDBMS environment easily accessible
to\nstatisticians and data analysts familiar with R but not fluent\nin SQL or
familiar with the database environment. It also\nfacilitates the benchmarking and
testing of ODM functionality\nincluding the production of summary statistics,
performance\nmetrics and graphics. It enables the scripting and control
of\nproduction data mining methodologies from a high-level\nenvironment. Oracle
Data Mining (ODM) is an option of Oracle\nRelational Database Management System
(RDBMS) Enterprise\nEdition (EE).
It contains several data mining and data analysis\nalgorithms for classification,
prediction, regression,\nclustering, associations, feature selection, anomaly
detection,\nfeature extraction, and specialized analytics. It provides\nmeans for
the creation, management and operational deployment\nof data mining models inside
the database environment. For more\ninformation consult the entry for \"Oracle Data
Mining\" in\nWikipedia (en.wikipedia.org).","License":"LGPL (>=
2)","NeedsCompilation":"no","Package":"RODM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"RODBC, mlbench, verification, PASWR,
scatterplot3d","Title":"R interface to Oracle Data Mining","URL":"http:\/\/www.r-
project.org","Version":"1.1"},"ROI":{"Author":"Kurt Hornik [aut],\nDavid Meyer
[aut],\nStefan Theussl [aut, cre]","Description":"The R Optimization Infrastructure
(ROI) package provides a\nsophisticated framework for handling optimization
problems in R.","Imports":"methods, registry, slam","License":"GPL-
3","NeedsCompilation":"no","Package":"ROI","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"ROI.plugin.glpk, ROI.plugin.symphony,
ROI.plugin.quadprog,\nnumDeriv","Title":"R Optimization
Infrastructure","URL":"http:\/\/R-Forge.R-
project.org\/projects\/roi","Version":"0.1-0"},"ROI.plugin.glpk":{"Author":"Stefan
Theussl [aut, cre]","Description":"This package enhances the R Optimization
Infrastructure (ROI) package\nwith the GLPK solver for solving mixed integer linear
programming (MILP)\nproblems as well as all variants\/combinations of LP,
IP.","Imports":"methods, ROI (>= 0.1-0), Rglpk","License":"GPL-
3","NeedsCompilation":"no","Package":"ROI.plugin.glpk","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"ROI-plugin GLPK","URL":"http:\/\/R-Forge.R-
project.org\/projects\/roi","Version":"0.0-2"},"ROI.plugin.quadprog":
{"Author":"Stefan Theussl [aut, cre]","Description":"This package enhances the R
Optimization Infrastructure (ROI) package\nwith the quadprog solver for solving
quadratic programming (QP)\nproblems.","Imports":"methods, quadprog, ROI (>= 0.1-
0), slam","License":"GPL-
3","NeedsCompilation":"no","Package":"ROI.plugin.quadprog","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Title":"ROI-plugin quadprog","URL":"http:\/\/R-
Forge.R-project.org\/projects\/roi","Version":"0.0-2"},"ROI.plugin.symphony":
{"Author":"Stefan Theussl [aut, cre]","Description":"This package enhances the R
Optimization Infrastructure (ROI) package\nwith the symphony solver from the COIN-
OR suite for solving mixed integer\nlinear programming (MILP) problems as well as
all variants\/combinations of LP, IP.","Imports":"methods, ROI (>= 0.1-0),
Rsymphony, slam","License":"GPL-
3","NeedsCompilation":"no","Package":"ROI.plugin.symphony","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Title":"ROI-plugin symphony","URL":"http:\/\/R-
Forge.R-project.org\/projects\/roi","Version":"0.0-2"},"ROMIplot":{"Author":"Roland
Rau, Tim Riffe","Depends":"MortalitySmooth, RCurl","Description":"Provides the
possibility to plot Lexis surface maps (heat maps) of rates of mortality
improvement. Raw data to be plotted can be read from the Human Mortality Database
using code originally written by Tim Riffe. The European Research Council has
provided financial support under the European Community's Seventh Framework
Programme (FP7\/2007-2013) \/ ERC grant agreement no. 263744.","License":"GPL-
2","NeedsCompilation":"no","Package":"ROMIplot","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Plots Surfaces of Rates of Mortality
Improvement","Version":"1.0"},"ROSE":{"Author":"Nicola Lunardon, Giovanna Menardi,
Nicola Torelli","Description":"The package provides functions to deal with binary
classification\nproblems in the presence of imbalanced classes. Synthetic balanced
samples are\ngenerated according to ROSE (Menardi and Torelli, 2013).\nFunctions
that implement more traditional remedies to the class imbalance\nare also provided,
as well as different metrics to evaluate a learner accuracy.\nThese are estimated
by holdout, bootstrap or cross-validation methods.","License":"GPL-
2","NeedsCompilation":"no","Package":"ROSE","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"MASS, nnet, rpart, tree","Title":"ROSE: Random Over-
Sampling Examples","Version":"0.0-3"},"RObsDat":{"Author":"Dominik
Reusser","Depends":"R (>= 2.11.0), methods, zoo","Description":"Data management in
hydrology and other fields is facilitated with functions to enter and modify data
in a database according to the Observations Data Model (ODM) standard by CUASHI
(Consortium of Universities for the Advancement of Hydrologic Science). While this
data model has been developed in hydrology, it is also useful for other fields.
RObsDat helps in the setup of the database within one of the free database systems
MariaDB, PostgreSQL or SQLite. It imports the controlled water vocabulary from the
CUASHI web service and provides a smart interface between the analyst and the
database: Already existing data entries are detected and duplicates avoided. The
data import function converts different data table designs to make import simple.
Cleaning and modifications of data are handled with a simple version control
system. Variable and location names are treated in a user friendly way, accepting
and processing multiple versions. When querying data from the database, it is
stored in a spacetime objects within R for subsequent
processing.","Imports":"spacetime, xts, DBI, vwr, e1071,
sp","License":"GPL","NeedsCompilation":"no","Package":"RObsDat","Repository":"http:
\/\/cran.csiro.au\/src\/contrib","Suggests":"RSQLite, testthat, RColorBrewer,
maptools, SSOAP, XML,\ngeonames","Title":"Data Management for Hydrology and Beyond
Using the Observations\nData Model","Version":"16.03"},"ROpenWeatherMap":
{"Author":"Mukul Chaware[aut,cre]","Description":"OpenWeatherMap (OWM)
<http:\/\/openweathermap.org\/api> is a service providing weather related
data.\nThis package can be used to access current weather data for one location or
several locations.\nIt can also be used to forecast weather for 5 days with data
for every 3 hours.","Imports":"httr,RCurl,jsonlite","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"ROpenWeatherMap","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Title":"R Interface to OpenWeatherMap
API","Version":"1.1"},"ROptEst":{"Author":"Matthias Kohl, Peter
Ruckdeschel","Depends":"R(>= 2.14.0), methods, distr(>= 2.5.2), distrEx(>=
2.4),\ndistrMod(>= 2.5.2), RandVar(>= 0.9.2), RobAStBase(>=
0.9)","Description":"Optimally robust estimation in general smoothly parameterized
models using S4 classes and methods.","License":"LGPL-
3","NeedsCompilation":"no","Package":"ROptEst","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"RobLox, MASS","Title":"Optimally robust
estimation","URL":"http:\/\/robast.r-forge.r-
project.org\/","Version":"0.9"},"ROptEstOld":{"Author":"Matthias
Kohl","Depends":"R(>= 2.14.0), methods, distr(>= 2.5.2), distrEx(>=
2.4),\nRandVar(>= 0.9.2), evd","Description":"Optimally robust estimation using S4
classes and methods. Old version still needed\nfor current versions of ROptRegTS
and RobRex.","License":"LGPL-
3","NeedsCompilation":"no","Package":"ROptEstOld","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Optimally robust estimation - old
version","URL":"http:\/\/robast.r-forge.r-
project.org\/","Version":"0.9.2"},"ROptRegTS":{"Author":"Matthias Kohl
<Matthias.Kohl@stamats.de>, Peter Ruckdeschel","Depends":"R (>= 2.14.0),
ROptEstOld(>= 0.9.2)","Description":"Optimally robust estimation for regression-
type models using S4 classes and\nmethods","Imports":"methods, RandVar(>= 0.9.2),
distr(>= 2.5.2), distrEx(>= 2.4)","License":"LGPL-
3","NeedsCompilation":"no","Package":"ROptRegTS","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Optimally robust estimation for regression-type
models","URL":"http:\/\/robast.r-forge.r-
project.org\/","Version":"0.9.1"},"ROptimizely":{"Author":"Keerthi Chandra [aut,
cre],\nChris Johannessen [aut],\nSiddharth Somayajula [ctb]","Depends":"R (>=
3.0.0)","Description":"R package extracts optimizely test results and test
information using Optimizely REST API. Only read functionality is supported for
analysis and reporting.","Imports":"httr, jsonlite","License":"GPL-
2","NeedsCompilation":"no","Package":"ROptimizely","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"R Optimizely
API","URL":"https:\/\/github.com\/kanaku\/ROptimizely","Version":"0.2.0"},"ROracle"
:{"Author":"Denis Mukhin, David A. James and Jake Luciani","Depends":"methods, DBI
(>= 0.2-5)","Description":"Oracle Database interface (DBI) driver for R.\nThis is a
DBI-compliant Oracle driver based on the
OCI.","Imports":"utils","License":"LGPL","NeedsCompilation":"yes","Package":"ROracl
e","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"OCI Based Oracle
Database Interface for R","URL":"http:\/\/www.oracle.com","Version":"1.2-
2"},"RPANDA":{"Author":"HÃ©lÃ¨ne Morlon [aut, cre, cph]","Depends":"R (>= 2.14.2),
picante","Description":"Implements macroevolutionary analyses on phylogenetic
trees. See Morlon et al. (2010) <DOI:10.1371\/journal.pbio.1000493>, Morlon et al.
(2011) <DOI:10.1073\/pnas.1102543108>, Condamine et al. (2013)
<DOI:10.1111\/ele.12062>, Morlon et al. (2014) <DOI:10.1111\/ele.12251>, Manceau et
al. (2015) <DOI:10.1111\/ele.12415>, Lewitus & Morlon (2016)
<DOI:10.1093\/sysbio\/syv116>, and Drury et al. (2016)
<DOI:10.1093\/sysbio\/syw020>.","Imports":"ape, pspline, deSolve, igraph, TESS,
cluster, fpc, pvclust,\ncorpcor, phytools, stats, graphics, grDevices,
2","NeedsCompilation":"no","Package":"RPANDA","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat","Title":"Phylogenetic ANalyses of
DiversificAtion","URL":"https:\/\/github.com\/hmorlon\/PANDA","Version":"1.2"},"RPC
LR":{"Author":"Raji
Balasubramanian","Depends":"MASS, survival","Description":"This package implements
the R-PCLR (Random-Penalized\nConditional Logistic Regression) algorithm for
obtaining\nvariable importance. The algorithm is applicable for the\nanalysis of
high dimensional data from matched case-control\nstudies.","License":"GPL-
2","NeedsCompilation":"no","Package":"RPCLR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"RPCLR (Random-Penalized Conditional Logistic
Regression)","Version":"1.0"},"RPEnsemble":{"Author":"Timothy I. Cannings and
Richard J. Samworth","Depends":"R (>= 3.0.0), MASS","Description":"Implements the
methodology of \"Cannings, T. I. and Samworth, R. J. (2015) Random projection
ensemble classification. http:\/\/arxiv.org\/abs\/1504.04595\". The random
projection ensemble classifier is a very general method for classification of high-
dimensional data, based on careful combination of the results of applying an
arbitrary base classifier to random projections of the feature vectors into a
lower-dimensional space. The random projections are divided into non-overlapping
blocks, and within each block the projection yielding the smallest estimate of the
test error is selected. The random projection ensemble classifier then aggregates
the results of applying the base classifier on the selected projections, with a
data-driven voting threshold to determine the final assignment.","Imports":"class,
parallel, stats","License":"GPL-
3","NeedsCompilation":"no","Package":"RPEnsemble","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Random Projection Ensemble
Classification","URL":"http:\/\/arxiv.org\/abs\/1504.04595,\nhttp:\/\/www.statslab.
cam.ac.uk\/~tc325\/","Version":"0.2"},"RPMG":{"Author":"Jonathan M.
Lees","Description":"Really Poor Man's Graphical User Interface, used to create
interactive R analysis sessions with simple R commands.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RPMG","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Graphical User Interface (GUI) for Interactive R
Analysis\nSessions","Version":"2.2-1"},"RPMM":{"Author":"E. Andres Houseman, Sc.D.
and Devin C. Koestler, Ph.D.","Depends":"R (>= 2.3.12),
cluster","Description":"\nRecursively Partitioned Mixture Model for Beta and
Gaussian Mixtures.\nThis is a model-based clustering algorithm that returns a
hierarchy\nof classes, similar to hierarchical clustering, but also similar
to\nfinite mixture models.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RPMM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Recursively Partitioned Mixture
Model","Version":"1.20"},"RPPairwiseDesign":{"Author":"Mohamed Laib, Imane Rezgui
and Zebida Gheribi-Aoulmi","Description":"Using some association schemes to obtain
a new series of resolvable partially pairwise balanced designs (RPPBD) and space-
filling designs.","License":"GPL-
3","NeedsCompilation":"no","Package":"RPPairwiseDesign","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Resolvable partially pairwise balanced design and
Space-filling\ndesign via association scheme","Version":"1.0"},"RPPanalyzer":
{"Author":"Heiko Mannsperger with contributions of Stephan Gade","Depends":"R (>=
2.14)","Description":"Reads in sample description and slide description files
and\nannotates the expression values taken from GenePix results files\n(text file
format used by many microarray scanner and software providers).\nAfter
normalization data can be visualized as boxplot, heatmap or
dotplot.","Imports":"quantreg, limma, lattice, stats4, gam, gplots, grid,
ggplot2,\nHmisc, Biobase, methods, utils,
graphics","License":"LGPL","NeedsCompilation":"no","Package":"RPPanalyzer","Reposit
ory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Reads, Annotates, and
Normalizes Reverse Phase Protein Array\nData","Version":"1.4.3"},"RPostgreSQL":
{"Author":"Joe Conway, Dirk Eddelbuettel, Tomoaki Nishiyama, Sameer Kumar\nPrayaga
(during 2008), Neil Tiffin","Depends":"R (>= 2.9.0), methods, DBI (>= 0.1-
4)","Description":"Database interface and PostgreSQL driver for R This\npackage
provides a Database Interface (DBI) compliant driver\nfor R to access PostgreSQL
database systems.\n\nIn order to build and install this package from source,
PostgreSQL\nitself must be present your system to provide PostgreSQL\nfunctionality
via its libraries and header files. These files\nare provided as postgresql-devel
package under some Linux\ndistributions.\n\nOn Microsoft Windows system the
attached libpq library source will be\nused.\n\nA wiki and issue tracking system
for the package are available at\nGoogle Code at
https:\/\/code.google.com\/p\/rpostgresql\/ .","License":"GPL-2 | file
LICENSE","NeedsCompilation":"yes","Package":"RPostgreSQL","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"R interface to the PostgreSQL database
system","URL":"https:\/\/code.google.com\/p\/rpostgresql\/,\nhttp:\/\/www.stat.bell
-labs.com\/RS-DBI, http:\/\/www.postgresql.org","Version":"0.4"},"RPresto":
{"Author":"Onur Ismail Filiz [aut, cre],\nSergey Goder [aut],\nJohn Myles White
[ctb]","Depends":"R (>= 3.1.0), methods","Description":"Implements a 'DBI'
compliant interface to Presto. Presto is\nan open source distributed SQL query
engine for running interactive\nanalytic queries against data sources of all sizes
ranging from\ngigabytes to petabytes: <https:\/\/prestodb.io\/>.","Imports":"DBI
(>= 0.3.0), httr (>= 0.6), RCurl, jsonlite, stringi, stats","License":"BSD_3_clause
+ file
LICENSE","NeedsCompilation":"no","Package":"RPresto","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat, dplyr (>= 0.4.3)","Title":"DBI
Connector to
Presto","URL":"https:\/\/github.com\/prestodb\/RPresto","Version":"1.2.1"},"RProtoB
uf":{"Author":"Romain Francois, Dirk Eddelbuettel, Murray Stokely and Jeroen
Ooms","Depends":"R (>= 3.0.0), methods","Description":"Protocol Buffers are a way
of encoding structured data in an\nefficient yet extensible format. Google uses
Protocol Buffers for almost all\nof its internal RPC protocols and file formats.
Additional\ndocumentation is available in the arXiv.org
preprint \"RProtoBuf:\nEfficient Cross-Language Data Serialization in R\" by
Eddelbuettel,\nStokely, and Ooms (2014) at
<http:\/\/arxiv.org\/abs\/1401.7372>.","Imports":"utils, stats, tools, Rcpp,
RCurl","License":"GPL-
2","NeedsCompilation":"yes","Package":"RProtoBuf","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"RUnit, highlight","Title":"R Interface to the
Protocol Buffers
API","URL":"https:\/\/github.com\/eddelbuettel\/rprotobuf","Version":"0.4.3"},"RPub
lica":{"Author":"Thomas J. Leeper [aut, cre],\nJeroen Ooms
[ctb]","Description":"Client for accessing data journalism APIs from ProPublica
<http:\/\/www.propublica.org\/>.","Imports":"jsonlite, httr, curl","License":"GPL-
2","NeedsCompilation":"no","Package":"RPublica","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"ProPublica API
Client","URL":"https:\/\/github.com\/rOpenGov\/RPublica","Version":"0.1.3"},"RPushb
ullet":{"Author":"Dirk Eddelbuettel","Description":"An R interface to the
Pushbullet messaging service which\nprovides fast and efficient notifications (and
file transfer) between\ncomputers, phones and tablets. An account has to be
registered at the site\nhttp:\/\/www.pushbullet.com site to obtain a (free) API
key.","Imports":"utils, RJSONIO","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RPushbullet","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"R Interface to the Pushbullet Messaging
Service","Version":"0.2.0"},"RPyGeo":{"Author":"Alexander
Brenning","Depends":"shapefiles, RSAGA","Description":"Provide access to (virtually
any) ArcGIS Geoprocessing\ntool from within R by running Python geoprocessing
scripts\nwithout writing Python code or touching ArcGIS. Requires ArcGIS\n>=9.2, a
suitable version of Python (for ArcGIS 9.2: Python\n2.4; for ArcGIS 10.0: 2.6), and
Windows.","License":"GPL","NeedsCompilation":"no","Package":"RPyGeo","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Title":"ArcGIS Geoprocessing in R via
Python","Version":"0.9-3"},"RQDA":{"Author":"HUANG Ronggui","Depends":"R (>=
2.8.0), RSQLite(>= 1.0.0), gWidgetsRGtk2 (>= 0.0-36)","Description":"R package for
Qualitative Data Analysis. Current version only supports plain text, but it can
import PDF highlights if the Enhance package of rjpod, which is available on R-
Forge, is installed.","Enhances":"tcltk, rjpod, d3Network","Imports":"RGtk2 (>=
2.20), DBI, igraph, gWidgets (>= 0.0-31)","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"RQDA","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"R-based Qualitative Data
Analysis","URL":"http:\/\/rqda.r-forge.r-project.org\/","Version":"0.2-
7"},"RQuantLib":{"Author":"Dirk Eddelbuettel, Khanh Nguyen (during 2009-
2010)","Depends":"R (>= 2.10.0)","Description":"The 'RQuantLib' package makes parts
of 'QuantLib' accessible from R\nThe 'QuantLib' project aims to provide a
comprehensive software framework\nfor quantitative finance. The goal is to provide
a standard open source library\nfor quantitative analysis, modeling, trading, and
risk management of financial\nassets.","Imports":"methods, Rcpp (>= 0.11.0), stats,
graphics","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"RQuantLib","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"rgl, zoo, RUnit, shiny","Title":"R Interface to the
'QuantLib'
Library","URL":"http:\/\/quantlib.org\nhttp:\/\/dirk.eddelbuettel.com\/code\/rquant
lib.html","Version":"0.4.2"},"RRF":{"Author":"Fortran original by Leo Breiman and
Adele Cutler, R port by\nAndy Liaw and Matthew Wiener, Regularized random forest
by\nHoutao Deng.","Depends":"R (>= 2.5.0), stats","Description":"Feature Selection
with Regularized Random Forest. This\npackage is based on the 'randomForest'
package by Andy Liaw.\nThe
key difference is the RRF function that builds a\nregularized random
forest.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"RRF","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"RColorBrewer, MASS","Title":"Regularized Random
Forest","URL":"https:\/\/sites.google.com\/site\/houtaodeng\/rrf","Version":"1.6"},
"RRNA":{"Author":"JP Bida","Description":"Functions for creating and manipulating
RNA secondary structure plots.","License":"GPL-
3","NeedsCompilation":"no","Package":"RRNA","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Secondary Structure Plotting for
RNA","Version":"1.0"},"RRTCS":{"Author":"Beatriz Cobo RodrÃguez, MarÃa del Mar
Rueda GarcÃa, Antonio Arcos\nCebriÃ¡n","Description":"Point and interval estimation
of linear parameters with data\nobtained from complex surveys (including stratified
and clustered samples)\nwhen randomization techniques are used. The randomized
response technique\nwas developed to obtain estimates that are more valid when
studying\nsensitive topics. Estimators and variances for 14 randomized
response\nmethods for qualitative variables and 7 randomized response methods
for\nquantitative variables are also implemented. In addition, some data sets\nfrom
surveys with these randomization methods are included in the
package.","Imports":"sampling, samplingVarEst, stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RRTCS","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"knitr","Title":"Randomized Response Techniques for
Complex Surveys","Version":"0.0.3"},"RRreg":{"Author":"Daniel W. Heck [aut, cre],
Morten Moshagen [aut]","Depends":"R (>= 3.0.0)","Description":"Univariate and
multivariate methods to analyze\nrandomized response (RR) survey designs (e.g.,
Warner, S. L. (1965).\nRandomized response: A survey technique for eliminating
evasive answer\nbias. Journal of the American Statistical Association, 60,
63â€“69).\nBesides univariate estimates of true proportions, RR variables can be
used\nfor correlations, as dependent variable in a logistic regression (with
or\nwithout random effects), as predictors in a linear regression, or as\ndependent
variable in a beta-binomial ANOVA. For simulation and bootstrap\npurposes, RR data
can be generated according to several models.","Imports":"parallel, doParallel,
foreach, stats, grDevices, graphics,\nlme4","License":"GPL-
2","NeedsCompilation":"no","Package":"RRreg","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr","Title":"Correlation and Regression Analyses for
Randomized Response Data","URL":"http:\/\/psycho3.uni-
mannheim.de\/Home\/Research\/Software\/RRreg\/","Version":"0.6.1"},"RSA":
{"Author":"Felix SchÃ¶nbrodt","Depends":"R (>= 2.15.0), lavaan (>= 0.5.20),
ggplot2, lattice, tkrplot,\ntcltk","Description":"Advanced response surface
analysis. The main function RSA computes\nand compares several nested polynomial
regression models (full polynomial,\nshifted and rotated squared differences,
rising ridge surfaces, basic\nsquared differences). The package provides plotting
functions for 3d\nwireframe surfaces, interactive 3d plots, and contour plots.
Calculates\nmany surface parameters (a1 to a4, principal axes, stationary
point,\neigenvalues) and provides standard, robust, or bootstrapped standard
errors\nand confidence intervals for them.","Imports":"plyr, RColorBrewer,
aplpack","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RSA","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"fields, SDMTools, rgl, qgraph,
AICcmodavg","Title":"Response Surface Analysis","Version":"0.9.10"},"RSADBE":
{"Author":"Prabhanjan Tattar","Description":"The package contains all the data sets
related to the book\nwritten by the maintainer of the package.","License":"GPL-
2","NeedsCompilation":"no","Package":"RSADBE","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Data related to the book \"R Statistical Application
Development\nby Example\"","Version":"1.0"},"RSAGA":{"Author":"Alexander Brenning
and Donovan Bangs","Depends":"R (>= 2.10), gstat, shapefiles,
plyr","Description":"Provides access to geocomputing and terrain
analysis\nfunctions of the geographical information system (GIS) 'SAGA' (System
for\nAutomated Geoscientific Analyses) from within R by running the command\nline
version of SAGA. This package furthermore provides several R functions\nfor
handling ASCII grids, including a flexible framework for applying local\nfunctions
(including predict methods of fitted models) and focal functions to\nmultiple
grids. SAGA GIS is available under GPLv2 \/ LGPLv2 licence
from\nhttp:\/\/sourceforge.net\/projects\/saga-gis\/.","License":"GPL-2 | file
LICENSE","NeedsCompilation":"no","Package":"RSAGA","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr","Title":"SAGA Geoprocessing and Terrain
Analysis in R","Version":"0.94-5"},"RSAP":{"Author":"Piers Harding
<piers@ompka.net>","Depends":"R (>= 2.12.0), utils, yaml,
reshape","Description":"The SAP Netweaver RFC connector for R","License":"GPL-
3","NeedsCompilation":"yes","Package":"RSAP","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"SAP Netweaver RFC connector for
R","URL":"http:\/\/github.com\/piersharding\/RSAP","Version":"0.9"},"RSDA":
{"Author":"Oldemar Rodriguez R. with contributions from Olger Calderon, Roberto
Zuniga and Jorge Arce","Depends":"R (>= 2.10), XML, scales, ggplot2, princurve,
sqldf","Description":"Symbolic Data Analysis (SDA) was proposed by professor Edwin
Diday in 1987, the main purpose of SDA is to substitute the set of rows (cases) in
the data table for a concept (second order statistical unit). This package
implements, to the symbolic case, certain techniques of automatic classification,
as well as some linear models.","Imports":"RJSONIO, glmnet, abind, scatterplot3d,
graphics, stats, utils,\nFactoMineR","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RSDA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"R to Symbolic Data
Analysis","URL":"http:\/\/www.oldemarrodriguez.com","Version":"1.3"},"RSEIS":
{"Author":"Jonathan M. Lees","Depends":"R (>= 2.12)","Description":"Multiple
interactive codes to view and analyze seismic data, via spectrum analysis, wavelet
transforms, particle motion, hodograms. Includes general time-series tools,
plotting, filtering, interactive display.","Imports":"RPMG, Rwave","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"RSEIS","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"stats","Title":"Seismic Time Series Analysis
Tools","Version":"3.5-2"},"RSGHB":{"Author":"Jeff Dumont [aut, cre],\nJeff Keller
[aut],\nChase Carpenter [ctb]","Depends":"methods","Description":"Functions for
estimating models using a Hierarchical Bayesian (HB) framework. The flexibility
comes in allowing the user to specify the likelihood function directly instead of
assuming predetermined model structures. Types of models that can be estimated with
this code include the family of discrete choice models (Multinomial Logit, Mixed
Logit, Nested Logit, Error Components Logit and Latent Class) as well ordered
response models like ordered probit and ordered logit. In addition, the package
allows for flexibility in specifying parameters as either fixed (non-varying across
individuals) or random with continuous distributions. Parameter distributions
supported include normal, positive\/negative log-normal, positive\/negative
censored normal, and the Johnson SB distribution. Kenneth Train's Matlab and Gauss
code for doing Hierarchical Bayesian estimation has served as the basis for a few
of the functions included in this package. These Matlab\/Gauss functions have been
rewritten to be optimized within R. Considerable code has been added to increase
the flexibility and usability of the code base. Train's original Gauss and Matlab
code can be found here:
http:\/\/elsa.berkeley.edu\/Software\/abstracts\/train1006mxlhb.html See Train's
chapter on HB in Discrete Choice with Simulation here:
http:\/\/elsa.berkeley.edu\/books\/choice2.html; and his paper on using HB with
non-normal distributions here:
http:\/\/eml.berkeley.edu\/\/~train\/trainsonnier.pdf.","Imports":"graphics,
3","NeedsCompilation":"yes","Package":"RSGHB","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Functions for Hierarchical Bayesian Estimation: A
Flexible\nApproach","URL":"https:\/\/github.com\/RSGInc\/RSGHB","Version":"1.1.2"},
"RSKC":{"Author":"Yumi Kondo","Depends":"flexclust, stats, R (>=
2.14.0)","Description":"This package contains a function RSKC which runs the robust
sparse K-means clustering algorithm.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"RSKC","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Robust sparse K-means","Version":"2.4.1"},"RSMET":
{"Author":"Emanuele Cordano","Depends":"R (>= 2.10), stringr","Description":"It
manages snow and weather local time series as provided by MeteoIO
(<http:\/\/models.slf.ch\/docserver\/meteoio\/html\/index.html>,
<http:\/\/www.slf.ch\/ueber\/organisation\/schnee_permafrost\/projekte\/MeteoIO\/in
dex_EN>, <https:\/\/www.openhub.net\/p\/MeteoIO>). MeteoIO is a C\/C++ Open Source
library which \"has been designed to accomodate both the needs of carefully crafted
simulations for a specific purpose\/study and for the needs of operational
simulations that run automatically and unattended\". It is integrated in physical
spatially-distributed models and tackles several issues with weather input\/output
data. Here a SMET S4 class object is defined and can be imported from\/ exported to
a SMET ini files of MeteoIO , allowing interoperability from R to MeteoIO and other
SMET-compliant software.","Imports":"methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RSMET","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"ggmap","Title":"Get
Real-Time Meteorological Data in SMET
Format","URL":"https:\/\/github.com\/ecor\/RSMET","Version":"1.2.9"},"RSNNS":
{"Author":"Christoph Bergmeir and JosÃ© M. BenÃtez","Depends":"R (>= 2.10.0),
methods, Rcpp (>= 0.8.5)","Description":"The Stuttgart Neural Network Simulator
(SNNS) is a library\ncontaining many standard implementations of neural networks.
This\npackage wraps the SNNS functionality to make it available from\nwithin R.
Using the RSNNS low-level interface, all of the\nalgorithmic functionality and
flexibility of SNNS can be accessed.\nFurthermore, the package contains a
convenient high-level\ninterface, so that the most common neural network topologies
and\nlearning algorithms integrate seamlessly into R.","License":"LGPL (>= 2) |
file
LICENSE","NeedsCompilation":"yes","Package":"RSNNS","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"scatterplot3d,NeuralNetTools","Title":"Neural
Networks in R using the Stuttgart Neural Network\nSimulator
(SNNS)","URL":"http:\/\/sci2s.ugr.es\/dicits\/software\/RSNNS","Version":"0.4-
7"},"RSNPset":{"Author":"Chanhee Yi, Alexander Sibley, and Kouros
Owzar","Description":"An implementation of the use of efficient score
statistics\nin genome-wide SNP set analysis with complex traits. Three standard
score statistics\n(Cox, binomial, and Gaussian) are provided, but the package is
easily extensible to\ninclude others. Code implementing the inferential procedure
is primarily written in C++ and\nutilizes parallelization of the analysis to reduce
runtime. A supporting function offers\nsimple computation of observed, permutation,
and FWER and FDR adjusted p-values.","Imports":"fastmatch (>= 1.0-4), foreach (>=
1.4.1), doRNG (>= 1.5.3),\nqvalue (>= 1.34), Rcpp (>= 0.10.4)","License":"GPL-
3","NeedsCompilation":"yes","Package":"RSNPset","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr","Title":"Efficient Score Statistics for Genome-
Wide SNP Set Analysis","Version":"0.5"},"RSPS":{"Author":"Milan Bimali, Joseph
Usset, Brooke L. Fridley","Description":"Provides functions for estimating power or
sample size for RNA-Seq studies. Empirical approach is used and the data is assumed
to be count in nature. The underlying distribution of data is assumed to be Poisson
or negative binomial. The package contains 6 function; 4 functions provide
estimates of sample size or power for Poisson and Negative Binomial distribution; 2
functions provide plots of power for given sample size or sample size for given
power.","Imports":"lattice,plyr,gridExtra","License":"GPL-
2","NeedsCompilation":"no","Package":"RSPS","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"RNA-Seq Power Simulation","Version":"1.0"},"RSQLServer":
{"Author":"Imanuel Costigan [aut, cre],\nThe jTDS Project (for MSSQL Server driver)
[aut],\nSimon Urbanek [ctb],\nHadley Wickham [ctb],\nRomain Francois
[ctb],\nRStudio [cph],\nThe Legion Of The Bouncy Castle [cph, ctb]","Depends":"R
(>= 3.2.0), DBI (>= 0.3.1)","Description":"Utilises The jTDS Project's JDBC 3.0 SQL
Server\ndriver to extend the RJDBC classes and DBI methods. It defines
a\nSQLServerDriver, SQLServerConnection & SQLServerRsult S4 classes as\nextensions
of the RJDBC equivalent classes with most DBI\nmethods being thin extensions of the
methods defined by RJDBC classes.\nHowever, the dbConnect interface is more
convenient, and the data reading\nand writing capabilities found in RJDBC's fetch
and dbWriteTable methods\nhave been refined. The package also implements a SQL
backend to the dplyr\npackage.","Imports":"methods (>= 3.2.0), rJava (>= 0.9.6),
RJDBC (>= 0.2-4), dplyr\n(>= 0.4), assertthat (>= 0.1), yaml (>= 2.1.13), lubridate
(>=\n1.3.3)","License":"GPL-
2","NeedsCompilation":"no","Package":"RSQLServer","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat","Title":"SQL Server R Database Interface
(DBI) and dplyr SQL
Backend","URL":"https:\/\/github.com\/imanuelcostigan\/RSQLServer","Version":"0.2.0
"},"RSQLite":{"Author":"Hadley Wickham [aut, cre],\nDavid A. James [aut],\nSeth
Falcon [aut],\nSQLite Authors [ctb] (for the included SQLite sources),\nLiam Healy
[ctb] (for the include SQLite extensions),\nRStudio [cph]","Depends":"R (>=
2.10.0), DBI (>= 0.3.1), methods","Description":"This package embeds the SQLite
database engine in R and\nprovides an interface compliant with the DBI
package.\nThe source for the SQLite engine (version 3.8.6) is
included.","License":"LGPL (>=
2)","NeedsCompilation":"yes","Package":"RSQLite","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat","Title":"SQLite Interface for
R","URL":"https:\/\/github.com\/rstats-
db\/RSQLite","Version":"1.0.0"},"RSVGTipsDevice":{"Author":"Tony Plate
<tplate@acm.org>, based on RSvgDevice by T Jake Luciani
<jakeluciani@yahoo.com>","Depends":"R (>= 2.6)","Description":"A graphics device
for R that uses the w3.org xml standard\nfor Scalable Vector Graphics. This
version supports\ntooltips with 1 to 3 lines, hyperlinks, and line
styles.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"RSVGTipsDevice","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"An R SVG graphics device with dynamic tips and
hyperlinks","Version":"1.0-4"},"RSclient":{"Author":"Simon Urbanek
<Simon.Urbanek@r-project.org>","Depends":"R (>= 2.7.0)","Description":"Client for
Rserve, allowing to connect to Rserve instances and issue
commands.","License":"GPL-2 | file
LICENSE","NeedsCompilation":"yes","Package":"RSclient","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Client for
Rserve","URL":"http:\/\/www.rforge.net\/RSclient\/","Version":"0.7-3"},"RSeed":
{"Author":"Claus Jonathan Fritzemeier","Depends":"R (>= 2.15.0), methods, sybil,
RBGL, graph","Description":"an implementation of the analysis about seed
components\nfrom borenstein 2008","License":"GNU General Public
License","NeedsCompilation":"no","Package":"RSeed","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"Rgraphviz","Title":"borenstein
analysis","Version":"0.1.31"},"RSelenium":{"Author":"John Harrison
<johndharrison0@gmail.com>","Depends":"R (>=
3.0.0),RCurl,RJSONIO,XML","Description":"The RSelenium package provides a set of R
bindings for the\nSelenium 2.0 WebDriver using the JsonWireProtocol. Selenium
automates web\nbrowsers (commonly referred to as browsers). Using RSelenium you
can\nautomate browsers locally or
remotely.","Imports":"methods,caTools,tools","License":"AGPL-
3","NeedsCompilation":"no","Package":"RSelenium","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat, knitr, Rcompression","Title":"R bindings
for Selenium
WebDriver","URL":"http:\/\/ropensci.github.io\/RSelenium","Version":"1.3.5"},"RSien
a":{"Author":"Ruth Ripley, Krists Boitmanis, Tom A.B. Snijders","Depends":"R (>=
2.15.0)","Description":"Fits models to longitudinal network
data","Imports":"Matrix","License":"GPL-
2","NeedsCompilation":"yes","Package":"RSiena","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"tcltk, network, codetools, lattice, MASS, parallel,
xtable,\ntools","Title":"Siena - Simulation Investigation for Empirical Network
Analysis","URL":"http:\/\/www.stats.ox.ac.uk\/~snijders\/siena","Version":"1.1-
232"},"RSiteCatalyst":{"Author":"Willem Paling, Randy Zwitch & Jowanza
Joseph","Depends":"R (>= 3.0)","Description":"Functions for interacting with the
Adobe Analytics API
V1.4\n(https:\/\/api.omniture.com\/admin\/1.4\/rest\/).","Imports":"jsonlite (>=
0.9.5), httr (>= 0.3), plyr, base64enc, digest,\nstringr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"RSiteCatalyst","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Suggests":"testthat","Title":"R Client for Adobe
Analytics API V1.4","Version":"1.4.8"},"RSocrata":{"Author":"Hugh Devlin, Ph. D.,
Tom Schenk, Jr., and John Malc","Depends":"R (>= 3.0.0)","Description":"Provides
easier interaction with\nSocrata open data portals http:\/\/dev.socrata.com.\nUsers
can provide a 'Socrata' data set resource URL,\nor a 'Socrata' Open Data API (SoDA)
web query,\nor a 'Socrata' \"human-friendly\" URL,\nreturns an R data frame.
Converts dates to 'POSIX'\nformat and manages throttling by 'Socrata'.\nUsers can
upload data to Socrata portals directly\nfrom R.","Imports":"httr (>= 1.0.0),
jsonlite (>= 0.9.16), mime (>= 0.3)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"RSocrata","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat (>= 0.10.0), roxygen2 (>= 4.1.0), readr
(>= 0.2.2)","Title":"Download or Upload 'Socrata' Data
Sets","URL":"https:\/\/github.com\/Chicago\/RSocrata","Version":"1.7.0-
14"},"RSofia":{"Author":"Michael King <wmichaelking1@gmail.com> and Fernando Cela
Diaz <fcela@sloan.mit.edu>. Original sofia-ml code by D. Sculley
<dsculley@google.com>.","Depends":"methods, Rcpp (>= 0.9.6)","Description":"sofia-
ml is a suite of fast incremental algorithms for machine learning that can be used
for training models for classification or ranking","License":"Apache License
2.0","NeedsCompilation":"yes","Package":"RSofia","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"RUnit","Title":"Port of sofia-ml
(http:\/\/code.google.com\/p\/sofia-ml\/) to R","Version":"1.1"},"RSpectra":
{"Author":"Yixuan Qiu [aut, cre],\nJiali Mei [aut] (Function interface of matrix
operation),\nGael Guennebaud [ctb] (Eigenvalue solvers from the 'Eigen'
library),\nJitse Niesen [ctb] (Eigenvalue solvers from the 'Eigen'
library)","Depends":"R (>= 3.0.2)","Description":"R interface to the 'Spectra'
library\n<http:\/\/yixuan.cos.name\/spectra\/> for large scale eigenvalue and
SVD\nproblems. It is typically used to compute a few\neigenvalues\/vectors of an n
by n matrix, e.g., the k largest eigenvalues,\nwhich is usually more efficient than
eigen() if k << n. This package\nprovides the 'eigs()' function which does the
similar job as in 'Matlab',\n'Octave',
'Python SciPy' and 'Julia'. It also provides the 'svds()' function\nto calculate
the largest k singular values and corresponding\nsingular vectors of a real matrix.
Matrices can be given in either dense\nor sparse form.","Imports":"Matrix (>= 1.1-
0), Rcpp (>= 0.11.5)","License":"MPL (>=
2)","NeedsCompilation":"yes","Package":"RSpectra","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Solvers for Large Scale Eigenvalue and SVD
Problems","URL":"https:\/\/github.com\/yixuan\/RSpectra","Version":"0.11-
0"},"RSpincalc":{"Author":"Jose Gama [aut, cre],\nJohn Fuller [aut, cph],\nPaolo
Leva [aut, cph]","Description":"Conversion between attitude representations: DCM,
Euler angles, Quaternions, and Euler vectors.\nPlus conversion between 2 Euler
angle set types (xyx, yzy, zxz, xzx, yxy, zyz, xyz, yzx, zxy, xzy, yxz,
zyx).\nFully vectorized code, with warnings\/errors for Euler angles (singularity,
out of range, invalid angle order),\nDCM (orthogonality, not proper, exceeded
tolerance to unity determinant) and Euler vectors(not unity).\nAlso quaternion and
other useful functions.\nBased on SpinCalc by John Fuller and SpinConv by Paolo de
Leva.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"RSpincalc","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Conversion Between Attitude Representations of DCM,
Euler\nAngles, Quaternions, and Euler Vectors","Version":"1.0.2"},"RStars":
{"Author":"William Kyle Hamilton <kyle.hamilton@gmail.com>","Depends":"R (>=
3.0.3), RJSONIO, RCurl","Description":"Access to the Digital Universe Data set API
pulls data on\nexoplants, stars, and galaxies.","License":"GPL-
3","NeedsCompilation":"no","Package":"RStars","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Access to the Digital Universe Data set
API","URL":"https:\/\/github.com\/kylehamilton\/RStars","Version":"1.0"},"RStata":
{"Author":"Luca Braglia [aut, cre]","Description":"A simple R -> Stata interface
allowing the user to\nexecute Stata commands (both inline and from a .do
file)\nfrom R.","Imports":"foreign, tools, utils","License":"GPL-
3","NeedsCompilation":"no","Package":"RStata","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"A Bit of Glue Between R and
Stata","URL":"http:\/\/github.com\/lbraglia\/RStata","Version":"1.0.0"},"RStoolbox"
:{"Author":"Benjamin Leutner [cre, aut],\nNed Horning [aut]","Depends":"R (>=
3.1.0)","Description":"Toolbox for remote sensing image processing and analysis
such as\ncalculating spectral indices, principal component transformation,
unsupervised\nand supervised classification or fractional cover
analyses.","Imports":"raster (>= 2.3-40), caret (>= 6.0-52), sp, XML,
geosphere,\nggplot2, plyr, reshape2, rgeos, codetools, parallel,\ndoParallel,
foreach, Rcpp, methods","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"RStoolbox","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"rgdal, randomForest, kernlab, e1071, gridExtra,
pls, testthat","Title":"Tools for Remote Sensing Data
Analysis","URL":"http:\/\/bleutner.github.io\/RStoolbox,\nhttps:\/\/github.com\/ble
utner\/RStoolbox","Version":"0.1.4"},"RStorm":{"Author":"Maurits
Kaptein","Depends":"plyr","Description":"While streaming processing provides
opportunities to deal with extremely large and ever growing data sets in (near)
real time, the development of streaming algorithms for complex models is often
cumbersome: the software packages that facilitate streaming processing in
production environments do not provide statisticians with the simulation,
estimation, and plotting tools they are used to. Developers of streaming algorithms
would thus benefit from the flexibility of [R] to create, plot and compute data
while developing streaming algorithms. Package RStorm implements a streaming
architecture modeled on Storm for easy development and testing of streaming
algorithms in [R]. RStorm is not intended as a production package, but rather a
development tool for streaming algorithms.","License":"GPL-
2","NeedsCompilation":"no","Package":"RStorm","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Simulate and Develop Streaming Processing in
[R]","Version":"0.902"},"RSurveillance":{"Author":"Evan
Sergeant","Description":"This package provides a range of functions for the design
and\nanalysis of disease surveillance activities. These functions were\noriginally
developed for animal health surveillance activities but can be\nequally applied to
aquatic animal, wildlife, plant and human health\nsurveillance activities.
Utilities are included for sample size calculation\nand analysis of representative
surveys for disease freedom, risk-based\nstudies for disease freedom and for
prevalence estimation.","Imports":"epitools, epiR","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"RSurveillance","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Design and Analysis of Disease Surveillance
Activities","Version":"0.1.0"},"RSurvey":{"Author":"Jason C. Fisher","Depends":"R
(>= 3.1.0)","Description":"A processing program for spatially distributed data.\nIt
features graphing tools, query building, and polygon clipping.\nA graphical user
interface is provided.","Imports":"tcltk, sp, rgeos, MBA","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RSurvey","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"rgdal, tripack, colorspace, dichromat, rgl,
XML","Title":"Analysis of Spatially Distributed
Data","URL":"https:\/\/github.com\/jfisher-usgs\/RSurvey","Version":"0.8-
3"},"RTConnect":{"Author":"Yusuke Miyazaki","Depends":"R (>= 2.14),
graphics","Description":"Tools for analyzing sales report files of iTunes
Connect.","License":"GPL-
3","NeedsCompilation":"no","Package":"RTConnect","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Tools for analyzing sales report files of iTunes
Connect","Version":"0.1.4"},"RTDE":{"Author":"Christophe Dutang [aut, cre], Armelle
Guillou [ctb], Yuri Goegebeur [ctb]","Depends":"R (>= 3.0.0),
parallel","Description":"Robust tail dependence estimation for bivariate models.
This package is based on two papers by the authors:'Robust and bias-corrected
estimation of the coefficient of tail dependence' and 'Robust and bias-corrected
estimation of probabilities of extreme failure sets'. This work was supported by a
research grant (VKR023480) from VILLUM FONDEN and an international project for
scientific cooperation (PICS-6416).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RTDE","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"tseries","Title":"Robust Tail Dependence
Estimation","Version":"0.2-0"},"RTOMO":{"Author":"Jonathan M. Lees","Depends":"R
(>= 2.12)","Description":"Aimed at seismic tomography, the package\nplots
tomographic images, and allows one to interact and query\nthree-dimensional
tomographic models.\nVertical cross-sectional cuts can be extracted by mouse
click.\nGeographic information can be added easily.","Imports":"RPMG, GEOmap,
RSEIS, splancs","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RTOMO","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Visualization for Seismic Tomography","Version":"1.1-
3"},"RTextTools":{"Author":"Timothy P. Jurka, Loren Collingwood, Amber E.
Boydstun,\nEmiliano Grossman, Wouter van Atteveldt","Depends":"R (>= 2.15.0),
SparseM","Description":"RTextTools is a machine learning package for
automatic\ntext classification that makes it simple for novice users to\nget
started with machine learning, while allowing experienced\nusers to easily
experiment with different settings and\nalgorithm combinations. The package
includes nine algorithms\nfor ensemble classification (svm, slda, boosting,
bagging,\nrandom forests, glmnet, decision trees, neural networks,\nmaximum
entropy), comprehensive analytics, and
thorough\ndocumentation.","Imports":"methods, randomForest, tree, nnet, tm, e1071,
ipred, caTools,\nmaxent, glmnet, tau","License":"GPL-
3","NeedsCompilation":"yes","Package":"RTextTools","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Automatic Text Classification via Supervised
Learning","URL":"http:\/\/www.rtexttools.com\/","Version":"1.4.2"},"RTextureMetrics
":{"Author":"Hans-Joachim Klemmt","Description":"This package contains several
functions for calculation of texture metrics for Grey Level Co-occurrence
matrices","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RTextureMetrics","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Functions for calculation of texture metrics for
Grey Level\nCo-occurrence Matrices","Version":"1.1"},"RTriangle":
{"Author":"Jonathan Shewchuk, David C. Sterratt
<david.c.sterratt@ed.ac.uk>","Depends":"R (>= 3.0.0)","Description":"This is a port
of Jonathan Shewchuk's Triangle library to\nR. From his description: \"Triangle
generates exact Delaunay\ntriangulations, constrained Delaunay triangulations,
conforming\nDelaunay triangulations, Voronoi diagrams, and high-quality\ntriangular
meshes. The latter can be generated with no small or\nlarge angles, and are thus
suitable for finite element analysis.\"","License":"CC BY-NC-SA
4.0","NeedsCompilation":"yes","Package":"RTriangle","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Triangle - A 2D Quality Mesh Generator and Delaunay
Triangulator","URL":"http:\/\/triangle.R-Forge.R-
project.org,\nhttp:\/\/www.cs.cmu.edu\/~quake\/triangle.html","Version":"1.6-
0.6"},"RUnit":{"Author":"Matthias Burger <burgerm@users.sourceforge.net>,
Klaus\nJuenemann <k.junemann@gmx.net>, Thomas
Koenig\n<thomas.koenig@epigenomics.com>","Depends":"R (>= 2.5.0), utils (>= 2.5.0),
methods (>= 2.5.0), graphics\n(>= 2.5.0)","Description":"R functions implementing a
standard Unit Testing\nframework, with additional code inspection and
report\ngeneration tools.","License":"GPL-
2","NeedsCompilation":"no","Package":"RUnit","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"XML
(>= 3.1.0)","Title":"R Unit Test Framework","Version":"0.4.31"},"RVAideMemoire":
{"Author":"Maxime Hervé","Description":"Contains diverse more or less complicated
functions, written to simplify user's life: simplifications of existing functions,
basic but not implemented tests, easy-to-use tools, bridges between functions of
different packages... All functions are presented in the French book 'Aide-memoire
de statistique appliquee a la biologie', written by the same author and available
on CRAN.","Imports":"ade4, boot, car, cramer, graphics, grDevices, lme4 (>= 1.0-
4),\nMASS, mixOmics (>= 5.0.2), multcompView, nnet, pls, pspearman,\nstatmod,
stats, utils, vegan","License":"GPL-
2","NeedsCompilation":"no","Package":"RVAideMemoire","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"EMT, lsmeans, npsm, ordinal,
survival","Title":"Diverse Basic Statistical and Graphical
Functions","Version":"0.9-54"},"RVFam":{"Author":"Ming-Huei Chen <mhchen@bu.edu>
and Qiong Yang <qyang@bu.edu>","Depends":"R (>= 3.0.0)","Description":"The RVFam
package provides functions to perform single SNP association analyses and gene-
based tests for continuous, binary and survival traits against sequencing data
(e.g. exome chip) using family data.","Imports":"coxme, survival, lme4, kinship2,
MASS, Matrix","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RVFam","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Rare Variants Association Analyses with Family
Data","Version":"1.1"},"RVPedigree":{"Author":"Karim Oualkacha [aut, cre],\nM'Hamed
Lajmi Lakhal-Chaieb [aut],\nCelia M.T. Greenwood [aut],\nLennart C. Karssen
[aut],\nSodbo Sharapov [aut]","Depends":"R (>= 3.2.2), foreach, doParallel,
utils","Description":"This is a collection of the five region-based\nrare-variant
genetic association tests. The following tests are\ncurrently implemented: ASKAT,
ASKAT-Normalized, VC-C1, VC-C2 and\nVC-C3.","Imports":"ks, CompQuadForm, Matrix,
snpStats, kinship2","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"RVPedigree","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"GenABEL, knitr, methods","Title":"Methods for
Family-Based Rare-Variant Genetic Association
Tests","Version":"0.0.3"},"RVideoPoker":{"Author":"Roland Rau Cards were created by
Byron Knoll and released into\nthe public domain. They were downloaded
from\nhttp:\/\/code.google.com\/p\/vector-playing-cards\/downloads\/detail?
name=PNG-cards-1.2.zip\non 2012-06-08. Byron Knoll stated in his blog that the
cards\nwere released by him into the public
domain:\nhttp:\/\/byronknoll.blogspot.de\/2011\/03\/vector-playing-cards.html\nThe
backside of the cards were created by Roland Rau using the\nR-
Logo.","Depends":"pixmap, tkrplot, rpanel","Description":"Play Video Poker with R,
complete with a graphical user\ninterface. So far, only \"Jacks or Better\" is
implemented.","License":"GPL-
2","NeedsCompilation":"no","Package":"RVideoPoker","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Play Video Poker with R","Version":"0.3"},"RViennaCL":
{"Author":"Charles Determan Jr.","Description":"ViennaCL is a free open-source
linear algebra library\nfor computations on many-core architectures (GPUs, MIC)
and\nmulti-core CPUs. The library is written in C++ and supports CUDA,\nOpenCL, and
OpenMP (including switches at runtime).\nI have placed these libraries in this
package as a more efficient\ndistribution system for CRAN. The idea is that you can
write a package\nthat depends on the ViennaCL library and yet you do not need
to\ndistribute a copy of this code with your package.","License":"GPL-
3","NeedsCompilation":"no","Package":"RViennaCL","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"gpuR","Title":"ViennaCL C++ Header
Files","URL":"http:\/\/github.com\/cdeterman\/RViennaCL","Version":"1.7.1-
1"},"RVsharing":{"Author":"Alexandre Bureau, Ingo Ruczinski, Samuel G.
Younkin","Depends":"R (>= 2.15.2)","Description":"Computes estimates of the
probability of related individuals sharing a rare variant.","Imports":"utils,
methods, kinship2","License":"GPL-
2","NeedsCompilation":"no","Package":"RVsharing","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Probability of Sharing Rare Variants among
Relatives","Version":"1.4.0"},"RVtests":{"Author":"C. Xu, and C. M.
Greenwood","Depends":"R (>= 2.12.1), glmnet, spls, pls","Description":"Use multiple
regression methods to test rare variants\nassociation with disease
traits.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RVtests","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Rare Variant Tests","Version":"1.2"},"RWBP":
{"Author":"Sigal Shaked & Ben Nasi","Depends":"RANN, igraph, lsa,
SnowballC","Description":"a Bipartite graph and is constructed based on the spatial
and\/or non-spatial attributes of the spatial objects in the dataset. Secondly, RW
techniques are utilized on the graphs to compute the outlierness for each point
(the differences between spatial objects and their spatial neighbours). The top k
objects with higher outlierness are recognized as outliers.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RWBP","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Detects spatial outliers using a Random Walk on Bipartite
Graph","Version":"1.0"},"RWeather":{"Author":"Paolo Sonego
<paolo.sonego@gmail.com>","Depends":"R (>= 2.11.0), XML","Description":"This
package provides programmatic access to Yahoo!\nWeather and NOAA
APIs","License":"GPL-
2","NeedsCompilation":"no","Package":"RWeather","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"R wrapper around the Yahoo! Weather, Google Weather and
NOAA\nAPIs","Version":"0.4"},"RWebLogo":{"Author":"Omar
Wagih","Description":"RWebLogo is a wrapper for the WebLogo python package\nthat
allows generating of customised sequence logos. Sequence logos are\ngraphical
representations of the sequence conservation of nucleotides (in a\nstrand of
DNA\/RNA) or amino acids (in protein sequences). Each logo\nconsists of stacks of
symbols, one stack for each position in the sequence.\nThe overall height of the
stack indicates the sequence conservation at that\nposition, while the height of
symbols within the stack indicates the\nrelative frequency of each amino or nucleic
acid at that position. In\ngeneral, a sequence logo provides a richer and more
precise description of,\nfor example, a binding site, than would a consensus
sequence.","Imports":"findpython","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"RWebLogo","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"plotting custom sequence
logos","Version":"1.0.3"},"RWeka":{"Author":"Kurt Hornik [aut, cre],\nChristian
Buchta [ctb],\nTorsten Hothorn [ctb],\nAlexandros Karatzoglou [ctb],\nDavid Meyer
[ctb],\nAchim Zeileis [ctb]","Depends":"R (>= 2.6.0)","Description":"An R interface
to Weka (Version 3.7.13).\nWeka is a collection of machine learning algorithms for
data mining\ntasks written in Java, containing tools for data pre-
processing,\nclassification, regression, clustering, association rules,
and\nvisualization. Package 'RWeka' contains the interface code, the\nWeka jar is
in a separate package 'RWekajars'. For more information\non Weka see
<http:\/\/www.cs.waikato.ac.nz\/ml\/weka\/>.","Imports":"RWekajars (>= 3.7.13),
rJava (>= 0.6-3), graphics, stats,\nutils, grid","License":"GPL-
2","NeedsCompilation":"no","Package":"RWeka","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"partykit (>= 0.8.0), mlbench, e1071","Title":"R\/Weka
Interface","Version":"0.4-26"},"RWekajars":{"Author":"Kurt Hornik [aut,
cre],\nUniversity of Waikato [ctb, cph] (Weka Java
library)","Description":"External jars required for package
'RWeka'.","Imports":"rJava (>= 0.6-3)","License":"GPL-
2","NeedsCompilation":"no","Package":"RWekajars","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"R\/Weka Interface Jars","Version":"3.7.13-1"},"RWiener":
{"Author":"Dominik Wabersich","Depends":"R (>= 2.15.0)","Description":"This package
provides Wiener process distribution functions,\nnamely the Wiener first passage
time density, CDF, quantile and random\nfunctions.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"RWiener","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"MASS","Title":"Wiener process distribution
functions","URL":"https:\/\/sourceforge.net\/projects\/rwiener\/","Version":"1.2-
0"},"RWinEdt":{"Author":"Uwe Ligges <Uwe.Ligges@R-project.org>\nwith contributions
(the original R-Sweave mode) from Gilbert Ritschard and Karl Koeller","Depends":"R
(>= 2.11.0)","Description":"A plug in for using WinEdt as an editor for
R.","Imports":"utils","License":"GPL-
2","NeedsCompilation":"yes","Package":"RWinEdt","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"R Interface to WinEdt","URL":"http:\/\/www.winedt.com\/,
http:\/\/www.winedt.org\/","Version":"2.0-5"},"RXKCD":{"Author":"Paolo Sonego
<paolo.sonego@gmail.com>","Depends":"R (>= 2.11.0), RJSONIO, png,
jpeg","Description":"This package allows the visualization of your favorite\nXKCD
comic strip directly from R. XKCD web comic content is\nprovided under the Creative
Commons Attribution-NonCommercial\n2.5 License.","Imports":"utils,
plyr","License":"GPL-
2","NeedsCompilation":"no","Package":"RXKCD","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Get XKCD comic from R","Version":"1.7-5"},"RXMCDA":
{"Author":"Patrick Meyer and Sebastien Bigaret, with contributions from Krzysztof
Ciomek.","Depends":"XML","Description":"Functions which allow to read many XMCDA
tags and transform them into R variables which are then usable in MCDA algorithms
written in R. It also allows to write certain R variables into XML files respecting
the XMCDA standard.","Imports":"kappalab","License":"CeCILL-
2","NeedsCompilation":"no","Package":"RXMCDA","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Functions
to Parse and Create XMCDA
Files","URL":"https:\/\/github.com\/paterijk\/RXMCDA","Version":"1.5.5"},"RXshrink"
:{"Author":"Bob Obenchain <wizbob@att.net>","Depends":"R (>= 1.8.0),
lars","Description":"Identify and display TRACEs for a specified shrinkage path and
determine\nthe extent of shrinkage most likely, under normal distribution theory,
to produce an\noptimal reduction in MSE Risk in estimates of regression (beta)
coefficients.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RXshrink","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Maximum Likelihood Shrinkage via Generalized Ridge or
Least\nAngle Regression","URL":"http:\/\/www.r-project.org,
http:\/\/members.iquest.net\/~softrx","Version":"1.0-8"},"RYandexTranslate":
{"Author":"Mukul Chaware[aut,cre]","Description":"'Yandex Translate'
(https:\/\/translate.yandex.com\/) is a statistical machine translation
system.\nThe system translates separate words, complete texts, and webpages.\nThis
package can be used to detect language from text and to translate it to supported
target language.\nFor more info:
https:\/\/tech.yandex.com\/translate\/doc\/dg\/concepts\/About-
docpage\/ .","Imports":"httr,RCurl,jsonlite","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"RYandexTranslate","Repository":"http:\/
\/cran.csiro.au\/src\/contrib","Title":"R Interface to Yandex Translate
API","URL":"https:\/\/github.com\/mukul13\/RYandexTranslate","Version":"1.0"},"RYou
daoTranslate":{"Author":"Ke-Hao Wu","Depends":"RCurl, rjson","Description":"You can
use this package to translate thousands of words. The Youdao translation open API
is applied in this package. But, it just translates less than 1000 English words
into Chinese.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RYoudaoTranslate","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"R package provide functions to translate English
words into\nChinese","Version":"1.0"},"RadOnc":{"Author":"Reid F. Thompson
<reid.thompson@gmail.com>","Depends":"R (>= 3.0.0), graphics, grDevices, methods,
rgl, geometry,\noro.dicom (>= 0.5.0), ptinpoly","Description":"Designed for the
import, analysis, and visualization of dosimetric and volumetric data in Radiation
Oncology, the tools herein enable import of dose-volume histogram information from
multiple treatment planning system platforms and 3D structural representations and
dosimetric information from 'DICOM-RT' files. These tools also enable subsequent
visualization and statistical analysis of these data.","Imports":"stats,
2)","NeedsCompilation":"no","Package":"RadOnc","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Analytical Tools for Radiation
Oncology","Version":"1.1.1"},"RadTran":{"Author":"Francisco Lopes","Depends":"R (>=
2.10), ReacTran","Description":"Contains 4 different functions for radon and soil
gas transport in a porous medium.","Imports":"rootSolve","License":"GPL-
2","NeedsCompilation":"no","Package":"RadTran","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Radon and Soil Gas Transport in 2D Porous
Medium","Version":"1.0"},"RadioSonde":{"Author":"Doug Nychka, Eric Gilleland,
Liangying Zhang, Tim Hoar","Description":"RadioSonde is a collection of programs
for reading and\nplotting SKEW-T,log p diagrams and wind profiles for
data\ncollected by radiosondes (the typical weather balloon-borne\ninstrument),
which we will call \"flights\", \"sondes\", or\n\"profiles\" throughout the
associated documentation. The raw\ndata files are in a common format that has a
header followed by\nspecific variables. Use \"help(ExampleSonde)\" for the
full\nexplanation of the data files.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RadioSonde","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Tools for plotting skew-T diagrams and wind
profiles","URL":"http:\/\/www.image.ucar.edu\/Software\/RadioSonde","Version":"1.4"
},"Rambo":{"Author":"Charles Bouveyron, Yacine Jernite, Pierre Latouche, Laetitia
Nouedoui","Depends":"stats, sna","Description":"Estimate the parameters, the number
of classes and cluster vertices of a random network into groups with homogeneous
connection profiles. The clustering is performed for directed graphs with typed
edges (edges are assumed to be drawn from multinomial distributions) for which a
partition of the vertices is available.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"Rambo","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"The Random Subgraph Model","Version":"1.1"},"Ramd":
{"Author":"Robert Krzyzanowski <technoguyrob@gmail.com>","Depends":"R (>=
3.0.0)","Description":"A \"define\" function is provided that allows\nfor inclusion
of external scripts without polluting\nthe global namespace and makes it easier
to\nwrite modular R code.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Ramd","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat, testthatsomemore","Title":"Tools For Managing
File\/function Dependencies In R","Version":"0.2"},"RandVar":{"Author":"Matthias
Kohl, Peter Ruckdeschel","Depends":"R (>= 2.14.0), methods, distr(>= 2.0),
distrEx(>= 2.0)","Description":"Implementation of random variables by means of S4
classes and methods","License":"LGPL-
3","NeedsCompilation":"no","Package":"RandVar","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Implementation of random
variables","URL":"http:\/\/robast.r-forge.r-
project.org\/","Version":"0.9.2"},"RandomFields":{"Author":"Martin Schlather [aut,
cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut],
Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix
Ballani [aut], Olga Moreva [aut], Christoph Berreth [ctr], Peter Menck [ctr],
Sebastian Gross [ctr], Ulrike Ober [ctb], Katharina Burmeister [ctb], Juliane
Manitz [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core
Team [ctb]","Depends":"R (>= 3.0.2), sp, RandomFieldsUtils (>=
0.0.14)","Description":"Methods for the inference on and the simulation of Gaussian
fields are provided, as well as methods for the simulation of extreme value random
fields.","Imports":"graphics, methods, grDevices, stats, utils","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"RandomFields","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"colorspace, RColorBrewer, mvtnorm, raster,
tcltk2, tcltk,\ntkrplot, spam, tools, geoR, minqa, soma, optimx, nloptr,
pso,\nGenSA","Title":"Simulation and Analysis of Random
Fields","URL":"http:\/\/ms.math.uni-
mannheim.de\/de\/publications\/software","Version":"3.1.8"},"RandomFieldsUtils":
{"Author":"Martin Schlather [aut, cre], Reinhard Furrer [ctb], Martin Kroll
[ctb]","Depends":"R (>= 3.0)","Description":"Various utilities are provided that
might be used in spatial statistics and elsewhere. It delivers a method for solving
linear equations that checks the sparsity of the matrix before any algorithm is
used. Furthermore, it includes the Struve
functions.","Imports":"utils","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"RandomFieldsUtils","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Title":"Utilities for the Simulation and Analysis of
Random Fields","URL":"http:\/\/ms.math.uni-
mannheim.de\/de\/publications\/software","Version":"0.0.14"},"RankAggreg":
{"Author":"Vasyl Pihur <vpihur@gmail.com>, Somnath
Datta\n<somnath.datta@louisville.edu>, Susmita
Datta\n<susmita.datta@louisville.edu>","Depends":"R (>=
2.12.0)","Description":"This package performs aggregation of ordered lists
based\non the ranks using several different algorithms: Borda count,\nCross-Entropy
Monte Carlo algorithm, Genetic algorithm, and a\nbrute force algorithm (for small
problems)","Imports":"gtools","License":"LGPL","NeedsCompilation":"yes","Package":"
RankAggreg","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"xtable,
kohonen, mclust, clValid","Title":"Weighted rank
aggregation","Version":"0.5"},"RankResponse":{"Author":"Hsiuying Wang, Yu-Chun
Lin","Description":"Methods for ranking responses of a single response question or
a multiple response question","License":"GPL-
2","NeedsCompilation":"no","Package":"RankResponse","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Ranking Responses in a Single Response Question or a
Multiple\nResponse Question","Version":"3.1.1"},"Rankcluster":{"Author":"Quentin
Grimonprez, Julien Jacques","Depends":"R (>= 2.10),
methods","Description":"Implementation of a model-based clustering algorithm
for\nranking data. Multivariate rankings as well as partial rankings are
taken\ninto account. This algorithm is based on an extension of the
Insertion\nSorting Rank (ISR) model for ranking data, which is a meaningful
and\neffective model parametrized by a position parameter (the modal
ranking,\nquoted by mu) and a dispersion parameter (quoted by pi). The
heterogeneity\nof the rank population is modelled by a mixture of ISR, whereas
conditional\nindependence assumption is considered for multivariate
rankings.","Imports":"Rcpp","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"Rankcluster","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Model-Based Clustering for Multivariate Partial
Ranking Data","Version":"0.93.1"},"RapidPolygonLookup":{"Author":"Markus Loecher
<markus.loecher@gmail.com> and Madhav Kumar
<madhavkumar2005@gmail.com>","Depends":"R(>= 2.10.0), sp, RANN, PBSmapping,
RgoogleMaps","Description":"Facilitates efficient polygon search using kd
trees.\nCoordinate level spatial data can be aggregated to higher
geographical\nidentities like census blocks, ZIP codes or police district
boundaries.\nThis process requires mapping each point in the given data set to
a\nparticular identity of the desired geographical hierarchy. Unless
efficient\ndata structures are used, this can be a daunting task.
The operation\npoint.in.polygon() from the package sp is computationally
expensive.\nHere, we exploit kd-trees as efficient nearest neighbor search
algorithm\nto dramatically reduce the effective number of polygons being
searched.","License":"GPL","NeedsCompilation":"no","Package":"RapidPolygonLookup","
Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Polygon lookup using kd
trees","Version":"0.1"},"Rarity":{"Author":"Boris
Leroy","Depends":"methods,graphics,stats","Description":"Allows calculation of
rarity weights for species and indices of rarity for assemblages of species
according to different methods (Leroy et al. 2012, 2013).","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"Rarity","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Calculation of Rarity Indices for Species and
Assemblages of\nSpecies","Version":"1.3-4"},"RaschSampler":{"Author":"Patrick Mair
[cre, aut],\nReinhold Hatzinger [aut],\nNorman D. Verhelst [aut]","Depends":"R (>=
3.0.0)","Description":"MCMC based sampling of binary matrices with fixed margins as
used in exact Rasch model tests.","Imports":"stats","License":"GPL-
2","NeedsCompilation":"yes","Package":"RaschSampler","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Rasch Sampler","Version":"0.8-8"},"RateDistortion":
{"Author":"Chris R. Sims","Description":"An implementation of routines for solving
rate-distortion problems.\nRate-distortion theory is a field within information
theory that\nexamines optimal lossy compression. That is, given that
some\ninformation must be lost, how can a communication channel be designed\nthat
minimizes the cost of communication error? Rate-distortion\ntheory is concerned
with the optimal (minimal cost) solution to such\ntradeoffs. An important tool for
solving rate-distortion problems is\nthe Blahut algorithm, developed by Richard
Blahut and described in:\n\nBlahut, R. E. (1972). Computation of channel capacity
and\nrate-distortion functions. IEEE Transactions on Information Theory,\nIT-18(4),
460-473.\n\nThis package implements the basic Blahut algorithm, and additionally
contains a number of `helper' functions, including a routine for searching for an
information channel that minimizes cost subject to a constraint on information
rate.","License":"GPL-
2","NeedsCompilation":"no","Package":"RateDistortion","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Routines for Solving Rate-Distortion
Problems","Version":"1.01"},"RbioRXN":{"Author":"Byoungnam Min, Byeonghyeok Park,
Kyoung Heon Kim and In-Geol Choi","Depends":"R (>= 3.0.3), fmcsR,
ChemmineR","Description":"To facilitate retrieving and processing biochemical
reaction data such as Rhea, MetaCyc, KEGG and Unipathway, the package provides the
functions to download and parse data, instantiate generic reaction and check mass-
balance. The package aims to construct an integrated metabolic network and genome-
scale metabolic model.","Imports":"plyr, RCurl, gdata, KEGGREST, data.table,
2)","NeedsCompilation":"no","Package":"RbioRXN","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Process Rhea, KEGG, MetaCyc, Unipathway Biochemical
Reaction\nData","Version":"1.5.1"},"Rbitcoin":{"Author":"Jan Gorecki","Depends":"R
(>= 2.10), data.table","Description":"Utilities related to Bitcoin. Unified markets
API interface\n(bitstamp, kraken, btce, bitmarket). Both public and private API
calls.\nIntegration of data structures for all markets. Support SSL. Read
Rbitcoin\ndocumentation (command: ?btc) for more information.","Imports":"RCurl,
digest, RJSONIO","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"Rbitcoin","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"R & bitcoin
integration","URL":"https:\/\/github.com\/jangorecki\/Rbitcoin","Version":"0.9.2"},
"Rblpapi":{"Author":"Whit Armstrong, Dirk Eddelbuettel and John
Laing","Description":"An R Interface to Bloomberg is provided via the Blp
API.","Imports":"Rcpp (>= 0.11.0), utils","License":"file
LICENSE","NeedsCompilation":"yes","Package":"Rblpapi","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"fts, xts, zoo, knitr, RUnit","Title":"R
Interface to Bloomberg","Version":"0.3.3"},"Rborist":{"Author":"Mark
Seligman","Depends":"Rcpp (>= 0.10.1), R(>= 3.1)","Description":"Scalable decision
tree training and prediction.","License":"MPL (>= 2) | GPL (>= 2) | file
LICENSE","NeedsCompilation":"yes","Package":"Rborist","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat","Title":"Extensible, Parallelizable
Implementation of the Random
Forest\nAlgorithm","URL":"http:\/\/www.suiji.org\/arborist,
https:\/\/github.com\/suiji\/Arborist","Version":"0.1-0"},"Rcapture":
{"Author":"Louis-Paul Rivest and Sophie Baillargeon","Description":"Estimation of
abundance and other of demographic parameters for closed\npopulations, open
populations and the robust design in capture-recapture experiments\nusing loglinear
models.","Imports":"stats, graphics","License":"GPL-
2","NeedsCompilation":"no","Package":"Rcapture","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Loglinear Models for Capture-Recapture
Experiments","Version":"1.4-2"},"RcellData":{"Author":"Alan Bush
<abush@fbmc.fcen.uba.ar>","Depends":"R (>= 2.15.0)","Description":"Example dataset
for 'Rcell' package. Contains images and cell data object.","License":"GPL-
2","NeedsCompilation":"no","Package":"RcellData","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Example Dataset for 'Rcell'
Package","URL":"http:\/\/www.embnet.qb.fcen.uba.ar,\nhttp:\/\/sourceforge.net\/proj
ects\/cell-id","Version":"1.3-2"},"Rcereal":{"Author":"Wush Wu, Randolph Voorhies,
and Shane Grant","Description":"To facilitate using 'cereal' with Rcpp.\n'cereal'
is a header-only C++11 serialization library.\n'cereal' takes arbitrary data types
and reversibly turns them into\ndifferent representations, such as compact binary
encodings, XML,\nor JSON. 'cereal' was designed to be fast, light-weight, and
easy\nto extend - it has no external dependencies and can be easily\nbundled with
other code or used standalone.","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"yes","Package":"Rcereal","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"Rcpp, git2r, httr, testthat, tools,
devtools","Title":"C++ Header Files of 'cereal'","Version":"1.1.2"},"Rcgmin":
{"Author":"John C. Nash","Description":"Conjugate gradient minimization of
nonlinear functions\nwith box constraints incorporating the Dai\/Yuan update.
This\nimplementation should be used in place of the \"CG\" algorithm\nof the
optim() function.","Imports":"numDeriv","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Rcgmin","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Conjugate Gradient Minimization of Nonlinear
Functions","Version":"2013-2.21"},"Rchoice":{"Author":"Mauricio Sarrias
<msarrias86@gmail.com>","Depends":"R (>= 3.1.2), Formula, maxLik","Description":"An
implementation of simulated maximum likelihood method for the estimation of Binary
(Probit and Logit), Ordered (Probit and Logit) and Poisson models with random
parameters for cross-sectional and longitudinal data.","Imports":"msm, plm,
plotrix, stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Rchoice","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"car, lmtest, memisc, pglm, sandwich","Title":"Discrete
Choice (Binary, Poisson and Ordered) Models with
Random\nParameters","URL":"http:\/\/msarrias.weebly.com\/rchoice-package-in-
r.html","Version":"0.3"},"Rclusterpp":{"Author":"Michael Linderman [aut],\nRobert
Bruggner [cre]","Depends":"R (>= 2.12.0), Rcpp (>= 0.10.4), RcppEigen (>=
0.1.2)","Description":"Provide flexible native clustering routines that can
be\nlinked against in downstream packages.","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"Rclusterpp","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"RUnit, rbenchmark, fastcluster,
inline","Title":"Linkable C++
clustering","URL":"https:\/\/github.com\/nolanlab\/Rclusterpp","Version":"0.2.3"},"
Rcmdr":{"Author":"John Fox [aut, cre],\nMilan Bouchet-Valat [aut],\nLiviu Andronic
[ctb],\nMichael Ash [ctb],\nTheophilius Boye [ctb],\nStefano Calza [ctb],\nAndy
Chang [ctb],\nPhilippe Grosjean [ctb],\nRichard Heiberger [ctb],\nKosar Karimi Pour
[ctb],\nG. Jay Kerns [ctb],\nRenaud Lancelot [ctb],\nMatthieu Lesnoff [ctb],\nUwe
Ligges [ctb],\nSamir Messad [ctb],\nMartin Maechler [ctb],\nRobert Muenchen
[ctb],\nDuncan Murdoch [ctb],\nErich Neuwirth [ctb],\nDan Putler [ctb],\nBrian
Ripley [ctb],\nMiroslav Ristic [ctb],\nPeter Wolf [ctb],\nKevin Wright
[ctb]","Depends":"R (>= 3.2.0), grDevices, utils, splines, RcmdrMisc (>= 1.0-
3),\ncar (>= 2.1-2)","Description":"\nA platform-independent basic-statistics GUI
(graphical user interface) for R, based on the tcltk package.","Imports":"tcltk,
tcltk2 (>= 1.2-6), abind, graphics, methods, stats,\nrelimp (>= 1.0-
5)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Rcmdr","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"aplpack, colorspace, effects (>= 3.0-1), e1071,
foreign,\ngrid, Hmisc, knitr, lattice, leaps, lmtest, markdown, MASS,\nmgcv,
multcomp (>= 0.991-2), nlme, nnet, readxl, rgl,\nrglwidget, rmarkdown (>= 0.9.5),
sem (>= 2.1-1)","Title":"R Commander","URL":"http:\/\/www.r-
project.org,\nhttp:\/\/socserv.socsci.mcmaster.ca\/jfox\/Misc\/Rcmdr\/","Version":"
2.2-4"},"RcmdrMisc":{"Author":"John Fox [aut, cre],\nRobert Muenchen [ctb],\nDan
Putler [ctb]","Depends":"R (>= 3.0.0), utils, car,
sandwich","Description":"\nVarious statistical, graphics, and data-management
functions used by the Rcmdr package in the R Commander GUI for
R.","Imports":"abind, colorspace, Hmisc, MASS, e1071, readxl, graphics,\ngrDevices,
2)","NeedsCompilation":"no","Package":"RcmdrMisc","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"R
Commander Miscellaneous Functions","URL":"http:\/\/www.r-project.org,
http:\/\/socserv.socsci.mcmaster.ca\/jfox\/","Version":"1.0-4"},"RcmdrPlugin.BCA":
{"Author":"Dan Putler","Depends":"R (>= 3.0.0), Rcmdr (>= 2.1-0), BCA (>= 0.9-3),
flexclust","Description":"An Rcmdr \"plug-in\" to accompany the book Customer
and\nBusiness Analytics: Applied Data Mining for Business Decision\nMaking Using R
by Daniel S. Putler and Robert E. Krider.","Imports":"car (>= 2.0-21), RcmdrMisc
(>= 1.0-1), nnet, foreign, rpart,\nrpart.plot","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.BCA","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"rgl","Title":"Rcmdr Plug-In for Business and
Customer Analytics","URL":"http:\/\/www.customeranalyticsbook.com","Version":"0.9-
8"},"RcmdrPlugin.DoE":{"Author":"Ulrike Groemping [aut, cre],\nFox John
[ctb]","Depends":"R (>= 2.10.0), utils, DoE.base (>= 0.22-8), FrF2 (>= 1.2-
10),\nDoE.wrapper (>= 0.8-6), tcltk, relimp","Description":"The package provides a
platform-independent GUI for design of experiments.\nIt is implemented as a plugin
to the R-Commander, which is a more general\ngraphical user interface for
statistics in R based on tcl\/tk.\nDoE functionality can be accessed through the
menu Design that is added to the\nR-Commander menus.","Imports":"Rcmdr,
RcmdrMisc","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.DoE","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"FrF2.catlg128","Title":"R Commander Plugin for
(industrial) Design of Experiments","URL":"http:\/\/prof.beuth-
hochschule.de\/groemping\/DoE","Version":"0.12-3"},"RcmdrPlugin.EACSPIR":
{"Author":"Maribel Pero <mpero@ub.edu>, David Leiva <dleivaur@ub.edu>,\nJoan
Guardia <jguardia@ub.edu>, Antonio Solanas
<antonio.solanas@ub.edu>","Depends":"R2HTML, abind, ez, nortest,
reshape","Description":"Este paquete proporciona una interfaz grafica de usuario
(GUI) para algunos de los procedimientos estadisticos detallados en un curso de
'Estadistica aplicada a las Ciencias Sociales mediante el programa informatico R'
(EACSPIR). LA GUI se ha desarrollado como un Plugin del programa R-
Commander.","Imports":"Rcmdr (>= 2.1-6), RcmdrMisc","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.EACSPIR","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Title":"Plugin de R-Commander para el Manual
'EACSPIR'","Version":"0.2-2"},"RcmdrPlugin.EBM":{"Author":"Daniel-Corneliu Leucuta
<danny.ldc@gmail.com>","Depends":"R (>= 2.10), Rcmdr (>= 1.7.0), epiR,
abind","Description":"Rcmdr plug-in GUI extension for Evidence Based Medicine
medical indicators calculations (Sensitivity, specificity, absolute risk reduction,
relative risk, ...).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.EBM","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Rcmdr Evidence Based Medicine Plug-in
Package","Version":"1.0-10"},"RcmdrPlugin.EZR":{"Author":"Yoshinobu
Kanda","Depends":"R (>= 3.0.0)","Description":"EZR (Easy R) adds a variety of
statistical functions, including survival analyses, ROC analyses, metaanalyses,
sample size calculation, and so on, to the R commander. EZR enables point-and-click
easy access to statistical functions, especially for medical statistics. EZR is
platform-independent and runs on Windows, Mac OS X, and UNIX. Its complete manual
is available only in Japanese (Chugai Igakusha, ISBN: 978-4-498-10901-8 or Nankodo,
ISBN: 978-4-524-26158-1), but an report that introduced the investigation of EZR
was published in Bone Marrow Transplantation (Nature Publishing Group) as an Open
article. This report can be used as a simple manual. It can be freely downloaded
from the journal website as shown below.","Imports":"Rcmdr (>=
2.2.0)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.EZR","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"abind, aod, aplpack, car, clinfun, cmprsk,
foreign, meta,\nmetatest, multcomp, mvtnorm, optmatch, pROC, tableone,
readxl","Title":"R Commander Plug-in for the EZR (Easy R)
Package","URL":"\nhttp:\/\/www.nature.com\/bmt\/journal\/vaop\/ncurrent\/pdf\/bmt20
12244a.pdf\nhttp:\/\/www.jichi.ac.jp\/saitama-
sct\/SaitamaHP.files\/statmedEN.html","Version":"1.32"},"RcmdrPlugin.EcoVirtual":
{"Author":"Alexandre Adalardo de Oliveira and Paulo Inacio Prado
<ecovirtualpackage@gmail.com>","Depends":"Rcmdr (>= 1.4-0),
EcoVirtual","Description":"This package provides an Rcmdr \"plug-in\" for the
EcoVirtual package and was designed primarily for teaching ecological models using
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.EcoVirtual","Repository":"http:\
/\/cran.csiro.au\/src\/contrib","Title":"Rcmdr EcoVirtual
Plugin","URL":"http:\/\/ecovirtual.ib.usp.br","Version":"0.1"},"RcmdrPlugin.Export"
:{"Author":"Liviu Andronic","Depends":"Rcmdr (>= 2.2-2), xtable,
Hmisc","Description":"Export Rcmdr output to LaTeX or HTML code. The\nplug-in was
originally intended to facilitate exporting Rcmdr\noutput to formats other than
ASCII text and to provide R\nnovices with an easy-to-use, easy-to-access reference
on\nexporting R objects to formats suited for printed output. The\npackage
documentation contains several pointers on creating\nreports, either by using
conventional word processors or\nLaTeX\/LyX.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.Export","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Title":"Export R Output to LaTeX or
HTML","Version":"0.3-1"},"RcmdrPlugin.FactoMineR":{"Author":"Francois Husson, Julie
Josse, Sebastien Le","Depends":"FactoMineR","Description":"Rcmdr Plugin for the
'FactoMineR' package.","Imports":"Rcmdr (>= 2.0-0), tcltk","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.FactoMineR","Repository":"http:\
/\/cran.csiro.au\/src\/contrib","Title":"Graphical User Interface for
FactoMineR","URL":"http:\/\/factominer.free.fr, http:\/\/www.agrocampus-
ouest.fr\/math\/","Version":"1.6-0"},"RcmdrPlugin.GWRM":{"Author":"Silverio
Vilchez-Lopez [aut, cre],\nAntonio Jose Saez-Castillo [aut],\nMaria Jose Olmo-
Jimenez [aut]","Depends":"R (>= 3.0.0), GWRM (>= 2.1.0.1), RcmdrMisc (>= 1.0-
2)","Description":"Provides an Rcmdr plug-in based on the 'GWRM'
package.","Imports":"Rcmdr (>= 2.0-0)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.GWRM","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"R Commander Plug-in for Fitting Generalized
Waring Regression\nModels","Version":"1.0.1"},"RcmdrPlugin.HH":{"Author":"Richard
M. Heiberger, with contributions from Burt Holland","Depends":"R (>= 3.0.2),
HH","Description":"Rcmdr menu support for many of the functions in the HH
package.\nThe focus is on menu items for functions we use in our
introductory\ncourses.","Imports":"Rcmdr (>= 2.0-0), lattice, mgcv","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.HH","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Rcmdr Support for the HH Package","Version":"1.1-
45"},"RcmdrPlugin.IPSUR":{"Author":"G. Jay Kerns [aut, cre],\nTheophilus Boye
[ctb],\nTyler Drombosky [ctb]","Description":"\nThis package is an R Commander
plugin that accompanies IPSUR, an Introduction to Probability and Statistics Using
R.","Imports":"Rcmdr (>= 2.1-0)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.IPSUR","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"abind, car, distr, distrEx, e1071, effects
(>= 1.0-7),\nforeign, grid, lattice, lmtest, MASS, mgcv, multcomp (>=\n0.991-2),
nlme, nnet, qcc, relimp, RODBC","Title":"An IPSUR Plugin for the R
Commander","URL":"http:\/\/www.r-project.org, http:\/\/ipsur.org\/","Version":"0.2-
1"},"RcmdrPlugin.KMggplot2":{"Author":"Triad sou. and Kengo NAGASHIMA","Depends":"R
(>= 3.1.3), grid, Rcmdr (>= 2.1-7), ggplot2 (>= 2.0.0)","Description":"A GUI front-
end for ggplot2 allows Kaplan-Meier plot, histogram,\nQ-Q plot, box plot, errorbar
plot, scatter plot, line chart, pie chart,\nbar chart, contour plot, and
distribution plot.","Imports":"stats, methods, utils, grDevices, graphics, ggthemes
(>=\n3.0.0), plyr (>= 1.8.3), RColorBrewer (>= 1.1-2), scales (>=\n0.3.0), survival
(>= 2.38-3), tcltk2 (>= 1.2-11)","License":"GPL-
2","NeedsCompilation":"no","Package":"RcmdrPlugin.KMggplot2","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Suggests":"extrafont, knitr, rmarkdown","Title":"An
Rcmdr Plug-in for Kaplan-Meier Plots and Other Plots by Using\nthe ggplot2
Package","Version":"0.2-3"},"RcmdrPlugin.MA":{"Author":"A. C. Del Re","Depends":"R
(>= 2.15)","Description":"Easy to use interface for conducting meta-analysis in R.
This\npackage is an Rcmdr-plugin, which allows the user to conduct analyses in
a\nmenu-driven, graphical user interface environment (e.g., CMA, SPSS). It\nuses
recommended procedures as described in The Handbook of Research\nSynthesis and
Meta-Analysis (Cooper, Hedges, & Valentine, 2009).","Imports":"Rcmdr, MAd,
metafor","License":"GPL-
2","NeedsCompilation":"no","Package":"RcmdrPlugin.MA","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"knitr, rmarkdown, compute.es, ggplot2,
gridExtra, scales","Title":"Graphical User Interface for Conducting Meta-Analyses
in R","URL":"http:\/\/acdelre.weebly.com\/","Version":"0.0-
2"},"RcmdrPlugin.MPAStats":{"Author":"Andrew Heiss, Richard Payne, Christa Schank,
Jessica Reese","Depends":"Rcmdr (>= 1.4-0), ordinal","Description":"Extends R
Commander with a unified menu of new and pre-existing\nstatistical functions
related to public management and policy analysis\nstatistics. Functions and menus
have been renamed according to the\nusage in PMGT 630 in the Master of Public
Administration program at\nBrigham Young University.","License":"GPL (>
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.MPAStats","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Title":"R
Commander Plug-in for MPA Statistics","Version":"1.2.0"},"RcmdrPlugin.NMBU":
{"Author":"Kristian Hovde Liland [aut, cre],\nSolve Sæbø [aut]","Depends":"R (>=
3.0.0), mixlm (>= 1.1.1), MASS, pls, xtable","Description":"An R Commander \"plug-
in\" extending functionality of linear models and providing an interface to Partial
Least Squares Regression and Linear and Quadratic Discriminant analysis. Several
statistical summaries are extended, predictions are offered for additional types of
analyses, and extra plots, tests and mixed models are available.","Imports":"Rcmdr
(>= 2.1-7), tcltk","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.NMBU","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"lme4, leaps, mvtnorm, gmodels, abind,
lattice, pbkrtest, vcd,\nmultcomp, e1071, nnet","Title":"R Commander Plug-in for
University Level Applied Statistics","Version":"1.8.5"},"RcmdrPlugin.RMTCJags":
{"Author":"Marcelo Goulart Correia <mgoulart.inc@gmail.com>","Depends":"R (>=
3.0.0)","Description":"Mixed Treatment Comparison is a methodology to compare
directly and\/or indirectly health strategies (drugs, treatments, devices). This
package provides an Rcmdr \"plug-in\" to perform Mixed Treatment Comparison for
binary outcome using BUGS code from Bristol University (Lu and
Ades).","Imports":"Rcmdr (>= 2.0.0), runjags, rmeta, igraph, coda","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.RMTCJags","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Title":"R MTC Jags Rcmdr Plugin","Version":"1.0-
1"},"RcmdrPlugin.ROC":{"Author":"Daniel-Corneliu Leucuta [aut, cre],\nMihaela
Hedesiu [ctb],\nAndrei Achimas [ctb],\nOana Almasan [ctb]","Depends":"R (>= 2.10),
Rcmdr (>= 1.7.0), ROCR, pROC, ResourceSelection","Description":"Rcmdr GUI extension
plug-in for Receiver Operator Characteristic tools from pROC and ROCR packages.
Also it ads a Rcmdr GUI extension for Hosmer and Lemeshow GOF test from the package
ResourceSelection.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.ROC","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Rcmdr Receiver Operator Characteristic Plug-In
PACKAGE","Version":"1.0-18"},"RcmdrPlugin.SCDA":{"Author":"Isis Bulte and Patrick
Onghena","Depends":"SCVA, SCRT, SCMA","Description":"Provides a GUI for the SCVA,
SCRT and SCMA packages. The package is written as an Rcmdr
plugin.","Imports":"Rcmdr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.SCDA","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Rcmdr Plugin for Designing and Analyzing Single-
case Experiments","Version":"1.1"},"RcmdrPlugin.SLC":{"Author":"Antonio Solanas
<antonio.solanas@ub.edu>, Rumen Manolov\n<rrumenov13@ub.edu & Patrick
Onghena\n<patrick.onghena@ped.kuleuven.be>.","Depends":"SLC","Description":"This
package provides a GUI for the SLC package, it is\nwritten as an Rcmdr plug-
in.","Imports":"Rcmdr (>= 1.9-3)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.SLC","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"SLC Rcmdr Plug-
in","Version":"0.2"},"RcmdrPlugin.SM":{"Author":"Stéphane Champely <champely@univ-
lyon1.fr>","Depends":"Rcmdr (>= 1.3-0), tcltk, car, RColorBrewer,
colorspace,vcd","Description":"This package provides an Rcmdr \"plug-in\" for
studying\nsport management data.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.SM","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"tkrplot","Title":"Rcmdr Sport Management Plug-
In","Version":"0.3.1"},"RcmdrPlugin.TeachingDemos":{"Author":"John Fox
<jfox@mcmaster.ca>","Depends":"rgl, TeachingDemos (>= 2.9)","Description":"This
package provides an Rcmdr \"plug-in\" based on the\nTeachingDemos package, and is
primarily for illustrative\npurposes.","Imports":"Rcmdr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.TeachingDemos","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Suggests":"tkrplot","Title":"Rcmdr Teaching
Demos Plug-In","Version":"1.0-7"},"RcmdrPlugin.UCA":{"Author":"Manuel Munoz-Marquez
<manuel.munoz@uca.es>","Depends":"Rcmdr (>= 1.6), randtests,
tseries","Description":"Some extension to Rcmdr (R Commander) made by R-UCA project
and used in teaching statistics at University of Cadiz (UCA).","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"RcmdrPlugin.UCA","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"UCA Rcmdr Plug-
in","URL":"http:\/\/knuth.uca.es\/RcmdrPlugin.UCA","Version":"2.0-
5"},"RcmdrPlugin.coin":{"Author":"Daniel-Corneliu Leucuta
<danny.ldc@gmail.com>","Depends":"R (>= 2.10), Rcmdr (>= 1.7.0), coin, survival,
multcomp","Description":"This package provides a Rcmdr \"plug-in\" based on coin
(Conditional Inference Procedures in a Permutation Test Framework).","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.coin","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Rcmdr Coin Plug-In","Version":"1.0-
22"},"RcmdrPlugin.depthTools":{"Author":"Sara Lopez-Pintado <sl2929@columbia.edu>
and Aurora Torrente\n<etorrent@est-econ.uc3m.es>.","Depends":"Rcmdr (>= 1.4-0),
tcltk, depthTools","Description":"This package provides an Rcmdr plug-in based on
the\ndepthTools package, which implements different robust\nstatistical tools for
the description and analysis of gene\nexpression data based on the Modified Band
Depth, namely, the\nscale curves for visualizing the dispersion of one or
various\ngroups of samples (e.g. types of tumors), a rank test to decide\nwhether
two groups of samples come from a single distribution\nand two methods of
supervised classification techniques, the DS\nand TAD methods.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.depthTools","Repository":"http:\
/\/cran.csiro.au\/src\/contrib","Title":"R commander Depth Tools Plug-
In","Version":"1.3"},"RcmdrPlugin.doex":{"Author":"Erin
Hodgess<hodgesse@uhd.edu>","Depends":"Rcmdr (>= 1.7-0),
multcomp","Description":"This package provides an Rcmdr \"plug-in\" based on
the\nDesign of experiments class Stat 4309","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.doex","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Rcmdr plugin for Stat 4309
course","Version":"0.2.0"},"RcmdrPlugin.epack":{"Author":"Erin
Hodgess<hodgesse@uhd.edu>","Depends":"Rcmdr (>= 1.8-3), TeachingDemos,
tseries,\nabind,MASS,xts,forecast","Description":"This package provides an
Rcmdr \"plug-in\" based on the time\nseries functions. Contributors: G. Jay Kerns,
John Fox, and\nRichard Heiberger.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.epack","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Rcmdr plugin for time
series","Version":"1.2.5"},"RcmdrPlugin.lfstat":{"Author":"Daniel Koffler and
Gregor Laaha","Depends":"R (>= 2.14.0), lfstat","Description":"This package
provides an Rcmdr \"plug-in\" based on the\nlfstat package for low flow
analysis.","Imports":"Rcmdr (>= 1.9-5)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.lfstat","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Title":"Rcmdr Plug-In for low flow
analysis","Version":"0.7"},"RcmdrPlugin.mosaic":{"Author":"Erich Neuwirth
<erich.neuwirth@univie.ac.at>","Depends":"ENmisc, vcd (>= 1.2-11), Hmisc,
Rcmdr","Description":"Rcmdr menu items to display mosaic and assoc plots Allows\nto
visually restructure the underlying structables Developed\nafter extended
discussions with Rich Heiberger","License":"GPL-
2","NeedsCompilation":"no","Package":"RcmdrPlugin.mosaic","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Adds menu items to produce mosaic plots and
assoc plots to Rcmdr","Version":"1.0-7"},"RcmdrPlugin.orloca":{"Author":"Fernando
Fernandez-Palacin <fernando.fernandez@uca.es> and\nManuel Munoz-Marquez
<manuel.munoz@uca.es>","Depends":"orloca (>= 4.1), orloca.es (>=
4.1)","Description":"This package provides a GUI for the orloca package, it
is\ndeveloped as an Rcmdr plug-in.","Imports":"Rcmdr","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"RcmdrPlugin.orloca","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Title":"orloca Rcmdr Plug-
in","URL":"http:\/\/knuth.uca.es\/orloca","Version":"4.1"},"RcmdrPlugin.plotByGroup
":{"Author":"Poul Svante Eriksen with contributions by Ege Rubak","Depends":"R (>=
2.13.0), Rcmdr (>= 1.4-6),lattice,grid,grDevices","Description":"Rcmdr menu support
for some of the graphics by group in\nthe lattice package","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.plotByGroup","Repository":"http:
\/\/cran.csiro.au\/src\/contrib","Title":"Rcmdr plots by group using
lattice","Version":"0.1-0"},"RcmdrPlugin.pointG":{"Author":"Stephane Champely
<champely@univ-lyon1.fr>","Depends":"tcltk, Rcmdr,
RColorBrewer","Description":"This package provides a Rcmdr \"plug-in\" to analyze
questionnaire data.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.pointG","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Suggests":"YaleToolkit, MASS, lattice, qgraph, maps,
ade4, effects,\nabind, nnet, vcd, car, gpairs, Hmisc","Title":"Graphical POINT of
view for questionnaire data Rcmdr Plug-In","Version":"0.6.6"},"RcmdrPlugin.qual":
{"Author":"Erin Hodgess<hodgesse@uhd.edu>","Depends":"R (>=
3.0)","Description":"This package provides an Rcmdr \"plug-in\" based on
the\nQuality control class Stat 4300","Imports":"Rcmdr (>= 2.0-0),
tcltk,stats","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"RcmdrPlugin.qual","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"qcc,sp,vcd,MASS","Title":"Rcmdr plugin for
quality control course","Version":"2.2.6"},"RcmdrPlugin.sampling":{"Author":"Susie
Jentoft and Johan Heldal","Depends":"lpSolve, sampling, MASS","Description":"This
package includes tools for calculating sample sizes and\nselecting samples using
various
sampling designs. This package is an extension\nof RcmdrPlugin.EHESsampling which
was developed as part of the EHES pilot project.\nThe EHES Pilot project has
received funding from the European Commission and\nDG Sanco. The views expressed
here are those of the authors and they do not represent\nCommission's official
position.","Imports":"Rcmdr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.sampling","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Title":"Tools for sampling in Official Statistical
Surveys","Version":"1.1"},"RcmdrPlugin.seeg":{"Author":"Miguel F.
Acevedo","Depends":"Rcmdr, seeg, spatstat, sgeostat","Description":"Supports the
text book Acevedo, M.F (2013) \"Data Analysis\nand Statistics for Geography,
Environmental Science, and\nEngineering\" CRC Press","License":"GPL-
2","NeedsCompilation":"no","Package":"RcmdrPlugin.seeg","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Rcmdr Plugin for
seeg","Version":"1.0"},"RcmdrPlugin.sos":{"Author":"Liviu Andronic","Depends":"sos
(>= 1.2-3)","Description":"Rcmdr interface to the 'sos' package. The plug-in
renders\nthe 'sos' searching functionality easily accessible via the Rcmdr\nmenus.
It also simplifies the task of performing multiple searches and\nsubsequently
obtaining the union or the intersection of the results.","Imports":"Rcmdr (>= 2.0-
1), tcltk, tcltk2 (>= 1.2-7)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.sos","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Efficiently search the R help
pages","Version":"0.3-0"},"RcmdrPlugin.steepness":{"Author":"David Leiva
<dleivaur@ub.edu> & Han de Vries\n<J.deVries@bio.uu.nl>","Depends":"Rcmdr (>= 2.1-
2), tcltk, steepness","Description":"This package provides a GUI for the steepness
package, it\nis written as an Rcmdr plug-in.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.steepness","Repository":"http:\/
\/cran.csiro.au\/src\/contrib","Title":"Steepness Rcmdr Plug-in","Version":"0.3-
2"},"RcmdrPlugin.survival":{"Author":"John Fox","Depends":"R (>= 2.10), survival,
date, stats","Description":"An R Commander plug-in for the survival\npackage, with
dialogs for Cox models, parametric survival regression models,\nestimation of
survival curves, and testing for differences in survival\ncurves, along with data-
management facilities and a variety of tests,\ndiagnostics and
graphs.","Imports":"Rcmdr (>= 2.2-1)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.survival","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Title":"R Commander Plug-in for the 'survival'
Package","Version":"1.1-0"},"RcmdrPlugin.temis":{"Author":"Milan Bouchet-Valat
[aut, cre],\nGilles Bastin [aut]","Depends":"methods, tm (>= 0.6), NLP, slam, zoo,
lattice","Description":"An 'R Commander' plug-in providing an integrated solution
to perform\na series of text mining tasks such as importing and cleaning a corpus,
and\nanalyses like terms and documents counts, vocabulary tables, terms\nco-
occurrences and documents similarity measures, time series
analysis,\ncorrespondence analysis and hierarchical clustering. Corpora can be
imported\nfrom spreadsheet-like files, directories of raw text files, 'Twitter'
queries,\nas well as from 'Dow Jones Factiva', 'LexisNexis', 'Europresse' and
'Alceste' files.","Imports":"Rcmdr (>= 2.1-1), tcltk, tcltk2, utils, ca, R2HTML (>=
2.3.0),\nRColorBrewer, latticeExtra, stringi","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RcmdrPlugin.temis","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"SnowballC, ROpenOffice, RODBC,
tm.plugin.factiva (>= 1.4),\ntm.plugin.lexisnexis (>= 1.1), tm.plugin.europresse
(>= 1.1),\ntm.plugin.alceste (>= 1.1), twitteR","Title":"Graphical Integrated Text
Mining Solution","URL":"https:\/\/r-forge.r-project.org\/projects\/r-
temis\/","Version":"0.7.5"},"Rcolombos":{"Author":"Paolo Sonego
<paolo.sonego@fmach.it>","Depends":"httr","Description":"Provides programmatic
access to Colombos, a web based\ninterface for exploring and analyzing
comprehensive organism-specific\ncross-platform expression compendia of bacterial
organisms.","License":"GPL-
3","NeedsCompilation":"no","Package":"Rcolombos","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Interface to Colombos Compendia using the Exposed REST
API","URL":"http:\/\/colombos.net\/,http:\/\/legacyv2.colombos.net\/","Version":"2.
0.2"},"Rcplex":{"Author":"Hector Corrada Bravo, with contributions from Stefan
Theussl and Kurt Hornik","Depends":"R (>= 2.6.0), slam","Description":"R interface
to CPLEX solvers for linear, quadratic, and (linear and quadratic) mixed integer
programs. Support for quadratically constrained programming is available. A working
installation of CPLEX is required for usage of the Rcplex package. See the
file \"INSTALL\" for details on how to install the Rcplex package in Linux\/Unix-
like systems and Windows systems. Support for sparse matrices is provided by an S3-
style class \"simple_triplet_matrix\" from package slam and by objects from the
Matrix package class hierarchy.","Enhances":"Matrix","License":"LGPL (>=
2.0)","NeedsCompilation":"yes","Package":"Rcplex","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"R interface to CPLEX","URL":"http:\/\/R-Forge.R-
project.org\/projects\/rcplex","Version":"0.3-2"},"Rcpp":{"Author":"Dirk
Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey,\nQiang Kou, Douglas Bates
and John Chambers","Depends":"R (>= 3.0.0)","Description":"The 'Rcpp' package
provides R functions as well as C++ classes which\noffer a seamless integration of
R and C++. Many R data types and objects can be\nmapped back and forth to C++
equivalents which facilitates both writing of new\ncode as well as easier
integration of third-party libraries. Documentation\nabout 'Rcpp' is provided by
several vignettes included in this package, via the\n'Rcpp Gallery' site at
<http:\/\/gallery.rcpp.org>, the paper by Eddelbuettel and\nFrancois (2011, JSS),
and the book by Eddelbuettel (2013, Springer); see\n'citation(\"Rcpp\")' for
details on these last two.","Imports":"methods, utils","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"Rcpp","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"RUnit, inline, rbenchmark, highlight, pkgKitten (>=
0.1.2)","Title":"Seamless R and C++ Integration","URL":"http:\/\/www.rcpp.org,
http:\/\/dirk.eddelbuettel.com\/code\/rcpp.html,\nhttps:\/\/github.com\/RcppCore\/R
cpp","Version":"0.12.4"},"Rcpp11":{"Author":"Romain Francois [aut, cre],\nKevin
Ushey [aut],\nJohn Chambers [ctb]","Depends":"R (>= 3.1.2)","Description":"Rcpp11
includes a header only C++11 library that facilitates\nintegration between R and
modern C++.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"Rcpp11","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"R and C++11","Version":"3.1.2.0"},"RcppAnnoy":
{"Author":"Dirk Eddelbuettel","Depends":"R (>= 3.1)","Description":"'Annoy' is a
small C++ library for Approximate Nearest Neighbors\nwritten for efficient memory
usage as well an ability to load from \/ save to\ndisk. This package provides an R
interface by relying on the 'Rcpp' package,\nexposing the same interface as the
original Python wrapper to 'Annoy'. See\n<https:\/\/github.com\/spotify\/annoy> for
more on 'Annoy'. 'Annoy' is released\nunder Version 2.0 of the Apache License. Also
included is a small Windows\nport of 'mmap' which is released under the MIT
license.","Imports":"methods, Rcpp (>= 0.11.3)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"RcppAnnoy","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"RUnit","Title":"'Rcpp' Bindings for 'Annoy', a
Library for Approximate Nearest\nNeighbors","Version":"0.0.7"},"RcppArmadillo":
{"Author":"Dirk Eddelbuettel, Romain Francois and Doug
Bates","Description":"'Armadillo' is a templated C++ linear algebra library (by
Conrad\nSanderson) that aims towards a good balance between speed and ease of use.
Integer,\nfloating point and complex numbers are supported, as well as a subset
of\ntrigonometric and statistics functions. Various matrix decompositions
are\nprovided through optional integration with LAPACK and ATLAS libraries.\nThe
'RcppArmadillo' package includes the header files from the templated\n'Armadillo'
library. Thus users do not need to install 'Armadillo' itself in\norder to use
'RcppArmadillo'. 'Armadillo' is licensed under the MPL 2.0, while\n'RcppArmadillo'
(the 'Rcpp' bindings\/bridge to Armadillo) is licensed under the\nGNU GPL version 2
or later, as is the rest of 'Rcpp'.","Imports":"Rcpp (>= 0.11.0), stats,
2)","NeedsCompilation":"yes","Package":"RcppArmadillo","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"RUnit, Matrix, pkgKitten","Title":"'Rcpp'
Integration for the 'Armadillo' Templated Linear
Algebra\nLibrary","URL":"https:\/\/github.com\/RcppCore\/RcppArmadillo,\nhttp:\/\/a
rma.sourceforge.net\/,\nhttp:\/\/dirk.eddelbuettel.com\/code\/rcpp.armadillo.html",
"Version":"0.6.700.3.0"},"RcppBDT":{"Author":"Dirk Eddelbuettel and Romain
Francois","Depends":"R (>= 3.1.0)","Description":"This package provides R with
access to Boost Date_Time\nfunctionality by using Rcpp modules.\n\nFunctionality
from Boost Date_Time for dates, durations (both for days\nand datetimes),
timezones, and posix time (\"ptime\") is provided. The posix\ntime implementation
can support high-resolution of up to nano-second\nprecision by using 96 bits
(instead of R's 64) to present a ptime object.","Imports":"Rcpp (>= 0.11.0),
2)","NeedsCompilation":"yes","Package":"RcppBDT","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Rcpp bindings for the Boost Date_Time
library","Version":"0.2.3"},"RcppCNPy":{"Author":"Dirk Eddelbuettel and Wush
Wu","Depends":"R (>= 3.1.0)","Description":"The
cnpy library written by Carl Rogers provides read and write\nfacilities for files
created with (or for) the NumPy extension for Python.\nVectors and matrices of
numeric types can be read or written to and from\nfiles as well as compressed
files. Support for integer files is available if\nthe package has been built with
-std=c++11 which is the default starting\nwith release 0.2.3 following the release
of R 3.1.0.","Imports":"methods, Rcpp","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"RcppCNPy","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"highlight","Title":"Read-Write Support for NumPy
Files via Rcpp","Version":"0.2.4"},"RcppClassic":{"Author":"Dirk Eddelbuettel and
Romain Francois, with contributions by David Reiss,\nand based on code written
during 2005 and 2006 by Dominick Samperi","Depends":"R (>=
2.12.0)","Description":"The RcppClassic package provides a deprecated C++ library
which\nfacilitates the integration of R and C++.\n\nNew projects should use the new
Rcpp API in the Rcpp package.","Imports":"Rcpp (>= 0.10.2), methods","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"RcppClassic","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"RUnit, inline, highlight","Title":"Deprecated
'classic' Rcpp API","Version":"0.9.6"},"RcppClassicExamples":{"Author":"Dirk
Eddelbuettel and Romain Francois, based on code written\nduring 2005 and 2006 by
Dominick Samperi","Depends":"R (>= 2.15.2), Rcpp (>= 0.10.2), RcppClassic (>=
0.9.3)","Description":"The Rcpp package contains a C++ library that
facilitates\nthe integration of R and C++ in various ways via a rich API.\nThis API
was preceded by an earlier version which has been\ndeprecated since 2010 (but is
still supported to provide\nbackwards compatability in the package RcppClassic).
This\npackage RcppClassicExamples provides usage examples for the\nolder,
deprecated API. There is also a corresponding package\nRcppExamples package with
examples for the newer, current API\nwhich we strongly recommend as the basis for
all new\ndevelopment.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"RcppClassicExamples","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Suggests":"RUnit","Title":"Examples using
RcppClassic to interface R and C+
+","URL":"http:\/\/dirk.eddelbuettel.com\/code\/rcpp.html,\nhttp:\/\/romainfrancois
.blog.free.fr\/index.php?category\/R-package\/Rcpp","Version":"0.1.1"},"RcppDE":
{"Author":"Dirk Eddelbuettel extending DEoptim (by David Ardia, Katharine
Mullen,\nBrian Peterson, Joshua Ulrich) which itself is based on DE-Engine (by
Rainer Storn)","Description":"An efficient C++ based implementation of the
'DEoptim'\nfunction which performs global optimization by differential
evolution.\nIts creation was motivated by trying to see if the old
approximation \"easier,\nshorter, faster: pick any two\" could in fact be extended
to achieving all\nthree goals while moving the code from plain old C to modern C++.
The\ninitial version did in fact do so, but a good part of the gain was due to\nan
implicit code review which eliminated a few inefficiencies which have\nsince been
eliminated in 'DEoptim'.","Imports":"Rcpp","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"RcppDE","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"inline, DEoptim, lattice","Title":"Global Optimization
by Differential Evolution in C++","Version":"0.1.5"},"RcppDL":{"Author":"Qiang Kou,
Yusuke Sugomori","Description":"This package is based on the C++ code from Yusuke
Sugomori,\nwhich implements basic machine learning methods with\nmany layers (deep
learning), including dA (Denoising Autoencoder),\nSdA (Stacked Denoising
Autoencoder), RBM (Restricted Boltzmann machine) and\nDBN (Deep Belief
Nets).","Imports":"methods, Rcpp (>= 0.11.2)","License":"GPL-
3","NeedsCompilation":"yes","Package":"RcppDL","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Deep Learning Methods via
Rcpp","URL":"https:\/\/github.com\/thirdwing\/RcppDL","Version":"0.0.5"},"RcppEigen
":{"Author":"Douglas Bates, Dirk Eddelbuettel, Romain Francois, and Yixuan
Qiu;\nthe authors of Eigen for the included version of Eigen","Depends":"R (>=
2.15.1)","Description":"R and 'Eigen' integration using 'Rcpp'.\n'Eigen' is a C++
template library for linear algebra: matrices,\nvectors, numerical solvers and
related algorithms. It supports dense\nand sparse matrices on integer, floating
point and complex numbers,\ndecompositions of such matrices, and solutions of
linear systems. Its\nperformance on many algorithms is comparable with some of the
best\nimplementations based on 'Lapack' and level-3 'BLAS'.\n\nThe 'RcppEigen'
package includes the header files from the 'Eigen' C++\ntemplate library (currently
version 3.2.8). Thus users do not need to\ninstall 'Eigen' itself in order to use
'RcppEigen'.\n\nSince version 3.1.1, 'Eigen' is licensed under the Mozilla Public
License\n(version 2); earlier version were licensed under the GNU LGPL version 3
or\nlater. 'RcppEigen' (the 'Rcpp' bindings\/bridge to 'Eigen') is licensed
under\nthe GNU GPL version 2 or later, as is the rest of 'Rcpp'.","Imports":"Matrix
(>= 1.1-0), Rcpp (>= 0.11.0), stats, utils","License":"GPL (>= 2) | file
LICENSE","NeedsCompilation":"yes","Package":"RcppEigen","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"inline, RUnit, pkgKitten","Title":"'Rcpp'
Integration for the 'Eigen' Templated Linear
Algebra\nLibrary","URL":"http:\/\/eigen.tuxfamily.org","Version":"0.3.2.8.1"},"Rcpp
Examples":{"Author":"Dirk Eddelbuettel and Romain Francois","Depends":"R (>=
2.15.1)","Description":"Examples for Seamless R and C++ integration\nThe 'Rcpp'
package contains a C++ library that facilitates the integration of\nR and C++ in
various ways. This package provides some usage examples.\n\nNote that the
documentation in this package currently does not cover all the\nfeatures in the
package. It is not even close. On the other hand, the
site\n<http:\/\/gallery.rcpp.org> is regrouping a large number of examples for
'Rcpp'.","Imports":"Rcpp","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"RcppExamples","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"RUnit","Title":"Examples using 'Rcpp' to
Interface R and C+
+","URL":"http:\/\/dirk.eddelbuettel.com\/code\/rcpp.html","Version":"0.1.7"},"Rcpp
Faddeeva":{"Author":"Baptiste Auguie [aut, cre],\nDirk Eddelbuettel [aut],\nSteven
G. Johnson [aut] (Author of Faddeeva)","Description":"Access to a family of Gauss
error functions for arbitrary complex arguments is provided via the 'Faddeeva'
package by Steven G. Johnson (see <http:\/\/ab-
initio.mit.edu\/wiki\/index.php\/Faddeeva_Package> for more
information).","Imports":"Rcpp (>= 0.11.0), knitr","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"RcppFaddeeva","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat","Title":"'Rcpp' Bindings for the
'Faddeeva' Package","Version":"0.1.0"},"RcppGSL":{"Author":"Dirk Eddelbuettel and
Romain Francois","Description":"'Rcpp' integration for 'GNU GSL' vectors and
matrices\nThe 'GNU Scientific Library' (or 'GSL') is a collection of numerical
routines for\nscientific computing. It is particularly useful for C and C++
programs as it\nprovides a standard C interface to a wide range of mathematical
routines\nsuch as special functions, permutations, combinations, fast
fourier\ntransforms, eigensystems, random numbers, quadrature, random
distributions,\nquasi-random sequences, Monte Carlo integration, N-tuples,
differential\nequations, simulated annealing, numerical differentiation,
interpolation,\nseries acceleration, Chebyshev approximations, root-finding,
discrete\nHankel transforms physical constants, basis splines and wavelets.
There\nare over 1000 functions in total with an extensive test suite.\n\nThe
'RcppGSL' package provides an easy-to-use interface between 'GSL' data\nstructures
and R using concepts from 'Rcpp' which is itself a package that\neases the
interfaces between R and C++.\n\nThis package also serves as a prime example of how
to build a package\nthat uses 'Rcpp' to connect to another third-party library. The
'autoconf'\nscript, 'inline' plugin and example package can all be used as a stanza
to\nwrite a similar package against another library.","Imports":"Rcpp (>= 0.11.0),
2)","NeedsCompilation":"yes","Package":"RcppGSL","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"RUnit, inline, highlight","Title":"'Rcpp' Integration
for 'GNU GSL' Vectors and Matrices","Version":"0.3.0"},"RcppOctave":
{"Author":"Renaud Gaujoux","Depends":"R (>= 3.0.0), methods, utils, stats, Rcpp (>=
0.10.1),\npkgmaker (>= 0.20)","Description":"Direct interface to Octave. The
primary goal is to facilitate the\nport of Matlab\/Octave scripts to R. The package
enables to call any Octave\nfunctions from R and as well as browsing their
documentation, passing\nvariables between R and Octave, using R core RNGs in
Octave, which ensures\nthat stochastic computations are also
reproducible.","Imports":"digest, stringr, tools","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"RcppOctave","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"RUnit, knitr, bibtex","Title":"Seamless Interface
to Octave -- And
Matlab","URL":"http:\/\/renozao.github.io\/RcppOctave","Version":"0.18.1"},"RcppPar
allel":{"Author":"JJ Allaire [aut, cre],\nRomain Francois [aut, cph],\nGregory
Vandenbrouck [aut],\nMarcus Geelnard [aut, cph] (TinyThread
library,\nhttp:\/\/tinythreadpp.bitsnbites.eu\/),\nRStudio [cph],\nIntel [aut, cph]
(Intel TBB library,\nhttps:\/\/www.threadingbuildingblocks.org\/),\nMicrosoft
[cph]","Description":"High level functions for doing parallel programming with
'Rcpp'.\nFor example, the parallelFor() function can be used to convert the work
of\na standard serial \"for\" loop into
a parallel one and the parallelReduce()\nfunction can be used for accumulating
aggregate or other values.","License":"GPL-
2","NeedsCompilation":"yes","Package":"RcppParallel","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"Rcpp, RUnit","Title":"Parallel Programming Tools
for
'Rcpp'","URL":"http:\/\/rcppcore.github.io\/RcppParallel,\nhttps:\/\/github.com\/Rc
ppCore\/RcppParallel","Version":"4.3.15"},"RcppProgress":{"Author":"Karl Forner
<karl.forner@quartzbio.com>","Description":"This package allows to display a
progress bar in the R\nconsole for long running computations taking place in c++
code,\nand support for interrupting those computations even in multithreaded\ncode,
typically using OpenMP.","Imports":"Rcpp (>= 0.9.4)","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"RcppProgress","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"An Interruptible Progress Bar with OpenMP Support
for C++ in
R\nPackages","URL":"https:\/\/github.com\/kforner\/rcpp_progress","Version":"0.2.1"
},"RcppRedis":{"Author":"Dirk Eddelbuettel
<edd@debian.org>","Description":"Connection to the 'Redis' key\/value store using
the\nC-language client library 'hiredis'.","Imports":"methods, Rcpp (>= 0.11.0),
RApiSerialize","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"RcppRedis","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"rredis, RUnit","Title":"'Rcpp' Bindings for 'Redis'
using the 'hiredis' Library","Version":"0.1.6"},"RcppRoll":{"Author":"Kevin
Ushey","Depends":"R (>= 2.15.1)","Description":"Provides fast and efficient
routines for\ncommon rolling \/ windowed operations. Routines for the\nefficient
computation of windowed mean, median,\nsum, product, minimum, maximum, standard
deviation\nand variance are provided.","Imports":"Rcpp","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"RcppRoll","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"zoo, microbenchmark, testthat,
RcppArmadillo","Title":"Efficient Rolling \/ Windowed
Operations","Version":"0.2.2"},"RcppSMC":{"Author":"Dirk Eddelbuettel and Adam M.
Johansen","Description":"This package provides R with access to the
Sequential\nMonte Carlo Template Classes by Johansen (Journal of
Statistical\nSoftware, 2009, v30, i6).\n\nAt present, two additional examples have
been added, and the first\nexample from the JSS paper has been extended. Further
integration\nand extensions are planned.","Imports":"Rcpp (>= 0.11.0),
2)","NeedsCompilation":"yes","Package":"RcppSMC","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Rcpp bindings for Sequential Monte
Carlo","Version":"0.1.4"},"RcppShark":{"Author":"Aydin
Demircioglu","Description":"An R interface to the C++\/Boost Shark machine learning
library.","Imports":"Rcpp (>= 0.11.6), checkmate (>= 1.5.1)","License":"LGPL (>=
2)","NeedsCompilation":"yes","Package":"RcppShark","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr, testthat","Title":"R Interface to the Shark
Machine Learning
Library","URL":"http:\/\/github.com\/aydindemircioglu\/RcppShark","Version":"0.1"},
"RcppStreams":{"Author":"Dirk Eddelbuettel <edd@debian.org>","Depends":"R (>=
3.0.0)","Description":"The Streamulus (template, header-only) library by\nIrit
Katriel (at https:\/\/github.com\/iritkatriel\/streamulus)\nprovides a very
powerful yet convenient framework for stream\nprocessing.\n\nThis package connects
Streamulus to R by providing both the header\nfiles and all
examples.","Imports":"Rcpp","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"RcppStreams","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Rcpp Integration of the Streamulus DSEL for Stream
Processing","Version":"0.1.0"},"RcppXts":{"Author":"Dirk
Eddelbuettel","Depends":"methods, Rcpp (>= 0.10.2), xts (>= 0.9-
2)","Description":"This package provides access to some of the C level\nfunctions
of the xts package.\n\nIn its current state, the package is mostly a proof-of-
concept to\nsupport adding useful functions, and does not yet add any of\nits
own.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"RcppXts","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Interface the xts API via
Rcpp","Version":"0.0.4"},"RcppZiggurat":{"Author":"Dirk Eddelbuettel
<edd@debian.org>","Depends":"R (>= 3.0.0)","Description":"The Ziggurat generator
for normally distributed random numbers,\noriginally proposed by Marsaglia and
Tsang (JSS, 2000), has been improved\nupon a few times starting with Leong et al
(JSS, 2005). This package provides\nan aggregation in order to compare different
implementations. The goal is to\nprovide an 'faster but good enough' alternative
for use with R and C++ code.\n\nThe package is still in an early state. Unless you
know what you are doing,\nsticking with the generators provided by R may be a good
idea as these have\nbeen extremely diligently tested.","Imports":"Rcpp, parallel,
graphics, stats, utils","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"RcppZiggurat","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"highlight, rbenchmark, microbenchmark,
lattice","Title":"'Rcpp' Integration of Different \"Ziggurat\" Normal
RNG\nImplementations","Version":"0.1.3"},"Rcsdp":{"Author":"Hector Corrada Bravo
(CSDP by Brian Borchers)","Description":"R interface to the CSDP semidefinite
programming library. Installs version 6.1.1 of CSDP from the COIN-OR website if
required. An existing installation of CSDP may be used by passing the proper
configure arguments to the installation command. See the INSTALL file for further
details.","Enhances":"Matrix","License":"CPL-
1.0","NeedsCompilation":"yes","Package":"Rcsdp","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"R interface to the CSDP semidefinite programming
library","URL":"https:\/\/projects.coin-
or.org\/Csdp\/","Version":"0.1.53"},"Rd2roxygen":{"Author":"Hadley Wickham
[aut],\nYihui Xie [aut, cre]","Description":"Functions to convert Rd to roxygen
documentation. It can parse an\nRd file to a list, create the roxygen documentation
and update the original\nR script (e.g. the one containing the definition of the
function)\naccordingly. This package also provides utilities which can help
developers\nbuild packages using roxygen more easily. The formatR package can be
used\nto reformat the R code in the examples sections so that the code will
be\nmore readable.","Imports":"roxygen2 (>= 4.0.0), formatR (>=
1.0)","License":"GPL","NeedsCompilation":"no","Package":"Rd2roxygen","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Suggests":"knitr (>= 1.9),
rmarkdown","Title":"Convert Rd to Roxygen
Documentation","URL":"http:\/\/yihui.name\/Rd2roxygen","Version":"1.6"},"Rdistance"
:{"Author":"Trent McDonald [cre, aut],\nRyan Nielson [aut],\nJason Carlisle
[aut],\nBen Augustine [ctb],\nJames Griswald [ctb],\nJoel Reynolds [ctb],\nPham
Quang [ctb],\nEarl Becker [ctb],\nAaron Christ [ctb],\nBrook Russelland
[ctb],\nPatrick McKann [ctb]","Description":"Analysis of distance sampling data
collected on line transect surveys. Estimates distance-based detection functions
and abundances.","Imports":"graphics, stats, utils","License":"GNU General Public
License","NeedsCompilation":"no","Package":"Rdistance","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"knitr","Title":"Distance Sampling
Analyses","URL":"https:\/\/github.com\/tmcd82070\/Rdistance\/wiki","Version":"1.3.2
"},"Rdpack":{"Author":"Georgi N. Boshnakov","Depends":"R (>= 2.15.0), methods,
tools, gbRd","Description":"Functions for manipulation of Rd objects, including
function\nreprompt() for updating existing Rd documentation for\nfunctions, methods
and classes, and function rebib() for\nimport of references from bibtex
files.","Imports":"bibtex","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Rdpack","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Update and Manipulate Rd Documentation
Objects","Version":"0.4-18"},"Rdsdp":{"Author":"Zhisu Zhu, Yinyu Ye (DSDP by Steve
Benson, Yinyu Ye and Xiong Zhang)","Description":"R interface to DSDP semidefinite
programming library. The DSDP software is a free open source implementation of an
interior-point method for semidefinite programming. It provides primal and dual
solutions, exploits low-rank structure and sparsity in the data, and has relatively
low memory requirements for an interior-point method.","Imports":"utils,
3","NeedsCompilation":"yes","Package":"Rdsdp","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"R Interface to DSDP Semidefinite Programming
Library","URL":"http:\/\/www.mcs.anl.gov\/hs\/software\/DSDP","Version":"1.0.4"},"R
eCiPa":{"Author":"Juan C. Vivar","Description":"Pathways in a database could have
many redundancies among\nthem. This package allows the user to set a maximum value
for\nthe proportion of these redundancies.","License":"GPL-
2","NeedsCompilation":"no","Package":"ReCiPa","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Redundancy Control in Pathways
databases","Version":"3.0"},"ReacTran":{"Author":"Karline Soetaert
<karline.soetaert@nioz.nl>,\nFilip Meysman <filip.meysman@nioz.nl>","Depends":"R
(>= 2.10), rootSolve, deSolve, shape","Description":"Routines for developing models
that describe reaction and advective-diffusive transport in one, two or three
dimensions.\nIncludes transport routines in porous media, in estuaries, and in
bodies with variable shape.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"ReacTran","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Reactive transport modelling in 1D, 2D and
3D","Version":"1.4.2"},"RealVAMS":{"Author":"Andrew Karl, Jennifer Broatch, and
Jennifer Green","Depends":"R (>= 3.0.0), Matrix","Description":"The RealVAMs
package fits a multivariate value-added model (VAM) (see Broatch and
Lohr 2012) with normally distributed test scores and a binary outcome indicator.
This material is based upon work supported by the National Science Foundation under
grants DRL-1336027 and DRL-1336265.","Imports":"numDeriv, Rcpp (>= 0.11.2),
methods, stats, utils","License":"GPL-
2","NeedsCompilation":"yes","Package":"RealVAMS","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Multivariate VAM Fitting","Version":"0.3-
2"},"Rearrangement":{"Author":"Wesley Graybill, Mingli Chen, Victor Chernozhukov,
Ivan\nFernandez-Val, Alfred Galichon","Depends":"quantreg,
splines","Description":"The rearrangement operator (Hardy,\nLittlewood, and Polya
1952) for univariate, bivariate, and\ntrivariate point estimates of monotonic
functions. The package\nadditionally provides a function that creates
simultaneous\nconfidence intervals for univariate functions and applies
the\nrearrangement operator to these confidence intervals.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Rearrangement","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Monotonize Point and Interval Functional Estimates
by\nRearrangement","Version":"2.1"},"RecordLinkage":{"Author":"Andreas Borg
<borga@uni-mainz.de>, Murat Sariyar <murat.sariyar@charite.de>","Depends":"R (>=
2.10.0), DBI, RSQLite(>= 0.9-1), ff, ffbase","Description":"Provides functions for
linking and de-duplicating data sets.\nMethods based on a stochastic approach are
implemented as well as\nclassification algorithms from the machine learning
domain.","Imports":"e1071, rpart, ada, ipred, stats, evd, methods, data.table
(>=\n1.7.8), nnet, xtable","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"RecordLinkage","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"RUnit","Title":"Record Linkage in
R","URL":"https:\/\/r-forge.r-
project.org\/projects\/recordlinkage\/,\nhttp:\/\/journal.r-
project.org\/archive\/2010-2\/RJournal_2010-2_Sariyar+Borg.pdf","Version":"0.4-
8"},"Records":{"Author":"Magdalena Chrapek","Description":"Functions for generating
k-record values and k-record\ntimes","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Records","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Record Values and Record
Times","Version":"1.0"},"RedditExtractoR":{"Author":"Ivan Rivera
<ivan.s.rivera@gmail.com>","Depends":"R (>= 3.2.0)","Description":"Reddit is an
online bulletin board and a social networking website\nwhere registered users can
submit and discuss content. This package uses\nReddit API to extract Reddit data
using Reddit API. Note that due to the API\nlimitations, the number of comments
that can extracted is limited to 500 per\nthread. The package consists of 4
functions, one for extracting relevant URLs,\none for extracting features out of
given URLs, one that does both together and\none that constructs graphs based on
the structure of a thread.","Imports":"RJSONIO, utils, igraph, grDevices,
3","NeedsCompilation":"no","Package":"RedditExtractoR","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Reddit Data Extraction
Toolkit","Version":"2.0.2"},"RefFreeEWAS":{"Author":"E. Andres Houseman,
Sc.D.","Depends":"R (>= 3.2.2), isva, quadprog","Description":"\nReference-free
method for conducting EWAS while deconvoluting DNA methylation arising as mixtures
of cell types.\nThe older method (Houseman et al., 2014) is similar to surrogate
variable analysis (SVA and ISVA), except that it makes additional use of a
biological mixture assumption.\nThe newer method (Houseman et al., 2016) is similar
to non-negative matrix factorization, with additional constraints and additional
utilities.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RefFreeEWAS","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"EWAS using Reference-Free DNA Methylation Mixture
Deconvolution","Version":"2.0"},"RefManageR":{"Author":"Mathew W. McLean [aut,
cre]","Depends":"R (>= 3.0)","Description":"Provides tools for importing and
working with\nbibliographic references. It greatly enhances the 'bibentry' class
by\nproviding a class 'BibEntry' which stores 'BibTeX' and 'BibLaTeX'
references,\nsupports 'UTF-8' encoding, and can be easily searched by any field, by
date\nranges, and by various formats for name lists (author by last
names,\ntranslator by full names, etc.). Entries can be updated, combined,
sorted,\nprinted in a number of styles, and exported. 'BibTeX' and 'BibLaTeX'
'.bib' files\ncan be read into 'R' and converted to 'BibEntry' objects. Interfaces
to 'NCBI Entrez',\n'CrossRef', and 'Zotero' are provided for importing references
and\nreferences can be created from locally stored 'PDF' files using 'Poppler'.
Includes\nfunctions for citing and generating a bibliography with hyperlinks
for\ndocuments prepared with 'RMarkdown' or 'RHTML'.","Imports":"XML, RCurl,
RJSONIO, utils, plyr, tools, httr, bibtex,\nlubridate (>= 1.5.0), stringr,
methods","License":"GPL-2 | GPL-3 | BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"RefManageR","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"knitr, testthat","Title":"Straightforward
'BibTeX' and 'BibLaTeX' Bibliography Management","Version":"0.10.13"},"RegClust":
{"Author":"Weichao Bao, Xin Tong, Meredith Ray, Hongmei Zhang","Depends":"R (>=
3.0.2)","Description":"This package clusters regression coefficients using the
methods of clustering through linear regression models (CLM) (Qin and Self 2006).
Maximum likelihood approach is used to infer the parameters for each cluster.
Bayesian information criterion (BIC) combined with Bootstrapped maximum volume
(BMV) criterion are used to determine the number of clusters.","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"RegClust","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Cluster analysis via regression
coefficients","Version":"1.0"},"RegressionFactory":{"Author":"Alireza S. Mahani,
Mansour T.A. Sharabiani","Description":"The expander functions rely on the
mathematics developed for the Hessian-definiteness invariance theorem for linear
projection transformations of variables, described in authors' paper, to generate
the full, high-dimensional gradient and Hessian from the lower-dimensional
derivative objects. This greatly relieves the computational burden of generating
the regression-function derivatives, which in turn can be fed into any optimization
routine that utilizes such derivatives. The theorem guarantees that Hessian
definiteness is preserved, meaning that reasoning about this property can be
performed in the low-dimensional space of the base distribution. This is often a
much easier task than its equivalent in the full, high-dimensional space.
Definiteness of Hessian can be useful in selecting optimization\/sampling
algorithms such as Newton-Raphson optimization or its sampling equivalent, the
Stochastic Newton Sampler. Finally, in addition to being a computational tool, the
regression expansion framework is of conceptual value by offering new opportunities
to generate novel regression problems.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RegressionFactory","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"sns, MfUSampler, dglm","Title":"Expander
Functions for Generating Full Gradient and Hessian from\nSingle- and Multi-Slot
Base Distributions","Version":"0.7.1"},"RelValAnalysis":{"Author":"Ting-Kam Leonard
Wong [aut, cre]","Depends":"zoo","Description":"Classes and functions for analyzing
the performance of portfolios relative to a benchmark.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"RelValAnalysis","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Relative Value
Analysis","Version":"1.0"},"Relatedness":{"Author":"Fabien
Laporte","Description":"Inference of relatedness coefficients from a bi-allelic
genotype matrix using a Maximum Likelihood estimation.","License":"AGPL-
3","NeedsCompilation":"yes","Package":"Relatedness","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"An Algorithm to Infer
Relatedness","Version":"1.3"},"Reliability":{"Author":"Andreas Wittmann
<andreas_wittmann@gmx.de>","Depends":"R (>= 2.4.0)","Description":"Functions for
estimating parameters in software reliability models.\nOnly infinite failure models
are implemented so
far.","License":"Unlimited","NeedsCompilation":"no","Package":"Reliability","Reposi
tory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Functions for estimating
parameters in software reliability\nmodels","Version":"0.0-2"},"ReliabilityTheory":
{"Author":"Louis Aslett <aslett@stats.ox.ac.uk>","Depends":"igraph (>=
1.0.1)","Description":"A variety of tools useful for performing
structural\nreliability analysis, such as with structure function and\nsystem
signatures. Plans to expand more widely.","Imports":"sfsmisc, combinat, FRACTION,
mcmc, PhaseType (>= 0.1.3),\nactuar, HI","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"ReliabilityTheory","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Tools for Structural
Reliability
Analysis","URL":"http:\/\/www.louisaslett.com\/","Version":"0.1.5"},"Renext":
{"Author":"Yves Deville <deville.yves@alpestat.com>, IRSN
<renext@irsn.fr>","Depends":"R (>= 2.8.0), stats, graphics,
evd","Description":"Peaks Over Threshold (POT) or 'methode du renouvellement'. The
distribution for the exceedances can be chosen, and heterogeneous data (including
historical data or block data) can be used in a Maximum-Likelihood
framework.","Imports":"numDeriv, splines","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Renext","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"MASS, ismev, XML","Title":"Renewal Method for Extreme
Values Extrapolation","Version":"3.0-0"},"RenextGUI":{"Author":"Yves Deville
<deville.yves@alpestat.com> and IRSN <renext@irsn.fr>","Depends":"graphics,
stats, utils, gWidgets, gWidgetstcltk(>= 0.0-44),\nRenext(>= 2.1-
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2)","NeedsCompilation":"no","Package":"RenextGUI","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"R2HTML","Title":"GUI for Renext","Version":"1.3-
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<bomeara@utk.edu>","Depends":"R (>= 2.13.0)","Description":"An R interface to the
Encyclopedia of Life API. Includes functions for downloading and extracting
information off the EOL pages.","Imports":"XML, RCurl, ape","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Reol","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"geiger","Title":"R interface to the Encyclopedia of
Life","Version":"1.55"},"ReorderCluster":{"Author":"Natalia Novoselova,Frank
Klawonn, Junxi Wang","Depends":"R (>= 2.10),gplots,graphics","Description":"Tools
for performing the leaf reordering for the dendrogram that preserves the
hierarchical clustering result and at the same time tries to group instances from
the same class together.","Imports":"Rcpp (>= 0.11.0)","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"ReorderCluster","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Reordering the dendrogram according to the class
labels","Version":"1.0"},"RepeatABEL":{"Author":"Lars Ronnegard","Depends":"R (>=
2.10), hglm, GenABEL","Description":"Performs genome-wide association studies on
individuals that are both related and have repeated
measurements.","Imports":"methods,
stats","License":"GPL","NeedsCompilation":"no","Package":"RepeatABEL","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Title":"GWAS for Multiple Observations on
Related Individuals","Version":"1.0"},"RepeatedHighDim":{"Author":"Klaus
Jung","Depends":"MASS, nlme","Description":"Global tests for expression data of
high-dimensional sets of\nmolecular features.","License":"GPL-
2","NeedsCompilation":"no","Package":"RepeatedHighDim","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Global tests for expression data of high-
dimensional sets of\nmolecular features","Version":"2.0.0"},"ReporteRs":
{"Author":"David Gohel [aut, cre],\nBootstrap [ctb, cph] (Bootstrap development
team),\njQuery [ctb, cph] (The jQuery Foundation)","Depends":"R (>= 3.0),
ReporteRsjars (>= 0.0.2)","Description":"Create 'Microsoft Word' document
(>=2007),\n'Microsoft PowerPoint' document (>=2007) and 'HTML' documents from R.
There are\nseveral features to let you format and present R outputs ; e.g.
Editable\nVector Graphics, functions for complex tables reporting, reuse of
corporate\ntemplate document. You can use the package as a tool for fast
reporting\nand as a tool for reporting automation. The package does not
require\nany installation of Microsoft product to be able to write Microsoft
files.","Imports":"grDevices, rJava, utils, rvg (>= 0.0.8), xml2, gdtools,
png,\nR.utils, knitr, shiny","License":"GPL-
3","NeedsCompilation":"no","Package":"ReporteRs","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"ggplot2, jpeg, bmp, testthat, magrittr, rmarkdown,
ggiraph","Title":"Microsoft Word, Microsoft PowerPoint and HTML
Documents\nGeneration","URL":"http:\/\/davidgohel.github.io\/ReporteRs\/index.html,
\nhttp:\/\/groups.google.com\/group\/reporters-
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[ctb, cph] (Apache Commons java libraries\nand log4j),\nSLF4J [ctb, cph] (Simple
Logging Facade for Java)","Depends":"R (>= 3.0)","Description":"External jars
required for package ReporteRs. ReporteRs is an\nR package for creating Microsoft
Word document (>=2007), Microsoft\nPowerpoint document (>=2007) and HTML documents
from R.","Imports":"rJava","License":"GPL-
3","NeedsCompilation":"no","Package":"ReporteRsjars","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"External jars required for package
ReporteRs","Version":"0.0.2"},"ResistorArray":{"Author":"Robin K. S.
Hankin","Description":"electrical properties of resistor networks.","License":"GPL-
2","NeedsCompilation":"no","Package":"ResistorArray","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"electrical properties of resistor
networks","Version":"1.0-28"},"ResourceSelection":{"Author":"Subhash R. Lele, Jonah
L. Keim, Peter Solymos","Depends":"R (>= 2.13.0)","Description":"Resource Selection
(Probability) Functions for\nuse-availability wildlife data as described in\nLele
and Keim (2006, Ecology 87, 3021--3028),\nand Lele (2009, J. Wildlife Management
73, 122--127).","Imports":"MASS, pbapply","License":"GPL-
2","NeedsCompilation":"no","Package":"ResourceSelection","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Resource Selection (Probability) Functions for
Use-
Availability\nData","URL":"https:\/\/github.com\/psolymos\/ResourceSelection","Vers
ion":"0.2-6"},"RevEcoR":{"Author":"Yang Cao, Fei Li","Depends":"R (>=
2.14)","Description":"An implementation of the reverse ecology framework. Reverse
ecology\nrefers to the use of genomics to study ecology with no a priori
assumptions\nabout the organism(s) under consideration, linking organisms to
their\nenvironment. It allows researchers to reconstruct the metabolic networks
and\nstudy the ecology of poorly characterized microbial species from
their\ngenomic information, and has substantial potentials for microbial
community\necological analysis.","Imports":"Matrix, igraph, XML, stringr, magrittr,
gtools, plyr, purrr,\nmethods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RevEcoR","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr","Title":"Reverse Ecology Analysis on
Microbiome","Version":"0.99.3"},"Rexperigen":{"Author":"Daniel Szeredi [aut,
cre]","Depends":"R (>= 3.2.3)","Description":"Provides convenience functions to
communicate with\nan Experigen server. It is especially helpful with registered
experiments, as\nauthentication with the server has to happen.","Imports":"RCurl,
digest, jsonlite","License":"GPL-
3","NeedsCompilation":"yes","Package":"Rexperigen","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat","Title":"R Interface to
Experigen","URL":"https:\/\/github.com\/aquincum\/Rexperigen","Version":"0.2.0"},"R
facebook":{"Author":"Pablo Barbera <pablo.barbera@nyu.edu>, Michael
Piccirilli\n<mrp2181@columbia.edu>, Andrew Geisler","Depends":"R (>= 2.12.0), httr,
rjson, httpuv","Description":"Provides an interface to the Facebook
2","NeedsCompilation":"no","Package":"Rfacebook","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Access to Facebook API via
R","URL":"https:\/\/github.com\/pablobarbera\/Rfacebook","Version":"0.6.3"},"Rfit":
{"Author":"John Kloke, Joseph McKean","Depends":"methods,
quantreg","Description":"R estimation and inference for linear models.
Estimation\nis for general scores and a library of commonly used score\nfunctions
is included.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"Rfit","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat","Title":"Rank Estimation for Linear
Models","Version":"0.22.0"},"Rfmtool":{"Author":"Gleb Beliakov [aut, cre],\nQuan Vu
[ctb],\nAndrei Kelarev [ctb],\nMichel Berkelaar [ctb],\nKjell \tEikland
[ctb],\nSamuel E. Buttrey and others [ctb]","Depends":"R (>=
2.9.2)","Description":"Various tools for handling fuzzy measures, calculating
Shapley value and Interaction index, Choquet and Sugeno integrals, as well as
fitting fuzzy measures to empirical data are provided. Construction of fuzzy
measures from empirical data is done by solving a linear programming problem by
using 'lpsolve' package, whose source in C adapted to the R environment\nis
included. The description of the basic theory of fuzzy measures is in the manual in
the Doc folder in this package.","License":"LGPL-
3","NeedsCompilation":"yes","Package":"Rfmtool","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Fuzzy Measure Tools for R","Version":"1.2"},"Rgbp":
{"Author":"Joseph Kelly, Hyungsuk Tak, and Carl Morris","Depends":"R (>= 2.2.0), sn
(>= 0.4-18), mnormt (>= 1.5-1)","Description":"We utilize approximate Bayesian
machinery to fit two-level conjugate hierarchical models on overdispersed Gaussian,
Poisson, and Binomial data and evaluates whether the resulting approximate Bayesian
interval estimates for random effects meet the nominal confidence levels via
frequency coverage evaluation. The data that Rgbp assumes comprise observed
sufficient statistic for each random effect, such as an average or a proportion of
each group, without population-level data. The approximate Bayesian tool equipped
with the adjustment for density maximization produces approximate point and
interval estimates for model parameters including second-level variance component,
regression coefficients, and random effect. For the Binomial data, the package
provides an option to produce posterior samples of all the model parameters via
the acceptance-rejection method. The package provides a quick way to evaluate
coverage rates of the resultant Bayesian interval estimates for random effects via
a parametric bootstrapping, which we call frequency method
checking.","License":"GPL-
2","NeedsCompilation":"no","Package":"Rgbp","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Hierarchical Modeling and Frequency Method Checking
on\nOverdispersed Gaussian, Poisson, and Binomial Data","Version":"1.1.1"},"Rglpk":
{"Author":"Stefan Theussl [aut, cre],\nKurt Hornik [aut],\nChristian Buchta
[ctb],\nHeinrich Schuchardt [ctb],\nAndrew Makhorin [cph],\nTimothy A. Davis
[cph],\nNiklas Sorensson [cph],\nMark Adler [cph],\nJean-loup Gailly
[cph]","Depends":"slam (>= 0.1-9)","Description":"R interface to the GNU
Linear Programming Kit.\nGLPK is open source software for solving large-scale
linear programming (LP),\nmixed integer linear programming (MILP) and other related
problems.","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"Rglpk","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"R\/GNU Linear Programming Kit Interface","URL":"http:\/\/R-
Forge.R-
project.org\/projects\/rglp\/,\nhttp:\/\/www.gnu.org\/software\/glpk\/","Version":"
0.6-1"},"Rgnuplot":{"Author":"Jose Gama [aut, cre],\nNicolas Devillard
[aut],\nMauricio Galo [ctb],\nPatrick J. Bartlein [ctb],\nOscar PerpiÃ±Ã¡n
Lamigueiro [ctb]","Depends":"R (>= 2.7.0), methods","Description":"Interface for
gnuplot\nBased on gnuplot_i version 1.11, the GPL code from Nicolas
Devillard.","Enhances":"colorspace, png, rgdal, sp","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"Rgnuplot","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"R Interface for
Gnuplot","Version":"1.0.3"},"RgoogleMaps":{"Author":"Markus Loecher","Depends":"R
(>= 2.10)","Description":"This package serves two purposes: (i) Provide
a\ncomfortable R interface to query the Google server for static\nmaps, and (ii)
Use the map as a background image to overlay\nplots within R. This requires proper
coordinate scaling.","Imports":"graphics, stats, utils, png,
RJSONIO","License":"GPL","NeedsCompilation":"no","Package":"RgoogleMaps","Repositor
y":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"PBSmapping, maptools, sp,
rgdal, loa, RColorBrewer","Title":"Overlays on Google map tiles in
R","Version":"1.2.0.7"},"Rhpc":{"Author":"Junji NAKANO <nakanoj@ism.ac.jp> and Ei-
ji Nakama<nakama@com-one.com>","Depends":"R (>= 3.0.0)","Description":"Function of
apply style using 'MPI' provides better 'HPC' environment on R.\nand this package
supports long vector, can deal with slightly big
data.","Imports":"parallel","License":"AGPL-
3","NeedsCompilation":"yes","Package":"Rhpc","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Permits *apply() Style Dispatch for
'HPC'","URL":"http:\/\/prs.ism.ac.jp\/~nakama\/Rhpc\/","Version":"0.15-
244"},"RhpcBLASctl":{"Author":"Junji NAKANO <nakanoj@ism.ac.jp> and Ei-ji
Nakama<nakama@com-one.com>","Description":"Control the number of threads on 'BLAS'
(Aka 'GotoBLAS', 'ACML' and 'MKL').\nand possible to control the number of threads
in 'OpenMP'.\nget a number of logical cores and physical cores if
feasible.","License":"AGPL-
3","NeedsCompilation":"yes","Package":"RhpcBLASctl","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Control the Number of Threads on
'BLAS'","URL":"http:\/\/prs.ism.ac.jp\/~nakama\/Rhpc\/","Version":"0.15-
148"},"RidgeFusion":{"Author":"Bradley S. Price","Depends":"R (>= 3.0.0),mvtnorm,
methods","Description":"This package implements ridge fusion methodology for
inverse covariance matrix estimation for use in quadratic discriminant analysis.
The package also contains function for model based clustering using ridge fusion
for inverse matrix estimation, as well as tuning parameter selection functions. We
have also implemented QDA using joint inverse covariance
estimation.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"RidgeFusion","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"R Package for Ridge Fusion in Statistical
Learning","Version":"1.0-3"},"Ridit":{"Author":"SeyedMahmood
TaghaviShahri","Description":"An extension of the Kruskal-Wallis Test that
allow\nselection of arbitrary reference group. Also provide Mean Ridit\nfor each
group. Mean Ridit of a group is an estimate of\nprobability a random observation
from that group will be\ngreater than or equal to a random observation from
reference\ngroup.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"Ridit","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Ridit Analysis (An extension of the Kruskal-Wallis
Test.)","Version":"1.1"},"Ritc":{"Author":"Yingyun
Liu","Depends":"minpack.lm","Description":"This package implements the simulation
and regression of\nintegrated Isothermal Titration Calorimetry (ITC) data
using\nthe most commonly used one-to-one binding reaction model.","License":"GPL-
3","NeedsCompilation":"no","Package":"Ritc","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Isothermal Titration Calorimetry (ITC) Data
Analysis","Version":"1.0.1"},"Rivivc":{"Author":"Aleksander Mendyk [aut, cre],
Sebastian Polak [aut]","Depends":"signal, compiler","Description":"This package is
devoted to the IVIVC linear level A with\nnumerical deconvolution method. The
latter is working for\ninequal and incompatible timepoints between impulse
and\nresponse curves. A numerical convolution method is also\navailable.
Application domains include pharamaceutical industry\nQA\/QC and R&D together with
academic research.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"Rivivc","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"graphics","Title":"In vitro in vivo correlation linear
level A","Version":"0.9"},"Rjpstatdb":{"Author":"Kiwamu
Ishikura","Depends":"methods, RCurl, XML","Description":"R interface to statistical
database organized by Japanese government
(http:\/\/statdb.nstac.go.jp\/)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Rjpstatdb","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"R interface of the Gateway to Advanced and User-
friendly\nStatistics Service","URL":"https:\/\/github.com\/i-
kiwamu\/Rjpstatdb","Version":"0.1"},"Rknots":{"Author":"Federico Comoglio and
Maurizio Rinaldi","Depends":"R (>= 2.14.0), methods, rgl, rSymPy,
bio3d","Description":"Contains functions for the topological analysis of polymers,
with a focus on protein structures.","License":"GPL-
2","NeedsCompilation":"no","Package":"Rknots","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"knitr","Title":"Topological Analysis of Knotted
Proteins, Biopolymers and 3D\nStructures","Version":"1.3.1"},"Rlab":
{"Author":"Dennis D. Boos, Douglas Nychka","Depends":"R (>= 2.10),
utils","Description":"Functions and Datasets Required for ST370
class","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Rlab","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Functions and Datasets Required for ST370
class","URL":"http:\/\/www.r-
project.org,\nhttp:\/\/courses.ncsu.edu\/ST370\/distance\/rlab","Version":"2.15.1"}
,"Rlabkey":{"Author":"Peter Hussey","Depends":"RCurl, rjson (>=
0.1.3)","Description":"Allow a user to discover, query and modify data from a
LabKey Server.","License":"Apache License
2.0","NeedsCompilation":"yes","Package":"Rlabkey","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Data Exchange Between R and LabKey
Server","Version":"2.1.129"},"Rlibeemd":{"Author":"Jouni Helske [aut, cre] (R
interface),\nPerttu Luukko [aut] (Original libeemd C library)","Description":"An R
interface for C library libeemd for performing the ensemble\nempirical mode
decomposition (EEMD), its complete variant (CEEMDAN) or the\nregular empirical mode
decomposition (EMD).","Imports":"stats, Rcpp (>= 0.11.0)","License":"GPL-
3","NeedsCompilation":"yes","Package":"Rlibeemd","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat","Title":"Ensemble Empirical Mode
Decomposition (EEMD) and Its Complete\nVariant
(CEEMDAN)","Version":"1.3.7"},"Rlinkedin":{"Author":"Michael Piccirilli
<michael.r.piccirilli@gmail.com>","Depends":"R (>= 2.12.0), httr, XML,
httpuv","Description":"A series of functions that allow users\nto access the
LinkedIn API to get information about connections,\nsearch for people and jobs,
share updates with their network,\nand create group discussions. For more
information about using\nthe API please visit
https:\/\/developer.linkedin.com\/.","License":"GPL-
2","NeedsCompilation":"no","Package":"Rlinkedin","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Access to the LinkedIn API via
R","URL":"https:\/\/github.com\/mpiccirilli\/Rlinkedin","Version":"0.1"},"Rlof":
{"Author":"Yingsong Hu, Wayne Murray and Yin Shan, Australia.","Depends":"R (>=
2.14.0), doParallel, foreach","Description":"R parallel implementation of Local
Outlier Factor(LOF) which uses multiple CPUs to significantly speed up the LOF
computation for large datasets. (Note: The overall performance depends on the
computers especially the number of the cores).It also supports multiple k values to
be calculated in parallel, as well as various distance measures in addition to the
default Euclidean distance.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"Rlof","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"R Parallel Implementation of Local Outlier
Factor(LOF)","Version":"1.1.1"},"Rmalschains":{"Author":"Christoph Bergmeir, Daniel
Molina, JosÃ© M. BenÃtez","Depends":"Rcpp (>= 0.9.10)","Description":"This package
implements an algorithm family for continuous\noptimization called memetic
algorithms with local search chains\n(MA-LS-Chains). Memetic algorithms are
hybridizations of genetic\nalgorithms with local search methods. They are
especially suited\nfor continuous optimization.","License":"GPL-3 | file
LICENSE","NeedsCompilation":"yes","Package":"Rmalschains","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"inline","Title":"Continuous Optimization
using Memetic Algorithms with Local\nSearch Chains (MA-LS-Chains) in
R","URL":"http:\/\/sci2s.ugr.es\/dicits\/software\/Rmalschains","Version":"0.2-
2"},"Rmisc":{"Author":"Ryan M. Hope <rmh3093@gmail.com>","Depends":"lattice,
plyr","Description":"The Rmisc library contains many functions useful for data
analysis\nand utility operations.","License":"GPL-
3","NeedsCompilation":"no","Package":"Rmisc","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"latticeExtra, Hmisc, stats4","Title":"Rmisc: Ryan
Miscellaneous","Version":"1.5"},"Rmixmod":{"Author":"Remi Lebret [aut, cre],\nSerge
Iovleff [aut],\nFlorent Langrognet [aut],\nBenjamin Auder [ctb],\nC. Biernacki
[ctb],\nG. Celeux [ctb],\nG. Govaert [ctb]","Depends":"R(>= 2.12.0), Rcpp(>=
0.8.0), methods, stats, graphics","Description":"A collection of functions designed
to run supervised and\nunsupervised classification with MIXture
MODelling.","License":"GPL-
3","NeedsCompilation":"yes","Package":"Rmixmod","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"An Interface for
MIXMOD","URL":"http:\/\/www.mixmod.org","Version":"2.0.3"},"RmixmodCombi":
{"Author":"J.-P. Baudry and G. Celeux","Depends":"R(>= 3.0.2), Rmixmod(>= 2.0.1),
Rcpp(>= 0.8.0), methods,\ngraphics","Description":"The Rmixmod package provides
model-based clustering by fitting a mixture model (e.g. Gaussian components for
quantitative continuous data) to the data and identifying each cluster with one of
its components. The number of components can be determined from the data, typically
using the BIC criterion. In practice, however, individual clusters can be poorly
fitted by Gaussian distributions, and in that case model-based clustering tends to
represent one non-Gaussian cluster by a mixture of two or more Gaussian components.
If the number of mixture components is interpreted as the number of clusters, this
can lead to overestimation of the number of clusters. This is because BIC selects
the number of mixture components needed to provide a good approximation to the
density. This package, RmixmodCombi, according to \\emph{Combining Mixture
Components for Clustering} by J.P. Baudry, A.E. Raftery, G. Celeux, K. Lo, R.
Gottardo, combines the components of the EM\/BIC solution (provided by Rmixmod)
hierarchically according to an entropy criterion. This yields a clustering for each
number of clusters less than or equal to K. These clusterings can be compared on
substantive grounds, and we also provide a way of selecting the number of clusters
via a piecewise linear regression fit to the (possibly rescaled) entropy
plot.","License":"GPL-
3","NeedsCompilation":"no","Package":"RmixmodCombi","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Combining Mixture Components for
Clustering","Version":"1.0"},"Rmonkey":{"Author":"Thomas J. Leeper [aut,
cre],\nKevin Little [ctb],\nStephan Renatus [ctb]","Description":"Programmatic
access to the Survey Monkey API <https:\/\/developer.surveymonkey.com\/>, which
currently provides extensive functionality for monitoring surveys and retrieving
survey results and some functionality for creating new surveys and data
collectors.","Imports":"stats, utils, httr, jsonlite, curl, plyr","License":"GPL-
2","NeedsCompilation":"no","Package":"Rmonkey","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"A Survey Monkey R
Client","URL":"https:\/\/github.com\/cloudyr\/Rmonkey","Version":"0.3.1"},"Rmosek":
{"Author":"Henrik Alsing Friberg","Depends":"R(>= 2.10.0), Matrix(>= 0.9996875-
3)","Description":"An interface to the MOSEK optimization library designed
to\nsolve large-scale mathematical optimization problems. Supports\nlinear,
quadratic and second order cone optimization\nwith\/without integer variables, in
addition to the more general\nseparable convex problems. Trial and free academic
licenses\navailable at http:\/\/www.mosek.com.","License":"LGPL (>=
2.1)","NeedsCompilation":"yes","Package":"Rmosek","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"The R-to-MOSEK Optimization
Interface","URL":"http:\/\/rmosek.r-forge.r-project.org\/,
http:\/\/www.mosek.com\/","Version":"1.2.5.1"},"Rmpfr":{"Author":"Martin
Maechler","Depends":"gmp (>= 0.5-8), R (>= 3.0.1)","Description":"Arithmetic (via
S4 classes and methods) for\narbitrary precision floating point numbers, including
transcendental\n(\"special\") functions. To this end, Rmpfr interfaces to\nthe
LGPL'ed MPFR (Multiple Precision Floating-Point Reliable) Library\nwhich itself is
based on the GMP (GNU Multiple Precision) Library.","Imports":"stats, utils,
2)","NeedsCompilation":"yes","Package":"Rmpfr","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"MASS, polynom, sfsmisc (>= 1.0-20), Matrix","Title":"R
MPFR - Multiple Precision Floating-Point Reliable","URL":"http:\/\/rmpfr.r-forge.r-
project.org\/","Version":"0.6-0"},"Rmpi":{"Author":"Hao Yu","Depends":"R (>=
2.15.1)","Description":"Rmpi provides an interface (wrapper) to MPI APIs. It
also\nprovides interactive R slave environment.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"Rmpi","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"parallel","Title":"Interface (Wrapper) to MPI (Message-
Passing
Interface)","URL":"http:\/\/www.stats.uwo.ca\/faculty\/yu\/Rmpi","Version":"0.6-
5"},"RnavGraph":{"Author":"Adrian R. Waddell and R. Wayne Oldford","Depends":"R (>=
2.10.0), methods, graphics, tcltk, graph","Description":"GUI to explore high
dimensional data (including image data) using graphs as navigational
infrastructure.","Imports":"scagnostics, rgl","License":"GPL-
2","NeedsCompilation":"yes","Package":"RnavGraph","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"PairViz, MASS, hexbin, RDRToolbox, vegan,
RnavGraphImageData,\npng, Rgraphviz","Title":"Using Graphs as a Navigational
Infrastructure","URL":"http:\/\/www.navgraph.com","Version":"0.1.8"},"RnavGraphImag
eData":{"Author":"Adrian R. Waddell and R. Wayne Oldford","Depends":"R (>=
2.10.0)","Description":"Image data used as examples in the RnavGraph R
package.\nSee the demos in the RnavGraph package.","License":"GPL-
2","NeedsCompilation":"no","Package":"RnavGraphImageData","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"RnavGraph","Title":"Some image data used in
the RnavGraph package
demos","URL":"http:\/\/www.navgraph.com","Version":"0.0.3"},"RndTexExams":
{"Author":"Marcelo Perlin [aut, cre]","Depends":"R (>= 3.2.3)","Description":"Using
as input a 'LaTeX' file with a multiple choice exam, this package will produce
random versions of the same exam.","Imports":"tools, stringr, stringi,
data.table","License":"GPL-
2","NeedsCompilation":"no","Package":"RndTexExams","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr, rmarkdown, testthat","Title":"Build Random
Multiple Choice Exams","Version":"1.1.1"},"RobAStBase":{"Author":"Matthias Kohl,
Peter Ruckdeschel","Depends":"R(>= 2.14.0), methods, rrcov, distr(>= 2.5.2),
distrEx(>=\n2.4), distrMod(>= 2.5.2), RandVar(>= 0.9.2)","Description":"Base S4-
classes and functions for robust asymptotic statistics.","License":"LGPL-
3","NeedsCompilation":"no","Package":"RobAStBase","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"ROptEst, RUnit (>= 0.4.26)","Title":"Robust
Asymptotic Statistics","URL":"http:\/\/robast.r-forge.r-
project.org\/","Version":"0.9"},"RobLox":{"Author":"Matthias Kohl
<Matthias.Kohl@stamats.de>","Depends":"R(>= 2.14.0), stats, distrMod(>= 2.5.2),
RobAStBase(>= 0.9)","Description":"Functions for the determination of optimally
robust influence curves and\nestimators in case of normal location and\/or
scale","Imports":"lattice, RColorBrewer, Biobase, RandVar(>= 0.9.2),
distr(>=\n2.5.2)","License":"LGPL-
3","NeedsCompilation":"no","Package":"RobLox","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"MASS","Title":"Optimally robust influence curves and
estimators for location\nand scale","URL":"http:\/\/robast.r-forge.r-
project.org\/","Version":"0.9"},"RobLoxBioC":{"Author":"Matthias Kohl
<Matthias.Kohl@stamats.de>","Depends":"R(>= 2.14.0), methods, RobLox(>= 0.9),
affy","Description":"Functions for the determination of optimally robust influence
curves and\nestimators for preprocessing omics data, in particular gene expression
data.","Imports":"BiocGenerics, Biobase, beadarray, lattice,
RColorBrewer,\ndistr(>= 2.5.2)","License":"LGPL-
3","NeedsCompilation":"no","Package":"RobLoxBioC","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Infinitesimally robust estimators for preprocessing
omics data","URL":"http:\/\/robast.r-forge.r-
project.org\/","Version":"0.9"},"RobPer":{"Author":"Anita M. Thieler
[aut],\nJonathan Rathjens [aut, cre],\nRoland Fried [aut],\nBrenton R. Clarke [ctb]
(function betaCvMfit()),\nUwe Ligges [ctb] (function TK95()),\nMatias Salibian-
Barrera [ctb] (functions FastS() and FastTau()),\nGert Willems [ctb] (function
FastTau()),\nVictor Yohai [ctb] (function FastS())","Depends":"robustbase,
quantreg, splines, BB, rgenoud","Description":"Calculates periodograms based on
(robustly) fitting periodic functions to light curves (irregularly observed time
series, possibly with measurement accuracies, occurring in astroparticle physics).
Three main functions are included: RobPer() calculates the periodogram. Outlying
periodogram bars (indicating a period) can be detected with betaCvMfit().
Artificial light curves can be generated using the function tsgen(). For more
details see the corresponding article: Thieler, Fried and Rathjens (2016), Journal
of Statistical Software 69(9), 1-36, <doi:10.18637\/jss.v069.i09>.","License":"GPL-
3","NeedsCompilation":"no","Package":"RobPer","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Robust Periodogram and Periodicity Detection
Methods","Version":"1.2.2"},"RobRSVD":{"Author":"Lingsong Zhang and Chao
Pan","Description":"This package provides the function to calculate SVD,
regularized SVD, robust SVD and robust regularized SVD method. The robust SVD
methods use alternating iteratively reweighted least squares methods. The
regularized SVD uses generalized cross validation to choose the optimal smoothing
parameters.","License":"GPL","NeedsCompilation":"no","Package":"RobRSVD","Repositor
y":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Robust Regularized Singular
Value Decomposition","Version":"1.0"},"RobRex":{"Author":"Matthias Kohl
<Matthias.Kohl@stamats.de>","Depends":"R (>= 2.14.0), ROptRegTS(>=
0.9)","Description":"Functions
for the determination of optimally robust influence curves in case of\nlinear
regression with unknown scale and standard normal distributed errors where
the\nregressor is random.","License":"LGPL-
3","NeedsCompilation":"no","Package":"RobRex","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Optimally robust influence curves for regression and
scale","URL":"http:\/\/robast.r-forge.r-
project.org\/","Version":"0.9"},"RobustAFT":{"Author":"Alfio Marazzi
<Alfio.Marazzi@chuv.ch>, Jean-Luc Muralti","Depends":"R (>= 2.9.2), robustbase,
stats, graphics, survival","Description":"R functions for the computation of the
truncated maximum\nlikelihood and the robust accelerated failure time
regression\nfor gaussian and log-Weibull case.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"RobustAFT","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Truncated Maximum Likelihood Fit and Robust
Accelerated Failure\nTime Regression for Gaussian and Log-Weibull
Case","Version":"1.4-1"},"RobustEM":{"Author":"Aishat Aloba, Kai Yu, Xin Dang,
Yixin Chen, and Henry Bart Jr.","Depends":"R (>= 2.15.0)","Description":"The
Spatial-EM is a new robust EM algorithm for the finite\nmixture learning
procedures. The algorithm utilizes median-\nbased location and rank-based scatter
estimators to replace sample\nmean and sample covariance matrix in each M step,
hence enhancing\nstability and robustness of the algorithm. To understand more
about\nthis algorithm, read the article\n''Yu, K., Dang, X., Bart Jr, H. and Chen,
Y. (2015). Robust Model-\nbased Learning via Spatial-EM Algorithm. IEEE
Transactions on\nKnowledge and Data Engineering, 27(6), 1670-
1682.\ndoi:10.1109\/TKDE.2014.2373355''.","Imports":"mvtnorm,e1071,ggplot2,ellipse,
doParallel,grid, foreach","License":"GPL-
3","NeedsCompilation":"yes","Package":"RobustEM","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Robust Mixture Modeling Fitted via Spatial-EM Algorithm
for\nModel-Based Clustering and Outlier
Detection","Version":"1.0"},"RobustRankAggreg":{"Author":"Raivo Kolde, Sven
Laur","Depends":"methods","Description":"Methods for aggregating ranked lists,
especially lists of\ngenes. It implements the Robust Rank Aggregation (Kolde et.
al\nin preparation) and some other simple algorithms for the task.\nRRA method uses
a probabilistic model for aggregation that is\nrobust to noise and also facilitates
the calculation of\nsignificance probabilities for all the elements in the
final\nranking.","License":"GPL-
2","NeedsCompilation":"no","Package":"RobustRankAggreg","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Methods for robust rank
aggregation","Version":"1.1"},"RockFab":{"Author":"Jeffrey R.
Webber","Depends":"methods","Description":"Provides functions to complete three-
dimensional rock fabric and strain analyses following the Rf Phi, Fry, and
normalized Fry methods. Also allows for plotting of results and interactive 3D
visualization functionality.","Imports":"rgl,
EBImage","License":"GPL","NeedsCompilation":"no","Package":"RockFab","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Title":"Rock fabric and strain analysis
tools","Version":"1.2"},"Rook":{"Author":"Jeffrey Horner
<jeffrey.horner@gmail.com>","Depends":"R (>= 2.13.0)","Description":"This package
contains the Rook specification and\nconvenience software for building and running
Rook applications. To\nget started, be sure and read the 'Rook' help file
first.","Imports":"utils, tools, methods, brew","License":"GPL-
2","NeedsCompilation":"yes","Package":"Rook","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Rook - a web server interface for R","Version":"1.1-
1"},"RootsExtremaInflections":{"Author":"Demetris T.
Christopoulos","Description":"Implementation of the Taylor Regression Estimator
method described in Christopoulos
(2014,<https:\/\/www.researchgate.net\/publication\/261562841>)\nfor finding the
root, extreme or inflection point of a curve, when we only have a set of probably
noisy xy points for it. The method uses a suitable\npolynomial regression in order
to find the coefficients of the relevant Taylor polynomial for the function that
has generated our data.","License":"GPL-
2","NeedsCompilation":"no","Package":"RootsExtremaInflections","Repository":"http:\
/\/cran.csiro.au\/src\/contrib","Title":"Finds roots, extrema and inflection points
of a curve","Version":"1.0"},"Rothermel":{"Author":"Giorgio Vacchiano, Davide
Ascoli","Depends":"R (>= 3.0.0), GA, ftsa","Description":"R build of Rothermel's
(1972) model for surface fire rate of spread with some additional utilities
(uncertainty propagation, standard fuel model selection, fuel model optimization by
genetic algorithm) and sample datasets.","License":"GPL-
2","NeedsCompilation":"no","Package":"Rothermel","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Rothermel fire spread model for
R","Version":"1.2"},"RoughSetKnowledgeReduction":{"Author":"Alber
Sanchez","Depends":"methods","Description":"Rough Sets were introduced by Zdzislaw
Pawlak on his book \"Rough Sets: Theoretical Aspects of Reasoning About Data\".
Rough Sets provide a formal method to approximate crisp sets when the set-element
belonging relationship is either known or undetermined. This enables the use of
Rough Sets for reasoning about incomplete or contradictory knowledge. A decision
table is a prescription of the decisions to make given some conditions. Such
decision tables can be reduced without losing prescription ability. This package
provides the classes and methods for knowledge reduction from decision tables as
presented in the chapter 7 of the aforementioned book. This package provides
functions for calculating the both the discernibility matrix and the essential
parts of decision tables.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"RoughSetKnowledgeReduction","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Simplification of Decision Tables
using Rough Sets","Version":"0.1"},"RoughSets":{"Author":"Lala Septem Riza
[aut],\nAndrzej Janusz [aut],\nDominik ÅšlÄ™zak [ctb],\nChris Cornelis
[ctb],\nFrancisco Herrera [ctb],\nJose Manuel Benitez [ctb],\nChristoph Bergmeir
[ctb, cre],\nSebastian Stawicki
[ctb]","Depends":"Rcpp","Description":"Implementations of algorithms for data
analysis\nbased on the rough set theory (RST) and the fuzzy rough set theory
(FRST). We\nnot only provide implementations for the basic concepts of RST and FRST
but also\npopular algorithms that derive from those theories. The methods included
in the\npackage can be divided into several categories based on their
functionality:\ndiscretization, feature selection, instance selection, rule
induction and classification\nbased on nearest neighbors. RST was introduced by
ZdzisÅ‚aw Pawlak in 1982\nas a sophisticated mathematical tool to\nmodel and
process imprecise or incomplete information. By using\nthe indiscernibility
relation for objects\/instances, RST does not require\nadditional parameters to
analyze the data. FRST is an extension of RST. The\nFRST combines concepts of
vagueness and indiscernibility that are expressed\nwith fuzzy sets (as proposed by
Zadeh, in 1965) and RST.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"RoughSets","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"class","Title":"Data Analysis Using Rough Set and
Fuzzy Rough Set
Theories","URL":"https:\/\/github.com\/janusza\/RoughSets","Version":"1.3-
0"},"Rpdb":{"Author":"Julien IdÃ©","Depends":"R (>= 3.0), rgl (>=
0.93)","Description":"Provides tools to read, write, visualize PDB files and
perform some structural
manipulations.","License":"GPL","NeedsCompilation":"no","Package":"Rpdb","Repositor
y":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Read, write, visualize and
manipulate PDB files","Version":"2.2"},"Rphylip":{"Author":"Liam J. Revell, Scott
A. Chamberlain","Depends":"R (>= 2.10), ape (>= 3.0-10)","Description":"Rphylip
provides an R interface for the PHYLIP package. All users\nof Rphylip will thus
first have to install the PHYLIP phylogeny methods\nprogram package (Felsenstein
2013). See http:\/\/www.phylip.com for more\ninformation about installing
PHYLIP.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Rphylip","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"An R interface for
PHYLIP","URL":"http:\/\/www.phytools.org\/Rphylip","Version":"0.1-
23"},"Rphylopars":{"Author":"Eric W. Goolsby, Jorn Bruggeman, Cecile
Ane","Depends":"ape","Description":"Tools for performing phylogenetic comparative
methods for datasets with with multiple observations per species (intraspecific
variation or measurement error) and\/or missing data. Performs ancestral state
reconstruction and missing data imputation on the estimated evolutionary model,
which can be specified as Brownian Motion, Ornstein-Uhlenbeck, Early-Burst, Pagel's
lambda, kappa, or delta, or a star phylogeny.","Imports":"Rcpp, doBy, geiger,
phylolm, phytools, mvnmle, Matrix","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"Rphylopars","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Phylogenetic Comparative Tools for Missing Data
and\nWithin-Species Variation","Version":"0.2.1"},"Rquake":{"Author":"Jonathan M.
Lees","Depends":"R (>= 2.12)","Description":"Hypocenter estimation and analysis of
seismic data collected continuously, or in trigger mode. The functions organize
other functions from RSEIS and GEOmap to help researchers pick, locate, and store
hypocenters for detailed seismic investigation.","Imports":"RPMG, RSEIS, GEOmap,
MBA, minpack.lm, rgl, cda","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Rquake","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Seismic Hypocenter Determination","Version":"2.3-
1"},"Rramas":{"Author":"Marcelino de la
Cruz","Depends":"diagram","Description":"Analyzes and predicts
from matrix population models in the way of the Ramas (c) software","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"Rramas","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Matrix population models","Version":"0.1-4"},"Rrdrand":
{"Author":"Ei-ji Nakama <nakama@com-one.com>, Junji NAKANO
<nakanoj@ism.ac.jp>","Depends":"R (>= 3.0.0)","Description":"Make use of the
hardware random number accessed by the 'RdRand'\ninstruction in recent Intel CPUs
(Ivy Bridge and later).\n'DRNG' is \"Digital Random Number
Generator\".","License":"AGPL-
3","NeedsCompilation":"yes","Package":"Rrdrand","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"'DRNG' on Intel CPUs with the 'RdRand' Instruction for
R","URL":"http:\/\/prs.ism.ac.jp\/~nakama\/Rrdrand\/","Version":"0.1-
14"},"Rsampletrees":{"Author":"Kelly Burkett, Brad McNeney, Jinko
Graham","Depends":"haplo.stats, ape","Description":"Contains functions that are
useful for pre- and post-processing the tree output from the MCMC-based C++ program
sampletrees. The program sampletrees is used to sample gene genealogies conditional
on either phased or unphased SNP genotype data. More information about sampletrees
can be found at http:\/\/stat.sfu.ca\/statgen\/research\/sampletrees.html . Pre-
processing tasks involve creating the settings file, the haplotype estimation files
(if input data is genotype), and error checking the settings. Post-processing
involves reading in the MCMC output from a run of sampletrees and computing summary
2","NeedsCompilation":"no","Package":"Rsampletrees","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Sampletrees Input\/Output
Processing","Version":"0.1"},"Rserve":{"Author":"Simon Urbanek <Simon.Urbanek@r-
project.org>","Depends":"R (>= 1.5.0)","Description":"Rserve acts as a socket
server (TCP\/IP or local sockets)\nwhich allows binary requests to be sent to R.
Every\nconnection has a separate workspace and working\ndirectory. Client-side
implementations are available\nfor popular languages such as C\/C++ and Java,
allowing\nany application to use facilities of R without the need of\nlinking to R
code. Rserve supports remote connection,\nuser authentication and file transfer. A
simple R client\nis included in this package as well.","License":"GPL-2 | file
LICENSE","NeedsCompilation":"yes","Package":"Rserve","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"RSclient","Title":"Binary R
server","URL":"http:\/\/www.rforge.net\/Rserve\/","Version":"1.7-3"},"RsimMosaic":
{"Author":"Alberto Krone-Martins","Depends":"R (>= 3.1.0)","Description":"This
package provides a way to transform an image into a mosaic composed from a set of
smaller images (tiles). It also contains a simple function for creating the tiles
from a folder of images directly through R, without the need of any external code.
At this moment only the JPEG format is supported, either as input (image and tiles)
or output (mosaic transformed image).","Imports":"jpeg, fields,
RANN","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RsimMosaic","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"R Simple IMage Mosaic creation
library","Version":"1.0.2"},"Rsolnp":{"Author":"Alexios Ghalanos and Stefan
Theussl","Depends":"R (>= 2.10.0)","Description":"General Non-linear Optimization
Using Augmented Lagrange Multiplier Method.","Imports":"truncnorm, parallel,
stats","License":"GPL","NeedsCompilation":"no","Package":"Rsolnp","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Title":"General Non-Linear
Optimization","Version":"1.16"},"Rsomoclu":{"Author":"Peter Wittek [aut], Shichao
Gao [cre]","Depends":"Rcpp","Description":"Somoclu is a massively parallel
implementation of self-organizing maps. It exploits multicore CPUs and it can be
accelerated by CUDA. The topology of the map can be planar or toroid and the grid
of neurons can be rectangular or hexagonal .","Imports":"kohonen,
class","License":"GPL-
3","NeedsCompilation":"yes","Package":"Rsomoclu","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Somoclu","URL":"http:\/\/peterwittek.github.io\/somoclu\
/","Version":"1.6.1"},"Rssa":{"Author":"Anton Korobeynikov, Alex Shlemov,
Konstantin Usevich, Nina Golyandina","Depends":"R (>= 3.1), svd (>= 0.3.3),
forecast","Description":"Methods and tools for Singular Spectrum Analysis including
decomposition, forecasting and gap-filling for univariate and multivariate time
series.","Imports":"lattice","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"Rssa","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat (>= 0.7)","Title":"A Collection of Methods for
Singular Spectrum Analysis","URL":"http:\/\/github.com\/asl\/rssa","Version":"0.13-
1"},"Rstem":
{"License":"BSD","NeedsCompilation":"yes","Package":"Rstem","Repository":"http:\/\/
www.stats.ox.ac.uk\/pub\/RWin\/src\/contrib","Version":"0.4-1"},"Rsundials":
{"Author":"Selwyn-Lloyd McPherson <smcphers@cwru.edu>","Depends":"R (>=
2.3.0)","Description":"This package provides an interface for the package
of\nnonlinear differential algebraic equation solvers that comprise\nSUNDIALS. ODEs
are expressed as R functions or as
compiled\ncode.","License":"GPL","NeedsCompilation":"yes","Package":"Rsundials","Re
pository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Suite of Nonlinear
Differential Algebraic Equations Solvers in R","Version":"1.6"},"Rsurrogate":
{"Author":"Layla Parast","Description":"Provides functions to estimate the
proportion of treatment effect on the primary outcome that is explained by the
treatment effect on the surrogate
marker.","Imports":"stats","License":"GPL","NeedsCompilation":"no","Package":"Rsurr
ogate","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Robust
Estimation of the Proportion of Treatment Effect\nExplained by Surrogate Marker
Information","Version":"1.0"},"Rsymphony":{"Author":"Reinhard Harter [aut],\nKurt
Hornik [aut, cre],\nStefan Theussl [aut],\nCyrille Szymanski [ctb]","Depends":"R
(>= 2.6.0)","Description":"An R interface to the SYMPHONY solver for mixed-integer
linear
programs.","Enhances":"slam","License":"EPL","NeedsCompilation":"yes","Package":"Rs
ymphony","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"SYMPHONY in
R","URL":"http:\/\/R-Forge.R-
project.org\/projects\/rsymphony,\nhttps:\/\/projects.coin-
or.org\/SYMPHONY,\nhttp:\/\/www.coin-
or.org\/download\/source\/SYMPHONY\/","Version":"0.1-21"},"Rtsne":{"Author":"Jesse
Krijthe <jkrijthe@gmail.com>","Description":"An R wrapper around the fast T-
distributed Stochastic\nNeighbor Embedding implementation by Van der
Maaten.","Imports":"Rcpp (>= 0.11.0)","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"yes","Package":"Rtsne","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat","Title":"T-Distributed Stochastic
Neighbor Embedding using Barnes-
Hut\nImplementation","URL":"https:\/\/github.com\/jkrijthe\/Rtsne","Version":"0.10"
},"Rttf2pt1":{"Author":"Winston Chang,\nAndrew Weeks,\nFrank M. Siegert,\nMark
Heath,\nThomas Henlick,\nSergey Babkin,\nTurgut Uyar,\nRihardas Hepas,\nSzalay
Tamas,\nJohan Vromans,\nPetr Titera,\nLei Wang,\nChen Xiangyang,\nZvezdan
Petkovic,\nRigel,\nI. Lee Hetherington","Depends":"R (>= 2.15)","Description":"This
package contains the program ttf2pt1, for use with the\nextrafont package. This
product includes software developed by the TTF2PT1\nProject and its
contributors.","License":"file
LICENSE","NeedsCompilation":"yes","Package":"Rttf2pt1","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Package for ttf2pt1
program","URL":"https:\/\/github.com\/wch\/Rttf2pt1","Version":"1.3.3"},"Rtts":
{"Author":"Xiaodong Deng","Depends":"RCurl","Description":"Convert text into speech
(voice file in 'wav' format) with API offered by ITRI TTS (Text-To-Speech service,
Industrial Technology Research Institute, Taiwan. http:\/\/tts.itri.org.tw\/). One
main function is given, tts_ITRI(). English and Chinese (both traditional and
simplified) are supported, and user can specify the speaker accent, speed and
volume. Using this package requires internet connection.","License":"GPL-
3","NeedsCompilation":"no","Package":"Rtts","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Convert Text into
Speech","URL":"http:\/\/me.seekingqed.com\/","Version":"0.3.3"},"RtutoR":
{"Author":"Anup Nair [aut, cre]","Depends":"R (>= 3.1.0)","Description":"Contains
functions for launching R Tutorial & Plotting Apps. The R Tutorial app\nprovides a
set of most commonly performed data manipulation tasks in R. The\napp structures
the contents into different topics and provides an interactive & dynamic
interface\nfor navigation.\nThe plotting app provides an automated interface for
generating plots using the ggplot2 package.\nCurrent version of this app supports
10 different plot types along with options to manipulate specific\naesthetics and
controls related to each plot type.","Imports":"dplyr, ggplot2, shiny,
shinydashboard, rmarkdown, DT, shinyBS,\nshinyjs, ggthemes,
plotly","License":"GPL","NeedsCompilation":"no","Package":"RtutoR","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"Tutorial App for Learning
R","Version":"0.2"},"Rtwalk":{"Author":"J Andres Christen","Depends":"R (>=
2.8.0)","Description":"The 't-walk' is a general-purpose MCMC sampler
for\narbitrary continuous distributions that requires no tuning.","License":"GPL-
3","NeedsCompilation":"no","Package":"Rtwalk","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"The R Implementation of the 't-walk' MCMC
Algorithm","URL":"http:\/\/www.cimat.mx\/~jac\/twalk\/","Version":"1.8.0"},"Ruchard
et":{"Author":"Heewon Jeon","Depends":"R (>= 3.0.2)","Description":"R port of
'universalchardet', that is the encoding detector\nlibrary of
Mozilla.","Imports":"Rcpp (>=
0.11.0)","License":"MPL","NeedsCompilation":"yes","Package":"Ruchardet","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"testthat
(>= 0.7.1)","Title":"R package to detect character
encoding","URL":"https:\/\/github.com\/haven-jeon\/Ruchardet\/","Version":"0.0-
3"},"Runiversal":{"Author":"Mehmet Hakan Satman","Description":"This package
contains some functions for converting R\nobjects to Java style variables and XML.
Generated Java code is\ninterpretable by dynamic Java libraries such as
Beanshell.\nCalling R externally and handling the Java or XML output is an\nother
way to call R from other languages without native\ninterfaces. For a Java
implementation of this approach visit\nhttp:\/\/www.mhsatman.com\/rcaller.php
and\nhttp:\/\/stdioe.blogspot.com\/search\/label\/rcaller","License":"GPL","NeedsCo
mpilation":"no","Package":"Runiversal","Repository":"http:\/\/cran.csiro.au\/src\/c
ontrib","Title":"Runiversal - Package for converting R objects to Java
variables\nand XML","Version":"1.0.2"},"Runuran":{"Author":"Josef Leydold and
Wolfgang H\\\"ormann","Depends":"R (>= 3.0.0)","Description":"Interface to the
UNU.RAN library for Universal Non-Uniform RANdom variate generators.\nThus it
allows to build non-uniform random number generators from quite
arbitrary\ndistributions. In particular, it provides an algorithm for fast
numerical inversion\nfor distribution with given density function.\nIn addition,
the package contains densities, distribution functions and quantiles\nfrom a couple
of distributions.","Imports":"methods, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"Runuran","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"R Interface to the UNU.RAN Random Variate
Generators","URL":"http:\/\/statmath.wu.ac.at\/unuran\/","Version":"0.23.0"},"Runur
anGUI":{"Author":"Josef Leydold","Depends":"R (>= 2.11.0), methods, Runuran (>=
0.15.0), rvgtest (>=\n0.5.0), gWidgets (>= 0.0-41), gWidgetsRGtk2(>= 0.0-
69),\ncairoDevice","Description":"This package provides a GUI (Graphical User
Interface) for\nthe UNU.RAN random variate generators. Thus it allows to
build\nnon-uniform random number generators interactively for quite\narbitrary
distributions. In addition, R code for the required\ncalls from package Runuran can
be displayed and stored for\nlater use. Some basic analysis like goodness-of-fit
tests can\nbe performed.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"RunuranGUI","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"A GUI for the UNU.RAN random variate
generators","Version":"0.1"},"Rvcg":{"Author":"Stefan Schlager; the authors of
VCGLIB for the included version of the\ncode","Depends":"R (>=
3.0.0)","Description":"Operations on triangular meshes based on 'VCGLIB'. This
package\nintegrates nicely with the R-package 'rgl' to render the meshes processed
by\n'Rvcg'. The Visualization and Computer Graphics Library (VCG for short) is\nan
open source portable C++ templated library for manipulation, processing\nand
displaying with OpenGL of triangle and tetrahedral meshes. The library,\ncomposed
by more than 100k lines of code, is released under the GPL license,\nand it is the
base of most of the software tools of the Visual Computing Lab of\nthe Italian
National Research Council Institute ISTI (http:\/\/vcg.isti.cnr.it),\nlike 'metro'
and 'MeshLab'. The 'VCGLIB' source is pulled from trunk
(svn:\/\/\nsvn.code.sf.net\/p\/vcg\/code\/trunk\/vcglib) and patched to work with
options\ndetermined by the configure script as well as to work with the header
files\nincluded by 'RcppEigen'.","Imports":"Rcpp, grDevices, stats,
utils","License":"GPL (>= 2) | file
LICENSE","NeedsCompilation":"yes","Package":"Rvcg","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"Morpho, rgl","Title":"Manipulations of Triangular
Meshes Based on the 'VCGLIB' API","URL":"http:\/\/github.com\/zarquon42b\/Rvcg,
http:\/\/vcg.sf.net\/","Version":"0.13.1.2"},"Rvmmin":{"Author":"John C. Nash [aut,
cre]","Depends":"optextras","Description":"Variable metric nonlinear function
minimization with bounds constraints.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Rvmmin","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Variable Metric Nonlinear Function
Minimization","Version":"2013-11.12"},"Rwave":{"Author":"S original by Rene Carmona
<rcarmona@princeton.edu> and Bruno\nTorresani <bruno.torresani@cmi.univ-mrs.fr>; R
port by Brandon\nWhitcher <bjw34032@users.sourceforge.net>; upgrade by Jonathan M.
Lees<jonathan.lees@unc.edu>","Depends":"R (>= 2.14)","Description":"A set of R
functions which provide an\nenvironment for the Time-Frequency analysis of 1-D
signals (and\nespecially for the wavelet and Gabor transforms of noisy\nsignals).
It was originally written for Splus by Rene Carmona,\nBruno Torresani, and Wen L.
Hwang, first at the University of\nCalifornia at Irvine and then at Princeton
University. Credit\nshould also be given to Andrea Wang whose functions on
the\ndyadic wavelet transform are included. Rwave is based on
the\nbook: \"Practical Time-Frequency Analysis: Gabor and Wavelet\nTransforms with
an Implementation in S\", by Rene Carmona, Wen\nL. Hwang and Bruno Torresani,
Academic Press, 1998.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"Rwave","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Time-Frequency Analysis of 1-D
Signals","URL":"http:\/\/www.orfe.princeton.edu\/~rcarmona\/TFbook\/tfbook.html,\nh
ttp:\/\/r-forge.r-project.org\/projects\/rwave\/","Version":"2.4"},"Rwinsteps":
{"Author":"Anthony Albano <tony.d.albano@gmail.com>, Ben
Babcock\n<ben.babcock@arrt.org>","Depends":"R (>= 2.12.0)","Description":"The
Rwinsteps package facilitates communication between R\nand the Rasch modeling
software Winsteps. The package currently\nincludes functions for reading and
writing command files,\nsending them to Winsteps, reading and writing data
according to\ncommand file specifications, reading output into R, and\nplotting
various results.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Rwinsteps","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Running Winsteps in R","URL":"http:\/\/www.r-
project.org","Version":"1.0-1"},"RxCEcolInf":{"Author":"D. James Greiner, Paul
Baines, and Kevin M. Quinn","Depends":"MASS, MCMCpack, mvtnorm,
lattice","Description":"Fits the R x C inference model described in Greiner
and\nQuinn (2009). Allows incorporation of survey
results.","License":"GPL","NeedsCompilation":"yes","Package":"RxCEcolInf","Reposito
ry":"http:\/\/cran.csiro.au\/src\/contrib","Title":"R x C Ecological Inference With
Optional Incorporation of Survey\nInformation","Version":"0.1-3"},"RxODE":
{"Author":"Melissa Hallow [aut, cre], Wenping Wang [aut], David A. James
[aut]","Depends":"R (>= 3.0.0)","Description":"Facilities for running simulations
from ordinary\ndifferential equation (ODE) models, such as pharmacometrics and
other\ncompartmental models. A compilation manager translates the ODE model\ninto
C, compiles it, and dynamically loads the object code into R for\nimproved
computational efficiency. An event table object facilitates\nthe specification of
complex dosing regimens (optional) and sampling\nschedules. NB: The use of this
package requires both C and\nFortran compilers, for details on their use with R
please see\nSection 6.3, Appendix A, and Appendix D in the \"R Administration
and\nInstallation\" manual.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"RxODE","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr, nlme, shiny","Title":"Facilities for Simulating
from ODE-Based Models","URL":"https:\/\/www.r-project.org,
https:\/\/github.com\/hallowkm\/RxODE","Version":"0.5-1"},"RxnSim":{"Author":"Varun
Giri [aut, cre]","Depends":"R (>= 2.5.0)","Description":"Methods to compute
chemical similarity between two or more reactions and molecules. Allows masking of
chemical substructures for weighted similarity computations. Uses packages 'rCDK'
and 'fingerprint' for cheminformatics functionality.","Imports":"rJava,
fingerprint, data.table, rcdk (>=
3.3.2)","License":"GPL","NeedsCompilation":"no","Package":"RxnSim","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"Functions to Compute Chemical Reaction
Similarity","Version":"1.0.1"},"Ryacas":{"Author":"Rob Goedman <goedman@mac.com>,
Gabor Grothendieck <ggrothendieck@gmail.com>, Søren Højsgaard
<Soren.Hojsgaard@agrsci.dk>, Ayal Pinkus <apinkus@xs4all.nl>","Description":"An
interface to the yacas computer algebra system.","Imports":"XML","License":"GPL-
2","NeedsCompilation":"no","Package":"Ryacas","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"R interface to the yacas computer algebra
system","URL":"http:\/\/ryacas.googlecode.com","Version":"0.2-12.1"},"Rz":
{"Author":"Masahiro Hayashi","Depends":"R (>= 2.14), methods, grid, foreign,
memisc, psych, ggplot2\n(>= 0.9.2)","Description":"R is very powerful but it lacks
some of the functionalities found in\nStata or SPSS to manage survey data. The
'memisc' package provides these\n(variable labels, value labels, definable missing
values and so on), but to\nefficiently work these functions need a graphical
interface to allow the user\nto get an overview of the data. This package provides
such a graphical interface,\nsimilar in fashion to SPSS's Variable View and data
managing system. It uses the\n'memisc' package as its backend. Additionally, 'Rz'
has a powerful plot assistant\ninterface based on 'ggplot2'.","Imports":"RGtk2 (>=
2.20), formatR","License":"GPL (>= 3) + file
LICENSE","NeedsCompilation":"no","Package":"Rz","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"quantreg, Hmisc, cairoDevice, vcd","Title":"GUI Tool
for Data Management like SPSS or
Stata","URL":"http:\/\/m884.jp\/Rz.html","Version":"0.9-1"},"S2sls":{"Author":"Taha
Zaghdoudi","Depends":"R (>= 2.12.0)","Description":"Fit a spatial instrumental-
variable regression by two-stage least squares.","Imports":"stats,
spanel","License":"GPL-
3","NeedsCompilation":"no","Package":"S2sls","Repository":"http:\/\/cran.csiro.au\/
src\
/contrib","Title":"Spatial Two Stage Least Squares
Estimation","Version":"0.1"},"SACCR":{"Author":"Tasos
Grivas","Description":"Computes the Exposure-At-Default based on standardized
approach\nof the Basel III Regulatory framework (SA-CCR). Currently, trade types of
all\nthe five major asset classes have been created and, given the
inheritance-\nbased structure of the application, the addition of further trade
types is\nstraightforward. The application automatically separates the trades on
the\ncorresponding hedging and netting sets including the basis and
volatility\ntransactions. All the examples appearing on the regulatory paper
(including the\nmargined and the un-margined workflow) have been
implemented.","Imports":"methods","License":"GPL-
3","NeedsCompilation":"no","Package":"SACCR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"SA Counterparty Credit Risk under Basel
III","URL":"www.openriskcalculator.com","Version":"1.5"},"SACOBRA":
{"Author":"Wolfgang Konen <wolfgang.konen@fh-koeln.de> [aut], Samineh Bagheri [cre,
aut], Patrick Koch [aut]","Depends":"R (>= 2.14.0),","Description":"Performs
constrained optimization for expensive black-box problems.","Imports":"testit,
2)","NeedsCompilation":"no","Package":"SACOBRA","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"nloptr, FNN, MASS, dfoptim, DEoptim, lhs, rgl,
grDevices,\nscales","Title":"Self-Adjusting COBRA","Version":"0.7"},"SAENET":
{"Author":"Stephen Hogg [aut, cre],\nEugene Dubossarsky [aut]","Description":"An
implementation of a stacked sparse autoencoder for dimension reduction of features
and pre-training of feed-forward neural networks\nwith the 'neuralnet' package is
contained within this package. The package also includes a predict function for the
stacked autoencoder object to generate the compressed\nrepresentation of new data
if required. For the purposes of this package, 'stacked' is defined in line with
http:\/\/ufldl.stanford.edu\/wiki\/index.php\/Stacked_Autoencoders .\nThe
underlying sparse autoencoder is defined in the documentation of
'autoencoder'.","Imports":"autoencoder, neuralnet","License":"GPL-
3","NeedsCompilation":"no","Package":"SAENET","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"A Stacked Autoencoder Implementation with Interface
to\n'neuralnet'","URL":"http:\/\/ufldl.stanford.edu\/wiki\/index.php\/Stacked_Autoe
ncoders ,\nhttp:\/\/cran.r-
project.org\/package=autoencoder","Version":"1.1"},"SAFD":{"Author":"Wolfgang
Trutschnig <wolfgang@trutschnig.net>, Asun
Lubiano\n<lubiano@uniovi.es>","Depends":"R (>= 3.0.1)","Description":"The aim of
the package is to provide some basic functions\nfor doing statistics with one
dimensional Fuzzy Data (in the\nform of polygonal fuzzy numbers). In particular,
the package\ncontains functions for the basic operations on the class of\nfuzzy
numbers (sum, scalar product, mean, median, Hukuhara difference)\nas well as for
calculating (Bertoluzza) distance,\nsample variance, sample covariance, and
the\nDempster-Shafer (levelwise) histogram. Moreover a function to\nsimulate fuzzy
random variables, bootstrap tests for the\nequality of means, and a function to do
linear regression given\ntrapezoidal fuzzy data is included. Version 1.0 fixes some
bugs\nof previous versions.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SAFD","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Statistical Analysis of Fuzzy Data","Version":"1.0-
1"},"SAGA":{"Author":"Heath Blackmon and Jeffery P.
Demuth","Description":"Implements an information theory approach to the analysis of
line\ncross data providing model averaged results of parameter estimates
and\nunconditional standard errors. Also includes functions to provide
a\nvisualization of models space, custom plots of multi-model inference results,
and traditional\nline cross analysis plots.","Imports":"plotrix,
viridis","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SAGA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr","Title":"Software for the Analysis of Genetic
Architecture","URL":"https:\/\/github.com\/coleoguy\/SAGA","Version":"2.0.0"},"SALE
S":{"Author":"Yuwen Gu <guxxx192@umn.edu>, Hui Zou
<zouxx019@umn.edu>","Depends":"Matrix","Description":"A coordinate descent
algorithm for computing the solution path of the sparse and coupled sparse
asymmetric least squares, including the elastic net and (adaptive) Lasso penalized
SALES and COSALES regressions.","Imports":"grDevices, graphics, stats,
2","NeedsCompilation":"yes","Package":"SALES","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Elastic Net and (Adaptive) Lasso Penalized Sparse
Asymmetric\nLeast Squares (SALES) and Coupled Sparse Asymmetric Least\nSquares
(COSALES) using Coordinate Descent and Proximal\nGradient
Algorithms","Version":"1.0.0"},"SALTSampler":{"Author":"Hannah Director, Scott
Vander Wiel, James Gattiker","Depends":"R (>= 3.0.0), lattice","Description":"The
SALTSampler package facilitates Monte Carlo Markov Chain (MCMC)\nsampling of random
variables on a simplex. A Self-Adjusting Logit Transform\n(SALT) proposal is used
so that sampling is still efficient even in difficult\ncases, such as those in high
dimensions or with parameters that differ by orders\nof magnitude. Special care is
also taken to maintain accuracy even when some\ncoordinates approach 0 or 1
numerically. Diagnostic and graphic functions are\nincluded in the package,
enabling easy assessment of the convergence and mixing\nof the chain within the
constrained space.","Imports":"graphics, methods, stats","License":"BSD_3_clause +
file
LICENSE","NeedsCompilation":"no","Package":"SALTSampler","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"knitr, coda","Title":"Efficient Sampling on
the Simplex","Version":"0.1"},"SAM":{"Author":"Tuo Zhao, Xingguo Li, Han Liu, and
Kathryn Roeder","Depends":"R (>= 2.14), splines","Description":"The package SAM
targets at high dimensional predictive\nmodeling (regression and classification)
for complex data\nanalysis. SAM is short for sparse additive modeling, and
adopts\nthe computationally efficient basis spline technique. We solve\nthe
optimization problems by various computational algorithms\nincluding the block
coordinate descent algorithm, fast\niterative soft-thresholding algorithm, and
newton method. The\ncomputation is further accelerated by warm-start and active-
set\ntricks.","License":"GPL-
2","NeedsCompilation":"yes","Package":"SAM","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Sparse Additive Modelling","Version":"1.0.5"},"SAMUR":
{"Author":"Mansour T.A. Sharabiani, Alireza S. Mahani","Description":"Augmenting a
matched data set by generating multiple stochastic, matched samples from the data
using a\nmulti-dimensional histogram constructed from dropping the input matched
data into a multi-dimensional grid built on\nthe full data set. The resulting
stochastic, matched sets will likely provide a collectively higher coverage of the
full\ndata set compared to the single matched set. Each stochastic match is without
duplication, thus allowing downstream\nvalidation techniques such as cross-
validation to be applied to each set without concern for
overfitting.","Imports":"Matching","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SAMUR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Stochastic Augmentation of Matched Data Using
Restriction\nMethods","Version":"0.6"},"SAMURAI":{"Author":"Noory Y. Kim. Advisors:
Shrikant I. Bangdiwala, Gerald Gartlehner.","Depends":"R (>= 3.0.0),
metafor","Description":"This package contains R functions to gauge the impact of
unpublished studies upon the meta-analytic summary effect of a set of published
studies. (Credits: The research leading to these results has received funding from
the European Union's Seventh Framework Programme (FP7\/2007-2013) under grant
agreement no. 282574.)","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"SAMURAI","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Sensitivity Analysis of a Meta-analysis with Unpublished
but\nRegistered Analytical Investigations","Version":"1.2.1"},"SAPP":{"Author":"The
Institute of Statistical Mathematics","Depends":"R (>= 2.14.0),
graphics","Description":"Functions for statistical analysis of point
processes.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"SAPP","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Statistical Analysis of Point
Processes","Version":"1.0.4"},"SASPECT":{"Author":"Pei Wang <pwang@fhcrc.org>, Yan
Liu <yanliu@fhcrc.org>","Description":"A statistical method for significant
analysis of\ncomparative proteomics based on LC-MS\/MS Experiments","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"SASPECT","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Significant AnalysiS of PEptide CounTs","Version":"0.1-
1"},"SAScii":{"Author":"Anthony Joseph Damico [aut, cre]","Depends":"R (>=
2.14)","Description":"Using any importation code designed for SAS users to
read\nASCII files into sas7bdat files, the SAScii package parses\nthrough the INPUT
block of a (.sas) syntax file to design the\nparameters needed for a read.fwf
function call. This allows\nthe user to specify the location of the ASCII (often a
.dat)\nfile and the location of the .sas syntax file, and then load\nthe data frame
directly into R in just one step.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SAScii","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Import ASCII files directly into R using only a SAS input
script","URL":"https:\/\/github.com\/ajdamico\/SAScii","Version":"1.0"},"SASmixed":
{"Author":"Original by Littell, Milliken, Stroup, and Wolfinger,\nmodifications by
Douglas Bates <bates@stat.wisc.edu>, Martin Maechler,\nBen Bolker
and Steven Walker","Depends":"R (>= 2.14.0),","Description":"Data sets and sample
lmer analyses corresponding\nto the examples in Littell, Milliken, Stroup and
Wolfinger\n(1996), \"SAS System for Mixed Models\", SAS Institute.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"SASmixed","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"lme4, lattice","Title":"Data sets from \"SAS System
for Mixed Models\"","Version":"1.0-4"},"SASxport":{"Author":"Unless otherwise
noted, the contents of this package were written by\nGregory R. Warnes
<greg@warnes.net> and are provided under the\nterms of the GNU General Public
License, version 2.0 or later.\n--\nThe files 'src\/ieee2ibm.c' and
'src\/ibm2ieee.c' were extracted from\nBRL-CAD file \/brlcad\/src\/libbu\/htond.c
written by Michael John\nMuuss, Copyright (c) 2004-2007 United States Government
as\nrepresented by the U.S. Army Research Laboratory, and is utilized\nand
redistributed under the terms of the GNU Lesser General Public\nLicense, version
2.1.\n--\nThe files 'R\/AFirst.lib.s',
'R\/all.is.numeric.R',\n'R\/importConvertDateTime.R', 'R\/in.opererator.R',
'R\/makeNames.R',\n'R\/read.xport.R', and 'R\/testDateTime.R' are copied or adapted
from the\n'Hmisc' package created by Frank E. Harrell,
Jr.\n<f.harrell@vanderbilt.edu>, and are utilized and redistributed under\nthe
terms of the GNU General Public License, version 2.0 or later.\n--\nThe files
'R\/xport.R', 'src\/SASxport.c', 'src\/SASxport.h', and\n'src\/foreign.h' are
copied or adapted from the 'R' 'foreign' package\ncreated by Douglas M. Bates
<bates@stat.wisc.edu> and Saikat DebRoy\n<saikat@stat.wisc.edu>, and are utilized
and redistributed under the\nterms of the GNU General Public License, version 2.0
or later.\n--\nThe creation of this package was partially funded by Metrum
Institute\n<http:\/\/metruminstitute.org>.","Depends":"R (>=
2.4.0)","Description":"Functions for reading, listing\nthe contents of, and writing
'SAS' 'xport' format files.\nThe functions support reading and writing of
either\nindividual data frames or sets of data frames. Further,\na mechanism has
been provided for customizing how\nvariables of different data types are
stored.","Imports":"chron, Hmisc, utils","License":"GPL-
2","NeedsCompilation":"yes","Package":"SASxport","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Read and Write 'SAS' 'XPORT'
Files","URL":"https:\/\/github.com\/mangothecat\/SASxport","Version":"1.5.3"},"SAVE
":{"Author":"Jesus Palomo [aut, cre],\nGonzalo Garcia-Donato [aut],\nRui Paulo
[aut],\nJames Berger [ctb],\nMaria Jesus Bayarri [ctb],\nJerome Sacks
[ctb]","Description":"Implements Bayesian statistical methodology for the\nanalysis
of complex computer models.\nIt allows for the emulation, calibration, and
validation of computer models,\nfollowing methodology described in Bayarri et al
2007, Technometrics.","Imports":"coda, DiceKriging, methods","License":"GPL-2 |
GPL-
3","NeedsCompilation":"yes","Package":"SAVE","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"MASS","Title":"Bayesian Emulation, Calibration and
Validation of
Computer\nModels","URL":"http:\/\/vangogh.fcjs.urjc.es\/~jesus\/SAVE,\nhttp:\/\/van
gogh.fcjs.urjc.es\/~jesus","Version":"1.0"},"SBRect":{"Author":"Paul Fischer [aut,
cre, cph],\nAstrid Hilbert [ctb, cph]","Depends":"rJava","Description":"The package
uses fitting axes-aligned rectangles to a time series in order to find structural
breaks. The algorithm enclose the time series in a number of axes-aligned
rectangles and tries to minimize their area and number. As these are conflicting
aims, the user has to specify a parameter alpha in [0.0,1.0]. Values close to 0
result in more breakpoints, values close to 1 in fewer. The left edges of the
rectangles are the breakpoints. The package supplies two methods,
computeBreakPoints(series,alpha) which returns the indices of the break points and
computeRectangles(series,alpha) which returns the rectangles. The algorithm is
randomised; it uses a genetic algorithm. Therefore, the break point sequence found
can be different in different executions of the method on the same data, especially
when used on longer series of some thousand observations. The algorithm uses a
range-tree as background data structure which makes i very fast and suited to
analyse series with millions of observations. A detailed description can be found
in Paul Fischer, Astrid Hilbert, Fast detection of structural breaks, Proceedings
of Compstat 2014.","License":"GPL-
2","NeedsCompilation":"no","Package":"SBRect","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"MASS","Title":"Detecting structural breaks using
rectangle covering\n(non-parametric
method)","URL":"http:\/\/www2.imm.dtu.dk\/~pafi\/StructBreak\/index.html","Version"
:"0.26"},"SBSA":{"Author":"Davor Cubranic and Paul Gustafson","Depends":"R (>=
3.0.2)","Description":"Simplified Bayesian Sensitivity Analysis","Imports":"Rcpp
(>= 0.8.6)","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"SBSA","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"MASS, xtable","Title":"Simplified Bayesian Sensitivity
Analysis","URL":"http:\/\/sbsa.r-forge.r-
project.org\/","Version":"0.2.3"},"SCBmeanfd":{"Author":"David Degras","Depends":"R
(>= 2.10), stats, graphics","Description":"This package implements statistical
methods for estimating and inferring the mean of functional data. The methods are
based on simultaneous confidence bands and local polynomial fitting. They feature:
bandwidth selection by plug-in and cross-validation, goodness-of-fit tests for
parametric models, equality tests for two-sample problems, and plotting
functions.","Imports":"boot, KernSmooth","License":"GPL-
3","NeedsCompilation":"no","Package":"SCBmeanfd","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Simultaneous Confidence Bands for the Mean of Functional
Data","URL":"http:\/\/www.r-project.org","Version":"1.1"},"SCEPtER":
{"Author":"Matteo Dell'Omodarme [aut, cre],\nGiada Valle [aut]","Depends":"R (>=
3.1.0), MASS, parallel","Description":"SCEPtER pipeline for estimating the stellar
age, mass, and radius\ngiven observational\neffective temperature, [Fe\/H], and
astroseismic\nparameters. The results are obtained adopting a maximum
likelihood\ntechnique over a grid of pre-computed stellar models.","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"SCEPtER","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"lattice","Title":"Stellar CharactEristics Pisa
Estimation gRid","Version":"0.2-1"},"SCEPtERbinary":{"Author":"Matteo Dell'Omodarme
[aut, cre],\nGiada Valle [aut]","Depends":"R (>= 2.10), MASS, parallel,
SCEPtER","Description":"SCEPtER pipeline for estimating the stellar age for double-
lined detached binary systems. The observational constraints adopted in the
recovery are the effective temperature, the metallicity [Fe\/H], the mass, and the
radius of the two stars. The results are obtained adopting a maximum likelihood
technique over a grid of pre-computed stellar models.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"SCEPtERbinary","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"lattice","Title":"Stellar CharactEristics Pisa
Estimation gRid for Binary Systems","Version":"0.1-1"},"SCGLR":{"Author":"Guillaume
Cornu [cre, aut],\nFrederic Mortier [aut],\nCatherine Trottier [aut],\nXavier Bry
[aut]","Depends":"R (>= 3.0.0)","Description":"The Fisher Scoring Algorithm is
extended so as to combine Partial\nLeast Squares regression with Generalized Linear
Model estimation in the\nmultivariate
context.","Imports":"Matrix,Formula,expm,graphics,grid,ggplot2
(>=\n2.0.0),pROC,scales","License":"CeCILL-2 | GPL-
2","NeedsCompilation":"no","Package":"SCGLR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"parallel,gridExtra,knitr","Title":"Supervised Component
Generalized Linear Regression","Version":"2.0.3"},"SCI":{"Author":"Lukas
Gudmundsson & James H. Stagge","Depends":"fitdistrplus,
lmomco","Description":"Functions for generating Standardized Climate Indices
(SCI).\nSCI is a transformation of (smoothed) climate (or environmental)\ntime
series that removes seasonality and forces the data to\ntake values of the
standard normal distribution. SCI was\noriginally developed for precipitation. In
this case it is\nknown as the Standardized Precipitation Index
(SPI).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SCI","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"evd","Title":"Standardized Climate Indices such as SPI,
SRI or SPEI","Version":"1.0-1"},"SCMA":{"Author":"Isis Bulte","Depends":"R (>=
2.11.1)","Description":"An R package for single-case meta-analysis.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"SCMA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Single-Case Meta-Analysis","Version":"1.1.1"},"SCORER2":
{"Author":"Craig T. Armstrong, Thomas L. Vincent <tlfvincent@gmail.com>, Peter J.
Green and Derek N. Woolfson <D.N.Woolfson@bristol.ac.uk>","Depends":"R (>=
2.12)","Description":"This package contains the functions necessary to run the
SCORER 2.0 algorithm. SCORER 2.0 can be used to differentiate between parallel
dimeric and trimeric coiled-coil sequence, which are the two most more frequent
coiled-coil structures observed naturally. As such, SCORER 2.0 is particularly
useful for researchers looking to characterize novel coiled-coil sequences. It may
also be used to assist in the structural characterization of synthetic coiled-coil
sequences. Also included in this package are functions that allows the user to
retrain the SCORER 2.0 algorithm using user-defined training data.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"SCORER2","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"SCORER 2.0: an algorithm for distinguishing parallel
dimeric
and\ntrimeric coiled-coil
sequences","URL":"http:\/\/coiledcoils.chm.bris.ac.uk\/Scorer\/","Version":"0.99.0"
},"SCRT":{"Author":"Isis Bulte and Patrick Onghena","Depends":"R (>=
2.14.1)","Description":"A package for designing single-case phase, alternation and
multiple-baseline experiments, as well as for conducting randomization tests on
data gathered by means of such designs.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SCRT","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Single-Case Randomization Tests","Version":"1.1.1"},"SCVA":
{"Author":"Isis Bulte and Patrick Onghena","Depends":"R (>=
2.15.2)","Description":"A package to make graphical representations of single case
data and to transform graphical displays back to raw data. The package also
includes tools for visually analyzing single-case data, by displaying central
location, variability and trend.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SCVA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Single-Case Visual Analysis","Version":"1.1.1"},"SCperf":
{"Author":"Marlene Silva Marchena","Description":"The package implements different
inventory models, the\nbullwhip effect and other supply chain performance
2)","NeedsCompilation":"no","Package":"SCperf","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Supply Chain Perform","Version":"1.0"},"SDD":
{"Author":"Luca Bagnato, Lucio De Capitani, Angelo Mazza and Antonio
Punzo","Depends":"R (>= 2.15.0)","Description":"Allows for computing (and by
default plotting) different types of serial dependence
diagrams.","Imports":"Hmisc,sm,tseries,stats,rpanel,rgl","License":"GPL-
2","NeedsCompilation":"no","Package":"SDD","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Serial Dependence Diagrams","Version":"1.2"},"SDDE":
{"Author":"Etienne Lord, Margaux Le Cam, Eric Bapteste, Vladimir Makarenkov and
Francois-Joseph Lapointe","Depends":"R (>= 3.0), igraph (>= 1.0.0), doParallel,
foreach, iterators,\nparallel","Description":"Compares the evolution of an original
network X to an augmented network Y by counting the number of Shortcuts, Detours,
Dead Ends (SDDE), equal paths and disconnected nodes.","License":"GPL-
3","NeedsCompilation":"yes","Package":"SDDE","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Shortcuts, Detours and Dead Ends (SDDE) Path Types in
Genome\nSimilarity Networks","Version":"1.0.1"},"SDMTools":{"Author":"Jeremy
VanDerWal, Lorena Falconi, Stephanie Januchowski, Luke Shoo and\nCollin
Storlie","Description":"This packages provides a set of tools for post processing
the\noutcomes of species distribution modeling exercises. It includes
novel\nmethods for comparing models and tracking changes in distributions
through\ntime. It further includes methods for visualizing outcomes,
selecting\nthresholds, calculating measures of accuracy and landscape
fragmentation\nstatistics, etc.. This package was made possible in part by
financial\nsupport from the Australian Research Council & ARC Research Network
for\nEarth System Science.","Imports":"R.utils","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"SDMTools","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"adehabitat, raster, sp","Title":"Species
Distribution Modelling Tools: Tools for processing data\nassociated with species
distribution modelling
exercises","URL":"http:\/\/www.rforge.net\/SDMTools\/","Version":"1.1-221"},"SDR":
{"Author":"Angel M. Garcia [aut, cre],\nPedro Gonzalez [aut, cph],\nCristobal J.
Carmona [aut, cph],\nFrancisco Charte [ctb]","Depends":"R (>=
3.0.0)","Description":"Implementation of some algorithms for the data mining task
called\n\"subgroup discovery\" without package dependencies. It also provide a
Shiny App\nfor make the analysis easier. The algorithms works with data sets
provided in\nKEEL or ARFF format files or data.frame objects. If you want more
information about KEEL format, please\nrefer to < http:\/\/www.keel.es
> .","Imports":"methods, parallel, stats, utils","License":"LGPL (>= 3) | file
LICENSE","NeedsCompilation":"no","Package":"SDR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr, shiny (>= 0.11)","Title":"Subgroup Discovery
Algorithms for
R","URL":"https:\/\/github.com\/aklxao2\/SDR","Version":"0.7.0.0"},"SDaA":
{"Author":"Tobias Verbeke","Description":"Functions and Datasets from Lohr, S.
(1999), Sampling:\nDesign and Analysis, Duxbury.","License":"GPL-
3","NeedsCompilation":"no","Package":"SDaA","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"survey, ggplot2 (>= 0.8.2)","Title":"Sampling: Design and
Analysis","Version":"0.1-3"},"SEAsic":{"Author":"Anne Corinne Huggins-Manley [aut,
cre], Douglas Whitaker [aut]","Depends":"R (>= 3.1.1)","Description":"This package
conducts Score Equity Assessment (SEA; Dorans, 2004) by calculating and plotting
multiple SEA indices as introduced by a variety of authors and summarized by
Huggins and Penfield (2012).","License":"GPL-
3","NeedsCompilation":"no","Package":"SEAsic","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Score Equity Assessment- summary index
computation","Version":"0.1"},"SECP":{"Author":"Pavel V. Moskalev","Depends":"R (>=
2.14.0), SPSL (>= 0.1-6)","Description":"SECP package provides functionality for
estimating\nparameters of site clusters on 2D & 3D square lattice with\nvarious
lattice sizes, relative fractions of accessible sites\n(occupation probability),
iso- & anisotropy, von Neumann &\nMoore (1,d)-neighborhoods","License":"GPL-
3","NeedsCompilation":"no","Package":"SECP","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Statistical Estimation of Cluster Parameters
(SECP)","URL":"http:\/\/www.r-project.org","Version":"0.1-4"},"SEER2R":
{"Author":"Jun Luo","Description":"read and write SEER*STAT data
files","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SEER2R","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"reading and writing SEER*STAT data
files","Version":"1.0"},"SEERaBomb":{"Author":"Tomas
Radivoyevitch","Depends":"dplyr, ggplot2","Description":"Creates SEER
(Surveillance, Epidemiology and End Results) and A-bomb data binaries\nfrom ASCII
sources and provides tools for estimating SEER second cancer
risks.","Imports":"Rcpp (>= 0.11.3), reshape2, mgcv, LaF, DBI, RSQLite,
rgl,\nXLConnect, scales, plyr","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"SEERaBomb","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"bbmle","Title":"SEER and Atomic Bomb Survivor Data
Analysis Tools","URL":"http:\/\/epbi-
radivot.cwru.edu\/SEERaBomb\/SEERaBomb.html","Version":"2015.2"},"SEHmodel":
{"Author":"Emily Walker [aut],\nJean-Francois Rey [aut, cre],\nMelen Leclerc
[aut],\nSamuel Soubeyrand [ctb],\nMarc Bourotte [ctb]","Depends":"methods,
grDevices (>= 3.0.0), graphics (>= 3.0.0), R (>=\n3.0.0)","Description":"A model
coupling polygon and point processes for assessing\nrisk due to contaminant sources
and their impact on exposed individuals.","Imports":"sp (>= 1.0-17), stats (>=
3.0.2), rgeos(>= 0.3), fields(>=\n7.1), MASS(>= 7.3.29), deldir(>= 0.1), pracma(>=
1.8.3),\nraster(>= 2.3.0), fftwtools(>= 0.9.6), mvtnorm(>= 1.0.2), rgdal\n(>=
0.9)","License":"GPL (>= 2) | file
LICENSE","NeedsCompilation":"no","Package":"SEHmodel","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Spatial Exposure-Hazard Model for Exposure and
Impact Assessment\non Exposed Individuals","Version":"0.0.11"},"SEL":
{"Author":"Bjoern Bornkamp","Depends":"splines, quadprog,
lattice","Description":"This package implements a novel method for fitting
a\nbounded probability distribution to quantiles (for example\nstated by an
expert), see Bornkamp and Ickstadt (2009) for\ndetails. For this purpose B-splines
are used, and the density\nis obtained by penalized least squares based on a Brier
entropy\npenalty. The package provides methods for fitting the\ndistribution as
well as methods for evaluating the underlying\ndensity and cdf. In addition methods
for plotting the\ndistribution, drawing random numbers and calculating
quantiles\nof the obtained distribution are
provided.","License":"GPL","NeedsCompilation":"yes","Package":"SEL","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Title":"Semiparametric
elicitation","Version":"1.0-2"},"SEMID":{"Author":"Rina Foygel Barber
<rina@uchicago.edu>, Mathias Drton <md5@uw.edu>, Luca\nWeihs
<lucaw@uw.edu>.","Depends":"R (>= 2.10.1), igraph","Description":"Provides routines
to check identifiability or non-identifiability\nof linear structural equation
models as described in Drton, Foygel &\nSullivant (Ann. Statist., 2011) and Foygel,
Draisma & Drton (Ann. Statist.,\n2012). The routines are based on the graphical
representation of\nstructural equation models by a path diagram\/mixed
graph.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SEMID","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat","Title":"Identifiability of Linear Structural
Equation Models","URL":"http:\/\/www.r-project.org
http:\/\/www.stat.washington.edu\/~md5","Version":"0.2"},"SEMModComp":
{"Author":"Roy Levy","Depends":"mvtnorm","Description":"Conduct tests of difference
in fit for mean and covariance\nstructure models as in structural equation modeling
(SEM)","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"SEMModComp","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Model Comparisons for
SEM","URL":"http:\/\/www.public.asu.edu\/~rlevy2\/papers&software.html","Version":"
1.0"},"SETPath":{"Author":"Patrick Danaher","Description":"Tests gene expression
data from a biological pathway for biologically meaningful differences in the
eigenstructure between two classes. Specifically, it tests the null hypothesis
that the two classes' leading eigenvalues and sums of eigenvalues are equal. A
pathway's
leading eigenvalue arguably represents the total variability due to variability in
pathway activity, while the sum of all its eigenvalues represents the variability
due to pathway activity and to other, unregulated causes. Implementation of the
method described in Danaher (2015), \"Covariance-based analyses of biological
pathways\".","License":"GPL-
2","NeedsCompilation":"no","Package":"SETPath","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Spiked Eigenvalue Test for Pathway
data","Version":"1.0"},"SEchart":{"Author":"Rutger M. van den Bor and Willem M. van
der Wal","Depends":"JM","Description":"Displays state-event charts, for graphical
presentation of longitudinal data.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SEchart","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"SEchart","Version":"0.1"},"SGCS":{"Author":"Tuomas
Rajala","Depends":"spatstat","Description":"Graph based clustering summaries for
spatial point patterns. Includes Connectivity function,\nCumulative connectivity
function and clustering function, plus the triangle\/triplet intensity function
T.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"SGCS","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Spatial Graph Based Clustering Summaries for Spatial
Point\nPatterns","Version":"2.3"},"SGL":{"Author":"Noah Simon, Jerome Friedman,
Trevor Hastie, and Rob Tibshirani","Description":"Fit a regularized generalized
linear model via penalized\nmaximum likelihood. The model is fit for a path of
values of\nthe penalty parameter. Fits linear, logistic and Cox
models.","License":"GPL","NeedsCompilation":"yes","Package":"SGL","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Title":"Fit a GLM (or cox model) with a
combination of lasso and group\nlasso regularization","Version":"1.1"},"SGP":
{"Author":"Damian W. Betebenner [aut, cre],\nAdam R. Van Iwaarden [aut],\nBen
Domingue [aut],\nYi Shang [aut],\nJonathan Weeks [ctb],\nJohn Stewart
[ctb],\nJinnie Choi [ctb],\nXin Wei [ctb],\nHi Shin Shim [ctb],\nXiaoyuan Tan [ctb]
(Arizona Department of Education),\nCarrie Giovannini [ctb] (Arizona Department of
Education),\nSarah Polasky [ctb] (Arizona State University),\nRebecca Gau [ctb]
(Arizona Charter School Association),\nJeffrey Dean [ctb] (University of
Arkansas),\nWilliam Bonk [ctb] (Colorado Department of Education),\nMarie Huchton
[ctb] (Colorado Department of Education),\nAllison Timberlake [ctb] (Georgia
Department of Education),\nQi Qin [ctb] (Georgia Department of Education),\nMelissa
Fincher [ctb] (Georgia Department of Education),\nKiran Athota [ctb] (Georgia
Department of Education),\nTravis Allen [ctb] (Georgia Department of
Education),\nGlenn Hirata [ctb] (Hawaii Department of Education),\nGlenn Nochi
[ctb] (Hawaii Department of Education),\nJoshua Lee [ctb] (Hawaii Department of
Education),\nAyaka Nukui [ctb] (Idaho Department of Education),\nCarissa Miller
[ctb] (Idaho Department of Education),\nMatthew Raimondi [ctb] (Elgin Area School
District U46 (Illinois)),\nWes Bruce [ctb] (Indiana Department of
Education),\nRobert Hochsegang [ctb] (Indiana Department of Education),\nTony Moss
[ctb] (Kansas State Department of Education),\nXuewen Sheng [ctb] (Kansas State
Department of Education),\nKathy Flanagan [ctb] (Massachusetts Department of
Elementary and Secondary Education),\nRobert Lee [ctb] (Massachusetts Department of
Elementary and Secondary Education),\nJi Zeng [ctb] (Michigan Department of
Education),\nSteve Viger [ctb] (Michigan Department of Education),\nJoe DeCastra
[ctb] (Mississippi Department of Education),\nKen Thompson [ctb] (Mississippi
Department of Education),\nSoo Yeon Cho [ctb] (Missouri Department of
Education),\nJeff Halsell [ctb] (Clark County School District, Nevada),\nSelcuk
Ozdemir [ctb] (Washoe County School District, Nevada),\nRoger Silva [ctb] (Nevada
Department of Education),\nDeb Wiswell [ctb] (New Hampshire Department of
Education),\nKatya Levitan-Reiner [ctb] (New Haven Public Schools),\nCatherine
McCaslin [ctb] (New Haven Public Schools),\nJoshua Marland [ctb] (New York
Education Department),\nW Joshua Rew [ctb] (Oregon Department of Education),\nJason
Becker [ctb] (Rhode Island Department of Education),\nJessica Bailey [ctb] (Rhode
Island Department of Education),\nAna Karantonis [ctb] (Rhode Island Department of
Education),\nDeborah Jonas [ctb] (Virginia Department of Education),\nJuan D'Brot
[ctb] (West Virginia Department of Education),\nNate Hixson [ctb] (West Virginia
Department of Education),\nDeb Came [ctb] (Washington Office of Superintendent of
Public Instruction),\nAshley Colburn [ctb] (Washington Office of Superintendent of
Public Instruction),\nNick Hassell [ctb] (Washington Office of Superintendent of
Public Instruction),\nKrissy Johnson [ctb] (Washington Office of Superintendent of
Public Instruction),\nDaniel Bush [ctb] (Wisconsin Department of
Education),\nJustin Meyer [ctb] (Wisconsin Department of Education),\nJoseph Newton
[ctb] (Wisconsin Department of Education),\nNick Stroud [ctb] (Wisconsin Department
of Education),\nJohn Paul [ctb] (Wyoming Department of Education),\nMichael Flicek
[ctb] (Michael Flicek Projects LLC working with Wyoming Department of
Education),\nPhyllis Clay [ctb] (Albuquerque Public Schools),\nPeter Kinyua [ctb]
(Albuquerque Public Schools),\nBrendan Houng [ctb] (University of Melbourne,
Australia, NAPLAN),\nLeslie Rosale [ctb] (Ministry of Education,
Guatemala),\nNathan Wall [ctb] (eMetric working with Nevada Department of Education
and South Dakota Department of Education),\nNarek Sahakyan [ctb] (World Class
Instruction and Design (WIDA))","Depends":"R (>= 2.13)","Description":"Functions to
calculate student growth percentiles and percentile growth
projections\/trajectories for students using large scale,\nlongitudinal assessment
data. Functions use quantile regression to estimate the conditional density
associated\nwith each student's achievement history. Percentile growth
projections\/trajectories are calculated using the coefficient matrices derived
from\nthe quantile regression analyses and specify what percentile growth is
required for students to reach future achievement targets.","Imports":"Cairo,
colorspace, datasets, data.table (>= 1.9.6),\ndoParallel, doRNG, equate, foreach,
graphics, grid, grDevices,\ngridBase, iterators, gtools, jsonlite, matrixStats,
methods,\nparallel, quantreg, RSQLite, randomNames (>= 0.0-5), sn (>=\n1.0-0),
splines, stats, toOrdinal, utils","License":"GPL-
3","NeedsCompilation":"no","Package":"SGP","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"SGPdata (>= 13.0-0)","Title":"Student Growth Percentiles &
Percentile Growth Trajectories","URL":"http:\/\/sgp.io,
https:\/\/github.com\/CenterForAssessment\/SGP,\nhttp:\/\/cran.r-
project.org\/package=SGP","Version":"1.5-0.0"},"SGPdata":{"Author":"Damian W.
Betebenner [aut, cre],\nAdam Van Iwaarden [aut],\nBen Domingue [aut]","Depends":"R
(>= 2.12)","Description":"Data sets utilized by the SGP Package as exemplars for
users to conduct their own SGP analyses.","License":"GPL-
3","NeedsCompilation":"no","Package":"SGPdata","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"SGP (>= 1.4-0.0)","Title":"Exemplar Data Sets for SGP
Analyses","URL":"http:\/\/cran.r-
project.org\/package=SGPdata,\nhttps:\/\/github.com\/CenterForAssessment\/SGPdata",
"Version":"13.0-0.0"},"SHELF":{"Author":"Jeremy Oakley","Depends":"R (>=
3.2.2)","Description":"Implements various methods for eliciting a probability
distribution\nfor a single parameter from an expert or a group of experts. The
expert\nprovides a small number of probability or quantile judgements,
corresponding\nto points on his or her cumulative distribution function. A range of
parametric\ndistributions can then be fitted and displayed, with feedback provided
in the\nform of additional quantiles. A graphical interface for the roulette
elicitation\nmethod is also provided. For multiple experts, a weighted linear pool
can be\ncalculated. Also includes functions for eliciting beliefs about population
distributions.","Imports":"ggplot2, grid, shiny, stats, graphics","License":"GPL-2
| GPL-
3","NeedsCompilation":"no","Package":"SHELF","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat","Title":"Tools to Support the Sheffield
Elicitation Framework
(SHELF)","URL":"https:\/\/github.com\/OakleyJ\/SHELF","Version":"1.1.0"},"SHIP":
{"Author":"Monika Jelizarow and Vincent Guillemot","Description":"The SHIP-package
allows the estimation of various types of\nshrinkage covariance matrices. These
types differ in terms of\nthe so-called covariance target (to be chosen by the
user), the\nhighly structured matrix which the standard unbiased sample\ncovariance
matrix is shrunken towards and which optionally\nincorporates prior biological
knowledge extracted from the\ndatabase KEGG. The shrinkage intensity is obtained
via an\nanalytical procedure.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SHIP","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"SHrinkage covariance Incorporating Prior
knowledge","Version":"1.0.2"},"SHLR":{"Author":"Satria Sajuthi","Description":"A
statistical method designed to take advantage of population genetics and
microevolutionary theory, specifically by testing the association between haplotype
sharing length and trait of interest.","Imports":"stringr, geepack, Matrix,
FactoMineR, kinship2, foreach, MASS,\ndoParallel","License":"GPL-
3","NeedsCompilation":"no","Package":"SHLR","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Shared Haplotype Length Regression","Version":"1.0"},"SIBER":
{"Author":"Andrew Jackson and Andrew Parnell","Depends":"R (>=
2.10)","Description":"Fits bi-variate ellipses to stable isotope data using
Bayesian\ninference with the aim being to describe and compare their
isotopic\nniche.","Imports":"rjags,
mnormt, hdrcde, graphics, stats, grDevices","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"SIBER","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr, viridis","Title":"Stable Isotope Bayesian
Ellipses in R","Version":"2.0.2"},"SID":{"Author":"Jonas Peters","Description":"The
code computes the structural intervention distance (SID) between a true directed
acyclic graph (DAG) and an estimated DAG. Definition and details about the
implementation can be found in J. Peters and P. BÃ¼hlmann: \"Structural
intervention distance (SID) for evaluating causal graphs\", Neural Computation 27,
pages 771-799, 2015.","Imports":"pcalg, igraph, RBGL,
Matrix","License":"FreeBSD","NeedsCompilation":"no","Package":"SID","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Title":"Structural Intervention
Distance","Version":"1.0"},"SII":{"Author":"Gregory R.
Warnes","Description":"\nThis package calculates ANSI S3.5-1997 Speech
Intelligibility Index\n(SII), a standard method for computing the intelligibility
of\nspeech from acoustical measurements of speech, noise, and hearing\nthresholds.
This package includes data frames corresponding to\nTables 1 - 4 in the ANSI
standard as well as a function utilizing\nthese tables and user-provided hearing
threshold and noise level\nmeasurements to compute the SII score. The methods
implemented\nhere extend the standard computations to allow calculation of
SII\nwhen the measured frequencies do not match those required by the\nstandard by
applying interpolation to obtain values for the\nrequired
frequencies\n--\nDevelopment of this package was funded by the Center for
Bioscience\nEducation and Technology (CBET) of the Rochester Institute
of\nTechnology (RIT).","License":"GPL-
2","NeedsCompilation":"no","Package":"SII","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"splines, gdata, xtable","Title":"Calculate ANSI S3.5-1997
Speech Intelligibility Index","Version":"1.0.3"},"SIMMS":{"Author":"Syed Haider,
Michal Grzadkowski, Paul C. Boutros","Depends":"R (>= 2.15.0), survival (>= 2.36-
2), MASS (>= 7.3-12), glmnet\n(>= 1.9-8)","Description":"Algorithms to create
prognostic biomarkers using biological networks.","Imports":"xtable (>= 1.7-
4)","License":"GPL-
2","NeedsCompilation":"no","Package":"SIMMS","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr","Title":"Subnetwork Integration for Multi-Modal
Signatures","Version":"1.0.2"},"SIN":{"Author":"Mathias Drton
<md5@uw.edu>.","Depends":"R (>= 1.8.0)","Description":"This package provides
routines to perform SIN model selection\nas described in Drton & Perlman (2004,
2008). The selected models are\nrepresented in the format of the 'ggm' package,
which allows in\nparticular parameter estimation in the selected
2)","NeedsCompilation":"no","Package":"SIN","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"A SINful Approach to Selection of Gaussian Graphical
Markov\nModels","URL":"http:\/\/www.r-project.org,
http:\/\/www.stat.washington.edu\/~md5","Version":"0.6"},"SIS":{"Author":"Jianqing
Fan, Yang Feng, Diego Franco Saldana, Richard Samworth, Yichao Wu","Depends":"R
(>= 3.1.1), glmnet, ncvreg, survival","Description":"Variable selection techniques
are essential tools for model selection and estimation in high-dimensional
statistical models. Through this publicly available package, we provide a unified
environment to carry out variable selection using iterative sure independence
screening (SIS) and all of its variants in generalized linear models and the Cox
proportional hazards model.","License":"GPL-
2","NeedsCompilation":"no","Package":"SIS","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Sure Independence Screening","Version":"0.7-6"},"SKAT":
{"Author":"Seunggeun (Shawn) Lee, with contributions from Larisa Miropolsky and
Michael Wu","Depends":"R (>= 2.13.0)","Description":"Functions for kernel-
regression-based association tests including Burden test, SKAT and SKAT-O. These
methods aggregate individual SNP score statistics in a SNP set and efficiently
compute SNP-set level p-values.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"SKAT","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"SNP-Set (Sequence) Kernel Association
Test","Version":"1.1.2"},"SLC":{"Author":"Antonio Solanas, Rumen Manolov, and
Patrick Onghena","Depends":"R (>= 2.14.0)","Description":"Estimates the slope and
level change present in data after\nremoving phase A trend. Represents graphically
the original and\nthe detrended data.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SLC","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Slope and level change","Version":"0.3"},"SLHD":
{"Author":"Shan Ba","Description":"Generate the optimal Latin Hypercube Designs
(LHDs) for computer experiments with quantitative factors and the optimal Sliced
Latin Hypercube Designs (SLHDs) for computer experiments with both quantitative and
qualitative factors. Details of the algorithm can be found in Ba, S., Brenneman, W.
A. and Myers, W. R. (2015), \"Optimal Sliced Latin Hypercube Designs,\"
Technometrics. Important function in this package
is \"maximinSLHD\".","License":"LGPL-
2.1","NeedsCompilation":"yes","Package":"SLHD","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Maximin-Distance (Sliced) Latin Hypercube
Designs","Version":"2.1-1"},"SLOPE":{"Author":"Malgorzata Bogdan, Ewout van den
Berg, Chiara Sabatti, Weijie Su,\nEmmanuel Candes, Evan
Patterson","Description":"Efficient procedures for Sorted L1 Penalized Estimation
(SLOPE).\nThe sorted L1 norm is useful for statistical estimation and
testing,\nparticularly for variable selection in the linear
model.","Imports":"Rcpp","License":"GPL-
3","NeedsCompilation":"yes","Package":"SLOPE","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"knitr, testthat, isotone, R.matlab","Title":"Sorted L1
Penalized Estimation (SLOPE)","Version":"0.1.3"},"SMC":{"Author":"Gopi Goswami
<goswami@stat.harvard.edu>","Depends":"R (>= 1.9.0)","Description":"particle
filtering, auxiliary particle filtering and sequential Monte Carlo
algorithms","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"SMC","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Sequential Monte Carlo (SMC)
Algorithm","Version":"1.1"},"SMCP":{"Author":"Jin (Gordon) Liu","Description":"A
package containing functions for genome-wide
association\nstudies.","License":"GPL","NeedsCompilation":"yes","Package":"SMCP","R
epository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Smoothed minimax concave
penalization (SMCP) method for\ngenome-wide association
studies","Version":"1.1.3"},"SMCRM":{"Author":"Tobias Verbeke, based on datasets
provided on the book's website","Description":"Data Sets for Kumar and Petersen
(2012).\nStatistical Methods in Customer Relationship Management,\nWiley: New
York.","License":"GPL-
3","NeedsCompilation":"no","Package":"SMCRM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Data Sets for Statistical Methods in Customer
Relationship\nManagement by Kumar and Petersen (2012)","Version":"0.0-3"},"SMFI5":
{"Author":"Bruno Remillard","Depends":"ggplot2, reshape, corpcor","Description":"R
functions and data from Chapter 5 of 'Statistical\nMethods for Financial
Engineering', by Bruno Remillard, CRC\nPress, (2013).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SMFI5","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"R functions and data from Chapter 5 of 'Statistical Methods
for\nFinancial Engineering'","URL":"http:\/\/www.r-project.org,
http:\/\/www.brunoremillard.com","Version":"1.0"},"SMIR":{"Author":"Murray Aitkin,
Brian Francis, John Hinde, Ross Darnell\n<ross.darnell@csiro.au>","Depends":"R (>=
2.6.0),","Description":"This package accompanies Aitkin et al,
Statistical\nModelling in R, OUP, 2009. The package contains some functions\nand
datasets used in the text.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SMIR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"lattice, foreign, gdata, car, dglm, gnm, MASS,
npmlreg,\nsurvival","Title":"Companion to Statistical Modelling in
R","Version":"0.02"},"SML":{"Author":"Tuo Zhao","Depends":"glmnet, Matrix,
lattice,","Description":"The SML package is a collection of statistical machine
learning methods.","License":"GPL-
2","NeedsCompilation":"no","Package":"SML","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Statistical Machine Learning","Version":"0.1"},"SMNCensReg":
{"Author":"Aldo M. Garay <medina_garay@yahoo.com>, Monique Bettio Massuia
<moniquemassuia@gmail.com> and Victor Lachos <hlachos@ime.unicamp.br>","Depends":"R
(>= 3.1.2)","Description":"Fit univariate right, left or interval censored
regression model under the scale mixture of normal
distributions","Imports":"Matrix, PerformanceAnalytics","License":"GPL (>=
3.0)","NeedsCompilation":"no","Package":"SMNCensReg","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Fitting Univariate Censored Regression Model Under
the Family of\nScale Mixture of Normal
Distributions","Version":"3.0"},"SMPracticals":{"Author":"Anthony Davison
<Anthony.Davison@epfl.ch>","Depends":"R (>= 1.14.0), ellipse","Description":"This
package contains the datasets and a few functions for\nuse with the practicals
outlined in Appendix A of the book\nStatistical Models (Davison, 2003, Cambridge
University Press).\nThe practicals themselves can be found
at\nhttp:\/\/statwww.epfl.ch\/davison\/SM\/","Imports":"MASS, nlme,
survival","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SMPracticals","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Practicals for use with Davison (2003) Statistical
Models","URL":"http:\/\/statwww.epfl.ch\/davison\/SM\/","Version":"1.4-2"},"SMR":
{"Author":"Ben Deivide de Oliveira Batista, Daniel Furtado
Ferreira","Description":"Computes the studentized midrange distribution (pdf, cdf
and quantile) and generates random numbers","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SMR","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Externally Studentized Midrange
Distribution","URL":"www.dex.ufla.br\/~danielff\/r_resources.html","Version":"2.0.1
"},"SMVar":{"Author":"Guillemette Marot","Depends":"R (>=
2.6.0)","Description":"Implements the structural model for variances in order
to\ndetect differentially expressed genes from gene expression
data","License":"GPL","NeedsCompilation":"no","Package":"SMVar","Repository":"http:
\/\/cran.csiro.au\/src\/contrib","Title":"Structural Model for
variances","Version":"1.3.3"},"SNFtool":{"Author":"Bo Wang, Aziz Mezlini, Feyyaz
Demir, Marc Fiume, Zhuowen Tu, Michael Brudno, Benjamin Haibe-Kains, Anna
Goldenberg","Description":"Similarity Network Fusion takes multiple views of a
network and fuses them together to construct an overall status matrix. The input to
our algorithm can be feature vectors, pairwise distances, or pairwise similarities.
The learned status matrix can then be used for retrieval, clustering, and
classification.","Imports":"heatmap.plus","License":"GPL","NeedsCompilation":"no","
Package":"SNFtool","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Sim
ilarity Network Fusion","Version":"2.2"},"SNPMClust":{"Author":"Stephen W. Erickson
and Joshua Callaway","Depends":"R (>= 2.14.0), MASS,
mclust","Description":"Bivariate Gaussian genotype clustering and calling for
Illumina microarrays, building on the package 'mclust'. Pronounced snip-em-
clust.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SNPMClust","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Bivariate Gaussian Genotype Clustering and Calling for
Illumina\nMicroarrays","Version":"1.2"},"SNPassoc":{"Author":"Juan R González,
Lluís Armengol, Elisabet Guinó, Xavier Solé, and Víctor Moreno","Depends":"R (>=
3.0.0), haplo.stats, survival, mvtnorm, parallel","Description":"This package
carries out most common analysis when performing whole genome association studies.
These analyses include descriptive statistics and exploratory analysis of missing
values, calculation of Hardy-Weinberg equilibrium, analysis of association based on
generalized linear models (either for quantitative or binary traits), and analysis
of multiple SNPs (haplotype and epistasis analysis). Permutation test and related
tests (sum statistic and truncated product) are also implemented. Max-statistic and
genetic risk-allele score exact distributions are also possible to be
estimated.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SNPassoc","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"SNPs-based whole genome association
studies","URL":"http:\/\/www.creal.cat\/jrgonzalez\/software.htm","Version":"1.9-
2"},"SNPmaxsel":{"Author":"Anne-Laure Boulesteix <boulesteix@ibe.med.uni-
muenchen.de>","Depends":"R (>= 2.2.1), mvtnorm, combinat","Description":"This
package implements asymptotic methods related to\nmaximally selected statistics,
with applications to SNP data.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SNPmaxsel","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"mvtnorm, combinat","Title":"Maximally selected
statistics for SNP data","URL":"http:\/\/cran.r-
project.org\/web\/packages\/SNPmaxsel\/index.html","Version":"1.0-3"},"SNPtools":
{"Author":"Daniel Gatti","Depends":"R (>= 2.10), IRanges, GenomicRanges,
Biostrings, Rsamtools","Description":"This package queries the SNPs data sets and
makes plots of\ngenes and SNPs. This package allows users to access these
data\nsets once they have been compiled into one file and indexed\nwith Tabix
(http:\/\/samtools.sourceforge.net\/tabix.shtml). There\nare functions to retrieve
SNPs, subset them for specific\nstrains, obtain only SNPs that are polymorphic for
a subset of\nstrains, plot SNPs and look for certain allele patterns in\nSNPs. We
have also added functions to access indels and\nstructural
variants.","License":"GPL-
3","NeedsCompilation":"no","Package":"SNPtools","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Accessing, subsetting and plotting mouse
SNPs","Version":"1.1"},"SNSequate":{"Author":"Jorge Gonzalez Burgos [cre,
aut],\nDaniel Acu<c3><b1>a Leon [ctb]","Depends":"R (>= 2.10), magic,
stats","Description":"Contains functions to perform various models and\nmethods for
test equating. It currently implements the traditional\nmean, linear and
equipercentile equating methods, as well as the\nmean-mean, mean-sigma, Haebara and
Stocking-Lord IRT linking methods.\nIt also supports newest methods such that local
equating, kernel\nequating (using Gaussian, logistic and uniform kernels) with
presmoothing,\nand IRT parameter linking methods based on asymmetric item
characteristic\nfunctions. Functions to obtain both standard error of equating
(SEE)\nand standard error of equating difference between two equating\nfunctions
(SEED) are also implemented for the kernel method
of\nequating.","Imports":"methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SNSequate","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat","Title":"Standard and Nonstandard
Statistical Models and Methods for
Test\nEquating","URL":"http:\/\/www.mat.puc.cl\/~jgonzale","Version":"1.2.1"},"SNsc
an":{"Author":"Tai-Chi Wang [aut,cre,ths] <taichi53719@gmail.com>,\nTun-Chieh Hsu
[aut] <htj801116@gmail.com>,\nFrederick Kin Hing Phoa [ths]
<fredphoa@stat.sinica.edu.tw>","Depends":"R (>= 3.1.0)","Description":"Scan
statistics applied in social network data can be used to test the cluster
characteristics among a social network.","Imports":"igraph, poweRlaw,
Rmpfr","License":"GPL-
2","NeedsCompilation":"no","Package":"SNscan","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Scan Statistics in Social
Networks","Version":"1.0"},"SOAR":{"Author":"Bill Venables, based on original code
by David Brahm","Depends":"R (>= 2.9.0)","Description":"Allows objects to be stored
on disc and automatically\nrecalled into memory, as required, by delayed
assignment.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"SOAR","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Memory management in R by delayed
assignments","Version":"0.99-11"},"SOD":{"Author":"Martin Jakt","Depends":"methods,
Rcpp (>= 0.10.5)","Description":"SOD (Self-Organising-Deltoids) provides
multidimensional scaling by gradually reducing the dimensionality of an initial
space and using the resulting stress in the configuration to re-arrange nodes.
Stress is calculated from the errors in the inter-node distances, and the sum of
the stresses at each node is combined to create N-dimensional force vectors that
direct the movement of nodes as the dimensionality is iteratively
reduced.","License":"GPL-
2","NeedsCompilation":"yes","Package":"SOD","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"SOD for multidimensional scaling","Version":"1.0"},"SODC":
{"Author":"Yanhong Wang","Depends":"magic,ppls,psych,MASS","Description":"To
implement two clustering methods, ODC and SODC, for\nclustering datasets using
optimal scoring, can also be used as\nan dimension reduction tool.","License":"GPL-
2","NeedsCompilation":"no","Package":"SODC","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Optimal Discriminant Clustering(ODC) and Sparse
Optimal\nDiscriminant Clustering(SODC)","Version":"1.0"},"SOLOMON":{"Author":"Mark
Christie","Depends":"tcltk","Description":"Parentage analysis using Bayes'
theorem","License":"GPL-
2","NeedsCompilation":"no","Package":"SOLOMON","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Parentage analysis","Version":"1.0-1"},"SOMbrero":
{"Author":"Laura Bendhaiba [aut],\nJulien Boelaert [aut],\nMadalina Olteanu
[aut],\nNathalie Villa-Vialaneix [aut, cre]","Depends":"R (>= 3.1.0), knitr, igraph
(>= 0.6)","Description":"The stochastic (also called on-line) version of the Self-
Organising\nMap (SOM) algorithm is provided. Different versions of the\nalgorithm
are implemented, for numeric and relational data and for\ncontingency tables. The
package also contains many plotting\nfeatures (to help the user interpret the
results) and a graphical\nuser interface based on shiny (which is also available
on-line at\nhttp:\/\/shiny.nathalievilla.org\/sombrero).","Imports":"wordcloud,
scatterplot3d, RColorBrewer, shiny, grDevices,\ngraphics, stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SOMbrero","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"SOM Bound to Realize Euclidean and Relational
Outputs","Version":"1.1"},"SOPIE":{"Author":"Willem Daniel Schutte","Depends":"R
(>= 3.2), circular, ADGofTest","Description":"Provides functions to non-
parametrically estimate the off-pulse interval of a source\nfunction originating
from a pulsar. The technique is based on a sequential application of P-
values\nobtained from goodness-of-fit tests for the uniform distribution, such as
the Kolmogorov-Smirnov,\nCramer-von Mises, Anderson-Darling and Rayleigh goodness-
of-fit tests.","Imports":"stats, grDevices, graphics","License":"GPL-
3","NeedsCompilation":"no","Package":"SOPIE","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Non-Parametric Estimation of the Off-Pulse Interval of a
Pulsar","Version":"1.5"},"SOR":{"Author":"Lee S. McDaniel, Jonathan S.
Schildcrout","Depends":"Matrix, stats","Description":"Estimation for longitudinal
data following outcome dependent sampling using the sequential offsetted regression
technique. Includes support for binary, count, and continuous
2)","NeedsCompilation":"no","Package":"SOR","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Estimation using Sequential Offsetted
Regression","Version":"0.22"},"SOUP":{"Author":"Federico
Mattiello [aut, cre]","Depends":"R (>= 3.0.0), methods,
tensor","Description":"Construct a ranking of a set of treatments\/groups
by\ngathering together information coming from several response variables.\nIt can
be used with both balanced and unbalanced experiments\n(with almost all test
statistics) as well as in presence of either\ncontinuous covariates or a
stratifying (categorical) variable.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SOUP","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"flip","Title":"Stochastic Ordering Using Permutations
(and Pairwise\nComparisons)","Version":"1.1"},"SPA3G":{"Author":"Shaoyu Li and
Yuehua Cui","Description":"The package implements the model-based kernel
machine\nmethod for detecting gene-centric gene-gene interactions of Li\nand Cui
(2012).","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"SPA3G","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"SPA3G: R package for the method of Li and Cui
(2012)","Version":"1.0"},"SPACECAP":{"Author":"Arjun M. Gopalaswamy, Andrew J.
Royle, Michael E. Meredith, Pallavi\nSingh, Devcharan Jathanna, N. Samba Kumar and
K. Ullas Karanth","Depends":"R (>= 2.15.3), tcltk, coda","Description":"SPACECAP is
a user-friendly software package for\nestimating animal densities using closed
model\ncapture-recapture sampling based on photographic captures using\nBayesian
spatially-explicit capture-recapture models. This\napproach offers advantage such
as: substantially dealing with\nproblems posed by individual heterogeneity in
capture\nprobabilities in conventional capture-recapture analyses. It\nalso offers
non-asymptotic inferences which are more\nappropriate for small samples of capture
data typical of\nphoto-capture studies.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SPACECAP","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"A Program to Estimate Animal Abundance and Density
using\nBayesian Spatially-Explicit Capture-Recapture
Models","Version":"1.1.0"},"SPARQL":{"Author":"Willem Robert van Hage
<willem.van.hage@synerscope.com>, with contributions from: Tomi Kauppinen, Benedikt
Graeler, Christopher Davis, Jesper Hoeksema, Alan Ruttenberg, and Daniel
Bahls.","Depends":"XML, RCurl","Description":"Use SPARQL to pose SELECT or UPDATE
queries to an end-point.","License":"GPL-
3","NeedsCompilation":"no","Package":"SPARQL","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"SPARQL client","Version":"1.16"},"SPAr":{"Author":"Ruixue
Fan","Description":"This package performs robust nonparametric tests for rare
variants\nassociation analysis using summation of partition approaches that
incorporate\ngene-gene and gene-environmental interactions","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SPAr","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Perform rare variants association analysis based on
summation of\npartition approaches","Version":"0.1"},"SPCALDA":{"Author":"Yue S.
Niu, Ning Hao, and Bin Dong","Depends":"R (>= 3.1.1), MASS","Description":"A new
reduced-rank LDA method which works for high dimensional multi-class
2","NeedsCompilation":"no","Package":"SPCALDA","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"A New Reduced-Rank Linear Discriminant Analysis
Method","Version":"1.0"},"SPECIES":{"Author":"Ji-Ping Wang,
<jzwang@northwestern.edu>","Description":"SPECIES is an R package for estimation of
species richness\nor diversity.","License":"GPL-
2","NeedsCompilation":"yes","Package":"SPECIES","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Statistical package for species richness
estimation","Version":"1.0"},"SPEI":{"Author":"Santiago BeguerÃa [aut,
cre],\nSergio M. Vicente-Serrano [aut]","Depends":"lmomco,
parallel","Description":"A set of functions for computing potential
evapotranspiration and several widely used drought indices including the
Standardized Precipitation-Evapotranspiration Index (SPEI).","License":"GPL-
2","NeedsCompilation":"no","Package":"SPEI","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Calculation of the Standardised Precipitation-
Evapotranspiration\nIndex","URL":"http:\/\/sac.csic.es\/spei","Version":"1.6"},"SPI
Assay":{"Author":"Francesca Demichelis <demichelis@science.unitn.it>,
Davide\nPrandi <prandi@science.unitn.it>","Depends":"R (>=
1.8.0)","Description":"The SNP Panel Identification Assay (SPIA) is a package\nthat
enables an accurate determination of cell line identity\nfrom the genotype of
single nucleotide polymorphisms (SNPs).\nThe SPIA test allows to discern when two
cell lines are close\nenough to be called similar and when they are
not.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SPIAssay","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"A genetic-based assay for the identification of cell
lines","URL":"http:\/\/www.r-project.org","Version":"1.0.0"},"SPIn":{"Author":"Ying
Liu","Depends":"R (>= 1.8.0), quadprog","Description":"An optimal weighting
strategy to compute\nsimulation-efficient shortest probability intervals
(spins).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SPIn","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Simulation-efficient Shortest Probability
Intervals","Version":"1.1"},"SPODT":{"Author":"Jean Gaudart, Nathalie Graffeo,
Guillaume Barbet, Bernard Fichet, Roch Giorgi (Aix-Marseille
University)","Depends":"methods, graphics, rgdal, sp, tree","Description":"SPODT is
a spatial partitioning method based on oblique decision trees, in order to classify
study area into zones of different risks, determining their
boundaries","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"SPODT","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Spatial Oblique Decision Tree","Version":"0.9-1"},"SPOT":
{"Author":"Thomas Bartz-Beielstein [aut],\nMartin Zaefferer [cre, ctb],\nJoerg
Ziegenhirt [ctb],\nWolfgang Konen [ctb],\nOliver Flasch [ctb],\nPatrick Koch
[ctb],\nMartina Friese [ctb]","Depends":"R (>= 2.14.0)","Description":"The
Sequential Parameter Optimization Toolbox provides a set of tools for Parameter-
tuning, based on modelling techniques, DoE and statistical
methods.","Imports":"rpart, emoa, twiddler, rgl, AlgDesign, randomForest,
rsm,\nMASS, mco","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SPOT","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"BB, cmaes, DEoptim, dfoptim, DiceKriging, DoE.wrapper,
e1071,\nearth, fields, FrF2, GenSA, ggplot2, gtools, kernlab, lattice,\nlhs, lme4,
minqa, mlegp, monmlp, nloptr, neuralnet,\npenalizedSVM, plotmo, pso, qrnn, rgenoud,
rgp (>= 0.3-4), tgp","Title":"Sequential Parameter Optimization
Toolbox","Version":"1.0.5543"},"SPREDA":{"Author":"Yili Hong, Yimeng Xie, and
Zhibing Xu","Depends":"survival, nlme","Description":"The Statistical Package for
REliability Data Analysis (SPREDA) implements recently-developed statistical
methods for the analysis of reliability data. Modern technological developments,
such as sensors and smart chips, allow us to dynamically track product\/system
usage as well as other environmental variables, such as temperature and humidity.
We refer to these variables as dynamic covariates. The package contains functions
for the analysis of time-to-event data with dynamic covariates and degradation data
with dynamic covariates. The package also contains functions that can be used for
analyzing time-to-event data with right censoring, and with left truncation and
right censoring. Financial support from NSF and DuPont are
acknowledged.","License":"GPL-
2","NeedsCompilation":"no","Package":"SPREDA","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Statistical Package for Reliability Data
Analysis","Version":"1.0"},"SPRT":{"Author":"Stephane Mikael
Bottine","Description":"Perform Wald's Sequential Probability Ratio Test on
variables with a Normal, Bernoulli, Exponential and Poisson distribution. Plot
acceptance and continuation regions, or create your own with the help of
closures.","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"SPRT","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Wald's Sequential Probability Ratio
Test","Version":"1.0"},"SPSL":{"Author":"Pavel V. Moskalev","Depends":"R (>=
2.14.0)","Description":"SPSL package provides functionality for labeling
of\npercolation clusters on 2D & 3D square lattice with various\nlattice size,
relative fraction of accessible sites (occupation\nprobability), iso- & anisotropy,
von Neumann & Moore\n(1,d)-neighborhood","License":"GPL-
3","NeedsCompilation":"yes","Package":"SPSL","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"lattice","Title":"Site Percolation on Square Lattice
(SPSL)","URL":"http:\/\/cran.r-project.org\/package=SPSL","Version":"0.1-
8"},"SPmlficmcm":{"Author":"Moliere Nguile-Makao [aut, cre], Alexandre Bureau
[aut]","Depends":"nleqslv","Description":"Implements the method of general
semiparametric maximum likelihood estimation for logistic models in case-mother
control-mother designs.","License":"GPL-
2","NeedsCompilation":"no","Package":"SPmlficmcm","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Semiparametric Maximum Likelihood Method for
Interactions\nGene-Environment in Case-Mother Control-Mother
Designs","Version":"1.4"},"SQDA":{"Author":"Jiehuan Sun","Depends":"R (>=
2.10)","Description":"Sparse Quadratic Discriminant Analysis (SQDA) can be
performed. In SQDA, the covariance matrix are assumed to be block-diagonal.And, for
each block, sparsity assumption is imposed on the covariance matrix. It is useful
in high-dimensional setting.","Imports":"limma (>= 3.18.13), PDSCE (>= 1.2),
mvtnorm (>= 0.9.99992)","License":"GPL-
3","NeedsCompilation":"no","Package":"SQDA","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Sparse Quadratic Discriminant
Analysis","Version":"1.0"},"SQN":{"Author":"Zhijin(Jean) Wu, Martin
Aryee","Depends":"R (>= 2.6.0), mclust(>= 3.2), nor1mix(>= 1.0-
7)","Description":"Normalization based a subset of negative control probes
as\ndescribed in 'Subset quantile normalization using negative\ncontrol features'.
Wu Z, Aryee MJ, J Comput Biol. 2010\nOct;17(10):1385-95 [PMID
20976876].","License":"LGPL (>=
2.0)","NeedsCompilation":"no","Package":"SQN","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"subset quantile
normalization","Version":"1.0.5"},"SQUAREM":{"Author":"Ravi Varadhan","Depends":"R
(>= 2.10.0)","Description":"Algorithms for accelerating the convergence of
slow,\nmonotone sequences from smooth, contraction mapping such as the\nEM
algorithm. It can be used to accelerate any smooth, linearly\nconvergent
acceleration scheme. A tutorial style introduction\nto this package is available
in a vignette on the CRAN download\npage or, when the package is loaded in an R
session, with\nvignette(\"SQUAREM\").","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SQUAREM","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"setRNG","Title":"Squared extrapolation methods for
accelerating fixed-
point\niterations","URL":"\nhttp:\/\/www.jhsph.edu\/agingandhealth\/People\/Faculty
_personal_pages\/Varadhan.html","Version":"2014.8-1"},"SRCS":{"Author":"Pablo J.
Villacorta <pjvi@decsai.ugr.es>","Description":"Implementation of the SRCS method
for a color-based visualization of the\nresults of multiple pairwise tests on a
large number of problem configurations, proposed in:\nI.G. del Amo, D.A. Pelta.
SRCS: a technique for comparing multiple algorithms under several\nfactors in
dynamic optimization problems. In: E. Alba, A. Nakib, P. Siarry\n(Eds.),
Metaheuristics for Dynamic Optimization. Series: Studies in\nComputational
Intelligence 433, Springer, Berlin\/Heidelberg, 2012.","Imports":"parallel,
graphics, stats, grDevices, methods","License":"LGPL (>=
3)","NeedsCompilation":"no","Package":"SRCS","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"R.rsp","Title":"Statistical Ranking Color Scheme for
Multiple Pairwise\nComparisons","URL":"http:\/\/decsai.ugr.es\/~pjvi\/r-
packages.html","Version":"1.1"},"SRRS":{"Author":"Frederick Kin Hing Phoa and Shu-
Ching Lin","Depends":"tcltk,tcltk2,gtools","Description":"This package implements
the SRRS method introduced in Phoa (2013) into a graphical user interface (GUI) R
program.","License":"GPL-
2","NeedsCompilation":"no","Package":"SRRS","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"The Stepwise Response Refinement Screener
(SRRS)","Version":"0.1.1"},"SSDM":{"Author":"Sylvain Schmitt, Robin Pouteau,
Dimitri Justeau, Philippe Birnbaum","Depends":"R (>= 3.2.2)","Description":"Allows
to map species richness and endemism based on stacked\nspecies distribution models
(SSDM). Individuals SDMs can be created using a\nsingle or multiple algorithms
(ensemble SDMs). For each species, an SDM can\nyield a habitat suitability map, a
binary map, a between-algorithm variance\nmap, and can assess variable importance,
algorithm accuracy, and between-\nalgorithm correlation. Methods to stack
individual SDMs include summing\nindividual probabilities and thresholding then
summing. Thresholding can be\nbased on a specific evaluation metric or by drawing
repeatedly from a Bernoulli\ndistribution. The SSDM package also provides a user-
friendly interface.","Imports":"sp (>= 1.2.0), raster (>= 2.4.20), methods (>=
3.2.2),\nSDMTools (>= 1.1.221), mgcv (>= 1.8.7), earth (>= 4.4.3), rpart\n(>=
4.1.10), gbm (>= 2.1.1), randomForest (>= 4.6.10), dismo\n(>= 1.0.12), nnet (>=
7.3.10), e1071 (>= 1.6.7), shiny (>=\n0.12.2), shinydashboard (>= 0.5.1), gplots
(>= 0.1.0), spThin\n(>= 0.1.0)","License":"GPL (>= 3) | file
LICENSE","NeedsCompilation":"no","Package":"SSDM","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"shinyFiles (>= 0.6.0)","Title":"Stacked Species
Distribution Modelling","Version":"0.1.1"},"SSDforR":{"Author":"Charles Auerbach
[aut, cre],\nWendy Zeitlin [aut]","Depends":"R (>= 2.10.0)
,psych,TTR,MASS,tcltk,TSA","Description":"Functions to visually and statistically
analyze single system
data.","Imports":"stats,graphics,grDevices,utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SSDforR","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Functions to Analyze Single System
Data","Version":"1.4.12"},"SSN":{"Author":"Jay Ver Hoef and Erin
Peterson","Depends":"R (>= 3.0.2), RSQLite, sp","Description":"Geostatistical
modeling for data on stream networks, including models based on in-stream distance.
Models are created using moving average constructions. Spatial linear models,
including covariates, can be fit with ML or REML. Mapping and other graphical
functions are included.","Imports":"MASS, igraph (>= 1.0.0), maptools, lattice,
2","NeedsCompilation":"yes","Package":"SSN","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Spatial Modeling on Stream
Networks","Version":"1.1.7"},"SSRMST":{"Author":"Miki
Horiguchi","Description":"Calculates the power and sample size based on the
difference in Restricted Mean Survival Times.","Imports":"survival,
survRM2","License":"GPL-
2","NeedsCompilation":"no","Package":"SSRMST","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"knitr","Title":"Sample Size Calculation using Restricted
Mean Survival Time","Version":"0.1.0"},"SSrat":{"Author":"Hans
Landsheer","Depends":"plyr, sna","Description":"SSRAT is a computer program for
two-dimensional sociometric status\ndetermination with rating scales. For each
person assessed, SSRAT computes\nprobability distributions of the total scores for
`sympathy' (S),\nàntipathy' (A), `social preference' (P) and `social impact' (I),
and\napplies the criteria for sociometric status categorization.","License":"GPL-
2","NeedsCompilation":"no","Package":"SSrat","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Two-dimensional sociometric status determination with
rating\nscales","Version":"1.0"},"SSsimple":{"Author":"Dave
Zes","Depends":"mvtnorm","Description":"Simulate, solve state space
models","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SSsimple","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"maps","Title":"State space
models","Version":"0.6.4"},"STAND":{"Author":"E. L. Frome <fromeEL@ornl.gov> and D.
P. Frome","Depends":"survival","Description":"Provides functions for the analysis
of\noccupational and environmental data with non-detects. Maximum\nlikelihood (ML)
methods for censored log-normal data and\nnon-parametric methods based on the
product limit estimate (PLE)\nfor left censored data are used to calculate all of
the\nstatistics recommended by the American Industrial Hygiene\nAssociation (AIHA)
for the complete data case. Functions for\nthe analysis of complete samples using
exact methods are also\nprovided for the lognormal model. Revised from 2007-11-
05\n'survfit~1'.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"STAND","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Statistical Analysis of Non-
Detects","URL":"http:\/\/www.csm.ornl.gov\/esh\/statoed\/","Version":"2.0"},"STAR":
{"Author":"Christophe Pouzat","Depends":"R (>= 2.10), survival, mgcv, R2HTML, gss,
codetools","Description":"Functions to analyze neuronal spike trains from a
single\nneuron or from several neurons recorded simultaneously.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"STAR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"lattice, HiddenMarkov, snow, rstream","Title":"Spike
Train Analysis with
R","URL":"http:\/\/sites.google.com\/site\/spiketrainanalysiswithr","Version":"0.3-
7"},"STEPCAM":{"Author":"Thijs Janzen & Fons van der Plas","Description":"STEPwise
Community Assembly Model collection, applying ABC-SMC in order to infer different
community assembly processes. Also includes several plotting functions in order to
visualize found estimates.","Imports":"gtools, MASS, vcd, FD, ade4, grid, geometry,
ape","License":"GPL-
2","NeedsCompilation":"no","Package":"STEPCAM","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"ABC-SMC Inference of STEPCAM","Version":"1.1.1"},"STI":
{"Author":"Marc Fasel [aut, cre]","Description":"A set of functions for computing
the Standardized Temperature Index (STI).","Imports":"fitdistrplus,
3","NeedsCompilation":"no","Package":"STI","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Calculation of the Standardized Temperature
Index","Version":"0.1"},"STMedianPolish":{"Author":"William Martinez, Carlos Melo
<cmelo@udistrital.edu.co>","Depends":"R (>= 2.15.0), maptools, reshape2, sp,
spacetime, zoo","Description":"Analysis by spatio-temporal data using the
decomposition in n-dimensional arrays and using median polish
technique.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"STMedianPolish","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Spatio-Temporal Median
Polish","Version":"0.1"},"STPGA":{"Author":"Deniz Akdemir","Description":"Can be
utilized to select a test data calibrated training population in high dimensional
prediction problems and assumes that the explanatory variables are observed for all
of the individuals. Once a \"good\" training set is identified, the response
variable can be obtained only for this set to build a model for predicting the
response in the test set.","License":"GPL-
2","NeedsCompilation":"no","Package":"STPGA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Selection of Training Populations by Genetic
Algorithm","Version":"1.0"},"SUE":{"Author":"Jim Yi","Description":"This is a
package for the subsampling method of robust\nestimation of linear regression
models","License":"GPL-
2","NeedsCompilation":"no","Package":"SUE","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"MASS","Title":"Subsampling
method","Version":"1.0"},"SVMMaj":{"Author":"Hoksan Yip, Patrick J.F. Groenen,
Georgi Nalbantov","Depends":"R (>= 2.9.0), kernlab","Description":"Implements the
SVM-Maj algorithm to train data with\nSupport Vector Machine, this algorithm uses
two efficient\nupdates, one for linear kernel and one for the
nonlinear\nkernel.","Imports":"graphics, stats, MASS, methods","License":"GPL-
2","NeedsCompilation":"no","Package":"SVMMaj","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"SVMMaj algorithm","Version":"0.2-2"},"SVMMatch":
{"Author":"Marc Ratkovic","Depends":"R (>= 3.0.2)","Description":"Causal effect
estimation in observational data often requires identifying a set of untreated
observations that are comparable to some treated group of interest. This package
provides a suite of functions for identifying such a set of observations and for
implementing standard and new diagnostics tools. The primary function, svmmatch(),
uses support vector machines to identify a region of common support between
treatment and control groups. A sensitivity analysis, balance checking, and
assessment of the region of overlap between treated and control groups is included.
The Bayesian implementation allows for recovery of uncertainty estimates for the
treatment effect and all other parameters.","Imports":"Rcpp (>=
0.11.0)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"SVMMatch","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Causal Effect Estimation and Diagnostics with Support
Vector\nMachines","Version":"1.1"},"SWATmodel":{"Author":"Fuka, DR, Walter, MT,
Steenhuis, TS, and Easton, ZM","Depends":"R (>= 2.10),
EcoHydRology","Description":"The Soil and Water Assessment Tool is a river basin
or\nwatershed scale model developed by Dr. Jeff Arnold for the\nUSDA-
ARS.","License":"GPL-
2","NeedsCompilation":"yes","Package":"SWATmodel","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"A multi-OS implementation of the TAMU SWAT
model","Version":"0.5.9"},"SWMPr":{"Author":"Marcus W. Beck [aut,
cre]","Depends":"R (>= 3.1.1), ggplot2, zoo","Description":"Tools for retrieving,
organizing, and analyzing environmental\ndata from the System Wide Monitoring
Program of the National Estuarine\nResearch Reserve System. These tools address
common challenges\nassociated with continuous time series data for environmental
decision\nmaking.","Imports":"data.table, httr, ggmap, gridExtra, maptools, oce,
dplyr,\nRColorBrewer, reshape2, tictoc, tidyr, wq,
XML","License":"CC0","NeedsCompilation":"no","Package":"SWMPr","Repository":"http:\
/\/cran.csiro.au\/src\/contrib","Suggests":"colorspace","Title":"Retrieving,
Organizing, and Analyzing Estuary Monitoring Data","Version":"2.1.5"},"SYNCSA":
{"Author":"Vanderlei Julio Debastiani","Depends":"vegan, mice,
FD","Description":"Analysis of metacommunities based on functional traits and
phylogeny of the community components. The functions that are offered here
implement for the R environment methods that have been available in the SYNCSA
application written in C++ (by Valerio Pillar, available at
http:\/\/ecoqua.ecologia.ufrgs.br\/ecoqua\/SYNCSA.html).","License":"GPL-
2","NeedsCompilation":"no","Package":"SYNCSA","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"SYNCSA - Analysis of functional and phylogenetic patterns
in\nmetacommunities","Version":"1.3.2"},"Sabermetrics":{"Author":"Peter Xenopoulos,
Fernando Crema <www.peterxeno.com>","Description":"A collection of baseball
analytics functions for sabermetrics\npurposes. Among these functions include
popular metrics such as FIP, wOBA, and\nruns created and other advanced
metrics.","Imports":"XML","License":"GPL-
3","NeedsCompilation":"no","Package":"Sabermetrics","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Sabermetrics Functions for Baseball
Analytics","Version":"2.0"},"SafeQuant":{"Author":"Erik Ahrne","Description":"Tools
for the statistical analysis and visualization of (relative and absolute)
quantitative (LFQ,TMT,HRM) Proteomics data.","Imports":"limma, gplots, seqinr,
corrplot, optparse, data.table, epiR,\nBiobase","License":"GPL-
3","NeedsCompilation":"no","Package":"SafeQuant","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"A Toolbox for the Analysis of Proteomics
Data","Version":"2.2.2"},"Sample.Size":{"Author":"Wei Jiang, Jonathan Mahnken,
Matthew Mayo","Description":"Computes the required sample size using the optimal
designs with multiple constraints proposed in Mayo et al.(2010). This optimal
method is designed for two-arm, randomized phase II clinical trials, and the
required sample size can be optimized either using fixed or flexible randomization
allocation ratios.","License":"GPL-
2","NeedsCompilation":"no","Package":"Sample.Size","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Sample size
calculation","Version":"1.0"},"SampleSizeMeans":{"Author":"Lawrence Joseph
<lawrence.joseph@mcgill.ca> and Patrick
Belisle\n<pbelisle@epimgh.mcgill.ca>","Description":"A set of R functions for
calculating sample size\nrequirements using three different Bayesian criteria in
the\ncontext of designing an experiment to estimate a normal mean or\nthe
difference between two normal means. Functions for\ncalculation of required sample
sizes for the Average Length\nCriterion, the Average Coverage Criterion and the
Worst Outcome\nCriterion in the context of normal means are provided.\nFunctions
for both the fully Bayesian and the mixed\nBayesian\/likelihood approaches are
2)","NeedsCompilation":"no","Package":"SampleSizeMeans","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Sample size calculations for normal
means","Version":"1.1"},"SampleSizeProportions":{"Author":"Lawrence Joseph
<lawrence.joseph@mcgill.ca>, Roxane du Berger\nand Patrick Belisle
<pbelisle@epimgh.mcgill.ca>","Description":"A set of R functions for calculating
sample size\nrequirements using three different Bayesian criteria in the\ncontext
of designing an experiment to estimate the difference\nbetween two binomial
proportions. Functions for calculation of\nrequired sample sizes for the Average
Length Criterion, the\nAverage Coverage Criterion and the Worst Outcome Criterion
in\nthe context of binomial observations are provided. In all\ncases, estimation of
the difference between two binomial\nproportions is considered. Functions for both
the fully\nBayesian and the mixed Bayesian\/likelihood approaches
are\nprovided.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SampleSizeProportions","Repository":"http:\/
\/cran.csiro.au\/src\/contrib","Title":"Calculating sample size requirements when
estimating the\ndifference between two binomial
proportions","Version":"1.0"},"SamplerCompare":{"Author":"Madeleine Thompson,
except dchud.f and dchdd.f, which were written by\nG. W. Stewart.","Depends":"R (>=
2.15.1), mvtnorm","Description":"A framework for running sets of MCMC samplers on
sets of\ndistributions with a variety of tuning parameters, along with
plotting\nfunctions to visualize the results of those simulations. See sc-
intro.pdf\nfor an introduction.","License":"GPL-
2","NeedsCompilation":"yes","Package":"SamplerCompare","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"ggplot2 (>= 0.9.2), synchronicity","Title":"A
Framework for Comparing the Performance of MCMC
Samplers","Version":"1.2.7"},"SamplingStrata":{"Author":"Giulio Barcaroli, Daniela
Pagliuca, Egon Willighagen,\nDiego Zardetto","Depends":"R (>= 2.15.0),
memoise","Description":"In the field of stratified sampling design, this
package\noffers an approach for the determination of the best\nstratification of a
sampling frame, the one that ensures the\nminimum sample cost under the condition
to satisfy precision\nconstraints in a multivariate and multidomain case.
This\napproach is based on the use of the genetic algorithm: each\nsolution (i.e. a
particular partition in strata of the sampling\nframe) is considered as an
individual in a population; the\nfitness of all individuals is evaluated applying
the\nBethel-Chromy algorithm to calculate the sampling size\nsatisfying precision
constraints on the target estimates.\nFunctions in the package allows to: (a)
analyse the obtained\nresults of the optimisation step; (b) assign the new
strata\nlabels to the sampling frame; (c) select a sample from the new\nframe
accordingly to the best allocation.\nFunctions for the execution of the genetic
algorithm are a modified\nversion of the functions in the 'genalg'
2)","NeedsCompilation":"no","Package":"SamplingStrata","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Optimal Stratification of Sampling Frames for
Multipurpose\nSampling Surveys","Version":"1.1"},"Scale":{"Author":"Nikolaos
Giallousis","Depends":"psych, Hmisc, MASS","Description":"Provides the Scale class
and corresponding functions, in order to facilitate data input for scale
construction. Reverse items and alternative orders of administration are dealt with
by the program. Computes reliability statistics, confirmatory, single factor
loadings. It suggests item deletions and produces basic text output in English, for
incorporation in reports. Returns list objects of all relevant functions from other
packages (see Depends).","License":"GPL-
2","NeedsCompilation":"no","Package":"Scale","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Likert Type Questionnaire Item
Analysis","Version":"1.0.4"},"SchemaOnRead":{"Author":"Michael North [aut,
cre]","Depends":"R (>= 3.2.1)","Description":"Provides schema-on-read tools
including a single function call (e.g., schemaOnRead('filename')) that reads text
('TXT'), comma separated value ('CSV'), raster image ('BMP', 'PNG', 'GIF', 'TIFF',
and 'JPG'), R data ('RDS'), HDF5 ('H5'), NetCDF ('CS'), spreadsheet ('XLS', 'XLSX',
'ODS', and 'DIF'), Weka Attribute-Relation
File Format ('ARFF'), Epi Info ('REC'), SPSS ('SAV'), Systat ('SYS'), and Stata
('DTA') files. It also recursively reads folders (e.g., schemaOnRead('folder')),
returning a nested list of the contained elements.","Imports":"caTools (>= 1.17.1),
foreign (>= 0.8-66), ncdf4 (>= 1.14),\nnetwork (>= 1.12.0), readbitmap (>= 0.1-4),
readODS (>= 1.4),\ntiff (>= 0.1-5), xml2 (>= 0.1.2), haven (>= 0.2.0), readxl
(>=\n0.1.0)","License":"GPL-
3","NeedsCompilation":"no","Package":"SchemaOnRead","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"knitr (>= 1.11), rmarkdown (>= 0.8.1), testthat
(>= 0.10.0)","Title":"Automated Schema on
Read","URL":"https:\/\/github.com\/drmichaelnorth\/SchemaOnRead","Version":"1.0.2"}
,"SciViews":{"Author":"Philippe Grosjean","Depends":"R (>= 2.6.0), stats,
grDevices, graphics, MASS","Description":"Functions to install SciViews additions
to R, and more (various)
tools","Enhances":"base","Imports":"ellipse","License":"GPL-
2","NeedsCompilation":"no","Package":"SciViews","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"SciViews GUI API - Main
package","URL":"http:\/\/www.sciviews.org\/SciViews-R","Version":"0.9-
5"},"SciencesPo":{"Author":"Daniel Marcelino [aut, cre]","Depends":"R (>= 3.2.0),
ggplot2 (>= 2.0.0), stats, utils, graphics,\ngrDevices,
methods","Description":"Provides functions for analyzing political behavior data,
including measures of political fragmentation, seat apportionment, and graphical
demonstrations.","Imports":"RSQLite (>= 1.0.0), data.table (>= 1.9.4), grid (>=
3.0.0),\ngridExtra, magrittr, stringr, shiny, lazyeval, dplyr, vcd","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"SciencesPo","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat, scales, knitr","Title":"A Tool Set for
Analyzing Political Behavior Data","URL":"http:\/\/CRAN.R-
project.org\/package=SciencesPo","Version":"1.3.9"},"ScoreGGUM":{"Author":"David R.
King and James S. Roberts","Description":"Estimate GGUM Person Parameters Using
Pre-Calibrated Item Parameters and Binary or Graded Disagree-Agree
Responses","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ScoreGGUM","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Score Persons Using the Generalized Graded Unfolding
Model","Version":"1.0"},"ScottKnott":{"Author":"Enio Jelihovschi
<eniojelihovs@gmail.com>\nJosé Cláudio Faria <joseclaudio.faria@gmail.com>\nIvan
Bezerra Allaman <ivanalaman@gmail.com>","Depends":"R (>= 2.6.0), stats,
base","Description":"Division of an ANOVA experiment treatment means
into\nhomogeneous distinct groups using the clustering method of\nScott &
Knott","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ScottKnott","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"The ScottKnott Clustering
Algorithm","URL":"https:\/\/github.com\/jcfaria\/ScottKnott,\nhttp:\/\/nbcgib.uesc.
br\/lec\/software\/pac-r\/scottknott","Version":"1.2-5"},"ScrabbleScore":
{"Author":"Will Kurt","Depends":"R (>= 2.10)","Description":"Given a word will
produce that word's scrabble score. Unlike many naive implementations this package
takes into consideration the distribution of letter in scrabble. So a word like
'zzz' will be scored '10' rather than '30'.","License":"MIT
License","NeedsCompilation":"no","Package":"ScrabbleScore","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Suggests":"testthat (>= 0.7)","Title":"Calculates
Scrabble score for strings","Version":"1.0"},"ScreenClean":{"Author":"Pengsheng Ji,
Jiashun Jin, Qi Zhang","Description":"Routines for a collection of screen-and-clean
type\nvariable selection procedures, including UPS and GS.","Imports":"MASS,
Matrix, quadprog","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ScreenClean","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Screen and clean variable selection
procedures","Version":"1.0.1"},"SearchTrees":{"Author":"Gabriel
Becker","Depends":"methods","Description":"This package provides an implementation
of the QuadTree\ndata structure. It uses this to implement fast k-Nearest\nNeighbor
and Rectangular range lookups in 2 dimenions. The\nprimary target is high
performance interactive
graphics.","License":"LGPL","NeedsCompilation":"yes","Package":"SearchTrees","Repos
itory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Spatial Search
Trees","Version":"0.5.2"},"SegCorr":{"Author":"Eleni Ioanna Delatola, Emilie
Lebarbier, Tristan Mary-Huard, Francois\nRadvanyi, Stephane Robin, Jennifer
Wong","Depends":"cghseg, methods","Description":"Performs correlation matrix
segmentation and applies a test\nprocedure to detect highly correlated regions in
gene expression.","License":"GPL-
2","NeedsCompilation":"no","Package":"SegCorr","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Detecting Correlated Genomic
Regions","Version":"1.1"},"Segmentor3IsBack":{"Author":"Alice Cleynen, Guillem
Rigaill, Michel Koskas","Depends":"R (>= 2.0.0), methods","Description":"This
package performs a fast exact segmentation on data and allows for use of various
cost functions","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"Segmentor3IsBack","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"A Fast Segmentation
Algorithm","Version":"1.8"},"Sejong":{"Author":"Heewon Jeon","Depends":"R (>=
2.14.0)","Description":"Sejong(http:\/\/www.sejong.or.kr\/) corpus
and\nHannanum(http:\/\/semanticweb.kaist.ac.kr\/home\/index.php\/HanNanum)\ndiction
aries for KoNLP","License":"GPL-
3","NeedsCompilation":"no","Package":"Sejong","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"KoNLP static dictionaries and Sejong project
resources","URL":"https:\/\/github.com\/haven-
jeon\/Sejong","Version":"0.01"},"SeleMix":{"Author":"Ugo Guarnera, M. Teresa
Buglielli","Depends":"mvtnorm, Ecdat, xtable","Description":"Detection of outliers
and influential errors using a latent variable
model.","License":"EUPL","NeedsCompilation":"no","Package":"SeleMix","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Title":"Selective Editing via Mixture
models","Version":"0.9.1"},"SelvarMix":{"Author":"Mohammed Sedki, Gilles Celeux,
Cathy Maugis-Rabusseau","Description":"Performs a regularization approach to
variable selection in the\nmodel-based clustering and classification
frameworks.\nFirst, the variables are arranged in order with a lasso-like
procedure.\nSecond, the method of Maugis, Celeux, and Martin-Magniette (2009,
2011)\nis adapted to define the role of variables in the two
frameworks.","Imports":"Rcpp (>= 0.11.1), glasso, parallel, Rmixmod,
3)","NeedsCompilation":"yes","Package":"SelvarMix","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Regularization for Variable Selection in Model-Based
Clustering\nand Discriminant Analysis","Version":"1.1"},"SemiCompRisks":
{"Author":"Kyu Ha Lee and Sebastien Haneuse","Depends":"MASS, survival, R (>=
3.2.3)","Description":"Parametric and semi-parametric analyses of semi-competing
risks\/univariate survival data.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"SemiCompRisks","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Hierarchical Models for Parametric and Semi-
Parametric Analyses\nof Semi-Competing Risks Data","Version":"2.4"},"SemiMarkov":
{"Author":"Agnieszka Listwon-Krol, Philippe Saint-Pierre","Depends":"R (>= 2.10.0),
numDeriv, MASS, Rsolnp","Description":"Functions for fitting multi-state semi-
Markov models to longitudinal data. A parametric maximum likelihood estimation
method adapted to deal with Exponential, Weibull and Exponentiated Weibull
distributions is considered. Right-censoring can be taken into account and both
constant and time-varying covariates can be included using a Cox proportional
2)","NeedsCompilation":"no","Package":"SemiMarkov","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Multi-States Semi-Markov
Models","Version":"1.4.3"},"SemiPar":{"Author":"Matt Wand
<mwand@uts.edu.au>","Description":"Functions for semiparametric regression
analysis, to\ncomplement the book: Ruppert, D., Wand, M.P. and Carroll,
R.J.\n(2003). Semiparametric Regression. Cambridge University
Press.","Imports":"MASS, cluster, nlme","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SemiPar","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"lattice","Title":"Semiparametic
Regression","URL":"http:\/\/www.use-r.com\/SPmanu.pdf","Version":"1.0-
4.1"},"SemiParBIVProbit":{"Author":"Giampiero Marra <giampiero.marra@ucl.ac.uk> and
Rosalba Radice <r.radice@bbk.ac.uk>","Depends":"R (>= 3.2.1),
mgcv","Description":"Routines for fitting copula bivariate models for binary and
continuous responses with linear and nonlinear effects in the presence of
associated error equations, endogeneity, non-random sample selection or partial
observability.","Enhances":"sp","Imports":"magic, VGAM, survey, trust, VineCopula,
graphics, stats,\nutils, grDevices, ggplot2, matrixStats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SemiParBIVProbit","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Semiparametric Copula Bivariate Regression
Models","URL":"http:\/\/www.ucl.ac.uk\/statistics\/people\/giampieromarra","Version
":"3.7"},"SemiParSampleSel":{"Author":"Giampiero Marra, Rosalba Radice, Malgorzata
Wojtys and Karol Wyszynski","Depends":"R (>= 3.1.1), copula, mgcv, mvtnorm,
gamlss.dist","Description":"Routine for fitting continuous or discrete response
copula sample selection models with semiparametric predictors, including linear and
nonlinear effects.","Imports":"magic, trust, VGAM, Matrix, graphics, grDevices,
2)","NeedsCompilation":"no","Package":"SemiParSampleSel","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Semiparametric Sample Selection Modelling with
Continuous or\nDiscrete
Response","URL":"http:\/\/www.ucl.ac.uk\/statistics\/people\/giampieromarra","Versi
on":"1.3"},"SenSrivastava":{"Author":"Kj
etil B Halvorsen <kjetil1001@gmail.com>","Depends":"R (>= 2.5.0),
stats","Description":"Collection of datasets from Sen &
Srivastava: \"Regression\nAnalysis, Theory, Methods and Applications\", Springer.
Sources\nfor individual data files are more fully documented in
the\nbook.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SenSrivastava","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"leaps, car","Title":"Datasets from Sen &
Srivastava","Version":"2015.6.25"},"SensMixed":{"Author":"Alexandra Kuznetsova
[aut, cre],\nPer Bruun Brockhoff [aut, ths],\nRune Haubo Bojesen Christensen
[aut]","Depends":"stats, methods, lmerTest","Description":"Functions that
facilitate analysis of\nSensory as well as Consumer data within a mixed effects
model\nframework are provided. The so-called mixed assessor models,\nthat correct
for the scaling effect are implemented.\nThe generation of the d-tilde plots forms
part of the package.\nThe shiny application for the functionalities\nforms part of
the package.","Imports":"Hmisc, parallel, plyr, doBy, xtable, reshape2, ggplot2,
shiny,\nshinyBS, lme4","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SensMixed","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"pbkrtest","Title":"Analysis of Sensory and Consumer
Data in a Mixed Model Framework","Version":"2.0-9"},"SensitivityCaseControl":
{"Author":"Dylan Small","Description":"This package performs sensitivity analysis
for case-control studies in which some cases may meet a more narrow definition of
being a case compared to other cases which only meet a broad definition. The
sensitivity analyses are described in Small, Cheng, Halloran and Rosenbaum
(2013, \"Case Definition and Sensitivity Analysis\", Journal of the American
Statistical Association, 1457-1468). The functions sens.analysis.mh and
sens.analysis.aberrant.rank provide sensitivity analyses based on the Mantel-
Haenszel test statistic and aberrant rank test statistic as described in Rosenbaum
(1991, \"Sensitivity Analysis for Matched Case Control Studies\", Biometrics); see
also Section 1 of Small et al. The function adaptive.case.test provides adaptive
inferences as described in Section 5 of Small et al. The function
adaptive.noether.brown provides a sensitivity analysis for a matched cohort study
based on an adaptive test. The other functions in the package are internal
2)","NeedsCompilation":"no","Package":"SensitivityCaseControl","Repository":"http:\
/\/cran.csiro.au\/src\/contrib","Title":"Sensitivity Analysis for Case-Control
Studies","Version":"2.1"},"SensoMineR":{"Author":"Francois Husson, Sebastien Le,
Marine Cadoret","Depends":"R (>= 2.12.0), FactoMineR (>= 1.23)","Description":"an R
package for analysing sensory data","Imports":"cluster,KernSmooth","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"SensoMineR","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Sensory data analysis with
R","URL":"http:\/\/sensominer.free.fr","Version":"1.20"},"SensusR":
{"Author":"Matthew S. Gerber","Description":"Provides access and analytic functions
for Sensus data.","Imports":"jsonlite (>= 0.9.14), lubridate (>= 1.3.3), rworldmap
(>=\n1.3-1), plyr (>= 1.8.1), sp (>= 1.0-16)","License":"GPL-
3","NeedsCompilation":"no","Package":"SensusR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Sensus
Analytics","URL":"https:\/\/github.com\/MatthewGerber\/sensus\/wiki","Version":"1.0
"},"SeqFeatR":{"Author":"Bettina Budeus","Depends":"R(>=
3.2.2),tcltk,tcltk2,Biostrings, plotrix, ape","Description":"Provides user friendly
methods for the identification of sequence patterns that are statistically
significantly associated with a property of the sequence. For instance, SeqFeatR
allows to identify viral immune escape mutations for hosts of given HLA types. The
underlying statistical method is Fisher's exact test, with appropriate corrections
for multiple testing, or Bayes. Patterns may be point mutations or n-tuple of
mutations. SeqFeatR offers several ways to visualize the results of the statistical
analyses.","Imports":"plyr, phangorn, qvalue, widgetTools, calibrate,
ggplot2,\nR2jags, coda, scales","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"SeqFeatR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"xtable","Title":"A Tool to Associate FASTA Sequences
and Features","Version":"0.2.2"},"SeqGrapheR":{"Author":"Petr Novak","Depends":"R
(>= 2.14.0)","Description":"The SeqGrapheR package provide interactive GUI for
visualization of DNA sequence clusters. Details and principles of usage are
described in user manual and (2010 BMC Bioinformatics 11:378). For full
functionality installed NCBI blast is
required.","Imports":"Biostrings,igraph,rggobi,gWidgets,gWidgetsRGtk2,cairoDevice",
"License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SeqGrapheR","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Simple GUI for Graph Based Visualization of Cluster of
DNA\nSequence Reads","Version":"0.4.8.5"},"Sequential":{"Author":"Ivair Ramos Silva
and Martin Kulldorff","Description":"Functions to calculate exact critical values,
statistical power, expected time to\t\t\t\tsignal and required sample sizes for
performing exact sequential analysis. All these\t\t\t\tcalculations can be done
for either Poisson or binomial data, for continuous or group\t\t\t\tsequential
analyses, and for different types of rejection boundaries. In case of
group\t\t\t\tsequential analyses, the group sizes do not have to be specified in
advance and, for\t\t\t\tbinomial data, the alpha spending can be arbitrarily
settled.","License":"GPL-
2","NeedsCompilation":"no","Package":"Sequential","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Exact Sequential Analysis for Poisson and Binomial
Data","Version":"2.0.2"},"SetMethods":{"Author":"Mario
Quaranta","Depends":"lattice, betareg, R (>= 2.14.0)","Description":"SetMethods is
a package companion to the book by C. Q.\nSchneider and C. Wagemann \"Set-Theoretic
Methods for the Social\nSciences\", Cambridge University Press. It contains
some\nadditional functions not present in other packages and data to\nreplicate the
examples in the book and in the online appendix.","Imports":"lattice,
betareg","License":"GPL-
2","NeedsCompilation":"no","Package":"SetMethods","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"SetMethods: A Package Companion to \"Set-Theoretic
Methods for\nthe Social Sciences\"","Version":"1.0"},"SetRank":{"Author":"Cedric
Simillion","Description":"Implements an algorithm to conduct advanced\ngene set
enrichment analysis on the results of genomics experiments.","Imports":"XML,
data.table, igraph","License":"GPL-
3","NeedsCompilation":"no","Package":"SetRank","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"R.rsp","Title":"Advanced Gene Set Enrichment
Analysis","Version":"1.0.1"},"ShapeChange":{"Author":"Xiyue Liao and Mary C
Meyer","Depends":"coneproj(>= 1.8), quadprog(>= 1.5-5), R(>=
3.2.0)","Description":"In a scatterplot where the response variable is Gaussian,
Poisson or binomial, we consider the case in which the mean function is smooth with
a change-point, which is a mode, an inflection point or a jump point. The main
routine estimates the mean curve and the change-point as well using shape-
restricted B-splines. An optional subroutine delivering a bootstrap confidence
interval for the change-point is incorporated in the main routine.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"ShapeChange","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"stats, MASS, graphics, grDevices,
utils","Title":"Change-Point Estimation using Shape-Restricted
Splines","Version":"1.3"},"ShapeSelectForest":{"Author":"Mary C. Meyer, Xiyue Liao,
Elizabeth Freeman, Gretchen G. Moisen","Depends":"coneproj (>= 1.6), raster (>=
2.3-40), rgdal (>= 0.8-12), R\n(>= 3.0.2)","Description":"Landsat satellites
collect important data about global forest conditions. Documentation about
Landsat's role in forest disturbance estimation is available at the site
<http:\/\/landsat.gsfc.nasa.gov\/?p=9513>. By constrained quadratic B-splines, this
package delivers an optimal shape-restricted trajectory to a time series of Landsat
imagery for the purpose of modeling annual forest disturbance dynamics to behave in
an ecologically sensible manner assuming one of seven possible \"shapes\", namely,
flat, decreasing, one-jump (decreasing, jump up, decreasing), inverted vee
(increasing then decreasing), vee (decreasing then increasing), linear increasing,
and double-jump (decreasing, jump up, decreasing, jump up, decreasing). The main
routine selects the best shape according to the minimum Bayes information criterion
(BIC) or the cone information criterion (CIC), which is defined as the log of the
estimated predictive squared error. The package also provides parameters
summarizing the temporal pattern including year(s) of inflection, magnitude of
change, pre- and post-inflection rates of growth or recovery. In addition, it
contains routines for converting a flat map of disturbance agents to time-series
disturbance maps and a graphical routine displaying the fitted trajectory of
Landsat imagery.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ShapeSelectForest","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"stats, MASS, graphics, grDevices,
utils","Title":"Shape Selection for Landsat Time Series of Forest
Dynamics","Version":"1.2"},"SharpeR":{"Author":"Steven E. Pav [aut,
cre]","Depends":"R (>= 3.0.0)","Description":"A collection of tools for analyzing
significance of trading\nstrategies, based on the Sharpe ratio and overfit of the
same.","Imports":"matrixcalc, sadists (>= 0.2.0)","License":"LGPL-
3","NeedsCompilation":"no","Package":"SharpeR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"xtable,
xts, timeSeries, quantmod, MASS, TTR, testthat,\nsandwich,
knitr","Title":"Statistical Significance of the Sharpe
Ratio","URL":"https:\/\/github.com\/shabbychef\/SharpeR","Version":"1.1.0"},"Shrink
CovMat":{"Author":"Anestis Touloumis","Depends":"R (>=
2.10)","Description":"Provides nonparametric Steinian shrinkage estimators of the
covariance matrix that are suitable in high dimensional settings, that is when the
number of variables is larger than the sample size.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"ShrinkCovMat","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Shrinkage Covariance Matrix
Estimators","Version":"1.1.1"},"Shrinkage":{"Author":"Corey M. Yanofsky, Zahra
Montazeri, Marta Padilla, Alaa Ali and David R. Bickel","Depends":"R (>= 2.14.0),
methods, PsiHat, multtest, limma","Description":"Several shrinkage estimators of
the effect-size of a parameter of interest.","License":"GPL-
3","NeedsCompilation":"no","Package":"Shrinkage","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Several Shrinkage Effect-Size
Estimators","URL":"http:\/\/www.r-project.org,
http:\/\/www.bioconductor.org","Version":"1.0"},"SiZer":{"Author":"Derek
Sonderegger <derek.sonderegger@gmail.com>","Depends":"R (>= 2.4.0), splines,
boot","Description":"Calculates and plots the SiZer map for scatterplot data.\nA
SiZer map is a way of examining when the p-th derivative of a\nscatterplot-smoother
is significantly negative, possibly zero\nor significantly positive across a range
of smoothing\nbandwidths.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SiZer","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"SiZer: Significant Zero Crossings","URL":"http:\/\/www.r-
project.org","Version":"0.1-4"},"SigTree":{"Author":"John R. Stevens and Todd R.
Jones","Description":"Takes a phylogenetic tree (of class phylo) and a data frame
(or matrix) of corresponding tip labels and p-values, and determines the
significance of the branches (families of p-values) and plots the tree with colored
branches (corresponding to families) according to their levels of significance.
Also produces a CSV file with the p-values of all of the branches as well as which
tips belong to which branches. Finally, it exports a file that can be opened in
FigTree that produces a colored plot (colored branches according to their
significance of corresponding groups of p-values) with p-value
annotations.","Imports":"ape, phylobase, phyext2, RColorBrewer, phyloseq,
graphics,\nutils, stats","License":"GPL-
3","NeedsCompilation":"yes","Package":"SigTree","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Identify and Visualize Significantly Responsive Branches
in a\nPhylogenetic Tree","Version":"1.10.3"},"SightabilityModel":{"Author":"John
Fieberg","Description":"Uses logistic regression to model the probability of
detection as a function of covariates.\nThis model is then used with observational
survey data to estimate population size, while\naccounting for uncertain detection.
See Steinhorst and Samuel (1989).","License":"GPL-
2","NeedsCompilation":"no","Package":"SightabilityModel","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Wildlife Sightability
Modeling","Version":"1.3"},"Sim.DiffProc":{"Author":"Arsalane Chouaib Guidoum,
Kamal Boukhetala","Depends":"R (>= 2.15.1)","Description":"Provides the functions
for simulation and modeling of stochastic differential equations (SDE's) the type
Ito and Stratonovich. This package contains many objects, the numerical methods to
find the solutions to SDE's (1, 2 and 3-dim), with a possibility for simulates a
flows trajectories,with good accuracy. Many theoretical problems on the SDE's have
become the object of practical research, as statistical analysis and simulation of
solution of SDE's, enabled many searchers in different domains to use these
equations to modeling and to analyse practical problems, in financial and actuarial
modeling and other areas of application, for example modelling and simulate of
dispersion in shallow water using the attractive center (Boukhetala K, 1996). We
hope that the package presented here and the updated survey on the subject might be
of help for practitioners, postgraduate and PhD students, and researchers in the
field who might want to implement new methods.","Imports":"scatterplot3d,
rgl","License":"GPL (>= 3) | file
LICENCE","NeedsCompilation":"yes","Package":"Sim.DiffProc","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Title":"Simulation of Diffusion
Processes","Version":"3.2"},"SimComp":{"Author":"Mario Hasler","Depends":"R (>=
2.10.0)","Description":"Simultaneous tests and confidence intervals are provided
for one-way experimental designs with one or many normally distributed, primary
response variables (endpoints). Differences (Hasler and Hothorn, 2011) or ratios
(Hasler and Hothorn, 2012) of means can be considered. Various contrasts can be
chosen, unbalanced sample sizes are allowed as well as heterogeneous variances
(Hasler and Hothorn, 2008) or covariance matrices (Hasler,
2014).","Imports":"mvtnorm, multcomp,
mratios","License":"GPL","NeedsCompilation":"no","Package":"SimComp","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Title":"Simultaneous Comparisons for
Multiple Endpoints","Version":"2.2"},"SimCorMultRes":{"Author":"Anestis
Touloumis","Depends":"R(>= 2.15.0)","Description":"Simulates correlated multinomial
responses by utilizing threshold\napproaches under a marginal model
specification.","Imports":"evd, stats","License":"GPL-
3","NeedsCompilation":"no","Package":"SimCorMultRes","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"multgee(>= 1.2)","Title":"Simulates Correlated
Multinomial Responses","Version":"1.4.0"},"SimDesign":{"Author":"Phil Chalmers
[aut, cre]","Depends":"R (>= 3.0.2)","Description":"Provides tools to help safely
and efficiently organize Monte Carlo simulations in R.\nThe package controls the
structure and back-end of Monte Carlo simulations\nby utilizing a general generate-
analyse-summarise strategy. The functions provided control\ncommon simulation
issues such as re-simulating non-convergent results, support parallel\nback-end and
MPI distributed computations, save and restore temporary files,\naggregate results
across independent nodes, and provide native support for
debugging.","Imports":"foreach, methods, parallel, plyr, stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SimDesign","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr, dplyr, ggplot2, doMPI","Title":"Structure for
Organizing Monte Carlo Simulation Designs","Version":"0.8"},"SimHaz":
{"Author":"Danyi Xiong, Teeranan Pokaprakarn, Hiroto Udagawa, Nusrat
Rabbee","Depends":"R (>= 3.1.1)","Description":"Generate power for the Cox
proportional hazards model by simulating survival events data with time dependent
exposure status for subjects. A dichotomous exposure variable is considered with a
single transition from unexposed to exposed status during the subject's time on
study.","Imports":"survival","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SimHaz","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Simulated Survival and Hazard Analysis for Time-
Dependent\nExposure","URL":"http:\/\/www.stat.berkeley.edu\/~rabbee\/research_webpa
ge.htm","Version":"0.1"},"SimInf":{"Author":"Stefan Widgren (National Veterinary
Institute, Sweden),\nPavol Bauer (Uppsala University, Sweden),\nStefan Engblom
(Uppsala University, Sweden)","Depends":"R(>= 3.0.2),
methods","Description":"Livestock movements are important for the spread of
many\ninfectious diseases between herds. The package provides an\nefficient and
flexible framework for stochastic disease spread\nmodelling that integrates within-
herd disease dynamics as\ncontinuous-time Markov chains and livestock movements
between\nherds as scheduled events. The core simulation solver is\nimplemented in C
and uses 'OpenMP' (if available) to divide work\nover multiple processors. The
package contains template models and\ncan be extended with user defined
models.","Imports":"graphics, Matrix","License":"GPL-
3","NeedsCompilation":"yes","Package":"SimInf","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"A Framework for Stochastic Disease Spread
Simulations","URL":"https:\/\/github.com\/stewid\/SimInf","Version":"1.0.0"},"SimRA
D":{"Author":"Olivier Lepais [aut, cre],\nJason Weir [aut]","Depends":"Biostrings,
ShortRead, zlibbioc","Description":"Provides a number of functions to simulate
restriction enzyme digestion, library construction and fragments size selection to
predict the number of loci expected from most of the Restriction site Associated
DNA (RAD) and Genotyping By Sequencing (GBS) approaches. SimRAD estimates the
number of loci expected from a particular genome depending on the protocol type and
parameters allowing to assess feasibility, multiplexing capacity and the amount of
sequencing required.","Imports":"stats, graphics","License":"GPL-
2","NeedsCompilation":"no","Package":"SimRAD","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"seqinr","Title":"Simulations to Predict the Number of
RAD and GBS Loci","Version":"0.96"},"SimReg":{"Author":"Daniel Greene","Depends":"R
(>= 3.0.0)","Description":"Functions for performing Bayesian `similarity
regression',\nspecialised for modelling the association between a HPO-encoded
phenotype\nand binary genotype. A `no association' model is compared with one in
which\nthe log odds of having a rare genotype is linked to the semantic
similarity\nbetween patient phenotype and a latent characteristic phenotype. The
method\nestimates the probability of an association together with an HPO-coded
phenotype\ncharacteristic of the disease.","Imports":"Rcpp (>= 0.11.1),
ontologyIndex, ontologySimilarity,\nontologyPlot, plotrix","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"SimReg","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Sugg
ests":"knitr","Title":"Similarity Regression Functions","Version":"1.4"},"SimSeq":
{"Author":"Samuel Benidt","Depends":"R (>= 2.10.0)","Description":"RNA sequencing
analysis methods are often derived by relying on hypothetical parametric models for
read counts that are not likely to be precisely satisfied in practice. Methods are
often tested by analyzing data that have been simulated according to the assumed
model. This testing strategy can result in an overly optimistic view of the
performance of an RNA-seq analysis method. We develop a data-based simulation
algorithm for RNA-seq data. The vector of read counts simulated for a given
experimental unit has a joint distribution that closely matches the distribution of
a source RNA-seq dataset provided by the user. Users control the proportion of
genes simulated to be differentially expressed (DE) and can provide a vector of
weights to control the distribution of effect sizes. The algorithm requires a
matrix of RNA-seq read counts with large sample sizes in at least two treatment
groups. Many datasets are available that fit this
standard.","Imports":"fdrtool","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SimSeq","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Nonparametric Simulation of RNA-Seq
Data","Version":"1.4.0"},"SimilarityMeasures":{"Author":"Kevin
Toohey","Description":"Functions to run and assist four\ndifferent similarity
measures. The similarity\nmeasures included are: longest common\nsubsequence
(LCSS), Frechet distance, edit distance\nand dynamic time warping (DTW). Each of
these\nsimilarity measures can be calculated from two\nn-dimensional trajectories,
both in matrix form.","License":"GPL-
3","NeedsCompilation":"no","Package":"SimilarityMeasures","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Trajectory Similarity
Measures","Version":"1.4"},"Simile":{"Author":"Simulistics
Ltd","Depends":"tcltk","Description":"Allows a Simile model saved as a compiled
binary to be\nloaded, parameterized, executed and interrogated. This version
works\nwith Simile v5.97
on.","License":"Unlimited","NeedsCompilation":"no","Package":"Simile","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Title":"Interact with Simile
Models","Version":"1.3.3"},"SimpleTable":{"Author":"Kevin M. Quinn
<kevin_quinn@harvard.edu>,","Depends":"R (>= 2.5.1), hdrcde, locfit, MCMCpack,
tcltk","Description":"SimpleTable provides a series of methods to conduct\nBayesian
inference and sensitivity analysis for causal effects\nfrom 2 x 2 and 2 x 2 x K
tables when unmeasured confounding is\npresent or suspected.","License":"GPL-
2","NeedsCompilation":"no","Package":"SimpleTable","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Bayesian Inference and Sensitivity Analysis for Causal
Effects\nfrom 2 x 2 and 2 x 2 x K Tables in the Presence of
Unmeasured\nConfounding","Version":"0.1-2"},"SimplicialCubature":{"Author":"John P.
Nolan, with parts based on code by Alan Genz","Depends":"R (>=
3.0)","Description":"Provides methods to integrate functions over m-dimensional
simplices\nin n-dimensional Euclidean space. There are exact methods for
polynomials and\nadaptive methods for integrating an arbitrary function. Dirichlet
probabilities\nare calculated in certain cases.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SimplicialCubature","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Title":"Integration of Functions Over
Simplices","Version":"1.1"},"Simpsons":{"Author":"Rogier Kievit & Sacha
Epskamp","Depends":"R (>= 2.14.0), mclust","Description":"This package detects
instances of Simpson's Paradox in\ndatasets. It examines subpopulations in the
data, either\nuser-defined or by means of cluster analysis, to test whether
a\nregression at the level of the group is in the opposite\ndirection at the level
of subpopulations.","License":"GPL-
2","NeedsCompilation":"no","Package":"Simpsons","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Detecting Simpson's
Paradox","Version":"0.1.0"},"SimuChemPC":{"Author":"Mohsen
Ahmadi","Depends":"stats, graphics, grDevices, utils, rcdk, R (>=
2.13)","Description":"This package provides simulation process of 4 selection
methods in predicting potent compounds","License":"GPL-
3","NeedsCompilation":"no","Package":"SimuChemPC","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Simulation process of 4 selection methods in predicting
chemical\npotent compounds","Version":"1.3"},"SimultAnR":{"Author":"Amaya Zarraga,
Beatriz Goitisolo","Description":"This package performs classical correspondence
analysis (CA) and\nsimultaneous analysis (SA). Simultaneous analysis is a
factorial\nmethodology developed for the joint treatment of a set of
several\ncontingency tables. In SA tables having the same rows, are
concatenated\nrow-wise.\nIn this version of the package a multiple option have been
included for\nthe simultaneous analysis\nof tables having the same columns,
concatenated column-wise.\nThis way, a MSA allows to perform the analysis of an
indicator matrix\nwhere the rows represent individuals.\nIn this package, functions
for computation, summaries\nand graphical visualization in two dimensions are
provided, including\noptions to display partial and supplementary
points.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SimultAnR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Correspondence and Simultaneous
Analysis","Version":"1.1"},"SixSigma":{"Author":"Emilio L. Cano, Javier M.
Moguerza, Mariano Prieto and AndrÃ©s Redchuk","Depends":"R (>=
2.14.0)","Description":"Functions and utilities to perform\nStatistical Analyses in
the Six Sigma way.\nThrough the DMAIC cycle (Define, Measure, Analyze, Improve,
Control),\nyou can manage several Quality Management studies:\nGage R&R, Capability
Analysis, Control Charts, Loss Function Analysis,\netc. Data frames used in the
books \"Six Sigma with R\" (Springer, 2012)\nand \"Quality Control with R\"
(Springer, 2015)\nare also included in the package.","Imports":"grDevices, stats,
graphics, qcc, lattice, ggplot2, reshape2,\nnortest, e1071, scales, testthat,
2)","NeedsCompilation":"no","Package":"SixSigma","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Six Sigma Tools for Quality Control and
Improvement","URL":"http:\/\/www.sixsigmawithr.com","Version":"0.9-
3"},"SkewHyperbolic":{"Author":"David Scott <d.scott@auckland.ac.nz>, Fiona
Grimson","Depends":"R (>= 2.3.0), DistributionUtils, GeneralizedHyperbolic,
RUnit","Description":"Functions are provided for the density
function,\ndistribution function, quantiles and random number generation\nfor the
skew hyperbolic t-distribution. There are also\nfunctions that fit the distribution
to data. There are\nfunctions for the mean, variance, skewness, kurtosis and
mode\nof a given distribution and to calculate moments of any order\nabout any
centre. To assess goodness of fit, there are\nfunctions to generate a Q-Q plot, a
P-P plot and a tail plot.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SkewHyperbolic","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"The Skew Hyperbolic Student t-
Distribution","Version":"0.3-2"},"Skillings.Mack":{"Author":"Patchanok
Srisuradetchai","Depends":"R (>= 3.1.1)","Description":"A generalization of the
statistic used in Friedman's ANOVA method and in Durbin's rank test. This
nonparametric statistical test is useful for the data obtained from block designs
with missing observations occurring randomly. A resulting p-value is based on the
chi-squared distribution and Monte Carlo method.","Imports":"MASS, stats,
matrixcalc","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Skillings.Mack","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"The Skillings-Mack Test Statistic for Block
Designs with Missing\nObservations","Version":"1.10"},"Sky":{"Author":"Benedicte
Bachelot","Depends":"R (>= 2.10),EBImage","Description":"Provides an alternative to
manually process hemispherical pictures. The algorithm processes each picture one
by one to determine the proportion of sky pixel. The algorithm uses the Ridler and
Calvard method (Ridler and Calvard 1978).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Sky","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Canopy Openness Analyzer Package","Version":"1.0"},"Sleuth2":
{"Author":"Original by F.L. Ramsey and D.W. Schafer,\nmodifications by Daniel W.
Schafer, Jeannie Sifneos and Berwin\nA. Turlach, vignettes contributed by Nicholas
Horton, Kate Aloisio\nand Ruobing Zhang","Depends":"R (>=
3.1.0)","Description":"Data sets from Ramsey, F.L. and Schafer, D.W.
(2002), \"The\nStatistical Sleuth: A Course in Methods of Data Analysis
(2nd\ned)\", Duxbury.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Sleuth2","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"lattice, knitr, MASS, agricolae, car, gmodels, leaps,
mosaic","Title":"Data Sets from Ramsey and Schafer's \"Statistical Sleuth
(2nd\nEd)\"","URL":"http:\/\/r-forge.r-
project.org\/projects\/sleuth2\/","Version":"2.0-3"},"Sleuth3":{"Author":"Original
by F.L. Ramsey and D.W. Schafer,\nmodifications by Daniel W. Schafer, Jeannie
Sifneos and Berwin\nA. Turlach, vignettes contributed by Nicholas Horton, Linda
Loi,\nKate Aloisio and Ruobing Zhang","Depends":"R (>= 3.1.0)","Description":"Data
sets from Ramsey, F.L. and Schafer, D.W. (2013), \"The\nStatistical Sleuth: A
Course in Methods of Data Analysis (3rd\ned)\", Cengage Learning.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"Sleuth3","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"CCA, Hmisc, MASS,agricolae, car, gmodels, knitr,
lattice,\nleaps, mosaic, multcomp","Title":"Data Sets from Ramsey and
Schafer's \"Statistical Sleuth (3rd\nEd)\"","URL":"http:\/\/r-forge.r-
project.org\/projects\/sleuth2\/","Version":"1.0-1"},"SmarterPoland":
{"Author":"Przemyslaw
Biecek (Foundation SmarterPoland.pl)","Depends":"R (>= 3.0), ggplot2, httr,
htmltools","Description":"Tools for accessing and processing datasets prepared by
the Foundation SmarterPoland.pl. Among all: access to API of Google Maps, Central
Statistical Office of Poland, MojePanstwo, Eurostat, WHO and other
sources.","Imports":"jsonlite, rjson","License":"GPL-
3","NeedsCompilation":"no","Package":"SmarterPoland","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Tools for Accessing Various Datasets Developed by
the Foundation\nSmarterPoland.pl","Version":"1.7"},"SmithWilsonYieldCurve":
{"Author":"Phil Joubert","Description":"Constructs a yield curve by the Smith-
Wilson method from a\ntable of LIBOR and SWAP rates","License":"GPL-
3","NeedsCompilation":"no","Package":"SmithWilsonYieldCurve","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Smith-Wilson Yield
Curve Construction","Version":"1.0.1"},"SmoothHazard":{"Author":"Celia Touraine,
Pierre Joly, Thomas A. Gerds","Depends":"R (>= 1.9.1)","Description":"SmoothHazard
is a package for fitting illness-death (and survival)\nmodel with possibly
interval-censored data for transition toward transient\nstate. Left-truncated and
right-censored data are also allowed.\nProportional intensities regression models
allow for covariates on each of\nthe 3 transitions. We use either a parametric
approach with Weibull\nbaseline intensities or a semi-parametric approach with M-
splines\napproximation of baseline intensities in order to obtain smooth
estimates.\nEstimation of parameters is conducted by likelihood maximization in
the\nparametric approach or penalized likelihood maximization in the\nsemi-
parametric approach.","Imports":"lava, mvtnorm, prodlim","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"SmoothHazard","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Fitting illness-death model for interval-censored
data","Version":"1.2.3"},"SnowballC":{"Author":"Milan Bouchet-Valat [aut,
cre]","Description":"An R interface to the C libstemmer library that
implements\nPorter's word stemming algorithm for collapsing words to a common\nroot
to aid comparison of vocabulary. Currently supported languages are\nDanish, Dutch,
English, Finnish, French, German, Hungarian, Italian,\nNorwegian, Portuguese,
Romanian, Russian, Spanish, Swedish\nand Turkish.","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"yes","Package":"SnowballC","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Snowball stemmers based on the C libstemmer UTF-8
library","URL":"https:\/\/r-forge.r-project.org\/projects\/r-
temis\/","Version":"0.5.1"},"SoDA":{"Author":"John M Chambers","Depends":"R(>=
2.5),methods,graphics","Description":"Functions, examples and other software
related to the book\n\"Software for Data Analysis: Programming with R\".
See\npackage?SoDA for an overview.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"SoDA","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Functions and Examples for \"Software for Data
Analysis\"","Version":"1.0-6"},"SocialMediaLab":{"Author":"Timothy Graham & Robert
Ackland, with contribution from Chung-hong Chan","Description":"A suite of tools
for collecting and constructing networks from\nsocial media data. Provides easy-to-
use functions for collecting data across\npopular platforms (Instagram, Facebook,
Twitter, and YouTube) and generating\ndifferent types of networks for
analysis.","Imports":"\ntm,stringr,twitteR,RCurl,bitops,rjson,plyr,igraph,Rfacebook
,Hmisc,data.table,httpuv,instaR,methods,httr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SocialMediaLab","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"magrittr","Title":"Tools for Collecting Social
Media Data and Generating Networks\nfor
Analysis","Version":"0.22.0"},"SocialMediaMineR":{"Author":"Marco T.
Bastos","Description":"Social media search and analytic tool that takes one or
multiple URL(s) and returns the information about the popularity and reach of the
URL(s) on social media. The function get_socialmedia() retrieves the number of
shares, likes, pins, and hits on Facebook (www.facebook.com), Pinterest
(www.pinterest.com), StumbleUpon (www.stumbleupon.com), LinkedIn
(www.linkedin.com), and Reddit (www.reddit.com). The package also includes
dedicated functions for each social network platform and a function to resolve
shortened URLs.","Imports":"RCurl, jsonlite, httr, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SocialMediaMineR","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"A Social Media Search and Analytic
Tool","Version":"0.3"},"SocialNetworks":{"Author":"Glenna Nightingale, Peter
Nightingale","Description":"Generates social networks using either of
two\napproaches: using either pairwise distances or territorial area
intersections.","Imports":"Rcpp (>=
0.11.0)","License":"GPL","NeedsCompilation":"yes","Package":"SocialNetworks","Repos
itory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Generates social networks
based on distance","Version":"1.1"},"SocialPosition":{"Author":"Julie Falcon
(University of Lausanne)","Description":"Provides to sociologists (and related
scientists) a toolbox to facilitate the construction of social position indicators
from survey data. Social position indicators refer to what is commonly known as
social class and social status. There exists in the sociological literature many
theoretical conceptualisation and empirical operationalization of social class and
social status. This first version of the package offers tools to construct the
International Socio-Economic Index of Occupational Status (ISEI) and the Oesch
social class schema. It also provides tools to convert several occupational
classifications (PCS82, PCS03, and ISCO08) into a common one (ISCO88) to facilitate
data harmonisation work, and tools to collapse (i.e. group) modalities of social
position indicators.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"SocialPosition","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Social Position Indicators Construction
Toolbox","Version":"1.0.1"},"Sofi":{"Author":"Jose D. Loera","Depends":"R (>=
3.1.0), shiny","Description":"Este paquete tiene la finalidad de ayudar a aprender
de una forma interactiva, teniendo ejemplos y la posibilidad de resolver nuevos al
mismo tiempo. Apuntes de clase interactivos.","Imports":"sampling,
foreign","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Sofi","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"ggplot2, VGAM, shinyjs, ggExtra, grid,
gridExtra","Title":"Interfaz interactiva con fines
didacticos","URL":"http:\/\/www.sofi.uno\/","Version":"0.16.4.8"},"SoftClustering":
{"Author":"G. Peters (Ed.)","Depends":"R (>= 3.0.2)","Description":"It contains
soft clustering algorithms, in particular approaches derived from rough set theory:
Lingras & West original rough k-means, Peters' refined rough k-means, and PI rough
k-means. It also contains classic k-means and a corresponding illustrative
demo.","License":"GPL-
2","NeedsCompilation":"no","Package":"SoftClustering","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Soft Clustering
Algorithms","Version":"1.1502"},"SoilR":{"Author":"Carlos A. Sierra <csierra@bgc-
jena.mpg.de>, Markus Mueller\n<mamueller@bgc-
jena.mpg.de>","Depends":"deSolve,methods,parallel,RUnit","Description":"This
package contains functions for modeling Soil Organic\nMatter decomposition in
terrestrial ecosystems.","License":"GPL-
3","NeedsCompilation":"no","Package":"SoilR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"FME,lattice,MASS","Title":"Models of Soil Organic Matter
Decomposition","Version":"1.1-23"},"SortableHTMLTables":{"Author":"John Myles
White","Depends":"testthat, brew","Description":"SortableHTMLTables writes a data
frame to an HTML file\nthat contains a sortable table. The sorting is done using
the\njQuery plugin Tablesorter. The appearance is controlled through\na CSS file
and several
GIF's.","License":"MIT","NeedsCompilation":"no","Package":"SortableHTMLTables","Rep
ository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Turns a data frame into an
HTML file containing a sortable\ntable","Version":"0.1-3"},"SoundexBR":
{"Author":"Daniel Marcelino","Depends":"R (>=
3.0),stats,utils,graphics,grDevices","Description":"The SoundexBR package provides
an algorithm for decoding names\ninto phonetic codes, as pronounced in Portuguese.
The goal is for\nhomophones to be encoded to the same representation so that they
can be\nmatched despite minor differences in spelling. The algorithm mainly
encodes\nconsonants; a vowel will not be encoded unless it is the first letter.
The\nsoundex code resultant consists of a four digits long string composed by\none
letter followed by three numerical digits: the letter is the first\nletter of the
name, and the digits encode the remaining
consonants.","Enhances":"RecordLinkage","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"SoundexBR","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"SciencesPo, stringr","Title":"Phonetic-Coding for
Portuguese","Version":"1.2"},"SoyNAM":{"Author":"Alencar Xavier, William Beavis,
James Specht, Brian Diers, Reka Howard, William Muir, Katy Rainey.","Depends":"R
(>= 3.0.2)","Description":"Genomic and multi-environmental soybean data. Soybean
Nested Association Mapping (SoyNAM) project dataset funded by the United Soybean
Board (USB), pre-formatted for general analysis and genome-wide association
analysis using the NAM package.","Imports":"NAM, lme4, reshape2","License":"GPL-
3","NeedsCompilation":"yes","Package":"SoyNAM","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Soybean Nested Association Mapping
Dataset","Version":"1.2"},"SpaDES":{"Author":"Alex M Chubaty [aut, cre],\nEliot J B
McIntire [aut],\nYong Luo [ctb],\nSteve Cumming [ctb],\nHer Majesty the Queen in
Right of Canada, as represented by the\nMinister of Natural Resources Canada
[cph]","Depends":"R (>= 3.2.2)","Description":"Easily implement a variety of
simulation models, with a focus on\nspatially explicit agent based models. These
include raster-based,\nevent-based, and agent-based models. The core simulation
components are\nbuilt upon a discrete event simulation framework that
facilitates\nmodularity, and easily enables the user to include additional
functionality\nby running user-built simulation modules. Included are numerous
tools to\nvisualize raster and other maps. The suggested package `fastshp` can
be\ninstalled with ìnstall.packages(\"fastshp\",
repos=\"http:\/\/rforge.net\",\ntype=\"source\")`.","Imports":"archivist (>= 2.0),
CircStats, data.table, DiagrammeR (>=\n0.8.2), digest, dplyr, ff, ffbase,
fpCompare, ggplot2,\ngraphics, grid, gridBase, httr, igraph, lazyeval, lubridate
(>=\n1.3.3), methods, R.utils, RandomFields, raster, secr, sp,\nstringi,
stringr","License":"GPL-
3","NeedsCompilation":"no","Package":"SpaDES","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"covr, fastshp, knitr, Matrix, png, RColorBrewer,
rgdal,\nrmarkdown, testthat, tkrplot","Title":"Develop and Run Spatially Explicit
Discrete Event
Simulation\nModels","URL":"https:\/\/github.com\/PredictiveEcology\/SpaDES","Versio
n":"1.1.1"},"SparseFactorAnalysis":{"Author":"Marc Ratkovic, In Song Kim, John
Londregan, and Yuki Shiraito","Depends":"directlabels, proto,
ggplot2","Description":"Multidimensional scaling provides a means of uncovering a
latent structure underlying observed data, while estimating the number of latent
dimensions. This package presents a means for scaling binary and count data, for
example the votes and word counts for legislators. Future work will include an EM
implementation and extend this work to ordinal and continuous
data.","Imports":"Rcpp (>= 0.11.4), MASS, VGAM, truncnorm","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"SparseFactorAnalysis","Repository":"http:\/
\/cran.csiro.au\/src\/contrib","Title":"Scaling Count and Binary Data with Sparse
Factor Analysis","Version":"1.0"},"SparseGrid":{"Author":"Jelmer
Ypma","Description":"SparseGrid is a package to create sparse grids for numerical
integration, based on code from www.sparse-
grids.de","License":"GPL","NeedsCompilation":"no","Package":"SparseGrid","Repositor
y":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"testthat, statmod,
mvtnorm","Title":"Sparse grid integration in R","Version":"0.8.2"},"SparseLearner":
{"Author":"Pi Guo, Yuantao Hao","Depends":"R (>= 3.0.2),
glmnet","Description":"Coefficient estimation and model prediction based on the
LASSO sparse\nlearning algorithm and its improved versions such as Bolasso,
bootstrap ranking\nLASSO, two-stage hybrid LASSO and others. These LASSO estimation
procedures are\napplied in the fields of variable selection, graphical modeling and
ensemble\nlearning. The bagging LASSO model uses a Monte Carlo cross-entropy
algorithm to\ndetermine the best base-level models and improve predictive
performance.","Imports":"SIS, mlbench, RankAggreg, SiZer, lqa,
qgraph","License":"GPL-
2","NeedsCompilation":"no","Package":"SparseLearner","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Sparse Learning Algorithms Using a LASSO-Type
Penalty for\nCoefficient Estimation and Model
Prediction","URL":"https:\/\/www.researchgate.net\/profile\/Pi_Guo3","Version":"1.0
-2"},"SparseM":{"Author":"Roger Koenker <rkoenker@uiuc.edu> and Pin Ng
<Pin.Ng@NAU.EDU>","Depends":"R (>= 2.15), methods","Description":"Some basic linear
algebra functionality for sparse matrices is\nprovided: including Cholesky
decomposition and backsolving as well as\nstandard R subsetting and Kronecker
products.","Imports":"graphics, stats, utils","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"SparseM","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Sparse Linear
Algebra","URL":"http:\/\/www.econ.uiuc.edu\/~roger\/research\/sparse\/sparse.html",
"Version":"1.7"},"SparseTSCGM":{"Author":"Fentaw Abegaz and Ernst
Wit","Depends":"R(>= 3.1.2)","Description":"Computes sparse vector autoregressive
coefficients and precision\nmatrices for time series chain graphical
models.","Imports":"glasso, longitudinal, flare, MASS, mvtnorm, network,
abind,\nstats","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"SparseTSCGM","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Sparse Time Series Chain Graphical
Models","Version":"2.2"},"SpatPCA":{"Author":"Wen-Ting Wang and Hsin-Cheng
Huang","Description":"Provide regularized principal component analysis
incorporating smoothness, sparseness and orthogonality of eigenfunctions by using
the alternating direction method of multipliers algorithm. The method can be
applied to either regularly or irregularly spaced data.","Imports":"Rcpp,
RcppParallel (>= 0.11.2)","License":"GPL-
2","NeedsCompilation":"yes","Package":"SpatPCA","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Regularized Principal Component Analysis for Spatial
Data","Version":"1.1.1.0"},"SpatialEpi":{"Author":"Cici Chen [ctb],\nAlbert Y. Kim
[aut, cre],\nMichelle Ross [ctb],\nJon Wakefield [aut]","Depends":"R (>= 3.0.2),
sp","Description":"\nMethods and data for cluster detection and disease
mapping.","Imports":"Rcpp, MASS, maptools, spdep, methods, grDevices,
graphics,\nstats","License":"GPL-
2","NeedsCompilation":"yes","Package":"SpatialEpi","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Methods and Data for Spatial
Epidemiology","Version":"1.2.2"},"SpatialExtremes":{"Author":"Mathieu Ribatet [aut,
cre],\nRichard Singleton [ctb],\nR Core team [ctb]","Depends":"R (>=
1.8.0)","Description":"Tools for the statistical modelling of spatial extremes
using max-stable processes, copula or Bayesian hierarchical
models.","Imports":"maps, fields","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"SpatialExtremes","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Modelling Spatial
Extremes","URL":"http:\/\/spatialextremes.r-forge.r-project.org\/","Version":"2.0-
2"},"SpatialNP":{"Author":"Seija Sirkia, Jari Miettinen, Klaus Nordhausen, Hannu
Oja, Sara Taskinen","Depends":"R (>= 2.4.0)","Description":"This package contains
test and estimates of location,\ntests of independence, tests of sphericity and
several\nestimates of shape all based on spatial signs, symmetrized\nsigns, ranks
and signed ranks.","License":"GPL-
2","NeedsCompilation":"yes","Package":"SpatialNP","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"ICSNP, MNM","Title":"Multivariate nonparametric
methods based on spatial signs and\nranks","Version":"1.1-1"},"SpatialPack":
{"Author":"Felipe Osorio <felipe.osorios@usm.cl> and Ronny
Vallejos\n<ronny.vallejos@usm.cl>, with contributions of Francisco Cuevas\nand
Diego Mancilla.","Description":"This package provides tools to assess the
association between two spatial processes.\nCurrently, three methodologies are
implemented: An adapted t-test to perform hypothesis\ntesting about the
independence between the processes, a suitable nonparametric
correlation\ncoefficient, and the codispersion coefficient. SpatialPack gives
methods to complement\nmethodologies that are available in geoR for one spatial
process.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"SpatialPack","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"geoR","Title":"Package for analysis of spatial
data","URL":"http:\/\/spatialpack.mat.utfsm.cl","Version":"0.2-
3"},"SpatialPosition":{"Author":"TimothÃ©e Giraud [cre, aut],\nHadrien Commenges
[aut],\nJoÃ«l Boulier [ctb]","Depends":"R (>= 3.0.0),
raster","Description":"Computes spatial position models: Stewart potentials,
Reilly\ncatchment areas, Huff catchment areas.","Imports":"sp, grDevices, graphics,
3","NeedsCompilation":"no","Package":"SpatialPosition","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"rgeos, cartography, knitr,
rmarkdown","Title":"Spatial Position Models","URL":"https:\/\/github.com\/Groupe-
ElementR\/SpatialPosition","Version":"1.1"},"SpatialTools":{"Author":"Joshua French
<joshua.french@ucdenver.edu>","Depends":"R (>= 3.0.2)","Description":"Tools for
spatial data analysis. Emphasis on kriging. Provides functions for prediction and
simulation. Intended to be relatively straightforward, fast, and
flexible.","Imports":"spBayes (>= 0.3.0), Rcpp","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"SpatialTools","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Tools for Spatial Data
Analysis","Version":"1.0.2"},"SpatialVx":{"Author":"Eric Gilleland
<EricG@ucar.edu>","Depends":"R (>= 2.10.0), spatstat (>= 1.37-0), fields (>=
6.8),\nsmoothie, smatr, turboEM","Description":"Spatial forecast verification arose
from verifying high-resolution forecasts, where coarser-resolution models generally
are favored even when a human forecaster finds the higher-resolution model to be
considerably better. Most newly proposed methods, which largely come from image
analysis, computer vision, and similar, are available, with more on the
way.","Imports":"distillery, maps, boot, CircStats, fastcluster,
waveslim","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SpatialVx","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"shapes","Title":"Spatial Forecast
Verification","URL":"http:\/\/www.ral.ucar.edu\/projects\/icp\/SpatialVx","Version"
:"0.4"},"SpatioTemporal":{"Author":"Johan Lindstrom, Adam Szpiro, Paul D. Sampson,
Silas Bergen, Assaf P.\nOron","Depends":"R (>= 2.12.0),
Matrix","Description":"Utilities that estimate, predict and cross-validate
the\nspatio-temporal model developed for MESA
Air.","Imports":"MASS","License":"GPL-
2","NeedsCompilation":"yes","Package":"SpatioTemporal","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests
":"maps, plotrix, fields","Title":"Spatio-Temporal Model
Estimation","Version":"1.1.7"},"SpecHelpers":{"Author":"Bryan A. Hanson DePauw
University, Greencastle Indiana USA","Depends":"R (>= 3.0)","Description":"Utility
functions for spectroscopy. 1. Functions to simulate\nspectra for use in teaching
or testing. 2. Functions to process files created by\n'LoggerPro' and
'SpectraSuite' software.","Imports":"gsubfn, utils, stats, graphics,
splancs","License":"GPL-
3","NeedsCompilation":"no","Package":"SpecHelpers","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Spectroscopy Related
Utilities","URL":"https:\/\/github.com\/bryanhanson\/SpecHelpers","Version":"0.2.2"
},"SpeciesMix":{"Author":"Piers K Dunstan, Scott D Foster and Ross
Darnell","Depends":"R(>= 2.15.0),MASS,stats,numDeriv","Description":"Mixtures using
BFGS and analytical derivatives","License":"GPL-
2","NeedsCompilation":"yes","Package":"SpeciesMix","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Fit Mixtures of Archetype
species","Version":"0.3.1"},"SpecsVerification":{"Author":"Stefan Siegert [aut,
cre]","Description":"A collection of new forecast verification routines for the
SPECS FP7 project. The emphasis is on comparative verification of ensemble
forecasts.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"SpecsVerification","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Title":"Forecast Verification Routines for the SPECS
FP7 Project","Version":"0.4-1"},"SpherWave":{"Author":"Hee-Seok Oh
<heeseok.oh@gmail.com>, Donghoh Kim\n<donghoh.kim@gmail.com>","Depends":"R (>=
2.15.1), fields (>= 6.7.6)","Description":"This package carries out spherical
wavelet transform\ndeveloped by Li (1999) and Oh (1999), and implements
wavelet\nthresholding approaches proposed by Oh and Li (2004).","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"SpherWave","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Spherical Wavelets and SW-based Spatially Adaptive
Methods","URL":"http:\/\/stat.snu.ac.kr\/heeseok\/SpherWave.html","Version":"1.2.2"
},"SphericalCubature":{"Author":"John P. Nolan, American University","Depends":"R
(>= 2.1.15), cubature","Description":"This package defines several methods to
integrate\nfunctions over the unit sphere and ball in n-dimensional\nEuclidean
space. Routines for converting to\/from multivariate\npolar\/spherical coordinates
are also provided.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SphericalCubature","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Numerical integration over spheres and balls in
n-dimensions;\nmultivariate polar coordinates","Version":"1.0.1"},"SphericalK":
{"Author":"Scott Robeson, Ao Li, Chunfeng Huang","Description":"Spherical K-
function for point-pattern analysis on the sphere.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SphericalK","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Spherical K-
Function","Version":"1.2"},"SportsAnalytics":{"Author":"Manuel J. A. Eugster
<manuel.eugster@stat.uni-muenchen.de>","Depends":"R (>= 2.10), methods,
stats","Description":"The aim of this package is to provide infrastructure
for\nsports analysis. Anyway, currently it is a selection of data\nsets, functions
to fetch sports data, examples, and demos --\nwith the ambition to develop bit by
bit a set of classes to\nrepresent general concepts of sports
2)","NeedsCompilation":"no","Package":"SportsAnalytics","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"archetypes","Title":"Infrastructure for Sports
Analytics","URL":"http:\/\/soccer.r-forge.r-
project.org\/","Version":"0.2"},"StAMPP":{"Author":"LW Pembleton","Depends":"R (>=
2.14.0), pegas","Description":"Allows users to calculate pairwise Nei's Genetic
Distances (Nei 1972), pairwise Fixation\nIndexes (Fst) (Weir & Cockerham 1984) and
also Genomic Relationship matrixes following Yang et al. (2010) in mixed and
single\nploidy populations. Bootstrapping across loci is implemented during Fst
calculation to generate confidence intervals and p-values\naround pairwise Fst
values. StAMPP utilises SNP genotype data of any ploidy level (with the ability to
handle missing data) and is coded to\nutilise multithreading where available to
allow efficient analysis of large datasets. StAMPP is able to handle genotype data
from genlight objects\nallowing integration with other packages such
adegenet.\nPlease refer to LW Pembleton, NOI Cogan & JW Forster, 2013, Molecular
Ecology Resources, 13(5), 946-952. doi:10.1111\/1755-0998.12129 for the appropriate
citation and user manual. Thank you in advance.","Imports":"parallel, doParallel,
foreach, adegenet, methods, utils","License":"GPL-
3","NeedsCompilation":"no","Package":"StAMPP","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Statistical Analysis of Mixed Ploidy
Populations","Version":"1.4"},"StMoMo":{"Author":"Andres Villegas
<andresmauriciovillegas@gmail.com>,\nPietro Millossovich
<Pietro.Millossovich.1@city.ac.uk>,\nVladimir Kaishev
<Vladimir.Kaishev.1@city.ac.uk>","Depends":"R (>= 3.2.0), gnm (>= 1.0), forecast(>=
6.1)","Description":"Implementation of the family of generalised age-period-
cohort\nstochastic mortality models. This family of models encompasses many
models\nproposed in the actuarial and demographic literature including the Lee-
Carter\nmodel and the Cairns-Blake-Dowd model. It includes functions for
fitting\nmortality models, analysing their goodness-of-fit and performing
mortality\nprojections and simulations.","Imports":"MASS, rootSolve (>= 1.6.5.1),
fanplot (>= 3.4), reshape2 (>=\n1.4.1), fields (>= 8.2),
RColorBrewer","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"StMoMo","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr, xtable","Title":"Stochastic Mortality
Modelling","URL":"http:\/\/github.com\/amvillegas\/StMoMo","Version":"0.3.1"},"StMo
Sim":{"Author":"Matthias
Salvisberg","Depends":"methods,RcppParallel,Rcpp","Description":"Plots a QQ-Norm
Plot with several Gaussian simulations.","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"StMoSim","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Plots a QQ-Norm Plot with several Gaussian
simulations","Version":"3.0"},"StableEstim":{"Author":"Tarak Kharrat, Georgi N.
Boshnakov","Depends":"R(>=
2.10.0),methods,Matrix,stats,utils,stabledist,testthat","Description":"Compute the
maximum-likelihood(ML), generalised method of moment with finite and continuum
number of points, the iterative Koutrouvelis regression and the Kogon-McCulloch
methods to estimate the 4 parameters of stable law. The asymptotic properties of
the estimator (covariance matrix, confidence intervals) are also
provided.","Imports":"numDeriv,xtable,fBasics,MASS","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"StableEstim","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Estimate the 4 parameters of stable law using
different methods","Version":"2.0"},"Stack":{"Author":"Mike Malecki <Mike.Malecki
at yougov.com>","Description":"Stacks rectangular datasets on top of each other,
possibly\nperforming several type coercions along the way. For large
datasets,\ndepends on the ff package. Provides an aggressive version
of\nffbase::compact for data that may appear be real-typed but is in
fact\nint\/short\/byte. For many purposes plyr::rbind.fill may be more
appropriate,\nbut for some kinds of survey data, the rules here work
better.","Imports":"plyr, stringr, methods, ff, ffbase, bit","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"Stack","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Stylized concatenation of data.frames or
ffdfs","Version":"2.0-1"},"StanHeaders":{"Author":"Ben Goodrich [cre, aut],\nJoshua
Pritikin [ctb],\nAndrew Gelman [aut],\nBob Carpenter [aut],\nMatt Hoffman
[aut],\nDaniel Lee [aut],\nMichael Betancourt [aut],\nMarcus Brubaker
[aut],\nJiqiang Guo [aut],\nPeter Li [aut],\nAllen Riddell [aut],\nMarco Inacio
[aut],\nMitzi Morris [aut],\nJeffrey Arnold [aut],\nRob Goedman [aut],\nBrian Lau
[aut],\nRob Trangucci [aut],\nJonah Gabry [aut],\nAlp Kucukelbir [aut],\nRobert
Grant [aut],\nDustin Tran [aut],\nMichael Malecki [aut],\nYuanjun Gao
[aut]","Description":"The C++ header files of the Stan project are provided by this
package, but it contains no R code, shared objects, vignettes, or function
documentation. It is only useful for developers who want to utilize the LinkingTo
directive of their package's DESCRIPTION file to build on the Stan library without
incurring unnecessary dependencies. The Stan project develops a probabilistic
programming language that implements full Bayesian statistical inference via Markov
Chain Monte Carlo and (optionally penalized) maximum likelihood estimation via
optimization. The Stan library includes an advanced automatic differentiation
scheme, templated statistical and linear algebra functions that can handle the
automatically differentiable scalar types (and doubles, ints, etc.), and a parser
for the Stan language. The 'rstan' package provides user-facing R functions to
parse, compile, test, estimate, and analyze Stan models.","License":"BSD_3_clause +
file
LICENSE","NeedsCompilation":"no","Package":"StanHeaders","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"RcppEigen, BH","Title":"C++ Header Files for
Stan","URL":"http:\/\/mc-stan.org\/","Version":"2.9.0"},"StandardizeText":
{"Author":"David Nepomechie","Description":"Standardizes text according to a
template; particularly\nuseful for country names.","License":"GPL-
3","NeedsCompilation":"no","Package":"StandardizeText","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Standardize Text","Version":"1.0"},"Stat2Data":
{"Author":"Robin Lock","Depends":"R (>= 2.10)","Description":"Datasets for Stat2
textbook (by Cannon, et. al., published\nby
WH Freeman)","License":"GPL-
3","NeedsCompilation":"no","Package":"Stat2Data","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Datasets for Stat2","Version":"1.6"},"StatDA":
{"Author":"Peter Filzmoser","Depends":"R (>= 2.10), geoR, methods,
sgeostat","Description":"This package offers different possibilities to make
statistical analysis for Environmental Data.","Imports":"cluster, e1071, MASS, MBA,
mgcv, rgl, robustbase, xtable","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"StatDA","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"mclust","Title":"Statistical Analysis for Environmental
Data","URL":"http:\/\/www.statistik.tuwien.ac.at\/public\/filz\/","Version":"1.6.9"
},"StatDataML":{"Author":"David Meyer [aut, cre],\nTorsten Hothorn
[aut],\nFriedrich Leisch [aut]","Depends":"R (>= 2.0.0), XML,
utils","Description":"Support for reading and writing files in StatDataML---an XML-
based data exchange format.","License":"GPL-
2","NeedsCompilation":"no","Package":"StatDataML","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Read and Write StatDataML Files","Version":"1.0-
26"},"StatMatch":{"Author":"Marcello D'Orazio","Depends":"R (>= 2.7.0), proxy,
clue, survey, RANN, lpSolve","Description":"Integration of two data sources
referred to the same target population which share a number of common variables
(aka data fusion). Some functions can also be used to impute missing values in data
sets through hot deck imputation methods. Methods to perform statistical matching
when dealing with data from complex sample surveys are available
too.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"StatMatch","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"MASS, Hmisc","Title":"Statistical
Matching","Version":"1.2.4"},"StatMeasures":{"Author":"Akash Jain","Depends":"R (>=
3.1.3)","Description":"Offers useful functions to perform day-to-day data
manipulation\noperations, data quality checks and post modelling statistical
checks.\nOne can effortlessly change class of a number of variables to
factor,\nremove duplicate observations from the data, create deciles of
a\nvariable, perform data quality checks for continuous (integer or
numeric),\ncategorical (factor) and date variables, and compute goodness of
fit\nmeasures such as auc for statistical models. The functions are consistent\nfor
objects of class 'data.frame' and 'data.table', which is an enhanced\n'data.frame'
implemented in the package 'data.table'.","Imports":"data.table (>=
2","NeedsCompilation":"no","Package":"StatMeasures","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Easy Data Manipulation, Data Quality and Statistical
Checks","Version":"1.0"},"StatMethRank":{"Author":"Li
Qinglong","Description":"Functions and datasets to support Mayer Alvo and Philip
L.H. Yu (2014). \"Statistical Methods for Ranking Data\", Springer. In this
packages, smaller ranks stand for more preferred items.","Imports":"stats,
graphics, datasets, Rcpp (>= 0.11.5), MASS, utils,\nrjags, pmr","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"StatMethRank","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Statistical Methods for Ranking
Data","Version":"1.3"},"StatRank":{"Author":"Hossein Azari Soufiani, William
Chen","Description":"A set of methods to implement Generalized Method of Moments
and Maximal\nLikelihood methods for Random Utility Models. These methods are meant
to\nprovide inference on rank comparison data. These methods accept full,\npartial,
and pairwise rankings, and provides methods to break down full or\npartial rankings
into their pairwise components. Please see Generalized\nMethod-of-Moments for Rank
Aggregation from NIPS 2013 for a description of\nsome of our
methods.","Imports":"truncdist, plyr, ggplot2","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"StatRank","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"gridExtra, grid, testthat,
lattice","Title":"Statistical Rank Aggregation: Inference, Evaluation,
and\nVisualization","Version":"0.0.6"},"Statomica":{"Author":"Zahra Montazeri, Alaa
Ali, Kyle Leckett, Marta Padilla and David R. Bickel","Depends":"R (>= 2.14.0),
Biobase, multtest, distr, fBasics, methods","Description":"Statomica is a suite of
R functions that are needed for\ncertain packages such as LFDR.MLE, PsiHat,
HistogramLFDR, combine and LFDRenrich.","License":"CC BY-NC
4.0","NeedsCompilation":"no","Package":"Statomica","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Statomica utility package","URL":"http:\/\/www.cran.r-
project.org,
http:\/\/www.bioconductor.org,\nhttp:\/\/www.statomics.com","Version":"1.0"},"Stein
IV":{"Author":"Cedric E Ginestet <cedric.ginestet@kcl.ac.uk>","Depends":"R (>=
2.10.1)","Description":"Routines for computing different types of linear
estimators, based on instrumental variables (IVs), including the semi-parametric
Stein-like (SPS) estimator, originally introduced by Judge and Mittelhammer (2004)
<DOI:10.1198\/016214504000000430>.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SteinIV","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Semi-Parametric Stein-Like Estimator with Instrumental
Variables","URL":"https:\/\/cran.r-project.org\/package=SteinIV","Version":"0.1-
1"},"Stem":{"Author":"Michela Cameletti","Depends":"R (>= 2.7.0), mvtnorm,
MASS","Description":"Estimation of the parameters of a spatio-temporal model\nusing
the EM algorithm, estimation of the parameter standard\nerrors using a spatio-
temporal parametric bootstrap, spatial\nmapping.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Stem","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Spatio-temporal models in R","Version":"1.0"},"StereoMorph":
{"Author":"Aaron Olsen, Annat Haber","Depends":"R (>=
2.11.0)","Description":"Functions for the collection of 3D points and curves using
a stereo camera setup.","Imports":"grDevices, graphics, stats, utils, bezier (>=
1.1), grid,\nrjson, shiny (>= 0.13.0), Rcpp (>= 0.9.9), jpeg, tiff, png,\nsvgViewR
(>= 1.0.1)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"StereoMorph","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"rgl","Title":"Stereo Camera Calibration and
Reconstruction","URL":"http:\/\/home.uchicago.edu\/~aolsen\/software\/stereomorph.s
html","Version":"1.5"},"StockChina":{"Author":"Xiaodong Deng","Description":"With
this package, users can obtain the real-time price and volume information of stocks
in China market, as well as the information of the stock index. This package
adopted the API from Sina Finance
(http:\/\/finance.sina.com.cn\/).","License":"GPL-
2","NeedsCompilation":"no","Package":"StockChina","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Real-Time Stock Price & Volume in China
Market","URL":"https:\/\/github.com\/XD-
DENG\/StockChina","Version":"0.3.1"},"Storm":{"Author":"Allen Day","Depends":"R (>=
2.1.0), methods, permute, rjson","Description":"Storm is a distributed real-time
computation system. Similar to how\nHadoop provides a set of general primitives for
doing batch processing, Storm\nprovides a set of general primitives for doing real-
time computation.\n\nStorm includes a \"Multi-Language\" (or \"Multilang\")
Protocol to allow\nimplementation of Bolts and Spouts in languages other than Java.
This R\nextension provides implementations of utility functions to allow an
application\ndeveloper to focus on application-specific functionality rather than
Storm\/R\ncommunications plumbing.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Storm","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Write Storm Bolts in R using the Storm Multi-Language
Protocol","Version":"1.2"},"StrainRanking":{"Author":"Soubeyrand, S., Tollenaere,
C., Haon-Lasportes, E. and Laine, A.-L.","Depends":"R (>= 3.0.0),
methods","Description":"Regression-based ranking of pathogen strains with respect
to their contributions to natural epidemics, using demographic and genetic data
sampled in the curse of the epidemics","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"StrainRanking","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Ranking of pathogen
strains","Version":"1.1"},"StratSel":{"Author":"Lucas Leemann","Depends":"R (>=
3.0.0), MASS, memisc, Formula, mnormt","Description":"This package provides
functions to estimate a strategic selection estimator. A strategic selection
estimator is an agent error model in which the two random components are not
assumed to be orthogonal. In addition this package provides generic functions to
print and plot objects of the class \"StratSel\" as well as the necessary functions
to create tables for LaTeX. There is also a function to create dyadic data
2)","NeedsCompilation":"no","Package":"StratSel","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Strategic Selection
Estimator","Version":"1.1"},"StreamMetabolism":{"Author":"Stephen A Sefick
Jr.","Depends":"zoo, chron, maptools","Description":"I provide functions to
calculate Gross Primary Productivity, Net Ecocsystem Production, and Ecosystem
Respiration from single station diurnal Oxygen curves.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"StreamMetabolism","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Calculate Single Station Metabolism from Diurnal
Oxygen Curves","Version":"1.1.1"},"StressStrength":{"Author":"Alessandro Barbiero
<alessandro.barbiero@unimi.it>, Riccardo Inchingolo
<riccardo.arner@libero.it>","Description":"The package provide functions for
computing the reliability of stress-strength models and for building two-sided or
one-sided confidence intervals according to different approximate
procedures","License":"GPL","NeedsCompilation":"no","Package":"StressStrength","Rep
ository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Computation
and estimation of reliability of stress-
strength\nmodels","Version":"1.0.1"},"SubCultCon":{"Author":"Mary C Meyer, Jeffrey
G Snodgrass, Michael Lacy","Depends":"graphics, grDevices, stats,
utils","Description":"The three functions in the package compute the maximum
likelihood estimates of the informants' competence scores, tests for two answer
keys with known groups, and finds \"best\" split of the informants into sub-culture
groups.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"SubCultCon","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Maximum-Likelihood Cultural Consensus Analysis with
Sub-Cultures","Version":"1.0"},"SubLasso":{"Author":"Fengfeng Zhou, Youxi Luo,
Qinghan Meng, Ruiquan Ge, Guoqin Mai, Jikui Liu","Depends":"R(>= 2.10), glmnet,
psych, gplots","Description":"The package implements a convenient procedure for
microarray study, which is to do gene selection and classification simultaneously
for binary outcomes. Users needn't to tune the parameters and can fix any genes
that they desire to keep in the model. The K-folds cross validation results are
returned.","License":"GPL","NeedsCompilation":"no","Package":"SubLasso","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Gene selection using Lasso for
Microarray data with user-defined\ngenes fixed in
model","Version":"1.0"},"SubpathwayGMir":{"Author":"Li Feng, Chunquan Li and Xia
Li","Depends":"R (>= 3.0.2), XML, igraph","Description":"Routines for identifying
metabolic subpathways mediated by microRNAs (miRNAs) through topologically locating
miRNAs and genes within reconstructed Kyoto Encyclopedia of Genes and Genomes
(KEGG) metabolic pathway graphs embedded by miRNAs. (1) This package can obtain the
reconstructed KEGG metabolic pathway graphs with genes and miRNAs as nodes, through
converting KEGG metabolic pathways to graphs with genes as nodes and compounds as
edges, and then integrating miRNA-target interactions verified by low-throughput
experiments from four databases (TarBase, miRecords, mirTarBase and miR2Disease)
into converted pathway graphs. (2) This package can locate metabolic subpathways
mediated by miRNAs by topologically analyzing the \"lenient distance\" of miRNAs
and genes within reconstructed KEGG metabolic pathway graphs.(3) This package can
identify significantly enriched miRNA-mediated metabolic subpathways based on
located subpathways by hypergenomic test. (4) This package can support six species
for metabolic subpathway identification, such as caenorhabditis elegans, drosophila
melanogaster, danio rerio, homo sapiens, mus musculus and rattus norvegicus, and
user only need to update interested organism-specific environment
2)","NeedsCompilation":"no","Package":"SubpathwayGMir","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Identify Metabolic Subpathways Mediated by
MicroRNAs","Version":"1.0"},"SubpathwayLNCE":{"Author":"Xinrui Shi, Chunquan Li and
Xia Li","Depends":"R (>= 2.10), igraph, RBGL, utils, BiasedUrn, graph,
graphics,\nstats","Description":"Identify dysfunctional subpathways competitively
regulated by lncRNAs through integrating lncRNA-mRNA expression profile and pathway
topologies.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SubpathwayLNCE","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"XML","Title":"Identify Signal Subpathways
Competitively Regulated by LncRNAs\nBased on ceRNA
Theory","Version":"1.0"},"Sunder":{"Author":"Filippo Botta, Casper Eriksen, Gilles
Guillot","Depends":"mnormt","Description":"Quantification of the effect of
geographic versus environmental isolation on genetic
differentiation","License":"GPL","NeedsCompilation":"yes","Package":"Sunder","Repos
itory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Quantification of the effect
of geographic versus environmental\nisolation on genetic
differentiation","URL":"http:\/\/www2.imm.dtu.dk\/~gigu\/Sunder","Version":"0.0.4"}
,"SunterSampling":{"Author":"Alessandro Barbiero, Giancarlo
Manzi","Description":"Functions for drawing samples according to Sunter's\nsampling
design, and for computing first and second order\ninclusion
probabilities","License":"GPL","NeedsCompilation":"no","Package":"SunterSampling","
Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Sunter's sampling
design","Version":"1.0.1"},"SuperExactTest":{"Author":"Minghui Wang, Yongzhong Zhao
and Bin Zhang","Depends":"grid (>= 3.1.0), methods, R (>=
3.1.0)","Description":"Efficient statistical testing and scalable visualization of
intersections among multiple sets.","License":"GPL-
3","NeedsCompilation":"yes","Package":"SuperExactTest","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"knitr, rmarkdown","Title":"Exact Test and
Visualization of Multi-Set Intersections","Version":"0.99.2"},"SuperLearner":
{"Author":"Eric Polley, Erin LeDell, Mark van der Laan","Depends":"R (>= 2.14.0),
nnls","Description":"Implements the super learner prediction method and contains a
library of prediction algorithms to be used in the super
learner.","Imports":"cvAUC","License":"GPL-
3","NeedsCompilation":"no","Package":"SuperLearner","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"arm, caret, class, e1071, earth, gam, gbm,
genefilter,\nggplot2, glmnet, Hmisc, ipred, lattice, LogicReg, MASS, mda,\nmlbench,
nloptr, nnet, party, polspline, quadprog,\nrandomForest, ROCR, rpart, SIS, spls,
stepPlr, sva","Title":"Super Learner
Prediction","URL":"https:\/\/github.com\/ecpolley\/SuperLearner","Version":"2.0-
19"},"SuppDists":{"Author":"Bob Wheeler <bwheelerg@gmail.com>","Description":"Ten
distributions supplementing those built into R.\nInverse Gauss, Kruskal-Wallis,
Kendall's Tau, Friedman's chi\nsquared, Spearman's rho, maximum F ratio, the
Pearson product\nmoment correlation coefficiant, Johnson distributions,
normal\nscores and generalized hypergeometric distributions. In\naddition two
random number generators of George Marsaglia are\nincluded.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"SuppDists","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Supplementary Distributions","URL":"no longer
valid","Version":"1.1-9.2"},"Surrogate":{"Author":"Wim Van der Elst, Paul Meyvisch,
Ariel Alonso, Hannah M. Ensor, Christopher J. Weir & Geert
Molenberghs","Depends":"MASS, msm","Description":"In a clinical trial, it
frequently occurs that the most credible outcome to evaluate the effectiveness of a
new therapy (the true endpoint) is difficult to measure. In such a situation, it
can be an effective strategy to replace the true endpoint by a biomarker that is
easier to measure and that allows for a prediction of the treatment effect on the
true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an
evaluation of the appropriateness of a candidate surrogate endpoint based on the
meta-analytic, information-theoretic, and causal-inference frameworks. Part of this
software has been developed using funding provided from the European Union's 7th
Framework Programme for research, technological development and demonstration under
Grant Agreement no 602552.","Imports":"rgl, lattice, latticeExtra, survival, nlme,
lme4,\nOrdinalLogisticBiplot, logistf, rms","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Surrogate","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Evaluation of Surrogate Endpoints in Clinical
Trials","Version":"0.1-71"},"SurvCorr":{"Author":"Meinhard Ploner, Alexandra Kaider
and Georg Heinze","Depends":"R (>= 3.0.2)","Description":"Estimates correlation
coefficients with associated\nconfidence limits\nfor bivariate, partially censored
survival times. Uses\nthe iterative multiple imputation approach proposed\nby
Schemper, Kaider, Wakounig and Heinze, Statistics\nin Medicine 2013. Provides a
scatterplot function to visualize the bivariate\ndistribution, either on the
original time scale or as copula.","Imports":"survival,
fields","License":"GPL","NeedsCompilation":"no","Package":"SurvCorr","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Title":"Correlation of Bivariate Survival
Times","Version":"1.0"},"SurvLong":{"Author":"Hongyuan Cao, Mathew M. Churpek,
Donglin Zeng, Jason P. Fine, and Shannon T. Holloway","Description":"Kernel
weighting methods for estimation of proportional hazards models with intermittently
observed longitudinal covariates.","License":"GPL-
2","NeedsCompilation":"no","Package":"SurvLong","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Analysis of Proportional Hazards Model with Sparse
Longitudinal\nCovariates","Version":"1.0"},"SurvRank":{"Author":"Michael
Laimighofer [aut, cre, ctb]","Depends":"R (>= 3.0.0), survival(>= 2.37-6),
foreach(>= 1.0.11)","Description":"Estimation of the prediction accuracy in a
unified survival AUC\napproach. Model selection and prediction estimation based on
a survival AUC.\nStepwise model selection, based on several ranking
approaches.","Imports":"ipred(>= 0.9-3), sampling(>= 2.6), glmnet(>= 1.9-8),
utils(>=\n3.1.0), survAUC(>= 1.0-5), randomForestSRC(>= 1.5.4),\nggplot2(>= 1.0.0),
reshape(>= 0.8), gplots(>= 2.16.0),\nmboost(>= 2.3-0), parallel(>= 3.2.0),
doParallel(>= 1.0.8),\nrpart(>= 4.1-8)","License":"GPL-
2","NeedsCompilation":"no","Package":"SurvRank","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr","Title":"Rank Based Survival
Modelling","Version":"0.1"},"SurvRegCensCov":{"Author":"Stanislas Hubeaux
<stanislas.hubeaux@alumni.epfl.ch> and Kaspar Rufibach
<kaspar.rufibach@gmail.com>","Depends":"R (>= 2.10), survival, stats,
graphics","Description":"The main function of this package allows estimation of a
Weibull Regression for a right-censored endpoint, one interval-censored covariate,
and an arbitrary number of non-censored covariates. Additional functions allow to
switch between different parametrizations of Weibull regression
used by different R functions, inference for the mean difference of two
arbitrarily censored Normal samples, and estimation of canonical parameters from
censored samples for several distributional
assumptions.","Imports":"numDeriv","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"SurvRegCensCov","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Weibull Regression for a Right-Censored Endpoint
with\nInterval-Censored Covariate","Version":"1.4"},"Survgini":{"Author":"Chiara
Gigliarano and Marco Bonetti","Depends":"R (>= 2.11.0),
survival","Description":"The Gini concentration test for survival data is a
nonparametric test based on the Gini index for testing the equality of two survival
distributions from the point of view of concentration. The package compares
different nonparametric tests (asymptotic Gini test, permutation Gini test, log-
rank test, Gray-Tsiatis test and Wilcoxon test) and computes their p-
values.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Survgini","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"The Gini concentration test for survival
data","Version":"1.0"},"SvyNom":{"Author":"Mithat Gonen, Marinela
Capanu","Description":"Builds, evaluates and validates a nomogram with survey data
and right-censored outcomes.","Imports":"survival,rms,Hmisc,survey","License":"GPL-
2","NeedsCompilation":"no","Package":"SvyNom","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Nomograms for Right-Censored Outcomes from Survey
Designs","Version":"1.1"},"SwarmSVM":{"Author":"Tong He <hetong007@gmail.com>,
Aydin Demircioglu <aydin.demircioglu@ini.ruhr-uni-bochum.de>","Depends":"R (>=
3.0.2)","Description":"Three ensemble learning algorithms based on support vector
machines.\nThey all train support vector machines on subset of data and combine the
result.","Imports":"e1071, LiblineaR, Matrix, SparseM, kernlab, methods,
checkmate\n(>= 1.6.0), BBmisc","License":"GPL-
2","NeedsCompilation":"yes","Package":"SwarmSVM","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat, knitr, rmarkdown","Title":"Ensemble
Learning Algorithms Based on Support Vector
Machines","Version":"0.1"},"SweaveListingUtils":{"Author":"Peter
Ruckdeschel","Depends":"R(>= 2.14.0), startupmsg","Description":"provides utilities
for defining R \/ Rd as Tex-package-listings \"language\" and\nincluding R \/ Rd
source file (sniplets) copied from R-forge in its most recent version\n(or another
url) thereby avoiding inconsistencies between vignette and documented\nsource
code","License":"LGPL-
3","NeedsCompilation":"no","Package":"SweaveListingUtils","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"distr, MASS, survival, distrEx, Matrix,
splines","Title":"Utilities for Sweave together with TeX listings
package","Version":"0.6.2"},"SwissAir":{"Author":"Rene Locher","Depends":"R(>=
2.13.1)","Description":"Ozone, NOx (= Sum of Nitrogenmonoxide
and\nNitrogendioxide), Nitrogenmonoxide, ambient temperature, dew\npoint, wind
speed and wind direction at 3 sites around lake of\nLucerne in Central Switzerland
in 30 min time resolution for\nyear 2004.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"SwissAir","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"IDPmisc(>= 1.1.17)","Title":"Air Quality Data of
Switzerland for one year in 30 min\nResolution","Version":"1.1.4"},"SyNet":
{"Author":"Daniel A. Dos Santos","Depends":"tkrplot, tcltk","Description":"Infers
sympatry matrices from distributional data and analyzes them in order to identify
groups of species cohesively
connected.","License":"GPL","NeedsCompilation":"no","Package":"SyNet","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Title":"Inference and Analysis of Sympatry
Networks","Version":"2.0"},"SyncMove":{"Author":"Martin Rimmler [aut, cre],\nThomas
Mueller [aut]","Depends":"R (>= 3.1.0)","Description":"The function 'syncSubsample'
subsamples temporal data of different entities so that the result only contains
synchronal events. The function 'mci' calculates the Movement Coordination Index
(MCI, see reference on help page for function 'mci') of a data set created with the
function 'syncSubsample'.","Imports":"utils","License":"GPL-
2","NeedsCompilation":"no","Package":"SyncMove","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Subsample Temporal Data to Synchronal Events and Compute
the MCI","Version":"0.1-0"},"SynchWave":{"Author":"Matlab original by Eugene
Brevdo; R port by Dongik Jang, Hee-Seok Oh and Donghoh Kim","Depends":"R (>= 2.13),
fields (>= 6.7.6)","Description":"This package carries out synchrosqueezed wavelet
transform. The package is a translation of MATLAB Synchrosqueezing Toolbox, version
1.1 originally developed by Eugene Brevdo (2012). The C code for curve_ext was
authored by Jianfeng Lu, and translated to Fortran by Dongik Jang. Synchrosqueezing
is based on the papers: [1] Daubechies, I., Lu, J. and Wu, H. T. (2011)
Synchrosqueezed wavelet transforms: An empirical mode decomposition-like tool.
Applied and Computational Harmonic Analysis, 30. 243-261. [2] Thakur, G., Brevdo,
E., Fukar, N. S. and Wu, H-T. (2013) The Synchrosqueezing algorithm for time-
varying spectral analysis: Robustness properties and new paleoclimate applications.
Signal Processing, 93, 1079-1094.","License":"LGPL (>=
2)","NeedsCompilation":"yes","Package":"SynchWave","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Synchrosqueezed Wavelet
Transform","Version":"1.1.1"},"SynergizeR":{"Author":"Paolo Sonego
<paolo.sonego@gmail.com>","Depends":"R (>= 2.11.0), RJSONIO,
RCurl","Description":"This package provides programmatic access to\nThe Synergizer
service for translating between sets of\nbiological identifiers.","License":"GPL-
2","NeedsCompilation":"no","Package":"SynergizeR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Interface to The Synergizer service for translating
between sets\nof biological identifiers","Version":"0.2"},"Synth":{"Author":"Jens
Hainmueller <jhain@stanford.edu> and Alexis Diamond
<adiamond@fas.harvard.edu>","Description":"Implements the synthetic control group
method for comparative case studies as described in Abadie and Gardeazabal (2003)
and Abadie, Diamond, and Hainmueller (2010, 2011, 2014). The synthetic control
method allows for effect estimation in settings where a single unit (a state,
country, firm, etc.) is exposed to an event or intervention. It provides a data-
driven procedure to construct synthetic control units based on a weighted
combination of comparison units that approximates the characteristics of the unit
that is exposed to the intervention. A combination of comparison units often
provides a better comparison for the unit exposed to the intervention than any
comparison unit alone.","Imports":"kernlab, optimx","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Synth","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"rgenoud, LowRankQP","Title":"Synthetic Control Group
Method for Comparative Case
Studies","URL":"http:\/\/www.stanford.edu\/~jhain","Version":"1.1-5"},"TAM":
{"Author":"\nThomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu
[aut]","Depends":"R (>= 2.15.1), CDM","Description":"\nIncludes marginal maximum
likelihood estimation of uni- and\nmultidimensional item response models (Rasch,
2PL, 3PL,\nGeneralized Partial Credit, Multi Facets,\nNominal Item Response,
Structured Latent Class Analysis,\nMixture Distribution IRT Models, Located Latent
Class Models)\nand joint maximum likelihood estimation for models\nfrom the Rasch
family.\nLatent regression models and plausible value imputation are\nalso
supported.","Imports":"GPArotation, graphics, grDevices, lavaan, lattice,
MASS,\nmethods, msm, mvtnorm, plyr, psych, Rcpp, sfsmisc, stats,\nutils, tensor,
WrightMap","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"TAM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"miceadds, sirt","Title":"Test Analysis
Modules","URL":"http:\/\/www.edmeasurementsurveys.com\/TAM\/Tutorials\/","Version":
"1.17-0"},"TANOVA":{"Author":"Baiyu Zhou <zhouby98@stanford.edu> and Weihong
Xu\n<weihongx@stanford.edu>","Depends":"R (>= 2.3.0), MASS,
splines","Description":"Functions for performing analysis of variance on
time\ncourse microarray
data","License":"LGPL","NeedsCompilation":"no","Package":"TANOVA","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Title":"Time Course Analysis of Variance for
Microarray","URL":"Wing Wong's lab (http:\/\/www.stanford.edu\/group\/wonglab\/)
&\nStanford Genome Technology
Center\n(http:\/\/gluegrant1.stanford.edu\/~DIC\/)","Version":"1.0.0"},"TAQMNGR":
{"Author":"Francesco Calvori, Fabrizio Cipollini, Giampiero M. Gallo and 'gzstream'
authors.","Depends":"R (>= 3.0-2)","Description":"Manager of tick-by-tick
transaction data that performs 'cleaning', 'aggregation' and 'import' in an
efficient and fast way. The package engine, written in C++, exploits the 'zlib' and
'gzstream' libraries to handle gzipped data without need to uncompress them.
'Cleaning' and 'aggregation' are performed according to Brownlees and Gallo (2006).
Currently, TAQMNGR processes raw data from WRDS (Wharton Research Data
Service).","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"TAQMNGR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Manage Tick-by-Tick Transaction
Data","URL":"http:\/\/www.r-project.org","Version":"2015.2-1"},"TBEST":
{"Author":"Guoli Sun, Alex Krasnitz","Depends":"parallel, signal,
fdrtool","Description":"Our method introduces mathematically well-defined measures
for tightness of branches in a hierarchical tree. Statistical significance of the
findings is determined, for all branches of the tree, by performing permutation
tests, optionally with generalized Pareto p-value estimation.","License":"GPL-
2","NeedsCompilation":"no","Package":"TBEST","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Tree
Branches Evaluated Statistically for Tightness","Version":"5.0"},"TBSSurvival":
{"Author":"Adriano Polpo <polpo@ufscar.br>, Cassio de Campos <cassiopc@acm.org>, D.
Sinha <sinhad@stat.fsu.edu>, Stuart Lipsitz <slipsitz@partners.org>, Jianchang Lin
<jlin@stat.fsu.edu>","Depends":"R (>= 3.1.2)","Description":"Functions to perform
the reliability\/survival\nanalysis using a parametric Transform-both-sides (TBS)
model.","Imports":"normalp, survival, mcmc, R.utils, coda, Rsolnp,
BMS","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"TBSSurvival","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Survival Analysis using a Transform-Both-Sides
model","URL":"http:\/\/code.google.com\/p\/tbssurvival\/","Version":"1.2"},"TCGA2ST
AT":{"Author":"Ying-Wooi Wan, Genevera I. Allen, Matthew L. Anderson, Zhandong
Liu","Depends":"R (>= 3.0.0)","Description":"Automatically downloads and processes
TCGA genomics and clinical data into a format convenient for statistical analyses
in the R environment.","Imports":"XML, parallel, CNTools","License":"GPL-
2","NeedsCompilation":"no","Package":"TCGA2STAT","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr","Title":"Simple TCGA Data Access for
Integrated Statistical Analysis in
R","URL":"http:\/\/www.liuzlab.org\/TCGA2STAT\/","Version":"1.2"},"TDA":
{"Author":"Brittany T. Fasy, Jisu Kim, Fabrizio Lecci, Clement Maria, Vincent
Rouvreau. The included GUDHI is authored by Clement Maria, Dionysus by Dmitriy
Morozov, and PHAT by Ulrich Bauer, Michael Kerber, and Jan
Reininghaus.","Depends":"R (>= 3.1.0)","Description":"Tools for the statistical
analysis of persistent homology and for density clustering. For that, this package
provides an R interface for the efficient algorithms of the C++ libraries GUDHI,
Dionysus, and PHAT.","Imports":"FNN, igraph, parallel, scales, Rcpp (>=
3","NeedsCompilation":"yes","Package":"TDA","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Statistical Tools for Topological Data
Analysis","Version":"1.4.1"},"TDAmapper":{"Author":"Paul Pearson [aut, cre,
trl],\nDaniel Muellner [aut, ctb],\nGurjeet Singh [aut, ctb]","Depends":"R (>=
3.1.2)","Description":"Topological Data Analysis using Mapper (discrete Morse
theory).\nGenerate a 1-dimensional simplicial complex from a filter\nfunction
defined on the data: 1. Define a filter function (lens) on the\ndata. 2. Perform
clustering within within each level set and generate\none node (vertex) for each
cluster. 3. For each pair of clusters in\nadjacent level sets with a nonempty
intersection, generate one edge\nbetween vertices. The function mapper1D uses a
filter function with\ncodomain R, while the the function mapper2D uses a filter
function with\ncodomain R^2.","License":"GPL-
3","NeedsCompilation":"no","Package":"TDAmapper","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"fastcluster, igraph","Title":"Analyze High-
Dimensional Data Using Discrete Morse
Theory","URL":"https:\/\/github.com\/paultpearson\/TDAmapper\/","Version":"1.0"},"T
DCor":{"Author":"Julien Lavenus","Depends":"R (>= 3.1.2),
deSolve","Description":"The Time-Delay Correlation algorithm (TDCor) reconstructs
the topology of a gene regulatory network (GRN) from time-series transcriptomic
data. The algorithm is described in details in Lavenus et al., Plant Cell, 2015.
It was initially developed to infer the topology of the GRN controlling lateral
root formation in Arabidopsis thaliana. The time-series transcriptomic dataset
which was used in this study is included in the package to illustrate how to use
it.","Imports":"parallel","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"TDCor","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Gene Network Inference from Time-Series Transcriptomic
Data","Version":"0.1-2"},"TDD":{"Author":"Jake Anderson","Depends":"R (>= 2.10),
signal, RSEIS, pracma","Description":"Deconvolution of instrument responses from
seismic traces and seismogram lists from RSEIS. Includes pre-calculated instrument
responses for several common
instruments.","License":"GPL","NeedsCompilation":"no","Package":"TDD","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Title":"Time-Domain Deconvolution of
Seismometer Response","Version":"0.4"},"TDMR":{"Author":"Wolfgang Konen
<wolfgang.konen@fh-koeln.de>, Patrick Koch\n<patrick.koch@fh-
koeln.de>","Depends":"R (>= 2.14.0), SPOT, twiddler","Description":"Tuned Data
Mining in R (TDMR) performs a complete tuning of a data\nmining
task.","Imports":"testit, adabag","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"TDMR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"cmaes, parallel, e1071, powell, ROCR, randomForest,
rCMA,\nrSFA","Title":"Tuned Data Mining in R","Version":"1.3"},"TDboost":
{"Author":"Yi Yang <yi.yang6@mcgill.ca>, Wei Qian <wxqsma@rit.edu>, Hui Zou
<hzou@stat.umn.edu>","Depends":"R (>= 2.12.0), lattice","Description":"A boosted
Tweedie compound Poisson model using the gradient boosting. It is capable of
fitting a flexible nonlinear Tweedie compound Poisson model (or a gamma model) and
capturing interactions among predictors.","License":"GPL-
3","NeedsCompilation":"yes","Package":"TDboost","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"A Boosted Tweedie Compound Poisson
Model","Version":"1.2"},"TED":{"Author":"Yanfei Kang, Danijel Belusic and Kate
Smith-Miles","Depends":"R (>= 3.0.2)","Description":"TED performs Turbulence time
series Event Detection and classification.","Imports":"foreach, zoo, fields,
animation, geoR, tcltk, utils,\nRcppArmadillo","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"TED","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"doMC","Title":"Turbulence Time Series Event Detection and
Classification","Version":"1.1.1"},"TEEReg":{"Author":"Wei Jiang and Matthew S.
Mayo","Description":"For fitting multiple linear regressions, the ordinary least
squares approach is sensitive to outliers and\/or violations of model assumptions.
The trimmed elemental estimators are more robust to such situations. This package
contains functions for computing the trimmed elemental estimates, as well as for
creating the bias-corrected and accelerated bootstrap confidence intervals in the
context of trimmed elemental regressions.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"TEEReg","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Trimmed Elemental Estimation for Linear
Models","Version":"1.0"},"TEQR":{"Author":"M. Suzette Blanchard","Description":"The
TEQR package contains software to calculate the operating characteristics for the
TEQR and the ACT designs.The TEQR (toxicity equivalence range) design is a toxicity
based cumulative cohort design with added safety rules. The ACT (Activity
constrained for toxicity) design is also a cumulative cohort design with
additional safety rules. The unique feature of this design is that dose is
escalated based on lack of activity rather than on lack of toxicity and is de-
escalated only if an unacceptable level of toxicity is
experienced.","License":"GPL-
2","NeedsCompilation":"no","Package":"TEQR","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Target Equivalence Range Design","Version":"6.0-
0"},"TERAplusB":{"Author":"Eun-Kyung Lee","Description":"This package is for the
comparison of various types of A+B\nescalation rules for dose finding
trials.","License":"LGPL-
2.1","NeedsCompilation":"no","Package":"TERAplusB","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Test for A+B Traditional Escalation
Rule","Version":"1.0"},"TESS":{"Author":"Sebastian Hoehna and Michael R.
May","Depends":"ape, coda, deSolve","Description":"Simulation of reconstructed
phylogenetic trees under tree-wide time-heterogeneous birth-death processes and
estimation of diversification parameters under the same model. Speciation and
extinction rates can be any function of time and mass-extinction events at specific
times can be provided. Trees can be simulated either conditioned on the number of
species, the time of the process, or both. Additionally, the likelihood equations
are implemented for convenience and can be used for Maximum Likelihood (ML)
estimation and Bayesian inference.","Imports":"Rcpp (>= 0.11.0)","License":"GPL-
3","NeedsCompilation":"yes","Package":"TESS","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr","Title":"Diversification Rate Estimation and Fast
Simulation of\nReconstructed Phylogenetic Trees under Tree-Wide\nTime-Heterogeneous
Birth-Death Processes Including\nMass-Extinction
Events","Version":"2.1.0"},"TExPosition":{"Author":"Derek Beaton, Jenny Rieck,
Cherise R. Chin Fatt, Herve Abdi","Depends":"prettyGraphs (>= 2.1.4), ExPosition
(>= 2.0.0)","Description":"TExPosition is an extension of ExPosition for two table
analyses, specifically, discriminant analyses.","License":"GPL-
2","NeedsCompilation":"no","Package":"TExPosition","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Two-table ExPosition","Version":"2.6.10"},"TFDEA":
{"Author":"Tom Shott [aut, cre],\nDong-Joon Lim [aut]","Depends":"R (>= 3.0.0),
lpSolveAPI","Description":"The TFDEA algorithm for technology forecasts when future
products\nwill be introduced based upon their features.\nIt also includes DEA (Data
Envelopment Analysis) functions including extensions dealing with\nwith
infeasibility.\nIn addition it includes some standard technology forecasting data
sets.","License":"GPL-
2","NeedsCompilation":"no","Package":"TFDEA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Technology Forecasting using DEA (Data Envelopment
Analysis)","URL":"\nhttp:\/\/www.pdx.edu\/extreme-technology-analytics\/open-tfdea-
r-package","Version":"0.9.8.3"},"TFMPvalue":{"Author":"Ge Tan
<ge.tan09@imperial.ac.uk>","Depends":"R (>= 3.0.1)","Description":"In putative
Transcription
Factor Binding Sites (TFBSs)\nidentification from sequence\/alignments,\nwe are
interested in the significance of certain match score.\nTFMPvalue provides the
accurate calculation of P-value with\nscore threshold for Position Weight
Matrices,\nor the score with given P-value.\nThis package is an interface to code
originally made available by\nHelene Touzet and Jean-Stephane Varre,
2007,\nAlgorithms Mol Biol:2, 15.","Imports":"Rcpp(>= 0.11.1)","License":"GPL-
2","NeedsCompilation":"yes","Package":"TFMPvalue","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat","Title":"Efficient and Accurate P-Value
Computation for Position
Weight\nMatrices","URL":"https:\/\/github.com\/ge11232002\/TFMPvalue","Version":"0.
0.6"},"TFX":{"Author":"Garrett See","Depends":"R(>=
2.15.0)","Description":"Connects R to TrueFX(tm) for free streaming real-time
and\nhistorical tick-by-tick market data for dealable interbank\nforeign exchange
rates with millisecond detail.","Imports":"XML","License":"GPL-
3","NeedsCompilation":"no","Package":"TFX","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"R API to
TrueFX(tm)","URL":"http:\/\/www.truefx.com","Version":"0.1.0"},"TH.data":
{"Author":"Torsten Hothorn [aut, cre]","Depends":"R (>= 2.10.0), survival,
MASS","Description":"Contains data sets used in other packages Torsten
Hothorn\nmaintains.","License":"GPL-
3","NeedsCompilation":"no","Package":"TH.data","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"dplyr, gdata, plyr","Title":"TH's Data
Archive","Version":"1.0-7"},"TIMP":{"Author":"Katharine M. Mullen, Joris J.
Snellenburg, Sergey P. Laptenok, David Nicolaides, Ivo H.M. van
Stokkum","Depends":"R (>= 2.10.0), methods, fields (>= 4.1)","Description":"A
problem-solving environment (PSE) for fitting\nseparable nonlinear models to
measurements arising in physics\nand chemistry experiments; has been extensively
applied to\ntime-resolved spectroscopy and FLIM-FRET data.","Imports":"deSolve,
nnls (>= 1.1), colorspace, splines, minpack.lm (>=\n1.1-1), gclus, gplots,
grDevices, graphics, stats, utils","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"TIMP","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Fitting Separable Nonlinear Models in Spectroscopy
and\nMicroscopy","URL":"http:\/\/timp.r-forge.r-project.org\/
http:\/\/timpgui.org\/","Version":"1.13.0"},"TITAN2":{"Author":"Matthew E. Baker
[aut, cph],\nRyan S. King [aut, cph],\nDavid Kahle [aut, cph, cre]","Depends":"R
(>= 2.15.0)","Description":"Uses indicator species scores across binary partitions
of\na sample set to detect congruence in taxon-specific changes of abundance\nand
occurrence frequency along an environmental gradient as evidence of\nan ecological
community threshold. Relevant references include: Baker,\nME and RS King. 2010. A
new method for detecting and interpreting\nbiodiversity and ecological community
thresholds. Methods in Ecology and\nEvolution 1(1): 25:37. King, RS and ME Baker.
2010. Considerations for\nidentifying and interpreting ecological community
thresholds. Journal\nof the North American Benthological Association 29(3):998-
1008. Baker ME\nand RS King. 2013. Of TITAN and straw men: an appeal for
greater\nunderstanding of community data. Freshwater Science 32(2):489-
506.","Imports":"parallel","License":"GPL-
2","NeedsCompilation":"no","Package":"TITAN2","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"knitr, rmarkdown","Title":"Threshold Indicator Taxa
Analysis","Version":"2.1"},"TInPosition":{"Author":"Derek Beaton, Jenny Rieck,
Herve Abdi","Depends":"prettyGraphs (>= 2.1.4), TExPosition (>= 2.6.10),
ExPosition\n(>= 2.8.19), InPosition (>= 0.12.7)","Description":"Non-parametric
resampling-based inference tests for TExPosition.","License":"GPL-
2","NeedsCompilation":"no","Package":"TInPosition","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Inference tests for
TExPosition","Version":"0.13.6"},"TKF":{"Author":"Ge Tan
<ge.tan09@imperial.ac.uk>","Depends":"R (>= 3.0.2)","Description":"Pairwise
evolutionary distance estimation between protein sequences with the TKF91 and TKF92
model, which consider all the possible paths of transforming from one sequence to
another.","Imports":"methods, expm, numDeriv, ape (>= 3.2), phytools (>= 0.4-
45),\nphangorn (>= 1.99-12)","License":"GPL-
2","NeedsCompilation":"yes","Package":"TKF","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"RUnit, seqinr","Title":"Pairwise Distance Estimation with
TKF91 and TKF92 Model","Version":"0.0.8"},"TLBC":{"Author":"Katherine
Ellis","Depends":"R(>= 2.10)","Description":"Contains functions for training and
applying two-level random forest and hidden Markov models for human behavior
classification from raw tri-axial accelerometer and\/or GPS data. Includes
functions for training a two-level model, applying the model to data, and computing
performance.","Imports":"stringr,randomForest,HMM,tools,signal,caret","License":"GP
L-
2","NeedsCompilation":"no","Package":"TLBC","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Two-Level Behavior
Classification","Version":"1.0"},"TLdating":{"Author":"David Strebler [aut,
cre],\nDominik Brill [ths],\nHelmut BrÃ¼ckner [ths]","Depends":"R (>=
2.0.0)","Description":"A series of function to make thermoluminescence dating using
the MAAD or the SAR protocol.\nThis package completes the R
package \"Luminescence.\"","Imports":"methods, Luminescence (>= 0.5.0),
gplots","License":"GPL-
3","NeedsCompilation":"no","Package":"TLdating","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Tools for Thermoluminescences
Dating","Version":"0.1.1"},"TMB":{"Author":"Kasper Kristensen [aut, cre,
cph],\nBrad Bell [cph],\nHans Skaug [ctb],\nArni Magnusson [ctb],\nCasper Berg
[ctb],\nAnders Nielsen [ctb],\nMartin Maechler [ctb],\nTheo Michelot [ctb],\nMollie
Brooks [ctb],\nCole Monnahan [ctb]","Depends":"R (>= 3.0.0)","Description":"With
this tool, a user should be able to quickly implement complex\nrandom effect models
through simple C++ templates. The package combines\nCppAD (C++ automatic
differentiation), Eigen (templated matrix-vector\nlibrary) and CHOLMOD (sparse
matrix routines available from R) to obtain an\nefficient implementation of the
applied Laplace approximation with exact\nderivatives. Key features are: Automatic
sparseness detection, parallelism\nthrough BLAS and parallel user
templates.","Imports":"graphics, methods, stats, utils, Matrix (>= 1.0-
2","NeedsCompilation":"yes","Package":"TMB","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"numDeriv, parallel","Title":"Template Model Builder: A
General Random Effect Tool Inspired by\nADMB","URL":"http:\/\/tmb-
project.org","Version":"1.7.0"},"TMDb":{"Author":"Andrea Capozio
<andreacapozio@gmail.com>","Depends":"R (>= 3.1.3), httr(>= 0.4), jsonlite(>=
0.9.15)","Description":"Provides an R-interface to the TMDb API (see TMDb API on
<http:\/\/docs.themoviedb.apiary.io\/#>). The Movie Database (TMDb) is a popular
user editable database for movies and TV shows (see
<https:\/\/www.themoviedb.org>).","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"TMDb","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Access to TMDb API - Apiary","Version":"1.0"},"TOC":
{"Author":"Robert G. Pontius <rpontius@clarku.edu>, Alí Santacruz, Amin Tayyebi,
Benoit Parmentier, Kangping Si","Depends":"R (>= 2.14.0), raster, bit, rgdal,
methods","Description":"Construction of the Total Operating Characteristic (TOC)
Curve and the Receiver (aka Relative) Operating Characteristic (ROC) Curve for
spatial and non-spatial data. The TOC method is a modification of the ROC method
which measures the ability of an index variable to diagnose either presence or
absence of a characteristic. The diagnosis depends on whether the value of an index
variable is above a threshold. Each threshold generates a two-by-two contingency
table, which contains four entries: hits (H), misses (M), false alarms (FA), and
correct rejections (CR). While ROC shows for each threshold only two ratios, H\/(H
+ M) and FA\/(FA + CR), TOC reveals the size of every entry in the contingency
table for each threshold (Pontius Jr., R.G., Si, K. 2014. The total operating
characteristic to measure diagnostic ability for multiple thresholds. Int. J.
Geogr. Inf. Sci. 28 (3), 570-583).","Imports":"graphics, grDevices,
2)","NeedsCompilation":"no","Package":"TOC","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Total Operating Characteristic Curve and ROC
Curve","URL":"http:\/\/amsantac.co\/software.html","Version":"0.0-4"},"TP.idm":
{"Author":"Vanesa Balboa-Barreiro, Jacobo de Una-Alvarez <jacobo@uvigo.es>\nand
Luis Meira-Machado >lmachado@math.uminho.pt>","Depends":"R (>= 3.1.1), graphics,
stats","Description":"Estimation of transition probabilities for the illness-death
model. Both the Aalen-Johansen estimator for a Markov model and a novel non-
Markovian estimator (de Una-Alvarez and Meira-Machado, 2015) are
2","NeedsCompilation":"yes","Package":"TP.idm","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Estimation of Transition Probabilities for the Illness-
Death\nModel","Version":"1.0"},"TPmsm":{"Author":"Artur Araujo, Javier Roca-
Pardinas <roca@uvigo.es>\nand Luis Meira-Machado
<lmachado@math.uminho.pt>","Depends":"R (>=
2.12.0),graphics,grDevices,KernSmooth","Description":"Estimation of transition
probabilities for the\nillness-death model and or the three-state progressive
model.","Enhances":"p3state.msm,etm","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"TPmsm","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Estimation of Transition Probabilities in Multistate
Models","Version":"1.2.1"},"TR8":{"Author":"Gionata Bocci
<boccigionata@gmail.com>","Depends":"R (>= 2.10), methods","Description":"Plant
ecologists often need to collect \"traits\" data\nabout plant species which are
often scattered among various\ndatabases: TR8 contains a set of tools which take
care of\nautomatically retrieving some of those functional traits data\nfor plant
species from publicly available databases (Biolflor,\nThe Ecological Flora of the
British Isles, LEDA traitbase, Ellenberg\nvalues for Italian Flora, Mycorrhizal
intensity databases, Catminat, BROT,\nPLANTS, Jepson Flora Project).\nThe TR8 name,
inspired by \"car plates\" jokes, was chosen since\nit both reminds of the main
object of the package and is\nextremely short to type.","Imports":"RCurl, XML,
plyr, reshape, rappdirs, gWidgets, gWidgetstcltk,\nreadxl, taxize","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"TR8","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"A Tool for Downloading Functional Traits Data for Plant
Species","URL":"https:\/\/github.com\/GioBo\/TR8","Version":"0.9.14"},"TRADER":
{"Author":"Pavel Fibich <pavel.fibich@prf.jcu.cz>, Jan Altman
<altman.jan@gmail.com>, Tuomas Aakala <tuomas.aakala@helsinki.fi>, Jiri Dolezal
<jiriddolezal@gmail.com>","Description":"Tree Ring Analysis of Disturbance Events
in R (TRADER) package provides only one way for disturbance reconstruction from
tree-ring data.","Imports":"dplR","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"TRADER","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Tree Ring Analysis of Disturbance Events in
R","URL":"https:\/\/github.com\/pavel-fibich\/TRADER","Version":"1.2-1"},"TRAMPR":
{"Author":"Rich FitzJohn & Ian Dickie","Depends":"R (>= 2.4)","Description":"TRAMPR
is an R package for matching terminal restriction\nfragment length polymorphism
(TRFLP) profiles between unknown\nsamples and a database of knowns. TRAMPR
facilitates analysis\nof many unknown profiles at once, and provides tools
for\nworking directly with electrophoresis output through to\ngenerating summaries
suitable for community analyses with R's\nrich set of statistical functions.
TRAMPR also resolves the\nissues of multiple TRFLP profiles within a species, and
shared\nTRFLP profiles across species.","License":"GPL-
2","NeedsCompilation":"no","Package":"TRAMPR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"TRFLP Analysis and Matching Package for R","Version":"1.0-
7"},"TRD":{"Author":"Lam Opal Huang","Depends":"Rlab (>=
2.15.1)","Description":"Transmission Ratio Distortion (TRD) is a genetic phenomenon
where the two alleles from either parent are not transmitted to the offspring at
the expected 1:1 ratio under Mendelian inheritance, leading to spurious signals in
genetic association studies. Functions in this package are developed to account for
this phenomenon using loglinear model and Transmission Disequilibrium Test (TDT).
Some population information can also be calculated.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"TRD","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Transmission Ratio Distortion","Version":"1.1"},"TROM":
{"Author":"Jingyi Jessica Li <jli@stat.ucla.edu>, Wei Vivian Li
<liw@ucla.edu>","Depends":"R (>= 2.10), lattice, methods","Description":"A new
bioinformatic tool for comparing transcriptomes of two biological samples from the
same or different species. The mapping is conducted based on the overlap of the
associated genes of different samples. More examples and detailed explanations are
available in the vignette.","Imports":"AnnotationDbi, openxlsx, GO.db, gtools,
RColorBrewer, gplots,\ntopGO","License":"GPL-
2","NeedsCompilation":"no","Package":"TROM","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Transcriptome Overlap
Measure","URL":"http:\/\/www.stat.ucla.edu\/~jingyi.li\/software-and-
data\/trom.html,\nhttp:\/\/www.stat.ucla.edu\/~jingyi.li\/packages\/TROM\/vignette.
pdf","Version":"1.1"},"TRSbook":{"Author":"Lafaye de Micheaux Pierre, Drouilhet
Remy, Liquet Benoit","Depends":"xtable, RColorBrewer, gdata,
IndependenceTests","Description":"Functions and datasets for the reader of the book
\"The R Software: Fundamentals of Programming and Statistical
Analysis\".","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"TRSbook","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Functions and Datasets to Accompany the Book \"The R
Software:\nFundamentals of Programming and Statistical
Analysis\"","Version":"1.0.1"},"TSA":{"Author":"Kung-Sik Chan, Brian
Ripley","Depends":"R (>= 2.5.1),leaps, locfit, mgcv,
tseries","Description":"Contains R functions and datasets detailed in the
book\n\"Time Series Analysis with Applications in R (second edition)\"\nby Jonathan
Cryer and Kung-Sik Chan","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"TSA","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Time Series
Analysis","URL":"http:\/\/www.stat.uiowa.edu\/~kchan\/TSA.htm","Version":"1.01"},"T
SHRC":{"Author":"Jun Sheng, Peihua Qiu <qiu@stat.umn.edu>, and Charles J.
Geyer\n<charlie@stat.umn.edu>","Depends":"R (>= 2.6.0)","Description":"two-stage
procedure for comparing hazard rate functions\nwhich may or may not cross each
other","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"TSHRC","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Two Stage Hazard Rate Comparison","Version":"0.1-
3"},"TSMining":{"Author":"Cheng Fan","Depends":"R (>=
3.0.1)","Description":"Implementations of a number of functions used to mine
numeric time-series data. It covers the implementation of SAX transformation,
univariate motif discovery (based on the random projection method), multivariate
motif discovery (based on graph clustering), and several functions used for the
ease of visualizing the motifs discovered. The details of SAX transformation can be
found in J. Lin. E. Keogh, L. Wei, S. Lonardi, Experiencing SAX: A novel symbolic
representation of time series, Data Mining and Knowledge Discovery 15 (2) (2007)
107-144. Details on univariate motif discovery method implemented can be found in
B. Chiu, E. Keogh, S. Lonardi, Probabilistic discovery of time series motifs, ACM
SIGKDD, Washington, DC, USA, 2003, pp. 493-498. Details on the multivariate motif
discovery method implemented can be found in A. Vahdatpour, N. Amini, M.
Sarrafzadeh, Towards unsupervised activity discovery using multi-dimensional motif
detection in time series, IJCAI 2009 21st International Joint Conference on
Artificial Intelligence.","Imports":"foreach, ggplot2, plyr,
reshape2","License":"GPL-
3","NeedsCompilation":"no","Package":"TSMining","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr","Title":"Mining Univariate and Multivariate
Motifs in Time-Series Data","Version":"1.0"},"TSMySQL":{"Author":"Paul Gilbert
<pgilbert.ttv9z@ncf.ca>","Depends":"R (>= 2.8.0), TSdbi (>= 2015.1-
1)","Description":"A 'MySQL' interface for 'TSdbi'.\nComprehensive examples of all
the 'TS*' packages is provided in the\nvignette Guide.pdf with the 'TSdata'
package.","Imports":"methods, DBI (>= 0.3.1), tframe, TSsql (>= 2015.1-1),
RMySQL\n(>= 0.10.3)","License":"GPL-
2","NeedsCompilation":"no","Package":"TSMySQL","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"zoo, tseries, tfplot, tframePlus,
timeSeries","Title":"'TSdbi' Extensions for 'MySQL'","URL":"http:\/\/tsdbi.r-
forge.r-project.org\/","Version":"2015.4-1"},"TSP":{"Author":"Michael Hahsler [aut,
cre, cph],\nKurt Hornik [aut, cph]","Depends":"R (>= 2.14.0)","Description":"Basic
infrastructure and some algorithms for the traveling\nsalesperson problem (also
traveling salesman problem; TSP).\nThe package provides some simple algorithms
and\nan interface to the Concorde TSP solver and its implementation of
the\nChained-Lin-Kernighan heuristic. Concorde\nitself is not included in the
package and has to be obtained separately\nfrom
http:\/\/www.math.uwaterloo.ca\/tsp\/concorde.html.","Imports":"graphics, foreach,
utils, methods, stats, grDevices","License":"GPL-
3","NeedsCompilation":"yes","Package":"TSP","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"maps, sp, maptools, testthat","Title":"Traveling
Salesperson Problem
(TSP)","URL":"http:\/\/lyle.smu.edu\/IDA\/seriation","Version":"1.1-
4"},"TSPostgreSQL":{"Author":"Paul Gilbert <pgilbert.ttv9z@ncf.ca>","Depends":"R
(>= 2.8.0), TSdbi (>= 2015.1-1)","Description":"A 'PostgreSQL' interface for
'TSdbi'.\nComprehensive examples of all the 'TS*' packages is provided in
the\nvignette Guide.pdf with the 'TSdata' package.","Imports":"methods, DBI (>=
0.3.1), tframe, tframePlus, TSsql (>=\n2015.1-1), RPostgreSQL","License":"GPL-
2","NeedsCompilation":"no","Package":"TSPostgreSQL","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"zoo, tseries, tfplot","Title":"'TSdbi' Extensions
for 'PostgreSQL'","URL":"http:\/\/tsdbi.r-forge.r-project.org\/","Version":"2015.4-
1"},"TSPred":{"Author":"Rebecca Pontes Salles [aut, cre, cph] (CEFET\/RJ),\nEduardo
Ogasawara [ths] (CEFET\/RJ)","Depends":"R (>= 2.10), forecast,
stats","Description":"Functions for time series prediction and accuracy assessment
using automatic ARIMA modelling. The generated ARIMA models and its yielded
prediction errors are intended to be used as baseline for evaluating the practical
value of other time series prediction methods and creating a demand for the
refinement of such methods. For this purpose, benchmark data from prediction
competitions may be used.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"TSPred","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Functions for Baseline-Based Time Series
Prediction","URL":"https:\/\/sourceforge.net\/p\/gpca\/wiki\/TSPred\/","Version":"2
.0"},"TSSQLite":{"Author":"Paul Gilbert <pgilbert.ttv9z@ncf.ca>","Depends":"R (>=
2.8.0), TSdbi (>= 2015.1-1)","Description":"An 'SQLite' interface for
'TSdbi'.\nComprehensive examples of all the 'TS*' packages is provided in
the\nvignette
Guide.pdf with the 'TSdata' package.","Imports":"methods, DBI (>= 0.3.1), tframe,
tframePlus, TSsql (>=\n2015.1-1), RSQLite","License":"GPL-
2","NeedsCompilation":"no","Package":"TSSQLite","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"zoo, tseries, tfplot","Title":"'TSdbi' Extensions for
'SQLite'","URL":"http:\/\/tsdbi.r-forge.r-project.org\/","Version":"2015.4-
1"},"TSTr":{"Author":"Ricardo Merino [aut, cre],\nSamantha Fernandez
[ctb]","Depends":"R (>= 3.2.0)","Description":"A ternary search tree is a type of
prefix tree with up to three children and the ability for incremental string
search. The package uses this ability for word auto-completion and spell checking.
Includes a dataset with the 10001 most frequent English words.","Imports":"stringr,
stringdist, stats, data.table","License":"GPL-
2","NeedsCompilation":"no","Package":"TSTr","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"knitr","Title":"Ternary Search Tree for Auto-Completion
and Spell Checking","Version":"1.2"},"TSTutorial":{"Author":"Alberto Lopez
Moreno","Depends":"methods, grDevices, graphics, stats, tools,
MASS","Description":"Interactive laboratory of Time Series based in Box-Jenkins
methodology.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"TSTutorial","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Fitting and Predict Time Series Interactive
Laboratory","Version":"1.2.3"},"TSclust":{"Author":"Pablo Montero Manso, JosÃ©
Antonio Vilar","Depends":"R (>= 3.0.1), wmtsa, pdc, cluster","Description":"This
package contains a set of measures of dissimilarity between time series to perform
time series clustering. Metrics based on raw data, on generating models and on the
forecast behavior are implemented. Some additional utilities related to time series
clustering are also provided, such as clustering algorithms and cluster evaluation
metrics.","Imports":"locpol, KernSmooth, dtw, longitudinalData","License":"GPL-
2","NeedsCompilation":"no","Package":"TSclust","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Time Series Clustering
Utilities","URL":"http:\/\/www.jstatsoft.org\/v62\/i01\/","Version":"1.2.3"},"TScom
pare":{"Author":"Paul Gilbert <pgilbert.ttv9z@ncf.ca>","Depends":"R (>= 2.10.0),
TSdbi (>= 2015.1-1)","Description":"Utilities for comparing the equality of series
on two databases.\nComprehensive examples of all the 'TS*' packages is provided in
the\nvignette Guide.pdf with the 'TSdata' package.","Enhances":"TSPostgreSQL,
TSodbc, TSfame","Imports":"tframe, tfplot, DBI (>= 0.3.1),","License":"GPL-
2","NeedsCompilation":"no","Package":"TScompare","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"tframePlus, TSsql, TSMySQL, TSSQLite, TSmisc,
zoo","Title":"'TSdbi' Database Comparison","URL":"http:\/\/tsdbi.r-forge.r-
project.org\/","Version":"2015.4-1"},"TSdata":{"Author":"Paul Gilbert
<pgilbert.ttv9z@ncf.ca>","Depends":"R (>= 2.8.0)","Description":"Illustrates the
various 'TSdbi' packages with a vignette using time series\ndata from several
sources. The vignette also illustrates some simple time series\nmanipulation and
plotting using packages 'tframe' and 'tfplot'.","License":"GPL-
2","NeedsCompilation":"no","Package":"TSdata","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"tframe, tframePlus, tfplot, TSdbi (>= 2015.1-1), TSsql
(>=\n2015.1-1), TSPostgreSQL (>= 2015.1-1), TSMySQL (>= 2015.4-1),\nTSSQLite (>=
2015.1-1), TSodbc (>= 2015.1-1), TSsdmx, TSmisc,\nTScompare (>= 2015.1-1), zoo,
xts, tseries, its, WriteXLS, DBI\n(>= 0.3.1), RPostgreSQL, RSQLite, RMySQL, RODBC,
RJSDMX","Title":"'TSdbi' Illustration","URL":"http:\/\/tsdbi.r-forge.r-
project.org\/","Version":"2015.4-2"},"TSdbi":{"Author":"Paul Gilbert
<pgilbert.ttv9z@ncf.ca>","Depends":"R (>= 2.8.0)","Description":"Provides a common
interface to time series databases. The\nobjective is to define a standard
interface so users can retrieve time\nseries data from various sources with a
simple, common, set of\ncommands, and so programs can be written to be portable
with respect\nto the data source. The SQL implementations also provide a
database\ntable design, so users needing to set up a time series database\nhave a
reasonably complete way to do this easily. The interface\nprovides for a variety of
options with respect to the representation\nof time series in R. The interface, and
the SQL implementations, also\nhandle vintages of time series data (sometime called
editions or\nrealtime data). There is also a (not yet well tested) mechanism
to\nhandle multilingual data documentation.\nComprehensive examples of all the TS*
packages is provided in the\nvignette Guide.pdf with the TSdata
package.","Imports":"methods, DBI(>= 0.3.1), tframe (>= 2015.1-1)","License":"GPL-
2","NeedsCompilation":"no","Package":"TSdbi","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"zoo, tseries, tis, tfplot, tframePlus","Title":"Time
Series Database Interface","URL":"http:\/\/tsdbi.r-forge.r-
project.org\/","Version":"2015.7-1"},"TSdist":{"Author":"Usue Mori, Alexander
Mendiburu, J.A. Lozano","Depends":"R (>= 3.0.3), proxy","Description":"A set of
commonly used distance measures and some additional functions which, although
initially not designed for this purpose, can be used to measure the dissimilarity
between time series. These measures can be used to perform clustering,
classification or other data mining tasks which require the definition of a
distance measure between time series.","Imports":"zoo, xts, dtw, TSclust,
KernSmooth, locpol, pdc,\nlongitudinalData, cluster, methods, graphics,
2)","NeedsCompilation":"yes","Package":"TSdist","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"testthat","Title":"Distance Measures for Time Series
Data","Version":"3.2"},"TSfame":{"Author":"Paul Gilbert
1)","Description":"A 'fame' interface for 'TSdbi'.\nComprehensive examples of all
package.","Imports":"methods, DBI (>= 0.3.1), tframe, tframePlus, fame (>=
2.12),\ntis","License":"GPL-
2","NeedsCompilation":"no","Package":"TSfame","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"tseries, tfplot, zoo","Title":"'TSdbi' Extensions for
Fame","URL":"http:\/\/tsdbi.r-forge.r-project.org\/","Version":"2015.4-
1"},"TSmisc":{"Author":"Paul Gilbert <pgilbert.ttv9z@ncf.ca>","Depends":"R (>=
2.8.0), TSdbi (>= 2015.1-1)","Description":"Methods to\nretrieve data from several
different sources. This include historical\nquote data from Yahoo and Oanda,
economic data from FRED, and xls and\ncsv data from different
sources.\nComprehensive examples of all the 'TS*' packages is provided in
0.3.1), tframe, tframePlus, zoo, xts, its,\ntseries(>= 0.10-33), quantmod (>= 0.4-
0), gdata","License":"GPL-
2","NeedsCompilation":"no","Package":"TSmisc","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"tfplot, timeSeries, tis","Title":"'TSdbi' Extensions to
Wrap Miscellaneous Data Sources","URL":"http:\/\/tsdbi.r-forge.r-
project.org\/","Version":"2015.1-3"},"TSodbc":{"Author":"Paul Gilbert
1)","Description":"An ODBC interface for 'TSdbi'.\nComprehensive examples of all
package.","Imports":"methods, DBI (>= 0.3.1), tframe, tframePlus , TSsql
(>=\n2015.1-1), RODBC (>= 0.6-0)","License":"GPL-
2","NeedsCompilation":"no","Package":"TSodbc","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"zoo, tseries, tfplot","Title":"'TSdbi' Extensions for
ODBC","URL":"http:\/\/tsdbi.r-forge.r-project.org\/","Version":"2015.4-
1"},"TSsdmx":{"Author":"Paul Gilbert <pgilbert.ttv9z@ncf.ca>","Depends":"R (>=
2.8.0), TSdbi (>= 2015.1-1)","Description":"Methods to\nretrieve data in the
Statistical Data and Metadata Exchange ('SDMX') format\nfrom several database. (For
example,\nEuroStat, the European Central Bank, the Organisation for Economic\nCo-
operation and Development, the Unesco Institute for Statistics,\nand the
International Labor Organization.)\nThis is a wrapper for package
'RJSDMX'.\nComprehensive examples of all the 'TS*' packages is provided in
0.3.1), tframe, tframePlus, RJSDMX(>= 1.3),\nrJava","License":"GPL-
2","NeedsCompilation":"no","Package":"TSsdmx","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"tfplot","Title":"'TSdbi' Extension to Connect with
'SDMX'","URL":"http:\/\/tsdbi.r-forge.r-project.org\/","Version":"2015.12-
1"},"TSsql":{"Author":"Paul Gilbert <pgilbert.ttv9z@ncf.ca>","Depends":"R (>=
2.8.0)","Description":"Standard SQL query functions used by\nSQL plugins packages
for the 'TSdbi' interface to time series databases.\nIt will mainly be used by
other packages rather than directly by end\nusers. The one exception is the
function 'TSquery' which can be used to\nconstruct a time series from a database
containing observations over\ntime (e.g. balance statements for multiple years),
but where the database\nis not specifically designed to store time series (as with
other\n'TSdbi' SQL plugin packages).\nComprehensive examples of all the 'TS*'
packages is provided in the\nvignette Guide.pdf with the 'TSdata'
package.","Imports":"methods, DBI, tframe (>= 2015.1-1), TSdbi (>= 2015.1-
1),\ntframePlus, zoo","License":"GPL-
2","NeedsCompilation":"no","Package":"TSsql","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"tseries, tis, tfplot, RMySQL, RSQLite","Title":"Generic
SQL Helper Functions for 'TSdbi' SQL Plugins","URL":"http:\/\/tsdbi.r-forge.r-
project.org\/","Version":"2015.1-2"},"TTAinterfaceTrendAnalysis":{"Author":"David
DEVREKER [aut],\nAlain LEFEBVRE [aut, cre]","Depends":"R (>= 3.0.0), base, stats,
grDevices","Description":"This interface was created to develop a standard
procedure\nto analyse temporal trend in the framework of the OSPAR convention.\nThe
analysis process run through 4 successive steps : 1) manipulate your data,
2)\nselect the parameters you want to analyse, 3) build your regulated\ntime
series, 4) perform diagnosis and analysis and 5) read the results.\nStatistical
analysis call other package function such as Kendall tests\nor cusum()
function.","Imports":"pastecs, reshape, wq, e1071, relimp, multcomp ,
nlme,\nlubridate, tcltk, tcltk2, mvtnorm","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"TTAinterfaceTrendAnalysis","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Title":"Temporal Trend Analysis Graphical
Interface","URL":"http:\/\/cran.at.r-
project.org\/package=TTAinterfaceTrendAnalysis","Version":"1.5.2"},"TTR":
{"Author":"Joshua Ulrich","Description":"Functions and data to construct technical
trading rules with R.","Enhances":"quantmod","Imports":"xts (>= 0.9-3),
2","NeedsCompilation":"yes","Package":"TTR","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"RUnit","Title":"Technical Trading
Rules","URL":"https:\/\/github.com\/joshuaulrich\/TTR","Version":"0.23-1"},"TTS":
{"Author":"Antonio Meneses <antoniomenesesfreire@hotmail.com>,\nSalvador Naya
<salva@udc.es>, Javier Tarrio-Saavedra <jtarrio@udc.es>","Depends":"R (>= 3.0.1),
mgcv, sfsmisc, splines","Description":"Time-Temperature Superposition analysis is
often applied to frequency modulated data obtained by Dynamic\nMechanic Analysis
(DMA) and Rheometry in the analytical chemistry and physics\nareas. These
techniques provide estimates of material mechanical properties\n(such as moduli) at
different temperatures in a wider range of time. This\npackage provides the Time-
Temperature superposition Master Curve at a referred\ntemperature by the three
methods: the two wider used methods, Arrhenius based\nmethods and WLF, and the
newer methodology based on derivatives procedure.\nThe Master Curve is smoothed by
B-splines basis. The package output is composed\nof plots of experimental data,
horizontal and vertical shifts, TTS data, and TTS\ndata fitted using B-splines with
bootstrap confidence intervals.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"TTS","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Master Curve Estimates Corresponding to Time-
Temperature\nSuperposition","Version":"1.0"},"TTmoment":{"Author":"Hsiu J. Ho,
Tsung-I Lin, Wan-Lun Wang, Aldo M. Garay, Victor H. Lachos, and Mauricio
Castro","Depends":"mvtnorm","Description":"Computing the first two moments of the
truncated multivariate t (TMVT) distribution under the double truncation. Appling
the slice sampling algorithm to generate random variates from the TMVT
2","NeedsCompilation":"no","Package":"TTmoment","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Sampling and Calculating the First and Second Moments for
the\nDoubly Truncated Multivariate t Distribution","Version":"1.0"},"TUWmodel":
{"Author":"Alberto Viglione [aut, cre],\nJuraj Parajka [aut]","Depends":"R (>=
3.0.0), stats","Description":"The model, developed at the Vienna University of
Technology, is a lumped conceptual rainfall-runoff model, following the structure
of the HBV model.\nThe model runs on a daily or shorter time step and consists of a
snow routine, a soil moisture routine and a flow routing routine.\nSee Parajka, J.,
R. Merz, G. Bloeschl (2007) Uncertainty and multiple objective calibration in
regional water balance modelling: case study in 320 Austrian catchments,
Hydrological Processes, 21, 435-446.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"TUWmodel","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Lumped Hydrological Model for Education
Purposes","Version":"0.1-6"},"Table1Heatmap":{"Author":"Philip C
Schouten","Depends":"colorRamps","Description":"Table 1 is the classical way to
describe the patients in a\nclinical study. The amount of splits in the data in
such a table is\nlimited. Table1Heatmap draws a heatmap of all crosstables that can
be\ngenerated with the data. Users can choose between showing the
actual\ncrosstables or direction of effect of associations, and
highlight\nassociations by number of patients or p-values.","License":"LGPL-
3","NeedsCompilation":"no","Package":"Table1Heatmap","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Table 1 Heatmap","Version":"1.1"},"TableMonster":
{"Author":"Grant Izmirlian Jr
<izmirlig@mail.nih.gov>","Depends":"xtable","Description":"Provides a user friendly
interface to generation of booktab style\ntables using xtable.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"TableMonster","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Table Monster","Version":"1.2"},"TableToLongForm":
{"Author":"Jimmy Oh [aut, cre]","Description":"TableToLongForm automatically
converts hierarchical Tables intended for a human reader into a simple LongForm
Dataframe that is machine readable.","License":"GPL-
3","NeedsCompilation":"no","Package":"TableToLongForm","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"TableToLongForm","URL":"https:\/\/www.stat.aucklan
d.ac.nz\/~joh024\/Research\/TableToLongForm\/","Version":"1.3.1"},"TaoTeProgramming
":{"Author":"Pat Burns","Description":"Art-like behavior based on
randomness","License":"Unlimited","NeedsCompilation":"no","Package":"TaoTeProgrammi
ng","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Illustrations from
Tao Te Programming","Version":"1.0"},"TapeR":{"Author":"Edgar Kublin
[aut],\nJohannes Breidenbach [ctb, cre]","Depends":"nlme, splines,
pracma","Description":"Implementation of functions for fitting taper curves (a
semiparametric linear mixed effects taper model) to diameter measurements along
stems. Further functions are provided to estimate the uncertainty around the
predicted curves, to calculate timber volume (also by sections) and marginal (e.g.,
upper) diameters. For cases where tree\nheights are not measured, methods for
estimating\nadditional variance in volume predictions resulting from uncertainties
in\ntree height models (tariffs) are provided. The example data include the taper
curve parameters for Norway spruce used in the 3rd German NFI fitted to 380 trees
and a subset of section-wise diameter measurements of these trees. The functions
implemented here are detailed in the following publication: Kublin, E.,
Breidenbach, J., Kaendler, G. (2013) A flexible stem taper and volume prediction
method based on mixed-effects B-spline regression, Eur J For Res, 132:983-
2)","NeedsCompilation":"no","Package":"TapeR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Flexible Tree Taper Curves Based on Semiparametric Mixed
Models","Version":"0.3.3"},"Tariff":{"Author":"Zehang Li, Tyler McCormick, Sam
Clark","Description":"Implement the Tariff algorithm for coding cause-of-death from
verbal autopsies. The Tariff method was originally proposed in James et al (2011)
<DOI:10.1186\/1478-7954-9-31> and later refined as Tariff 2.0 in Serina, et al.
(2015) <DOI:10.1186\/s12916-015-0527-9>. Note that this package was not developed
by authors affiliated with the Institute for Health Metrics and Evaluation and thus
unintentional discrepancies may exist between the this implementation and the
implementation available from IHME.","License":"GPL-
2","NeedsCompilation":"no","Package":"Tariff","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Replicate Tariff Method for Verbal
Autopsy","Version":"1.0.2"},"TauP.R":{"Author":"Jake Anderson, Jonathan Lees;
largely translated from the TTBOX\nMatlab toolbox by Martin
Knapmeyer\n(http:\/\/www.dr-knapmeyer.de\/downloads\/)","Description":"Evaluates
traveltimes and ray paths using predefined Earth\n(or other planet) models.
Includes phase plotting routines.\nThe IASP91 and AK135 Earth models are included,
and most\nimportant arrival phases can be
evaluated.","License":"GPL","NeedsCompilation":"no","Package":"TauP.R","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"RSEIS","Title":"Earthquake
Traveltime Calculations for 1-D Earth Models","Version":"1.1"},"TauStar":
{"Author":"Luca Weihs [aut, cre],\nEmin Martinian [ctb] (Created the red-black tree
library included in\npackage.)","Description":"Computes the t* statistic
corresponding to the tau* population\ncoefficient introduced by Bergsma and Dassios
(2014) <DOI:10.3150\/13-BEJ514>\nand does so in O(n^2*log(n)) time following the
algorithm of Weihs,\nDrton, and Leung (2016) <DOI:10.1007\/s00180-015-0639-x>. Also
allows for\nindependence testing using the asymptotic distribution of t* as
described by\nNandy, Weihs, and Drton (2016)
<http:\/\/arxiv.org\/abs\/1602.04387>.","Imports":"Rcpp (>= 0.11.4)","License":"GPL
(>=
3)","NeedsCompilation":"yes","Package":"TauStar","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat","Title":"Efficient Computation and Testing
of the Bergsma-Dassios Sign\nCovariance","Version":"1.1.0"},"Taxonstand":
{"Author":"Luis Cayuela, Jari Oksanen","Description":"Automated standardization of
taxonomic names and removal of orthographic errors in plant species names using
'The Plant List' website (www.theplantlist.org).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Taxonstand","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Taxonomic Standardization of Plant Species
Names","Version":"1.8"},"TcGSA":{"Author":"Boris P. Hejblum [aut, cre],\nDamien
Chimits [aut]","Depends":"R (>= 3.0.2), ggplot2 (>=
2.0.0)","Description":"Implementation of TcGSA, a method for analyzing
longitudinal\ngene-expression data at the gene set level.","Imports":"lme4 (>= 1.0-
4),
reshape2, GSA, multtest, gtools, cluster,\nstringr, splines, gplots, stats,
graphics, grDevices, utils","License":"GPL-2 | file
LICENSE","NeedsCompilation":"no","Package":"TcGSA","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"foreach, parallel, doParallel","Title":"Time-Course
Gene Set Analysis","Version":"0.10.1"},"TeachNet":{"Author":"Georg
Steinbuss","Depends":"methods","Description":"Can fit neural networks with up to
two hidden layer and two different error functions. Also able to handle a weight
decay. But just able to compute one output neuron and very slow.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"TeachNet","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Fits neural networks to learn about back
propagation","Version":"0.7"},"TeachingDemos":{"Author":"Greg
Snow","Description":"Demonstration functions that can be used in a classroom to
demonstrate statistical concepts, or on your own to better understand the concepts
or the programming.","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"TeachingDemos","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"tkrplot, lattice, MASS, rgl, tcltk, tcltk2,
png, ggplot2,\nlogspline, maptools, R2wd, manipulate","Title":"Demonstrations for
Teaching and Learning","Version":"2.10"},"TeachingSampling":{"Author":"Hugo Andres
Gutierrez Rojas <hugogutierrez@usantotomas.edu.co>","Depends":"R (>=
2.6.0)","Description":"Allows the user to draw probabilistic samples and make
inferences from a finite population based on several sampling
designs.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"TeachingSampling","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Selection of Samples and Parameter Estimation in
Finite\nPopulation","Version":"3.2.2"},"TestScorer":{"Author":"Manel
Salamero","Description":"GUI for entering test items and obtaining raw\nand
transformed scores. The results are shown on the\nconsole and can be saved to a
tabular text file for further\nstatistical analysis. The user can define his own
tests and\nscoring procedures through a GUI.","Imports":"tcltk,
2","NeedsCompilation":"no","Package":"TestScorer","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"GUI for Entering Test Items and Obtaining Raw and
Transformed\nScores","Version":"1.7.2"},"TestSurvRec":{"Author":"Dr. Carlos
Martinez","Depends":"survrec, boot, R(>= 3.0.2)","Description":"These are weighted
tests type logrank for recurrent events.","License":"GPL-
2","NeedsCompilation":"no","Package":"TestSurvRec","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Statistical tests to compare two survival curves with
recurrent\nevents","URL":"http:\/\/www.r-
project.org","Version":"1.2.1"},"TestingSimilarity":{"Author":"Kathrin
Moellenhoff","Description":"Provides a bootstrap test which decides whether two
dose response curves can be assumed as equal concerning their maximum absolute
deviation. A plenty of choices for the model types are available, which can be
found in the 'DoseFinding' package, which is used for the fitting of the
models.","Imports":"lattice, DoseFinding, alabama","License":"GPL-
3","NeedsCompilation":"no","Package":"TestingSimilarity","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Bootstrap Test for Similarity of Dose Response
Curves Concerning\nthe Maximum Absolute Deviation","Version":"1.0"},"TextoMineR":
{"Author":"Monica Becue-Bertaut, Daria M. Hernandez, Belchin Kostov, Josep A.
Sanchez","Depends":"FactoMineR, stringr, tm, gdata,
MASS","Description":"Multidimensional statistical methods for textual
2.0)","NeedsCompilation":"no","Package":"TextoMineR","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Textual Statistics","Version":"1.1"},"Thermimage":
{"Author":"Glenn J. Tattersall, PhD","Depends":"R (>= 2.10)","Description":"A
collection of functions and routines for inputting thermal image video files,
plotting and converting binary raw data into estimates of
temperature.","License":"GPL-
2","NeedsCompilation":"no","Package":"Thermimage","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"fields","Title":"Functions for Handling Thermal
Images","URL":"http:\/\/github.com\/gtatters\/Thermimage","Version":"1.0.1"},"Think
num":{"Author":"Gregory Ugwi","Description":"This package interacts directly with
the Thinknum API to offer data\nin a number of formats usable in
R","Imports":"RCurl, RJSONIO","License":"GPL-
2","NeedsCompilation":"no","Package":"Thinknum","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Thinknum Data
Connection","Version":"1.3.0"},"ThreeArmedTrials":{"Author":"Tobias
Muetze","Depends":"R (>= 3.0.0)","Description":"Design and analyze three-armed non-
inferiority or superiority trials which follow a gold-standard design, i.e. trials
with an experimental treatment, an active and a placebo control. The following
distribution of endpoints is covered: negative binomial
distribution.","Imports":"stats, MASS","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ThreeArmedTrials","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Design and Analysis of Clinical Non-inferiority
or Superiority\nTrials with Active and Placebo Control","Version":"0.1-
0"},"ThreeGroups":{"Author":"Holger L. Kern [aut]","Description":"Implements the
Maximum Likelihood estimator for baseline, placebo, and treatment groups (three-
group) experiments with non-compliance proposed by Gerber, Green, Kaplan, and Kern
(2010).","Imports":"stats","License":"GPL-
2","NeedsCompilation":"no","Package":"ThreeGroups","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"ML Estimator for Baseline-Placebo-Treatment (Three-
Group)\nExperiments","Version":"0.21"},"ThreeWay":{"Author":"Maria Antonietta Del
Ferraro, Henk A.L. Kiers, Paolo Giordani","Depends":"R(>= 2.8.1), base, stats,
graphics, grDevices","Description":"Component analysis for three-way data arrays by
means of Candecomp\/Parafac, Tucker3, Tucker2 and Tucker1 models.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"ThreeWay","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Three-Way Component
Analysis","Version":"1.1.3"},"ThresholdROC":{"Author":"Sara Perez-Jaume, Natalia
Pallares, Konstantina Skaltsa","Depends":"R (>= 3.1.0), MASS, numDeriv,
pROC","Description":"Point and interval estimations of optimum thresholds for
continuous diagnostic tests (two- and three- state settings).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ThresholdROC","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Threshold Estimation","Version":"2.3"},"TickExec":
{"Author":"HKUST","Description":"Functions to execute orders in backtesting using
tick data. A testing platform was established by the four major execution
functions, namely 'LimitBuy', 'LimitSell', 'MarketBuy' and 'MarketSell', which
enclosed all tedious aspects (such as queueing for order executions and calculate
actual executed volumes) for order execution using tick data. Such that one can
focus on the logic of strategies, rather than its execution.","License":"GPL-
3","NeedsCompilation":"no","Package":"TickExec","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Execution Functions for Tick Data Back
Test","Version":"1.1"},"TiddlyWikiR":{"Author":"David Montaner
<dmontaner@cipf.es>","Depends":"R (>= 2.14),","Description":"Utilities to generate
wiki reports in TiddlyWiki format.","Imports":"methods","License":"GPL-
2","NeedsCompilation":"no","Package":"TiddlyWikiR","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr","Title":"Create dynamic reports using a
TiddlyWiki
template","URL":"https:\/\/github.com\/dmontaner\/TiddlyWikiR","Version":"1.0.1"},"
TideCurves":{"Author":"Moritz Mueller-Navarra [aut, cre], Sylvin Mueller-Navarra
[aut]","Depends":"R (>= 3.2.2)","Description":"Tidal analysis of evenly spaced
observed time series (time step 1 to 60 min) with or\nwithout shorter gaps.\nThe
analysis should preferably cover an observation period of at least 19 years.\nFor
shorter periods low frequency constituents are not taken into account, in
accordance with the Rayleigh-Criterion.\nThe main objective of this package is to
synthesize or predict a tidal time series.","Imports":"chron (>= 2.3-47),
data.table (>= 1.9.6), fields (>= 8.3-6)","License":"GPL-
3","NeedsCompilation":"no","Package":"TideCurves","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Analysis and Prediction of
Tides","Version":"0.0.1"},"TideHarmonics":{"Author":"Alec Stephenson.","Depends":"R
(>= 2.10)","Description":"Implements harmonic analysis of tidal and sea-level
data.\nOver 400 harmonic tidal constituents can be estimated, all with\ndaily nodal
corrections. Time-varying mean sea-levels can also\nbe
used.","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"TideHarmonics","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Title":"Harmonic Analysis of Tides","Version":"0.1-
0"},"TideTables":{"Author":"Moritz Mueller-Navarra [aut, cre],\nSylvin Mueller-
Navarra [aut]","Depends":"R (>= 3.2.2)","Description":"Tide analysis and prediction
of predominantly semi-diurnal tides\nwith two high waters and two low waters during
one lunar day (~24.842 hours,\n~1.035 days). The analysis should preferably cover
an observation period of at\nleast 19 years. For shorter periods, for example, the
nodal cycle can not be\ntaken into account, which particularly affects the height
calculation. The main\nobjective of this package is to produce tide
tables.","Imports":"chron (>= 2.3-47), data.table (>= 1.9.6)","License":"GPL-
3","NeedsCompilation":"no","Package":"TideTables","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Tide Analysis and Prediction of Predominantly Semi-
Diurnal Tides","Version":"0.0.1"},"Tides":{"Author":"Tom Cox
<tom.cox@uantwerp.be>","Depends":"R
(>= 2.10)","Description":"Calculate Characteristics of Qasi-Periodic Time Series,
e.g. Estuarine Water
Levels.","License":"GPL","NeedsCompilation":"no","Package":"Tides","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"Quasi-Periodic Time Series
Characteristics","Version":"1.1"},"TilePlot":{"Author":"Ian
Marshall","Description":"This package is intended for processing the output
from\nfunctional gene tiling DNA microarray experiments. It produces\nhybridization
pattern plots for each gene on the array, and\nstatistics for each gene including
mean probe intensity, median\nprobe intensity, bright probe fraction, bright
segment length\ndependent score, bright probe mean intensity, and bright
probe\nmedian intensity. Output is generated in order of bright\nsegment length
dependent score in both a latex\/eps format and\ntab-delimited text file. The
package works in two modes: single\narray, and comparison of two arrays. Array
comparison includes\narray comparison statistics: median of logarithm of one
array\nprobe divided by its counterpart on the other array, median\nabsolute
deviation of that value, and the binomial test to see\nwhether the genes are
equally abundant in both arrays.","License":"GPL-
2","NeedsCompilation":"no","Package":"TilePlot","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Characterization of functional genes in complex
microbial\ncommunities using tiling DNA
microarrays","Version":"1.3.1"},"TimeMachine":{"Author":"Gianluca Campanella [aut,
cre],\nMarc Chadeau-Hyam [aut],\nMaria De Iorio [ctb],\nAjay Jasra
[ctb]","Depends":"R (>= 2.15), methods","Description":"Implements the Time Machine,
a simulation approach for stochastic\ntrees.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"TimeMachine","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Time Machine","Version":"1.2"},"TimeProjection":
{"Author":"Jeffrey Wong","Depends":"lubridate, timeDate,
Matrix","Description":"Extract useful time components of a date object, such
as\nday of week, weekend, holiday, day of month, etc, and put it in\na data frame.
This can be used to create many predictor\nvariables out of a single time variable,
which can then be used\nin a regression or decision tree. Also includes
function\nplotCalendarHeatmap which draws a calendar and overlays a\nheatmap based
on values.","License":"GPL-
3","NeedsCompilation":"no","Package":"TimeProjection","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat, roxygen2, ggplot2, plyr","Title":"Time
Projections","URL":"https:\/\/github.com\/jeffwong\/TimeProjection","Version":"0.2.
0"},"TimeWarp":{"Author":"Tony Plate, Jeffrey Horner, Lars Hansen","Depends":"R (>=
2.6)","Description":"Date sequence, relative date calculations, and date
manipulation with business days\nand holidays. Works with Date and POSIXt
classes.","License":"GPL","NeedsCompilation":"no","Package":"TimeWarp","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"scriptests,
Holidays","Title":"Date Calculations and
Manipulation","Version":"1.0.12"},"Tinflex":{"Author":"Josef Leydold, Carsten Botts
and Wolfgang H\\\"ormann","Description":"A universal non-uniform random number
generator\nfor quite arbitrary distributions with piecewise twice\ndifferentiable
densities.","Imports":"graphics, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"Tinflex","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"Runuran, rvgtest","Title":"Tinflex - Universal Non-
Uniform Random Number Generator","Version":"1.1"},"TipDatingBeast":
{"Author":"Adrien Rieux, Camilo Khatchikian","Depends":"R (>=
3.1.2)","Description":"Assist performing tip-dating of phylogenetic trees with
BEAST.","Imports":"mclust, utils, stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"TipDatingBeast","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Using Tip Dates with Phylogenetic Trees in
BEAST","URL":"http:\/\/www.r-project.org","Version":"0.1-6"},"Tmisc":
{"Author":"Stephen Turner <vustephen@gmail.com>","Depends":"R (>=
3.0.0)","Description":"Miscellaneous data and utility functions\nfor manipulating
data and your R environment.","Imports":"dplyr, utils","License":"GPL-
3","NeedsCompilation":"no","Package":"Tmisc","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Turner Miscellaneous","Version":"0.1.5"},"TopKLists":
{"Author":"Michael G. Schimek, Eva Budinska, Jie Ding, Karl G. Kugler, Vendula
Svendova, Shili Lin","Depends":"R (>= 3.0.0)","Description":"For multiple ranked
input lists (full or partial) representing the same set of N objects, the package
TopKLists offers (1) statistical inference on the lengths of informative top-k
lists, (2) stochastic aggregation of full or partial lists, and (3) graphical tools
for the statistical exploration of input lists, and for the visualization of
aggregation results.","Imports":"Hmisc,grid,gplots","License":"LGPL-
3","NeedsCompilation":"yes","Package":"TopKLists","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr,RGtk2,gWidgets2,gWidgetsRGtk2","Title":"Infere
nce, Aggregation and Visualization for Top-K Ranked
Lists","URL":"http:\/\/topklists.r-forge.r-
project.org","Version":"1.0.6"},"TotalCopheneticIndex":{"Author":"Martin R.
Smith","Description":"Quantifies how balanced a phylogenetic tree is, using the
Total Cophenetic Index\n- per A. Mir, F. Rossello, L. A. Rotger (2013), A new
balance index for phylogenetic trees.\nMath. Biosci. 241, 125-136
<DOI:10.1016\/j.mbs.2012.10.005>.","Imports":"ape","License":"Unlimited","NeedsComp
ilation":"no","Package":"TotalCopheneticIndex","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Total Cophenetic
Index","URL":"https:\/\/github.com\/ms609\/tci","Version":"0.1"},"TraMineR":
{"Author":"Alexis Gabadinho [aut, cph],\nMatthias Studer [aut, cph],\nNicolas
Muller [aut],\nReto Buergin [aut],\nGilbert Ritschard [aut, cre, cph]","Depends":"R
(>= 2.8.1),","Description":"Toolbox for the manipulation, description and rendering
of sequences, and more generally the mining of sequence data in the field of social
sciences. Although the toolbox is primarily intended for analyzing state or event
sequences that describe life courses such as family formation histories or
professional careers, its features also apply to many other kinds of categorical
sequence data. It accepts many different sequence representations as input and
provides tools for converting sequences from one format to another. It offers
several functions for describing and rendering sequences, for computing distances
between sequences with different metrics (among which optimal matching), original
dissimilarity-based analysis tools, and simple functions for extracting the most
frequent subsequences and identifying the most discriminating ones among them. A
user's guide can be found on the TraMineR web page.","Imports":"utils,
RColorBrewer, boot, graphics, grDevices, stats, Hmisc","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"TraMineR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"cluster, xtable","Title":"Trajectory Miner: a
Toolbox for Exploring and
Rendering\nSequences","URL":"http:\/\/mephisto.unige.ch\/traminer","Version":"1.8-
11.1"},"TraMineRextras":{"Author":"Gilbert Ritschard [aut, cre, ths,
cph],\nMatthias Studer [aut],\nReto Buergin [aut],\nAlexis Gabadinho
[ctb],\nNicolas Muller [ctb],\nPatrick Rousset [ctb]","Depends":"R (>= 2.8.1),
TraMineR (>= 1.8-9), RColorBrewer, survival,\ncluster","Description":"Collection of
ancillary functions and utilities to be used in conjunction with the TraMineR
package for sequence data exploration. Most of the functions are in test phase,
lack systematic consistency check of the arguments and are subject to changes. Once
fully checked, some of the functions of this collection could be included in a next
release of TraMineR.","Imports":"combinat, grDevices, graphics,
2)","NeedsCompilation":"yes","Package":"TraMineRextras","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"TraMineR
Extension","URL":"http:\/\/traminer.unige.ch\/","Version":"0.2.4"},"TrackReconstruc
tion":{"Author":"Brian Battaile","Depends":"R(>= 2.10.0), fields,
RColorBrewer","Description":"Reconstructs animal tracks from magnetometer,
accelerometer, depth and optional speed data. Designed primarily using data from
Wildlife Computers Daily Diary tags deployed on northern fur seals.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"TrackReconstruction","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Suggests":"lattice, onion, plotrix, rgl,
scatterplot3d","Title":"Reconstruct animal tracks from magnetometer,
accelerometer,\ndepth and optional speed data","Version":"1.1"},"Traitspace":
{"Author":"Chaitanya Joshi, Xin Li, Daniel Laughlin","Depends":"permute, mclust,
graphics, grDevices, stats, utils","Description":"Implements a predictive model of
community assembly called 'Traitspace' (Laughlin et al. 2012, Ecology Letters).
Traitspace is a hierarchical Bayesian model that translates the theory of trait-
based environmental filtering into a statistical model that incorporates
intraspecific trait variation to predict the relative abundances and the
distributions of species.\nThe package includes functions to plot the predicted and
the observed values. It also includes functions to compare the predicted values
against the observed values using a variety of different distance measures and to
implement permutation tests to test their statistical significance.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"Traitspace","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"A Predictive Model for Trait Based Community Assembly
of Plant\nSpecies","Version":"1.1"},"TransModel":{"Author":"Jie Zhou, Jiajia Zhang,
Wenbin Lu","Depends":"stats,graphics,survival","Description":"A unified
estimation procedure for the analysis of censored data using linear transformation
models.","License":"GPL-
2","NeedsCompilation":"no","Package":"TransModel","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Fit Linear Transformation Models for Censored
Data","Version":"1.0"},"TransP":{"Author":"Somenath
Sit","Description":"Implementation of two transportation problem algorithms.\n1.
North West Corner Method\n2. Minimum Cost Method or Least cost method.\nFor more
technical details about the algorithms please refer below
URLs.\n<http:\/\/www.universalteacherpublications.com\/univ\/ebooks\/or\/Ch5\/nw.ht
m>.\n<http:\/\/personal.maths.surrey.ac.uk\/st\/J.F\/chapter7.pdf>.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"TransP","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Implementation of Transportation Problem
Algorithms","URL":"https:\/\/github.com\/Somenath24\/TransP","Version":"0.1"},"Tran
sferEntropy":{"Author":"ANN Library: David Mount, Sunil Arya (see
src\/ann_1.1.2\/Copyright.txt).\nTransfer Entropy Packge: Ghazaleh Haratinezhad
Torbati, Glenn Lawyer.","Depends":"R (>= 3.0.0)","Description":"Estimates the
transfer entropy from one time series to another, where each time series consists
of continuous random variables. The transfer entropy is an extension of mutual
information which takes into account the direction of information flow, under the
assumption that the underlying processes can be described by a Markov model. Two
estimation methods are provided. The first calculates transfer entropy as the
difference of mutual information. Mutual information is estimated using the Kraskov
method, which builds on a nearest-neighbor framework (see package references). The
second estimation method estimate transfer entropy via the a generalized
correlation sum.","Imports":"Rcpp (>= 0.11.6)","License":"GPL (>= 2) | file
LICENSE","NeedsCompilation":"yes","Package":"TransferEntropy","Repository":"http:\/
\/cran.csiro.au\/src\/contrib","Title":"The Transfer Entropy
Package","URL":"https:\/\/github.com\/Healthcast\/TransEnt","Version":"1.2"},"Treat
mentSelection":{"Author":"Marshall Brown and Holly Janes","Description":"Evaluate
the performance of markers used to guide treatment selection decisions. Package
includes functions to plot risk curves, evaluate marker performance, assess model
calibration, and compare markers.","Imports":"ggplot2","License":"GPL-
2","NeedsCompilation":"no","Package":"TreatmentSelection","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Evaluate Treatment Selection
Biomarkers","URL":"http:\/\/mdbrown.github.io\/TreatmentSelection\/","Version":"1.2
.0"},"TreePar":{"Author":"Tanja Stadler","Depends":"ape, Matrix, subplex, TreeSim
(>= 2.1), deSolve","Description":"(i) For a given species phylogeny on present day
data which is calibrated to calendar-time, a method for estimating maximum
likelihood speciation and extinction processes is provided. The method allows for
non-constant rates. Rates may change (1) as a function of time, i.e. rate shifts at
specified times or mass extinction events (likelihood implemented as LikShifts,
optimization as bd.shifts.optim and visualized as bd.shifts.plot) or (2) as a
function of the number of species, i.e. density-dependence (likelihood implemented
as LikDD and optimization as bd.densdep.optim) or (3) extinction rate may be a
function of species age (likelihood implemented as LikAge and optimization as
bd.age.optim.matlab). Note that the methods take into account the whole phylogeny,
in particular it accounts for the \"pull of the present\" effect. (1-3) can take
into account incomplete species sampling, as long as each species has the same
probability of being sampled. For a given phylogeny on higher taxa (i.e. all but
one species per taxa are missing), where the number of species is known within each
higher taxa, speciation and extinction rates can be estimated under model (1)
(implemented within LikShifts and bd.shifts.optim with groups !=0). (ii) For a
given phylogeny with sequentially sampled tips, e.g. a virus phylogeny, rates can
be estimated under a model where rates vary across time using bdsky.stt.optim based
on likelihood LikShiftsSTT (extending LikShifts and bd.shifts.optim). Furthermore,
rates may vary as a function of host types using LikTypesSTT (multitype branching
process extending functions in R package diversitree). This function can
furthermore calculate the likelihood under an epidemiological model where infected
individuals are first exposed and then infectious.","License":"GPL-
2","NeedsCompilation":"no","Package":"TreePar","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Estimating birth and death rates based on
phylogenies","Version":"3.3"},"TreeSim":{"Author":"Tanja Stadler","Depends":"ape,
laser, geiger","Description":"Simulation methods for phylogenetic trees where (i)
all tips are sampled at one time point or (ii) tips are sampled sequentially
through time. (i) For sampling at one time point, simulations are performed under a
constant rate birth-death process, conditioned on having a fixed number of final
tips (sim.bd.taxa()), or a fixed age (sim.bd.age()), or a fixed age and number of
tips (sim.bd.taxa.age()). When conditioning on the number of final tips, the method
allows for shifts in rates and mass extinction events during the birth-death
process (sim.rateshift.taxa()). The function sim.bd.age() (and sim.rateshift.taxa()
without extinction) allow the speciation rate to change in a density-dependent way.
The LTT plots of the simulations can be displayed using LTT.plot(), LTT.plot.gen()
and LTT.average.root(). TreeSim further samples trees with n final tips from a set
of trees generated by the common sampling algorithm stopping when a fixed number
m>>n of tips is first reached (sim.gsa.taxa()). This latter method is appropriate
for m-tip trees generated under a big class of models (details in the
sim.gsa.taxa() man page). For incomplete phylogeny, the missing speciation events
can be added through simulations (corsim()). (ii) sim.rateshifts.taxa() is
generalized to sim.bdsky.stt() for serially sampled trees, where the trees are
conditioned on either the number of sampled tips or the age. Furthermore, for a
multitype-branching process with sequential sampling, trees on a fixed number of
tips can be simulated using sim.bdtypes.stt.taxa(). This function further allows to
simulate under epidemiological models with an exposed class. The function
sim.genespeciestree() simulates coalescent gene trees within birth-death species
trees, and sim.genetree() simulates coalescent gene trees.","License":"GPL-
2","NeedsCompilation":"no","Package":"TreeSim","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Simulating Phylogenetic
Trees","Version":"2.2"},"TreeSimGM":{"Author":"Oskar Hagen, Tanja
Stadler","Depends":"TreeSim","Description":"The package is a flexible simulation
tool for phylogenetic trees under a general model. It is possible to assume any
probability distribution for the waiting time until speciation and extinction
independently. Thus, TreeSimGM allows to simulate stochastic phylogenetic trees
using any probability distribution and parameters for speciation and extinction.
The speciation modes have all binary splits and are: (i) symmetric, where for every
speciation event new waiting times until speciation and extinction are drawn for
both daughter lineages; and (ii) asymmetric, where a speciation event results in
one species with new waiting times, and another that carries the extinction time
and age of its ancestor. Those two modes were inspired by allopatric and peripatric
speciation respectively.Both models (symmetric and asymmetric) were created and
implemented so that different processes (distributions) for speciation and
extinction could be independently and explicitly specified. It is also possible to
have an implicit extinction process by setting the extinction rate to
zero.","License":"GPL-
2","NeedsCompilation":"no","Package":"TreeSimGM","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Simulating Phylogenetic Trees under a General
Model","Version":"1.2"},"TriMatch":{"Author":"Jason Bryer
<jason@bryer.org>","Depends":"ggplot2, scales, reshape2, ez, R (>=
3.0)","Description":"Propensity score matching for non-binary
treatments.","Imports":"psych, stats, PSAgraphics, compiler, grid,
gridExtra","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"TriMatch","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"MASS, xtable","Title":"Propensity Score Matching of
Non-Binary Treatments","URL":"http:\/\/jason.bryer.org\/TriMatch,
http:\/\/github.com\/jbryer\/TriMatch","Version":"0.9.7"},"TrialSize":{"Author":"Ed
Zhang ; Vicky Qian Wu ; Shein-Chung Chow ; Harry G.Zhang\n(Quality check)
<ed.zhang.jr@gmail.com>","Description":"functions and examples in Sample Size
Calculation in\nClinical Research.","License":"GPL (>=
2.15.1)","NeedsCompilation":"yes","Package":"TrialSize","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"R functions in Chapter
3,4,6,7,9,10,11,12,14,15","Version":"1.3"},"TripleR":{"Author":"F. D. SchÃ¶nbrodt,
M. D. Back, S. C. Schmukle","Depends":"ggplot2 (>= 0.9.3)","Description":"Social
Relation Model (SRM) analyses for single or multiple\nround-robin groups are
performed. These analyses are either based on one\nmanifest variable, one latent
construct measured by two manifest variables,\ntwo manifest variables and their
bivariate relations, or two latent\nconstructs each measured by two manifest
variables. Within-group t-tests\nfor variance components and covariances are
provided for single groups.\nFor multiple groups two types of significance tests
are provided:\nbetween-groups t-tests (as in SOREMO) and enhanced standard errors
based on\nLashley and Bond (1997) <DOI:10.1037\/1082-989X.2.3.278>. Handling for
missing
values is provided.","Imports":"reshape2, plyr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"TripleR","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"lme4","Title":"Social Relation Model (SRM) Analyses
for Single or Multiple\nGroups","Version":"1.5.1"},"TruncatedNormal":
{"Author":"Zdravko I. Botev","Depends":"randtoolbox","Description":"A collection of
functions to deal with the truncated univariate and multivariate normal
distributions.","License":"GPL-
3","NeedsCompilation":"no","Package":"TruncatedNormal","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Truncated Multivariate
Normal","Version":"1.0"},"Tsphere":{"Author":"Genevera I. Allen","Depends":"glasso,
rms","Description":"Adjusts for correlations among the rows and columns via\nthe
Transposable Sphering Algorithm when conducting large-scale\ninference on the rows
of a data matrix.","License":"GPL-
2","NeedsCompilation":"no","Package":"Tsphere","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Transposable Sphering for Large-Scale Inference with
Correlated\nData","URL":"http:\/\/www.stat.rice.edu\/~gallen\/","Version":"1.0"},"T
ukeyC":{"Author":"José Cláudio Faria <joseclaudio.faria@gmail.com>\nEnio G.
Jelihovschi <eniojelihovs@gmail.com>\nIvan Bezerra Allaman
<ivanalaman@gmail.com>","Depends":"R (>= 2.6.0), base","Description":"Perform the
conventional Tukey test from aov and aovlist\nobjects","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"TukeyC","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Conventional Tukey Test","Version":"1.1-5"},"TunePareto":
{"Author":"Christoph MÃ¼ssel, Ludwig Lausser, Hans Kestler","Description":"Generic
methods for parameter tuning of classification algorithms using multiple scoring
functions","License":"GPL-
2","NeedsCompilation":"yes","Package":"TunePareto","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"snowfall, desire, igraph, gsl, class, tree,
e1071,\nrandomForest, klaR","Title":"Multi-objective parameter tuning for
classifiers","Version":"2.4"},"TurtleGraphics":{"Author":"Anna Cena [aut],\nMarek
Gagolewski [aut],\nMarcin Kosinski [aut],\nNatalia Potocka [aut],\nBarbara Zogala-
Siudem [aut, cre]","Depends":"R (>= 3.0), grid","Description":"An implementation of
turtle graphics\n(http:\/\/en.wikipedia.org\/wiki\/Turtle_graphics) in R.\nTurtle
graphics comes from Papert's language Logo and has\nbeen used to teach concepts of
computer programming.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"TurtleGraphics","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"knitr","Title":"Turtle graphics in
R","URL":"http:\/\/TurtleGraphics.rexamine.com","Version":"1.0-5"},"TwoCop":
{"Author":"Bruno Remillard and Jean-Francois Plante","Description":"This package
implements the nonparametric test of equality\nbetween two copulas proposed by
Remillard and Scaillet in their\n2009 JMVA paper.","License":"GPL-
2","NeedsCompilation":"yes","Package":"TwoCop","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Nonparametric test of equality between two
copulas","Version":"1.0"},"TwoPhaseInd":{"Author":"James Dai [aut, cre],\nXiaoyu
Wang [aut]","Description":"Estimation of gene-treatment interactions in randomized
clinical trials exploiting gene-treatment
independence.","Imports":"survival","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"TwoPhaseInd","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Estimate Gene-Treatment Interaction Exploiting
Randomization","Version":"1.1.1"},"TwoStepCLogit":{"Author":"Radu V. Craiu, Thierry
Duchesne, Daniel Fortin and Sophie Baillargeon","Description":"Conditional logistic
regression with longitudinal follow up and\nindividual-level random coefficients: A
stable and efficient\ntwo-step estimation method.","Imports":"survival,
2","NeedsCompilation":"no","Package":"TwoStepCLogit","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Conditional Logistic Regression: A Two-Step
Estimation Method","Version":"1.2.5"},"UBCRM":{"Author":"Benjamin Esterni with
contribution from Baboukar Mane","Description":"Two Phase I designs are implemented
in the package: the classical 3+3 and the Continual Reassessment Method.
Simulations tools are also available to estimate the operating characteristics of
the methods with several user-dependent options.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"UBCRM","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Functions to Simulate and Conduct Dose-Escalation Phase
I\nStudies","Version":"1.0.1"},"UNF":{"Author":"Thomas Leeper [aut, cre],\nMicah
Altman [aut]","Depends":"R (>= 2.0)","Description":"Computes a universal numeric
fingerprint (UNF) for an R data object. UNF is a cryptographic hash or signature
that can be used to uniquely identify (a version of) a rectangular dataset, or a
subset thereof. UNF can be used, in tandem with a DOI, to form a persistent
citation to a versioned dataset.","Imports":"base64enc, digest,
tools","License":"GPL-
2","NeedsCompilation":"no","Package":"UNF","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"knitr, testthat","Title":"Tools for Creating Universal
Numeric Fingerprints for
Data","URL":"https:\/\/github.com\/leeper\/UNF","Version":"2.0.1"},"UPMASK":
{"Author":"Alberto Krone-Martins, Andre Moitinho","Depends":"R (>=
3.0)","Description":"An implementation of the UPMASK method for performing
membership\nassignment in stellar clusters in R. It is prepared to use photometry
and\nspatial positions, but it can take into account other types of data.
The\nmethod is able to take into account arbitrary error models, and it
is\nunsupervised, data-driven, physical-model-free and relies on as
few\nassumptions as possible. The approach followed for membership assessment
is\nbased on an iterative process, principal component analysis, a
clustering\nalgorithm and a kernel density estimation.","Imports":"parallel, MASS,
RSQLite, DBI","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"UPMASK","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Unsupervised Photometric Membership Assignment in
Stellar\nClusters","Version":"1.0"},"USAboundaries":{"Author":"Lincoln Mullen [aut,
cre],\nDr. William M. Scholl Center for American History and Culture, The\nNewberry
Library [cph],\nUnited States Census Bureau [cph]","Depends":"R (>=
3.1.1)","Description":"The boundaries for geographical units in the United States
of\nAmerica contained in this package include state, county,
congressional\ndistrict, and zip code tabulation area. Contemporary boundaries are
provided\nby the U.S. Census Bureau (public domain). Historical boundaries for
the\nyears from 1629 to 2000 are provided form the Newberry Library's 'Atlas
of\nHistorical County Boundaries' (licensed CC BY-NC-SA). Additional
high\nresolution data is provided in the 'USAboundariesData' package;\nthis package
provides an interface to access that data.","Imports":"sp (>=
1.0.15)","License":"CC BY-NC-SA
4.0","NeedsCompilation":"no","Package":"USAboundaries","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"USAboundariesData (>= 0.2.0), knitr, testthat
(>= 0.9.1)","Title":"Historical and Contemporary Boundaries of the United States
of\nAmerica","URL":"https:\/\/github.com\/ropensci\/USAboundaries","Version":"0.2.0
"},"UScancer":{"Author":"Jonathan Lee","Depends":"R (>= 3.0.0),
rgdal","Description":"This package contains functions to read cancer data from SEER
(http:\/\/seer.cancer.gov\/) and IARC (http:\/\/www.iarc.fr) to create datasets at
the county level based on US census information.","License":"GPL-
2","NeedsCompilation":"no","Package":"UScancer","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"diseasemapping","Title":"Create US cancer datasets
from SEER, IARC, and US Census data","Version":"0.1-2"},"UScensus2000cdp":
{"Author":"Zack W. Almquist <almquist@uci.edu>","Depends":"R (>= 2.10), maptools,
sp, foreign, methods, grDevices, base,\nstats, utils","Description":"US Census 2000
Designated Places shapefiles and additional\ndemographic data from the SF1 100
percent files. This data set\ncontains polygon files in lat\/lon coordinates and
the\ncorresponding demographic data for a number of
different\nvariables.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"UScensus2000cdp","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"US Census 2000 Designated Places Shapefiles and
Additional\nDemographic
Data","URL":"http:\/\/disasternets.calit2.uci.edu\/census2000\/","Version":"0.03"},
"UScensus2000tract":{"Author":"Zack W. Almquist <almquist@uci.edu>","Depends":"R
(>= 2.10), maptools, sp, foreign, methods, grDevices, base,\nstats,
utils","Description":"US 2000 Census Tract shapefiles and additional
demographic\ndata from the SF1 100 percent files. This data set contains\npolygon
files in lat\/lon coordinates and the corresponding\ndemographic data for a number
of different variables.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"UScensus2000tract","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"US Census 2000 Tract Level Shapefiles and
Additional
Demographic\nData","URL":"http:\/\/disasternets.calit2.uci.edu\/census2000\/","Vers
ion":"0.03"},"UScensus2010":{"Author":"Zack W. Almquist
<almquist@uci.edu>","Depends":"R (>= 2.10), maptools, sp, foreign, methods,
grDevices, base,\nstats, utils","Description":"US Census 2010 shape files and
additional demographic data\nfrom the SF1 100 percent files. This package contains
a number\nof helper functions for the UScensus2010blk,\nUScensus2010blkgrp,
UScensus2010tract, UScensus2010cdp\npackages.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"UScensus2010","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"rgdal,gpclib","Title":"US Census 2010 Suite of R
Packages","URL":"http:\/\/www.ncasd.org\/census2000\/","Version":"0.11"},"UWHAM":
{"Author":"Zhiqiang
Tan and Emilio Gallicchio","Depends":"R (>= 2.9.1), trust","Description":"A method
for estimating log-normalizing constants (or free\nenergies) and expectations from
multiple distributions (such as\nmultiple generalized ensembles).","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"UWHAM","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Unbinned weighted histogram analysis method
(UWHAM)","URL":"http:\/\/www.stat.rutgers.edu\/~ztan,
http:\/\/hpcp.rutgers.edu\/~emilio","Version":"1.0"},"Ultimixt":{"Author":"Kaniav
Kamary, Kate Lee","Depends":"coda, gtools, graphics, grDevices,
stats","Description":"A generic reference Bayesian analysis of unidimensional
mixtures of Gaussian distributions obtained by a location-scale parameterisation of
the model is implemented. Included functions can be applied to produce a Bayesian
analysis of Gaussian mixtures with an arbitrary number of components, with no need
to define the prior distribution.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"Ultimixt","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Bayesian Analysis of a Non-Informative Parametrization
for\nGaussian Mixture Distributions","Version":"2.0"},"UncerIn2":{"Author":"Tomas
Burian <Buri777@seznam.cz>","Depends":"R (>= 3.0.0), sp, RandomFields, automap,
fields, gstat","Description":"Provides a basic (random) data, grids, 6 models of
uncertainty, 3 automatic interpolations (idw, spline, kriging), variogram and basic
data visualization.","Imports":"geoR, methods, stats, Rcpp, utils","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"UncerIn2","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Implements Models of Uncertainty into the
Interpolation\nFunctions","Version":"2.0"},"Unicode":{"Author":"Kurt Hornik [aut,
cre]","Depends":"R (>= 2.10.0)","Description":"Data from Unicode 8.0.0 and related
utilities.","Imports":"utils","License":"GPL-
2","NeedsCompilation":"no","Package":"Unicode","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Unicode Data and Utilities","Version":"8.0.0-1"},"UpSetR":
{"Author":"Jake Conway [cre],\nNils Gehlenborg [aut]","Depends":"R (>=
3.0)","Description":"Creates visualizations of intersecting sets using a novel
matrix\ndesign, along with visualizations of several common set, element and
attribute\nrelated tasks.","Imports":"ggplot2, gridExtra, plyr, utils, stats,
methods, grDevices","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"UpSetR","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"knitr","Title":"A More Scalable Alternative to
Venn and Euler Diagrams for\nVisualizing Intersecting
Sets","URL":"http:\/\/github.com\/hms-dbmi\/UpSetR","Version":"1.2.0"},"UsingR":
{"Author":"John Verzani <verzani@math.csi.cuny.edu>","Depends":"R (>= 2.15.0),
MASS, HistData, Hmisc","Description":"A collection of data sets to accompany
the\ntextbook \"Using R for Introductory Statistics,\"
second\nedition.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"UsingR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"zoo, coin, ggplot2, vcd, lubridate,
aplpack","Title":"Data Sets, Etc. for the Text \"Using R for
Introductory\nStatistics\", Second Edition","Version":"2.0-5"},"V8":
{"Author":"Jeroen Ooms","Description":"An R interface to Google's open source
JavaScript engine.\nV8 is written in C++ and implements ECMAScript as specified in
ECMA-262,\n5th edition. In addition, this package implements typed arrays
as\nspecified in ECMA 6 used for high-performance computing and libraries\ncompiled
with 'emscripten'.","Imports":"Rcpp (>= 0.12), jsonlite (>= 0.9.14), curl (>= 0.5),
LICENSE","NeedsCompilation":"yes","Package":"V8","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat, knitr, rmarkdown","Title":"Embedded
JavaScript Engine for
R","URL":"https:\/\/github.com\/jeroenooms\/v8,\nhttps:\/\/developers.google.com\/v
8\/intro","Version":"1.0.1"},"VAR.etp":{"Author":"Jae. H.
Kim","Description":"Estimation, Hypothesis Testing, Prediction for Stationary
Vector Autoregressive Models","License":"GPL-
2","NeedsCompilation":"no","Package":"VAR.etp","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"VAR modelling: estimation, testing, and
prediction","Version":"0.7"},"VARSEDIG":{"Author":"Cástor Guisande
González","Depends":"R (>= 3.1.1), adehabitatHS, kulife, MASS, car, stats,
utils,\ngrDevices, graphics, ade4","Description":"An algorithm which identifies the
morphometric features that significantly discriminate two taxa and validates the
morphological distinctness between them via a Monte-Carlo test, polar coordinates
and overlap of the area under the density
curve.","Imports":"IDPmisc","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"VARSEDIG","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"An Algorithm for Morphometric Characters Selection
and\nStatistical Validation in Morphological Taxonomy","Version":"1.1"},"VARsignR":
{"Author":"Christian Danne [aut, cre]","Depends":"R (>=
3.2)","Description":"Provides routines for identifying structural shocks in vector
autoregressions (VARs) using sign restrictions.","Imports":"HI, minqa, mvnfast,
utils, stats, methods, grDevices, graphics","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"VARsignR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr","Title":"Sign Restrictions, Bayesian, Vector
Autoregression Models","Version":"0.1.3"},"VBLPCM":{"Author":"Michael Salter-
Townshend","Depends":"ergm, network","Description":"Fit and simulate latent
position and cluster\nmodels for network data, using a fast Variational Bayes
approximation.","Imports":"mclust, sna","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"VBLPCM","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Variational Bayes Latent Position Cluster Model for
Networks","URL":"http:\/\/www.r-
project.org,\nhttps:\/\/sites.google.com\/site\/mikesaltertownshend\/software\/","V
ersion":"2.4.4"},"VCA":{"Author":"Andre Schuetzenmeister
<andre.schuetzenmeister@roche.com>","Depends":"R (>= 3.0.0)","Description":"\nANOVA
and REML estimation of linear mixed models is implemented, once following\nSearle
et al. (1991, ANOVA for unbalanced data), once making use of the 'lme4'
package.\nThe primary objective of this package is to a perform variance component
analysis (VCA)\naccording to CLSI EP05-A3 guideline \"Evaluation of Precision of
Quantitative Measurement\nProcedures\" (2014). There are plotting methods for
visualization of an experimental design,\nplotting random effects and residuals.
For ANOVA type estimation two methods for computing\nANOVA mean squares are
implemented (SWEEP and quadratic forms). The covariance matrix of\nvariance
components can be derived, which is used in estimating confidence intervals.
Linear\nhypotheses of fixed effects and LS means can be computed. LS means can be
computed at specific\nvalues of covariables and with custom weighting schemes for
factor variables. See ?VCA for a\nmore comprehensive description of the
features.","Imports":"stats, graphics, grDevices, lme4, Matrix, methods,
numDeriv","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"VCA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Variance Component Analysis","Version":"1.3.1"},"VDA":
{"Author":"Edward Grant, Xia Li, Kenneth Lange, Tong Tong
Wu","Depends":"rgl","Description":"Multicategory Vertex Discriminant Analysis: A
novel supervised multicategory classification method","License":"GPL-
2","NeedsCompilation":"yes","Package":"VDA","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"VDA","Version":"1.3"},"VGAM":{"Author":"Thomas W. Yee
<t.yee@auckland.ac.nz>","Depends":"R (>= 3.0.0), methods, stats, stats4,
splines","Description":"An implementation of about 6 major classes of\nstatistical
regression models. At the heart of it are the\nvector generalized linear and
additive model (VGLM\/VGAM)\nclasses, and the book \"Vector Generalized Linear
and\nAdditive Models: With an Implementation in R\" (Yee, 2015)\ngives details of
the statistical framework and VGAM package.\nCurrently only fixed-effects models
are implemented,\ni.e., no random-effects models. Many (150+) models
and\ndistributions are estimated by maximum likelihood estimation\n(MLE) or
penalized MLE, using Fisher scoring. VGLMs can be\nloosely thought of as
multivariate GLMs. VGAMs are data-driven\nVGLMs (i.e., with smoothing). The other
classes are RR-VGLMs\n(reduced-rank VGLMs), quadratic RR-VGLMs, reduced-rank
VGAMs,\nRCIMs (row-column interaction models)---these classes perform\nconstrained
and unconstrained quadratic ordination (CQO\/UQO)\nmodels in ecology, as well as
constrained additive ordination\n(CAO). Note that these functions are subject to
change;\nsee the NEWS and ChangeLog files for latest changes.","License":"GPL-2 |
GPL-
3","NeedsCompilation":"yes","Package":"VGAM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"VGAMdata, MASS","Title":"Vector Generalized Linear and
Additive
Models","URL":"https:\/\/www.stat.auckland.ac.nz\/~yee\/VGAM","Version":"1.0-
1"},"VGAMdata":{"Author":"Thomas Yee [aut, cre, cph],\nJames Gray
[dtc]","Depends":"R (>= 3.0.0)","Description":"Data sets to accompany the VGAM
package and\nthe book \"Vector Generalized Linear and\nAdditive Models: With an
Implementation in R\" (Yee, 2015).\nThese are used to illustrate vector
generalized\nlinear and additive models (VGLMs\/VGAMs), and associated
models\n(Reduced-Rank VGLMs, Quadratic RR-VGLMs, Row-Column\nInteraction Models,
and constrained and unconstrained ordination\nmodels in ecology).","License":"GPL-
2","NeedsCompilation":"no","Package":"VGAMdata","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"VGAM","Title":"Data Supporting the 'VGAM'
Package","URL":"http:\/\/www.stat.auckland.ac.nz\/~yee\/VGAMdata","Version":"1.0-
0"},"VHDClassification":{"Author":"Robin
Girard","Depends":"methods, e1071, lattice, stats","Description":"This package
provides an implementation of Linear discriminant analysis and quadratic
discriminant analysis that works fine in very high dimension (when there are many
more variables than observations).","License":"GPL-
2","NeedsCompilation":"no","Package":"VHDClassification","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"pamr,randomForest","Title":"Discrimination\/C
lassification in very high dimension with linear\nand quadratic
rules","Version":"0.3"},"VIF":{"Author":"Dongyu Lin
<dongyu.lin@gmail.com>","Description":"This package implements a fast regression
algorithm for\nbuilding linear model for large data as defined in the paper\n\"VIF-
Regression: A Fast Regression Algorithm for Large Data\n(2011), Journal of the
American Statistical Association, Vol.\n106, No. 493: 232-247\" by Dongyu Lin, Dean
P. Foster, and Lyle\nH. Ungar.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"VIF","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"VIF Regression: A Fast Regression Algorithm For Large
Data","URL":"http:\/\/gosset.wharton.upenn.edu\/~foster\/auction\/auction.html","Ve
rsion":"1.0"},"VIFCP":{"Author":"Xiaoping Shi, Xiangsheng Wang, Dongwei Wei, Yuehua
Wu","Depends":"R (>= 3.1.3)","Description":"Contains a function to support the
paper 'A sequential multiple change-point detection\nprocedure via VIF regression'
(Accepted by Computational Statistics).","License":"LGPL-
3","NeedsCompilation":"yes","Package":"VIFCP","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Detecting Change-Points via VIFCP
Method","Version":"1.1"},"VIGoR":{"Author":"Akio Onogi and Hiroyoshi
Iwata","Description":"Conducts linear regression using variational Bayesian
inference, particularly optimized for genome-wide association mapping and whole-
genome prediction which use a number of DNA markers as the explanatory variables.
Provides seven regression models which select the important variables (i.e., the
variables related to response variables) among the given explanatory variables in
different ways (i.e., model structures).","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"VIGoR","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Variational Bayesian Inference for Genome-Wide
Regression","Version":"1.0"},"VIM":{"Author":"Matthias Templ, Andreas Alfons,
Alexander Kowarik, Bernd Prantner","Depends":"R (>=
3.1.0),colorspace,grid,data.table(>= 1.9.4)","Description":"New tools for the
visualization of missing\nand\/or imputed values are introduced, which can be used
for exploring the data and the\nstructure of the missing and\/or imputed values.
Depending on this structure\nof the missing values, the corresponding methods may
help to identify the\nmechanism generating the missing values and allows to explore
the data\nincluding missing values. In addition, the quality of imputation can
be\nvisually explored using various univariate, bivariate, multiple
and\nmultivariate plot methods. A graphical user interface available in
the\nseparate package VIMGUI allows an easy handling of the implemented
plot\nmethods.","Imports":"car, grDevices, robustbase, stats,
sp,\nvcd,MASS,nnet,e1071,methods,Rcpp,utils,graphics","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"VIM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Visualization and Imputation of Missing
Values","URL":"https:\/\/github.com\/alexkowa\/VIM","Version":"4.4.1"},"VIMGUI":
{"Author":"Daniel Schopfhauser, Matthias Templ, Andreas Alfons, Alexander
Kowarik,\nBernd Prantner","Depends":"R (>= 2.13), tcltk, tkrplot,VIM
(>=\n4.0.0),survey,gWidgetsRGtk2","Description":"This package introduces new tools
for the visualization of missing\nand\/or imputed values, which can be used for
exploring the data and the\nstructure of the missing and\/or imputed values.
Depending on this structure\nof the missing values, the corresponding methods may
help to identify the\nmechanism generating the missings and allows to explore the
data including\nmissing values. In addition, the quality of imputation can be
visually\nexplored using various univariate, bivariate, multiple and
multivariate\nplot methods. A graphical user interface allows an easy handling of
the\nimplemented plot methods.","Imports":"foreign,RGtk2,Cairo,
Hmisc","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"VIMGUI","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Visualization and Imputation of Missing
Values","URL":"https:\/\/github.com\/alexkowa\/VIMGUI","Version":"0.9.0"},"VLF":
{"Author":"Taryn B. T. Athey and Paul D. McNicholas","Depends":"R (>=
2.10)","Description":"Using frequency matrices, very low frequency variants (VLFs)
are assessed for amino acid and nucleotide sequences. The VLFs are then compared
to see if they occur in only one member of a species, singleton VLFs, or if they
occur in multiple members of a species, shared VLFs. The amino acid and nucleotide
VLFs are then compared to see if they are concordant with one another. Amino acid
VLFs are also assessed to determine if they lead to a change in amino acid residue
type, and potential changes to protein structures.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"VLF","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Frequency Matrix Approach for Assessing Very Low
Frequency\nVariants in Sequence Records","Version":"1.0"},"VLMC":{"Author":"Martin
Maechler <maechler@stat.math.ethz.ch>","Depends":"R (>=
2.15.1)","Description":"Functions, Classes & Methods for estimation, prediction,
and\nsimulation (bootstrap) of Variable Length Markov Chain ('VLMC')
Models.","Imports":"stats, MASS","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"VLMC","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Variable Length Markov Chains ('VLMC')
Models","Version":"1.4-1"},"VNM":{"Author":"Seung Won Hyun, Weng Kee Wong, and
Yarong Yang","Depends":"methods","Description":"Using V-algorithm and Newton-
Raphson method to obtain multiple-objective optimal design for estimating the shape
of dose-response, the ED50 (the dose producing an effect midway between the
expected responses at the extreme doses) and the MED (the minimum effective dose
level) for the 2,3,4-parameter logistic models and for evaluating its efficiencies
for the three objectives.","Imports":"graphics, Rcpp","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"VNM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Using V-algorithm and Newton-Raphson Method to
Obtain\nMultiple-objective Optimal Design","Version":"4.1"},"VPdtw":
{"Author":"David Clifford, Glenn Stone","Description":"Variable Penalty Dynamic
Time Warping for aligning GC-MS chromatograms to a master signal and more. With the
appropriate penalty this method performs good alignment without altering the shape
of peaks in GC-MS data.","License":"GPL-
2","NeedsCompilation":"yes","Package":"VPdtw","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Variable Penalty Dynamic Time Warping","Version":"2.1-
11"},"VSE":{"Author":"Musaddeque Ahmed
<musa.ahmed@utoronto.ca>","Depends":"GenomicRanges","Description":"Calculates the
enrichment of associated variant set (AVS) for an array of genomic regions. The AVS
is the collection of disjoint LD blocks computed from a list of disease associated
SNPs and their linked (LD) SNPs. VSE generates a null distribution of matched
random variant sets (MRVSs) from 1000 Genome Project Phase III data that are
identical to AVS, LD block by block. It then computes the enrichment of AVS
intersecting with user provided genomic features (e.g., histone marks or
transcription factor binding sites) compared with the null
distribution.","Imports":"igraph, car, IRanges, parallel","License":"GPL-
3","NeedsCompilation":"no","Package":"VSE","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"knitr, rmarkdown, ggplot2","Title":"Variant Set
Enrichment","Version":"0.99"},"VSURF":{"Author":"Robin Genuer [aut, cre],\nJean-
Michel Poggi [aut],\nChristine Tuleau-Malot [aut]","Description":"Three steps
variable selection procedure based on random forests.\nInitially developed to
handle high dimensional data (for which number of\nvariables largely exceeds number
of observations), the package is very\nversatile and can treat most dimensions of
data, for regression and\nsupervised classification problems. First step is
dedicated to eliminate\nirrelevant variables from the dataset. Second step aims to
select all\nvariables related to the response for interpretation purpose. Third
step\nrefines the selection by eliminating redundancy in the set of
variables\nselected by the second step, for prediction
purpose.","Imports":"doParallel, foreach, parallel, randomForest,
rpart","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"VSURF","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat","Title":"Variable Selection Using Random
Forests","URL":"https:\/\/github.com\/robingenuer\/VSURF","Version":"1.0.2"},"VTrac
k":{"Author":"Ross G. Dwyer, Mathew E. Watts, Hamish A. Campbell & Craig E.
Franklin","Depends":"R (>= 3.1.0), foreach(>= 1.2.0), parallel,
doParallel","Description":"Designed to facilitate the assimilation, analysis and
synthesis of animal location and movement data collected by the VEMCO suite of
acoustic transmitters and receivers. As well as database and geographic information
capabilities the principal feature of VTrack is the qualification and
identification of ecologically relevant events from the acoustic detection and
sensor data. This procedure condenses the acoustic detection database by orders of
magnitude, greatly enhancing the synthesis of acoustic detection
data.","Imports":"plotKML, sp, spacetime","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"VTrack","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat","Title":"A
Collection of Tools for the Analysis of Remote Acoustic\nTelemetry
Data","URL":"http:\/\/www.uq.edu.au\/eco-lab\/v-track","Version":"1.11"},"VaRES":
{"Author":"Saralees Nadarajah, Stephen Chan and Emmanuel Afuecheta","Depends":"R
(>= 2.15.0)","Description":"Computes Value at risk and expected shortfall, two most
popular measures of financial risk, for over one hundred parametric distributions,
including all commonly known distributions. Also computed are the corresponding
probability density function and cumulative distribution function.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"VaRES","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Computes value at risk and expected shortfall for over
100\nparametric distributions","Version":"1.0"},"VarSelLCM":{"Author":"Matthieu
Marbac and Mohammed Sedki","Description":"Uses a finite mixture model for
performing the cluster analysis with variable selection of continuous data by
assuming independence between classes. The package deals dataset with missing
values by assuming that values are missing at random. The one-dimensional marginals
of the components follow Gaussian distributions for facilitating both model
interpretation and model selection. The variable selection is led by the Maximum
Integrated Complete-Data Likelihood criterion. The maximum likelihood inference is
done by an EM algorithm for the selected model. This package also performs the
imputation of missing values.","Imports":"methods, Rcpp (>= 0.11.1),
2)","NeedsCompilation":"yes","Package":"VarSelLCM","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Variable Selection for Model-Based Clustering using
the\nIntegrated Complete-Data Likelihood of a Latent Class
Model","Version":"1.2"},"VarSwapPrice":{"Author":"Paolo
Zagaglia","Description":"Computes a portfolio of European options that
replicates\nthe cost of capturing the realised variance of an equity
index.","License":"GPL-
3","NeedsCompilation":"no","Package":"VarSwapPrice","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Pricing a variance swap on an equity
index","Version":"1.0"},"VarfromPDB":{"Author":"Zongfu Cao","Depends":"R (>=
3.0.0), XML, XML2R, RCurl, stringr","Description":"Captures and compiles the genes
and variants related to a disease, a phenotype or a clinical feature based on the
public databases including HPO (Human Phenotype Ontology, http:\/\/human-phenotype-
ontology.github.io\/about.html), Orphanet (http:\/\/www.orpha.net\/consor\/cgi-
bin\/index.php), OMIM (Online Mendelian Inheritance in Man, http:\/\/www.omim.org),
ClinVar (http:\/\/www.ncbi.nlm.nih.gov\/clinvar), and Uniprot (Universal Protein
Resource, http:\/\/www.uniprot.org) and Pubmed. HPO provides a standardized
vocabulary of phenotypic abnormalities encountered in human disease. HPO currently
contains approximately 11,000 terms and over 115,000 annotations to hereditary
diseases. Orphanet is the reference portal for information on rare diseases and
orphan drugs, whose aim is to help improve the diagnosis, care and treatment of
patients with rare diseases. OMIM is a continuously updated catalog of human genes
and genetic disorders and traits, with particular focus on the molecular
relationship between genetic variation and phenotypic expression. ClinVar is a
freely accessible, public archive of reports of the relationships among human
variations and phenotypes, with supporting evidence. Uniprot focuses on amino acid
altering variants imported from Ensembl Variation databases. For Homo sapiens, the
variants including human polymorphisms and disease mutations in the Uniprot are
manually curated from UniProtKB\/Swiss-Prot.","Imports":"stringi,
RISmed","License":"GPL-
2","NeedsCompilation":"no","Package":"VarfromPDB","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"tools","Title":"Capture the Genes and Variants
Related to a Genetic Disease from\nPublic Databases","Version":"2.0.5"},"VariABEL":
{"Author":"Maksim Struchalin","Depends":"R (>= 2.13.0)","Description":"Presence of
interaction between a SNP and another SNP (or another factor) can result\nin
heterogeneity of variance between the genotypes of an interacting SNP.\nDetecting
such heterogeneity gives prior knowledge for constructing a genetic
model\nunderlying complex trait.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"VariABEL","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"GenABEL, DatABEL","Title":"Testing of genotypic
variance heterogeneity to detect\npotentially interacting SNP","Version":"0.9-
2"},"VarianceGamma":{"Author":"David Scott <d.scott@auckland.ac.nz> and Christine
Yang Dong\n<c.dong@auckland.ac.nz>","Depends":"R (>= 2.3.0), DistributionUtils,
GeneralizedHyperbolic, RUnit","Description":"This package provides functions for
the variance gamma\ndistributions. Density, distribution and quantile
functions.\nFunctions for random number generation and fitting of the\nvariance
gamma to data. Also, functions for computing moments\nof the variance gamma
distribution of any order about any\nlocation. In addition, there are functions for
checking the\nvalidity of parameters and to interchange different sets
of\nparameterizatons for the variance gamma distribution.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"VarianceGamma","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"The Variance Gamma
Distribution","URL":"http:\/\/www.r-project.org","Version":"0.3-1"},"VdgRsm":
{"Author":"Patchanok Srisuradetchai, John J. Borkowski","Depends":"R (>=
3.1.2)","Description":"Functions for creating variance dispersion graphs, fraction
of design space plots, and contour plots of scaled prediction variances for second-
order response surface designs in spherical and cuboidal regions. Also, some
standard response surface designs can be generated.","Imports":"permute,
AlgDesign","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"VdgRsm","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"akima","Title":"Plots of Scaled Prediction Variances
for Response Surface\nDesigns","Version":"1.5"},"Vdgraph":{"Author":"John Lawson
<lawson@byu.edu>, with contributions from G. Vining","Description":"Uses a
modification of the published FORTRAN code in \"A Computer Program for Generating
Variance Dispersion Graphs\" by G. Vining, Journal of Quality Technology, Vol. 25
No. 1 January 1993, to produce variance dispersion graphs. Also produces fraction
of design space plots, and contains data frames for several minimal run response
surface designs.","License":"GPL-
2","NeedsCompilation":"yes","Package":"Vdgraph","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Variance dispersion graphs and Fraction of design space
plots\nfor response surface designs","Version":"2.2-2"},"VecStatGraphs2D":
{"Author":"Ruiz-Cuetos J.C., Felicisimo A.M., Cuartero A., Polo M.E., Rodriguez
P.G.","Depends":"R (>= 2.10.1), MASS","Description":"This package performs a 2D
statistical analysis, both numerical and graphical, of a set of vectors. Since a
vector has two components (module and azimuth) vector analysis is performed in
three stages: modules are analyzed by means of linear statistics, azimuths are
analyzed by circular statistics, and the joint analysis of modules and azimuths is
done using density maps that allow detecting another distribution properties (i.e.
anisotropy) and outliers. Tests and circular statistic parameters have associated a
full range of graphing: histograms, maps of distributions, point maps, vector maps,
density maps, distribution modules and azimuths.","License":"GPL-
3","NeedsCompilation":"no","Package":"VecStatGraphs2D","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Vector analysis using graphical and analytical
methods in
2D","URL":"http:\/\/gim.unex.es\/VecStatGraphs2D\/","Version":"1.7"},"VecStatGraphs
3D":{"Author":"Angel Felicisimo, Juan Carlos Ruiz Cuetos, Maria Eugenia Polo
Garcia, Aurora Cuartero,\nPablo Garcia Rodriguez","Depends":"R (>= 2.10.1), rgl,
misc3d, tcltk, MASS","Description":"This package performs a 3D statistical
analysis, both numerical and graphical, of a set of vectors. Since a vector has
three components (a module and two angles) vectorial analysis is performed in two
stages: modules are analyzed by means of linear statistics and orientations are
analyzed by spherical statistics. Tests and spherical statistic parameters are
accompanied by a graphs as: density maps, distribution modules and angles. The
tests, spherical statistic parameters and graphs allow us detecting another
distribution properties (i.e. anisotropy) and outliers.","License":"GPL-
3","NeedsCompilation":"no","Package":"VecStatGraphs3D","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Vector analysis using graphical and analytical
methods in
3D","URL":"http:\/\/gim.unex.es\/VecStatGraphs3D\/","Version":"1.6"},"VennDiagram":
{"Author":"Hanbo Chen","Depends":"R (>= 2.14.1), grid (>= 2.14.1),
futile.logger","Description":"A set of functions to generate high-resolution Venn
and Euler plots. Includes handling for several special cases, including two-case
scaling, and extensive customization of plot shape and structure.","License":"GPL-
2","NeedsCompilation":"no","Package":"VennDiagram","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat","Title":"Generate High-Resolution Venn
and Euler Plots","Version":"1.6.16"},"VertexSimilarity":{"Author":"Rishabh
Singh","Description":"Creates Vertex Similarity matrix of an undirected graph
based\non the method stated by E. A. Leicht, Petter Holme, AND M. E. J. Newman
in\ntheir paper
<DOI:10.1103\/PhysRevE.73.026120>.","Imports":"igraph","License":"GPL-
2","NeedsCompilation":"no","Package":"VertexSimilarity","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Creates Vertex Similarity Matrix for an
Undirected
Graph","Version":"0.1"},"ViSiElse":{"Author":"Nastasia Fouret [aut, cre,
cph],\nMederic Descoins [aut, cph],\nCEPOI - EA 7388 [cph]","Depends":"R (>=
3.2.0), methods (>= 3.2.0), grid (>= 3.2.0), chron (>=\n2.3-46), Matrix (>= 1.2-0),
colorspace (>= 1.2-6), stringr (>=\n1.0.0)","Description":"A graphical tool
designed to visualize and to give an overview of behavioural observations realized
on individuals or groups. ViSiElse allows visualization of raw data during
experimental observations of the realization of a procedure. It graphically
presents an overview of individuals and group actions usually acquired from
timestamps during video recorded sessions. Options of the package allow adding
graphical information as statistical indicators (mean, standard deviation, quantile
or statistical test) but also for each action green or black zones providing visual
information about the accuracy of the realized actions.","License":"AGPL-
3","NeedsCompilation":"no","Package":"ViSiElse","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr, rmarkdown","Title":"A Visual Tool for Behaviour
Analysis","URL":"https:\/\/github.com\/CEPOI\/ViSiElse","Version":"1.0.1"},"VideoCo
mparison":{"Author":"Silvia Espinosa, Joaquin Ordieres, Antonio Bello, Jose Maria
Perez","Depends":"R (>= 2.15.2), zoo, RCurl, RJSONIO, stats, pracma, Rcpp
(>=\n0.10.3)","Description":"It will take the vectors of motion for two
videos\n(coming from a variant of shotdetect code allowing to store\ndetailed
motion vectors in JSON format, for instance) and it\nwill look for comparing taking
out the common chunk.\nThen, provided you have some image's hashes it will
compare\ntheir signature in order to make up the decision about\nchunk similarity
of two video files.\nShotDetect is a free software which detects shots and
scenes\nfrom a video (http:\/\/johmathe.name\/shotdetect.html).","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"VideoComparison","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"MASS","Title":"Video Comparison
Tool","URL":"http:\/\/www.r-project.org","Version":"0.15"},"VineCopula":
{"Author":"Ulf Schepsmeier, Jakob Stoeber, Eike Christian Brechmann, Benedikt
Graeler, Thomas Nagler, Tobias Erhardt","Depends":"R (>=
2.11.0)","Description":"Tools for bivariate exploratory data analysis, bivariate
copula selection and (vine) tree construction are provided. Vine copula models can
be estimated either sequentially or by joint maximum likelihood estimation.
Sampling algorithms and plotting methods are included. Data is assumed to lie in
the unit hypercube (so-called copula data). For C- and D-vines links to the package
'CDVine' are provided.","Imports":"graphics, grDevices, stats, utils, MASS,
mvtnorm, igraph (>=\n1.0.0), methods, copula, ADGofTest, lattice","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"VineCopula","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"TSP","Title":"Statistical Inference of Vine
Copulas","Version":"1.6-1"},"VisuClust":{"Author":"Michael Sieger [cre, aut], Georg
Ohmayer [aut, ths], Hochschule Weihenstephan-Triesdorf
[cph]","Depends":"aplpack","Description":"Displays multivariate data, based on
Sammon's nonlinear mapping.","License":"LGPL (>=
3)","NeedsCompilation":"no","Package":"VisuClust","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"MASS, cluster","Title":"Visualisation of Clusters in
Multivariate Data","Version":"1.2"},"VizOR":{"Author":"Drew Griffin Levy
[aut],\nDavid C. Norris [aut, cre]","Depends":"lattice,
grid,","Description":"Provides individual- and aggregate-level graphical depictions
of\npatterns of treatment and response in patient registries, and a graphical\ntool
for examining potential for confounding in analyses of
observational\ndata.","Imports":"rms","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"VizOR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"rpanel","Title":"Graphical visualization tools for
complex observational data\nwith focus on health sciences (VizOR)","Version":"0.7-
9"},"Voss":{"Author":"Pavel V. Moskalev","Depends":"R (>= 2.14.0),
fields","Description":"Voss package provides functionality for
generating\nrealizations of a fractal Brownian function on uniform 1D & 2D\ngrid
with classic and generic versions of the Voss algorithm\n(random sequential
additions)","License":"GPL-
3","NeedsCompilation":"no","Package":"Voss","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Generic Voss algorithm (random sequential
additions)","URL":"http:\/\/www.r-project.org","Version":"0.1-4"},"VoxR":
{"Author":"Bastien Lecigne, Sylvain Delagrange and Christian Messier","Depends":"R
(>= 2.10)","Description":"Tools for tree crown structure description based on T-
LiDAR data voxelisation","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"VoxR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"rgl, raster, sp","Title":"Metrics extraction of trees
from T-LiDAR data","Version":"0.5.1"},"W2CWM2C":{"Author":"Josue M. Polanco-
Martinez","Depends":"R (>= 2.14.1), waveslim, wavemulcor,
colorspace","Description":"Set of functions that improves the graphical
presentations of the functions 'wave.correlation' and 'spin.correlation' (waveslim
package, Whitcher 2012) and the 'wave.multiple.correlation' and
'wave.multiple.cross.correlation' (wavemulcor package, Fernandez-Macho 2012b). The
plot outputs (heatmaps) can be displayed in the screen or can be saved as PNG or
JPG images or as PDF or EPS formats. The W2CWM2C package also helps to handle the
(input data) multivariate time series easily as a list of N elements (times series)
and provides a multivariate data set (dataexample) to exemplify its use. A
description of the package was published in Computing in Science & Engineering
(Volume:16, Issue: 6) on Sep. 09, 2014, doi:10.1109\/MCSE.2014.96.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"W2CWM2C","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"A Graphical Tool for Wavelet (Cross) Correlation and
Wavelet\nMultiple (Cross) Correlation
Analysis","Version":"2.0"},"W3CMarkupValidator":{"Author":"Kurt Hornik [aut,
cre]","Depends":"R (>= 3.2.0)","Description":"\nR interface to a W3C Markup
Validation service.\nSee <http:\/\/validator.w3.org\/> for more
information.","Imports":"curl, utils, xml2","License":"GPL-
2","NeedsCompilation":"no","Package":"W3CMarkupValidator","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"R Interface to W3C Markup Validation
Services","Version":"0.1-5"},"WACS":{"Author":"Denis Allard [aut, cre], Ronan
Trepos [aut]","Depends":"R (>= 2.10), mclust, mnormt, tmvtnorm,
mvtnorm","Description":"Multivariate weather generator for daily climate variables
based\non weather-states using a Markov chain for modeling the succession of
weather states.\nConditionally to the weather states, the multivariate variables
are modeled using the family\nof Complete Skew-Normal distributions. Parameters are
estimated on measured series. Data must\ninclude the variable 'Rain' and can accept
as many other variables as desired.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"WACS","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"R.rsp","Title":"Multivariate Weather-State Approach
Conditionally Skew-Normal\nGenerator","URL":"http:\/\/informatique-
mia.inra.fr\/biosp\/allard#WACS","Version":"1.0"},"WARN":{"Author":"Takumi
Tsutaya","Depends":"R (>= 3.0.0)","Description":"This estimates precise weaning
ages\nfor a given skeletal population\nby analyzing the stable nitrogen isotope
ratios of them.\nBone collagen turnover rates estimated anew and\nthe approximate
Bayesian computation (ABC)\nwere adopted in this package.","Imports":"graphics,
grDevices, MASS, stats","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"WARN","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Weaning Age Reconstruction with Nitrogen Isotope
Analysis","Version":"1.2-0"},"WCE":{"Author":"Marie-Pierre Sylvestre <marie-
pierre.sylvestre@umontreal.ca>, Marie-Eve Beauchamp <marie-
eve.beauchamp@clinepi.mcgill.ca>, Ryan Patrick Kyle <ryan.kyle@mail.mcgill.ca>,
Michal Abrahamowicz <michal.abrahamowicz@mcgill.ca>","Depends":"R (>=
2.10)","Description":"WCE implements a flexible method for modeling cumulative
effects of time-varying exposures, weighted according to their relative proximity
in time, and represented by time-dependent covariates. The current implementation
estimates the weight function in the Cox proportional hazards model. The function
that assigns weights to doses taken in the past is estimated using cubic regression
splines.","Imports":"plyr, survival, splines","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"WCE","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"R.rsp","Title":"Weighted Cumulative Exposure
Models","Version":"1.0"},"WCQ":{"Author":"Jan Michael Yap","Description":"The
package contains the WCQ method for detection of QTL\neffects in a small mapping
population. It also contains\nimplementation of the Chen-Qin two-sample and one-
sample test\nof means.","License":"GPL-
3","NeedsCompilation":"no","Package":"WCQ","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Detection of QTL effects in a small mapping
population","Version":"0.2"},"WDI":{"Author":"Vincent Arel-Bundock
<varel@umich.edu>","Depends":"RJSONIO","Description":"Search, extract and format
data from the World Bank's\nWorld Development Indicators","License":"GPL-
3","NeedsCompilation":"no","Package":"WDI","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"World Development Indicators (World
Bank)","URL":"http:\/\/www.umich.edu\/~varel
,\nhttps:\/\/www.github.com\/vincentarelbundock\/WDI","Version":"2.4"},"WGCNA":
{"Author":"Peter Langfelder <Peter.Langfelder@gmail.com> and Steve Horvath
<SHorvath@mednet.ucla.edu> with contributions
by Chaochao Cai, Jun Dong, Jeremy Miller, Lin Song, Andy Yip, and Bin
Zhang","Depends":"R (>= 3.0), dynamicTreeCut (>= 1.62),
fastcluster","Description":"Functions necessary to perform Weighted Correlation
Network Analysis on high-dimensional data. Includes functions for rudimentary data
cleaning, construction of correlation networks, module identification,
summarization, and relating of variables and modules to sample traits. Also
includes a number of utility functions for data manipulation and
visualization.","Imports":"stats, grDevices, utils, matrixStats (>= 0.8.1),
Hmisc,\nimpute, splines, foreach, doParallel, preprocessCore, survival,\nparallel,
GO.db, AnnotationDbi","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"WGCNA","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"org.Hs.eg.db, org.Mm.eg.db, infotheo, entropy,
minet","Title":"Weighted Correlation Network
Analysis","URL":"\nhttp:\/\/www.genetics.ucla.edu\/labs\/horvath\/CoexpressionNetwo
rk\/Rpackages\/WGCNA\/","Version":"1.51"},"WHO":{"Author":"Eric Persson [aut,
cre]","Description":"Provides programmatic access to the World Health Organization
API.","Imports":"httr,
dplyr","License":"CC0","NeedsCompilation":"no","Package":"WHO","Repository":"http:\
/\/cran.csiro.au\/src\/contrib","Suggests":"ggplot2, knitr, testthat,
rmarkdown","Title":"R Client for the World Health Organization
API","URL":"https:\/\/www.github.com\/expersso\/WHO ,
http:\/\/www.who.int","Version":"0.2"},"WMCapacity":{"Author":"R. D. Morey
<richarddmorey@gmail.com>","Depends":"R (>= 2.10), gtools, gWidgets, gWidgetsRGtk2,
coda,\ncairoDevice","Description":"A GUI R implementation of hierarchical Bayesian
models of working memory, used for analyzing change detection
data.","Imports":"RGtk2, grDevices, XML","License":"GPL-
2","NeedsCompilation":"yes","Package":"WMCapacity","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"GUI Implementing Bayesian Working Memory
Models","URL":"http:\/\/wmcapacity.r-forge.r-
project.org\/","Version":"0.9.6.7"},"WMDB":{"Author":"Bingpei
Wu","Description":"Distance discriminant analysis method is one of\nclassification
methods according to multiindex performance\nparameters.However,the traditional
Mahalanobis distance\ndiscriminant method treats with the importance of
all\nparameters equally,and exaggerates the role of parameters which\nchanges a
little.The weighted Mahalanobis distance is used in\ndiscriminant analysis method
to distinguish the importance of\neach parameter.In the concrete
application,firstly based on the\nprincipal component analysis scheme,a new group
of parameters\nand their corresponding percent contributions of the parameters\nare
calculated ,and the weighted matrix is regarded as the\ndiagonal matrix of the
contributions rates.Setting data to\nstandardization,then the weighted Mahalanobis
distance can be\ncalculated.Besides the methods metioned above,bayes method
is\nalso given.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"WMDB","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Discriminant Analysis Methods by Weight Mahalanobis Distance
and\nbayes","Version":"1.0"},"WRS2":{"Author":"Patrick Mair [cre, aut],\nRand
Wilcox [aut],\nFelix Schoenbrodt [ctr]","Depends":"R (>= 3.0.0)","Description":"A
collection of robust statistical methods based on Wilcox' WRS functions. It
implements t-tests (independent and dependent samples), ANOVA (including between-
within subject designs) and nonparametric ANCOVA models based on robust location
measures.","Imports":"MASS, reshape, plyr, stats, graphics, grDevices,
3","NeedsCompilation":"yes","Package":"WRS2","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr, beanplot, car, colorspace, ez","Title":"A
Collection of Robust Statistical Methods","URL":"https:\/\/r-forge.r-
project.org\/projects\/psychor\/","Version":"0.4-0"},"WWGbook":{"Author":"Shu Chen,
Andrzej Galecki <agalecki@umich.edu>","Depends":"R (>= 1.4.1)","Description":"Book
is \"Linear Mixed Models: A Practical Guide Using\nStatistical Software\" published
in 2006 by Chapman Hall \/ CRC\nPress","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"WWGbook","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Functions and datasets for WWGbook","URL":"http:\/\/www-
personal.umich.edu\/~bwest\/almmussp.html","Version":"1.0.1"},"WaterML":
{"Author":"Jiri Kadlec [aut, cre]","Depends":"R (>= 3.0)","Description":"Lets you
connect to any of the Consortium of Universities for the Advancement\nof Hydrologic
Sciences, Inc. ('CUAHSI') Water Data Center 'WaterOneFlow' web services\nand read
any 'WaterML' hydrological time series data file. To see list of available\nweb
services, see <http:\/\/hiscentral.cuahsi.org>. All versions of 'WaterML'\n(1.0,
1.1 and 2.0) and both types of the web service protocol ('SOAP' and 'REST') are
supported.\nThe package has six data download functions: GetServices(): show all
public web\nservices from the HIS Central Catalog. HISCentral_GetSites() and
HISCentral_GetSeriesCatalog():\nsearch for sites or time series from the HIS
Central catalog based on geographic bounding box,\nserver, or keyword.
GetVariables(): Show a data.frame with all variables on the server.\nGetSites():
Show a data.frame with all sites on the server. GetSiteInfo(): Show what
variables,\nmethods and quality control levels are available at the specific site.
GetValues(): Given a site\ncode, variable code, start time and end time, fetch a
data.frame of all the observation time\nseries data values. The GetValues()
function can also parse 'WaterML' data from a custom URL or\nfrom a local file. The
package also has five data upload functions:\nAddSites(), AddVariables(),
AddMethods(), AddSources(), and AddValues().\nThese functions can be used for
uploading data to a 'HydroServer Lite' Observations\nData Model ('ODM') database
via the 'JSON' data upload web service interface.","Imports":"stats, XML, RJSONIO,
httr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"WaterML","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"knitr","Title":"Fetch and Analyze Data from
'WaterML' and 'WaterOneFlow'
Web\nServices","URL":"https:\/\/github.com\/jirikadlec2\/waterml","Version":"1.7.1"
},"Watersheds":{"Author":"J.A. Torres-Matallana","Depends":"R (>= 2.10), methods,
sp, maptools, rgeos, lattice, splancs","Description":"Methods for watersheds
aggregation and spatial drainage network analysis.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Watersheds","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Spatial Watershed Aggregation and Spatial Drainage
Network\nAnalysis","Version":"1.1"},"Wats":{"Author":"Will Beasley [aut, cre], Joe
Rodgers [aut], Matthew Schuelke [ctb],\nRonnie Coleman [ctb], Mark Joseph Lachowicz
[ctb]","Depends":"R (>= 3.0.0), stats","Description":"Wrap-around Time Series
(WATS) plots for interrupted time series\ndesigns with seasonal
patterns.","Imports":"colorspace, ggplot2, grid, lubridate, plyr,
RColorBrewer,\ntestit, zoo","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"Wats","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"BayesSingleSub, boot, devtools, knitr, scales,
testthat","Title":"Wrap Around Time Series
Graphics","URL":"https:\/\/github.com\/OuhscBbmc\/Wats","Version":"0.10.3"},"Wavele
tComp":{"Author":"Angi Roesch and Harald Schmidbauer","Depends":"R (>=
2.10)","Description":"Wavelet analysis and reconstruction of time series, cross-
wavelets and phase-difference (with filtering options), significance with
simulation algorithms.","License":"GPL-
2","NeedsCompilation":"no","Package":"WaveletComp","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Computational Wavelet
Analysis","URL":"\nhttp:\/\/www.hs-
stat.com\/projects\/WaveletComp\/WaveletComp_guided_tour.pdf","Version":"1.0"},"Wav
erR":{"Author":"Olivia Cheronet, John A. Finarelli","Depends":"MASS (>= 7.3-33),
kimisc (>= 0.2-1)","Description":"For multivariate datasets, this function enables
the estimation of missing data using the Weighted AVERage of all possible
Regressions using the data available.","License":"GPL-
2","NeedsCompilation":"no","Package":"WaverR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Data Estimation using Weighted Averages of Multiple
Regressions","Version":"1.0"},"Weighted.Desc.Stat":{"Author":"Abbas Parchami
(Department of Statistics, Faculty of Mathematics and Computer, Shahid Bahonar
University of Kerman, Kerman, Iran)","Description":"Weighted descriptive statistics
is the discipline of quantitatively describing the main features of real-valued
fuzzy data which usually given from a fuzzy population. One can summarize this
special kind of fuzzy data numerically or graphically using this package. To
interpret some of the properties of one or several sets of real-valued fuzzy data,
numerically summarize is possible by some weighted statistics which are designed in
this package such as mean, variance, covariance and correlation coefficent. Also,
graphically interpretation can be given by weighted histogram and weighted scatter
plot using this package to describe properties of real-valued fuzzy data
set.","License":"LGPL (>=
3)","NeedsCompilation":"no","Package":"Weighted.Desc.Stat","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Title":"Weighted Descriptive
Statistics","Version":"1.0"},"WeightedCluster":{"Author":"Matthias Studer [aut,
cre]","Depends":"R (>= 3.0.0), TraMineR(>= 1.8-8), cluster","Description":"The
WeightedCluster library provides functions to cluster states sequences and weighted
data. These functionalities include aggregating replicated cases, an optimized
weighted PAM algorithm, function computing cluster quality measures for a range of
clustering solutions and miscellaneous functions to plot clustering solutions of
state sequences.","Imports":"utils,
2)","NeedsCompilation":"yes","Package":"WeightedCluster","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"RUnit, knitr, isotone, vegan,
lattice","Title":"Clustering of Weighted
Data","URL":"http:\/\/mephisto.unige.ch\/weightedcluster","Version":"1.2"},"Weighte
dPortTest":{"Author":"Thomas J. Fisher and Colin M. Gallagher","Description":"This
packages contains the Weighted Portmanteau Tests as\ndescribed in \"New Weighted
Portmanteau Statistics for Time\nSeries Goodness-of-Fit Testing' accepted for
publication by the\nJournal of the American Statistical
Association.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"WeightedPortTest","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Weighted Portmanteau Tests for Time Series
Goodness-of-fit","Version":"1.0"},"WhatIf":{"Author":"Heather Stoll
<hstoll@polsci.ucsb.edu>,\nGary King <king@harvard.edu>,\nLangche Zeng
<zeng@ucsd.edu>,","Depends":"R (>= 2.3.1), lpSolve","Description":"Inferences about
counterfactuals are essential for prediction,\nanswering what if questions, and
estimating causal effects.\nHowever, when the counterfactuals posed are too far
from the data at\nhand, conclusions drawn from well-specified statistical
analyses\nbecome based largely on speculation hidden in convenient
modeling\nassumptions that few would be willing to defend.
Unfortunately,\nstandard statistical approaches assume the veracity of the
model\nrather than revealing the degree of model-dependence, which makes
this\nproblem hard to detect. WhatIf offers easy-to-apply methods to\nevaluate
counterfactuals that do not require sensitivity testing over\nspecified classes of
models. If an analysis fails the tests offered\nhere, then we know that
substantive inferences will be sensitive to at\nleast some modeling choices that
are not based on empirical evidence,\nno matter what method of inference one
chooses to use. WhatIf\nimplements the methods for evaluating counterfactuals
discussed in\nGary King and Langche Zeng, 2006, \"The Dangers of
Extreme\nCounterfactuals,\" Political Analysis 14 (2); and Gary\nKing and Langche
Zeng, 2007, \"When Can History Be Our Guide? The\nPitfalls of Counterfactual
Inference,\" International Studies\nQuarterly 51 (March).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"WhatIf","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"WhatIf: Software for Evaluating
Counterfactuals","URL":"http:\/\/gking.harvard.edu\/whatif","Version":"1.5-
6"},"WhiteStripe":{"Author":"Taki Shinohara, John Muschelli","Depends":"R (>=
2.10), methods","Description":"Shinohara et. al introduced Whitestripe,
an\nintensity-based normalization of T1 and T2 images, where normal\nappearing
white matter performs well, but requires segmentation.\nThis method performs white
matter mean and standard deviation\nestimates on data that has been rigidly-
registered to the MNI\ntemplate and uses histogram-based
methods.","Imports":"oro.nifti (>= 0.5.0), mgcv","License":"GPL-
3","NeedsCompilation":"no","Package":"WhiteStripe","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"fslr","Title":"White Matter Normalization for
Magnetic Resonance Images using\nWhitestripe","Version":"1.1.1"},"WhopGenome":
{"Author":"Ulrich Wittelsbuerger [aut, cre], Heng Li [ctb], Bob Handsaker
[ctb]","Depends":"R (>= 1.8.0)","Description":"Provides very fast access to whole
genome, population scale variation data\nfrom VCF files and sequence data from
FASTA-formatted files.\nIt also reads in alignments from FASTA, Phylip, MAF and
other file formats.\nProvides easy-to-use interfaces to genome annotation from UCSC
and Bioconductor and gene ontology data\nfrom AmiGO and is capable to read, modify
and write PLINK .PED-format pedigree files.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"WhopGenome","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"RMySQL, DBI, AnnotationDbi","Title":"High-Speed
Processing of VCF, FASTA and Alignment Data","Version":"0.9.3"},"WiSEBoot":
{"Author":"Megan Heyman, Snigdhansu Chatterjee","Depends":"R (>=
3.1.0)","Description":"Perform the Wild Scale-Enhanced (WiSE) bootstrap.
Specifically, the user may supply a single or multiple equally-spaced time series
and use the WiSE bootstrap to select a wavelet-smoothed model. Conversely, a pre-
selected smooth level may also be specified for the time series. Quantities such
as the bootstrap sample of wavelet coefficients, smoothed bootstrap samples, and
specific hypothesis testing and confidence region results of the wavelet
coefficients may be obtained. Additional functions are available to the user which
help format the time series before analysis. This methodology is recommended to
aid in model selection and signal extraction.\nNote: This package specifically
uses wavelet bases in the WiSE bootstrap methodology, but the theoretical construct
is much more versatile.","Imports":"wavethresh, FAdist","License":"GPL-
2","NeedsCompilation":"no","Package":"WiSEBoot","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr","Title":"Wild Scale-Enhanced
Bootstrap","Version":"1.4.0"},"WikiSocio":{"Author":"person(\"Leo\", \"Joubert\",
email = \"joubert.leo@gmail.com\", role =\nc(\"aut\", \"cre\"))","Depends":"R (>=
3.0.0)","Description":"\nMediaWiki is wiki platform. Providing the infrastructure
of Wikipedia, it also offers very sophisticated archiving functionalities.\nThis
package is built to store these wiki's archives to R object - data-frame, lists,
vector and variables. All data are downloaded\nwith the help of MediaWiki REST API.
For instance, you can get all revisions made by a contributor - contrib_list(), all
the revisions\nof a page page_revisions(), or create corpus of contributors -
corpus_contrib_create() - and pages corpus_page_create(). Then, you can\nmake these
corpus rich of data about contributors or pages - corpus_contrib_data() or
corpus_page_data().","Imports":"httr,igraph,pbapply,plyr,XML,RCurl,stringr","Licens
e":"GPL-
3","NeedsCompilation":"no","Package":"WikiSocio","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"A MediaWiki API Wrapper","Version":"0.7.0"},"WikidataR":
{"Author":"Oliver Keyes [aut, cre], Christian Graul [ctb]","Description":"An API
client for the Wikidata <http:\/\/wikidata.org\/> store of\nsemantic
data.","Imports":"httr, jsonlite, WikipediR","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"WikidataR","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat, knitr, pageviews","Title":"API Client
Library for
'Wikidata'","URL":"https:\/\/github.com\/Ironholds\/WikidataR\/issues","Version":"1
.0.1"},"WikipediR":{"Author":"Oliver Keyes","Depends":"httr,
jsonlite","Description":"A wrapper for the MediaWiki API, aimed particularly at
the\nWikimedia 'production' wikis, such as Wikipedia. It can be used to
retrieve\npage text, information about users or the history of pages, and elements
of\nthe category tree.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"WikipediR","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat, knitr, WikidataR,
pageviews","Title":"A MediaWiki API
Wrapper","URL":"https:\/\/github.com\/Ironholds\/WikipediR\/","Version":"1.3.0"},"W
ikipediaR":{"Author":"Avner Bar-Hen [aut, cre],\nLouise Baschet [ctb],\nFrancois-
Xavier Jollois [ctb],\nJeremie Riou [ctb]","Depends":"R (>= 2.10.0), XML (>=
2.6.3), httr (>= 1.0.0)","Description":"Provides an interface to the Wikipedia web
application programming\ninterface (API), using internet connexion.Three functions
provide details for\na specific Wikipedia page : all links that are present, all
pages that link\nto, all the contributions (revisions for main pages, and
discussions for talk\npages). Two functions provide details for a specific user :
all contributions,\nand general information (as name, gender, rights or groups). It
provides\nadditional information compared to others packages, as WikipediR. It does
not\nneed login. The multiplex network that can be constructed from the results\nof
the functions of WikipediaR can be modeled as Stochastic Block Model as
in\nBarbillon P., Donnet, S., Lazega E., and Bar-Hen A. : Stochastic Block
Models\nfor Multiplex networks: an application to networks of researchers,
ArXiv\n1501.06444, http:\/\/arxiv.org\/abs\/1501.06444.","License":"GPL (>
2)","NeedsCompilation":"no","Package":"WikipediaR","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"R-Based Wikipedia Client","URL":"http:\/\/www.r-
project.org","Version":"1.1"},"WilcoxCV":{"Author":"Anne-Laure Boulesteix
<boulesteix@ibe.med.uni-muenchen.de>.","Depends":"R (>= 2.0.0)","Description":"This
package provides functions to perform fast variable\nselection based on the
Wilcoxon rank sum test in the\ncross-validation or Monte-Carlo cross-validation
settings, for\nuse in microarray-based binary classification.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"WilcoxCV","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Wilcoxon-based variable selection in cross-
validation","URL":"http:\/\/cran.r-
project.org\/web\/packages\/WilcoxCV\/index.html","Version":"1.0-2"},"WordPools":
{"Author":"Michael Friendly","Depends":"R (>= 2.10)","Description":"This package
collects several classical word pools used\nmost often to provide lists of words in
psychological studies\nof learning and memory.","License":"GPL-
2","NeedsCompilation":"no","Package":"WordPools","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Classical word pools used in studies of learning and
memory","Version":"1.0-2"},"WrightMap":{"Author":"David Torres Irribarra & Rebecca
Freund","Depends":"R (>= 3.0.0)","Description":"A powerful yet simple graphical
tool available in the field of psychometrics is the Wright Map (also known as item
maps or item-person maps),
which presents the location of both respondents and items on the same scale.
Wright Maps are commonly used to present the results of dichotomous or polytomous
item response models. The 'WrightMap' package provides functions to create these
plots from item parameters and person estimates stored as R objects. Although the
package can be used in conjunction with any software used to estimate the IRT model
(e.g. 'TAM', 'mirt', 'eRm' or 'IRToys' in 'R', or 'Stata', 'Mplus', etc.),
'WrightMap' features special integration with 'ConQuest' to facilitate reading and
plotting its output directly.The 'wrightMap' function creates Wright Maps based on
person estimates and item parameters produced by an item response analysis. The
'CQmodel' function reads output files created using 'ConQuest' software and creates
a set of data frames for easy data manipulation, bundled in a 'CQmodel' object. The
'wrightMap' function can take a 'CQmodel' object as input or it can be used to
create Wright Maps directly from data frames of person and item
parameters.","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"WrightMap","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"IRT Item-Person Map with 'ConQuest'
Integration","Version":"1.2.1"},"WriteXLS":{"Author":"Marc Schwartz
<marc_schwartz@me.com> and various authors for Perl modules listed in each .pm
file.","Description":"Cross-platform Perl based R function to create Excel 2003
(XLS) and Excel 2007 (XLSX)\nfiles from one or more data frames. Each data frame
will be\nwritten to a separate named worksheet in the Excel spreadsheet.\nThe
worksheet name will be the name of the data frame it contains\nor can be specified
by the user.","Imports":"utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"WriteXLS","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Cross-Platform Perl Based R Function to Create Excel
2003 (XLS)\nand Excel 2007 (XLSX)
Files","URL":"https:\/\/github.com\/marcschwartz\/WriteXLS","Version":"4.0.0"},"Wuf
ooR":{"Author":"John Malc [aut, cre] (@dmpe),\nMaksim Pecherskiy [ctb]
(@MrMaksimize)","Depends":"R (>= 3.2.2)","Description":"Allows form managers to
download entries from their respondents\nusing Wufoo JSON API. Additionally, the
Wufoo reports - when public - can be\nalso acquired programmatically. Note that
building new forms within this package\nis not supported.","Imports":"httr (>=
1.1.0), jsonlite (>= 0.9.19), dplyr (>= 0.4.3)","License":"Apache License
2.0","NeedsCompilation":"no","Package":"WufooR","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"roxygen2 (>= 5.0.1), knitr (>= 1.12.3), testthat (>=
0.11.0)","Title":"R Wrapper for the 'Wufoo.com' - The Form Building
Service","URL":"http:\/\/github.com\/dmpe\/wufoor","Version":"0.6.1"},"XBRL":
{"Author":"Roberto Bertolusso and Marek Kimmel","Description":"\nFunctions to
extract business financial information from\nan Extensible Business Reporting
Language ('XBRL') instance file and the\nassociated collection of files that
defines its 'Discoverable' Taxonomy\nSet ('DTS').","Imports":"Rcpp (>=
0.10.4)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"XBRL","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Extraction of Business Financial Information from
'XBRL'\nDocuments","Version":"0.99.16"},"XGR":{"Author":"Hai Fang, Bogdan Knezevic,
Katie L Burnham, Julian C Knight","Depends":"R (>= 3.1.0), igraph,
dnet","Description":"The central goal of XGR is to provide a data interpretation
system. It is designed to make a user-defined gene or SNP list more interpretable
by comprehensively utilising ontology and network information to reveal
relationships and enhance opportunities for biological discovery. XGR is unique in
supporting a broad range of ontologies (including knowledge of biological and
molecular functions, pathways, diseases and phenotypes - in both human and mouse)
and different types of networks (including functional, physical and pathway
interactions). There are two core functionalities of the XGR. The first is basic
infrastructures for easy access to built-in ontologies and networks. The second is
extensible functions, now including 1) enrichment analysis using either built-in or
custom ontologies, 2) similarity analysis for calculating semantic similarity
between genes (or SNPs) based on their ontology annotation profiles, and 3) network
analysis for identification of gene networks given a query list of (significant)
genes or SNPs. Together with its web app, XGR aims to provide a user-friendly tool
for exploring genomic relations at the gene and SNP level.","Imports":"Matrix,
GenomicRanges, RCircos, ggplot2, ggbio, MASS,\ngrDevices","License":"GPL-
2","NeedsCompilation":"no","Package":"XGR","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"foreach, doMC","Title":"Exploring Genomic Relations at the
Gene and SNP Level Through\nEnrichment, Similarity and Network
Analysis","URL":"http:\/\/galahad.well.ox.ac.uk\/XGR, http:\/\/xgr.r-forge.r-
project.org","Version":"1.0.0"},"XHWE":{"Author":"Xiao-Ping You, Qi-Lei Zou, Jian-
Long Li, Ji-Yuan Zhou","Description":"Conduct the likelihood ratio tests for Hardy-
Weinberg equilibrium at marker loci on the X chromosome.","License":"GPL-
2","NeedsCompilation":"no","Package":"XHWE","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"X Chromosome Hardy-Weinberg
Equilibrium","Version":"1.0"},"XLConnect":{"Author":"Mirai Solutions GmbH
[aut],\nMartin Studer [cre],\nThe Apache Software Foundation [ctb, cph] (Apache
POI, Apache Commons\nCodec),\nStephen Colebourne [ctb, cph] (Joda-Time Java
library)","Depends":"R (>= 2.10.0), XLConnectJars (== 0.2-
9)","Description":"Provides comprehensive functionality to read, write and format
Excel data.","Imports":"methods, rJava","License":"GPL-
3","NeedsCompilation":"no","Package":"XLConnect","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"RUnit, lattice, ggplot2 (>= 0.9.3),
zoo","Title":"Excel Connector for R","URL":"http:\/\/www.mirai-solutions.com
,\nhttp:\/\/miraisolutions.wordpress.com","Version":"0.2-11"},"XLConnectJars":
{"Author":"Mirai Solutions GmbH [aut],\nMartin Studer [cre],\nThe Apache Software
Foundation [ctb, cph] (Apache POI, Apache XMLBeans)","Description":"Provides
external JAR dependencies for the XLConnect
package","Imports":"rJava","License":"GPL-
3","NeedsCompilation":"no","Package":"XLConnectJars","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"JAR dependencies for the XLConnect
package","URL":"http:\/\/www.mirai-solutions.com
,\nhttp:\/\/miraisolutions.wordpress.com","Version":"0.2-9"},"XML":
{"Author":"Duncan Temple Lang and the CRAN Team","Depends":"R (>= 2.13.0), methods,
utils","Description":"Many approaches for both reading and\ncreating XML (and HTML)
documents (including DTDs), both local\nand accessible via HTTP or FTP. Also
offers access to an\n'XPath' \"interpreter\".","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"yes","Package":"XML","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"bitops, RCurl","Title":"Tools for Parsing and
Generating XML Within R and S-
Plus","URL":"http:\/\/www.omegahat.net\/RSXML","Version":"3.98-1.4"},"XML2R":
{"Author":"Carson Sievert <sievert@iastate.edu>","Depends":"R (>= 2.15.1),
XML","Description":"XML2R is a framework that reduces the effort required to
transform\nXML content into number of tables while preserving parent to
child\nrelationships.","Imports":"RCurl, plyr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"XML2R","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"EasieR XML data
collection","URL":"http:\/\/cpsievert.github.com\/XML2R","Version":"0.0.6"},"XMRF":
{"Author":"Ying-Wooi Wan, Genevera I. Allen, Yulia Baker, Eunho Yang, Pradeep
Ravikumar, Zhandong Liu","Depends":"R (>= 3.0.2)","Description":"Fit Markov
Networks to a wide range of high-throughput genomics data.","Imports":"igraph,
glmnet, MASS, snowfall, parallel, Matrix","License":"GPL-
2","NeedsCompilation":"yes","Package":"XMRF","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Markov Random Fields for High-Throughput Genetics
Data","URL":"http:\/\/www.liuzlab.org\/XMRF\/","Version":"1.0"},"XNomial":
{"Author":"Bill Engels <wrengels@wisc.edu>","Depends":"R (>=
2.14)","Description":"Tests whether a set of counts fit a given expected ratio.
For\nexample, a genetic cross might be expected to produce four types in
the\nrelative frequencies of 9:3:3:1. To see whether a set of observed counts\nfits
this expectation, one can examine all possible outcomes with xmulti() or a\nrandom
sample of them with xmonte() and find the probability of an observation\ndeviating
from the expectation by at least as much as the observed. As a\nmeasure of
deviation from the expected, one can use the log-likelihood\nratio, the multinomial
probability, or the classic chi-square statistic. A\nhistogram of the test
statistic can also be plotted and compared with the\nasymptotic
curve.","License":"GPL","NeedsCompilation":"yes","Package":"XNomial","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Suggests":"knitr","Title":"Exact Goodness-
of-Fit Test for Multinomial Data with
Fixed\nProbabilities","Version":"1.0.4"},"XiMpLe":{"Author":"Meik Michalke [aut,
cre]","Depends":"R (>= 2.9.0),methods","Description":"Provides a simple XML tree
parser\/generator. It includes functions\nto read XML files into R objects, get
information out of and into nodes, and\nwrite R objects back to XML code. It's not
as powerful as the 'XML' package\nand doesn't aim to be, but for simple XML
handling it could be useful. It was\noriginally developed for the R GUI and IDE
RKWard (https:\/\/rkward.kde.org), to\nmake plugin development
easier.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"XiMpLe","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat","Title":"A
Simple XML Tree Parser and Generator","URL":"http:\/\/reaktanz.de\/?
c=hacking&s=XiMpLe","Version":"0.03-23"},"Xmisc":{"Author":"Xiaobei Zhao [aut, cre,
cph]","Depends":"R (>= 3.1.0)","Description":"This is Xiaobei's miscellaneous
classes and functions useful when\ndeveloping R packages, particularly for OOP
using R Reference Class.","Imports":"methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Xmisc","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"RUnit, datasets, data.table","Title":"Xiaobei's
miscellaneous classes and functions","URL":"http:\/\/CRAN.R-
project.org\/package=Xmisc","Version":"0.2.1"},"YPmodel":{"Author":"Junlong Sun and
Song Yang","Depends":"R (>= 2.10.0)","Description":"Inference procedures
accommodate a flexible range of hazard ratio patterns with a two-sample semi-
parametric model. This model contains the proportional hazards model and the
proportional odds model as sub-models, and accommodates non-proportional hazards
situations to the extreme of having crossing hazards and crossing survivor
functions. Overall, this package has four major functions: 1) the parameter
estimation, namely short-term and long-term hazard ratio parameters; 2) 95 percent
and 90 percent point-wise confidence intervals and simultaneous confidence bands
for the hazard ratio function; 3) p-value of the adaptive weighted log-rank test;
4) p-values of two lack-of-fit tests for the model. See the
included \"read_me_first.pdf\" for brief instructions. In this version (1.1), there
is no need to sort the data before applying this package.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"YPmodel","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"The Short-Term and Long-Term Hazard Ratio Model for
Survival\nData","Version":"1.3"},"YaleToolkit":{"Author":"John W. Emerson and
Walton A. Green","Depends":"grid","Description":"This collection of data
exploration tools was developed at\nYale University for the graphical exploration
of complex\nmultivariate data; barcode and gpairs now have their own\npackages.
The new big.read.table() provided here may be\nuseful for large files when only a
subset is needed.","Imports":"foreach, iterators","License":"LGPL-
3","NeedsCompilation":"no","Package":"YaleToolkit","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Data exploration tools from Yale
University","Version":"4.2.2"},"YieldCurve":{"Author":"Sergio Salvino
Guirreri","Depends":"R (>= 2.10), xts","Description":"Modelling the yield curve
with some parametric models.\nThe models implemented are: Nelson-Siegel, Diebold-Li
and\nSvensson. The package also includes the data of the term\nstructure of
interest rate of Federal Reserve Bank and European\nCentral Bank.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"YieldCurve","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Modelling and estimation of the yield
curve","URL":"http:\/\/www.guirreri.host22.com","Version":"4.1"},"YplantQMC":
{"Author":"Remko Duursma. QuasiMC by Mik Cieslak. Uses code by Robert
Pearcy\n(Yplant) and Belinda Medlyn (MAESTRA)","Depends":"R (>= 2.10), rgl,
geometry, LeafAngle, gplots","Description":"An R implementation of Yplant, combined
with the QuasiMC\nraytracer. Calculate radiation absorption, transmission and
scattering,\nphotosynthesis and transpiration of virtual 3D
plants.","License":"GPL-
2","NeedsCompilation":"yes","Package":"YplantQMC","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"maps","Title":"Plant Architectural Analysis with
Yplant and
QuasiMC","URL":"http:\/\/www.remkoduursma.com\/yplantqmc,\nhttps:\/\/www.bitbucket.
org\/remkoduursma\/yplantqmc\/","Version":"0.6-4"},"YuGene":{"Author":"Kim-Anh Le
Cao, Florian Rohart, Leo McHugh, Othmar Korn, Christine A.
Wells","Depends":"mixOmics ,R (>= 2.10)","Description":"Simple method for
comparison of gene\nexpression generated across different experiments, and
on\ndifferent platforms; that does not require global\nrenormalization, and is not
restricted to comparison of\nidentical probes. YuGene works on a range of
microarray dataset\ndistributions, such as between manufacturers. The
resulting\noutput allows direct comparisons of gene expression between\nexperiments
and experimental platforms.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"YuGene","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"A Simple Approach to Scale Gene Expression Data Derived
from\nDifferent Platforms for Integrated Analyses","Version":"1.1.5"},"ZIM":
{"Author":"Ming Yang, Gideon K. D. Zamba, and Joseph E.
Cavanaugh","Depends":"MASS","Description":"Fits observation-driven and parameter-
driven models for zero-inflated time series","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ZIM","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Zero-Inflated Models for Count Time Series with Excess
Zeros","Version":"1.0.2"},"ZRA":{"Author":"David Beiner","Depends":"R (>= 3.0.2),
forecast, dygraphs, stats","Description":"Combines a forecast of a time series,
using the function forecast(), with the dynamic plots from
dygraphs.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ZRA","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Dynamic Plots for Time Series
Forecasting","Version":"0.2"},"ZeBook":{"Author":"Francois Brun (ACTA), David
Makowski (INRA), Daniel Wallach\n(INRA), James W. Jones (U.of
Florida).","Depends":"triangle, deSolve, R(>= 2.10.0)","Description":"R package
accompanying the book Working with dynamic\nmodels for agriculture and environment,
by Daniel Wallach\n(INRA), David Makowski (INRA), James W. Jones (U.of
Florida),\nFrancois Brun (ACTA), in preparation for June 2013.","License":"LGPL-
3","NeedsCompilation":"no","Package":"ZeBook","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"ZeBook Working with dynamic models for agriculture
and\nenvironment","Version":"0.5"},"Zelig":{"Author":"Christine Choirat, James
Honaker, Kosuke Imai, Gary King, Olivia Lau","Description":"A framework that brings
together an abundance of common\nstatistical models found across packages into a
unified interface, and\nprovides a common architecture for estimation and
interpretation, as well\nas bridging functions to absorb increasingly more models
into the\ncollective library. Zelig allows each individual package, for
each\nstatistical model, to be accessed by a common uniformly structured call
and\nset of arguments. Moreover, Zelig automates all the surrounding
building\nblocks of a statistical work-flow --procedures and algorithms that may
be\nessential to one user's application but which the original package\ndeveloper
did not use in their own research and might not themselves\nsupport. These include
bootstrapping, jackknifing, and re-weighting of data.\nIn particular, Zelig
automatically generates predicted and simulated\nquantities of interest (such as
relative risk ratios, average treatment\neffects, first differences and predicted
and expected values) to interpret\nand visualize complex
models.","Imports":"sandwich, methods, MASS, survival, VGAM, jsonlite, AER,
plyr,\ndplyr (>= 0.3.0.2), quantreg, geepack, MCMCpack, coda, Amelia,\nMatchIt,
maxLik, survey","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"Zelig","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat, knitr","Title":"Everyone's Statistical
Software","Version":"5.0-12"},"ZeligChoice":{"Author":"Christine Choirat, James
Honaker, Kosuke Imai, Gary King, Olivia Lau","Depends":"R (>=
2.10)","Description":"Add-on package for Zelig 5. Enables the use of a variety of
logit\nand probit regressions.","Imports":"methods, Zelig (>= 5.0-9), MASS, VGAM,
jsonlite, dplyr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ZeligChoice","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat, knitr","Title":"Zelig Choice
Models","Version":"0.9-0"},"ZillowR":{"Author":"Justin Brantley
<fascinatingfingers@icloud.com>","Description":"Zillow, an online real estate
company, provides real estate and\nmortgage data for the United States through a
REST API. The ZillowR package\nprovides an R function for each API service, making
it easy to make API\ncalls and process the response into convenient, R-friendly
data structures.\nSee <http:\/\/www.zillow.com\/howto\/api\/APIOverview.htm> for
the Zillow API\nDocumentation.","Imports":"methods, utils, RCurl,
XML","License":"GPL-
3","NeedsCompilation":"no","Package":"ZillowR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat","Title":"R Interface to Zillow Real Estate
and Mortgage Data
API","URL":"https:\/\/github.com\/fascinatingfingers\/ZillowR","Version":"0.1.0"},"
aCRM":{"Author":"Dirk Van den Poel, Michel Ballings, Andrey Volkov, Jeroen D'haen,
Michiel Van Herwegen","Description":"Convenience functions for data preparation and
modeling often used in aCRM.","Imports":"dummies, randomForest, kernelFactory,
ada","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"aCRM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Convenience functions for analytical Customer
Relationship\nManagement","Version":"0.1.1"},"aLFQ":{"Author":"George Rosenberger,
Hannes Roest, Christina Ludwig, Ruedi Aebersold, Lars Malmstroem","Depends":"R (>=
2.15.0)","Description":"Determination of absolute protein quantities is necessary
for multiple applications, such as mechanistic modeling of biological systems.
Quantitative liquid chromatography tandem mass spectrometry (LC-MS\/MS) proteomics
can measure relative protein abundance on a system-wide scale. To estimate absolute
quantitative information using these relative abundance measurements requires
additional information such as heavy-labeled references of known concentration.
Multiple methods have been using different references and strategies; some are
easily available whereas others
require more effort on the users end. Hence, we believe the field might benefit
from making some of these methods available under an automated framework, which
also facilitates validation of the chosen strategy. We have implemented the most
commonly used absolute label-free protein abundance estimation methods for LC-
MS\/MS modes quantifying on either MS1-, MS2-levels or spectral counts together
with validation algorithms to enable automated data analysis and error estimation.
Specifically, we used Monte-carlo cross-validation and bootstrapping for model
selection and imputation of proteome-wide absolute protein quantity estimation. Our
open-source software is written in the statistical programming language R and
validated and demonstrated on a synthetic sample.","Imports":"data.table, plyr,
caret, seqinr, lattice, randomForest, ROCR,\nreshape2, protiq,
bio3d","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"aLFQ","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat","Title":"Estimating Absolute Protein Quantities
from Label-Free LC-MS\/MS\nProteomics
Data","URL":"https:\/\/github.com\/aLFQ","Version":"1.3.3"},"aRpsDCA":
{"Author":"Derrick Turk [aut, cre, cph]","Description":"Functions for Arps decline-
curve analysis on oil and gas data. Includes exponential, hyperbolic, harmonic, and
hyperbolic-to-exponential models as well as the preceding with initial curtailment
or a period of linear rate buildup. Functions included for computing rate,
cumulative production, instantaneous decline, EUR, time to economic limit, and
performing least-squares best fits.","Imports":"stats","License":"LGPL-
2.1","NeedsCompilation":"no","Package":"aRpsDCA","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Arps Decline Curve Analysis in
R","URL":"https:\/\/github.com\/derrickturk\/aRpsDCA","Version":"1.1.0"},"aRxiv":
{"Author":"Karthik Ram [aut],\nKarl Broman [aut, cre]","Depends":"R (>=
3.0.0)","Description":"An interface to the API for arXiv, a repository
of\nelectronic preprints for computer science, mathematics, physics,\nquantitative
biology, quantitative finance, and statistics.","Imports":"httr, utils,
XML","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"aRxiv","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"devtools, knitr, roxygen2,
testthat","Title":"Interface to the arXiv
API","URL":"https:\/\/github.com\/ropensci\/aRxiv","Version":"0.5.10"},"aSPU":
{"Author":"Il-Youp Kwak and others (See Author(s) in each function
manual)","Depends":"R(>= 3.1.0), gee, MASS, mvtnorm, matrixStats","Description":"R
codes for the (adaptive) Sum of Powered Score ('SPU' and 'aSPU') tests, inverse
variance weighted Sum of Powered score ('SPUw' and 'aSPUw') tests and gene-based
and some pathway based association tests (Pathway based Sum of Powered Score tests
('SPUpath'), adaptive 'SPUpath' ('aSPUpath') test, 'GEEaSPU' test for multiple
traits - single 'SNP' (single-nucleotide-polymorphism) association in generalized
estimation equations, 'MTaSPUs' test for multiple traits - single 'SNP' association
with Genome Wide Association Studies ('GWAS') summary statistics, Gene-based
Association Test that uses an extended Simes procedure ('GATES'), Hybrid Set-based
Test ('HYST') and extended version of 'GATES' test for pathway-based association
testing ('GATES-Simes'). ). The tests can be used with genetic and other data sets
with covariates. The response variable is binary or quantitative. Summary; (1)
Single trait-'SNP' set association with individual-level data ('aSPU', 'aSPUw'),
(2) Single trait-'SNP' set association with summary statistics ('aSPUs'), (3)
Single trait-pathway association with individual-level data ('aSPUpath'), (4)
Single trait-pathway association with summary statistics ('aSPUsPath'), (5)
Multiple traits-single 'SNP' association with individual-level data ('GEEaSPU'),
(6) Multiple traits-single SNP association with summary statistics
('MTaSPUs').","Imports":"Rcpp (>= 0.12.1)","License":"GPL-
3","NeedsCompilation":"yes","Package":"aSPU","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr","Title":"Adaptive Sum of Powered Score
Test","URL":"https:\/\/github.com\/ikwak2\/aSPU","Version":"1.41"},"aTSA":
{"Author":"Debin Qiu","Description":"Contains some tools for testing, analyzing
time series data and\nfitting popular time series models such as ARIMA, Moving
Average and Holt\nWinters, etc. Most functions also provide nice and clear outputs
like SAS\ndoes, such as identify, estimate and forecast, which are the same
statements\nin PROC ARIMA in SAS.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"aTSA","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Alternative Time Series
Analysis","Version":"3.1.2"},"abbyyR":{"Author":"Gaurav Sood [aut,
cre]","Depends":"R (>= 3.2.0)","Description":"Get text from images of text using
Abbyy Cloud Optical Character\nRecognition (OCR) API. Easily OCR images, barcodes,
forms, documents with\nmachine readable zones, e.g. passports. Get the results in a
variety of formats\nincluding plain text and XML. To learn more about the Abbyy OCR
API, see http:\/\/\nocrsdk.com\/.","Imports":"httr, XML, curl, RecordLinkage,
readr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"abbyyR","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat, knitr (>= 1.11)","Title":"Access to
Abbyy Optical Character Recognition (OCR)
API","URL":"http:\/\/github.com\/soodoku\/abbyyR","Version":"0.3"},"abc":
{"Author":"Csillery Katalin [aut],\nLemaire Louisiane [aut],\nFrancois Olivier
[aut],\nBlum Michael [aut, cre]","Depends":"R (>= 2.10), abc.data, nnet, quantreg,
MASS, locfit","Description":"Implements several ABC algorithms for\nperforming
parameter estimation, model selection, and goodness-of-fit.\nCross-validation tools
are also available for measuring the\naccuracy of ABC estimates, and to calculate
the\nmisclassification probabilities of different models.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"abc","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Tools for Approximate Bayesian Computation
(ABC)","Version":"2.1"},"abc.data":{"Author":"Csillery Katalin [aut],\nLemaire
Louisiane [aut],\nFrancois Olivier [aut],\nBlum Michael [aut, cre]","Depends":"R
(>= 2.10)","Description":"Contains data which are used by functions of the 'abc'
3)","NeedsCompilation":"no","Package":"abc.data","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Data Only: Tools for Approximate Bayesian Computation
(ABC)","Version":"1.0"},"abcdeFBA":{"Author":"Abhilash Gangadharan, Neha
Rohatgi","Depends":"Rglpk,rgl,corrplot,lattice,R (>=
2.10)","Description":"Functions for Constraint Based Simulation using Flux\nBalance
Analysis and informative analysis of the data generated\nduring
simulation.","License":"GPL-
2","NeedsCompilation":"no","Package":"abcdeFBA","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"LIM,sybil","Title":"ABCDE_FBA: A-Biologist-Can-Do-
Everything of Flux Balance\nAnalysis with this package","Version":"0.4"},"abcrf":
{"Author":"Jean-Michel Marin [aut, cre],\nPierre Pudlo [aut],\nChristian P. Robert
[ctb],\nArnaud Estoup [ctb]","Depends":"R(>= 2.10.0)","Description":"Performs
Approximate Bayesian Computation (ABC) model choice via random
forests.","Imports":"MASS, randomForest, parallel, foreach, doParallel,
doRNG","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"abcrf","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Approximate Bayesian Computation via Random
Forests","Version":"1.2"},"abctools":{"Author":"Matt Nunes [aut, cre],\nDennis
Prangle [aut]","Depends":"R (>= 2.10), abc, abind, parallel,
plyr","Description":"Tools for approximate Bayesian computation including summary
statistic selection and assessing coverage.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"abctools","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"ggplot2, abc.data","Title":"Tools for ABC
Analyses","URL":"https:\/\/github.com\/dennisprangle\/abctools","Version":"1.0.4"},
"abd":{"Author":"Kevin M. Middleton <middletonk@missouri.edu>, Randall
Pruim\n<rpruim@calvin.edu>","Depends":"R (>= 3.0), nlme, lattice, grid,
mosaic","Description":"The abd package contains data sets and sample code for
The\nAnalysis of Biological Data by Michael Whitlock and Dolph Schluter
(2009;\nRoberts & Company Publishers).","License":"GPL-
2","NeedsCompilation":"no","Package":"abd","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"boot, car, ggplot2, plyr, HH, ICC, vcd, Hmisc","Title":"The
Analysis of Biological Data","Version":"0.2-8"},"abf2":{"Author":"Matthew
Caldwell","Description":"Loads ABF2 files containing gap-free data from
electrophysiological recordings, as created by Axon Instruments\/Molecular Devices
software such as pClamp 10.","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"abf2","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Load Gap-Free Axon ABF2 Files","Version":"0.7-1"},"abind":
{"Author":"Tony Plate <tplate@acm.org> and Richard Heiberger","Depends":"R (>=
1.5.0)","Description":"Combine multidimensional arrays into a single array.\nThis
is a generalization of 'cbind' and 'rbind'. Works with\nvectors, matrices, and
higher-dimensional arrays. Also\nprovides functions 'adrop', 'asub', and 'afill'
for manipulating,\nextracting and replacing data in arrays.","License":"LGPL (>=
2)","NeedsCompilation":"no","Package":"abind","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Combine Multidimensional Arrays","Version":"1.4-3"},"abn":
{"Author":"Fraser Ian Lewis [aut], Marta Pittavino [cre, ctb], Reinhard Furrer
[ctb]","Depends":"Cairo, R (>= 2.15.1)","Description":"Bayesian network analysis is
a form of probabilistic graphical models which derives from empirical
data a directed acyclic graph, DAG, describing the dependency structure between
random variables. An additive Bayesian network model consists of a form of a DAG
where each node comprises a generalized linear model, GLM. Additive Bayesian
network models are equivalent to Bayesian multivariate regression using graphical
modelling, they generalises the usual multivariable regression, GLM, to multiple
dependent variables. 'abn' provides routines to help determine optimal Bayesian
network models for a given data set, where these models are used to identify
statistical dependencies in messy, complex data. The additive formulation of these
models is equivalent to multivariate generalised linear modelling (including mixed
models with iid random effects). The usual term to describe this model selection
process is structure discovery. The core functionality is concerned with model
selection - determining the most robust empirical model of data from interdependent
variables. Laplace approximations are used to estimate goodness of fit metrics and
model parameters, and wrappers are also included to the INLA package which can be
obtained from http:\/\/www.r-inla.org. It is recommended the testing version, which
can be downloaded by running: source(\"http:\/\/www.math.ntnu.no\/inla\/givemeINLA-
testing.R\"). A comprehensive set of documented case studies, numerical
accuracy\/quality assurance exercises, and additional documentation are available
from the abn website.","Imports":"methods","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"abn","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"INLA, Rgraphviz","Title":"Modelling Multivariate Data
with Additive Bayesian Networks","URL":"http:\/\/www.r-bayesian-
networks.org","Version":"1.0"},"abodOutlier":{"Author":"Jose Jimenez
<jose@jimenezluna.com>","Depends":"cluster, R (>= 3.1.2)","Description":"Performs
angle-based outlier detection on a given dataframe. Three methods are available, a
full but slow implementation using all the data that has cubic complexity, a fully
randomized one which is way more efficient and another using k-nearest neighbours.
These algorithms are specially well suited for high dimensional data outlier
detection.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"abodOutlier","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Angle-Based Outlier
Detection","Version":"0.1"},"abundant":{"Author":"Adam J. Rothman","Depends":"R (>=
2.10), QUIC","Description":"Fit and predict with the high-dimensional principal
fitted\ncomponents model.","License":"GPL-
2","NeedsCompilation":"yes","Package":"abundant","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Abundant regression and high-dimensional principal
fitted\ncomponents","Version":"1.0"},"acc":{"Author":"Jaejoon Song, Matthew G.
Cox","Depends":"R (>= 2.10), zoo, mhsmm, PhysicalActivity, nleqslv,
plyr,\nmethods","Description":"Processes accelerometer data from uni-axial and tri-
axial devices, and generates data summaries. Also includes functions to plot,
analyze, and simulate accelerometer data.","License":"GNU General Public License
(>=
3)","NeedsCompilation":"no","Package":"acc","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Functions for Processing and Analyzing Accelerometer
Data","Version":"1.2.4"},"accelerometry":{"Author":"Dane R. Van
Domelen","Depends":"R (>= 3.0.0)","Description":"A collection of functions that
perform operations on time-series accelerometer data, such as identify non-wear
time, flag minutes that are part of an activity bout, and find the maximum 10-
minute average count value. The functions are generally very flexible, allowing for
a variety of algorithms to be implemented. Most of the functions are written in C++
for efficiency.","Imports":"Rcpp (>= 0.11.0)","License":"GPL-
2","NeedsCompilation":"yes","Package":"accelerometry","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Functions for Processing Minute-to-Minute
Accelerometer Data","Version":"2.2.5"},"accelmissing":{"Author":"Jung Ae Lee
<jungaeleeb@gmail.com>","Depends":"R (>= 2.10), mice,
pscl","Description":"Imputation for the missing count values in accelerometer data.
The methodology includes both parametric and semi-parametric multiple imputations
under the zero-inflated Poisson lognormal model. This package also provides
multiple functions to pre-process the accelerometer data previous to the missing
data imputation. These includes detecting wearing and non-wearing time, selecting
valid days and subjects, and creating plots.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"accelmissing","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Missing Value Imputation for Accelerometer
Data","Version":"1.0"},"accrual":{"Author":"Yu Jiang, Cen Wu, Steve Simon, Matthew
S. Mayo , Rama Raghavan, Byron J. Gajewski","Depends":"R(>=
2.8.0)","Description":"Subject recruitment for medical research is challenging.
Slow patient accrual leads to delay in research. Accrual monitoring during the
process of recruitment is critical. Researchers need reliable tools to manage the
accrual rate. We developed a Bayesian method that integrates researcher's
experience on previous trials and data from the current study, providing reliable
prediction on accrual rate for clinical studies. In this R package, we present
functions for Bayesian accrual prediction which can be easily used by statisticians
and clinical researchers.","Imports":"fgui,SMPracticals,tcltk","License":"GPL-
2","NeedsCompilation":"no","Package":"accrual","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Bayesian Accrual Prediction","Version":"1.1"},"accrued":
{"Author":"Julie Eaton and Ian Painter","Depends":"R (>= 2.14.1),
grid","Description":"Package for visualizing data quality of partially accruing
3","NeedsCompilation":"no","Package":"accrued","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Data Quality Visualization Tools for Partially Accruing
Data","Version":"1.3.5"},"acepack":{"Author":"Phil Spector, Jerome Friedman, Robert
Tibshirani, Thomas Lumley","Description":"ACE and AVAS methods for choosing
regression\ntransformations.","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"acepack","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"ace() and avas() for selecting regression
transformations","Version":"1.3-3.3"},"acid":{"Author":"Alexander
Sohn","Depends":"gamlss,gamlss.dist,Hmisc,stats,graphics,splines","Description":"Fu
nctions for the analysis of income distributions for subgroups of the population as
defined by a set of variables like age, gender, region, etc. This entails a
Kolmogorov-Smirnov test for a mixture distribution as well as functions for
moments, inequality measures, entropy measures and polarisation measures of income
distributions. This package thus aides the analysis of income inequality by
offering tools for the exploratory analysis of income distributions at the
disaggregated level.","Imports":"grDevices,utils,datasets,methods","License":"GPL-
3","NeedsCompilation":"no","Package":"acid","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"ineq","Title":"Analysing Conditional Income
Distributions","Version":"1.1"},"acm4r":{"Author":"Andrea Benedetti, Sahir Rai
Bhatnagar, Xiaofei Zhao","Depends":"MASS","Description":"Fragment lengths or
molecular weights from pairs of lanes are\ncompared, and a number of matching bands
are calculated using the\nAlign-and-Count
Method.","License":"GPL","NeedsCompilation":"no","Package":"acm4r","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"Align-and-Count Method comparisons of
RFLP data","Version":"1.0"},"acmeR":{"Author":"Robert Wolpert [aut, cre],\nJacob
Coleman [aut]","Depends":"R (>= 3.1.1)","Description":"Implementation of estimator
ACME, described in Wolpert (2015), ACME: A \t\tPartially Periodic Estimator of
Avian & Chiropteran Mortality at Wind\nTurbines (submitted). Unlike most other
models, this estimator\nsupports decreasing-hazard Weibull model for
persistence;\ndecreasing search proficiency as carcasses age; variable\nbleed-
through at successive searches; and interval mortality\nestimates. The package
provides, based on search data, functions\nfor estimating the mortality inflation
factor in Frequentist and\nBayesian settings.","Imports":"foreign (>= 0.8-63),
grDevices (>= 3.1.1), graphics (>=\n3.1.1), stats (>= 3.1.1), utils (>=
LICENSE","NeedsCompilation":"no","Package":"acmeR","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr, devtools","Title":"Implements ACME Estimator
of Bird and Bat Mortality by Wind\nTurbines","Version":"1.1.0"},"acnr":
{"Author":"Morgane Pierre-Jean and Pierre Neuvial","Depends":"R (>= 2.10), R.utils,
xtable","Description":"This data package contains SNP array data from different
types of copy-number regions. These regions were identified manually by the
authors of the package and may be used to generate realistic data sets with known
truth.","License":"LGPL (>=
2.1)","NeedsCompilation":"no","Package":"acnr","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Annotated Copy-Number
Regions","Version":"0.2.4"},"acopula":{"Author":"Tomas
Bacigal","Description":"Archimax copulas are mixture of Archimedean and EV copulas.
The package provides definitions of several parametric families of generator and
dependence function, computes CDF and PDF, estimates parameters, tests for goodness
of fit, generates random sample and checks copula properties for custom constructs.
In 2-dimensional case explicit formulas for density are used, in the contrary to
higher dimensions when all derivatives are linearly approximated. Several non-
archimax families (normal, FGM, Plackett) are provided as well.","License":"GPL-
2","NeedsCompilation":"no","Package":"acopula","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"mvtnorm","Title":"Modelli
ng dependence with multivariate Archimax (or any\nuser-defined continuous)
copulas","Version":"0.9.2"},"acp":{"Author":"Siakoulis
Vasileios","Depends":"tseries,quantmod","Description":"Analysis of count data
exhibiting autoregressive properties, using the Autoregressive Conditional Poisson
model (ACP(p,q)) proposed by Heinen (2003).","License":"GPL-
2","NeedsCompilation":"no","Package":"acp","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Autoregressive Conditional Poisson","Version":"2.1"},"acs":
{"Author":"Ezra Haber Glenn [aut, cre]","Depends":"R (>= 2.10), stringr, methods,
plyr, XML","Description":"Provides a general toolkit for downloading,
managing,\nanalyzing, and presenting data from the U.S. Census, including
SF1\n(Decennial short-form), SF3 (Decennial long-form), and the American\nCommunity
Survey (ACS). Confidence intervals provided with ACS data\nare converted to
standard errors to be bundled with estimates in\ncomplex acs objects. Package
provides new methods to conduct\nstandard operations on acs objects and
present\/plot data in\nstatistically appropriate ways. Current version is 2.0
+\/- .033.","Imports":"graphics, stats, utils, RCurl","License":"GPL-
3","NeedsCompilation":"no","Package":"acs","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Download, Manipulate, and Present American Community Survey
and\nDecennial Data from the US
Census","URL":"http:\/\/dusp.mit.edu\/faculty\/ezra-
glenn,\nhttp:\/\/eglenn.scripts.mit.edu\/citystate\/,\nhttp:\/\/mailman.mit.edu\/ma
ilman\/listinfo\/acs-r","Version":"2.0"},"acss":{"Author":"Nicolas Gauvrit
[aut],\nHenrik Singmann [aut, cre],\nFernando Soler Toscano [ctb],\nHector Zenil
[ctb]","Depends":"R (>= 2.15.0), acss.data","Description":"Main functionality is to
provide the algorithmic complexity for\nshort strings, an approximation of the
Kolmogorov Complexity of a short\nstring using the coding theorem method (see ?
acss). The database containing\nthe complexity is provided in the data only package
acss.data, this package\nprovides functions accessing the data such as prob_random
returning the\nposterior probability that a given string was produced by a random
process.\nIn addition, two traditional (but problematic) measures of complexity
are\nalso provided: entropy and change complexity.","Imports":"zoo","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"acss","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"effects, lattice","Title":"Algorithmic Complexity for
Short
Strings","URL":"http:\/\/complexitycalculator.com\/methodology.html","Version":"0.2
-5"},"acss.data":{"Author":"Fernando Soler Toscano [aut],\nNicolas Gauvrit
[aut],\nHector Zenil [aut],\nHenrik Singmann [aut, cre]","Depends":"R (>=
2.10)","Description":"Data only package providing the algorithmic complexity of
short strings, computed using the coding theorem method. For a given set of symbols
in a string, all possible or a large number of random samples of Turing machines
(TM) with a given number of states (e.g., 5) and number of symbols corresponding to
the number of symbols in the strings were simulated until they reached a halting
state or failed to end. This package contains data on 4.5 million strings from
length 1 to 12 simulated on TMs with 2, 4, 5, 6, and 9 symbols. The complexity of
the string corresponds to the distribution of the halting states of the
TMs.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"acss.data","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Data Only: Algorithmic Complexity of Short Strings
(Computed via\nCoding Theorem
Method)","URL":"http:\/\/complexitycalculator.com\/methodology.html","Version":"1.0
"},"activity":{"Author":"Marcus Rowcliffe
<marcus.rowcliffe@ioz.ac.uk>","Depends":"methods","Description":"Provides functions
to fit kernel density functions\nto animal activity time data; plot activity
distributions;\nquantify overall levels of activity; statistically
compare\nactivity metrics through bootstrapping; and evaluate variation\nin linear
variables with time (or other circular variables).","Imports":"circular, overlap,
pbapply,","License":"GPL-
3","NeedsCompilation":"no","Package":"activity","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Animal Activity
Statistics","Version":"1.0"},"activpalProcessing":{"Author":"Kate
Lyden","Depends":"R (>= 2.10), graphics, grDevices, stats,
utils","Description":"Performs estimation of physical activity and sedentary
behavior variables from activPAL (PAL Technologies, Glasgow, Scotland) events
files. See <http:\/\/paltechnologies.com> for more information on the
activPAL.","Imports":"chron","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"activpalProcessing","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Process activPAL Events
Files","Version":"1.0.1"},"actuar":{"Author":"Vincent Goulet, SÃ©bastien Auclair,
Christophe Dutang, Xavier Milhaud, Tommy Ouellet, Louis-Philippe Pouliot, Mathieu
Pigeon","Depends":"R (>= 2.6.0)","Description":"Various actuarial science
functionalities, mostly in the\nfields of loss distributions, risk theory
(including ruin theory),\nsimulation of compound hierarchical models and
credibility theory.\nThe package also features 17 probability laws commonly used
in\ninsurance, mostly heavy tailed distributions.","Imports":"stats,
2)","NeedsCompilation":"yes","Package":"actuar","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"MASS","Title":"Actuarial Functions and Heavy Tailed
Distributions","Version":"1.2-0"},"ada":{"Author":"Mark Culp, Kjell Johnson, and
George Michailidis","Depends":"R(>= 2.10),rpart","Description":"Performs discrete,
real, and gentle boost under both\nexponential and logistic loss on a given data
set. The package\nada provides a straightforward, well-documented, and
broad\nboosting routine for classification, ideally suited for small\nto moderate-
sized data sets. Please refer to the Url below for\nmore
information.","License":"GPL","NeedsCompilation":"no","Package":"ada","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Title":"ada: an R package for stochastic
boosting","Version":"2.0-3"},"adabag":{"Author":"Alfaro, Esteban; Gamez, Matias and
Garcia, Noelia; with contributions from Li Guo","Depends":"rpart, mlbench,
caret","Description":"It implements Freund and Schapire's Adaboost.M1 algorithm and
Breiman's Bagging\nalgorithm using classification trees as individual classifiers.
Once these classifiers have been\ntrained, they can be used to predict on new data.
Also, cross validation estimation of the error can\nbe done. Since version 2.0 the
function margins() is available to calculate the margins for these\nclassifiers.
Also a higher flexibility is achieved giving access to the rpart.control()
argument\nof 'rpart'. Four important new features were introduced on version 3.0,
AdaBoost-SAMME (Zhu\net al., 2009) is implemented and a new function errorevol()
shows the error of the ensembles as\na function of the number of iterations. In
addition, the ensembles can be pruned using the option\n'newmfinal' in the
predict.bagging() and predict.boosting() functions and the posterior probability
of\neach class for observations can be obtained. Version 3.1 modifies the relative
importance measure\nto take into account the gain of the Gini index given by a
variable in each tree and the weights of\nthese trees. Version 4.0 includes the
margin-based ordered aggregation for Bagging pruning (Guo\nand Boukir, 2013) and a
function to auto prune the 'rpart' tree. Moreover, three new plots are
also\navailable importanceplot(), plot.errorevol() and plot.margins(). Version 4.1
allows to predict on\nunlabeled data.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"adabag","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Applies Multiclass AdaBoost.M1, SAMME and
Bagging","Version":"4.1"},"adagio":{"Author":"Hans Werner Borchers","Depends":"R
(>= 3.0.0)","Description":"\nThe R package 'adagio' will provide methods and
algorithms for\ndiscrete optimization and (evolutionary) global
optimization.","Imports":"graphics, stats, quadprog","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"adagio","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Discrete and Global Optimization
Routines","Version":"0.6.3"},"adaptDA":{"Author":"Charles
Bouveyron","Depends":"MASS","Description":"The adaptive mixture discriminant
analysis (AMDA) allows to adapt a model-based classifier to the situation where a
class represented in the test set may have not been encountered earlier in the
learning phase.","License":"GPL-
2","NeedsCompilation":"no","Package":"adaptDA","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Adaptive Mixture Discriminant
Analysis","Version":"1.0"},"adaptMCMC":{"Author":"Andreas Scheidegger,
<andreas.scheidegger@eawag.ch>,\n<scheidegger.a@gmail.com>","Depends":"R (>=
2.14.1), parallel, coda, Matrix","Description":"This package provides an
implementation of the generic\nadaptive Monte Carlo Markov chain sampler proposed
by Vihola\n(2011).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"adaptMCMC","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Implementation of a generic adaptive Monte Carlo Markov
Chain\nsampler","Version":"1.1"},"adaptTest":{"Author":"Marc
Vandemeulebroecke","Depends":"lattice","Description":"The functions defined in this
program serve for\nimplementing adaptive two-stage tests. Currently, four
tests\nare included: Bauer and Koehne (1994), Lehmacher and Wassmer\n(1999),
Vandemeulebroecke (2006), and the horizontal\nconditional error function. User-
defined tests can also be\nimplemented. Reference: Vandemeulebroecke, An
investigation of\ntwo-stage tests, Statistica Sinica 2006.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"adaptTest","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Adaptive
two-stage tests","Version":"1.0"},"adaptivetau":{"Author":"Philip
Johnson","Depends":"R (>= 2.10.1)","Description":"Implements adaptive tau leaping
to approximate the\ntrajectory of a continuous-time stochastic process
as\ndescribed by Cao et al. (2007) The Journal of Chemical\nPhysics. This package
is based upon work supported by\nNSF DBI-0906041 and NIH K99-GM104158 to Philip
Johnson and\nNIH R01-AI049334 to Rustom
Antia.","Enhances":"compiler","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"adaptivetau","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Tau-leaping stochastic
simulation","Version":"2.2"},"adaptsmoFMRI":{"Author":"Max Hughes","Depends":"R(>=
2.15.2), Matrix, coda, mvtnorm, MCMCpack, spatstat,\nparallel","Description":"This
package contains R functions for estimating the blood\noxygenation level dependent
(BOLD) effect by using functional\nMagnetic Resonance Imaging (fMRI) data, based on
adaptive Gauss\nMarkov random fields, for real as well as simulated data.
The\nimplemented simulations make use of efficient Markov Chain\nMonte Carlo
methods.","License":"GPL-
2","NeedsCompilation":"no","Package":"adaptsmoFMRI","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Adaptive Smoothing of FMRI
Data","Version":"1.1"},"addhaz":{"Author":"Renata T C Yokota, Caspar W N Looman,
Wilma J Nusselder,\nHerman Van Oyen, Geert Molenberghs","Depends":"R (>= 3.1.0),
stats, boot (>= 1.3-17), Matrix (>= 1.2-3), MASS","Description":"Functions to fit
the binomial and multinomial additive hazards models and to calculate the
contribution of diseases\/conditions to the disability prevalence, as proposed by
Nusselder and Looman (2004) <DOI:10.1353\/dem.2004.0017>.","License":"GPL-
3","NeedsCompilation":"no","Package":"addhaz","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Binomial and Multinomial Additive Hazards
Models","Version":"0.3"},"addhazard":{"Author":"Jie (Kate) Hu [aut, cre],\nNorman
Breslow [aut],\nGary Chan [aut]","Depends":"R (>= 3.1.2)","Description":"Contains
tools to fit additive hazards model to random sampling, two-phase sampling and two-
phase sampling with auxiliary information. This package provides regression
parameter estimates and their model-based and robust standard errors. It also
offers tools to make prediction of individual specific hazards.","Imports":"ahaz,
survival, rootSolve","License":"GPL-
2","NeedsCompilation":"no","Package":"addhazard","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Fit Additive Hazards Models for Survival
Analysis","Version":"1.0.0"},"additivityTests":{"Author":"Marie Simeckova [aut],
Thomas Rusch [aut], Petr Simecek [cre]","Description":"Implementation of the Tukey,
Mandel, Johnson-Graybill, LBI, Tusell\nand modified Tukey non-additivity
tests.","License":"GPL-
3","NeedsCompilation":"no","Package":"additivityTests","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"knitr","Title":"Additivity Tests in the Two Way
Anova with Single Sub-
class\nNumbers","URL":"https:\/\/github.com\/simecek\/additivityTests","Version":"1
.1-4"},"addreg":{"Author":"Mark W. Donoghoe <mark.donoghoe@mq.edu.au>","Depends":"R
(>= 3.0.1)","Description":"Methods for fitting identity-link GLMs and GAMs to
discrete data,\nusing EM-type algorithms with more stable convergence properties
than standard methods.","Imports":"splines, combinat, glm2","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"addreg","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Additive Regression for Discrete
Data","Version":"2.0"},"ade4":{"Author":"StÃ©phane Dray <stephane.dray@univ-
lyon1.fr>, Anne-BÃ©atrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean
Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut
Jombart, Sandrine Pavoine, Jean R. Lobry, SÃ©bastien Ollier, and AurÃ©lie
Siberchicot. Based on earlier work by Daniel Chessel.","Depends":"R (>=
2.10)","Description":"Multivariate data analysis and graphical
display.","Imports":"graphics, grDevices, methods, stats, utils","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ade4","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"ade4TkGUI, adegraphics, ape, CircStats, deldir,
lattice,\nmaptools, MASS, pixmap, sp, spdep, splancs, waveslim","Title":"Analysis
of Ecological Data : Exploratory and Euclidean Methods\nin Environmental
Sciences","URL":"http:\/\/pbil.univ-lyon1.fr\/ADE-4, Mailing
list:\nhttp:\/\/listes.univ-lyon1.fr\/wws\/info\/adelist","Version":"1.7-
4"},"ade4TkGUI":{"Author":"Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>,
StÃ©phane Dray <stephane.dray@univ-lyon1.fr>, AurÃ©lie Siberchicot
<aurelie.siberchicot@univ-lyon1.fr>","Depends":"ade4 (>= 1.4-3),
adegraphics","Description":"A Tcl\/Tk GUI for some basic functions in the 'ade4'
package.","Imports":"graphics, grDevices, lattice, stats, tcltk, tkrplot,
2)","NeedsCompilation":"no","Package":"ade4TkGUI","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"pixmap","Title":"'ade4' Tcl\/Tk Graphical User
Interface","URL":"http:\/\/pbil.univ-lyon1.fr\/ade4TkGUI, Mailing
9"},"adegenet":{"Author":"Thibaut Jombart, Zhian N. Kamvar, Roman Lustrik, Caitlin
Collins, Marie-\nPauline Beugin, Brian Knaus, Peter Solymos, Klaus Schliep, Ismail
Ahmed, Anne\nCori, Federico Calboli","Depends":"R (>= 2.14), methods,
ade4","Description":"Toolset for the exploration of genetic and genomic data.
Adegenet\nprovides formal (S4) classes for storing and handling various genetic
data,\nincluding genetic markers with varying ploidy and hierarchical
population\nstructure ('genind' class), alleles counts by populations ('genpop'),
and\ngenome-wide SNP data ('genlight'). It also implements original
multivariate\nmethods (DAPC, sPCA), graphics, statistical tests, simulation tools,
distance\nand similarity measures, and several spatial methods. A range of both
empirical\nand simulated datasets is also provided to illustrate various
methods.","Imports":"utils, stats, grDevices, MASS, igraph, ape, shiny,
ggplot2,\nseqinr, parallel, spdep, boot, reshape2, dplyr (>=
0.4.1),\nvegan","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"adegenet","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"pegas, hierfstat, akima, maps, splancs, adehabitat,
tripack,\ntestthat","Title":"Exploratory Analysis of Genetic and Genomic
Data","URL":"http:\/\/adegenet.r-forge.r-
project.org\/","Version":"2.0.1"},"adegraphics":{"Author":"StÃ©phane Dray
<stephane.dray@univ-lyon1.fr> and AurÃ©lie Siberchicot <aurelie.siberchicot@univ-
lyon1.fr>, with contributions from Jean Thioulouse. Based on earlier work by Alice
Julien-LaferriÃ¨re.","Depends":"R (>= 3.0.2)","Description":"Graphical
functionalities for the representation of multivariate data. It is a complete re-
implementation of the functions available in the 'ade4' package.","Imports":"ade4,
graphics, grid, KernSmooth, lattice, methods,\nRColorBrewer, sp (>= 1.1-1),
2)","NeedsCompilation":"no","Package":"adegraphics","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"Guerry, knitr, maptools, pixmap, rmarkdown, spdep,
splancs","Title":"An S4 Lattice-Based Package for the Representation
of\nMultivariate Data","URL":"http:\/\/pbil.univ-lyon1.fr\/ADE-4, Mailing
5"},"adehabitat":{"Author":"Clement Calenge, contributions from Mathieu Basille,
Stephane Dray and Scott Fortmann-Roe","Depends":"R (>= 2.10.0), ade4, tkrplot,
shapefiles, sp, graphics","Description":"A collection of tools for the analysis of
habitat selection by animals.","Imports":"grDevices, methods, stats,
2)","NeedsCompilation":"yes","Package":"adehabitat","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"spatstat, MASS, CircStats","Title":"Analysis of
Habitat Selection by Animals","Version":"1.8.18"},"adehabitatHR":{"Author":"Clement
Calenge, contributions from Scott Fortmann-Roe","Depends":"R (>= 3.0.1), sp,
methods, deldir, ade4, adehabitatMA,\nadehabitatLT","Description":"A collection of
tools for the estimation of animals home range.","Imports":"graphics, grDevices,
2)","NeedsCompilation":"yes","Package":"adehabitatHR","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"maptools, tkrplot, MASS, rgeos","Title":"Home
Range Estimation","Version":"0.4.14"},"adehabitatHS":{"Author":"Clement Calenge,
contributions from Mathieu Basille","Depends":"R (>= 3.0.1), sp, methods, ade4,
adehabitatMA, adehabitatHR","Description":"A collection of tools for the analysis
of habitat selection.","Imports":"graphics, grDevices, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"adehabitatHS","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"maptools, tkrplot, MASS,
rgeos","Title":"Analysis of Habitat Selection by
Animals","Version":"0.3.12"},"adehabitatLT":{"Author":"Clement Calenge,
contributions from Stephane Dray and Manuela Royer","Depends":"R (>= 2.10.0), sp,
methods, ade4, adehabitatMA, CircStats,\nstats","Description":"A collection of
tools for the analysis of animal movements.","Imports":"graphics, grDevices,
2)","NeedsCompilation":"yes","Package":"adehabitatLT","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"maptools, tkrplot, MASS","Title":"Analysis of
Animal Movements","Version":"0.3.20"},"adehabitatMA":{"Author":"Clement Calenge,
contributions from Mathieu Basille","Depends":"R (>= 2.10.0), sp,
methods","Description":"A collection of tools to deal with raster
maps.","Imports":"utils, graphics, grDevices, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"adehabitatMA","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"maptools,
tkrplot, MASS","Title":"Tools to Deal with Raster
Maps","Version":"0.3.10"},"adephylo":{"Author":"Thibaut Jombart
<t.jombart@imperial.ac.uk>, Stephane Dray <stephane.dray@univ-
lyon1.fr>","Depends":"methods, ade4","Description":"Multivariate tools to analyze
comparative data, i.e. a phylogeny and some traits measured for each
taxa.","Imports":"phylobase, ape, adegenet","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"adephylo","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"adephylo: exploratory analyses for the phylogenetic
comparative\nmethod","Version":"1.1-6"},"adhoc":{"Author":"Gontran
Sonet","Depends":"R (>= 2.15), spider, ape, polynom","Description":"An ad hoc
distance threshold can be calculated for each particular reference library of DNA
barcodes. Specimen identification at this ad hoc distance threshold (using the best
close match method) will produce identifications with an estimated relative error
probability that can be fixed by the user (e.g. 5%)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"adhoc","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"calculate ad hoc distance thresholds for DNA
barcoding\nidentification","URL":"http:\/\/jemu.myspecies.info\/computer-
programs","Version":"1.0"},"adimpro":{"Author":"Karsten Tabelow <tabelow@wias-
berlin.de>, Joerg Polzehl\n<polzehl@wias-berlin.de>","Depends":"R (>= 2.12.0),
grDevices","Description":"This package implements tools for manipulation of
digital\nimages and the Propagation Separation approach by Polzehl and\nSpokoiny
(2006) for smoothing digital images.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"adimpro","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Adaptive Smoothing of Digital
Images","URL":"http:\/\/www.wias-
berlin.de\/software\/imaging\/","Version":"0.7.8"},"adlift":{"Author":"Matt Nunes
<m.nunes@lancs.ac.uk> Marina
Knight","Depends":"EbayesThresh","Description":"Adaptive Wavelet transforms for
signal
denoising","License":"GPL","NeedsCompilation":"yes","Package":"adlift","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Title":"An adaptive lifting scheme
algorithm","Version":"1.3-2"},"ads":{"Author":"R. Pelissier and F.
Goreaud","Description":"Perform first- and second-order multi-scale analyses
derived from Ripley K-function, for univariate,\nmultivariate and marked mapped
data in rectangular, circular or irregular shaped sampling windows, with tests
of\nstatistical significance based on Monte Carlo simulations.","Imports":"ade4,
spatstat","License":"GPL-
2","NeedsCompilation":"yes","Package":"ads","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Spatial point patterns analysis","Version":"1.5-
2.2"},"adwave":{"Author":"Jean
Sanderson","Depends":"waveslim","Description":"Implements wavelet-based approaches
for describing population admixture. Principal Components Analysis (PCA) is used to
define the population structure and produce a localized admixture signal for each
individual. Wavelet summaries of the PCA output describe variation present in the
data and can be related to population-level demographic processes. For more
details, see Sanderson et al. (2015).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"adwave","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Wavelet Analysis of Genomic Data from Admixed
Populations","Version":"1.1"},"aemo":{"Author":"Imanuel Costigan [aut,
cre],\nAustralian Energy Market Operator [cph]","Depends":"R (>=
3.1.0)","Description":"Download and process real time trading prices and demand
data\nfreely provided by the Australian Energy Market Operator (AEMO). Note
that\nthis includes a sample data set.","Imports":"dplyr (>= 0.2), stringr (>=
0.6.2), assertthat (>= 0.1),\nlubridate (>= 1.3.3)","License":"GPL-
2","NeedsCompilation":"no","Package":"aemo","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"testthat, httr (>= 0.3)","Title":"Download and process
AEMO price and demand data","Version":"0.1.0"},"afex":{"Author":"Henrik Singmann
[aut, cre],\nBen Bolker [aut],\nJake Westfall [aut],\nFrederik Aust [aut],\nSÃ¸ren
HÃ¸jsgaard [ctb],\nJohn Fox [ctb],\nMichael A. Lawrence [ctb],\nUlf Mertens
[ctb]","Depends":"R (>= 3.1.0), lme4 (>= 1.1-8), reshape2, lsmeans (>=
2.17)","Description":"Provides convenience functions for analyzing
factorial\nexperiments using ANOVA or mixed models. aov_ez(), aov_car(), and
aov_4() allow\nspecification of between, within (i.e., repeated-measures), or mixed
between-\nwithin (i.e., split-plot) ANOVAs for data in long format (i.e., one
observation\nper row), potentially aggregating multiple observations per individual
and\ncell of the design. mixed() fits mixed models using lme4::lmer() and
computes\np-values for all fixed effects using either Kenward-Roger approximation
for\ndegrees of freedom (LMM only), parametric bootstrap (LMMs and GLMMs),
or\nlikelihood ratio tests (LMMs and GLMMs). afex uses type 3 sums of squares
as\ndefault (imitating commercial statistical software).","Imports":"stringr, coin,
Matrix (>= 1.1.1), pbkrtest (>= 0.4-1), car,\nstats, utils, methods","License":"GPL
(>=
3)","NeedsCompilation":"no","Package":"afex","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"ascii, xtable, parallel, plyr, optimx, nloptr,
knitr,\nlattice, multcomp, testthat, mlmRev, dplyr","Title":"Analysis of Factorial
Experiments","URL":"https:\/\/github.com\/singmann\/afex","Version":"0.16-
1"},"aftgee":{"Author":"Sy Han (Steven) Chiou, Sangwook Kang, Jun
Yan","Description":"This package features both rank-based estimates and
least\nsquare estimates to the Accelerated Failure Time (AFT) model.\nFor rank-
based estimation, it provides approaches that include\nthe computationally
efficient Gehan's weight and the general's\nweight such as the logrank weight.\nFor
the least square estimation, the estimating equation is\nsolved with Generalized
Estimating Equations (GEE).\nMoreover, in multivariate cases, the dependence
working\ncorrelation structure can be specified in GEE's setting.","Imports":"MASS,
BB, survival, geepack","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"aftgee","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"copula","Title":"Accelerated Failure Time Model with
Generalized Estimating\nEquations","Version":"1.0-0"},"agRee":{"Author":"Dai
Feng","Depends":"R (>= 3.0.2), miscF (>= 0.1-2), lme4 (>= 1.0-
4)","Description":"Bland-Altman plot and scatter plot with identity line\nfor
visualization and point and\ninterval estimates for different metrics related
to\nreproducibility\/repeatability\/agreement including\nthe concordance
correlation coefficient,\nintraclass correlation coefficient,\nwithin-subject
coefficient of variation,\nsmallest detectable difference,\nand mean normalized
smallest detectable difference.","Imports":"R2jags (>= 0.03-11), coda (>= 0.16-
1)","License":"GPL","NeedsCompilation":"no","Package":"agRee","Repository":"http:\/
\/cran.csiro.au\/src\/contrib","Title":"Various Methods for Measuring
Agreement","Version":"0.4-0"},"agop":{"Author":"Marek Gagolewski [aut, cre],\nAnna
Cena [ctb]","Depends":"R (>= 2.12.0), stats, grDevices, graphics, Matrix,
igraph","Description":"Tools supporting multi-criteria decision making,
including\nvariable number of criteria, by means of aggregation operators\nand
preordered sets. Possible applications include, but are not\nlimited to,
scientometrics and bibliometrics.","License":"LGPL (>=
3)","NeedsCompilation":"yes","Package":"agop","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Aggregation Operators and Preordered
Sets","URL":"http:\/\/agop.rexamine.com\/","Version":"0.1-4"},"agricolae":
{"Author":"Felipe de Mendiburu","Description":"Original idea was presented in the
thesis \"A statistical analysis tool for agricultural research\" to obtain the
degree of Master on science, National Engineering University (UNI), Lima-Peru. Some
experimental data for the examples come from the CIP and others research. Agricolae
offers extensive functionality on experimental design especially for agricultural
and plant breeding experiments, which can also be useful for other purposes. It
supports planning of lattice, Alpha, Cyclic, Complete Block, Latin Square, Graeco-
Latin Squares, augmented block, factorial, split and strip plot designs. There are
also various analysis facilities for experimental data, e.g. treatment comparison
procedures and several non-parametric tests comparison, biodiversity indexes and
consensus cluster.","Imports":"klaR, MASS, nlme, cluster, spdep, AlgDesign,
graphics","License":"GPL","NeedsCompilation":"no","Package":"agricolae","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Statistical Procedures for
Agricultural
Research","URL":"http:\/\/tarwi.lamolina.edu.pe\/~fmendiburu","Version":"1.2-
3"},"agridat":{"Author":"Kevin Wright","Description":"Datasets from books, papers,
and websites related to agriculture.\nExample analyses are included. Includes
functions for plotting field\ndesigns and GGE biplots.","Imports":"graphics,
grDevices, grid, lattice, reshape2, stats","License":"GPL-
2","NeedsCompilation":"no","Package":"agridat","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"AER, agricolae (>= 1.2), betareg, car, coin,
corrgram,\neffects, equivalence, FrF2, gam, gstat, HH, knitr,\nlatticeExtra, lme4
(>= 1.1-5), lucid, mapproj, maps, MASS,\nMCMCglmm, mgcv, nlme, ordinal, pls, pscl,
qtl, sp, survival,\nvcd","Title":"Agricultural
Datasets","URL":"https:\/\/github.com\/kwstat\/agridat","Version":"1.12"},"agrmt":
{"Author":"Didier Ruedin","Description":"Calculate agreement or consensus in
ordered rating scales. The package implements van der Eijk's (2001) <DOI:
10.1023\/A:1010374114305> measure of agreement A, which can be used to describe
agreement, consensus, or polarization among respondents. It also implements
measures of
consensus (dispersion) by Leik, Tatsle and Wierman, Blair and Lacy, Kvalseth,
Berry and Mielke, and Garcia-Montalvo and Reynal-Querol. Furthermore, an
implementation of Galtungs AJUS-system is provided to classify distributions, as
well as a function to identify the position of multiple modes.","License":"GPL-
3","NeedsCompilation":"no","Package":"agrmt","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Calculate Agreement or Consensus in Ordered Rating
Scales","URL":"http:\/\/agrmt.r-forge.r-
project.org","Version":"1.40.4"},"agsemisc":{"Author":"Lutz Prechelt [aut,
cre]","Depends":"R (>= 2.12.0), lattice","Description":"High-featured panel
functions for bwplot and xyplot,\nsome plot management helpers, various convenience
functions","Imports":"grid, MASS","License":"GPL-
2","NeedsCompilation":"no","Package":"agsemisc","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Miscellaneous plotting and utility
functions","URL":"https:\/\/github.com\/prechelt\/agsemisc","Version":"1.3-
1"},"ahaz":{"Author":"Anders Gorst-Rasmussen <agorstras@gmail.com>","Depends":"R
(>= 2.10), survival, Matrix","Description":"Computationally efficient procedures
for regularized\nestimation with the semiparametric additive hazards
regression\nmodel.","License":"GPL-
2","NeedsCompilation":"yes","Package":"ahaz","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Regularization for semiparametric additive hazards
regression","URL":"http:\/\/www.gorst.dk\/software.htm","Version":"1.14"},"ahp":
{"Author":"Christoph Glur","Depends":"R (>= 3.2.0)","Description":"Model and
analyse complex decision making problems\nusing the Analytic Hierarchy Process
(AHP) by Thomas Saaty.","Imports":"utils, data.tree, yaml, formattable,
DiagrammeR","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ahp","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"shiny, shinyAce, shinythemes, shinyjs, testthat,
knitr,\nrmarkdown","Title":"Analytic Hierarchy
Process","URL":"http:\/\/github.com\/gluc\/ahp","Version":"0.2.8"},"aidar":
{"Author":"Andreas Pfeiffer
<apfeiffer1@gmail.com>","Depends":"XML","Description":"Read objects from the AIDA
file and make them available\nas dataframes in R","License":"LGPL (>=
2)","NeedsCompilation":"no","Package":"aidar","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat","Title":"Tools for reading AIDA
(http:\/\/aida.freehep.org\/) files into R","Version":"1.0.0"},"akima":
{"Author":"Hiroshi Akima [aut, cph] (Fortran code (TOMS 526, 761, 697 and
433)),\nAlbrecht Gebhardt [aut, cre, cph] (R port (interp* functions),
bicubic*\nfunctions),\nThomas Petzold [ctb, cph] (aspline function),\nMartin
Maechler [ctb, cph] (interp2xyz function + enhancements),\nYYYY Association for
Computing Machinery, Inc. [cph] (covers code from\nTOMS 526, 761, 697 and
433)","Depends":"R (>= 2.0.0)","Description":"Several cubic spline interpolation
methods of H. Akima for irregular and\nregular gridded data are available through
this package, both for the bivariate case\n(irregular data: ACM 526 and ACM 761,
regular data: ACM 433) and univariate case (ACM 697).\nLinear interpolation of
irregular gridded data is also covered by reusing D. J. Renkas\ntriangulation code
which is part of Akimas Fortran code.","Imports":"sp","License":"ACM | file
LICENSE","NeedsCompilation":"yes","Package":"akima","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Interpolation of Irregularly and Regularly Spaced
Data","Version":"0.5-12"},"akmeans":{"Author":"Jungsuk
Kwac","Description":"Adaptive K-means algorithm with various threshold
settings.\nIt support two distance metric:\nEuclidean distance, Cosine distance (1
- cosine similarity)\nIn version 1.1, it contains one more threshold
condition.","License":"GPL-
2","NeedsCompilation":"no","Package":"akmeans","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Adaptive Kmeans algorithm based on
threshold","Version":"1.1"},"alabama":{"Author":"Ravi Varadhan (with contributions
from Gabor Grothendieck)","Depends":"R (>= 2.10.1),
numDeriv","Description":"Augmented Lagrangian Adaptive Barrier
Minimization\nAlgorithm for optimizing smooth nonlinear objective functions\nwith
constraints. Linear or nonlinear equality and inequality\nconstraints are
allowed.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"alabama","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Constrained Nonlinear Optimization","Version":"2015.3-
1"},"alakazam":{"Author":"Jason Vander Heiden [aut, cre],\nNamita Gupta
[aut],\nDaniel Gadala-Maria [ctb],\nSusanna Marquez [ctb],\nRoy Jiang
[ctb],\nSteven Kleinstein [aut, cph]","Depends":"R (>= 3.1.2), ggplot2 (>=
2.0.0)","Description":"Provides immunoglobulin (Ig) sequence lineage
reconstruction,\ndiversity profiling, and amino acid property analysis. Also
provides\ncore functionality for other tools in the Change-O
suite.","Imports":"dplyr, graphics, grid, igraph (>= 1.0.0), lazyeval,
methods,\nscales, seqinr, stats, stringi, utils","License":"CC BY-NC-SA
4.0","NeedsCompilation":"no","Package":"alakazam","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr, rmarkdown, testthat","Title":"Immunoglobulin
Clonal Lineage and Diversity
Analysis","URL":"http:\/\/clip.med.yale.edu\/changeo","Version":"0.2.3"},"ald":
{"Author":"Christian E. Galarza <cgalarza88@gmail.com> and Victor H. Lachos
<hlachos@ime.unicamp.br>","Description":"It provides the density, distribution
function, quantile function,\nrandom number generator, likelihood function, moments
and Maximum Likelihood estimators for a given sample, all this for\nthe three
parameter Asymmetric Laplace Distribution defined\nin Koenker and Machado (1999)
useful for quantile regression.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ald","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"The Asymmetric Laplace
Distribution","Version":"1.0"},"algstat":{"Author":"David Kahle [aut, cre],\nLuis
Garcia-Puente [aut]","Depends":"mpoly","Description":"algstat provides
functionality for algebraic statistics in R.\nCurrent applications include exact
inference in log-linear models for\ncontingency table data, analysis of ranked and
partially ranked data, and\ngeneral purpose tools for multivariate polynomials,
building on the mpoly\npackage. To aid in the process, algstat has ports to
Macaulay2, Bertini,\nLattE-integrale and 4ti2.","Imports":"stringr, reshape2,
Rcpp","License":"GPL-
2","NeedsCompilation":"yes","Package":"algstat","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Algebraic statistics in R","Version":"0.0.2"},"alineR":
{"Author":"Sean Downey [aut, cre],\nGuowei Sun [aut]","Description":"Functions are
provided to calculate the 'ALINE' Distance between words. The score is based on
phonetic features represented using the Unicode-compliant International Phonetic
Alphabet (IPA). Parameterized features weights are used to determine the optimal
alignment and functions are provided to estimate optimum values.","License":"GPL-
3","NeedsCompilation":"yes","Package":"alineR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Alignment of Phonetic Sequences Using the 'ALINE'
Algorithm","Version":"1.1.3"},"allan":{"Author":"Alan
Lee","Depends":"biglm","Description":"Automated fitting of linear regression models
and a\nstepwise
routine","License":"GPL","NeedsCompilation":"no","Package":"allan","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"Automated Large Linear Analysis
Node","Version":"1.01"},"allanvar":{"Author":"Javier Hidalgo Carrio","Depends":"R
(>= 2.10.0), gplots","Description":"A collection of tools for stochastic sensor
error\ncharacterization using the Allan Variance technique originally\ndeveloped by
D. Allan.","License":"GPL-
2","NeedsCompilation":"no","Package":"allanvar","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Allan Variance Analysis","Version":"1.1"},"alleHap":
{"Author":"Nathan Medina-Rodriguez and Angelo Santana","Description":"Simulation of
alphanumeric alleles, imputation of genetic missing data and reconstruction of non-
recombinant haplotypes from pedigree databases in a deterministic way. Allelic
simulations can be implemented taking into account many different factors (such as
number of families, markers, alleles per marker, probability and proportion of
missing genotypes, recombination rate, etc). Genotype imputation can be used either
simulated datasets or loaded databases (in .ped file biallelic format). Haplotype
reconstruction can be performed even with missing data because of alleHap, firstly
imputes the genotypes. All this considering that each member (due to meiosis)
should unequivocally have two alleles, one inherited from each
parent.","Imports":"abind, tools, stats, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"alleHap","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr","Title":"Allele Imputation and Haplotype
Reconstruction from Pedigree\nDatabases","Version":"0.9.2"},"allelematch":
{"Author":"Paul Galpern
<pgalpern@gmail.com>","Depends":"dynamicTreeCut","Description":"This package
provides tools for the identification of unique of multilocus genotypes when both
genotyping error and missing data may be present. The package is targeted at those
working with large datasets and databases containing multiple samples of each
individual, a situation that is common in conservation genetics, and particularly
in non-invasive wildlife sampling applications. Functions explicitly incorporate
missing data, and can tolerate allele mismatches created by genotyping error. If
you use this tool, please cite the package using the journal article in Molecular
Ecology Resources (Galpern et al., 2012). Please use citation('allelematch') to
find this. Due to changing CRAN policy, and the size and compile time of the
vignettes, they can no longer be distributed
with this package. Please contact the package primary author, or visit the
allelematch site for a complete vignette
(http:\/\/nricaribou.cc.umanitoba.ca\/allelematch\/). For users with access to
academic literature, tutorial material is also available as supplementary material
to the article describing this software.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"allelematch","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Identifying unique multilocus genotypes where
genotyping error\nand missing data may be
present","URL":"http:\/\/nricaribou.cc.umanitoba.ca\/allelematch\/","Version":"2.5"
},"allelic":{"Author":"Karl Forner <Karl.Forner@gmail.com>","Description":"This is
the implementation in R+C of a new association\ntest described in \"A fast,
unbiased and exact allelic exact\ntest for case-control association studies\"
(Submitted). It\nappears that in most cases the classical chi-square test
used\nfor testing for allelic association on genotype data is biased.\nOur test is
unbiased, exact but fast throught careful\noptimization.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"allelic","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"A fast, unbiased and exact allelic exact
test","Version":"0.1"},"alm":{"Author":"Scott Chamberlain [aut, cre],\nCarl
Boettiger [aut],\nKarthik Ram [aut],\nFenner Martin [aut]","Description":"An R
interface to the open source article level metrics
platform\n<https:\/\/github.com\/articlemetrics\/lagotto\/> created by the Public
Library\nof Science (PLOS). A number of publishers are using the open source
app\ncreated by PLOS, so you can drop in a different base URL to the functions\nin
this package to get to not only PLOS data, but data for Crossref,\nand more as the
open source PLOS software is used.","Imports":"ggplot2, plyr, stringr, reshape,
reshape2, httr, grid,\njsonlite, lubridate","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"alm","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat, roxygen2, rplos, knitr","Title":"R Client
for the Lagotto Altmetrics
Platform","URL":"https:\/\/github.com\/ropensci\/alm","Version":"0.4.0"},"alphaOutl
ier":{"Author":"Andre Rehage, Sonja Kuhnt","Depends":"Rsolnp, nleqslv,
quantreg","Description":"Given the parameters of a distribution, the package uses
the concept of alpha-outliers by Davies and Gather (1993) to flag outliers in a
data set. See Davies, L.; Gather, U. (1993): The identification of multiple
outliers, JASA, 88 423, 782-792, doi: 10.1080\/01621459.1993.10476339 for
details.","License":"GPL-
3","NeedsCompilation":"no","Package":"alphaOutlier","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Obtain Alpha-Outlier Regions for Well-Known
Probability\nDistributions","Version":"1.1.0"},"alphahull":{"Author":"Beatriz
Pateiro-Lopez [aut, cre], Alberto Rodriguez-Casal,
[aut].","Description":"Computation of the alpha-shape and alpha-convex\nhull of a
given sample of points in the plane. The concepts of\nalpha-shape and alpha-convex
hull generalize the definition of\nthe convex hull of a finite set of points. The
programming is\nbased on the duality between the Voronoi diagram and
Delaunay\ntriangulation. The package also includes a function that\nreturns the
Delaunay mesh of a given sample of points and its\ndual Voronoi diagram in one
single object.","Imports":"ggplot2, tripack, R.utils, sgeostat, spatstat,
splancs","License":"file
LICENSE","NeedsCompilation":"yes","Package":"alphahull","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Generalization of the Convex Hull of a Sample of
Points in the\nPlane","Version":"2.1"},"alphashape3d":{"Author":"Thomas Lafarge,
Beatriz Pateiro-Lopez","Depends":"geometry, rgl","Description":"Implementation in R
of the alpha-shape of a finite set of points in the three-dimensional space. The
alpha-shape generalizes the convex hull and allows to recover the shape of non-
convex and even non-connected sets in 3D, given a random sample of points taken
into it. Besides the computation of the alpha-shape, this package provides users
with functions to compute the volume of the alpha-shape, identify the connected
components and facilitate the three-dimensional graphical visualization of the
estimated set.","License":"GPL-
2","NeedsCompilation":"yes","Package":"alphashape3d","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"alphahull","Title":"Implementation of the 3D
Alpha-Shape for the Reconstruction of\n3D Sets from a Point
Cloud","Version":"1.2"},"alr3":{"Author":"Sanford Weisberg
<sandy@umn.edu>","Depends":"R (>= 2.1.1), car","Description":"This package is a
companion to the textbook S. Weisberg (2005),\n\"Applied Linear Regression,\" 3rd
edition, Wiley. It includes all the\ndata sets discussed in the book (except one),
and a few functions that\nare tailored to the methods discussed in the book. As of
version 2.0.0,\nthis package depends on the car package. Many functions
formerly\nin alr3 have been renamed and now reside in car.\nData files have beeen
lightly modified to make some data columns row labels.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"alr3","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Data to accompany Applied Linear Regression 3rd
edition","URL":"http:\/\/www.r-project.org,
http:\/\/www.stat.umn.edu\/alr","Version":"2.0.5"},"alr4":{"Author":"Sanford
Weisberg <sandy@umn.edu>","Depends":"R (>= 2.1.1), car,
effects","Description":"This package is a companion to the textbook S. Weisberg
(2014),\n\"Applied Linear Regression,\" 4rd edition, Wiley. It includes all
the\ndata sets discussed in the book and one function to access the
textbook's\nwebsite.\nThis package depends on the car package. Many data files in
this package\nare included in the alr3 package as well, so only one of them should
be\nloaded.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"alr4","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Data to accompany Applied Linear Regression 4rd
edition","URL":"http:\/\/www.r-project.org,
http:\/\/www.z.umn.edu\/alr4ed","Version":"1.0.5"},"altmeta":{"Author":"Lifeng Lin
and Haitao Chu","Depends":"R (>= 2.14.0)","Description":"Provides alternative
statistical methods for meta-analysis, including new heterogeneity tests and
measures that are robust to outliers, and measures of publication
bias.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"altmeta","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Alternative Meta-Analysis
Methods","Version":"2.0"},"amap":{"Author":"Antoine Lucas","Depends":"R (>=
2.10.0)","Description":"Tools for Clustering and Principal Component
Analysis\n(With robust methods, and parallelized
functions).","License":"GPL","NeedsCompilation":"yes","Package":"amap","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"Biobase","Title":"Another
Multidimensional Analysis
Package","URL":"http:\/\/mulcyber.toulouse.inra.fr\/projects\/amap\/","Version":"0.
8-14"},"ameco":{"Author":"Eric Persson [aut, cre]","Depends":"R(>=
2.10.0)","Description":"Annual macro-economic database provided by the European
Commission.","License":"CC0","NeedsCompilation":"no","Package":"ameco","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"knitr, rmarkdown, dplyr,
ggplot2, testthat, xml2","Title":"European Commission Annual Macro-Economic (AMECO)
Database","URL":"http:\/\/github.com\/expersso\/ameco","Version":"0.2.2"},"amei":
{"Author":"Daniel Merl <danmerl@gmail.com>, Leah R. Johnson
<lrjohnson@uchicago.edu>, Robert B. Gramacy <rbgramacy@chicagobooth.edu>, and Marc
S. Mangel <msmangel@ams.ucsc.edu>","Description":"\nThis package provides a
flexible statistical framework for generating optimal\nepidemiological
interventions that are designed to minimize the total expected\ncost of an emerging
epidemic while simultaneously propagating uncertainty regarding\nunderlying disease
parameters through to the decision process via Bayesian posterior\ninference. The
strategies produced through this framework are adaptive: vaccination\nschedules are
iteratively adjusted to reflect the anticipated trajectory of the\nepidemic given
the current population state and updated parameter
estimates.","License":"GPL","NeedsCompilation":"yes","Package":"amei","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Title":"Adaptive Management of
Epidemiological Interventions","Version":"1.0-7"},"amen":{"Author":"Peter Hoff,
Bailey Fosdick, Alex Volfovsky, Yanjun He","Depends":"R (>=
3.2.0)","Description":"Analysis of dyadic network and relational data using
additive and\nmultiplicative effects (AME) models. The basic model
includes\nregression terms, the covariance structure of the social relations
model\n(Warner, Kenny and Stoto (1979), Wong (1982)), and multiplicative
factor\nmodels (Hoff(2009)). Four different link functions accommodate
different\nrelational data structures, including binary\/network data (bin),
normal\nrelational data (nrm), ordinal relational data (ord) and data from\nfixed-
rank nomination schemes (frn). Several of these link functions are\ndiscussed in
Hoff, Fosdick, Volfovsky and Stovel (2013). Development of this\nsoftware was
supported in part by NIH grant R01HD067509.","License":"GPL-
3","NeedsCompilation":"no","Package":"amen","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"coda,network,knitr","Title":"Additive and Multiplicative
Effects Models for Networks and\nRelational Data","Version":"1.1"},"aml":
{"Author":"Dong Wang","Depends":"R (>= 2.10), lars","Description":"This package
implements the adaptive mixed lasso (AML) method proposed by Wang et al.(2011).
AML applies adaptive lasso penalty to a large number of predictors, thus producing
a sparse model, while accounting for the population structure in the linear mixed
model framework. The package here is primarily
designed for application to genome wide association studies or genomic prediction
in plant breeding populations, though it could be applied to other settings of
linear mixed models.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"aml","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"MASS","Title":"Adaptive Mixed
LASSO","URL":"http:\/\/www.r-project.org","Version":"0.1-1"},"anacor":
{"Author":"Patrick Mair [aut, cre], Jan De Leeuw [aut]","Depends":"R (>=
3.0.2)","Description":"Performs simple and canonical CA (covariates on
rows\/columns) on a two-way frequency table (with missings) by means of SVD.
Different scaling methods (standard, centroid, Benzecri, Goodman) as well as
various plots including confidence ellipsoids are provided.","Imports":"graphics,
stats, car, scatterplot3d, colorspace, fda, rgl,\nsplines,
2","NeedsCompilation":"yes","Package":"anacor","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Simple and Canonical Correspondence
Analysis","URL":"http:\/\/r-forge.r-
project.org\/projects\/psychor\/","Version":"1.0-6"},"analogsea":{"Author":"Scott
Chamberlain [aut, cre],\nHadley Wickham [aut],\nWinston Chang [aut],\nRStudio
[cph]","Description":"Provides a set of functions for interacting with
the\n'Digital Ocean' 'API' at
https:\/\/developers.digitalocean.com\/documentation\/v2\/,\nincluding creating
images, destroying them, 'rebooting',\ngetting details on regions, and available
images.","Imports":"stats, utils, httr (>= 1.0.0), jsonlite (>= 0.9.17),
magrittr,\nyaml","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"analogsea","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat, knitr","Title":"Interface to 'Digital
Ocean'","URL":"https:\/\/github.com\/sckott\/analogsea","Version":"0.3.0"},"analogu
e":{"Author":"Gavin L. Simpson [aut, cre],\nJari Oksanen [aut]","Depends":"R (>=
2.15.0), vegan (>= 2.2-0)","Description":"Fits Modern Analogue Technique and
Weighted Averaging transfer\nfunction models for prediction of environmental data
from species\ndata, and related methods used in palaeoecology.","Imports":"mgcv,
MASS, stats, graphics, grid, brglm, princurve, lattice","License":"GPL-
2","NeedsCompilation":"yes","Package":"analogue","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat","Title":"Analogue and Weighted Averaging
Methods for
Palaeoecology","URL":"https:\/\/github.com\/gavinsimpson\/analogue","Version":"0.17
-0"},"analogueExtra":{"Author":"Gavin L. Simpson [aut, cre]","Depends":"vegan3d (>=
0.65-0), analogue (>= 0.16-0)","Description":"Provides additional functionality for
the analogue package\nthat is not required by all users of the main
package.","Imports":"rgl","License":"GPL-
2","NeedsCompilation":"yes","Package":"analogueExtra","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat","Title":"Additional Functions for Use
with the Analogue
Package","URL":"https:\/\/github.com\/gavinsimpson\/analogueExtra","Version":"0.1-
1"},"analyz":{"Author":"Rodrigo Buhler","Depends":"R (>=
2.15.1)","Description":"Class with methods to read and execute R commands described
as steps in a CSV file.","Imports":"methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"analyz","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Model Layer for Automatic Data Analysis via CSV
File\nInterpretation","Version":"1.4"},"anametrix":{"Author":"Roman
Jugai","Depends":"R (>= 1.8.0), RCurl, XML, pastecs","Description":"Bidirectional
connector to Anametrix
API","License":"LGPL","NeedsCompilation":"no","Package":"anametrix","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Title":"Bidirectional connector to Anametrix
API","Version":"1.6"},"anapuce":{"Author":"J. Aubert (INRA)","Description":"This
package contains functions for\nnormalisation,differentially analysis of microarray
data and\nothers functions implementing recent methods developed by the\nStatistic
and Genom Team from UMR 518 AgroParisTech\/INRA Appl.\nMath. Comput.
Sc.","License":"GPL-
2","NeedsCompilation":"no","Package":"anapuce","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Tools for microarray data
analysis","Version":"2.2"},"anchors":{"Author":"Wand, Jonathan and Gary King, and
Olivia Lau","Depends":"R (>= 2.4.0), rgenoud, MASS","Description":"Tools for
analyzing survey responses with anchors.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"anchors","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Statistical analysis of surveys with anchoring
vignettes","URL":"http:\/\/wand.stanford.edu\/anchors","Version":"3.0-
8"},"andrews":{"Author":"Jaroslav Myslivec
<jaroslav.myslivec@upce.cz>","Depends":"R (>= 2.9.1)","Description":"Andrews curves
for visualization of multidimensional data","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"andrews","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Andrews curves","Version":"1.0"},"anesrake":
{"Author":"Josh Pasek","Depends":"Hmisc","Description":"This package provides a
comprehensive system for selecting\nvariables and weighting data to match the
specifications of the\nAmerican National Election Studies. The package
includes\nmethods for identifying discrepant variables, raking data, and\nassessing
the effects of the raking algorithm. It also allows\nautomated re-raking if target
variables fall outside identified\nbounds and allows greater user specification
than other\navailable raking algorithms. A variety of simple weighted\nstatistics
that were previously in this package (version .55\nand earlier) have been moved to
the package 'weights.'","License":"GPL-
2","NeedsCompilation":"no","Package":"anesrake","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"ANES Raking Implementation","Version":"0.70"},"anfis":
{"Author":"Cristobal Fresno, Andrea S. Llera and Elmer A. Fernandez","Depends":"R
(>= 3.0), methods, parallel","Description":"The package implements ANFIS Type 3
Takagi and Sugeno's fuzzy\nif-then rule network with the following features: (1)
Independent number of\nmembership functions(MF) for each input, and also different
MF extensible\ntypes. (2) Type 3 Takagi and Sugeno's fuzzy if-then rule (3) Full
Rule\ncombinations, e.g. 2 inputs 2 membership funtions -> 4 fuzzy rules
(4)\nHibrid learning, i.e. Descent Gradient for precedents and Least
Squares\nEstimation for consequents (5) Multiple outputs.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"anfis","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Adaptive Neuro Fuzzy Inference System in
R","URL":"http:\/\/www.bdmg.com.ar","Version":"0.99.1"},"anim.plots":
{"Author":"David Hugh-Jones <davidhughjones@gmail.com>","Description":"Simple
animated versions of basic R plots, using the 'animation'\npackage. Includes
animated versions of plot, barplot, persp, contour,\nfilled.contour, hist, curve,
points, lines, text, symbols, segments,
and\narrows.","Imports":"animation","License":"GPL-
2","NeedsCompilation":"no","Package":"anim.plots","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"maps, knitr","Title":"Simple Animated Plots For
R","Version":"0.1"},"animalTrack":{"Author":"Ed Farrell and Lee
Fuiman","Depends":"R (>= 2.10.0), rgl","Description":"2D and 3D animal tracking
data can be used to reconstruct tracks through time\/space with correction based on
known positions. 3D visualization of animal position and attitude.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"animalTrack","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Animal track reconstruction for high frequency 2-
dimensional\n(2D) or 3-dimensional (3D) movement
data","Version":"1.0.0"},"animation":{"Author":"Yihui Xie [cre, aut],\nChristian
Mueller [ctb],\nLijia Yu [ctb],\nWeicheng Zhu [ctb]","Depends":"R (>=
2.14.0)","Description":"Provides functions for animations in statistics, covering
topics in\nprobability theory, mathematical statistics, multivariate
statistics,\nnonparametric statistics, sampling survey, linear models, time
series,\ncomputational statistics, data mining and machine learning. These
functions\nmay be helpful in teaching statistics and data analysis. Also provided
in\nthis package are a series of functions to save animations to various
formats,\ne.g. Flash, GIF, HTML pages, PDF and videos (saveSWF(),
saveGIF(),\nsaveHTML(), saveLatex(), and saveVideo() respectively). PDF animations
can\nbe inserted into Sweave\/knitr
easily.","License":"GPL","NeedsCompilation":"no","Package":"animation","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"MASS, testit","Title":"A
Gallery of Animations in Statistics and Utilities to
Create\nAnimations","URL":"http:\/\/yihui.name\/animation","Version":"2.4"},"anoint
":{"Author":"Ravi Varadhan <rvaradhan@jhmi.edu> and Stephanie
Kovalchik","Depends":"R (>= 2.13.0), stats, survival, MASS, graphics,
grid","Description":"The tools in this package are intended to help researchers
assess multiple treatment-covariate interactions with data from a parallel-group
randomized controlled clinical trial.","Imports":"methods, glmnet","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"anoint","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Analysis of Interactions","Version":"1.4"},"anominate":
{"Author":"Royce Carroll <rcarroll@rice.edu>, Christopher Hare <chare@uga.edu>,
Jeffrey B. Lewis <jblewis@ucla.edu>, James Lo <lo@uni-mannheim.de>, Keith T. Poole
<ktpoole@uga.edu>, and Howard Rosenthal <hl31@nyu.edu>","Depends":"coda, wnominate,
oc, pscl, MCMCpack","Description":"Fits ideal point model described in Carroll,
Lewis, Lo, Poole and Rosenthal, \"The Structure of Utility in Models of Spatial
Voting,\" American Journal of Political Science 57(4): 1008--1028.","License":"GPL-
2","NeedsCompilation":"yes","Package":"anominate","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"alpha-NOMINATE
Ideal Point
Estimator","URL":"http:\/\/www.voteview.com\/alphanominate.asp","Version":"0.5"},"a
nonymizer":{"Author":"Paul Hendricks [aut, cre]","Depends":"R (>=
3.1.2)","Description":"Allows users to quickly and easily anonymize data
containing\nPersonally Identifiable Information (PII) through convenience
functions.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"anonymizer","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"digest, testthat","Title":"Anonymize Data
Containing Personally Identifiable
Information","URL":"https:\/\/github.com\/paulhendricks\/anonymizer","Version":"0.2
.0"},"antitrust":{"Author":"Charles Taragin and Michael Sandfort","Description":"A
collection of tools for antitrust practitioners, including the ability to calibrate
different consumer demand systems and simulate the effects mergers under different
competitive regimes.","Imports":"methods, MASS, evd, BB, numDeriv,
ggplot2","License":"Unlimited","NeedsCompilation":"no","Package":"antitrust","Repos
itory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Tools for Antitrust
Practitioners","Version":"0.95.1"},"aod":{"Author":"Matthieu Lesnoff
<matthieu.lesnoff@cirad.fr> and Renaud\nLancelot
<renaud.lancelot@cirad.fr>","Depends":"R (>= 2.0.0), methods,
stats","Description":"This package provides a set of functions to
analyse\noverdispersed counts or proportions. Most of the methods are\nalready
available elsewhere but are scattered in different\npackages. The proposed
functions should be considered as\ncomplements to more sophisticated methods such
as generalized\nestimating equations (GEE) or generalized linear mixed
effect\nmodels (GLMM).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"aod","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"MASS, boot, lme4","Title":"Analysis of Overdispersed
Data","URL":"http:\/\/cran.r-project.org\/package=aod","Version":"1.3"},"aods3":
{"Author":"Matthieu Lesnoff <matthieu.lesnoff@cirad.fr> and Renaud\nLancelot
<renaud.lancelot@cirad.fr>","Depends":"R (>= 3.0.0), methods, stats, lme4,
boot","Description":"This package provides functions to analyse
overdispersed\ncounts or proportions. These functions should be considered
as\ncomplements to more sophisticated methods such as generalized\nestimating
equations (GEE) or generalized linear mixed effect\nmodels (GLMM). aods3 is an S3
re-implementation of the\ndeprecated S4 package aod.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"aods3","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"MASS, gamlss","Title":"Analysis of Overdispersed Data
using S3 methods","Version":"0.4-1"},"aoos":{"Author":"Sebastian Warnholz [aut,
cre]","Depends":"methods, R(>= 3.2.0)","Description":"Another implementation of
object-orientation in R. It provides\nsyntactic sugar for the S4 class system and
two alternative new\nimplementations. One is an experimental version built around
S4\nand the other one makes it more convenient to work with lists as
objects.","Imports":"magrittr, utils, roxygen2","License":"GPL-3 | file
LICENSE","NeedsCompilation":"no","Package":"aoos","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat, knitr, microbenchmark,
R6","Title":"Another Object Orientation
System","URL":"https:\/\/wahani.github.io\/aoos","Version":"0.4.0"},"aop":
{"Author":"Lyle D. Burgoon <Lyle.D.Burgoon@usace.army.mil>","Description":"Provides
tools for analyzing adverse outcome pathways\n(AOPs) for pharmacological and
toxicological research. Functionality\nincludes the ability to perform causal
network analysis of networks\ndeveloped in and exported from Cytoscape or existing
as R graph objects, and\nidentifying the point of departure\/screening\/risk value
from concentration-\nresponse data.","Imports":"graph (>= 1.38.3), rjson (>=
0.2.14), igraph (>= 0.7.1),\nRgraphviz (>= 2.10.0), methods, plyr (>= 1.8.3),
ggplot2 (>=\n1.0.1),
splines","License":"CC0","NeedsCompilation":"no","Package":"aop","Repository":"http
:\/\/cran.csiro.au\/src\/contrib","Suggests":"RUnit, knitr, rmarkdown,
BiocGenerics","Title":"Adverse Outcome Pathway
Analysis","Version":"1.0.0"},"aoristic":{"Author":"George
Kikuchi","Depends":"ggplot2, spatstat, GISTools","Description":"'Aoristic' is one
of the past tenses in Greek and represents an\nuncertain occurrence time. Aoristic
analysis suggested by Ratcliffe (2002)\nis a method to analyze events that do not
have exact times of occurrence\nbut have starting times and ending times. For
example, a property crime\ndatabase (e.g., burglary) typically has a starting time
and ending time of\nthe crime that could have occurred. Aoristic analysis
allocates the\nprobability of a crime incident occurring at every hour over a 24-
hour\nperiod. The probability is aggregated over a study area to create
an\naoristic graph.\nUsing crime incident data with lat\/lon, DateTimeFrom,
and\nDateTimeTo, functions in this package create a total of three (3) kml\nfiles
and corresponding aoristic graphs: 1) density and contour; 2) grid\ncount; and 3)
shapefile boundary. (see
also:\nhttps:\/\/sites.google.com\/site\/georgekick\/software)","Imports":"lubridat
e, classInt, reshape2, rgdal, plotKML, MASS, sp,\nmaptools,
2)","NeedsCompilation":"no","Package":"aoristic","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"aoristic analysis with spatial output
(kml)","Version":"0.6"},"apTreeshape":{"Author":"Nicolas Bortolussi, Eric Durand,
Michael Blum\n<michael.blum@imag.fr>, Olivier
Francois\n<olivier.francois@imag.fr>","Depends":"R (>= 2.0.0),
ape","Description":"apTreeshape is mainly dedicated to simulation and analysis\nof
phylogenetic tree topologies using statistical indices. It\nis a companion library
of the 'ape' package. It provides\nadditional functions for reading, plotting,
manipulating\nphylogenetic trees. It also offers convenient web-access to\npublic
databases, and enables testing null models of\nmacroevolution using corrected test
statistics. Trees of class\n\"phylo\" (from 'ape' package) can be converted
easily.","Imports":"quantreg","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"apTreeshape","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Analyses of Phylogenetic Treeshape","Version":"1.4-
5"},"apaStyle":{"Author":"Jort de Vreeze [aut, cre]","Depends":"R (>=
3.0.0)","Description":"Most psychological journals require that tables in a
manuscript comply to APA (American Association of Psychology) standards. Creating
APA tables manually is often time consuming and prone to transcription errors. This
package generates tables for MS Word ('.docx' extension) in APA format
automatically with just a few lines of code.","Imports":"ReporteRs, stats,
3","NeedsCompilation":"no","Package":"apaStyle","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"testthat","Title":"Generate APA Tables for MS
Word","Version":"0.2"},"apaTables":{"Author":"David Stanley [aut,
cre]","Depends":"R (>= 3.1.2)","Description":"A common task faced by researchers is
the creation of APA style (i.e., American Psychological Association style) tables
from statistical output. In R a large number of function calls are often needed to
obtain all of the desired information for a single APA style table. As well, the
process of manually creating APA style tables in a word processor is prone to
transcription errors. This package creates Word files (.doc files) containing APA
style tables for several types of analyses. Using this package minimizes
transcription errors and reduces the number commands needed by the
user.","Imports":"rockchalk, stats, utils, methods, MBESS,
car","License":"Unlimited","NeedsCompilation":"no","Package":"apaTables","Repositor
y":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Create American Psychological
Association (APA) Style Tables","Version":"1.0.4"},"apc":{"Author":"Bent
Nielsen","Description":"Functions for age-period-cohort analysis. The data can be
organised in matrices indexed by age-cohort, age-period or cohort-period. The data
can include dose and response or just doses. The statistical model is a
generalized linear model (GLM) allowing for 3,2,1 or 0 of the age-period-cohort
factors. The canonical parametrisation of Kuang, Nielsen and Nielsen (2008) is
used. Thus, the analysis does not rely on ad hoc
identification.","Imports":"lattice","License":"GPL-
3","NeedsCompilation":"no","Package":"apc","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Age-Period-Cohort Analysis","Version":"1.2"},"apcluster":
{"Author":"Ulrich Bodenhofer, Johannes Palme, Chrats Melkonian, Andreas
Kothmeier","Depends":"R (>= 3.0.0)","Description":"Implements Affinity Propagation
clustering introduced by Frey and\nDueck (2007) <DOI:10.1126\/science.1136800>. The
algorithms are largely\nanalogous to the 'Matlab' code published by Frey and
Dueck.\nThe package further provides leveraged affinity propagation and
an\nalgorithm for exemplar-based agglomerative clustering that can also be\nused to
join clusters obtained from affinity propagation. Various\nplotting functions are
available for analyzing clustering results.","Imports":"Rcpp (>= 0.11.1), methods,
Matrix, stats, graphics, grDevices","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"apcluster","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"Biostrings, kebabs, knitr","Title":"Affinity
Propagation
Clustering","URL":"http:\/\/www.bioinf.jku.at\/software\/apcluster\/","Version":"1.
4.3"},"ape":{"Author":"Emmanuel Paradis [aut, cre, cph],\nSimon Blomberg [aut,
cph],\nBen Bolker [aut, cph],\nJulien Claude [aut, cph],\nHoa Sien Cuong [aut,
cph],\nRichard Desper [aut, cph],\nGilles Didier [aut, cph],\nBenoit Durand [aut,
cph],\nJulien Dutheil [aut, cph],\nOlivier Gascuel [aut, cph],\nChristoph Heibl
[aut, cph],\nAnthony Ives [aut, cph],\nDaniel
Lawson [aut, cph],\nVincent Lefort [aut, cph],\nPierre Legendre [aut, cph],\nJim
Lemon [aut, cph],\nRosemary McCloskey [aut, cph],\nJohan Nylander [aut,
cph],\nRainer Opgen-Rhein [aut, cph],\nAndrei-Alin Popescu [aut, cph],\nManuela
Royer-Carenzi [aut, cph],\nKlaus Schliep [aut, cph],\nKorbinian Strimmer [aut,
cph],\nDamien de Vienne [aut, cph]","Depends":"R (>=
3.0.0)","Description":"Functions for reading, writing, plotting, and manipulating
phylogenetic trees, analyses of comparative data in a phylogenetic framework,
ancestral character analyses, analyses of diversification and macroevolution,
computing distances from allelic and nucleotide data, reading and writing
nucleotide sequences as well as importing from BioConductor, and several tools such
as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic
data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-
like trees using mean path lengths and penalized likelihood. Phylogeny estimation
can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several
methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the
corresponding triangle method). Some functions call external applications (PhyML,
Clustal, T-Coffee, Muscle) whose results are returned into R.","Imports":"nlme,
lattice, graphics, methods, stats, tools, utils,\nparallel","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ape","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"gee, expm","Title":"Analyses of Phylogenetics and
Evolution","URL":"http:\/\/ape-package.ird.fr\/","Version":"3.4"},"apex":
{"Author":"Thibaut Jombart [aut, cre],\nZhian Namir Kamvar [aut],\nKlaus Schliep
[aut],\nEric Archer [aut],\nRebecca Harris [aut]","Depends":"R (>= 3.1.3), methods,
ape, phangorn","Description":"Toolkit for the analysis of multiple gene data. Apex
implements\nthe new S4 classes 'multidna', 'multiphyDat' and associated methods to
handle\naligned DNA sequences from multiple genes.","Imports":"utils, graphics,
stats, grDevices, adegenet","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"apex","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat, knitr, rmarkdown","Title":"Phylogenetic Methods
for Multiple Gene
Data","URL":"https:\/\/github.com\/thibautjombart\/apex","Version":"1.0.2"},"aplore
3":{"Author":"\"Luca Braglia\" [aut, cre]","Depends":"R (>=
3.1.1)","Description":"This package is a unofficial companion to the
textbook \"Applied\nLogistic Regression\" by D.W. Hosmer, S. Lemeshow and\nR.X.
Sturdivant (3rd ed.). See ?aplore3 for more info.","License":"GPL-
3","NeedsCompilation":"no","Package":"aplore3","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr, MASS, vcdExtra, nnet, survival,
pROC","Title":"Datasets from Hosmer, Lemeshow and Sturdivant, \"Applied
Logistic\nRegression\" (3rd
ed.)","URL":"https:\/\/github.com\/lbraglia\/aplore3","Version":"0.7"},"aplpack":
{"Author":"Hans Peter Wolf, Uni Bielefeld","Depends":"R (>= 2.8.0),
tcltk","Description":"set of functions for drawing some special plots:\nstem.leaf
plots a stem and leaf plot,\nstem.leaf.backback plots back-to-back versions of stem
and leafs,\nbagplot plots a bagplot,\nskyline.hist plots several histgramm in one
plot of a one dimensional data set,\nplotsummary plots a graphical summary of a
data set with one or more variables,\nplothulls plots sequentially hulls of a
bivariate data set,\nfaces plots chernoff faces,\nspin3R for an inspection of a 3-
dim point cloud,\nslider functions for interactive graphics.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"aplpack","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"tkrplot","Title":"Another Plot PACKage: stem.leaf,
bagplot, faces, spin3R,\nplotsummary, plothulls, and some slider
functions","URL":"http:\/\/www.wiwi.uni-
bielefeld.de\/com\/wolf\/software\/aplpack.html","Version":"1.3.0"},"apmsWAPP":
{"Author":"Martina Fischer","Depends":"R (>= 3.0.1)","Description":"apmsWAPP
provides a complete workflow for the analysis of AP-MS data (replicate single-bait
purifications including negative controls) based on spectral counts.\nIt comprises
pre-processing, scoring and postprocessing of protein interactions.\nA final list
of interaction candidates is reported: it provides a ranking of the candidates
according\nto their p-values which allow estimating the number of false-positive
interactions.","Imports":"genefilter, Biobase, seqinr, multtest, gtools, edgeR,
DESeq,\naroma.light","License":"LGPL-
3","NeedsCompilation":"no","Package":"apmsWAPP","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Pre- and Postprocessing for AP-MS data analysis based
on\nspectral counts","Version":"1.0"},"appell":{"Author":"Daniel Sabanes Bove
<daniel.sabanesbove@ifspm.uzh.ch> with\ncontributions by F. D. Colavecchia, R. C.
Forrey, G. Gasaneo,\nN. L. J. Michel, L. F. Shampine, M. V. Stoitsov and H.
A.\nWatts.","Depends":"R (>= 2.14.0)","Description":"This package wraps Fortran
code by F. D. Colavecchia and\nG. Gasaneo for computing the Appell's F1
hypergeometric\nfunction. Their program uses Fortran code by L. F. Shampine and\nH.
A. Watts. Moreover, the hypergeometric function with complex\narguments is computed
with Fortran code by N. L. J. Michel and\nM. V. Stoitsov or with Fortran code by R.
C. Forrey. See the\nfunction documentations for the references and please cite
them\naccordingly.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"appell","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Compute Appell's F1 hypergeometric
function","Version":"0.0-4"},"apple":{"Author":"Yi Yu, Yang
Feng","Depends":"MASS","Description":"Approximate Path for Penalized Likelihood
Estimators for\nGeneralized Linear Models penalized by LASSO or
MCP","License":"GPL-
2","NeedsCompilation":"yes","Package":"apple","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Approximate Path for Penalized Likelihood
Estimators","Version":"0.3"},"appnn":{"Author":"Carlos FamÃlia, Sarah R. Dennison,
Alexandre Quintas, David A. Phoenix","Description":"Amyloid propensity prediction
neural network (APPNN) is an amyloidogenicity propensity predictor based on a
machine learning approach through recursive feature selection and feed-forward
neural networks, taking advantage of newly published sequences with experimental,
in vitro, evidence of amyloid formation.","License":"GPL-
3","NeedsCompilation":"no","Package":"appnn","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Amyloid Propensity Prediction Neural
Network","Version":"1.0-0"},"approximator":{"Author":"Robin K. S.
Hankin","Depends":"R (>= 2.0.0), emulator (>= 1.2-11)","Description":"Performs
Bayesian prediction of complex computer codes\nwhen fast approximations are
available: M. C. Kennedy and A. O'Hagan\n2000, Biometrika 87(1):1-
13","License":"GPL","NeedsCompilation":"no","Package":"approximator","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Title":"Bayesian prediction of complex
computer codes","Version":"1.2-6"},"aprean3":{"Author":"Luca Braglia [aut,
cre]","Depends":"R (>= 3.1.1)","Description":"An unofficial companion to the
textbook \"Applied Regression\nAnalysis\" by N.R. Draper and H. Smith (3rd Ed.,
1998) including all the\naccompanying datasets.","License":"GPL-
3","NeedsCompilation":"no","Package":"aprean3","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Datasets from Draper and Smith \"Applied Regression
Analysis\"\n(3rd Ed.,
1998)","URL":"https:\/\/github.com\/lbraglia\/aprean3","Version":"1.0.1"},"apricom"
:{"Author":"Romin Pajouheshnia [aut, cre],\nWiebe Pestman [aut],\nRolf Groenwold
[aut]","Depends":"R (>= 3.1.1)","Description":"Tools to compare several model
adjustment and validation methods prior to application in a final
analysis.","Imports":"logistf, penalized, rms, graphics, stats,
shrink","License":"GPL-
2","NeedsCompilation":"no","Package":"apricom","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr, testthat, rmarkdown","Title":"Tools for the a
Priori Comparison of Regression Modelling\nStrategies","Version":"1.0.0"},"aprof":
{"Author":"Marco D. Visser","Description":"Assists the evaluation of whether
and\nwhere to focus code optimization, using Amdahl's law and visual aids\nbased on
line profiling. Amdahl's profiler organises profiling output\nfiles (including
memory profiling) in a visually appealing way.\nIt is meant to help to balance
development\nvs. execution time by helping to identify the most promising
sections\nof code to optimize and projecting potential gains. The package is\nan
addition to R's standard profiling tools and is not a wrapper for
them.","Imports":"graphics, grDevices, stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"aprof","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Amdahl's Profiler, Directed Optimization Made
Easy","URL":"http:\/\/github.com\/MarcoDVisser\/aprof","Version":"0.3.2"},"apsimr":
{"Author":"Bryan Stanfill","Depends":"R (>= 3.0), ggplot2, XML","Description":"The
Agricultural Production Systems sIMulator (APSIM) is a widely\nused simulator of
agricultural systems. This package includes\nfunctions to create, edit and run
APSIM simulations from R. It\nalso includes functions to visualize the results of
an APSIM simulation\nand perform sensitivity\/uncertainty analysis of APSIM either
via functions\nin the sensitivity package or by novel emulator-based
functions.\nFor more on APSIM including download instructions go
to\n\\url{www.apsim.info}.","Imports":"lubridate, reshape2, MASS,
mgcv","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"apsimr","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr","Title":"Edit, Run and Evaluate APSIM
Simulations Easily Using R","Version":"1.2"},"apsrtable":{"Author":"Michael
Malecki","Depends":"R (>= 2.14.0),
methods","Description":"Formats latex tables from one or more model objects\nside-
by-side with standard errors below, not unlike tables\nfound in such journals as
the American Political Science\nReview.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"apsrtable","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"apsrtable model-output formatter for social
science","Version":"0.8-8"},"apt":{"Author":"Changyou Sun
<cs258@msstate.edu>","Depends":"R (>= 3.0.0), erer,
gWidgets","Description":"Asymmetric price transmission between two time series is
assessed. Several functions are available for linear and nonlinear threshold
cointegration, and furthermore, symmetric and asymmetric error correction model. A
graphical user interface is also included for major functions included in the
package, so users can also use these functions in a more intuitive
way.","Imports":"car, urca,
copula","License":"GPL","NeedsCompilation":"no","Package":"apt","Repository":"http:
\/\/cran.csiro.au\/src\/contrib","Suggests":"RGtk2, gWidgetsRGtk2,
cairoDevice","Title":"Asymmetric Price Transmission","Version":"2.5"},"aqfig":
{"Author":"Jenise Swall, with contributions from Kristen
Foley","Depends":"geoR","Description":"This package contains functions to help
display air quality model output and monitoring data, such as creating color
scatterplots, color legends,
etc.","License":"Unlimited","NeedsCompilation":"no","Package":"aqfig","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"maps","Title":"Functions to help
display air quality model output and\nmonitoring data","Version":"0.8"},"aqp":
{"Author":"Dylan Beaudette <debeaudette@ucdavis.edu>, Pierre Roudier
<roudierp@landcareresearch.co.nz>","Depends":"R (>= 3.0.0)","Description":"A
collection of algorithms related to modeling of soil resources, soil
classification, soil profile aggregation, and visualization.","Imports":"grDevices,
graphics, stats, utils, methods, plyr, reshape,\ngrid, lattice, cluster, sp, Hmisc,
stringr, scales, plotrix,\nRColorBrewer, MASS, digest","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"aqp","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"colorspace, maptools, foreign, ape, soilDB,
latticeExtra,\nmaps, compositions, sharpshootR","Title":"Algorithms for
Quantitative Pedology","URL":"http:\/\/aqp.r-forge.r-
project.org\/","Version":"1.9.3"},"aqr":{"Author":"Ulrich Staudinger, ActiveQuant
GmbH","Depends":"R (>= 2.1), xts, RCurl","Description":"This R extension provides
methods to use a standalone ActiveQuant\nMaster Server from within R. Currently
available features include fetching\nand storing historical data, receiving and
sending live data. Several\nutility methods for simple data transformations are
included, too. For\nsupport requests, please join the mailing list at\nhttps:\/\/r-
forge.r-project.org\/mail\/?group_id=1518","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"aqr","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Interface methods to use with an ActiveQuant Master
Server","URL":"http:\/\/www.activequant.com","Version":"0.4"},"archdata":
{"Author":"David L. Carlson and Georg Roth","Description":"The archdata package
provides several types of data that are typically used in archaeological
research.","License":"GPL","NeedsCompilation":"no","Package":"archdata","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"ca, circular, plotrix, MASS,
rgl","Title":"Example Datasets from Archaeological
Research","Version":"1.1"},"archetypes":{"Author":"Manuel J. A. Eugster [aut,
cre],\nFriedrich Leisch [aut],\nSohan Seth [ctb]","Depends":"methods, stats,
modeltools, nnls (>= 1.1)","Description":"The main function archetypes implements
a\nframework for archetypal analysis supporting arbitrary\nproblem solving
mechanisms for the different conceptual\nparts of the algorithm.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"archetypes","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"MASS, vcd, mlbench, ggplot2,
TSP","Title":"Archetypal Analysis","Version":"2.2-0"},"archiDART":
{"Author":"Benjamin M Delory, Caroline Baudson, Yves Brostaux, Guillaume Lobet,
Patrick du Jardin, Loic Pages, Pierre Delaplace","Description":"Analysis of complex
plant root system architectures (RSA) using the output files created by Data
Analysis of Root Tracings (DART), an open-access software dedicated to the study of
plant root architecture and development across time series (Le Bot et al
(2010) \"DART: a software to analyse root system architecture and development from
captured images\", Plant and Soil, <DOI:10.1007\/s11104-009-0005-2>), and RSA data
encoded with the Root System Markup Language (RSML) (Lobet et al (2015) \"Root
System Markup Language: toward a unified root architecture description language\",
Plant Physiology, <DOI:10.1104\/pp.114.253625>). More information can be found in
Delory et al (2016) \"archiDART: an R package for the automated computation of
plant root architectural traits\", Plant and Soil, <DOI:10.1007\/s11104-015-2673-
4>.","Imports":"stats, utils, graphics, grDevices, XML","License":"GPL-
2","NeedsCompilation":"no","Package":"archiDART","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Plant Root System Architecture Analysis Using DART and
RSML\nFiles","Version":"1.4"},"archivist":{"Author":"Przemyslaw Biecek [aut,
cre],\nMarcin Kosinski [aut],\nWitold Chodor [ctb]","Depends":"R (>=
3.2.0)","Description":"Data exploration and modelling is a process in which a lot
of data\nartifacts are produced. Artifacts like: subsets, data aggregates,
plots,\nstatistical models, different versions of data sets and different
versions\nof results. The more projects we work with the more artifacts are
produced\nand the harder it is to manage these artifacts. Archivist helps to
store\nand manage artifacts created in R. Archivist allows you to store
selected\nartifacts as a binary files together with their metadata and
relations.\nArchivist allows to share artifacts with others, either through
shared\nfolder or github. Archivist allows to look for already created artifacts
by\nusing it's class, name, date of the creation or other properties. Makes
it\neasy to restore such artifacts. Archivist allows to check if new artifact\nis
the exact copy that was produced some time ago. That might be useful\neither for
testing or caching.","Imports":"RCurl, digest, httr, DBI, lubridate, RSQLite,
magrittr","License":"GPL-
2","NeedsCompilation":"no","Package":"archivist","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"shiny, dplyr, testthat, ggplot2, devtools,
knitr","Title":"Tools for Storing, Restoring and Searching for R
Objects","Version":"2.0.3"},"archivist.github":{"Author":"Marcin Kosinski [aut,
cre],\nPrzemyslaw Biecek [aut]","Depends":"R (>= 3.2.0),
archivist","Description":"The extension of the 'archivist' package integrating the
archivist with GitHub via GitHub API, 'git2r' packages and 'httr'
package.","Imports":"httr, git2r, jsonlite, digest","License":"GPL-
2","NeedsCompilation":"no","Package":"archivist.github","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Tools for Archiving, Managing and Sharing R
Objects via
GitHub","URL":"http:\/\/marcinkosinski.github.io\/archivist.github\/","Version":"0.
1.1"},"arf3DS4":{"Author":"Wouter D. Weeda","Depends":"R (>= 2.15.0), methods,
graphics, tcltk, corpcor","Description":"Activated Region Fitting (ARF) is an
analysis method for fMRI data.","License":"GPL-
2","NeedsCompilation":"yes","Package":"arf3DS4","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Activated Region Fitting, fMRI data analysis
(3D)","URL":"http:\/\/arf.r-forge.r-project.org\/","Version":"2.5-10"},"arfima":
{"Author":"Justin Q. Veenstra [aut, cre],\nA.I. McLeod [aut]","Depends":"R (>=
2.14.0), ltsa","Description":"Simulates, fits, and predicts long-memory and anti-
persistent time\nseries, possibly mixed with ARMA, regression, transfer-function
components.\nExact methods (MLE, forecasting, simulation) are
used.","Imports":"parallel","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"arfima","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Fractional ARIMA (and Other Long Memory) Time Series
Modeling","Version":"1.3-4"},"argosfilter":{"Author":"Carla
Freitas","Description":"Functions to filters animal satellite tracking
data\nobtained from Argos. It is especially indicated for telemetry\nstudies of
marine animals, where Argos locations are\npredominantly of low-
quality.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"argosfilter","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Argos locations filter","Version":"0.63"},"argparse":
{"Author":"Trevor L Davis. Ports examples from the argparse Python module by
the\nPython Software Foundation. Ports examples from the getopt package by
Allen\nDay.","Depends":"proto","Description":"A command line parser to\nbe used
with Rscript to write \"#!\" shebang scripts that gracefully\naccept positional and
optional arguments and automatically generate usage.","Imports":"findpython, getopt
(>= 1.19), rjson","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"argparse","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr, testthat","Title":"Command line optional and
positional argument
parser","URL":"https:\/\/github.com\/trevorld\/argparse","Version":"1.0.1"},"argpar
ser":{"Author":"David J. H. Shih","Depends":"methods","Description":"Cross-platform
command-line argument parser written purely in R\nwith no external dependencies. It
is useful with the Rscript\nfront-end and facilitates turning an R script into an
executable script.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"argparser","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Command-Line Argument
Parser","URL":"https:\/\/bitbucket.org\/djhshih\/argparser","Version":"0.4"},"arm":
{"Author":"Andrew
Gelman [aut],\nYu-Sung Su [aut, cre],\nMasanao Yajima [ctb],\nJennifer Hill
[ctb],\nMaria Grazia Pittau [ctb],\nJouni Kerman [ctb],\nTian Zheng [ctb],\nVicent
Dorie [ctb]","Depends":"R (>= 3.1.0), MASS, Matrix (>= 1.0), stats, lme4 (>=
1.0)","Description":"R functions for processing 'lm', 'glm', 'svy.glm', 'merMod'
and 'polr' outputs.","Imports":"abind, coda, graphics, grDevices, methods, nlme,
2)","NeedsCompilation":"no","Package":"arm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Data Analysis Using Regression and
Multilevel\/Hierarchical\nModels","URL":"http:\/\/CRAN.R-
project.org\/package=arm","Version":"1.8-6"},"arnie":{"Author":"'Imanuel Costigan'
[aut, cre]","Depends":"R (>= 3.1.0)","Description":"Arnold Schwarzenegger movie
weekend box office records from\n1982-2014","License":"CC BY-SA
4.0","NeedsCompilation":"no","Package":"arnie","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"\"Arnie\" box office records 1982-
2014","URL":"https:\/\/github.com\/imanuelcostigan\/arnie","Version":"0.1.2"},"arom
a.affymetrix":{"Author":"Henrik Bengtsson [aut, cre, cph],\nJames Bullard
[ctb],\nKasper Hansen [ctb],\nPierre Neuvial [ctb],\nElizabeth Purdom [ctb],\nMark
Robinson [ctb],\nKen Simpson [ctb]","Depends":"R (>= 3.1.2), R.utils (>= 2.2.0),
aroma.core (>= 3.0.0)","Description":"A cross-platform R framework that facilitates
processing of any number of Affymetrix microarray samples regardless of computer
system. The only parameter that limits the number of chips that can be processed
is the amount of available disk space. The Aroma Framework has successfully been
used in studies to process tens of thousands of arrays. This package has actively
been used since 2006.","Imports":"methods, R.methodsS3 (>= 1.7.0), R.oo (>=
1.19.0), R.cache (>=\n0.12.0), R.devices (>= 2.13.2), R.filesets (>=
2.10.0),\naroma.apd (>= 0.6.0), MASS, splines, matrixStats (>= 0.50.1),\nlistenv,
future","License":"LGPL (>=
2.1)","NeedsCompilation":"no","Package":"aroma.affymetrix","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Suggests":"DBI (>= 0.3.1), gsmoothr (>= 0.1.7),
RColorBrewer (>= 1.1-2),\nBiobase (>= 2.28.0), BiocGenerics (>= 0.14.0), affxparser
(>=\n1.40.0), affy (>= 1.46.0), affyPLM (>= 1.44.0), aroma.light (>=\n2.4.0), gcrma
(>= 2.40.0), limma (>= 3.24.1), oligo (>=\n1.32.0), oligoClasses (>= 1.30.0),
pdInfoBuilder (>= 1.32.0),\npreprocessCore (>= 1.28.0), AffymetrixDataTestFiles,
dChipIO\n(>= 0.1.1)","Title":"Analysis of Large Affymetrix Microarray Data
Sets","URL":"http:\/\/www.aroma-
project.org\/,\nhttps:\/\/github.com\/HenrikBengtsson\/aroma.affymetrix","Version":
"3.0.0"},"aroma.apd":{"Author":"Henrik Bengtsson [aut, cre, cph]","Depends":"R (>=
3.0.0)","Description":"DEPRECATED. Do not start building new projects based on this
package. (The (in-house) APD file format was initially developed to store
Affymetrix probe-level data, e.g. normalized CEL intensities. Chip types can be
added to APD file and similar to methods in the affxparser package, this package
provides methods to read APDs organized by units (probesets). In addition, the
probe elements can be arranged optimally such that the elements are guaranteed to
be read in order when, for instance, data is read unit by unit. This speeds up the
read substantially. This package is supporting the Aroma framework and should not
be used elsewhere.)","Imports":"R.methodsS3 (>= 1.7.0), R.oo (>= 1.18.0), R.utils
(>= 1.34.0),\nR.huge (>= 0.9.0)","License":"LGPL (>=
2.1)","NeedsCompilation":"no","Package":"aroma.apd","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"affxparser","Title":"A Probe-Level Data File
Format Used by 'aroma.affymetrix'\n[deprecated]","URL":"URL: http:\/\/www.aroma-
project.org\/,\nhttps:\/\/github.com\/HenrikBengtsson\/aroma.apd","Version":"0.6.0"
},"aroma.cn":{"Author":"Henrik Bengtsson [aut, cre, cph],\nPierre Neuvial
[aut]","Depends":"R (>= 3.1.1), R.utils (>= 2.1.0), aroma.core (>=
2.14.0)","Description":"Methods for analyzing DNA copy-number data.
Specifically,\nthis package implements the multi-source copy-number normalization
(MSCN)\nmethod for normalizing copy-number data obtained on various platforms
and\ntechnologies. It also implements the TumorBoost method for
normalizing\npaired tumor-normal SNP data.","Imports":"R.methodsS3 (>= 1.7.0), R.oo
(>= 1.19.0), R.filesets (>=\n2.9.0), R.cache (>= 0.10.0), matrixStats (>= 0.15.0),
PSCBS (>=\n0.50.0)","License":"LGPL (>=
2.1)","NeedsCompilation":"no","Package":"aroma.cn","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"aroma.light (>= 2.2.1), DNAcopy (>= 1.40.0), GLAD
(>= 1.12.0)","Title":"Copy-Number Analysis of Large Microarray Data
Sets","URL":"http:\/\/www.aroma-
project.org\/,\nhttps:\/\/github.com\/HenrikBengtsson\/aroma.cn","Version":"1.6.1"}
,"aroma.core":{"Author":"Henrik Bengtsson [aut, cre, cph],\nMark Robinson
[ctb],\nKen Simpson [ctb]","Depends":"R (>= 3.1.2), R.utils (>= 2.2.0), R.filesets
(>= 2.10.0),\nR.devices (>= 2.13.2)","Description":"Core methods and classes used
by higher-level aroma.* packages\npart of the Aroma Project, e.g. aroma.affymetrix
and aroma.cn.","Imports":"stats, utils, R.methodsS3 (>= 1.7.0), R.oo (>=
1.19.0),\nR.cache (>= 0.12.0), R.rsp (>= 0.21.0), matrixStats (>=\n0.50.1),
RColorBrewer (>= 1.1-2), PSCBS (>= 0.60.0), listenv,\nfuture","License":"LGPL (>=
2.1)","NeedsCompilation":"no","Package":"aroma.core","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"png (>= 0.1-7), Cairo (>= 1.5-6), EBImage (>=
4.8.3),\npreprocessCore (>= 1.28.0), aroma.light (>= 2.2.1), DNAcopy (>=\n1.40.0),
GLAD (>= 2.30.0), sfit (>= 0.1.8), expectile (>=\n0.2.5), HaarSeg (>= 0.0.2), mpcbs
(>= 1.1.1)","Title":"Core Methods and Classes Used by 'aroma.*' Packages Part of
the\nAroma
Framework","URL":"https:\/\/github.com\/HenrikBengtsson\/aroma.core,\nhttp:\/\/www.
aroma-project.org\/","Version":"3.0.0"},"arrApply":{"Author":"Serguei
Sokol","Description":"High performance variant of apply() for a fixed set of
functions.\nHowever, a considerable speedup is a trade-off for universality.\nOnly
the following functions can be applied: sum(), prod(), all(), any(),\nmin(), max(),
mean(), median(), sd(), var().","Imports":"Rcpp (>= 0.12.0),","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"arrApply","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat","Title":"Apply a Function to a Margin of
an Array","Version":"1.0.4"},"arrayhelpers":{"Author":"C. Beleites
<Claudia.Beleites@ipht-jena.de>","Depends":"methods","Description":"Some convenient
functions to work with
arrays","License":"GPL","NeedsCompilation":"no","Package":"arrayhelpers","Repositor
y":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"svUnit","Title":"Convenience
functions for arrays","URL":"http:\/\/arrayhelpers.r-forge.r-
project.org\/","Version":"0.76-20120816"},"ars":{"Author":"Paulino Perez Rodriguez
<perpdgo@colpos.mx> original C++ code\nfrom Arnost Komarek based on ars.f written
by P. Wild and W. R.\nGilks","Depends":"R (>= 3.1.2)","Description":"Adaptive
Rejection Sampling, Original version","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ars","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Adaptive Rejection Sampling","Version":"0.5"},"artfima":
{"Author":"A. I. McLeod, Mark M. Meerschaert, Farzad Sabzikar","Depends":"R (>=
2.1.0)","Description":"Fit and simulate ARTFIMA. Theoretical autocovariance
function and spectral density function for stationary ARTFIMA.","Imports":"ltsa,
gsl","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"artfima","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"ARTFIMA Model
Estimation","URL":"http:\/\/www.stats.uwo.ca\/faculty\/aim","Version":"1.2"},"arule
s":{"Author":"Michael Hahsler [aut, cre, cph],\nChristian Buchta [aut,
cph],\nBettina Gruen [aut, cph],\nKurt Hornik [aut, cph],\nChristian Borgelt [ctb,
cph]","Depends":"R (>= 3.2.0), Matrix (>= 1.2-0)","Description":"Provides the
infrastructure for representing,\nmanipulating and analyzing transaction data and
patterns (frequent\nitemsets and association rules). Also provides interfaces to\nC
implementations of the association mining algorithms Apriori and Eclat\nby C.
Borgelt.","Imports":"stats, methods, graphics, utils","License":"GPL-
3","NeedsCompilation":"yes","Package":"arules","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"pmml, XML, arulesViz, testthat","Title":"Mining
Association Rules and Frequent
Itemsets","URL":"http:\/\/lyle.smu.edu\/IDA\/arules","Version":"1.4-
0"},"arulesNBMiner":{"Author":"Michael Hahsler","Depends":"R (>= 2.10), arules (>=
0.6-6), rJava (>= 0.6-3)","Description":"NBMiner is an implementation of the model-
based mining algorithm\nfor mining NB-frequent itemsets presented in \"Michael
Hahsler. A\nmodel-based frequency constraint for mining associations
from\ntransaction data. Data Mining and Knowledge Discovery, 13(2):137-
166,\nSeptember 2006.\" In addition an extension for NB-precise rules
is\nimplemented.","Imports":"methods, stats, graphics","License":"GPL-
2","NeedsCompilation":"no","Package":"arulesNBMiner","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Mining NB-Frequent Itemsets and NB-Precise
Rules","URL":"http:\/\/R-Forge.R-
project.org\/projects\/arules\/,\nhttp:\/\/lyle.smu.edu\/IDA\/arules\/","Version":"
0.1-5"},"arulesViz":{"Author":"Michael Hahsler and Sudheer
Chelluboina","Depends":"arules (>= 1.2.0), grid","Description":"Extends package
arules with various visualization techniques for association rules and itemsets.
The package also includes several interactive visualizations for rule
exploration.","Imports":"scatterplot3d, vcd, seriation, igraph (>= 1.0.0),
graphics,\nmethods, utils, grDevices, stats, colorspace","License":"GPL-
3","NeedsCompilation":"no","Package":"arulesViz","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"graph,
Rgraphviz, iplots","Title":"Visualizing Association Rules and Frequent
Itemsets","URL":"http:\/\/lyle.smu.edu\/IDA\/arules\/","Version":"1.1-0"},"asVPC":
{"Author":"Eun-Kyung Lee","Description":"The visual predictive checks are well-
known method to validate the\nnonlinear mixed effect model, especially in
pharmacometrics area.\nThe average shifted visual predictive checks are the
newly\ndeveloped method of Visual predictive checks combined with\nthe idea of the
average shifted histogram.","Imports":"ggplot2,plyr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"asVPC","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"Hmisc","Title":"Average Shifted Visual Predictive
Checks","Version":"1.0.2"},"asaur":{"Author":"Dirk F. Moore","Description":"Data
sets are referred to in the text \"Applied Survival Analysis Using R\"\nby Dirk F.
Moore,\nto be published by Springer in 2016.","License":"LGPL-
2","NeedsCompilation":"no","Package":"asaur","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Data Sets for \"Applied Survival Analysis Using
R\"\"","Version":"0.44"},"asbio":{"Author":"Ken Aho","Depends":"R (>= 2.15.1),
tcltk","Description":"Contains functions from: Aho, K. (2014) Foundational and
Applied Statistics for Biologists using R. CRC\/Taylor and Francis, Boca Raton,
FL, ISBN: 978-1-4398-7338-0.","Imports":"scatterplot3d, pixmap, plotrix, mvtnorm,
deSolve, lattice,\nmultcompView, grDevices, graphics, stats, utils","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"asbio","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"akima, boot","Title":"A Collection of Statistical Tools
for Biologists","Version":"1.3-1"},"ascii":{"Author":"David Hajage","Depends":"R
(>= 2.13), utils, methods","Description":"Coerce R object to asciidoc, txt2tags,
restructuredText,\norg, textile or pandoc syntax. Package comes with a set
of\ndrivers for Sweave.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ascii","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"survival, Hmisc, xtable, R2HTML, cacheSweave,
weaver","Title":"Export R objects to several markup
languages","URL":"http:\/\/eusebe.github.com\/ascii\/,
http:\/\/github.com\/eusebe\/ascii\/","Version":"2.1"},"asd":{"Author":"Nick
Parsons","Depends":"mvtnorm","Description":"Package runs simulations for adaptive
seamless designs with and without early outcomes\nfor treatment selection and
subpopulation type designs.","License":"GPL-
3","NeedsCompilation":"no","Package":"asd","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Simulations for adaptive seamless
designs","Version":"2.0"},"asdreader":{"Author":"Pierre Roudier [aut,
cre]","Depends":"R (>= 3.0)","Description":"A simple driver that reads binary data
created by the ASD Inc.\nportable spectrometer instruments, such as the FieldSpec
(for more information,\nsee <http:\/\/www.asdi.com\/products\/fieldspec-
spectroradiometers>). Spectral data\ncan be extracted from the ASD files as raw
(DN), white reference, radiance, or\nreflectance. Additionally, the metadata
information contained in the ASD file\nheader can also be
accessed.","License":"GPL-
3","NeedsCompilation":"no","Package":"asdreader","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Reading ASD Binary Files in
R","URL":"http:\/\/github.com\/pierreroudier\/asdreader","Version":"0.1-2"},"ash":
{"Author":"S original by David W. Scott\nR port by Albrecht Gebhardt
<albrecht.gebhardt@aau.at>\nadopted to recent S-PLUS by Stephen Kaluzny
<spk@insightful.com>","Description":"David Scott's ASH routines ported from S-PLUS
to R.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ash","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"David Scott's ASH Routines","Version":"1.0-15"},"asht":
{"Author":"Michael P. Fay","Depends":"stats, exact2x2, exactci, bpcp, ssanv,
coin","Description":"Some hypothesis test functions with a focus on non-asymptotic
methods that have matching confidence intervals.","License":"GPL-
3","NeedsCompilation":"no","Package":"asht","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Applied Statistical Hypothesis
Tests","Version":"0.5"},"asnipe":{"Author":"Damien R. Farine
<dfarine@orn.mpg.de>","Depends":"R (>= 2.10)","Description":"Implements several
tools that are used in animal social network analysis. In particular, this package
provides the tools to generate networks from observation data, perform permutation
tests on the data, calculate lagged association rates, and performed multiple
regression analysis on social network data.","License":"GPL-
2","NeedsCompilation":"no","Package":"asnipe","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"ape, igraph, raster, sna","Title":"Animal Social Network
Inference and Permutations for Ecologists","Version":"0.90"},"aspace":
{"Author":"Randy Bui, Ron N. Buliung, Tarmo K. Remmel","Depends":"R (>= 2.15.1),
splancs, Hmisc, shapefiles","Description":"A collection of functions for computing
centrographic\nstatistics (e.g., standard distance, standard deviation\nellipse,
standard deviation box) for observations taken at\npoint locations. Separate
plotting functions have been\ndeveloped for each measure. Users interested in
writing results\nto ESRI shapefiles can do so by using results from
aspace\nfunctions as inputs to the convert.to.shapefile and\nwrite.shapefile
functions in the shapefiles library. The aspace\nlibrary was originally conceived
to aid in the analysis of\nspatial patterns of travel behaviour (see Buliung and
Remmel,\n2008). Major changes in the current version include (1) removal\nof
dependencies on several external libraries (e.g., gpclib,\nmaptools, sp), (2) the
separation of plotting and estimation\ncapabilities, (3) reduction in the number of
functions, and (4)\nexpansion of analytical capabilities with additional
functions\nfor descriptive analysis and visualization (e.g., standard\ndeviation
box, centre of minimum distance, central feature).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"aspace","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"A collection of functions for estimating
centrographic\nstatistics and computational geometries for spatial
point\npatterns","Version":"3.2"},"aspect":{"Author":"Patrick Mair [cre, aut],\nJan
De Leeuw [aut]","Depends":"R (>= 3.0.0)","Description":"Contains various functions
for optimal scaling. One function performs optimal scaling by maximizing an aspect
(i.e. a target function such as the sum of eigenvalues, sum of squared
correlations, squared multiple correlations, etc.) of the corresponding correlation
matrix. Another function performs implements the LINEALS approach for optimal
scaling by minimization of an aspect based on pairwise correlations and correlation
ratios. The resulting correlation matrix and category scores can be used for
further multivariate methods such as structural equation models.","Imports":"stats,
graphics, grDevices","License":"GPL-
2","NeedsCompilation":"yes","Package":"aspect","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"sem, polycor","Title":"A General Framework for
Multivariate Analysis with Optimal\nScaling","URL":"http:\/\/R-forge.R-
project.org\/projects\/psychor\/","Version":"1.0-4"},"asremlPlus":{"Author":"Chris
Brien <Chris.Brien@unisa.edu.au>.","Depends":"R (>= 2.10.0)","Description":"Assists
in automating the testing of terms in mixed models when 'asreml' is used\nto fit
the models. The content falls into the following natural groupings: (i) Data, (ii)
Object\nmanipulation functions, (iii) Model modification functions, (iv) Model
testing functions,\n(v) Model diagnostics functions, (vi) Prediction production and
presentation functions,\n(vii) Response transformation functions, and (viii)
Miscellaneous functions. A history of the\nfitting of a sequence of models is kept
in a data frame. Procedures are available for choosing\nmodels that conform to the
hierarchy or marginality principle and for displaying predictions\nfor significant
terms in tables and graphs. The package 'asreml' provides a
computationally\nefficient algorithm for fitting mixed models using Residual
Maximum Likelihood. It can be\npurchased from 'VSNi' (http:\/\/www.vsni.co.uk\/) as
'asreml-R', who will supply a zip file for\nlocal
installation\/updating.","Enhances":"asreml","Imports":"dae, ggplot2, stats,
methods, utils, grDevices","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"asremlPlus","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Augments the Use of 'Asreml' in Fitting Mixed
Models","URL":"http:\/\/chris.brien.name","Version":"2.0-3"},"assertive":
{"Author":"Richard Cotton [aut, cre]","Depends":"R (>= 3.0.0)","Description":"Lots
of predicates (is_* functions) to check the state of your\nvariables, and
assertions (assert_* functions) to throw errors if they\naren't in the right
form.","Imports":"assertive.base (>= 0.0-4), assertive.properties (>= 0.0-
2),\nassertive.types (>= 0.0-2), assertive.numbers,\nassertive.strings,
assertive.datetimes, assertive.files,\nassertive.sets (>= 0.0-2),
assertive.matrices,\nassertive.models, assertive.data,
assertive.data.uk,\nassertive.data.us, assertive.reflection (>= 0.0-
2),\nassertive.code, knitr","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"assertive","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat","Title":"Readable Check Functions to
Ensure Code
Integrity","URL":"https:\/\/bitbucket.org\/richierocks\/assertive","Version":"0.3-
3"},"assertive.base":{"Author":"Richard Cotton [aut, cre],\nSunkyu Choi
[trl],\nIvanka Skakun [trl],\nGergely Dar<c3><b3>czi [trl],\nAnton Antonov
[trl],\nHisham Ben Hamidane [trl],\nAnja Billing [trl],\nAditya Bhagwat
[trl],\nRasmus B<c3><a5><c3><a5>th [trl],\nMine Cetinkaya-Rundel [trl],\nAspasia
Chatziefthymiou [trl]","Depends":"R (>= 3.0.0)","Description":"A
minimal set of predicates and assertions used by the assertive\npackage. This is
mainly for use by other package developers who want to\ninclude run-time testing
features in their own packages. End-users will\nusually want to use assertive
directly.","Imports":"methods, utils","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"assertive.base","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat","Title":"A Lightweight Core of the
'assertive'
Package","URL":"https:\/\/bitbucket.org\/richierocks\/assertive.base","Version":"0.
0-5"},"assertive.code":{"Author":"Richard Cotton [aut, cre]","Depends":"R (>=
3.0.0)","Description":"A set of predicates and assertions for checking the
properties of\ncode. This is mainly for use by other package developers who want to
include\nrun-time testing features in their own packages. End-users will usually
want to\nuse assertive directly.","Imports":"assertive.base (>= 0.0-2),
assertive.properties,\nassertive.types, methods","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"assertive.code","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat, devtools","Title":"Assertions to
Check Properties of
Code","URL":"https:\/\/bitbucket.org\/richierocks\/assertive.code","Version":"0.0-
1"},"assertive.data":{"Author":"Richard Cotton [aut, cre]","Depends":"R (>=
properties of\n(country independent) complex data types. This is mainly for use by
other\npackage developers who want to include run-time testing features in\ntheir
own packages. End-users will usually want to use assertive
directly.","Imports":"assertive.base (>= 0.0-2), assertive.strings","License":"GPL
(>=
3)","NeedsCompilation":"no","Package":"assertive.data","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat, devtools","Title":"Assertions to
Check Properties of
Data","URL":"https:\/\/bitbucket.org\/richierocks\/assertive.data","Version":"0.0-
1"},"assertive.data.uk":{"Author":"Richard Cotton [aut, cre]","Depends":"R (>=
properties of\nUK-specific complex data types. This is mainly for use by other
package\ndevelopers who want to include run-time testing features in their
own\npackages. End-users will usually want to use assertive
(>=
3)","NeedsCompilation":"no","Package":"assertive.data.uk","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"testthat, devtools","Title":"Assertions to
Check Properties of
Strings","URL":"https:\/\/bitbucket.org\/richierocks\/assertive.data.uk","Version":
"0.0-1"},"assertive.data.us":{"Author":"Richard Cotton [aut, cre]","Depends":"R (>=
properties of\nUS-specific complex data types. This is mainly for use by other
package\ndevelopers who want to include run-time testing features in their
own\npackages. End-users will usually want to use assertive
(>=
3)","NeedsCompilation":"no","Package":"assertive.data.us","Repository":"http:\/\/cr
Check Properties of
Strings","URL":"https:\/\/bitbucket.org\/richierocks\/assertive.data.us","Version":
"0.0-1"},"assertive.datetimes":{"Author":"Richard Cotton [aut, cre]","Depends":"R
(>= 3.0.0)","Description":"A set of predicates and assertions for checking the
properties of\ndates and times. This is mainly for use by other package developers
who\nwant to include run-time testing features in their own packages. End-
users\nwill usually want to use assertive directly.","Imports":"assertive.base (>=
0.0-2), assertive.types","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"assertive.datetimes","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Suggests":"testthat, devtools","Title":"Assertions to
Check Properties of Dates and
Times","URL":"https:\/\/bitbucket.org\/richierocks\/assertive.datetimes","Version":
"0.0-1"},"assertive.files":{"Author":"Richard Cotton [aut, cre]","Depends":"R (>=
properties of\nfiles and connections. This is mainly for use by other package
developers\nwho want to include run-time testing features in their own
packages.\nEnd-users will usually want to use assertive
directly.","Imports":"assertive.base (>= 0.0-2), assertive.numbers","License":"GPL
(>=
3)","NeedsCompilation":"no","Package":"assertive.files","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"testthat, devtools","Title":"Assertions to
Check Properties of
Files","URL":"https:\/\/bitbucket.org\/richierocks\/assertive.files","Version":"0.0
-1"},"assertive.matrices":{"Author":"Richard Cotton [aut, cre]","Depends":"R (>=
properties of\nmatrices. This is mainly for use by other package developers who
want to\ninclude run-time testing features in their own packages. End-users
will\nusually want to use assertive directly.","Imports":"assertive.base (>= 0.0-
3)","NeedsCompilation":"no","Package":"assertive.matrices","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Suggests":"testthat, devtools","Title":"Assertions to
Check Properties of
Matrices","URL":"https:\/\/bitbucket.org\/richierocks\/assertive.matrices","Version
":"0.0-1"},"assertive.models":{"Author":"Richard Cotton [aut, cre]","Depends":"R
properties of\nmodels. This is mainly for use by other package developers who want
to\ninclude run-time testing features in their own packages. End-users
2), stats","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"assertive.models","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"testthat, devtools","Title":"Assertions to
Check Properties of
Models","URL":"https:\/\/bitbucket.org\/richierocks\/assertive.models","Version":"0
.0-1"},"assertive.numbers":{"Author":"Richard Cotton [aut, cre]","Depends":"R (>=
properties of\nnumbers. This is mainly for use by other package developers who
3)","NeedsCompilation":"no","Package":"assertive.numbers","Repository":"http:\/\/cr
Check Properties of
Numbers","URL":"https:\/\/bitbucket.org\/richierocks\/assertive.numbers","Version":
"0.0-1"},"assertive.properties":{"Author":"Richard Cotton [aut, cre]","Depends":"R
properties of\nvariables, such as length, names and attributes. This is mainly for
use by\nother package developers who want to include run-time testing features
in\ntheir own packages. End-users will usually want to use assertive
directly.","Imports":"assertive.base (>= 0.0-3), methods","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"assertive.properties","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Assertions to Check
Properties of
Variables","URL":"https:\/\/bitbucket.org\/richierocks\/assertive.properties","Vers
ion":"0.0-2"},"assertive.reflection":{"Author":"Richard Cotton [aut,
cre]","Depends":"R (>= 3.0.0)","Description":"A set of predicates and assertions
for checking the state and\ncapabilities of R, the operating system it is running
on, and the IDE\nbeing used. This is mainly for use by other package developers
who\nwant to include run-time testing features in their own packages.\nEnd-users
will usually want to use assertive directly.","Imports":"assertive.base (>= 0.0-5),
3)","NeedsCompilation":"no","Package":"assertive.reflection","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Assertions for
Checking the State of
R","URL":"https:\/\/bitbucket.org\/richierocks\/assertive.reflection","Version":"0.
0-3"},"assertive.sets":{"Author":"Richard Cotton [aut, cre]","Depends":"R (>=
properties of\nsets. This is mainly for use by other package developers who want
3)","NeedsCompilation":"no","Package":"assertive.sets","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat, withr","Title":"Assertions to Check
Properties of
Sets","URL":"https:\/\/bitbucket.org\/richierocks\/assertive.sets","Version":"0.0-
2"},"assertive.strings":{"Author":"Richard Cotton [aut, cre]","Depends":"R (>=
properties of\nstrings. This is mainly for use by other package developers who
2), assertive.types","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"assertive.strings","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Assertions to Check
Properties of
Strings","URL":"https:\/\/bitbucket.org\/richierocks\/assertive.strings","Version":
"0.0-2"},"assertive.types":{"Author":"Richard Cotton [aut, cre]","Depends":"R
types of\nvariables. This is mainly for use by other package developers who want
3), assertive.properties, methods,\nstats","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"assertive.types","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"testthat, data.table,
dplyr","Title":"Assertions to Check Types of
Variables","URL":"https:\/\/bitbucket.org\/richierocks\/assertive.types","Version":
"0.0-2"},"assertr":{"Author":"Tony Fischetti [aut, cre]","Description":"Provides
functionality to assert conditions\nthat have to be met so that errors in data used
in\nanalysis pipelines can fail quickly. Similar to\n'stopifnot()' but more
powerful, friendly, and easier\nfor use in pipelines.","Imports":"dplyr, MASS,
lazyeval","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"assertr","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"knitr, testthat, magrittr","Title":"Assertive
Programming for R Analysis
Pipelines","URL":"https:\/\/github.com\/tonyfischetti\/assertr","Version":"1.0.0"},
"assertthat":{"Author":"'Hadley Wickham' [aut, cre]","Description":"assertthat is
an extension to stopifnot() that makes it\neasy to declare the pre and post
conditions that you code should\nsatisfy, while also producing friendly error
messages so that your\nusers know what they've done wrong.","License":"GPL-
3","NeedsCompilation":"no","Package":"assertthat","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat","Title":"Easy pre and post
assertions","Version":"0.1"},"assist":{"Author":"Yuedong Wang
<yuedong@pstat.ucsb.edu>, and\nChunlei Ke <chunlei_ke@yahoo.com>.","Depends":"R (>=
3.0.2), nlme, lattice","Description":"A comprehensive package for fitting various
non-parametric\/semi-parametric linear\/nonlinear fixed\/mixed smoothing spline
2)","NeedsCompilation":"yes","Package":"assist","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"A Suite of R Functions Implementing Spline Smoothing
Techniques","URL":"http:\/\/www.pstat.ucsb.edu\/faculty\/yuedong\/software.html","V
ersion":"3.1.3"},"assortnet":{"Author":"Damien Farine
<dfarine@orn.mpg.de>","Description":"Functions to calculate the assortment of
vertices in social networks. This can be measured on both weighted and binary
networks, with discrete or continuous vertex values.","License":"GPL-
2","NeedsCompilation":"no","Package":"assortnet","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Calculate the Assortativity Coefficient of Weighted and
Binary\nNetworks","Version":"0.12"},"aster":{"Author":"Charles J. Geyer
<charlie@stat.umn.edu>.","Depends":"R (>= 2.10.0), trust","Description":"Aster
models are exponential family regression models for life\nhistory analysis. They
are like generalized linear models except that\nelements of the response vector can
have different families (e. g.,\nsome Bernoulli, some Poisson, some zero-truncated
Poisson, some normal)\nand can be dependent, the dependence indicated by a
graphical structure.\nDiscrete time survival analysis, zero-inflated Poisson
regression, and\ngeneralized linear models that are exponential family (e. g.,
logistic\nregression and Poisson regression with log link) are special cases.\nMain
use is for data in which there is survival over discrete time periods\nand there is
additional data about what happens conditional on survival\n(e. g., number of
offspring). Uses the exponential family canonical\nparameterization (aster
transform of usual parameterization).","Imports":"stats","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"aster","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Aster
Models","URL":"http:\/\/www.stat.umn.edu\/geyer\/aster\/","Version":"0.8-
31"},"aster2":{"Author":"Charles J. Geyer <charlie@stat.umn.edu>.","Depends":"R (>=
2.10.0)","Description":"Aster models are exponential family regression models for
life\nhistory analysis. They are like generalized linear models except
that\nelements of the response vector can have different families (e. g.,\nsome
Bernoulli, some Poisson, some zero-truncated Poisson, some normal)\nand can be
dependent, the dependence indicated by a graphical structure.\nDiscrete time
survival analysis, zero-inflated Poisson regression, and\ngeneralized linear models
that are exponential family (e. g., logistic\nregression and Poisson regression
with log link) are special cases.\nMain use is for data in which there is survival
over discrete time periods\nand there is additional data about what happens
conditional on survival\n(e. g., number of offspring). Uses the exponential family
canonical\nparameterization (aster transform of usual parameterization).\nUnlike
the aster package, this package does dependence groups (nodes of\nthe graph need
not be conditionally independent given their predecessor\nnode), including
multinomial and two-parameter normal as families. Thus\nthis package also
generalizes mark-capture-recapture analysis.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"aster2","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"aster","Title":"Aster
Models","URL":"http:\/\/www.stat.umn.edu\/geyer\/aster\/","Version":"0.2-
1"},"astro":{"Author":"Lee Kelvin","Depends":"MASS,plotrix","Description":"The
astro package provides a series of functions, tools and routines in everyday use
within astronomy. Broadly speaking, one may group these functions into 7 main
areas, namely: cosmology, FITS file manipulation, the Sersic function, plotting,
data manipulation, statistics and general convenience functions and scripting
tools.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"astro","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Astronomy Functions, Tools and
Routines","Version":"1.2"},"astroFns":{"Author":"Andrew
Harris","Description":"Miscellaneous astronomy functions, utilities, and
2)","NeedsCompilation":"no","Package":"astroFns","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Astronomy: time and position functions, misc.
utilities","Version":"4.1-0"},"astrochron":{"Author":"Stephen
Meyers","Description":"Routines for astrochronologic testing, astronomical time
scale construction, and time series analysis. Also included are a range of
statistical analysis and modeling routines that are relevant to time scale
development and paleoclimate analysis.","Imports":"multitaper, IDPmisc,
fields","License":"GPL-
3","NeedsCompilation":"yes","Package":"astrochron","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"A Computational Tool for
Astrochronology","Version":"0.5"},"astrodatR":{"Author":"Eric D.
Feigelson","Description":"A collection of 19 datasets from contemporary
astronomical research. They are described the textbook `Modern Statistical Methods
for Astronomy with R Applications' by Eric D. Feigelson and G. Jogesh Babu
(Cambridge University Press, 2012, Appendix C) or on the website of Penn State's
Center for Astrostatistics (http:\/\/astrostatistics.psu.edu\/datasets). These
datasets can be used to exercise methodology involving: density estimation;
heteroscedastic measurement errors; contingency tables; two-sample hypothesis
tests; spatial point processes; nonlinear regression; mixture models; censoring and
truncation; multivariate analysis; classification and clustering; inhomogeneous
Poisson processes; periodic and stochastic time series
analysis.","License":"GPL","NeedsCompilation":"no","Package":"astrodatR","Repositor
y":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Astronomical
Data","Version":"0.1"},"astrolibR":{"Author":"Arnab Chakraborty and Eric D.
Feigelson","Description":"Several dozen low-level utilities and codes from the
Interactive Data Language (IDL) Astronomy Users Library
(http:\/\/idlastro.gsfc.nasa.gov) are implemented in R. They treat: time,
coordinate and proper motion transformations; terrestrial precession and nutation,
atmospheric refraction and aberration, barycentric corrections, and related
effects; utilities for astrometry, photometry, and spectroscopy; and utilities for
planetary, stellar, Galactic, and extragalactic
science.","License":"GPL","NeedsCompilation":"no","Package":"astrolibR","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Astronomy Users
Library","Version":"0.1"},"astsa":{"Author":"David Stoffer","Description":"Data
sets and scripts for Time Series Analysis and Its Applications: With R Examples by
Shumway and Stoffer, 3rd edition","License":"GPL-
2","NeedsCompilation":"no","Package":"astsa","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Applied Statistical Time Series
Analysis","URL":"http:\/\/www.stat.pitt.edu\/stoffer\/tsa3\/","Version":"1.3"},"asy
mLD":{"Author":"Richard M. Single","Description":"Computes asymmetric LD measures
(ALD) for multi-allelic genetic data. These measures are identical to the
correlation measure (r) for bi-allelic data.","License":"GPL-
2","NeedsCompilation":"no","Package":"asymLD","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"haplo.stats, fields","Title":"Asymmetric Linkage
Disequilibrium (ALD) for Polymorphic Genetic\nData","Version":"0.1"},"asympTest":
{"Author":"Cqls Team","Depends":"R (>= 1.8.0)","Description":"Asymptotic
testing","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"asympTest","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Asymptotic statistic","URL":"http:\/\/www.r-
project.org","Version":"0.1.3"},"asypow":{"Author":"S original by Barry W. Brown,
James Lovato and Kathy Russel.\nR port by Kjetil B Halvorsen
<kjetil1001@gmail.com>","Depends":"R (>= 2.2.0), stats","Description":"A
set of routines written in the S language\nthat calculate power and related
quantities utilizing asymptotic\nlikelihood ratio methods.","License":"ACM | file
LICENSE","NeedsCompilation":"no","Package":"asypow","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Calculate Power Utilizing Asymptotic Likelihood Ratio
Methods","Version":"2015.6.25"},"atmcmc":{"Author":"Jinyoung
Yang","Description":"Uses adaptive diagnostics to tune and run a random walk
Metropolis MCMC algorithm, to converge to a specified target distribution and
estimate means of functionals.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"atmcmc","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Automatically Tuned Markov Chain Monte
Carlo","Version":"1.0"},"atsd":{"Author":"Axibase Corporation","Depends":"R (>=
3.1.2)","Description":"Provides functions for retrieving time-series and
related\nmeta-data such as entities, metrics, and tags from the Axibase\nTime-
Series Database (ATSD). ATSD is a non-relational clustered\ndatabase used for
storing performance measurements from IT infrastructure\nresources: servers,
network devices, storage systems, and applications.","Imports":"RCurl (>=
1.95.4.5), httr (>= 0.6.1)","License":"Apache License
2.0","NeedsCompilation":"no","Package":"atsd","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"zoo, knitr, pander","Title":"Support Querying Axibase
Time-Series Database","URL":"https:\/\/github.com\/axibase\/atsd-api-
r\/","Version":"1.0.8441"},"attribrisk":{"Author":"Louis Schenck, Elizabeth
Atkinson, Cynthia Crowson, Terry
Therneau","Depends":"survival,boot","Description":"Estimates population
(etiological) attributable risk for\nunmatched, pair-matched or set-matched case-
control designs and returns a\nlist containing the estimated attributable risk,
estimates of coefficients,\nand their standard errors, from the (conditional, If
necessary) logistic\nregression used for estimating the relative
risk.","License":"LGPL (>=
2)","NeedsCompilation":"no","Package":"attribrisk","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr,xtable,testthat","Title":"Population
Attributable Risk","Version":"0.1"},"auRoc":{"Author":"Dai Feng","Depends":"R (>=
3.0.2), rjags (>= 3-11), ProbYX(>= 1.1)","Description":"Estimate the AUC using a
variety of methods as follows:\n(1) frequentist nonparametric methods based on the
Mann-Whitney statistic or kernel methods.\n(2) frequentist parametric methods using
the likelihood ratio test based on higher-order\nasymptotic results, the signed
log-likelihood ratio test, the Wald test,\nor the approximate ''t'' solution to the
Behrens-Fisher problem.\n(3) Bayesian parametric MCMC methods.","Imports":"coda(>=
0.16-1), MBESS(>=
3.3.3)","License":"GPL","NeedsCompilation":"no","Package":"auRoc","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Title":"Various Methods to Estimate the
AUC","Version":"0.1-0"},"aucm":{"Author":"Youyi Fong <youyifong@gmail.com>,
Krisztian Sebestyen <ksebestyen@gmail.com>, Shuxin Yin <yinshuxin05@gmail.com>,
Ying Huang <yhuang124@gmail.com>","Depends":"R (>= 3.0.0),
kyotil","Description":"Implements methods for identifying linear and nonlinear
marker combinations that maximizes the Area Under the AUC Curve
(AUC).","License":"GPL-
2","NeedsCompilation":"yes","Package":"aucm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"RUnit, mvtnorm","Title":"AUC
Maximization","Version":"2016.1-2"},"audio":{"Author":"Simon Urbanek
<simon.urbanek@r-project.org>","Depends":"R (>= 2.0.0)","Description":"Interfaces
to audio devices (mainly sample-based) from R to allow recording and playback of
audio. Built-in devices include Windows MM, Mac OS X AudioUnits and PortAudio (the
last one is very experimental).","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"audio","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Audio Interface for
R","URL":"http:\/\/www.rforge.net\/audio\/","Version":"0.1-5"},"audiolyzR":
{"Author":"Eric Stone, Jesse Garrison","Depends":"hexbin, RJSONIO,
plotrix","Description":"Creates audio representations of common plots in
R","License":"GPL-
2","NeedsCompilation":"no","Package":"audiolyzR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"audiolyzR: Give your data a listen","Version":"0.4-
9"},"audit":{"Author":"Glen Meeden <glen@stat.umn.edu>.","Description":"Two
Bayesian methods for Accounting
Populations","License":"MIT","NeedsCompilation":"no","Package":"audit","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Title":"Bounds for Accounting
Populations","Version":"0.1-1"},"autoencoder":{"Author":"Eugene Dubossarsky
(project leader, chief designer), Yuriy Tyshetskiy (design, implementation,
testing)","Description":"Implementation of the sparse autoencoder in R environment,
following the notes of Andrew Ng
(http:\/\/www.stanford.edu\/class\/archive\/cs\/cs294a\/cs294a.1104\/sparseAutoenco
der.pdf). The features learned by the hidden layer of the autoencoder (through
unsupervised learning of unlabeled data) can be used in constructing deep belief
neural networks.","License":"GPL-
2","NeedsCompilation":"no","Package":"autoencoder","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Sparse Autoencoder for Automatic Learning of
Representative\nFeatures from Unlabeled Data","Version":"1.1"},"automap":
{"Author":"Paul Hiemstra <paul@numbertheory.nl>","Depends":"R (>= 2.10.0), sp (>=
0.9-55)","Description":"This package performs an automatic interpolation by
automatically estimating the variogram and then calling gstat.","Imports":"gstat,
lattice,
reshape","License":"GPL","NeedsCompilation":"no","Package":"automap","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Suggests":"ggplot2, maptools,
gpclib","Title":"Automatic interpolation package","Version":"1.0-14"},"autopls":
{"Author":"Sebastian Schmidtlein, with contributions from C. Oldenburg and H.
Feilhauer\nand with a code snipped borrowed from Bjorn-Helge
Mevik","Depends":"pls","Description":"Some convenience functions for pls
regression, including backward\nvariable selection and validation procedures, image
based predictions\nand plotting.","License":"GPL-
2","NeedsCompilation":"no","Package":"autopls","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"rgdal, raster","Title":"Partial Least Squares
Regression with Backward Selection of\nPredictors","Version":"1.3"},"autovarCore":
{"Author":"Ando Emerencia [aut, cre]","Description":"Automatically find the best
vector autoregression\nmodels and networks for a given time series data set.
'AutovarCore'\nevaluates eight kinds of models: models with and without
log\ntransforming the data, lag 1 and lag 2 models, and models with and\nwithout
day dummy variables. For each of these 8 model configurations,\n'AutovarCore'
evaluates all possible combinations for including\noutlier dummies (at 2.5x the
standard deviation of the residuals)\nand retains the best model. Model evaluation
includes the Eigenvalue\nstability test and a configurable set of residual tests.
These eight\nmodels are further reduced to four models because
'AutovarCore'\ndetermines whether adding day dummies improves the model
fit.","Imports":"Rcpp (>= 0.11.4), Amelia, jsonlite, parallel, stats,
urca,\nvars","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"autovarCore","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"testthat, roxygen2","Title":"Automated
Vector Autoregression Models and Networks","Version":"1.0-0"},"averisk":
{"Author":"John Ferguson [aut, cre]","Description":"Average population attributable
fractions are calculated for a set of risk factors (either binary or ordinal
valued) for both prospective and case-control designs. Confidence intervals are
found by Monte Carlo simulation. The method can be applied to either prospective or
case control designs, provided an estimate of disease prevalence is provided. In
addition to an exact calculation of AF, an approximate calculation, based on
randomly sampling permutations has been implemented to ensure the calculation is
computationally tractable when the number of risk factors is
large.","Imports":"MASS (>=
7.3.0)","License":"CC0","NeedsCompilation":"no","Package":"averisk","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Title":"Calculation of Average Population
Attributable Fractions and\nConfidence Intervals","Version":"1.0.1"},"aws":
{"Author":"Joerg Polzehl [aut, cre],\nFelix Anker [ctb]","Depends":"R (>= 2.14.0),
methods, awsMethods (>= 1.0-1), gsl","Description":"The package contains R-
functions implementing the\nPropagation-Separation Approach to adaptive smoothing
as\ndescribed in J. Polzehl and V. Spokoiny (2006),\nPropagation-Separation
Approach for Local Likelihood Estimation,\nProb. Theory and Rel. Fields,
135(3):335--362.\nand J. Polzehl and V. Spokoiny (2004) Spatially
adaptive\nregression estimation: Propagation-separation approach,\nWIAS-Preprint
2)","NeedsCompilation":"yes","Package":"aws","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Adaptive Weights Smoothing","URL":"http:\/\/www.wias-
berlin.de\/projects\/matheon_a3\/","Version":"1.9-4"},"aws.signature":
{"Author":"Thomas J. Leeper","Description":"Generates request signatures for Amazon
Web Services (AWS) APIs.","Imports":"digest","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"aws.signature","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat","Title":"Amazon Web Services Request
Signatures","URL":"https:\/\/github.com\/cloudyr\/aws.signature","Version":"0.2.0"}
,"awsMethods":{"Author":"Joerg Polzehl [aut, cre],\nFelix Anker [ctb]","Depends":"R
(>= 2.14.0), methods","Description":"The package defines method extract and
provides OpenMP support needed in several packages.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"awsMethods","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Class
and Methods Definitions for Packages 'aws', 'adimpro',\n'fmri' and
'dti'","URL":"http:\/\/www.wias-berlin.de\/projects\/matheon_a3\/","Version":"1.0-
3.1"},"aylmer":{"Author":"Robin K. S. Hankin (R) and Luke J. West (C+
+)","Depends":"R (>= 2.10), methods, Brobdingnag","Description":"A generalization
of Fisher's exact test that allows for\nstructural zeros.","License":"GPL-
2","NeedsCompilation":"yes","Package":"aylmer","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"partitions","Title":"A generalization of Fisher's exact
test","Version":"1.0-11"},"b6e6rl":{"Author":"Marek Spruzina","Description":"This
package contains b6e6rl algorithm, adaptive\ndifferential evolution for global
optimization.","License":"GPL-
2","NeedsCompilation":"no","Package":"b6e6rl","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Adaptive differential evolution, b6e6rl
variant","Version":"1.1"},"bPeaks":{"Author":"Jawad MERHEJ and Gaelle
LELANDAIS","Depends":"R (>= 2.10)","Description":"bPeaks is a simple approach to
identify transcription factor binding sites from ChIP-seq data. Our general
philosophy is to provide an easy-to-use tool, well-adapted for small eukaryotic
genomes (< 20 Mb). bPeaks uses a combination of 4 cutoffs (T1, T2, T3 and T4) to
mimic \"good peak\" properties as described by biologists who visually inspect the
ChIP-seq data on a genome browser. For yeast genomes, bPeaks calculates the
proportion of peaks that fall in promoter sequences. These peaks are good
candidates as transcription factor binding
sites.","License":"GPL","NeedsCompilation":"no","Package":"bPeaks","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"bPeaks: an intuitive peak-calling
strategy to detect\ntranscription factor binding sites from ChIP-seq data in
small\neukaryotic genomes","Version":"1.2"},"bReeze":{"Author":"Christian Graul and
Carsten Poppinga","Depends":"R (>= 2.14.2)","Description":"A collection of
functions to analyse, visualize and interpret wind data\nand to calculate the
potential energy production of wind turbines.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"bReeze","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"RColorBrewer, RgoogleMaps, XML","Title":"Functions for
wind resource
assessment","URL":"https:\/\/github.com\/chgrl\/bReeze","Version":"0.4-0"},"bWGR":
{"Author":"Alencar Xavier, William Muir, Katy Rainey.","Depends":"R (>=
3.2.0)","Description":"Designed for whole-genome regressions using Bayesian models
fitted via Gibbs sampling with optional resampling techniques and polygenic term
with reduced dimensionality.","Imports":"Rcpp","License":"GPL-
3","NeedsCompilation":"yes","Package":"bWGR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Bagging Whole-Genome Regression","Version":"1.3.1"},"babar":
{"Author":"Lydia Rickett, Matthew Hartley, Richard Morris and Nick
Pullen","Description":"Babar is designed to use nested sampling (a Bayesian
analysis technique) to compare possible models for bacterial growth curves, as well
as extracting parameters. It allows model evidence and parameter likelihood values
to be extracted, and also contains helper functions for comparing distributions as
well as direct access to the underlying nested sampling code.","License":"GPL-
2","NeedsCompilation":"no","Package":"babar","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr, R.rsp","Title":"Bayesian Bacterial Growth Curve
Analysis in R","Version":"1.0"},"babel":{"Author":"Adam B. Olshen, Richard A.
Olshen, Barry S. Taylor","Depends":"R (>= 2.14.0), edgeR","Description":"Implements
babel routines for identifying unusual ribosome protected fragment counts given
mRNA counts","Imports":"parallel","License":"LGPL (>=
2.1)","NeedsCompilation":"no","Package":"babel","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"R.rsp, R.devices, R.utils","Title":"Ribosome profiling
data analysis","Version":"0.2-6"},"babynames":{"Author":"Hadley Wickham [aut,
cre],\nRStudio [cph]","Depends":"R (>= 2.10)","Description":"US baby names provided
by the SSA. This package contains all\nnames used for at least 5 children of either
sex.","License":"CC0","NeedsCompilation":"no","Package":"babynames","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Title":"US Baby Names 1880-
2014","URL":"http:\/\/github.com\/hadley\/babynames","Version":"0.2.1"},"backShift"
:{"Author":"Christina Heinze <heinze@stat.math.ethz.ch>","Depends":"R (>=
3.1.0)","Description":"Code for 'backShift', an algorithm to estimate the
connectivity\nmatrix of a directed (possibly cyclic) graph with hidden variables.
The\nunderlying system is required to be linear and we assume that
observations\nunder different shift interventions are available. For more
details,\nsee <http:\/\/arxiv.org\/abs\/1506.02494>.","Imports":"jointDiag, clue,
pcalg, igraph, matrixcalc, reshape2,
ggplot2","License":"GPL","NeedsCompilation":"no","Package":"backShift","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"knitr, pander, fields,
testthat","Title":"Learning Causal Cyclic Graphs from Unknown Shift
Interventions","URL":"https:\/\/github.com\/christinaheinze\/backShift","Version":"
0.1.3"},"backblazer":{"Author":"Authors@R: person(\"Phill\", \"Clarke\", email
= \"phill@starkingdom.co.uk\",\nrole = c(\"aut\", \"cre\"))","Depends":"R (>=
3.2.3)","Description":"Provides convenience functions for the Backblaze B2 cloud
storage\nAPI (see https:\/\/www.backblaze.com\/b2\/docs\/). All B2 API calls are
mapped\nto equivalent R functions. Files can be easily uploaded, downloaded
and\ndeleted from B2, all from within R programs.","Imports":"httr (>= 1.0.0),
jsonlite (>= 0.9.19), openssl (>= 0.9.1),\ntools (>= 3.2.3)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"backblazer","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"knitr (>= 1.12), rmarkdown","Title":"Bindings
to the Backblaze B2
API","URL":"https:\/\/github.com\/phillc73\/backblazer","Version":"0.1.0"},"backpip
e":{"Author":"Christopher Brown [cre, aut],\nDecision Patterns [cph]","Depends":"R
(>= 3.1.0)","Description":"Provides a backward-pipe operator for 'magrittr' (%<%)
or\n'pipeR' (%<<%) that allows for a performing operations from right-to-
left.\nThis is useful in instances where there is right-to-left ordering
commonly\nobserved with nested structures such as trees\/directories and
markup\nlanguages such as HTML and XML.","License":"GPL-2 | file
LICENSE","NeedsCompilation":"no","Package":"backpipe","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"magrittr (>= 1.5), pipeR (>= 0.6.0.6), R6 (>=
2.1.1),\ntestthat (>= 0.10.0), shiny (>= 0.12.1), knitr (>=
1.11)","Title":"Backward Pipe
Operator","URL":"https:\/\/github.com\/decisionpatterns\/backpipe","Version":"0.1.5
"},"backports":{"Author":"Michel Lang <michellang@gmail.com>","Depends":"R (>=
3.0.0)","Description":"Provides implementations of functions which have been
introduced in\nR since version 3.0.0. The backports are conditionally exported
which\nresults in R resolving the function names to the version shipped with R
(if\navailable) and uses the implemented backports as fallback. This way
package\ndevelopers can make use of the new functions without worrying about
the\nminimum required R version.","Imports":"stringi","License":"GPL-
2","NeedsCompilation":"no","Package":"backports","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat","Title":"Reimplementations of Functions
Introduced Since R-3.0.0","Version":"1.0.2"},"backtest":{"Author":"Jeff Enos
<jeff@kanecap.com> and David Kane <dave@kanecap.com>,\nwith contributions from Kyle
Campbell\n<kyle.w.campbell@williams.edu>, Daniel Gerlanc\n<daniel@gerlanc.com>,
Aaron Schwartz\n<Aaron.J.Schwartz@williams.edu>, Daniel Suo\n<danielsuo@gmail.com>,
Alexei Colin <acolin@fas.harvard.edu>,\nand Luyi Zhao
<luyizhao@gmail.com>","Depends":"R (>= 2.10), methods, grid,
lattice","Description":"The backtest package provides facilities for
exploring\nportfolio-based conjectures about financial instruments\n(stocks, bonds,
swaps, options, et cetera).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"backtest","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Exploring Portfolio-Based Conjectures About
Financial\nInstruments","Version":"0.3-4"},"backtestGraphics":
{"Author":"as.person(c(\n\"David Kane <dave.kane@gmail.com> [aut]\",\n\"Ziqi Lu
<ziqi.lu@williams.edu> [aut]\",\n\"Fan Zhang <fan.zhang@williams.edu>
[aut]\",\n\"Miller Zijie Zhu <zijie.miller.zhu@gmail.com> [aut]\"\n))","Depends":"R
(>= 2.10)","Description":"Creates an interactive graphics\ninterface to visualize
backtest results of different financial\ninstruments, such as equities, futures,
and credit default swaps.\nThe package does not run backtests on the given data set
but\ndisplays a graphical explanation of the backtest results. Users can\nlook at
backtest graphics for different instruments, investment\nstrategies, and
portfolios. Summary statistics of different\nportfolio holdings are shown in the
left panel, and interactive\nplots of profit and loss (P\\&L), net market value
(NMV) and\ngross market value (GMV) are displayed in the right
panel.","Imports":"dygraphs, dplyr, scales, xts, shiny","License":"GPL-
3","NeedsCompilation":"no","Package":"backtestGraphics","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Interactive Graphics for
Portfolio Data","Version":"0.1.6"},"bacr":{"Author":"Chi Wang
<chi.wang@uky.edu>","Depends":"R(>= 2.13.0), graphics, stats,
MCMCpack","Description":"Estimating the average causal effect based on the Bayesian
Adjustment for Confounding (BAC) algorithm.","License":"GPL-
2","NeedsCompilation":"no","Package":"bacr","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Bayesian Adjustment for
Confounding","Version":"1.0"},"bagRboostR":{"Author":"Shannon
Rush <shannonmrush@gmail.com>","Description":"bagRboostR is a set of ensemble
classifiers for multinomial\nclassification. The bagging function is the
implementation of Breiman's\nensemble as described by Opitz & Maclin (1999). The
boosting function is\nthe implementation of Stagewise Additive Modeling using a
Multi-class\nExponential loss function (SAMME) created by Zhu et al (2006). Both
bagging\nand SAMME implementations use randomForest as the weak classifier
and\nexpect a character outcome variable. Each ensemble classifier returns
a\ncharacter vector of predictions for the test
set.","Imports":"randomForest","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"bagRboostR","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Ensemble bagging and
boosting classifiers","Version":"0.0.2"},"bamdit":{"Author":"Pablo Emilio Verde
[aut, cre]","Depends":"R (>= 3.1.0)","Description":"Functions for Bayesian meta-
analysis of diagnostic test data which are based on a scale mixtures bivariate
random-effects model.","Imports":"rjags (>= 3.4.0), ggplot2 (>= 0.9.3.1), grid,
gridExtra,\nR2jags (>= 0.04-03)","License":"GPL (<=
2)","NeedsCompilation":"no","Package":"bamdit","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Bayesian Meta-Analysis of Diagnostic Test
Data","Version":"2.0.1"},"bandit":{"Author":"Thomas Lotze and Markus
Loecher","Description":"A set of functions for doing analysis of A\/B split test
data and web metrics in general.","Imports":"boot, gam (>= 1.09)","License":"GPL-
3","NeedsCompilation":"no","Package":"bandit","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Functions for simple A\/B split test and multi-armed
bandit\nanalysis","Version":"0.5.0"},"bapred":{"Author":"Roman Hornung, David
Causeur","Depends":"R (>= 3.1.0), glmnet, lme4, MASS, sva","Description":"Various
tools dealing with batch effects, in particular enabling the\nremoval of
discrepancies between training and test sets in prediction scenarios.\nThe
following batch effect removal methods are implemented: FAbatch, ComBat,
(f)SVA,\nmean-centering, standardization, Ratio-A and Ratio-G. For each of these we
provide\nan additional function which enables a posteriori ('addon') batch effect
removal\nin independent batches ('test data'). Here, the (already batch effect
adjusted)\ntraining data is not altered. For evaluating the success of batch effect
adjustment\nseveral metrics are provided. Moreover, the package implements a plot
for the\nvisualization of batch effects using principal component analysis. The
main functions\nof the package are ba() and baaddon() which enable batch effect
removal and addon\nbatch effect removal, respectively, with one of the seven
methods mentioned above.\nAnother important function is bametric() which is a
wrapper function for all implemented\nmethods for evaluating the success of batch
effect removal.","Imports":"FNN, fuzzyRankTests, mnormt","License":"GPL-
2","NeedsCompilation":"no","Package":"bapred","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Batch Effect Removal (in Phenotype Prediction using Gene
Data)","Version":"0.3"},"barcode":{"Author":"John W. Emerson and Walton A. Green
and John A. Hartigan","Depends":"grid, lattice","Description":"This package
includes the function \\code{barcode()}, which\nproduces a histogram-like plot of a
distribution that shows\ngranularity in the
data.","Enhances":"gpairs","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"barcode","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Barcode distribution
plots","Version":"1.1"},"bartMachine":{"Author":"Adam Kapelner and Justin Bleich (R
package)","Depends":"R (>= 2.14.0), rJava (>= 0.9-8), bartMachineJARs (>=
1.0),\ncar, randomForest, missForest","Description":"An advanced implementation of
Bayesian Additive Regression Trees with expanded features for data analysis and
visualization.","Imports":"graphics, grDevices, stats","License":"GPL-
3","NeedsCompilation":"no","Package":"bartMachine","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Bayesian Additive Regression
Trees","Version":"1.2.2"},"bartMachineJARs":{"Author":"Adam Kapelner and Justin
Bleich (R package), see COPYRIGHTS file for the authors of the java
libraries","Depends":"R (>= 2.14.0), rJava (>= 0.9-8)","Description":"These are
bartMachine's Java dependency libraries. Note: this package has no functionality of
its own and should not be installed as a standalone package without
bartMachine.","License":"GPL-
3","NeedsCompilation":"no","Package":"bartMachineJARs","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"bartMachine JARs","Version":"1.0"},"base64":
{"Author":"Romain Francois, based on code by Bob Trower available
at\nhttp:\/\/base64.sourceforge.net\/","Description":"Base 64
encoder\/decoder","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"base64","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Base 64
encoder\/decoder","URL":"\nhttp:\/\/romainfrancois.blog.free.fr\/index.php?
category\/R-package\/base64","Version":"1.1"},"base64enc":{"Author":"Simon Urbanek
<Simon.Urbanek@r-project.org>","Depends":"R (>= 2.9.0)","Description":"This package
provides tools for handling base64 encoding. It is more flexible than the orphaned
base64 package.","Enhances":"png","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"base64enc","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Tools for base64
encoding","URL":"http:\/\/www.rforge.net\/base64enc","Version":"0.1-3"},"basefun":
{"Author":"Torsten Hothorn [aut, cre]","Depends":"variables (>= 0.0-
30)","Description":"Some very simple infrastructure for basis
functions.","Imports":"stats, polynom, Matrix, orthopolynom,
2","NeedsCompilation":"yes","Package":"basefun","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Infrastructure for Computing with Basis
Functions","Version":"0.0-30"},"baseline":{"Author":"Kristian Hovde Liland [aut,
cre],\nBjÃ¸rn-Helge Mevik [aut],\nRoberto Canteri [ctb]","Depends":"R (>=
2.15)","Description":"Collection of baseline correction algorithms, along with a
framework and a GUI for optimising baseline algorithm parameters. Typical use of
the package is for removing background effects from spectra originating from
various types of spectroscopy and spectrometry, possibly optimizing this with
regard to regression or classification results. Correction methods include
polynomial fitting, weighted local smoothers and many more.","Imports":"graphics,
SparseM, grDevices, stats, methods","License":"GPL-
2","NeedsCompilation":"no","Package":"baseline","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"gWidgets, IDPmisc, lattice, pls,
MASS","Title":"Baseline Correction of Spectra","Version":"1.2-1"},"basicspace":
{"Author":"Keith Poole <ktpoole@uga.edu>, Howard Rosenthal\n<hr31@nyu.edu>, Jeffrey
Lewis <jblewis@ucla.edu>,\nJames Lo <jameslo@princeton.edu> and Royce
Carroll\n<rcarroll@rice.edu>","Depends":"R (>= 3.0.0), tools (>=
2.0.0)","Description":"Conducts Aldrich-McKelvey and Blackbox Scaling to
Recover\nLatent Dimensions of Judgment.","License":"GPL-
2","NeedsCompilation":"yes","Package":"basicspace","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Recovering a Basic Space from Issue
Scales","Version":"0.17"},"batade":{"Author":"Ichikawa
Daisuke","Depends":"hwriter","Description":"This package provides some utility
functions (e.g HTML\nreport maker).","License":"GPL-
2","NeedsCompilation":"no","Package":"batade","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"HTML reports and so on","Version":"0.1"},"batch":
{"Author":"Thomas Hoffmann <tjhoffm@gmail.com>","Depends":"R (>=
2.14)","Description":"Functions to allow you to easily pass command-line\narguments
into R, and functions to aid in submitting your R\ncode in parallel on a cluster
and joining the results afterward\n(e.g. multiple parameter values for simulations
running in\nparallel, splitting up a permutation test in parallel, etc.).\nSee
`parseCommandArgs(...)' for the main example of how to use\nthis
package.","License":"GPL","NeedsCompilation":"no","Package":"batch","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Suggests":"parallel","Title":"Batching
Routines in Parallel and Passing Command-Line Arguments\nto
R","URL":"http:\/\/sites.google.com\/site\/thomashoffmannproject\/","Version":"1.1-
4"},"batchmeans":{"Author":"Murali Haran <mharan@stat.psu.edu> and John Hughes
<hughesj@umn.edu>","Depends":"utils","Description":"batchmeans provides consistent
batch means estimation of Monte\nCarlo standard errors.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"batchmeans","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Consistent Batch Means Estimation of Monte Carlo
Standard Errors","URL":"http:\/\/stat.psu.edu\/~mharan ,
http:\/\/www.biostat.umn.edu\/~johnh","Version":"1.0-2"},"batman":{"Author":"Oliver
Keyes [aut, cre], Ruben C. Arslan [ctb], Christopher Akiki [ctb], Mine Cetinkaya-
Rundel [ctb], Peter Meissner [ctb],\nIlaria Prosdocimi [ctb], Thomas Leeper [ctb],
Amy Lee [ctb], Adolfo Ãlvarez [ctb]","Description":"Survey systems and other
third-party data sources commonly use non-standard representations of logical
values when\nit comes to qualitative data - \"Yes\", \"No\" and \"N\/A\", say.
batman is a package designed to seamlessly convert these into logicals.\nIt is
highly localised, and contains equivalents to boolean values in languages including
German, French, Spanish, Italian,\nTurkish, Chinese and
Polish.","Imports":"Rcpp","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"batman","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat","Title":"Convert Categorical
Representations of Logicals to
Actual\nLogicals","URL":"https:\/\/github.com\/ironholds\/batman","Version":"0.1.0"
},"batteryreduction":{"Author":"Chunqiao
Luo [aut, cre],\nRalph D'Agostino [aut] (This package is derived from Battery
Reduction\nMacro at
http:\/\/www.lexjansen.com\/nesug\/nesug92\/NESUG92090.pdf)","Depends":"R (>=
3.0.2)","Description":"Battery reduction is a method used in data reduction. It
uses Gram-Schmidt orthogonal rotations to find out a subset of variables best
representing the original set of variables.","Imports":"stats,
pracma","License":"GPL","NeedsCompilation":"no","Package":"batteryreduction","Repos
itory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"An R Package for Data
Reduction by Battery Reduction","Version":"0.1.1"},"bayesDccGarch":{"Author":"Jose
A Fiorucci <jafioruci@gmail.com>, Ricardo S Ehlers <ehlers@icmc.usp.br>, Francisco
Louzada <louzada@icmc.usp.br>","Depends":"R (>= 2.0), numDeriv,
coda","Description":"Bayesian estimation of dynamic conditional correlation GARCH
model for multivariate time series volatility (Fioruci, J.A., Ehlers, R.S. and
Andrade-Filho, M.G., (2014), DOI:10.1080\/02664763.2013.839635).","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"bayesDccGarch","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"The Bayesian Dynamic Conditional Correlation GARCH
Model","URL":"http:\/\/arxiv.org\/abs\/1412.2967","Version":"2.0"},"bayesDem":
{"Author":"Hana Sevcikova <hanas@uw.edu>","Depends":"R (>= 2.14.2), gWidgets,
gWidgetsRGtk2, bayesTFR (>= 5.0-0),\nbayesLife (>= 3.0-0), bayesPop (>= 6.0-
0)","Description":"Provides graphical user interface for the packages 'bayesTFR',
'bayesLife' and 'bayesPop'.","Imports":"RGtk2, wpp2015","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"bayesDem","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"wpp2012, wpp2010","Title":"Graphical User Interface
for bayesTFR, bayesLife and
bayesPop","URL":"http:\/\/bayespop.csss.washington.edu","Version":"2.5-
0"},"bayesGARCH":{"Author":"David Ardia [aut, cre]","Description":"Provides the
bayesGARCH function which performs the\nBayesian estimation of the GARCH(1,1) model
with Student's t innovations.","Imports":"mvtnorm, coda","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"bayesGARCH","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Bayesian Estimation of the GARCH(1,1) Model with
Student-
t\nInnovations","URL":"http:\/\/perso.unifr.ch\/david.ardia\/","Version":"2.0.2"},"
bayesLife":{"Author":"Hana Sevcikova, Adrian Raftery; original WinBugs code written
by Jennifer Chunn","Depends":"bayesTFR (>= 4.1-2)","Description":"Making
probabilistic projections of life expectancy for all countries of the world, using
a Bayesian hierarchical model.","Imports":"wpp2015, hett, car, coda","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"bayesLife","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"wpp2012, wpp2010","Title":"Bayesian Projection of
Life Expectancy","URL":"http:\/\/bayespop.csss.washington.edu","Version":"3.0-
0"},"bayesMCClust":{"Author":"Christoph Pamminger
<christoph.pamminger@gmail.com>","Depends":"R (>= 2.14.1), gplots, xtable,
grDevices, mnormt, MASS,\nbayesm, boa, e1071, gtools","Description":"This package
provides various Markov Chain Monte Carlo\n(MCMC) sampler for model-based
clustering of discrete-valued\ntime series obtained by observing a categorical
variable with\nseveral states (in a Bayesian approach). In order to analyze\ngroup
membership, we provide also an extension to the\napproaches by formulating a
probabilistic model for the latent\ngroup indicators within the Bayesian
classification rule using\na multinomial logit model.","License":"GPL-
2","NeedsCompilation":"no","Package":"bayesMCClust","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"nnet","Title":"Mixtures-of-Experts Markov Chain
Clustering and Dirichlet\nMultinomial Clustering","Version":"1.0"},"bayesPop":
{"Author":"Hana Sevcikova, Adrian Raftery, Thomas Buettner","Depends":"R (>=
2.14.2), bayesTFR (>= 4.2-0), bayesLife (>= 2.2-0)","Description":"Generating
population projections for all countries of the world using several probabilistic
components, such as total fertility rate (TFR) and life
expectancy.","Imports":"parallel, abind, plyr, wpp2015, wpp2012, graphics,
grDevices,\nstats, utils, rworldmap, fields, googleVis","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"bayesPop","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"wpp2010","Title":"Probabilistic Population
Projection","Version":"6.0-1"},"bayesQR":{"Author":"Dries F. Benoit, Rahim Al-
Hamzawi, Keming Yu, Dirk Van den Poel","Depends":"R (>=
3.0)","Description":"Bayesian quantile regression using the asymmetric Laplace
distribution, both continuous as well as binary dependent variables are supported.
The package consists of implementations of the methods of Yu & Moyeed (2001),
Benoit & Van den Poel (2012) and Al-Hamzawi, Yu & Benoit (2012). To speed up the
calculations, the Markov Chain Monte Carlo core of all algorithms is programmed in
Fortran and called from R.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"bayesQR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Bayesian quantile
regression","Version":"2.2"},"bayesSurv":{"Author":"ArnoÅ¡t KomÃ¡rek
<arnost.komarek@mff.cuni.cz>","Depends":"R (>= 3.0.0), survival, coda,
smoothSurv","Description":"Contains Bayesian implementations of Mixed-Effects
Accelerated Failure Time (MEAFT) models\nfor censored data. Those can be not only
right-censored but also interval-censored,\ndoubly-interval-censored or
misclassified interval-censored.","Imports":"graphics, stats, utils","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"bayesSurv","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Bayesian Survival Regression with Flexible Error and
Random\nEffects
Distributions","URL":"http:\/\/msekce.karlin.mff.cuni.cz\/~komarek","Version":"2.6"
},"bayesTFR":{"Author":"Hana Sevcikova (hanas@uw.edu), Leontine Alkema
(alkema@nus.edu.sg), Adrian Raftery (raftery@uw.edu) with code contribution from
Bailey Fosdick (bfosdick@uw.edu) and Patrick Gerland (gerland@un.org)","Depends":"R
(>= 2.14.2)","Description":"Making probabilistic projections of total fertility
rate for all countries of the world, using a Bayesian hierarchical
model.","Imports":"mvtnorm, MASS, coda, wpp2015, graphics, grDevices,
stats,\nutils","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"bayesTFR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"rworldmap, snowFT, googleVis, rgdal, rworldxtra, sp,
wpp2012,\nwpp2010","Title":"Bayesian Fertility
Projection","URL":"http:\/\/bayespop.csss.washington.edu","Version":"5.0-
1"},"bayesboot":{"Author":"Rasmus BÃ¥Ã¥th [aut, cre]","Depends":"R (>=
3.2.0)","Description":"Functions for performing the Bayesian bootstrap as
introduced by\nRubin (1981) <doi:10.1214\/aos\/1176345338> and for summarizing the
result.\nThe implementation can handle both summary statistics that works on
a\nweighted version of the data and summary statistics that works on a\nresampled
data set.","Imports":"plyr (>= 1.8.3), HDInterval(>= 0.1.1)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"bayesboot","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat, doParallel, boot","Title":"An
Implementation of Rubin's (1981) Bayesian
Bootstrap","URL":"https:\/\/github.com\/rasmusab\/bayesboot","Version":"0.2.1"},"ba
yescount":{"Author":"Matthew Denwood [aut, cre]","Depends":"R (>=
2.14.0)","Description":"A set of functions to allow analysis of count data
(such\nas faecal egg count data) using Bayesian MCMC methods. Returns\ninformation
on the possible values for mean count, coefficient\nof variation and zero inflation
(true prevalence) present in\nthe data. A complete faecal egg count reduction test
(FECRT)\nmodel is implemented, which returns inference on the true\nefficacy of the
drug from the pre- and post-treatment data\nprovided, using non-parametric
bootstrapping as well as using\nBayesian MCMC. Functions to perform power analyses
for faecal\negg counts (including FECRT) are also provided.","Imports":"runjags (>=
2.0.1), rjags, coda, stats, utils","License":"GPL-
2","NeedsCompilation":"yes","Package":"bayescount","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Power Calculations and Bayesian Analysis of Count
Distributions\nand FECRT Data using
MCMC","URL":"http:\/\/bayescount.sourceforge.net","Version":"0.9.99-5"},"bayesm":
{"Author":"Peter Rossi <perossichi@gmail.com>","Depends":"R (>=
2.10)","Description":"Covers many important models used\nin marketing and micro-
econometrics applications.\nThe package includes:\nBayes Regression (univariate or
multivariate dep var),\nBayes Seemingly Unrelated Regression (SUR),\nBinary and
Ordinal Probit,\nMultinomial Logit (MNL) and Multinomial Probit
(MNP),\nMultivariate Probit,\nNegative Binomial (Poisson) Regression,\nMultivariate
Mixtures of Normals (including clustering),\nDirichlet Process Prior Density
Estimation with normal base,\nHierarchical Linear Models with normal prior and
covariates,\nHierarchical Linear Models with a mixture of normals prior and
covariates,\nHierarchical Multinomial Logits with a mixture of normals prior\nand
covariates,\nHierarchical Multinomial Logits with a Dirichlet Process prior and
covariates,\nHierarchical Negative Binomial Regression Models,\nBayesian analysis
of choice-based conjoint data,\nBayesian treatment of linear instrumental variables
models,\nAnalysis of Multivariate Ordinal survey data with scale\nusage
heterogeneity (as in Rossi et al, JASA (01)),\nBayesian Analysis of Aggregate
Random Coefficient Logit Models as in BLP (see\nJiang, Manchanda, Rossi 2009)\nFor
further reference, consult our book, Bayesian Statistics and\nMarketing by Rossi,
Allenby and McCulloch (Wiley 2005) and Bayesian Non- and Semi-Parametric\nMethods
and Applications (Princeton U Press 2014).","Imports":"Rcpp
(>= 0.11.3)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"bayesm","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Bayesian Inference for Marketing\/Micro-
Econometrics","URL":"http:\/\/www.perossi.org\/home\/bsm-1","Version":"3.0-
2"},"bayesmeta":{"Author":"Christian Roever [aut, cre], Tim Friede
[ctb]","Description":"A collection of functions allowing to derive the posterior
distribution of the two parameters in a random-effects meta-analysis, and providing
functionality to evaluate joint and marginal posterior probability distributions,
predictive distributions, etc.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"bayesmeta","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"metafor, compute.es, knitr,
rmarkdown","Title":"Bayesian Random-Effects Meta-
Analysis","Version":"1.1"},"bayesmix":{"Author":"Bettina Gruen [aut, cre],\nMartyn
Plummer [ctb]","Depends":"R (>= 2.10),","Description":"The fitting of finite
mixture models of univariate\nGaussian distributions using JAGS within a
Bayesian\nframework is provided.","Imports":"graphics, stats, methods, rjags (>=
2.1.0), coda (>= 0.13)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"bayesmix","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Bayesian Mixture Models with
JAGS","URL":"http:\/\/ifas.jku.at\/gruen\/BayesMix","Version":"0.7-4"},"bayespref":
{"Author":"Zachariah Gompert and James A. Fordyce","Depends":"coda, lattice, MASS,
MCMCpack, RColorBrewer","Description":"This program implements a hierarchical
Bayesian analysis\nof count data, such as preference experiments. It
provides\npopulation-level and individual-level preference parameter\nestimates
obtained via MCMC. It also allows for model\ncomparison using Deviance Information
Criterion.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"bayespref","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Hierarchical Bayesian analysis of ecological count
data","Version":"1.0"},"bayess":{"Author":"Christian P. Robert, Universite Paris
Dauphine, and Jean-Michel\nMarin, Universite Montpellier 2","Depends":"stats, MASS,
mnormt, gplots, combinat","Description":"bayess contains a collection of functions
that allows the\nreenactment of the R programs used in the
book \"Bayesian\nEssentials with R\" (revision of \"Bayesian Core\")
without\nfurther programming. R code being available as well, they can\nbe modified
by the user to conduct one's own simulations.","License":"GPL-
2","NeedsCompilation":"no","Package":"bayess","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Bayesian Essentials with R","Version":"1.4"},"bayou":
{"Author":"Josef C. Uyeda, Jon Eastman and Luke Harmon","Depends":"ape (>= 3.0-6),
geiger(>= 2.0), R (>= 2.15.0), phytools, coda","Description":"Tools for fitting and
simulating multi-optima Ornstein-Uhlenbeck\nmodels to phylogenetic comparative data
using Bayesian reversible-jump\nmethods.","Imports":"Rcpp (>= 0.10.3), MASS,
mnormt, fitdistrplus, denstrip,\nforeach, stats, grDevices,
2)","NeedsCompilation":"yes","Package":"bayou","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"doParallel","Title":"Bayesian Fitting of Ornstein-
Uhlenbeck Models to Phylogenies","Version":"1.1.0"},"bbefkr":{"Author":"Han Lin
Shang","Depends":"R (>= 3.0.3), splines","Description":"Estimating optimal
bandwidths for the regression mean function approximated by the functional
Nadaraya-Watson estimator and the error density approximated by a kernel density of
residuals simultaneously in a scalar-on-function regression. As a by-product of
Markov chain Monte Carlo, the optimal choice of semi-metric is selected based on
largest marginal likelihood.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"bbefkr","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Bayesian bandwidth estimation and semi-metric selection
for the\nfunctional kernel regression with unknown error
density","URL":"https:\/\/sites.google.com\/site\/hanlinshangswebsite\/","Version":
"4.2"},"bbemkr":{"Author":"Han Lin Shang and Xibin Zhang","Depends":"R (>= 3.0.1),
MASS","Description":"Bayesian bandwidth estimation for Nadaraya-Watson
type\nmultivariate kernel regression with Gaussian error density","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"bbemkr","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Bayesian bandwidth estimation for multivariate kernel
regression\nwith Gaussian
error","URL":"https:\/\/sites.google.com\/site\/hanlinshangswebsite\/","Version":"2
.0"},"bbmle":{"Author":"Ben Bolker <bolker@mcmaster.ca>, R Development Core
Team","Depends":"R (>= 3.0.0), stats4","Description":"Methods and functions for
fitting maximum likelihood models in R.\nThis package modifies and extends the
'mle' classes in the 'stats4' package.","Imports":"stats, numDeriv, lattice, MASS,
methods","License":"GPL","NeedsCompilation":"no","Package":"bbmle","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Suggests":"emdbook, rms, ggplot2, RUnit,
MuMIn, AICcmodavg, Hmisc,\noptimx (>= 2013.8.6), knitr, testthat","Title":"Tools
for General Maximum Likelihood Estimation","Version":"1.0.18"},"bbo":
{"Author":"Sarvesh Nikumbh (BBO originally invented by Prof. Dan Simon,\nCleveland
State University, Ohio)","Description":"This package provides an R implementation
of\nBiogeography-Based Optimization (BBO), originally invented by\nProf. Dan Simon,
Cleveland State University, Ohio. This method\nis an application of the concept of
biogeography, a study of\nthe geographical distribution of biological organisms,
to\noptimization problems. More information about this method can\nbe found here:
http:\/\/academic.csuohio.edu\/simond\/bbo\/.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"bbo","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Biogeography-Based Optimization","Version":"0.2"},"bc3net":
{"Author":"Ricardo de Matos Simoes [aut, cre],\nFrank Emmert-Streib
[aut]","Depends":"R (>= 2.10.0), c3net, infotheo, igraph, Matrix,
lattice","Description":"Implementation of the BC3NET algorithm for gene regulatory
network inference (de Matos Simoes and Frank Emmert-Streib, Bagging Statistical
Network Inference from Large-Scale Gene Expression Data, PLoS ONE 7(3):
e33624).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"bc3net","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Gene Regulatory Network Inference with
Bc3net","Version":"1.0.3"},"bcRep":{"Author":"Julia Bischof","Depends":"R (>=
3.2.2)","Description":"Methods for advanced analysis of B cell receptor
repertoire\ndata, like gene usage, mutations, clones, diversity, distance measures
and\nmultidimensional scaling and their visualisation.","Imports":"vegan, parallel,
doParallel, foreach, gplots, ineq, ape,\nstringdist, proxy,
2","NeedsCompilation":"no","Package":"bcRep","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"stats, utils, graphics, grDevices, knitr, rmarkdown,
pander","Title":"Advanced Analysis of B Cell Receptor Repertoire
Data","Version":"1.3.2"},"bclust":{"Author":"Vahid PARTOVI NIA and Anthony C.
DAVISON","Depends":"R (>= 3.2.1), stats, grDevices, graphics","Description":"Builds
a dendrogram using log posterior as a natural distance defined by the model and
meanwhile waits the clustering variables. It is also capable to computing
equivalent Bayesian discrimination probabilities. The adopted method suites small
sample large dimension setting. The model parameter estimation maybe difficult,
depending on data structure and the chosen distribution family.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"bclust","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Bayesian Hierarchical Clustering Using Spike and Slab
Models","URL":"http:\/\/bclust.r-forge.r-project.org\/","Version":"1.5"},"bcp":
{"Author":"Xiaofei Wang, Chandra Erdman, and John W. Emerson","Depends":"graphics,
methods, grid","Description":"Provides an implementation of the Barry and Hartigan
(1993) product partition model for the normal errors change point problem using
Markov Chain Monte Carlo. It also extends the methodology to regression models on
a connected graph (Wang and Emerson, 2015); this allows estimation of change point
models with multivariate responses. Parallel MCMC, previously available in bcp
v.3.0.0, is currently not implemented.","Imports":"Rcpp (>= 0.9.2)","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"bcp","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"DNAcopy, coda, strucchange, vegan, ggplot2,
igraph","Title":"Bayesian Analysis of Change Point
Problems","Version":"4.0.0"},"bcpa":{"Author":"Eliezer Gurarie
<eliezg@uw.edu>","Depends":"Rcpp (>= 0.10.2), plyr","Description":"The Behavioral
Change Point Analysis (BCPA) is a method of\nidentifying hidden shifts in the
underlying parameters of a time series,\ndeveloped specifically to be applied to
animal movement data which is\nirregularly sampled. The method is based on:
E.\nGurarie, R. Andrews and K. Laidre A novel method for identifying\nbehavioural
changes in animal movement data (2009) Ecology Letters 12:5\n395-
408.","License":"Unlimited","NeedsCompilation":"yes","Package":"bcpa","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"knitr,
circular","Title":"Behavioral change point analysis of animal
movement","Version":"1.1"},"bcpmeta":{"Author":"Yingbo Li","Depends":"R (>=
2.14.0)","Description":"A Bayesian approach to detect mean shifts in AR(1) time
series while accommodating metadata (if available). In addition, a linear trend
component is allowed.","Imports":"mvtnorm","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"bcpmeta","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Bayesian Multiple Changepoint Detection Using
Metadata","Version":"1.0"},"bcrm":{"Author":"Michael
Sweeting","Description":"Implements a wide variety of one and two-parameter
Bayesian CRM\ndesigns. The program can run interactively, allowing the user to
enter outcomes\nafter each cohort has been recruited, or via simulation to assess
operating\ncharacteristics.","Imports":"mvtnorm, ggplot2 (>= 1.0.1),
grid","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"bcrm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"R2WinBUGS, BRugs, rjags","Title":"Bayesian Continual
Reassessment Method for Phase I\nDose-Escalation
Trials","Version":"0.4.6"},"bcrypt":{"Author":"Jeroen Ooms [cre, aut],\nDamien
Miller [cph],\nNiels Provos [cph]","Description":"An R interface to the OpenBSD
'blowfish' password hashing algorithm,\nas described in \"A Future-Adaptable
Password Scheme\" by Niels Provos. The\nimplementation is derived from the 'py-
bcrypt' module for Python which is a\nwrapper for the OpenBSD
implementation.","Imports":"openssl","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"yes","Package":"bcrypt","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"'Blowfish' Password Hashing
Algorithm","URL":"https:\/\/github.com\/jeroenooms\/bcrypt\nhttps:\/\/www.usenix.or
g\/legacy\/events\/usenix99\/full_papers\/provos\/provos.pdf","Version":"0.2"},"bcv
":{"Author":"Patrick O. Perry","Description":"\nMethods for choosing the rank of an
SVD approximation via cross\nvalidation. The package provides both Gabriel-
style \"block\"\nholdouts and Wold-style \"speckled\" holdouts. It also includes
an\nimplementation of the SVDImpute algorithm. For more information about\nBi-
cross-validation, see Owen & Perry's 2009 AoAS article\n(at
http:\/\/arxiv.org\/abs\/0908.2062) and Perry's 2009 PhD thesis\n(at
http:\/\/arxiv.org\/abs\/0909.3052).","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"yes","Package":"bcv","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Cross-Validation for the SVD (Bi-Cross-
Validation)","Version":"1.0.1"},"bda":{"Author":"Bin Wang
<bwang@southalabama.edu>.","Depends":"R (>= 2.10.0)","Description":"Functions for
density estimation based on grouped (or pre-
binned)\ndata.","License":"Unlimited","NeedsCompilation":"yes","Package":"bda","Rep
ository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Density Estimation for
Grouped Data","Version":"5.1.6"},"bde":{"Author":"Guzman Santafe, Borja Calvo,
Aritz Perez and Jose A. Lozano","Depends":"R (>=
2.0),shiny,ggplot2","Description":"A collection of S4 classes which implements
different methods to estimate and deal with densities in bounded domains. That is,
densities defined within the interval [lower.limit, upper.limit], where lower.limit
and upper.limit are values that can be set by the
user.","Imports":"methods","License":"GPL-
2","NeedsCompilation":"no","Package":"bde","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Bounded Density Estimation","Version":"1.0.1"},"bdots":
{"Author":"Michael Seedorff, Jacob Oleson, Grant Brown, Joseph Cavanaugh, and Bob
McMurray","Depends":"nlme, mvtnorm","Description":"Analyze differences among time
series curves with p-value adjustment for multiple comparisons introduced in Oleson
et al (2015) <DOI:10.1177\/0962280215607411>.","Imports":"doParallel, doRNG,
foreach","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"bdots","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Bootstrapped Differences of Time
Series","Version":"0.1.7"},"bdpopt":{"Author":"Sebastian Jobjörnsson [aut,
cre]","Depends":"R (>= 3.0.2)","Description":"Optimisation of the expected utility
in single-stage and multi-stage Bayesian decision problems. The expected utility is
estimated by simulation. For single-stage problems, JAGS is used to draw MCMC
samples.","Imports":"rjags (>= 3-15), coda (>= 0.17-1), parallel (>=
2","NeedsCompilation":"no","Package":"bdpopt","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Optimisation of Bayesian Decision Problems","Version":"1.0-
1"},"bdpv":{"Author":"Frank Schaarschmidt [aut, cre]","Description":"Computation of
asymptotic confidence intervals for negative and positive predictive values in
binary diagnostic tests in case-control studies. Experimental design for hypothesis
tests on predictive values.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"bdpv","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Inference and design for predictive values in binary
diagnostic\ntests","Version":"1.1"},"bdrift":{"Author":"Markus Peter Auer [aut,
cre]","Depends":"R (>= 3.2.3), graphics, stats, xts, zoo","Description":"Beta drift
poses a serious challenge to asset managers\nand financial researchers. Beta drift
causes problems in asset\npricing models and can have serious ramifications for
hedging\nattempts. Providing users with a tool that allows them to\nquantify beta
drift and form educated opinions about it is\nthe primary purpose of this
package.\nThis package contains the BDA() function that performs a beta\ndrift
analysis, typically for multi-factor asset pricing models.\nThe BDA() function
tests the underlying model parameters for\ndrift across time, drift across model
horizon, and applies a\njackknife procedure to the baseline model. This allows the
users\nto draw conclusions about the stability of model parameters or\nmake
inferences about the behavior of funds. For example, the\ndrift of parameters for
active funds could be interpreted as\nimplicit style drift or, in the case of
passive funds, management's\ninability to track a benchmark
completely.","Imports":"Quandl, quantmod, scales","License":"GPL-
3","NeedsCompilation":"no","Package":"bdrift","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Beta Drift
Analysis","URL":"http:\/\/github.com\/MeanerReversion\/bdrift","Version":"1.2.2"},"
bdscale":{"Author":"Dave Mills [aut, cre]","Depends":"R (>=
3.2.0)","Description":"Provides a continuous date scale, omitting weekends and
holidays.","Imports":"ggplot2 (>= 2.1.0), scales (>= 0.3.0)","License":"GPL-
2","NeedsCompilation":"no","Package":"bdscale","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr (>= 1.12.3), testthat (>= 0.11.0), rmarkdown (>=
0.9.5)","Title":"Remove Weekends and Holidays from ggplot2
Axes","URL":"http:\/\/github.com\/dvmlls\/bdscale","Version":"2.0.0"},"bdsmatrix":
{"Author":"Terry Therneau","Depends":"methods, R (>= 2.0.0)","Description":"This is
a special case of sparse matrices, used by coxme","License":"LGPL-
2","NeedsCompilation":"yes","Package":"bdsmatrix","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Routines for Block Diagonal Symmetric
matrices","URL":"http:\/\/r-forge.r-project.org","Version":"1.3-2"},"bdvis":
{"Author":"Vijay Barve <vijay.barve@gmail.com>, Javier
Otegui\n<javier.otegui@gmail.com>","Description":"Provides a set of functions to
create basic visualizations to quickly\npreview different aspects of biodiversity
information such as inventory\ncompleteness, extent of coverage (taxonomic,
temporal and geographic), gaps\nand biases.","Imports":"maps, plotrix, sqldf, plyr,
taxize, treemap, ggplot2, lattice,\nchron, leafletR","License":"GPL-
3","NeedsCompilation":"no","Package":"bdvis","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"rinat","Title":"Biodiversity Data
Visualizations","Version":"0.2.0"},"bdynsys":{"Author":"Shyam Ranganathan, Viktoria
Spaiser, Richard P. Mann, David J.T. Sumpter","Depends":"R (>= 2.10), stats,
graphics, grDevices","Description":"The package bdynsys for panel\/longitudinal
data combines methods to model\nchanges in up to four indicators over times as a
function of the indicators\nthemselves and up to three predictors using ordinary
differential equations\n(ODEs) with polynomial terms that allow to model complex
and nonlinear\neffects. A Bayesian model selection approach is implemented. The
package\nprovides also visualisation tools to plot phase portraits of the
dynamic\nsystem, showing the complex co-evolution of two indicators over time with
the\npossibility to highlight trajectories for specified entities (e.g.
countries,\nindividuals). Furthermore the visualisation tools allow for
making\npredictions of the trajectories of specified entities with respect to
the\nindicators.","Imports":"plm, Formula, MASS, Hmisc, deSolve, pracma,
caTools,\nmatrixStats","License":"GNU General Public License (>=
2)","NeedsCompilation":"no","Package":"bdynsys","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Bayesian Dynamical System
Model","Version":"1.3"},"beadarrayFilter":{"Author":"Anyiawung Chiara Forcheh,
Geert Verbeke, Adetayo Kasim, Dan\nLin, Ziv Shkedy, Willem Talloen, Hinrich WH
Gohlmann, Lieven\nClement.","Depends":"beadarray, RColorBrewer","Description":"This
package contains functions to fit the filtering model\nof Forcheh et al., (2012)
which is used to derive the\nintra-cluster correlation (ICC). Model fitting is done
using\nthe modified version of the ``MLM.beadarray\" function of Kim\nand Lin
(2011).","License":"GPL-
2","NeedsCompilation":"no","Package":"beadarrayFilter","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"beadarrayExampleData, lumi","Title":"Bead
filtering for Illumina bead arrays","Version":"1.1.0"},"beadarrayMSV":
{"Author":"Lars Gidskehaug","Depends":"R (>= 2.10.0), Biobase (>= 2.5.5), methods,
geneplotter","Description":"Imports bead-summary data from Illumina scanner.\nPre-
processes using a suite of optional normalizations and\ntransformations. Clusters
and automatically calls genotypes,\ncritically able to handle markers in duplicated
regions of the\ngenome (multisite variants; MSVs). Interactive clustering
if\nneeded. MSVs with variation in both paralogs may be resolved\nand mapped to
their respective chromosomes. Quality control\nincluding pedigree checking and
visual assessment of clusters.\nToo large data-sets are handled by
working on smaller subsets\nof the data in sequence.","Imports":"rggobi,
limma","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"beadarrayMSV","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Analysis of Illumina BeadArray SNP data including
MSV markers","Version":"1.1.0"},"beanplot":{"Author":"Peter
Kampstra","Description":"Plots univariate comparison graphs, an alternative
to\nboxplot\/stripchart\/violin plot.","License":"GPL-
2","NeedsCompilation":"no","Package":"beanplot","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"vioplot, lattice","Title":"Visualization via Beanplots
(like Boxplot\/Stripchart\/Violin\nPlot)","Version":"1.2"},"bedr":{"Author":"Daryl
Waggott, Syed Haider, Emilie Lalonde, Clement Fung, Paul C. Boutros","Depends":"R
(>= 3.0)","Description":"Genomic region processing using tools such as bedtools,
bedops and tabix.","Imports":"testthat (>= 0.7.1), VennDiagram (>= 1.6.4),
data.table (>=\n1.8.11), R.utils (>= 2.0.2), yaml (>= 2.1.10), parallel,
2","NeedsCompilation":"no","Package":"bedr","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"knitr (>= 1.4)","Title":"Genomic Region Processing using
Tools Such as Bedtools, Bedops\nand Tabix","Version":"1.0.2"},"beepr":
{"Author":"Rasmus BÃ¥Ã¥th <rasmus.baath@gmail.com>","Description":"The sole
function of this package is beep(), with the purpose to\nmake it easy to play
notification sounds on whatever platform you are on.\nIt is intended to be useful,
for example, if you are running a long analysis\nin the background and want to know
when it is ready.","Imports":"stringr (>= 1.0.0), audio","License":"GPL-
3","NeedsCompilation":"no","Package":"beepr","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Easily Play Notification Sounds on any
Platform","Version":"1.2"},"beeswarm":{"Author":"Aron Eklund","Description":"The
bee swarm plot is a one-dimensional scatter plot like \"stripchart\", but with
closely-packed, non-overlapping points.","Imports":"stats, graphics, grDevices,
utils","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"beeswarm","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"The Bee Swarm Plot, an Alternative to
Stripchart","URL":"http:\/\/www.cbs.dtu.dk\/~eklund\/beeswarm\/","Version":"0.2.1"}
,"benchden":{"Author":"Thoralf Mildenberger, Henrike Weinert, Sebastian
Tiemeyer","Description":"Full implementation of the 28 distributions introduced
as\nbenchmarks for nonparametric density estimation by Berlinet and\nDevroye
(1994). Includes densities, cdfs, quantile functions\nand generators for samples as
well as additional information on\nfeatures of the densities. Also contains the 4
histogram\ndensities used in Rozenholc\/Mildenberger\/Gather
(2010).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"benchden","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"28 benchmark densities from Berlinet\/Devroye
(1994)","Version":"1.0.5"},"benchmark":{"Author":"Manuel J. A. Eugster [aut,
cre]","Depends":"R (>= 2.10), utils, proto, ggplot2, relations,
psychotools","Description":"The benchmark package provides a toolbox for setup,
execution\nand analysis of benchmark experiments. Main focus is the analysis
of\ndata accumulating during the execution -- one primary objective is
the\nstatistical correct computation of the candidate algorithms'
order.","Imports":"reshape, scales, plyr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"benchmark","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"coin, multcomp, lme4, e1071, entropy, archetypes,
Rgraphviz,\npsychotree","Title":"Benchmark Experiments
Toolbox","URL":"http:\/\/benchmark.r-forge.r-project.org\/","Version":"0.3-
6"},"benchmarkme":{"Author":"Colin Gillespie [aut, cre]","Description":"Benchmark
your CPU and compare against other CPUs. Also provides\nfunctions for obtaining
system specifications, such as\nRAM, CPU type, and R version.","Imports":"Matrix,
compiler, httr, methods, benchmarkmeData(>= 0.2.2),\nutils,
3","NeedsCompilation":"no","Package":"benchmarkme","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"RcppZiggurat, testthat, DT, knitr, ggplot2,
shiny","Title":"Crowd Sourced System
Benchmarks","URL":"https:\/\/github.com\/csgillespie\/benchmarkme","Version":"0.2.3
"},"benchmarkmeData":{"Author":"Colin Gillespie [aut, cre]","Description":"Crowd
sourced benchmarks from running the 'benchmarkme' package.","Imports":"graphics,
utils,","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"benchmarkmeData","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat, DT, shiny, ggplot2,
benchmarkme","Title":"Data Set for the 'benchmarkme'
Package","URL":"https:\/\/github.com\/csgillespie\/benchmarkme-
data","Version":"0.2.2"},"benford.analysis":{"Author":"Carlos Cinelli","Depends":"R
(>= 3.0.0)","Description":"The Benford Analysis package provides tools that make it
easier to\nvalidate data using Benford's
Law.","Imports":"data.table","License":"GPL-
3","NeedsCompilation":"no","Package":"benford.analysis","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Benford Analysis for Data
Validation and Forensic
Analytics","URL":"http:\/\/github.com\/carloscinelli\/benford.analysis","Version":"
0.1.3"},"bentcableAR":{"Author":"\nGrace Chiu <bentcable@gmail.com>,\nCSIRO,\nCSIT
Bldg, ANU Campus, Acton, ACT 2601, Australia","Description":"\nIncluded are two
main interfaces for fitting and diagnosing\nbent-cable regressions for
autoregressive time-series data or\nindependent data (time series or otherwise):
'bentcable.ar()' and\n'bentcable.dev.plot()'. Some components in the package can
also be\nused as stand-alone functions. The bent cable\n(linear-quadratic-linear)
generalizes the broken stick\n(linear-linear), which is also handled by this
package. Version 0.2\ncorrects a glitch in the computation of confidence intervals
for the\nCTP. References that were updated from Versions 0.2.1 and 0.2.2 appear\nin
Version 0.2.3 and up. Version 0.3.0 improves robustness of the\nerror-message
producing mechanism. It is the author's intention to\ndistribute any future updates
via GitHub.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"bentcableAR","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Bent-Cable Regression for Independent Data or
Autoregressive\nTime Series","Version":"0.3.0"},"ber":{"Author":"Marco
Giordan","Depends":"MASS","Description":"The functions in this package remove batch
effects from\nmicroarrary normalized data. The expression levels of the genes\nare
represented in a matrix where rows correspond to\nindependent samples and columns
to genes (variables). The\nbatches are represented by categorical variables
(objects of\nclass factor). When further covariates of interest are\navailable they
can be used to remove efficiently the batch\neffects and adjust the
2","NeedsCompilation":"no","Package":"ber","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Batch Effects Removal","Version":"4.0"},"berryFunctions":
{"Author":"Berry Boessenkool","Description":"Draw horizontal histograms, color
scatterpoints by 3rd dimension, enhance date- and log-axis plots, zoom in X11
graphics, use the unit hydrograph in a linear storage cascade, convert lists to
data.frames, fit multiple functions by regression (power, reciprocal, exponential,
logarithmic, polynomial, rational).","Imports":"graphics, stats, utils,
2","NeedsCompilation":"no","Package":"berryFunctions","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"RColorBrewer","Title":"Function Collection
Related to Plotting and
Hydrology","URL":"https:\/\/github.com\/brry\/berryFunctions","Version":"1.9.0"},"b
estglm":{"Author":"A.I. McLeod and Changjiang Xu","Depends":"R (>= 2.0.0),
leaps","Description":"Best subset glm using AIC, BIC, EBIC, BICq or Cross-
Validation. For the normal case, the 'leaps' is used. Otherwise, a slower
exhaustive search. The 'xtable' package is needed for vignette
'SimExperimentBICq.Rnw' accompanying this package.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"bestglm","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"xtable","Title":"Best Subset
GLM","URL":"http:\/\/www.stats.uwo.ca\/faculty\/aim","Version":"0.34"},"betafam":
{"Author":"Wei Guo <wei.guo3@nih.gov>","Depends":"R (>= 2.4.0)","Description":"To
detecting rare variants for quantitative traits using\nnuclear families, the linear
combination methods are proposed\nusing the estimated regression coefficients from
the multiple\nregression and regularized regression as the weights.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"betafam","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Detecting rare variants for quantitative traits using
nuclear\nfamilies","Version":"1.0"},"betalink":{"Author":"Timothee Poisot
<tim@poisotlab.io>","Depends":"R (>= 2.12.0)","Description":"Measures of beta-
diversity in networks, and easy visualization of why two networks are
different.","Imports":"plyr, stringr, igraph","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"betalink","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat, covr","Title":"Beta-Diversity of
Species
Interactions","URL":"http:\/\/poisotlab.io\/software","Version":"2.2.1"},"betapart"
:{"Author":"Andres Baselga, David Orme, Sebastien Villeger, Julien De Bortoli and
Fabien Leprieur","Depends":"R (>= 2.10)","Description":"betapart allows computing
pair-wise dissimilarities (distance matrices) and multiple-site dissimilarities,
separating the turnover and nestedness-resultant components of taxonomic (incidence
and abundance based), functional and phylogenetic beta diversity.","Imports":"ape,
geometry, picante, rcdd","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"betapart","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"vegan","Title":"Partitioning beta diversity into
turnover and nestedness\ncomponents","Version":"1.3"},"betaper":{"Author":"Luis
Cayuela and Marcelino de la Cruz","Depends":"vegan,
ellipse","Description":"Permutational method to incorporate taxonomic
uncertainty\nand some functions to assess its effects on parameters of some\nwidely
used multivariate methods in ecology","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"betaper","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Functions to incorporate taxonomic uncertainty on
multivariate\nanalyses of ecological data","Version":"1.1-0"},"betareg":
{"Author":"Achim Zeileis [aut, cre],\nFrancisco Cribari-Neto [aut],\nBettina Gruen
[aut],\nIoannis Kosmidis [aut],\nAlexandre B. Simas [ctb] (earlier version
by),\nAndrea V. Rocha [ctb] (earlier version by)","Depends":"R (>=
2.10.0)","Description":"Beta regression for modeling beta-distributed dependent
variables, e.g., rates and proportions.\nIn addition to maximum likelihood
regression (for both mean and precision of a beta-distributed\nresponse), bias-
corrected and bias-reduced estimation as well as finite mixture models
and\nrecursive partitioning for beta regressions are
provided.","Imports":"graphics, methods, stats, flexmix, Formula,
lmtest,\nmodeltools, sandwich","License":"GPL-
2","NeedsCompilation":"no","Package":"betareg","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"car, lattice, party, strucchange","Title":"Beta
Regression","Version":"3.0-5"},"betas":{"Author":"Andrea Cantieni [aut,
cre]","Depends":"R (>= 3.1.1)","Description":"Computes standardized beta
coefficients and corresponding\nstandard errors for the following models:\nlinear
regression models with numerical covariates only,\nlinear regression models with
numerical and factorial covariates,\nweighted linear regression models,\nall these
linear regression models with interaction terms, and\nrobust linear regression
models with numerical covariates only.","Imports":"robust","License":"GPL-
3","NeedsCompilation":"no","Package":"betas","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Standardized Beta
Coefficients","URL":"https:\/\/github.com\/andreaphsz\/betas","Version":"0.1.1"},"b
etategarch":{"Author":"Genaro Sucarrat","Depends":"R (>= 2.15.0),
zoo","Description":"Simulation, estimation and forecasting of first-order Beta-
Skew-t-EGARCH models with leverage (one-component, two-component, skewed
versions).","License":"GPL-
2","NeedsCompilation":"yes","Package":"betategarch","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Simulation, estimation and forecasting of Beta-Skew-
t-EGARCH\nmodels","URL":"http:\/\/www.sucarrat.net\/","Version":"3.2"},"bethel":
{"Author":"Michele De Meo","Depends":"R (>= 2.5.0)","Description":"The sample size
according to the Bethel's procedure.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"bethel","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Bethel's algorithm","Version":"0.2"},"bezier":
{"Author":"Aaron Olsen <aolsen@uchicago.edu>","Description":"The bezier package is
a toolkit for working with Bezier curves and splines. The package provides
functions for point generation, arc length estimation, degree elevation and curve
fitting.","License":"GPL-
2","NeedsCompilation":"no","Package":"bezier","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Bezier Curve and Spline Toolkit","Version":"1.1"},"bfa":
{"Author":"Jared Murray","Description":"This package provides model fitting
for\nseveral Bayesian factor models including Gaussian,\nordinal probit, mixed and
semiparametric Gaussian\ncopula factor models under a range of
priors.","Imports":"coda, Rcpp (>= 0.10.6), RcppArmadillo (>=
3","NeedsCompilation":"yes","Package":"bfa","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Bayesian Factor Analysis","Version":"0.3.1"},"bfast":
{"Author":"Jan Verbesselt [aut, cre], Achim Zeileis [aut], Rob Hyndman
[ctb]","Depends":"R (>= 2.15.0)","Description":"BFAST integrates the decomposition
of time series into trend,\nseasonal, and remainder components with methods for
detecting\nand characterizing abrupt changes within the trend and
seasonal\ncomponents. BFAST can be used to analyze different types of\nsatellite
image time series and can be applied to other disciplines\ndealing with seasonal or
non-seasonal time series, such as hydrology,\nclimatology, and econometrics. The
algorithm can be extended to\nlabel detected changes with information on the
parameters of the\nfitted piecewise linear models. BFAST monitoring functionality
is added\nbased on a paper that has been submitted to Remote Sensing of
Environment.\nBFAST monitor provides functionality to detect disturbance in near
real-time based on BFAST-type models.\nBFAST approach is flexible approach that
handles missing data without interpolation.\nFurthermore now different models can
be used to fit the time series data and detect structural changes
(breaks).","Imports":"graphics, stats, strucchange, zoo, forecast, sp,
raster","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"bfast","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Breaks For Additive Season and Trend
(BFAST)","URL":"http:\/\/bfast.R-Forge.R-project.org\/","Version":"1.5.7"},"bfp":
{"Author":"Daniel Sabanes Bove <sabanesd@roche.com>","Depends":"R (>=
2.10)","Description":"Implements the Bayesian paradigm for fractional\npolynomial
models under the assumption of normally distributed error terms.","Imports":"Rcpp
(>= 0.11.0)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"bfp","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"doBy, SoDA, Hmisc, mfp","Title":"Bayesian Fractional
Polynomials","Version":"0.0-30"},"bgeva":{"Author":"Giampiero Marra, Raffaella
Calabrese and Silvia Angela Osmetti","Depends":"R (>= 2.15.1),
mgcv","Description":"Routine for fitting regression models for binary rare events
with linear and nonlinear covariate effects when using the quantile function of the
Generalized Extreme Value random variable.","Imports":"magic, trust","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"bgeva","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Binary Generalized Extreme Value Additive
Models","URL":"http:\/\/www.ucl.ac.uk\/statistics\/people\/giampieromarra","Version
":"0.3"},"bglm":{"Author":"Nicolas Molano-Gonzalez, Edilberto Cepeda-
Cuervo","Depends":"R (>= 3.0.2), mvtnorm, methods","Description":"Implementation of
Bayesian estimation in generalized linear models following Gamerman
2","NeedsCompilation":"no","Package":"bglm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"car, coda, faraway","Title":"Bayesian Estimation in
Generalized Linear Models","Version":"1.0"},"bgmm":{"Author":"Przemyslaw Biecek \\&
Ewa Szczurek","Depends":"R (>= 2.0), mvtnorm, car, lattice,
combinat","Description":"Two partially supervised mixture modeling methods:\nsoft-
label and belief-based modeling are implemented.\nFor completeness, we equipped the
package also with the\nfunctionality of unsupervised, semi- and fully
supervised\nmixture modeling. The package can be applied also to selection\nof the
best-fitting from a set of models with different\ncomponent numbers or constraints
on their structures.\nFor detailed introduction see:\nPrzemyslaw Biecek, Ewa
Szczurek, Martin Vingron, Jerzy\nTiuryn (2012), The R Package bgmm: Mixture
Modeling with\nUncertain Knowledge, Journal of Statistical
Software.","License":"GPL-
3","NeedsCompilation":"no","Package":"bgmm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Gaussian Mixture Modeling Algorithms And The Belief-
based\nMixture
Modeling","URL":"http:\/\/bgmm.molgen.mpg.de\/","Version":"1.7"},"biasbetareg":
{"Author":"Luana Cecilia Meireles","Depends":"betareg","Description":"Bias
correction of second order of the maximum likelihood\nestimators of the parameters
of the beta regression
model.","License":"GPL","NeedsCompilation":"no","Package":"biasbetareg","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Bias correction of the parameter
estimates of the beta\nregression model","Version":"1.0"},"bibtex":
{"Author":"Romain Francois [aut, cre],\nKurt Hornik [ctb],\nMichael Koohafkan
[ctb]","Depends":"R (>= 3.0.2)","Description":"Utility to parse a bibtex
file","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"bibtex","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"bibtex
parser","URL":"https:\/\/github.com\/romainfrancois\/bibtex","Version":"0.4.0"},"bi
clust":{"Author":"Sebastian Kaiser, Rodrigo Santamaria, Tatsiana
Khamiakova,\nMartin Sill, Roberto Theron, Luis Quintales, Friedrich\nLeisch and
Ewoud De Troyer.","Depends":"R (>= 2.10), MASS, grid, colorspace,
lattice","Description":"The main function biclust provides several algorithms
to\nfind biclusters in two-dimensional data: Cheng and Church,\nSpectral, Plaid
Model, Xmotifs and Bimax. In addition, the\npackage provides methods for data
preprocessing (normalization\nand discretisation), visualisation, and validation of
bicluster\nsolutions.","Imports":"methods, flexclust","License":"GPL-
3","NeedsCompilation":"yes","Package":"biclust","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"isa2","Title":"BiCluster
Algorithms","Version":"1.2.0"},"bifactorial":{"Author":"Peter
Frommolt","Depends":"mvtnorm,multcomp,lattice,graphics,methods,Rcpp (>=
0.8.8)","Description":"This package makes global and multiple inferences for\ngiven
bi- and trifactorial clinical trial designs using\nbootstrap methods and a
classical
approach.","License":"GPL","NeedsCompilation":"yes","Package":"bifactorial","Reposi
tory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Inferences
for bi- and trifactorial trial designs","URL":"http:\/\/cecad.uni-
koeln.de\/Bioinformatics-Facility.268.0.html","Version":"1.4.7"},"bigRR":
{"Author":"Xia Shen, Moudud Alam and Lars Ronnegard","Depends":"R (>= 2.10), utils,
hglm, DatABEL","Description":"The package fits large-scale (generalized) ridge
regression for various distributions of response. The shrinkage parameters
(lambdas) can be pre-specified or estimated using an internal update routine
(fitting a heteroscedastic effects model, or HEM). It gives possibility to shrink
any subset of parameters in the model. It has special computational advantage for
the cases when the number of shrinkage parameters exceeds the number of
observations. For example, the package is very useful for fitting large-scale omics
data, such as high-throughput genotype data (genomics), gene expression data
(transcriptomics), metabolomics data, etc.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"bigRR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Generalized Ridge Regression (with special advantage for p
>> n\ncases)","Version":"1.3-10"},"bigalgebra":{"Author":"Michael J. Kane, Bryan
Lewis, and John W. Emerson","Depends":"bigmemory (>= 4.0.0)","Description":"This
package provides arithmetic functions for R matrix and big.matrix
objects.","Imports":"methods","License":"LGPL-3 | Apache License
2.0","NeedsCompilation":"yes","Package":"bigalgebra","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"BLAS routines for native R matrices and big.matrix
objects","URL":"http:\/\/www.bigmemory.org","Version":"0.8.4"},"biganalytics":
{"Author":"John W. Emerson <jayemerson@gmail.com> and Michael J.
Kane\n<kaneplusplus@gmail.com>","Depends":"methods, stats, utils, bigmemory (>=
4.0.0), foreach, biglm","Description":"Extend the 'bigmemory' package with various
analytics.\nFunctions 'bigkmeans' and 'binit' may also be used with native R
objects.\nFor 'tapply'-like functions, the bigtabulate package may also be
helpful.\nFor linear algebra support, see 'bigalgebra'. For mutex (locking)
support\nfor advanced shared-memory usage, see 'synchronicity'.","License":"LGPL-3
| Apache License
2.0","NeedsCompilation":"yes","Package":"biganalytics","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Utilities for 'big.matrix' Objects from Package
'bigmemory'","URL":"http:\/\/www.bigmemory.org","Version":"1.1.14"},"bigdata":
{"Author":"Han Liu, Tuo Zhao","Depends":"glmnet, Matrix,
lattice,","Description":"The big data package is a collection of scalable
methods\nfor large-scale data analysis.","License":"GPL-
2","NeedsCompilation":"no","Package":"bigdata","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Big Data Analytics","Version":"0.1"},"biglars":
{"Author":"Mark Seligman, Chris Fraley, Tim Hesterberg","Depends":"R (>= 2.10),
ff","Description":"Least-angle regression, lasso and stepwise regression
for\nnumeric datasets in which the number of observations is greater\nthan the
number of predictors. The functions can be used with\nthe ff library to accomodate
datasets that are too large to be\nheld in memory.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"biglars","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Scalable Least-Angle Regression and
Lasso","Version":"1.0.2"},"biglasso":{"Author":"Yaohui Zeng [aut,cre], Patrick
Breheny [ctb]","Depends":"bigmemory, Matrix, parallel,
ncvreg","Description":"Extend lasso and elastic-net model fitting for ultrahigh-
dimensional, multi-gigabyte data sets that cannot be loaded into memory. Compared
to existing lasso-fitting packages, it preserves equivalently fast computation
speed but is much more memory-efficient, thus allowing for very powerful big data
analysis even with only a single laptop.","Imports":"Rcpp (>= 0.12.1),
2","NeedsCompilation":"yes","Package":"biglasso","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Big Lasso: Extending Lasso Model Fitting to Big Data in
R","Version":"1.0-1"},"biglm":{"Author":"Thomas Lumley","Depends":"DBI,
methods","Description":"Regression for data too large to fit in
memory","Enhances":"leaps","License":"GPL","NeedsCompilation":"yes","Package":"bigl
m","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"RSQLite,
RODBC","Title":"bounded memory linear and generalized linear
models","Version":"0.9-1"},"bigmemory":{"Author":"Michael J. Kane
<kaneplusplus@gmail.com>, John W. Emerson\n<jayemerson@gmail.com>, Peter Haverty
<haverty.peter@gene.com>, and Charles\nDeterman Jr.
<cdetermanjr@gmail.com>","Depends":"R (>= 3.2.0), methods, utils,
bigmemory.sri","Description":"Create, store, access, and manipulate massive
matrices.\nMatrices are allocated to shared memory and may use memory-
mapped\nfiles. Packages 'biganalytics', 'bigtabulate', 'synchronicity',
and\n'bigalgebra' provide advanced functionality.","Enhances":"biganalytics,
bigtabulate, synchronicity","Imports":"Rcpp","License":"LGPL-3 | Apache License
2.0","NeedsCompilation":"yes","Package":"bigmemory","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"knitr, testthat","Title":"Manage Massive Matrices
with Shared Memory and Memory-
Mapped\nFiles","URL":"http:\/\/www.bigmemory.org","Version":"4.5.19"},"bigmemory.sr
i":{"Author":"Michael J. Kane","Description":"This package provides a shared
resource interface for the bigmemory and synchronicity
packages.","Enhances":"bigmemory,
synchronicity","Imports":"methods","License":"LGPL-3 | Apache License
2.0","NeedsCompilation":"no","Package":"bigmemory.sri","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"A shared resource interface for Bigmemory Project
packages","Version":"0.1.3"},"bigml":{"Author":"Leon Hwang [cre,
aut]","Description":"The 'bigml' package contains bindings for the BigML API.\nThe
package includes methods that provide straightforward access\nto basic API
functionality, as well as methods that accommodate\nidiomatic R data types and
concepts.","Imports":"RJSONIO, RCurl, plyr","License":"LGPL-
3","NeedsCompilation":"no","Package":"bigml","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Bindings for the BigML
API","URL":"https:\/\/github.com\/bigmlcom\/bigml-
r","Version":"0.1.2"},"bigrquery":{"Author":"Hadley Wickham [aut, cre],\nRStudio
[cph]","Depends":"R (>= 3.1.0)","Description":"Easily talk to Google's 'BigQuery'
database from R.","Imports":"httr, jsonlite, assertthat, R6 (>= 2.0.0), dplyr (>=
3","NeedsCompilation":"no","Package":"bigrquery","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat","Title":"An Interface to Google's
'BigQuery' 'API'","Version":"0.2.0"},"bigsplines":{"Author":"Nathaniel E. Helwig
<helwig@umn.edu>","Description":"Fits smoothing spline regression models using
scalable algorithms designed for large samples. Six marginal spline types are
supported: cubic, different cubic, cubic periodic, cubic thin-plate, ordinal, and
nominal. Random effects and parametric effects are also supported. Response can be
Gaussian or non-Gaussian: Binomial, Poisson, Gamma, Inverse Gaussian, or Negative
Binomial.","Imports":"stats, graphics, grDevices","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"bigsplines","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Smoothing Splines for Large Samples","Version":"1.0-
8"},"bigtabulate":{"Author":"Michael J. Kane <kaneplusplus@gmail.com> and John W.
Emerson\n<jayemerson@gmail.com>","Depends":"methods, bigmemory (>= 4.0.0),
biganalytics","Description":"Extend the bigmemory package with 'table', 'tapply',
and 'split'\nsupport for 'big.matrix' objects. The functions may also be used with
native R\nmatrices for improving speed and memory-efficiency.","License":"LGPL-3 |
Apache License
2.0","NeedsCompilation":"yes","Package":"bigtabulate","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Table, Apply, and Split Functionality for Matrix
and\n'big.matrix'
Objects","URL":"http:\/\/www.bigmemory.org","Version":"1.1.5"},"bild":{"Author":"M.
Helena Gonçalves, M. Salomé Cabral and Adelchi Azzalini,\napart from a set of
Fortran-77 subroutines written by R. Piessens\nand E. de Doncker, belonging to the
suite \"Quadpack\".","Depends":"R (>= 2.10.0), methods, stats, graphics,
utils","Description":"Performs logistic regression for binary longitudinal\ndata,
allowing for serial dependence among observations from a given\nindividual and a
random intercept term. Estimation is via maximization\nof the exact likelihood of a
suitably defined model. Missing values and\nunbalanced data are allowed, with some
restrictions.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"bild","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"BInary Longitudinal Data","Version":"1.1-5"},"bimetallic":
{"Author":"Andrew McDavid","Description":"A power calculator for Genome-wide
association studies\n(GWAs) with combined gold (error-free) and silver
(erroneous)\nphenotyping per McDavid A, Crane PK, Newton KM, Crosslin DR, et\nal.
(2011)","License":"GPL-
2","NeedsCompilation":"no","Package":"bimetallic","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Power for SNP analyses using silver standard
cases","Version":"1.0"},"bimixt":{"Author":"Michelle Winerip, Garrick Wallstrom,
Joshua LaBaer","Depends":"pROC","Description":"Estimates non-Gaussian mixture
models of case-control data. The four types of models supported are binormal, two
component constrained, two component unconstrained, and four component. The most
general model is the four component model, under which both cases and controls are
distributed according to a mixture of two unimodal distributions. In the four
component model, the two component distributions of the control mixture may be
distinct from the two components of the case mixture distribution. In the two
component unconstrained model,
the components of the control and case mixtures are the same; however the mixture
probabilities may differ for cases and controls. In the two component constrained
model, all controls are distributed according to one of the two components while
cases follow a mixture distribution of the two components. In the binormal model,
cases and controls are distributed according to distinct unimodal distributions.
These models assume that Box-Cox transformed case and control data with a common
lambda parameter are distributed according to Gaussian mixture distributions.
Model parameters are estimated using the expectation-maximization (EM) algorithm.
Likelihood ratio test comparison of nested models can be performed using the
lr.test function. AUC and PAUC values can be computed for the model-based and
empirical ROC curves using the auc and pauc functions, respectively. The model-
based and empirical ROC curves can be graphed using the roc.plot function. Finally,
the model-based density estimates can be visualized by plotting a model object
created with the bimixt.model function.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"bimixt","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Estimates Mixture Models for Case-Control
Data","Version":"1.0"},"binGroup":{"Author":"Boan Zhang, Christopher Bilder, Brad
Biggerstaff, Frank\nSchaarschmidt","Description":"This package provides methods for
estimation and\nhypothesis testing of proportions in group testing designs.
It\ninvolves methods for estimating a proportion in a single\npopulation (assuming
sensitivity and specificity 1 in designs\nwith equal group sizes), as well as
hypothesis tests and\nfunctions for experimental design for this situation.
For\nestimating one proportion or the difference of proportions, a\nnumber of
confidence interval methods are included, which can\ndeal with various different
pool sizes. Further, regression\nmethods are implemented for simple pooling and
matrix
pooling\ndesigns.","License":"GPL","NeedsCompilation":"no","Package":"binGroup","Re
pository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Evaluation and
experimental design for binomial group testing","Version":"1.1-0"},"binMto":
{"Author":"Frank Schaarschmidt","Description":"Asymptotic simultaneous confidence
intervals for comparison of many treatments with one control,\nfor the difference
of binomial proportions, allows for Dunnett-like-adjustment, Bonferroni or
unadjusted intervals.\nSimulation of power of the above interval methods,
approximate calculation of any-pair-power, and sample size\niteration based on
approximate any-pair power.\nExact conditional maximum test for many-to-one
comparisons to a control.","Imports":"mvtnorm","License":"GPL-
2","NeedsCompilation":"no","Package":"binMto","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Asymptotic simultaneous confidence intervals for many-to-
one\ncomparisons of proportions","Version":"0.0-6"},"binaryLogic":{"Author":"Daniel
DÃ¶rrhÃ¶fer <ddo@openmailbox.org>","Depends":"R (>= 3.0.2)","Description":"Convert
to binary numbers (Base2). Shift, rotate, summary. Based on logical
vector.","License":"GPL-3 + file
LICENSE","NeedsCompilation":"no","Package":"binaryLogic","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Binary
Logic","URL":"https:\/\/github.com\/d4ndo\/binaryLogic","Version":"0.3.4"},"binda":
{"Author":"Sebastian Gibb and Korbinian Strimmer.","Depends":"R (>= 3.0.2), entropy
(>= 1.2.1)","Description":"The \"binda\" package implements functions for multi-
class\ndiscriminant analysis using binary predictors, for corresponding\nvariable
selection, and for dichotomizing continuous data.","Imports":"graphics, stats,
3)","NeedsCompilation":"no","Package":"binda","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"crossval","Title":"Multi-Class Discriminant Analysis
using Binary
Predictors","URL":"http:\/\/strimmerlab.org\/software\/binda\/","Version":"1.0.3"},
"bindata":{"Author":"Friedrich Leisch and Andreas Weingessel and Kurt
Hornik","Depends":"R (>= 2.10)","Description":"Generation of correlated artificial
binary data.","Imports":"e1071, mvtnorm (>= 0.7-0)","License":"GPL-
2","NeedsCompilation":"no","Package":"bindata","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Generation of Artificial Binary Data","Version":"0.9-
19"},"binequality":{"Author":"Samuel V. Scarpino, Paul von Hippel, and Igor
Holas","Depends":"R (>= 2.10), gamlss (>= 4.2.7), gamlss.cens (>=
4.2.7),\ngamlss.dist (>= 4.3.0)","Description":"Methods for model selection, model
averaging, and calculating metrics, such as the Gini, Theil, Mean Log Deviation,
etc, on binned income data where the topmost bin is right-censored. We provide
both a non-parametric method, termed the bounded midpoint estimator (BME), which
assigns cases to their bin midpoints; except for the censored bins, where cases are
assigned to an income estimated by fitting a Pareto distribution. Because the usual
Pareto estimate can be inaccurate or undefined, especially in small samples, we
implement a bounded Pareto estimate that yields much better results. We also
provide a parametric approach, which fits distributions from the generalized beta
(GB) family. Because some GB distributions can have poor fit or undefined
estimates, we fit 10 GB-family distributions and use multimodel inference to obtain
definite estimates from the best-fitting distributions. We also provide binned
income data from all United States of America school districts, counties, and
states.","Imports":"survival (>= 2.37-7), ineq (>= 0.2-11)","License":"GPL (>=
3.0)","NeedsCompilation":"no","Package":"binequality","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Methods for Analyzing Binned Income
Data","Version":"0.6.1"},"bingat":{"Author":"Terrence Brooks, Berkley Shands, Skye
Buckner-Petty, Patricio S. La Rosa, Elena Deych, William D. Shannon","Depends":"R
(>= 2.14.0)","Description":"Tools to analyze binary graph
objects.","Imports":"matrixStats, network, gplots, genalg, doParallel,
foreach,\nparallel","License":"Apache License (==
2.0)","NeedsCompilation":"no","Package":"bingat","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Binary Graph Analysis Tools","Version":"1.2.2"},"binhf":
{"Author":"Matt Nunes <m.nunes@lancaster.ac.uk>","Depends":"R (>= 2.10),
wavethresh, adlift (>= 0.9.2)","Description":"Binomial Haar-Fisz transforms for
Gaussianization","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"binhf","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Haar-Fisz functions for binomial data","Version":"1.0-
1"},"binom":{"Author":"Sundar Dorai-Raj <sundar.dorai-
raj@pdf.com>","Description":"Constructs confidence intervals on the probability
of\nsuccess in a binomial experiment via several
parameterizations","License":"GPL","NeedsCompilation":"yes","Package":"binom","Repo
sitory":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"lattice, polynom, tcltk,
ggplot2","Title":"Binomial Confidence Intervals For Several
Parameterizations","Version":"1.1-1"},"binomSamSize":{"Author":"Michael Hoehle with
contributions by Wei Liu","Depends":"binom","Description":"\nA suite of functions
to compute confidence intervals and necessary\nsample sizes for the parameter p of
the Bernoulli B(p)\ndistribution under simple random sampling or under
pooled\nsampling. Such computations are e.g. of interest when investigating\nthe
incidence or prevalence in populations.\nThe package contains functions to compute
coverage probabilities and\ncoverage coefficients of the provided confidence
intervals\nprocedures. Sample size calculations are based on expected
length.","License":"GPL-
3","NeedsCompilation":"yes","Package":"binomSamSize","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Confidence intervals and sample size determination
for a\nbinomial proportion under simple random sampling and
pooled\nsampling","Version":"0.1-3"},"binomTools":{"Author":"Rune Haubo B
Christensen and Merete K Hansen","Description":"This package provides a range of
diagnostic methods for\nbinomial regression models.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"binomTools","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Performing diagnostics on binomial regression
models","Version":"1.0-1"},"binomen":{"Author":"Scott Chamberlain [aut,
cre]","Description":"Includes functions for working with taxonomic data,\nincluding
functions for combining, separating, and filtering\ntaxonomic groups by any rank or
name. Allows standard (SE)\nand non-standard evaluation (NSE).","Imports":"methods,
stats, jsonlite, lazyeval, dplyr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"binomen","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat, knitr, taxize","Title":"'Taxonomic'
Specification and Parsing
Methods","URL":"https:\/\/github.com\/ropensci\/binomen","Version":"0.1.0"},"binomi
alcftp":{"Author":"Francisco Juretig","Description":"Binomial random numbers are
generated via the perfect\nsampling algorithm. At each iteration dual markov chains
are\ngenerated and coalescence is checked. In case coalescence\noccurs, the
resulting number is outputted. In case not, then\nthe algorithm is restarted from
T(t)=2*T(t) until coalescence\noccurs.","License":"GPL-
2","NeedsCompilation":"no","Package":"binomialcftp","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Generates binomial random numbers via the coupling
from the past\nalgorithm","Version":"1.0"},"binomlogit":{"Author":"Agnes
Fussl","Description":"The R package contains different MCMC schemes to estimate the
regression coefficients of a binomial (or binary) logit model within a Bayesian
framework: a data-augmented independence MH-sampler, an auxiliary mixture sampler
and a hybrid auxiliary mixture
(HAM) sampler. All sampling procedures are based on algorithms using data
augmentation, where the regression coefficients are estimated by rewriting the
logit model as a latent variable model called difference random utility model
(dRUM).","License":"GPL-
3","NeedsCompilation":"no","Package":"binomlogit","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Efficient MCMC for Binomial Logit
Models","Version":"1.2"},"binr":{"Author":"Sergei Izrailev","Depends":"R (>=
2.15),","Description":"Implementation of algorithms for cutting numerical
values\nexhibiting a potentially highly skewed distribution into evenly
distributed\ngroups (bins). This functionality can be applied for binning
discrete\nvalues, such as counts, as well as for discretization of continuous
values,\nfor example, during generation of features used in machine
learning\nalgorithms.","License":"Apache License (==
2.0)","NeedsCompilation":"no","Package":"binr","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Cut Numeric Values into Evenly Distributed
Groups","URL":"http:\/\/github.com\/jabiru\/binr","Version":"1.1"},"binseqtest":
{"Author":"Jenn Kirk, Michael P. Fay","Depends":"methods, graphics, stats,
clinfun","Description":"For a series of binary responses, create stopping boundary
with exact results after stopping, allowing updating for missing
assessments.","License":"GPL-
3","NeedsCompilation":"no","Package":"binseqtest","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Exact Binary Sequential Designs and
Analysis","Version":"1.0.1"},"bio.infer":{"Author":"Lester L. Yuan","Depends":"R
(>= 2.10), tcltk","Description":"Imports benthic count data, reformats this data,
and\ncomputes environmental inferences from this data.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"bio.infer","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Predict environmental conditions from biological
observations","Version":"1.3-3"},"bio3d":{"Author":"Barry Grant, Xin-Qiu Yao, Lars
Skjaerven, Julien Ide","Depends":"R (>= 3.1.0)","Description":"Utilities to
process, organize and explore protein structure, sequence and dynamics data.
Features include the ability to read and write structure, sequence and dynamic
trajectory data, perform sequence and structure database searches, data summaries,
atom selection, alignment, superposition, rigid core identification, clustering,
torsion analysis, distance matrix analysis, structure and sequence conservation
analysis, normal mode analysis, principal component analysis of heterogeneous
structure data, and correlation network analysis from normal mode and molecular
dynamics data. In addition, various utility functions are provided to enable the
statistical and graphical power of the R environment to work with biological
sequence and structural data. Please refer to the URLs below for more
information.","Imports":"parallel, grid, graphics, grDevices, stats,
2)","NeedsCompilation":"yes","Package":"bio3d","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"XML, RCurl, lattice, ncdf4, igraph, bigmemory,
knitr,\ntestthat (>= 0.9.1)","Title":"Biological Structure
Analysis","URL":"http:\/\/thegrantlab.org\/bio3d\/,
http:\/\/bitbucket.org\/Grantlab\/bio3d","Version":"2.2-4"},"bioPN":
{"Author":"Roberto Bertolusso and Marek Kimmel","Description":"\nbioPN is a package
suited to perform simulation of deterministic and stochastic systems of biochemical
reaction\nnetworks.\nModels are defined using a subset of Petri Nets, in a way that
is close at how chemical reactions\nare defined.\nFor deterministic solutions,
bioPN creates the associated system of differential equations \"on the fly\",
and\nsolves it with a Runge Kutta Dormand Prince 45 explicit algorithm.\nFor
stochastic solutions, bioPN offers variants of Gillespie algorithm, or SSA.\nFor
hybrid deterministic\/stochastic,\nit employs the Haseltine and Rawlings algorithm,
that partitions the system in fast and slow reactions.\nbioPN algorithms are
developed in C to achieve adequate performance.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"bioPN","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Simulation of deterministic and stochastic biochemical
reaction\nnetworks using Petri Nets","Version":"1.2.0"},"biogas":{"Author":"Sasha
D. Hafner [aut, cre], Charlotte Rennuit [aut], Jin Mi Triolo [ctb], Ali Heidarzadeh
Vazifehkhoran [ctb]","Description":"Functions for working with biogas data. Both
low- and high-level functions are included for carrying out common tasks for
analysis of biogas and related data. Molar mass and calculated oxygen demand (COD')
can be determined from a chemical formula. Measured gas volume can be corrected for
water vapor and to (possibly user-defined) standard temperature and pressure. Gas
composition, cumulative production, or other variables can be interpolated to a
specified time. Cumulative biogas and methane production (and rates) can be
calculated from individual biogas volume (or reactor mass) and biogas composition
measurements for any number of reactors. With cumulative methane production data
and data on reactor contents, biochemical methane potential (BMP) can be calculated
and summarized, including subtraction of the inoculum contribution and
normalization by substrate mass. Cumulative production and production rates can be
summarized in several different ways (e.g., omitting normalization) using the same
function. Lastly, biogas and methane production can be predicted from substrate
composition and additional, optional data.","License":"GPL-
2","NeedsCompilation":"no","Package":"biogas","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"knitr, ggplot2, testthat","Title":"Process Biogas Data
and Predict Biogas Production","Version":"1.2.1"},"biogeo":{"Author":"Mark
Robertson","Depends":"R (>= 3.1.0)","Description":"Functions for error detection
and correction in point data quality datasets that are used in species distribution
modelling. Includes functions for parsing and converting coordinates into decimal
degrees from various formats.","Imports":"raster, stringr, maptools, vegan,
sp","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"biogeo","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"dismo (>= 0.9-3)","Title":"Point Data Quality
Assessment and Coordinate
Conversion","URL":"http:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/ecog.02118\/abst
ract","Version":"1.0"},"biogram":{"Author":"Michal Burdukiewicz [cre, aut],\nPiotr
Sobczyk [aut],\nChris Lauber [aut]","Depends":"R (>= 3.0.0),
slam","Description":"Tools for extraction and analysis of various\nn-grams (k-mers)
derived from biological sequences (proteins\nor nucleic acids). Uses QuiPT (quick
permutation test) for fast\nfeature-filtering to deal with the dimensionality of
the n-gram data.","Imports":"bit, entropy","License":"GPL-
3","NeedsCompilation":"no","Package":"biogram","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"ggplot2, testthat","Title":"N-Gram Analysis of
Biological
Sequences","URL":"https:\/\/github.com\/michbur\/biogram","Version":"1.2"},"bioinac
tivation":{"Author":"Alberto Garre [aut, cre],\nPablo S. Fernandez [aut],\nJose A.
Egea [aut]","Description":"Prediction and adjustment to experimental data of
microbial\ninactivation. Several models available in the literature are
implemented.","Imports":"dplyr (>= 0.4.1), deSolve (>= 1.11), FME (>= 1.3.2),
lazyeval\n(>= 0.1.10), ggplot2 (>= 2.0.0), MASS (>= 7.3-39), graphics (>=\n3.1.3),
stats (>= 3.1.3)","License":"GPL-
3","NeedsCompilation":"no","Package":"bioinactivation","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"knitr (>= 1.9), testthat (>=
0.9.1)","Title":"Simulation of Dynamic Microbial
Inactivation","Version":"1.1.2"},"biom":{"Author":"Paul J. McMurdie
<mcmurdie@stanford.edu> and the\nbiom-format team http:\/\/biom-
format.org\/","Depends":"R (>= 3.0.0), methods","Description":"This is an R package
for interfacing with the\nBIOM format. This package includes basic tools
for\nreading biom-format files, accessing and subsetting\ndata tables from a biom
object (which is more complex\nthan a single table), as well as limited support
for\nwriting a biom-object back to a biom-format file. The\ndesign of this API is
intended to match the python API\nand other tools included with the biom-format
project,\nbut with a decidedly \"R flavor\" that should be familiar\nto R users.
This includes S4 classes and methods, as\nwell as extensions of common core
functions\/methods.","Imports":"plyr (>= 1.8), RJSONIO (>= 1.0.3), Matrix (>=
2","NeedsCompilation":"no","Package":"biom","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"testthat (>= 0.7.1), knitr (>= 1.3)","Title":"An interface
package (beta) for the BIOM file
format","URL":"https:\/\/github.com\/joey711\/biom\/, http:\/\/biom-
format.org\/","Version":"0.3.12"},"biomartr":{"Author":"Hajk-Georg
Drost","Depends":"R (>= 3.1.1)","Description":"Perform biological data retrieval
and functional annotation with\nR. This tool provides API functions to the BioMart
database and genome retrieval\nfunctions for bulk retrieval of
genomes.","Imports":"biomaRt, Biostrings, data.table (>= 1.9.4), dplyr (>=
0.3.0),\nreadr (>= 0.2.2), downloader (>= 0.3), RCurl (>= 1.95-4.5), XML\n(>= 3.98-
1.1), httr (>= 0.6.1), stringr (>= 0.6.2)","License":"GPL-
3","NeedsCompilation":"yes","Package":"biomartr","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr (>= 1.6), rmarkdown (>= 0.3.3), devtools (>=
1.6.1),\ntestthat","Title":"Functional Annotation and Biological Data Retrieval
with R","URL":"https:\/\/github.com\/HajkD\/biomartr","Version":"0.0.3"},"biomod2":
{"Author":"Wilfried Thuiller [aut, cre],\nDamien Georges [aut, cre],\nRobin Engler
[aut],\nFrank Breiner [aut]","Depends":"R (>= 3.2.1),
stats, utils, sp, raster, parallel, reshape,\nggplot2","Description":"Functions
for species distribution modeling, calibration and\nevaluation, ensemble of
models.","Imports":"abind, rasterVis, pROC, nnet, gbm, mda, randomForest,
rpart,\nMASS, methods, PresenceAbsence, dismo, maxent, earth","License":"GPL-
2","NeedsCompilation":"no","Package":"biomod2","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"ade4, foreign, Hmisc, mgcv, gam, testthat, ecospat,
caret","Title":"Ensemble Platform for Species Distribution
Modeling","Version":"3.3-7"},"bionetdata":{"Author":"Matteo Re, Giorgio Valentini
-- Universita' degli Studi di Milano","Depends":"R (>= 2.10)","Description":"Data
Package that includes several examples of chemical and biological data networks,
i.e. data graph structured.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"bionetdata","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Biological and chemical data
networks","Version":"1.0.1"},"biorxivr":{"Author":"Edmund Hart [aut,
cre]","Depends":"XML","Description":"The bioRxiv preprint server
(http:\/\/www.biorxiv.org) is a website where scientists can post preprints of
scholarly texts in biology. Users can search and download PDFs in bulk from the
preprint server. The text of abstracts are stored as raw text within R, and PDFs
can easily be saved and imported for text mining with packages such as
'tm'.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"biorxivr","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"knitr","Title":"Search and Download Papers from
the bioRxiv Preprint Server","Version":"0.1.3"},"bios2mds":{"Author":"Julien Pele
with Jean-Michel Becu, Herve Abdi, and Marie\nChabbert","Depends":"R (>= 2.12),
amap, e1071, scales, cluster, rgl","Description":"Bios2mds is primarily dedicated
to the analysis of\nbiological sequences by metric MultiDimensional Scaling
with\nprojection of supplementary data. It contains functions for\nreading multiple
sequence alignment files, calculating distance\nmatrices, performing metric
multidimensional scaling and\nvisualizing
results.","License":"GPL","NeedsCompilation":"no","Package":"bios2mds","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Title":"From BIOlogical Sequences to
MultiDimensional Scaling","Version":"1.2.2"},"biosignalEMG":{"Author":"J.A.
Guerrero, J.E. Macias-Diaz","Description":"Data processing tools to compute the
rectified, integrated and the averaged EMG. Routines for automatic detection of
activation phases. A routine to compute and plot the ensemble average of the EMG.
An EMG signal simulator for general purposes.","Imports":"signal, graphics, stats,
2)","NeedsCompilation":"no","Package":"biosignalEMG","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Tools for Electromyogram Signals (EMG)
Analysis","Version":"2.0.0"},"biotools":{"Author":"Anderson Rodrigo da
Silva","Depends":"R (>= 2.15), rpanel, tkrplot, MASS, lattice,
SpatialEpi","Description":"Tools designed to perform and work with cluster analysis
(including Tocher's algorithm),\ndiscriminant analysis and path analysis (standard
and under collinearity), as well as some\nuseful miscellaneous tools for dealing
with sample size and optimum plot size calculations.\nMantel's permutation test can
be found in this package. A new approach for calculating its\npower is implemented.
biotools also contains the new tests for genetic covariance
components.","Imports":"utils, stats, graphics, boot, grDevices,
datasets","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"biotools","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"soilphysics","Title":"Tools for Biometry and Applied
Statistics in Agricultural\nScience","Version":"3.0"},"bipartite":
{"Author":"Carsten F. Dormann, Jochen Fruend and Bernd Gruber, with additional code
from Mariano Devoto, Jose Iriondo, Rouven Strauss and Diego Vazquez, also based on
C-code developed by Nils Bluethgen, Aaron Clauset\/Rouven Strauss and Miguel
Rodriguez-Girones.","Depends":"vegan, sna","Description":"Bipartite provides
functions to visualise webs and calculate a series of indices commonly used to
describe pattern in ecological webs. It focuses on webs consisting of only two
trophic levels, e.g. pollination webs or predator-prey-webs. Visualisation is
important to get an idea of what we are actually looking at, while the indices
summarise different aspects of the webs topology.","Imports":"fields, igraph, MASS,
methods,
permute","License":"GPL","NeedsCompilation":"yes","Package":"bipartite","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Visualising bipartite networks
and calculating some (ecological)\nindices","Version":"2.05"},"biplotbootGUI":
{"Author":"Ana Belen Nieto Librero<ananieto@usal.es>, Purificacion Galindo
Villardon<pgalindo@usal.es>","Depends":"R (>= 3.1.1)","Description":"A GUI with
which the user can construct and interact with Bootstrap methods on Classical
Biplots and with Clustering and\/or Disjoint Biplot.","Imports":"rgl, tkrplot,
tcltk, tcltk2, shapes, cluster, dendroextras,\nMASS","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"biplotbootGUI","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Bootstrap on Classical Biplots and Clustering
Disjoint Biplot","Version":"1.1"},"birdring":{"Author":"Fraenzi Korner-Nievergelt,
Rob Robinson","Depends":"R (>= 2.10.1), stats","Description":"R functions to read
EURING data and analyse re-encounter data of birds marked by metal rings. For a
tutorial, go to
http:\/\/www.tandfonline.com\/doi\/full\/10.1080\/03078698.2014.933053.","Imports":
"geosphere, ks, lazyData, raster, rgdal, rgeos, rworldmap,\nrworldxtra, sp,
methods, graphics","License":"GPL-
2","NeedsCompilation":"no","Package":"birdring","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Methods to Analyse Ring Re-Encounter
Data","Version":"1.3"},"birk":{"Author":"Matthew A. Birk","Description":"Collection
of tools to make R more convenient. Includes tools to\nconvert between units and
dimensions of measurement and to summarize data\nusing statistics not available
with base R.","Imports":"grDevices, stats","License":"GPL-
3","NeedsCompilation":"no","Package":"birk","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"MA Birk's Functions","Version":"2.1.0"},"bisectr":
{"Author":"Winston Chang <winston@stdout.org>","Depends":"R (>=
2.14)","Description":"Tools to find bad commits with git bisect.
See\nhttps:\/\/github.com\/wch\/bisectr for examples and test
script\ntemplates.","Imports":"devtools","License":"GPL-
2","NeedsCompilation":"no","Package":"bisectr","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Tools to find bad commits with git
bisect","URL":"https:\/\/github.com\/wch\/bisectr","Version":"0.1.0"},"bisoreg":
{"Author":"S. McKay Curtis <s.mckay.curtis@gmail.com>","Depends":"R (>= 2.7.0),
bootstrap, monreg, R2WinBUGS, coda (>= 0.17.1)","Description":"Provides functions
for fitting Bayesian monotonic regression models to data.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"bisoreg","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Bayesian Isotonic Regression with Bernstein
Polynomials","Version":"1.4"},"bit":{"Author":"Jens Oehlschlägel
<Jens.Oehlschlaegel@truecluster.com>","Depends":"R (>=
2.9.2)","Description":"bitmapped vectors of booleans (no NAs),\ncoercion from and
to logicals, integers and integer subscripts;\nfast boolean operators and fast
summary statistics.\nWith 'bit' vectors you can store true binary booleans
{FALSE,TRUE} at the\nexpense of 1 bit only, on a 32 bit architecture this means
factor 32 less\nRAM and ~ factor 32 more speed on boolean operations. Due to
overhead of\nR calls, actual speed gain depends on the size of the vector: expect
gains\nfor vectors of size > 10000 elements. Even for one-time boolean
operations\nit can pay-off to convert to bit, the pay-off is obvious, when
such\ncomponents are used more than once.\nReading from and writing to bit is
approximately as fast as accessing\nstandard logicals - mostly due to R's time for
memory allocation. The package\nallows to work with pre-allocated memory for return
values by calling .Call()\ndirectly: when evaluating the speed of C-access with
pre-allocated vector\nmemory, coping from bit to logical requires only 70% of the
time for copying\nfrom logical to logical; and copying from logical to bit comes at
a\nperformance penalty of 150%. the package now contains further classes
for\nrepresenting logical selections: 'bitwhich' for very skewed selections
and\n'ri' for selecting ranges of values for chunked processing. All three
index\nclasses can be used for subsetting 'ff' objects (ff-2.1-0 and
higher).","License":"GPL-
2","NeedsCompilation":"yes","Package":"bit","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"A class for vectors of 1-bit booleans","URL":"http:\/\/ff.r-
forge.r-project.org\/","Version":"1.1-12"},"bit64":{"Author":"Jens Oehlschlägel
<Jens.Oehlschlaegel@truecluster.com>","Depends":"R (>= 3.0.1), bit (>= 1.1-12),
utils, methods, stats","Description":"\nPackage 'bit64' provides serializable S3
atomic 64bit (signed) integers\nthat can be used in vectors, matrices, arrays and
data.frames. Methods are\navailable for coercion from and to logicals, integers,
doubles, characters\nand factors as well as many elementwise and summary functions.
Many fast\nalgorithmic operations such as 'match' and 'order' support interactive
data\nexploration and manipulation and optionally leverage
caching.","License":"GPL-
2","NeedsCompilation":"yes","Package":"bit64","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"A S3 Class for Vectors of 64bit
Integers","URL":"http:\/\/ff.r-forge.r-project.org\/","Version":"0.9-5"},"bitops":
{"Author":"S original by Steve Dutky <sdutky@terpalum.umd.edu> initial
R\nport and extensions by Martin Maechler; revised and modified\nby Steve
Dutky","Description":"Functions for bitwise operations on integer
vectors.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"bitops","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Bitwise Operations","Version":"1.0-6"},"bivarRIpower":
{"Author":"W. Scott Comulada and Robert E. Weiss","Description":"Implements sample
size calculations for bivariate random\nintercept regression model that are
described in Comulada and\nWeiss (2010)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"bivarRIpower","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Sample size calculations for bivariate longitudinal
data","Version":"1.2"},"biwavelet":{"Author":"Tarik C. Gouhier, Aslak
Grinsted","Description":"This is a port of the WTC MATLAB package written by Aslak
Grinsted\nand the wavelet program written by Christopher Torrence and Gibert
P.\nCompo. This package can be used to perform univariate and bivariate\n(cross-
wavelet, wavelet coherence, wavelet clustering)
analyses.","Imports":"fields","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"biwavelet","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Conduct Univariate and Bivariate Wavelet
Analyses","URL":"http:\/\/github.com\/tgouhier\/biwavelet","Version":"0.17.10"},"bi
wt":{"Author":"Jo Hardin <jo.hardin@pomona.edu>","Depends":"R (>= 2.1.0), rrcov,
MASS","Description":"Compute multivariate location, scale, and
correlation\nestimates based on Tukey's biweight M-estimator.","License":"GPL-
2","NeedsCompilation":"no","Package":"biwt","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Functions to compute the biweight mean vector and covariance
&\ncorrelation matrices","Version":"1.0"},"bizdays":{"Author":"Wilson Freitas
<wilson.freitas@gmail.com>","Depends":"R (>= 2.15)","Description":"Business days
calculations based on a list of holidays and\nnonworking weekdays. Quite useful for
fixed income and derivatives pricing.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"bizdays","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"knitr","Title":"Business Days Calculations and
Utilities","URL":"https:\/\/github.com\/wilsonfreitas\/R-
bizdays","Version":"0.2.2"},"blatr":{"Author":"Stefan Milton
Bache","Description":"A wrapper around the 'Blat' command line SMTP mailer for
Windows.\n'Blat' is public domain software, but be sure to read the license before
use.\nIt can be found at the Blat website http:\/\/www.blat.net.","License":"MIT +
file
LICENSE","NeedsCompilation":"no","Package":"blatr","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Send Emails Using 'Blat' for
Windows","Version":"1.0.1"},"blavaan":{"Author":"Edgar Merkle [aut, cre],\nYves
Rosseel [aut]","Depends":"R(>= 3.2.0), methods, runjags, lavaan(>= 0.5-
20)","Description":"Fit a variety of Bayesian latent variable models, including
confirmatory\nfactor analysis, structural equation models, and latent growth curve
models.","Imports":"stats, utils, graphics, MASS, MCMCpack, mnormt, nonnest2,
loo","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"blavaan","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"modeest, rjags, semTools","Title":"Bayesian Latent
Variable Analysis","Version":"0.1-3"},"blender":{"Author":"David J. Harris
<DavHarris@UCDavis.edu>","Depends":"R (>= 2.10), vegan","Description":"Tools for
assessing exotic species' contributions to\nlandscape homogeneity using average
pairwise Jaccard similarity\nand an analytical approximation derived in Harris et
al. (2011,\n\"Occupancy is nine-tenths of the law,\" The American\nNaturalist).
Also includes a randomization method for assessing\nsources of model
error.","License":"GPL-2 | Artistic-
2.0","NeedsCompilation":"no","Package":"blender","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Analyze biotic homogenization of
landscapes","Version":"0.1.2"},"blighty":{"Author":"David Lucy
<d.lucy@lancaster.ac.uk>","Depends":"utils","Description":"Function for drawing the
coastline of the British Isles","License":"GPL-
2","NeedsCompilation":"no","Package":"blighty","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"United Kingdom coastlines","Version":"3.1-4"},"blkergm":
{"Author":"Xiaolin Yang [aut, cre],\nStephen E. Fienberg [aut],\nAlessandro Rinaldo
[aut],\nHan Liu [aut],\nMichael Rosenblum [aut]","Depends":"network (>= 1.7-1),
ergm (>= 3.1-0), statnet.common (>= 3.1-0)","Description":"This package is an
extension to the \"ergm\" package which implements the block
ergms.","License":"GPL-
3","NeedsCompilation":"yes","Package":"blkergm","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Fitting block ERGM given the block structure on social
networks","URL":"http:\/\/statnet.org","Version":"1.1"},"blm":{"Author":"S.
Kovalchik","Depends":"R (>= 2.10.1), methods","Description":"Implements regression
models for binary data on the absolute risk scale. These models are applicable to
cohort and population-based case-control data.","Imports":"stats,
stats4","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"blm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Binomial linear and linear-expit
regression","Version":"2013.2.4.4"},"blme":{"Author":"Vincent Dorie
<vjd4@nyu.edu>","Depends":"R (>= 3.0-0), lme4 (>= 1.0-6)","Description":"Maximum a
posteriori estimation for linear and generalized\nlinear mixed-effects models in a
Bayesian setting. Extends\n'lme4' by Douglas Bates, Martin Maechler, Ben Bolker,
and Steve Walker.","Imports":"methods, stats, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"blme","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat (>= 0.9-0)","Title":"Bayesian Linear Mixed-
Effects Models","URL":"https:\/\/github.com\/vdorie\/blme","Version":"1.0-
4"},"blmeco":{"Author":"Fraenzi Korner-Nievergelt, Tobias Roth, Stefanie von
Felten, Jerome Guelat, Bettina Almasi, Pius Korner-Nievergelt","Depends":"R (>=
3.0.0), stats, MASS","Description":"Data files and functions accompanying the book
Korner-Nievergelt, Roth, von Felten, Guelat, Almasi, Korner-Nievergelt
(2015) \"Bayesian Data Analysis in Ecology using R, BUGS and Stan\", Elsevier, New
York.","Imports":"MuMIn, arm, lme4","License":"GPL-
2","NeedsCompilation":"no","Package":"blmeco","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Data Files and Functions Accompanying the Book \"Bayesian
Data\nAnalysis in Ecology using R, BUGS and Stan\"","Version":"1.1"},"blockTools":
{"Author":"Ryan T. Moore and Keith Schnakenberg","Description":"Blocks units into
experimental blocks, with one unit per treatment condition, by creating a measure
of multivariate distance between all possible pairs of units. Maximum, minimum, or
an allowable range of differences between units on one variable can be set.
Randomly assign units to treatment conditions. Diagnose potential interference
between units assigned to different treatment conditions. Write outputs to .tex
and .csv files.","Imports":"MASS","License":"GPL (>= 2) | file
LICENSE","NeedsCompilation":"yes","Package":"blockTools","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"nbpMatching, RItools, xtable","Title":"Block,
Assign, and Diagnose Potential Interference in
Randomized\nExperiments","Version":"0.6-2"},"blockcluster":{"Author":"Serge Iovleff
[aut, cre],\nParmeet Singh Bhatia [aut],\nVincent Kubicki [ctb],\nGerard Goavert
[ctb],\nVincent Brault [ctb],\nChristophe Biernacki [ctb],\nGilles Celeux
[ctb]","Depends":"R (>= 3.0.2), rtkore (>= 1.0.0)","Description":"Simultaneous
clustering of rows and columns, usually designated by\nbiclustering, co-clustering
or block clustering, is an important technique\nin two way data analysis. It
consists of estimating a mixture model which\ntakes into account the block
clustering problem on both the individual and\nvariables sets. The blockcluster
package provides a bridge between the C++\ncore library and the R statistical
computing environment. This package\nallows to co-cluster binary, contingency,
continuous and categorical\ndata-sets. It also provides utility functions to
visualize the results.\nThis package may be useful for various applications in
fields of Data\nmining,Information retrieval, Biology, computer vision and many
more. More\ninformation about the project and comprehensive tutorial can be found
on\nthe link mentioned in URL.","Imports":"methods","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"blockcluster","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Coclustering Package for Binary, Categorical,
Contingency and\nContinuous Data-
Sets","URL":"https:\/\/gforge.inria.fr\/projects\/cocluster\/","Version":"4.0.2"},"
blockmatrix":{"Author":"Emanuele Cordano","Depends":"R (>=
2.13)","Description":"Some elementary matrix algebra tools are implemented to
manage\nblock matrices or partitioned matrix, i.e. \"matrix of
matrices\"\n(http:\/\/en.wikipedia.org\/wiki\/Block_matrix). The block matrix is
here\ndefined as a new S3 object. In this package, some methods
for \"matrix\"\nobject are rewritten for \"blockmatrix\" object. New methods are
implemented.\nThis package was created to solve equation systems with block
matrices for\nthe analysis of environmental vector time series
.\nBugs\/comments\/questions\/collaboration of any kind are warmly
welcomed.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"blockmatrix","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"blockmatrix: Tools to solve algebraic systems with
partitioned\nmatrices","URL":"\nhttp:\/\/cri.gmpf.eu\/Research\/Sustainable-Agro-
Ecosystems-and-Bioresources\/Dynamics-in-the-agro-ecosystems\/people\/Emanuele-
Cordano","Version":"1.0"},"blockmodeling":{"Author":"Ales
Ziberna","Description":"The package is primarly ment as
an implementation of\nGeneralized blockmodeling for valued networks. In
addition,\nmeasurese of similarity or dissimilarity based on
structural\nequivalence and regular equivalence (REGE algorithem) can be\ncomputed
and partitioned matrices can be ploted.","Imports":"stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"blockmodeling","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"sna, Matrix","Title":"An R package for
Generalized and classical blockmodeling of\nvalued
networks","Version":"0.1.8"},"blockmodels":{"Author":"INRA, Jean-Benoist Leger
<jbleger@bordeaux.inra.fr>","Depends":"Rcpp (>= 0.10.6), parallel, methods,
digest","Description":"Latent and Stochastic Block Model estimation by a
Variational EM algorithm.\nVarious probability distribution are provided
(Bernoulli,\nPoisson...), with or without covariates.","License":"LGPL-
2.1","NeedsCompilation":"yes","Package":"blockmodels","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Latent and Stochastic Block Model Estimation by a
'V-EM'\nAlgorithm","Version":"1.1.1"},"blockrand":{"Author":"Greg Snow
<greg.snow@imail.org>","Description":"Create randomizations for block random
clinical trials.\nCan also produce a pdf file of randomization
cards.","License":"GPL-
2","NeedsCompilation":"no","Package":"blockrand","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Randomization for block random clinical
trials","Version":"1.3"},"blocksdesign":{"Author":"R. N. Edmondson","Depends":"R
(>= 3.1.0)","Description":"Constructs nested and crossed block designs\nfor
unstructured treatment sets with arbitrary replication not necessarily all
equal.\nBlocks can be nested to any required depth of nesting and blocks are
optimized\nhierarchically from the top down with successive nested blocks strata
optimized within\nthe levels of all preceding blocks strata. Block sizes are all
equal in any one stratum if the number\nof blocks in that stratum exactly divides
the number of plots, otherwise they differ by at most one plot.\nThe design output
is a data table showing a randomised allocation of treatments to blocks together
with\nplans showing the allocation of treatments to blocks for each block in the
bottom stratum of the design.\nD and A-efficiency factors are shown for each
stratum together with A-efficiency upper bounds,\nwhere
available.","Imports":"crossdes","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"blocksdesign","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Nested Block Designs for Unstructured
Treatments","URL":"http:\/\/www.expdesigns.co.uk","Version":"2.1"},"blockseg":
{"Author":"Julien Chiquet [aut, cre],\nVincent Brault
[aut]","Description":"Segments a matrix in blocks with constant
values.","Imports":"Rcpp (>= 0.12.1), Matrix, ggplot2, reshape2,
2.0)","NeedsCompilation":"yes","Package":"blockseg","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Two Dimensional Change-Points
Detection","Version":"0.2"},"blsAPI":{"Author":"Michael Silva
<mike.a.silva@gmail.com>","Depends":"R (>= 3.1.1)","Description":"Allows users to
request data for one or multiple series through the\nU.S. Bureau of Labor
Statistics API. Users provide parameters as specified
in\nhttp:\/\/www.bls.gov\/developers\/api_signature.htm and the function returns a
JSON\nstring.","Imports":"rjson, RCurl","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"blsAPI","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Request Data from the U.S. Bureau of Labor Statistics
API","Version":"0.1.3"},"bmd":{"Author":"Christian Ritz
<ritz@life.ku.dk>","Depends":"R (>= 2.6.0), drc","Description":"Benchmark dose
analysis for continuous and quantal\ndose-response data.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"bmd","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Benchmark dose analysis for dose-response
data","URL":"http:\/\/www.r-project.org","Version":"0.5"},"bmem":{"Author":"Zhiyong
Zhang and Lijuan Wang","Depends":"R (>= 1.7), Amelia, MASS, lavaan, sem,
snowfall","Description":"Four methods for mediation analysis with missing data:
Listwise deletion, Pairwise deletion, Multiple imputation, and Two Stage Maximum
Likelihood algorithm. For MI and TS-ML, auxiliary variables can be included.
Bootstrap confidence intervals for mediation effects are obtained. The robust
method is also implemented for TS-ML. Since version 1.4, bmem adds the capability
to conduct power analysis for mediation models.","License":"GPL-
2","NeedsCompilation":"no","Package":"bmem","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Mediation analysis with missing data using
bootstrap","URL":"http:\/\/nd.psychstat.org","Version":"1.5"},"bmeta":
{"Author":"Tao Ding, Gianluca
Baio","Depends":"R2jags,forestplot","Description":"Provides a collection of
functions for conducting meta-analyses under Bayesian context in R. The package
includes functions for computing various effect size or outcome measures (e.g. odds
ratios, mean difference and incidence rate ratio) for different types of data based
on MCMC simulations. Users are allowed to fit fixed- and random-effects models with
different priors to the data. Meta-regression can be carried out if effects of
additional covariates are observed. Furthermore, the package provides functions for
creating posterior distribution plots and forest plot to display main model output.
Traceplots and some other diagnostic plots are also available for assessing model
fit and performance.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"bmeta","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Bayesian Meta-Analysis and Meta-
Regression","URL":"http:\/\/www.statistica.it\/gianluca\/bmeta,\nhttp:\/\/www.stati
stica.it\/gianluca","Version":"0.1.2"},"bmk":{"Author":"Matthew Krachey and Edward
L. Boone","Depends":"coda, plyr, functional","Description":"MCMC diagnostic package
that contains tools to diagnose\nconvergence as well as to evaluate sensitivity
studies,\nIncludes summary functions which output mean, median,\n95percentCI,
Gelman & Rubin diagnostics and the Hellinger\ndistance based diagnostics, Also
contains functions to\ndetermine when an MCMC chain has converged via
Hellinger\ndistance, A function is also provided to compare outputs
from\nidentically dimensioned chains for determining sensitivy to\nprior
distribution assumptions","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"bmk","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"MCMC diagnostics package","Version":"1.0"},"bmmix":
{"Author":"Thibaut Jombart <t.jombart@imperial.ac.uk>","Depends":"R (>=
3.0.0)","Description":"Bayesian multinomial mixture model","Imports":"utils,
ggplot2, reshape2","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"bmmix","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Bayesian multinomial mixture","Version":"0.1-2"},"bmp":
{"Author":"Gregory Jefferis","Description":"Reads Windows BMP format images.
Currently limited to 8 bit\ngreyscale images and 24,32 bit (A)RGB images. Pure R
implementation without\nexternal dependencies.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"bmp","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"pixmap, testthat","Title":"Read Windows Bitmap (BMP)
images","Version":"0.2"},"bmrm":{"Author":"Julien Prados","Depends":"R (>=
3.0.2)","Description":"Bundle methods for minimization of convex and non-convex
risk\nunder L1 or L2 regularization. Implements the algorithm proposed by Teo
et\nal. (JMLR 2010) as well as the extension proposed by Do and Artieres
(JMLR\n2012). The package comes with lot of loss functions for machine
learning\nwhich make it powerful for big data analysis. The applications
includes:\nstructured prediction, linear SVM, multi-class SVM, f-beta
optimization,\nROC optimization, ordinal regression, quantile regression,\nepsilon
insensitive regression, least mean square, logistic regression,\nleast absolute
deviation regression (see package examples), etc... all with\nL1 and L2
regularization.","Imports":"lpSolve, LowRankQP","License":"GPL-
3","NeedsCompilation":"no","Package":"bmrm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Bundle Methods for Regularized Risk Minimization
Package","Version":"3.0"},"bnclassify":{"Author":"Mihaljevic Bojan [aut,
cre],\nBielza Concha [aut],\nLarranaga Pedro [aut],\nWickham Hadley [ctb] (some
code extracted from memoise package)","Depends":"R (>=
3.2.0)","Description":"Implements state-of-the art algorithms for learning discrete
Bayesian network classifiers from data, as well as functions for using these
classifiers for prediction, assessing their predictive performance, and inspecting
their properties.","Imports":"assertthat (>= 0.1), entropy(>= 1.2.0), graph(>=
1.42.0),\nmatrixStats(>= 0.14.0), RBGL(>= 1.40.1), rpart(>= 4.1-8)","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"bnclassify","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"gRain(>= 1.2-3), gRbase(>= 1.7-0.1), mlr(>= 2.2),
testthat(>=\n0.8.1), knitr(>= 1.10.5), microbenchmark(>= 1.4-2),\nParamHelpers(>=
1.5), Rgraphviz(>= 2.8.1), rmarkdown(>= 0.7),\ncovr","Title":"Learning Discrete
Bayesian Network Classifiers from
Data","URL":"http:\/\/github.com\/bmihaljevic\/bnclassify","Version":"0.3.2"},"bnle
arn":{"Author":"Marco Scutari","Depends":"R (>= 2.14.0),
methods","Description":"Bayesian network structure learning, parameter learning
and\ninference.\nThis package implements constraint-based (GS, IAMB, Inter-IAMB,
Fast-IAMB,\nMMPC, Hiton-PC), pairwise (ARACNE and Chow-Liu), score-based (Hill-
Climbing\nand Tabu Search) and hybrid (MMHC and RSMAX2) structure learning
algorithms\nfor discrete, Gaussian and conditional Gaussian networks, along with
many\nscore functions and conditional independence tests.\nThe Naive
Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are\nalso
implemented.\nSome utility functions (model comparison and manipulation, random
data\ngeneration, arc orientation testing, simple and advanced plots)
are\nincluded, as well as support for parameter estimation (maximum likelihood\nand
Bayesian) and inference, conditional probability queries and\ncross-validation.
Development snapshots with the latest bugfixes are\navailable from
www.bnlearn.com.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"bnlearn","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"parallel, graph, Rgraphviz, lattice,
gRain","Title":"Bayesian Network Structure Learning, Parameter Learning
and\nInference","URL":"http:\/\/www.bnlearn.com\/","Version":"3.9"},"bnnSurvival":
{"Author":"Marvin N. Wright","Description":"Implements a bootstrap aggregated
(bagged) version of\nthe k-nearest neighbors survival probability prediction method
(Lowsky et\nal. 2013). In addition to the bootstrapping of training samples,
the\nfeatures can be subsampled in each baselearner to break the
correlation\nbetween them. The Rcpp package is used to speed up the
computation.","Imports":"prodlim, pec, Rcpp (>= 0.11.2), parallel,
3","NeedsCompilation":"yes","Package":"bnnSurvival","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"survival, testthat","Title":"Bagged k-Nearest
Neighbors Survival Prediction","Version":"0.1.4"},"bnormnlr":{"Author":"Nicolas
Molano-Gonzalez, Marta Corrales Bossio, Maria Fernanda Zarate, Edilberto Cepeda-
Cuervo.","Depends":"mvtnorm, numDeriv","Description":"Implementation of Bayesian
estimation in normal heteroscedastic nonlinear regression Models following Cepeda-
Cuervo, (2001).","License":"GPL-
2","NeedsCompilation":"no","Package":"bnormnlr","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"car, coda, MASS","Title":"Bayesian Estimation for
Normal Heteroscedastic Nonlinear\nRegression Models","Version":"1.0"},"bnpmr":
{"Author":"Bjoern Bornkamp","Description":"Implements the Bayesian nonparametric
monotonic regression\nmethod described in Bornkamp & Ickstadt (2009), Biometrics,
65,\n198-
205.","License":"GPL","NeedsCompilation":"yes","Package":"bnpmr","Repository":"http
:\/\/cran.csiro.au\/src\/contrib","Title":"Bayesian monotonic nonparametric
regression","Version":"1.1"},"bnstruct":{"Author":"Francesco Sambo [aut,
cre],\nAlberto Franzin [aut]","Depends":"R (>= 2.10), bitops, Matrix,
methods","Description":"Bayesian Network Structure Learning from Data with Missing
Values.\nThe package implements the Silander-Myllymaki complete search,\nthe Max-
Min Hill-climbing heuristic search, and the Structural\nExpectation-Maximization
algorithm. Available scoring functions are\nBDeu, AIC, BIC. The package also
implements methods for generating and using\nbootstrap samples, imputed data,
inference.","Imports":"igraph","License":"GPL (>= 2) | file
LICENSE","NeedsCompilation":"yes","Package":"bnstruct","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"graph, Rgraphviz, knitr,
testthat","Title":"Bayesian Network Structure Learning from Data with
Missing\nValues","Version":"1.0"},"boa":{"Author":"Brian J. Smith","Depends":"R (>=
2.7)","Description":"A menu-driven program and library of functions for carrying
out\nconvergence diagnostics and statistical and graphical analysis of
Markov\nchain Monte Carlo sampling output.","License":"GPL-
2","NeedsCompilation":"no","Package":"boa","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Bayesian Output Analysis Program (BOA) for
MCMC","URL":"http:\/\/www.jstatsoft.org\/v21\/i11","Version":"1.1.8-
1"},"bodenmiller":{"Author":"Yann Abraham [aut, cre],\nBernd Bodenmiller
[aut]","Depends":"R (>= 3.1.0)","Description":"This data package contains a subset
of the Bodenmiller et al, Nat Biotech 2012 dataset for testing single cell, high
dimensional analysis and visualization
methods.","License":"CC0","NeedsCompilation":"no","Package":"bodenmiller","Reposito
ry":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"ggplot2, dplyr, reshape2,
RColorBrewer, knitr, rmarkdown","Title":"Profilling of Peripheral Blood Mononuclear
Cells using
CyTOF","URL":"https:\/\/github.com\/yannabraham\/bodenmiller","Version":"0.1"},"boi
lerpipeR":{"Author":"See AUTHORS file.","Description":"Generic Extraction of main
text content from HTML files; removal\nof ads, sidebars and headers using the
boilerpipe\n(http:\/\/code.google.com\/p\/boilerpipe\/) Java library.
The\nextraction heuristics from boilerpipe show a robust performance for a
wide\nrange of web site templates.","Imports":"rJava","License":"Apache License (==
2.0)","NeedsCompilation":"no","Package":"boilerpipeR","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"RCurl","Title":"Interface to the Boilerpipe Java
Library","URL":"https:\/\/github.com\/mannau\/boilerpipeR","Version":"1.3"},"bold":
{"Author":"Scott Chamberlain [aut, cre]","Description":"A programmatic interface to
the Web Service methods provided by\nBold Systems for genetic 'barcode' data.
Functions include methods for\nsearching by sequences by taxonomic names, ids,
collectors, and\ninstitutions; as well as a function for searching for specimens,
and\ndownloading trace files.","Imports":"methods, utils, stats, xml2, httr,
stringr, assertthat,\njsonlite, reshape, plyr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"bold","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"sangerseqR, knitr, testthat,
covr","Title":"Interface to Bold Systems
'API'","URL":"https:\/\/github.com\/ropensci\/bold","Version":"0.3.5"},"boolean3":
{"Author":"Jason W. Morgan <morgan.746@osu.edu>","Depends":"R (>= 3.0),
utils","Description":"This package implements a\npartial-observability procedure
for testing Boolean\nhypotheses that generalizes the binary response GLM
as\noutlined in Braumoeller (2003).","Imports":"stats, optimx (>= 2013.8.6),
numDeriv, lattice, rgenoud,\nparallel, mvtnorm, rlecuyer","License":"GPL-
3","NeedsCompilation":"no","Package":"boolean3","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Boolean Binary Response
Models","Version":"3.1.6"},"boostSeq":{"Author":"c(person(\"Milan
Hiersche\", \"Developer\", email =\n\"mihi@uni-muenster.de\")","Depends":"R (>=
2.11.0), genetics, lpSolveAPI","Description":"This package contains functionality
to select a subsample\nof a genotyped cohort e.g. from a GWAS that is preferential
for\nresequencing under the assumtion that causal variants share a\nhaplotype with
the risk allele of associated variants. The\nsubsample is selected such that is
contains risk alleles at\nmaximum frequency for all SNPs specified. Phentoypes can
also\nbe included as additional variables to obtain a higher fraction\nof extreme
phenotypes. An arbitrary number of SNPs and\/or\nphentoypes can be specified for
enrichment in a single\nsubsample.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"boostSeq","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Optimized GWAS cohort subset selection for resequencing
studies","URL":"http:\/\/www.r-project.org","Version":"1.0"},"boostmtree":
{"Author":"Hemant Ishwaran <hemant.ishwaran@gmail.com>, Amol Pande
<amoljpande@gmail.com>","Depends":"R (>= 3.1.0)","Description":"Implements
Friedman's gradient descent boosting algorithm for longitudinal data using
multivariate tree base learners. A time-covariate interaction effect is modeled
using penalized B-splines (P-splines) with estimated adaptive smoothing
parameter.","Imports":"randomForestSRC (>= 2.1.0), parallel, splines,
nlme","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"boostmtree","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Boosted Multivariate Trees for Longitudinal
Data","URL":"http:\/\/web.ccs.miami.edu\/~hishwaran
http:\/\/www.kogalur.com","Version":"1.0.0"},"boostr":{"Author":"Steven Pollack
<steven@pollackphoto.net>","Depends":"R (>= 3.0.2)","Description":"boostr provides
a modular framework that return the focus of\nensemble learning back to 'learning'
(instead of programming).","Imports":"foreach, iterators, stringr","License":"GPL-
2","NeedsCompilation":"no","Package":"boostr","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"knitr, xtable, mlbench, nnet, class, e1071,
randomForest","Title":"A modular framework to bag or boost any estimation
procedure","Version":"1.0.0"},"boot":{"Author":"Angelo Canty [aut],\nBrian Ripley
[aut, trl, cre] (author of parallel support)","Depends":"R (>= 3.0.0), graphics,
stats","Description":"Functions and datasets for bootstrapping from
the\nbook \"Bootstrap Methods and Their Application\" by A. C. Davison and\nD. V.
Hinkley (1997, CUP), originally written by Angelo Canty for
S.","License":"Unlimited","NeedsCompilation":"no","Package":"boot","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Suggests":"MASS, survival","Title":"Bootstrap
Functions (Originally by Angelo Canty for S)","Version":"1.3-18"},"bootES":
{"Author":"Daniel Gerlanc <dgerlanc@enplusadvisors.com> and Kris Kirby
<kkirby@williams.edu>","Depends":"R (>= 2.10.1), boot","Description":"Calculate
robust measures of effect sizes using the bootstrap.","Imports":"stats,
2)","NeedsCompilation":"no","Package":"bootES","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Bootstrap Effect
Sizes","URL":"http:\/\/www.enplusadvisors.com","Version":"1.2"},"bootLR":
{"Author":"Keith A. Marill and Ari B. Friedman","Description":"Computes appropriate
confidence intervals for the likelihood ratio tests commonly used in
medicine\/epidemiology. It is particularly useful when the sensitivity or
specificity in the sample is 100%. Note that this does not perform the test on
nested models--for that, see 'epicalc::lrtest'.","Imports":"boot,
stats","License":"LGPL-
2.1","NeedsCompilation":"no","Package":"bootLR","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"testthat",
"Title":"Bootstrapped Confidence Intervals for (Negative) Likelihood\nRatio
Tests","Version":"1.0"},"bootRes":{"Author":"Christian Zang","Depends":"base,
stats, utils","Description":"Calculation of Bootstrapped Response and
Correlation\nFunctions for Use in Dendroclimatology","License":"GPL-
3","NeedsCompilation":"no","Package":"bootRes","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"dplR","Title":"Bootstrapped Response and Correlation
Functions","Version":"1.2.3"},"bootSVD":{"Author":"Aaron Fisher
<fisher@jhu.edu>","Depends":"R (>= 3.0.2)","Description":"Implements fast, exact
bootstrap Principal Component Analysis and\nSingular Value Decompositions for high
dimensional data, as described in\n<http:\/\/arxiv.org\/abs\/1405.0922>. For data
matrices that are too large to operate\non in memory, users can input objects with
class 'ff' (see the 'ff'\npackage), where the actual data is stored on disk. In
response, this\npackage will implement a block matrix algebra procedure for
calculating the\nprincipal components (PCs) and bootstrap PCs. Depending on options
set by\nthe user, the 'parallel' package can be used to parallelize the calculation
of\nthe bootstrap PCs.","Imports":"ff, parallel","License":"GPL-
2","NeedsCompilation":"no","Package":"bootSVD","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Fast, Exact Bootstrap Principal Component Analysis for
High\nDimensional
Data","URL":"http:\/\/arxiv.org\/abs\/1405.0922","Version":"0.5"},"bootStepAIC":
{"Author":"Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>","Depends":"R(>= 2.3.0),
MASS","Description":"Model selection by bootstrapping the stepAIC()
procedure.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"bootStepAIC","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Bootstrap stepAIC","Version":"1.2-
0"},"bootTimeInference":{"Author":"Michael Wolf [aut],\nOliver Ledoit
[aut],\nAleksandar Spasojevic [cre]","Depends":"stats","Description":"Applied
researchers often test for the difference of the Sharpe\nratios of two investment
strategies. A very popular tool to this end is the test\nof Jobson and Korkie,
which has been corrected by Memmel. Unfortunately, this\ntest is not valid when
returns have tails heavier than the normal distribution\nor are of time series
nature. Instead, we propose the use of robust inference\nmethods. In particular, we
suggest to construct a studentized time series\nbootstrap confidence interval for
the difference of the Sharpe ratios and\nto declare the two ratios different if
zero is not contained in the obtained\ninterval. This approach has the advantage
that one can simply resample from the\nobserved data as opposed to some null-
restricted data.","Imports":"Rcpp (>= 0.12.3.3)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"bootTimeInference","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Suggests":"R.rsp","Title":"Robust Performance
Hypothesis Testing with the Sharpe Ratio","Version":"0.1.0"},"bootnet":
{"Author":"Sacha Epskamp","Depends":"ggplot2, R (>=
3.0.0)","Description":"Bootstrap standard errors on various network estimation
routines, such as EBICglasso() from the 'qgraph' package and IsingFit() from the
'IsingFit' package.","Imports":"methods, IsingFit, qgraph, dplyr (>= 0.3.0.2),
gtools,\ncorpcor, IsingSampler, mvtnorm, abind, Matrix","License":"GPL-
2","NeedsCompilation":"no","Package":"bootnet","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"psych","Title":"Bootstrap Methods for Various Network
Estimation Routines","Version":"0.2"},"bootruin":{"Author":"Benjamin Baumgartner
<benjamin@baumgrt.com>, Riccardo Gatto <gatto@stat.unibe.ch>","Description":"This
package provides a framework for testing the probability of ruin in the classical
(compound Poisson) risk process. It also includes some procedures for assessing and
comparing the performance between the bootstrap test and the test using asymptotic
normality.","License":"AGPL-
3","NeedsCompilation":"yes","Package":"bootruin","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"A bootstrap test for the probability of ruin in the
classical\nrisk process","Version":"1.2-1"},"bootsPLS":{"Author":"Florian Rohart
[aut, cre], Kim-Anh Le Cao [boss], Christine Wells
[boss]","Depends":"mixOmics","Description":"Applicable to any classification
problem with more than 2 classes. It relies on bootstrap subsamplings of sPLS-DA
and provides tools to select the most stable variables (defined as the ones
consistently selected over the bootstrap subsamplings) and to predict the class of
test samples.","License":"GPL-
3","NeedsCompilation":"no","Package":"bootsPLS","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Bootstrap Subsamplings of Sparse Partial Least Squares
-\nDiscriminant Analysis for Classification and
Signature\nIdentification","Version":"1.0.3"},"bootspecdens":{"Author":"Tatjana
Kinsvater","Depends":"MASS","Description":"Bootstrap for testing the hypothesis
that the spectral\ndensities of a number m, m>=2, not necessarily independent
time\nseries are equal","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"bootspecdens","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Testing equality of spectral
densities","Version":"3.0"},"bootstrap":{"Author":"S original, from StatLib, by Rob
Tibshirani. R port by\nFriedrich Leisch.","Depends":"stats, R (>=
2.10.0)","Description":"Software (bootstrap, cross-validation, jackknife) and
data\nfor the book \"An Introduction to the Bootstrap\" by B. Efron and\nR.
Tibshirani, 1993, Chapman and
Hall.\n_____________________________________________________________\nThis package
is primarily provided for projects already based\non it, and for support of the
book. New projects should\npreferentially use the recommended
package \"boot\".","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"yes","Package":"bootstrap","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Functions for the Book \"An Introduction to the
Bootstrap\"","Version":"2015.2"},"boottol":{"Author":"Garrett
Schiltgen","Depends":"R (>= 3.1.2), boot, plyr","Description":"Used to create
bootstrap tolerance levels for the Kolmogorov-Smirnov (KS) statistic, the area
under receiver operator characteristic curve (AUROC) statistic, and the Gini
coefficient for each score cutoff. Also provides a bootstrap alternative to the
Vasicek test.","License":"GPL-
2","NeedsCompilation":"no","Package":"boottol","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Bootstrap Tolerance Levels for Credit Scoring
Validation\nStatistics","Version":"2.0"},"boral":{"Author":"Francis K.C.
Hui","Depends":"coda","Description":"Bayesian approaches for analyzing multivariate
data in ecology. Estimation is performed using Markov Chain Monte Carlo (MCMC)
methods via JAGS. Three types of models may be fitted: 1) With explanatory
variables only, boral fits independent column GLMs to each column of the response
matrix; 2) With latent variables only, boral fits a purely latent variable model
for model-based unconstrained ordination; 3) With explanatory and latent variables,
boral fits correlated column GLMs with latent variables to account for any residual
correlation between the columns of the response matrix.","Imports":"R2jags,
mvtnorm, fishMod, MASS, stats, graphics, grDevices","License":"GPL-
2","NeedsCompilation":"no","Package":"boral","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"mvabund (>= 3.8.4), corrplot, testthat","Title":"Bayesian
Ordination and Regression AnaLysis","Version":"0.9.1"},"boussinesq":
{"Author":"Emanuele Cordano","Depends":"R (>= 2.10)","Description":"This package is
a collection of R functions implemented\nfrom published and available analytic
solutions for the\nOne-Dimensional Boussinesq Equation (ground-water).
In\nparticular, the function \"beq.lin\" is the analytic solution of\nthe
linearized form of Boussinesq Equation between two\ndifferent head-based boundary
(Dirichlet) conditions;\n\"beq.song\" is the non-linear power-series analytic
solution of\nthe motion of a wetting front over a dry bedrock (Song at al,\n2007,
see complete reference on function
documentation).\nBugs\/comments\/questions\/collaboration of any kind are
warmly\nwelcomed.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"boussinesq","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Analytic Solutions for (ground-water) Boussinesq
Equation","URL":"http:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/wrcr.20072\/abstra
ct","Version":"1.0.3"},"boxplotdbl":{"Author":"Shinichiro
Tomizono","Description":"Correlation chart of two set (x and y) of data.\nUsing
Quartiles with boxplot style.\nVisualize the effect of factor.","License":"MIT +
file
LICENSE","NeedsCompilation":"no","Package":"boxplotdbl","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Double Box Plot for Two-Axes
Correlation","Version":"1.2.2"},"boxr":{"Author":"Brendan Rocks [aut,
cre]","Description":"An R interface for the remote file hosting service 'Box'
(https:\/\/\nwww.box.com\/). In addition to uploading and downloading files, this
package\nincludes functions which mirror base R operations for local files,
(e.g.\nbox_load(), box_save(), box_read(), box_setwd(), etc.), as well as
'git'\nstyle functions for entire directories (e.g. box_fetch(),
box_push()).","Imports":"httr (>= 1.1.0), httpuv, assertthat, stringr, dplyr,
digest,\nbit64, rio, mime, utils, stats","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"boxr","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat, knitr, rmarkdown","Title":"Interface for
the 'Box.com API'","URL":"https:\/\/github.com\/brendan-
R\/boxr\/","Version":"0.3.2"},"bpa":{"Author":"Brandon Greenwell [aut,
cre]","Depends":"base","Description":"Run basic pattern analyses on character sets,
digits, or combined\ninput containing
both characters and numeric digits. Useful for data\ncleaning and for identifying
columns containing multiple or nonstandard\nformats.","Imports":"magrittr,
2)","NeedsCompilation":"no","Package":"bpa","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"testthat, knitr, rmarkdown","Title":"Basic Pattern
Analysis","URL":"https:\/\/github.com\/bgreenwell\/bpa","Version":"0.1.1"},"bpca":
{"Author":"José Cláudio Faria, Clarice Garcia Borges Demétrio and Ivan Bezerra
Allaman","Depends":"R (>= 2.6.0), scatterplot3d, rgl","Description":"Implements
biplot (2d and 3d) of multivariate data based\non principal components analysis and
diagnostic tools of the quality of the reduction.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"bpca","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Biplot of Multivariate Data Based on Principal
Components\nAnalysis","Version":"1.2-2"},"bpcp":{"Author":"Michael P.
Fay","Depends":"stats","Description":"Calculates nonparametric pointwise confidence
intervals for the survival distribution for right censored data. Has two-sample
tests for dissimilarity (e.g., difference, ratio or odds ratio) in survival at a
fixed time. Especially important for small sample sizes or heavily censored data.
Includes mid-p options.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"bpcp","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"survival","Title":"Beta Product Confidence Procedure for
Right Censored Data","Version":"1.3.2"},"bpkde":{"Author":"Kjell Konis
<kjell.konis@me.com>,\nVictor M. Panaretos
<victor.panaretos@epfl.ch>.","Description":"Nonparametric multivariate kernel
density \\\nestimation using a back-projected kernel.","License":"GPL-
2","NeedsCompilation":"yes","Package":"bpkde","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"mvtnorm, KernSmooth","Title":"Back-Projected Kernel
Density Estimation","Version":"1.0-7"},"bqtl":{"Author":"Charles C. Berry
<cberry@ucsd.edu>","Depends":"R (>= 2.6.0)","Description":"QTL mapping toolkit for
inbred crosses and recombinant\ninbred lines. Includes maximum likelihood and
Bayesian tools.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"bqtl","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Bayesian QTL Mapping
Toolkit","URL":"http:\/\/famprevmed.ucsd.edu\/faculty\/cberry\/bqtl\/","Version":"1
.0-32"},"braQCA":{"Author":"C. Ben Gibson [aut, cre],\nBurrel Vann Jr
[aut]","Depends":"R (>= 3.2.3), QCAGUI, bootstrap","Description":"Test the
robustness of a user's Qualitative Comparative Analysis solutions to randomness,
using the bootstrapped assessment: baQCA(). This package also includes a function
that provides recommendations for improving solutions to reach typical significance
levels: brQCA().","License":"GPL-
2","NeedsCompilation":"no","Package":"braQCA","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Bootstrapped Robustness Assessment for Qualitative
Comparative\nAnalysis","Version":"0.9.7.0"},"braidReports":{"Author":"Nathaniel R.
Twarog","Depends":"ggplot2, braidrm, stats","Description":"Provides functions to
generate, format, and style surface plots for visualizing combined action data.
Also provides functions for reporting on a BRAID analysis, including plotting
curve-shifts, calculating IAE values, and producing full BRAID analysis
reports.","Imports":"utils, grid","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"braidReports","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"gtable, gridExtra (>= 2.0.0)","Title":"Visualize
Combined Action Response Surfaces and Report
BRAID\nAnalyses","Version":"0.5.3"},"braidrm":{"Author":"Nathaniel R.
Twarog","Depends":"stats","Description":"Contains functions for evaluating,
analyzing, and fitting combined action dose response surfaces with the Bivariate
Response to Additive Interacting Dose (BRAID) model of combined
action.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"braidrm","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Fitting Dose Response with the BRAID Combined Action
Model","Version":"0.71"},"brainGraph":{"Author":"Christopher G. Watson
<cgwatson@bu.edu>","Depends":"R (>= 3.0.0), igraph (>= 1.0.0), RGtk2,
cairoDevice","Description":"A set of tools for performing graph theory analysis of
brain MRI\ndata. It is best suited to data from a Freesurfer analysis
(cortical\nthickness, volumes, local gyrification index, surface area), but also
works\nwith e.g., tractography data from FSL. It contains a graphical
user\ninterface for graph visualization and data exploration.","Imports":"abind,
ade4, boot, data.table, foreach, ggplot2, Hmisc,\nmethods, oro.nifti, parallel,
plyr, scales","License":"GPL-
3","NeedsCompilation":"no","Package":"brainGraph","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Graph Theory Analysis of Brain MRI
Data","URL":"https:\/\/github.com\/cwatson\/brainGraph","Version":"0.55.0"},"brainR
":{"Author":"John Muschelli III","Depends":"rgl, misc3d,
oro.nifti","Description":"This includes functions for creating 3D and 4D images
using WebGL, RGL, and JavaScript Commands. This package relies on the X ToolKit
(XTK, https:\/\/github.com\/xtk\/X#readme).","License":"GPL-
2","NeedsCompilation":"no","Package":"brainR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Helper functions to misc3d and rgl packages for brain
imaging","Version":"1.2"},"brainwaver":{"Author":"Sophie Achard
<sophie.achard@gipsa-lab.inpg.fr>","Depends":"R (>= 1.10.0),
waveslim","Description":"This package computes the correlation matrix for
each\nscale of a wavelet decomposition, namely the one performed by\nthe R package
waveslim (Whitcher, 2000). An hypothesis test is\napplied to each entry of one
matrix in order to construct an\nadjacency matrix of a graph. The graph obtained is
finally\nanalysed using the small-world theory (Watts and Strogatz,\n1998) and
using the computation of efficiency (Latora, 2001),\ntested using simulated
attacks. The brainwaver project is\ncomplementary to the camba project for brain-
data\npreprocessing. A collection of scripts (with a makefile) is\navalaible to
download along with the brainwaver package, see\ninformation on the webpage
mentioned below.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"brainwaver","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Basic wavelet analysis of multivariate time series
with a\nvisualisation and parametrisation using graph
theory","URL":"http:\/\/www.gipsa-lab.grenoble-
inp.fr\/~sophie.achard\/","Version":"1.6"},"breakage":{"Author":"Matthew Caldwell
<m.caldwell@ucl.ac.uk>","Depends":"Imap","Description":"Estimates geometry of SICM
pipette tips by fitting a physical model to recorded breakage-current
data.","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"breakage","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"SICM pipette tip geometry estimation","Version":"1.1-
1"},"breakaway":{"Author":"Amy Willis and John Bunge","Description":"Species
richness estimation is an important problem in biodiversity analysis. This package
provides methods for total species richness estimation (observed plus unobserved)
and a method for modelling total diversity with covariates. breakaway() estimates
total (observed plus unobserved) species richness. Microbial diversity datasets are
characterized by a large number of rare species and a small number of highly
abundant species. The class of models implemented by breakaway() is flexible enough
to model both these features. breakaway_nof1() implements a similar procedure
however does not require a singleton count. betta() provides a method for modelling
total diversity with covariates in a way that accounts for its estimated nature and
thus accounts for unobserved taxa, and betta_random() permits random effects
modelling.","License":"GPL-
2","NeedsCompilation":"no","Package":"breakaway","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Species Richness Estimation and
Modeling","Version":"3.0"},"breakpoint":{"Author":"Priyadarshana W.J.R.M. and
Georgy Sofronov","Depends":"R (>= 2.5)","Description":"Implements the Cross-Entropy
(CE) method, which is a model based stochastic optimization technique to estimate
both the number and their corresponding locations of break-points in continuous and
discrete measurements (Priyadarshana and Sofronov (2015), Priyadarshana and
Sofronov (2012a), Priyadarshana and Sofronov (2012b)).","Imports":"ggplot2 (>=
1.0.0), MASS, msm (>= 1.0.1), foreach (>= 1.2.0),\nparallel, doParallel (>=
1.0.10)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"breakpoint","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"An R Package for Multiple Break-Point Detection via
the\nCross-Entropy
Method","URL":"https:\/\/github.com\/madawaweer\/breakpoint","Version":"1.2"},"brew
":{"Author":"Jeffrey Horner","Description":"brew implements a templating framework
for mixing text and\nR code for report generation. brew template syntax is
similar\nto PHP, Ruby's erb module, Java Server Pages, and Python's
psp\nmodule.","License":"GPL-
2","NeedsCompilation":"no","Package":"brew","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Templating Framework for Report Generation","Version":"1.0-
6"},"brewdata":{"Author":"Nathan Welch","Depends":"RCurl, XML, stringdist,
tools","Description":"Retrieves and parses graduate admissions survey data from the
Grad Cafe website (http:\/\/thegradcafe.com).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"brewdata","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"rgl, scatterplot3d","Title":"Extracting Usable Data
from the Grad Cafe Results Search","Version":"0.4"},"brglm":{"Author":"Ioannis
Kosmidis <i.kosmidis@ucl.ac.uk>","Depends":"R (>= 2.6.0),
profileModel","Description":"Fit generalized linear
models with binomial responses using either an adjusted-score approach to bias
reduction or maximum penalized likelihood where penalization is by Jeffreys
invariant prior. These procedures return estimates with improved frequentist
properties (bias, mean squared error) that are always finite even in cases where
the maximum likelihood estimates are infinite (data separation). Fitting takes
place by fitting generalized linear models on iteratively updated pseudo-data. The
interface is essentially the same as 'glm'. More flexibility is provided by the
fact that custom pseudo-data representations can be specified and used for model
fitting. Functions are provided for the construction of confidence intervals for
the reduced-bias estimates.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"brglm","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"MASS","Title":"Bias reduction in binomial-response
generalized linear
models","URL":"http:\/\/www.ucl.ac.uk\/~ucakiko\/index.html","Version":"0.5-
9"},"bride":{"Author":"Stefan Siegert","Description":"Decomposes the empirical
Brier score into reliability, resolution and uncertainty. Two different estimators
for the components are provided: The original estimators proposed by Murphy (1974),
and the bias-corrected estimators proposed by Ferro and Fricker (2012). Sampling
variances of all the components are estimated. This package applies only to
probabilistic predictions of binary events.","License":"GPL-
2","NeedsCompilation":"no","Package":"bride","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Brier score decomposition of probabilistic forecasts for
binary\nevents","Version":"1.3"},"brms":{"Author":"Paul-Christian Buerkner [aut,
cre]","Depends":"R (>= 3.1.0), rstan (>= 2.9.0), ggplot2 (>= 2.0.0),
methods","Description":"Fit Bayesian generalized (non-)linear mixed models using
Stan for full\nBayesian inference.","Imports":"loo (>= 0.1.4), shinystan (>=
2.1.0), gridExtra (>= 2.0.0),\nlme4 (>= 1.1-11), Matrix (>= 1.1.1), coda, abind,
statmod,\nstats, graphics, utils, parallel, grDevices, grid","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"brms","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat (>= 0.9.1), mvtnorm, KernSmooth, R.rsp,
knitr,\nrmarkdown","Title":"Bayesian Regression Models using
Stan","URL":"http:\/\/github.com\/paul-buerkner\/brms","Version":"0.8.0"},"brnn":
{"Author":"Paulino Perez Rodriguez, Daniel Gianola","Depends":"R (>= 3.1.2),
Formula","Description":"Bayesian regularization for feed-forward neural
networks.","License":"GPL-
2","NeedsCompilation":"yes","Package":"brnn","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Bayesian Regularization for Feed-Forward Neural
Networks","Version":"0.6"},"broman":{"Author":"Karl W Broman
<kbroman@biostat.wisc.edu>, with contributions from Aimee\nTeo Broman","Depends":"R
(>= 2.15.0)","Description":"Miscellaneous R functions.","Imports":"utils, graphics,
grDevices, stats, assertthat, RPushbullet,\njsonlite, ggplot2,
3","NeedsCompilation":"yes","Package":"broman","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat, devtools, roxygen2","Title":"Karl Broman's R
Code","URL":"https:\/\/github.com\/kbroman\/broman","Version":"0.62-1"},"broom":
{"Author":"David Robinson [aut, cre],\nMatthieu Gomez [ctb],\nBoris Demeshev
[ctb],\nDieter Menne [ctb],\nBenjamin Nutter [ctb],\nLuke Johnston [ctb],\nBen
Bolker [ctb],\nFrancois Briatte [ctb],\nHadley Wickham
[ctb]","Description":"Convert statistical analysis objects from R into tidy data
frames,\nso that they can more easily be combined, reshaped and otherwise
processed\nwith tools like 'dplyr', 'tidyr' and 'ggplot2'. The package provides
three S3\ngenerics: tidy, which summarizes a model's statistical findings such
as\ncoefficients of a regression; augment, which adds columns to the original\ndata
such as predictions, residuals and cluster assignments; and glance,\nwhich provides
a one-row summary of model-level statistics.","Imports":"plyr, dplyr, tidyr, psych,
stringr, reshape2, nlme","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"broom","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr, boot, survival, gam, glmnet, lfe, Lahman,
MASS, sp,\nmaps, maptools, multcomp, testthat, lme4, zoo, lmtest, plm,\nbiglm,
ggplot2, nnet, geepack, AUC, ergm, network,\nstatnet.common, xergm, btergm,
binGroup, Hmisc, bbmle, gamlss,\nrstan, coda","Title":"Convert Statistical Analysis
Objects into Tidy Data
Frames","URL":"http:\/\/github.com\/dgrtwo\/broom","Version":"0.4.0"},"brotli":
{"Author":"Jeroen Ooms [aut, cre],\nGoogle, Inc [aut, cph] (Brotli C++
library)","Description":"A lossless compressed data format that uses a combination
of the\nLZ77 algorithm and Huffman coding. Brotli is similar in speed to deflate
(gzip)\nbut offers more dense compression.","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"brotli","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"knitr, R.rsp, microbenchmark, ggplot2","Title":"A
Compression Format Optimized for the Web","URL":"http:\/\/www.ietf.org\/id\/draft-
alakuijala-brotli\nhttps:\/\/github.com\/google\/brotli","Version":"0.6"},"brr":
{"Author":"StÃ©phane Laurent","Depends":"R (>=
3.0.0)","Description":"Implementation of the Bayesian inference for the two
independent Poisson samples model, using the semi-conjugate family of prior
distributions.","Imports":"gsl, SuppDists, TeachingDemos, hypergeo, pander,
stringr,\nmethods","License":"GPL-
2","NeedsCompilation":"no","Package":"brr","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"testthat, R.rsp, magrittr","Title":"Bayesian Inference on
the Ratio of Two Poisson Rates","Version":"1.0.0"},"brranching":{"Author":"Scott
Chamberlain [aut, cre]","Description":"Includes methods for fetching 'phylogenies'
from a variety\nof sources, currently includes
'Phylomatic'\n(http:\/\/phylodiversity.net\/phylomatic\/), with more in the
future.","Imports":"httr, ape, taxize","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"brranching","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Fetch 'Phylogenies' from
Many
Sources","URL":"https:\/\/github.com\/ropensci\/brranching","Version":"0.1.0"},"bsh
azard":{"Author":"Paola Rebora,Agus Salim, Marie Reilly","Depends":"R(>=
3.0.2),splines,survival,Epi","Description":"The function estimates the hazard
function non parametrically from a survival object (possibly adjusted for
covariates). The smoothed estimate is based on B-splines from the perspective of
generalized linear mixed models. Left truncated and right censoring data are
allowed.","License":"GPL-
2","NeedsCompilation":"no","Package":"bshazard","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Nonparametric Smoothing of the Hazard
Function","Version":"1.0"},"bspec":{"Author":"Christian
Roever","Description":"Bayesian inference on the (discrete) power spectrum of time
series.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"bspec","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Bayesian Spectral Inference","Version":"1.5"},"bspmma":
{"Author":"Deborah Burr","Description":"Some functions for nonparametric and
semiparametric\nBayesian models for random effects meta-analysis","License":"GPL-
2","NeedsCompilation":"no","Package":"bspmma","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"bspmma: Bayesian Semiparametric Models for Meta-
Analysis","Version":"0.1-1"},"bssn":{"Author":"Rocio Paola Maehara
<rmaeharaa@gmail.com> and Luis Benites Sanchez
<lbenitesanchez@gmail.com>","Description":"It provides the density, distribution
function, quantile function, random number generator, reliability function, failure
rate, likelihood function,\nmoments and EM algorithm for Maximum Likelihood
estimators, also empirical quantile and generated envelope for a given sample, all
this for the three parameter\nBirnbaum-Saunders model based on Skew-Normal
Distribution.\nAdditionally, it provides the random number generator for the
mixture of Birnbaum-Saunders model based on Skew-Normal
distribution.","Imports":"sn","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"bssn","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Birnbaum-Saunders Model Based on Skew-Normal
Distribution","Version":"0.7"},"bst":{"Author":"Zhu Wang [aut, cre],\nTorsten
Hothorn [ctb]","Depends":"gbm","Description":"Functional gradient descent algorithm
for a variety of convex and nonconvex loss functions, for both classical and robust
regression and classification problems. HingeBoost is implemented for binary and
multi-class classification, with unequal misclassification costs for binary case.
The algorithm can fit linear and nonlinear classifiers.","Imports":"rpart, methods,
foreach, doParallel","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"bst","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"hdi, pROC, R.rsp, knitr","Title":"Gradient
Boosting","Version":"0.3-13"},"bsts":{"Author":"Steven L. Scott
<stevescott@google.com>","Depends":"BoomSpikeSlab (>= 0.5.3), zoo, xts, Boom (>=
0.3), R(>= 3.1.0)","Description":"Time series regression using dynamic linear
models fit using MCMC.","License":"LGPL-2.1 | file
LICENSE","NeedsCompilation":"yes","Package":"bsts","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Bayesian Structural Time
Series","Version":"0.6.3"},"btergm":{"Author":"Philip Leifeld [aut, cre],\nSkyler
J. Cranmer [ctb],\nBruce A. Desmarais [ctb]","Depends":"R (>= 2.14.0), xergm.common
(>= 1.7.0)","Description":"Temporal Exponential Random Graph Models (TERGM)
estimated by maximum pseudolikelihood with bootstrapped confidence intervals or
Markov Chain Monte Carlo maximum likelihood. Goodness of fit assessment for ERGMs,
TERGMs, and SAOMs.
Micro-level interpretation of ERGMs and TERGMs.","Imports":"stats4, utils,
methods, graphics, statnet (>= 2015.11.0),\nstatnet.common (>= 3.3.0), network (>=
1.13.0), sna (>= 2.3.2),\nergm (>= 3.5.1), texreg (>= 1.34.4), parallel, Matrix
(>=\n1.2.2), boot (>= 1.3.17), coda (>= 0.18.1), stats, ROCR (>=\n1.0.7), speedglm
(>= 0.3.1), igraph (>= 0.7.1)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"btergm","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"RSiena (>= 1.0.12.169), xergm","Title":"Temporal
Exponential Random Graph Models by
Bootstrapped\nPseudolikelihood","Version":"1.7.0"},"btf":{"Author":"Edward A.
Roualdes","Depends":"R (>= 3.1.0)","Description":"Trend filtering uses the
generalized\nlasso framework to fit an adaptive polynomial of degree k to\nestimate
the function f_0 at each input x_i in the model: y_i =\nf_0(x_i) + epsilon_i, for i
= 1, ..., n, and epsilon_i\nis sub-Gaussian with E(epsilon_i) = 0. Bayesian trend
filtering adapts\nthe genlasso framework to a fully Bayesian hierarchical model,
estimating\nthe penalty parameter lambda within a tractable Gibbs
sampler.","Imports":"Matrix, coda,","License":"GPL (>=
2.0)","NeedsCompilation":"yes","Package":"btf","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Estimates univariate function via Bayesian trend
filtering","Version":"1.1"},"bujar":{"Author":"Zhu Wang and others (see
COPYRIGHTS)","Depends":"R (>= 2.10)","Description":"Buckley-James regression for
right-censoring survival data with high-dimensional covariates. Implementations for
survival data include boosting with componentwise linear least squares,
componentwise smoothing splines, regression trees and MARS. Other high-dimensional
tools include penalized regression for survival data.","Imports":"mda, mpath,
mboost, gbm, earth, elasticnet, rms, methods,\nmodeltools, bst,
2","NeedsCompilation":"no","Package":"bujar","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"TH.data, survival, R.rsp","Title":"Buckley-James
Regression for Survival Data with High-Dimensional\nCovariates","Version":"0.2-
1"},"bursts":{"Author":"Jeff Binder [aut, cre]","Description":"An implementation of
Jon Kleinberg's burst detection algorithm. Uses an infinite Markov model to detect
periods of increased activity in a series of discrete events with known times, and
provides a simple visualization of the results.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"bursts","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Markov model for bursty behavior in
streams","Version":"1.0-1"},"bvarsv":{"Author":"Fabian
Krueger","Description":"R\/C++ implementation of the model proposed by Primiceri
(\"Time Varying Structural Vector Autoregressions and Monetary Policy\", Review of
Economic Studies, 2005), with functionality for computing posterior predictive
distributions and impulse responses.","Imports":"Rcpp (>= 0.11.0)","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"bvarsv","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Bayesian Analysis of a Vector Autoregressive Model
with\nStochastic Volatility and Time-Varying
Parameters","URL":"https:\/\/sites.google.com\/site\/fk83research\/code","Version":
"1.1"},"bvenn":{"Author":"Raivo Kolde
<rkolde@gmail.com>","Depends":"grid","Description":"This package implements a
simple alternative to the\ntraditional Venn diagram. It depicts each overlap as a
separate\nbubble with area proportional to the overlap size. Relation of\nthe
bubbles to input sets is shown by their their arrangement.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"bvenn","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"A Simple alternative to proportional Venn
diagrams","Version":"0.1"},"bvls":{"Author":"Katharine M. Mullen","Description":"An
R interface to the Stark-Parker implementation of an\nalgorithm for bounded-
variable least squares","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"bvls","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"The Stark-Parker algorithm for bounded-variable least
squares","Version":"1.4"},"bvpSolve":{"Author":"Karline Soetaert
<karline.soetaert@nioz.nl>,\nJeff Cash <j.cash@imperial.ac.uk>,\nFrancesca Mazzia
<mazzia@dm.uniba.it>","Depends":"R (>= 2.01), deSolve","Description":"Functions
that solve boundary value problems ('BVP') of systems of ordinary\ndifferential
equations ('ODE') and differential algebraic equations ('DAE').\nThe functions
provide an interface to the FORTRAN functions\n'twpbvpC', 'colnew\/colsys', and an
R-implementation of the shooting method.","Imports":"rootSolve, stats, graphics,
2)","NeedsCompilation":"yes","Package":"bvpSolve","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Solvers for Boundary Value Problems of Differential
Equations","Version":"1.3.2"},"c060":{"Author":"Martin Sill, Thomas Hielscher,
Manuela Zucknick, Natalia Becker.","Description":"c060 provides additional
functions to perform stability selection, model validation and parameter tuning for
glmnet models","Imports":"glmnet, survival, parallel, mlegp, tgp, peperr,
penalizedSVM,\nlattice","License":"GPL-
2","NeedsCompilation":"no","Package":"c060","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Extended Inference for Lasso and Elastic-Net Regularized Cox
and\nGeneralized Linear Models","Version":"0.2-4"},"c3net":{"Author":"Gokmen Altay,
Frank Emmert-Streib","Depends":"R (>= 2.12.1), igraph","Description":"This package
allows inferring gene regulatory networks\nwith direct physical interactions from
microarray expression\ndata using C3NET.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"c3net","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Infering large-scale gene networks with
C3NET","Version":"1.1.1"},"cAIC4":{"Author":"Benjamin Saefken and David Ruegamer,
with contributions from Sonja Greven and Thomas Kneib","Depends":"lme4(>= 1.1-6),
methods, Matrix","Description":"Provides functions for the estimation of the
conditional Akaike\ninformation in generalized mixed-effects models fitted with
(g)lmer\nform lme4.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"cAIC4","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"gamm4","Title":"Conditional Akaike information criterion
for lme4","Version":"0.2"},"cIRT":{"Author":"Steve Culpepper [aut, cph],\nJames
Balamuta [aut, cre, ctb, com, cph]","Description":"Jointly model the accuracy of
cognitive responses and item choices within a bayesian hierarchical framework as
described by Culpepper and Balamuta (2015) <doi:10.1007\/s11336-015-9484-7>. In
addition, the package contains the datasets used within the analysis of the
paper.","Imports":"Rcpp (>= 0.12.2)","License":"GPL-
3","NeedsCompilation":"yes","Package":"cIRT","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Choice Item Response Theory","Version":"1.1.0"},"cOde":
{"Author":"Daniel Kaschek","Depends":"R (>= 3.0)","Description":"Generates all
necessary C functions allowing the user to work with the compiled-code interface of
ode() and bvptwp(). The implementation supports \"forcings\" and \"events\". Also
provides functions to symbolically compute Jacobians, sensitivity equations and
adjoint sensitivities being the basis for sensitivity analysis.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"cOde","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"deSolve, bvpSolve","Title":"Automated C Code Generation
for Use with the 'deSolve' and\n'bvpSolve' Packages","Version":"0.2.1"},"cSFM":
{"Author":"Meng Li, Ana-Maria Staicu, and Howard D. Bondell","Depends":"R (>=
2.15.3), sn","Description":"cSFM is a method to model skewed functional data when
considering covariates via a copula-based approach.","Imports":"mgcv, mnormt, MASS,
moments, splines","License":"GPL-
2","NeedsCompilation":"no","Package":"cSFM","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Covariate-adjusted Skewed Functional Model
(cSFM)","Version":"1.1"},"ca":{"Author":"Michael Greenacre [aut], Oleg Nenadic
[aut, cre], Michael Friendly [ctb]","Depends":"R (>=
2.8.0)","Description":"Computation and visualization of simple, multiple and joint
correspondence
analysis.","License":"GPL","NeedsCompilation":"no","Package":"ca","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Suggests":"rgl (>= 0.64-10),
vcd","Title":"Simple, Multiple and Joint Correspondence
Analysis","URL":"http:\/\/www.carme-n.org\/","Version":"0.64"},"caRpools":
{"Author":"Jan Winter, Florian Heigwer","Depends":"R (>=
3.1.0)","Description":"CRISPR-Analyzer for pooled CRISPR screens (caRpools)
provides an end-to-end analysis of CRISPR screens including quality control, hit
candidate analysis, visualization and automated report generation using R markdown.
Needs MAGeCK (http:\/\/sourceforge.net\/p\/mageck\/wiki\/Home\/), bowtie2 for all
functions. CRISPR (clustered regularly interspaced short palindromic repeats) is a
method to perform genome editing. See <https:\/\/en.wikipedia.org\/wiki\/CRISPR>
for more information
on\nCRISPR.","Imports":"\nrmarkdown,VennDiagram,DESeq2,sm,biomaRt,seqinr,scatterplo
t3d,xlsx","License":"GPL","NeedsCompilation":"no","Package":"caRpools","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"BiocGenerics,knitr,stringi","Ti
tle":"CRISPR AnalyzeR for Pooled CRISPR Screens","URL":"http:\/\/www.crispr-
analyzer.de,\nhttps:\/\/github.com\/boutroslab\/caRpools","Version":"0.83"},"caTool
s":{"Author":"Jarek Tuszynski <jaroslaw.w.tuszynski@saic.com>","Depends":"R (>=
2.2.0)","Description":"Contains several basic utility functions including:
moving\n(rolling, running) window statistic functions, read\/write for\nGIF and
ENVI binary files, fast calculation of AUC, LogitBoost\nclassifier, base64
encoder\/decoder, round-off-error-free
sum\nand cumsum, etc.","Imports":"bitops","License":"GPL-
3","NeedsCompilation":"yes","Package":"caTools","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"MASS, rpart","Title":"Tools: moving window statistics,
GIF, Base64, ROC AUC, etc","Version":"1.17.1"},"cabootcrs":{"Author":"T.J.
Ringrose","Description":"Performs correspondence analysis on a two-way
contingency\ntable and produces bootstrap-based elliptical confidence\nregions
around the projected coordinates for the category\npoints. Includes routines to
plot the results in a variety of\nstyles. Also reports the standard numerical
output for\ncorrespondence analysis.","Imports":"methods, utils","License":"GPL-
2","NeedsCompilation":"no","Package":"cabootcrs","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Bootstrap Confidence Regions for Correspondence
Analysis","Version":"1.0"},"cacIRT":{"Author":"Quinn N.
Lathrop","Description":"Computes classification accuracy and consistency indices
under Item Response Theory. Implements the total score IRT-based methods in Lee,
Hanson & Brennen (2002) and Lee (2010), the IRT-based methods in Rudner (2001,
2005), and the total score nonparametric methods in Lathrop & Cheng (2014). For
dichotomous and polytomous tests.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"cacIRT","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Classification Accuracy and Consistency under Item
Response\nTheory","Version":"1.4"},"cairoDevice":{"Author":"Michael
Lawrence","Depends":"R (>= 2.12.0)","Description":"This device uses Cairo and GTK
to draw to the screen,\nfile (png, svg, pdf, and ps) or memory (arbitrary
GdkDrawable\nor Cairo context). The screen device may be embedded into
RGtk2\ninterfaces and supports all interactive features of other graphics\ndevices,
including
getGraphicsEvent().","Imports":"grDevices","License":"GPL","NeedsCompilation":"yes"
,"Package":"cairoDevice","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title
":"Embeddable Cairo Graphics Device Driver","Version":"2.23"},"calACS":
{"Author":"Alan Gu","Description":"Implements several string comparison algorithms,
including calACS (count all common subsequences), lenACS (calculate the lengths of
all common subsequences), and lenLCS (calculate the length of the longest common
subsequence). Some algorithms differentiate between the more strict definition of
subsequence, where a common subsequence cannot be separated by any other items,
from its looser counterpart, where a common subsequence can be interrupted by other
items. This difference is shown in the suffix of the algorithm (-Strict vs -Loose).
For example, q-w is a common subsequence of q-w-e-r and q-e-w-r on the looser
definition, but not on the more strict definition. calACSLoose Algorithm from Wang,
H. All common subsequences (2007) IJCAI International Joint Conference on
Artificial Intelligence, pp. 635-
640.","License":"GPL","NeedsCompilation":"no","Package":"calACS","Repository":"http
:\/\/cran.csiro.au\/src\/contrib","Title":"Calculations for All Common
Subsequences","Version":"2.2.2"},"calibrar":{"Author":"Ricardo Oliveros-Ramos [aut,
cre]","Depends":"R (>= 2.15)","Description":"Automated parameter estimation for
complex (ecological) models in R.\nThis package allows the parameter estimation or
calibration of complex models,\nincluding stochastic ones. It is a generic tool
that can be used for fitting\nany type of models, especially those with non-
differentiable objective functions.\nIt supports multiple phases and constrained
optimization.\nIt implements maximum likelihood estimation methods and automated
construction\nof the objective function from simulated model outputs.\nSee
<http:\/\/roliveros-ramos.github.io\/calibrar> for more details.","Imports":"cmaes,
optimx, foreach, parallel, stats, utils","License":"GPL-
2","NeedsCompilation":"no","Package":"calibrar","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"deSolve","Title":"Automated Parameter Estimation for
Complex (Ecological) Models","URL":"http:\/\/roliveros-
ramos.github.io\/calibrar","Version":"0.2.0"},"calibrate":{"Author":"Jan Graffelman
<jan.graffelman@upc.edu>","Depends":"R (>= 1.8.0), MASS","Description":"Package for
drawing calibrated scales with tick marks on (non-orthogonal)\nvariable vectors in
scatterplots and biplots.","License":"GPL-
2","NeedsCompilation":"no","Package":"calibrate","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Calibration of Scatterplot and Biplot
Axes","Version":"1.7.2"},"calibrator":{"Author":"Robin K. S. Hankin","Depends":"R
(>= 2.0.0), emulator (>= 1.2-11)","Description":"Performs Bayesian calibration of
computer models as per\nKennedy and O'Hagan 2001. The package includes routines to
find the\nhyperparameters and parameters; see the help page for stage1() for
a\nworked example using the toy dataset. A tutorial is provided in the\ncalex.Rnw
vignette; and a suite of especially simple one dimensional\nexamples appears in
inst\/doc\/one.dim\/.","Imports":"cubature","License":"GPL","NeedsCompilation":"no"
,"Package":"calibrator","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title"
:"Bayesian calibration of complex computer codes","Version":"1.2-6"},"calmate":
{"Author":"Maria Ortiz [aut, ctb],\nAnder Aramburu [ctb],\nHenrik Bengtsson [aut,
cre, cph],\nPierre Neuvial [aut, ctb],\nAngel Rubio [aut, ctb]","Depends":"R (>=
3.0.3), R.utils (>= 2.1.0), aroma.core (>= 2.14.0)","Description":"A multi-array
post-processing method of allele-specific copy-number estimates
(ASCNs).","Imports":"utils, MASS, R.methodsS3 (>= 1.7.0), R.oo (>=
1.19.0),\nmatrixStats (>= 0.14.2), R.filesets (>= 2.9.0)","License":"LGPL (>=
2.1)","NeedsCompilation":"no","Package":"calmate","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"DNAcopy","Title":"Improved Allele-Specific Copy
Number of SNP Microarrays for\nDownstream
Segmentation","URL":"https:\/\/github.com\/HenrikBengtsson\/calmate\/","Version":"0
.12.1"},"camel":{"Author":"Xingguo Li, Tuo Zhao, and Han Liu","Depends":"R (>=
2.15.0), lattice, igraph, MASS, Matrix","Description":"The package \"camel\"
provides the implementation of a family of high-dimensional calibrated machine
learning tools, including (1) LAD, SQRT Lasso and Calibrated Dantzig Selector for
estimating sparse linear models; (2) Calibrated Multivariate Regression for
estimating sparse multivariate linear models; (3) Tiger, Calibrated Clime for
estimating sparse Gaussian graphical models. We adopt the combination of the dual
smoothing and monotone fast iterative soft-thresholding algorithm (MFISTA). The
computation is memory-optimized using the sparse matrix output, and accelerated by
the path following and active set tricks.","License":"GPL-
2","NeedsCompilation":"yes","Package":"camel","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Calibrated Machine Learning","Version":"0.2.0"},"camtrapR":
{"Author":"Juergen Niedballa [aut, cre],\nAlexandre Courtiol [aut],\nRahel Sollmann
[aut],\nJohn Mathai [ctb],\nSeth Timothy Wong [ctb],\nAn The Truong Nguyen
[ctb],\nAzlan bin Mohamed [ctb],\nAndrew Tilker [ctb],\nAndreas Wilting [ctb,
ths]","Depends":"R (>= 3.1.0)","Description":"Management of and data extraction
from camera trap photographs in wildlife studies. The package provides a workflow
for storing and sorting camera trap photographs, computes record databases and
detection\/non-detection matrices for occupancy and spatial capture-recapture
analyses with great flexibility. In addition, it provides simple mapping functions
(number of species, number of independent species detections by station) and can
visualise activity data.","Imports":"methods, overlap, secr, rgdal,
2)","NeedsCompilation":"no","Package":"camtrapR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"unmarked","Title":"Camera Trap Data Management and
Preparation of Occupancy and\nSpatial Capture-Recapture
Analyses","Version":"0.98.0"},"cancerGI":{"Author":"Audrey Qiuyan Fu and Xiaoyue
Wang","Depends":"R (>= 2.10)","Description":"Functions to perform the following
analyses: i) inferring epistasis from RNAi double knockdown data; ii) identifying
gene pairs of multiple mutation patterns; iii) assessing association between gene
pairs and survival; and iv) calculating the smallworldness of a graph (e.g., a gene
interaction network). Data and analyses are described in Wang, X., Fu, A. Q.,
McNerney, M. and White, K. P. (2014). Widespread genetic epistasis among breast
cancer genes. Nature Communications. 5 4828.
<doi:10.1038\/ncomms5828>.","Imports":"systemfit, qvalue, survival, reshape2,
igraph","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"cancerGI","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Analyses of Cancer Gene
Interaction","Version":"1.0.0"},"cancerTiming":{"Author":"Elizabeth
Purdom","Depends":"R (>= 2.11.0)","Description":"Timing copy number changes using
estimates of mutational allele frequency from resequencing of tumor
samples.","Imports":"utils, stats, grDevices, graphics, LearnBayes,
2)","NeedsCompilation":"no","Package":"cancerTiming","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"GenomicRanges, IRanges,
S4Vectors","Title":"Estimation of Temporal Ordering of Cancer
Abnormalities","Version":"3.1.8"},"candisc":{"Author":"Michael Friendly [aut, cre],
John Fox [aut]","Depends":"R (>= 2.10), car, heplots (>= 0.8.6), graphics,
stats","Description":"Functions for computing and visualizing\ngeneralized
canonical discriminant analyses and canonical correlation analysis\nfor a
multivariate linear model.\nTraditional canonical discriminant analysis is
restricted to a one-way 'MANOVA'\ndesign and is equivalent to canonical correlation
analysis between a set of quantitative\nresponse variables and a set of dummy
variables coded from the factor variable.\nThe
'candisc' package generalizes this to higher-way 'MANOVA' designs\nfor all factors
in a multivariate linear model,\ncomputing canonical scores and vectors for each
term. The graphic functions provide low-rank (1D, 2D, 3D)\nvisualizations of terms
in an 'mlm' via the 'plot.candisc' and 'heplot.candisc' methods. Related plots
are\nnow provided for canonical correlation analysis when all predictors are
quantitative.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"candisc","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"rgl, corrplot","Title":"Visualizing Generalized
Canonical Discriminant and Canonical\nCorrelation Analysis","Version":"0.6-
7"},"cape":{"Author":"Anna L. Tyler, Wei Lu, Justin J. Hendrick, Vivek M. Philip,
and Greg W.\nCarter","Depends":"R (>= 3.2.2)","Description":"Combines complementary
information across multiple related\nphenotypes to infer directed epistatic
interactions between genetic markers.\nThis analysis can be applied to a variety of
engineered and natural populations.","Imports":"grDevices, graphics, stats, utils,
corpcor, evd, qpcR, Matrix,\nigraph, fdrtool, shape, parallel, doParallel,
RColorBrewer,\nforeach, HardyWeinberg, regress","License":"GPL-
3","NeedsCompilation":"no","Package":"cape","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Combined Analysis of Pleiotropy and
Epistasis","Version":"2.0.1"},"caper":{"Author":"David Orme, Rob Freckleton, Gavin
Thomas, Thomas Petzoldt, Susanne Fritz, Nick Isaac, Will Pearse","Depends":"R (>=
2.10), ape (>= 3.0-6) , MASS, mvtnorm","Description":"Functions for performing
phylogenetic comparative analyses.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"caper","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"xtable","Title":"Comparative Analyses of Phylogenetics
and Evolution in R","Version":"0.5.2"},"capm":{"Author":"Oswaldo Santos Baquero
[aut, cre],\nMarcos Amaku [ctb],\nFernando Ferreira [ctb]","Depends":"R (>=
3.2.2)","Description":"Quantitative analysis to support companion animal
population\nmanagement.","Imports":"deSolve, FME, survey, ggplot2, reshape2, shiny,
grid, rgdal,\nmaptools, sp","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"capm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Companion Animal Population
Management","URL":"http:\/\/oswaldosantos.github.io\/capm","Version":"0.9.1"},"capt
ioner":{"Author":"Letaw Alathea [aut, cre]","Description":"Provides a method for
automatically numbering figures,\ntables, or other objects. Captions can be
displayed in full, or as citations.\nThis is especially useful for adding figures
and tables to R markdown\ndocuments without having to numbering them
manually.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"captioner","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"knitr","Title":"Numbers Figures and Creates
Simple
Captions","URL":"https:\/\/github.com\/adletaw\/captioner","Version":"2.2.3"},"capt
r":{"Author":"Gaurav Sood [aut, cre]","Depends":"R (>= 3.2.0)","Description":"Get
text from images of text using Captricity Optical Character\nRecognition (OCR) API.
Captricity allows you to get text from handwritten\nforms --- think surveys --- and
other structured paper documents. And it can\noutput data in form a delimited file
keeping field information intact. For more\ninformation, read
https:\/\/shreddr.captricity.com\/developer\/overview\/.","Imports":"curl,
jsonlite","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"captr","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat, rmarkdown, knitr (>=
1.11)","Title":"Client for the Captricity
API","URL":"http:\/\/github.com\/soodoku\/captR","Version":"0.1.5"},"capushe":
{"Author":"Sylvain Arlot, Vincent Brault, Jean-Patrick Baudry, Cathy Maugis and
Bertrand Michel","Depends":"methods, graphics, MASS","Description":"Calibration of
penalized criteria for model selection. The calibration methods available are based
on the slope heuristics.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"capushe","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"CAlibrating Penalities Using Slope
HEuristics","URL":"http:\/\/www.math.u-
psud.fr\/~brault\/capushe.html","Version":"1.1"},"capwire":{"Author":"Matthew W.
Pennell and Craig R. Miller","Description":"Fits models from Miller et al. 2005 to
estimate population\nsizes from natural populations. Several models are
implemented.\nPackage also includes functions to perform a likelihood ratio\ntest
to choose between models, perform parametric bootstrapping\nto obtain confidence
intervals and multiple functions to\nsimulate data.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"capwire","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Estimates population size from non-invasive
sampling","Version":"1.1.4"},"car":{"Author":"John Fox [aut, cre],\nSanford
Weisberg [aut],\nDaniel Adler [ctb],\nDouglas Bates [ctb],\nGabriel Baud-Bovy
[ctb],\nSteve Ellison [ctb],\nDavid Firth [ctb],\nMichael Friendly [ctb],\nGregor
Gorjanc [ctb],\nSpencer Graves [ctb],\nRichard Heiberger [ctb],\nRafael Laboissiere
[ctb],\nGeorges Monette [ctb],\nDuncan Murdoch [ctb],\nHenric Nilsson [ctb],\nDerek
Ogle [ctb],\nBrian Ripley [ctb],\nWilliam Venables [ctb],\nDavid Winsemius
[ctb],\nAchim Zeileis [ctb],\nR-Core [ctb]","Depends":"R (>=
3.2.0)","Description":"\nFunctions and Datasets to Accompany J. Fox and S.
Weisberg,\nAn R Companion to Applied Regression, Second Edition, Sage,
2011.","Imports":"MASS, mgcv, nnet, pbkrtest (>= 0.4-4), quantreg,
grDevices,\nutils, stats, graphics","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"car","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"alr4, boot, coxme, leaps, lme4, lmtest, Matrix,
MatrixModels,\nnlme, rgl (>= 0.93.960), sandwich, SparseM, survival,
survey","Title":"Companion to Applied Regression","URL":"https:\/\/r-forge.r-
project.org\/projects\/car\/,\nhttp:\/\/CRAN.R-
project.org\/package=car,\nhttp:\/\/socserv.socsci.mcmaster.ca\/jfox\/Books\/Compan
ion\/index.html","Version":"2.1-2"},"carcass":{"Author":"Fraenzi Korner-Nievergelt,
Ivo Niermann, Oliver Behr, Matthew A. Etterson, Robert Brinkmann, Pius Korner,
Barbara Hellriegel, Tobias Roth, Manuela M. P. Huso, Dan Dalthorp","Depends":"R (>=
3.1.0), stats, lme4, survival","Description":"The number of bird or bat fatalities
from collisions with buildings, towers or wind energy turbines can be estimated
based on carcass searches and experimentally assessed carcass persistence times and
searcher efficiency. Functions for estimating the probability that a bird or bat
that died is found by a searcher are provided. Further functions calculate the
posterior distribution of the number of fatalities based on the number of carcasses
found and the estimated detection probability.","Imports":"expm, arm,
MASS","License":"GPL-
2","NeedsCompilation":"no","Package":"carcass","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Estimation of the Number of Fatalities from Carcass
Searches","Version":"1.6"},"cardidates":{"Author":"Susanne Rolinski [aut], René
Sachse [aut], Thomas Petzoldt [aut, cre]","Depends":"R (>= 3.0.0), boot, pastecs,
lattice","Description":"Identification of cardinal dates\n(begin, time of maximum,
end of mass developments)\nin ecological time series using fitted Weibull
functions.","Imports":"graphics, grDevices, stats, methods, utils","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"cardidates","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Identification of Cardinal Dates in Ecological Time
Series","URL":"http:\/\/cardidates.r-forge.r-
project.org","Version":"0.4.7"},"cardioModel":{"Author":"Daniela J Conrado [aut,
cre], Gregory J Hather [aut], William S Denney [aut], Danny Chen
[ctb]","Depends":"R (>= 2.10.0)","Description":"Includes over 100 mixed-effects
model structures describing the relationship between drug concentration and QT
interval, heart rate\/pulse rate or blood pressure. Given an exposure-response
dataset, the tool fits each model structure to the observed data.","Imports":"nlme,
lubridate","License":"GPL-
3","NeedsCompilation":"no","Package":"cardioModel","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Cardiovascular Safety Exposure-Response Modeling in
Early-Phase\nClinical Studies","Version":"1.4"},"care":{"Author":"Verena Zuber and
Korbinian Strimmer.","Depends":"R (>= 3.0.2), corpcor (>=
1.6.8)","Description":"Implements the regression approach\nof Zuber and Strimmer
(2011) \"High-dimensional regression and variable\nselection using CAR scores\"
SAGMB 10: 34.\nCAR scores measure the correlation between the response and
the\nMahalanobis-decorrelated predictors. The squared CAR score is a\nnatural
measure of variable importance and provides a canonical\nordering of variables.
This package provides functions for estimating\nCAR scores, for variable selection
using CAR scores, and for estimating\ncorresponding regression coefficients. Both
shrinkage as well as\nempirical estimators are
available.","Imports":"stats","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"care","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"crossval","Title":"High-Dimensional Regression and CAR
Score Variable
Selection","URL":"http:\/\/strimmerlab.org\/software\/care\/","Version":"1.1.9"},"c
aret":{"Author":"Max Kuhn. Contributions from Jed Wing, Steve Weston,
Andre\nWilliams, Chris Keefer, Allan Engelhardt, Tony Cooper, Zachary
Mayer,\nBrenton Kenkel, the R Core Team, Michael Benesty, Reynald
Lescarbeau,\nAndrew Ziem, Luca Scrucca, Yuan Tang, and Can Candan.","Depends":"R
(>= 2.10), lattice (>= 0.20), ggplot2","Description":"Misc functions for training
and plotting classification and\nregression models.","Imports":"car, foreach,
methods, plyr, nlme, reshape2,
stats, stats4,\nutils, grDevices","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"caret","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"BradleyTerry2, e1071, earth (>= 2.2-3), fastICA, gam,
ipred,\nkernlab, klaR, MASS, ellipse, mda, mgcv, mlbench, nnet, party\n(>= 0.9-
99992), pls, pROC (>= 1.8), proxy, randomForest, RANN,\nspls, subselect, pamr,
superpc, Cubist, testthat (>= 0.9.1)","Title":"Classification and Regression
Training","URL":"https:\/\/github.com\/topepo\/caret\/","Version":"6.0-
68"},"caretEnsemble":{"Author":"Zachary A. Deane-Mayer [aut, cre],\nJared E.
Knowles [aut]","Depends":"R (>= 3.2.0)","Description":"Functions for creating
ensembles of caret models: caretList\nand caretStack. caretList is a convenience
function for fitting multiple\ncaret::train models to the same dataset. caretStack
will make linear or\nnon-linear combinations of these models, using a caret::train
model as a\nmeta-model, and caretEnsemble will make a robust linear combination
of\nmodels using a glm.","Imports":"methods, pbapply, ggplot2, digest, plyr,
lattice, gridExtra,\ndata.table, caret","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"caretEnsemble","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Suggests":"caTools, testthat, lintr, randomForest,
glmnet, rpart,\nkernlab, nnet, e1071, ipred, pROC, knitr, mlbench, MASS,
gbm,\nklaR","Title":"Ensembles of Caret
Models","URL":"https:\/\/github.com\/zachmayer\/caretEnsemble","Version":"2.0.0"},"
caribou":{"Author":"Helene Crepeau <Helene.Crepeau@mat.ulaval.ca> and Louis-
Paul\nRivest <Louis-Paul.Rivest@mat.ulaval.ca> and Serge
Couturier\n<tuttu@videotron.ca> and Sophie
Baillargeon\n<Sophie.Baillargeon@mat.ulaval.ca>","Description":"This is a package
for estimating the population size of\nmigratory caribou herds based on large scale
aggregations\nmonitored by radio telemetry. It implements the methodology\nfound in
the article by Rivest et al. (1998) about caribou\nabundance estimation. It also
includes a function based on the\nLincoln-Petersen Index as applied to radio
telemetry data by\nWhite and Garrott (1990).","License":"GPL-
2","NeedsCompilation":"no","Package":"caribou","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Estimation of caribou abundance based on large
scale\naggregations monitored by radio telemetry","Version":"1.1"},"caroline":
{"Author":"David Schruth","Depends":"R (>= 1.8.0)","Description":"The caroline R
library contains dozens of functions useful\nfor: database migration
(dbWriteTable2), database style joins &\naggregation (nerge, groupBy & bestBy),
data structure\nconversion (nv, tab2df), legend table making (sstable &\nleghead),
plot annotation (labsegs & mvlabs), data\nvisualization (violins, pies & raPlot),
character string\nmanipulation (m & pad), file I\/O (write.delim), batch
scripting\nand more. The package's greatest\ncontributions lie in the database
style merge, aggregation and\ninterface functions as well as in it's extensive use
and\npropagation of row, column and vector names in most
functions.","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"caroline","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"sm, MASS, RSQLite, grid","Title":"A Collection of
Database, Data Structure, Visualization, and\nUtility Functions for
R","Version":"0.7.6"},"cartography":{"Author":"TimothÃ©e Giraud [cre,
aut],\nNicolas Lambert [aut]","Depends":"R (>= 2.10), sp","Description":"Create and
integrate maps in your R workflow. This package allows\nvarious cartographic
representations such as proportional symbols, chroropleth,\ntypology, flows,
discontinuities. In addition it also proposes some additional useful\nfeatures as
cartographic palettes, layout (scale, north arrow, title...), labels,\nlegends,
access to cartographic API to ease the graphic presentation of
maps.","Imports":"classInt, stats, graphics, utils, methods","License":"GPL-
3","NeedsCompilation":"no","Package":"cartography","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"rgeos, rosm, raster, rgdal, knitr,
rmarkdown","Title":"Thematic Cartography","URL":"https:\/\/github.com\/Groupe-
ElementR\/cartography\/","Version":"1.2"},"carx":{"Author":"Chao Wang [aut,
cre],\nKung-Sik Chan [aut]","Depends":"R (>= 1.9.0)","Description":"A censored time
series class is designed. An estimation procedure\nis implemented to estimate the
Censored AutoRegressive time series with\neXogenous covariates (CARX), assuming
normality of the innovations. Some other\nfunctions that might be useful are also
included.","Imports":"tmvtnorm, mvtnorm, matrixStats, xts, zoo, nlme,
grDevices,\ngraphics, stats","License":"GPL-
3","NeedsCompilation":"no","Package":"carx","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Censored Autoregressive Model with Exogenous
Covariates","Version":"0.6.2"},"caschrono":{"Author":"Yves
Aragon","Depends":"forecast, Hmisc, its, timeSeries","Description":"Functions, data
sets and exercises solutions for the book 'Séries temporelles avec R - Méthodes et
cas' (Yves Aragon, Springer, 2011). For all chapters, a vignette is available with
some additional material and exercises solutions.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"caschrono","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"dse, e1071, expsmooth, fBasics, FitARMA, fGarch,
polynom,\nTSA, xtable","Title":"Séries temporelles avec R - Méthodes et
cas","URL":"http:\/\/www.seriestemporelles.com","Version":"1.4"},"caseMatch":
{"Author":"Rich Nielsen","Description":"Allows users to identify similar cases for
qualitative case studies using statistical matching methods.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"caseMatch","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Identify Similar Cases for Qualitative Case
Studies","Version":"1.0.6"},"cat":{"Author":"Ported to R by Ted Harding and
Fernando Tusell. Original by\nJoseph L. Schafer
<jls@stat.psu.edu>.","Description":"Analysis of categorical-variable with missing
values","License":"file
LICENSE","NeedsCompilation":"yes","Package":"cat","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Analysis of categorical-variable datasets with missing
values","URL":"http:\/\/www.stat.psu.edu\/~jls\/misoftwa.html#aut","Version":"0.0-
6.5"},"catIrt":{"Author":"Steven W. Nydick","Depends":"R (>= 2.11.0), numDeriv (>=
2012.3-1)","Description":"Functions designed to simulate data that conform to
basic\nunidimensional IRT models (for now 3-parameter binary response models\nand
graded response models) along with Post-Hoc CAT simulations of\nthose models with
various item selection methods, ability estimation\nmethods, and termination
criteria.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"catIrt","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"irtoys, ltm, catR","Title":"An R Package for
Simulating IRT-Based Computerized Adaptive\nTests","Version":"0.5-0"},"catR":
{"Author":"David Magis (U Liege, Belgium), Gilles Raiche (UQAM, Canada), Juan Ramon
Barrada (U Zaragoza, Spain)","Depends":"R (>= 2.8.0)","Description":"Generation of
response patterns under dichotomous and polytomous computerized adaptive testing
(CAT) framework.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"catR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Procedures to Generate Patterns under Computerized
Adaptive\nTesting","Version":"3.6"},"catdap":{"Author":"The Institute of
Statistical Mathematics","Depends":"R (>= 3.0.1)","Description":"Categorical data
analysis program package.","Imports":"graphics, grDevices","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"catdap","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"utils, datasets, methods","Title":"Categorical Data
Analysis Program Package","Version":"1.2.2"},"catdata":{"Author":"Gunther
Schauberger, Gerhard Tutz","Depends":"MASS","Description":"This R-package contains
examples from the book \"Regression for Categorical Data\", Tutz 2011, Cambridge
University Press. The names of the examples refer to the chapter and the data set
that is used.","License":"GPL-
2","NeedsCompilation":"no","Package":"catdata","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"rms, qvcalc, glmmML, nnet, pscl, VGAM, gee, mlogit,
Ecdat,\ngeepack, mgcv, rpart, party, ordinal, lme4, vcdExtra, glmnet,\nmboost,
class, e1071, flexmix, lqa, lpSolve, GAMBoost,\npenalized","Title":"Categorical
Data","Version":"1.2.1"},"cate":{"Author":"Jingshu Wang [aut],\nQingyuan Zhao [aut,
cre]","Description":"Provides several methods for factor analysis in high dimension
(both n,p >> 1) and methods to adjust for possible confounders in multiple
hypothesis testing.","Imports":"MASS, esaBcv, ruv, sva, corpcor,
leapp","License":"GPL-
2","NeedsCompilation":"no","Package":"cate","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"knitr, ggplot2, gridExtra","Title":"High Dimensional
Factor Analysis and Confounder Adjusted Testing\nand
Estimation","Version":"1.0.4"},"catenary":{"Author":"Jonathan Tuke [aut,
cre],\nMatthew Roughan [aut]","Depends":"R (>= 2.15.0),","Description":"Gives
methods to create a catenary object and then plot it and get\nproperties of it. Can
construct from parameters or endpoints. Also can get\ncatenary fitted to
data.","Imports":"ggplot2, boot, methods","License":"GPL-
3","NeedsCompilation":"no","Package":"catenary","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Fits a Catenary to Given
Points","Version":"1.1.1"},"cati":{"Author":"Adrien Taudiere, Cyrille Violle with
contribution by Francois Munoz","Depends":"R (>= 3.0.2), nlme, ade4,
ape,","Description":"Detect and quantify community assembly processes using trait
values of individuals or populations, the T-statistics and other metrics, and
dedicated null models.","Imports":"e1071,
mice, rasterVis, hypervolume, FD, geometry, vegan","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"cati","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"lattice, spacodiR, entropart, fBasics, picante,
knitr","Title":"Community Assembly by Traits: Individuals and
Beyond","URL":"https:\/\/github.com\/adrientaudiere\/cati","Version":"0.99.1"},"cat
net":{"Author":"Nikolay Balov, Peter Salzman","Depends":"R (>=
3.0.2)","Description":"Structure learning and parameter estimation of discrete
Bayesian networks using likelihood-based criteria. Exhaustive search for fixed
node orders and stochastic search of optimal orders via simulated annealing
algorithm are implemented.","Imports":"methods, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"catnet","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Categorical Bayesian Network
Inference","Version":"1.14.8"},"catspec":{"Author":"John Hendrickx
<John_Hendrickx@yahoo.com>","Description":"`ctab' creates (multiway) percentage
tables. `sqtab'\ncontains a set of functions for estimating models for
square\ntables such as quasi-independence, symmetry, uniform\nassociation. Examples
show how to use these models in a\nloglinear model using glm or in a multinomial
logistic model\nusing mlogit or clogit","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"catspec","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"mlogit,survival","Title":"Special models for
categorical variables","Version":"0.97"},"causaldrf":{"Author":"Douglas Galagate
[cre],\nJoseph Schafer [aut]","Depends":"R(>= 3.1.2)","Description":"Functions and
data to estimate causal dose response functions given continuous, ordinal, or
binary treatments.","Imports":"mgcv, splines, stats, survey,","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"causaldrf","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"BayesTree, dplyr, foreign, Hmisc, knitr, MASS,
nnet,\nreshape2, rmarkdown, sas7bdat, testthat, tidyr","Title":"Tools for
Estimating Causal Dose Response Functions","Version":"0.3"},"causaleffect":
{"Author":"Santtu Tikka","Description":"Functions for identification and
transportation of causal effects. Provides a conditional causal effect
identification algorithm (IDC) by Ilya Shpitser and Judea Pearl, and algorithms for
z-identifiability, transportability, z-transportability and meta-transportability
of causal effects by Elias Bareinboim and Judea Pearl. All of the previously
mentioned algorithms are based on a causal effect identification algorithm by Jin
Tian.","Imports":"ggm, igraph, XML","License":"GPL-
2","NeedsCompilation":"no","Package":"causaleffect","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"R.rsp","Title":"Deriving Expressions of Joint
Interventional Distributions and\nTransport Formulas in Causal
Models","Version":"1.2.4"},"causalsens":{"Author":"Matthew Blackwell
<mblackwell@gov.harvard.edu.edu>","Depends":"R (>= 3.0.0)","Description":"The
causalsens package provides functions to perform sensitivity analyses and to study
how various assumptions about selection bias affects estimates of causal
effects.","Imports":"stats, graphics, grDevices","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"causalsens","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr","Title":"Selection Bias Approach to
Sensitivity Analysis for
Causal\nEffects","URL":"http:\/\/www.mattblackwell.org\/software\/causalsens\/","Ve
rsion":"0.1.1"},"cba":{"Author":"Christian Buchta and Michael Hahsler","Depends":"R
(>= 2.4.1), grid, proxy","Description":"Implements clustering techniques such as
Proximus and Rock, utility functions for efficient computation of cross distances
and data manipulation.","Imports":"stats, graphics, grDevices,
2","NeedsCompilation":"yes","Package":"cba","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"gclus, colorspace","Title":"Clustering for Business
Analytics","Version":"0.2-15"},"cbsodataR":{"Author":"Edwin de
Jonge","Description":"The data and meta data from Statistics\nNetherlands
(www.cbs.nl) can be browsed and downloaded. The client uses\nthe open data API of
Statistics Netherlands.","Imports":"whisker, jsonlite, yaml, utils","License":"GPL-
2","NeedsCompilation":"no","Package":"cbsodataR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr, rmarkdown, dplyr","Title":"Statistics
Netherlands (CBS) Open Data API
Client","URL":"https:\/\/github.com\/edwindj\/cbsodataR","Version":"0.2.1"},"ccChoo
ser":{"Author":"Marcin Studnicki and Konrad Debski","Depends":"R(>= 2.14.1),
cluster (>= 1.13.1)","Description":"ccChooser can be used to developing and
evaluation of core\ncollections for germplasm collections (entire collection).
This\npackage used to develop a core collection for biological\nresources like
genbanks. A core collection is defined as a\nsample of accessions that represent,
with the lowest possible\nlevel of redundancy, the genetic diversity (the richness
of\ngene or genotype categories) of the entire collection. The\nestablishing a core
collection that represents genetic\ndiversity of the entire collection with minimum
loss of its\noriginal diversity and minimum redundancies is an important\nproblem
for gene-banks curators and crop breeders. ccChooser\nestablish core collection
base on phenotypic data (agronomic,\nmorphological, phenological).","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"ccChooser","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Developing a core
collections","Version":"0.2.6"},"ccaPP":{"Author":"Andreas Alfons [aut,
cre],\nDavid Simcha [ctb]","Depends":"R (>= 3.2.0), parallel, pcaPP (>= 1.8-1),
robustbase","Description":"Canonical correlation analysis and maximum correlation
via\nprojection pursuit, as well as fast implementations of
correlation\nestimators, with a focus on robust and non-parametric
methods.","Imports":"Rcpp (>= 0.11.0)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ccaPP","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr, mvtnorm","Title":"(Robust) Canonical Correlation
Analysis via Projection Pursuit","Version":"0.3.2"},"cccd":{"Author":"David J.
Marchette <dmarchette@gmail.com>","Depends":"igraph","Description":"Class Cover
Catch Digraphs, neighborhood graphs, and\nrelatives.","Imports":"proxy, deldir,
FNN","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"cccd","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"Matrix","Title":"Class Cover Catch
Digraphs","Version":"1.5"},"cccp":{"Author":"Bernhard Pfaff [aut, cre],\nLieven
Vandenberghe [cph] (copyright holder of cvxopt),\nMartin Andersen [cph] (copyright
holder of cvxopt),\nJoachim Dahl [cph] (copyright holder of cvxopt)","Depends":"R
(>= 3.0.1), methods","Description":"Routines for solving convex optimization
problems with cone constraints by means of interior-point methods. The implemented
algorithms are partially ported from CVXOPT, a Python module for convex
optimization (see <http:\/\/cvxopt.org> for more information).","Imports":"Rcpp (>=
0.11.2)","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"cccp","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"RUnit, numDeriv","Title":"Cone Constrained Convex
Problems","Version":"0.2-4"},"cccrm":{"Author":"Josep Lluis Carrasco
<jlcarrasco@ub.edu>, Josep Puig Martinez\n<j.puig04@gmail.com>","Depends":"R (>=
3.1.0), nlme, gdata","Description":"Estimates the Concordance Correlation
Coefficient to assess agreement. The scenarios considered are non-repeated
measures, non-longitudinal repeated measures (replicates) and longitudinal repeated
measures. The estimation approaches implemented are variance components and U-
statistics approaches.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"cccrm","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Concordance Correlation Coefficient for Repeated (and\nNon-
Repeated) Measures","Version":"1.2.1"},"ccda":{"Author":"Solt Kovacs, Jozsef
Kovacs, Peter Tanos","Depends":"MASS","Description":"This package implements the
combined cluster and discriminant analysis method for finding homogeneous groups of
data with known origin as described in Kovacs et. al (2014): Classification into
homogeneous groups using combined cluster and discriminant analysis (CCDA).
Environmental Modelling & Software. DOI:
http:\/\/dx.doi.org\/10.1016\/j.envsoft.2014.01.010","License":"GPL-
2","NeedsCompilation":"no","Package":"ccda","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Combined Cluster and Discriminant
Analysis","Version":"1.1"},"ccgarch":{"Author":"Tomoaki Nakatani
<naktom2@gmail.com>","Depends":"R (>= 2.15.2)","Description":"Functions for
estimating and simulating the family of the\nCC-GARCH models.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ccgarch","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Conditional Correlation GARCH
models","Version":"0.2.3"},"cchs":{"Author":"E. Jones","Depends":"R (>= 2.15.0),
survival (>= 2.36-12)","Description":"Contains a function, also called cchs, that
calculates Estimator III of Borgan et al (2000), Exposure-stratified Case-cohort
Designs. This estimator is for fitting a Cox proportional hazards model to data
from a case-cohort study where the subcohort was selected by stratified simple
random sampling.","License":"GPL-
3","NeedsCompilation":"no","Package":"cchs","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Cox Model for Case-Cohort Data with Stratified\nSubcohort-
Selection","Version":"0.2.0"},"cclust":{"Author":"Evgenia Dimitriadou [aut],\nKurt
Hornik [ctb, cre]","Description":"Convex Clustering methods, including K-means
algorithm,\nOn-line Update algorithm (Hard Competitive Learning) and Neural
Gas\nalgorithm (Soft Competitive Learning),
and calculation of several\nindexes for finding the number of clusters in a data
set.","Imports":"stats","License":"GPL-
2","NeedsCompilation":"yes","Package":"cclust","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Convex Clustering Methods and Clustering
Indexes","Version":"0.6-20"},"cda":{"Author":"Baptiste Auguie [aut, cre],\nLAPACK
authors [cph] (copyrights apply to src\/zgels.f)","Depends":"methods,
dielectric","Description":"Solves the electromagnetic problem of coupled-dipoles
(scattering\nand absorption by a cluster of subwavelength particles in arbitrary
3D\nconfiguration) by setting up the interaction matrix and solving the
linear\nsystem for multiple incident fields. Functions are provided for
linear\npolarisation as well as circular polarisation with full angular
averaging\n(optical activity). Retardation is included in the dipole-
dipole\ninteraction.","Imports":"Rcpp, statmod, randtoolbox, reshape2,
3","NeedsCompilation":"yes","Package":"cda","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"rgl, grid, ggplot2, gridExtra, testthat,
knitr","Title":"Coupled dipole approximation of light scattering by clusters
of\nnanoparticles","URL":"https:\/\/github.com\/baptiste\/cda","Version":"1.5.1"},"
cdb":{"Author":"Emilio Torres Manzanera [aut,
cre]","Depends":"bitops","Description":"A constant database is a data structure
created by Daniel\nJ. Bernstein in his cdb package. Its format consists on
a\nsequence of (key,value)-pairs. This R package replicates the\nbasic utilities
for reading (cdbget) and writing (cdbdump)\nconstant databases.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"cdb","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"methods","Title":"Reading and Writing Constant
DataBases","URL":"http:\/\/cdb.r-forge.r-
project.org\/","Version":"0.0.1"},"cdcfluview":{"Author":"Bob Rudis
(@hrbrmstr)","Depends":"R (>= 3.0.0)","Description":"The U.S. Centers for Disease
Control (CDC) maintains a
portal\n<http:\/\/gis.cdc.gov\/grasp\/fluview\/fluportaldashboard.html>
for\naccessing state, regional and national influenza statistics. The
Flash\ninterface makes it difficult and time-consuming to select and
retrieve\ninfluenza data. This package provides functions to access the data
provided\nby the portal's underlying API.","Imports":"httr (>= 0.3.0), pbapply,
xml2, dplyr, utils","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"cdcfluview","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Retrieve U.S. Flu Season
Data from the CDC FluView
Portal","URL":"http:\/\/github.com\/hrbrmstr\/cdcfluview","Version":"0.4.0"},"cdcsi
s":{"Author":"Canhong Wen, Wenliang Pan, Mian Huang, and Xueqin
Wang","Depends":"R(>= 3.0.1), stats","Description":"Gives conditional distance
correlation and performs the conditional distance correlation sure independence
screening procedure for ultrahigh dimensional data. The conditional distance
correlation is a novel conditional dependence measurement of two random variables
given a third variable. The conditional distance correlation sure independence
screening is used for screening variables in ultrahigh dimensional
setting.","Imports":"ks","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"cdcsis","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"MASS, energy","Title":"Conditional Distance
Correlation and Its Related Feature\nScreening
Method","Version":"1.0"},"cdfquantreg":{"Author":"Yiyun Shou [aut, cre],\nMichael
Smithson [aut]","Depends":"R (>= 3.1.0)","Description":"Employs a two-parameter
family of\ndistributions for modelling random variables on the (0, 1) interval
by\napplying the cumulative distribution function (cdf) of one parent\ndistribution
to the quantile function of another.","Imports":"pracma (>= 1.8), Formula (>= 1.2),
stats, MASS","License":"GPL-
3","NeedsCompilation":"no","Package":"cdfquantreg","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr, R2OpenBUGS","Title":"Quantile Regression for
Random Variables on the Unit Interval","Version":"1.0.4"},"cdom":
{"Author":"Philippe Massicotte [aut, cre]","Depends":"R (>=
3.0)","Description":"Wrapper functions to model and extract various quantitative
information from absorption spectra of chromophoric dissolved organic matter
(CDOM).","Imports":"minpack.lm, ggplot2, tidyr, broom","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"cdom","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"eemR","Title":"R Functions to Model CDOM
Spectra","URL":"https:\/\/github.com\/PMassicotte\/cdom","Version":"0.1.0"},"cds":
{"Author":"Pieter Schoonees [aut, cre]","Depends":"R(>= 3.2.3),
parallel","Description":"This is an implementation of constrained dual scaling
for\ndetecting response styles in categorical data, including utility functions.
The\nprocedure involves adding additional columns to the data matrix representing
the\nboundaries between the rating categories. The resulting matrix is then
doubled\nand analyzed by dual scaling. One-dimensional solutions are sought which
provide\noptimal scores for the rating categories. These optimal scores are
constrained\nto follow monotone quadratic splines. Clusters are introduced within
which the\nresponse styles can vary. The type of response style present in a
cluster can\nbe diagnosed from the optimal scores for said cluster, and this can be
used to\nconstruct an imputed version of the data set which adjusts for response
styles.","Imports":"MASS, limSolve, clue, colorspace, copula, graphics,
methods,\nstats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"cds","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Constrained Dual Scaling for Detecting Response
Styles","Version":"1.0.3"},"cec2005benchmark":{"Author":"Yasser Gonzalez-Fernandez
[aut, cre],\nMarta Soto [aut]","Description":"This package is a wrapper for the C
implementation of the 25 benchmark functions for the CEC 2005 Special Session on
Real-Parameter Optimization. The original C code by Santosh Tiwari and related
documentation are available at
http:\/\/www.ntu.edu.sg\/home\/EPNSugan\/index_files\/CEC-
05\/CEC05.htm.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"cec2005benchmark","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Benchmark for the CEC 2005 Special Session on
Real-
Parameter\nOptimization","URL":"https:\/\/github.com\/yasserglez\/cec2005benchmark"
,"Version":"1.0.4"},"cec2013":{"Author":"Mauricio Zambrano-Bigiarini [aut, cre],
Yasser Gonzalez-Fernandez [aut]","Depends":"R (>= 2.13.0)","Description":"This
package provides R wrappers for the C implementation of 28 benchmark functions
defined for the Special Session and Competition on Real-Parameter Single Objective
Optimization at CEC-2013. The focus of this package is to provide an open-source
and multi-platform implementation of the CEC2013 benchmark functions, in order to
make easier for researchers to test the performance of new optimization algorithms
in a reproducible way. The original C code (Windows only) was provided by Jane Jing
Liang, while GNU\/Linux comments were made by Janez Brest. This package was gently
authorised for publication on CRAN by Ponnuthurai Nagaratnam Suganthan. The
official documentation is available at
http:\/\/www.ntu.edu.sg\/home\/EPNSugan\/index_files\/CEC2013\/CEC2013.htm. Bugs
reports\/comments\/questions are very welcomed (in English, Spanish or
Italian).","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"cec2013","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Benchmark functions for the Special Session and
Competition on\nReal-Parameter Single Objective Optimization at CEC-
2013","URL":"http:\/\/www.rforge.net\/cec2013,\nhttp:\/\/cran.r-
project.org\/web\/packages\/cec2013","Version":"0.1-5"},"celestial":
{"Author":"Aaron Robotham","Depends":"R (>= 3.00), RANN","Description":"Contains a
number of common astronomy conversion routines, particularly the HMS and degrees
schemes, which can be fiddly to convert between on mass due to the textural nature
of the former. It allows users to coordinate match datasets quickly. It also
contains functions for various cosmological calculations.","License":"GPL-
3","NeedsCompilation":"no","Package":"celestial","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Collection of Common Astronomical Conversion Routines
and\nFunctions","Version":"1.3"},"cellVolumeDist":{"Author":"Katharine M. Mullen,
Michael Halter, John Lu and Nathan Dodder","Depends":"minpack.lm (>= 1.1-1),
gplots","Description":"This package implements a methodology for using cell\nvolume
distributions to estimate cell growth rates and division\ntimes that is described
in the paper entitled \"Cell Volume\nDistributions Reveal Cell Growth Rates and
Division Times\", by\nMichael Halter, John T. Elliott, Joseph B. Hubbard,
Alessandro\nTona and Anne L. Plant, which is in press in the Journal
of\nTheoretical Biology. In order to reproduce the analysis used\nto obtain Table
1 in the paper, execute the command\n\"example(fitVolDist)\".","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"cellVolumeDist","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Functions to fit cell volume distributions and
thereby estimate\ncell growth rates and division
times","Version":"1.3"},"cellranger":{"Author":"Jennifer Bryan [cre, aut],\nHadley
Wickham [ctb]","Depends":"R (>= 3.0.0)","Description":"Helper functions to work
with spreadsheets and the \"A1:D10\" style\nof cell range
specification.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"cellranger","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"covr, testthat","Title":"Translate Spreadsheet
Cell Ranges to Rows and
Columns","URL":"https:\/\/github.com\/jennybc\/cellranger","Version":"1.0.0"},"cem"
:{"Author":"Iacus,
Stefano M., King, Gary, Porro, Giuseppe","Depends":"tcltk,
lattice","Description":"Implementation of the Coarsened Exact Matching
algorithm.","Imports":"MatchIt, combinat, randomForest, nlme","License":"GPL-
2","NeedsCompilation":"no","Package":"cem","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"Amelia(>= 1.2-0)","Title":"Coarsened Exact
Matching","URL":"http:\/\/gking.harvard.edu\/cem\/","Version":"1.1.17"},"cems":
{"Author":"Samuel Gerber <sgerber@uoregon.edu>","Depends":"R (>=
2.10)","Description":"Conditional expectation manifolds are an approach to compute
principal curves and surfaces.","Imports":"plotrix, rgl, vegan, stats, graphics,
2","NeedsCompilation":"yes","Package":"cems","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Conditional Expectation
Manifolds","Version":"0.4"},"censNID":{"Author":"A. I. McLeod and N. M.
Mohammad","Depends":"R (>= 2.1.0),","Description":"Implements AS138,
AS139.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"censNID","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"censored NID samples","Version":"0-0-1"},"censReg":
{"Author":"Arne Henningsen <arne.henningsen@gmail.com>","Depends":"R (>= 2.4.0),
maxLik (>= 0.7-3)","Description":"Estimation of censored regression (Tobit)
models\nwith cross-section and panel data","Imports":"glmmML (>= 0.81-6), sandwich
(>= 2.2-6), miscTools (>=\n0.6-11), stats (>= 2.15.0)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"censReg","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"plm, AER, lmtest (>= 0.9-27)","Title":"Censored
Regression (Tobit) Models","URL":"http:\/\/www.sampleSelection.org","Version":"0.5-
20"},"censorcopula":{"Author":"Yan Li, Yang Li, Yichen Qin, and Jun
yan","Depends":"copula","Description":"Implement an interval censor method\nto
break ties when using data with ties to fitting a\nbivariate
copula.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"censorcopula","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Estimate Parameter of Bivariate
Copula","Version":"2.0"},"censusr":{"Author":"Greg Macfarlane [cre, aut],\nJosie
Kressner [aut]","Depends":"dplyr (>= 0.4.3), httr (>= 1.0.0)","Description":"Use
the US Census API to collect summary data tables\nfor SF1 and ACS datasets at
arbitrary geographies.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"censusr","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"knitr","Title":"Collect Data from the Census
API","Version":"0.0.2"},"cents":{"Author":"A.I. McLeod, Nagham M. Mohammad, Justin
Veenstra and Abdel El-Shaarawi","Depends":"R (>= 2.1.0)","Description":"Fit
censored time series","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"cents","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Censored time series","Version":"0.1-41"},"cepp":
{"Author":"Mohit Dayal","Depends":"R (>= 2.10), trust","Description":"Functions and
Data to support Context Driven Exploratory Projection
Pursuit.","Imports":"randtoolbox","License":"GPL-
3","NeedsCompilation":"no","Package":"cepp","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Context Driven Exploratory Projection
Pursuit","Version":"1.7"},"cernn":{"Author":"Eric C. Chi
<ecchi1105@gmail.com>","Depends":"R (>= 3.1.3)","Description":"An implementation of
the covariance estimation method\nproposed in Chi and Lange (2014), \"Stable
estimation of a covariance matrix guided by nuclear norm
penalties,\"\nComputational Statistics and Data Analysis 80:117-
128.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"cernn","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Covariance Estimation Regularized by Nuclear Norm
Penalties","Version":"0.1"},"cffdrs":{"Author":"Xianli Wang, Alan Cantin, Marc-
Andre Parisien, Mike Wotton, Kerry Anderson, Brett Moore, and Mike
Flannigan","Depends":"R(>= 3.2.2), rgdal, raster, foreach, data.table,
spatial.tools","Description":"This project provides a group of new functions to
calculate the outputs of the two main components of the Canadian Forest Fire Danger
Rating System (CFFDRS) at various time scales: the Fire Weather Index (FWI) System
and the Fire Behaviour Prediction (FBP) System. Some functions have two versions,
table and raster based.","Imports":"doParallel","License":"GPL-
2","NeedsCompilation":"no","Package":"cffdrs","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Canadian Forest Fire Danger Rating
System","URL":"https:\/\/r-forge.r-
project.org\/projects\/cffdrs\/","Version":"1.7.3"},"cg":{"Author":"Bill Pikounis
[aut, cre, cph], John Oleynick [aut], Eva Ye [ctb]","Depends":"R (>= 3.2.3), Hmisc
(>= 3.17-1)","Description":"Comprehensive data analysis software, and the
name \"cg\" stands for \"compare groups.\" Its genesis and evolution are driven by
common needs to compare administrations, conditions, etc. in medicine research and
development. The current version provides comparisons of unpaired samples, i.e. a
linear model with one factor of at least two levels. It also provides comparisons
of two paired samples. Good data graphs, modern statistical methods, and useful
displays of results are emphasized.","Imports":"VGAM (>= 1.0-0), methods,
grDevices, graphics, stats, utils,\ngrid, MASS, lattice, survival, multcomp, nlme,
rms","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"cg","Repository":"http:\/\/cran.csiro.au\/src
\/contrib","Title":"Compare Groups, Analytically and Graphically","Version":"1.0-
3"},"cgAUC":{"Author":"Yuan-chin I. Chang, Yu-chia Chang, and Ling-wan
Chen","Description":"The cgAUC can calculate the AUC-type measure of
Obuchowski(2006) when gold standard is continuous, and find the optimal linear
combination of variables with respect to this measure.","Imports":"Rcpp (>=
0.11.2)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"cgAUC","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Calculate AUC-type measure when gold standard is
continuous and\nthe corresponding optimal linear combination of variables
with\nrespect to it","Version":"1.2.1"},"cgam":{"Author":"Mary C. Meyer and Xiyue
Liao","Depends":"coneproj(>= 1.3), R(>= 3.0.2)","Description":"A constrained
generalized additive model is fitted by the cgam routine. Given a set of predictors
with or without shape or order restrictions, the maximum likelihood estimator for
the constrained generalized additive model is found using an iteratively re-
weighted cone projection algorithm. The cone information criterion (CIC) may be
used to select the best combination of variables and shapes. This package depends
on the R package coneproj.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"cgam","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"stats, MASS, graphics, grDevices,
utils","Title":"Constrained Generalized Additive Model","Version":"1.3"},"cgdsr":
{"Author":"Anders Jacobsen <jacobsen@cbio.mskcc.org>","Depends":"R (>=
2.12.0)","Description":"Provides a basic set of R functions for querying the
Cancer\nGenomics Data Server (CGDS), hosted by the Computational Biology Center
at\nMemorial-Sloan-Kettering Cancer Center (MSKCC).","Imports":"R.oo,
R.methodsS3","License":"LGPL-
3","NeedsCompilation":"no","Package":"cgdsr","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat","Title":"R-Based API for Accessing the MSKCC
Cancer Genomics Data
Server\n(CGDS)","URL":"https:\/\/github.com\/cBioPortal\/cgdsr","Version":"1.2.5"},
"cggd":{"Author":"Cun-Hui Zhang and Ofer Melnik","Depends":"R (>= 2.10), grDevices,
graphics, stats, utils","Description":"Efficient procedures for fitting an entire
regression\nsequences with different model types.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"cggd","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Continuous Generalized Gradient
Descent","Version":"0.8"},"cgh":{"Author":"Tom Price
<t0mpr1c3@gmail.com>","Depends":"R (>= 2.6.0)","Description":"Functions to analyze
microarray comparative genome\nhybridization data using the Smith-Waterman
algorithm","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"cgh","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Microarray CGH analysis using the Smith-Waterman
algorithm","URL":"http:\/\/sgdp.iop.kcl.ac.uk\/tprice\/software.html","Version":"1.
0-7.1"},"cghFLasso":{"Author":"Nicholas Austin Johnson <nickaj@stanford.edu>,
Robert\nTibshirani <tibs@stat.stanford.edu>, Pei
Wang\n<pwang@fhcrc.org>.","Description":"Spatial smoothing and hot spot detection
using the fused\nlasso regression","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"cghFLasso","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Detecting hot spot on CGH array data with fused
lasso\nregression","Version":"0.2-1"},"cghseg":{"Author":"Franck Picard, Mark
Hoebeke, Emilie Lebarbier, Vincent Miele,\nGuillem Rigaill, Stephane
Robin","Depends":"methods, parallel","Description":"cghseg is an R package
dedicated to the analysis of CGH\nprofiles using segmentation
2)","NeedsCompilation":"yes","Package":"cghseg","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Segmentation Methods for Array CGH
Analysis","Version":"1.0.2-1"},"cgwtools":{"Author":"Carl
Witthoft","Description":"A set of tools the author has found useful for performing
quick observations or evaluations of data, including a variety of ways to list
objects by size, class, etc. Several other tools mimic Unix shell commands,
including 'head', 'tail' ,'pushd' ,and 'popd'. The functions 'seqle' and
'reverse.seqle' mimic the base 'rle' but can search for linear sequences. The
function 'splatnd' allows the user to generate zero-argument commands without the
need for 'makeActiveBinding' .","License":"LGPL-
3","NeedsCompilation":"no","Package":"cgwtools","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Miscellaneous
Tools","Version":"3.0"},"changepoint":{"Author":"Rebecca Killick [aut,
cre],\nKaylea Haynes [aut],\nIdris Eckley [ths, aut],\nPaul Fearnhead [ctb,
ths],\nJamie Lee [ctr]","Depends":"R(>= 3.0), methods, stats, zoo(>= 0.9-
1)","Description":"Implements various mainstream and specialised changepoint
methods for finding single and multiple changepoints within data. Many popular
non-parametric and frequentist methods are included. The cpt.mean(), cpt.var(),
cpt.meanvar() functions should be your first point of
call.","License":"GPL","NeedsCompilation":"yes","Package":"changepoint","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Methods for
Changepoint
Detection","URL":"https:\/\/github.com\/rkillick\/changepoint\/","Version":"2.2.1"}
,"cheb":{"Author":"Jan de Leeuw <deleeuw@stat.ucla.edu>","Description":"Discrete
Linear Chebyshev Approximation","License":"GPL-
3","NeedsCompilation":"yes","Package":"cheb","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Discrete Linear Chebyshev
Approximation","Version":"0.3"},"chebpol":{"Author":"Simen Gaure, Ragnar Frisch
Centre for Economic Research, Oslo, Norway","Description":"Contains methods for
creating multivariate Chebyshev\napproximation of functions on a hypercube. Some
methods for\nnon-Chebyshev grids are also provided.","Imports":"compiler,
stats","License":"Artistic-
2.0","NeedsCompilation":"yes","Package":"chebpol","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Multivariate Chebyshev Interpolation","Version":"1.3-
1789"},"checkmate":{"Author":"Michel Lang <michellang@gmail.com>,\nBernd Bischl
<bernd_bischl@gmx.net>","Depends":"R (>= 3.0.0)","Description":"Tests and
assertions to perform frequent argument checks. A\nsubstantial part of the package
was written in C to minimize any worries\nabout execution time
overhead.","Imports":"backports, utils","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"yes","Package":"checkmate","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"data.table, devtools, dplyr, ggplot2, knitr,
rmarkdown,\nmagrittr, microbenchmark, testthat","Title":"Fast and Versatile
Argument
Checks","URL":"https:\/\/github.com\/mllg\/checkmate","Version":"1.7.4"},"checkpoin
t":{"Author":"Revolution Analytics","Depends":"R(>= 3.0.0)","Description":"The goal
of checkpoint is to solve the problem of package\nreproducibility in R.
Specifically, checkpoint allows you to install\npackages as they existed on CRAN on
a specific snapshot date as if you had\na CRAN time machine. To achieve
reproducibility, the checkpoint() function\ninstalls the packages required or
called by your project and scripts to a\nlocal library exactly as they existed at
the specified point in time. Only\nthose packages are available to your project,
thereby avoiding any package\nupdates that came later and may have altered your
results. In this way,\nanyone using checkpoint's checkpoint() can ensure the
reproducibility of\nyour scripts or projects at any time. To create the snapshot
archives, once\na day (at midnight UTC) Revolution Analytics refreshes the Austria
CRAN mirror, on the \"Managed\nR Archived Network\" server
(http:\/\/mran.revolutionanalytics.com\/).\nImmediately after completion of the
rsync mirror process, the process takes a\nsnapshot, thus creating the archive.
Snapshot archives exist starting from\n2014-09-
17.","Imports":"utils","License":"GPL-
2","NeedsCompilation":"no","Package":"checkpoint","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr, testthat(>= 0.9), MASS","Title":"Install
Packages from Snapshots on the Checkpoint Server
for\nReproducibility","URL":"http:\/\/projects.revolutionanalytics.com\/documents\/
rrt\/rrtpkgs\/","Version":"0.3.15"},"cheddar":{"Author":"Lawrence Hudson with
contributions from Dan Reuman and Rob Emerson","Description":"Provides a flexible,
extendable representation of an ecological community and a range of functions for
analysis and visualisation, focusing on food web, body mass and numerical abundance
data. Allows inter-web comparisons such as examining changes in community structure
over environmental, temporal or spatial gradients.","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"yes","Package":"cheddar","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Analysis and Visualisation of Ecological
Communities","URL":"https:\/\/github.com\/quicklizard99\/cheddar\/","Version":"0.1-
630"},"chemCal":{"Author":"Johannes Ranke [aut, cre, cph]","Description":"Simple
functions for plotting linear\ncalibration functions and estimating standard errors
for measurements\naccording to the Handbook of Chemometrics and Qualimetrics: Part
A\nby Massart et al. There are also functions estimating the limit\nof detection
(LOD) and limit of quantification (LOQ).\nThe functions work on model objects from
- optionally weighted - linear\nregression (lm) or robust linear regression ('rlm'
from the 'MASS' package).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"chemCal","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"MASS","Title":"Calibration Functions for Analytical
Chemistry","URL":"http:\/\/www.r-project.org,\nhttp:\/\/chem.uft.uni-
bremen.de\/ranke\/?page=chemCal,\nhttp:\/\/cgit.jrwb.de\/chemCal","Version":"0.1-
37"},"chemometrics":{"Author":"Peter Filzmoser and Kurt Varmuza","Depends":"R (>=
2.10), rpart","Description":"This package is the R companion to the
book \"Introduction to Multivariate Statistical Analysis in Chemometrics\" written
by K. Varmuza and P. Filzmoser (2009)","Imports":"class, e1071, MASS, nnet, pcaPP,
robustbase, som, lars, pls,\nmclust","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"chemometrics","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"gclus","Title":"Multivariate Statistical Analysis
in
Chemometrics","URL":"http:\/\/www.statistik.tuwien.ac.at\/public\/filz\/","Version"
:"1.3.9"},"cherry":{"Author":"Jelle Goeman, Aldo Solari, Rosa
Meijer","Depends":"methods, bitops, lpSolve, Matrix, slam","Description":"Provides
an alternative approach to multiple testing\nby calculating a simultaneous upper
confidence bounds for the\nnumber of true null hypotheses among any subset of the
hypotheses of interest.\nSome of the functions in this package are optionally
enhanced by the 'gurobi'\nsoftware and its accompanying R package. For their
installation, please follow the\ninstructions at www.gurobi.com and
http:\/\/www.gurobi.com\/documentation, respectively.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"cherry","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"MASS, multtest, gurobi","Title":"Multiple Testing
Methods for Exploratory Research","Version":"0.6-11"},"childsds":{"Author":"Mandy
Vogel [aut, cre]","Depends":"R (>= 3.1.1), methods","Description":"Calculation of
standard deviation scores from different\ngrowth standards","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"childsds","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Calculation of standard deviation scores adduced from
different\ngrowth standards","Version":"0.5"},"chillR":{"Author":"Eike
Luedeling","Description":"The phenology of plants (i.e. the timing of their annual
life\nphases) depends on climatic cues. For temperate trees and many other
plants,\nspring phases, such as leaf emergence and flowering, have been found to
result\nfrom the effects of both cool (chilling) conditions and heat. Fruit
tree\nscientists (pomologists) have developed some metrics to quantify
chilling\nand heat. 'chillR' contains functions for processing temperature records
into\nchilling (Chilling Hours, Utah Chill Units and Chill Portions) and heat
units\n(Growing Degree Hours). Regarding chilling metrics, Chill Portions are
often\nconsidered the most promising, but they are difficult to calculate. This
package\nmakes it easy. 'chillR' also contains procedures for conducting a PLS
analysis\nrelating phenological dates (e.g. bloom dates) to either mean
temperatures or\nmean chill and heat accumulation rates, based on long-term weather
and phenology\nrecords.","Imports":"pls, Kendall, fields, sp, readxl, XML, httr,
grDevices,\ngraphics, stats, utils","License":"GPL-
3","NeedsCompilation":"no","Package":"chillR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Statistical Methods for Phenology Analysis in Temperate
Fruit\nTrees","Version":"0.62"},"chipPCR":{"Author":"Stefan Roediger [cre,
aut],\nMichal Burdukiewicz [aut],\nKonstantin A. Blagodatskikh [ctb]","Depends":"R
(>= 3.0.0), methods","Description":"A collection of functions to pre-process
amplification curve data from polymerase chain reaction (PCR) or isothermal
amplification reactions. Contains functions to normalize and baseline amplification
curves, to detect both the start and end of an amplification reaction, several
smoothers (e.g., LOWESS, moving average, cubic splines, Savitzky-Golay), a function
to detect false positive amplification reactions and a function to determine the
amplification efficiency. Quantification point (Cq) methods include the first (FDM)
and second approximate derivative maximum (SDM) methods (calculated by a 5-point-
stencil) and the cycle threshold method. Data sets of experimental nucleic acid
amplification systems (VideoScan HCU, capillary convective PCR (ccPCR)) and
commercial systems are included. Amplification curves were generated by helicase
dependent amplification (HDA), ccPCR or PCR. As detection system intercalating dyes
(EvaGreen, SYBR Green) and hydrolysis probes (TaqMan) were
used.","Imports":"lmtest, MASS, outliers, ptw, quantreg, Rfit, robustbase,\nshiny,
signal","License":"GPL-
3","NeedsCompilation":"no","Package":"chipPCR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"drc, knitr, markdown, MBmca (>= 0.0.3-4), qpcR, RDML,
xtable","Title":"Toolkit of Helper Functions
to Pre-Process Amplification
Data","URL":"https:\/\/github.com\/michbur\/chipPCR","Version":"0.0.8-
10"},"chngpt":{"Author":"Youyi Fong","Depends":"R (>= 3.0.0), kyotil,
MASS","Description":"Change point regression models are also called two-phase
regression, break-point regression, split-point regression structural change models
and threshold regression models. Hypothesis testing in change point logistic
regression with or without interaction terms. Several options are provided for
testing in models with interaction, including a maximum of likelihood ratios test
that determines p-value through Monte Carlo. Estimation under change point model is
also included, but less developed at this
point.","Imports":"survival","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"chngpt","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"RUnit, mvtnorm","Title":"Change Point
Regression","Version":"2015.9-5"},"choiceDes":{"Author":"Jack Horne [aut,
cre]","Depends":"R (>= 2.15.2), AlgDesign","Description":"This package consists of
functions to design DCMs and other types of choice\nstudies (including MaxDiff and
other tradeoffs)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"choiceDes","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Design Functions for Choice Studies","Version":"0.9-
1"},"choplump":{"Author":"Michael P. Fay","Depends":"R (>= 2.5.0),
stats","Description":"Choplump Tests are Permutation Tests for Comparing Two Groups
with Some Positive but Many Zero Responses","License":"GPL-
3","NeedsCompilation":"no","Package":"choplump","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"coin, survival","Title":"Choplump
tests","Version":"1.0-0.4"},"chopthin":{"Author":"Axel Gandy and F. Din-Houn
Lau","Description":"Resampling is a standard step in particle filtering and
in\nsequential Monte Carlo. This package implements the chopthin resampler,
which\nkeeps a bound on the ratio between the largest and the smallest weights
after\nresampling.","Imports":"Rcpp (>= 0.11.2)","License":"GPL-
3","NeedsCompilation":"yes","Package":"chopthin","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat","Title":"The Chopthin
Resampler","Version":"0.2.1"},"chords":{"Author":"Jonathan
Rosenblatt","Description":"Maximum likelihood estimation in respondent driven
samples.","Imports":"MASS","License":"GPL-
2","NeedsCompilation":"no","Package":"chords","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Estimation in respondent driven
samples","Version":"0.90"},"choroplethr":{"Author":"Ari Lamstein
<arilamstein@gmail.com>[cre, aut],\nBrian P Johnson <brian@pjohnson.info> [ctb,
frontend animation code]","Depends":"R (>= 3.0.0), acs","Description":"Choropleths
are thematic maps where geographic regions, such as\nstates, are colored according
to some metric, such as the number of people\nwho live in that state. This package
simplifies this process by 1.\nProviding ready-made functions for creating
choropleths of common maps. 2.\nProviding data and API connections to interesting
data sources for making\nchoropleths. 3. Providing a framework for creating
choropleths from\narbitrary shapefiles. 4. Overlaying those maps over reference
maps from\nGoogle Maps. Please see the vignettes for more
details.","Imports":"scales, Hmisc, stringr, ggplot2 (>= 2.0.0), dplyr, R6,
WDI,\nggmap, RgoogleMaps","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"choroplethr","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"testthat, knitr, choroplethrMaps,
choroplethrAdmin1 (>=\n1.1.0)","Title":"Simplify the Creation of Choropleth Maps in
R","URL":"http:\/\/www.arilamstein.com\/,\nhttps:\/\/github.com\/arilamstein\/choro
plethr\/,\nhttps:\/\/groups.google.com\/forum\/#!
forum\/choroplethr","Version":"3.5.2"},"choroplethrAdmin1":{"Author":"Ari Lamstein
<arilamstein@gmail.com>","Description":"Contains an administrative-level-1 map of
the world.\nAdministrative-level-1 is the generic term for the largest sub-
national\nsubdivision of a country. This package was created for use with
the\nchoroplethr package.","Imports":"ggplot2","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"choroplethrAdmin1","Repository":"http:\
/\/cran.csiro.au\/src\/contrib","Title":"Contains an Administrative-Level-1 Map of
the
World","URL":"http:\/\/www.arilamstein.com,\nhttps:\/\/github.com\/arilamstein\/cho
roplethrAdmin1,\nhttps:\/\/groups.google.com\/forum\/#!
forum\/choroplethr","Version":"1.1.0"},"choroplethrMaps":{"Author":"Ari Lamstein
<arilamstein@gmail.com>","Description":"Contains 3 maps. 1) US States 2) US
Counties 3) Countries of the\nworld.","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"choroplethrMaps","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Suggests":"ggplot2","Title":"Contains maps used by
the choroplethr
package","URL":"https:\/\/github.com\/trulia\/choroplethrMaps\/,\nhttps:\/\/groups.
google.com\/forum\/#!forum\/choroplethr","Version":"1.0"},"chromer":
{"Author":"Matthew Pennell [aut, cre]","Depends":"R (>= 2.15)","Description":"A
programmatic interface to the Chromosome Counts
Database\n(http:\/\/ccdb.tau.ac.il\/). This package is part of the rOpenSci
suite\n(http:\/\/ropensci.org)","Imports":"dplyr, httr,
data.table","License":"CC0","NeedsCompilation":"no","Package":"chromer","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"testthat,
roxygen2","Title":"Interface to Chromosome Counts Database
API","URL":"http:\/\/www.github.com\/ropensci\/chromer","Version":"0.1"},"chromoR":
{"Author":"Yoli Shavit","Depends":"R (>= 2.15.2), haarfisz,
gdata","Description":"chromoR provides users with a statistical pipeline for
analysing chromosomal interactions data (Hi-C data).It combines wavelet methods and
a Bayesian approach for correction (bias and noise) and comparison (detecting
significant changes between Hi-C maps) of Hi-C contact maps.In addition, it also
support detection of change points in 1D Hi-C contact
profiles.","License":"GPL","NeedsCompilation":"no","Package":"chromoR","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Title":"Analysis of chromosomal
interactions data (correction,\nsegmentation and
comparison)","Version":"1.0"},"chron":{"Author":"David James [aut] (S
original),\nKurt Hornik [aut, trl, cre],\nGabor Grothendieck [ctb]","Depends":"R
(>= 2.12.0)","Description":"Chronological objects which can handle dates and
times.","Enhances":"zoo","Imports":"graphics, stats","License":"GPL-
2","NeedsCompilation":"yes","Package":"chron","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"scales, ggplot2","Title":"Chronological Objects which
can Handle Dates and Times","Version":"2.3-47"},"chunked":{"Author":"Edwin de
Jonge","Depends":"dplyr","Description":"Text data can be processed chunkwise using
'dplyr' commands. These\nare recorded and executed per data chunk, so large files
can be processed with\nlimited memory using the 'LaF' package.","Imports":"LaF,
utils, lazyeval","License":"GPL-
2","NeedsCompilation":"no","Package":"chunked","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat, RSQLite","Title":"Chunkwise Text-File
Processing for
'dplyr'","URL":"https:\/\/github.com\/edwindj\/chunked","Version":"0.2.1"},"cin":
{"Author":"Xi (Rossi) LUO with contributions from Dylan Small, Chiang-shan Li, and
Paul Rosenbaum","Description":"Many experiments in neuroscience involve randomized
and fast stimulation while the continuous outcome measures respond at much slower
time scale, for example event-related fMRI. This package provide valid statistical
tools with causal interpretation under these challenging settings, without imposing
model assumptions.","License":"GPL-
2","NeedsCompilation":"no","Package":"cin","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Causal Inference for
Neuroscience","Version":"0.1"},"circlize":{"Author":"Zuguang Gu","Depends":"R (>=
2.10.0), graphics","Description":"Circular layout is an efficient way for the
visualization of huge\namounts of information. Here the circlize package provides
an implementation\nof circular layout generation in R as well as an enhancement of
available\nsoftware. The flexibility of this package is based on the usage of low-
level\ngraphics functions such that self-defined high-level graphics can be
easily\nimplemented by users for specific purposes. Together with the
seamless\nconnection between the powerful computational and visual environment in
R,\ncirclize gives users more convenience and freedom to design figures for\nbetter
understanding complex patterns behind multi-dimensional
data.","Imports":"GlobalOptions (>= 0.0.9), shape, grDevices, utils,
stats,\ncolorspace, methods, grid","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"circlize","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr, dendextend (>= 1.0.1)","Title":"Circular
Visualization","URL":"https:\/\/github.com\/jokergoo\/circlize","Version":"0.3.5"},
"circular":{"Author":"Ulric Lund <ulund@calpoly.edu>, Claudio Agostinelli
<claudio@unive.it>","Depends":"R (>= 3.0.0)","Description":"Circular Statistics,
from \"Topics in circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta,
World Scientific.","Imports":"boot","License":"GPL-
2","NeedsCompilation":"yes","Package":"circular","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Circular Statistics","Version":"0.4-7"},"cit":
{"Author":"Joshua Millstein","Description":"A likelihood-based hypothesis testing
approach is implemented for assessing causal mediation. For example, it could be
used to test for mediation of a known causal association between a DNA variant, the
'instrumental variable', and a clinical outcome or phenotype by gene expression or
DNA methylation, the potential mediator. Another example would be testing mediation
of the effect of
a drug on a clinical outcome by the molecular target. The hypothesis test
generates a p-value or permutation-based FDR value with confidence intervals to
quantify uncertainty in the causal inference. The outcome can be represented by
either a continuous or binary variable, the potential mediator is continuous, and
the instrumental variable can be continuous or binary and is not limited to a
single variable but may be a design matrix representing multiple
variables.","License":"Artistic-
2.0","NeedsCompilation":"yes","Package":"cit","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Causal Inference Test","Version":"2.0"},"citbcmst":
{"Author":"Laetitia Marisa, Aurelien de Reynies, Mickael Guedj","Depends":"R(>=
2.10.0)","Description":"This package implements the approach to assign tumor gene
expression dataset to the 6 CIT Breast Cancer Molecular Subtypes described in Guedj
et al 2012.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"citbcmst","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"CIT Breast Cancer Molecular SubTypes
Prediction","URL":"http:\/\/cit.ligue-cancer.net","Version":"1.0.4"},"citccmst":
{"Author":"Laetitia Marisa","Description":"This package implements the approach to
assign tumor gene expression dataset to the 6 CIT Colon Cancer Molecular Subtypes
described in Marisa et al 2013.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"citccmst","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"CIT Colon Cancer Molecular SubTypes
Prediction","URL":"http:\/\/cit.ligue-cancer.net","Version":"1.0.2"},"cjoint":
{"Author":"Anton Strezhnev, Elissa Berwick, Jens Hainmueller, Daniel Hopkins,
Teppei Yamamoto","Depends":"R (>= 2.0.0), sandwich, lmtest, ggplot2,
survey","Description":"An R implementation of the Average Marginal Component-
specific Effects (AMCE) estimator presented in Hainmueller, J., Hopkins, D., and
Yamamoto T. (2014) Causal Inference in Conjoint Analysis: Understanding Multi-
Dimensional Choices via Stated Preference Experiments. Political Analysis 22(1):1-
30.","Imports":"stats, utils, methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"cjoint","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat","Title":"AMCE Estimator for Conjoint
Experiments","Version":"2.0.4"},"ckanr":{"Author":"Scott Chamberlain [aut,
cre],\nImanuel Costigan [ctb],\nWush Wu [ctb],\nFlorian Mayer
[ctb]","Description":"Client for 'CKAN' 'API' (http:\/\/ckan.org\/). Includes
interface\nto 'CKAN' 'APIs' for search, list, show for packages, organizations,
and\nresources. In addition, provides an interface to the 'datastore'
'API'.","Imports":"methods, stats, utils, httr (>= 1.0.0), jsonlite (>=
0.9.17),\nmagrittr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"ckanr","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr, maptools, readxl, testthat,
xml2","Title":"Client for the Comprehensive Knowledge Archive Network
('CKAN')\n'API'","URL":"https:\/\/github.com\/ropensci\/ckanr","Version":"0.1.0"},"
clValid":{"Author":"Guy Brock <guy.brock@louisville.edu>, Vasyl Pihur
<vasyl.pihur@louisville.edu>,\nSusmita Datta <susmita.datta@louisville.edu>,
and\nSomnath Datta <somnath.datta@louisville.edu>","Depends":"R (>= 2.0),
cluster","Description":"Statistical and biological validation of clustering
results.","Imports":"methods, class","License":"LGPL-
3","NeedsCompilation":"no","Package":"clValid","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"Biobase, annotate, GO.db, moe430a.db, RankAggreg,
kohonen,\nmclust","Title":"Validation of Clustering
Results","URL":"http:\/\/guybrock.gpbrock.net\/research","Version":"0.6-
6"},"cladoRcpp":{"Author":"Nicholas J. Matzke [aut, cre, cph]","Description":"This
package implements in C++\/Rcpp various cladogenesis-related calculations that are
slow in pure R. These include the calculation of the probability of various
scenarios for the inheritance of geographic range at the divergence events on a
phylogenetic tree, and other calculations necessary for models which are not
continuous-time markov chains (CTMC), but where change instead occurs
instantaneously at speciation events. Typically these models must assess the
probability of every possible combination of (ancestor state, left descendent
state, right descendent state). This means that there are up to (# of states)^3
combinations to investigate, and in biogeographical models, there can easily be
hundreds of states, so calculation time becomes an issue. C++ implementation plus
clever tricks (many combinations can be eliminated a priori) can greatly speed the
computation time over naive R implementations. CITATION INFO: This package is the
result of my Ph.D. research, please cite the package if you use it! Type:
citation(package=\"cladoRcpp\") to get the citation
information.","Imports":"Rcpp","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"cladoRcpp","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"C++ implementations of phylogenetic cladogenesis
calculations","URL":"http:\/\/phylo.wikidot.com\/biogeobears","Version":"0.14.4"},"
clarifai":{"Author":"Gaurav Sood [aut, cre]","Depends":"R (>=
3.2.0)","Description":"Get description of images from Clarifai API. For more
information,\nsee http:\/\/clarifai.com. Clarifai uses a large deep learning cloud
to come\nup with descriptive labels of the things in an image. It also provides
how\nconfident it is about each of the labels.","Imports":"curl,
LICENSE","NeedsCompilation":"no","Package":"clarifai","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"knitr, testthat","Title":"Access to Clarifai
API","URL":"http:\/\/github.com\/soodoku\/clarifai","Version":"0.2"},"class":
{"Author":"Brian Ripley [aut, cre, cph],\nWilliam Venables [cph]","Depends":"R (>=
3.0.0), stats, utils","Description":"Various functions for classification,
including k-nearest\nneighbour, Learning Vector Quantization and Self-Organizing
Maps.","Imports":"MASS","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"class","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Functions for
Classification","URL":"http:\/\/www.stats.ox.ac.uk\/pub\/MASS4\/","Version":"7.3-
14"},"classGraph":{"Author":"Martin Maechler partly based on code from Robert
Gentleman","Depends":"methods","Description":"Construct directed graphs of S4 class
hierarchies and\nvisualize them. In general, these graphs typically are DAGs
(directed\nacyclic graphs), often simple trees in practice.","Imports":"graphics,
stats, utils, graph,
Rgraphviz","License":"GPL","NeedsCompilation":"no","Package":"classGraph","Reposito
ry":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"Matrix","Title":"Construct
Graphs of S4 Class Hierarchies","Version":"0.7-5"},"classInt":{"Author":"Roger
Bivand [aut, cre],\nHisaji Ono [ctb],\nRichard Dunlap [ctb],\nMatthieu Stigler
[ctb]","Depends":"R (>= 2.2)","Description":"Selected commonly used methods for
choosing univariate class intervals for mapping or other graphics
purposes.","Imports":"grDevices, stats, graphics, e1071, class","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"classInt","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Choose Univariate Class Intervals","Version":"0.1-
23"},"classifly":{"Author":"Hadley Wickham
<h.wickham@gmail.com>","Description":"Given $p$-dimensional training data
containing\n$d$ groups (the design space), a classification\nalgorithm (classifier)
predicts which group new data\nbelongs to. Generally the input to these algorithms
is\nhigh dimensional, and the boundaries between groups\nwill be high dimensional
and perhaps curvilinear or\nmulti-faceted. This package implements methods
for\nunderstanding the division of space between the groups.","Imports":"class,
stats, plyr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"classifly","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"e1071, rggobi, rpart, MASS","Title":"Explore
classification models in high
dimensions","URL":"http:\/\/had.co.nz\/classifly","Version":"0.4"},"classify":
{"Author":"Dr Chris Wheadon and Dr Ian Stockford","Description":"IRT classification
uses the probability that candidates of\na given ability, will answer correctly
questions of a specified\ndifficulty to calculate the probability of their
achieving\nevery possible score in a test. Due to the IRT assumption
of\nconditional independence (that is every answer given is assumed\nto depend only
on the latent trait being measured) the\nprobability of candidates achieving these
potential scores can\nbe expressed by multiplication of probabilities for
item\nresponses for a given ability. Once the true score and the\nprobabilities of
achieving all other scores have been\ndetermined for a candidate the probability of
their score lying\nin the same category as that of their true
score\n(classification accuracy), or the probability of consistent\nclassification
in a category over administrations\n(classification consistency), can be
calculated.","Imports":"Rcpp (>= 0.9.10), plyr, ggplot2, lattice, methods,
R2jags,\nreshape2","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"classify","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"R2WinBUGS","Title":"Classification Accuracy and
Consistency under IRT models","Version":"1.3"},"classyfire":{"Author":"Eleni
Chatzimichali <ea.chatzimichali@gmail.com> and Conrad Bessant
<c.bessant@qmul.ac.uk>","Depends":"R (>= 3.0.0), snowfall (>= 1.84-6), e1071 (>=
1.6-3), boot (>=\n1.3-11), neldermead (>= 1.0-9)","Description":"A collection of
functions for the creation and application of highly optimised, robustly evaluated
ensembles of support vector machines (SVMs). The package takes care of training
individual SVM classifiers using a fast parallel heuristic algorithm,
and combines individual classifiers into ensembles. Robust metrics of
classification performance are offered by bootstrap resampling and permutation
testing.","Imports":"ggplot2 (>= 1.0-0), optimbase (>= 1.0-9)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"classyfire","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"RUnit, knitr","Title":"Robust multivariate
classification using highly optimised SVM\nensembles","Version":"0.1-
2"},"cleangeo":{"Author":"Emmanuel Blondel
<emmanuel.blondel1@gmail.com>","Depends":"R (>= 2.15)","Description":"\nProvides a
set of utility tools to inspect spatial objects, facilitate\nhandling and reporting
of topology errors and geometry validity issues.\nFinally, it provides a geometry
cleaner that will fix all geometry problems,\nand eliminate (at least reduce) the
likelihood of having issues when doing\nspatial data
processing.","Imports":"methods, sp, rgeos, maptools","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"cleangeo","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat, knitr","Title":"Cleaning Geometries from
Spatial Objects","URL":"https:\/\/github.com\/eblondel\/cleangeo","Version":"0.1-
1"},"clere":{"Author":"Loic Yengo, Mickael Canouil","Depends":"R (>= 2.10),
parallel, methods, lasso2","Description":"Implements an empirical Bayes approach
for simultaneous variable clustering and regression. This version also
(re)implements in C++ an R script proposed by Howard Bondell that fits the Pairwise
Absolute Clustering and Sparsity (PACS) methodology (see Sharma et al (2013)
<DOI:10.1080\/15533174.2012.707849>).","Imports":"Rcpp","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"clere","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Simultaneous Variables Clustering and
Regression","Version":"1.1.4"},"clhs":{"Author":"Pierre Roudier","Depends":"R (>=
2.14.0)","Description":"Conditioned Latin hypercube sampling, as published by
Minasny and McBratney (2006). This method proposes to stratify sampling in presence
of ancillary data. An extension of this method, which propose to associate a cost
to each individual and take it into account during the optimisation process, is
also proposed (Roudier et al., 2012).","Imports":"utils, methods, grid, ggplot2,
sp, raster, reshape2, plyr,\nscales","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"clhs","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Conditioned Latin Hypercube Sampling","Version":"0.5-
5"},"clickstream":{"Author":"Michael Scholz","Depends":"R (>= 3.0.1), methods,
igraph, stats, utils","Description":"A set of tools to read, analyze and write
lists of click sequences\non websites (i.e., clickstream). A click can be
represented by a number,\ncharacter or string. Clickstreams can be modeled as zero-
(only computes\noccurrence probabilities), first- or higher-order Markov
chains.","Imports":"plyr, Rsolnp, data.table, arules, linprog","License":"GPL-
2","NeedsCompilation":"no","Package":"clickstream","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Analyzes Clickstreams Based on Markov
Chains","Version":"1.1.7"},"clifro":{"Author":"Blake Seers [aut,
cre]","Description":"CliFlo is a web portal to the New Zealand National
Climate\nDatabase and provides public access (via subscription) to around
6,500\nvarious climate stations. Collating and manipulating data from
CliFlo\n(hence clifro) and importing into R for further analysis, exploration
and\nvisualisation is now straightforward and coherent. The user is required
to\nhave an internet connection, and a current CliFlo subscription (free) if\ndata
from stations, other than the public Reefton electronic weather\nstation, is
sought.","Imports":"methods, lubridate, XML, selectr, RCurl, utils, ggplot2
(>=\n2.0.0), scales, RColorBrewer, reshape2","License":"GPL-
2","NeedsCompilation":"no","Package":"clifro","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"knitr, rmarkdown, ggmap (>= 2.6),
pander","Title":"Easily Download and Visualise Climate Data from
CliFlo","URL":"http:\/\/cliflo.niwa.co.nz\/
https:\/\/github.com\/ropensci\/clifro","Version":"2.4-1"},"climdex.pcic":
{"Author":"David Bronaugh <bronaugh@uvic.ca> for the Pacific Climate
Impacts\nConsortium","Depends":"R (>= 2.12.0), PCICt (>= 0.5-
4)","Description":"PCIC's implementation of Climdex routines for computation
of\nextreme climate indices.","Imports":"caTools (>= 1.0), methods, Rcpp (>=
3","NeedsCompilation":"yes","Package":"climdex.pcic","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"compiler, RUnit","Title":"PCIC Implementation of
Climdex Routines","URL":"http:\/\/www.r-project.org","Version":"1.1-6"},"clime":
{"Author":"T. Tony Cai, Weidong Liu and Xi (Rossi)
Luo","Depends":"lpSolve","Description":"A robust constrained L1 minimization method
for estimating\na large sparse inverse covariance matrix (aka precision\nmatrix),
and recovering its support for building graphical\nmodels. The computation uses
linear programming.","License":"GPL-
2","NeedsCompilation":"no","Package":"clime","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"lorec, scio","Title":"Constrained L1-minimization for
Inverse (covariance) Matrix\nEstimation","Version":"0.4.1"},"climtrends":
{"Author":"Jose Gama [aut, cre]","Depends":"R (>= 2.7.0)","Description":"Absolute
homogeneity tests SNHT absolute 1-breaks, 1-break,\nSD different from 1, 2-breaks,
Buishand, Pettitt, von Neumann ratio and\nratio-rank, Worsley, and Craddock,
Relative homogeneity tests SNHT\nabsolute 1-breaks, 1-break SD different from 1, 2-
breaks, Peterson\nand Easterling, and Vincent, Differences in scale between two
groups Siegelâ€“Tukey,\nCreate reference time series mean, weights\/correlation,
finding outliers Grubbs,\nESD, MAD, Tietjen Moore, Hampel, etc.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"climtrends","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Statistical Methods for Climate
Sciences","Version":"1.0.5"},"climwin":{"Author":"Liam D. Bailey and Martijn van de
Pol","Depends":"R (>= 2.10), ggplot2, gridExtra","Description":"Contains functions
to detect and visualise periods of climate sensitivity (climate windows) for a
given biological response.","Imports":"evd, lme4, lubridate, MuMIn,
reshape","License":"GPL-
2","NeedsCompilation":"no","Package":"climwin","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat, knitr","Title":"Climate Window
Analysis","Version":"0.1.2"},"clinUtiDNA":{"Author":"Thuy Trang
Nguyen","Description":"This package provides the estimation of an index
measuring\nthe clinical utility of DNA testing in the context of\ngene-environment
interactions on a disease. The corresponding\ngene-environment interaction effect
on the additive scale can\nalso be obtained. The estimation is based on case-
control or\ncohort data. The method was developed by Nguyen et al.
2013.","License":"GPL-
3","NeedsCompilation":"no","Package":"clinUtiDNA","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Clinical Utility of DNA
Testing","Version":"1.0"},"clinfun":{"Author":"Venkatraman E. Seshan","Depends":"R
(>= 2.0.0), graphics, stats","Description":"Utilities to make your clinical
collaborations easier if not fun.","Imports":"mvtnorm","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"clinfun","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"survival","Title":"Clinical Trial Design and Data
Analysis Functions","Version":"1.0.11"},"clinsig":{"Author":"Jim Lemon
<drjimlemon@gmail.com>,","Description":"Functions for calculating clinical
significance.","Imports":"grDevices, graphics, stats, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"clinsig","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Clinical Significance
Functions","Version":"1.1"},"clipr":{"Author":"Matthew Lincoln [aut, cre],\nLouis
Maddox [ctb]","Description":"Simple utility functions to read from and write to the
system\nclipboards of Windows, OS X, and Linux.","Imports":"utils","License":"GPL-
3","NeedsCompilation":"no","Package":"clipr","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat","Title":"Read and Write from the System
Clipboard","URL":"https:\/\/github.com\/mdlincoln\/clipr","Version":"0.2.0"},"clisy
mbols":{"Author":"Gabor Csardi [aut, cre],\nSindre Sorhus [aut]","Description":"A
small subset of Unicode symbols, that are useful\nwhen building command line
applications. They fall back to\nalternatives on terminals that do not support
Unicode.\nMany symbols were taken from the 'figures' 'npm' package\n(see
<https:\/\/github.com\/sindresorhus\/figures>).","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"clisymbols","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Unicode Symbols at the R
Prompt","URL":"https:\/\/github.com\/gaborcsardi\/clisymbols","Version":"1.0.0"},"c
logitL1":{"Author":"Stephen Reid and Robert Tibshirani","Depends":"Rcpp (>=
0.10.2)","Description":"Tools for the fitting and cross validation of exact
conditional logistic regression models with lasso and elastic net penalties. Uses
cyclic coordinate descent and warm starts to compute the entire path
efficiently.","License":"GPL-
2","NeedsCompilation":"yes","Package":"clogitL1","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Fitting exact conditional logistic regression with lasso
and\nelastic net penalties","Version":"1.4"},"clogitboost":{"Author":"Haolun Shi
and Guosheng Yin","Description":"A set of functions to fit a boosting conditional
logit model.","Imports":"Rcpp (>= 0.11.6)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"clogitboost","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Boosting Conditional Logit
Model","Version":"1.1"},"cloudUtil":{"Author":"Christian
Panse <cp@fgcz.ethz.ch>, Ermir Qeli <ermir.qeli@gmail.com>","Depends":"R (>=
2.11.0), methods","Description":"Provides means of plots for comparing utilization
data of compute systems.","License":"GPL-
2","NeedsCompilation":"no","Package":"cloudUtil","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Cloud Util Plots","URL":"http:\/\/fgcz-
data.uzh.ch\/~cpanse\/cloudUtil\/","Version":"0.1.10"},"clpAPI":{"Author":"Gabriel
Gelius-Dietrich [aut, cre]","Depends":"R (>= 2.6.0)","Description":"R Interface to
C API of COIN-OR Clp, depends on COIN-OR Clp Version >=
1.12.0","Imports":"methods","License":"GPL-
3","NeedsCompilation":"yes","Package":"clpAPI","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"R Interface to C API of COIN-OR
Clp","Version":"1.2.6"},"clttools":{"Author":"Simiao Ye, Jingning
Mei","Description":"Central limit theorem experiments presented by data frames or
plots. Functions include generating theoretical sample space, corresponding
probability, and simulated results as well.","License":"GPL-
2","NeedsCompilation":"no","Package":"clttools","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Central Limit Theorem Experiments (Theoretical and
Simulation)","Version":"1.3"},"clue":{"Author":"Kurt Hornik [aut, cre],\nWalter
BÃ¶hm [ctb]","Depends":"R (>= 2.10)","Description":"CLUster
Ensembles.","Enhances":"RWeka, ape, cba, cclust, flexclust, flexmix, kernlab,
mclust,\nmovMF, modeltools","Imports":"stats, cluster, graphics,
2","NeedsCompilation":"yes","Package":"clue","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"e1071, lpSolve (>= 5.5.7), quadprog (>= 1.4-8),
relations","Title":"Cluster Ensembles","Version":"0.3-51"},"clues":{"Author":"Fang
Chang <changf@mathstat.yorku.ca>, Vincent Carey\n<stvjc@channing.harvard.edu>,
Weiliang Qiu\n<stwxq@channing.harvard.edu>, Ruben H. Zamar\n<ruben@stat.ubc.ca>,
Ross Lazarus\n<ross.lazarus@channing.harvard.edu>, Xiaogang
Wang\n<stevenw@mathstat.yorku.ca>","Depends":"R (>= 3.1.0), stats,
utils","Description":"We developed the clues R package to provide functions\nfor
automatically estimating the number of clusters and\ngetting the final cluster
partition without any input\nparameter except the stopping rule for
convergence.\nThe package also provides functions to\nevaluate and compare the
performances of partitions of a data\nset both numerically and
graphically.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"clues","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"cluster","Title":"Clustering Method Based on Local
Shrinking","Version":"0.5.6"},"clusrank":{"Author":"Yujing Jiang [aut, cre],\nJun
Yan [ctb]","Depends":"R (>= 3.1.0)","Description":"Non-parametric tests (Wilcoxon
rank sum test and Wilcoxon signed rank test) for clustered
data.","Imports":"stats","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"clusrank","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr","Title":"Wilcoxon Rank Sum Test for Clustered
Data","Version":"0.1-1"},"clustMD":{"Author":"Damien
McParland","Description":"Model-based clustering of mixed data (i.e. data which
consist of continuous, binary, ordinal or nominal variables) using a parsimonious
mixture of latent Gaussian variable models.","Imports":"tmvtnorm, mvtnorm,
truncnorm, MASS, mclust, msm","License":"GPL-
2","NeedsCompilation":"no","Package":"clustMD","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Model Based Clustering for Mixed
Data","Version":"1.1"},"clustMixType":{"Author":"Gero
Szepannek","Description":"Functions to perform k-prototypes partitioning clustering
for\nmixed variable-type data according to Z.Huang (1998): Extensions to the k-
Means\nAlgorithm for Clustering Large Data Sets with Categorical Variables, Data
Mining\nand Knowledge Discovery 2, 283-304,
<DOI:10.1023\/A:1009769707641>.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"clustMixType","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"k-Prototypes Clustering for Mixed Variable-Type
Data","Version":"0.1-16"},"cluster":{"Author":"Martin Maechler [aut, cre],\nPeter
Rousseeuw [aut] (Fortran original),\nAnja Struyf [aut] (S original),\nMia Hubert
[aut] (S original),\nKurt Hornik [trl, ctb] (port to R; maintenance(1999-
2000)),\nMatthias Studer [ctb],\nPierre Roudier [ctb]","Depends":"R (>= 2.15.0),
utils","Description":"Methods for Cluster analysis. Much extended the original
from\nPeter Rousseeuw, Anja Struyf and Mia Hubert,\nbased on Kaufman and Rousseeuw
(1990) \"Finding Groups in Data\".","Imports":"graphics, grDevices,
2)","NeedsCompilation":"yes","Package":"cluster","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"MASS","Title":"\"Finding Groups in Data\": Cluster
Analysis Extended Rousseeuw et\nal.","Version":"2.0.3"},"cluster.datasets":
{"Author":"Frederick Novomestky <fnovomes@poly.edu>","Depends":"R (>=
2.0.1)","Description":"A collection of data sets for teaching cluster
2)","NeedsCompilation":"no","Package":"cluster.datasets","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Cluster Analysis Data Sets","Version":"1.0-
1"},"clusterCrit":{"Author":"Bernard Desgraupes (University of Paris Ouest - Lab
Modal'X)","Description":"Compute clustering validation indices.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"clusterCrit","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"RUnit, rbenchmark","Title":"Clustering
Indices","URL":"http:www.r-project.org","Version":"1.2.6"},"clusterGeneration":
{"Author":"Weiliang Qiu <stwxq@channing.harvard.edu>, Harry
Joe\n<harry@stat.ubc.ca>.","Depends":"R (>= 2.9.1), MASS","Description":"We
developed the clusterGeneration package to provide functions\nfor generating random
clusters, generating random\ncovariance\/correlation matrices,\ncalculating a
separation index (data and population version)\nfor pairs of clusters or cluster
distributions, and 1-D and 2-D\nprojection plots to visualize clusters. The
package also\ncontains a function to generate random clusters based on\nfactorial
designs with factors such as degree of separation,\nnumber of clusters, number of
variables, number of noisy\nvariables.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"clusterGeneration","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Random Cluster Generation (with Specified
Degree of Separation)","Version":"1.3.4"},"clusterGenomics":{"Author":"Gro Nilsen
and Ole Christian Lingjaerde","Description":"The Partitioning Algorithm based on
Recursive Thresholding\n(PART) is used to recursively uncover clusters and
subclusters\nin the data. Functionality is also available for visualization\nof the
clustering.","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"clusterGenomics","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Identifying clusters in genomics data by
recursive partitioning","Version":"1.0"},"clusterPower":{"Author":"Nicholas G.
Reich <nick@schoolph.umass.edu>, Daniel Obeng
<dobeng@gmail.com>","Description":"This package enables researchers to calculate
power for cluster-randomized crossover trials by employing a simulation-based
approach. A particular study design is specified, with fixed sample sizes for all
clusters and an assumed treatment effect, and the empirical power for that study
design is calculated by simulating hypothetical datasets.","Imports":"lme4 (>=
2)","NeedsCompilation":"no","Package":"clusterPower","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Power calculations for cluster-randomized and
cluster-randomized\ncrossover trials","Version":"0.5"},"clusterRepro":
{"Author":"Amy Kapp <Amy_Kapp@hotmail.com> and Rob
Tibshirani\n<robert.tibshirani@stanford.edu>","Depends":"R (>=
2.2.0)","Description":"A function for validating microarry clusters
via\nreproducibility","License":"GPL-
2","NeedsCompilation":"no","Package":"clusterRepro","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Reproducibility of gene expression
clusters","Version":"0.5-1.1"},"clusterSEs":{"Author":"Justin Esarey [aut,
cre]","Depends":"R (>= 3.2.1), AER, Formula, plm, stats","Description":"Calculate
p-values and confidence intervals using cluster-adjusted t-statistics (based on
Ibragimov and Muller 2010, Journal of Business and Economic Statistics 28(4)),
pairs cluster bootstrapped t-statistics, and wild cluster bootstrapped t-statistics
(the latter two techniques based on Cameron, Gelbach, and Miller 2008, Review of
Economics and Statistics 90(3)). Procedures are included for use with GLM, ivreg,
plm (fixed effects), and mlogit models.","Imports":"sandwich, lmtest, mlogit,
2)","NeedsCompilation":"no","Package":"clusterSEs","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Calculate Cluster-Robust p-Values and Confidence
Intervals","Version":"2.1"},"clusterSim":{"Author":"Marek Walesiak
<marek.walesiak@ue.wroc.pl> Andrzej Dudek
<andrzej.dudek@ue.wroc.pl>","Depends":"cluster, MASS","Description":"Distance
measures (GDM1, GDM2,\tSokal-Michener, Bray-Curtis, for symbolic interval-valued
data), cluster quality indices (Calinski-Harabasz, Baker-Hubert, Hubert-Levine,
Silhouette, Krzanowski-Lai, Hartigan, Gap,\tDavies-Bouldin),\tdata normalization
formulas, data generation (typical and non-typical data), HINoV
method,\treplication analysis, linear ordering methods, spectral clustering,
agreement indices between two partitions, plot functions (for categorial and
symbolic interval-valued data).","Imports":"ade4, e1071, rgl,
R2HTML","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"clusterSim","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"mlbench","Title":"Searching for Optimal Clustering
Procedure for a Data
Set","URL":"http:\/\/keii.ue.wroc.pl\/clusterSim","Version":"0.44-2"},"clusterfly":
{"Author":"Hadley
Wickham <h.wickham@gmail.com>","Depends":"rggobi","Description":"Visualise
clustering algorithms with GGobi. Contains both\ngeneral code for visualising
clustering results and specific\nvisualisations for model-based, hierarchical and
SOM clustering.","Imports":"e1071, reshape2, plyr, RGtk2","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"clusterfly","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"som, mclust, kohonen,
ggplot2","Title":"Explore clustering interactively using R and
GGobi","URL":"http:\/\/had.co.nz\/clusterfly","Version":"0.4"},"clustering.sc.dp":
{"Author":"Tibor Szkaliczki [aut, cre],\nJ. Song [ctb]","Depends":"R (>=
2.10.0)","Description":"A dynamic programming algorithm for optimal clustering
multidimensional data with sequential constraint. The algorithm minimizes the sum
of squares of within-cluster distances. The sequential constraint allows only
subsequent items of the input data to form a cluster. The sequential constraint is
typically required in clustering data streams or items with time stamps such as
video frames, GPS signals of a vehicle, movement data of a person, e-pen data, etc.
The algorithm represents an extension of Ckmeans.1d.dp to multiple dimensional
spaces. Similarly to the one-dimensional case, the algorithm guarantees optimality
and repeatability of clustering. Method clustering.sc.dp can find the optimal
clustering if the number of clusters is known. Otherwise, methods
findwithinss.sc.dp and backtracking.sc.dp can be used.","License":"LGPL (>=
3)","NeedsCompilation":"yes","Package":"clustering.sc.dp","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Optimal Distance-Based Clustering for
Multidimensional Data with\nSequential Constraint","Version":"1.0"},"clustertend":
{"Author":"Luo YiLan, Zeng RuTong","Description":"Calculate some statistics aiming
to help analyzing the clustering tendency of given data. In the first version,
Hopkins' statistic is implemented.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"clustertend","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Check the Clustering
Tendency","Version":"1.4"},"clusteval":{"Author":"John A. Ramey","Depends":"R (>=
2.15)","Description":"An R package that provides a suite of tools to
evaluate\nclustering algorithms, clusterings, and individual
clusters.","Imports":"parallel, mvtnorm, Rcpp (>=
0.9.13)","License":"MIT","NeedsCompilation":"yes","Package":"clusteval","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Evaluation of Clustering
Algorithms","Version":"0.1"},"clustrd":{"Author":"Angelos Markos [aut,
cre],\nAlfonso Iodice D' Enza [aut],\nMichel Van de Velden
[aut]","Depends":"corpcor, e1071, ggplot2, irlba","Description":"A collection of
methods for joint dimension reduction
and\nclustering","License":"GPL","NeedsCompilation":"no","Package":"clustrd","Repos
itory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Methods for joint dimension
reduction and clustering","Version":"0.1.2"},"clustsig":{"Author":"Douglas Whitaker
<whitaker@ufl.edu> and Mary Christman\n<mcxman@ufl.edu>","Depends":"R (>=
3.0.2)","Description":"A complimentary package for use with hclust; simprof
tests\nto see which (if any) clusters are statistically different. The\nnull
hypothesis is that there is no a priori group structure.\nSee Clarke, K.R.,
Somerfield, P.J., and Gorley R.N. 2008.\nTesting of null hypothesis in exploratory
community analyses:\nsimilarity profiles and biota-environment linkage. J. Exp.
Mar.\nBiol. Ecol. 366, 56-69.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"clustsig","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Significant Cluster
Analysis","URL":"http:\/\/www.douglaswhitaker.com","Version":"1.1"},"clustvarsel":
{"Author":"Nema Dean, Adrian E. Raftery, and Luca Scrucca","Depends":"R (>= 3.2),
mclust (>= 5.1), BMA (>= 3.18), foreach, iterators","Description":"A function which
implements variable selection methodology for model-based clustering which allows
to find the (locally) optimal subset of variables in a data set that have
group\/cluster information. A greedy or headlong search can be used, either in a
forward-backward or backward-forward direction, with or without sub-sampling at the
hierarchical clustering stage for starting MCLUST models. By default the algorithm
uses a sequential search, but parallelisation is also available.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"clustvarsel","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"MASS, parallel, doParallel","Title":"Variable
Selection for Model-Based Clustering","Version":"2.2"},"clv":{"Author":"Lukasz
Nieweglowski <wookashn@gmail.com>","Depends":"cluster,
class","Description":"Package contains most of the popular internal and
external\ncluster validation methods ready to use for the most of the\noutputs
produced by functions coming from package \"cluster\".\nPackage contains also
functions and examples of usage for\ncluster stability approach that might be
applied to algorithms\nimplemented in \"cluster\" package as well as user
defined\nclustering algorithms.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"clv","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Cluster Validation Techniques","Version":"0.3-2.1"},"cmaes":
{"Author":"Heike Trautmann <trautmann@statistik.tu-dortmund.de> and Olaf\nMersmann
<olafm@statistik.tu-dortmund.de> and David Arnu\n<david.arnu@statistik.tu-
dortmund.de>","Depends":"R (>= 2.9.0)","Description":"Single objective optimization
using a CMA-ES.","License":"GPL-
2","NeedsCompilation":"no","Package":"cmaes","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"RUnit","Title":"Covariance Matrix Adapting Evolutionary
Strategy","Version":"1.0-11"},"cmaesr":{"Author":"Jakob Bossek [aut,
cre]","Depends":"ParamHelpers (>= 1.3), BBmisc (>= 1.6), checkmate (>= 1.1),\nsmoof
(>= 1.1)","Description":"Pure R implementation of the Covariance Matrix Adaptation
-\nEvolution Strategy (CMA-ES) with optional restarts (IPOP-CMA-
ES).","Imports":"ggplot2","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"cmaesr","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat","Title":"Covariance Matrix Adaptation
Evolution
Strategy","URL":"https:\/\/github.com\/jakobbossek\/cmaesr","Version":"1.0.1"},"cmm
":{"Author":"Wicher Bergsma and Andries van der Ark","Description":"Quite extensive
package for the estimation of marginal models for categorical data.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"cmm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Categorical Marginal Models","Version":"0.8"},"cmna":
{"Author":"\"James P. Howard, II\" <jh@jameshoward.us>","Depends":"R (>=
2.10)","Description":"Provides the source and examples for James P. Howard,
II,\n\"Computational Methods for Numerical Analysis with
R,\"\n<https:\/\/jameshoward.us\/cmna>, a forthcoming book on\nnumerical methods in
R.","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"cmna","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat","Title":"Computational Methods for
Numerical Analysis","Version":"0.1.2"},"cmprsk":{"Author":"Bob Gray
<gray@jimmy.harvard.edu>","Depends":"R (>= 2.15.0),
survival","Description":"Estimation, testing and regression modeling
of\nsubdistribution functions in competing risks, as described in Gray\n(1988), A
class of K-sample tests for comparing the cumulative\nincidence of a competing
risk, Ann. Stat. 16:1141-1154, and Fine JP and\nGray RJ (1999), A proportional
hazards model for the subdistribution\nof a competing risk, JASA, 94:496-
2)","NeedsCompilation":"yes","Package":"cmprsk","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Subdistribution Analysis of Competing
Risks","URL":"http:\/\/www.r-project.org","Version":"2.2-7"},"cmprskQR":
{"Author":"Stephan Dlugosz, based on code from Limin Peng and Ruosha
Li","Depends":"R (>= 2.13.0)","Description":"Estimation, testing and regression
modeling of\nsubdistribution functions in competing risks using quantile
regressions,\nas described in Peng and Fine (2009)
<DOI:10.1198\/jasa.2009.tm08228>.","Imports":"graphics, quantreg, stats,
survival","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"cmprskQR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Analysis of Competing Risks Using Quantile
Regressions","URL":"https:\/\/bitbucket.org\/sdlugosz\/cmprskqr","Version":"0.9.1"}
,"cmrutils":{"Author":"Andrey Paramonov","Depends":"grDevices,
chron","Description":"A collection of useful helper routines developed by\nstudents
of the Center for the Mathematical Research, Stankin,\nMoscow.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"cmrutils","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Misc Functions of the Center for the Mathematical
Research","URL":"http:\/\/aparamon.msk.ru\/svn\/study\/R-
packages\/cmrutils\/","Version":"1.3"},"cmsaf":{"Author":"Steffen Kothe
<Steffen.Kothe@dwd.de>","Depends":"ncdf4, sp, raster, stats,
fields","Description":"The Satellite Application Facility on Climate Monitoring (CM
SAF)\nis a ground segment of the European Organization for the Exploitation
of\nMeteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite
Application\nFacilities. The CM SAF contributes to the sustainable observing of the
climate\nsystem by providing Essential Climate Variables related to the energy and
water\ncycle of the atmosphere (www.cmsaf.eu). It is a joint cooperation of
seven\nNational Meteorological and Hydrological Services, including the
Deutscher\nWetterdienst (DWD).\nThe cmsaf R-package provides a small collection of
R-functions, which are\ninspired by the Climate Data Operators (cdo). This gives
the opportunity to\nanalyse and manipulate CM SAF data
without the need of installing cdo.\nThe cmsaf R-package is tested for CM SAF
netcdf data, which are structured\nin three-dimensional arrays (longitude,
latitude, time) on a rectangular grid.\nLayered CM SAF data have to be converted
with the provided `levbox_mergetime`\nfunction. The cmsaf R-package functions have
only minor checks for deviations\nfrom the recommended data structure, and give
only few specific error messages.\nThus, there is no warranty of accurate
results.\nA Windows binary file and scripts for an easy application of the
functions are\nprovided at the CM SAF homepage
(http:\/\/www.cmsaf.eu\/EN\/Products\/Tools\/Tools_node.html).","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"cmsaf","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Tools for CM SAF Netcdf Data","Version":"1.6.1"},"cmvnorm":
{"Author":"Robin K. S. Hankin","Depends":"emulator (>= 1.2-
15)","Description":"Various utilities for the complex multivariate Gaussian
distribution.","Imports":"elliptic","License":"GPL-
2","NeedsCompilation":"no","Package":"cmvnorm","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"The Complex Multivariate Gaussian
Distribution","Version":"1.0-3"},"cna":{"Author":"Ambuehl, Mathias, Michael
Baumgartner, Ruedi Epple, Alexis Kauffmann and Alrik Thiem","Depends":"R (>=
2.13.0), utils","Description":"Provides functions for performing Coincidence
Analysis (CNA).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"cna","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"A Package for Coincidence Analysis (CNA)","Version":"1.0-
3"},"cncaGUI":{"Author":"Ana Belen Nieto Librero <ananieto@usal.es>, Priscila
Willems\n<pwillems@bariloche.inta.gov.ar>, Purificacion Galindo\nVillardon
<pgalindo@usal.es>","Depends":"R (>= 3.1.1)","Description":"A GUI with which users
can construct and interact\nwith Canonical Correspondence Analysis and Canonical
Non-Symmetrical Correspondence Analysis and provides inferential results by using
Bootstrap Methods.","Imports":"rgl, tkrplot, tcltk, tcltk2, shapes, plotrix,
2)","NeedsCompilation":"no","Package":"cncaGUI","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Canonical Non-Symmetrical Correspondence Analysis in
R","Version":"1.0"},"cnmlcd":{"Author":"Yu Liu, Yong
Wang","Depends":"lsei","Description":"Contains functions for computing the
nonparametric maximum\nlikelihood estimate of a log-concave density function
from\nunivariate observations. The log-density estimate is always a\npiecewise
linear function.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"cnmlcd","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Maximum Likelihood Estimation of a Log-Concave Density
Function","Version":"1.0-0"},"coala":{"Author":"Paul Staab [aut, cre],\nDirk
Metzler [aut, ths]","Depends":"R (>= 3.1.0)","Description":"Coalescent simulators
can rapidly simulate biological sequences\nevolving according to a given model of
evolution.\nYou can use this package to specify such models, to conduct the
simulations\nand to calculate additional statistics from the results.\nIt relies on
existing simulators for doing the simulation, and currently\nsupports the programs
'ms', 'msms' and 'scrm'. It also supports finite-sites\nmutation models by
combining the simulators with the program 'seq-gen'.","Imports":"assertthat (>=
0.1), methods, parallel, R6 (>= 2.0.1), Rcpp\n(>= 0.11.0), rehh (>= 1.11), scrm (>=
1.6.0-2), stats, utils","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"coala","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"abc (>= 2.0), knitr, PopGenome (>= 2.1.0),
phyclust (>=\n0.1-16), rmarkdown, testthat (>= 0.11.0)","Title":"A Framework for
Coalescent
Simulation","URL":"https:\/\/github.com\/statgenlmu\/coala","Version":"0.4.0"},"coa
lescentMCMC":{"Author":"Emmanuel Paradis [aut, cre, cph]","Depends":"ape, coda,
lattice","Description":"Flexible framework for coalescent analyses in R. It
includes a main function running the MCMC algorithm, auxiliary functions for tree
rearrangement, and some functions to compute population genetic
parameters.","Imports":"Matrix, phangorn, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"coalescentMCMC","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"MCMC Algorithms for the
Coalescent","Version":"0.4-1"},"coarseDataTools":{"Author":"Nicholas G. Reich
<nick@schoolph.umass.edu>, Justin Lessler\n<jlessler@jhsph.edu>, Andrew Azman
<andrewazman@gmail.com>","Description":"Functions to analyze coarse
data.\nSpecifically, it contains functions to (1) fit parametric
accelerated\nfailure time models to interval-censored survival time data, and
(2)\nestimate the case-fatality ratio in scenarios with under-reporting.\nThis
package's development was motivated by applications to infectious\ndisease: in
particular, problems with estimating the incubation period and\nthe case fatality
ratio of a given disease. Sample data files are included\nin the
package.","Imports":"MCMCpack, graphics, stats, methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"coarseDataTools","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"A Collection of Functions to Help with Analysis
of Coarsely\nObserved Data","URL":"http:\/\/cran.r-
project.org\/package=coarseDataTools","Version":"0.6-3"},"cobs":{"Author":"Pin T.
Ng <Pin.Ng@nau.edu> and Martin Maechler","Depends":"R (>=
2.15.1)","Description":"Qualitatively Constrained (Regression) Smoothing Splines
via\nLinear Programming and Sparse Matrices.","Imports":"SparseM (>= 1.6), quantreg
(>= 4.65),\ngrDevices,graphics,methods,stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"cobs","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"COnstrained B-Splines (Sparse Matrix
Based)","URL":"http:\/\/curves-etc.r-forge.r-project.org\/\nhttp:\/\/r-forge.r-
project.org\/R\/?group_id=846","Version":"1.3-1"},"cocor":{"Author":"Birk
Diedenhofen [aut, cre]","Depends":"methods","Description":"Statistical tests for
the comparison between two\ncorrelations based on either independent or dependent
groups.\nDependent correlations can either be overlapping or\nnonoverlapping. A web
interface is available at\nhttp:\/\/comparingcorrelations.org. A plugin for the R
GUI and\nIDE RKWard is included. Please install RKWard
from\nhttps:\/\/rkward.kde.org to use this feature. The respective R\npackage
'rkward' cannot be installed directly from a\nrepository, as it is a part of
RKWard.","Enhances":"rkward","Imports":"stats","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"cocor","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat","Title":"Comparing
Correlations","URL":"http:\/\/comparingcorrelations.org","Version":"1.1-
2"},"cocorresp":{"Author":"Original Matlab routines by C.J.F. ter Braak and A.P.
Schaffers. R port by Gavin L. Simpson.\nFunction simpls based on simpls.fit
(package pls) by Ron Wehrens and Bjorn-Helge Mevik.","Depends":"vegan (>= 2.2-0), R
(>= 3.0.0)","Description":"Fits predictive and symmetric co-correspondence analysis
(CoCA) models to relate one data matrix\nto another data matrix. More specifically,
CoCA maximises the weighted covariance\nbetween the weighted averaged species
scores of one community and the weighted averaged species\nscores of another
community. CoCA attempts to find patterns that are common to both
communities.","Imports":"stats, graphics, utils, grDevices","License":"GPL-
2","NeedsCompilation":"no","Package":"cocorresp","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat, knitr","Title":"Co-Correspondence Analysis
Methods","URL":"https:\/\/github.com\/gavinsimpson\/cocorresp","Version":"0.3-
0"},"cocron":{"Author":"Birk Diedenhofen [aut,
cre]","Depends":"methods","Description":"Statistical tests for the comparison
between two or more alpha\ncoefficients based on either dependent or independent
groups of individuals.\nA web interface is available at
http:\/\/comparingcronbachalphas.org. A plugin\nfor the R GUI and IDE RKWard is
included. Please install RKWard from https:\/\/\nrkward.kde.org to use this
feature. The respective R package 'rkward' cannot be\ninstalled directly from a
repository, as it is a part of
RKWard.","Enhances":"rkward","Imports":"stats","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"cocron","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat","Title":"Statistical Comparisons of Two or
more Alpha
Coefficients","URL":"http:\/\/comparingcronbachalphas.org","Version":"1.0-
1"},"coda":{"Author":"Martyn Plummer [aut, cre, trl],\nNicky Best [aut],\nKate
Cowles [aut],\nKaren Vines [aut],\nDeepayan Sarkar [aut],\nDouglas Bates
[aut],\nRussell Almond [aut],\nArni Magnusson [aut]","Depends":"R (>=
2.14.0)","Description":"Provides functions for summarizing and plotting the\noutput
from Markov Chain Monte Carlo (MCMC) simulations, as\nwell as diagnostic tests of
convergence to the equilibrium\ndistribution of the Markov
chain.","Imports":"lattice","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"coda","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Output Analysis and Diagnostics for MCMC","Version":"0.18-
1"},"codadiags":{"Author":"Yann Richet, Xavier Bay, Olivier Jacquet, Alexis
Jinaphanh","Depends":"R (>= 3.0.0), coda","Description":"Markov chain Monte Carlo
burn-in based on \"bridge\" statistics, in the way of coda::heidel.diag, but
including non asymptotic tabulated statistics.","License":"GPL-
3","NeedsCompilation":"yes","Package":"codadiags","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Markov chain Monte Carlo burn-in based on \"bridge\"
statistics","Version":"1.0"},"codep":{"Author":"Guillaume Guenard and Pierre
Legendre, with contributions from Bertrand Pages","Depends":"R (>= 3.0.0),
grDevices, graphics, stats","Description":"Computation
of Multiscale Codependence Analysis and spatial eigenvector maps, as an additional
feature.","License":"GPL-
2","NeedsCompilation":"yes","Package":"codep","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"vegan","Title":"Multiscale Codependence
Analysis","Version":"0.5-1"},"codetools":{"Author":"Luke Tierney <luke-
tierney@uiowa.edu>","Depends":"R (>= 2.1)","Description":"Code analysis tools for
R.","License":"GPL","NeedsCompilation":"no","Package":"codetools","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Title":"Code Analysis Tools for
R","Version":"0.2-14"},"codingMatrices":{"Author":"Bill
Venables","Depends":"stats","Description":"A collection of coding functions as
alternatives to the standard\nfunctions in the stats package, which have names
starting with 'contr.'. Their\nmain advantage is that they provide a consistent
method for defining marginal\neffects in multi-way factorial models. In a simple
one-way ANOVA model the\nintercept term is always the simple average of the class
means.","Imports":"Matrix, methods, fractional, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"codingMatrices","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"knitr, MASS, dplyr, car,
ggplot2","Title":"Alternative Factor Coding Matrices for Linear Model
Formulae","Version":"0.2.0"},"codyn":{"Author":"Lauren Hallett [aut],\nSydney K.
Jones [aut],\nAndrew A. MacDonald [aut],\nDan F. B. Flynn [aut],\nPeter Slaughter
[aut],\nJulie Ripplinger [aut],\nScott L. Collins [aut],\nCorinna Gries
[aut],\nMatthew B. Jones [aut, cre]","Depends":"R (>= 3.2.0)","Description":"A
toolbox of ecological community dynamics metrics that are\nexplicitly temporal.
Functions fall into two categories: temporal diversity\nindices and community
stability metrics. The diversity indices are temporal\nanalogs to traditional
diversity indices such as richness and rank-abundance\ncurves. Specifically,
functions are provided to calculate species turnover, mean\nrank shifts, and lags
in community similarity between time points. The community\nstability metrics
calculate overall stability and patterns of species covariance\nand synchrony over
time.","Imports":"assertthat, stats","License":"Apache License (==
2.0)","NeedsCompilation":"no","Package":"codyn","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"testthat, knitr, ggplot2, reshape2, devtools,
dplyr","Title":"Community Dynamics
Metrics","URL":"https:\/\/github.com\/laurenmh\/codyn\/","Version":"1.0.1"},"coeffi
cientalpha":{"Author":"Zhiyong Zhang and Ke-Hai Yuan","Depends":"rsem,
lavaan","Description":"Cronbach's alpha and McDonald's omega are widely used
reliability or internal consistency measures in social, behavioral and education
sciences. Alpha is reported in nearly every study that involves measuring a
construct through multiple test items. The package 'coefficientalpha' calculates
coefficient alpha and coefficient omega with missing data and non-normal data.
Robust standard errors and confidence intervals are also provided. A test is also
available to test the tau-equivalent and homogeneous assumptions. Version 0.5 added
the bootstrap confidence
intervals.","License":"GPL","NeedsCompilation":"no","Package":"coefficientalpha","R
epository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Robust Coefficient Alpha
and Omega with Missing and Non-Normal\nData","Version":"0.5"},"coefplot":
{"Author":"Jared P. Lander","Depends":"ggplot2 (>= 2.0.0)","Description":"Plots the
coefficients from model objects. This very quickly shows the user the point
estimates and confidence intervals for fitted models.","Enhances":"glmnet,
maxLik","Imports":"plyr, reshape2, useful, stats","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"coefplot","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat","Title":"Plots Coefficients from
Fitted Models","Version":"1.2.4"},"coenocliner":{"Author":"Gavin L. Simpson [aut,
cre],\nJari Oksanen [ctb],\nFrancisco Rodriguez-Sanchez
[ctb]","Description":"Simulate species occurrence and abundances (counts)
along\ngradients.","Imports":"stats","License":"GPL-
2","NeedsCompilation":"no","Package":"coenocliner","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat, knitr","Title":"Coenocline
Simulation","URL":"https:\/\/github.com\/gavinsimpson\/coenocliner\/","Version":"0.
2-1"},"coenoflex":{"Author":"David W. Roberts
<droberts@montana.edu>","Depends":"mgcv","Description":"Simulates the composition
of samples of vegetation\naccording to gradient-based vegetation theory. Features
a\nflexible algorithm incorporating competition and complex\nmulti-gradient
interaction.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"coenoflex","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Gradient-Based Coenospace Vegetation
Simulator","Version":"2.1-0"},"coexist":{"Author":"Youhua
Chen","Description":"species coexistence modeling under asymmetric dispersal\nand
fluctuating source-sink dynamics;testing the proportion of\ncoexistence scenarios
driven by neutral and niche processes","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"coexist","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Species coexistence modeling and
analysis","Version":"1.0"},"cofeatureR":{"Author":"Fong Chun Chan [aut,
cre]","Depends":"R (>= 3.1.0)","Description":"Generate cofeature (feature by
sample) matrices. The package\nutilizes ggplot2::geom_tile() to generate the matrix
allowing for easy\nadditions from the base matrix.","Imports":"ggplot2 (>= 1.0.0),
dplyr (>= 0.4.3), lazyeval (>= 0.1.10)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"cofeatureR","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Generate Cofeature
Matrices","URL":"https:\/\/github.com\/tinyheero\/cofeatureR","Version":"1.0.1"},"c
oin":{"Author":"Torsten Hothorn [aut, cre],\nKurt Hornik [aut],\nMark A. van de
Wiel [aut],\nHenric Winell [aut],\nAchim Zeileis [aut]","Depends":"R (>= 2.14.0),
methods, survival","Description":"Conditional inference procedures for the general
independence\nproblem including two-sample, K-sample (non-parametric ANOVA),
correlation,\ncensored, ordered and multivariate problems.","Imports":"stats,
modeltools (>= 0.2-9), mvtnorm (>= 1.0-3), multcomp","License":"GPL-
2","NeedsCompilation":"yes","Package":"coin","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"parallel, xtable, e1071, vcd,
TH.data","Title":"Conditional Inference Procedures in a Permutation Test
Framework","URL":"http:\/\/coin.r-forge.r-project.org","Version":"1.1-2"},"cold":
{"Author":"M. Helena Gonçalves and M. Salomé Cabral,\napart from a set of Fortran-
77 subroutines written by R. Piessens\nand E. de Doncker, belonging to the
suite \"Quadpack\".","Depends":"R (>= 2.10.0), methods, stats, graphics,
utils","Description":"Performs regression analysis for longitudinal count\ndata
using a self-decomposable probability distribution,\na random intercept term is
also allowed. Estimation is via maximization\nof the exact likelihood of a suitably
defined model. Missing values and\nunbalanced data are allowed.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"cold","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Count Longitudinal Data","Version":"1.0-4"},"collUtils":
{"Author":"Kaiyin Zhong, Fan Liu","Depends":"R (>= 3.1.3), rJava (>= 0.9-6), Rcpp
(>= 0.11.2)","Description":"Provides some low level functions for processing PLINK
input and output files.","License":"GPL-
3","NeedsCompilation":"yes","Package":"collUtils","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat","Title":"Auxiliary Package for Package
'CollapsABEL'","URL":"https:\/\/bitbucket.org\/kindlychung\/collutils","Version":"1
.0.5"},"coloc":{"Author":"Chris Wallace [aut, cre],\nClaudia Giambartolomei
[aut],\nVincent Plagnol [ctb]","Depends":"methods, colorspace, MASS,
BMA","Description":"Performs the colocalisation tests described in Plagnol et
al\n(2009), Wallace et al (2013) and Giambartolomei et al
(2013).","License":"GPL","NeedsCompilation":"no","Package":"coloc","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Suggests":"ggplot2,
snpStats","Title":"Colocalisation tests of two genetic
traits","URL":"https:\/\/github.com\/chr1swallace\/coloc","Version":"2.3-
1"},"colorRamps":{"Author":"Tim Keitt","Description":"Builds gradient color
maps","License":"GPL","NeedsCompilation":"no","Package":"colorRamps","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Title":"Builds color
tables","Version":"2.3"},"coloredICA":{"Author":"Lee, S., Shen, H., Truong, Y. and
Zanini, P.","Depends":"MASS","Description":"It implements colored Independent
Component Analysis (Lee et al., 2011) and spatial colored Independent Component
Analysis (Shen et al., 2014). They are two algorithms to perform ICA when sources
are assumed to be temporal or spatial stochastic processes,
respectively.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"coloredICA","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"fastICA","Title":"Implementation of Colored
Independent Component Analysis and\nSpatial Colored Independent Component
Analysis","Version":"1.0.0"},"colorfulVennPlot":{"Author":"Elliot Noma, Aliona
Manvae","Depends":"grid","Description":"Given 2-,3- or 4-dimensional data, plots a
Venn diagram, i.e. 'crossing circles'. The user can specify values, labels for each
circle-group and unique colors for each plotted part. Here is what it would look
like for a 3-dimensional plot:
http:\/\/elliotnoma.files.wordpress.com\/2011\/02\/venndiagram.png. To see what the
4-dimensional plot looks like, go to
http:\/\/elliotnoma.files.wordpress.com\/2013\/03\/4dplot.png.","License":"GPL-
2","NeedsCompilation":"no","Package":"colorfulVennPlot","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"MASS","Title":"Plot
and add custom coloring to Venn diagrams for 2-dimensional,\n3-dimensional and 4-
dimensional data","Version":"2.4"},"colorhcplot":{"Author":"Damiano
Fantini","Depends":"graphics","Description":"This function takes a hierarchical
cluster-class object and a factor describing the groups as arguments and generates
colorful dendrograms in which leaves belonging to different groups are identified
by colors.","License":"GPL-
2","NeedsCompilation":"no","Package":"colorhcplot","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"Biobase, stats, grDevices","Title":"Colorful
Hierarchical Clustering Dendrograms","Version":"1.0"},"colorscience":
{"Author":"Jose Gama [aut, cre]","Depends":"R (>= 2.10), Hmisc, munsellinterpol,
pracma, sp","Description":"Methods and data for color science - color conversions
by observer,\nilluminant and gamma. Color matching functions and chromaticity
diagrams.\nColor indices, color differences and spectral data
conversion\/analysis.","Enhances":"png","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"colorscience","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Color Science Methods and
Data","Version":"1.0.2"},"colorspace":{"Author":"Ross Ihaka [aut],\nPaul Murrell
[aut],\nKurt Hornik [aut],\nJason C. Fisher [aut],\nAchim Zeileis [aut,
cre]","Depends":"R (>= 2.13.0), methods","Description":"Carries out mapping between
assorted color spaces including\nRGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar
CIELUV),\nCIELAB and polar CIELAB. Qualitative, sequential, and\ndiverging color
palettes based on HCL colors are
provided.","Imports":"graphics","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"yes","Package":"colorspace","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"KernSmooth, MASS, kernlab, mvtnorm, vcd,
dichromat, tcltk","Title":"Color Space Manipulation","Version":"1.2-
6"},"colortools":{"Author":"Gaston Sanchez","Description":"R package with handy
functions to help users select and play with\ncolor schemes in an HSV color
model","License":"GPL-
3","NeedsCompilation":"no","Package":"colortools","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Tools for colors in a Hue-Saturation-Value (HSV) color
model","URL":"http:\/\/www.gastonsanchez.com","Version":"0.1.5"},"colourlovers":
{"Author":"Thomas J. Leeper","Description":"Provides access to the COLOURlovers
<http:\/\/www.colourlovers.com\/> API, which offers color inspiration and color
palettes.","Imports":"XML, jsonlite, png, graphics, utils","License":"GPL-
2","NeedsCompilation":"no","Package":"colourlovers","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat","Title":"R Client for the COLOURlovers
API","URL":"https:\/\/github.com\/leeper\/colourlovers","Version":"0.2.0"},"comato"
:{"Author":"Andreas Muehling","Description":"Provides methods for the
import\/export and automated analysis of concept maps.","Imports":"igraph, Matrix,
lattice, gdata, XML, cluster, clusterSim","License":"GPL-
3","NeedsCompilation":"no","Package":"comato","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Analysis of Concept Maps","Version":"1.0"},"combinat":
{"Author":"Scott Chasalow","Description":"routines for
combinatorics","License":"GPL-
2","NeedsCompilation":"no","Package":"combinat","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"combinatorics utilities","Version":"0.0-8"},"comclim":
{"Author":"Benjamin Blonder","Depends":"methods, R (>=
3.0.0)","Description":"Computes community climate statistics for volume and
mismatch using species' climate niches either unscaled or scaled relative to a
regional species pool. These statistics can be used to describe biogeographic
patterns and infer community assembly processes. Includes a vignette outlining
usage.","License":"GPL-
3","NeedsCompilation":"no","Package":"comclim","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Community climate
statistics","Version":"0.9.4"},"cometExactTest":{"Author":"Max Leiserson [aut,
cre],\nHsin-Ta Wu [aut],\nFabio Vandin [ctb],\nVivian Hsiao [ctb],\nBenjamin
Raphael [ctb]","Depends":"R (>= 2.15.0)","Description":"An algorithm for
identifying combinations of mutually exclusive alterations in cancer genomes. CoMEt
represents the mutations in a set M of k genes with a 2^k dimensional contingency
table, and then computes the tail probability of observing T(M) exclusive
alterations using an exact statistical test.","Imports":"dplyr","License":"MIT +
file
LICENSE","NeedsCompilation":"yes","Package":"cometExactTest","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Title":"Exact Test from the Combinations of Mutually
Exclusive\nAlterations (CoMEt)
Algorithm","URL":"http:\/\/compbio.cs.brown.edu\/projects\/comet,\nhttp:\/\/www.r-
project.org","Version":"0.1.3"},"comf":{"Author":"Marcel Schweiker [aut, cre] and
Sophia Mueller [aut] and Michael Kleber [ctr] and Boris Kingma [ctr] and Masanori
Shukuya [ctr]","Description":"Functions to calculate various common and less common
thermal comfort indices.","License":"GPL-
2","NeedsCompilation":"no","Package":"comf","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Calculation of Thermal Comfort
Indices","Version":"0.1.2"},"commandr":{"Author":"Michael
Lawrence","Depends":"methods","Description":"An S4 representation of the Command
design pattern. The\nOperation class is a simple implementation using closures and
supports\nforward and reverse (undo) evaluation. The more complicated
Protocol\nframework represents each type of command (or analytical protocol) by\na
formal S4 class. Commands may be grouped and consecutively executed\nusing the
Pipeline class. Example use cases include logging, do\/undo,\nanalysis pipelines,
GUI actions, parallel processing, etc.","Imports":"utils","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"commandr","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Command pattern in R","Version":"1.0.1"},"commentr":
{"Author":"Erik Bulow","Description":"Functions to\nproduce nicely formatted
comments to use in R-scripts (or\nLatex\/HTML\/markdown etc). A comment with
formatting is printed to the\nconsole and can then be copied to a
script.","Imports":"stringr","License":"GPL-
2","NeedsCompilation":"no","Package":"commentr","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"testthat","Title":"Print Nicely Formatted Comments for
Use in Script Files","Version":"1.0.4"},"commonmark":{"Author":"Jeroen Ooms [aut,
cre],\nJohn MacFarlane [cph] (Author of cmark)","Description":"The CommonMark
specification defines a rationalized version of markdown\nsyntax. This package uses
the libcmark reference implementation for converting\nmarkdown text into various
formats including html, latex and groff man. In\naddition it exposes the markdown
parse tree in xml format.","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"yes","Package":"commonmark","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"curl","Title":"Bindings to the CommonMark
Reference
Implementation","URL":"https:\/\/github.com\/jeroenooms\/commonmark\nhttp:\/\/commo
nmark.org\/help\/","Version":"0.8"},"compHclust":{"Author":"Gen Nowak and Robert
Tibshirani","Description":"Performs the complementary hierarchical clustering
procedure and returns X' (the expected residual matrix) and a vector of the
relative gene importances.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"compHclust","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Complementary Hierarchical
Clustering","Version":"1.0-2"},"compactr":{"Author":"Carlisle
Rainey","Description":"Creates empty plots with compact axis notation to which
users can\nadd whatever they like (points, lines, text, etc.) The notation is
more\ncompact in the sense that the axis-labels and tick-labels are closer to
the\naxis and the tick-marks are shorter. Also, if the plot appears as part of
a\nmatrix, the x-axis notation is suppressed unless the plot appears along
the\nbottom row and the y-axis notation is suppress unless the plot appears\nalong
the left column.","License":"GPL-
2","NeedsCompilation":"no","Package":"compactr","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Creates empty plots with compact axis
notation","Version":"0.1"},"compare":{"Author":"Paul
Murrell","Description":"Functions to compare a model object to a comparison
object.\nIf the objects are not identical, the functions can be instructed
to\nexplore various modifications of the objects (e.g., sorting rows,\ndropping
names) to see if the modified versions are identical.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"compare","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Comparing Objects for Differences","Version":"0.2-
6"},"compareC":{"Author":"Le Kang, Weijie Chen","Description":"Proposed by Harrell,
the C index or concordance C, is considered an overall measure of discrimination in
survival analysis between a survival outcome that is possibly right censored and a
predictive-score variable, which can represent a measured biomarker or a composite-
score output from an algorithm that combines multiple biomarkers. This package aims
to statistically compare two C indices with right-censored survival outcome, which
commonly arise from a paired design and thus resulting two correlated C
indices.","License":"GPL (>=
2.0)","NeedsCompilation":"yes","Package":"compareC","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Compare Two Correlated C Indices with Right-censored
Survival\nOutcome","Version":"1.3.1"},"compareDF":{"Author":"Alex Joseph [aut,
cre]","Depends":"R (>= 3.0.0)","Description":"Compares two dataframes which have
the same column\nstructure to show the rows that have changed. Also gives a git
style diff format\nto quickly see what has changes in addition to summary
statistics.","Imports":"dplyr (>= 0.4.3), tidyr (>= 0.4.1)","License":"MIT
+ file
LICENSE","NeedsCompilation":"no","Package":"compareDF","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"htmlTable (>= 1.5), testthat","Title":"Do a Git
Style Diff of the Rows Between Two Dataframes with\nSimilar
Structure","Version":"1.0.0"},"compareGroups":{"Author":"Isaac Subirana, Joan Vila,
Héctor Sanz, Gavin Lucas, judith Peñafiel and David Giménez","Depends":"R (>=
2.13.1), Hmisc, gdata, xtable, SNPassoc","Description":"Create data summaries for
quality control, extensive reports for exploring data, as well as publication-ready
univariate or bivariate tables in several formats (plain text, HTML,LaTeX, PDF,
Word or Excel. Perform figures to quickly visualise the distribution of your data
(boxplots, barplots, normality-plots, etc.). Display statistics (mean, median,
frequencies, incidences, etc.). Perform the appropriate tests (t-test, Analysis of
variance, Kruskal-Wallis, Fisher, log-rank, ...) depending on the nature of the
described variable (normal, non-normal or qualitative). Summarize genetic
data (Single Nucleotids Polymorphisms) data displaying Allele Frequencies and
performing Hardy-Weinberg Equilibrium tests among other typical statistics and
tests for these kind of data.","Imports":"survival, epitools, tools, HardyWeinberg,
rmarkdown, knitr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"compareGroups","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"tcltk2, car, XLConnect, shiny, shinyBS, shinyjs,
shinythemes,\nDT, xlsx","Title":"Descriptive Analysis by
Groups","URL":"http:\/\/www.comparegroups.eu","Version":"3.2"},"compareODM":
{"Author":"Martin Dugas","Depends":"R (>= 2.15.0), XML","Description":"Input: 2 ODM
files (ODM version 1.3) Output: list of\nidentical, matching, similar and differing
data
items","License":"GPL","NeedsCompilation":"no","Package":"compareODM","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Title":"comparison of medical forms in
CDISC ODM format","Version":"1.2"},"comparison":{"Author":"David Lucy
<d.lucy@lancaster.ac.uk>","Description":"Functions for calculating and evaluating
likelihood ratios from uni\/multivariate continuous
observations","Imports":"isotone, methods","License":"GPL-
2","NeedsCompilation":"no","Package":"comparison","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Multivariate likelihood ratio calculation and
evaluation","Version":"1.0-4"},"compeir":{"Author":"Nadine Grambauer, Andreas
Neudecker","Depends":"grid, lattice, etm","Description":"The package enables to
compute event-specific incidence\nrates for competing risks data, to compute rate
ratios,\nevent-specific incidence proportions and cumulative incidence\nfunctions
from these, and to plot these in a comprehensive\nmulti-state type
graphic.","License":"GPL-
2","NeedsCompilation":"no","Package":"compeir","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Event-specific incidence rates for competing risks
data","Version":"1.0"},"compendiumdb":{"Author":"Umesh K. Nandal
<u.k.nandal@amc.uva.nl> and Perry D.
Moerland\n<p.d.moerland@amc.uva.nl>","Depends":"Biobase, GEOquery,
RMySQL","Description":"Package for the systematic retrieval and storage
of\nfunctional genomics data via a MySQL
database.","Imports":"methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"compendiumdb","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"inSilicoDb, genefilter, GEOmetadb, gplots, GSVA,
limma,\nmogene10sttranscriptcluster.db, RColorBrewer","Title":"Tools for Retrieval
and Storage of Functional Genomics
Data","URL":"\nhttp:\/\/wiki.bioinformaticslaboratory.nl\/foswiki\/bin\/view\/BioLa
b\/CompendiumDB","Version":"1.0.3"},"complmrob":{"Author":"David Kepplinger
<david.kepplinger@gmail.com>","Description":"Provides functionality to perform
robust regression\non compositional data. To get information on the distribution of
the\nestimates, various bootstrapping methods are implemented for
the\ncompositional as well as for standard robust regression models, to provide\na
direct comparison between them.","Imports":"robustbase, ggplot2, boot, parallel,
scales","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"complmrob","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Robust Linear Regression with Compositional Data as
Covariates","Version":"0.6.1"},"compoisson":{"Author":"Jeffrey
Dunn","Depends":"stats, MASS","Description":"Provides routines for density and
moments of the\nConway-Maxwell-Poisson distribution as well as functions
for\nfitting the COM-Poisson model for over\/under-dispersed
count\ndata.","License":"BSD","NeedsCompilation":"no","Package":"compoisson","Repos
itory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Conway-Maxwell-Poisson
Distribution","Version":"0.3"},"compositions":{"Author":"K. Gerald van den Boogaart
<boogaart@hzdr.de>,\nRaimon Tolosana, Matevz Bren","Depends":"R (>= 2.2.0),
tensorA, robustbase, energy, bayesm","Description":"The package provides functions
for the consistent analysis of\ncompositional data (e.g. portions of substances)
and positive numbers\n(e.g. concentrations) in the way proposed by Aitchison and
Pawlowsky-Glahn.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"compositions","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"rgl","Title":"Compositional Data
Analysis","URL":"http:\/\/www.stat.boogaart.de\/compositions","Version":"1.40-
1"},"compound.Cox":{"Author":"Takeshi Emura & Yi-Hau Chen","Depends":"numDeriv,
survival","Description":"Calculate regression coefficients and their standard
deviations under the Cox proportional hazard model with a large number of
covariates. A shrinkage type estimation based on the compound covariate method
(Emura, Chen & Chen, 2012 PLoS ONE) and a univariate gene selection method under
dependent censoring (Emura & Chen, 2014 Statistical Methods in Medical Research)
are implemented. Algorithms for simulating gene expressions in these references are
also given.","License":"GPL-
2","NeedsCompilation":"no","Package":"compound.Cox","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Regression Estimation Based on the Compound Covariate
Method\nUnder the Cox Proportional Hazard Model","Version":"2.0"},"compute.es":
{"Author":"AC Del Re","Depends":"R (>= 2.10.1)","Description":"This package
contains several functions for calculating the most\nwidely used effect sizes (ES),
along with their variances, confidence\nintervals and p-values. The output
includes ES's of d (mean difference), g\n(unbiased estimate of d), r (correlation
coefficient), z' (Fisher's z), and\nOR (odds ratio and log odds ratio). In
addition, NNT (number needed to\ntreat), U3, CLES (Common Language Effect Size) and
Cliff's Delta are\ncomputed. This package uses recommended formulas as described in
The\nHandbook of Research Synthesis and Meta-Analysis (Cooper, Hedges,
&\nValentine, 2009).","License":"GPL-
2","NeedsCompilation":"no","Package":"compute.es","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Compute Effect
Sizes","URL":"http:\/\/acdelre.weebly.com","Version":"0.2-4"},"concor":
{"Author":"R. Lafosse <lafosse@lsp.ups-tlse.fr>","Depends":"R (>=
0.99)","Description":"The four functions svdcp (cp for column partitioned),\nsvdbip
or svdbip2 (bip for bi-partitioned), and svdbips (s for\na simultaneous
optimization of one set of r solutions),\ncorrespond to a \"SVD by blocks\" notion,
by supposing each block\ndepending on relative subspaces, rather than on two
whole\nspaces as usual SVD does. The other functions, based on this\nnotion, are
relative to two column partitioned data matrices x\nand y defining two sets of
subsets xi and yj of variables and\namount to estimate a link between xi and yj for
the pair (xi,\nyj) relatively to the links associated to all the other
pairs.","License":"GPL","NeedsCompilation":"no","Package":"concor","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"Concordance","Version":"1.0-
0.1"},"concordance":{"Author":"Feng Zhu, In Song Kim","Depends":"R (>=
2.10.1)","Description":"A set of utilities for matching products in different
classification codes used in international trade research. It supports concordance
between HS (Combined), ISIC Rev. 2,3, and SITC1,2,3,4 product classification codes,
as well as BEC, NAICS, and SIC classifications. It also provides code
nomenclature \/ descriptions look-up, Rauch classification look-up (via concordance
to SITC2) and trade elasticity look-up (via concordance to SITC2\/3 or
HS3.ss).","License":"GPL-
2","NeedsCompilation":"no","Package":"concordance","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Product Concordance","Version":"1.6"},"concreg":
{"Author":"Georg Heinze, Meinhard Ploner, Daniela Dunkler","Depends":"R (>=
2.15.1), survival","Description":"Concordance
regression","License":"GPL","NeedsCompilation":"yes","Package":"concreg","Repositor
y":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Concordance
regression","Version":"0.5"},"cond":{"Author":"S original by Alessandra R. Brazzale
<alessandra.brazzale@unipd.it>.\nR port by Alessandra R. Brazzale
<alessandra.brazzale@unipd.it>, following\nearlier work by Douglas
Bates.","Depends":"R (>= 3.0.0), statmod, survival","Description":"Higher order
likelihood-based inference for logistic and\nloglinear models","License":"GPL (>=
2) | file
LICENCE","NeedsCompilation":"no","Package":"cond","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"boot, csampling, marg, nlreg","Title":"Approximate
conditional inference for logistic and loglinear\nmodels","URL":"http:\/\/www.r-
project.org, http:\/\/statwww.epfl.ch\/AA\/","Version":"1.2-3"},"condGEE":
{"Author":"David Clement","Description":"Solves for the mean parameters, the
variance parameter, and their asymptotic variance in a conditional GEE for
recurrent event gap times, as described by Clement and Strawderman (2009) in the
journal
Biostatistics. Makes a parametric assumption for the length of the censored gap
time.","Imports":"numDeriv, rootSolve","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"condGEE","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Parameter estimation in conditional GEE for recurrent
event gap\ntimes","Version":"0.1-4"},"condMVNorm":{"Author":"Ravi Varadhan [aut,
cre]","Depends":"R(>= 1.9.0), mvtnorm","Description":"Computes conditional
multivariate normal probabilities, random deviates and
densities.","Imports":"stats","License":"GPL-
2","NeedsCompilation":"no","Package":"condMVNorm","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Conditional Multivariate Normal
Distribution","Version":"2015.2-1"},"condformat":{"Author":"Sergio Oller Moreno
[aut, cph, cre]","Description":"Apply and visualize conditional formatting to data
frames in R.\nIt presents a data frame as an HTML table with cells CSS formatted
according to\ncriteria defined by rules, using a syntax similar to 'ggplot2'. The
table is printed\neither opening a web browser or within the 'RStudio' viewer if
available. The\nconditional formatting rules allow to highlight cells matching a
condition or\nadd a gradient background to a given column based on a column
values.","Imports":"htmlTable, scales, dplyr, assertthat, lazyeval,
knitr","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"condformat","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Conditional Formatting in
Data
Frames","URL":"http:\/\/github.com\/zeehio\/condformat","Version":"0.2.0"},"condmix
t":{"Author":"Julie Carreau","Depends":"evd","Description":"Conditional density
estimation with mixtures for\nheavy-tailed distributions","License":"GPL-
2","NeedsCompilation":"yes","Package":"condmixt","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Conditional Density Estimation with Neural Network
Conditional\nMixtures","Version":"1.0"},"condvis":{"Author":"Mark O'Connell [aut,
cre],\nCatherine Hurley [ths],\nKatarina Domijan [ths],\nAchim Zeileis [ctb],\nAnja
Struyf [ctb],\nMia Hubert [ctb],\nPeter Rousseeuw [ctb],\nMartin Maechler [ctb],\nR
Core Team [ctb]","Depends":"R (>= 2.1.0)","Description":"Exploring fitted model
structures by interactively taking 2-D and\n3-D sections in data
space.","Imports":"graphics, grDevices, stats, utils, MASS","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"condvis","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"RColorBrewer, shiny, scagnostics, cluster, hdrcde,
gplots,\nTSP","Title":"Conditional Visualization for Statistical
Models","Version":"0.2-2"},"coneproj":{"Author":"Mary C. Meyer and Xiyue
Liao","Depends":"R(>= 3.0.2)","Description":"Routines doing cone projection and
quadratic programming, as well as doing estimation and inference for constrained
parametric regression and shape-restricted regression problems.","Imports":"Rcpp
(>= 0.10.4)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"coneproj","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"stats, graphics, grDevices, utils","Title":"Primal
or Dual Cone Projections with Routines for
Constrained\nRegression","Version":"1.9"},"conf.design":{"Author":"Bill
Venables","Description":"This small library contains a series of simple tools
for\nconstructing and manipulating confounded and fractional\nfactorial
designs.","License":"GPL-
2","NeedsCompilation":"no","Package":"conf.design","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"stats, utils","Title":"Construction of factorial
designs","Version":"2.0.0"},"confidence":{"Author":"Willem M. G. M. van Loon [aut,
cph],\nDennis J. J. Walvoort [aut, cre]","Depends":"R (>= 3.0.0),
tcltk","Description":"Functions for estimating and reporting multiyear averages
and\ncorresponding confidence intervals and distributions. A potential use case\nis
reporting the chemical and ecological status of surface waters according\nto the
European Water Framework Directive.","Imports":"knitr, markdown, plyr, xtable,
ggplot2","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"confidence","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat","Title":"Confidence Estimation of
Environmental State Classifications","Version":"1.1-0"},"conformal":
{"Author":"Isidro Cortes <isidrolauscher@gmail.com>","Depends":"R (>= 2.12.0),
caret, ggplot2, e1071, methods, grid","Description":"Implementation of conformal
prediction using caret models for classification and
regression.","Imports":"randomForest","License":"GPL","NeedsCompilation":"no","Pack
age":"conformal","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"ke
rnlab","Title":"Conformal Prediction for Regression and
Classification","Version":"0.2"},"confreq":{"Author":"Joerg-Henrik Heine, R.W.
Alexandrowicz (function stirling_cfa() )\nand intensive package testing by Mark
Stemmler","Depends":"R (>= 2.10.1), stats, gmp","Description":"Offers several
functions for Configural Frequencies\nAnalysis (CFA), which is a useful statistical
tool for the analysis of\nmultiway contingency tables. CFA was introduced by G. A.
Lienert as\n'Konfigurations Frequenz Analyse - KFA'.","License":"GPL-
3","NeedsCompilation":"no","Package":"confreq","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Configural Frequencies Analysis Using Log-Linear
Modeling","Version":"1.4"},"conicfit":{"Author":"Jose Gama [aut, cre],\nNikolai
Chernov [aut, cph]","Depends":"R (>= 2.7.0), pracma,
geigen","Description":"Geometric circle fitting with Levenberg-Marquardt (a, b, R),
Levenberg-Marquardt reduced (a, b), Landau, Spath and Chernov-Lesort. Algebraic
circle fitting with Taubin, Kasa, Pratt and Fitzgibbon-Pilu-Fisher. Geometric
ellipse fitting with ellipse LMG (geometric parameters) and conic LMA (algebraic
parameters). Algebraic ellipse fitting with Fitzgibbon-Pilu-Fisher and
Taubin.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"conicfit","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Algorithms for Fitting Circles, Ellipses and Conics
Based on the\nWork by Prof. Nikolai Chernov","Version":"1.0.4"},"conics":
{"Author":"Bernard Desgraupes (University of Paris Ouest - Lab
Modal'X)","Description":"plot conics (ellipses, hyperbolas,
parabolas)","Imports":"graphics","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"conics","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Plot Conics","URL":"http:\/\/www.r-
project.org","Version":"0.3"},"conjoint":{"Author":"Andrzej Bak
<andrzej.bak@ue.wroc.pl>, Tomasz
Bartlomowicz\n<tomasz.bartlomowicz@ue.wroc.pl>","Description":"Conjoint is a simple
package that implements a conjoint\nanalysis method to measure the
preferences.","Imports":"AlgDesign, clusterSim","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"conjoint","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Conjoint analysis package","URL":"www.r-project.org,
http:\/\/keii.ue.wroc.pl\/conjoint","Version":"1.39"},"connect3":
{"Author":"Chunqiao Luo [aut, cre]","Depends":"R (>=
3.0.2)","Description":"Converts 'LaTeX' files (with extension '.tex') generated by
R Sweave using package 'knitr' to Rich Text Format files (with extension '.rtf').
Rich Text Format files can be read and written by most word
processors.","License":"GPL","NeedsCompilation":"no","Package":"connect3","Reposito
ry":"http:\/\/cran.csiro.au\/src\/contrib","Title":"A Tool for Reproducible
Research by Converting 'LaTeX' Files\nGenerated by R Sweave to Rich Text Format
Files","Version":"0.1.0"},"conover.test":{"Author":"Alexis Dinno
<alexis.dinno@pdx.edu>","Description":"Computes the Conover-Iman test (1979) for
stochastic dominance and reports the results among multiple pairwise comparisons
after a Kruskal-Wallis test for stochastic dominance among k groups (Kruskal and
Wallis, 1952). The interpretation of stochastic dominance requires an assumption
that the CDF of one group does not cross the CDF of the other. conover.test makes
k(k-1)\/2 multiple pairwise comparisons based on Conover-Iman t-test-statistic of
the rank differences. The null hypothesis for each pairwise comparison is that the
probability of observing a randomly selected value from the first group that is
larger than a randomly selected value from the second group equals one half; this
null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test.
Like the rank-sum test, if the data can be assumed to be continuous, and the
distributions are assumed identical except for a difference in location, Conover-
Iman test may be understood as a test for median difference. conover.test accounts
for tied ranks. The Conover-Iman test is strictly valid if and only if the
corresponding Kruskal-Wallis null hypothesis is rejected.","License":"GPL-
2","NeedsCompilation":"no","Package":"conover.test","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Conover-Iman Test of Multiple Comparisons Using Rank
Sums","Version":"1.1.1"},"constrainedKriging":{"Author":"Christoph
Hofer","Depends":"R (>= 2.9.0), sp(>= 0.9-60), spatialCovariance(>= 0.6-
4),\nmethods","Description":"Provides functions for\nefficient computations of
nonlinear spatial predictions with\nlocal change of support. This package supplies
functions for\ntow-dimensional spatial interpolation by constrained,\ncovariance-
matching constrained and universal (external drift)\nkriging for points or block of
any shape for data with a\nnonstationary mean function and an isotropic weakly
stationary\nvariogram. The linear spatial interpolation methods,\nconstrained and
covariance-matching constrained kriging,\nprovide approximately unbiased prediction
for nonlinear target\nvalues under change of support. This package\nextends the
range of geostatistical tools available in R and\nprovides a veritable alternative
to conditional simulation
for\nnonlinear spatial prediction problems with local change
of\nsupport.","Imports":"rgeos(>= 0.2-17), RandomFields(>= 1.3.41),","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"constrainedKriging","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Suggests":"spdep(>= 0.5-43)","Title":"Constrained,
Covariance-Matching Constrained and Universal Point\nor Block
Kriging","Version":"0.2.4"},"contfrac":{"Author":"Robin K. S.
Hankin","Description":"Various utilities for evaluating continued
fractions","License":"GPL-
2","NeedsCompilation":"yes","Package":"contfrac","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Continued fractions","Version":"1.1-9"},"conting":
{"Author":"Antony M. Overstall","Depends":"R (>= 2.15.0)","Description":"Bayesian
analysis of complete and incomplete contingency tables.","Imports":"mvtnorm, BMS,
gtools, tseries, coda","License":"GPL-
2","NeedsCompilation":"no","Package":"conting","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Bayesian Analysis of Contingency
Tables","Version":"1.5"},"contoureR":{"Author":"Nicholas
Hamilton","Depends":"geometry","Description":"Create contour lines for a non
regular series of points, potentially from a non-regular canvas.","Imports":"Rcpp
(>= 0.11.5), reshape, plyr","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"contoureR","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"ggplot2","Title":"Contouring of Non-Regular Three-
Dimensional Data","URL":"http:\/\/contoureR.com","Version":"1.0.5"},"contrast":
{"Author":"Max Kuhn, contributions from Steve Weston, Jed Wing,\nJames Forester and
Thorn Thaler","Depends":"R (>= 2.2.1), rms","Description":"Contrast methods, in the
style of the Design package,\nfor fit objects produced by the lm, glm, gls, and
geese functions.","License":"GPL-
2","NeedsCompilation":"no","Package":"contrast","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"lattice, nlme, Hmisc, geepack, MASS,
sandwich","Title":"A collection of contrast
methods","Version":"0.19"},"controlTest":{"Author":"Eric Kawaguchi","Depends":"R
(>= 3.1.0)","Description":"Nonparametric two-sample procedure for comparing the
median survival time.","Imports":"survival (>= 2.38)","License":"GPL-
2","NeedsCompilation":"no","Package":"controlTest","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Median Comparison for Two-Sample Right-Censored
Survival Data","Version":"1.0"},"convevol":{"Author":"\"C. Tristan Stayton\" [aut,
cre]","Depends":"R (>= 3.1.2), ape, geiger, MASS,
phytools","Description":"Quantifies and assesses the significance of convergent
evolution.","Imports":"cluster","License":"GPL-
2","NeedsCompilation":"no","Package":"convevol","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Quantifies and assesses the significance of convergent
evolution","Version":"1.0"},"convoSPAT":{"Author":"Mark D. Risser [aut,
cre]","Depends":"R (>= 3.1.2)","Description":"Fits convolution-based
nonstationary\nGaussian process models to point-referenced spatial data. The
nonstationary\ncovariance function allows the user to specify the underlying
correlation\nstructure and which spatial dependence parameters should be allowed
to\nvary over space: the anisotropy, nugget variance, and process variance.\nThe
parameters are estimated via maximum likelihood, using a local\nlikelihood
approach. Also provided are functions to fit stationary spatial\nmodels for
comparison, calculate the kriging predictor and standard errors,\nand create
various plots to visualize nonstationarity.","Imports":"stats, graphics, ellipse,
fields, geoR, MASS, plotrix,\nStatMatch","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"convoSPAT","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Convolution-Based Nonstationary Spatial
Modeling","URL":"http:\/\/github.com\/markdrisser\/convoSPAT","Version":"1.0"},"coo
ccur":{"Author":"Daniel M. Griffith, Joseph A. Veech, and Charles J.
Marsh","Description":"This R package applies the probabilistic model of species co-
occurrence (Veech 2013) to a set of species distributed among a set of survey or
sampling sites. The algorithm calculates the observed and expected frequencies of
co-occurrence between each pair of species. The expected frequency is based on the
distribution of each species being random and independent of the other species. The
analysis returns the probabilities that a more extreme (either low or high) value
of co-occurrence could have been obtained by chance. The package also includes
functions for visualizing species co-occurrence results and preparing data for
downstream analyses.","Imports":"reshape2, gmp, ggplot2","License":"GPL-
2","NeedsCompilation":"no","Package":"cooccur","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Probabilistic Species Co-Occurrence Analysis in
R","Version":"1.3"},"coop":{"Author":"Drew Schmidt [aut, cre],\nChristian
Heckendorf [ctb] (Caught some memory errors.)","Depends":"R (>=
3.1.0)","Description":"Fast implementations of the co-operations:
covariance,\ncorrelation, and cosine similarity. The implementations are\nfast and
memory-efficient and their use is resolved\nautomatically based on the input data,
handled by R's S3\nmethods. Full descriptions of the algorithms and
benchmarks\nare available in the package vignettes.","Enhances":"slam (>= 0.1.32),
Matrix","License":"BSD 2-clause License + file
LICENSE","NeedsCompilation":"yes","Package":"coop","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"memuse, knitr, rmarkdown","Title":"Co-Operation:
Fast Covariance, Correlation, and Cosine\nSimilarity
Operations","URL":"https:\/\/github.com\/wrathematics\/coop","Version":"0.4-
0"},"cooptrees":{"Author":"Manuel Fontenla","Depends":"R (>= 2.7.0), igraph (>=
0.7.1), optrees (>= 1.0)","Description":"Computes several cooperative games and
allocation rules associated with minimum cost spanning tree problems and minimum
cost arborescence problems.","Imports":"gtools","License":"GPL-
3","NeedsCompilation":"no","Package":"cooptrees","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Cooperative aspects of optimal trees in weighted
graphs","Version":"1.0"},"copBasic":{"Author":"William Asquith","Depends":"R (>=
2.10)","Description":"Extensive functions for bivariate copula (bicopula)
computations and related mathematical operations oriented around the oft cited and
fundamental bicopula theory described by Nelsen (2006), Joe (2014), and other
selected works. The lower, upper, product, and a few select other bicopula are
implemented. Individual copula support is deliberately limited to keep the package
focused on an educational API to major bicopula theory. Expressions for an
arbitrary bicopula include the diagonal, survival copula, the dual of a copula, co-
copula, and numerical bicopula density. Level curves (sets) as well as horizontal
and vertical sections and derivatives of such sections also are supported. The
numerical derivatives of a bicopula are provided as well as inverses; simulation by
the conditional distribution method thus are supported. Composition, convex
combination, and products of bicopula are provided. Copula properties include
Kendall Function and L-moments thereof, Kendall Tau, Spearman Rho and Footrule,
Gini Gamma, Blomqvist Beta, Hoeffding Phi, Schweizer-Wolff Sigma, tail dependency
and order, and skewness. Evaluators of positively\/negatively quadrant dependency,
left-tail decreasing, and right-tail increasing are available. Kullback-Leibler
divergence, Vuong's procedure, and L-comoments for copula inference are available.
Quantile and median regressions for V with respect to U and U with respect to V are
available. Empirical copulas (EC) are
supported.","Imports":"lmomco","License":"GPL-
2","NeedsCompilation":"no","Package":"copBasic","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"General Bivariate Copula Theory and Many Utility
Functions","Version":"2.0.1"},"copCAR":{"Author":"Emily Goren
<emily.goren@gmail.com> and John Hughes <hughesj@umn.edu>","Depends":"numDeriv,
Rcpp, spam","Description":"Provides tools for fitting the copCAR regression model
for discrete areal data. Three types of estimation are supported: continuous
extension, composite marginal likelihood, and distributional
transform.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"copCAR","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"lattice","Title":"Fitting the copCAR Regression Model
for Discrete Areal
Data","URL":"http:\/\/www.biostat.umn.edu\/~johnh","Version":"1.0-1"},"cope":
{"Author":"Max Sommerfeld [aut, cre]","Depends":"maps (>= 2.3-
7)","Description":"Provides functions to compute and plot Coverage\nProbability
Excursion (CoPE) sets\nfor real valued functions on a 2-dimensional domain. CoPE
sets are obtained\nfrom repeated noisy observations of the function on the entire
domain.\nThey are designed to bound the excursion\nset of the target function at a
given level from above and below with\na predefined probability. The
target\nfunction can be a parameter in spatially-indexed linear
regression.","Imports":"fields (>= 7.1), MASS (>= 7.3-34), mvtnorm (>= 1.0-
0)","License":"GPL-
2","NeedsCompilation":"no","Package":"cope","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Coverage Probability Excursion (CoPE)
Sets","Version":"0.1"},"copula":{"Author":"Marius Hofert
<marius.hofert@uwaterloo.ca>,\nIvan Kojadinovic <ivan.kojadinovic@univ-
pau.fr>,\nMartin Maechler <maechler@stat.math.ethz.ch>, and\nJun Yan
<jun.yan@uconn.edu>","Depends":"R (>= 3.0.1)","Description":"Classes (S4) of
commonly used elliptical, Archimedean, extreme\nvalue and some more copula
families. Methods for density, distribution,\nrandom number generation, bivariate
dependence measures, perspective and\ncontour plots. Fitting copula models
including variance estimates.\nIndependence
and serial (univariate and multivariate) independence tests,\nand other copula
related tests. Empirical copula and multivariate CDF.\nGoodness-of-fit tests for
copulas based on multipliers, the parametric\nbootstrap with several transformation
options.\nMerged former package 'nacopula' for nested Archimedean copulas:
Efficient\nsampling algorithms, various estimators, goodness-of-fit tests and
related\ntools and special functions.","Enhances":"nor1mix","Imports":"stats,
graphics, methods, stats4, Matrix, lattice, colorspace,\ngsl, ADGofTest, stabledist
(>= 0.6-4), mvtnorm, pspline","License":"GPL (>= 3) | file
LICENCE","NeedsCompilation":"yes","Package":"copula","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"MASS, KernSmooth, sfsmisc, scatterplot3d, Rmpfr,
bbmle,\nknitr, parallel, mvnormtest, partitions, polynom, randtoolbox,\nrugarch,
Runuran, tseries, VGAM, VineCopula, zoo","Title":"Multivariate Dependence with
Copulas","URL":"http:\/\/copula.r-forge.r-project.org\/","Version":"0.999-
14"},"copulaedas":{"Author":"Yasser Gonzalez-Fernandez [aut, cre],\nMarta Soto
[aut]","Depends":"methods","Description":"Provides a platform where EDAs
(estimation of\ndistribution algorithms) based on copulas can be implemented
and\nstudied. The package offers complete implementations of various\nEDAs based on
copulas and vines, a group of well-known\noptimization problems, and utility
functions to study the\nperformance of the algorithms. Newly developed EDAs can be
easily\nintegrated into the package by extending an S4 class with
generic\nfunctions for their main components.","Imports":"copula, vines, mvtnorm,
truncnorm","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"copulaedas","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"cec2005benchmark, cec2013","Title":"Estimation of
Distribution Algorithms Based on
Copulas","URL":"https:\/\/github.com\/yasserglez\/copulaedas","Version":"1.4.2"},"c
orHMM":{"Author":"Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Jeffrey C. Oliver
<jeffreycoliver@gmail.com>, Brian O'Meara <bomeara@utk.edu>","Depends":"ape,
nloptr, GenSA","Description":"Fits a hidden rates model that allows different
transition rate classes on different portions of a phylogeny by treating rate
classes as hidden states in a Markov process and various other functions for
evaluating models of binary character evolution.","Imports":"expm, numDeriv,
corpcor, phangorn, parallel","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"corHMM","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Analysis of Binary Character
Evolution","Version":"1.18"},"corTools":{"Author":"Angela
Fan","Description":"Designed for analysis of the results of a Genome Wide
Association Study. Includes tools to pull lists of Chromosome number and SNP
position below a certain significance threshold, refine gene networks (including
data I\/O for Cytoscape), and check SNP base pair changes.","License":"Artistic
License
2.0","NeedsCompilation":"no","Package":"corTools","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Tools for processing data after a Genome Wide
Association Study","Version":"1.0"},"corclass":{"Author":"Andrei
Boutyline","Depends":"igraph","Description":"Perform a correlational class analysis
of the data, resulting in a partition of the data into separate
modules.","License":"GPL-
2","NeedsCompilation":"no","Package":"corclass","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"Cairo","Title":"Correlational Class
Analysis","Version":"0.1.1"},"corcounts":{"Author":"Vinzenz
Erhardt","Description":"Generate high-dimensional correlated count
random\nvariables with a prespecified Pearson correlation.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"corcounts","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Generate correlated count random
variables","Version":"1.4"},"cord":{"Author":"Xi (Rossi) LUO, Florentina Bunea,
Christophe Giraud","Description":"Partition data points (variables) into
communities\/clusters, similar to clustering algorithms, such as k-means and
hierarchical clustering. This package implements a clustering algorithm based on a
new metric CORD, defined for high dimensional parametric or semi-parametric
distributions. Read http:\/\/arxiv.org\/abs\/1508.01939 for more
details.","Imports":"Rcpp","License":"GPL-
3","NeedsCompilation":"yes","Package":"cord","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"pcaPP","Title":"Community Estimation in G-Models via
CORD","Version":"0.1.1"},"coreNLP":{"Author":"Taylor Arnold, Lauren
Tilton","Description":"Provides a minimal interface for applying\nannotators from
the 'Stanford CoreNLP' java library. Methods\nare provided for tasks such as
tokenisation, part of speech\ntagging, lemmatisation, named entity recognition,
coreference\ndetection and sentiment analysis.","Imports":"rJava, XML,
2","NeedsCompilation":"no","Package":"coreNLP","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Wrappers Around Stanford CoreNLP Tools","Version":"0.4-
1"},"coreTDT":{"Author":"Yu Jiang, Andrew S Allen","Description":"Use to analysis
case-parent trio sequencing studies. Test the compound heterozygous and recessive
disease models","License":"GPL-
3","NeedsCompilation":"no","Package":"coreTDT","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"TDT for compound heterozygous and recessive
models","Version":"1.0"},"corkscrew":{"Author":"Navin Loganathan [aut],\nMohan
Manivannan [aut],\nSanthosh Sasanapuri [aut, cre],\nLatentView Analytics
[ctb]","Depends":"R (>= 3.0.1), ggplot2, gplots, RColorBrewer, igraph,
stats,\ngrDevices","Description":"Includes binning categorical variables into
lesser number of categories based on t-test, converting categorical variables into
continuous features\nusing the mean of the response variable for the respective
categories, understanding the relationship between the response variable and
predictor variables\nusing data transformations.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"corkscrew","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"datasets","Title":"Preprocessor for Data
Modeling","Version":"1.1"},"corpcor":{"Author":"Juliane Sch\\\"afer, Rainer Opgen-
Rhein, Verena Zuber, Miika Ahdesm\\\"aki,\nA. Pedro Duarte Silva, and Korbinian
Strimmer.","Depends":"R (>= 3.0.2)","Description":"Implements a James-Stein-type
shrinkage estimator for\nthe covariance matrix, with separate shrinkage for
variances and correlations.\nThe details of the method are explained in Sch\\\"afer
and Strimmer (2005) and\nOpgen-Rhein and Strimmer (2007). The approach is both
computationally as well\nas statistically very efficient, it is applicable
to \"small n, large p\" data,\nand always returns a positive definite and well-
conditioned covariance matrix.\nIn addition to inferring the covariance matrix the
package also provides\nshrinkage estimators for partial correlations and partial
variances.\nThe inverse of the covariance and correlation matrix\ncan be
efficiently computed, as well as any arbitrary power of the\nshrinkage correlation
matrix. Furthermore, functions are available for fast\nsingular value
decomposition, for computing the pseudoinverse, and for\nchecking the rank and
positive definiteness of a matrix.","Imports":"stats","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"corpcor","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Efficient Estimation of Covariance and (Partial)
Correlation","URL":"http:\/\/strimmerlab.org\/software\/corpcor\/","Version":"1.6.8
"},"corpora":{"Author":"Stefan Evert
[http:\/\/purl.org\/stefan.evert]","Depends":"R (>= 2.10.0)","Description":"Utility
functions and data sets for the statistical\nanalysis of corpus frequency data,
used in the SIGIL statistics\ncourse.","License":"GPL-
3","NeedsCompilation":"no","Package":"corpora","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Statistics and data sets for corpus frequency
data","URL":"http:\/\/SIGIL.R-Forge.R-Project.org\/","Version":"0.4-3"},"corregp":
{"Author":"Koen Plevoets [aut, cre]","Depends":"R (>= 3.1.0), graphics, rgl,
stats","Description":"A collection of tools for correspondence regression, i.e.
the\ncorrespondence analysis of the crosstabulation of a categorical variable Y\nin
function of another one X, where X can in turn be made up of the\ncombination of
various categorical variables. Consequently, correspondence\nregression can be used
to analyze the effects for a polytomous or\nmultinomial outcome
variable.","Imports":"ellipse, gplots","License":"GPL-
3","NeedsCompilation":"no","Package":"corregp","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"datasets, grDevices, MASS,
polytomous","Title":"Functions and Methods for Correspondence
Regression","Version":"0.1.4"},"corrgram":{"Author":"Kevin Wright [aut,
cre]","Description":"Calculates correlation of variables and displays the results
graphically.\nIncluded panel functions can display points, shading, ellipses, and
correlation\nvalues with confidence intervals.","Imports":"graphics, grDevices,
seriation, stats","License":"GPL-
2","NeedsCompilation":"no","Package":"corrgram","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr, Matrix","Title":"Plot a
Correlogram","URL":"https:\/\/github.com\/kwstat\/corrgram","Version":"1.8"},"corrp
lot":{"Author":"Taiyun Wei","Description":"The corrplot package is a graphical
display of a\ncorrelation matrix, confidence interval. It also contains
some\nalgorithms to do matrix
reordering.","License":"GPL","NeedsCompilation":"no","Package":"corrplot","Reposito
ry":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"seriation,
knitr","Title":"Visualization of a correlation
matrix","URL":"https:\/\/github.com\/taiyun\/corrplot","Version":"0.73"},"corrsieve
":{"Author":"Michael
G. Campana <mcampana63@gmail.com>","Depends":"methods","Description":"Statistical
summary of Structure output.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"corrsieve","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"CorrSieve","URL":"\nhttp:\/\/www.mcdonald.cam.ac.uk\/pr
ojects\/genetics\/projects\/CorrSieve\/CorrSieve.htm","Version":"1.6-8"},"cosinor":
{"Author":"Michael Sachs <sachsmc@gmail.com>","Depends":"R (>=
2.11.0)","Description":"cosinor is a set of simple functions that transforms
longitudinal\ndata to estimate the cosinor linear model as described in Tong
(1976).\nMethods are given to summarize the mean, amplitude and acrophase,
to\npredict the mean annual outcome value, and to test the
coefficients.","Imports":"ggplot2, shiny","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"cosinor","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"knitr","Title":"Tools for estimating and
predicting the cosinor
model","URL":"http:\/\/github.com\/sachsmc\/cosinor","Version":"1.1"},"cosmoFns":
{"Author":"Andrew Harris","Description":"Package encapsulates standard expressions
for distances,\ntimes, luminosities, and other quantities useful in\nobservational
cosmology, including molecular line observations.\nCurrently coded for a flat
universe only.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"cosmoFns","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Functions for cosmological distances, times,
luminosities, etc","Version":"1.0-1"},"cosmosR":{"Author":"Maxime
Wack","Depends":"xlsx","Description":"This package aims at the easy production of
descriptive and\nbivariate statistics tables in HTML. It can load files in csv,
xls\/xlsx\nformats, and read labels and formats from SAS or plain text files. It
is\nintended to be usable by absolute R beginners. Ce paquet permet la\nproduction
facile de tableaux HTML descriptifs et comparatifs, meme pour\nles debutants sous
R.","License":"GPL-
3","NeedsCompilation":"no","Package":"cosmosR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"cosmosR","Version":"1.0"},"cosso":{"Author":"Hao Helen
Zhang <hzhang@math.arizona.edu> and Chen-Yen
Lin\n<clin5@ncsu.edu>","Depends":"quadprog, Rglpk, parallel,
glmnet","Description":"COSSO is a new regularization method that
automatically\nestimates and selects important function components by a\nsoft-
thresholding penalty in the context of smoothing spline\nANOVA models. Implemented
models include mean regression,\nquantile regression, logistic regression and the
Cox regression\nmodels.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"cosso","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Fit Regularized Nonparametric Regression Models Using
COSSO\nPenalty","URL":"http:\/\/www4.stat.ncsu.edu\/~hzhang\/cosso.html","Version":
"2.1-1"},"costat":{"Author":"Guy Nason, Alessandro Cardinali","Depends":"R (>=
2.14), wavethresh (>= 4.6.1)","Description":"Contains functions that can determine
whether a time series\nis second-order stationary or not (and hence evidence
for\nlocally stationarity). Given two non-stationary series (i.e.\nlocally
stationary series) this package can then discover\ntime-varying linear combinations
that are second-order stationary.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"costat","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"parallel","Title":"Time series costationarity
determination","Version":"2.3"},"cotrend":{"Author":"A. Christian
Silva","Depends":"xts","Description":"Implements cointegration\/cotrending rank
selection\nalgorithm in Guo and Shintani(2011). Paper: \"Consistant\nCotrending
rank selection when both stochastic and nonlinear\ndeterministic trends are
present\", Preprint, Feb
2011.","License":"GPL","NeedsCompilation":"no","Package":"cotrend","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"Consistant Cotrend Rank
Selection","Version":"1.0"},"couchDB":{"Author":"Aleksander
Dietrichson","Depends":"R (>= 3.0.0), RCurl, bitops, httr,
rjson","Description":"Interface to couchDB","License":"AGPL-
3","NeedsCompilation":"no","Package":"couchDB","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Connect and work with couchDB
databases","Version":"1.3.0"},"countrycode":{"Author":"Vincent Arel-Bundock
<vincent.arel-bundock@umontreal.ca>","Description":"Standardize country names,
convert them into one of\neleven coding schemes, convert between coding schemes,
and\nassign region descriptors.","License":"GPL-
3","NeedsCompilation":"no","Package":"countrycode","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat (>= 0.5)","Title":"Convert Country Names
and Country
Codes","URL":"https:\/\/github.com\/vincentarelbundock\/countrycode","Version":"0.1
8"},"covBM":{"Author":"Oliver Stirrup [aut, cre]","Depends":"nlme (>=
3.0)","Description":"Allows Brownian motion, fractional Brownian motion,\nand
integrated Ornstein-Uhlenbeck process components to\nbe added to linear and non-
linear mixed effects models\nusing the structures and methods of the 'nlme'
package.","Imports":"stats","License":"GPL-
3","NeedsCompilation":"yes","Package":"covBM","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Brownian Motion Processes for 'nlme'-
Models","Version":"0.1.0"},"covLCA":{"Author":"Aurelie Bertrand
<aurelie.bertrand@uclouvain.be> and Christian\nM. Hafner
<christian.hafner@uclouvain.be>","Depends":"Matrix, mlogit,
poLCA","Description":"Estimation of latent class models with covariate effects\non
underlying and measured variables. The measured variables\nare dichotomous or
polytomous, all with the same number of\ncategories.","License":"GPL-
2","NeedsCompilation":"no","Package":"covLCA","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Latent Class Models with Covariate Effects on Underlying
and\nMeasured Variables","Version":"1.0"},"covRobust":{"Author":"Naisyin Wang
<nwangaa@umich.edu> and Adrian Raftery\n<raftery@uw.edu> with contributions from
Chris Fraley\n<fraley@uw.edu>","Depends":"R (>= 2.15.1)","Description":"The
cov.nnve() function for robust covariance estimation\nby the nearest neighbor
variance estimation (NNVE) method of\nWang and Raftery (2002,JASA)","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"covRobust","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Robust Covariance Estimation via Nearest Neighbor
Cleaning","Version":"1.1-0"},"covTest":{"Author":"Richard Lockhart, Jon Taylor,
Ryan Tibshirani, Rob Tibshirani","Depends":"lars,glmnet,glmpath (>=
0.97),MASS","Description":"This package computes covariance test for the
lasso.","License":"GPL-
2","NeedsCompilation":"no","Package":"covTest","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Computes covariance test for adaptive linear
modelling","Version":"1.02"},"covafillr":{"Author":"Christoffer Moesgaard Albertsen
[aut, cre]","Depends":"R (>= 3.0.0),","Description":"Facilitates local polynomial
regression for state dependent covariates in state-space models. The functionality
can also be used from 'C++' based model builder tools such as 'Rcpp'\/'inline',
'TMB', or 'JAGS'.","Imports":"methods","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"yes","Package":"covafillr","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"TMB, rjags, inline,","Title":"Local Polynomial
Regression of State Dependent Covariates in\nState-Space
Models","Version":"0.2.1"},"covmat":{"Author":"Rohit Arora","Depends":"mvtnorm,
RMTstat, grid","Description":"We implement a collection of techniques for
estimating covariance matrices.\nCovariance matrices can be built using missing
data. Stambaugh Estimation and\nFMMC methods can be used to construct such
matrices. Covariance matrices can\nbe built by denoising or shrinking the
eigenvalues of a sample covariance\nmatrix. Such techniques work by exploiting the
tools in Random Matrix Theory\nto analyse the distribution of eigenvalues.
Covariance matrices can also\nbe built assuming that data has many underlying
regimes. Each regime is\nallowed to follow a Dynamic Conditional Correlation model.
Robust covariance\nmatrices can be constructed by multivariate cleaning and
smoothing of noisy data.","Imports":"zoo, xts, robust, robustbase, VIM, ggplot2,
reshape2, Matrix,\nparallel, doParallel, fGarch, lhs, scales, gridExtra,
optimx,\nDEoptim, foreach","License":"Artistic-
2.0","NeedsCompilation":"yes","Package":"covmat","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr, knitcitations, roxygen2, quantmod,
PortfolioAnalytics,\nrmgarch","Title":"Covariance Matrix
Estimation","Version":"1.0"},"covr":{"Author":"Jim Hester [aut, cre]","Depends":"R
(>= 3.1.0), methods","Description":"Track and report code coverage for your package
and (optionally)\nupload the results to a coverage service like Codecov
(http:\/\/codecov.io) or\nCoveralls (http:\/\/coveralls.io). Code coverage is a
measure of the amount of\ncode being exercised by the tests. It is an indirect
measure of test quality.\nThis package is compatible with any testing methodology
or framework and tracks\ncoverage of both R code and compiled C\/C++\/Fortran
code.","Imports":"stats, utils, jsonlite, rex, httr, crayon, withr","License":"MIT
+ file
LICENSE","NeedsCompilation":"yes","Package":"covr","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"R6, knitr, rmarkdown, shiny (>= 0.11.1), htmltools,
DT,\ntestthat, rstudioapi (>= 0.2), devtools","Title":"Test Coverage for
Packages","URL":"https:\/\/github.com\/jimhester\/covr","Version":"2.0.1"},"covreg"
:{"Author":"Xiaoyue Niu and Peter Hoff","Description":"This package fits a
simultaneous regression model for the mean vectors and covariance matrices of
multivariate response variables, as described in Hoff and Niu (2012). The
explanatory variables can be continuous or discrete. The current
version of the package provides the Bayesian estimates.","License":"GPL-
2","NeedsCompilation":"no","Package":"covreg","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"A simultaneous regression model for the mean and
covariance","Version":"1.0"},"covsep":{"Author":"Shahin Tavakoli [aut,
cre],\nDavide Pigoli [ctb],\nJohn Aston [ctb]","Depends":"R (>=
3.2.3)","Description":"Functions for testing if the covariance structure of 2-
dimensional data\n(e.g. samples of surfaces X_i = X_i(s,t)) is separable, i.e. if
covariance(X) = C_1 x C_2.\nA complete descriptions of the implemented tests can be
found in the paper\narXiv:1505.02023.","Imports":"mvtnorm (>=
2","NeedsCompilation":"no","Package":"covsep","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Tests for Determining if the Covariance Structure of\n2-
Dimensional Data is
Separable","URL":"http:\/\/arxiv.org\/abs\/1505.02023","Version":"1.0.0"},"cowplot"
:{"Author":"Claus O. Wilke [aut, cre],\nHadley Wickham [cph]","Depends":"R (>=
3.2.0), ggplot2 (>= 2.0.0),","Description":"Some helpful extensions and
modifications to the 'ggplot2'\nlibrary. In particular, this package makes it easy
to combine multiple\n'ggplot2' plots into one and label them with letters, e.g. A,
B, C, etc.,\nas is often required for scientific publications. The package also
provides\na streamlined and clean theme that is used in the Wilke lab, hence
the\npackage name, which stands for Claus O. Wilke's plot library.","Imports":"grid
(>= 3.0.0), gtable (>= 0.1.2), plyr (>= 1.8.2),\ngrDevices, methods,
2","NeedsCompilation":"no","Package":"cowplot","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr","Title":"Streamlined Plot Theme and Plot
Annotations for
'ggplot2'","URL":"https:\/\/github.com\/wilkelab\/cowplot","Version":"0.6.1"},"cows
ay":{"Author":"Scott Chamberlain [aut, cre],\nTyler Rinker [aut],\nThomas Leeper
[aut],\nNoam Ross [aut],\nRich FitzJohn [aut],\nCarson Sievert [aut],\nKiyoko
Gotanda [aut],\nAndy Teucher [aut],\nKarl Broman [aut],\nFranz-Sebastian Krah
[aut]","Description":"Allows printing of character strings as
messages\/warnings\/etc.\nwith ASCII animals, including cats, cows, frogs,
chickens, ghosts, and
more.","Enhances":"magrittr","Imports":"fortunes","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"cowsay","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"jsonlite, testthat, knitr","Title":"Messages,
Warnings, Strings with Ascii
Animals","URL":"https:\/\/github.com\/sckott\/cowsay","Version":"0.4.0"},"coxinterv
al":{"Author":"Audrey Boruvka and Richard J. Cook","Depends":"R (>= 2.15.2),
survival, timereg","Description":"Fits Cox-type models based on interval-censored
data from a survival\nor illness-death process.","Imports":"Matrix","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"coxinterval","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Cox-Type Models for Interval-Censored
Data","URL":"https:\/\/github.com\/aboruvka\/coxinterval","Version":"1.2"},"coxme":
{"Author":"Terry M. Therneau [aut, cre]","Depends":"survival (>= 2.36.14), methods,
bdsmatrix(>= 1.3)","Description":"Cox proportional hazards models containing
Gaussian random\neffects, also known as frailty models.","Imports":"nlme, Matrix
(>= 1.0)","License":"LGPL-
2","NeedsCompilation":"yes","Package":"coxme","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"mvtnorm, kinship2","Title":"Mixed Effects Cox
Models","URL":"http:\/\/r-forge.r-project.org","Version":"2.2-5"},"coxphf":
{"Author":"R by Meinhard Ploner, Fortran by Georg Heinze","Depends":"R (>=
3.0.2)","Description":"Cox regression with Firth's penalized
likelihood","Imports":"survival","License":"GPL","NeedsCompilation":"yes","Package"
:"coxphf","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Cox
regression with Firth's penalized likelihood","Version":"1.11"},"coxphw":
{"Author":"R by Meinhard Ploner, Georg Heinze, Daniela Dunkler, Fortran by Georg
Heinze","Depends":"R (>= 3.0.2), survival","Description":"This package implements
weighted estimation in Cox regression as proposed by\nSchemper, Wakounig and Heinze
(Statistics in Medicine, 2009). Weighted Cox regression\nprovides unbiased average
hazard ratio estimates also in case of non-proportional hazards.\nApproximated
generalized concordance probability an effect size measure for clear-cut\ndecisions
can be obtained.\nAdditionally estimation of nonlinear effects using fractional
polynomials similar to the\nMFP algorithm (Royston, Sauerbrei, 2008) is provided.
This feature can also be used to\nestimate the interaction of a covariate with a
nonlinear function of time.","License":"GPL-
2","NeedsCompilation":"yes","Package":"coxphw","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Weighted Estimation in Cox
Regression","Version":"3.0.0"},"coxrobust":{"Author":"Tadeusz Bednarski
<t.bednarski@prawo.uni.wroc.pl>, Filip\nBorowicz
<f.borowicz@prawo.uni.wroc.pl>","Depends":"R (>= 2.0.0),
survival","Description":"Fit robustly proportional hazards regression
2)","NeedsCompilation":"yes","Package":"coxrobust","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Robust Estimation in Cox
Model","Version":"1.0"},"coxsei":{"Author":"Feng Chen
<feng.chen@unsw.edu.au>","Description":"It fits a CoxSEI (Cox type Self-Exciting
Intensity) model to right-censored counting process data.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"coxsei","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Fitting a CoxSEI Model","Version":"0.1"},"cp4p":
{"Author":"Quentin Giai Gianetto, Florence Combes, Claire Ramus, Christophe Bruley,
Yohann CoutÃ©, Thomas Burger","Depends":"R (>= 3.2.0), MESS, graphics, stats,
multtest, qvalue, limma","Description":"Functions to check whether a vector of p-
values respects the assumptions of FDR (false discovery rate) control procedures
and to compute adjusted p-values.","License":"GPL-
3","NeedsCompilation":"no","Package":"cp4p","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Calibration Plot for Proteomics","Version":"0.3.4"},"cpa":
{"Author":"Alessandro Bellino and Daniela
Baldantoni","Depends":"tcltk","Description":"The package includes functions to test
and compare causal models.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"cpa","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Confirmatory Path Analysis through the d-sep
tests","Version":"1.0"},"cpca":{"Author":"Andrey Ziyatdinov [aut, cre],\nSamir
Kanaan-Izquierdo [aut],\nNickolay T. Trendafilov [aut],\nAlexandre Perera-Lluna
[aut]","Depends":"R (>= 3.0.1)","Description":"This package contains methods to
perform Common Principal\nComponent Analysis (CPCA). The stepwise method by
Trendafilov is published\nin the current version. Please see Trendafilov (2010).
Stepwise estimation\nof common principal components. Computational Statistics &
Data Analysis,\n54(12), 3446-3457. doi:10.1016\/j.csda.2010.03.010","License":"GPL
(>=
3)","NeedsCompilation":"no","Package":"cpca","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"abind, plyr","Title":"Methods to perform Common Principal
Component Analysis
(CPCA)","URL":"https:\/\/github.com\/variani\/cpca","Version":"0.1.2"},"cpgen":
{"Author":"Claas Heuer","Depends":"R(>= 3.1.0), Matrix(>= 1.0-5), pedigreemm(>=
0.3-3)","Description":"Frequently used methods in genomic applications with
emphasis on parallel computing (OpenMP).\nAt its core, the package has a Gibbs
Sampler that allows running univariate linear\nmixed models that have both, sparse
and dense design matrices. The parallel sampling method\nin case of dense design
matrices (e.g. Genotypes) allows running Ridge Regression or BayesA for\na very
large number of individuals. The Gibbs Sampler is capable of running Single Step
Genomic Prediction models.\nIn addition, the package offers parallelized functions
for common tasks like genome-wide\nassociation studies and cross validation in a
memory efficient way.","Imports":"methods, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"cpgen","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Parallelized Genomic Prediction and
GWAS","URL":"https:\/\/github.com\/cheuerde\/cpgen","Version":"0.1"},"cpk":
{"Author":"Oscar A. Linares [aut, cre],\nDavid T. Daly [aut]","Depends":"R (>=
2.10.0)","Description":"The package cpk provides simplified clinical
pharmacokinetic functions for dose regimen design and modification at the point-of-
care. Currently, the following functions are available: (1) ttc.fn for target
therapeutic concentration, (2) dr.fn for dose rate, (3) di.fn for dosing interval,
(4) dm.fn for maintenance dose, (5) bc.ttc.fn for back calculation, (6) ar.fn for
accumulation ratio, (7) dpo.fn for orally administered dose, (8) cmax.fn for peak
concentration, (9) css.fn for steady-state concentration, (10) cmin.fn for trough,
(11) ct.fn for concentration-time predictions, (12) dlcmax.fn for calculating
loading dose based on drug's maximum concentration, (13) dlar.fn for calculating
loading dose based on drug's accumulation ratio, and (14) R0.fn for calculating
drug infusion rate. Reference: Linares O, Linares A. Computational opioid
prescribing: A novel application of clinical pharmacokinetics. J Pain Palliat Care
Pharmacother 2011;25:125-135.","License":"GPL-
2","NeedsCompilation":"no","Package":"cpk","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Clinical Pharmacokinetics","Version":"1.3-1"},"cplexAPI":
{"Author":"C. Jonathan Fritzemeier [cre, ctb], Gabriel Gelius-Dietrich
[aut]","Depends":"R (>= 2.6.0)","Description":"This is the R Interface to the C API
of IBM ILOG CPLEX. It necessarily depends on IBM ILOG CPLEX (>=
12.1).","Imports":"methods","License":"GPL-3 | file
LICENSE","NeedsCompilation":"yes","Package":"cplexAPI","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"R
Interface to C API of IBM ILOG CPLEX","Version":"1.3.1"},"cplm":{"Author":"Yanwei
(Wayne) Zhang","Depends":"R (>= 2.10), coda, Matrix, splines,
methods","Description":"Likelihood-based and Bayesian methods for various compound
Poisson linear models.","Imports":"biglm, ggplot2, minqa, nlme, reshape2, statmod,
stats, stats4,\ntweedie","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"cplm","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Compound Poisson Linear
Models","URL":"http:\/\/code.google.com\/p\/cplm\/","Version":"0.7-4"},"cpm":
{"Author":"Gordon J. Ross","Depends":"R (>= 2.15.0),
methods","Description":"Sequential and batch change detection for univariate data
streams, using the change point model framework. Functions are provided to allow
nonparametric distribution-free change detection in the mean, variance, or general
distribution of a given sequence of observations. Parametric change detection
methods are also provided for Gaussian, Bernoulli and Exponential sequences. Both
the batch (Phase I) and sequential (Phase II) settings are supported, and the
sequences may contain either a single or multiple change points.","License":"GPL-
3","NeedsCompilation":"yes","Package":"cpm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Sequential and Batch Change Detection Using Parametric
and\nNonparametric Methods","Version":"2.2"},"cqrReg":{"Author":"Jueyu Gao &
Linglong Kong","Depends":"Rcpp (>= 0.10.0),quantreg,R (>=
2.6)","Description":"Estimate quantile regression(QR) and composite quantile
regression (cqr) and with adaptive lasso penalty using interior point (IP),
majorize and minimize(MM), coordinate descent (CD), and alternating direction
method of multipliers algorithms(ADMM).","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"cqrReg","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Quantile, Composite Quantile Regression and Regularized
Versions","Version":"1.2"},"cquad":{"Author":"Francesco Bartolucci (University of
Perugia), Claudia Pigini (University of Ancona \"Politecnica delle
Marche\")","Depends":"R (>= 2.0.0), MASS, plm","Description":"Estimation, based on
conditional maximum likelihood, of the quadratic exponential model proposed by
Bartolucci, F. & Nigro, V. (2010, Econometrica) and of a simplified and a modified
version of this model. The quadratic exponential model is suitable for the analysis
of binary longitudinal data when state dependence (further to the effect of the
covariates and a time-fixed individual intercept) has to be taken into account.
Therefore, this is an alternative to the dynamic logit model having the advantage
of easily allowing conditional inference in order to eliminate the individual
intercepts and then getting consistent estimates of the parameters of main interest
(for the covariates and the lagged response). The simplified version of this model
does not distinguish, as the original model does, between the last time occasion
and the previous occasions. The modified version formulates in a different way the
interaction terms and it may be used to test in a easy way state dependence as
shown in Bartolucci, F., Nigro, V. & Pigini, C. (2013, Econometric Reviews). The
package also includes estimation of the dynamic logit model by a pseudo conditional
estimator based on the quadratic exponential model, as proposed by Bartolucci, F. &
Nigro, V. (2012, Journal of Econometrics).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"cquad","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Conditional Maximum Likelihood for Quadratic Exponential
Models\nfor Binary Panel Data","Version":"1.3"},"crackR":{"Author":"Keith
Halbert","Depends":"Hmisc (>= 3.14-3), evd (>= 2.3-0)","Description":"Using a
sampling-based approach (either sequential importance sampling or explicit Monte
Carlo), this package can be used to perform a probabilistic damage tolerance for
aircraft structures. It can model a single crack, or two simultaneously growing
fatigue cracks (the so-called continuing damage problem). With a single crack,
multiple types of future repairs are possible.","License":"GPL-
3","NeedsCompilation":"no","Package":"crackR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Probabilistic damage tolerance analysis for fatigue
cracking of\nmetallic aerospace structures","Version":"0.3-9"},"cramer":
{"Author":"Carsten Franz <carsten.franz@gmail.com>","Depends":"R (>= 0.65),
boot","Description":"Provides R routine for the so called two-sample\nCramer-Test.
This nonparametric two-sample-test on equality\nof the underlying distributions can
be applied to\nmultivariate data as well as univariate data. It offers
two\npossibilities to approximate the critical value both of which\nare included in
this package.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"cramer","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Multivariate nonparametric Cramer-Test for the\ntwo-
sample-problem","Version":"0.9-1"},"crandatapkgs":{"Author":"Thomas J. Leeper [aut,
cre]","Description":"Provides a data.frame listing of known data-only and data-
heavy\npackages available on CRAN.","Imports":"utils","License":"GPL-
3","NeedsCompilation":"no","Package":"crandatapkgs","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat","Title":"Find Data-Only Packages on
CRAN","URL":"http:\/\/github.com\/leeper\/crandatapkgs","Version":"0.1.3"},"crank":
{"Author":"Jim Lemon <drjimlemon@gmail.com>,","Description":"Functions for
completing and recalculating rankings.","Imports":"stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"crank","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Completing Ranks","Version":"1.1"},"cranlogs":
{"Author":"Gabor Csardi [aut, cre]","Description":"'API' to the database of 'CRAN'
package downloads from the\n'RStudio' 'CRAN mirror'. The database itself is at
<http:\/\/cranlogs.r-pkg.org>,\nsee <https:\/\/github.com\/metacran\/cranlogs.app>
for the raw 'API'.","Imports":"httr, jsonlite","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"cranlogs","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Download Logs from the 'RStudio' 'CRAN'
Mirror","URL":"https:\/\/github.com\/metacran\/cranlogs","Version":"2.1.0"},"cranta
stic":{"Author":"Bjorn Arild Maeland
<bjorn.maeland@gmail.com>","Description":"Various R tools for
http:\/\/crantastic.org\/","License":"GPL-
2","NeedsCompilation":"no","Package":"crantastic","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Various R tools for
http:\/\/crantastic.org\/","URL":"http:\/\/github.com\/hadley\/crantastic\/tree\/R-
package,\nhttp:\/\/crantastic.org","Version":"0.1"},"crawl":{"Author":"Devin S.
Johnson","Depends":"R (>= 2.10)","Description":"The Correlated Random Walk Library
of\nR functions was designed for fitting continuous-time\ncorrelated random walk
models with time indexed\ncovariates. The model is fit using the Kalman-filter
on\na state space version of the continuous-time stochastic\nmovement
process.","Imports":"mvtnorm, Rcpp (>= 0.11.1), methods,
shiny","License":"CC0","NeedsCompilation":"yes","Package":"crawl","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Suggests":"ggplot2, knitr, rmarkdown, sp,
rgdal, argosfilter, tidyr,\ndplyr, lubridate, xts, doParallel","Title":"Fit
Continuous-Time Correlated Random Walk Models to Animal\nMovement
Data","Version":"2.0"},"crayon":{"Author":"Gabor Csardi [aut,
cre]","Description":"Colored terminal output on terminals that support
'ANSI'\ncolor and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI'\ncolor
support is automatically detected. Colors and highlighting can\nbe combined and
nested. New styles can also be created easily.\nThis package was inspired by the
'chalk' 'JavaScript' project.","Imports":"memoise, grDevices, methods,
LICENSE","NeedsCompilation":"no","Package":"crayon","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat","Title":"Colored Terminal
Output","URL":"https:\/\/github.com\/gaborcsardi\/crayon","Version":"1.3.1"},"crblo
cks":{"Author":"David Allingham, D.J. Best","Description":"Implements a statistical
test for comparing bar plots or\nhistograms of categorical data derived from a
randomized block\nrepeated measures layout.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"crblocks","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Categorical Randomized Block Data
Analysis","URL":"http:\/\/carma.newcastle.edu.au\/davida\/","Version":"0.9-
1"},"crch":{"Author":"Jakob Messner [aut, cre],\nAchim Zeileis [aut]","Depends":"R
(>= 2.10.0)","Description":"Different approaches to censored or truncated
regression with\nconditional heteroscedasticity are provided. First,
continuous\ndistributions can be used for the (right and\/or left censored or
truncated)\nresponse with separate linear predictors for the mean and
variance.\nSecond, cumulative link models for ordinal data\n(obtained by interval-
censoring continuous data) can be employed for\nheteroscedastic extended logistic
regression (HXLR). In the latter type of\nmodels, the intercepts depend on the
thresholds that define the intervals.","Imports":"stats, Formula,
ordinal","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"crch","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"glmx, lmtest","Title":"Censored Regression with
Conditional Heteroscedasticity","Version":"0.9-2"},"creditr":
{"Author":"c(person(\"Heidi\", \"Chen\", role = c(\"aut\"),\nemail
= \"s.heidi.chen@gmail.com\"),\nperson(\"Yuanchu\", \"Dang\", role =
c(\"aut\"),\nemail = \"yuanchu.dang@gmail.com\"),\nperson(\"David\", \"Kane\", role
= c(\"aut\"),\nemail = \"dave.kane@gmail.com\"),\nperson(\"Yang\", \"Lu\", role =
c(\"aut\", \"cre\"),\nemail
= \"yang.lu2014@gmail.com\"),\nperson(\"Skylar\", \"Smith\", role
= c(\"aut\"),\nemail = \"sws2@williams.edu\"),\nperson(\"Kanishka\", \"Malik\",
role = c(\"aut\"),\nemail = \"kanishkamalik@gmail.com\"),\nperson(\"Miller Zijie\",
\"Zhu\", role = c(\"aut\"),\nemail = \"zijie.zhu@williams.com\"))","Depends":"R (>=
3.1.0)","Description":"Provides tools for pricing credit default swaps using\nC
code for the International Swaps and Derivatives\nAssociation (ISDA) CDS Standard
Model. See\n<http:\/\/www.cdsmodel.com\/cdsmodel\/documentation.html>\nfor more
information about the model and\n<http:\/\/www.cdsmodel.com\/cdsmodel\/cds-
disclaimer.html>\nfor license details for the C code.","Imports":"utils, quantmod,
devtools, methods, Rcpp (>= 0.10.6), RCurl,\nXML, zoo, xts","License":"file
LICENSE","NeedsCompilation":"yes","Package":"creditr","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat","Title":"Credit Default Swaps in
R","URL":"https:\/\/github.com\/davidkane9\/creditr","Version":"0.6.1"},"credule":
{"Author":"Bertrand Le Nezet [cre, aut, cph],\nRichard Brent [ctb, cph],\nJohn
Burkardt [ctb, cph]","Depends":"R (>= 2.14.1)","Description":"It provides functions
to bootstrap Credit Curves from market quotes (Credit Default Swap - CDS - spreads)
and price Credit Default Swaps - CDS.","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"credule","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"knitr","Title":"Credit Default Swap
Functions","URL":"https:\/\/github.com\/lampalork\/credule","Version":"0.1.3"},"cri
cketr":{"Author":"Tinniam V Ganesh","Depends":"R (>= 3.1.2)","Description":"Tools
for analyzing performances of cricketers based on stats in\nESPN Cricinfo
Statsguru. The toolset can be used for analysis of Tests,ODIs\nand Twenty20
matches of both batsmen and bowlers.","Imports":"dplyr, plotrix, ggplot2,
scatterplot3d, forecast, lubridate,\nXML, graphics, grDevices, stats,
LICENSE","NeedsCompilation":"no","Package":"cricketr","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Analyze Cricketers Based on ESPN Cricinfo
Statsguru","URL":"https:\/\/github.com\/tvganesh\/cricketr","Version":"0.0.12"},"cr
imCV":{"Author":"Jason D. Nielsen <jdn@math.carleton.ca>","Depends":"R (>= 2.10.0),
splines","Description":"This package fits discrete mixtures of Zero-
Inflated\nPoisson (ZIP) models for analyzing criminal trajectories.","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"crimCV","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Group-Based Modelling of Longitudinal
Data","Version":"0.9.3"},"crimelinkage":{"Author":"Michael Porter [aut,
cre],\nBrian Reich [aut]","Depends":"R (>= 3.1.0)","Description":"Statistical
Methods for Crime Series Linkage. This package provides\ncode for criminal case
linkage, crime series identification, crime series\nclustering, and suspect
identification.","Imports":"igraph, geosphere, grDevices, graphics, stats,
3","NeedsCompilation":"no","Package":"crimelinkage","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"fields, knitr, gbm","Title":"Statistical Methods
for Crime Series Linkage","Version":"0.0.4"},"crmPack":{"Author":"Daniel Sabanes
Bove <sabanesd@roche.com>,\nWai Yin Yeung <w.yeung1@lancaster.ac.uk>,\nGiuseppe
Palermo <giuseppe.palermo@roche.com>,\nThomas Jaki
<jaki.thomas@gmail.com>","Depends":"R (>= 3.0.0), ggplot2 (>= 2.0.0),
graphics","Description":"Implements a wide range of model-based dose\nescalation
designs, ranging from classical and modern continual\nreassessment methods (CRMs)
based on dose-limiting toxicity endpoints to\ndual-endpoint designs taking into
account a biomarker\/efficacy outcome. The\nfocus is on Bayesian inference, making
it very easy to setup a new design\nwith its own JAGS code. However, it is also
possible to implement 3+3\ndesigns for comparison or models with non-Bayesian
estimation. The whole\npackage is written in a modular form in the S4 class system,
making it very\nflexible for adaptation to new models, escalation or stopping
rules.","Imports":"methods, grid, gridExtra, GenSA, mvtnorm, parallel,\nBayesLogit,
rjags, utils, tools, MASS","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"crmPack","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"ggmcmc, R2WinBUGS, Rcpp,
RcppArmadillo","Title":"Object-Oriented Implementation of CRM
Designs","Version":"0.1.9"},"crmn":{"Author":"Henning Redestig","Depends":"R (>=
2.10), pcaMethods (>= 1.56.0), Biobase, methods","Description":"Implements the
Cross-contribution Compensating Multiple\nstandard Normalization (CCMN) method and
other normalization\nalgorithms.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"crmn","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"CCMN and other noRMalizatioN methods for metabolomics
data","Version":"0.0.20"},"crn":{"Author":"Steven Mosher","Depends":"R (>= 2.11.0),
chron, RCurl","Description":"The crn package provides the core functions required
to\ndownload and format data from the Climate Reference Network.\nBoth daily and
hourly data are downloaded from the ftp, a\nconsolidated file of all stations is
created, station metadata\nis extracted. In addition functions for selecting
individual\nvariables and creating R friendly datasets for them
is\nprovided.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"crn","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Downloads and Builds datasets for Climate Reference
Network","URL":"http:\/\/stevemosher.wordpress.com\/","Version":"1.1"},"crop":
{"Author":"Marius Hofert [aut, cre]","Depends":"R (>= 3.0.0)","Description":"A
device closing function which is able to crop graphics (e.g.,\nPDF, PNG files) on
Unix-like operating systems with the required underlying\ncommand-line tools
installed.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"crop","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Graphics Cropping Tool","Version":"0.0-2"},"crossReg":
{"Author":"Sunbok Lee","Description":"\nThis package provides functions to
calculate confidence intervals for crossover points of two simple linear regression
lines using\nthe non-linear regression, the delta method, the Fieller method, and
the bootstrap methods.","License":"GPL-
2","NeedsCompilation":"no","Package":"crossReg","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"boot, MASS","Title":"Confidence intervals for
crossover points of two simple\nregression lines","Version":"1.0"},"crossdes":
{"Author":"Martin Oliver Sailer","Depends":"AlgDesign,
gtools","Description":"Contains functions for the construction of
carryover\nbalanced crossover designs. In addition contains functions to\ncheck
given designs for balance.","License":"GPL-
2","NeedsCompilation":"no","Package":"crossdes","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Construction of Crossover Designs","Version":"1.1-
1"},"crossmatch":{"Author":"Ruth Heller <ruheller@post.tau.ac.il>, Dylan
Small\n<dsmall@wharton.upenn.edu>, Paul
Rosenbaum\n<rosenbap@wharton.upenn.edu>","Depends":"survival,nbpMatching","Descript
ion":"This package performs a test for comparing two\nmultivariate distributions by
using the distance between\nobservations. The input is a distance matrix and the
labels of\nthe two groups to be compared, the output is the number of\ncross-
matches and a p-value.","License":"GPL-
2","NeedsCompilation":"no","Package":"crossmatch","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"MASS","Title":"The Cross-match Test","Version":"1.3-
1"},"crossval":{"Author":"Korbinian Strimmer.","Depends":"R (>=
3.0.2)","Description":"Contains generic functions for performing\ncross validation
and for computing diagnostic errors.","Imports":"stats","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"crossval","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"MASS, sda, care, binda","Title":"Generic Functions
for Cross Validation","URL":"http:\/\/cran.r-
project.org\/package=crossval","Version":"1.0.3"},"crp.CSFP":{"Author":"Kevin
Jakob, Dr. Matthias Fischer & Stefan Kolb","Description":"Modelling credit risks
based on the concept of \"CreditRisk+\", First Boston Financial Products, 1997
and \"CreditRisk+ in the Banking Industry\", Gundlach & Lehrbass, Springer,
2003.","Imports":"methods, MASS,utils,graphics","License":"GPL-
2","NeedsCompilation":"no","Package":"crp.CSFP","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"CreditRisk+ Portfolio Model","Version":"2.0.1"},"crqa":
{"Author":"Moreno I. Coco and Rick Dale with contributions of James D. Dixon and
John Nash","Depends":"R (>= 3.0.0), Matrix, tseriesChaos, fields, plot3D,
pracma","Description":"\nCross-recurrence quantification analysis\nof two time-
series, of either categorical or\ncontinuous values. It provides different
methods\nfor profiling cross-recurrence, i.e., only looking\nat the diagonal
recurrent points, as well as more\nin-depth measures of the whole cross-recurrence
plot,\ne.g., recurrence rate.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"crqa","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Cross-Recurrence Quantification Analysis for Categorical
and\nContinuous Time-Series","Version":"1.0.6"},"crrSC":{"Author":"Bingqing Zhou
and Aurelien Latouche","Depends":"survival","Description":"Extension of cmprsk to
Stratified and Clustered data.\nGoodness of fit test for Fine-Gray
2","NeedsCompilation":"yes","Package":"crrSC","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Competing risks regression for Stratified and Clustered
data","Version":"1.1"},"crrp":{"Author":"Zhixuan Fu","Depends":"survival, Matrix,
cmprsk","Description":"In competing risks regression, the proportional
subdistribution hazards(PSH) model is popular for its direct assessment of
covariate effects on the cumulative incidence
function. This package allows for penalized variable selection for the PSH model.
Penalties include LASSO, SCAD, MCP, and their group versions.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"crrp","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Penalized Variable Selection in Competing Risks
Regression","Version":"1.0"},"crrstep":{"Author":"Ravi Varadhan & Deborah
Kuk","Depends":"cmprsk","Description":"Performs forward and backwards stepwise
regression for the Proportional subdistribution hazards model in competing risks
(Fine & Gray 1999). Procedure uses AIC, BIC and BICcr as selection criteria. BICcr
has a penalty of k = log(n*), where n* is the number of primary
events.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"crrstep","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Stepwise Covariate Selection for the Fine & Gray
Competing Risks\nRegression Model","Version":"2015-2.1"},"crs":{"Author":"Jeffrey
S. Racine [aut, cre],\nZhenghua Nie [aut],\nBrian D. Ripley [ctb]
(stepCV.R)","Description":"Regression splines that handle a mix of continuous and
categorical (discrete) data often encountered in applied settings. I would like to
gratefully acknowledge support from the Natural Sciences and Engineering Research
Council of Canada (NSERC:www.nserc.ca), the Social Sciences and Humanities Research
Council of Canada (SSHRC:www.sshrc.ca), and the Shared Hierarchical Academic
Research Computing Network (SHARCNET:www.sharcnet.ca).","Imports":"boot, stats, np,
quantreg,
rgl","License":"GPL","NeedsCompilation":"yes","Package":"crs","Repository":"http:\/
\/cran.csiro.au\/src\/contrib","Suggests":"logspline, npRmpi,
quadprog","Title":"Categorical Regression
Splines","URL":"https:\/\/github.com\/JeffreyRacine\/R-Package-
crs\/","Version":"0.15-24"},"crskdiag":{"Author":"Jianing Li","Depends":"R (>=
3.0.0), cmprsk","Description":"Provides the implementation of analytical and
graphical approaches for checking the assumptions of the Fine and Gray
2)","NeedsCompilation":"yes","Package":"crskdiag","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Diagnostics for Fine and Gray
Model","Version":"1.0"},"crsnls":{"Author":"Josef TvrdÃk [aut],\nTomÃ¡Å¡ Goryl
[trl, cre]","Description":"Functions for nonlinear regression parameters estimation
by algorithms based on Controlled Random Search algorithm.\nBoth functions
(crs4hc(), crs4hce()) adapt current search strategy by four heuristics competition.
In addition, crs4hce() improves adaptability by adaptive stopping
condition.","License":"GPL-
2","NeedsCompilation":"no","Package":"crsnls","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Nonlinear Regression Parameters Estimation by 'CRS4HC'
and\n'CRS4HCe'","Version":"0.1"},"crunch":{"Author":"Neal Richardson [aut,
cre]","Depends":"R (>= 3.0.0)","Description":"The Crunch.io service
(http:\/\/crunch.io\/) provides a cloud-based\ndata store and analytic engine, as
well as an intuitive web interface.\nUsing this package, analysts can interact with
and manipulate Crunch\ndatasets from within R. Importantly, this allows technical
researchers to\ncollaborate naturally with team members, managers, and clients who
prefer a\npoint-and-click interface.","Imports":"httr (>= 1.0.0), httpcache,
jsonlite (>= 0.9.15), methods,\ncurl","License":"LGPL (>=
3)","NeedsCompilation":"no","Package":"crunch","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr, testthat","Title":"Crunch.io Data
Tools","URL":"https:\/\/github.com\/Crunch-io\/rcrunch","Version":"1.9.4"},"cruts":
{"Author":"Benjamin M. Taylor","Depends":"R (>= 3.2.1)","Description":"Functions
for reading in and manipulating CRU TS3.21: Climatic Research Unit (CRU) Time-
Series (TS) Version 3.21 data.","Imports":"sp, raster, stringr, lubridate,
ncdf4","License":"GPL-
3","NeedsCompilation":"no","Package":"cruts","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Interface to Climatic Research Unit Time-Series Version
3.21\nData","Version":"0.2"},"csSAM":{"Author":"Shai Shen-Orr, Rob Tibshirani,
Narasimhan Balasubramanian,\nDavid Wang","Depends":"R (>= 2.15),
compiler","Description":"Cell-type specific differential expression of a
microarray\nexperiment of heterogeneous tissue samples, using
SAM.","License":"LGPL","NeedsCompilation":"no","Package":"csSAM","Repository":"http
:\/\/cran.csiro.au\/src\/contrib","Title":"csSAM - cell-specific Significance
Analysis of Microarrays","Version":"1.2.4"},"csampling":{"Author":"S original by
Alessandra R. Brazzale <alessandra.brazzale@unipd.it>.\nR port by Alessandra R.
Brazzale <alessandra.brazzale@unipd.it>.","Depends":"R (>= 3.0.0), marg, statmod,
survival","Description":"Monte Carlo conditional inference for the parameters of
a\nlinear nonnormal regression model","License":"GPL (>= 2) | file
LICENCE","NeedsCompilation":"no","Package":"csampling","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Functions for Conditional Simulation in
Regression-Scale Models","URL":"http:\/\/www.r-project.org,
http:\/\/statwww.epfl.ch\/AA\/","Version":"1.2-2"},"cshapes":{"Author":"Nils B.
Weidmann <nils.weidmann@uni-konstanz.de>, Kristian Skrede Gleditsch
<ksg@essex.ac.uk>","Depends":"R (>= 2.8.0), sp (>= 1.0-5), maptools (>= 0.8-21),
plyr (>=\n1.8)","Description":"Package for CShapes, a GIS dataset of country
boundaries (1946-2015). Includes functions for data extraction and the computation
of distance matrices and -lists.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"cshapes","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"CShapes Dataset and
Utilities","URL":"http:\/\/nils.weidmann.ws\/projects\/cshapes,\nhttps:\/\/r-
forge.r-
project.org\/scm\/viewvc.php\/*checkout*\/pkg\/inst\/shp\/cshapes_shapefile_documen
tation.txt?root=cshapes","Version":"0.5-1"},"cslogistic":{"Author":"Alejandro Jara
[aut, cre], Maria Jose Garcia-Zattera [ctb]","Depends":"R (>= 2.10),
mvtnorm","Description":"This package contains functions for likelihood
and\nposterior analysis of conditionally specified logistic\nregression models.
All calculus and simulation is done in\ncompiled FORTRAN.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"cslogistic","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Conditionally Specified Logistic
Regression","URL":"http:\/\/www.mat.puc.cl\/~ajara","Version":"0.1-3"},"csn":
{"Author":"Dmitry Pavlyuk, Eugene Girtcius","Depends":"R (>=
2.2.0)","Description":"Provides functions for computing the density\nand the log-
likelihood function of closed-skew normal variates,\nand for generating random
vectors sampled from this distribution.\nSee Gonzalez-Farias, G., Dominguez-Molina,
J., and Gupta, A. (2004).\nThe closed skew normal distribution,\nSkew-elliptical
distributions and their applications: a journey beyond normality,\nChapman and
Hall\/CRC, Boca Raton, FL, pp. 25-42.","Imports":"mvtnorm","License":"GPL-
2","NeedsCompilation":"no","Package":"csn","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Closed Skew-Normal Distribution","Version":"1.1.3"},"csrplus":
{"Author":"Sarah Smith <smirks2@hotmail.com>","Depends":"R (>=
3.0.2)","Description":"Includes two functions to evaluate the hypothesis of
complete spatial randomness (csr) in point processes. The function 'mwin'
calculates quadrat counts to estimate the intensity of a spatial point process
through the moving window approach proposed by Bailey and Gatrell (1995). Event
counts are computed within a window of a set size over a fine lattice of points
within the region of observation. The function 'pielou' uses the nearest neighbor
test statistic and asymptotic distribution proposed by Pielou (1959) to compare the
observed point process to one generated under csr. The value can be compared to
that given by the more widely used test proposed by Clark and Evans
(1954).","Imports":"sp","License":"GPL-
2","NeedsCompilation":"no","Package":"csrplus","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Methods to Test Hypotheses on the Distribution of Spatial
Point\nProcesses","Version":"1.03-0"},"cstar":{"Author":"Justin
Esarey","Description":"Functions that allow a researcher to examine the robustness
of the substantive significance of their findings. Implements ideas set out in
Esarey and Danneman (2014).","License":"GPL-
2","NeedsCompilation":"no","Package":"cstar","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"MASS","Title":"Substantive significance testing for
regression estimates and\nmarginal effects","Version":"1.0"},"csvread":
{"Author":"Sergei Izrailev","Depends":"R (>= 2.15),
methods","Description":"Functions for loading large (10M+ lines) CSV\nand other
delimited files, similar to read.csv, but typically faster and\nusing less memory
than the standard R loader. While not entirely general,\nit covers many common use
cases when the types of columns in the CSV file\nare known in advance. In addition,
the package provides a class 'int64',\nwhich represents 64-bit integers exactly
when reading from a file. The\nlatter is useful when working with 64-bit integer
identifiers exported from\ndatabases. The CSV file loader supports common column
types including\n'integer', 'double', 'string', and 'int64', leaving further
type\ntransformations to the user.","Enhances":"bit64","License":"Apache License
(==
2.0)","NeedsCompilation":"yes","Package":"csvread","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Fast Specialized CSV File
Loader","URL":"http:\/\/github.com\/jabiru\/csvread","Version":"1.2"},"ctmcmove":
{"Author":"Ephraim Hanks","Depends":"R (>= 2.10), crawl, raster,
Matrix","Description":"Software to facilitates taking movement data in xyt format
and pairing it with raster covariates within a continuous time Markov chain (CTMC)
framework. As described in Hanks et al. (2015) <DOI:10.1214\/14-AOAS803>
, this allows flexible modeling of movement in response to covariates (or
covariate gradients) with model fitting possible within a Poisson GLM
framework.","License":"GPL-
2","NeedsCompilation":"no","Package":"ctmcmove","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"mgcv, dismo","Title":"Modeling Animal Movement with
Continuous-Time Discrete-Space\nMarkov Chains","Version":"1.2.1"},"ctmm":
{"Author":"Chris H. Fleming and J. M. Calabrese","Depends":"R (>=
2.10)","Description":"Functions for identifying, fitting, and applying continuous-
space, continuous-time stochastic movement models to animal tracking
data.","Imports":"expm, graphics, grDevices, manipulate, MASS, Matrix,
methods,\nnumDeriv, pbivnorm, raster, rgdal, scales, sp, stats,
3","NeedsCompilation":"no","Package":"ctmm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"knitr, move","Title":"Continuous-Time Movement
Modeling","Version":"0.3.1"},"cts":{"Author":"Fortran original by G. Tunnicliffe-
Wilson and Zhu Wang, R port by Zhu Wang with contribution from John Nash, Netlib
and NAG authors","Description":"Functions to Fit Continuous Time Autoregressive
Models with the Kalman Filter.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"cts","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Continuous Time Autoregressive Models","Version":"1.0-
20"},"ctsem":{"Author":"Manuel Voelkle [aut, cph] (Original development of
continuous time\nmodel specification within OpenMx, advisor for further
development),\nHan Oud [aut, cph] (Original development of continuous time
model\nspecification within OpenMx),\nCharles Driver [aut, cre, cph] (Further
development of continuous time\nmodel specification within OpenMx, package
development,\ndocumentation and maintenance)","Depends":"R (>= 3.0.0), OpenMx (>=
2.5.0)","Description":"An easily accessible continuous (and discrete) time
dynamic\nmodelling package for panel and time series data, reliant upon the
OpenMx.\npackage (http:\/\/openmx.psyc.virginia.edu\/) for computation. Most
dynamic\nmodelling approaches to longitudinal data rely on the assumption that
time\nintervals between observations are consistent. When this assumption
is\nadhered to, the data gathering process is necessarily limited to a
specific\nschedule, and when broken, the resulting parameter estimates may be
biased\nand reduced in power. Continuous time models are conceptually similar
to\nvector autoregressive models (thus also the latent change models
popularised\nin a structural equation modelling context), however by explicitly
including\nthe length of time between observations, continuous time models are
freed\nfrom the assumption that measurement intervals are consistent. This
allows:\ndata to be gathered irregularly; the elimination of noise and bias due
to\nvarying measurement intervals; parsimonious structures for complex
dynamics.\nThe application of such a model in this SEM framework allows full-
information\nmaximum-likelihood estimates for both N = 1 and N > 1 cases, multiple
measured\nindicators per latent process, and the flexibility to incorporate
additional\nelements, including individual heterogeneity in the latent process
and\nmanifest intercepts, and time dependent and independent exogenous
covariates.\nFurthermore, due to the SEM implementation we are able to estimate a
random\neffects model where the impact of time dependent and time independent
predictors\ncan be assessed simultaneously, but without the classic problems of
random\neffects models assuming no covariance between unit level effects and
predictors.","Imports":"MASS, Matrix, stats, utils,graphics,methods,
3","NeedsCompilation":"no","Package":"ctsem","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr, testthat, PSM, cts, yuima","Title":"Continuous
Time Structural Equation Modelling","URL":"http:\/\/ctsem.r-forge.r-
project.org\/","Version":"1.1.5.2"},"ctv":{"Author":"Achim Zeileis [aut,
cre],\nKurt Hornik [aut]","Depends":"R (>= 2.13.0), utils","Description":"Server-
side and client-side tools for task views\nto CRAN-style
repositories","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"ctv","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"XML","Title":"CRAN Task Views","Version":"0.8-
1"},"cubature":{"Author":"C code by Steven G. Johnson, R by Balasubramanian
Narasimhan","Description":"Adaptive multivariate integration over
hypercubes","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"cubature","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Adaptive multivariate integration over
hypercubes","Version":"1.1-2"},"cubfits":{"Author":"Wei-Chen Chen [aut,
cre],\nRussell Zaretzki [aut],\nWilliam Howell [aut],\nCedric Landerer [aut],\nDrew
Schmidt [aut],\nMichael A. Gilchrist [aut],\nPreston Hewgley [ctb],\nStudents REU13
[ctb]","Depends":"R(>= 3.0.0), methods, coda, foreach, parallel, stats,\ngraphics,
utils","Description":"Estimating mutation and selection coefficients on
synonymous\ncodon bias usage based on models of ribosome overhead cost
(ROC).\nMultinomial logistic regression and Markov Chain Monte Carlo are used
to\nestimate and predict protein production rates with\/without the presence\nof
expressions and measurement errors. Work flows with examples for\nsimulation,
estimation and prediction processes are also provided\nwith parallelization
speedup. The whole framework is tested with\nyeast genome and gene expression data
of Yassour (2009).","Enhances":"pbdMPI (>= 0.3-1)","License":"Mozilla Public
License
2.0","NeedsCompilation":"yes","Package":"cubfits","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"seqinr, VGAM, EMCluster","Title":"Codon Usage Bias
Fits","URL":"https:\/\/github.com\/snoweye\/cubfits","Version":"0.1-
2"},"cudaBayesreg":{"Author":"Adelino Ferreira da Silva
<afs@fct.unl.pt>","Depends":"R (>= 3.0.0), cudaBayesregData,
oro.nifti","Description":"Compute Unified Device Architecture (CUDA) is a
software\nplatform for massively parallel high-performance computing on\nNVIDIA
GPUs. This package provides a CUDA implementation of a\nBayesian multilevel model
for the analysis of brain fMRI data.\nA fMRI data set consists of time series of
volume data in 4D\nspace. Typically, volumes are collected as slices of 64 x
64\nvoxels. Analysis of fMRI data often relies on fitting linear\nregression models
at each voxel of the brain. The volume of the\ndata to be processed, and the type
of statistical analysis to\nperform in fMRI analysis, call for high-performance
computing\nstrategies. In this package, the CUDA programming model uses a\nseparate
thread for fitting a linear regression model at each\nvoxel in parallel. The global
statistical model implements a\nGibbs Sampler for hierarchical linear models with a
normal\nprior. This model has been proposed by Rossi, Allenby and\nMcCulloch in
`Bayesian Statistics and Marketing', Chapter 3,\nand is referred to as
`rhierLinearModel' in the R-package\nbayesm. A notebook equipped with a NVIDIA
`GeForce 8400M GS'\ncard having Compute Capability 1.1 has been used in the
tests.\nThe data sets used in the package's examples are available in\nthe separate
package cudaBayesregData.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"cudaBayesreg","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"CUDA Parallel Implementation of a Bayesian
Multilevel Model for\nfMRI Data Analysis","URL":"http:\/\/www.r-
project.org","Version":"0.3-16"},"cudaBayesregData":{"Author":"Adelino Ferreira da
Silva <afs@fct.unl.pt>","Depends":"R (>= 2.9.2)","Description":"FMRI data sets used
in the examples of \"cudaBayesreg\".\nData sets have been separated from the main
package\n\"cudaBayesreg\" for convenience.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"cudaBayesregData","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Data sets for the examples used in the
package \"cudaBayesreg\"","Version":"0.3-11"},"cudia":{"Author":"Yubin Park and
Joydeep Ghosh","Depends":"R (>= 2.14.1), MCMCpack,
mvtnorm","Description":"Reconstruct individual-level values from aggregate-
level\nsummaries.","License":"GPL-
2","NeedsCompilation":"no","Package":"cudia","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"MASS","Title":"CUDIA Cross-level
Imputation","Version":"0.1"},"cumSeg":{"Author":"Vito M.R.
Muggeo","Depends":"lars","Description":"Estimation of number and location of change
points in\nmean-shift (piecewise constant) models. Particularly useful to\nmodel
genomic sequences of continuous
measurements.","License":"GPL","NeedsCompilation":"no","Package":"cumSeg","Reposito
ry":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Change point detection in
genomic sequences","Version":"1.1"},"cumplyr":{"Author":"John Myles
White","Description":"Extends ddply to allow calculation of
cumulative\nquantities.","License":"MIT","NeedsCompilation":"no","Package":"cumplyr
","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Extends ddply to
allow calculation of cumulative quantities","Version":"0.1-1"},"curl":
{"Author":"Jeroen Ooms [cre, aut],\nHadley Wickham [ctb],\nRStudio
[cph]","Depends":"R (>= 3.0.0)","Description":"The curl() and curl_download()
functions provide highly\nconfigurable drop-in replacements for base url() and
download.file() with\nbetter performance, support for encryption (https, ftps),
gzip compression,\nauthentication, and other libcurl goodies. The core of the
package implements a\nframework for performing fully customized requests where data
can be processed\neither in memory, on disk, or streaming via the callback or
connection\ninterfaces. Some knowledge of libcurl is recommended; for a more-user-
friendly\nweb client see the 'httr' package which builds on this package with
http\nspecific tools and logic.","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"curl","Repository":"http:\/\/cran.csir
o.au\/src\/contrib
","Suggests":"testthat, knitr, jsonlite, rmarkdown, magrittr","Title":"A Modern and
Flexible Web Client for
R","URL":"https:\/\/github.com\/jeroenooms\/curl\nhttps:\/\/www.opencpu.org\/posts\
/curl-release-0-8\/","Version":"0.9.7"},"curlconverter":{"Author":"Bob Rudis [aut,
cre],\nNick Carneiro [ctb]","Depends":"R (>= 3.0.0)","Description":"Deciphering
web\/'REST' 'API' and 'XHR' calls can be tricky, which is one reason\nwhy internet
browsers provide \"Copy as cURL\" functionality within their \"Developer
Tools\"\npane(s). These 'cURL' command-lines can be difficult to wrangle into an
'httr' 'GET' or\n'POST' request, but you can now \"straighten\" these 'cURLs'
either from data copied to the\nsystem clipboard or by passing in a vector of
'cURL' command-lines and getting back a\nlist of parameter elements which can be
used to form 'httr' requests. You can also make a\ncomplete\/working\/callable
'httr::VERB' function right from the tools provided.","Imports":"V8, curl, httr,
purrr, clipr, stringi, formatR,
magrittr,\njsonlite","License":"AGPL","NeedsCompilation":"no","Package":"curlconver
ter","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"testthat,
knitr, rmarkdown","Title":"Tools to Transform 'cURL' Command-Line Calls to 'httr'
Requests","Version":"0.7.0"},"currentSurvival":{"Author":"Eva Janousova, Tomas
Pavlik, Jiri Mayer, Ladislav Dusek","Depends":"R (>= 2.13.0), survival,
cmprsk","Description":"The currentSurvival package contains functions for
the\nestimation of the current cumulative incidence (CCI) and the\ncurrent
leukaemia-free survival (CLFS). The CCI is the\nprobability that a patient is alive
and in any disease\nremission (e.g. complete cytogenetic remission in
chronic\nmyeloid leukaemia) after initiating his or her therapy (e.g.\ntyrosine
kinase therapy for chronic myeloid leukaemia). The\nCLFS is the probability that a
patient is alive and in any\ndisease remission after achieving the first disease
remission.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"currentSurvival","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Estimation of CCI and CLFS
Functions","Version":"1.0"},"curvHDR":{"Author":"Matt Wand [aut, cre],\nGeorge Luta
[aut],\nUlrike Naumann [aut],\nMathew W. McLean [ctb],\nDai Feng [ctb],\nLuke
Tierney [ctb],\nFlorian Hahne [ctb]","Description":"Filtering, also known as
gating, of\nflow cytometry samples using the curvHDR method.","Imports":"feature,
geometry, hdrcde, ks, misc3d, ptinpoly, rgl,\nKernSmooth","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"curvHDR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Filtering of Flow Cytometry Samples","Version":"1.1-
0"},"curvetest":{"Author":"Zhongfa Zhang","Depends":"locfit, R.oo, methods,
R.methodsS3","Description":"Test Equality of Curves with Homoscedastic
or\nHeteroscedastic Errors.","License":"GPL-
2","NeedsCompilation":"no","Package":"curvetest","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"The package will formally test two curves represented
by\ndiscrete data sets to be statistically equal or not when the\nerrors of the two
curves were assumed either equal or not using\nthe tube formula to calculate the
tail probabilities","Version":"2.2"},"cusp":{"Author":"Raoul P. P. P. Grasman [aut,
cre, cph]","Description":"Cobb's maximum likelihood method for cusp-catastrophe
modeling\n(Grasman, van der Maas, & Wagenmakers, 2009, JSS, 32:8;\nCobb, L, 1981,
Behavioral Science, 26:1, 75--78).\nIncludes a cusp() function for model fitting,
and several\nutility functions for plotting, and for comparing the\nmodel to linear
regression and logistic curve models.","Imports":"stats, graphics, grDevices,
2","NeedsCompilation":"yes","Package":"cusp","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"plot3D","Title":"Cusp-Catastrophe Model Fitting Using
Maximum Likelihood","Version":"2.3.3"},"customizedTraining":{"Author":"Scott
Powers, Trevor Hastie, Robert Tibshirani","Description":"Customized training is a
simple technique for transductive\nlearning, when the test covariates are known at
the time of training. The\nmethod identifies a subset of the training set to serve
as the training set\nfor each of a few identified subsets in the training set. This
package\nimplements customized training for the glmnet() and cv.glmnet()
functions.","Imports":"FNN, glmnet","License":"GPL-
2","NeedsCompilation":"no","Package":"customizedTraining","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Customized Training for Lasso and Elastic-Net
Regularized\nGeneralized Linear Models","Version":"1.0"},"cutoffR":
{"Author":"Lingbing Feng, Gen Nowak, Alan. H. Welsh, Terry. J.
O'Neill","Depends":"R (>= 3.1.0)","Description":"This package provides a set of
tools for spatio-temporal imputation\nin R. It includes the implementation for then
CUTOFF imputation method,\na useful cross-validation function that can be used not
only by the\nCUOTFF method but also by some other imputation functions to
help\nchoosing an optimal value for relevant parameters, such as the number\nof k-
nearest neighbors for the KNN imputation method, or the number of\ncomponents for
the SVD imputation method. It also contains tools for\nsimulating data with missing
values with respect to some specific\nmissing pattern, for example, block missing.
Some useful visualisation\nfunctions for imputation purposes are also provided in
the package.","Imports":"ggplot2, reshape2","License":"GPL-
2","NeedsCompilation":"no","Package":"cutoffR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"CUTOFF: A Spatio-temporal Imputation
Method","Version":"1.0"},"cuttlefish.model":{"Author":"Michael Gras and Jean-Paul
Robin","Depends":"R (>= 3.0.0)","Description":"This package can be used to
standardize abundance indices using the delta-GLM method and to model the English
Channel cuttlefish stock using a two-stage biomass model","License":"GPL-
3","NeedsCompilation":"no","Package":"cuttlefish.model","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"An R package to perform LPUE standardization and
stock\nassessment of the English Channel cuttlefish stock using a\ntwo-stage
biomass model","Version":"1.0"},"cvAUC":{"Author":"Erin LeDell, Maya Petersen, Mark
van der Laan","Depends":"ROCR, data.table","Description":"This package contains
various tools for working with and evaluating cross-validated area under the ROC
curve (AUC) estimators. The primary functions of the package are ci.cvAUC and
ci.pooled.cvAUC, which report cross-validated AUC and compute confidence intervals
for cross-validated AUC estimates based on influence curves for i.i.d. and pooled
repeated measures data, respectively. One benefit to using influence curve based
confidence intervals is that they require much less computation time than
bootstrapping methods. The utility functions, AUC and cvAUC, are simple wrappers
for functions from the ROCR package.","License":"Apache License (==
2.0)","NeedsCompilation":"no","Package":"cvAUC","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Cross-Validated Area Under the ROC Curve Confidence
Intervals","URL":"https:\/\/github.com\/ledell\/cvAUC","Version":"1.1.0"},"cvTools"
:{"Author":"Andreas Alfons","Depends":"R (>= 2.11.0), lattice,
robustbase","Description":"Tools that allow developers to write functions
for\ncross-validation with minimal programming effort and assist\nusers with model
selection.","Imports":"lattice, robustbase, stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"cvTools","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Cross-validation tools for regression
models","Version":"0.3.2"},"cvplogistic":{"Author":"Dingfeng Jiang
<dingfengjiang@gmail.com>","Depends":"R (>= 2.9.0)","Description":"The package uses
majorization minimization by coordinate\ndescent (MMCD) algorithm to compute the
solution surface for\nconcave penalized logistic regression model. The SCAD and
MCP\n(default) are two concave penalties considered in this\nimplementation. For
the MCP penalty, the package also provides\nthe local linear approximation by
coordinate descant (LLA-CD)\nand adaptive rescaling algorithms for computing the
solutions.\nThe package also provides a Lasso-concave hybrid penalty for\nfast
variable selection. The hybrid penalty applies the concave\npenalty only to the
variables selected by the Lasso. For all\nthe implemented methods, the solution
surface is computed along\nkappa, which is a more smooth fit for the logistic
model.\nTuning parameter selection method by k-fold cross-validated\narea under ROC
curve (CV-AUC) is implemented as well.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"cvplogistic","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Penalized Logistic Regression Model using
Majorization\nMinimization by Coordinate Descent (MMCD)
Algorithm","URL":"http:\/\/www.r-project.org","Version":"3.1-0"},"cvq2":
{"Author":"Torsten Thalheim","Depends":"methods, stats","Description":"The external
prediction capability of quantitative structure-activity relationship (QSAR) models
is often quantified using the predictive squared correlation coefficient. This
value can be calculated with an external data set or by cross
validation.","License":"GPL-
3","NeedsCompilation":"no","Package":"cvq2","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Calculate the predictive squared correlation
coefficient","Version":"1.2.0"},"cvxbiclustr":{"Author":"Eric C. Chi, Genevera I.
Allen, Richard G. Baraniuk","Depends":"R (>= 3.1.3), Matrix,
igraph,","Description":"An iterative algorithm for solving a convex\nformulation of
the biclustering problem.","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"cvxbiclustr","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Convex Biclustering
Algorithm","Version":"0.0.1"},"cvxclustr":{"Author":"Eric
C. Chi, Kenneth Lange","Depends":"R (>= 2.15.2), Matrix,
igraph","Description":"Alternating Minimization Algorithm (AMA) and Alternating
Direction\nMethod of Multipliers (ADMM) splitting methods for convex
clustering.","License":"CC BY-NC-SA
4.0","NeedsCompilation":"yes","Package":"cvxclustr","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"ggplot2","Title":"Splitting methods for convex
clustering","Version":"1.1.1"},"cwhmisc":{"Author":"Christian W. Hoffmann
<christian@echoffmann.ch> <http:\/\/www.echoffmann.ch>","Depends":"R (>= 2.0),
lattice, grid","Description":"Miscellaneous useful or interesting functions. Some
parameters of functions may have changed, so beware!","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"cwhmisc","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Miscellaneous Functions for Math, Plotting,
Printing,\nStatistics, Strings, and Tools","Version":"6.0"},"cwm":
{"Author":"Giorgio Spedicato, Simona C. Minotti","Depends":"R (>= 2.14),
MASS","Description":"This package estimates gaussian cluster weighted linear
regressions by EM algorithm.","Imports":"methods, stats, matlab,
permute","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"cwm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Cluster Weighted Models by EM
algorithm","Version":"0.0.3"},"cxxfunplus":{"Author":"Jiqiang Guo
<guojq28@gmail.com>","Depends":"inline","Description":"extend cxxfunction by saving
the dynamic shared objects\nfor reusing across R
sessions","Imports":"methods","License":"GPL-
3","NeedsCompilation":"no","Package":"cxxfunplus","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"Rcpp (>= 0.8.0)","Title":"extend cxxfunction by
saving the dynamic shared
objects","URL":"https:\/\/github.com\/maverickg\/cxxfunplus","Version":"1.0"},"cycl
eRtools":{"Author":"Jordan Mackie [aut, cre]","Depends":"R (>=
3.2.1)","Description":"A suite of functions for analysing cycling
data.","Imports":"Rcpp, xml2, stats, graphics, grDevices, utils","License":"MIT +
file
LICENSE","NeedsCompilation":"yes","Package":"cycleRtools","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"changepoint, minpack.lm, RCurl, raster,
pspline, leaflet,\nknitr, rmarkdown","Title":"Tools for Cycling Data
Analysis","URL":"https:\/\/github.com\/jmackie4\/cycleRtools","Version":"1.1.1"},"c
yclocomp":{"Author":"Gabor Csardi","Description":"Cyclomatic complexity is a
software metric (measurement), used to\nindicate the complexity of a program. It is
a quantitative measure of the number\nof linearly independent paths through a
program's source code. It was developed\nby Thomas J. McCabe, Sr. in
1976.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"cyclocomp","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat","Title":"Cyclomatic Complexity of R
Code","URL":"https:\/\/github.com\/MangoTheCat\/cyclocomp","Version":"1.0.0"},"cycl
oids":{"Author":"Peter Biber","Description":"Tools for calculating coordinate
representations of\nhypocycloids, epicyloids, hypotrochoids, and
epitrochoids\n(altogether called 'cycloids' here) with different scaling\nand
positioning options. The cycloids can be visualised with\nany appropriate graphics
function in R.","License":"GPL-
3","NeedsCompilation":"no","Package":"cycloids","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"cycloids","Version":"1.0"},"cymruservices":{"Author":"Bob
Rudis [aut, cre]","Depends":"R (>= 3.2.0)","Description":"A toolkit for querying
'Team Cymru' <http:\/\/team-cymru.org> 'IP'\naddress, Autonomous System Number
('ASN'), Border Gateway Protocol ('BGP'), Bogon\nand 'Malware' Hash Data
Services.","Imports":"utils, stringr, purrr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"cymruservices","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Query 'Team Cymru' 'IP'
Address, Autonomous System Number\n('ASN'), Border Gateway Protocol ('BGP'), Bogon
and 'Malware'\nHash Data Services","Version":"0.2.0"},"cyphid":{"Author":"Elizabeth
Crane","Depends":"fda","Description":"This library contains a primary function that
divides\nchewing sequences in cycles and cycles into phases. See\nget.all.breaks
for an example.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"cyphid","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Cycle and Phase Identification for mastication
data","Version":"1.1"},"cytoDiv":{"Author":"Francois Ribalet
<ribalet@u.washington.edu>","Depends":"R (>= 2.13.1), GenKern,
plotrix","Description":"Calculates ecological diversity indices for a
microbial\ncommunity","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"cytoDiv","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Cytometric diversity
indices","URL":"http:\/\/seaflow.ocean.washington.edu","Version":"0.5-
3"},"d3Network":{"Author":"Christopher Gandrud","Depends":"R (>=
3.0.0)","Description":"This packages is intended to make it easy to create D3
JavaScript\nnetwork, tree, dendrogram, and Sankey graphs from R using data
frames.\n!!! NOTE: Active development has moved to the networkD3
package. !!!","Imports":"plyr, rjson, whisker","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"d3Network","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"RCurl","Title":"Tools for creating D3 JavaScript
network, tree, dendrogram, and\nSankey graphs from
R","URL":"http:\/\/christophergandrud.github.io\/d3Network\/","Version":"0.5.2.1"},
"d3heatmap":{"Author":"Joe Cheng [aut, cre],\nTal Galili [aut],\nRStudio, Inc.
[cph],\nMichael Bostock [ctb, cph] (D3.js library),\nJustin Palmer [ctb, cph]
(d3.tip library)","Description":"Create interactive heat maps that are usable from
the R console, in\nthe 'RStudio' viewer pane, in 'R Markdown' documents, and in
'Shiny' apps. Hover\nthe mouse pointer over a cell to show details, drag a
rectangle to zoom, and\nclick row\/column labels to highlight.","Imports":"scales
(>= 0.2.5), htmlwidgets, png, base64enc, dendextend (>=\n0.18.0), stats,
grDevices","License":"GPL-3 | file
LICENSE","NeedsCompilation":"no","Package":"d3heatmap","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"shiny, knitr","Title":"Interactive Heat Maps
Using 'htmlwidgets' and
'D3.js'","URL":"https:\/\/github.com\/rstudio\/d3heatmap","Version":"0.6.1.1"},"dCh
ipIO":{"Author":"Henrik Bengtsson [aut, cre, cph]","Depends":"R (>=
2.6.0)","Description":"Functions for reading DCP and CDF.bin files generated by the
dChip software.","License":"LGPL (>=
2.1)","NeedsCompilation":"no","Package":"dChipIO","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Methods for Reading dChip
Files","URL":"https:\/\/github.com\/HenrikBengtsson\/dChipIO","Version":"0.1.5"},"d
CovTS":{"Author":"Maria Pitsillou [aut, cre],\nKonstantinos Fokianos
[aut]","Depends":"R (>= 3.1.0), doParallel (>= 1.0.8), energy (>=
1.5.0)","Description":"Computing and plotting the distance covariance and
correlation\nfunction of a univariate or a multivariate time series. Test
statistics for\ntesting pairwise independence are also implemented. Some data sets
are also included.","Imports":"foreach","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"dCovTS","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"MASS","Title":"Distance Covariance and Correlation for
Time Series Analysis","Version":"1.0"},"dHSIC":{"Author":"Niklas Pfister and Jonas
Peters","Description":"Contains an implementation of the\nd-variable Hilbert
Schmidt independence criterion\nand several hypothesis tests based on
it.","Imports":"stats","License":"GPL-
3","NeedsCompilation":"no","Package":"dHSIC","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Independence Testing via Hilbert Schmidt Independence
Criterion","Version":"1.0"},"dMod":{"Author":"Daniel Kaschek","Depends":"cOde,
trust, ggplot2","Description":"The framework provides functions to generate ODEs of
reaction networks, parameter transformations, observation functions, residual
functions, etc. The framework follows the paradigm that derivative information
should be used for optimization whenever possible. Therefore, all major functions
produce and can handle expressions for symbolic derivatives.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"dMod","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"MASS, inline, rPython, rootSolve","Title":"Dynamic
Modeling and Parameter Estimation in ODE Models","Version":"0.1"},"dad":
{"Author":"Rachid Boumaza, Pierre Santagostini, Smail Yousfi, Sabine Demotes-
Mainard","Depends":"R (>= 3.1.0), methods, stats, graphics, grDevices,
utils,\nlattice, e1071","Description":"The three-way data consists of a set of
variables measured on several groups of individuals. To each group is associated an
estimated probability density function. The package provides functional methods
(principal component analysis, multidimensional scaling, discriminant analysis...)
for such probability densities.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"dad","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"MASS","Title":"Three-Way Data Analysis Through
Densities","Version":"1.1.0"},"dae":{"Author":"Chris Brien
<Chris.Brien@unisa.edu.au>.","Depends":"R (>= 2.10.0), ggplot2","Description":"The
content falls into the following groupings: (i) Data, (ii) Factor
manipulation\nfunctions, (iii) Design functions, (iv) ANOVA functions, (v) Matrix
functions,\n(vi) Projector and canonical efficiency functions, and (vii)
Miscellaneous functions.\nA document 'daeDesignRandomization.pdf', available in the
doc subdirectory of the\ninstallation directory for 'dae', describes the use of the
package for generating randomized\nlayouts for experiments. The ANOVA functions
facilitate the extraction of information when\nthe 'Error' function has been used
in the call to
'aov'.","Imports":"graphics, methods, stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"dae","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Functions Useful in the Design and ANOVA of
Experiments","URL":"http:\/\/chris.brien.name","Version":"2.7-6"},"daewr":
{"Author":"John Lawson","Description":"Contains Data frames and functions used in
the book \"Design and Analysis of Experiments with R\".","Imports":"lattice, FrF2,
BsMD, graphics, grDevices, stats","License":"GPL-
2","NeedsCompilation":"no","Package":"daewr","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Design and Analysis of Experiments with R","Version":"1.1-
6"},"daff":{"Author":"Paul Fitzpatrick [aut] (JavaScript
original,\nhttp:\/\/paulfitz.github.io\/daff\/),\nEdwin de Jonge [aut, cre] (R
wrapper)","Description":"Diff, patch and merge for data frames. Document changes in
data sets and use them to apply patches.\nChanges to data can be made visible by
using render_diff. The V8 package is used to\nwrap the 'daff.js' JavaScript library
which is included in the package.","Imports":"V8 (>= 0.6), jsonlite","License":"MIT
+ file
LICENSE","NeedsCompilation":"no","Package":"daff","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat","Title":"Diff, Patch and Merge for
Data.frames","URL":"http:\/\/github.com\/edwindj\/daff","Version":"0.1.4"},"dafs":
{"Author":"James Curran, Danny Chang","Depends":"s20x","Description":"Data and
miscellanea to support the book \"Introduction to\nData analysis with R for
Forensic Scientists\", Curran, J.M.\n2010 CRC Press ISBN: 978-1-4200-8826-
7","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"dafs","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Data analysis for forensic scientists","Version":"1.0-
37"},"dagR":{"Author":"Lutz P Breitling","Description":"Functions to draw,
manipulate, evaluate directed\nacyclic graphs and simulate corresponding
2","NeedsCompilation":"no","Package":"dagR","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"R functions for directed acyclic
graphs","Version":"1.1.3"},"dagbag":{"Author":"Ru Wang, Jie
Peng","Description":"dagbag is a set of methods that learn DAGs via bootstrap
aggregating.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"dagbag","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Learning directed acyclic graphs (DAGs) through
bootstrap\naggregating","Version":"1.1"},"dagitty":{"Author":"Johannes Textor,
Benito van der Zander","Depends":"R (>= 3.0.0)","Description":"A port of the web-
based software 'DAGitty', available at\n<http:\/\/dagitty.net>, for analyzing
structural causal models\n(also known as directed acyclic graphs or DAGs).\nThis
package computes covariate adjustment sets for estimating causal\neffects,
enumerates instrumental variables, derives testable\nimplications (d-separation and
vanishing tetrads), generates equivalent\nmodels, and includes a simple facility
for data simulation.","Imports":"V8, jsonlite, boot, MASS, methods, grDevices,
stats, utils,\ngraphics","License":"GPL-
2","NeedsCompilation":"no","Package":"dagitty","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr, base64enc (>= 0.1-3), lavaan,
testthat","Title":"Graphical Analysis of Structural Causal
Models","URL":"http:\/\/www.dagitty.net,
https:\/\/github.com\/jtextor\/dagitty","Version":"0.1-10"},"dams":{"Author":"Gopi
Goteti <my.ration.shop@gmail.com>","Depends":"R (>= 2.10)","Description":"The
single largest source of dams in the United States is the\nNational Inventory of
Dams (NID, http:\/\/nid.usace.army.mil) from the US\nArmy Corps of Engineers.
Entire data from the NID cannot be obtained all at\nonce and NID's website limits
extraction of more than a couple of thousand\nrecords at a time. Moreover, selected
data from the NID's user interface\ncannot not be saved to a file. In order to make
the analysis of this data\neasier, all the data from NID was extracted manually.
Subsequently, the raw\ndata was checked for potential errors and cleaned. This
package provides\nsample cleaned data from the NID and provides functionality to
access the\nentire cleaned NID data.","Imports":"RCurl","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"dams","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"ggplot2, maps, mapproj","Title":"Dams in the United
States from the National Inventory of Dams\n(NID)","Version":"0.1"},"darch":
{"Author":"Martin Drees [aut, cre],\nJohannes Rueckert [ctb],\nGeoffrey Hinton
[cph],\nRuslan Salakhutdinov [cph],\nCarl Edward Rasmussen [cph],","Depends":"R (>=
3.0.0)","Description":"The darch package is built on the basis of the code from G.
E.\nHinton and R. R. Salakhutdinov (available under Matlab Code for deep
belief\nnets). This package is for generating neural networks with many layers
(deep\narchitectures) and train them with the method introduced by the
publications\n\"A fast learning algorithm for deep belief nets\" (G. E. Hinton, S.
Osindero,\nY. W. Teh; doi: 10.1162\/neco.2006.18.7.1527) and \"Reducing
the\ndimensionality of data with neural networks\" (G. E. Hinton, R.
R.\nSalakhutdinov; doi: 10.1126\/science.1127647). This method includes a
pre\ntraining with the contrastive divergence method published by G.E
Hinton\n(2002; doi: 10.1162\/089976602760128018) and a fine tuning with common
known\ntraining algorithms like backpropagation or conjugate
gradients.\nAdditionally, supervised fine-tuning can be enhanced with maxout
and\ndropout, two recently developed techniques to improve fine-tuning for
deep\nlearning.","Imports":"stats, methods, futile.logger (>= 1.4.1), ff (>= 2.2-
13)","License":"GPL (>= 2) | file
LICENSE","NeedsCompilation":"no","Package":"darch","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"gputools","Title":"Package for Deep Architectures
and Restricted Boltzmann
Machines","URL":"https:\/\/github.com\/maddin79\/darch","Version":"0.10.0"},"darts"
:{"Author":"Ryan Tibshirani","Description":"Are you aiming at the right spot in
darts? Maybe not! Use\nthis package to find your optimal aiming location. For a
better\nexplanation, go to\nhttp:\/\/www-stat.stanford.edu\/~ryantibs\/darts\/ or
see the paper\n\"A Statistician Plays
Darts\".","License":"GPL","NeedsCompilation":"yes","Package":"darts","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Title":"Statistical Tools to Analyze Your
Darts Game","Version":"1.0"},"dashboard":{"Author":"Johann Laurent","Depends":"R
(>= 2.13.0)","Description":"The dashboard package allows users to create web pages
which display\ninteractive data visualizations working in a standard modern
browser. It displays them locally\nusing the Rook server. Nor knowledge about web
technologies nor Internet connection are\nrequired. D3.js is a JavaScript library
for manipulating documents based on data.\nD3 helps the dashboard package bring
data to life using HTML, SVG and CSS.","Imports":"Rook","License":"GPL-
2","NeedsCompilation":"no","Package":"dashboard","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Interactive Data Visualization with
D3.js","Version":"0.1.0"},"data.table":{"Author":"M Dowle, A Srinivasan, T Short, S
Lianoglou with contributions from R Saporta, E Antonyan","Depends":"R (>=
2.14.1)","Description":"Fast aggregation of large data (e.g. 100GB in RAM), fast
ordered joins, fast add\/modify\/delete of columns by group using no copies at all,
list columns and a fast file reader (fread). Offers a natural and flexible syntax,
for faster development.","Imports":"methods, chron","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"data.table","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"ggplot2 (>= 0.9.0), plyr, reshape, reshape2,
testthat (>=\n0.4), hexbin, fastmatch, nlme, xts, bit64, gdata,\nGenomicRanges,
caret, knitr, curl, zoo, plm","Title":"Extension of
Data.frame","URL":"https:\/\/github.com\/Rdatatable\/data.table\/wiki","Version":"1
.9.6"},"data.tree":{"Author":"Christoph Glur","Depends":"R (>=
3.0)","Description":"Create tree structures from hierarchical data, and
traverse\nthe tree in various orders. Aggregate, cumulate, print, plot, convert to
and from\ndata.frame and more. Useful for decision trees, machine
learning,\nfinance, conversion from and to JSON, and many other
applications.","Imports":"R6, stringr, methods, DiagrammeR","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"data.tree","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"graphics, testthat, knitr, ape, yaml, networkD3,
jsonlite,\nigraph, treemap, doParallel, foreach, htmlwidgets","Title":"General
Purpose Hierarchical Data
Structure","URL":"http:\/\/github.com\/gluc\/data.tree","Version":"0.3.5"},"dataQua
lityR":{"Author":"Madhav Kumar <madhavkumar2005@gmail.com> and Shreyes
Upadhyay\n<shreyes.upadhyay@gmail.com>","Description":"The package performs
variable level data quality checks including\nmissing values, unique values,
frequency tables, and generates summary\nstatistics","License":"MIT | file
LICENSE","NeedsCompilation":"no","Package":"dataQualityR","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Performs variable level data quality checks and
generates\nsummary statistics","Version":"1.0"},"dataRetrieval":{"Author":"Robert
Hirsch [aut],\nLaura DeCicco [aut, cre],\nDavid Lorenz [aut],\nJordan Read
[ctb],\nLindsay Carr [ctb]","Depends":"R (>= 3.0)","Description":"Collection of
functions to help retrieve U.S. Geological Survey\n(USGS) and U.S. Environmental
Protection Agency (EPA) water quality and\nhydrology data from web services. USGS
web services are discovered from the\nNational Water Information System (NWIS)
tools. Both EPA and USGS water\nquality data are obtained from the Water Quality
Portal.","Imports":"XML, httr (>= 1.0.0), curl, reshape2, lubridate (>=
1.5.0),\nstats, utils, dplyr, readr
(>=
0.1.1.9000)","License":"CC0","NeedsCompilation":"no","Package":"dataRetrieval","Rep
ository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"xtable, knitr,
testthat","Title":"Retrieval Functions for USGS and EPA Hydrologic and
Water\nQuality Data","URL":"https:\/\/github.com\/USGS-
R\/dataRetrieval,\nhttp:\/\/pubs.usgs.gov\/tm\/04\/a10\/","Version":"2.5.3"},"datac
heck":{"Author":"\"Simon, Reinhard (CIP)\" <R.SIMON@CGIAR.ORG>, Jose Francisco Loff
<jfloff at phistat.com>","Depends":"R (>= 3.1.0),
grDevices","Description":"Functions to check variables against a\nset of data
quality rules. A rule file can be accompanied by look-up tables. In\naddition,
there are some convenience functions that may\nserve as an example for defining
clearer 'data rules'. An\nHTML based user interface facilitates initial exploration
of the\nfunctionality.","Imports":"stringr, Hmisc, shiny","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"datacheck","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Tools for Checking Data
Consistency","URL":"https:\/\/github.com\/c5sire\/datacheck","Version":"1.2.2"},"da
tacheckr":{"Author":"Joe Thorley [aut, cre]","Depends":"R (>=
3.1.0)","Description":"Checks column names,\ncolumn classes, values, keys, joins,
vectors and scalars.\nIf the user-defined conditions are met the function\nreturns
an invisible copy of the data frame, vector or scalar.\nOtherwise the function
throws an informative error.","Imports":"dplyr, magrittr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"datacheckr","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"assertr, knitr, nycflights13, rmarkdown,
testthat","Title":"Data
Checking","URL":"https:\/\/github.com\/poissonconsulting\/datacheckr","Version":"0.
1.1"},"datadr":{"Author":"Ryan Hafen [aut, cre],\nLandon Sego
[ctb]","Description":"Methods for dividing data into subsets, applying
analytical\nmethods to the subsets, and recombining the results. Comes with a
generic\nMapReduce interface as well. Works with key-value pairs stored in
memory,\non local disk, or on HDFS, in the latter case using the R and
Hadoop\nIntegrated Programming Environment (RHIPE).","Imports":"data.table (>=
1.9.6), digest, codetools, hexbin, parallel,\nmagrittr, dplyr,
methods","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"datadr","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat (>= 0.11.0), roxygen2 (>= 5.0.1),
Rhipe","Title":"Divide and Recombine for Large, Complex
Data","URL":"http:\/\/tessera.io\/docs-datadr","Version":"0.8.5"},"dataframes2xls":
{"Author":"Guido van Steen","Depends":"R (>= 2.0.0)","Description":"dataframes2xls
writes data frames to xls files. It\nsupports multiple sheets and basic
formatting.","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"dataframes2xls","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Title":"dataframes2xls writes data frames to xls
files","Version":"0.4.6"},"datafsm":{"Author":"Nay John J. [cre, aut],\nGilligan
Jonathan M. [aut]","Depends":"R (>= 3.1.1), methods, stats","Description":"Our
method automatically generates models of dynamic decision-making\nthat both have
strong predictive power and are interpretable in human terms.\nWe use an efficient
model representation and a genetic algorithm-based\nestimation process to generate
simple deterministic approximations that\nexplain most of the structure of complex
stochastic processes.\nWe have applied the software to empirical data, and
demonstrated it's\nability to recover known data-generating processes by
simulating\ndata with agent-based models and correctly deriving the underlying
decision\nmodels for multiple agent models and degrees of
stochasticity.","Imports":"caret, GA, Rcpp","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"datafsm","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"doParallel, testthat, diagram,
knitr","Title":"Estimating Finite State Machine Models from
Data","URL":"http:\/\/johnnay.github.io\/datafsm\/","Version":"0.1.0"},"datamap":
{"Author":"Jeffrey Horner
<jeffrey.horner@gmail.com>","Depends":"DBI","Description":"datamap utilizes
variable bindings and objects of class\n\"UserDefinedDatabase\" to provide a simple
mapping system to\nforeign objects. Maps can be used as environments or
attached\nto the search path, and changes to either are persistent.\nMapped foreign
objects are fetched in real-time and are never\ncached by the mapping
system.","License":"GPL-
2","NeedsCompilation":"yes","Package":"datamap","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"A system for mapping foreign objects to R variables
and\nenvironments","Version":"0.1-1"},"datamart":{"Author":"Karsten
Weinert","Description":"Provides an S4 infrastructure for unified handling\nof
internal datasets and web based data sources. The package is\ncurrently in beta;
things may break, change or go away without\nwarning.","Imports":"RJSONIO, XML,
RCurl, base64, gsubfn, methods, markdown","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"datamart","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Unified access to your data
sources","Version":"0.5.2"},"dataonderivatives":{"Author":"Imanuel Costigan [aut,
cre]","Description":"Post-GFC derivatives reforms have lifted the veil off\nover-
the-counter (OTC) derivative markets. Swap Execution Facilities (SEFs)\nand Swap
Data Repositories (SDRs) now publish data on swaps that are traded\non or reported
to those facilities (respectively). This package provides you\nthe ability to get
this data from supported sources.","Imports":"httr (>= 0.5), jsonlite (>= 0.9),
lubridate (>= 1.3.3), dplyr\n(>= 0.4), assertthat (>= 0.1), readr (>= 0.1),
downloader (>=\n0.4), utils (>= 3.2.2), stats (>= 3.2.2)","License":"GPL-
2","NeedsCompilation":"no","Package":"dataonderivatives","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"testthat (>= 0.1)","Title":"Easily Source
Publicly Available Data on
Derivatives","URL":"https:\/\/github.com\/imanuelcostigan\/dataonderivatives","Vers
ion":"0.2.1"},"datapack":{"Author":"Matthew B. Jones [aut, cre],\nPeter Slaughter
[aut],\nRegents of the University of California [cph]","Depends":"R (>=
3.1.1)","Description":"Provides a flexible container to transport and\nmanipulate
complex sets of data. These data may consist of multiple data files and\nassociated
meta data and ancillary files. Individual data objects have\nassociated system
level meta data, and data files are linked together using\nthe OAI-ORE standard
resource map which describes the relationships between the files.\nThe OAI-ORE
standard is described at <https:\/\/www.openarchives.org\/ore>. Data packages\ncan
be serialized and transported as structured files that have been created
following\nthe BagIt specification. The BagIt specification is described
at\n<https:\/\/tools.ietf.org\/html\/draft-kunze-bagit-08>.","Imports":"digest,
methods, redland, XML, hash, uuid","License":"Apache License (==
2.0)","NeedsCompilation":"no","Package":"datapack","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat, knitr","Title":"A Flexible Container to
Transport and Manipulate Data and\nAssociated
Resources","Version":"1.0.0"},"datastepr":{"Author":"Brandon Taylor","Depends":"R
(>= 3.1.3)","Description":"Based on a SAS data step. This allows for row-wise
dynamic building of data, iteratively importing slices of existing dataframes,
conducting analyses, and exporting to a results frame. This is particularly useful
for differential or time-series analyses, which are often not well suited to
vector-based operations.","Imports":"dplyr (>= 0.4.1), lazyeval (>= 0.1.10), R6 (>=
2.0.1),\nmagrittr (>= 1.5), rlist (>=
0.4)","License":"CC0","NeedsCompilation":"no","Package":"datastepr","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Suggests":"knitr","Title":"An Implementation
of a SAS-Style Data Step","Version":"0.0.1"},"datautils":{"Author":"Pierrick
Bruneau","Depends":"R (>= 2.10.0), deldir, gplots","Description":"Support functions
for packages VBmix, semisupKernelPCA,\nand
patchPlot.","Imports":"gtools","License":"LGPL-
3","NeedsCompilation":"yes","Package":"datautils","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Support functions for packages VBmix, semisupKernelPCA,
and\npatchPlot","Version":"0.1.4"},"dataview":{"Author":"Christofer Backlin [aut,
cre]","Description":"Tools for deciphering the contents of\nunknown objects or
environments from within the terminal,\na problem often encountered when working
with unfamiliar packages or debugging complex functions.\nIf working in xterm256 or
ANSI terminals the output is coloured by default\nto improve readability (e.g. the
standard Ubuntu terminal).","Imports":"data.table, xtermStyle (>=
3.0.5)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"dataview","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Data and Workspace Browser for
Terminals","URL":"http:\/\/github.com\/backlin\/dataview","Version":"2.1.1"},"date"
:{"Author":"Terry Therneau [aut],\nThomas Lumley [trl] (R port),\nKjetil Halvorsen
[trl] (R port),\nKurt Hornik [trl, ctb, cre] (R port)","Description":"Functions for
handling dates.","Imports":"graphics","License":"GPL-
2","NeedsCompilation":"yes","Package":"date","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Functions for handling dates","Version":"1.2-34"},"dave":
{"Author":"Otto Wildi","Depends":"R (>= 3.1.0), labdsv, vegan","Description":"A
collection of functions accompanying the book \"Data Analysis in Vegetation
Ecology\", Second edition. 2013, Wiley-Blackwell, Chichester","License":"LGPL (>=
2.0)","NeedsCompilation":"no","Package":"dave","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Functions for \"Data Analysis in Vegetation
Ecology\"","Version":"1.5"},"dawai":{"Author":"David
Conde, Miguel A. Fernandez, Bonifacio Salvador","Depends":"mvtnorm, ibdreg,
boot","Description":"In applications it is usual that some additional information
is available. This package dawai (an acronym for Discriminant Analysis With
Additional Information) performs linear and quadratic discriminant analysis with
additional information expressed as inequality restrictions among the populations
means. It also computes several estimations of the true error
rate.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"dawai","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"survival","Title":"Discriminant Analysis with Additional
Information","Version":"1.2.1"},"dbConnect":{"Author":"Dason Kurkiewicz, Heike
Hofmann, Ulrike Genschel","Depends":"RMySQL, gWidgets","Description":"Using widgets
provided by gWidgets this creates a nice\nusable interface to help facilitate the
learning of SQL. It\nalso just gives a nice interface for more advanced users.
Not\nall features are provided in the GUI but it is possible for\nmore advanced
users to achieve these goals inside the
GUI.","License":"GPL","NeedsCompilation":"no","Package":"dbConnect","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Suggests":"gWidgetsRGtk2","Title":"Provides a
graphical user interface to connect with databases\nthat use
MySQL","Version":"1.0"},"dbEmpLikeGOF":{"Author":"Lori A. Shepherd
<las65@buffalo.edu>Albert Vexler <avexler@buffalo.edu>Jeffrey C. Miecznikowski
<jcm38@buffalo.edu>","Depends":"R (>= 2.10)","Description":"Goodness-of-fit and two
sample comparison tests using sample entropy","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"dbEmpLikeGOF","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Goodness-of-fit and two sample comparison tests
using
sample\nentropy","URL":"\nhttp:\/\/sphhp.buffalo.edu\/biostat\/research\/software\/
EmpLike.GOF\/index.php","Version":"1.2.4"},"dbEmpLikeNorm":{"Author":"Lori A.
Shepherd <las65@buffalo.edu>, Wan-Min Tsai\n<wan-min.tsai@yale.edu>, Albert Vexler
<avexler@buffalo.edu>,\nJeffrey C. Miecznikowski <jcm38@buffalo.edu>","Depends":"R
(>= 2.10), dbEmpLikeGOF","Description":"Test for joint assessment of
normality","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"dbEmpLikeNorm","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Test for joint assessment of
normality","Version":"1.0.0"},"dbarts":{"Author":"Hugh Chipman
<hugh.chipman@gmail.com>, Robert McCulloch <robert.mcculloch1@gmail.com>, Vincent
Dorie <vjd4@nyu.edu>","Depends":"R (>= 3.1-0)","Description":"Fits Bayesian
additive regression trees (BART) while allowing the updating of predictors or
response so that BART can be incorporated as a conditional model in a Gibbs\/MH
sampler. Also serves as a drop-in replacement for package
BayesTree.","Imports":"methods, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"dbarts","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"testthat (>= 0.9-0)","Title":"Discrete Bayesian
Additive Regression Trees
Sampler","URL":"https:\/\/github.com\/vdorie\/dbarts","Version":"0.8-5"},"dblcens":
{"Author":"Mai Zhou, Li Lee, Kun Chen.","Depends":"R (>=
2.15.0)","Description":"Use EM algorithm to compute the NPMLE of CDF and also
the\ntwo censoring distributions. For doubly censored data (as\ndescribed in Chang
and Yang (1987) Ann. Stat. 1536-47). You can\nalso specify a constraint, it will
return the constrained NPMLE\nand the -2 log empirical likelihood ratio. This can
be used to\ntest the hypothesis about the constraint and find confidence\nintervals
for probability or quantile via empirical likelihood\nratio theorem. Influence
function of hat F may also be\ncalculated (but may be slow).","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"dblcens","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Compute the NPMLE of distribution from doubly censored
data","Version":"1.1.7"},"dbmss":{"Author":"Eric Marcon, Gabriel Lang, Stephane
Traissac, Florence Puech","Depends":"spatstat, Rcpp (>=
0.10.6)","Description":"Simple computation of spatial statistic functions of
distance to characterize the spatial structures of mapped objects, including
classical ones (Ripley's K and others) and more recent ones used by spatial
economists (Duranton and Overman's Kd, Marcon and Puech's M). Relies on spatstat
for some core calculation.","Imports":"cubature, stats,
RcppParallel","License":"GNU General Public
License","NeedsCompilation":"yes","Package":"dbmss","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Distance-Based Measures of Spatial
Structures","Version":"2.2-4"},"dbscan":{"Author":"Michael Hahsler [aut, cre,
cph],\nSunil Arya [ctb, cph],\nDavid Mount [ctb, cph]","Description":"A fast
reimplementation of several density-based algorithms of the DBSCAN family for
spatial data. Includes the DBSCAN (density-based spatial clustering of applications
with noise) and OPTICS (ordering points to identify the clustering structure)
clustering algorithms and the LOF (local outlier factor) algorithm. The
implementations uses the kd-tree data structure (from library ANN) for faster k-
nearest neighbor search. An R interface to fast kNN and fixed-radius NN search is
also provided.","Imports":"Rcpp, graphics, stats, methods","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"dbscan","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"fpc, microbenchmark, testthat","Title":"Density Based
Clustering of Applications with Noise (DBSCAN) and\nRelated
Algorithms","Version":"0.9-6"},"dbstats":{"Author":"Boj, Eva <evaboj@ub.edu>,
Caballe, Adria <adria.caballe@upc.edu>, Delicado, Pedro <pedro.delicado@upc.edu>
and Fortiana, Josep <fortiana@ub.edu>.","Depends":"R (>= 2.10.0), cluster,
pls","Description":"Prediction methods where explanatory information is coded as a
matrix of distances between individuals. Distances can either be directly input as
a distances matrix, a squared distances matrix, an inner-products matrix or
computed from observed predictors.","License":"GPL-
2","NeedsCompilation":"no","Package":"dbstats","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"proxy","Title":"Distance-Based
Statistics","Version":"1.0.4"},"dcGOR":{"Author":"Hai Fang and Julian
Gough","Depends":"R (>= 3.1.0), Matrix, igraph, dnet","Description":"There lacks a
package for analysing domain-centric ontologies and annotations, particularly those
in the dcGO database. The dcGO (http:\/\/supfam.org\/SUPERFAMILY\/dcGO) is a
comprehensive domain-centric database for annotating protein domains using a panel
of ontologies including Gene Ontology. With the package, users are expected to
analyse and visualise domain-centric ontologies and annotations. Supported analyses
include but are not limited to: easy access to a wide range of ontologies and their
domain-centric annotations; able to build customised ontologies and annotations;
domain-based enrichment analysis and visualisation; construction of a domain
(semantic similarity) network according to ontology annotations; significance
analysis for estimating a contact (statistical significance) network via Random
Walk with Restart; and high-performance parallel computing. The new functionalities
are: 1) to create domain-centric ontologies; 2) to predict ontology terms for input
protein sequences (precisely domain content in the form of architectures) plus to
assess the predictions; 3) to reconstruct ancestral discrete characters using
maximum likelihood\/parsimony.","Imports":"methods","License":"GPL-
2","NeedsCompilation":"no","Package":"dcGOR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"foreach, doMC, ape","Title":"Analysis of Ontologies and
Protein Domain Annotations","URL":"http:\/\/supfam.org\/dcGOR, http:\/\/cran.r-
project.org\/package=dcGOR,\nhttp:\/\/dcgor.r-forge.r-
project.org,\nhttps:\/\/github.com\/hfang-
bristol\/dcGOR","Version":"1.0.6"},"dcemriS4":{"Author":"Brandon Whitcher [aut,
cre],\nVolker Schmid [aut],\nAndrew Thornton [ctb]","Depends":"R (>= 2.14.0),
oro.nifti (>= 0.4.3)","Description":"A collection of routines and documentation
that allows one to\nperform voxel-wise quantitative analysis of dynamic contrast-
enhanced MRI\n(DEC-MRI) and diffusion-weighted imaging (DWI) data, with emphasis
on\noncology applications.","Imports":"utils, parallel,
LICENSE","NeedsCompilation":"yes","Package":"dcemriS4","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"bitops, minpack.lm, splines, XML, oro.dicom (>=
0.4.3),\ntestthat","Title":"A Package for Image Analysis of DCE-MRI (S4
Implementation)","URL":"http:\/\/www.dcemri.com\/,
http:\/\/dcemri.blogspot.com\/","Version":"0.55"},"dclone":{"Author":"Peter
Solymos","Depends":"R (>= 2.15.1), coda (>= 0.13), parallel,
Matrix","Description":"Low level functions for implementing\nmaximum likelihood
estimating procedures for\ncomplex models using data cloning and Bayesian\nMarkov
chain Monte Carlo methods.\nSequential and parallel MCMC support\nfor JAGS, WinBUGS
and OpenBUGS.","Imports":"methods, stats, rjags (>= 4-4), snow","License":"GPL-
2","NeedsCompilation":"no","Package":"dclone","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"MASS, lattice, R2WinBUGS, R2OpenBUGS, BRugs,
rlecuyer","Title":"Data Cloning and MCMC Tools for Maximum Likelihood
Methods","URL":"https:\/\/groups.google.com\/forum\/#!forum\/dclone-
users,\nhttp:\/\/datacloning.org","Version":"2.1-2"},"dcmle":{"Author":"Peter
Solymos","Depends":"R (>= 2.15.0), dclone (>= 2.0-0)","Description":"S4 classes
around infrastructure provided by the\n'coda' and 'dclone' packages to make package
development easy as a breeze\nwith data cloning for hierarchical
models.","Imports":"coda, methods, stats4, lattice","License":"GPL-
2","NeedsCompilation":"no","Package":"dcmle","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"MASS,
parallel, rjags","Title":"Hierarchical Models Made Easy with Data
Cloning","URL":"https:\/\/groups.google.com\/forum\/#!forum\/dclone-
users,\nhttp:\/\/datacloning.org","Version":"0.3-1"},"dcmr":
{"Author":"c( person(\"Diane\", family=\"Losardo\",
email='dlosardo@amplify.com\",\nrole = c(\"aut\", \"cre\", \"cph\")),
person(\"Margi\", family=\"Dubal\",\nemail='margidubal@gmail.com\", role =
c(\"aut\", \"cre\", \"cph\")))","Depends":"R (>= 3.0.2)","Description":"Analysis of
dichotomous response data to obtain attribute profile\nestimates for respondents
using Diagnostic Classification Model (DCM) and\nMarkov Chain Monte Carlo (MCMC)
method. The estimation procedure uses a\nloglinear cognitive diagnostic modeling
(LDCM) framework that allows for\nthe estimation of a host of DCMs such as NIDO,
NIDA, NC-RUM etc.","Imports":"ggplot2, KFAS, plyr, reshape2, tableplot,
3)","NeedsCompilation":"no","Package":"dcmr","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat","Title":"Attribute profile estimation using
Diagnostic Classification\nModels and MCMC","Version":"1.0"},"dcv":
{"Author":"Zongshan Li with contributions from Jinlong
Zhang","Depends":"lmtest","Description":"This package performs several
conventional\nCross-validation statistical methods for climate-growth model\nin the
climate reconstruction from tree rings, including Sign\nTest statistic, Reduction
of Error statistic, Product Mean\nTest, Durbin-Watson statistic etc. This package
is at its\nprimary stage, the functions have not been tested exhaustively\nand more
functions would be added in the comming days.","License":"GPL-
2","NeedsCompilation":"no","Package":"dcv","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Conventional Cross-validation statistics for climate-
growth\nmodel","Version":"0.1.1"},"ddR":{"Author":"Edward Ma, Indrajit Roy, Michael
Lawrence","Depends":"methods, R (>= 3.0.0)","Description":"Provides distributed
data structures and simplifies\ndistributed computing in R.","Imports":"parallel,
Rcpp","License":"GPL (>= 2) | file
LICENSE","NeedsCompilation":"yes","Package":"ddR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat, Matrix, knitr","Title":"Distributed Data
Structures in R","Version":"0.1.2"},"ddalpha":{"Author":"Oleksii Pokotylo [aut,
cre],\nPavlo Mozharovskyi [aut],\nRainer Dyckerhoff [aut]","Depends":"stats, utils,
graphics, grDevices, MASS, class, robustbase","Description":"Contains procedures
for depth-based supervised learning, which are entirely non-parametric, in
particular the DDalpha-procedure (Lange, Mosler and Mozharovskyi, 2014). The
training data sample is transformed by a statistical depth function to a compact
low-dimensional space, where the final classification is done. It also offers an
extension to functional data and routines for calculating certain notions of
statistical depth functions. 50 multivariate and 5 functional classification
problems are included.","Imports":"Rcpp (>= 0.11.0)","License":"GPL-
2","NeedsCompilation":"yes","Package":"ddalpha","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Depth-Based Classification and Calculation of Data
Depth","Version":"1.1.3.1"},"ddeploy":{"Author":"person(\"Niall\", \"McGearailt\",
role = c(\"aut\", \"cre\"),email = \"niall@dukeanalytics.com\")","Depends":"R (>=
3.0.0)","Description":"A wrapper for the Duke Analytics model deployment API. See
<http:\/\/www.dukeanalytics.com\/products\/dukedeployR.php> for more
details.","Imports":"httr,
jsonlite","License":"GPL","NeedsCompilation":"no","Package":"ddeploy","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Title":"Wrapper for the Duke Deploy REST
API","Version":"1.0.4"},"ddpcr":{"Author":"Dean Attali [aut, cre]","Depends":"R (>=
3.1.0)","Description":"An interface to explore, analyze, and visualize droplet
digital PCR\n(ddPCR) data in R. This is the first non-proprietary software for
analyzing\ntwo-channel ddPCR data. An interactive tool was also created and is
available\nonline to facilitate this analysis for anyone who is not comfortable
with\nusing R.","Imports":"DT (>= 0.1), dplyr (>= 0.4.0), ggplot2 (>=
1.0.1.9003),\nlazyeval (>= 0.1.10), magrittr (>= 1.5), mixtools (>= 1.0.2),\nplyr
(>= 1.8.1), readr (>= 0.1.0), shiny (>= 0.11.0), shinyjs\n(>=
LICENSE","NeedsCompilation":"no","Package":"ddpcr","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"ggExtra (>= 0.3.0), graphics, grid (>= 3.2.2),
gridExtra (>=\n2.0.0), knitr (>= 1.7), rmarkdown, stats, testthat (>=
0.9.1),\nutils","Title":"Analysis and Visualization of Droplet Digital PCR in R and
on\nthe
Web","URL":"https:\/\/github.com\/daattali\/ddpcr","Version":"1.1.2"},"ddst":
{"Author":"Przemyslaw Biecek (R code), Teresa Ledwina
(support,\ndescriptions)","Depends":"R (>= 2.7.0), orthopolynom,
evd","Description":"Support for data driven testing","License":"GPL-
2","NeedsCompilation":"no","Package":"ddst","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Data driven smooth test","Version":"1.03"},"deSolve":
{"Author":"Karline Soetaert [aut],\nThomas Petzoldt [aut, cre],\nR. Woodrow Setzer
[aut],\nodepack authors [cph]","Depends":"R (>= 2.15.0)","Description":"Functions
that solve initial value problems of a system\nof first-order ordinary differential
equations (ODE), of\npartial differential equations (PDE), of
differential\nalgebraic equations (DAE), and of delay differential\nequations. The
functions provide an interface to the FORTRAN\nfunctions lsoda, lsodar, lsode,
lsodes of the ODEPACK\ncollection, to the FORTRAN functions dvode and daspk and
a\nC-implementation of solvers of the Runge-Kutta family with\nfixed or variable
time steps. The package contains routines\ndesigned for solving ODEs resulting
from 1-D, 2-D and 3-D\npartial differential equations (PDE) that have been
converted\nto ODEs by numerical differencing.","Imports":"methods, graphics,
grDevices, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"deSolve","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"scatterplot3d","Title":"Solvers for Initial Value
Problems of Differential Equations\n(ODE, DAE, DDE)","URL":"http:\/\/desolve.r-
forge.r-project.org\/","Version":"1.13"},"deTestSet":{"Author":"Karline Soetaert
[aut, cre],\nJeff Cash [aut],\nFrancesca Mazzia [aut],\nLAPACK authors
[cph]","Depends":"R (>= 2.01), deSolve","Description":"Solvers and testset for
stiff and nonstiff differential equations, and\ndifferential algebraic
equations","License":"GPL","NeedsCompilation":"yes","Package":"deTestSet","Reposito
ry":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Testset for differential
equations","Version":"1.1.2"},"deal":{"Author":"Susanne Gammelgaard Bottcher, Claus
Dethlefsen.","Depends":"R (>= 2.0.0)","Description":"Bayesian networks with
continuous and\/or discrete\nvariables can be learned and compared from
2)","NeedsCompilation":"yes","Package":"deal","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Learning Bayesian Networks with Mixed
Variables","Version":"1.2-37"},"deamer":{"Author":"Julien Stirnemann, Adeline
Samson, Fabienne Comte. Contribution\nfrom Claire Lacour.","Description":"deamer
provides deconvolution algorithms for the\nnon-parametric estimation of the density
f of an error-prone\nvariable x with additive noise e. The model is y = x + e
where\nthe noisy variable y is observed, while x is unobserved.\nEstimation may be
performed for i) a known density of the error\nii) with an auxiliary sample of pure
noise and iii) with an\nauxiliary sample of replicate (repeated)
measurements.\nEstimation is performed using adaptive model selection
and\npenalized
contrasts.","License":"GPL","NeedsCompilation":"no","Package":"deamer","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Title":"Deconvolution density estimation
with adaptive methods for a\nvariable prone to measurement
error","Version":"1.0"},"debug":{"Author":"Mark V. Bravington
<mark.bravington@csiro.au>","Depends":"R (>= 2.13), tcltk","Description":"Debugger
for R functions, with code display, graceful\nerror recovery, line-numbered
conditional breakpoints, access\nto exit code, flow control, and full keyboard
input.","Imports":"mvbutils (>= 2.7)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"debug","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"MVB's debugger for R","Version":"1.3.1"},"decision":
{"Author":"Partha Sarathi Bishnu <psbishnu@gmail.com>","Description":"Contains a
function called dmur() which accepts four parameters like possible values,
probabilities of the values, selling cost and preparation cost. The dmur() function
generates various numeric decision parameters like MEMV (Maximum (optimum) expected
monitory value), best choice, EPPI (Expected profit with perfect information), EVPI
(Expected value of the perfect information), EOL (Expected opportunity loss), which
facilitate effective decision-making.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"decision","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Statistical Decision
Analysis","Version":"0.1.0"},"decisionSupport":{"Author":"Lutz GÃ¶hring [cre, aut]
(ICRAF and Lutz GÃ¶hring Consulting),\nEike Luedeling [aut] (ICRAF)","Depends":"R
(>= 3.1.3)","Description":"Supporting the quantitative analysis of binary welfare
based\ndecision making processes using Monte Carlo simulations. Decision
support\nis given on two levels: (i) The actual decision level is to choose
between\ntwo alternatives under probabilistic uncertainty. This package
calculates\nthe optimal decision based on maximizing expected welfare. (ii) The
meta\ndecision level is to allocate resources to reduce the uncertainty in
the\nunderlying decision problem, i.e to increase the current information
to\nimprove the actual decision making process.
This problem is dealt with\nusing the Value of Information Analysis. The Expected
Value of\nInformation for arbitrary prospective estimates can be calculated
as\nwell as Individual and Clustered Expected Value of Perfect Information.\nThe
probabilistic calculations are done via Monte Carlo\nsimulations. This Monte Carlo
functionality can be used on its own.","Imports":"msm (>= 1.5), mvtnorm (>= 1.0.2),
stats (>= 3.1.3)","License":"GPL-
3","NeedsCompilation":"no","Package":"decisionSupport","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"chillR (>= 0.54), eha (>= 2.4.2), mc2d (>=
0.1.15), nleqslv\n(>= 2.6), pls (>= 2.4.3), rriskDistributions (>= 2.0),
testthat\n(>= 0.9.1), knitr","Title":"Quantitative Support of Decision Making under
Uncertainty","URL":"http:\/\/www.worldagroforestry.org\/","Version":"1.101.1"},"dec
ode":{"Author":"Thomas Lui [aut, cre]","Depends":"R (>=
3.1.2)","Description":"Integrated differential expression (DE) and differential co-
expression (DC) analysis on gene expression data based on DECODE (DifferEntial CO-
expression and Differential Expression) algorithm.","License":"GPL-
3","NeedsCompilation":"no","Package":"decode","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"knitr","Title":"Differential Co-Expression and
Differential Expression Analysis","Version":"1.2"},"decompr":{"Author":"Bastiaan
Quast [aut, cre],\nFei Wang [aut],\nVictor Kummritz [aut]","Depends":"R (>=
2.10)","Description":"Two global-value-chain decompositions are
implemented.\nFirstly, the Wang-Wei-Zhu (Wang, Wei, and Zhu, 2013) algorithm splits
bilateral gross\nexports into 16 value-added components. Secondly, the Leontief
decomposition\n(default) derives the value added origin of exports by country
and\nindustry, which is also based on Wang, Wei, and Zhu\n(Wang, Z., S.-J. Wei, and
K. Zhu. 2013. \"Quantifying International Production Sharing at the Bilateral and
Sector Levels.\").","License":"GPL-
3","NeedsCompilation":"no","Package":"decompr","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"gvc, testthat, knitr","Title":"Global-Value-Chain
Decomposition","URL":"http:\/\/qua.st\/decompr,
https:\/\/github.com\/bquast\/decompr","Version":"4.1.0"},"decon":{"Author":"Xiao-
Feng Wang, Bin Wang","Description":"This package contains a collection of functions
to deal\nwith nonparametric measurement error problems using\ndeconvolution kernel
methods. We focus two measurement error\nmodels in the package: (1) an additive
measurement error model,\nwhere the goal is to estimate the density or
distribution\nfunction from contaminated data; (2) nonparametric regression\nmodel
with errors-in-variables. The R functions allow the\nmeasurement errors to be
either homoscedastic or\nheteroscedastic. To make the deconvolution
estimators\ncomputationally more efficient in R, we adapt the \"Fast
Fourier\nTransform\" (FFT) algorithm for density estimation with\nerror-free data
to the deconvolution kernel estimation. Several\nmethods for the selection of the
data-driven smoothing\nparameter are also provided in the package. See details
in:\nWang, X.F. and Wang, B. (2011). Deconvolution estimation in\nmeasurement error
models: The R package decon. Journal of\nStatistical Software, 39(10), 1-
3)","NeedsCompilation":"yes","Package":"decon","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Deconvolution Estimation in Measurement Error
Models","Version":"1.2-4"},"deconstructSigs":{"Author":"Rachel
Rosenthal","Description":"Takes sample information in the form of the fraction of
mutations\nin each of 96 trinucleotide contexts and identifies the weighted
combination\nof published signatures that, when summed, most closely reconstructs
the\nmutational profile.","Imports":"reshape2, BSgenome,
BSgenome.Hsapiens.UCSC.hg19, grDevices,\ngraphics, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"deconstructSigs","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Identifies Signatures Present in a Tumor
Sample","URL":"https:\/\/github.com\/raerose01\/deconstructSigs","Version":"1.6.0"}
,"deducorrect":{"Author":"Mark van der Loo, Edwin de Jonge, and
Sander\nScholtus","Depends":"editrules (>= 2.9.0)","Description":"A collection of
methods for automated data cleaning where all actions are
logged.","Imports":"stats, utils, methods","License":"GPL-
3","NeedsCompilation":"no","Package":"deducorrect","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Deductive Correction, Deductive Imputation, and
Deterministic\nCorrection","URL":"https:\/\/github.com\/data-
cleaning\/deducorrect","Version":"1.3.7"},"deductive":{"Author":"Mark van der Loo
[cre, aut],\nEdwin de Jonge [aut]","Depends":"R (>= 3.2.0)","Description":"Attempt
to repair inconsistencies and missing values in data\nrecords by using information
from valid values and validation rules\nrestricting the data.","Imports":"methods,
lintools (>= 0.1.1.1), validate, stringdist","License":"GPL-
3","NeedsCompilation":"yes","Package":"deductive","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat, knitr","Title":"Data Correction and
Imputation Using Deductive Methods","URL":"https:\/\/github.com\/data-
cleaning\/deductive","Version":"0.1.0"},"deepboost":{"Author":"Daniel Marcous [aut,
cre], Yotam Sandbank [aut], Google Inc. [cph]","Depends":"R (>=
3.1)","Description":"Provides deep boosting models training, evaluation, predicting
and\nhyper parameter optimising using grid search and cross validation.\nBased on
Google's Deep Boosting algorithm, and Google's C++ implementation.\nCortes, C.,
Mohri, M., & Syed, U. (2014)
<URL:\nhttp:\/\/machinelearning.wustl.edu\/mlpapers\/papers\/icml2014c2_cortesb14>.
","Imports":"Rcpp (>= 0.12.2), methods","License":"Apache License (==
2.0)","NeedsCompilation":"yes","Package":"deepboost","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat, ada, caret","Title":"Deep Boosting
Ensemble
Modeling","URL":"https:\/\/github.com\/dmarcous\/CRAN_deepboost","Version":"0.1.4"}
,"deepnet":{"Author":"Xiao Rong","Description":"Implement some deep learning
architectures and neural network\nalgorithms, including BP,RBM,DBN,Deep autoencoder
and so
on.","License":"GPL","NeedsCompilation":"no","Package":"deepnet","Repository":"http
:\/\/cran.csiro.au\/src\/contrib","Title":"deep learning toolkit in
R","Version":"0.2"},"deformula":{"Author":"Hiroyuki
Okamura","Description":"Numerical quadrature of functions of one variable over a
finite or infinite interval\nwith double exponential formulas.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"deformula","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Integration of One-Dimensional Functions with Double
Exponential\nFormulas","Version":"0.1.1"},"degenes":{"Author":"Klaus
Jung","Description":"Detection of differentially expressed genes between
two\ndistinct groups of samples.","License":"GPL-
2","NeedsCompilation":"no","Package":"degenes","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Detection of differentially expressed
genes","Version":"1.1"},"degreenet":{"Author":"Mark S. Handcock
<handcock@stat.ucla.edu>","Description":"Likelihood-based inference for skewed
count distributions used in network modeling. \"degreenet\" is a part of
the \"statnet\" suite of packages for network analysis.","Imports":"igraph,
network","License":"GPL-3 + file
LICENSE","NeedsCompilation":"yes","Package":"degreenet","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Models for Skewed Count Distributions Relevant to
Networks","URL":"http:\/\/statnet.org","Version":"1.3-1"},"deldir":{"Author":"Rolf
Turner","Depends":"R (>= 0.99)","Description":"Calculates the Delaunay
triangulation and the Dirichlet\nor Voronoi tessellation (with respect to the
entire plane) of\na planar point set. Plots triangulations and tessellations
in\nvarious ways. Clips tessellations to sub-windows. Calculates\nperimeters of
tessellations.","Imports":"graphics, grDevices","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"deldir","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"polyclip","Title":"Delaunay Triangulation and
Dirichlet (Voronoi) Tessellation","Version":"0.1-12"},"delt":{"Author":"Jussi
Klemela [aut, cre],\nSauli Herrala [ctb]","Description":"\nWe implement methods for
estimating multivariate densities.\nWe include a discretized kernel estimator,\nan
adaptive histogram (a greedy histogram and a CART-histogram),\nstagewise
minimization, and bootstrap aggregation.","Imports":"denpro (>=
0.9.2)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"delt","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Estimation of Multivariate Densities Using Adaptive
Partitions","URL":"http:\/\/jussiklemela.com\/delt\/","Version":"0.8.2"},"deltaPlot
R":{"Author":"David Magis (U Liege), Bruno Facon (Univ Lille-Nord de
France)","Depends":"R (>= 2.10.0), MASS","Description":"The deltaPlotR package
proposes an implementation of Angoff's Delta Plot method to detect dichotomous DIF.
Several detection thresholds are included, either from multivariate normality
assumption or by prior determination. Item purification is
supported.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"deltaPlotR","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Identification of dichotomous differential item
functioning\n(DIF) using Angoff's Delta Plot method","Version":"1.5"},"demi":
{"Author":"Sten Ilmjarv [aut, cre],\nHendrik Luuk [aut]","Depends":"R (>= 3.0.0),
utils","Description":"Implementation of the DEMI method for the analysis of high-
density microarray data.","Imports":"R.utils, affxparser, affy, oligo, plyr,
methods, devtools","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"demi","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"ggplot2, reshape","Title":"Differential
Expression from Multiple
Indicators","URL":"http:\/\/biit.cs.ut.ee\/demi","Version":"1.1.2"},"deming":
{"Author":"Terry Therneau","Description":"Generalized Deming regression, Theil-Sen
regression and Passing-Bablock regression
functions.","Imports":"boot","License":"LGPL (>=
2)","NeedsCompilation":"no","Package":"deming","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Deming, Thiel-Sen and Passing-Bablock
Regression","Version":"1.0-1"},"demoKde":{"Author":"Bill
Venables","Description":"Demonstration code showing how (univariate)
kernel\ndensity estimates are computed, at least conceptually,\nand allowing users
to experiment with different kernels,\nshould they so wish. NOTE: the density
function in the\nstats package should be used for computational
efficiency.","Imports":"stats","License":"GPL-
2","NeedsCompilation":"no","Package":"demoKde","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"MASS, graphics","Title":"Kernel Density Estimation for
Demonstration Purposes","Version":"0.9-3"},"demography":{"Author":"Rob J Hyndman
with contributions from Heather Booth, Leonie Tickle and John
Maindonald.","Depends":"R (>= 2.15.2), forecast (>= 3.09), rainbow, ftsa,
cobs","Description":"Functions for demographic analysis including
lifetable\ncalculations; Lee-Carter modelling; functional data analysis
of\nmortality rates, fertility rates, net migration numbers; and\nstochastic
population forecasting.","Imports":"mgcv, strucchange, RCurl","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"demography","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Forecasting mortality, fertility, migration and
population
data","URL":"http:\/\/robjhyndman.com\/software\/demography\/","Version":"1.18"},"d
endextend":{"Author":"Tal Galili [aut, cre, cph] (http:\/\/www.r-
statistics.com),\nGavin Simpson [ctb],\nGregory Jefferis [aut, ctb] (imported code
from his dendroextras\npackage),\nMarco Gallotta [ctb] (a.k.a: marcog),\nJohan
Renaudie [ctb] (https:\/\/github.com\/plannapus),\nThe R Core Team [ctb] (Thanks
for the Infastructure, and code in the\nexamples),\nKurt Hornik [ctb],\nUwe Ligges
[ctb],\nAndrej-Nikolai Spiess [ctb],\nSteve Horvath [ctb],\nPeter Langfelder
[ctb],\nskullkey [ctb],\nMark Van Der Loo [ctb]
(https:\/\/github.com\/markvanderloo d3dendrogram),\nAndrie de Vries [ctb]
(ggdendro author),\nZuguang Gu [ctb] (circlize author),\nYoav Benjamini
[ths]","Depends":"R (>= 3.0.0)","Description":"Offers a set of functions for
extending\ndendrogram objects in R, letting you visualize and compare trees
of\nhierarchical clusterings. You can (1) Adjust a tree's graphical parameters\n-
the color, size, type, etc of its branches, nodes and labels. (2)\nVisually and
statistically compare different dendrograms to one another.","Enhances":"ggdendro,
labeltodendro,dendroextras, data.table, rpart","Imports":"utils, stats, magrittr
(>= 1.0.1), whisker","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"dendextend","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"dendextendRcpp (>= 0.5.0), knitr, rmarkdown,
testthat,\ncolorspace, ggplot2, plyr, ape, profdpm, microbenchmark,\ngplots, NMF,
d3heatmap, dynamicTreeCut, pvclust, corrplot,\nDendSer, MASS, cluster, circlize (>=
0.2.5), covr","Title":"Extending R's Dendrogram
Functionality","URL":"http:\/\/cran.r-
project.org\/package=dendextend,\nhttps:\/\/github.com\/talgalili\/dendextend\/,\nh
ttp:\/\/www.r-
statistics.com\/tag\/dendextend\/,\nhttp:\/\/bioinformatics.oxfordjournals.org\/con
tent\/31\/22\/3718","Version":"1.1.8"},"dendextendRcpp":{"Author":"Tal Galili [aut,
cre, cph] (http:\/\/www.r-statistics.com),\nRomain Francois [ctb],\nDirk
Eddelbuettel [ctb],\nKevin Ushey [ctb],\nYoav Benjamini [ths]","Depends":"R (>=
3.0.0), Rcpp (>= 0.11.0), dendextend (>= 0.14.0)","Description":"Offers faster
manipulation of dendrogram objects in\nR. A dendrogram object in R is a list
structure with attributes in its\nnodes and leaves. Working with dendrogram objects
often require a function\nto recursively go through all (or most) element in the
list object.\nNaturally, such function are rather slow in R, but can become much
faster\nthanks to 'Rcpp'.","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"dendextendRcpp","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat, microbenchmark","Title":"Faster
Dendrogram Manipulation using
'Rcpp'","URL":"https:\/\/github.com\/talgalili\/dendextendRcpp\/,\nhttp:\/\/cran.r-
project.org\/web\/packages\/dendextendRcpp\/","Version":"0.6.1"},"dendroextras":
{"Author":"Gregory Jefferis","Description":"This package provides extra functions
to manipulate dendrograms\nthat build on the base functions provided by the stats
package. The main\nfunctionality it is designed to add is the ability to colour all
the edges\nin an object of class dendrogram according to cluster membership i.e.
each\nsubtree is coloured, not just the terminal leaves. In addition it
provides\nsome utility functions to cut dendrogram and hclust objects and to
set\/get\nlabels.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"dendroextras","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat","Title":"Extra functions to cut, label
and colour dendrogram clusters","Version":"0.2.1"},"dendrometeR":{"Author":"Olivier
Bouriaud, Ernst van der Maaten, Marieke van der Maaten-Theunissen and Marko
Smiljanic","Depends":"R (>= 3.2.0), forecast, graphics, grDevices, pspline,
stats,\nzoo","Description":"Various functions to import, verify, process and plot
high-resolution dendrometer using daily and stem-cycle
approaches.","Imports":"methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"dendrometeR","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"knitr, rmarkdown","Title":"Analyzing Dendrometer
Data","Version":"1.0.0"},"dendsort":{"Author":"Ryo Sakai","Description":"An
implementation of functions to optimize ordering of nodes in\na dendrogram, without
affecting the meaning of the dendrogram. A dendrogram can\nbe sorted based on the
average distance of subtrees, or based on the smallest\ndistance value. These
sorting methods improve readability and interpretability\nof tree structure,
especially for tasks such as comparison of different distance\nmeasures or linkage
types and identification of tight clusters and outliers. As\na result, it also
introduces more meaningful reordering for a coupled
heatmap\nvisualization.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"dendsort","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr, RColorBrewer, gplots, heatmap.plus, seriation,
gapmap","Title":"Modular Leaf Ordering Methods for Dendrogram
Nodes","URL":"https:\/\/bitbucket.org\/vda-
lab\/dendsort\/,\nhttp:\/\/f1000research.com\/articles\/3-
177\/v1","Version":"0.3.3"},"denovolyzeR":{"Author":"James Ware [aut, cre],\nJason
Homsy [ctb],\nKaitlin Samocha [ctb]","Depends":"R (>= 3.1.0)","Description":"An
integrated toolset for the analysis of de novo (sporadic) genetic sequence
variants. denovolyzeR implements a mutational model that estimates the probability
of a de novo genetic variant arising in each human gene, from which one can infer
the expected number of de novo variants in a given population size. Observed
variant frequencies can then be compared against expectation in a Poisson
framework. denovolyzeR provides a suite of functions to implement these analyses
for the interpretation of de novo variation in human disease.","Imports":"dplyr (>=
0.3), reshape (>= 0.8)","License":"GPL-
3","NeedsCompilation":"no","Package":"denovolyzeR","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr","Title":"Statistical Analyses of De Novo
Genetic
Variants","URL":"http:\/\/jamesware.github.io\/denovolyzeR","Version":"0.1.0"},"den
pro":{"Author":"Jussi Klemela <jussi.klemela@gmail.com>","Description":"\nWe
provide tools to\n(1) visualize multivariate density functions and density
estimates\nwith level set trees,\n(2) visualize level sets with shape trees,\n(3)
visualize multivariate data with tail trees,\n(4) visualize scales of multivariate
density estimates with\nmode graphs and branching maps, and\n(5) visualize
anisotropic spread with 2D volume functions and\n2D probability content
functions.\nLevel set trees visualize mode structure,\nshape trees visualize shapes
of level sets of unimodal densities,\nand tail trees visualize connected data
sets.\nThe kernel estimator is implemented\nbut the package may also be applied
for visualizing other density estimates.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"denpro","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Visualization of Multivariate Functions, Sets, and
Data","URL":"http:\/\/jussiklemela.com\/denpro\/","Version":"0.9.2"},"densityClust"
:{"Author":"Thomas Lin Pedersen [aut, cre],\nSean Hughes [aut]","Description":"An
implementation of the clustering algorithm described by Alex\nRodriguez and
Alessandro Laio (Science, 2014 vol. 344), along with tools to\ninspect and
visualize the results.","Imports":"Rcpp","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"densityClust","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat","Title":"Clustering by Fast Search and
Find of Density Peaks","Version":"0.2.1"},"densratio":{"Author":"Koji Makiyama
[aut, cre]","Description":"Density ratio estimation.\nThe estimated density ratio
function can be used in many applications such as\nthe inlier-based outlier
detection, covariate shift adaptation and etc.","Imports":"utils","License":"MIT +
file
LICENSE","NeedsCompilation":"no","Package":"densratio","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"graphics, knitr, mvtnorm, rmarkdown,
stats","Title":"Density Ratio Estimation","URL":"https:\/\/github.com\/hoxo-
m\/densratio","Version":"0.0.3"},"denstrip":{"Author":"Christopher
Jackson","Depends":"R (>= 2.15)","Description":"Graphical methods for compactly
illustrating probability distributions, including density strips, density regions,
sectioned density plots and varying width
strips.","Enhances":"survival","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"denstrip","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"vioplot,lattice,Hmisc","Title":"Density strips and
other methods for compactly
illustrating\ndistributions","Version":"1.5.3"},"depend.truncation":
{"Author":"Takeshi Emura","Depends":"mvtnorm","Description":"Suppose that one can
observe bivariate random variables (X, Y) only when X<=Y holds. Data (Xj, Yj),
subject to Xj<=Yj, for all j=1,...,n, are called truncated data. Parametric
approach (Emura & Konno 2012 Stat Papers), semiparametric approach (Chaieb et al.
2006 Biometrika; Emura et al. 2011 Sinica; Emura & Murotani 2015 TEST),
nonparametric maximum likelihood approach (Emura & Wang 2012 JMVA), and regression
approach (Emura & Wang 2015 AISM) are implemented for statistical inference on (X,
Y), when X and Y are dependent. Also included is truncated data on the number of
deaths at each year (1963-1980) for Japanese male centenarians (Emura & Murotani
2015 TEST).","License":"GPL-
2","NeedsCompilation":"no","Package":"depend.truncation","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Statistical Inference for Parametric and
Semiparametric Models\nBased on Dependently Truncated
Data","Version":"2.4"},"depmix":{"Author":"Ingmar Visser
<i.visser@uva.nl>","Depends":"R (>= 3.1.2), MASS","Description":"Fits (multigroup)
mixtures of latent or hidden Markov models on mixed categorical and continuous
(timeseries) data. The Rdonlp2 package can optionally be used for optimization of
the log-likelihood and is available from R-forge.","License":"GPL-
3","NeedsCompilation":"yes","Package":"depmix","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"Rdonlp2","Title":"Dependent Mixture
Models","Version":"0.9.14"},"depmixS4":{"Author":"Ingmar Visser <i.visser@uva.nl>,
Maarten Speekenbrink <m.speekenbrink@ucl.ac.uk>","Depends":"R (>= 3.0.1), nnet,
MASS, Rsolnp","Description":"Fits latent (hidden) Markov models on mixed
categorical and continuous (time series) data, otherwise known as dependent mixture
models.","Imports":"stats, stats4, methods","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"depmixS4","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"gamlss, gamlss.dist, Rdonlp2","Title":"Dependent
Mixture Models - Hidden Markov Models of GLMs and\nOther Distributions in
S4","URL":"http:\/\/depmix.r-forge.r-project.org\/","Version":"1.3-3"},"depth":
{"Author":"Maxime Genest <maxime.genest@clevislauzon.qc.ca>, Jean-Claude\nMasse
<jcmasse@mat.ulaval.ca>, Jean-Francois Plante\n<jfplante@hec.ca>.","Depends":"R (>=
2.5.0), abind, grDevices, rgl, circular","Description":"Depth functions methodology
applied to multivariate\nanalysis. Besides allowing calculation of depth values
and\ndepth-based location estimators, the package includes functions\nfor drawing
contour plots and perspective plots of depth\nfunctions. Euclidian and spherical
depths are supported.","License":"GPL-
2","NeedsCompilation":"yes","Package":"depth","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"robustbase, MASS","Title":"Depth functions tools for
multivariate analysis","Version":"2.0-0"},"depth.plot":{"Author":"Omker
Mahalanobish [aut],\nSomedip Karmakar [cre, aut]","Description":"Could be used to
obtain spatial depths, spatial ranks and outliers of multivariate random variables.
Could also be used to visualize DD-plots (a multivariate generalization of QQ-
plots).","Imports":"mvtnorm , stats , graphics","License":"GPL-
2","NeedsCompilation":"no","Package":"depth.plot","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Multivariate Analogy of
Quantiles","Version":"0.1"},"depthTools":{"Author":"Sara Lopez-Pintado
<sl2929@columbia.edu> and Aurora Torrente\n<etorrent@est-
econ.uc3m.es>.","Depends":"R (>= 2.8.0)","Description":"depthTools is a package
that implements different\nstatistical tools for the description and analysis of
gene\nexpression data based on the concept of data depth, namely, the\nscale curves
for visualizing the dispersion of one or various\ngroups of samples (e.g. types of
tumors), a rank test to decide\nwhether two groups of samples come from a single
distribution\nand two methods of supervised classification techniques, the DS\nand
TAD methods. All these techniques are based on the Modified\nBand Depth, which is a
recent notion of depth with a low\ncomputational cost, what renders it very
appropriate for high\ndimensional data such as gene expression
2)","NeedsCompilation":"no","Package":"depthTools","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Depth Tools Package","Version":"0.4"},"dequer":
{"Author":"Drew Schmidt [aut, cre]","Depends":"R (>= 3.1.0)","Description":"Offers
a special data structure called a 'deque'\n(pronounced like 'deck'), which is a
list-like structure. However,\nunlike R's list structure, data put into a 'deque'
is not necessarily\nstored contiguously, making insertions and deletions at the
front\/end\nof the structure much faster. The implementation here is new and\nuses
a doubly linked list, and whence does not rely on R's\nenvironments. To avoid
unnecessary data copying, most 'deque'\noperations are performed via side-
effects.","Imports":"utils","License":"BSD 2-clause License + file
LICENSE","NeedsCompilation":"yes","Package":"dequer","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"An R 'Deque'
Container","URL":"https:\/\/github.com\/wrathematics\/dequer","Version":"1.0"},"des
componer":{"Author":"Francisco Parra
<parra_fj@cantabria.es>","Depends":"taRifx,R(>= 2.10)","Description":"Decompose a
time series into seasonal, trend and irregular components using transformations to
amplitude-frequency domain.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"descomponer","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Seasonal Adjustment by Frequency
Analysis","Version":"1.2"},"descr":{"Author":"Jakson Aquino. Includes R source code
and\/or documentation\nwritten by Dirk Enzmann, Marc Schwartz, Nitin Jain, and
Stefan\nKraft","Description":"Weighted frequency and contingency tables of
categorical\nvariables and of the comparison of the mean value of a
numerical\nvariable by the levels of a factor, and methods to produce
xtable\nobjects of the tables and to plot them. There are also functions
to\nfacilitate the character encoding conversion of objects, to quickly\nconvert
fixed width files into csv ones, and to export a data.frame to\na text file with
the necessary R and SPSS codes to reread the data.","Imports":"xtable, utils,
grDevices, graphics, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"descr","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Descriptive
Statistics","URL":"https:\/\/github.com\/jalvesaq\/descr","Version":"1.1.2"},"descr
iber":{"Author":"Paul Hendricks [aut, cre]","Depends":"R (>=
3.1.2)","Description":"Allows users to quickly and easily describe data
using\ncommon descriptive statistics.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"describer","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"dplyr, testthat, lintr","Title":"Describe Data
in R Using Common Descriptive
Statistics","URL":"https:\/\/github.com\/paulhendricks\/describer","Version":"0.2.0
"},"deseasonalize":{"Author":"A. I. McLeod and Hyukjun Gweon","Depends":"R (>=
2.10),lattice, FitAR","Description":"Deseasonalize daily or monthly time
series.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"deseasonalize","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Optimal deseasonalization for geophysical time
series using AR\nfitting","Version":"1.35"},"desiR":{"Author":"Stanley E.
Lazic","Depends":"R (>= 2.10)","Description":"Functions for (1) ranking, selecting,
and prioritising genes,\nproteins, and metabolites from high dimensional biology
experiments, (2)\nmultivariate hit calling in high content screens, and (3)
combining data\nfrom diverse sources.","License":"GPL-
3","NeedsCompilation":"no","Package":"desiR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr","Title":"Desirability Functions for Ranking,
Selecting, and
Integrating\nData","URL":"https:\/\/github.com\/stanlazic\/desiR","Version":"1.2"},
"designGG":{"Author":"Yang Li <yang.li@rug.nl>, Morris Swertz
<m.a.swertz@rug.nl>,\nGonzalo Vera <gonzalo.vera.rodriguez@gmail.com>,
Rainer\nBreitling <r.breitling@rug.nl>, Ritsert
Jansen\n<r.c.jansen@rug.nl>","Depends":"R (>= 2.2.0)","Description":"The package
provides R scripts for designing genetical\ngenomics
experiments.","License":"GPL","NeedsCompilation":"no","Package":"designGG","Reposit
ory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Computational tool for
designing genetical genomics
experiments","URL":"http:\/\/www.rug.nl\/research\/bioinformatics\/","Version":"1.1
"},"designGLMM":{"Author":"Stephen Bush and Katya Ruggiero","Description":"Use
simulated annealing to find optimal designs for Poisson regression models with
blocks.","Imports":"stats","License":"GPL-
3","NeedsCompilation":"no","Package":"designGLMM","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Finding Optimal Block Designs for a Generalised Linear
Mixed\nModel","Version":"0.1.0"},"designmatch":{"Author":"Jose R. Zubizarreta
<zubizarreta@columbia.edu>, Cinar Kilcioglu
<ckilcioglu16@gsb.columbia.edu>","Depends":"R (>= 3.2), lattice, MASS, slam,
Rglpk","Description":"Includes functions for the construction of matched samples
that are balanced by design. Among others, these functions can be used for
matching in observational studies with treated and
control units, with cases and controls, in related settings with instrumental
variables, and in discontinuity designs. Also, they can be used for the design of
randomized experiments, for example, for matching before randomization. By
default, 'designmatch' uses the 'GLPK' optimization solver, but its performance is
greatly enhanced by the 'Gurobi' optimization solver and its associated R
interface. For their installation, please follow the instructions at
http:\/\/user.gurobi.com\/download\/gurobi-optimizer and
http:\/\/www.gurobi.com\/documentation\/6.5\/refman\/r_api_overview.html. We have
also included directions in the gurobi_installation file in the inst
folder.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"designmatch","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"gurobi, Rcplex, Rsymphony","Title":"Construction of
Optimally Matched Samples for Randomized\nExperiments and Observational Studies
that are Balanced by\nDesign","Version":"0.1.1"},"desirability":{"Author":"Max
Kuhn","Description":"S3 classes for multivariate optimization using the
desirability function by Derringer and Suich (1980).","License":"GPL-
2","NeedsCompilation":"no","Package":"desirability","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"lattice","Title":"Desirability Function
Optimization and
Ranking","URL":"https:\/\/github.com\/topepo\/desirability","Version":"1.9"},"desir
e":{"Author":"Heike Trautmann, Detlef Steuer and Olaf Mersmann","Depends":"R (>=
2.9.0), loglognorm","Description":"Harrington and Derringer-Suich type desirability
functions","License":"GPL-
2","NeedsCompilation":"yes","Package":"desire","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Desirability functions in R","Version":"1.0.7"},"desplot":
{"Author":"Kevin Wright [aut, cre]","Description":"A function for plotting maps of
agricultural field experiments that\nare laid out in grids.","Imports":"grid,
lattice, reshape2,","License":"GPL-
2","NeedsCompilation":"no","Package":"desplot","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"agridat, knitr","Title":"Plotting Field Plans for
Agricultural
Experiments","URL":"https:\/\/github.com\/kwstat\/desplot","Version":"1.0"},"detect
":{"Author":"Peter Solymos [cre, aut], Monica Moreno [aut], Subhash R. Lele
[aut]","Depends":"R (>= 2.13.0), Formula, stats4, pbapply","Description":"Models
for analyzing site occupancy and count data models\nwith detection error, including
single-visit based models,\nconditional distance sampling and time-removal
models.\nPackage development was supported by the\nAlberta Biodiversity Monitoring
Institute (www.abmi.ca)\nand the Boreal Avian Modelling Project
(borealbirds.ca).","License":"GPL-
2","NeedsCompilation":"no","Package":"detect","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"dclone, dcmle","Title":"Analyzing Wildlife Data with
Detection Error","URL":"https:\/\/github.com\/psolymos\/detect","Version":"0.4-
0"},"detector":{"Author":"Paul Hendricks [aut, cre]","Depends":"R (>=
3.1.2)","Description":"Allows users to quickly and easily detect data
containing\nPersonally Identifiable Information (PII) through convenience
functions.","Imports":"stringr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"detector","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat, generator","Title":"Detect Data
Containing Personally Identifiable
Information","URL":"https:\/\/github.com\/paulhendricks\/detector","Version":"0.1.0
"},"detrendeR":{"Author":"Filipe Campelo","Depends":"tcltk,
dplR","Description":"Simple GUI to perform some standard tree-ring
analyses.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"detrendeR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Start the detrendeR Graphical User Interface
(GUI)","Version":"1.0.4"},"devEMF":{"Author":"Philip Johnson","Depends":"R (>=
2.10.1)","Description":"Output graphics to EMF (enhanced
metafile).","License":"GPL-
3","NeedsCompilation":"yes","Package":"devEMF","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"EMF Graphics Output Device","Version":"2.0"},"devtools":
{"Author":"Hadley Wickham [aut, cre],\nWinston Chang [aut],\nRStudio [cph],\nR Core
team [ctb] (Some namespace and vignette code extracted from base\nR)","Depends":"R
(>= 3.0.2)","Description":"Collection of package development
tools.","Imports":"httr (>= 0.4), utils, tools, methods, memoise, whisker,\ndigest,
rstudioapi (>= 0.2.0), jsonlite, stats, git2r (>=\n0.11.0), withr","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"devtools","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"curl (>= 0.9), testthat (>= 0.7), BiocInstaller,
Rcpp (>=\n0.10.0), MASS, rmarkdown, knitr, lintr (>= 0.2.1), bitops,\nroxygen2 (>=
5.0.0), evaluate, rversions","Title":"Tools to Make Developing R Packages
Easier","URL":"https:\/\/github.com\/hadley\/devtools","Version":"1.10.0"},"df2json
":{"Author":"Nacho Caballero <nachocab@gmail.com>","Depends":"R (>= 2.15.1),
rjson","Description":"It handles numerics, characters, factors, and
logicals.","License":"GPL-
3","NeedsCompilation":"no","Package":"df2json","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat, roxygen2","Title":"Convert a dataframe to
JSON","URL":"http:\/\/github.com\/nachocab\/df2json","Version":"0.0.2"},"dfcomb":
{"Author":"Marie-Karelle Riviere and Jacques-Henri Jourdan","Depends":"R (>=
3.1.3)","Description":"Phase I\/II adaptive dose-finding design for
combination\nstudies. Several methods are proposed depending on the type
of\ncombinations: (1) the combination of two cytotoxic agents, and (2)\ncombination
of a molecularly targeted agent with a cytotoxic agent.","License":"GPL-
3","NeedsCompilation":"yes","Package":"dfcomb","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Phase I\/II Adaptive Dose-Finding Design for Combination
Studies","Version":"2.1-5"},"dfcrm":{"Author":"Ken Cheung
<yc632@columbia.edu>","Description":"This package provides functions to run the CRM
and\nTITE-CRM in phase I trials and calibration tools for trial\nplanning
purposes.","License":"GPL-
2","NeedsCompilation":"no","Package":"dfcrm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Dose-finding by the continual reassessment
method","URL":"http:\/\/www.columbia.edu\/~yc632","Version":"0.2-2"},"dfexplore":
{"Author":"Joris Muller","Depends":"ggplot2, methods","Description":"Quickly and
graphically show missing values and classes of each variable and each observation
of a data.frame. The aim is to show pattern of missing values and if there is wrong
class
attribution.","License":"GPL","NeedsCompilation":"no","Package":"dfexplore","Reposi
tory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Explore data.frames by
plotting NA and classes of each
variable","URL":"https:\/\/github.com\/jomuller\/dfexplore","Version":"0.2.1"},"dfm
ta":{"Author":"Marie-Karelle Riviere and Jacques-Henri Jourdan","Depends":"R (>=
3.1.0)","Description":"Phase I\/II adaptive dose-finding design for single-
agent\nMolecularly Targeted Agent (MTA), according to the paper \"Phase\nI\/II
Dose-Finding Design for Molecularly Targeted Agent: Plateau\nDetermination using
Adaptive Randomization\" (in review).","License":"GPL-
3","NeedsCompilation":"yes","Package":"dfmta","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Phase I\/II Adaptive Dose-Finding Design for
MTA","Version":"1.3-3"},"dfoptim":{"Author":"Ravi Varadhan, Johns Hopkins
University, and Hans W. Borchers,\nABB Corporate Research.","Depends":"R (>=
2.10.1)","Description":"Derivative-Free optimization algorithms. These
algorithms\ndo not require gradient information. More importantly, they can\nbe
used to solve non-smooth optimization problems.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"dfoptim","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Derivative-free
Optimization","URL":"\nhttp:\/\/www.jhsph.edu\/agingandhealth\/People\/Faculty_pers
onal_pages\/Varadhan.html","Version":"2011.8-1"},"dga":{"Author":"James Johndrow,
Kristian Lum, and Patrick Ball","Description":"Performs Bayesian model averaging
for capture-recapture. This includes code to stratify records, check the strata for
suitable overlap to be used for capture-recapture, and some functions to plot the
estimated population size.","Imports":"chron","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"dga","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Capture-Recapture Estimation using Bayesian Model
Averaging","Version":"1.2"},"dglars":{"Author":"Luigi Augugliaro","Depends":"R (>=
2.10)","Description":"dglars implements the differential geometric extension\nof
the least angle regression method for logistic and Poisson\nregression models. To
compute the implicitly defined solution\ncurve, two different algorithms are
implemented, i.e. the\npredictor-corrector method and the cyclic coordinate
descent\nmethod.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"dglars","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Differential Geometric LARS (dgLARS)
method","Version":"1.0.5"},"dglm":{"Author":"Peter K Dunn <pdunn2@usc.edu.au> and
Gordon K Smyth","Depends":"R (>= 2.8.0), statmod(>= 1.4.20)","Description":"Model
fitting and evaluation tools for double generalized linear models (DGLMs).\nThis
class of models uses one generalized linear model (GLM) to fit the specified
response and\na second GLM to fit the deviance of the first model.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"dglm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Double Generalized Linear Models","URL":"https:\/\/cran.r-
project.org\/package=dglm","Version":"1.8.2"},"dgmb":{"Author":"Alba Martinez-Ruiz
<amartine@ucsc.cl> and Claudia Martinez-Araneda <cmartinez@ucsc.cl>","Depends":"R
(>= 3.1.0), tcltk,
MASS, abind","Description":"A set of functions have been implemented to generate
random data to perform Monte Carlo simulations on structural models with formative
constructs and interaction and nonlinear effects (Two-Step PLS Mode B structural
models). The setup of the true model considers a simple structure with three
formative exogenous constructs related to one formative endogenous construct. The
routines take into account the interaction and nonlinear effects of the exogenous
constructs on the endogenous construct.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"dgmb","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Simulating Data for PLS Mode B Structural
Models","Version":"1.2"},"dgof":{"Author":"Taylor B. Arnold, John W. Emerson, R
Core Team and contributors\nworldwide","Description":"This package contains a
proposed revision to the\nstats::ks.test() function and the associated ks.test.Rd
help\npage. With one minor exception, it does not change the\nexisting behavior of
ks.test(), and it adds features necessary\nfor doing one-sample tests with
hypothesized discrete\ndistributions. The package also contains cvm.test(), for
doing\none-sample Cramer-von Mises goodness-of-fit tests.","License":"GPL (>=
2.0)","NeedsCompilation":"yes","Package":"dgof","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Discrete Goodness-of-Fit Tests","Version":"1.2"},"dhglm":
{"Author":"Youngjo Lee, Maengseok Noh","Depends":"R (>= 3.1.0), methods, Matrix,
numDeriv, boot","Description":"Double hierarchical generalized linear models in
which the mean, dispersion parameters for variance of random effects, and residual
variance (overdispersion) can be further modeled as random-effect
models.","License":"Unlimited","NeedsCompilation":"no","Package":"dhglm","Repositor
y":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Double Hierarchical Generalized
Linear Models","Version":"1.5"},"diagonals":{"Author":"Bastiaan Quast [aut,
cre]","Depends":"R (>= 2.10)","Description":"Several tools for handling block-
matrix diagonals and similar constructs are implemented. Block-diagonal matrices
can be extracted or removed using two small functions implemented here. In
addition, non-square matrices are supported. Block diagonal matrices occur when two
dimensions of a data set are combined along one edge of a matrix. For example,
trade-flow data in the 'decompr' and 'gvc' packages have each country-industry
combination occur along both edges of the matrix.","License":"GPL-
3","NeedsCompilation":"no","Package":"diagonals","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat, knitr","Title":"Block Diagonal Extraction
or Replacement","URL":"http:\/\/qua.st\/diagonals,
https:\/\/github.com\/bquast\/diagonals","Version":"0.4.0"},"diagram":
{"Author":"Karline Soetaert <karline.soetaert@nioz.nl>","Depends":"R (>= 2.01)
,shape","Description":"Visualises simple graphs (networks) based on a transition
matrix, utilities to plot flow diagrams,\nvisualising webs, electrical
networks, ...\nSupport for the books \"A practical guide to ecological modelling
-\nusing R as a simulation platform\"\nby Karline Soetaert and Peter M.J. Herman
(2009). Springer.\nand the book \"Solving Differential Equations in R\"\nby Karline
Soetaert, Jeff Cash and Francesca Mazzia. Springer.\nIncludes demo(flowchart),
demo(plotmat), demo(plotweb)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"diagram","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Functions for visualising simple graphs (networks),
plotting\nflow diagrams","Version":"1.6.3"},"diaplt":{"Author":"Shinichiro
Tomizono","Description":"Visualize one-factor data frame.\nBeads plot consists of
diamonds of each factor of each data series.\nA diamond indicates average and
range.\nLook over a data frame with many numeric columns and a factor
column.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"diaplt","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Beads Summary Plot of
Ranges","Version":"1.2.1"},"dice":{"Author":"Dylan Arena","Depends":"R (>= 2.0.0),
gtools","Description":"This package provides utilities to calculate the
probabilities of various dice-rolling events, such as the probability of rolling a
four-sided die six times and getting a 4, a 3, and either a 1 or 2 among the six
rolls (in any order); the probability of rolling two six-sided dice three times and
getting a 10 on the first roll, followed by a 4 on the second roll, followed by
anything but a 7 on the third roll; or the probabilities of each possible sum of
rolling five six-sided dice, dropping the lowest two rolls, and summing the
remaining dice.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"dice","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Calculate probabilities of various dice-rolling
events","Version":"1.2"},"dichromat":{"Author":"Thomas Lumley [aut, cre], Ken
Knoblauch [ctb], Scott Waichler\n[ctb], Achim Zeileis [ctb]","Depends":"R (>=
2.10), stats","Description":"Collapse red-green or green-blue distinctions to
simulate\nthe effects of different types of color-blindness.","License":"GPL-
2","NeedsCompilation":"no","Package":"dichromat","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Color Schemes for Dichromats","Version":"2.0-
0"},"dicionariosIBGE":{"Author":"Alexandre Rademaker
<alexandre.rademaker@fgv.br>","Depends":"R (>= 2.15.1)","Description":"This package
contains the dictionaries for reading microdata\nfrom IBGE (Brazilian Institute of
Geography and Statistics)\nsurveys PNAD, PME and POF.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"dicionariosIBGE","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Dictionaries for reading microdata surveys from
IBGE","URL":"http:\/\/github.com\/arademaker\/dicionariosIBGE","Version":"1.6"},"di
electric":{"Author":"Baptiste Auguie [aut, cre] (the original data have their
original\nsource listed in the help file.)","Depends":"R (>= 2.13),
methods","Description":"Physical constants. Gold, silver and glass
permittivities,\ntogether with spline interpolation functions.","License":"GPL-
3","NeedsCompilation":"no","Package":"dielectric","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"ggplot2","Title":"Defines some physical constants
and dielectric functions\ncommonly used in optics,
plasmonics","Version":"0.2.3"},"diezeit":{"Author":"Christian
Graul","Description":"A wrapper for the ZEIT ONLINE Content API, available at
<http:\/\/developer.zeit.de>. 'diezeit' gives access to articles and corresponding
metadata from the ZEIT archive and from ZEIT ONLINE. A personal API key is required
for usage.","Imports":"brew, grDevices, httr, jsonlite, methods,
LICENSE","NeedsCompilation":"no","Package":"diezeit","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"knitr","Title":"R Interface to the ZEIT ONLINE
Content API","Version":"0.1-0"},"difR":{"Author":"David Magis (U Liege), Sebastien
Beland (UQAM) and Gilles Raiche (UQAM)","Depends":"R (>= 3.0.0), lme4,
ltm","Description":"Collection of traditional methods to detect differential item
functioning among dichotomously scored items.","License":"file
LICENSE","NeedsCompilation":"no","Package":"difR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Collection of Methods to Detect Dichotomous
Differential Item\nFunctioning (DIF)","Version":"4.6"},"diffEq":{"Author":"Karline
Soetaert <karline.soetaert@nioz.nl>","Depends":"R (>= 2.01), deSolve, rootSolve,
bvpSolve, ReacTran, deTestSet","Description":"Functions and examples from the book
Solving Differential\nEquations in R by Karline Soetaert, Jeff R Cash and Francesca
Mazzia.\nSpringer,
2012.","Imports":"shape","License":"GPL","NeedsCompilation":"no","Package":"diffEq"
,"Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"scatterplot3d","Ti
tle":"Functions from the book Solving Differential Equations in R","Version":"1.0-
1"},"diffIRT":{"Author":"Dylan Molenaar","Depends":"statmod","Description":"Package
to fit diffusion-based IRT models to response and\nresponse time data. Models are
fit using marginal maximum\nlikelihood. Parameter restrictions (fixed value and
equality\nconstraints) are possible. In addition, factor scores (person drift\nrate
and person boundary separation) can be estimated. Model fit\nassessment tools are
also available. The traditional diffusion model\ncan be estimated as
well.","License":"GPL-
2","NeedsCompilation":"yes","Package":"diffIRT","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Diffusion IRT Models for Response and Response Time
Data","Version":"1.5"},"diffdepprop":{"Author":"Daniela Wenzel, Antonia
Zapf","Depends":"gee, rootSolve, PropCIs","Description":"The package includes
functions to calculate confidence\nintervals for the difference of dependent
proportions. There\nare two functions implemented to edit the data
(dichotomising\nwith the help of cutpoints, counting accordance and discordance\nof
two tests or situations). For the calculation of the\nconfidence intervals entries
of the fourfold table are
needed.","License":"GPL","NeedsCompilation":"no","Package":"diffdepprop","Repositor
y":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Calculates Confidence Intervals
for two Dependent Proportions","Version":"0.1-9"},"diffeR":{"Author":"Robert
Gilmore Pontius Jr. <rpontius@clarku.edu>, Alí Santacruz
<asantacruzdelgado@clarku.edu>","Depends":"R (>= 2.14.0), rgdal, raster, methods,
ggplot2","Description":"Metrics of difference for comparing pairs of maps
representing real or categorical variables at original and multiple
resolutions.","Imports":"graphics, grDevices","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"diffeR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Metrics of Difference for Comparing Pairs of
Maps","URL":"http:\/\/amsantac.co\/software.html","Version":"0.0-4"},"diffr":
{"Author":"John
Muschelli [aut, cre]","Depends":"R (>= 3.0)","Description":"An R interface to the
'codediff' JavaScript library (a copy of which is included in the package).\nAllows
for visualization of the difference between 2 files, usually text files or R
scripts, in a browser.","Imports":"htmlwidgets","License":"GPL-
2","NeedsCompilation":"no","Package":"diffr","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"shiny","Title":"Display Differences Between Two Files
using Codediff
Library","URL":"https:\/\/github.com\/danvk\/codediff.js","Version":"0.0.1"},"diffr
actometry":{"Author":"P.L. Davies, U. Gather, M. Meise, D.Mergel, T. Mildenberger.
Additional Code by T. Bernholt and T. Hofmeister","Description":"Residual-based
baseline identification and peak decomposition for x-ray diffractograms as
introduced in Davies\/Gather\/Mergel\/Meise\/Mildenberger (2008).","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"diffractometry","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Baseline identification and peak decomposition
for x-ray\ndiffractograms","Version":"0.1-8"},"diffusionMap":{"Author":"Joseph
Richards <joeyrichar@gmail.com>","Depends":"R (>= 2.4.0)","Description":"Implements
diffusion map method of data\nparametrization, including creation and visualization
of\ndiffusion map, clustering with diffusion K-means and\nregression using adaptive
regression model.","Imports":"scatterplot3d, igraph, Matrix","License":"GPL-
2","NeedsCompilation":"no","Package":"diffusionMap","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Diffusion map","URL":"http:\/\/www.r-
project.org,\nhttp:\/\/www.stat.berkeley.edu\/~jwrichar\/software.html","Version":"
1.1-0"},"digest":{"Author":"Dirk Eddelbuettel <edd@debian.org> with
contributions\nby Antoine Lucas, Jarek Tuszynski, Henrik Bengtsson, Simon
Urbanek,\nMario Frasca, Bryan Lewis, Murray Stokely, Hannes Muehleisen,\nDuncan
Murdoch, Jim Hester, Wush Wu and Thierry Onkelinx.","Depends":"R (>=
2.4.1)","Description":"Implementation of a function 'digest()' for the creation\nof
hash digests of arbitrary R objects (using the md5, sha-1, sha-256,\ncrc32, xxhash
and murmurhash algorithms) permitting easy comparison of R\nlanguage objects, as
well as a function 'hmac()' to create hash-based\nmessage authentication
code.\n\nThe md5 algorithm by Ron Rivest is specified in RFC 1321, the sha-1\nand
sha-256 algorithms are specified in FIPS-180-1 and FIPS-180-2,\nand the crc32
algorithm is described
in\nftp:\/\/ftp.rocksoft.com\/cliens\/rocksoft\/papers\/crc_v3.txt.\n\nFor md5,
sha-1, sha-256 and aes, this package uses small standalone\nimplementations that
were provided by Christophe Devine. For crc32, code\nfrom the zlib library is used.
For sha-512, an implementation by Aaron\nD. Gifford is used. For xxhash, the
implementation by Yann Collet is used.\nFor murmurhash, an implementation by Shane
Day is used.\n\nPlease note that this package is not meant to be deployed
for\ncryptographic purposes for which more comprehensive (and widely\ntested)
libraries such as OpenSSL should be used.","License":"GPL-
2","NeedsCompilation":"yes","Package":"digest","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr, rmarkdown","Title":"Create Compact Hash Digests
of R
Objects","URL":"http:\/\/dirk.eddelbuettel.com\/code\/digest.html","Version":"0.6.9
"},"digitalPCR":{"Author":"Xutao Deng","Depends":"stats","Description":"The assay
sensitivity is the minimum number of copies that the digital PCR assay can detect.
Users provide serial dilution results in the format of counts of positive and total
reaction wells. The output is the estimated assay sensitivity and the copy number
per well in the initial dilute.","License":"GPL-
2","NeedsCompilation":"no","Package":"digitalPCR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Estimate Copy Number for Digital
PCR","Version":"1.1.0"},"dils":{"Author":"Stephen R. Haptonstahl","Depends":"R (>=
3.0.1), igraph, Rcpp (>= 0.10.4)","Description":"Combine multiple-relationship
networks into a single weighted\nnetwork. The approach is similar to factor
analysis in the that\ncontribution from each constituent network varies so as to
maximize the\ninformation gleaned from the multiple-relationship networks.\nThis
implementation uses Principal Component Analysis calculated using\n'prcomp' with
bootstrap subsampling. Missing links are imputed using\nthe method of Chen et
al.\n(2012).","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"dils","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat, Matrix","Title":"Data-Informed Link
Strength. Combine multiple-relationship\nnetworks into a single weighted network.
Impute (fill-in)\nmissing network links","Version":"0.8.1"},"dina":
{"Author":"Steven Andrew Culpepper [aut, cph, cre]","Depends":"R (>=
3.0.1)","Description":"Estimate the Deterministic Input, Noisy `Ànd'' Gate (DINA)
cognitive diagnostic model parameters using the Gibbs sampler described by
Culpepper (2015) DOI: 10.3102\/1076998615595403.","Imports":"Rcpp","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"dina","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Bayesian Estimation of DINA
Model","Version":"1.0.1"},"dinamic":{"Author":"Vonn Walter, Andrew B. Nobel, and
Fred A. Wright","Description":"This function implements the DiNAMIC procedure
for\nassessing the statistical significance of recurrent DNA copy\nnumber
aberrations (Bioinformatics (2011) 27(5) 678 - 685).","License":"GPL-
2","NeedsCompilation":"no","Package":"dinamic","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"DiNAMIC A Method To Analyze Recurrent DNA Copy
Number\nAberrations in Tumors","Version":"1.0"},"diptest":{"Author":"Martin
Maechler (originally from Fortran and S-plus by Dario Ringach,
NYU.edu)","Description":"Compute Hartigan's dip test statistic for unimodality
\/\nmultimodality and provide a test with simulation based p-values, where\nthe
original public code has been corrected.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"diptest","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Hartigan's Dip Test Statistic for Unimodality -
Corrected","Version":"0.75-7"},"directPA":{"Author":"Pengyi Yang & Ellis
Patrick","Depends":"R (>= 2.10.0), rgl, calibrate","Description":"Direction
analysis is a set of tools designed to identify\ncombinatorial effects of multiple
treatments and\/or perturbations on pathways\nand kinases profiled by microarray,
RNA-seq, proteomics, or phosphoproteomics\ndata.","License":"GPL-
3","NeedsCompilation":"no","Package":"directPA","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Direction Analysis for Pathways and
Kinases","Version":"1.3"},"directlabels":{"Author":"Toby Dylan
Hocking","Description":"An extensible framework\nfor automatically placing direct
labels onto multicolor lattice or\nggplot2 plots.\nLabel positions are described
using Positioning Methods\nwhich can be re-used across several different
plots.\nThere are heuristics for examining \"trellis\" and \"ggplot\" objects\nand
inferring an appropriate Positioning Method.","Imports":"grid,
3","NeedsCompilation":"no","Package":"directlabels","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"MASS, inlinedocs, ggplot2 (>= 2.0), lattice,
alphahull, nlme,\nElemStatLearn, lars, latticeExtra","Title":"Direct Labels for
Multicolor Plots","URL":"http:\/\/directlabels.r-forge.r-
project.org\/","Version":"2015.12.16"},"dirmult":{"Author":"Torben Tvedebrink
<tvede@math.aau.dk>","Depends":"R (>= 2.5.0)","Description":"Estimate parameters in
Dirichlet-Multinomial and compute\nprofile log-likelihoods.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"dirmult","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Estimation in Dirichlet-Multinomial
distribution","Version":"0.1.3-4"},"discSurv":{"Author":"Thomas Welchowski
<welchow@imbie.meb.uni-bonn.de> and Matthias Schmid <matthias.schmid@imbie.uni-
bonn.de>","Description":"Provides data transformations, estimation
utilities,\npredictive evaluation measures and simulation functions for discrete
time\nsurvival analysis.","Imports":"functional, mvtnorm, mgcv","License":"GPL-
3","NeedsCompilation":"no","Package":"discSurv","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"Matrix, matrixcalc, numDeriv, caret, Ecdat, pec,
survival,\nrandomForest, nnet, VGAM","Title":"Discrete Time Survival
Analysis","Version":"1.1.2"},"disclap":{"Author":"Mikkel Meyer Andersen and Poul
Svante Eriksen","Description":"Discrete Laplace exponential family for models such
as a generalized linear model","License":"GPL-
2","NeedsCompilation":"no","Package":"disclap","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Discrete Laplace Exponential
Family","Version":"1.5"},"disclapmix":{"Author":"Mikkel Meyer Andersen and Poul
Svante Eriksen","Description":"Make inference in a mixture of discrete Laplace
distributions using the EM algorithm. This can e.g. be used for modelling the
distribution of Y chromosomal haplotypes as described in [1, 2] (refer to the URL
section).","Imports":"Rcpp (>= 0.11), disclap (>= 1.4), cluster (>= 1.14.4),
stats,\ngraphics, methods, utils","License":"GPL-
2","NeedsCompilation":"yes","Package":"disclapmix","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"ggplot2, gridExtra, ggdendro, scales,
seriation","Title":"Discrete Laplace Mixture Inference using the EM
Algorithm","URL":"http:\/\/dx.doi.org\/10.1016\/j.jtbi.2013.03.009\nhttp:\/\/arxiv.
org\/abs\/1304.2129","Version":"1.6.2"},"discreteMTP":{"Author":"Ruth Heller [aut],
Hadas Gur [aut], Shay Yaacoby [aut, cre]","Description":"Multiple testing
procedures for discrete test statistics,\nthat use the known discrete null
distribution of the p-values\nfor simultaneous inference.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"discreteMTP","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Multiple testing procedures for discrete test
statistics","URL":"http:\/\/www.math.tau.ac.il\/~ruheller\/","Version":"0.1-
2"},"discreteRV":{"Author":"Andreas Buja [aut],\nEric Hare [aut, cre],\nHeike
Hofmann [aut]","Depends":"R (>= 3.0.2)","Description":"Create, manipulate,
transform, and simulate from discrete random\nvariables. The syntax is modeled
after that which is used in mathematical\nstatistics and probability courses, but
with powerful support for more\nadvanced probability calculations. This includes
the creation of joint\nrandom variables, and the derivation and manipulation of
their conditional\nand marginal distributions.","Imports":"plyr,
3","NeedsCompilation":"no","Package":"discreteRV","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat, roxygen2, knitr","Title":"Create and
Manipulate Discrete Random
Variables","URL":"https:\/\/github.com\/erichare\/discreteRV","Version":"1.2.2"},"d
iscretization":{"Author":"HyunJi Kim","Description":"This package is a collection
of supervised discretization\nalgorithms. It can also be grouped in terms of top-
down or\nbottom-up, implementing the discretization
algorithms.","License":"GPL","NeedsCompilation":"no","Package":"discretization","Re
pository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Data preprocessing,
discretization for classification","Version":"1.0-1"},"discrimARTs":{"Author":"J.
Mark Rowland, Clifford Qualls, and Christian Gunning","Depends":"R (>= 2.10.0),
grid, RUnit","Description":"'discrimARTs' discriminates with explicit confidence
the alternative reproductive tactics (ARTs) in dimorphic systems with bimodal
traits by computing the maximum likelihood estimate of a mixture of distributions
of a measured ARTs trait. Supported distributions include a mixture of 2 normal
distributions and a mixture of 2 facing gamma distributions.","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"discrimARTs","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Discrimination of Alternative Reproductive Tactics
(ARTs)","Version":"0.2"},"diseasemapping":{"Author":"Patrick Brown
<patrick.brown@utoronto.ca>","Depends":"sp, R (>= 3.2)","Description":"Formatting
of population and case data, calculation of Standardized Incidence Ratios, and
fitting the BYM model using INLA.","Enhances":"INLA","Imports":"methods, stats,
utils","License":"GPL","NeedsCompilation":"no","Package":"diseasemapping","Reposito
ry":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"mgcv, spdep, geostatsp, XML,
mapmisc (>= 1.0), knitr","Title":"Modelling Spatial Variation in Disease Risk for
Areal Data","Version":"1.4.0"},"diskImageR":{"Author":"Aleeza Gerstein [aut,
cre],\nInbal Hecht [ctb]","Depends":"R (>= 3.0.3)","Description":"A pipeline to
analyze photographs of disk diffusion plates. This removes the need to analyze the
plates themselves, and thus analysis can be done separate from the assay.
Furthermore, diskImageR removes potential researcher bias, by quantitative
assessment of drug resistance as the zone diameter at multiple cutoff values of
growth inhibition. This method also extends the disk diffusion assay by measuring
drug tolerance (in addition to drug resistance) as the fraction of the
subpopulation that is able to grow above the resistance point (\"FoG\"), and drug
sensitivity as the rate of change from no growth to full growth
(\"slope\").","Imports":"zoo, subplex, tcltk, methods","License":"GPL-
3","NeedsCompilation":"no","Package":"diskImageR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr","Title":"A Pipeline to Analyze Resistance and
Tolerance from Drug Disk\nDiffusion Assays","Version":"1.0.0"},"dismo":
{"Author":"Robert J. Hijmans, Steven Phillips, John Leathwick and Jane
Elith","Depends":"R (>= 2.13.0), methods, raster (>= 2.3-40), sp (>= 1.0-
13)","Description":"Functions for species distribution modeling, that is,
predicting entire geographic distributions form occurrences at a number of
sites.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"dismo","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"rJava (>= 0.5-0), rgdal, rgeos, XML, ROCR, deldir,
gstat,\nrandomForest, kernlab, maptools, jsonlite, gbm (>= 2.1.1)","Title":"Species
Distribution Modeling","Version":"1.0-15"},"disp2D":{"Author":"Guillermo
Ayala","Depends":"geometry","Description":"An implementation of two exact
algorithms for testing the\nHausdorff and simplex dispersion
orderings","License":"GPL-
2","NeedsCompilation":"no","Package":"disp2D","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"mvtnorm","Title":"2D Hausdorff and Simplex Dispersion
Orderings","Version":"1.0"},"disparityfilter":{"Author":"Alessandro
Bessi","Depends":"R (>= 3.1.1), igraph","Description":"Disparity filter is a
network reduction algorithm to extract the backbone structure of both directed and
undirected weighted networks. Disparity filter can reduce the network without
destroying the multi-scale nature of the network. The algorithm has been developed
by M. Angeles Serrano, Marian Boguna, and Alessandro Vespignani in Extracting the
multiscale backbone of complex weighted networks, Proceedings of the national
academy of sciences 106 (16).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"disparityfilter","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Disparity Filter Algorithm of Weighted
Network","Version":"2.1"},"displayHTS":{"Author":"Xiaohua Douglas Zhang & Zhaozhi
Zhang","Description":"A package containing R functions for displaying data
and\nresults from high-throughput screening experiments.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"displayHTS","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"displayHTS","Version":"1.0"},"dispmod":{"Author":"Luca
Scrucca <luca@stat.unipg.it>","Depends":"R (>= 2.12)","Description":"Description:
Functions for modelling dispersion in GLM.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"dispmod","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Dispersion models","Version":"1.1"},"disposables":
{"Author":"Gabor Csardi","Depends":"methods","Description":"Create disposable R
packages for testing.\nYou can create, install and load multiple R packages with a
single\nfunction call, and then unload, uninstall and destroy them with
another\nfunction call. This is handy when testing how some R code or an R
package\nbehaves with respect to other packages.","Imports":"utils","License":"MIT
+ file
LICENSE","NeedsCompilation":"no","Package":"disposables","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Create Disposable R
Packages for
Testing","URL":"https:\/\/github.com\/gaborcsardi\/disposables","Version":"1.0.1"},
"dissUtils":{"Author":"Benjamin N. Taft","Depends":"R (>=
2.14)","Description":"This package has extensible C++ code for computing
dissimilarities between vectors. It also has a number of C++ functions for
assembling collections of dissimilarities. In particular, it lets you find a matrix
of dissimilarities between the rows of two input matrices. There are also functions
for finding the nearest neighbors of each row of a matrix, either within the matrix
itself or within another matrix.","License":"GPL (>= 2) | file
LICENSE","NeedsCompilation":"yes","Package":"dissUtils","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"MASS (>= 1.0)","Title":"Utilities for making
pairwise comparisons of multivariate data","Version":"1.0"},"distance.sample.size":
{"Author":"Robert Clark","Description":"Calculates the study size (either number of
detections, or\nproportion of region that should be covered) to achieve a target
precision for\nthe estimated abundance. The calculation allows for the penalty due
to unknown\ndetection function, and for overdispersion. The user must specify a
guess at the\ntrue detection function.","Imports":"MASS","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"distance.sample.size","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Title":"Calculates Study Size Required for Distance
Sampling","Version":"0.0"},"distcomp":{"Author":"Balasubramanian Narasimhan [aut,
cre],\nMarina Bendersky [aut],\nSam Gross [aut],\nTerry M. Therneau [ctb],\nThomas
Lumley [ctb]","Depends":"survival, stats, R (>= 3.1.0)","Description":"Implementing
algorithms and fitting models when sites (possibly remote) share\ncomputation
summaries rather than actual data over HTTP with a master R process
(using\n'opencpu', for example). A stratified Cox model and a singular value
decomposition are\nprovided. The former makes direct use of code from the R
'survival' package. (That is,\nthe underlying Cox model code is derived from that
in the R 'survival' package.)\nSites may provide data via several means: CSV files,
Redcap API, etc. An extensible\ndesign allows for new methods to be added in the
future. Web applications are provided\n(via 'shiny') for the implemented methods to
help in designing and deploying the\ncomputations.","Imports":"utils, shiny, httr
(>= 1.0.0), digest, jsonlite, stringr, R6\n(>= 2.0)","License":"LGPL (>=
2)","NeedsCompilation":"yes","Package":"distcomp","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"opencpu","Title":"Computations over Distributed Data
without
Aggregation","URL":"http:\/\/arxiv.org\/abs\/1412.6890","Version":"0.25.4"},"distfr
ee.cr":{"Author":"Zhiqiu Hu, Rong-cai Yang","Depends":"R (>=
2.10)","Description":"An R package that is developed for constructing
confidence\nregions without the need to know the sampling distribution
of\nbivariate data.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"distfree.cr","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Distribution-free confidence
region
(distfree.cr)","URL":"http:\/\/statgen.ualberta.ca","Version":"1.0"},"distillery":
{"Author":"Eric Gilleland","Depends":"R (>= 2.10.0)","Description":"Some very
simple method functions for confidence interval calculation and to distill
pertinent information from a potentially complex object; primarily used in common
with packages extRemes and SpatialVx.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"distillery","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Method Functions for Confidence Intervals and to
Distill\nInformation from an
Object","URL":"http:\/\/www.ral.ucar.edu\/staff\/ericg","Version":"1.0-
2"},"distory":{"Author":"John Chakerian and Susan Holmes","Depends":"ape (>= 2.3),
R (>= 2.6.0)","Description":"Geodesic distance between phylogenetic trees
and\nassociated
functions.","License":"BSD","NeedsCompilation":"yes","Package":"distory","Repositor
y":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Distance Between Phylogenetic
Histories","Version":"1.4.2"},"distr":{"Author":"Florian Camphausen
[aut],\nMatthias Kohl [aut, cph],\nPeter Ruckdeschel [cre, cph],\nThomas Stabla
[aut, cph],\nR Core Team [ctb, cph] (for source file ks.c\/ routines 'pKS2'
and\n'pKolmogorov2x')","Depends":"R(>= 2.14.0), methods, graphics, startupmsg,
sfsmisc,\nSweaveListingUtils","Description":"S4 Classes and Methods for
distributions","Imports":"stats","License":"LGPL-
3","NeedsCompilation":"yes","Package":"distr","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"distrEx, svUnit (>= 0.7-11)","Title":"Object oriented
implementation of distributions","URL":"http:\/\/distr.r-forge.r-
project.org\/","Version":"2.5.3"},"distrDoc":{"Author":"Florian Camphausen [ctb]
(contributed as student to the documented\npackages in the initial phase
--2005),\nMatthias Kohl [aut, cph],\nPeter Ruckdeschel [cre, cph],\nThomas Stabla
[ctb] (contributed as student to the documented packages\nin the initial phase
--2005)","Depends":"R(>= 2.14.0)","Description":"provides documentation in form of
a common vignette to packages distr, distrEx,\ndistrMod, distrSim, distrTEst,
distrTeach, and distrEllipse","Imports":"distr(>= 2.2.0), distrEx(>= 2.2.0),
distrSim(>= 2.2.0),\ndistrTEst(>= 2.2.0), distrTeach(>= 2.2.0), RandVar(>=
0.7),\ndistrMod(>= 2.2.0), MASS, methods,
SweaveListingUtils,\nstartupmsg","License":"LGPL-
3","NeedsCompilation":"no","Package":"distrDoc","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"Biobase","Title":"Documentation for Packages distr,
distrEx, distrSim, distrTEst,\ndistrTeach, distrMod, and
distrEllipse","URL":"http:\/\/distr.r-forge.r-
project.org\/","Version":"2.5.1"},"distrEllipse":{"Author":"Peter
Ruckdeschel","Depends":"R(>= 2.8.0), methods, graphics, mvtnorm, setRNG(>= 2006.2-
1),\ndistr(>= 2.2), distrEx(>= 2.2), distrSim(>= 2.2)","Description":"Distribution
(S4-)classes for elliptically contoured distributions (based on\npackage
distr)","License":"LGPL-
3","NeedsCompilation":"no","Package":"distrEllipse","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"distrMod(>= 2.2), distrTEst(>= 2.2)","Title":"S4
classes for elliptically contoured distributions","URL":"http:\/\/distr.r-forge.r-
project.org\/","Version":"2.5"},"distrEx":{"Author":"Matthias Kohl, Peter
Ruckdeschel, Nataliya Horbenko","Depends":"R (>= 2.10), methods, distr (>=
2.2)","Description":"Extensions of package distr and some additional
functionality","License":"LGPL-
3","NeedsCompilation":"yes","Package":"distrEx","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"tcltk","Title":"Extensions of package
distr","URL":"http:\/\/distr.r-forge.r-project.org\/","Version":"2.5"},"distrMod":
{"Author":"Matthias Kohl, Peter Ruckdeschel","Depends":"R(>= 2.14.0), distr(>=
2.5.2), distrEx(>= 2.4), RandVar(>=\n0.6.3), MASS, stats4,
methods","Description":"Object oriented implementation of probability models based
on packages 'distr' and\n'distrEx'","Imports":"sfsmisc,
startupmsg","License":"LGPL-
3","NeedsCompilation":"no","Package":"distrMod","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Object Oriented Implementation of Probability
Models","URL":"http:\/\/distr.r-forge.r-
project.org\/","Version":"2.5.3"},"distrRmetrics":{"Author":"Nataliya Horbenko,
Matthias Kohl, Daria Pupashenko, Myhailo Pupashenko,
Peter\nRuckdeschel","Depends":"R(>= 2.6.0), methods, distr(>= 2.4), fBasics(>=
270.73),\nfGarch(>= 270.73)","Description":"(S4-)distribution classes based on
package distr for distributions from packages\nfBasics and fGarch","License":"LGPL-
3","NeedsCompilation":"no","Package":"distrRmetrics","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"distrEx(>= 2.4), distrMod(>=
2.4)","Title":"Package distr classes for distributions from
Rmetrics","URL":"http:\/\/distr.r-forge.r-
project.org\/","Version":"2.5"},"distrSim":{"Author":"Florian Camphausen, Matthias
Kohl, Peter Ruckdeschel, Thomas Stabla","Depends":"R(>= 2.14.0), methods, graphics,
setRNG(>= 2006.2-1), distr(>=\n2.5.2)","Description":"Simulation (S4-)classes based
on package distr","License":"LGPL-
3","NeedsCompilation":"no","Package":"distrSim","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"distrEx(>= 2.2)","Title":"Simulation classes based on
package distr","URL":"http:\/\/distr.r-forge.r-
project.org\/","Version":"2.5.2"},"distrTEst":{"Author":"Florian Camphausen,
Matthias Kohl, Peter Ruckdeschel, Thomas Stabla","Depends":"R(>= 2.6.0), methods,
graphics, setRNG(>= 2006.2-1),\ndistrSim(>= 2.2),
startupmsg","Description":"Evaluation (S4-)classes based on package distr for
evaluating procedures\n(estimators\/tests) at data\/simulation in a unified
way.","License":"LGPL-
3","NeedsCompilation":"no","Package":"distrTEst","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"distrEx(>= 2.2)","Title":"Estimation and Testing
classes based on package distr","URL":"http:\/\/distr.r-forge.r-
project.org\/","Version":"2.5"},"distrTeach":{"Author":"Peter Ruckdeschel, Matthias
Kohl, Anja Hueller, Eleonara Feist","Depends":"R(>= 2.2.0), methods, distr(>= 2.2),
distrEx(>= 2.2)","Description":"Extensions of package distr and some additional
functionality","License":"LGPL-
3","NeedsCompilation":"no","Package":"distrTeach","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"tcltk","Title":"Extensions of package distr for
teaching Stochastics\/Statistics\nin secondary school","URL":"http:\/\/distr.r-
forge.r-project.org\/","Version":"2.5"},"distrom":{"Author":"Matt Taddy
<taddy@chicagobooth.edu>","Depends":"R (>= 2.15), Matrix, gamlr, parallel, methods,
stats","Description":"Estimation for a multinomial logistic regression factorized
into independent Poisson log regressions. See the textir package for applications
in multinomial inverse regression analysis of text.","License":"GPL-
3","NeedsCompilation":"no","Package":"distrom","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"MASS, textir","Title":"Distributed Multinomial
Regression","URL":"http:\/\/faculty.chicagobooth.edu\/matt.taddy\/research\/index.h
tml\nhttp:\/\/github.com\/TaddyLab\/distrom","Version":"0.3-3"},"divagis":
{"Author":"Reinhard Simon","Depends":"rgdal, sp","Description":"Provides tools for
quality checks of georeferenced plant\nspecies accessions.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"divagis","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Provides tools for quality checks of georeferenced plant
species\naccessions","Version":"1.0.0"},"diveMove":{"Author":"Sebastian P. Luque
<spluque@gmail.com>","Depends":"R (>= 2.13.0), methods,
stats4","Description":"Utilities to represent, visualize, filter, analyse, and
summarize\ntime-depth recorder (TDR) data. Miscellaneous functions for\nhandling
location data are also provided.","Imports":"caTools, KernSmooth, quantreg,
geosphere","License":"GPL-
3","NeedsCompilation":"no","Package":"diveMove","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"lattice, tcltk","Title":"Dive Analysis and
Calibration","URL":"https:\/\/github.com\/spluque\/diveMove","Version":"1.4.1"},"di
veRsity":{"Author":"Kevin Keenan <kkeenan02@qub.ac.uk>","Depends":"R (>=
3.0.0)","Description":"Allows the calculation of both genetic diversity
partition\nstatistics, genetic differentiation statistics, and locus
informativeness\nfor ancestry assignment.\nIt also provides users with various
option to calculate\nbootstrapped 95\\% confidence intervals both across loci,\nfor
pairwise population comparisons, and to plot these results interactively.\nParallel
computing capabilities and pairwise results without\nbootstrapping are
provided.\nWeir and Cockerham's 1984 F-statistics are also calculated.\nVarious
plotting features are also provided, as well as Chi-square tests of\ngenetic
heterogeneity are also provided.\nFunctionality for the calculation of various
diversity parameters is\npossible for RAD-seq derived SNP data sets containing
thousands of marker loci.\nA shiny application for the development of
microsatellite multiplexes is\nalso available.","Imports":"ggplot2, shiny, qgraph,
Rcpp, methods, stats, grid","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"diveRsity","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"xlsx, sendplot, plotrix, parallel,
HWxtest","Title":"A Comprehensive, General Purpose Population Genetics
Analysis\nPackage","URL":"http:\/\/diversityinlife.weebly.com\/","Version":"1.9.89"
},"diverse":{"Author":"Miguel R. Guevara <miguel.guevara@upla.cl>, Dominik
Hartmann\n<d.hartmann@uni-hohenheim.de>, Marcelo
Mendoza\n<marcelo.mendoza@usm.cl>","Depends":"proxy, reshape2,
foreign","Description":"Computes the most common diversity measures used in social
and natural sciences, and includes new measures from interdisciplinary
research.","License":"CC BY-SA
4.0","NeedsCompilation":"no","Package":"diverse","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"pheatmap,
igraph","Title":"Diversity Measures for Complex
Systems","URL":"https:\/\/github.com\/mguevara\/diverse","Version":"0.1.1"},"divers
itree":{"Author":"Richard G. FitzJohn <fitzjohn@zoology.ubc.ca>, with 'GeoSSE'
and\n'ClaSSE' by Emma E. Goldberg <eeg@uic.edu>, and 'BiSSE-ness' by
Karen\nMagnuson-Ford.","Depends":"R (>= 2.10), methods,
ape","Description":"Contains a number of comparative phylogenetic methods,\nmostly
focusing on analysing diversification and character\nevolution. Contains
implementations of 'BiSSE' (Binary State\nSpeciation and Extinction) and its
unresolved tree extensions,\n'MuSSE' (Multiple State Speciation and Extinction),
'QuaSSE',\n'GeoSSE', and 'BiSSE-ness' Other included methods include Markov\nmodels
of discrete and continuous trait evolution and constant rate\nspeciation and
extinction.","Imports":"deSolve (>= 1.7), graphics, grDevices, stats, subplex,
Rcpp\n(>= 0.10.0)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"diversitree","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"numDeriv, minqa, lubridate, expm, caper,
geiger","Title":"Comparative Phylogenetic Analyses of
Diversification","URL":"http:\/\/www.zoology.ubc.ca\/prog\/diversitree","Version":"
0.9-8"},"divo":{"Author":"Maciej Pietrzak, Michal Seweryn, Grzegorz
Rempala","Depends":"R (>= 3.1.0), RcppCNPy, cluster","Description":"A set of tools
for empirical analysis of diversity (a number and frequency of different types in
population) and similarity (a number and frequency of shared types in two
populations) in biological or ecological systems.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"divo","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Tools for Analysis of Diversity and Similarity in
Biological\nSystems","Version":"0.1.2"},"dixon":{"Author":"Marcelino de la Cruz Rot
and Philip M. Dixon","Depends":"splancs, spatstat","Description":"Function to test
spatial segregation and association based\nin contingency table analysis of nearest
neighbour counts\nfollowing Dixon (2002). Some fortran code has been included
to\nthe original dixon2002 function of the ecespa package to\nimprove
speed.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"dixon","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Nearest Neighbour Contingency Table
Analysis","Version":"0.0-5"},"dkDNA":{"Author":"Gota Morota and Masanori
Koyama","Description":"Compute diffusion kernels on DNA polymorphisms, including
SNP and bi-allelic genotypes.","License":"GPL-
2","NeedsCompilation":"yes","Package":"dkDNA","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Diffusion Kernels on a Set of
Genotypes","URL":"http:\/\/morotalab.org\/","Version":"0.1.1"},"dlm":
{"Author":"Giovanni Petris <GPetris@uark.edu>.\nOriginal C code for ARMS by Wally
Gilks.","Description":"Maximum likelihood, Kalman filtering and smoothing, and
Bayesian\nanalysis of Normal linear State Space models, also known as\nDynamic
Linear Models","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"dlm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"MASS","Title":"Bayesian and Likelihood Analysis of
Dynamic Linear Models","Version":"1.1-4"},"dlmap":{"Author":"Emma Huang and Andrew
George","Depends":"qtl, ibdreg, wgaim, nlme, mgcv","Description":"QTL mapping in a
mixed model framework with separate\ndetection and localization stages. The first
stage detects the\nnumber of QTL on each chromosome based on the genetic
variation\ndue to grouped markers on the chromosome; the second stage uses\nthis
information to determine the most likely QTL positions.\nThe mixed model can
accommodate general fixed and random\neffects, including spatial effects in field
trials and pedigree\neffects. Applicable to backcrosses, doubled
haploids,\nrecombinant inbred lines, F2 intercrosses, and association\nmapping
populations.","License":"GPL-
2","NeedsCompilation":"no","Package":"dlmap","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"asreml","Title":"Detection Localization Mapping for
QTL","Version":"1.13"},"dlmodeler":{"Author":"Cyrille Szymanski <cnszym@gmail.com>
[aut]","Depends":"R (>= 2.15.0)","Description":"dlmodeler is a set of user-friendly
functions to simplify the state-space modelling, fitting, analysis and forecasting
of Generalized Dynamic Linear Models (DLMs). It includes functions to name and
extract individual components of a DLM, build classical seasonal time-series models
(monthly, quarterly, yearly, etc. with calendar adjustments) and provides a unified
interface compatible with other state-space packages including: dlm, FKF and
KFAS.","Imports":"KFAS (>= 1.0.2)","License":"GPL (>= 2) | BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"dlmodeler","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"dlm (>= 1.1-3), FKF (>=
0.1.2)","Title":"Generalized Dynamic Linear Modeler","Version":"1.4-2"},"dlnm":
{"Author":"Antonio Gasparrini and Ben Armstrong","Depends":"R (>=
3.2)","Description":"Collection of functions for distributed lag linear and non-
linear models.","Imports":"stats, graphics, grDevices, utils, splines, nlme,
mgcv,\ntsModel","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"dlnm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"survival, lme4, gee, geepack,
mvmeta","Title":"Distributed Lag Non-Linear Models","URL":"http:\/\/www.ag-
myresearch.com\/package-dlnm","Version":"2.2.3"},"dma":{"Author":"Tyler H.
McCormick, Adrian Raftery, David Madigan","Description":"Dynamic model averaging
for binary and continuous\noutcomes.","Imports":"MASS, mnormt","License":"GPL-
2","NeedsCompilation":"no","Package":"dma","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Dynamic Model Averaging","Version":"1.2-3"},"dml":
{"Author":"Yuan Tang <terrytangyuan@gmail.com>, Gao Tao <joegaotao@gmail.com>, Xiao
Nan <road2stat@gmail.com>","Depends":"MASS","Description":"The state-of-the-art
algorithms for distance metric learning, including global and local methods such as
Relevant Component Analysis, Discriminative Component Analysis, Local Fisher
Discriminant Analysis, etc. These distance metric learning methods are widely
applied in feature extraction, dimensionality reduction, clustering,
classification, information retrieval, and computer vision
problems.","Imports":"lfda","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"dml","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat","Title":"Distance Metric Learning in
R","URL":"https:\/\/github.com\/terrytangyuan\/dml","Version":"1.1.0"},"dmm":
{"Author":"Neville Jackson","Depends":"MASS, Matrix, nadiv, robustbase,
pls","Description":"Dyadic mixed model analysis with multi-trait responses
and\npedigree-based partitioning of individual variation into a range
of\nenvironmental and genetic variance components for individual and\nmaternal
effects.","Imports":"stats, graphics, grDevices","License":"GPL-2 | GPL (>= 2) |
GPL-
3","NeedsCompilation":"no","Package":"dmm","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Dyadic Mixed Model for Pedigree Data","Version":"1.6-
3"},"dmt":{"Author":"Leo Lahti and Olli-Pekka Huovilainen","Depends":"R (>=
2.15.0), methods, mvtnorm, MASS","Description":"Probabilistic dependency modeling
toolkit.","Imports":"Matrix","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"dmt","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Dependency Modeling Toolkit","Version":"0.8.20"},"dna":
{"Author":"Ryan Gill, Somnath Datta, Susmita Datta","Depends":"R (>=
3.0.0)","Description":"Package for conducting differential network analysis
from\nmicroarray data.","Imports":"methods","License":"GPL-
2","NeedsCompilation":"yes","Package":"dna","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"igraph, lars","Title":"Differential Network
Analysis","Version":"1.1-1"},"dnet":{"Author":"Hai Fang and Julian
Gough","Depends":"R (>= 3.1.0), igraph, supraHex","Description":"The focus of the
dnet is to make sense of omics data (such as gene expression and mutations) from
different angles including: integration with molecular networks, enrichments using
ontologies, and relevance to gene evolutionary ages. Integration is achieved to
identify a gene subnetwork from the whole gene network whose nodes\/genes are
labelled with informative data (such as the significant levels of differential
expression or survival risks). To help make sense of identified gene networks,
enrichment analysis is also supported using a wide variety of pre-compiled
ontologies and phylostratific gene age information in major organisms including:
human, mouse, rat, chicken, C.elegans, fruit fly, zebrafish and arabidopsis. Add-on
functionalities are supports for calculating semantic similarity between ontology
terms (and between genes) and for calculating network affinity based on random
walk; both can be done via high-performance parallel computing.","Imports":"graph,
Rgraphviz, Matrix, Biobase","License":"GPL-
2","NeedsCompilation":"no","Package":"dnet","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"limma, survival, foreach, doMC","Title":"Integrative
Analysis of Omics Data in Terms of Network,\nEvolution and
Ontology","URL":"http:\/\/supfam.org\/dnet, http:\/\/cran.r-
project.org\/package=dnet,\nhttp:\/\/dnet.r-forge.r-
project.org,\nhttps:\/\/github.com\/hfang-bristol\/dnet","Version":"1.0.8"},"doBy":
{"Author":"Søren Højsgaard <sorenh@math.aau.dk> and Ulrich Halekoh
<uhalekoh@health.sdu.dk>","Depends":"R (>= 3.2.0), methods","Description":"The
facilities can roughly be grouped as:\n\n1) Facilities for groupwise computations
of summary statistics and\nother facilities for working with grouped data: 'do'
something to data\nstratified 'by' some variables.\n\n2) LSmeans (least-squares
means), general linear contrasts.\n\n3) Miscellaneous
other utilities.","Imports":"MASS, Matrix","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"doBy","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"pbkrtest (>= 0.4-6), ggplot2, multcomp, geepack,
lme4,\nsurvival","Title":"Groupwise Statistics, LSmeans, Linear Contrasts,
Utilities","URL":"http:\/\/people.math.aau.dk\/~sorenh\/software\/doBy\/","Version"
:"4.5-15"},"doMPI":{"Author":"Steve Weston","Depends":"R (>= 2.14.0), foreach(>=
1.3.0), iterators(>= 1.0.0), Rmpi(>=\n0.5-7)","Description":"Provides a parallel
backend for the %dopar% function using\nthe Rmpi package.","Imports":"parallel,
compiler, utils","License":"GPL-
2","NeedsCompilation":"no","Package":"doMPI","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"randomForest, itertools","Title":"Foreach parallel
adaptor for the Rmpi package","Version":"0.2.1"},"doParallel":{"Author":"Rich
Calaway [cre],\nRevolution Analytics [aut, cph],\nSteve Weston [aut],\nDan
Tenenbaum [ctb]","Depends":"R (>= 2.14.0), foreach(>= 1.2.0), iterators(>=
1.0.0),\nparallel, utils","Description":"Provides a parallel backend for the %dopar
% function using\nthe parallel package.","Enhances":"compiler,
RUnit","License":"GPL-
2","NeedsCompilation":"no","Package":"doParallel","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"caret, mlbench, rpart","Title":"Foreach Parallel
Adaptor for the 'parallel' Package","Version":"1.0.10"},"doRNG":{"Author":"Renaud
Gaujoux","Depends":"R (>= 3.0.0), foreach, rngtools (>= 1.2.4)","Description":"This
package provides functions to perform\nreproducible parallel foreach loops, using
independent\nrandom streams as generated by L'Ecuyer's combined\nmultiple-recursive
generator [L'Ecuyer (1999)]. It\nenables to easily convert standard %dopar% loops
into\nfully reproducible loops, independently of the number\nof workers, the task
scheduling strategy, or the chosen\nparallel environment and associated foreach
backend.","Imports":"stats, iterators, pkgmaker (>= 0.20)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"doRNG","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"doParallel, doMPI, doRedis, rbenchmark, RUnit,
devtools,\nknitr, bibtex","Title":"Generic Reproducible Parallel Backend for
foreach
Loops","URL":"https:\/\/renozao.github.io\/doRNG","Version":"1.6"},"doRedis":
{"Author":"B. W. Lewis <blewis@illposed.net>","Depends":"R (>= 2.5), rredis (>=
1.6.8), foreach(>= 1.3.0), iterators(>=\n1.0.0), utils","Description":"A Redis
parallel backend for the %dopar% function","License":"GPL-
2","NeedsCompilation":"yes","Package":"doRedis","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"boot","Title":"Foreach parallel adapter for the rredis
package","Version":"1.1.1"},"doSNOW":{"Author":"Rich Calaway [cre],\nRevolution
Analytics [aut, cph],\nStephen Weston [aut]","Depends":"R (>= 2.5.0), foreach(>=
1.2.0), iterators(>= 1.0.0), snow(>=\n0.3.0), utils","Description":"Provides a
parallel backend for the %dopar% function using\nLuke Tierney's snow
2","NeedsCompilation":"no","Package":"doSNOW","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"compiler, RUnit, caret, mlbench, rpart","Title":"Foreach
Parallel Adaptor for the 'snow' Package","Version":"1.0.14"},"docopt":
{"Author":"Edwin de Jonge
(edwindjonge@gmail.com)","Depends":"methods","Description":"Define a command-line
interface by just giving it\na description in the specific
format.","Imports":"stringr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"docopt","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat","Title":"Command-Line Interface
Specification
Language","URL":"https:\/\/github.com\/docopt\/docopt.R","Version":"0.4.3.3"},"doco
pulae":{"Author":"Andreas Rappold [aut, cre]","Depends":"R (>=
3.1.2)","Description":"A direct approach to optimal designs for copula models based
on the Fisher information. Provides flexible functions for building joint PDFs,
evaluating the Fisher information and finding optimal designs. It includes an
extensible solution to summation and integration called 'nint', functions for
transforming, plotting and comparing designs, as well as a set of tools for common
low-level tasks.","Imports":"graphics, grDevices, methods, stats,
LICENSE","NeedsCompilation":"no","Package":"docopulae","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"copula, numDeriv, Deriv, cubature, SparseGrid,
mvtnorm,\ntestthat","Title":"Optimal Designs for Copula
Models","URL":"https:\/\/github.com\/arappold\/docopulae","Version":"0.3.2"},"docum
air":{"Author":"Jean-Baptiste Denis <Jean-Baptiste.Denis@jouy.inra.fr>, Regis
Pouillot <RPouillot@yahoo.fr>, Kien Kieu
<Kien.Kieu@jouy.inra.fr>","Description":"Production of R packages from tagged
comments introduced within the code\nand a minimum of additional documentation
files.","License":"GPL (>=
2.15)","NeedsCompilation":"yes","Package":"documair","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Automatic Documentation for R
packages","Version":"0.6-0"},"docxtractr":{"Author":"Bob Rudis [aut,
cre]","Depends":"R (>= 3.0.0)","Description":"Microsoft Word docx files provide an
XML structure that is fairly\nstraightforward to navigate, especially when it
applies to Word tables. The\ndocxtractr package provides tools to determine table
count\/structure and\nextract\/clean tables from Microsoft Word docx
documents.","Imports":"tools, xml2, dplyr, utils","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"docxtractr","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Extract Data Tables from
Microsoft Word Documents","Version":"0.1.0.9000"},"domino":{"Author":"Jacek Glodek
<jacek@theiterators.com>","Description":"A wrapper on top of the 'Domino Command-
Line Client'. It lets you run 'Domino' commands
(e.g., \"run\", \"upload\", \"download\") directly from your R environment. Under
the hood, it uses R's system function to run the 'Domino' executable, which must be
installed as a prerequisite. 'Domino' is a service that makes it easy to run your
code on scalable hardware, with integrated version control and collaboration
features designed for analytical workflows (see <http:\/\/www.dominoup.com> for
more information).","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"domino","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"R Console Bindings for the 'Domino Command-Line
Client'","URL":"http:\/\/www.dominoup.com\/","Version":"0.2-7"},"dosresmeta":
{"Author":"Alessio Crippa","Depends":"mvmeta, aod, Matrix","Description":"It
estimates a dose-response relation from either a single or\nmultiple summarized
data. The trend estimation takes into account the\ncorrelation among sets of log
relative risks and use it to efficiently\nestimate the dose-response relation. To
obtain a pooled functional\nrelation, the study-specific trends are combined
according to principles of\nmultivariate random-effects meta-
2","NeedsCompilation":"no","Package":"dosresmeta","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Performing Multivariate Dose-Response Meta-
Analysis","Version":"1.3.2"},"dostats":{"Author":"Andrew Redd
<Andrew.Redd@hsc.utah.edu>","Depends":"R (>= 2.12.0)","Description":"A small
package containing helper utilities for creating function\nfor computing
statistics.","Imports":"stats","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"dostats","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"plyr, testthat","Title":"Compute Statistics Helper
Functions","URL":"https:\/\/github.com\/halpo\/dostats","Version":"1.3.2"},"dotenv"
:{"Author":"Gabor Csardi [aut, cre, cph]","Description":"Load configuration from a
'.env' file, that is\nin the current working directory, into environment
variables.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"dotenv","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Load Environment Variables from
'.env'","URL":"https:\/\/github.com\/gaborcsardi\/dotenv","Version":"1.0.1"},"dotwh
isker":{"Author":"Frederick Solt <frederick-solt@uiowa.edu>, Yue Hu <yue-hu-
1@uiowa.edu>","Depends":"R (>= 3.2.0), ggplot2, gtable","Description":"Quick and
easy dot-and-whisker plots of regression results.","Imports":"grid, gridExtra,
stats, broom, plyr, dplyr, stringr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"dotwhisker","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"mfx, ordinal, knitr","Title":"Dot-and-Whisker
Plots of Regression Results","Version":"0.2.0.5"},"downloader":{"Author":"Winston
Chang <winston@stdout.org>","Description":"Provides a wrapper for the download.file
function,\nmaking it possible to download files over HTTPS on Windows, Mac OS X,
and\nother Unix-like platforms. The 'RCurl' package provides this
functionality\n(and much more) but can be difficult to install because it must be
compiled\nwith external dependencies. This package has no external dependencies,
so\nit is much easier to install.","Imports":"utils, digest","License":"GPL-
2","NeedsCompilation":"no","Package":"downloader","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat","Title":"Download Files over HTTP and
HTTPS","URL":"https:\/\/github.com\/wch\/downloader","Version":"0.4"},"downscale":
{"Author":"Charles Marsh [aut, cre]","Depends":"raster (>= 2.4-20), R (>=
3.0.0)","Description":"A set of functions that downscales species occupancy
at\ncoarse grain sizes to predict species occupancy at fine grain
sizes.","Imports":"cubature (>= 1.1-2), graphics, grDevices, methods,
minpack.lm\n(>= 1.1-9), Rmpfr (>= 0.5-7), sp (>= 1.2-0), stats","License":"GPL-
2","NeedsCompilation":"no","Package":"downscale","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"rgeos,
rgbif (>= 0.9.2),","Title":"Downscaling Species Occupancy","Version":"1.2-
1"},"dpa":{"Author":"Emile Chappin <e.j.l.chappin@tudelft.nl>","Depends":"R (>=
2.9.0), tcltk, sem, igraph","Description":"A GUI or command-line operated data
analysis tool, for\nanalyzing time-dependent simulation data in which
multiple\ninstantaneous or time-lagged relations are assumed. This\npackage uses
Structural Equation Modeling (the sem package). It\nis aimed to deal with time-
dependent data and estimate whether\na causal diagram fits data from an (agent-
based) simulation\nmodel.","License":"LGPL (>=
2.0)","NeedsCompilation":"no","Package":"dpa","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Dynamic Path Approach","URL":"http:\/\/www.chappin.com -
http:\/\/www.r-project.org","Version":"1.0-3"},"dpcR":{"Author":"Michal
Burdukiewicz [cre, aut],\nStefan Roediger [aut],\nBart Jacobs [aut],\nPiotr Sobczyk
[ctb]","Depends":"R (>= 3.0.0), methods","Description":"Analysis, visualisation and
simulation of digital polymerase chain\nreaction (dPCR).","Imports":"binom,
chipPCR, e1071, dgof, multcomp, qpcR, pracma,\nrateratio.test, readxl, signal,
shiny, spatstat","License":"GPL-
3","NeedsCompilation":"no","Package":"dpcR","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"DT, ggplot2, knitr, markdown, rmarkdown, shinythemes,
xtable","Title":"Digital PCR
Analysis","URL":"https:\/\/github.com\/michbur\/dpcR","Version":"0.3"},"dpglasso":
{"Author":"Rahul Mazumder and Trevor Hastie","Description":"fits the primal
graphical lasso, via one-at-a-time\nblock-coordinate descent.","License":"GPL-
2","NeedsCompilation":"yes","Package":"dpglasso","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Primal Graphical Lasso","Version":"1.0"},"dplR":
{"Author":"Andy Bunn [aut, cph, cre, trl], Mikko Korpela [aut, trl], Franco Biondi
[aut, cph], Filipe Campelo [aut, cph], Pierre MÃ©rian [aut, cph], Fares Qeadan
[aut, cph], Christian Zang [aut, cph], Allan Buras [ctb], Jacob Cecile [ctb],
Manfred Mudelsee [ctb], Michael Schulz [ctb]","Depends":"R (>=
2.15.2)","Description":"Perform tree-ring analyses such as detrending,
chronology\nbuilding, and cross dating. Read and write standard file formats\nused
in dendrochronology.","Imports":"graphics, grDevices, grid, stats, utils, lattice
(>= 0.13-6),\nMatrix (>= 1.0-3), digest (>= 0.2.3), gmp (>= 0.5-5),\nmatrixStats
(>= 0.50.0), png (>= 0.1-1), R.utils (>= 1.32.0),\nstringi (>= 0.2-2), stringr (>=
0.4), XML (>= 2.1-0)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"dplR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"Biobase, Cairo (>= 1.5-0), dichromat (>= 1.2-3),
foreach,\nforecast, iterators, knitr, RColorBrewer, testthat (>= 0.8),\ntikzDevice,
waveslim","Title":"Dendrochronology Program Library in R","URL":"http:\/\/R-
Forge.R-project.org\/projects\/dplr\/","Version":"1.6.4"},"dplRCon":
{"Author":"Maryann Pirie","Depends":"R (>= 2.10)","Description":"The concordance
method is a non-parametric method based on bootstrapping that is used to test the
hypothesis that two subsets of time series are similar in terms of mean, variance
or both. This method was developed to address a concern within dendroclimatology
that young trees may produce a differing climate response to older more established
trees. Details of this method are available in Pirie, M. (2013). The Climate of
New Zealand reconstructed from kauri tree rings: Enhancement through the use of
novel statistical methodology. PhD. Dissertation, School of Environment and
Department of Statistics, University of Auckland, New Zealand. This package also
produces a figure with 3 panels, each panel is for a different climate variable. An
example of this figure in included in \"On the influence of tree size on the
climate - growth relationship of New Zealand kauri (Agathis australis): insights
from annual, monthly and daily growth patterns. J Wunder, AM Fowler, ER Cook, M
Pirie, SPJ McCloskey. Trees 27 (4), 937-948\". For further R functions for loading
your own dendroclimatology datasets and performing dendrochronology analysis refer
to the R package \"dplR: Dendrochronology Program Library in R\". The concordance
procedure is intended to add to the standard dendrochronology techniques provided
in \"dplR\".","License":"GPL","NeedsCompilation":"no","Package":"dplRCon","Reposito
ry":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Concordance for
Dendroclimatology","Version":"1.0"},"dplyr":{"Author":"Hadley Wickham [aut,
cre],\nRomain Francois [aut],\nRStudio [cph]","Depends":"R (>=
3.1.2)","Description":"A fast, consistent tool for working with data frame like
objects,\nboth in memory and out of memory.","Imports":"assertthat, utils, R6,
Rcpp, magrittr, lazyeval (>= 0.1.10),\nDBI (>= 0.3)","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"dplyr","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"RSQLite (>= 1.0.0), RMySQL, RPostgreSQL,
data.table,\ntestthat, knitr, microbenchmark, ggplot2, mgcv, Lahman (>=\n3.0-1),
nycflights13, methods","Title":"A Grammar of Data
Manipulation","URL":"https:\/\/github.com\/hadley\/dplyr","Version":"0.4.3"},"dpmix
sim":{"Author":"Adelino Ferreira da Silva <afs@fct.unl.pt>","Depends":"R (>=
2.10.0), oro.nifti, cluster","Description":"The package implements a Dirichlet
Process Mixture (DPM)\nmodel for clustering and image segmentation. The DPM model
is\na Bayesian nonparametric methodology that relies on MCMC\nsimulations for
exploring mixture models with an unknown number\nof components. The code
implements conjugate models with\nnormal structure (conjugate normal-normal DP
mixture model).\nThe package's applications are oriented towards
the\nclassification of magnetic resonance images according to tissue\ntype or
region of interest.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"dpmixsim","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Dirichlet Process Mixture model simulation for
clustering and\nimage segmentation","Version":"0.0-8"},"dpmr":
{"Author":"Christopher Gandrud [aut, cre],\nYann-Ael Le Borgne
[ctb]","Description":"Create, install, and summarise data packages that follow\nthe
Open Knowledge Foundation's Data Package Protocol.","Imports":"digest, httr,
jsonlite, magrittr, rio","License":"GPL-
3","NeedsCompilation":"no","Package":"dpmr","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"devtools, testthat","Title":"Data Package Manager for
R","URL":"http:\/\/cran.r-project.org\/package=dpmr","Version":"0.1.9"},"dprep":
{"Author":"Edgar Acuna and the CASTLE research group at The University of Puerto
Rico-Mayaguez","Depends":"R (>= 3.1.0), graphics, stats","Description":"Data
preprocessing techniques for classification. Functions for normalization, handling
of missing values,discretization, outlier detection, feature selection, and data
visualization are included.","Imports":"MASS, e1071, class, nnet, rpart, FNN,
StatMatch, rgl,
methods","License":"GPL","NeedsCompilation":"yes","Package":"dprep","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Title":"Data Pre-Processing and Visualization
Functions for\nClassification","Version":"3.0.2"},"dr":{"Author":"Sanford Weisberg
<sandy@umn.edu>,","Depends":"MASS","Description":"Functions, methods, and datasets
for fitting dimension\nreduction regression, using slicing (methods SAVE and SIR),
Principal\nHessian Directions (phd, using residuals and the response), and
an\niterative IRE. Partial methods, that condition on categorical\npredictors are
also available. A variety of tests, and stepwise\ndeletion of predictors, is also
included. Also included is\ncode for computing permutation tests of dimension.
Adding additional\nmethods of estimating dimension is straightforward.\nFor
documentation, see the vignette in the package. With version 3.0.4,\nthe
arguments for dr.step have been
modified.","Imports":"stats,graphics","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"dr","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Methods for Dimension Reduction for
Regression","URL":"https:\/\/cran.r-
project.org\/package=dr","Version":"3.0.10"},"drLumi":{"Author":"Hector Sanz [aut,
cre],\nJohn Aponte [aut],\nJaroslaw Harezlak [aut],\nYan Dong [aut],\nMagdalena
Murawska [aut],\nClarissa Valim [aut],\nAintzane Ayestaran [ctb],\nRuth Aguilar
[ctb],\nGemma Moncunill [ctb]","Depends":"R (>= 3.2.2)","Description":"Contains
quality control routines for multiplex immunoassay data,\nincluding several
approaches for: treating the background noise of the assay,\nfitting the dose-
response curves and estimating the limits of quantification.","Imports":"reshape,
Hmisc, chron, gdata, plyr, stringr, ggplot2,\nminpack.lm, stats, irr, rootSolve,
msm","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"drLumi","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr, testthat, xtable","Title":"Multiplex
Immunoassays Data Analysis","Version":"0.1.2"},"drat":{"Author":"Dirk Eddelbuettel
with contributions by Carl Boettiger, Sebastian\nGibb, Colin Gillespie, Matt Jones,
Thomas Leeper, Steven Pav and Jan Schulz.","Description":"Creation and Use of R
Repositories via two helper functions\nto insert packages into a repository, and to
add repository information\nto the current R session. Two primary types of
repositories are support:\ngh-pages at GitHub, as well as local repositories on
either the same machine\nor a local network. Drat is a recursive acronym: Drat R
Archive Template.","Imports":"utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"drat","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"git2r, knitr","Title":"Drat R Archive
Template","Version":"0.1.0"},"drawExpression":{"Author":"Sylvain
Loiseau","Depends":"R (>= 2.9.0), grid","Description":"Graphical display of R
expression, showing the\ninterpretation of an expression
by R and the various kind of R\ndata structure. The steps of the interpretation of
an\nexpression are obtained through the parsed
tree.","License":"BSD","NeedsCompilation":"no","Package":"drawExpression","Reposito
ry":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Visualising R syntax through
graphics","Version":"1.0"},"drc":{"Author":"Christian Ritz <ritz@bioassay.dk>, Jens
C. Strebig <streibig@bioassay.dk>","Depends":"R (>= 2.0.0), MASS,
stats","Description":"Analysis of dose-response data is made available through a
suite of flexible and versatile model fitting and after-fitting
functions.","Imports":"car, gtools, multcomp, plotrix, scales","License":"GPL-2 |
file
LICENCE","NeedsCompilation":"no","Package":"drc","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Analysis of Dose-Response Curves","URL":"http:\/\/www.r-
project.org, http:\/\/www.bioassay.dk","Version":"2.5-12"},"drfit":
{"Author":"Johannes Ranke [aut, cre]","Description":"A somewhat outdated package of
basic and easy-to-use functions for\nfitting dose-response curves to continuous
dose-response data, calculating some\n(eco)toxicological parameters and plotting
the results. Please consider using\nthe more powerful and actively developed 'drc'
package. Functions that are\nfitted are the cumulative density function of the
lognormal distribution\n(probit fit), of the logistic distribution (logit fit), of
the weibull\ndistribution (weibull fit) and a linear-logistic model (\"linlogit\"
fit),\nderived from the latter, which is used to describe data showing stimulation
at\nlow doses (hormesis). In addition, functions checking, plotting and
retrieving\ndose-response data retrieved from a database accessed via RODBC are
included.\nAs an alternative to the original fitting methods, the algorithms from
the drc\npackage can be used.","Imports":"graphics, grDevices, MASS,
drc","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"drfit","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"RODBC","Title":"Dose-Response Data
Evaluation","URL":"http:\/\/www.r-project.org,\nhttp:\/\/www.uft.uni-
bremen.de\/chemie\/ranke?
page=drfit,\nhttp:\/\/cgit.jrwb.de\/drfit\/","Version":"0.6.4"},"drgee":
{"Author":"Johan Zetterqvist <johan.zetterqvist@ki.se> , Arvid SjÃ¶lander
<arvid.sjolander@ki.se> with contributions from Alexander
Ploner.","Depends":"stats, nleqslv, survival, R (>= 3.0.0), Rcpp,
data.table","Description":"Fit restricted mean models for the conditional
association\nbetween an exposure and an outcome, given covariates. Three
methods\nare implemented: O-estimation, where a nuisance model for the\nassociation
between the covariates and the outcome is used;\nE-estimation where a nuisance
model for the association\nbetween the covariates and the exposure is used, and
doubly robust (DR)\nestimation where both nuisance models are used. In DR-
estimation,\nthe estimates will be consistent when at least one of the
nuisance\nmodels is correctly specified, not necessarily both.","License":"GPL-2 |
GPL-
3","NeedsCompilation":"yes","Package":"drgee","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Doubly Robust Generalized Estimating
Equations","Version":"1.1.4"},"drm":{"Author":"Jukka Jokinen
<jukka.jokinen@helsinki.fi>","Depends":"R(>= 1.0)","Description":"Likelihood-based
marginal regression and association\nmodelling for repeated, or otherwise
clustered, categorical\nresponses using dependence ratio as a measure of
the\nassociation","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"drm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Regression and association models for repeated categorical
data","URL":"http:\/\/www.helsinki.fi\/~jtjokine\/drm","Version":"0.5-8"},"drmdel":
{"Author":"Song Cai","Depends":"R (>= 2.11)","Description":"Dual empirical
likelihood (DEL) inference under semiparametric density ratio models (DRM) in the
presence of multiple samples, including population cumulative distribution function
estimation, quantile estimation and comparison, density estimation, composite
hypothesis testing for DRM parameters which encompasses testing for changes in
population distribution functions as a special case, etc.","License":"GPL-
3","NeedsCompilation":"yes","Package":"drmdel","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Dual Empirical Likelihood Inference under Density Ratio
Models\nin the Presence of Multiple Samples","Version":"1.3.1"},"dropR":
{"Author":"Matthias Bannert [aut, cre], Ulf-Dietrich Reips [aut]","Depends":"R (>=
3.0.0)","Description":"Drop out analysis for psychologists in a R based web
application.\nShiny is used to visualize and analyze drop outs tailored to the
methods of\nonline survey methodology. Concept and app presented at the SCIP
Conference\nin Long Beach, California.","Imports":"plyr,shiny","License":"GPL-
2","NeedsCompilation":"no","Package":"dropR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Analyze Drop Out of an Experiment or
Survey","Version":"0.1"},"drsmooth":{"Author":"Greg Hixon [aut],\nChad Thompson
[aut],\nAnne Bichteler [aut, cre],\nLiz Abraham [ctb]","Depends":"R (>=
3.0.1)","Description":"Provides tools for assessing the shape of a dose-
response\ncurve by testing linearity and non-linearity at user-defined cut-offs.
It\nalso provides two methods of estimating a threshold dose, or the dose at\nwhich
the dose-response function transitions to significantly increasing:\nbi-linear
(based on pkg 'segmented') and smoothed with splines (based on\npkg
'mgcv').","Imports":"boot, car, mgcv, multcomp, DTK, segmented,
lubridate,\npgirmess, stats","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"drsmooth","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat","Title":"Dose-Response Modeling with
Smoothing Splines","Version":"1.9.0"},"ds":{"Author":"Emmanuel
Arnhold","Description":"The package performs various analyzes of descriptive
statistics, including correlations","License":"GPL-
2","NeedsCompilation":"no","Package":"ds","Repository":"http:\/\/cran.csiro.au\/src
\/contrib","Title":"Descriptive Statistics","Version":"3.0"},"dsample":
{"Author":"Chel Hee Lee [aut, cre],\nLiqun Wang [aut]","Depends":"R (>=
2.7.0)","Description":"Two discretization-based Monte Carlo algorithms, namely the
Fu-Wang algorithm and the Wang-Lee algorithm, are provided for random sample
generation from a high dimensional distribution of complex structure. The
normalizing constant of the target distribution needs not to be
known.","Imports":"stats, graphics, MASS","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"dsample","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Discretization-Based Direct Random Sample
Generation","URL":"https:\/\/r-forge.r-
project.org\/projects\/wanglee\/","Version":"0.91.2.2"},"dse":{"Author":"Paul
Gilbert <pgilbert.ttv9z@ncf.ca>","Depends":"R (>= 2.5.0),
tfplot","Description":"Tools for multivariate, linear, time-invariant,\ntime series
models. This includes ARMA and state-space representations,\nand methods for
converting between them. It also includes simulation\nmethods and several
estimation functions. The package has functions\nfor looking at model roots,
stability, and forecasts at different\nhorizons. The ARMA model representation is
general, so that VAR, VARX,\nARIMA, ARMAX, ARIMAX can all be considered to be
special cases. Kalman\nfilter and smoother estimates can be obtained from the state
space\nmodel, and state-space model reduction techniques are implemented.\nAn
introduction and User's Guide is available in a vignette.","Imports":"tframe (>=
2007.5-3), stats, utils, graphics, grDevices,\nsetRNG (>= 2004.4-
1)","License":"GPL-
2","NeedsCompilation":"yes","Package":"dse","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Dynamic Systems Estimation (Time Series
Package)","URL":"http:\/\/tsanalysis.r-forge.r-project.org\/","Version":"2015.12-
1"},"dslice":{"Author":"Chao Ye and Bo Jiang","Depends":"R (>= 2.10), stats, utils,
Rcpp (>= 0.11.1), ggplot2 (>=\n0.9.3.1), scales","Description":"Dynamic slicing is
a method designed for dependency detection between a categorical variable and a
continuous variable. It could be applied for non-parametric hypothesis testing and
gene set enrichment analysis.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"dslice","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Dynamic Slicing","Version":"1.1.5"},"dsm":
{"Author":"David L. Miller, Eric Rexstad, Louise Burt, Mark V. Bravington,\nSharon
Hedley.","Depends":"R (>= 3.0), mgcv (>= 1.7), mrds (>=
2.1.8)","Description":"Density surface modelling of line transect data. A
Generalized Additive Model-based approach is used to calculate spatially-explicit
estimates of animal abundance from distance sampling (also presence\/absence and
strip transect) data. Several utility functions are provided for model checking,
plotting and variance estimation.","Imports":"nlme, ggplot2,
statmod","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"dsm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"Distance, tweedie","Title":"Density Surface Modelling of
Distance Sampling
Data","URL":"http:\/\/github.com\/DistanceDevelopment\/dsm","Version":"2.2.9"},"dst
":{"Author":"Claude Boivin, Stat.ASSQ <webapp.cb@gmail.com>","Description":"This
package allows you to make basic probability assignments on a set of\npossibilities
(events) and combine these events with Dempster's rule of
combination.","License":"GPL-
2","NeedsCompilation":"no","Package":"dst","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Using Dempster-Shafer Theory","Version":"0.3"},"dti":
{"Author":"Karsten Tabelow [aut, cre],\nJoerg Polzehl [aut],\nFelix Anker
[ctb]","Depends":"R (>= 3.1.0), awsMethods (>= 1.0-1), adimpro,
rgl","Description":"Diffusion Weighted Imaging (DWI) is a Magnetic Resonance
Imaging\nmodality,
that measures diffusion of water in tissues like the human\nbrain. The package
contains R-functions to process diffusion-weighted\ndata. The functionality
includes diffusion tensor imaging (DTI),\ndiffusion kurtosis imaging (DKI),
modeling for high angular resolution\ndiffusion weighted imaging (HARDI) using Q-
ball-reconstruction and\ntensor mixture models, several methods for structural
adaptive\nsmoothing including POAS and msPOAS, and a streamline fiber tracking\nfor
tensor and tensor mixture models.\nThe package provides functionality to manipulate
and visualize results\nin 2D and 3D.","Imports":"methods, parallel, oro.nifti (>=
0.3.9), oro.dicom, gsl,\nquadprog","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"dti","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Analysis of Diffusion Weighted Imaging (DWI)
Data","URL":"http:\/\/www.wias-berlin.de\/research\/ats\/imaging\/","Version":"1.2-
4.1"},"dtt":{"Author":"Lukasz Komsta","Description":"This package provides
functions for 1D and 2D Discrete\nCosine Transform (DCT), Discrete Sine Transform
(DST) and\nDiscrete Hartley Transform (DHT).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"dtt","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Discrete Trigonometric Transforms","URL":"http:\/\/www.r-
project.org, http:\/\/www.komsta.net\/","Version":"0.1-2"},"dtw":{"Author":"Toni
Giorgino <toni.giorgino@gmail.com>,","Depends":"R (>= 2.10.0),
proxy","Description":"A comprehensive implementation of dynamic time warping (DTW)
algorithms in R. DTW computes the optimal (least cumulative distance) alignment
between points of two time series. Common DTW variants covered include local
(slope) and global (window) constraints, subsequence matches, arbitrary distance
definitions, normalizations, minimum variance matching, and so on. Provides
cumulative distances, alignments, specialized plot styles,
etc.","Imports":"graphics, grDevices, stats, utils","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"dtw","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Dynamic Time Warping Algorithms","URL":"http:\/\/dtw.r-
forge.r-project.org\/","Version":"1.18-1"},"dtwSat":{"Author":"Victor Maus [aut,
cre]","Depends":"R (>= 3.0.0), methods, dtw, zoo","Description":"\nProvides a Time-
Weighted Dynamic Time Warping (TWDTW) algorithm to measure similarity between two
temporal sequences. This adaptation of the classical Dynamic Time Warping (DTW)
algorithm is flexible to compare events that have a strong time dependency, such as
phenological stages of cropland systems and tropical forests. This package provides
methods for visualization of minimum cost paths, time series alignment, and time
intervals classification.","Imports":"proxy, waveslim, graphics, ggplot2, scales,
reshape2,\ngrDevices, utils","License":"GPL (>= 2) | file
LICENSE","NeedsCompilation":"no","Package":"dtwSat","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat","Title":"Time-Weighted Dynamic Time
Warping for Remote Sensing Time\nSeries Analysis","Version":"0.1.0"},"dtwclust":
{"Author":"Alexis Sarda-Espinosa","Depends":"R (>= 3.2.0), proxy, dtw, ggplot2,
rngtools","Description":"Time series clustering along with optimized techniques
related\nto the Dynamic Time Warping distance and its corresponding lower
bounds.\nImplementations of k-Shape, TADPole and fuzzy clustering are
available.\nThe functionality can be easily extended with custom distance
measures\nand centroid definitions.","Imports":"stats, utils, methods, flexclust,
caTools, reshape2, foreach,\nparallel","License":"GPL-
3","NeedsCompilation":"yes","Package":"dtwclust","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"TSdist, TSclust, doParallel, testthat","Title":"Time
Series Clustering Along with Optimizations for the Dynamic\nTime Warping
Distance","URL":"https:\/\/github.com\/asardaes\/dtwclust","Version":"2.1.1"},"dual
Scale":{"Author":"Jose G. Clavel, Shizuiko Nishisato and Antonio
Pita","Depends":"matrixcalc, ff, vcd, lattice, Matrix","Description":"Functions to
analyze multiple choice data using Dual Scaling","License":"GPL-
2","NeedsCompilation":"no","Package":"dualScale","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Dual Scaling Analysis of Multiple Choice
Data","Version":"0.9.1"},"dummies":{"Author":"Christopher
Brown","Depends":"utils","Description":"Expands factors, characters and other
eligible classes\ninto dummy\/indicator variables.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"dummies","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Create dummy\/indicator variables flexibly and
efficiently","URL":"http:\/\/www.decisionpatterns.com","Version":"1.5.6"},"dummy":
{"Author":"Michel Ballings and Dirk Van den Poel","Description":"Efficiently create
dummies of all factors and character vectors in a data frame. Support is included
for learning the categories on one data set (e.g., a training set) and deploying
them on another (e.g., a test set).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"dummy","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Automatic Creation of Dummies with Support for
Predictive\nModeling","Version":"0.1.3"},"dunn.test":{"Author":"Alexis Dinno
<alexis.dinno@pdx.edu>","Description":"Computes Dunn's test (1964) for stochastic
dominance and reports the results among multiple pairwise comparisons after a
Kruskal-Wallis test for stochastic dominance among k groups (Kruskal and Wallis,
1952). The interpretation of stochastic dominance requires an assumption that the
CDF of one group does not cross the CDF of the other. 'dunn.test' makes k(k-1)\/2
multiple pairwise comparisons based on Dunn's z-test-statistic approximations to
the actual rank statistics. The null hypothesis for each pairwise comparison is
that the probability of observing a randomly selected value from the first group
that is larger than a randomly selected value from the second group equals one
half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-
sum test. Like the rank-sum test, if the data can be assumed to be continuous, and
the distributions are assumed identical except for a difference in location, Dunn's
test may be understood as a test for median difference. 'dunn.test' accounts for
tied ranks.","License":"GPL-
2","NeedsCompilation":"no","Package":"dunn.test","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Dunn's Test of Multiple Comparisons Using Rank
Sums","Version":"1.3.2"},"dupiR":{"Author":"Federico Comoglio and Maurizio
Rinaldi","Depends":"R (>= 2.15.1), methods, plotrix","Description":"Inference of
population sizes using a binomial likelihood and least informative discrete uniform
priors.","License":"GPL-
2","NeedsCompilation":"no","Package":"dupiR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Bayesian inference from count data using discrete uniform
priors","Version":"1.2"},"dvfBm":{"Author":"Jean-Francois
Coeurjolly","Depends":"wmtsa","Description":"Hurst exponent estimation of a
fractional Brownian motion\nby using discrete variations methods in presence of
outliers\nand\/or an additive noise","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"dvfBm","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Discrete variations of a fractional Brownian
motion","Version":"1.0"},"dvn":{"Author":"Thomas J. Leeper","Description":"Provides
access to The Dataverse Network APIs via the RCurl package, enabling access to
archived data (and metadata), and the ability to create and manipulate studies in a
user's dataverse(s).","Imports":"RCurl, XML","License":"GPL-
2","NeedsCompilation":"no","Package":"dvn","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Access to The Dataverse Network
APIs","URL":"https:\/\/github.com\/leeper\/dvn","Version":"0.3.3"},"dygraphs":
{"Author":"Dan Vanderkam [aut, cph] (dygraphs library in
htmlwidgets\/lib,\nhttp:\/\/dygraphs.com\/),\nJJ Allaire [aut, cre] (R
interface),\nRStudio [cph],\nJonathan Owen [aut, cph],\nDaniel Gromer [aut,
cph],\nPetr Shevtsov [aut, cph],\nBenoit Thieurmel [aut, cph],\njQuery Foundation
[cph] (jQuery library),\njQuery contributors [ctb, cph] (jQuery library; authors
listed in\ninst\/htmlwidgets\/lib\/jquery\/AUTHORS.txt)","Depends":"R (>=
3.0)","Description":"An R interface to the 'dygraphs' JavaScript charting
library\n(a copy of which is included in the package). Provides rich
facilities\nfor charting time-series data in R, including highly
configurable\nseries- and axis-display and interactive features like zoom\/pan
and\nseries\/point highlighting.","Enhances":"rmarkdown (>= 0.3.3), shiny (>=
0.10.2.1)","Imports":"magrittr, htmlwidgets (>= 0.3.2), zoo (>= 1.7-10), xts
(>=\n0.9-7)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"dygraphs","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat","Title":"Interface to 'Dygraphs'
Interactive Time Series Charting Library","Version":"0.8"},"dyn":{"Author":"G.
Grothendieck","Depends":"R (>= 2.6.0), zoo (>= 1.0-0)","Description":"Time series
regression. The dyn class interfaces ts,\nirts, its, zoo and zooreg time series
classes to lm, glm,\nloess, quantreg::rq, MASS::rlm,
MCMCpack::MCMCregress,\nquantreg::rq, randomForest::randomForest and other
regression\nfunctions allowing those functions to be used with time
series\nincluding specifications that may contain lags, diffs and\nmissing
values.","License":"GPL","NeedsCompilation":"no","Package":"dyn","Repository":"http
:\/\/cran.csiro.au\/src\/contrib","Suggests":"its (>= 1.0.9), lattice, MASS,
MCMCpack, quantreg (>= 3.82),\nrandomForest, sandwich, tseries","Title":"Time
Series Regression","Version":"0.2-9"},"dynBiplotGUI":{"Author":"Jaime Egido [aut,
cre]","Depends":"R (>= 2.15.0)","Description":"A GUI to solve dynamic biplots and
classical
biplot. Try matrices of 2-way and 3-way. The GUI can be run in multiple
languages.","Imports":"tcltk, tcltk2 (>= 1.2-10), tkrplot (>= 0.0-
2)","NeedsCompilation":"no","Package":"dynBiplotGUI","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"foreign (>= 0.8-61), xlsx (>=
0.5.7)","Title":"Full Interactive GUI for Dynamic Biplot in
R","Version":"1.1.3"},"dynCorr":{"Author":"Joel Dubin, Dandi Qiao, Hans-Georg
Mueller.","Depends":"lpridge","Description":"Computes dynamical correlation
estimates and percentile\nbootstrap confidence intervals for pairs of
longitudinal\nresponses, including consideration of lags and
derivatives.","License":"GPL-
2","NeedsCompilation":"no","Package":"dynCorr","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Dynamic Correlation Package","Version":"0.1-2"},"dynRB":
{"Author":"Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at>,\nWolfgang
Trutschnig <Wolfgang.Trutschnig@sbg.ac.at>,\nRobert R. Junker
<Robert.Junker@sbg.ac.at>,\nJonas Kuppler <Jonas.Kuppler@uni-duesseldorf.de>,\nArne
Bathke <Arne.Bathke@sbg.ac.at>","Description":"Improves the concept of multivariate
range boxes, which is highly susceptible for outliers and does not consider the
distribution of the data. The package uses dynamic range boxes to overcome these
problems.","Imports":"caTools, corrplot","License":"GPL-
2","NeedsCompilation":"no","Package":"dynRB","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat","Title":"Dynamic Range
Boxes","URL":"http:\/\/www.r-project.org","Version":"0.7"},"dynaTree":
{"Author":"Robert B. Gramacy <rbgramacy@chicagobooth.edu> and Matt A. Taddy
<taddy@chicagobooth.edu>","Depends":"R (>= 2.14.0),
methods","Description":"Inference by sequential Monte Carlo for\ndynamic tree
regression and classification models\nwith hooks provided for sequential design and
optimization,\nfully online learning with drift, variable selection,
and\nsensitivity analysis of inputs. Illustrative\nexamples from the original
dynamic trees paper are facilitated\nby demos in the package; see
demo(package=\"dynaTree\")","License":"LGPL","NeedsCompilation":"yes","Package":"dy
naTree","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"akima, tgp,
plgp, MASS","Title":"Dynamic trees for learning and
design","URL":"http:\/\/faculty.chicagobooth.edu\/robert.gramacy\/dynaTree.html","V
ersion":"1.2-7"},"dynamicGraph":{"Author":"Jens Henrik Badsberg
<coco@badsberg.eu>","Depends":"R (>= 1.8.1), methods, ggm,
tcltk","Description":"Interactive graphical tool for manipulating
graphs","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"dynamicGraph","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"dynamicGraph","URL":"http:\/\/www.badsberg.eu","Vers
ion":"0.2.2.6"},"dynamicTreeCut":{"Author":"Peter Langfelder
<Peter.Langfelder@gmail.com> and Bin Zhang <binzhang.ucla@gmail.com>,\nwith
contributions from Steve Horvath <SHorvath@mednet.ucla.edu>","Depends":"R (>=
2.3.0), stats","Description":"Contains methods for detection of clusters in
hierarchical clustering dendrograms.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"dynamicTreeCut","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Methods for Detection of Clusters in Hierarchical
Clustering\nDendrograms","URL":"\nhttp:\/\/www.genetics.ucla.edu\/labs\/horvath\/Co
expressionNetwork\/BranchCutting\/","Version":"1.63-1"},"dynatopmodel":
{"Author":"Peter Metcalfe, Keith Beven and Jim Freer","Depends":"R (>=
2.10),","Description":"A native R implementation and enhancement of the Dynamic
TOPMODEL\nsemi-distributed hydrological model. Includes some pre-processsing
and\noutput routines.","Imports":"deSolve, rgeos, maptools, rgdal, zoo, xts, sp,
raster,\nlubridate, topmodel, methods, grDevices, stats, utils,\ngraphics,
2","NeedsCompilation":"no","Package":"dynatopmodel","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Implementation of the Dynamic TOPMODEL Hydrological
Model","Version":"1.1"},"dynia":{"Author":"Jinkun Xiao and A.I.
McLeod","Depends":"R (>= 2.0.0)","Description":"Fit dynamic intervention model
using the arima() function.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"dynia","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Fit Dynamic Intervention
Model","URL":"http:\/\/www.stats.uwo.ca\/faculty\/aim","Version":"0.2"},"dynlm":
{"Author":"Achim Zeileis [aut, cre]","Depends":"R (>= 2.10.0),
zoo","Description":"Dynamic linear models and time series
regression.","Imports":"stats, car (>= 2.0-0), lmtest","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"dynlm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"datasets, sandwich, strucchange, TSA","Title":"Dynamic
Linear Regression","Version":"0.3-3"},"dynpred":{"Author":"Hein
Putter","Depends":"survival","Description":"The dynpred package contains functions
for dynamic prediction in survival analysis.","Imports":"graphics, stats,
2)","NeedsCompilation":"yes","Package":"dynpred","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"mstate","Title":"Companion Package to \"Dynamic
Prediction in Clinical
Survival\nAnalysis\"","URL":"http:\/\/www.msbi.nl\/putter","Version":"0.1.2"},"dyns
im":{"Author":"Christopher Gandrud [aut, cre],\nLaron K. Williams [aut],\nGuy D.
Whitten [aut]","Depends":"R (>= 3.0.0)","Description":"Dynamic simulations and
graphical depictions of autoregressive\nrelationships.","Imports":"ggplot2 (>=
1.0.1.9003), grid, gridExtra (>= 2.0.0), MASS","License":"GPL-
3","NeedsCompilation":"no","Package":"dynsim","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"DataCombine, knitr","Title":"Dynamic Simulations of
Autoregressive Relationships","URL":"http:\/\/cran.r-
project.org\/package=dynsim","Version":"1.2.1"},"dynsurv":{"Author":"Xiaojing Wang
<wangxj03@gmail.com>,\nJun Yan <jun.yan@uconn.edu>, and\nMing-Hui Chen <ming-
hui.chen@uconn.edu>","Depends":"R (>= 3.0.2), survival","Description":"Functions to
fit time-varying coefficient models for interval\ncensored and right censored
survival data. Three major\napproaches are implemented: 1) Bayesian Cox model
with\ntime-independent, time-varying or dynamic coefficients for\nright censored
and interval censored data; 2) Spline based\ntime-varying coefficient Cox model for
right censored data;\n3) Transformation model with time-varying coefficients
for\nright censored data using estimating equations.","Imports":"methods, reshape,
plyr, nleqslv, ggplot2, grid","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"dynsurv","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Dynamic models for survival data","Version":"0.2-
2"},"e1071":{"Author":"David Meyer [aut, cre],\nEvgenia Dimitriadou [aut,
cph],\nKurt Hornik [aut],\nAndreas Weingessel [aut],\nFriedrich Leisch
[aut],\nChih-Chung Chang [ctb, cph] (libsvm C++-code),\nChih-Chen Lin [ctb, cph]
(libsvm C++-code)","Description":"Functions for latent class analysis, short time
Fourier\ntransform, fuzzy clustering, support vector machines,\nshortest path
computation, bagged clustering, naive Bayes\nclassifier, ...","Imports":"graphics,
grDevices, class, stats, methods, utils","License":"GPL-
2","NeedsCompilation":"yes","Package":"e1071","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"cluster, mlbench, nnet, randomForest, rpart, SparseM,
xtable,\nMatrix, MASS","Title":"Misc Functions of the Department of Statistics,
Probability\nTheory Group (Formerly: E1071), TU Wien","Version":"1.6-7"},"eHOF":
{"Author":"Florian Jansen, Jari Oksanen","Depends":"R (>= 2.5.0), mgcv,
lattice","Description":"Extended and enhanced hierarchical logistic regression
models (called Huisman-Olff-Fresco in biology, see Huisman eta l. 1993 JVS) models.
Response curves along one-dimensional gradients including no response, monotone,
plateau, unimodal and bimodal models.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"eHOF","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"vegdata, vegan, knitr, testthat","Title":"Extended HOF
(Huisman-Olff-Fresco) Models","Version":"1.7"},"eRm":{"Author":"Patrick Mair [cre,
aut],\nReinhold Hatzinger [aut],\nMarco J. Maier [aut],\nThomas Rusch
[ctb]","Depends":"R (>= 3.0.0)","Description":"The eRm package fits Rasch models
(RM), linear logistic test models (LLTM), rating scale model (RSM), linear rating
scale models (LRSM), partial credit models (PCM), and linear partial credit models
(LPCM). Missing values are allowed in the data matrix. Additional features are
the ML estimation of the person parameters, Andersen's LR-test, item-specific Wald
test, Martin-LÃ¶f-Test, nonparametric Monte-Carlo Tests, itemfit and personfit
statistics including infit and outfit measures, various ICC and related plots,
automated stepwise item elimination, simulation module for various binary data
matrices. An eRm platform is provided at R-forge (see URL).","Imports":"graphics,
grDevices, stats, methods, MASS, splines, Matrix,\nlattice","License":"GPL-
2","NeedsCompilation":"yes","Package":"eRm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Extended Rasch Modeling","URL":"http:\/\/r-forge.r-
project.org\/projects\/erm\/","Version":"0.15-6"},"eVenn":{"Author":"Nicolas
Cagnard","Depends":"R (>= 2.10)","Description":"Compare lists (from 2 to infinite)
and plot the results in a Venn diagram if (N<=4) with regulation details. It allows
to produce a complete annotated file, merging the annotations of the compared
lists. It is also possible to compute an overlaps table to show the overlaps
proportions of all the couples of lists and draw proportional Venn
diagrams.","Imports":"grDevices, graphics, stats,
utils","License":"GPL","NeedsCompilation":"no","Package":"eVenn","Repository":"http
:\/\/cran.csiro.au\/src\/contrib","Title":"A Powerful Tool to Quickly
Compare Huge Lists and Draw Venn\nDiagrams","Version":"2.3"},"eaf":
{"Author":"Carlos Fonseca, Luis Paquete, Thomas StÃ¼tzle, Manuel LÃ³pez-IbÃ¡Ã±ez
and Marco Chiarandini.","Depends":"R (>= 2.10.0)","Description":"Plots of the
empirical attainment function for two
objectives.","Imports":"modeltools","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"eaf","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Plots of the Empirical Attainment
Function","URL":"http:\/\/iridia.ulb.ac.be\/~manuel\/eaftools","Version":"1.07"},"e
arlywarnings":{"Author":"Vasilis Dakos <vasilis.dakos@gmail.com>, with
contributions from S.R.\nCarpenter, T. Cline, L. Lahti","Depends":"R (>= 3.0.2),
ggplot2, moments, tgp, tseries","Description":"The Early-Warning-Signals Toolbox
provides methods for estimating\nstatistical changes in timeseries that can be used
for identifying nearby\ncritical transitions. Based on Dakos et al (2012) Methods
for Detecting\nEarly Warnings of Critical Transitions in Time Series Illustrated
Using\nSimulated Ecological Data. PLoS ONE 7(7):e41010","Imports":"fields, nortest,
quadprog, Kendall, KernSmooth, lmtest, som,\nspam,
stats","License":"FreeBSD","NeedsCompilation":"no","Package":"earlywarnings","Repos
itory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Early Warning Signals
Toolbox for Detecting Critical Transitions\nin
Timeseries","URL":"http:\/\/www.early-warning-
signals.org,\nhttp:\/\/vasilisdakos.wordpress.com","Version":"1.0.59"},"earth":
{"Author":"Stephen Milborrow. Derived from mda:mars by Trevor Hastie and\nRob
Tibshirani. Uses Alan Miller's Fortran utilities\nwith Thomas Lumley's leaps
wrapper.","Depends":"plotmo (>= 3.0.0), TeachingDemos","Description":"Build
regression models using the techniques in Friedman's\npapers \"Fast MARS\"
and \"Multivariate Adaptive Regression\nSplines\". (The term \"MARS\" is
trademarked and thus not used in\nthe name of the package.)","License":"GPL-
3","NeedsCompilation":"yes","Package":"earth","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"gam, mgcv, mda, MASS","Title":"Multivariate Adaptive
Regression
Splines","URL":"http:\/\/www.milbo.users.sonic.net\/earth","Version":"4.4.4"},"easy
PubMed":{"Author":"Damiano Fantini","Depends":"XML","Description":"Query NCBI
Entrez and retrieve PubMed records in XML format. A large number of records can be
easily downloaded via this simple-to-use interface to the NCBI PubMed
2","NeedsCompilation":"no","Package":"easyPubMed","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Search and Retrieve Scientific Publication Records from
Pubmed","Version":"1.5"},"easyVerification":{"Author":"Jonas Bhend [aut,
cre],\nJacopo Ripoldi [ctb],\nClaudia Mignani [ctb],\nIrina Mahlstein
[ctb],\nRebecca Hiller [ctb],\nChristoph Spirig [ctb],\nMark Liniger
[ctb],\nAndreas Weigel [ctb],\nJoaqu'in Bedia Jimenez [ctb],\nMatteo De Felice
[ctb]","Depends":"R (>= 3.0), SpecsVerification, stats, utils","Description":"Set
of tools to simplify application of atomic forecast verification\nmetrics for
(comparative) verification of ensemble forecasts to large data sets.\nThe forecast
metrics are imported from the 'SpecsVerification' package, and\nadditional forecast
metrics are provided with this package. Alternatively,\nnew user-defined forecast
scores can be implemented using the example scores\nprovided and applied using the
functionality of this package.","Imports":"RCurl, pbapply, Rcpp","License":"GPL-
3","NeedsCompilation":"yes","Package":"easyVerification","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"testthat, knitr, parallel,
R.rsp","Title":"Ensemble Forecast Verification for Large Data
Sets","URL":"http:\/\/www.meteoswiss.ch","Version":"0.2.0"},"easyanova":
{"Author":"Emmanuel Arnhold","Depends":"R (>= 3.0.0)","Description":"Perform
analysis of variance and other important complementary analyzes. The functions are
easy to use. Performs analysis in various designs, with balanced and unbalanced
data.","Imports":"car, nlme","License":"GPL-
2","NeedsCompilation":"no","Package":"easyanova","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Analysis of variance and other important complementary
analyzes","Version":"4.0"},"easynls":{"Author":"Emmanuel
Arnhold","Description":"The package fit and plot some nonlinear
models","License":"GPL-
2","NeedsCompilation":"no","Package":"easynls","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Easy nonlinear model","Version":"4.0"},"easypackages":
{"Author":"Jake Sherman [aut, cre]","Depends":"R (>= 3.0.0)","Description":"Easily
load and install multiple packages from different sources,\nincluding CRAN and
GitHub. The libraries function allows you to load or attach\nmultiple packages in
the same function call. The packages function will load one\nor more packages, and
install any packages that are not installed on your system\n(after prompting you).
Also included is a from_import function that allows you\nto import specific
functions from a package into the global environment.","Imports":"assertthat,
devtools, utils","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"easypackages","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"knitr, rmarkdown","Title":"Easy Loading and
Installing of Packages","Version":"0.1.0"},"easypower":{"Author":"Aaron
McGarvey","Description":"Power analysis is used in the estimation of sample sizes
for\nexperimental designs. Most programs and R packages will only output the
highest\nrecommended sample size to the user. Often the user input can be
complicated\nand computing multiple power analyses for different treatment
comparisons can\nbe time consuming. This package simplifies the user input and
allows the user\nto view all of the sample size recommendations or just the ones
they want to see.\nThe calculations used to calculate the recommended sample sizes
are from the\n'pwr' package.","Imports":"pwr (>= 1.1-3)","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"easypower","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr","Title":"Sample Size Estimation for
Experimental Designs","Version":"1.0.1"},"ebGenotyping":{"Author":"Na You
<youn@mail.sysu.edu.cn> and Gongyi
Huang<huanggyi@mail2.sysu.edu.cn>","Description":"Genotyping the population using
next generation sequencing data is essentially important for the rare variant
detection. In order to distinguish the genomic structural variation from sequencing
error, we propose a statistical model which involves the genotype effect through a
latent variable to depict the distribution of non-reference allele frequency data
among different samples and different genome loci, while decomposing the sequencing
error into sample effect and positional effect. An ECM algorithm is implemented to
estimate the model parameters, and then the genotypes and SNPs are inferred based
on the empirical Bayes method.","License":"GPL-
2","NeedsCompilation":"no","Package":"ebGenotyping","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Genotyping using Next Generation Sequencing
Data","Version":"1.0"},"ebSNP":{"Author":"Na You","Description":"Genotyping and SNP
calling tool for single-sample next generation sequencing data analysis using an
empirical Bayes method.","License":"GPL-
2","NeedsCompilation":"no","Package":"ebSNP","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Genotyping and SNP calling using single-sample next
generation\nsequencing data","Version":"1.0"},"eba":{"Author":"Florian
Wickelmaier","Depends":"R (>= 2.15.0), stats","Description":"Fitting and testing
multi-attribute probabilistic choice\nmodels, especially the Bradley-Terry-Luce
(BTL) model (Bradley\n& Terry, 1952; Luce, 1959), elimination-by-aspects (EBA)
models\n(Tversky, 1972), and preference tree (Pretree) models (Tversky\n& Sattath,
1979).","Imports":"nlme","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"eba","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Elimination-by-Aspects (EBA)
Models","URL":"http:\/\/homepages.uni-
tuebingen.de\/florian.wickelmaier","Version":"1.7-1"},"ebal":{"Author":"Jens
Hainmueller","Description":"Package implements entropy balancing, a data
preprocessing procedure that allows users to reweight a dataset such that the
covariate distributions in the reweighted data satisfy a set of user specified
moment conditions. This can be useful to create balanced samples in observational
studies with a binary treatment where the control group data can be reweighted to
match the covariate moments in the treatment group. Entropy balancing can also be
used to reweight a survey sample to known characteristics from a target
population.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ebal","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Entropy reweighting to create balanced
samples","URL":"http:\/\/www.stanford.edu\/~jhain\/","Version":"0.1-6"},"ebdbNet":
{"Author":"Andrea Rau <andrea.rau@jouy.inra.fr>","Depends":"R (>= 2.8.1),
igraph","Description":"This package is used to infer the adjacency matrix of
a\nnetwork from time course data using an empirical Bayes\nestimation procedure
based on Dynamic Bayesian Networks.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"ebdbNet","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"GeneNet","Title":"Empirical Bayes Estimation of
Dynamic Bayesian Networks","URL":"http:\/\/www.r-
project.org","Version":"1.2.3"},"ecb":{"Author":"Eric Persson [aut,
cre]","Description":"Provides an interface to the European Central Bank's
Statistical\nData Warehouse API, allowing for programmatic retrieval of a vast
quantity\nof statistical data.","Imports":"curl, rsdmx, xml2,
httr","License":"CC0","NeedsCompilation":"no","Package":"ecb","Repository":"http:\/
\/cran.csiro.au\/src\/contrib","Suggests":"knitr, rmarkdown, dplyr,
ggplot2, testthat","Title":"Programmatic Access to the European Central Bank's
Statistical\nData Warehouse (SDW)","URL":"https:\/\/sdw.ecb.europa.eu\/
https:\/\/www.ecb.int","Version":"0.2"},"ecd":{"Author":"Stephen H-T. Lihn [aut,
cre]","Depends":"R (>= 3.1.2)","Description":"An implementation of the univariate
elliptic distribution\nand elliptic option pricing model. It provides detailed
functionality\nand data sets for the distribution and modelling.\nEspecially, it
contains functions for the computation of\ndensity, probability, quantile, fitting
procedures, option prices,\nvolatility smile. It also comes with sample financial
data, and plotting routines.","Imports":"stats, Rmpfr, polynom, xts, zoo, optimx,
moments, parallel,\ngraphics, methods, yaml, RSQLite","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"ecd","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr, testthat, roxygen2, ghyp,
fOptions","Title":"Elliptic Distribution Based on Elliptic
Curves","Version":"0.6.4"},"ecespa":{"Author":"Marcelino de la Cruz Rot, with
contributions of Philip M. Dixon and Jose M. Blanco-Moreno","Depends":"splancs,
spatstat (>= 1.4.0)","Description":"Some wrappers, functions and data sets for for
spatial point pattern analysis (mainly based on spatstat), used in the
book \"Introduccion al Analisis Espacial de Datos en Ecologia y Ciencias
Ambientales: Metodos y Aplicaciones\".","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ecespa","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Functions for Spatial Point Pattern
Analysis","Version":"1.1-8"},"ecipex":{"Author":"Andreas
Ipsen","Description":"Provides a function that quickly computes the fine
structure\nisotope patterns of a set of chemical formulas to a given degree
of\naccuracy (up to the limit set by errors in floating point arithmetic). A\ndata-
set comprising the masses and isotopic abundances of individual\nelements is also
provided.","Imports":"CHNOSZ","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ecipex","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Efficient calculation of fine structure isotope patterns
via\nFourier transforms of simplex-based elemental models","Version":"1.0"},"eco":
{"Author":"Kosuke Imai <kimai@princeton.edu>,\nYing Lu <yl46@nyu.edu>,\nAaron B
Strauss <aaronbstrauss@gmail.com>.","Depends":"R (>= 2.0), MASS,
utils","Description":"We implement the Bayesian and likelihood methods proposed\nin
Imai, Lu, and Strauss (2008, 2011) for ecological inference in 2\nby 2 tables as
well as the method of bounds introduced by Duncan and\nDavis (1953). The package
fits both parametric and nonparametric\nmodels using either the Expectation-
Maximization algorithms (for\nlikelihood models) or the Markov chain Monte Carlo
algorithms (for\nBayesian models). For all models, the individual-level data can
be\ndirectly incorporated into the estimation whenever such data are
available.\nAlong with in-sample and out-of-sample predictions, the package
also\nprovides a functionality which allows one to quantify the effect of
data\naggregation on parameter estimation and hypothesis testing under
the\nparametric likelihood models.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"eco","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Ecological Inference in 2x2
Tables","URL":"http:\/\/imai.princeton.edu\/software\/eco.html","Version":"3.1-
7"},"ecodist":{"Author":"Sarah Goslee and Dean Urban","Depends":"R (>=
3.0.0)","Description":"Dissimilarity-based analysis functions including ordination
and Mantel test functions, intended for use with spatial and community
data.","Imports":"stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ecodist","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Dissimilarity-based functions for ecological
analysis","Version":"1.2.9"},"ecoengine":{"Author":"Karthik Ram [aut,
cre]","Depends":"R (>= 3.1.1)","Description":"The ecoengine provides access to more
than 5 million georeferenced specimen records from the University of California,
Berkeley's Natural History Museums.","Imports":"httr (>= 0.3), plyr, assertthat,
whisker, dplyr (>= 0.2),\njsonlite, lubridate, leafletR (>= 0.1-
1)","License":"CC0","NeedsCompilation":"no","Package":"ecoengine","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Suggests":"testthat, knitr,
ggplot2","Title":"Programmatic Interface to the API Serving UC Berkeley's
Natural\nHistory
Data","URL":"https:\/\/github.com\/ropensci\/ecoengine","Version":"1.9.1"},"ecolMod
":{"Author":"Karline Soetaert <karline.soetaert@nioz.nl>, Peter MJ Herman
<peter.herman@nioz.nl>","Depends":"R (>= 2.01), rootSolve, shape, diagram,
deSolve","Description":"Figures, data sets and examples from the book \"A practical
guide to ecological modelling - using R as a simulation platform\" by Karline
Soetaert and Peter MJ Herman (2009). Springer.\nAll figures from chapter x can be
generated by \"demo(chapx)\", where x = 1 to 11.\nThe R-scripts of the model
examples discussed in the book are in subdirectory \"examples\", ordered per
chapter.\nSolutions to model projects are in the same
subdirectories.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ecolMod","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"maps, seacarb, scatterplot3d, deldir","Title":"\"A
practical guide to ecological modelling - using R as a\nsimulation
platform\"","Version":"1.2.6"},"ecoreg":{"Author":"Christopher Jackson
<chris.jackson@mrc-bsu.cam.ac.uk>","Description":"Estimating individual-level
covariate-outcome associations\nusing aggregate data (\"ecological inference\") or
a combination of\naggregate and individual-level data (\"hierarchical related
regression\").","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ecoreg","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Ecological Regression using Aggregate and Individual
Data","Version":"0.2.1"},"ecoretriever":{"Author":"Daniel McGlinn [aut,
cre],\nEthan White [aut]","Depends":"R (>= 3.0.0)","Description":"Provides an R
interface to the EcoData Retriever\n(http:\/\/ecodataretriever.org\/) via the
EcoData Retriever's\ncommand line interface. The EcoData Retriever automates
the\ntasks of finding, downloading, and cleaning ecological datasets,\nand then
stores them in a local database.","Imports":"utils","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"ecoretriever","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"R Interface to the EcoData
Retriever","URL":"https:\/\/github.com\/ropensci\/ecoretriever\/","Version":"0.2.1"
},"ecosim":{"Author":"Peter Reichert","Depends":"methods, deSolve,
stoichcalc","Description":"Classes and methods for implementing aquatic ecosystem
models,\nfor running these models, and for visualizing their
2)","NeedsCompilation":"no","Package":"ecosim","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Toolbox for Aquatic Ecosystem
Modeling","Version":"1.2"},"ecospace":{"Author":"Phil Novack-Gottshall [aut,
cre]","Depends":"R (>= 3.1.0)","Description":"Implements stochastic simulations of
community assembly (ecological\ndiversification) using customizable ecospace
frameworks (functional trait\nspaces). Provides a wrapper to calculate common
ecological disparity and\nfunctional ecology statistical dynamics as a function of
species richness. Functions are written so they will work in a\nparallel-computing
environment.","Imports":"FD (>= 1.0-
12)","License":"CC0","NeedsCompilation":"no","Package":"ecospace","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Title":"Simulating Community Assembly and
Ecological Diversification\nUsing Ecospace
Frameworks","URL":"https:\/\/github.com\/pnovack-gottshall\/ecospace
,\nhttp:\/\/www.ben.edu\/faculty\/pnovack-
gottshall\/index.html","Version":"1.0.0"},"ecospat":{"Author":"Olivier Broennimann
<olivier.broennimann@unil.ch> and\nBlaise Petitpierre <bpetitpierre@gmail.com>
and\nChristophe Randin <christophe.randin@wsl.ch> and\nRobin Engler
<robin.engler@isb-sib.ch> and\nValeria Di Cola <valeria.dicola@unil.ch> and\nFrank
Breiner <frank.breiner@wsl.ch> and\nManuela DÀmen<manuela.damen@unil.ch> and\nLoic
Pellissier <loic.pellissier@unifr.ch> and\nJulien Pottier
<julien.pottier@clermont.inra.fr> and\nDorothea Pio <dorothea.pio@fauna-flora.org>
and\nRuben Garcia Mateo <rubeng.mateo@gmail.com> and\nWim Hordijk
<wim@WorldWideWanderings.net> and\nAnne Dubuis <anne.dubuis@gmail.com> and\nDaniel
Scherrer <daniel.scherrer@unil.ch> and\nNicolas Salamin <nicolas.salamin@unil.ch>
and\nAntoine Guisan <antoine.guisan@unil.ch>","Depends":"ade4, ape, gam, gbm,
sp","Description":"R package for the support of spatial analyses and modelling of
species niches and distributions, written by current and former members and
collaborators of the ecospat group of Antoine Guisan, Department of Ecology and
Evolution (DEE) & Institute of Earth Surface Dynamics (IDYST), University of
Lausanne, Switzerland.","Imports":"adehabitatHR, adehabitatMA, biomod2, dismo,
ecodist, maptools,\nrandomForest, spatstat, raster,
rms","License":"GPL","NeedsCompilation":"no","Package":"ecospat","Repository":"http
:\/\/cran.csiro.au\/src\/contrib","Suggests":"MigClim, rgdal, rJava,
XML","Title":"Spatial Ecology Miscellaneous
Methods","URL":"http:\/\/www.unil.ch\/ecospat\/home\/menuinst\/tools--
data\/tools.html","Version":"1.1"},"ecotoxicology":{"Author":"Jose Gama [aut, cre,
trl]","Depends":"R (>= 2.10)","Description":"Implementation of the EPA's Ecological
Exposure Research Division (EERD) tools (discontinued in 1999) for Probit and
Trimmed Spearman-Karber Analysis.\nProbit and Spearman-Karber methods from Finney's
book \"Probit analysis a statistical treatment of the sigmoid response curve\" with
options for most accurate results or identical results to the book.\nProbit and all
the tables
from Finney's book (code-generated, not copied) with the generating functions
included.\nControl correction: Abbott, Schneider-Orelli, Henderson-Tilton, Sun-
Shepard.\nToxicity scales: Horsfall-Barratt, Archer, Gauhl-Stover, Fullerton-Olsen,
etc.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"ecotoxicology","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Methods for
Ecotoxicology","Version":"1.0.1"},"ecoval":{"Author":"Nele Schuwirth
<nele.schuwirth@eawag.ch> and Peter Reichert <peter.reichert@eawag.ch>\nwith
contributions by Simone Langhans","Depends":"utility,
rivernet","Description":"Functions for evaluating and visualizing\necological
assessment procedures for surface waters\ncontaining physical, chemical and
biological assessments\nin the form of value functions.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ecoval","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Procedures for Ecological Assessment of Surface
Waters","Version":"1.0"},"ecp":{"Author":"Nicholas A. James and David S.
Matteson","Depends":"R (>= 3.00), Rcpp","Description":"Implements various
procedures for finding\nmultiple change-points through the use of U-
statistics.\nThe procedures do not make any distributional assumptions\nother than
the existence of certain absolute moments. Hierarchical\nand exact search methods
are included. All methods return the\nset of estimated change-points as well as
other summary information.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ecp","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"mvtnorm,MASS,combinat, R.rsp","Title":"Non-Parametric
Multiple Change-Point Analysis of Multivariate\nData","Version":"2.0.0"},"edcc":
{"Author":"Weicheng Zhu, Changsoon Park","Depends":"spc","Description":"This
package provides a unified approach for Economic\nDesign of Control Charts. The
main purpose of this package is\nto find out the optimal parameters to minimize the
ECH\n(Expected Cost per Hour) of the
process.","License":"GPL","NeedsCompilation":"no","Package":"edcc","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"Economic Design of Control
Charts","Version":"1.0-0"},"edeR":{"Author":"Jaynal Abedin","Depends":"rJava,
rjson, rJython","Description":"This package will allow to connect with email server
through Internet Message Access Protocol (IMAP) and extract header information e.g.
from, to, cc, subject, date and time. User will supply their email address and
password along with other options. Initially this package is developed only for
Gmail. To run the functions from this package user have to have IMAP enabled Gmail
account.","License":"GPL-
2","NeedsCompilation":"no","Package":"edeR","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Email Data Extraction Using R","Version":"1.0.0"},"edeaR":
{"Author":"Gert Janssenswillen","Depends":"R(>= 3.0.0)","Description":"Functions
for exploratory and descriptive analysis of event based data. Can be used to import
and export xes-files, the IEEE eXtensible Event Stream standard. Provides methods
for describing and selecting process
data.","Imports":"dplyr,ggplot2,lubridate,tidyr,XML","License":"GPL-
3","NeedsCompilation":"no","Package":"edeaR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr, rmarkdown","Title":"Exploratory and Descriptive
Event-Based Data Analysis","Version":"0.3.2"},"edesign":{"Author":"Claudia Gebhardt
[aut, cre],\nRobert Gentleman [ctb, cph] (covers file src\/chol1.f and
src\/ch2inv1.f),\nRoss Ihaka [ctb, cph] (covers file src\/chol1.f and
src\/ch2inv1.f),\nThe University of Tennessee and The University of Tennessee
Research\nFoundation [ctb, cph] (covers file src\/dschur.f),\nThe University of
California Berkeley [ctb, cph] (covers file\nsrc\/dschur.f),\nThe University of
Colorado Denver [ctb, cph] (covers file src\/dschur.f)","Description":"An
implementation of maximum entropy sampling for spatial\ndata is provided. An exact
branch-and-bound algorithm as well as greedy and\ndual greedy heuristics are
2.0)","NeedsCompilation":"yes","Package":"edesign","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Maximum Entropy Sampling","Version":"1.0-
13"},"edfReader":{"Author":"Jan Vis [aut, cre]","Depends":"R (>=
3.2.0)","Description":"Reads European Data Format files EDF and EDF+, see
http:\/\/www.edfplus.info,\nBioSemi Data Format files BDF, see
http:\/\/www.biosemi.com\/faq\/file_format.htm,\nand BDF+ files, see
http:\/\/www.teuniz.net\/edfbrowser\/bdfplus%20format%20description.html.\nThe
files are read in two steps: first the header is read\nand then the signals (using
the header object as a parameter).","License":"GPL-
3","NeedsCompilation":"no","Package":"edfReader","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat, knitr, rmarkdown","Title":"Reading EDF(+)
and BDF(+) Files","Version":"1.1.0"},"edgar":{"Author":"Gunratan Lonare
<lonare.gunratan@gmail.com>, Bharat Patil <bharatspatil@gmail.com>","Depends":"R
(>= 3.1),shiny, shinydashboard, rChoiceDialogs","Description":"EDGAR is the
Electronic Data Gathering, Analysis, and Retrieval system which performs automated
collection, validation, indexing, acceptance, and forwarding of submissions by
companies and others who are required by law to file forms with the U.S. Securities
and Exchange Commission (SEC). This package downloads EDGAR quarterly master index,
daily master index, filings from SEC.org site and do sentiment analysis of 10-K
statements.","Imports":"R.utils,tcltk,tm,XML,wordcloud,RColorBrewer,ggplot2","Licen
se":"GPL-
2","NeedsCompilation":"no","Package":"edgar","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Platform for EDGAR Filing
Management","Version":"1.0.4"},"edgeCorr":{"Author":"Glenna
Nightingale","Depends":"graphics","Description":"Facilitates basic spatial edge
correction to point pattern data.","License":"GPL-
2","NeedsCompilation":"no","Package":"edgeCorr","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Spatial Edge Correction","Version":"1.0"},"edgeRun":
{"Author":"Emmanuel Dimont","Depends":"edgeR, data.table","Description":"Extends
edgeR functionality by improving on exactTest using an unconditional exact test of
negative binomial means.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"edgeRun","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"More Powerful Unconditional Testing of Negative
Binomial Means\nfor Digital Gene Expression Data","Version":"1.0.9"},"edgebundleR":
{"Author":"Mike Bostock [aut, cph] (d3.js library and much of edgebundle code
in\nhtmlwidgets\/lib, http:\/\/d3js.org),\nEllis Patrick [aut],\nKent Russell
[ctb],\nGarth Tarr [aut, cre]","Depends":"R (>= 3.1.2)","Description":"Generates
interactive circle plots with the nodes around the\ncircumference and linkages
between the connected nodes using hierarchical\nedge bundling via the D3 JavaScript
library. See <http:\/\/d3js.org\/> for more\ninformation on
D3.","Imports":"htmlwidgets (>= 0.3.2), rjson, igraph, shiny","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"edgebundleR","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"knitr, huge","Title":"Circle Plot with Bundled
Edges","URL":"https:\/\/github.com\/garthtarr\/edgebundleR","Version":"0.1.4"},"edi
trules":{"Author":"Edwin de Jonge, Mark van der Loo","Depends":"R (>= 2.12.0),
igraph","Description":"Facilitates reading and manipulating (multivariate) data
restrictions\n(edit rules) on numerical and categorical data. Rules can be defined
with common R syntax\nand parsed to an internal (matrix-like format). Rules can be
manipulated with\nvariable elimination and value substitution methods, allowing for
feasibility checks\nand more. Data can be tested against the rules and erroneous
fields can be found based\non Fellegi and Holt's generalized principle. Rules
dependencies can be visualized with\nusing the igraph
package.","Imports":"lpSolveAPI","License":"GPL-
3","NeedsCompilation":"no","Package":"editrules","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Parsing, Applying, and Manipulating Data Cleaning
Rules","URL":"https:\/\/github.com\/data-
cleaning\/editrules","Version":"2.9.0"},"edmr":{"Author":"Sheng Li [aut, cre,
cph],\nFrancine Garrett-Bakelman [ctb],\nAltuna Akalin [ctb],\nPaul Zumbo
[ctb],\nAri Melnick [ctb],\nChris Mason [ctb, ths]","Depends":"R (>=
3.2.1)","Description":"Optimized DMR analysis based on bimodal normal
distribution\nmodel and cost function for regional methylation analysis
optimization.\nIt captures the regional methylation modification by taking the
spatial\ndistribution of CpGs into account for the enrichment DNA methylation
sequencing\ndata so as to optimize the definition of the empirical regions.
Combined with\nthe dependent adjustment for regional p-value combination and DMR
annotation.","Imports":"GenomicRanges, IRanges, data.table, mixtools,
S4Vectors","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"edmr","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Empirical Differentially Methylated Regions
Calculation","URL":"https:\/\/github.com\/ShengLi\/edmr","Version":"0.6.3.1"},"edrG
raphicalTools":{"Author":"RaphaÃ«l Coudret, BenoÃ®t Liquet and JÃ©rÃ´me
Saracco","Depends":"rgl, mvtnorm, MASS, lasso2","Description":"This package comes
to illustrate the articles \"A graphical\ntool for selecting the number of slices
and the dimension of\nthe model in SIR and SAVE approaches\" and \"Comparison of
sliced\ninverse regression approaches for underdetermined cases\"","License":"GPL
(>=
2.0)","NeedsCompilation":"yes","Package":"edrGraphicalTools","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Title":"Provides tools for dimension reduction
methods","Version":"2.1"},"eegAnalysis":{"Author":"Murilo Coutinho Silva
(University of Brasilia, Brazil), George
Freitas von Borries (University of Brasilia, Brazil)","Depends":"R (>= 3.0.0),
e1071 (>= 1.6), wmtsa (>= 2.0-0) , fields (>=\n6.9.1), splus2R (>= 1.2-
0)","Description":"Package with tools for classification of electroencephalography
(EEG) data. Feature extraction techniques such as Fourier Transform and Continuous
Wavelet Transform (CWT) are available. Support Vector Machines (SVM) can be used to
classify the extracted features. An algorithm using Analysis of Variance (ANOVA),
False Discovery Rate (FDR), and SVM is available to feature selection.
Additionally, the package contains functions to plot data and
features.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"eegAnalysis","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Tools for analysis and classification of
electroencephalography\n(EEG) data","Version":"0.0"},"eegkit":{"Author":"Nathaniel
E. Helwig <helwig@umn.edu>","Depends":"R (>= 3.1.1), bigsplines, eegkitdata, ica,
rgl","Description":"Analysis and visualization tools for electroencephalography
(EEG) data. Includes functions for plotting (a) EEG caps, (b) single- and multi-
channel EEG time courses, and (c) EEG spatial maps. Also includes smoothing and
Independent Component Analysis functions for EEG data analysis, and a function for
simulating event-related potential EEG data.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"eegkit","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Toolkit for Electroencephalography Data","Version":"1.0-
2"},"eegkitdata":{"Author":"Nathaniel E. Helwig <helwig@umn.edu>","Depends":"R (>=
2.10)","Description":"Contains the example EEG data used in the package eegkit.
Also contains code for easily creating larger EEG datasets from the EEG Database on
the UCI Machine Learning Repository.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"eegkitdata","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Data for package eegkit","Version":"1.0"},"eel":
{"Author":"Fan Wu and Yu Zhang","Depends":"emplik,
rootSolve","Description":"Compute the extended empirical log likelihood ratio (Tsao
& Wu, 2014) for the mean and parameters defined by estimating
equations.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"eel","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Extended Empirical Likelihood","Version":"1.1"},"eemR":
{"Author":"Philippe Massicotte [aut, cre]","Depends":"R (>=
3.2.1)","Description":"Provides various tools to calculate EEM fluorescence metrics
and preprocess EEM for PARAFAC analysis.","Imports":"stringr, fields, dplyr,
R.matlab, pracma, ggplot2, tidyr,\nreadr, stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"eemR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Tools for Pre-Processing Emission-Excitation-Matrix
(EEM)\nFluorescence
Data","URL":"https:\/\/github.com\/PMassicotte\/eemR","Version":"0.1.2"},"eeptools"
:{"Author":"Jason P. Becker [ctb],\nJared E. Knowles [aut, cre]","Depends":"R (>=
2.15.1), ggplot2","Description":"Collection of convenience functions to make
working with\nadministrative records easier and more consistent. Includes functions
to\nclean strings, identify cutpoints, and quickly combine shapefiles
and\ndataframes for plotting. Includes four alternative themes for ggplot2.
Also\nincludes three example datasets of administrative education records
for\nlearning how to process records with errors.","Imports":"maptools, arm,
data.table, vcd, memisc","License":"GPL-
3","NeedsCompilation":"no","Package":"eeptools","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"reshape, sp, plyr, mapproj, testthat, maps, stringr,
knitr,\nrmarkdown, MASS","Title":"Convenience Functions for Education
Data","Version":"0.9.1"},"effects":{"Author":"John Fox [aut, cre],\nSanford
Weisberg [aut],\nMichael Friendly [aut],\nJangman Hong [aut],\nRobert Andersen
[ctb],\nDavid Firth [ctb],\nSteve Taylor [ctb]","Depends":"R (>=
3.2.0)","Description":"\nGraphical and tabular effect displays, e.g., of
interactions, for\nvarious statistical models with linear
predictors.","Imports":"lme4, nnet, lattice, grid, colorspace, graphics,
grDevices,\nstats, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"effects","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"pbkrtest (>= 0.4-4), nlme, MASS, poLCA, heplots,
splines,\nordinal, car","Title":"Effect Displays for Linear, Generalized Linear,
and Other Models","URL":"http:\/\/www.r-project.org,
http:\/\/socserv.socsci.mcmaster.ca\/jfox\/","Version":"3.1-1"},"efflog":
{"Author":"Gloria Gheno [aut, cre]","Depends":"stats, R(>=
2.10.1)","Description":"Fitting a causal loglinear model and calculating the causal
effects for a causal loglinear model with the multiplicative interaction or without
the multiplicative interaction, obtaining the natural direct, indirect and the
total effect. It calculates also the cell effect, which is a new interaction
effect.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"efflog","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"The Causal Effects for a Causal Loglinear
Model","Version":"1.0"},"effsize":{"Author":"Marco Torchiano [aut,
cre]","Description":"A collection of functions to compute the standardized\neffect
sizes for experiments (Cohen d, Hedges g, Cliff delta, Vargha-Delaney A).\nThe
computation algorithms have been optimized to allow efficient computation
even\nwith very large data sets.","License":"GPL-
2","NeedsCompilation":"no","Package":"effsize","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Efficient Effect Size
Computation","URL":"http:\/\/github.com\/mtorchiano\/effsize\/","Version":"0.6.2"},
"efreadr":{"Author":"Marco Bascietto [aut, cre]","Depends":"R (>= 3.2.0), readr,
dplyr, ensurer, magrittr","Description":"The European Eddy Fluxes Database Cluster
distributes fluxes of different Green House Gases measured mainly using the eddy
covariance technique acquired in sites involved in EU projects but also single
sites in Europe, Africa and others continents that decided to share their
measurements in the database (cit. http:\/\/gaia.agraria.unitus.it ). The package
provides two functions to load and row-wise bind CSV files distributed by the
database. Currently only L3 and L4 (L=Level), half-hourly and daily (aggregation)
files are supported.","License":"GPL-
3","NeedsCompilation":"no","Package":"efreadr","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Read European Fluxes CSV Files","Version":"0.1.1"},"ega":
{"Author":"Daniel Schmolze [aut, cre]","Depends":"R (>=
2.14.0)","Description":"Functions for assigning Clarke or Parkes (Consensus) error
grid\nzones to blood glucose values, and for plotting both types of error
grids.","Imports":"ggplot2","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"ega","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr","Title":"Error Grid
Analysis","Version":"1.0.1"},"egcm":{"Author":"Matthew Clegg [aut, cre,
cph]","Depends":"zoo, xts, TTR","Description":"An easy-to-use implementation of the
Engle-Granger\ntwo-step procedure for identifying pairs of cointegrated series. It
is geared towards\nthe analysis of pairs of securities. Summary and plot functions
are provided,\nand the package is able to fetch closing prices of securities from
Yahoo.\nA variety of unit root tests are supported, and an improved unit root test
is included.","Imports":"grid, ggplot2, tseries, MASS, urca, parallel, fArma,
stats,\nmethods","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"egcm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Engle-Granger Cointegration
Models","Version":"1.0.8"},"eggCounts":{"Author":"Michaela Paul [aut], Reinhard
Furrer [cre, ctb]","Description":"An implementation of hierarchical models\nfor
faecal egg count data to assess anthelmintic\nefficacy. Bayesian inference is done
via MCMC sampling.","Imports":"actuar,boot,coda","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"eggCounts","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"lattice","Title":"Hierarchical Modelling of Faecal
Egg Counts","URL":"http:\/\/www.math.uzh.ch\/as\/index.php?
id=eggCounts","Version":"0.4-1"},"egonet":{"Author":"A. Sciandra, F. Gioachin, L.
Finos","Depends":"sna","Description":"A small tool for Social Network Analysis,
dealing with\nego-centric network measures, including Burt's effective size\nand
aggregate constraint and an import code suitable for a\nlarge number of adjacency
matrices. A free web application is\nalso available on
http:\/\/www.egonet.associazionerospo.org","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"egonet","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Tool for ego-centric measures in Social Network
Analysis","Version":"1.2"},"eha":{"Author":"GÃ¶ran BrostrÃ¶m [aut,
cre]","Depends":"R (>= 3.0.0), survival (>= 2.37-6)","Description":"Sampling of
risk sets in Cox regression, selections in\nthe Lexis diagram, bootstrapping.
Parametric proportional\nhazards fitting with left truncation and right censoring
for\ncommon families of distributions, piecewise constant hazards,\nand discrete
models. AFT regression for left truncated and\nright censored data. Binary and
Poisson regression for\nclustered data, fixed and random effects with
bootstrapping.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"eha","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Event History Analysis","Version":"2.4-3"},"ei":
{"Author":"Gary King <king@harvard.edu>, Molly Roberts
<molly.e.roberts@gmail.com>","Depends":"R (>= 2.5.0),
eiPack","Description":"Software accompanying Gary King's book: A Solution to the
Ecological Inference Problem. (1997). Princeton University Press. ISBN 978-
0691012407.","Imports":"mvtnorm, msm, tmvtnorm, ellipse, plotrix, MASS,
ucminf,\ncubature, mnormt,
foreach, sp","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ei","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"rgl","Title":"Ecological
Inference","URL":"http:\/\/gking.harvard.edu\/eiR,\nhttp:\/\/gking.harvard.edu\/eic
amera\/kinroot.html","Version":"1.3-2"},"eiCompare":{"Author":"Loren
Collingwood","Depends":"eiPack, methods, tmvtnorm, foreach","Description":"Compares
estimates from three ecological inferences routines, based on King et. al.'s
approach.","Imports":"plyr, data.table, ucminf, R.utils, mvtnorm, msm,
mnormt,\ncubature, ellipse, plotrix","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"eiCompare","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Compares EI, Goodman, RxC
Estimates","Version":"1.6"},"eiPack":{"Author":"Olivia Lau
<olivia.lau@post.harvard.edu>, Ryan T. Moore\n<rtm@wustl.edu>, Michael Kellermann
<kellerm@post.harvard.edu>","Depends":"R (>= 2.0.0), MASS, coda,
msm","Description":"Provides methods for analyzing RxC ecological
contingency\ntables using the extreme case analysis, ecological regression,\nand
Multinomial-Dirichlet ecological inference models. Also\nprovides tools for
manipulating higher-dimension data objects.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"eiPack","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"eiPack: Ecological Inference and Higher-Dimension
Data\nManagement","URL":"http:\/\/www.olivialau.org\/software","Version":"0.1-
7"},"eigeninv":{"Author":"Ravi Varadhan, Johns Hopkins University","Depends":"R (>=
2.10.1)","Description":"Solves the `ìnverse eigenvalue problem'' which is
to\ngenerate a real-valued matrix that has the specified real\neigenvalue spectrum.
It can generate infinitely many dense\nmatrices, symmetric or asymmetric, with the
given set of\neigenvalues. Algorithm can also generate stochastic and
doubly\nstochastic matrices.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"eigeninv","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Generates (dense) matrices that have a given set of
eigenvalues","URL":"\nhttp:\/\/www.jhsph.edu\/agingandhealth\/People\/Faculty_perso
nal_pages\/Varadhan.html","Version":"2011.8-1"},"eigenmodel":{"Author":"Peter
Hoff","Description":"This package estimates the parameters of a model
for\nsymmetric relational data (e.g., the above-diagonal part of a\nsquare matrix),
using a model-based eigenvalue decomposition\nand regression. Missing data is
accomodated, and a posterior\nmean for missing data is calculated under the
assumption that\nthe data are missing at random. The marginal distribution of\nthe
relational data can be arbitrary, and is fit with an\nordered probit
specification.","License":"GPL-
2","NeedsCompilation":"no","Package":"eigenmodel","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Semiparametric factor and regression models for
symmetric\nrelational
data","URL":"http:\/\/www.stat.washington.edu\/hoff","Version":"1.01"},"eigenprcomp
":{"Author":"Francisco Juretig","Description":"Computes confidence intervals for
the proportion explained by the first 1,2,k principal components, and computes
confidence intervals for each eigenvalue. Both computations are done via
nonparametric bootstrap.","License":"GPL-
2","NeedsCompilation":"no","Package":"eigenprcomp","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Computes confidence intervals for principal
components","Version":"1.0"},"eive":{"Author":"Mehmet Hakan Satman (PhD), Erkin
Diyarbakirlioglu (PhD)","Description":"EIVE performs a compact genetic algorithm
search to reduce errors-in-variables bias in linear regression.","Imports":"Rcpp
(>=
0.11.1)","License":"GPL","NeedsCompilation":"yes","Package":"eive","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"An algorithm for reducing errors-in-
variable bias in simple\nlinear regression","Version":"2.1"},"eiwild":
{"Author":"Thomas Schlesinger <tho.schlesinger@gmail.com>","Depends":"R (>=
2.15)","Description":"This package allows to use the hybrid Multinomial-Dirichlet-
Model\nof Ecological Inference for estimating inner Cells of RxC-Tables. This
was\nalready implemented in the eiPack-package. eiwild-package now has
the\npossibility to use individual level data to support the aggregate level\ndata
and using different Hyperpriori-Distributions.","Imports":"gtools, coda,
lattice","License":"GPL-
3","NeedsCompilation":"yes","Package":"eiwild","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Ecological Inference with individual and aggregate
data","URL":"http:\/\/CRAN.R-
project.org\/package=eiwild","Version":"0.6.7"},"elasso":{"Author":"Pi
Guo","Depends":"R (>= 3.0.2),glmnet,SiZer,datasets","Description":"Performs some
enhanced variable selection algorithms\nbased on the least absolute shrinkage and
selection operator for regression model.","License":"GPL-
2","NeedsCompilation":"no","Package":"elasso","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Enhanced Least Absolute Shrinkage and Selection
Operator\nRegression Model","Version":"1.1"},"elastic":{"Author":"Scott Chamberlain
[aut, cre]","Description":"Connect to 'Elasticsearch', a 'NoSQL' database built on
the 'Java'\nVirtual Machine. Interacts with the 'Elasticsearch' 'HTTP'
'API'\n(<https:\/\/www.elastic.co\/products\/elasticsearch>), including functions
for\nsetting connection details to 'Elasticsearch' instances, loading bulk
data,\nsearching for documents with both 'HTTP' query variables and 'JSON' based
body\nrequests. In addition, 'elastic' provides functions for interacting with
'APIs'\nfor 'indices', documents, nodes, clusters, an interface to the cat 'API',
and\nmore.","Imports":"utils, methods, httr (>= 1.0.0), curl (>= 0.9.4), jsonlite
(>=\n0.9.19)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"elastic","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat, knitr","Title":"General Purpose
Interface to
'Elasticsearch'","URL":"https:\/\/github.com\/ropensci\/elastic","Version":"0.6.0"}
,"elasticnet":{"Author":"Hui Zou <hzou@stat.umn.edu> and Trevor
Hastie\n<hastie@stanford.edu>","Depends":"R (>= 2.10), lars","Description":"This
package provides functions for fitting the entire\nsolution path of the Elastic-Net
and also provides functions\nfor estimating sparse Principal Components. The Lasso
solution\npaths can be computed by the same function. First version:\n2005-
2)","NeedsCompilation":"no","Package":"elasticnet","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Elastic-Net for Sparse Estimation and Sparse
PCA","URL":"http:\/\/www.stat.umn.edu\/~hzou","Version":"1.1"},"elec":
{"Author":"Luke Miratrix","Description":"This is a bizzare collection of functions
written to do\nvarious sorts of statistical election audits. There are
also\nfunctions to generate simulated voting data, and simulated\n\"truth\" so as
to do simulations to check charactaristics of\nthese methods.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"elec","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Collection of functions for statistical election
audits","Version":"0.1.2"},"elec.strat":{"Author":"Mike Higgins, Hua
Yang","Depends":"R (>= 2.10), elec","Description":"An extension of the elec package
intended for use on\nelection audits using stratified random samples.
Includes\nfunctions to obtain conservative and exact p-values, and\nfunctions that
give sample sizes that may make election audits\nmore efficient.","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"elec.strat","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Functions for election audits using stratified random
samples","Version":"0.1.1"},"elexr":{"Author":"Geoff Hing","Description":"Provides
R access to election results data. Wraps elex
(https:\/\/github.com\/newsdev\/elex\/), a Python package and command line tool for
fetching and parsing Associated Press election
results.","Imports":"utils","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"elexr","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Load Associated Press Election Results with
Elex","Version":"1.0"},"elliplot":{"Author":"Shinichiro
Tomizono","Description":"Correlation chart of two set (x and y) of data.\nUsing
Quantiles. Visualize the effect of factor.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"elliplot","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Ellipse Summary Plot of
Quantiles","Version":"1.1.1"},"ellipse":{"Author":"Duncan Murdoch
<murdoch@stats.uwo.ca> and E. D. Chow (porting\nto R by Jesus M. Frias Celayeta
<iosu@bureau.ucc.ie>)","Depends":"R (>= 2.0.0),graphics,stats","Description":"This
package contains various routines for drawing\nellipses and ellipse-like confidence
regions, implementing the\nplots described in Murdoch and Chow (1996), A graphical
display\nof large correlation matrices, The American Statistician 50,\n178-180.
There are also routines implementing the profile plots\ndescribed in Bates and
Watts (1988), Nonlinear Regression\nAnalysis and its Applications.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"ellipse","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"MASS","Title":"Functions for drawing ellipses and
ellipse-like confidence\nregions","Version":"0.3-8"},"elliptic":{"Author":"Robin K.
S. Hankin","Depends":"R (>= 2.5.0)","Description":"\nA suite of elliptic and
related functions including Weierstrass and\nJacobi forms. Also includes various
tools for manipulating and\nvisualizing complex
functions.","Imports":"MASS","License":"GPL-
2","NeedsCompilation":"no","Package":"elliptic","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"emulator, calibrator","Title":"elliptic
functions","Version":"1.3-5"},"elmNN":{"Author":"Alberto
Gosso","Depends":"MASS","Description":"Training
and predict functions for SLFN ( Single\nHidden-layer Feedforward Neural
Networks ) using the ELM\nalgorithm. ELM algorithm differs from the
traditional\ngradient-based algorithms for very short training times ( it\ndoesn't
need any iterative tuning, this makes learning time\nvery fast ) and there is no
need to set any other parameters\nlike learning rate, momentum, epochs,
etc.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"elmNN","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Implementation of ELM (Extreme Learning Machine ) algorithm
for\nSLFN ( Single Hidden Layer Feedforward Neural
Networks )","Version":"1.0"},"elrm":{"Author":"David Zamar, Jinko Graham, Brad
McNeney","Depends":"R(>= 2.7.2), coda, graphics, stats","Description":"elrm
implements a Markov Chain Monte Carlo algorithm to\napproximate exact conditional
inference for logistic regression\nmodels. Exact conditional inference is based on
the\ndistribution of the sufficient statistics for the parameters of\ninterest
given the sufficient statistics for the remaining\nnuisance parameters. Using model
formula notation, users\nspecify a logistic model and model terms of interest for
exact\ninference.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"elrm","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Exact Logistic Regression via MCMC","URL":"http:\/\/stat-
db.stat.sfu.ca:8080\/statgen\/research\/elrm","Version":"1.2.2"},"emIRT":
{"Author":"Kosuke Imai <kimai@princeton.edu>, James Lo <jameslo@princeton.edu>,
Jonathan Olmsted <jpolmsted@gmail.com>","Depends":"R (>= 2.10), pscl (>= 1.0.0),
Rcpp (>= 0.10.6)","Description":"Various Expectation-Maximization (EM) algorithms
are implemented for item response theory\n(IRT) models. The current implementation
includes IRT models for binary and ordinal\nresponses, along with dynamic and
hierarchical IRT models with binary responses. The\nlatter two models are derived
and implemented using variational EM. Subsequent edits\nalso include variational
network and text scaling models.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"emIRT","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"EM Algorithms for Estimating Item Response Theory
Models","Version":"0.0.6"},"embryogrowth":{"Author":"Marc Girondot
<marc.girondot@u-psud.fr>","Depends":"deSolve, polynom, parallel, HelpersMG (>=
1.2),R (>= 2.14.2)","Description":"Tools to analyze the embryo growth and the
sexualisation thermal reaction norms.","License":"GPL-
2","NeedsCompilation":"no","Package":"embryogrowth","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"entropy, shiny, coda, optimx,
numDeriv","Title":"Tools to Analyze the Thermal Reaction Norm of Embryo
Growth","Version":"6.2"},"emdbook":{"Author":"Ben Bolker","Description":"Auxiliary
functions and data sets for \"Ecological Models and Data\", a book presenting
maximum likelihood estimation and related topics for ecologists (ISBN 978-0-691-
12522-0).","Imports":"MASS, lattice, plyr, coda,
bbmle","License":"GPL","NeedsCompilation":"no","Package":"emdbook","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Suggests":"R2WinBUGS, ellipse, SuppDists,
numDeriv, testthat, rgl","Title":"Support Functions and Data for \"Ecological
Models and
Data\"","URL":"http:\/\/www.math.mcmaster.ca\/bolker\/emdbook","Version":"1.3.9"},"
emdist":{"Author":"Simon Urbanek <urbanek@research.att.com>, Yossi
Rubner","Description":"Package providing calculation of Earth Mover's
Distance\n(EMD).","License":"MIT","NeedsCompilation":"yes","Package":"emdist","Repo
sitory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Earth Mover's
Distance","URL":"http:\/\/www.rforge.net\/emd","Version":"0.3-1"},"emg":
{"Author":"Shawn Garbett, Mark Kozdoba","Depends":"R (>= 1.8.0), stats,
stats4","Description":"Provides basic distribution functions for a mixture model of
a Gaussian and exponential distribution.","License":"GPL-
2","NeedsCompilation":"no","Package":"emg","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Exponentially Modified Gaussian (EMG)
Distribution","Version":"1.0.6"},"emil":{"Author":"Christofer Backlin [aut,
cre],\nMats Gustafsson [aut]","Description":"A toolbox for designing and evaluating
predictive models with\nresampling methods. The aim of this package is to provide a
simple and\nefficient general framework for working with any type of
prediction\nproblem, be it classification, regression or survival analysis, that
is\neasy to extend and adapt to your specific setting. Some commonly used\nmethods
for classification, regression and survival analysis are
included.","Imports":"data.table, dplyr, ggplot2 (>= 1.0.1), graphics,
grDevices,\nlazyeval, magrittr, methods, Rcpp (>= 0.12.1), stats,
tidyr,\nutils","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"emil","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"caret, cmprsk, e1071, glmnet, Hmisc, MASS, parallel,
party,\npamr, randomForest, RColorBrewer, rpart, survival, testthat
(>=\n0.9.1)","Title":"Evaluation of Modeling without Information
Leakage","URL":"http:\/\/molmed.github.io\/emil","Version":"2.2.3"},"emma":
{"Author":"Laura Villanova <laura.villanova@monash.edu>, Kate Smith-
Miles\n<kate.smith-miles@monash.edu> and Rob J
Hyndman\n<rob.hyndman@monash.edu>.","Depends":"R (>= 2.9.2), earth,
clusterSim","Description":"The evolutionary model-based multiresponse approach
(EMMA)\nis a novel methodology to process optimisation and product\nimprovement.
The approach is suitable to contexts in which the\nexperimental cost and\/or time
limit the number of implementable\ntrials.","Imports":"methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"emma","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Evolutionary model-based multiresponse
approach","Version":"0.1-0"},"emme2":{"Author":"Ben Stabler
<benstabler@yahoo.com>","Depends":"R (>= 1.6.0), graphics,
reshape","Description":"This package includes functions to read and write to
an\nEMME\/2
databank","License":"GPL","NeedsCompilation":"no","Package":"emme2","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Title":"Read and Write to an EMME\/2
databank","Version":"0.9"},"emoa":{"Author":"Olaf Mersmann <olafm@statistik.tu-
dortmund.de>","Description":"Collection of building blocks for the design and
analysis\nof evolutionary multiobjective optimization algorithms.","License":"GPL-
2","NeedsCompilation":"yes","Package":"emoa","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"RUnit","Title":"Evolutionary Multiobjective Optimization
Algorithms","URL":"http:\/\/www.statistik.tu-
dortmund.de\/~olafm\/software\/emoa\/","Version":"0.5-0"},"emojifont":
{"Author":"Guangchuang Yu [aut, cre]","Depends":"R (>= 3.2.2)","Description":"An
implementation of using emoji font in both base and 'ggplot2'
graphics.","Imports":"proto, showtext, sysfonts, utils","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"emojifont","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr, ggplot2","Title":"Emoji Fonts for using in
R","URL":"https:\/\/github.com\/GuangchuangYu\/emojifont","Version":"0.3.2"},"emov"
:{"Author":"Simon Schwab <schw4b@gmail.com>","Depends":"R (>=
1.8.0)","Description":"Fixation and saccade detection in eye movement recordings.
This package implements a dispersion-based algorithm (I-DT) proposed by Salvucci &
Goldberg (2000) which detects fixation duration and position.","License":"GPL-
3","NeedsCompilation":"no","Package":"emov","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Eye Movement Analysis Package for Fixation and Saccade
Detection","URL":"https:\/\/github.com\/schw4b\/emov","Version":"0.1.1"},"empirical
FDR.DESeq2":{"Author":"Mikhail V.
Matz","Depends":"DESeq2,GenomicRanges","Description":"Auxiliary functions for the
DESeq2 package to simulate read counts according to the null hypothesis (i.e., with
empirical sample size factors, per-gene total counts and dispersions, but without
effects of predictor variables) and to compute the empirical false discovery
rate.","License":"GPL-
3","NeedsCompilation":"no","Package":"empiricalFDR.DESeq2","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Title":"Simulation-Based False Discovery Rate in RNA-
Seq","Version":"1.0.3"},"emplik":{"Author":"Mai Zhou. (Art Owen for el.test().
Yifan Yang for C code.)","Depends":"R (>= 3.0), quantreg","Description":"Empirical
likelihood ratio tests for means\/quantiles\/hazards\nfrom possibly censored
and\/or truncated data. Now does regression too.\nThis version contains some C
code.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"emplik","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"KMsurv, boot","Title":"Empirical Likelihood Ratio for
Censored\/Truncated
Data","URL":"http:\/\/www.ms.uky.edu\/~mai\/EmpLik.html","Version":"1.0-
2"},"emplik2":{"Author":"William H. Barton <williamhbarton1@gmail.com> under the
supervision of Dr. Mai Zhou <mai@ms.uky.edu>","Depends":"R (>=
2.15.0)","Description":"Calculates the p-value for a mean-type hypothesis (or
multiple mean-type hypotheses) based on two samples with censored
2)","NeedsCompilation":"no","Package":"emplik2","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Empirical Likelihood Ratio Test for Two Samples with
Censored\nData","Version":"1.20"},"emuR":{"Author":"Raphael Winkelmann [aut,
cre],\nKlaus Jaensch [aut, ctb],\nSteve Cassidy [aut, ctb],\nJonathan Harrington
[aut, ctb]","Depends":"R (>= 3.2.0)","Description":"Provides the next iteration of
the EMU Speech\nDatabase Management System (EMU_SDMS) with database management,
data\nextraction, data preparation and data visualization
facilities.","Imports":"MASS, tools, utils, stats, methods, graphics,
grDevices,\nstringr, uuid, base64enc, wrassp (>= 0.1.3), tidyjson (>=\n0.2.1),
jsonlite (>= 0.9.13), RSQLite (>= 1.0.0),
DBI (>=\n0.3.1), httpuv (>= 1.3.2), data.table (>= 1.9.4), dplyr
(>=\n0.4.3)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"emuR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat(>= 0.7.1.99), knitr(>= 1.7), compare(>=
0.2.4),\nggplot2(>= 1.0.1), rmarkdown(>= 0.9.2)","Title":"Main Package of the EMU
Speech Database Management System","URL":"https:\/\/github.com\/IPS-
LMU\/emuR","Version":"0.1.7"},"emulator":{"Author":"Robin K. S.
Hankin","Depends":"R (>= 3.0.1), mvtnorm","Description":"\nThis package allows one
to estimate the output of a computer program,\nas a function of the input
parameters, without actually running it.\nThe computer program is assumed to be a
Gaussian process, whose\nparameters are estimated using Bayesian techniques that
give a PDF of\nexpected program output. This PDF is conditional on a ``training
set''\nof runs, each consisting of a point in parameter space and the model\noutput
at that point. The emphasis is on complex codes that take\nweeks or months to run,
and that have a large number of undetermined\ninput parameters; many climate
prediction models fall into this\nclass. The emulator essentially determines
Bayesian posterior\nestimates of the PDF of the output of a model, conditioned on
results\nfrom previous runs and a user-specified prior linear model. A\nworking
example is given in the help page for function ìnterpolant()',\nwhich should be
the first point of
reference.","License":"GPL","NeedsCompilation":"no","Package":"emulator","Repositor
y":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Bayesian emulation of computer
programs","Version":"1.2-15"},"enRich":{"Author":"Yanchun Bao, Veronica
Vinciotti","Depends":"R(>= 3.2.2), parallel","Description":"An R package for joint
statistical modelling of ChIP-seq data, accounting for technical\/biological
replicates, multiple conditions and different ChIP efficiencies of the individual
experiments.","License":"GPL-
2","NeedsCompilation":"yes","Package":"enRich","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"An R Package for the Analysis of Multiple ChIP-Seq
Data","Version":"3.0"},"enaR":{"Author":"M.K. Lau, S.R. Borrett, D.E. Hines, P.
Singh","Depends":"R (>= 2.10), MASS, stringr, sna, network, gdata, stats,
utils,\ngraphics","Description":"Provides algorithms for the analysis of ecological
networks.","License":"GPL-
3","NeedsCompilation":"no","Package":"enaR","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"codetools, igraph, R.rsp","Title":"Tools for Ecological
Network
Analysis","URL":"https:\/\/github.com\/SEELab\/enaR","Version":"2.9.1"},"endogMNP":
{"Author":"Lane F. Burgette <lb131@stat.duke.edu>","Depends":"R (>= 2.1),
utils","Description":"endogMNP is an R package that fits a Bayesian
multinomial\nprobit model with endogenous selection, which is sometimes\ncalled an
endogenous switching model. This can be used to\nmodel discrete choice data when
respondents select themselves\ninto one of several groups. This package is based
on the MNP\npackage by Kosuke Imai and David A. van Dyk. This package\nmodifies
their code.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"endogMNP","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"R Package for Fitting Multinomial Probit Models with
Endogenous\nSelection","URL":"http:\/\/www.r-
project.org,\nhttp:\/\/fds.duke.edu\/db\/aas\/stat\/faculty\/lb131","Version":"0.2-
1"},"endorse":{"Author":"Yuki Shiraito <shiraito@princeton.edu>, Kosuke Imai
<kimai@princeton.edu>","Depends":"coda, utils","Description":"This R package
implements the statistical model proposed by Bullock, Imai, and Shapiro (2011;
Political Analysis) to analyze endorsement experiments. Endorsement experiments
are a survey methodology for eliciting truthful responses to sensitive questions.
This methodology is helpful when measuring support for socially sensitive political
actors such as militant groups. The model is fitted with the Markov chain Monte
Carlo algorithm and produces the output containing draws from the posterior
2)","NeedsCompilation":"yes","Package":"endorse","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"R Package for Analyzing Endorsement
Experiments","URL":"http:\/\/imai.princeton.edu\/software\/endorse.html","Version":
"1.4.1"},"energy":{"Author":"Maria L. Rizzo and Gabor J. Szekely","Description":"E-
statistics (energy) tests and statistics for comparing\ndistributions: multivariate
normality, multivariate distance\ncomponents and k-sample test for equal
distributions,\nhierarchical clustering by e-distances, multivariate\nindependence
tests, distance correlation, goodness-of-fit\ntests. Energy- statistics concept
based on a generalization of\nNewton's potential energy is due to Gabor J.
Szekely.","Imports":"boot","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"energy","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"E-statistics (energy
statistics)","Version":"1.6.2"},"english":{"Author":"John Fox and Bill
Venables.","Description":"Allow numbers to be presented in an English
language\nversion, one, two, three, ...","License":"GPL-
2","NeedsCompilation":"no","Package":"english","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Translate integers into English","Version":"1.0-
1"},"enigma":{"Author":"Scott Chamberlain [aut, cre]","Description":"The company
'Enigma' (https:\/\/enigma.io) holds many public 'datasets' from\ngovernments,
companies, universities, and organizations. 'Enigma' provides an\n'API' for data,
'metadata', and statistics on each of the 'datasets'. 'enigma' is\na client to
interact with the 'Enigma' 'API', including getting the data\nand 'metadata' for
'datasets' in 'Enigma', as well as collecting statistics on\n'datasets'. In
addition, you can download a 'gzipped' 'csv' file of a 'dataset'\nif you want the
whole 'dataset'. An 'API' key from 'Enigma' is required to
use\n'enigma'.","Imports":"methods, utils, httr (>= 1.0.0), jsonlite,
plyr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"enigma","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"knitr, testthat, dplyr, ggplot2,
ggthemes","Title":"Client for the 'Enigma'
'API'","URL":"https:\/\/github.com\/ropengov\/enigma","Version":"0.2.0"},"enpls":
{"Author":"Nan Xiao <road2stat@gmail.com>, Dong-Sheng Cao <oriental-
cds@163.com>,\nQing-Song Xu <dasongxu@gmail.com>","Description":"Ensemble partial
least squares regression, a unified\nframework for feature selection, outlier
detection, and ensemble learning.","Imports":"pls, foreach,
2)","NeedsCompilation":"no","Package":"enpls","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"knitr","Title":"Ensemble Partial Least Squares
Regression","URL":"https:\/\/github.com\/road2stat\/enpls","Version":"1.1"},"enrich
vs":{"Author":"Hiroaki YABUUCHI","Depends":"R (>= 0.99)","Description":"These
programs are used for calculating enrichment\nfactors, drawing enrichment curves to
evaluate virtual\nscreening
approaches.","License":"BSD","NeedsCompilation":"no","Package":"enrichvs","Reposito
ry":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Enrichment assessment of
virtual screening approaches","Version":"0.0.5"},"ensembleBMA":{"Author":"Chris
Fraley, Adrian E. Raftery, J. McLean Sloughter, Tilmann\nGneiting, University of
Washington.","Depends":"R (>= 2.10), chron","Description":"Bayesian Model Averaging
to create probabilistic forecasts\nfrom ensemble forecasts and weather
2)","NeedsCompilation":"no","Package":"ensembleBMA","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"fields, maps","Title":"Probabilistic Forecasting
using Ensembles and Bayesian Model\nAveraging","Version":"5.1.2"},"ensembleMOS":
{"Author":"RA Yuen, Tilmann Gneiting, Thordis Thorarinsdottir,
Chris\nFraley","Depends":"R (>= 2.10.0), ensembleBMA,
chron","Description":"Ensemble Model Output Statistics to create
probabilistic\nforecasts from ensemble forecasts and weather
2)","NeedsCompilation":"no","Package":"ensembleMOS","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"fields, maps","Title":"Ensemble Model Output
Statistics","Version":"0.7"},"ensurer":{"Author":"Stefan Milton
Bache","Description":"Add simple runtime contracts to R values. These ensure that
values\nfulfil certain conditions and will raise appropriate errors if they do
not.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"ensurer","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"magrittr, testthat, knitr","Title":"Ensure Values
at
Runtime","URL":"https:\/\/github.com\/smbache\/ensurer","Version":"1.1"},"entropart
":{"Author":"Eric Marcon, Bruno Herault","Description":"Measurement and
partitioning of diversity, based on Tsallis entropy.","Imports":"ade4, ape,
EntropyEstimation, geiger, graphics, grDevices,\nparallel, stats, utils,
vegan","License":"GNU General Public
License","NeedsCompilation":"no","Package":"entropart","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Entropy Partitioning to Measure
Diversity","Version":"1.4-5"},"entropy":{"Author":"Jean Hausser and Korbinian
Strimmer","Depends":"R (>= 2.15.1)","Description":"This package implements various
estimators of entropy, such\nas the shrinkage estimator by Hausser and Strimmer,
the maximum likelihood\nand the Millow-Madow estimator, various Bayesian
estimators, and the\nChao-Shen estimator. It also offers an R interface to the NSB
estimator.\nFurthermore, it provides functions for estimating Kullback-Leibler
divergence,\nchi-squared, mutual information, and chi-squared statistic of
independence.\nIn addition there are functions for discretizing continuous random
3)","NeedsCompilation":"no","Package":"entropy","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Estimation
of Entropy, Mutual Information and Related
Quantities","URL":"http:\/\/strimmerlab.org\/software\/entropy\/","Version":"1.2.1"
},"enveomics.R":{"Author":"Luis M. Rodriguez-R [aut, cre]","Depends":"R (>= 2.9),
stats, methods, parallel, modeest, fitdistrplus,\nsn","Description":"A collection
of R functions of common use in\nthe Kostas Lab for microbial
ecology.","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"enveomics.R","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"tools, vegan, ape, picante, gplots,
optparse","Title":"Various R Functions from the Kostas Lab","URL":"http:\/\/enve-
omics.gatech.edu\/","Version":"1.0.1"},"enviPat":{"Author":"Martin Loos, Christian
Gerber","Description":"Fast and very memory-efficient calculation of isotope
patterns,\nsubsequent convolution to theoretical envelopes (profiles) plus
valley\ndetection and centroidization or intensoid calculation. Batch
processing,\nresolution interpolation, wrapper, adduct calculations and
molecular\nformula parsing.","License":"GPL-
2","NeedsCompilation":"yes","Package":"enviPat","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Isotope Pattern, Profile and Centroid Calculation for
Mass\nSpectrometry","URL":"http:\/\/www.envipat.eawag.ch\/,\nhttp:\/\/pubs.acs.org\
/doi\/abs\/10.1021\/acs.analchem.5b00941","Version":"2.1"},"enviPick":
{"Author":"Martin Loos","Depends":"R (>= 3.0.1), shiny(>= 0.7.0), readMzXmlData(>=
2.7)","Description":"Sequential partitioning, clustering and peak detection
of\ncentroided LC-MS mass spectrometry data (.mzXML). Interactive result and
raw\ndata plot.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"enviPick","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Peak Picking for High Resolution Mass Spectrometry
Data","Version":"1.4"},"envlpaster":{"Author":"Daniel J. Eck
<eckxx049@umn.edu>","Depends":"R (>= 2.10.0), aster","Description":"Envelope
methodology and aster modeling are combined to provide users with precise
estimation of expected Darwinian fitness.","Imports":"caTools, MASS,
aster2","License":"GPL-
2","NeedsCompilation":"no","Package":"envlpaster","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Enveloping the Aster Model","Version":"0.1-2"},"epade":
{"Author":"Andreas Schulz","Depends":"plotrix, R (>= 2.14)","Description":"A
collection of nice plotting functions directly from a\ndata.frame with limited
customisation possibilities.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"epade","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"survival, Hmisc","Title":"Easy
Plots","Version":"0.3.8"},"epandist":{"Author":"Mathias Borritz Milfeldt [aut,
cre]","Depends":"R (>= 3.0.0)","Description":"Analyzing censored variables usually
requires the use of optimization algorithms. This package provides an alternative
algebraic approach to the task of determining the expected value of a random
censored variable with a known censoring point. Likewise this approach allows for
the determination of the censoring point if the expected value is known. These
results are derived under the assumption that the variable follows an Epanechnikov
kernel distribution with known mean and range prior to censoring. Statistical
functions related to the uncensored Epanechnikov distribution are also provided by
this
package.","License":"LGPL","NeedsCompilation":"no","Package":"epandist","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"knitr,
rmarkdown","Title":"Statistical Functions for the Censored and
Uncensored\nEpanechnikov Distribution","Version":"1.1.1"},"epanetReader":
{"Author":"Bradley J. Eck","Depends":"R (>= 3.0.0), graphics,
utils","Description":"Reads water network simulation data in Epanet's text-
based\n'.inp' and '.rpt' formats into R. Also reads results from Epanet-
msx.\nProvides basic summary information and plots.\nThe README file has a quick
introduction. See http:\/\/www2.epa.gov\/\nwater-research\/epanet for more
information on the Epanet software for modeling\nhydraulic and water quality
behavior of water piping systems.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"epanetReader","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Read Epanet Files into
R","Version":"0.3.1"},"epiDisplay":{"Author":"Virasakdi Chongsuvivatwong
<cvirasak@medicine.psu.ac.th>","Depends":"R (>= 2.6.2), foreign, survival, MASS,
nnet","Description":"Package for data exploration and result presentation.\nFull
'epicalc' package with data management functions is available\nat the author's
repository.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"epiDisplay","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Epidemiological Data Display
Package","URL":"http:\/\/CRAN.R-project.org\/","Version":"3.2.2.0"},"epiR":
{"Author":"Mark Stevenson <mark.stevenson1@unimelb.edu.au> with contributions from
Telmo Nunes, Cord Heuer, Jonathon Marshall, Javier Sanchez, Ron Thornton, Jeno
Reiczigel, Jim Robison-Cox, Paola Sebastiani, Peter Solymos, Kazuki Yoshida, Geoff
Jones, Sarah Pirikahu, Simon Firestone and Ryan Kyle","Depends":"R (>= 3.0.0),
survival","Description":"Tools for the analysis of epidemiological data. Contains
functions for directly and indirectly adjusting measures of disease frequency,
quantifying measures of association on the basis of single or multiple strata of
count data presented in a contingency table, and computing confidence intervals
around incidence risk and incidence rate estimates. Miscellaneous functions for use
in meta-analysis, diagnostic test interpretation, and sample size
calculations.","Imports":"BiasedUrn, methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"epiR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"MASS (>= 3.1-20)","Title":"Tools for the Analysis of
Epidemiological Data","URL":"http:\/\/fvas.unimelb.edu.au\/veam","Version":"0.9-
74"},"epibasix":{"Author":"Michael A Rotondi <mrotondi@yorku.ca>","Depends":"R (>=
2.01)","Description":"This package contains elementary tools for analysis
of\ncommon epidemiological problems, ranging from sample size\nestimation, through
2x2 contingency table analysis and basic\nmeasures of agreement (kappa,
sensitivity\/specificity).\nAppropriate print and summary statements are also
written to\nfacilitate interpretation wherever possible. Source code is\ncommented
throughout to facilitate modification. The target\naudience includes advanced
undergraduate and graduate students\nin epidemiology or biostatistics courses, and
clinical\nresearchers.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"epibasix","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Elementary Epidemiological Functions for Epidemiology
and\nBiostatistics","Version":"1.3"},"epifit":{"Author":"Kazutaka Doi
[aut,cre],\nKei Sakabe [ctb],\nMasataka Taruri [ctb]","Description":"Provides
flexible model fitting used in epidemiological data\nanalysis by a unified model
specification, along with some data manipulation\nfunctions. This package covers
fitting of variety models including Cox\nregression models, linear regression
models, Poisson regression models, logistic\nmodels and others whose likelihood is
expressed in negative binomial, gamma and\nWeibull
distributions.","Imports":"stats, MASS","License":"GPL-
3","NeedsCompilation":"yes","Package":"epifit","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"survival","Title":"Flexible Modelling Functions for
Epidemiological Data Analysis","Version":"0.0.6"},"epinet":{"Author":"Chris
Groendyke [aut, cre],\nDavid Welch [aut],\nDavid Hunter [ctb]","Description":"A
collection of epidemic\/network-related tools. Simulates transmission of diseases
through contact networks. Performs Bayesian inference on network and epidemic
parameters, given epidemic data.","Imports":"network","License":"GPL-
2","NeedsCompilation":"yes","Package":"epinet","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Epidemic\/Network-Related
Tools","Version":"2.1.7"},"episensr":{"Author":"Denis Haine [aut,
cre]","Depends":"R (>= 3.2.3)","Description":"Basic sensitivity analysis of the
observed relative risks adjusting\nfor unmeasured confounding and misclassification
of the\nexposure\/outcome, or both. It follows the bias analysis methods
and\nexamples from the book by Lash T.L, Fox M.P, and Fink A.K.\n\"Applying
Quantitative Bias Analysis to Epidemiologic Data\",\n('Springer',
2009).","Imports":"triangle, trapezoid, plyr, ggplot2, grid,
gridExtra","License":"GPL-
2","NeedsCompilation":"no","Package":"episensr","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"testthat","Title":"Basic Sensitivity Analysis of
Epidemiological Results","Version":"0.7.2"},"episplineDensity":{"Author":"Sam
Buttrey, Johannes Royset, and Roger Wets, based on\nthe Matlab code of Royset and
Wets","Depends":"nloptr, pracma","Description":"Produce one-dimensional density
estimates using\nexponential epi-splines. The user may incorporate soft
information, by\nimposing constraints that (i) require unimodality; (ii) require
that the\ndensity be monotone non-increase or non-decreasing; (iii) put upper
bounds\non first or second moments; (iv) bound the density's values at mesh
points;\n(v) require that the estimate be continuous or continuously
differentiable;\nand more.","License":"GPL-
2","NeedsCompilation":"no","Package":"episplineDensity","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Density Estimation with Soft Information by
Exponential\nEpi-splines","Version":"0.0-1"},"epitools":{"Author":"Tomas J. Aragon
Developer [aut, cre], Michael P. Fay User\n[ctb], Daniel Wollschlaeger User
[ctb]","Depends":"R (>= 2.1.0)","Description":"EpiTools: R Package for
Epidemiologic Data and Graphics","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"epitools","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Epidemiology
Tools","URL":"http:\/\/medepi.com\/epitools\/","Version":"0.5-7"},"epoc":
{"Author":"Rebecka Jornsten, Tobias Abenius, Sven Nelander","Depends":"R (>=
2.12.0), lassoshooting (>= 0.1.4), Matrix,
methods,\ngraph","Description":"Estimates sparse matrices A or G using fast lasso
regression from mRNA transcript levels Y and CNA profiles U. Two models are
provided, EPoC A where\nAY + U + R = 0\nand EPoC G where\nY = GU + E,\nthe matrices
R and E are so far treated as noise. For details see the reference and the manual
page of `lassoshooting'.","Imports":"irr, elasticnet, survival,
Rgraphviz","License":"LGPL-
3","NeedsCompilation":"no","Package":"epoc","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"RCytoscape","Title":"EPoC (Endogenous Perturbation
analysis of Cancer)","Version":"0.2.5-1"},"epr":{"Author":"Emmanuel
Arnhold","Depends":"R (>= 2.13), car","Description":"The package performs analysis
of polynomial regression in simple designs with quantitative
treatments","License":"GPL-
2","NeedsCompilation":"no","Package":"epr","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Easy polynomial regression","Version":"2.0"},"eqs2lavaan":
{"Author":"Craig M. Krebsbach","Depends":"lavaan,
stringr","Description":"Transitioning from EQS to R for structural equation
modeling (SEM)\nis made easier with a set of functions to convert .out files into R
code.\nThe EQS output can be converted into lavaan syntax and run in the
R\nenvironment. Other functions parse descriptive statistics and the covariance
matrix\nfrom an EQS .out file. A heat map plot of a covariance matrix is
also\nincluded.","License":"GPL-
2","NeedsCompilation":"no","Package":"eqs2lavaan","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"EQS Output Conversion to lavaan
Functions","Version":"3.0"},"eqtl":{"Author":"Ahmid A. Khalili and Olivier
Loudet","Depends":"R (>= 2.10), qtl (>= 1.7.12)","Description":"Analysis of
experimental crosses to identify genes (called\nquantitative trait loci, QTLs)
contributing to variation in\nquantitative traits.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"eqtl","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Tools for analyzing eQTL experiments: A complementary to
Karl\nBroman's 'qtl' package for genome-wide analysis","Version":"1.1-7"},"equate":
{"Author":"Anthony Albano <tony.d.albano@gmail.com>","Depends":"R (>=
3.0.0)","Description":"Contains methods for observed-score linking\nand equating
under the single-group, equivalent-groups,\nand nonequivalent-groups with anchor
test(s) designs.\nEquating types include identity, mean, linear, general\nlinear,
equipercentile, circle-arc, and composites of\nthese. Equating methods include
synthetic, nominal\nweights, Tucker, Levine observed score, Levine true\nscore,
Braun\/Holland, frequency estimation, and chained\nequating. Plotting and summary
methods, and methods for\nmultivariate presmoothing and bootstrap error
estimation\nare also provided.","License":"GPL (>= 2) | file
LICENSE","NeedsCompilation":"no","Package":"equate","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Observed-Score Linking and
Equating","URL":"http:\/\/www.r-project.org","Version":"2.0-3"},"equateIRT":
{"Author":"Michela Battauz","Description":"Computation of direct, chain and average
(bisector) equating coefficients with standard errors using Item Response Theory
(IRT) methods for dichotomous items. Test scoring can be performed by true score
equating and observed score equating methods.","Imports":"statmod, stats, utils,
mirt","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"equateIRT","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"ltm","Title":"Direct, Chain and Average Equating
Coefficients with Standard\nErrors Using IRT
Methods","Version":"2.0"},"equivalence":{"Author":"Andrew Robinson
<A.Robinson@ms.unimelb.edu.au>","Depends":"lattice, boot,
PairedData","Description":"Provides statistical tests and graphics for assessing
tests\nof equivalence. Such tests have similarity as the alternative\nhypothesis
instead of the null. Sample data sets are
included.","Imports":"grid","License":"GPL-
2","NeedsCompilation":"yes","Package":"equivalence","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Provides Tests and Graphics for Assessing Tests of
Equivalence","Version":"0.7.1"},"erboost":{"Author":"Yi Yang <yiyang@umn.edu>, Hui
Zou <hzou@stat.umn.edu>","Depends":"R (>= 2.12.0), lattice,
splines","Description":"Expectile regression is a nice tool for estimating the
conditional expectiles of a response variable given a set of covariates. This
package implements a regression tree based gradient boosting estimator for
nonparametric multiple expectile regression.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"erboost","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Nonparametric Multiple Expectile Regression via ER-
Boost","Version":"1.3"},"erer":{"Author":"Changyou Sun
<cs258@msstate.edu>","Depends":"R (>= 3.0.0), lmtest","Description":"Functions,
datasets, and sample codes related to the book of 'Empirical Research in Economics:
Growing up with R' by Dr. Changyou Sun are included. Marginal effects for binary or
ordered choice models can be calculated. Static and dynamic Almost Ideal Demand
System (AIDS) models can be estimated. A typical event analysis in finance can be
conducted with several functions included.","Imports":"systemfit, tseries,
urca","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"erer","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"MASS","Title":"Empirical Research in Economics with
R","Version":"2.5"},"ergm":{"Author":"Mark S. Handcock [aut],\nDavid R. Hunter
[aut],\nCarter T. Butts [aut],\nSteven M. Goodreau [aut],\nPavel N. Krivitsky [aut,
cre],\nMartina Morris [aut],\nLi Wang [ctb],\nKirk Li [ctb],\nSkye Bender-deMoll
[ctb]","Depends":"statnet.common (>= 3.3), network (>= 1.13)","Description":"An
integrated set of tools to analyze and simulate networks based on exponential-
family random graph models (ERGM). \"ergm\" is a part of the \"statnet\" suite of
packages for network analysis.","Imports":"robustbase (>= 0.9-10), coda (>= 0.18-
1), trust, Matrix,\nlpSolve, parallel, methods, MASS","License":"GPL-3 + file
LICENSE","NeedsCompilation":"yes","Package":"ergm","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"lattice, latticeExtra, sna, latentnet,
rmarkdown,\nergm.userterms, tergm, Rmpi","Title":"Fit, Simulate and Diagnose
Exponential-Family Models
for\nNetworks","URL":"http:\/\/statnet.org","Version":"3.6.0"},"ergm.count":
{"Author":"Pavel N. Krivitsky [aut, cre],\nMark S. Handcock [ctb],\nDavid R. Hunter
[ctb]","Depends":"statnet.common (>= 3.1), ergm (>= 3.4), network","Description":"A
set of extensions for the 'ergm' package to fit weighted networks whose edge
weights are counts.","License":"GPL-3 + file
LICENSE","NeedsCompilation":"yes","Package":"ergm.count","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Fit, Simulate and Diagnose Exponential-Family
Models for\nNetworks with Count
Edges","URL":"http:\/\/statnet.org","Version":"3.2.2"},"ergm.ego":{"Author":"Pavel
N. Krivitsky [aut, cre],\nSteven M. Goodreau [ctb],\nMartina Morris [ctb],\nKirk Li
[ctb],\nEmily N. Beylerian [ctb]","Depends":"ergm (>= 3.5),
network","Description":"Utilities for managing egocentrically sampled network data
and a wrapper around the 'ergm' package to facilitate ERGM inference and simulation
from such data.","Imports":"statnet.common, coda, RColorBrewer","License":"GPL-3 +
file
LICENSE","NeedsCompilation":"no","Package":"ergm.ego","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Fit, Simulate and Diagnose Exponential-Family
Random Graph\nModels to Egocentrically Sampled Network
Data","URL":"http:\/\/www.statnet.org","Version":"0.3.0"},"ergm.graphlets":
{"Author":"Omer Nebil Yaveroglu [aut, cre],\nSean M. Fitzhugh [aut],\nMaciej Kurant
[aut],\nAthina Markopoulou [aut],\nNatasa Przulj [aut],\nCarter T. Butts
[aut]","Depends":"network (>= 1.7-1), ergm (>= 3.1-0), statnet.common (>= 3.1-
0)","Description":"Integrates graphlet statistics based model terms for use in
exponential-family random graph models ('ergm') as part of the 'statnet' suite of
packages.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ergm.graphlets","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"parallel, rlecuyer","Title":"ERG Modeling
Based on Graphlet Properties","Version":"1.0.3"},"ergm.rank":{"Author":"Pavel N.
Krivitsky [aut, cre],\nCarter T. Butts [ctb],\nMark S. Handcock [ctb],\nDavid R.
Hunter [ctb]","Depends":"statnet.common (>= 3.1), ergm (>= 3.5),
network","Description":"A set of extensions for the 'ergm' package to fit weighted
networks whose edge weights are ranks.","License":"GPL-3 + file
LICENSE","NeedsCompilation":"yes","Package":"ergm.rank","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Fit, Simulate and Diagnose Exponential-Family
Models for\nRank-Order Relational
Data","URL":"http:\/\/statnet.org","Version":"1.0.1"},"ergm.userterms":
{"Author":"Mark S. Handcock [aut],\nDavid R. Hunter [aut],\nCarter T. Butts
[aut],\nSteven M. Goodreau [aut],\nPavel N. Krivitsky [aut, cre],\nMartina Morris
[aut]","Depends":"network (>= 1.7-1), ergm (>= 3.1-0), statnet.common (>= 3.1-
0)","Description":"A template package to demonstrate the use of user-specified
statistics for use in \"ergm\" models as part of the \"statnet\" suite of
packages.","License":"GPL-3 + file
LICENSE","NeedsCompilation":"yes","Package":"ergm.userterms","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Title":"User-specified terms for the statnet suite
of packages","URL":"http:\/\/statnet.org","Version":"3.1.1"},"ergmharris":
{"Author":"Jenine K. Harris","Description":"Data for use with the Sage Introduction
to Exponential\nRandom Graph Modeling
text by Jenine K. Harris. Network data\nset consists of 1283 local health
departments and the\ncommunication links among them along with several
attributes.","License":"GPL-
3","NeedsCompilation":"no","Package":"ergmharris","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Local Health Department network data
set","Version":"1.0"},"erp.easy":{"Author":"Travis Moore [aut, cre]","Depends":"R
(>= 3.2.0)","Description":"A set of user-friendly functions to aid in organizing,
plotting\nand analyzing event-related potential (ERP) data. Provides an easy-to-
learn\nmethod to explore ERP data. Should be useful to those without a
background\nin computer programming, and to those who are new to ERPs (or new to
the\nmore advanced ERP software available). Emphasis has been placed on
highly\nautomated processes using functions with as few arguments as
possible.\nExpects processed (cleaned) data.","Imports":"plyr (>= 1.8.3), signal
(>= 0.7-6)","License":"GPL-
3","NeedsCompilation":"no","Package":"erp.easy","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Event-Related Potential (ERP) Data Exploration Made
Easy","Version":"1.0.0"},"erpR":{"Author":"Giorgio Arcara, Anna
Petrova","Depends":"R (>= 3.0.2), rpanel","Description":"This package is dedicated
to the analysis of event-related potentials (ERPs). Event-related potentials are
the measured brain responses associated with a specific sensory, cognitive, or
motor event and are obtained from electroencephalographic (EEG) signal. The erpR
package contains a series of functions for importing ERP data, computing
traditional ERP measures, exploratory ERP analyses and plotting.","License":"GPL-
3","NeedsCompilation":"no","Package":"erpR","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"akima","Title":"Event-related potentials (ERP) analysis,
graphics and utility\nfunctions","Version":"0.2.0"},"errint":{"Author":"Jesus Prada
[aut,cre]","Depends":"VGAM, rootSolve","Description":"Build and analyze error
intervals for a particular model predictions assuming different distributions for
noise in the data.","License":"GPL-
2","NeedsCompilation":"no","Package":"errint","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Build Error
Intervals","URL":"http:\/\/link.springer.com\/chapter\/10.1007\/978-3-319-19222-
2_47","Version":"0.1"},"esaBcv":{"Author":"Art B. Owen [aut],\nJingshu Wang [aut,
cre]","Depends":"R (>= 3.0.2)","Description":"These functions estimate the latent
factors of a given matrix, no matter it is high-dimensional or not. It tries to
first estimate the number of factors using bi-cross-validation and then estimate
the latent factor matrix and the noise variances. For more information about the
method, see Art B. Owen and Jingshu Wang 2015 archived article on factor model
(http:\/\/arxiv.org\/abs\/1503.03515).","Imports":"corpcor, svd","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"esaBcv","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"MASS","Title":"Estimate Number of Latent Factors and
Factor Matrix for Factor\nAnalysis","Version":"1.2.1"},"estatapi":
{"Author":"Hiroaki Yutani [aut, cre]","Depends":"R (>=
3.1.2)","Description":"Provides an interface to e-Stat API, the one-stop service
for official statistics of the Japanese government.","Imports":"httr, dplyr,
purrr(>= 0.2), readr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"estatapi","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat","Title":"R Interface to e-Stat
API","Version":"0.2"},"estimability":{"Author":"Russell V.
Lenth","Depends":"stats","Description":"Provides tools for determining estimability
of linear functions of regression coefficients,\nand 'epredict' methods that handle
non-estimable cases correctly.","License":"GPL-
2","NeedsCompilation":"no","Package":"estimability","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Tools for Assessing Estimability of Linear
Predictions","Version":"1.1-1"},"estout":{"Author":"Felix Kaminsky <fkamins@uni-
goettingen.de>, inspired by the\nestout package for Stata.","Description":"This
package is intended to speedup the process of\ncreating model-comparing tables
common in Macroeconomics. The\nfunction collection stores the estimates of several
models and\nformats it to a table of the form estimate starred and std.err.\nbelow.
The default output is LaTeX but output to CSV for later\nediting in a spreadsheet
tool is possible as well. It works for\nlinear models (lm) and panel models from
the \"plm\"-package\n(plm). Two further implemented functions \"descsto\"
and\n\"desctab\" enable you to export descriptive statistics of\ndata-frames and
single variables to LaTeX and CSV.","License":"GPL-
2","NeedsCompilation":"no","Package":"estout","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Estimates
Output","URL":"http:\/\/www.toolswitch.net","Version":"1.2"},"etable":
{"Author":"Andreas Schulz","Depends":"R (>= 3.0.0), xtable, Hmisc","Description":"A
table function for descriptive statistics in tabular format, using variables in a
data.frame. You can create simple or highly customized tables.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"etable","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Easy Table","Version":"1.2.0"},"etasFLP":
{"Author":"Marcello Chiodi [aut, cre],\nGiada Adelfio [aut]","Depends":"R (>=
2.14.0),mapdata,rgl","Description":"Estimation of the components of an ETAS model
for earthquake description. Non-parametric background seismicity can be estimated
through FLP (Forward Likelihood Predictive), while parametric components are
estimated through maximum likelihood. The two estimation steps are alternated until
convergence is obtained. For each event the probability of being a background event
is estimated and used as a weight for declustering steps. Many options to control
the estimation process are present, together with some diagnostic tools. Some
descriptive functions for earthquakes catalogs are present; also plot, print,
summary, profile methods are defined for main output (objects of class
'etasclass').","Imports":"fields,maps","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"etasFLP","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"MASS","Title":"Mixed FLP and ML Estimation of ETAS
Space-Time Point Processes","Version":"1.3.0"},"etm":{"Author":"Arthur
Allignol","Depends":"R (>= 2.14), survival","Description":"Matrix of transition
probabilities for any time-inhomogeneous multistate model with finite state
space","Imports":"lattice","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"etm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"ggplot2, kmi, geepack","Title":"Empirical Transition
Matrix","Version":"0.6-2"},"etma":{"Author":"Chin Lin","Depends":"R (>= 2.10),
graphics, stats, utils","Description":"Traditional meta-regression based method has
been developed for using meta-analysis data, but it faced the challenge of
inconsistent estimates. This package purpose a new statistical method to detect
epistasis using incomplete information summary, and have proven it not only
successfully let consistency of evidence, but also increase the power compared with
traditional method (Detailed tutorial is shown in website).","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"etma","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr","Title":"Epistasis Test in Meta-
Analysis","Version":"1.1-1"},"eulerian":{"Author":"Ashis Saha, with contribution
from Jaewoo Kang","Depends":"R(>= 2.15.0), methods","Description":"An eulerian path
is a path in a graph which visits every edge exactly once. This package provides
methods to handle eulerian paths or cycles.","Imports":"graph","License":"GPL-
2","NeedsCompilation":"no","Package":"eulerian","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"eulerian: A package to find eulerian paths from
graphs","Version":"1.0"},"euroMix":{"Author":"Guro Dorum and Thore
Egeland","Depends":"R (>= 3.0), paramlink (>= 0.9-7), Familias,
forensim","Description":"Calculations for DNA mixtures accounting for possibly
inbred pedigrees (simulations with conditioning, LR). Calculation of exact p-
values.","Imports":"graphics, utils","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"euroMix","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Calculations for DNA
Mixtures","Version":"1.1.1"},"eurostat":{"Author":"Lahti Leo [aut, cre],\nBiecek
Przemyslaw [aut],\nKainu Markus [aut],\nHuovari Janne [aut]","Depends":"R (>=
3.0.2)","Description":"Tools to download data from the Eurostat
database\n<http:\/\/ec.europa.eu\/eurostat> together with search and
manipulation\nutilities.","Imports":"tidyr, jsonlite, httr","License":"BSD_2_clause
+ file
LICENSE","NeedsCompilation":"no","Package":"eurostat","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"devtools, dplyr, ggplot2, knitr, mapproj,
plotrix, rvest,\nstringi, testthat","Title":"Tools for Eurostat Open
Data","URL":"https:\/\/github.com\/ropengov\/eurostat","Version":"1.2.21"},"eva":
{"Author":"Brian Bader [aut, cre],\nJun Yan [ctb]","Depends":"R(>=
2.10.0)","Description":"Goodness-of-fit tests for selection of r in the r-largest
order\nstatistics (GEVr) model. Goodness-of-fit tests for threshold selection in
the\npeaks-over-threshold approach. Random number generation and density
functions\nfor the GEVr distribution. Profile likelihood for return level
estimation\nusing the GEVr and Generalized Pareto distributions. P-value
adjustments for\nsequential, multiple testing error control.","Imports":"parallel,
stats, graphics, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"eva","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"knitr","Title":"Extreme Value Analysis with Goodness-of-
Fit
Testing","URL":"https:\/\/github.com\/geekman1\/eva_package","Version":"0.2.1"},"ev
aluate":{"Author":"Hadley
Wickham [aut],\nYihui Xie [cre, ctb],\nMichael Lawrence [ctb],\nThomas Kluyver
[ctb],\nBarret Schloerke [ctb]","Depends":"R (>= 3.0.2)","Description":"Parsing and
evaluation tools that make it easy to recreate the\ncommand line behaviour of
R.","Imports":"methods, stringr (>= 0.6.2)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"evaluate","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat, lattice, ggplot2","Title":"Parsing and
Evaluation Tools that Provide More Details than
the\nDefault","URL":"https:\/\/github.com\/hadley\/evaluate","Version":"0.8.3"},"ev
d":{"Author":"Alec Stephenson. Function fbvpot by Chris
Ferro.","Description":"Extends simulation, distribution, quantile and
density\nfunctions to univariate and multivariate parametric extreme\nvalue
distributions, and provides fitting functions which\ncalculate maximum likelihood
estimates for univariate and\nbivariate maxima models, and for univariate and
bivariate\nthreshold models.","Imports":"stats, grDevices,
3","NeedsCompilation":"yes","Package":"evd","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"akima","Title":"Functions for Extreme Value
Distributions","Version":"2.3-2"},"evdbayes":{"Author":"Alec Stephenson and Mathieu
Ribatet.","Depends":"R (>= 1.8.0)","Description":"Provides functions for the
bayesian analysis of extreme\nvalue models, using MCMC methods.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"evdbayes","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Bayesian Analysis in Extreme Value
Theory","Version":"1.1-1"},"eventInterval":{"Author":"Jim Lemon
<drjimlemon@gmail.com>,","Description":"Functions for analysis of rate changes in
sequential events.","Imports":"MASS, graphics, stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"eventInterval","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Sequential Event Interval
Analysis","Version":"1.3"},"events":{"Author":"Will Lowe","Depends":"R (>=
2.10)","Description":"Stores, manipulates, aggregates and otherwise messes with
event\ndata from KEDS\/TABARI or any other extraction tool with similar
output","License":"GPL","NeedsCompilation":"no","Package":"events","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"Store and manipulate event
data","Version":"0.5"},"eventstudies":{"Author":"Ajay Shah, Vimal Balasubramaniam,
Vikram Bahure","Depends":"R (>= 2.12.0), zoo, xts,
boot","Description":"Implementation of short and long term event
study\nmethodology","License":"GPL-
2","NeedsCompilation":"no","Package":"eventstudies","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Event study and extreme event
analysis","Version":"1.1"},"evir":{"Author":"Bernhard Pfaff [aut, cre], Alexander
McNeil [aut] (S original\n(EVIS)), Alec Stephenson [trl] (R port of
EVIS)","Depends":"stats","Description":"Functions for extreme value theory, which
may be divided\ninto the following groups; exploratory data analysis,
block\nmaxima, peaks over thresholds (univariate and bivariate), point\nprocesses,
gev\/gpd distributions.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"evir","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Extreme Values in R","Version":"1.7-3"},"evmix":
{"Author":"Carl Scarrott and Yang Hu, University of Canterbury","Depends":"stats,
graphics, MASS, splines, gsl, SparseM","Description":"The usual distribution
functions, maximum likelihood inference and\nmodel diagnostics for univariate
stationary extreme value mixture models\nare provided. Kernel density estimation
including various boundary\ncorrected kernel density estimation methods and a wide
choice of kernels,\nwith cross-validation likelihood based bandwidth
estimator.\nReasonable consistency with the base functions in the 'evd' package
is\nprovided, so that users can safely interchange most code.","License":"GPL-
3","NeedsCompilation":"no","Package":"evmix","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Extreme Value Mixture Modelling, Threshold Estimation
and\nBoundary Corrected Kernel Density
Estimation","URL":"http:\/\/www.math.canterbury.ac.nz\/~c.scarrott\/evmix","Version
":"2.6"},"evobiR":{"Author":"Heath Blackmon and Richard H.
Adams","Description":"Comparative analysis of continuous traits influencing
discrete states, and utility tools to facilitate comparative analyses.
Implementations of ABBA\/BABA type statistics to test for introgression in genomic
data. Wright-Fisher, phylogenetic tree, and statistical distribution Shiny
interactive simulations for use in teaching.","Imports":"seqinr, ape, geiger,
shiny, phytools","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"evobiR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Comparative and Population Genetic
Analyses","URL":"http:\/\/www.uta.edu\/karyodb\/evobiR\/","Version":"1.1"},"evolqg"
:{"Author":"Ana Paula Assis, Diogo Melo, Edgar Zanella, Fabio Machado,
Guilherme\nGarcia","Depends":"R (>= 3.1.0), plyr (>=
1.7.1)","Description":"Provides functions for covariance matrix comparisons,
estimation\nof repeatabilities in measurements and matrices, and general
evolutionary\nquantitative genetics tools.","Imports":"Rcpp (>= 0.11), Matrix,
reshape2, ggplot2, magrittr, tidyr,\nvegan, ape, phytools, mvtnorm, coda, graphics,
grDevices,\nmethods, stats, depth, utils","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"evolqg","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat (>= 0.2), foreach, grid, gridExtra,
doParallel","Title":"Tools for Evolutionary Quantitative Genetics","Version":"0.2-
2"},"evolvability":{"Author":"Geir H. Bolstad [aut, cre]","Description":"An
implementation of the evolvability parameters defined in Hansen and Houle
(2008).","Imports":"coda","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"evolvability","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Calculation of Evolvability
Parameters","Version":"1.1.0"},"evt0":{"Author":"B G Manjunath and Frederico
Caeiro; guidance from Prof. M. Ivette Gomes and Prof. M. Isabel Fraga
Alves","Depends":"R (>= 1.9.0), evd, stats","Description":"Computes extreme value
index (EVI) estimate for heavy tailed models by Mean of order p (MOP)\nand peaks
over random threshold (PORT) Hill methodologies.\nBesides, also computes moment,
generalised Hill and mixed moment estimates for EVI.\nCompute high quantile or
value-at-risk (VaR) based on above EVI estimates.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"evt0","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Mean of order p, peaks over random threshold Hill and
high\nquantile estimates","URL":"http:\/\/www.r-project.org","Version":"1.1-
3"},"evtree":{"Author":"Thomas Grubinger [aut, cre],\nAchim Zeileis [aut],\nKarl-
Peter Pfeiffer [aut]","Depends":"R (>= 2.11.0), partykit","Description":"Commonly
used classification and regression tree methods like the CART algorithm\nare
recursive partitioning methods that build the model in a forward stepwise
search.\nAlthough this approach is known to be an efficient heuristic, the results
of recursive\ntree methods are only locally optimal, as splits are chosen to
maximize homogeneity at\nthe next step only. An alternative way to search over the
parameter space of trees is\nto use global optimization methods like evolutionary
algorithms. The evtree package\nimplements an evolutionary algorithm for learning
globally optimal classification and\nregression trees in R. CPU and memory-
intensive tasks are fully computed in C++ while\nthe partykit package is leveraged
to represent the resulting trees in R, providing\nunified infrastructure for
summaries, visualizations, and predictions.","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"evtree","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"Formula, kernlab, lattice, mlbench, multcomp, party,
rpart,\nxtable","Title":"Evolutionary Learning of Globally Optimal
Trees","Version":"1.0-0"},"exCon":{"Author":"Bryan Hanson [aut, cre],\nKristina
Mulry [ctb]","Depends":"R (>= 3.0)","Description":"Interactive tools to explore
topographic-like data\nsets. Such data sets take the form of a matrix in which the
rows and\ncolumns provide location\/frequency information, and the matrix
elements\ncontain altitude\/response information. Such data is found in
cartography,\n2D spectroscopy and chemometrics. The functions in this package
create\ninteractive web pages showing the contoured data, possibly with\nslices
from the original matrix parallel to each dimension. The interactive\nbehavior is
created using the D3.js 'JavaScript' library by Mike Bostock.","Imports":"jsonlite,
grDevices, utils","License":"GPL-
3","NeedsCompilation":"no","Package":"exCon","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"js","Title":"Interactive Exploration of Contour
Data","URL":"https:\/\/github.com\/bryanhanson\/exCon","Version":"0.1.14"},"exact2x
2":{"Author":"Michael P. Fay","Depends":"stats, exactci,
ssanv","Description":"Calculates Fisher's exact test, Blaker's exact test, or the
exact McNemar's test with appropriate matching confidence intervals. Provides power
and sample size calculations. Also gives melded confidence intervals for the
binomial case.","License":"GPL-
3","NeedsCompilation":"no","Package":"exact2x2","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Exact Conditional Tests and Confidence Intervals for 2x2
tables","Version":"1.4.1"},"exactLoglinTest":{"Author":"Brian Caffo
<bcaffo@gmail.com>","Depends":"R (>= 1.5)","Description":"Monte Carlo and MCMC
goodness of fit tests for log-
linear\nmodels","License":"GPL","NeedsCompilation":"yes","Package":"exactLoglinTest
","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"stats","Title":"M
onte Carlo Exact Tests for Log-linear
models","URL":"http:\/\/www.bcaffo.com","Version":"1.4.2"},"exactRankTests":
{"Author":"Torsten
Hothorn [aut, cre],\nKurt Hornik [aut]","Depends":"R (>= 2.4.0), stats,
utils","Description":"Computes exact conditional p-values and quantiles using
an\nimplementation of the Shift-Algorithm by Streitberg & Roehmel.","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"exactRankTests","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"survival","Title":"Exact Distributions for
Rank and Permutation Tests","Version":"0.8-28"},"exactci":{"Author":"Michael P.
Fay","Depends":"stats, ssanv","Description":"Calculates exact tests and confidence
intervals for one-sample binomial and one- or two-sample Poisson
cases.","License":"GPL-
3","NeedsCompilation":"no","Package":"exactci","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Exact P-Values and Matching Confidence Intervals for
Simple\nDiscrete Parametric Cases","Version":"1.3-1"},"exactmeta":{"Author":"Yilei
Yu and Lu Tian","Description":"Perform exact fixed effect meta analysis for rare
events data without the need of artificial continuity correction.","License":"GPL-
2","NeedsCompilation":"no","Package":"exactmeta","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Exact fixed effect meta analysis","Version":"1.0-
2"},"exams":{"Author":"Achim Zeileis [aut, cre],\nBettina Gruen [aut],\nFriedrich
Leisch [aut],\nNikolaus Umlauf [aut],\nDominik Ernst [ctb]","Depends":"R (>=
2.15.0)","Description":"Automatic generation of exams based on exercises in Sweave
(R\/LaTeX) or R\/Markdown format,\nincluding multiple-choice questions and
arithmetic problems. Exams can be produced in various formats,\nincluding PDF,
HTML, Moodle XML, QTI 1.2 (for OLAT\/OpenOLAT), QTI 2.1, ARSnova, and TCExam.\nIn
addition to fully customizable PDF exams, a standardized PDF format is provided
that can be\nprinted, scanned, and automatically evaluated.","Imports":"stats,
graphics, grDevices, tools, utils","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"exams","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"base64enc, knitr, parallel, png, RCurl, RJSONIO,
rmarkdown,\ntth","Title":"Automatic Generation of Exams in
R","URL":"http:\/\/exams.R-Forge.R-project.org\/","Version":"2.1-0"},"excel.link":
{"Author":"Gregory Demin <excel.link.feedback@gmail.com>. To comply CRAN
policy\nincludes source code from 'RDCOMClient'
(http:\/\/www.omegahat.org\/RDCOMClient) by\nDuncan Temple Lang
<duncan@wald.ucdavis.edu>.","Depends":"methods, grDevices,
utils","Description":"Allows access to data in running instance of Microsoft
Excel\n(e. g. 'xl[a1] = xl[b2]*3' and so on). Graphics can be transferred
with\n'xl[a1] = current.graphics()'. There is an Excel workbook with examples
of\ncalling R from Excel in the 'doc' folder. It tries to keep things as\nsimple as
possible - there are no needs in any additional\ninstallations besides R, only
'VBA' code in the Excel workbook.\nMicrosoft Excel is required for this
2)","NeedsCompilation":"yes","Package":"excel.link","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"knitr","Title":"Convenient Data Exchange with
Microsoft
Excel","URL":"https:\/\/github.com\/gdemin\/excel.link","Version":"0.9.3"},"excursi
ons":{"Author":"David Bolin <davidbolin@gmail.com> and Finn Lindgren
<finn.lindgren@gmail.com>","Depends":"Matrix, sp, spam","Description":"Functions
that compute probabilistic excursion sets, contour credibility regions, contour
avoiding regions, and simultaneous confidence bands for latent gaussian random
processes and fields. The package also contains functions that calculate these
quantities for models estimated with the INLA package.","Imports":"methods, stats,
3)","NeedsCompilation":"yes","Package":"excursions","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"INLA, testthat, rgeos","Title":"Excursion Sets and
Contour Credibility Regions for Random Fields","Version":"2.1.1"},"exifr":
{"Author":"Dewey Dunnington [aut, cre],\nPhil Harvey [aut]","Description":"Reads
EXIF data using ExifTool <http:\/\/www.sno.phy.queensu.ca\/~phil\/exiftool\/>\nand
returns results as a data frame.\nExifTool is a platform-independent Perl library
plus a command-line\napplication for reading, writing and editing meta information
in a wide variety\nof files. ExifTool supports many different metadata formats
including EXIF,\nGPS, IPTC, XMP, JFIF, GeoTIFF, ICC Profile, Photoshop IRB,
FlashPix, AFCP and\nID3, as well as the maker notes of many digital cameras by
Canon, Casio, FLIR,\nFujiFilm, GE, HP, JVC\/Victor, Kodak, Leaf, Minolta\/Konica-
Minolta, Motorola, Nikon,\nNintendo, Olympus\/Epson, Panasonic\/Leica,
Pentax\/Asahi, Phase One, Reconyx, Ricoh,\nSamsung, Sanyo, Sigma\/Foveon and
Sony.","Imports":"foreach, plyr, utils","License":"GPL-
2","NeedsCompilation":"no","Package":"exifr","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"EXIF Image Data in
R","URL":"https:\/\/github.com\/paleolimbot\/exifr","Version":"0.1.1"},"expands":
{"Author":"Noemi Andor","Depends":"R (>= 2.10)","Description":"Expanding Ploidy and
Allele Frequency on Nested Subpopulations (expands) characterizes coexisting
subpopulations in a single tumor sample using copy number and allele frequencies
derived from exome- or whole genome sequencing input data
(http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/24177718). The model detects coexisting
genotypes by leveraging run-specific tradeoffs between depth of coverage and
breadth of coverage. This package predicts the number of clonal expansions, the
size of the resulting subpopulations in the tumor bulk, the mutations specific to
each subpopulation, tumor purity and phylogeny. The main function runExPANdS()
provides the complete functionality needed to predict coexisting subpopulations
from single nucleotide variations (SNVs) and associated copy numbers. The
robustness of subpopulation predictions increases with the number of mutations
provided. It is recommended that at least 200 mutations are used as input to obtain
stable results. Updates in version 1.7 include: (1) Higher subpopulation detection
specificity, in particular for small subpopulations. (2) Higher accuracy for
mutation assignment to subpopulations. (3) Whenever possible, SNVs are assigned not
only to the subpopulation in which they first occurred, but also to descending
subpopulations. (4) Two additional output files are created: subpopulation specific
ploidy matrix and a summary file of all detected subpopulations, including
information on the inferred ancestor and the closest descendant of each
subpopulation. (5) New subpopulation plotting options (function plotSPs). (6) New
phylogeny plotting option: user can choose between consensus and germline
population to be included as control. (7) 50 simulated samples of various genetic
complexities and measurement precision included for user testing. Special thanks to
Dr. Ryan Morin for his contributions that have led to higher accuracy measures
during simulations for mutation assignment to subpopulations, as well as advanced
visualization features of assigned mutations. Further documentation and FAQ
available at http:\/\/dna-
discovery.stanford.edu\/software\/expands.","Imports":"rJava (>= 0.5-0), flexmix
(>= 2.3), matlab (>= 0.8.9), mclust\n(>= 4.2), moments (>= 0.13), ape (>= 3.2),
permute (>= 0.8)","License":"GPL-
2","NeedsCompilation":"no","Package":"expands","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"phylobase (>= 0.6.8)","Title":"Expanding Ploidy and
Allele-Frequency on Nested Subpopulations","URL":"http:\/\/dna-
discovery.stanford.edu\/software\/expands,\nhttps:\/\/github.com\/noemiandor\/expan
ds,\nhttps:\/\/groups.google.com\/d\/forum\/expands","Version":"1.7.2"},"expectreg"
:{"Author":"Fabian Sobotka <fabian.sobotka@wiwi.uni-goettingen.de>,\nSabine
Schnabel <sabine.schnabel@wur.nl>\nand Linda Schulze Waltrup
<lschulze_waltrup@stat.uni-muenchen.de>\nwith contributions from\nPaul Eilers
<p.eilers@erasmusmc.nl>,\nThomas Kneib <tkneib@uni-goettingen.de>\nand Goeran
Kauermann <goeran.kauermann@stat.uni-muenchen.de>.","Depends":"R (>= 2.14.0),
stats, parallel,mboost (>= 2.1.0), BayesX (>=\n0.2-4)","Description":"Expectile and
quantile regression of models with nonlinear effects\ne.g. spatial, random, ridge
using least asymmetric weighed squares \/ absolutes\nas well as boosting; also
supplies expectiles for common distributions.","Imports":"splines,
2","NeedsCompilation":"no","Package":"expectreg","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"SemiPar, fields","Title":"Expectile and Quantile
Regression","Version":"0.39"},"experiment":{"Author":"Kosuke Imai
<kimai@princeton.edu>","Depends":"boot, MASS, R (>= 2.4.0)","Description":"The
package provides various statistical methods for\ndesigning and analyzing
randomized experiments. One main\nfunctionality of the package is the
implementation of\nrandomized-block and matched-pair designs based on
possibly\nmultivariate pre-treatment covariates. The package also\nprovides the
tools to analyze various randomized experiments\nincluding cluster randomized
experiments, randomized\nexperiments with noncompliance, and randomized experiments
with\nmissing data.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"experiment","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"experiment: R package for designing and analyzing
randomized\nexperiments","URL":"http:\/\/imai.princeton.edu\/software\/experiment.h
tml","Version":"1.1-1"},"expert":{"Author":"Mathieu Pigeon, Michel Jacques, Vincent
Goulet","Depends":"R (>= 2.6.0), stats","Description":"Expert opinion (or judgment)
is a body of techniques to\nestimate the distribution of a random variable when
data is scarce\nor unavailable. Opinions on the quantiles of the distribution
are\nsought from experts in the field and aggregated into a final\nestimate. The
package supports aggregation by means of the Cooke,\nMendel-Sheridan and
predefined weights models.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"expert","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Modeling without data using expert
opinion","Version":"1.0-0"},"explor":{"Author":"Julien Barnier [aut,
cre]","Description":"Shiny interfaces and graphical functions for multivariate
analysis results exploration.","Imports":"shiny (>= 0.13), shinyBS, DT, dplyr,
tidyr, ggplot2, scatterD3\n(>= 0.6.1)","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"explor","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"FactoMineR, ade4, testthat, knitr,
rmarkdown","Title":"Interactive Interfaces for Results
Exploration","URL":"https:\/\/github.com\/juba\/explor","Version":"0.2.1"},"explore
R":{"Author":"Michael Coates [aut, cre]","Depends":"R (>=
3.2.3)","Description":"Simplifies some complicated and labor intensive processes
involved in exploring and explaining data. Allows you to quickly and efficiently
visualize the interaction between variables and simplifies the process of
discovering covariation in your data. Also includes some convenience features
designed to remove as much redundant typing as possible.","Imports":"ggplot2,
grDevices, stats","License":"GPL-
3","NeedsCompilation":"no","Package":"exploreR","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr, rmarkdown","Title":"Tools for Quickly Exploring
Data","Version":"0.1"},"expm":{"Author":"Vincent Goulet, Christophe Dutang, Martin
Maechler,\nDavid Firth, Marina Shapira, Michael Stadelmann,\nexpm-
developers@lists.R-forge.R-
project.org","Depends":"Matrix","Description":"Computation of the matrix
exponential, logarithm, and related quantities.","Imports":"methods","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"expm","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"RColorBrewer, sfsmisc, Rmpfr","Title":"Matrix
Exponential","URL":"http:\/\/R-Forge.R-
project.org\/projects\/expm\/","Version":"0.999-0"},"expoRkit":{"Author":"Roger B.
Sidje [aut, cph], Niels Richard Hansen [aut, cre, cph]","Depends":"R (>= 2.14.1),
methods","Description":"An R-interface to the Fortran package
Expokit.","Imports":"Matrix, SparseM","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"expoRkit","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Expokit in
R","URL":"https:\/\/bitbucket.org\/nielsrhansen\/exporkit\/","Version":"0.9"},"expo
Tree":{"Author":"Gabriel E Leventhal, partly adapted from MATLAB code by Awad H.
Al-Mohy and using the routines DLNAC1 and DLARPC by Sheung Hun Cheng, and DLAPST
from ScaLAPACK.","Depends":"R (>= 2.12.0), ape, deSolve","Description":"Calculates
the density dependent likelihood of a phylogenetic tree. It takes branching and
sampling times as an argument and integrates the likelihood function over the whole
tree.","License":"BSD_3_clause + file
LICENCE","NeedsCompilation":"yes","Package":"expoTree","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Calculate density dependent likelihood of a
phylogenetic tree","Version":"1.0.1"},"expp":{"Author":"Mihai Valcu, Lotte
Schlicht","Depends":"R (>= 3.0.0), methods, sp, spdep, rgeos,
deldir","Description":"Tools and data to accompany Schlicht, Valcu and
Kempenaers \"Spatial patterns of extra-pair paternity: beyond paternity gains and
losses\"","License":"GPL-
3","NeedsCompilation":"no","Package":"expp","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"knitr, spatstat, lme4","Title":"Spatial analysis of extra-
pair paternity","Version":"1.1"},"expsmooth":{"Author":"Rob J Hyndman
<Rob.Hyndman@monash.edu>","Depends":"R (>= 2.0.0), forecast","Description":"Data
sets from the book \"Forecasting with exponential smoothing: the state space
approach\" by\nHyndman, Koehler, Ord and Snyder (Springer, 2008).","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"expsmooth","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Data Sets from \"Forecasting with Exponential
Smoothing\"","URL":"https:\/\/github.com\/robjhyndman\/expsmooth","Version":"2.3"},
"exptest":{"Author":"Alexey Novikov, Ruslan Pusev, Maxim
Yakovlev","Description":"Tests for the composite hypothesis of
exponentiality","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"exptest","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Tests for Exponentiality","Version":"1.2"},"exreport":
{"Author":"Jacinto Arias [aut, cre],\nJavier Cozar [aut]","Depends":"R (>=
3.1.1)","Description":"Analysis of experimental results and automatic report
generation in both interactive HTML and LaTeX. This package ships with a rich
interface for data modeling and built in functions for the rapid application of
statistical tests and generation of common plots and tables with publish-ready
quality.","Imports":"ggplot2, grDevices, methods, reshape2, stats, tools,
2","NeedsCompilation":"no","Package":"exreport","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Fast, Reliable and Elegant Reproducible
Research","Version":"0.4.1"},"exsic":{"Author":"Reinhard Simon [aut, cre]
(CIP),\nDavid M. Spooner [aut] (USDA),\nInternational Potato Center
[cph]","Depends":"R (>= 2.15.1), stringr, markdown","Description":"The package
provides tools for botanists, plant taxonomists,\ncurators of plant genebanks and
perhaps other biological collections.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"exsic","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Convenience Functions for Botanists to Create
Specimens Indices","Version":"1.1.1"},"extRemes":{"Author":"Eric
Gilleland","Depends":"R (>= 2.10.0), Lmoments, distillery,
car","Description":"Functions for performing extreme value
analysis.","Imports":"graphics, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"extRemes","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"fields","Title":"Extreme Value
Analysis","URL":"http:\/\/www.assessment.ucar.edu\/toolkit\/","Version":"2.0-
7"},"extWeibQuant":{"Author":"Yang (Seagle) Liu","Description":"It implements the
subjectively censored Weibull MLE and censored Weibull mixture methods for the
lower quantile estimation. Quantile estimates from these two methods are robust to
model misspecification in the lower tail. It also includes functions to evaluation
the standard error of the resulting quantile estimates. Also, the methods here can
be used to fit the Weibull or Weibull mixture for the Type-I or Type-II right
censored data.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"extWeibQuant","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Estimate Lower Extreme Quantile with the Censored
Weibull MLE\nand Censored Weibull Mixture","Version":"1.1"},"extfunnel":
{"Author":"Dean Langan, Alexander Sutton, Julian PT Higgins,
Walter\nGregory","Depends":"rmeta","Description":"This is a package containing the
function extfunnel()\nwhich produces a funnel plot including additional
augmentations\nsuch as statistical significance contours and
heterogeneity\ncontours.","License":"GPL-
2","NeedsCompilation":"no","Package":"extfunnel","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Additional Funnel Plot
Augmentations","Version":"1.3"},"extlasso":{"Author":"B N Mandal
<mandal.stat@gmail.com> and Jun Ma <jun.ma@mq.edu.au>","Depends":"R (>=
3.1.1)","Description":"The package estimates coefficients of extended LASSO
penalized linear regression and generalized linear models. Currently lasso and
elastic net penalized linear regression and generalized linear models are
considered. The package currently utilizes an accurate approximation of L1 penalty
and then a modified Jacobi algorithm to estimate the coefficients. There is
provision for plotting of the solutions and predictions of coefficients at given
values of lambda. The package also contains functions for cross validation to
select a suitable lambda value given the data. The package also provides a function
for estimation in fused lasso penalized linear regression.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"extlasso","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Maximum penalized likelihood estimation with extended
lasso\npenalty","Version":"0.2"},"extraBinomial":{"Author":"Xin Yang, Chris
Wallace","Description":"This package tests for differences in minor
allele\nfrequency between groups and is based on an extra-binomial\nvariation model
for pooled sequencing data.","License":"GPL-
3","NeedsCompilation":"no","Package":"extraBinomial","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Extra-binomial approach for pooled sequencing
data","Version":"2.1"},"extraTrees":{"Author":"Jaak Simm, Ildefons Magrans de
Abril","Depends":"R (>= 2.7.0), rJava (>= 0.5-0)","Description":"Classification and
regression based on an ensemble of decision trees. The package also provides
extensions of ExtraTrees to multi-task learning and quantile regression. Uses Java
implementation of the method.","License":"Apache License
2.0","NeedsCompilation":"no","Package":"extraTrees","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat, Matrix","Title":"Extremely Randomized
Trees (ExtraTrees) Method for\nClassification and
Regression","URL":"http:\/\/github.com\/jaak-
s\/extraTrees","Version":"1.0.5"},"extracat":{"Author":"Alexander Pilhoefer
<alexander.pilhoefer@gmail.com>","Depends":"R (>=
3.1.0)","Description":"Categorical Data Analysis and
Visualization.","Imports":"grid, colorspace, hexbin, scales, ggplot2, plyr, TSP,
methods,\ndata.table, reshape2","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"extracat","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"ca, amap, MASS, proto","Title":"Categorical Data
Analysis and Visualization","Version":"1.7-4"},"extrafont":{"Author":"Winston
Chang <winston@stdout.org>,","Depends":"R (>= 2.15)","Description":"Tools to using
fonts other than the standard PostScript fonts.\nThis package makes it easy to use
system TrueType fonts and with PDF or\nPostScript output files, and with bitmap
output files in Windows. extrafont\ncan also be used with fonts packaged
specifically to be used with, such as\nthe fontcm package, which has Computer
Modern PostScript fonts with math\nsymbols. See
https:\/\/github.com\/wch\/extrafont for instructions
and\nexamples.","Imports":"extrafontdb, grDevices, utils, Rttf2pt1","License":"GPL-
2","NeedsCompilation":"no","Package":"extrafont","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"fontcm","Title":"Tools for using
fonts","URL":"https:\/\/github.com\/wch\/extrafont","Version":"0.17"},"extrafontdb"
:{"Author":"Winston Chang <winston@stdout.org>","Depends":"R (>=
2.14)","Description":"Package for holding the database for the extrafont
package","License":"GPL-
2","NeedsCompilation":"no","Package":"extrafontdb","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Package for holding the database for the extrafont
package","URL":"https:\/\/github.com\/wch\/extrafontdb","Version":"1.0"},"extremeva
lues":{"Author":"Mark van der Loo <mark.vanderloo@gmail.com>","Depends":"R (>=
2.8.0)","Description":"Detect outliers in one-dimensional
data.","Imports":"gWidgets, gWidgetstcltk, utils, stats, graphics","License":"GPL-
2","NeedsCompilation":"no","Package":"extremevalues","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Univariate Outlier
Detection","URL":"https:\/\/www.github.com\/markvanderloo\/extremevalues","Version"
:"2.3.2"},"extremogram":{"Author":"Nadezda Frolova, Ivor Cribben","Depends":"R (>=
3.1.0)","Description":"Estimation of the sample univariate, cross and return time
extremograms. The package can also add empirical confidence bands to each of the
extremogram plots via a permutation procedure under the assumption that the data
are independent. Finally, the stationary bootstrap allows us to construct credible
confidence bands for the extremograms.","Imports":"boot(>= 1.3-11), MASS(>= 7.3-
31), parallel(>= 3.1.1)","License":"GPL-
3","NeedsCompilation":"no","Package":"extremogram","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Estimation of Extreme Value Dependence for Time Series
Data","Version":"1.0.1"},"eyetracking":{"Author":"Ryan M. Hope","Description":"Misc
function for working with eyetracking data","License":"GPL-
3","NeedsCompilation":"no","Package":"eyetracking","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Eyetracking Helper
Functions","Version":"1.1"},"eyetrackingR":{"Author":"Jacob Dink [aut, cre],\nBrock
Ferguson [aut]","Depends":"R (>= 3.2.0)","Description":"A set of tools that address
tasks along the pipeline from raw\ndata to analysis and visualization for eye-
tracking data. Offers several\npopular types of analyses, including linear and
growth curve time analyses,\nonset-contingent reaction time analyses, as well as
several non-parametric\nbootstrapping approaches.","Imports":"broom (>= 0.3.7),
dplyr (>= 0.4.3), ggplot2 (>= 2.0), lazyeval\n(>= 0.1.10), zoo (>= 1.7-12), tidyr
(>= 0.3.1)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"eyetrackingR","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"pbapply, knitr, lme4 (>= 1.1-10), Matrix,
testthat,\nrmarkdown, doMC, foreach","Title":"Eye-Tracking Data
Analysis","URL":"http:\/\/eyetracking-r.com","Version":"0.1.6"},"ez":
{"Author":"Michael A. Lawrence <mike.lwrnc@gmail.com>","Depends":"R (>=
3.0.0)","Description":"Facilitates easy analysis of factorial experiments,
including purely within-Ss designs (a.k.a. \"repeated measures\"), purely between-
Ss designs, and mixed within-and-between-Ss designs. The functions in this package
aim to provide simple, intuitive and consistent specification of data analysis and
visualization. Visualization functions also include design visualization for pre-
analysis data auditing, and correlation matrix visualization. Finally, this package
includes functions for non-parametric analysis, including permutation tests and
bootstrap resampling. The bootstrap function obtains predictions either by cell
means or by more advanced\/powerful mixed effects models, yielding predictions and
confidence intervals that may be easily visualized at any level of the experiment's
design.","Imports":"car (>= 2.0-12), ggplot2 (>= 0.9.1), lme4 (>= 0.999999-
0),\nMASS (>= 7.3-29), Matrix (>= 1.0-6), mgcv (>= 1.7-13), plyr (>=\n1.7.1),
reshape2 (>= 1.2.1), scales (>= 0.2.1), stringr (>=\n0.6.1)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ez","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Easy Analysis and Visualization of Factorial
Experiments","URL":"http:\/\/github.com\/mike-
lawrence\/ez","Version":"4.3"},"ezec":{"Author":"Zhian N. Kamvar [cre,
aut],\nNiklaus J. Grunwald [ths, ctb]","Depends":"R (>=
3.2.0)","Description":"Because fungicide resistance is an important phenotypic
trait for\nfungi and oomycetes, it is necessary to have a standardized method
of\nstatistically analyzing the Effective Concentration (EC) values. This\npackage
is designed for those who are not terribly familiar with R to be\nable to analyze
and plot an entire set of isolates using the drc package.","Imports":"drc,
dplyr","License":"GPL-
3","NeedsCompilation":"no","Package":"ezec","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"testthat, readxl, knitr, rmarkdown","Title":"Easy
Interface to Effective Concentration Calculations","Version":"0.1.0"},"ezglm":
{"Author":"Yi Yang <yiyang@umn.edu>","Description":"This package implements a
simplified version of least\nsquares, and logistic regression for efficiently
selecting the\nsignificant non-additive interactions between two
variables.","License":"GPL-
2","NeedsCompilation":"yes","Package":"ezglm","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"selects significant non-additive interaction between
two\nvariables using fast GLM
implementation","URL":"http:\/\/code.google.com\/p\/ezglm\/","Version":"1.0"},"ezkn
itr":{"Author":"Dean Attali [aut, cre]","Depends":"R (>= 3.0.2)","Description":"An
extension of 'knitr' that adds flexibility in several\nways. One common source of
frustration with 'knitr' is that it assumes\nthe directory where the source file
lives should be the working directory,\nwhich is often not true. 'ezknitr'
addresses this problem by giving you\ncomplete control over where all the inputs
and outputs are, and adds several\nother convenient features to make rendering
markdown\/HTML documents easier.","Imports":"knitr (>= 1.7), markdown (>= 0.7),
R.utils (>= 1.34.0)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"ezknitr","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat (>= 0.9.1), rmarkdown","Title":"Avoid
the Typical Working Directory Pain When Using
'knitr'","URL":"https:\/\/github.com\/daattali\/ezknitr","Version":"0.3.1"},"ezsim"
:{"Author":"TszKin Julian Chan <ctszkin@gmail.com>","Description":"ezsim provides a
handy way to run simulation and examine its result","Imports":"foreach, ggplot2,
parallel, digest, plyr, reshape, Jmisc","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ezsim","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"provide an easy to use framework to conduct
simulation","Version":"0.5.5"},"ezsummary":{"Author":"Hao Zhu [aut,
cre]","Depends":"R (>= 3.1.2)","Description":"Functions that can fulfill the gap
between the outcomes of 'dplyr' and a print-ready summary table.","Imports":"dplyr
(>= 0.4), reshape2 (>= 1.4.1), tidyr (>= 0.3)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"ezsummary","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat","Title":"Summarise Data in the Quick
and Easy Way","Version":"0.1.9"},"fANCOVA":{"Author":"Xiao-Feng
Wang","Description":"This package contains a collection of R functions to\nperform
nonparametric analysis of covariance for regression\ncurves or surfaces. Testing
the equality or parallelism of\nnonparametric curves or surfaces is equivalent to
analysis of\nvariance (ANOVA) or analysis of covariance (ANCOVA) for\none-sample
functional data. Three different testing methods are\navailable in the package,
including one based on L-2 distance,\none based on an ANOVA statistic, and one
based on variance\nestimators.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"fANCOVA","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Nonparametric Analysis of Covariance","Version":"0.5-
1"},"fArma":{"Author":"Diethelm Wuertz and many others, see the SOURCE
file","Depends":"R (>= 2.4.0), methods, timeDate, timeSeries,
fBasics","Description":"Environment for teaching \"Financial Engineering
and\nComputational Finance\"","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"fArma","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"RUnit, tcltk","Title":"ARMA Time Series
Modelling","URL":"http:\/\/www.rmetrics.org","Version":"3010.79"},"fAsianOptions":
{"Author":"Diethelm Wuertz and many others, see the SOURCE file","Depends":"R (>=
2.4.0), timeDate, timeSeries, fBasics, fOptions","Description":"Environment for
teaching \"Financial Engineering and\nComputational Finance\"","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"fAsianOptions","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"RUnit","Title":"EBM and Asian Option
Valuation","URL":"http:\/\/www.rmetrics.org","Version":"3010.79"},"fAssets":
{"Author":"Rmetrics Core Team,\nDiethelm Wuertz [aut],\nTobias Setz [cre],\nYohan
Chalabi [ctb]","Depends":"R (>= 2.15.1), timeDate, timeSeries,
fBasics","Description":"Environment for teaching\n\"Financial Engineering and
Computational Finance\".","Imports":"fMultivar, robustbase, MASS, sn,
ecodist, mvnormtest, energy","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"fAssets","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"methods, mnormt, RUnit","Title":"Rmetrics - Analysing
and Modelling Financial
Assets","URL":"https:\/\/www.rmetrics.org","Version":"3011.83"},"fBasics":
Chalabi [ctb]","Depends":"R (>= 2.15.1), timeDate,
timeSeries","Description":"Environment for teaching\n\"Financial Engineering and
Computational Finance\".","Imports":"gss, stabledist, MASS","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"fBasics","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"methods, spatial, RUnit, tcltk,
akima","Title":"Rmetrics - Markets and Basic
Statistics","URL":"https:\/\/www.rmetrics.org","Version":"3011.87"},"fBonds":
2.4.0), timeDate, timeSeries, fBasics","Description":"Environment for
teaching \"Financial Engineering and\nComputational Finance\"","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"fBonds","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"RUnit","Title":"Bonds and Interest Rate
Models","URL":"http:\/\/www.rmetrics.org","Version":"3010.77"},"fCertificates":
{"Author":"Stefan Wilhelm <wilhelm@financial.com>","Depends":"R (>= 2.6.0),
fBasics, fOptions, fExoticOptions","Description":"Collection of pricing by
duplication methods for popular structured products
(\"Zertifikate\").","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"fCertificates","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Basics of Certificates and Structured Products
Valuation","URL":"http:\/\/www.r-project.org","Version":"0.5-4"},"fCopulae":
{"Author":"Rmetrics Core Team,\nDiethelm Wuertz [aut],\nTobias Setz [cre]\nYohan
Chalabi [ctb]","Depends":"R (>= 2.15.1), timeDate, timeSeries, fBasics,
fMultivar","Description":"Environment for teaching\n\"Financial Engineering and
Computational Finance\".","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"fCopulae","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"methods, RUnit, tcltk, mvtnorm, sn","Title":"Rmetrics
- Bivariate Dependence Structures with
Copulae","URL":"https:\/\/www.rmetrics.org","Version":"3011.81"},"fExoticOptions":
2.4.0), methods, timeDate, timeSeries, fBasics,
fOptions","Description":"Environment for teaching \"Financial Engineering
2)","NeedsCompilation":"no","Package":"fExoticOptions","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"RUnit","Title":"Exotic Option
Valuation","URL":"http:\/\/www.rmetrics.org","Version":"2152.78"},"fExpressCertific
ates":{"Author":"Stefan Wilhelm","Depends":"R (>= 2.15.0), mvtnorm, tmvtnorm,
fCertificates, Matrix","Description":"Collection of pricing by duplication and
Monte Carlo methods for Express Certificates products (also known as
Autocallables)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"fExpressCertificates","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Title":"fExpressCertificates - Structured Products
Valuation for\nExpressCertificates\/Autocallables","URL":"http:\/\/www.r-
project.org","Version":"1.2"},"fExtremes":{"Author":"Diethelm Wuertz and many
others, see the SOURCE file","Depends":"R (>= 2.4.0), timeDate, timeSeries,
fBasics, fGarch, fTrading","Description":"Environment for teaching \"Financial
Engineering and\nComputational Finance\"","Imports":"methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"fExtremes","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"RUnit, tcltk","Title":"Rmetrics - Extreme Financial
Market Data","URL":"http:\/\/www.rmetrics.org","Version":"3010.81"},"fGarch":
{"Author":"Diethelm Wuertz and Yohan Chalabi with contribution from
Michal\nMiklovic, Chris Boudt, Pierre Chausse and others","Depends":"R (>= 2.15.0),
stats, graphics, methods, timeDate, timeSeries,\nfBasics (>=
2100.78)","Description":"Environment for teaching \"Financial Engineering
2)","NeedsCompilation":"yes","Package":"fGarch","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"RUnit, Matrix, fastICA, tcltk","Title":"Rmetrics -
Autoregressive Conditional Heteroskedastic
Modelling","URL":"http:\/\/www.rmetrics.org","Version":"3010.82"},"fICA":
{"Author":"Jari Miettinen, Klaus Nordhausen, Hannu Oja, Sara
Taskinen","Description":"Algorithms for classical symmetric and deflation-based
FastICA, reloaded deflation-based FastICA algorithm and an algorithm for adaptive
deflation-based FastICA using multiple nonlinearities.","Imports":"stats, JADE,
Rcpp (>= 0.11.0)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"fICA","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"BSSasymp","Title":"Classical, Reloaded and Adaptive
FastICA Algorithms","Version":"1.0-3"},"fImport":{"Author":"Diethelm Wuertz and
many others","Depends":"R (>= 2.13.0), methods, timeDate,
timeSeries","Description":"Environment for teaching \"Financial Engineering
2)","NeedsCompilation":"no","Package":"fImport","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"RUnit","Title":"Rmetrics - Economic and Financial Data
Import","URL":"http:\/\/www.rmetrics.org","Version":"3000.82"},"fMultivar":
{"Author":"Rmetrics Core Team,\nDiethelm Wuertz [aut],\nTobias Setz [cre]\nYohan
Computational Finance\"","Imports":"cubature, mvtnorm, sn","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"fMultivar","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"methods, spatial, RUnit, tcltk,
akima","Title":"Rmetrics - Analysing and Modeling Multivariate Financial
Return\nDistributions","URL":"https:\/\/www.rmetrics.org","Version":"3011.78"},"fNo
nlinear":{"Author":"Diethelm Wuertz and many others, see the SOURCE
file","Depends":"R (>= 2.4.0), methods, timeDate, timeSeries, fBasics,
fGarch","Description":"Environment for teaching \"Financial Engineering
2)","NeedsCompilation":"yes","Package":"fNonlinear","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"RUnit, tcltk","Title":"Nonlinear and Chaotic Time
Series
Modelling","URL":"http:\/\/www.rmetrics.org","Version":"3010.78"},"fOptions":
Chalabi [ctb]","Depends":"timeDate, timeSeries, fBasics","Description":"Environment
for teaching\n\"Financial Engineering and Computational Finance\".\nPricing and
Evaluating Basic Options.","Imports":"graphics, methods, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"fOptions","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"RUnit, tcltk","Title":"Rmetrics - Pricing and
Evaluating Basic
Options","URL":"http:\/\/www.rmetrics.org","Version":"3022.85"},"fPortfolio":
Chalabi [ctb]","Depends":"R (>= 2.15.1), methods, timeDate, timeSeries, fBasics,
fAssets","Description":"Environment for teaching\n\"Financial Engineering and
Computational Finance\".","Imports":"fCopulae, robustbase, MASS, Rglpk, slam,
Rsymphony, Rsolnp,\nkernlab, quadprog, rneos","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"fPortfolio","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"Rsocp, Rnlminb2, Rdonlp2, dplR, bcp, fGarch,
mvoutlier","Title":"Rmetrics - Portfolio Selection and
Optimization","URL":"https:\/\/www.rmetrics.org","Version":"3011.81"},"fRegression"
:{"Author":"Rmetrics Core Team,\nDiethelm Wuertz [aut],\nTobias Setz [cre]\nYohan
Computational Finance\".","Imports":"lmtest, mgcv, nnet, polspline","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"fRegression","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"methods, MASS, RUnit","Title":"Rmetrics -
Regression Based Decision and
Prediction","URL":"http:\/\/www.rmetrics.org","Version":"3011.81"},"fSRM":
{"Author":"Felix SchÃ¶nbrodt, Lara Stas, Tom
Loeys","Depends":"lavaan","Description":"Social Relations Analysis with roles
(\"Family SRM\") are computed,\nusing a structural equation modeling approach.
Groups ranging from three members\nup to an unlimited number of members are
supported and the mean structure can\nbe computed. Means and variances can be
compared between different groups of\nfamilies and between roles.","Imports":"plyr,
reshape2, ggplot2, scales, foreign, tcltk, tcltk2,\ngridExtra,
2)","NeedsCompilation":"no","Package":"fSRM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Social Relations Analyses with Roles (\"Family
SRM\")","Version":"0.6.4"},"fTrading":{"Author":"Diethelm Wuertz and many others,
see the SOURCE file","Depends":"R (>= 2.4.0), methods, timeDate, timeSeries,
fBasics","Description":"Environment for teaching \"Financial Engineering
2)","NeedsCompilation":"no","Package":"fTrading","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"RUnit, tcltk","Title":"Technical Trading
Analysis","URL":"http:\/\/www.rmetrics.org","Version":"3010.78"},"fUnitRoots":
2.4.0), urca, methods, timeDate, timeSeries, fBasics","Description":"Environment
for teaching \"Financial Engineering and\nComputational
Finance\"","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"fUnitRoots","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"RUnit","Title":"Trends and Unit
Roots","URL":"http:\/\/www.rmetrics.org","Version":"3010.78"},"factorQR":
{"Author":"Lane Burgette <lb131@stat.duke.edu>,","Depends":"R (>= 2.1),
lattice","Description":"Package to fit Bayesian quantile regression models
that\nassume a factor structure for at least part of the
design\nmatrix.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"factorQR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Bayesian quantile regression factor
models","Version":"0.1-4"},"factorplot":{"Author":"Dave Armstrong (Department of
Political Science, UW-Milwaukee)","Depends":"multcomp,
nnet","Description":"Calculate, print, summarize and plot pairwise differences from
GLMs, GLHT or Multinomial Logit models","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"factorplot","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"factorplot","Version":"1.1-1"},"factualR":
{"Author":"Ethan McCallum","Depends":"methods, RJSONIO, RCurl","Description":"Per
the Factual.com website, \"Factual is a platform where\nanyone can share and mash
open, living data on any subject.\"\nThe data is in the form of tables and is
accessible via REST\nAPI. The factualR package is a thin wrapper around
the\nFactual.com API, to make it even easier for people working with\nR to explore
Factual.com data sets.","License":"Apache License
2.0","NeedsCompilation":"no","Package":"factualR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"thin wrapper for the Factual.com server
API","URL":"http:\/\/www.exmachinatech.net\/factualR\/","Version":"0.5"},"fail":
{"Author":"Michel Lang <michellang@gmail.com>","Description":"More comfortable
interface to work with R data or source files\nin a key-value
fashion.","Imports":"stats, utils, BBmisc, checkmate","License":"BSD_3_clause +
file
LICENSE","NeedsCompilation":"no","Package":"fail","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat","Title":"File Abstraction Interface Layer
(FAIL)","URL":"https:\/\/github.com\/mllg\/fail","Version":"1.3"},"faisalconjoint":
{"Author":"Faisal Afzal Siddiqui, Ghulam Hussain, and Mudassir
Uddin","Description":"It is used for systematic analysis of decisions based on
attributes and its levels.","License":"GPL-
3","NeedsCompilation":"no","Package":"faisalconjoint","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Faisal Conjoint Model: A New Approach to Conjoint
Analysis","Version":"1.15"},"falcon":{"Author":"Hao Chen and Nancy R.
Zhang","Depends":"R (>= 3.0.1)","Description":"This is a method for Allele-specific
DNA Copy Number Profiling using Next-Generation Sequencing. Given the allele-
specific coverage at the variant loci, this program segments the genome into
regions of homogeneous allele-specific copy number. It requires, as input, the
read counts for each variant allele in a pair of case and control samples. For
detection of somatic mutations, the case and control samples can be the tumor and
normal sample from the same individual.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"falcon","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Finding Allele-specific Copy Number in Next-
Generation\nSequencing Data","Version":"0.1"},"falsy":{"Author":"Gabor Csardi [aut,
cre]","Description":"A value is falsy if it is NULL, FALSE, the empty
string,\nzero, or an empty vector or list. Other values are truthy. The new\n%&&%
and %||% operators work with falsy and truthy values and\ncan be used for concise
conditional execution.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"falsy","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat","Title":"Define Truthy and Falsy
Values","URL":"https:\/\/github.com\/gaborcsardi\/falsy","Version":"1.0.1"},"fame":
{"Author":"Jeff Hallman <jeffrey.j.hallman@frb.gov>","Depends":"R (>=
2.3)","Description":"Read and write FAME
databases.","Imports":"tis","License":"Unlimited","NeedsCompilation":"yes","Package
":"fame","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Interface for
FAME Time Series Database","Version":"2.21"},"fanc":{"Author":"Kei Hirose, Michio
Yamamoto, Haruhisa Nagata","Depends":"Matrix","Description":"An R package \"fanc\"
computes the penalized maximum\nlikelihood estimates of factor loadings and unique
variances\nfor various tuning parameters. The pathwise coordinate descent\nalong
with EM algorithm is used. This package also includes a\nnew graphical tool which
outputs path diagram, goodness-of-fit\nindices and model selection criteria for
each regularization\nparameter. The user can change the regularization parameter
by\nmanipulating scrollbars, which is helpful to find a suitable\nvalue of
regularization parameter.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"fanc","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"RGtk2, tcltk, matlab","Title":"Penalized Likelihood
Factor Analysis via Nonconvex
Penalty","URL":"http:\/\/link.springer.com\/article\/10.1007%2Fs11222-014-9458-
0,\nhttp:\/\/www.sciencedirect.com\/science\/article\/pii\/S0167947314001510,\nhttp
:\/\/www.keihirose.com","Version":"1.25"},"fancycut":{"Author":"Adam Rich [aut,
cre]","Depends":"R (>= 3.2.2)","Description":"Provides the function fancycut()
which is like cut() except\nyou can mix left open and right open intervals with
point values,\nintervals that are closed on both ends and intervals that are open
on both
ends.","License":"CC0","NeedsCompilation":"no","Package":"fancycut","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Title":"A Fancy Version of
'base::cut'","Version":"0.1.0"},"fanovaGraph":{"Author":"Jana Fruth, Thomas
Muehlenstaedt, Olivier Roustant, Malte Jastrow","Depends":"sensitivity, igraph,
DiceKriging (>= 1.4)","Description":"Estimation and plotting of a function's FANOVA
graph to identify the interaction structure and fitting, prediction and simulation
of a Kriging model modified by the identified structure. The interactive function
plotManipulate() can only be run on the RStudio IDE with RStudio's package
'manipulate' loaded. RStudio is freely available (www.rstudio.org), and includes
package 'manipulate'. The equivalent function plotTk() bases on CRAN Repository
packages only.","License":"GPL-
3","NeedsCompilation":"no","Package":"fanovaGraph","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"manipulate, testthat","Title":"Building Kriging
Models from FANOVA Graphs","Version":"1.4.8"},"fanplot":{"Author":"Guy J.
Abel","Depends":"R (>= 2.10)","Description":"Visualise sequential distributions
using a range of plotting\nstyles. Sequential distribution data can be input as
either simulations or\nvalues corresponding to percentiles over time. Plots are
added to\nexisting graphic devices using the fan function. Users can choose from
four\ndifferent styles, including fan chart type plots, where a set of
coloured\npolygon, with shadings corresponding to the percentile values are
layered\nto represent different uncertainty levels.","License":"GPL-
2","NeedsCompilation":"no","Package":"fanplot","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"shiny, tsbugs,","Title":"Visualisation of Sequential
Probability Distributions Using
Fan\nCharts","URL":"http:\/\/gjabel.wordpress.com\/category\/r\/fanplot\/","Version
":"3.4.1"},"faoutlier":{"Author":"Phil Chalmers [aut, cre]","Depends":"R (>=
3.0.2), sem, mvtnorm, parallel","Description":"Tools for detecting and summarize
influential cases that\ncan affect exploratory and confirmatory factor analysis
models as well as\nstructural equation models more generally.","Imports":"methods,
lattice, lavaan, mirt (>= 1.14), MASS","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"faoutlier","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Influential Case Detection Methods for Factor Analysis
and\nStructural Equation
Models","URL":"https:\/\/github.com\/philchalmers\/faoutlier","Version":"0.6.1"},"f
ar":{"Author":"Damon Julien <julien.damon@gmail.com>\nGuillas Serge","Depends":"R
(>= 2.10.0), nlme, graphics, stats","Description":"Modelizations and previsions
functions for\nFunctional AutoRegressive processes using\nnonparametric methods:
functional kernel,\nestimation of the covariance operator in\na
subspace, ...","License":"LGPL-
2.1","NeedsCompilation":"yes","Package":"far","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Modelization for Functional AutoRegressive
Processes","URL":"https:\/\/github.com\/Looping027\/far","Version":"0.6-
5"},"faraway":{"Author":"Julian Faraway <jjf23@bath.ac.uk>","Depends":"R (>=
2.10)","Description":"Books are \"Practical Regression and ANOVA in R\" on
CRAN, \"Linear Models with R\" published 1st Ed. August 2004, 2nd Ed. July 2014 by
CRC press, ISBN 9781439887332, and \"Extending the Linear Model with R\" published
by CRC press in 1st Ed. December 2005 and 2nd Ed. March 2016, ISBN
9781584884248.","Imports":"lme4,nlme,methods","License":"GPL","NeedsCompilation":"n
o","Package":"faraway","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":
"Functions and Datasets for Books by Julian
Faraway","URL":"http:\/\/people.bath.ac.uk\/jjf23\/","Version":"1.0.7"},"farsi":
{"Author":"Sadegh Rasoulinejad","Description":"Allow numbers to be presented in an
persian language\nversion","License":"GPL-
2","NeedsCompilation":"no","Package":"farsi","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Translate integers into persian","Version":"1.0"},"fast":
{"Author":"Dominik Reusser","Depends":"zoo","Description":"The Fourier Amplitude
Sensitivity Test (FAST) is a method to determine global sensitivities of a model on
parameter changes with relatively few model runs. This package implements this
sensitivity
analysis method.","License":"GPL-
2","NeedsCompilation":"no","Package":"fast","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Implementation of the Fourier Amplitude Sensitivity Test
(FAST)","Version":"0.64"},"fastAdaboost":{"Author":"Sourav Chatterjee [aut,
cre]","Depends":"R (>= 3.1.2)","Description":"Implements Adaboost based on C++
backend code.\nThis is blazingly fast and especially useful for large, in memory
data sets.\nThe package uses decision trees as weak classifiers. Once the
classifiers\nhave been trained, they can be used to predict new data.\nCurrently,
we support only binary classification tasks.\nThe package implements the
Adaboost.M1 algorithm and the real\nAdaboost(SAMME.R) algorithm.","Imports":"Rcpp,
rpart","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"fastAdaboost","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Suggests":"testthat, knitr, MASS","Title":"a Fast
Implementation of
Adaboost","URL":"https:\/\/github.com\/souravc83\/fastAdaboost","Version":"1.0.0"},
"fastGHQuad":{"Author":"Alexander W Blocker","Depends":"Rcpp (>=
0.11.0)","Description":"Fast, numerically-stable Gauss-Hermite
quadrature","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"fastGHQuad","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Fast Rcpp implementation of Gauss-Hermite
quadrature","URL":"https:\/\/github.com\/awblocker\/fastGHQuad","Version":"0.2"},"f
astGraph":{"Author":"Steven T. Garren [aut, cre]","Depends":"R (>=
2.0)","Description":"Provides functionality to produce graphs of probability
density functions and cumulative distribution functions with few keystrokes, allows
shading under the curve of the probability density function to illustrate concepts
such as p-values and critical values, and fits a simple linear regression line on a
scatter plot with the equation as the main title.","License":"GPL-
3","NeedsCompilation":"no","Package":"fastGraph","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Fast Drawing and Shading of Graphs of Statistical
Distributions","Version":"1.0"},"fastHICA":{"Author":"Piercesare Secchi, Simone
Vantini, and Paolo Zanini","Depends":"fastICA, energy","Description":"It implements
HICA (Hierarchical Independent Component Analysis) algorithm. This approach,
obtained through the integration between treelets and Independent Component
Analysis, is able to provide a multi-scale non-orthogonal data-driven basis, whose
elements have a phenomenological interpretation according to the problem under
study.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"fastHICA","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Hierarchical Independent Component Analysis: a Multi-
Scale\nSparse Non-Orthogonal Data-Driven Basis","Version":"1.0.2"},"fastICA":
{"Author":"J L Marchini <marchini@stats.ox.ac.uk>, C
Heaton\n<chrisheaton99@yahoo.com> and B D
Ripley\n<ripley@stats.ox.ac.uk>","Depends":"R (>=
3.0.0)","Description":"Implementation of FastICA algorithm to perform
Independent\nComponent Analysis (ICA) and Projection Pursuit.","License":"GPL-2 |
GPL-
3","NeedsCompilation":"yes","Package":"fastICA","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"MASS","Title":"FastICA Algorithms to perform ICA and
Projection Pursuit","Version":"1.2-0"},"fastM":{"Author":"Lutz Duembgen, Klaus
Nordhausen, Heike Schuhmacher","Description":"The package implements the new
algorithm for fast computation of M-scatter matrices using a partial Newton-Raphson
procedure for several estimators.","Imports":"Rcpp (>= 0.11.0)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"fastM","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Fast Computation of Multivariate M-
estimators","Version":"0.0-2"},"fastR":{"Author":"Randall Pruim","Depends":"R (>=
3.0.0), mosaic","Description":"Data sets and utilities to accompany\n\"Foundations
and Applications of Statistics: an Introduction\nusing R\" (R Pruim, published by
AMS, 2011), a text covering\ntopics from probability and mathematical statistics at
an advanced\nundergraduate level. R is integrated throughout, and access to
all\nthe R code in the book is provided via the snippet
function.","Imports":"lattice, grid, mosaicData","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"fastR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"MASS, faraway, Hmisc, DAAG, multcomp, vcd, car,
alr3,\ncorrgram, BradleyTerry2, cubature, Devore7, knitr","Title":"Foundations and
Applications of Statistics Using R","Version":"0.10.2"},"fastSOM":{"Author":"Stefan
Kloessner <S.Kloessner@mx.uni-saarland.de>, Sven Wagner\n<sven.wagner@mx.uni-
saarland.de>","Description":"Functions for computing spillover measures,
especially\nspillover tables and spillover indices, as well as their\naverage,
minimal, and maximal values.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"fastSOM","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"parallel","Title":"Fast Calculation of Spillover
Measures","Version":"0.9"},"fastclime":{"Author":"Haotian Pang, Han Liu and Robert
Vanderbei","Depends":"R (>= 2.15.0), lattice, igraph, MASS,
Matrix","Description":"An efficient method of recovering precision matrices\nby
applying the parametric simplex method is provided in this package.\nThe
computation is based on a linear optimization solver.\nIt also contains a generic
Linear Programming solver and a\nparameterized Linear Programming solver based on
the parametric simplex method.","License":"GPL-
2","NeedsCompilation":"yes","Package":"fastclime","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"A Fast Solver for Parameterized Linear Programming
Problems and\nConstrained L1 Minimization Approach to Sparse Precision
Matrix\nEstimation","Version":"1.2.5"},"fastcluster":{"Author":"Daniel MÃ¼llner
[aut, cph, cre]","Depends":"R (>= 3.0.0)","Description":"This is a two-in-one
package which provides interfaces to\nboth R and Python. It implements fast
hierarchical, agglomerative\nclustering routines. Part of the functionality is
designed as drop-in\nreplacement for existing routines: linkage() in the SciPy
package\n'scipy.cluster.hierarchy', hclust() in R's 'stats' package, and
the\n'flashClust' package. It provides the same functionality with the\nbenefit of
a much faster implementation. Moreover, there are\nmemory-saving routines for
clustering of vector data, which go beyond\nwhat the existing packages provide. For
information on how to install\nthe Python files, see the file INSTALL in the source
distribution.","Enhances":"stats, flashClust","License":"FreeBSD | GPL-2 | file
LICENSE","NeedsCompilation":"yes","Package":"fastcluster","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Fast Hierarchical Clustering Routines for R and
Python","URL":"http:\/\/danifold.net\/fastcluster.html","Version":"1.1.20"},"fastco
x":{"Author":"Yi Yang <yiyang@umn.edu>, Hui Zou
<hzou@stat.umn.edu>","Depends":"Matrix","Description":"We implement a cocktail
algorithm, a good mixture of coordinate decent, the majorization-minimization
principle and the strong rule, for computing the solution paths of the elastic net
penalized Cox's proportional hazards model.","License":"GPL-
2","NeedsCompilation":"yes","Package":"fastcox","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Lasso and elastic-net penalized Cox's regression in
high\ndimensions models using the cocktail
algorithm","URL":"http:\/\/code.google.com\/p\/fastcox\/","Version":"1.1.1"},"fastd
igest":{"Author":"Gabriel Becker, Bob Jenkins (SpookyHash algorithm and C++
implementation)","Description":"Provides an R interface to Bob Jenkin's
streaming,\nnon-cryptographic 'SpookyHash' hash algorithm for use in digest-
based\ncomparisons of R objects. 'fastdigest' plugs directly into R's
internal\nserialization machinery, allowing digests of all R objects the
serialize()\nfunction supports, including reference-style objects via custom hooks.
Speed is\nhigh and scales linearly by object size; memory usage is constant
and\nnegligible.","License":"Artistic-
2.0","NeedsCompilation":"yes","Package":"fastdigest","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"RUnit","Title":"Fast, Low Memory-Footprint
Digests of R Objects","Version":"0.6-3"},"fastmatch":{"Author":"Simon Urbanek
<simon.urbanek@r-project.org>","Description":"Package providing a fast match()
replacement for cases\nthat require repeated look-ups. It is slightly faster that
R's\nbuilt-in match() function on first match against a table, but\nextremely fast
on any subsequent lookup as it keeps the hash\ntable in memory.","License":"GPL-
2","NeedsCompilation":"yes","Package":"fastmatch","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Fast match()
function","URL":"http:\/\/www.rforge.net\/fastmatch","Version":"1.0-
4"},"fastpseudo":{"Author":"Dayne Batten [aut, cre],\nMaja Pohar Perme
[ctb],\nMette Gerster [ctb]","Depends":"R (>= 3.1.1)","Description":"Computes
pseudo-observations for survival analysis on right-censored data based on
restricted mean survival time.","License":"GPL-
2","NeedsCompilation":"no","Package":"fastpseudo","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"geepack","Title":"Fast Pseudo
Observations","Version":"0.1"},"fasttime":{"Author":"Simon Urbanek
<simon.urbanek@r-project.org>","Description":"Fast functions for
timestamp\nmanipulation that avoid system calls and take shortcuts\nto facilitate
operations on very large data.","License":"GPL-
2","NeedsCompilation":"yes","Package":"fasttime","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Fast Utility Function for Time Parsing and
Conversion","URL":"http:\/\/www.rforge.net\/fasttime","Version":"1.0-
1"},"fat2Lpoly":{"Author":"Alexandre BUREAU <alexandre.bureau@msp.ulaval.ca> and
Jordie Croteau\n<jordie.croteau@crulrg.ulaval.ca>","Depends":"R (>=
3.2)","Description":"Performs family-based association tests with a polytomous
outcome under 2-locus and 1-locus models\ndefined by some design
matrix.","Imports":"kinship2,
multgee","License":"GPL","NeedsCompilation":"no","Package":"fat2Lpoly","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Title":"Two-Locus Family-Based Association
Test with Polytomic
Outcome","URL":"http:\/\/www.crulrg.ulaval.ca\/pages_perso_chercheurs\/bureau_a\/",
"Version":"1.2.2"},"favnums":{"Author":"Oliver Keyes [aut, cre], Alex Bellos
[cph]","Depends":"R (>= 2.10)","Description":"A dataset of favourite numbers,
selected from an online poll of over 30,000 people by Alex
Bellos\n(http:\/\/pages.bloomsbury.com\/favouritenumber).","License":"CC0","NeedsCo
mpilation":"no","Package":"favnums","Repository":"http:\/\/cran.csiro.au\/src\/cont
rib","Title":"A Dataset of Favourite Numbers","Version":"1.0.0"},"fbRads":
{"Author":"Ajaykumar Gopal <ajay@card.com>, Gergely Daroczi
<gergely.daroczi@card.com>","Description":"Wrapper functions around the Facebook
Marketing 'API' to create, read, update and delete custom audiences, images,
campaigns, ad sets, ads and related content.","Imports":"RCurl, jsonlite, digest,
futile.logger, bit64, plyr,\ndata.table","License":"AGPL-
3","NeedsCompilation":"no","Package":"fbRads","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Analyzing and Managing Facebook Ads from
R","URL":"https:\/\/github.com\/cardcorp\/fbRads","Version":"0.2"},"fbRanks":
{"Author":"Eli Holmes","Depends":"stats","Description":"This package uses time
dependent Poisson regression and a record of goals scored in matches to rank teams
via estimated attack and defense strengths. The statistical model is based on
Dixon and Coles (1997) Modeling Association Football Scores and Inefficiencies in
the Football Betting Market, Applied Statistics, Volume 46, Issue 2, 265-280. The
package has a some webscrapers to assist in the development and updating of a match
database. If the match database contains unconnected clusters (i.e. sets of teams
that have only played each other and not played teams from other sets), each
cluster is ranked separately relative to the median team strength in the cluster.
The package contains functions for predicting and simulating tournaments and
leagues from estimated models. The package allows fitting via the glm(),
speedglm(), and glmnet() functions. The latter allows fast and efficient fitting
of very large numbers of teams. The fitting algorithm will analyze the match data
and determine which teams form a cluster (a set of teams where there is a path of
matches connecting every team) and fit each cluster separately.","Imports":"igraph,
2","NeedsCompilation":"no","Package":"fbRanks","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"RJSONIO, RCurl, httr, XML, Rlab, xtable, tcltk,
speedglm,\nglmnet","Title":"Association Football (Soccer) Ranking via Poisson
Regression","URL":"http:\/\/www.lastplanetranking.blogspot.com\/","Version":"2.0"},
"fbati":{"Author":"Thomas Hoffmann <tjhoffm@gmail.com>","Depends":"pbatR(>=
2.0.0)","Description":"Does family-based gene by environment interaction tests,
joint gene, gene-environment interaction test, and a test of a set of genes
conditional on another set of genes.","Imports":"tcltk, fgui,
rootSolve","License":"GPL","NeedsCompilation":"yes","Package":"fbati","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Title":"Gene by Environment Interaction and
Conditional Gene Tests for\nNuclear
Families","URL":"http:\/\/www.people.fas.harvard.edu\/~tjhoffm\/fbati.html","Versio
n":"1.0-1"},"fbroc":{"Author":"Erik Peter [aut, cre]","Depends":"R (>= 3.2.0),
ggplot2, methods, stats, utils","Description":"Implements a very fast C++ algorithm
to quickly bootstrap\nreceiver operating characteristics (ROC) curves and derived
performance metrics, including the area under the\ncurve (AUC) as well as the true
and false positive rate. The analysis of paired\nreceiver operating curves is
supported as well, so that a comparison of two predictors is possible.\nYou can
also plot the results and calculate confidence intervals.\nCurrently the
calculation of 100000 bootstrap replicates for 500 observations\ntakes about one
second.","Imports":"Rcpp","License":"GPL-
2","NeedsCompilation":"yes","Package":"fbroc","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Fast Algorithms to Bootstrap Receiver Operating
Characteristics\nCurves","URL":"http:\/\/www.epeter-stats.de\/roc-curve-analysis-
with-fbroc\/","Version":"0.3.1"},"fcd":{"Author":"Yang Feng, Richard J. Samworth
and Yi Yu","Depends":"R (>= 2.15.1), glmnet, MASS,
combinat","Description":"Efficient procedures for community detection in network
studies, especially for sparse networks with not very obvious community structure.
The algorithms impose penalties on the differences of the coordinates which
represent the community labels of the nodes.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"fcd","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Fused Community Detection","Version":"0.1"},"fclust":
{"Author":"Paolo Giordani, Maria Brigida Ferraro","Depends":"R(>= 2.8.1), base,
stats, graphics, grDevices","Description":"Algorithms for fuzzy clustering, cluster
validity indices and plots for cluster validity and visualizing fuzzy clustering
2)","NeedsCompilation":"no","Package":"fclust","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Fuzzy Clustering","Version":"1.1.2"},"fcros":
{"Author":"Doulaye Dembele","Depends":"R (>= 2.10)","Description":"A fold change
rank ordering statistics method is presented to search for\ndifferentially
expressed genes and to detect recurrent chromosomal copy number aberrations.\nThis
method may be useful for high-throughput biological data (microarray,
sequencing, ...).\nProbabilities are associated with genes\/probes in the dataset
and there is no problem of\nmultiple tests when using this method. For aCGH data,
segmentation results are obtained by\nmerging the significant probes
detected.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"fcros","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"A Method to Search for Differentially Expressed Genes and
to\nDetect Recurrent Chromosomal Copy Number Aberrations","Version":"1.4.1"},"fda":
{"Author":"J. O. Ramsay <ramsay@psych.mcgill.ca>, Hadley
Wickham\n<h.wickham@gmail.com>, Spencer Graves\n<spencer.graves@prodsyse.com>,
Giles Hooker <gjh27@cornell.edu>","Depends":"R (>= 2.10.0), splines, Matrix,
graphics","Description":"These functions were developed to support functional
data\nanalysis as described in Ramsay, J. O. and Silverman, B. W.\n(2005)
Functional Data Analysis. New York: Springer. They were\nported from earlier
versions in Matlab and S-PLUS. An\nintroduction appears in Ramsay, J. O., Hooker,
Giles, and\nGraves, Spencer (2009) Functional Data Analysis with R and\nMatlab
(Springer). The package includes data sets and script\nfiles working many examples
including all but one of the 76\nfigures in this latter book. Matlab versions of
the code and\nsample analyses are no longer distributed through CRAN, as they\nwere
when the book was published. For those, ftp
from\nhttp:\/\/www.psych.mcgill.ca\/misc\/fda\/downloads\/FDAfuns\/\nThere you find
a set of .zip files containing the functions and\nsample analyses, as well as
two .txt files giving instructions for\ninstallation and some additional
information.\nThe changes from Version 2.4.1 are fixes of bugs in density.fd
and\nremoval of functions create.polynomial.basis, polynompen, and\npolynomial.
These were deleted because the monomial basis\ndoes the same thing and because
there were errors in the code.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"fda","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"deSolve, R.matlab, quadprog, nlme, lattice, RCurl,
zoo","Title":"Functional Data
Analysis","URL":"http:\/\/www.functionaldata.org","Version":"2.4.4"},"fda.usc":
{"Author":"Manuel Febrero Bande [aut],\nManuel Oviedo de la Fuente [aut,
cre],\nPedro Galeano [ctb],\nAlicia Nieto [ctb],\nEduardo Garcia-Portugues
[ctb]","Depends":"R (>= 2.10), fda, splines, MASS, mgcv,
rpart","Description":"Routines for exploratory and descriptive analysis of
functional data such as depth measurements, atypical curves detection, regression
models, supervised classification, unsupervised classification and functional
analysis of variance.","Imports":"methods, grDevices, graphics, utils,
2","NeedsCompilation":"yes","Package":"fda.usc","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Functional Data Analysis and Utilities for Statistical
Computing","URL":"http:\/\/www.jstatsoft.org\/v51\/i04\/","Version":"1.2.2"},"fdaMi
xed":{"Author":"Bo Markussen","Description":"Likelihood based analysis of 1-
dimension functional data\nin a mixed-effects model framework. Matrix computation
are\napproximated by semi-explicit operator equivalents with linear\ncomputational
complexity.","Imports":"Formula, Rcpp","License":"GPL-
2","NeedsCompilation":"yes","Package":"fdaMixed","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Functional data analysis in a mixed model
framework","Version":"0.4"},"fdaPDE":{"Author":"Eardi Lila [aut, cre],\nLaura M.
Sangalli [aut],\nJim Ramsay [aut],\nLuca Formaggia [aut]","Depends":"R (>= 3.0.0),
stats, grDevices, graphics, rgl","Description":"An implementation of regression
models with partial differential regularizations, making use of the Finite Element
Method. The models efficiently handle data distributed over irregularly shaped
domains and can comply with various conditions at the boundaries of the domain. A
priori information about the spatial structure of the phenomenon under study can be
incorporated in the model via the
differential regularization.","License":"CC BY-NC-SA
4.0","NeedsCompilation":"yes","Package":"fdaPDE","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"MASS","Title":"Functional Data Analysis and Partial
Differential Equations;\nStatistical Analysis of Functional and Spatial Data, Based
on\nRegression with Partial Differential Regularizations","Version":"0.1-
2"},"fdakma":{"Author":"Alice Parodi, Mirco Patriarca, Laura Sangalli, Piercesare
Secchi, Simone Vantini, Valeria Vitelli","Description":"It performs simultaneously
clustering and alignment of a multidimensional or unidimensional functional dataset
by means of k-mean alignment.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"fdakma","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Functional Data Analysis: K-Mean
Alignment","Version":"1.2.1"},"fdapace":{"Author":"Xiongtao Dai,\nPantelis Z.
Hadjipantelis,\nHao Ji,\nHans-Georg Mueller,\nJane-Ling
Wang","Description":"Provides implementation of various methods of Functional Data
Analysis (FDA) and Empirical Dynamics. The core of this package is Functional
Principal Component Analysis (FPCA), a key technique for functional data analysis,
for sparsely or densely sampled random trajectories and time courses, via the
Principal Analysis by Conditional Estimation (PACE) algorithm or numerical
integration. PACE is useful for the analysis of data that have been generated by a
sample of underlying (but usually not fully observed) random trajectories. It does
not rely on pre-smoothing of trajectories, which is problematic if functional data
are sparsely sampled. PACE provides options for functional regression and
correlation, for Longitudinal Data Analysis, the analysis of stochastic processes
from samples of realized trajectories, and for the analysis of underlying dynamics.
The core computational algorithms are implemented using the 'Eigen' C++ library for
numerical linear algebra and 'RcppEigen' \"glue\".","Imports":"Rcpp (>= 0.11.5),
Hmisc, plot3D, Matrix, pracma, numDeriv","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"yes","Package":"fdapace","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"rgl, aplpack, mgcv, ks, MASS,
gtools","Title":"Functional Data Analysis and Empirical
Dynamics","URL":"https:\/\/github.com\/hadjipantelis\/tPACE","Version":"0.1.1"},"fd
asrvf":{"Author":"J. Derek Tucker <jdtuck@sandia.gov>","Depends":"R (>=
3.1.0),","Description":"Functions to support functional data analysis using the
square root velocity framework.","Imports":"Rcpp (>= 0.12.1), foreach, mvtnorm,
matrixcalc, splines,\nparallel, fields, doParallel","License":"GPL-
3","NeedsCompilation":"yes","Package":"fdasrvf","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"akima","Title":"Elastic Functional Data
Analysis","Version":"1.6.0"},"fdatest":{"Author":"Alessia Pini, Simone
Vantini","Depends":"fda","Description":"Implementation of the Interval Testing
Procedure for functional data in different frameworks (i.e., one or two-population
frameworks, functional linear models) by means of different basis expansions (i.e.,
B-spline, Fourier, and phase-amplitude Fourier). The current version of the package
requires functional data evaluated on a uniform grid; it automatically projects
each function on a chosen functional basis; it performs the entire family of
multivariate tests; and, finally, it provides the matrix of the p-values of the
previous tests and the vector of the corrected p-values. The functional basis, the
coupled or uncoupled scenario, and the kind of test can be chosen by the user. The
package provides also a plotting function creating a graphical output of the
procedure: the p-value heat-map, the plot of the corrected p-values, and the plot
of the functional data.","License":"GPL-
2","NeedsCompilation":"no","Package":"fdatest","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Interval Testing Procedure for Functional
Data","Version":"2.1"},"fdrDiscreteNull":{"Author":"Xiongzhi Chen and R.W. Doerge
<doerge@purdue.edu>","Depends":"R(>= 3.1.0)","Description":"It is known that
current false discovery rate (FDR) procedures can be very conservative\nwhen
applied to p-values (and test statistics) with discrete (and heterogeneous) null
distributions.\nThis package implements the more powerful weighted generalized FDR
procedure that adapts to these two features of the discrete paradigm for multiple
testing.\nThe package takes in the original data set rather than the p-values in
order to carry out the adjustments needed for multiple testing in this paradigm.
The methodology applies also to multiple testing where the null p-values are
uniformly distributed.\nThe package implements the method for three types of test
statistics and their p-values:\n(a) binomial test on if two independent Poisson
distributions have the same means, (b) Fisher's exact test on if the conditional
distribution is the same as the marginal distribution for two binomial
distributions,\n(c) the exact negative binomial test on if two independent negative
binomial distributions with the same size parameter have the same means.\nIt
depends on the R packages ``MCMCpack'' to use its function ``dnoncenhypergeom'' for
hypergeometric distributions, and edgeR to uses its normalization techniques for
data that follow negative binomial distributions.","Imports":"MCMCpack,
edgeR","License":"LGPL","NeedsCompilation":"no","Package":"fdrDiscreteNull","Reposi
tory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"False Discovery Rate
Procedure Under Discrete Null
Distributions","URL":"http:\/\/www.princeton.edu\/~xiongzhi\/fdrDiscreteNull","Vers
ion":"1.0"},"fdrci":{"Author":"Joshua Millstein","Description":"FDR functions for
permutation-based estimators, including pi0 as well as FDR\nconfidence intervals.
The confidence intervals account for dependencies between\ntests by the
incorporation of an overdispersion parameter, which is estimated\nfrom the permuted
data.","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"fdrci","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Permutation-based FDR Point and Confidence Interval
Estimation","Version":"2.0"},"fdrtool":{"Author":"Bernd Klaus and Korbinian
Strimmer.","Depends":"R (>= 3.0.2)","Description":"Estimates both tail area-based
false\ndiscovery rates (Fdr) as well as local false discovery rates (fdr) for
a\nvariety of null models (p-values, z-scores, correlation coefficients,\nt-
scores). The proportion of null values and the parameters of the
null\ndistribution are adaptively estimated from the data. In addition, the
package\ncontains functions for non-parametric density estimation (Grenander
estimator),\nfor monotone regression (isotonic regression and antitonic regression
with weights),\nfor computing the greatest convex minorant (GCM) and the least
concave majorant (LCM),\nfor the half-normal and correlation distributions, and for
computing\nempirical higher criticism (HC) scores and the corresponding decision
threshold.","Imports":"graphics, grDevices, stats","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"fdrtool","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Estimation of (Local) False Discovery Rates and Higher
Criticism","URL":"http:\/\/strimmerlab.org\/software\/fdrtool\/","Version":"1.2.15"
},"fds":{"Author":"Han Lin Shang and Rob J Hyndman","Depends":"R (>= 2.10.0),
rainbow, RCurl","Description":"Functional data sets","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"fds","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Functional data
sets","URL":"https:\/\/sites.google.com\/site\/hanlinshangswebsite\/","Version":"1.
7"},"fdth":{"Author":"José Cláudio Faria, Enio G. Jelihovschi and Ivan B.
Allaman","Depends":"R (>= 2.6.0), stats, grDevices,
graphics","Description":"Perform frequency distribution tables, associated
histograms\nand polygons from vector, data.frame and matrix objects for\nnumerical
and categorical variables.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"fdth","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Frequency Distribution Tables, Histograms and
Polygons","Version":"1.2-1"},"feature":{"Author":"Tarn Duong <tarn.duong@gmail.com>
& Matt Wand <Matt.Wand@uts.edu.au>","Depends":"R (>= 1.4.0)","Description":"Local
inferential feature significance for multivariate kernel density
estimation.","Imports":"grDevices, graphics, ks (>= 1.10.0), misc3d, rgl, stats,
tcltk","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"feature","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"MASS","Title":"Local Inferential Feature Significance
for Multivariate Kernel\nDensity
Estimation","URL":"http:\/\/www.mvstat.net\/tduong","Version":"1.2.13"},"features":
{"Author":"Ravi Varadhan, Johns Hopkins University, and MKG Subramaniam,\nAT&T
Reserach Labs.","Depends":"lokern","Description":"Discretely-sampled function is
first smoothed. Features\nof the smoothed function are then extracted. Some of
the key\nfeatures include mean value, first and second derivatives,\ncritical
points (i.e. local maxima and minima), curvature of\ncunction at critical points,
wiggliness of the function, noise\nin data, and outliers in data.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"features","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Feature Extraction for Discretely-Sampled Functional
Data","URL":"\nhttp:\/\/www.jhsph.edu\/agingandhealth\/People\/Faculty_personal_pag
es\/Varadhan.html","Version":"2015.12-1"},"fechner":{"Author":"Ali Uenlue [aut,
cre], Thomas Kiefer [aut, trl] (Based on\noriginal MATLAB source by Ehtibar N.
Dzhafarov.)","Depends":"R (>= 2.15.1), base, graphics,
stats","Description":"Functions and example datasets for Fechnerian scaling
of\ndiscrete object sets. It computes Fechnerian distances among\nobjects
representing subjective dissimilarities, and other\nrelated information. See
package?fechner for an overview.","Imports":"base, graphics, stats","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"fechner","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Fechnerian Scaling of Discrete Object
Sets","Version":"1.0-2"},"federalregister":{"Author":"Thomas J.
Leeper","Description":"Access data from the Federal Register API
<https:\/\/www.federalregister.gov\/developers\/api\/v1>.","Imports":"httr, curl,
jsonlite","License":"GPL-
2","NeedsCompilation":"no","Package":"federalregister","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Client Package for the U.S. Federal Register
API","URL":"https:\/\/github.com\/rOpenGov\/federalregister","Version":"0.2.0"},"fe
rmicatsR":{"Author":"Pablo Saz Parkinson [aut, cre]","Depends":"R (>=
3.1.0)","Description":"Data from various catalogs of astrophysical gamma-ray
sources\ndetected by NASA's Large Area Telescope (The Astrophysical Journal, 697,
1071,\n2009 June 1), on board the Fermi gamma-ray satellite. More information
on\nFermi and its data products is available from the Fermi Science Support
Center\n(http:\/\/fermi.gsfc.nasa.gov\/ssc\/).","License":"CC0","NeedsCompilation":
"no","Package":"fermicatsR","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Su
ggests":"ggplot2","Title":"Fermi Large Area Telescope
Catalogs","URL":"https:\/\/github.com\/sazpark\/fermicatsR.git","Version":"1.4"},"f
f":{"Author":"Daniel Adler <dadler@uni-goettingen.de>,\nChristian Gläser
<christian_glaeser@gmx.de>,\nOleg Nenadic <onenadi@uni-goettingen.de>,\nJens
Oehlschlägel <Jens.Oehlschlaegel@truecluster.com>,\nWalter Zucchini <wzucchi@uni-
goettingen.de>","Depends":"R (>= 2.10.1), bit (>= 1.1-12),
utils","Description":"The ff package provides data structures that are stored
on\ndisk but behave (almost) as if they were in RAM by transparently\nmapping only
a section (pagesize) in main memory - the effective\nvirtual memory consumption per
ff object. ff supports R's standard\natomic data types 'double', 'logical', 'raw'
and 'integer' and\nnon-standard atomic types boolean (1 bit), quad (2 bit
unsigned),\nnibble (4 bit unsigned), byte (1 byte signed with NAs), ubyte (1
byte\nunsigned), short (2 byte signed with NAs), ushort (2 byte unsigned),\nsingle
(4 byte float with NAs). For example 'quad' allows efficient\nstorage of genomic
data as an 'A','T','G','C' factor. The unsigned\ntypes support 'circular'
arithmetic. There is also support for\nclose-to-atomic types 'factor', 'ordered',
'POSIXct', 'Date' and\ncustom close-to-atomic types.\nff not only has native C-
support for vectors, matrices and arrays\nwith flexible dimorder (major column-
order, major row-order and\ngeneralizations for arrays). There is also a ffdf class
not unlike\ndata.frames and import\/export filters for csv files.\nff objects store
raw data in binary flat files in native encoding,\nand complement this with
metadata stored in R as physical and virtual\nattributes. ff objects have well-
defined hybrid copying semantics,\nwhich gives rise to certain performance
improvements through\nvirtualization. ff objects can be stored and reopened across
R\nsessions. ff files can be shared by multiple ff R objects\n(using different data
en\/de-coding schemes) in the same process\nor from multiple R processes to exploit
parallelism. A wide choice of\nfinalizer options allows to work with 'permanent'
files as well as\ncreating\/removing 'temporary' ff files completely transparent to
the\nuser. On certain OS\/Filesystem combinations, creating the ff files\nworks
without notable delay thanks to using sparse file allocation.\nSeveral access
optimization techniques such as Hybrid Index\nPreprocessing and Virtualization are
implemented to achieve good\nperformance even with large datasets, for example
virtual matrix\ntranspose without touching a single byte on disk. Further, to
reduce\ndisk I\/O, 'logicals' and non-standard data types get stored native
and\ncompact on binary flat files i.e. logicals take up exactly 2 bits
to\nrepresent TRUE, FALSE and NA.\nBeyond basic access functions, the ff package
also provides\ncompatibility functions that facilitate writing code for ff and
ram\nobjects and support for batch processing on ff objects (e.g. as.ram,\nas.ff,
ffapply). ff interfaces closely with functionality from package\n'bit': chunked
looping, fast bit operations and coercions between\ndifferent objects that can
store subscript information ('bit',\n'bitwhich', ff 'boolean', ri range index, hi
hybrid index). This allows\nto work interactively with selections of large datasets
and quickly\nmodify selection criteria.\nFurther high-performance enhancements can
be made available upon request.","License":"GPL-2 | file
LICENSE","NeedsCompilation":"yes","Package":"ff","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"biglm","Title":"memory-efficient storage of large
data on disk and fast access\nfunctions","URL":"http:\/\/ff.r-forge.r-
project.org\/","Version":"2.2-13"},"ffbase":{"Author":"Edwin de Jonge, Jan
Wijffels, Jan van der Laan","Depends":"R (>= 2.12.0),ff(>= 2.2-
11)","Description":"Extends the out of memory vectors of 'ff' with\nstatistical
functions and other utilities to ease their usage.","Imports":"fastmatch,
bit","License":"GPL-
3","NeedsCompilation":"yes","Package":"ffbase","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat, parallel, LaF, biglm","Title":"Basic
Statistical Functions for Package
'ff'","URL":"http:\/\/github.com\/edwindj\/ffbase","Version":"0.12.3"},"ffmanova":
{"Author":"Øyvind Langsrud and Bjørn-Helge Mevik","Description":"This package
performs general linear modeling with\nmultiple responses (MANCOVA). An overall p-
value for each\nmodel term is calculated by the 50-50 MANOVA method, which\nhandles
collinear responses. Rotation testing is used to\ncompute adjusted single response
p-values according to\nfamilywise error rates and false discovery
rates.","License":"GPL-
2","NeedsCompilation":"no","Package":"ffmanova","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Fifty-fifty MANOVA","Version":"0.2-2"},"fftw":
{"Author":"Sebastian Krey <skrey@statistik.tu-dortmund.de> Uwe
Ligges\n<ligges@statistik.tu-dortmund.de> Olaf Mersmann\n<olafm@statistik.tu-
dortmund.de>","Depends":"R (>= 2.12.0)","Description":"Provides a simple and
efficient wrapper around the fastest\nFourier transform in the west (FFTW)
library.","License":"GPL-
2","NeedsCompilation":"yes","Package":"fftw","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Fast FFT and DCT based on FFTW","Version":"1.0-
3"},"fftwtools":{"Author":"Karim Rahim <karim.rahim@queensu.ca>","Depends":"R (>=
2.15.2)","Description":"Provides a wrapper for several FFTW functions. This package
provides access to the two-dimensional FFT, the multivariate FFT, and the one-
dimensional real to complex FFT using FFTW3. The package includes the functions
fftw and mvfftw which are designed to mimic the functionality of the R functions
fft and mvfft. The FFT functions have a parameter that allows them to not return
the redundant complex conjugate when the input is real data.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"fftwtools","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"fftw","Title":"Wrapper for FFTW3: Includes 1-D,
Univariate and Multivariate,\nand 2-D
Transform","URL":"http:\/\/github.com\/krahim\/fftwtools","Version":"0.9-
7"},"fgac":{"Author":"Veronica Andrea Gonzalez-Lopez
<veronica@ime.unicamp.br>","Description":"Bi-variate data fitting is done by two
stochastic\ncomponents: the marginal distributions and the dependency\nstructure.
The dependency structure is modeled through a\ncopula. An algorithm was implemented
considering seven families\nof copulas (Generalized Archimedean Copulas), the best
fitting\ncan be obtained looking all copula's options (totally positive\nof order 2
and stochastically increasing
models).","License":"GPL","NeedsCompilation":"no","Package":"fgac","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"Generalized Archimedean
Copula","Version":"0.6-1"},"fgof":{"Author":"Ivan Kojadinovic and Jun
Yan","Depends":"mvtnorm, numDeriv","Description":"Goodness-of-fit test with
multiplier or parametric\nbootstrap.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"fgof","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Fast Goodness-of-fit Test","Version":"0.2-1"},"fgpt":
{"Author":"Reinder Radersma & Ben Sheldon","Depends":"R (>= 2.10)","Description":"A
permutation technique to explore and control for spatial autocorrelation. This
package contains low level functions for performing permutations and calculating
statistics as well as higher level functions. Higher level functions are an easy to
use function for performing spatially restricted permutation tests and summarize
and plot
results.","License":"GPL","NeedsCompilation":"no","Package":"fgpt","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Suggests":"knitr","Title":"Floating Grid
Permutation Technique","Version":"2.3"},"fgui":{"Author":"Thomas Hoffmann
<tjhoffm@gmail.com>","Depends":"tools","Description":"Rapidly create a GUI
interface for a function you created\nby automatically creating widgets for
arguments of the\nfunction. Automatically parses help routines for\ncontext-
sensative help to these arguments. The interface\nessentially a wrapper to some
tcltk routines to both simplify\nand facilitate GUI creation. More advanced tcltk
routines\/GUI\nobjects can be incorporated into the interface for
greater\ncustomization for the more
experienced.","Imports":"tcltk","License":"GPL","NeedsCompilation":"no","Package":"
fgui","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"tcltk","Title
":"Function
GUI","URL":"http:\/\/www.people.fas.harvard.edu\/~tjhoffm\/fgui.html","Version":"1.
0-5"},"fheatmap":{"Author":"Vaishali
Tumulu and Sivasish Sindiri","Depends":"R (>= 3.0)","Description":"R function to
plot high quality, elegant heatmap using 'ggplot2' graphics .\nSome of the
important features of this package are, coloring of row\/column side tree
with\nrespect to the number of user defined cuts in the cluster, add annotations to
both columns\nand rows, option to input annotation palette for tree and column
annotations and multiple\nparameters to modify aesthetics (style, color, font) of
texts in the plot.","Imports":"grid, RColorBrewer , gdata, ggplot2, reshape2,
gplots","License":"GPL-
3","NeedsCompilation":"no","Package":"fheatmap","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Fantastic Heatmap","Version":"1.0.1"},"fields":
{"Author":"Douglas Nychka [aut, cre], Reinhard Furrer [aut], John Paige [aut],
Stephan Sain [aut]","Depends":"R (>= 3.0), methods, spam, maps","Description":"For
curve, surface and function\nfitting with an emphasis on splines, spatial data and
spatial\nstatistics. The major methods include cubic, and thin plate
splines,\nKriging and compact covariances for large data sets. The splines
and\nKriging methods are supporting by functions that can determine the\nsmoothing
parameter (nugget and sill variance) by cross validation\nand also by restricted
maximum likelihood. For Kriging there is\nan easy to function that also estimates
the correlation scale (range).\nA major feature is that\nany covariance function
implemented in R and following a simple fields\nformat can be used for spatial
prediction. There are also many useful\nfunctions for plotting and\nworking with
spatial data as images. This package also contains an\nimplementation of sparse
matrix methods for large spatial data sets and\ncurrently requires the sparse
matrix (spam) package.\nUse help(fields) to get started and for an\noverview. The
fields source code is deliberately commented and\nprovides useful explanations of
numerical details in addition to the\nmanual pages. The commented source code can
be viewed by expanding the\nsource code .tar.gz file and looking in R
subdirectory.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"fields","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Tools for Spatial
Data","URL":"http:\/\/www.image.ucar.edu\/Software\/Fields","Version":"8.3-
6"},"fifer":{"Author":"Dustin Fife <fife.dustin@gmail.com>","Depends":"xtable,
MASS","Description":"A collection of functions that assist in data\nmanipulation
analysis and plotting.","License":"GPL-
2","NeedsCompilation":"no","Package":"fifer","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"A collection of miscellaneous
functions","Version":"1.0"},"filehash":{"Author":"Roger D. Peng
<rdpeng@jhu.edu>","Depends":"R (>= 3.0.0), methods","Description":"Implements a
simple key-value style database where character string keys\nare associated with
data values that are stored on the disk. A simple interface is provided for
inserting,\nretrieving, and deleting data from the database. Utilities are provided
that allow 'filehash' databases to be\ntreated much like environments and lists are
already used in R. These utilities are provided to encourage\ninteractive and
exploratory analysis on large datasets. Three different file formats for
representing the\ndatabase are currently available and new formats can easily be
incorporated by third parties for use in the\n'filehash' framework.","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"filehash","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Simple Key-Value
Database","URL":"http:\/\/github.com\/rdpeng\/filehash","Version":"2.3"},"filehashS
QLite":{"Author":"Roger D. Peng <rpeng@jhsph.edu>","Depends":"R (>= 2.14.0),
methods, filehash (>= 1.0), DBI, RSQLite","Description":"Simple key-value database
using SQLite as the backend","Imports":"filehash, DBI","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"filehashSQLite","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Simple key-value database using
SQLite","URL":"http:\/\/github.com\/rdpeng\/filehashsqlite","Version":"0.2-
4"},"filematrix":{"Author":"Andrey
Shabalin","Depends":"methods","Description":"Interface for working with large
matrices stored in files, not in computer memory.\nSupports multiple data types
(double, integer, logical and raw) of different sizes (e.g. 4, 2, or 1 byte
integers).\nAccess to parts of the matrix is done by indexing, exactly as with
usual R matrices.\nSupports very large matrices (tested on 1 terabyte matrix),
allowing for more than 2^32 rows or columns.\nCross-platform as the package has R
code only, no C\/C++.","License":"LGPL-
3","NeedsCompilation":"no","Package":"filematrix","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"File-Backed Matrix Class with Convenient Read and Write
Access","Version":"1.0"},"filenamer":{"Author":"David J. H.
Shih","Depends":"methods","Description":"Create descriptive file names with ease.
New file names are\nautomatically (but optionally) time stamped and placed in date
stamped\ndirectories. Streamline your analysis pipeline with input and output
file\nnames that have informative tags and proper file extensions.","License":"GPL
(>=
3)","NeedsCompilation":"no","Package":"filenamer","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"io, testthat","Title":"Easy Management of File
Names","URL":"https:\/\/bitbucket.org\/djhshih\/filenamer","Version":"0.2.1"},"fina
ncial":{"Author":"Lukasz Komsta <lukasz.komsta@umlub.pl>","Depends":"R (>=
2.0)","Description":"Time value of money, cash flows and other
financial\nfunctions.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"financial","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Solving financial problems in R","URL":"http:\/\/www.r-
project.org, http:\/\/www.komsta.net\/","Version":"0.2"},"findpython":
{"Author":"Trevor L Davis and Paul Gilbert.","Description":"Package designed to
find an acceptable python binary.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"findpython","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Python tools to find an
acceptable python
binary","URL":"https:\/\/github.com\/trevorld\/findpython","Version":"1.0.1"},"fing
erprint":{"Author":"Rajarshi Guha
<rajarshi.guha@gmail.com>","Depends":"methods","Description":"This package contains
functions to manipulate binary fingerprints\nof arbitrary length. A fingerprint is
represented by an object of S4 class 'fingerprint'\nwhich is internally represented
a vector of integers, such\nthat each element represents the position in the
fingerprint that is set to 1.\nThe bitwise logical functions in R are overridden so
that they can be used directly\nwith 'fingerprint' objects. A number of distance
metrics are also\navailable (many contributed by Michael Fadock). Fingerprints\ncan
be converted to Euclidean vectors (i.e., points on the unit hypersphere) and\ncan
also be folded using OR. Arbitrary fingerprint formats can be handled via
line\nhandlers. Currently handlers are provided for CDK, MOE and BCI fingerprint
data.","License":"GPL","NeedsCompilation":"yes","Package":"fingerprint","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"RUnit","Title":"Functions to
operate on binary fingerprint data","Version":"3.5.2"},"finiteruinprob":
{"Author":"Benjamin Baumgartner [aut, cre],\nRiccardo Gatto [ctb,
ths]","Description":"In the CramÃ©râ€“Lundberg risk process perturbed by a
Wiener\nprocess, this packages provides approximations to the probability of\nruin
within a finite time horizon. Currently, there are three methods\nimplemented: The
first one uses saddlepoint approximation (two\nvariants are provided), the second
one uses importance sampling and\nthe third one is based on the simulation of a
dual process. This last\nmethod is not very accurate and only given here for
completeness.","Imports":"sdprisk, numDeriv","License":"AGPL-
3","NeedsCompilation":"no","Package":"finiteruinprob","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Computation of the probability of ruin within a
finite time\nhorizon","Version":"0.4"},"finreportr":{"Author":"Seward
Lee","Depends":"R (>= 2.10)","Description":"Download and display company financial
data from the U.S. Securities\nand Exchange Commission's EDGAR database. It
contains a suite of functions with\nweb scraping and XBRL parsing capabilities that
allows users to extract data from EDGAR\nin an automated and scalable manner. See
<https:\/\/www.sec.gov\/edgar\/searchedgar\/companysearch.html>\nfor more
information.","Imports":"xml2, dplyr, RCurl, rvest, XBRL","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"finreportr","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"knitr, rmarkdown, testthat","Title":"Financial
Data from U.S. Securities and Exchange
Commission","URL":"https:\/\/github.com\/sewardlee337\/finreportr","Version":"1.0.0
"},"fishMod":{"Author":"Scott D. Foster","Description":"Fits models to catch and
effort data. Single-species models are 1) delta log-normal, 2) Tweedie, or 3)
Poisson-gamma
(GL)Ms.","License":"GPL","NeedsCompilation":"yes","Package":"fishMod","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Title":"Fits Poisson-sum-of-Gammas GLMs,
Tweedie GLMs, and delta\nlog-normal mdoels","Version":"0.25"},"fisheyeR":
{"Author":"Eduardo San Miguel Martin","Depends":"tkrplot,
methods","Description":"fisheyeR provides tools for creating Interactive
Data\nVisualizations by implementing ideas from Furnas, Munzner,\nCosta and
Venturini.","License":"GPL-
2","NeedsCompilation":"no","Package":"fisheyeR","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Fisheye and Hyperbolic-space-alike Interactive
Visualization\nTools in R","Version":"0.9"},"fishmethods":{"Author":"Gary A. Nelson
<gary.nelson@state.ma.us>","Depends":"R (>=
3.2.0),MASS, boot, bootstrap, lme4","Description":"Fishery science methods and
models from published literature and contributions from colleagues.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"fishmethods","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Fishery Science Methods and Models in
R","Version":"1.9-0"},"fishmove":{"Author":"Johannes Radinger","Depends":"ggplot2,
plyr, MASS, boot","Description":"Functions to predict fish movement parameters
plotting leptokurtic fish dispersal kernels (see Radinger and Wolter, 2014:
Patterns and predictors of fish dispersal in rivers. Fish and Fisheries. 15:456-
473.)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"fishmove","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Prediction of Fish Movement
Parameters","URL":"http:\/\/dx.doi.org\/10.1111\/faf.12028","Version":"0.3-
3"},"fit.models":{"Author":"Kjell Konis <kjell.konis@me.com>.","Depends":"R (>=
2.15.0), lattice","Description":"A framework for comparing fitted
models","License":"GPL","NeedsCompilation":"no","Package":"fit.models","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"MASS","Title":"fit.models","Ver
sion":"0.5-10"},"fit4NM":{"Author":"Eun-Kyung Lee, Gyujeong
Noh","Depends":"gWidgets, tcltk, tkrplot, RGtk2, gWidgetsRGtk2,
cairoDevice","Description":"This package is for NONMEM user","License":"LGPL-
2.1","NeedsCompilation":"no","Package":"fit4NM","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"NONMEM platform","Version":"3.3.3"},"fitDRC":
{"Author":"Simon L. Rinderknecht and Peter Reichert
<peter.reichert@eawag.ch>","Description":"Fits Density Ratio Classes to
elicited\nprobability-quantile points or intervals","License":"GPL-
2","NeedsCompilation":"no","Package":"fitDRC","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Fitting Density Ratio Classes","Version":"1.1"},"fitTetra":
{"Author":"Roeland Voorrips and Gerrit Gort","Depends":"R (>=
2.10)","Description":"Package fitTetra contains three functions that can be
used\nto assign genotypes to a collection of tetraploid samples based\non
bialleleic marker assays. Functions fitTetra (to fit several\nmodels for one marker
from the data and select the best\nfitting) or saveMarkerModels (calls fitTetra for
multiple\nmarkers and saves the results to files) will probably be the\nmost
convenient to use. Function CodomMarker offers more\ncontrol and fits one specified
model for a given marker.","License":"GPL (>=
2.2)","NeedsCompilation":"no","Package":"fitTetra","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"doMC, foreach, RSvgDevice,
devEMF","Title":"fitTetra is an R package for assigning tetraploid
genotype\nscores","Version":"1.0"},"fitbitScraper":{"Author":"Cory Nissen
<corynissen@gmail.com> [aut, cre]","Depends":"R (>= 3.0.0)","Description":"Scrapes
data from Fitbit <http:\/\/www.fitbit.com>. This does not use the official\nAPI,
but instead uses the API that the web dashboard uses to generate the
graphs\ndisplayed on the dashboard after login at
<http:\/\/www.fitbit.com>.","Imports":"httr, stringr, jsonlite, methods,
LICENSE","NeedsCompilation":"no","Package":"fitbitScraper","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Title":"Scrapes Data from
Fitbit","URL":"https:\/\/github.com\/corynissen\/fitbitScraper","Version":"0.1.6"},
"fitdistrplus":{"Author":"Marie Laure Delignette-Muller [aut, cre],\nChristophe
Dutang [aut],\nRegis Pouillot [ctb],\nJean-Baptiste Denis [ctb]","Depends":"R (>=
3.2.0), MASS, grDevices","Description":"Extends the fitdistr function (of the MASS
package) with several functions to help the fit of a parametric distribution to
non-censored or censored data. Censored data may contain left censored, right
censored and interval censored values, with several lower and upper bounds. In
addition to maximum likelihood estimation (MLE), the package provides moment
matching (MME), quantile matching (QME) and maximum goodness-of-fit estimation
(MGE) methods (available only for non-censored data). Weighted versions of MLE, MME
and QME are available.","Imports":"stats, survival","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"fitdistrplus","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"actuar, rgenoud, mc2d, gamlss.dist","Title":"Help
to Fit of a Parametric Distribution to Non-Censored or\nCensored
Data","URL":"http:\/\/riskassessment.r-forge.r-project.org","Version":"1.0-
6"},"flacco":{"Author":"Pascal Kerschke [aut, cre],\nJan Dagefoerde
[aut]","Depends":"R (>= 3.0.0), BBmisc, checkmate","Description":"Contains tools
and features, which can be used for an exploratory\nlandscape analysis of
continuous optimization problems. Those are able to\nquantify rather complex
properties, such as the global structure,\nseparability, etc., of continuous
optimization problems.","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"flacco","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"devtools, e1071, expm, lhs, MASS, Matrix, mda,
mlbench, mlr,\nnumDeriv, parallel, parallelMap, plyr, RANN, rpart, shape,\nsmoof,
testthat","Title":"Feature-Based Landscape Analysis of Continuous and
Constraint\nOptimization
Problems","URL":"https:\/\/github.com\/kerschke\/flacco","Version":"1.2"},"flam":
{"Author":"Ashley Petersen","Description":"Implements the fused lasso additive
model as proposed in Petersen, A., Witten, D., and Simon, N. (2014). Fused Lasso
Additive Model. arXiv preprint arXiv:1409.5391.","Imports":"Rcpp (>= 0.11.6), MASS,
graphics, grDevices, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"flam","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Fits Piecewise Constant Models with Data-Adaptive
Knots","Version":"3.0"},"flare":{"Author":"Xingguo Li, Tuo Zhao, Lie Wang, Xiaoming
Yuan and Han Liu","Depends":"R (>= 2.15.0), lattice, MASS, Matrix,
igraph","Description":"The package \"flare\" provides the implementation of a
family of Lasso variants including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq
Lasso for estimating high dimensional sparse linear model. We adopt the alternating
direction method of multipliers and convert the original optimization problem into
a sequential L1 penalized least square minimization problem, which can be
efficiently solved by linearization algorithm. A multi-stage screening approach is
adopted for further acceleration. Besides the sparse linear model estimation, we
also provide the extension of these Lasso variants to sparse Gaussian graphical
model estimation including TIGER and CLIME using either L1 or adaptive penalty.
Missing values can be tolerated for Dantzig selector and CLIME. The computation is
memory-optimized using the sparse matrix output.","License":"GPL-
2","NeedsCompilation":"yes","Package":"flare","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Family of Lasso
Regression","Version":"1.5.0"},"flashClust":{"Author":"code by Fionn Murtagh and R
development team, modifications and\npackaging by Peter Langfelder","Depends":"R
(>= 2.3.0)","Description":"Fast implementation of hierarchical
clustering","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"flashClust","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Implementation of optimal hierarchical
clustering","Version":"1.01-2"},"flexCWM":{"Author":"Mazza A., Punzo A., Ingrassia
S.","Depends":"R (>= 3.0.0)","Description":"Allows for maximum likelihood fitting
of cluster-weighted models, a class of mixtures of regression models with random
covariates.","Imports":"\nparallel,numDeriv,mnormt,mclust,ellipse,mixture,Flury,ade
habitat,MASS,statmod","License":"GPL-
2","NeedsCompilation":"no","Package":"flexCWM","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Flexible Cluster-Weighted
Modeling","Version":"1.5"},"flexPM":{"Author":"Paolo Frumento
<paolo.frumento@ki.se>","Depends":"survival","Description":"Estimation of flexible
parametric models for survival data.","Imports":"splines, stats","License":"GPL-
2","NeedsCompilation":"no","Package":"flexPM","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Flexible Parametric Models for Censored and Truncated
Data","Version":"2.0"},"flexclust":{"Author":"Friedrich Leisch [aut, cre], Evgenia
Dimitriadou [ctb]","Depends":"R (>= 2.14.0), graphics, grid, lattice,
modeltools","Description":"The main function kcca implements a general framework
for\nk-centroids cluster analysis supporting arbitrary distance\nmeasures and
centroid computation. Further cluster methods\ninclude hard competitive learning,
neural gas, and QT\nclustering. There are numerous visualization methods
for\ncluster results (neighborhood graphs, convex cluster hulls,\nbarcharts of
centroids, ...), and bootstrap methods for the\nanalysis of cluster
stability.","Imports":"methods, parallel, stats, stats4","License":"GPL-
2","NeedsCompilation":"yes","Package":"flexclust","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"ellipse, clue, cluster, seriation","Title":"Flexible
Cluster Algorithms","Version":"1.3-4"},"flexmix":{"Author":"Bettina Gruen [aut,
cre],\nFriedrich Leisch [aut],\nDeepayan Sarkar [ctb],\nFrederic Mortier
[ctb],\nNicolas Picard [ctb]","Depends":"R (>= 2.15.0),
lattice","Description":"FlexMix implements a general framework for finite\nmixtures
of regression models using the EM algorithm.\nFlexMix provides the E-step and all
data handling, while the M-step can be\nsupplied by the user to easily define new
models. Existing drivers\nimplement mixtures of standard linear models, generalized
linear\nmodels and model-based clustering.","Imports":"grid, methods, modeltools
(>= 0.2-16), nnet, stats, stats4","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"flexmix","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"codetools, diptest, ellipse, gclus, glmnet,
lme4 (>= 1.0),\nMASS, mgcv (>= 1.8-0), mlbench, mlogit, multcomp,
mvtnorm,\nsurvival","Title":"Flexible Mixture Modeling","Version":"2.3-
13"},"flexsurv":{"Author":"Christopher Jackson <chris.jackson@mrc-
bsu.cam.ac.uk>","Depends":"survival,R (>= 2.15.0)","Description":"Flexible
parametric models for time-to-event data, including the Royston-Parmar spline
model, generalized gamma and generalized F distributions. Any user-defined
parametric distribution can be fitted, given at least an R function defining the
probability density or hazard. There are also tools for fitting and predicting
from fully parametric multi-state
models.","Imports":"mstate,muhaz,mvtnorm,deSolve,quadprog","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"flexsurv","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"eha,numDeriv,testthat,msm,ActuDistns,knitr,TH.data,co
lorspace","Title":"Flexible Parametric Survival and Multi-State
Models","URL":"https:\/\/github.com\/chjackson\/flexsurv-
dev","Version":"0.7.1"},"flip":{"Author":"Livio Finos, with contributions by Dario
Basso, Aldo Solari, Jelle Goeman and Marco Rinaldo. Special thanks are due to Ivan
Marin-Franch and Fredrik Nilsson for the debugging and the good
questions.","Depends":"methods, e1071, someMTP, cherry","Description":"It
implements many univariate and multivariate permutation (and rotation) tests.
Allowed tests: the t one and two samples, ANOVA, linear models, Chi Squared test,
rank tests (i.e. Wilcoxon, Mann-Whitney, Kruskal-Wallis), Sign test and McNemar.
Test on Linear Models are performed also in presence of covariates (i.e. nuisance
parameters). The permutation and the rotation methods to get the null distribution
of the test statistics are available. It also implements methods for multiplicity
control such as Westfall-Young minP procedure and Closed Testing (Marcus, 1976) and
k-FWER. Moreover, it allows to test for fixed effects in mixed effects
models.","Imports":"Rcpp,","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"flip","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Multivariate Permutation Tests","Version":"2.4.3"},"flora":
{"Author":"Gustavo Carvalho","Depends":"R (>= 3.0.0)","Description":"Tools to
quickly compile taxonomic and distribution data from\nthe Brazilian Flora 2020 at
http:\/\/floradobrasil.jbrj.gov.br\/.","Imports":"shiny, httr, dplyr,
2)","NeedsCompilation":"no","Package":"flora","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat","Title":"Tools for Interacting with the
Brazilian Flora
2020","URL":"http:\/\/www.github.com\/gustavobio\/flora","Version":"0.2.7"},"flowDi
v":{"Author":"Bruno M.S. Wanderley, MarÃa Victoria Quiroga, AndrÃ© M. Amado,
Fernando Unrein","Depends":"R (>= 3.0), flowWorkspace, flowCore,
vegan","Description":"Concatenates some 'flowWorkspace', 'flowCore', 'vegan' and
'gdata' packages functionalities to import 'FlowJo' workspaces and calculates
ecological diversity indices for gated populations, based on two dimensions
cytograms.","License":"GPL-
3","NeedsCompilation":"no","Package":"flowDiv","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Cytometric Diversity Indices from 'FlowJo'
Workspaces","Version":"1.0"},"flower":{"Author":"Xie WANG","Description":"Flowering
is an important life history trait of flowering plants. It has been mainly analyzed
with respect to flowering onset and duration of flowering. This tools provide some
functions to compute the temporal distribution of an flowering individual related
to other population members. fCV() measures the temporal variation in flowering.
RIind() measures the rank order of flowering for individual plants within a
population. SI(), SI2(), SI3(), and SI4() calculate flowering synchrony with
different methods.","License":"GPL (>=
1.0)","NeedsCompilation":"no","Package":"flower","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Tools for characterizing flowering
traits","Version":"1.0"},"flowfield":{"Author":"Kyle A. Caudle","Description":"Flow
field forecasting draws information from an interpolated flow field of the observed
time series to incrementally build a forecast.","License":"GPL-
3","NeedsCompilation":"no","Package":"flowfield","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"SemiPar","Title":"Forecasts future values of a
univariate time series","Version":"1.0"},"flowr":{"Author":"Sahil Seth [aut,
cre]","Depends":"R (>= 3.0.2), methods, params (>= 0.3), utils","Description":"This
framework allows you to design and implement complex\npipelines, and deploy them on
your institution's computing cluster. This has\nbeen built keeping in mind the
needs of bioinformatics workflows. However, it is\neasily extendable to any field
where a series of steps (shell commands) are to\nbe executed in a
(work)flow.","Imports":"diagram, whisker, tools","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"flowr","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"reshape2, knitr, ggplot2, openxlsx, testthat,
funr","Title":"Streamlining Design and Deployment of Complex
Workflows","URL":"https:\/\/github.com\/sahilseth\/flowr","Version":"0.9.9.5"},"flo
ws":{"Author":"TimothÃ©e Giraud [cre, aut],\nLaurent Beauguitte [aut],\nMarianne
GuÃ©rois [ctb]","Depends":"R (>= 2.10)","Description":"Selections on flow matrices,
statistics on selected flows, map and graph visualisations.","Imports":"reshape2,
igraph, sp, graphics, stats","License":"GPL-
3","NeedsCompilation":"no","Package":"flows","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr","Title":"Flow Selection and
Analysis","URL":"https:\/\/github.com\/rCarto\/flows","Version":"1.1"},"flsa":
{"Author":"Holger Hoefling","Depends":"R (>= 2.0.0)","Description":"This package
implements a path algorithm for the Fused\nLasso Signal Approximator. For more
details see the help files","License":"GPL-
2","NeedsCompilation":"yes","Package":"flsa","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat","Title":"Path algorithm for the general Fused
Lasso Signal Approximator","Version":"1.05"},"flux":{"Author":"Gerald Jurasinski,
Franziska Koebsch, Anke Guenther, Sascha Beetz","Depends":"R (>= 2.12.0),
caTools","Description":"Functions for the calculation of greenhouse gas flux
rates\nfrom closed chamber concentration measurements. The package follows\na
modular concept: Fluxes can be calculated in just two simple steps\nor in several
steps if more control in details is wanted. Additionally\nplot and preparation
functions as well as functions for modelling\ngpp and reco are
provided.","License":"GPL-
2","NeedsCompilation":"no","Package":"flux","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Flux rate calculation from dynamic closed chamber
measurements","Version":"0.3-0"},"fma":{"Author":"Rob J Hyndman
<Rob.Hyndman@monash.edu>","Depends":"R (>= 2.0.0), graphics, stats, tseries,
forecast","Description":"All data sets from \"Forecasting: methods and
applications\"\nby Makridakis, Wheelwright & Hyndman (Wiley, 3rd ed.,
1998).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"fma","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Data sets from \"Forecasting: methods and applications\"
by\nMakridakis, Wheelwright & Hyndman
(1998)","URL":"http:\/\/robjhyndman.com\/software\/fma\/","Version":"2.01"},"fmri":
{"Author":"Karsten Tabelow [aut, cre],\nJoerg Polzehl [aut],\nBrandon Whitcher
[ctb]","Description":"The package contains R-functions to perform an fmri
analysis\nas described in\nK. Tabelow, J. Polzehl, H.U. Voss, and V.
Spokoiny,\nAnalysing fMRI experiments with structure adaptive smoothing
procedures,\nNeuroImage, 33:55-62 (2006),\nJ. Polzehl, H.U. Voss, K. Tabelow,
Structural adaptive segmentation\nfor statistical parametric mapping, NeuroImage,
52:515-523 (2010)\nand\nK. Tabelow, J. Polzehl, Statistical Parametric Maps
for\nFunctional MRI Experiments in {R}: The Package {fmri}},\nJournal of
Statistical Software, 44(11):1--21 (2011).","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"fmri","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"tcltk, tkrplot, fastICA, adimpro,
oro.nifti","Title":"Analysis of fMRI experiments","URL":"http:\/\/www.wias-
berlin.de\/software\/imaging\/","Version":"1.5-1"},"fmsb":{"Author":"Minato
Nakazawa <minato-nakazawa@umin.net>","Depends":"R (>=
2.2.0)","Description":"Several utility functions for the book entitled\n\"Practices
of Medical and Health Data Analysis using R\"\n(Pearson Education Japan, 2007) with
Japanese demographic\ndata and some demographic analysis related
2)","NeedsCompilation":"no","Package":"fmsb","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Functions for Medical Statistics Book with some Demographic
Data","URL":"http:\/\/minato.sip21c.org\/msb\/","Version":"0.5.2"},"fmt":
{"Author":"Lianbo Yu, The Ohio State University","Description":"This package
computes posterior residual variances to be\nused in the denominator of a moderated
t-statistic from a\nlinear model analysis of microarray data. It is an
extension\nof the moderated t-statistic original proposed by Smyth (2004).\nLOESS
local regression and empirical Bayesian method are used\nto estimate gene specific
prior degrees of freedom and prior\nvariance based on average gene intensity level.
The posterior\nresidual variance in the denominator is a weighted average of\nprior
and residual variance and the weights are prior degrees\nof freedom and residual
variance degrees of freedom. The\ndegrees of freedom of the moderated t-statistic
is simply the\nsum of prior and residual variance degrees of
freedom.","License":"GPL-
2","NeedsCompilation":"no","Package":"fmt","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"limma","Title":"Variance estimation of FMT method (Fully
Moderated
t-statistic)","Version":"1.0"},"foba":{"Author":"Tong Zhang
<tongz@rci.rutgers.edu>","Depends":"R (>= 2.0.0)","Description":"foba is a package
that implements forward, backward, and foba sparse learning algorithms for ridge
regression, described in the paper \"Adaptive Forward-Backward Greedy Algorithm for
Learning Sparse Representations\".","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"foba","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"greedy variable selection","Version":"0.1"},"fontcm":
{"Author":"Winston Chang,\nAlexej Kryukov,\nPaul Murrell","Depends":"R (>=
2.14)","Description":"Computer Modern font for use with extrafont
2","NeedsCompilation":"no","Package":"fontcm","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"extrafont","Title":"Computer Modern font for use with
extrafont
package","URL":"https:\/\/github.com\/wch\/fontcm","Version":"1.1"},"foodweb":
{"Author":"Giselle Perdomo","Depends":"rgl","Description":"Calculates twelve
commonly-used, basic measures of food\nweb network structure from binary, predator-
prey matrices:\nspecies richness, connectance, total number of links,
link\ndensity, number of trophic positions, predator:prey ratio, and\nfraction of
carnivores, herbivores, top species and\nintermediate species. Employs food web
language in the code\nand output, translates between a couple of common food
web\nformats, can handle food webs consisting of multiple levels,\nand can automate
the analysis for a large number of webs. The\nprogram produces 3-dimensional graphs
of high quality that can\nbe customized by the user.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"foodweb","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"visualisation and analysis of food web
networks","Version":"1-0"},"forams":{"Author":"Rodrigo
Aluizio","Depends":"methods","Description":"SHE, FORAM Index and ABC Method
analyses and custom plot\nfunctions for community data.","Imports":"vegan, stats,
2)","NeedsCompilation":"no","Package":"forams","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Foraminifera and Community Ecology
Analyses","Version":"2.0-5"},"foreach":{"Author":"Rich Calaway [cre],\nRevolution
Analytics [aut, cph],\nSteve Weston [aut]","Depends":"R (>=
2.5.0)","Description":"Support for the foreach looping construct. Foreach is
an\nidiom that allows for iterating over elements in a collection,\nwithout the use
of an explicit loop counter. This package in\nparticular is intended to be used
for its return value, rather\nthan for its side effects. In that sense, it is
similar to the\nstandard lapply function, but doesn't require the evaluation\nof a
function. Using foreach without side effects also\nfacilitates executing the loop
in parallel.","Enhances":"compiler, doMC, RUnit, doParallel","Imports":"codetools,
utils, iterators","License":"Apache License (==
2.0)","NeedsCompilation":"no","Package":"foreach","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"randomForest","Title":"Provides Foreach Looping
Construct for R","Version":"1.4.3"},"forecTheta":{"Author":"Jose Augusto Fiorucci,
Francisco Louzada and Bao Yiqi","Depends":"R (>= 2.0), parallel,
forecast","Description":"Routines for forecasting univariate time series using
Theta Models. Contains several cross-validation routines.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"forecTheta","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Forecasting Time Series by Theta
Models","URL":"http:\/\/arxiv.org\/abs\/1503.03529","Version":"2.1"},"forecast":
{"Author":"Rob Hyndman [aut, cre, cph]","Depends":"R (>= 3.0.2), stats, graphics,
zoo, timeDate","Description":"Methods and tools for displaying and
analysing\nunivariate time series forecasts including exponential smoothing\nvia
state space models and automatic ARIMA modelling.","Imports":"tseries, fracdiff,
Rcpp (>= 0.11.0), nnet, colorspace,\nparallel, ggplot2 (>= 2.0.0)","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"forecast","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat, fpp","Title":"Forecasting Functions for
Time Series and Linear
Models","URL":"http:\/\/github.com\/robjhyndman\/forecast","Version":"7.0"},"forega
":{"Author":"Mehmet Hakan Satman","Depends":"robfilter,
forecast","Description":"The implemented algorithm performs a floating-point
genetic algorithm search with a statistical forecasting operator that generates
offspring which probably will be generated in future generations. Use of this
operator enhances the search capabilities of floating-point genetic algorithms
because offspring generated by usual genetic operators rapidly forecasted before
performing more generations.","Imports":"Rcpp (>= 0.11.6)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"forega","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Floating-Point Genetic Algorithms with Statistical
Forecast\nBased Inheritance Operator","Version":"1.0"},"foreign":{"Author":"R Core
Team [aut, cph, cre],\nRoger Bivand [ctb, cph],\nVincent J. Carey [ctb,
cph],\nSaikat DebRoy [ctb, cph],\nStephen Eglen [ctb, cph],\nRajarshi Guha [ctb,
cph],\nNicholas Lewin-Koh [ctb, cph],\nMark Myatt [ctb, cph],\nBen Pfaff
[ctb],\nBrian Quistorff [ctb],\nFrank Warmerdam [ctb, cph],\nStephen Weigand [ctb,
cph],\nFree Software Foundation, Inc. [cph]","Depends":"R (>=
3.0.0)","Description":"Functions for reading and writing data stored by some
versions of\nEpi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka\nand for
reading and writing some dBase files.","Imports":"methods, utils,
2)","NeedsCompilation":"yes","Package":"foreign","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Read Data Stored by Minitab, S, SAS, SPSS, Stata,
Systat, Weka,\ndBase, ...","Version":"0.8-66"},"forensic":{"Author":"Miriam
Marusiakova (Centre of Biomedical Informatics, Institute\nof Computer Science,
Academy of Sciences of the Czech Republic)","Depends":"R (>= 2.4.0), genetics,
combinat","Description":"The statistical evaluation of DNA mixtures, DNA
profile\nmatch
probability","License":"GPL","NeedsCompilation":"no","Package":"forensic","Reposito
ry":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Statistical Methods in Forensic
Genetics","Version":"0.2"},"forensim":{"Author":"Hinda Haned
<h.haned@nfi.minvenj.nl>","Depends":"methods,
tcltk,tcltk2,tkrplot","Description":"Statistical methods and simulation tools for
the\ninterpretation of forensic DNA mixtures","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"forensim","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Statistical tools for the interpretation of forensic
DNA\nmixtures","Version":"4.3"},"forestFloor":{"Author":"Soeren Havelund
Welling","Description":"Form visualizations of high dimensional mapping structures
of random forests and feature contributions.","Imports":"Rcpp (>= 0.11.3), rgl,
kknn","License":"GPL-
2","NeedsCompilation":"yes","Package":"forestFloor","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"randomForest, utils, devtools,
tools","Title":"Visualizes Random Forests with Feature
Contributions","URL":"http:\/\/forestFloor.dk","Version":"1.9.3"},"forestmodel":
{"Author":"Nick Kennedy <r@nick-kennedy.com>","Depends":"R (>= 3.2.0), ggplot2 (>=
1.0.1)","Description":"Produces forest plots using 'ggplot2' from models produced
by functions\nsuch as stats::lm(), stats::glm() and
survival::coxph().","Imports":"dplyr (>= 0.4.2), broom (>= 0.3.7), lazyeval (>=
2","NeedsCompilation":"no","Package":"forestmodel","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"survival, metafor","Title":"Forest Plots from
Regression Models","Version":"0.4.0"},"forestplot":{"Author":"Max Gordon [aut,
cre],\nThomas Lumley [aut, ctb]","Depends":"grid, magrittr","Description":"A forest
plot that allows for\nmultiple confidence intervals per row,\ncustom fonts for each
text element,\ncustom confidence intervals,\ntext mixed with expressions, and
more.\nThe aim is to extend the use of forest plots beyond meta-analyses.\nThis is
a more general version of the original 'rmeta' package's forestplot\nfunction and
relies heavily on the 'grid' package.","License":"GPL-
2","NeedsCompilation":"no","Package":"forestplot","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat, knitr","Title":"Advanced Forest Plot Using
'grid' Graphics","URL":"http:\/\/gforge.se\/packages\/","Version":"1.4"},"formatR":
{"Author":"Yihui Xie","Depends":"R (>= 3.0.2)","Description":"Provides a function
tidy_source() to format R source code. Spaces\nand indent will be added to the code
automatically, and comments will be\npreserved under certain conditions, so that R
code will be more\nhuman-readable and tidy. There is also a Shiny app as a user
interface in\nthis package (see
tidy_app()).","License":"GPL","NeedsCompilation":"no","Package":"formatR","Reposito
ry":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"codetools, shiny, testit,
knitr","Title":"Format R Code
Automatically","URL":"http:\/\/yihui.name\/formatR","Version":"1.3"},"formattable":
{"Author":"Kun Ren [aut, cre],\nKenton Russell [aut]","Depends":"R (>=
2.14.1)","Description":"Provides functions to create formattable vectors and data
frames.\nFormattable vectors are printed with text formatting, and
formattable\ndata frames are printed with multiple types of formatting in
markdown\nto improve the readability of data presented in tabular form rendered
as\nweb pages.","Imports":"htmltools, htmlwidgets, markdown, knitr,
shiny","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"formattable","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Formattable Data
Structures","URL":"http:\/\/renkun.me\/formattable,\nhttps:\/\/github.com\/renkun-
ken\/formattable","Version":"0.1.5"},"formula.tools":{"Author":"Christopher
Brown","Depends":"R (>= 3.0.0), operator.tools(>= 1.4.0), utils,
methods","Description":"These utilities facilitate the programmatic manipulations
of\nformulas, expressions, calls, names, symbols and other objects.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"formula.tools","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"magrittr, testthat","Title":"Utilities for
Formulas, Expressions, Calls and Other
Objects","URL":"https:\/\/github.com\/decisionpatterns\/formula.tools","Version":"1
.5.4"},"fortunes":{"Author":"Achim Zeileis (R code) and the R community
(fortunes).\nContributions (fortunes and\/or code) by Torsten Hothorn,\nPeter
Dalgaard, Uwe Ligges, Kevin Wright, Martin Maechler,\nKjetil Brinchmann Halvorsen,
Kurt Hornik, Duncan Murdoch,\nAndy Bunn, Ray Brownrigg, Roger Bivand, Spencer
Graves,\nJim Lemon, Christian Kleiber, David L. Reiner,\nBerton Gunter, Roger
Koenker, Charles Berry, Marc Schwartz,\nMichael Dewey, Ben Bolker, Peter Dunn,
Sarah Goslee, Simon\nBlomberg, Bill Venables, Roland Rau, Thomas Petzoldt,
Rolf\nTurner, Mark Leeds, Emmanuel Charpentier, Chris Evans, Paolo\nSonego, Peter
Ehlers, Detlef Steuer, Tal Galili, Greg Snow,\nBrian D. Ripley, Michael Sumner,
David Winsemius, Liviu\nAndronic, Brian Diggs, Matthieu Stigler, Michael
Friendly,\nDirk Eddelbuettel, Richard M. Heiberger, Patrick Burns,\nDieter Menne,
Andrie de Vries, Barry Rowlingson, Renaud\nLancelot, R. Michael Weylandt, Jon Olav
Skoien, Francois\nMorneau, Antony Unwin, Joshua Wiley, Terry Therneau,
Bryan\nHanson, Henrik Singmann, Eduard Szoecs.","Description":"R
Fortunes","Imports":"utils","License":"GPL-
2","NeedsCompilation":"no","Package":"fortunes","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"R Fortunes","Version":"1.5-2"},"forward":
{"Author":"Originally written for S-Plus by: Kjell Konis\n<kkonis@insightful.com>
and Marco Riani <mriani@unipr.it>\nPorted to R by Luca Scrucca
<luca@stat.unipg.it>","Depends":"R (>= 2.8), MASS","Description":"Forward search
approach to robust analysis in linear and\ngeneralized linear regression
2","NeedsCompilation":"no","Package":"forward","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Forward search","Version":"1.0.3"},"fossil":
{"Author":"Matthew J. Vavrek <matthew@matthewvavrek.com>","Depends":"sp, maps,
shapefiles","Description":"A set of analytical tools useful in analysing
ecological\nand geographical data sets, both ancient and modern. The\npackage
includes functions for estimating species richness\n(Chao 1 and 2, ACE, ICE,
Jacknife), shared species\/beta\ndiversity, species area curves and geographic
distances and\nareas.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"fossil","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Palaeoecological and Palaeogeographical Analysis
Tools","URL":"http:\/\/matthewvavrek.com\/programs-and-
code\/fossil\/","Version":"0.3.7"},"fourPNO":{"Author":"Steven Andrew Culpepper
[aut, cre]","Depends":"R (>= 3.0.1)","Description":"Estimate Barton & Lord's four
parameter IRT model with lower and upper asymptotes using Bayesian formulation
described by Culpepper (2015).","Imports":"Rcpp","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"fourPNO","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Bayesian 4 Parameter Item Response
Model","Version":"1.0.3"},"fpCompare":{"Author":"Alex M Chubaty [aut, cre],\nHer
Majesty the Queen in Right of Canada, as represented by the\nMinister of Natural
Resources Canada [cph]","Depends":"R (>= 3.1.2)","Description":"Comparisons of
floating point numbers are problematic due to errors\nassociated with the binary
representation of decimal numbers.\nDespite being aware of these problems, people
still use numerical methods\nthat fail to account for these and other rounding
errors (this pitfall is\nthe first to be highlighted in Circle 1 of Burns
(2012)\n[The R Inferno](http:\/\/www.burns-
stat.com\/pages\/Tutor\/R_inferno.pdf)).\nThis package provides new relational
operators useful for performing\nfloating point number comparisons with a set
tolerance.","License":"GPL-
3","NeedsCompilation":"no","Package":"fpCompare","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr, rmarkdown, testthat","Title":"Reliable
Comparison of Floating Point
Numbers","URL":"https:\/\/github.com\/PredictiveEcology\/fpCompare","Version":"0.2.
1"},"fpc":{"Author":"Christian Hennig <c.hennig@ucl.ac.uk>","Depends":"R (>=
2.0)","Description":"Various methods for clustering and cluster validation.\nFixed
point clustering. Linear regression clustering. Clustering by\nmerging Gaussian
mixture components. Symmetric\nand asymmetric discriminant projections for
visualisation of the\nseparation of groupings. Cluster validation statistics\nfor
distance based clustering including corrected Rand index.\nCluster-wise cluster
stability assessment. Methods for estimation of\nthe number of clusters: Calinski-
Harabasz, Tibshirani and Walther's\nprediction strength, Fang and Wang's bootstrap
stability.\nGaussian\/multinomial mixture fitting for
mixed\ncontinuous\/categorical variables. Variable-wise statistics for
cluster\ninterpretation. DBSCAN clustering. Interface functions for
many\nclustering methods implemented in R, including estimating the number
of\nclusters with kmeans, pam and clara. Modality diagnosis for Gaussian\nmixtures.
For an overview see package?fpc.","Imports":"MASS, cluster, mclust, flexmix,
prabclus, class, diptest,\nmvtnorm, robustbase, kernlab, trimcluster, grDevices,
graphics,\nmethods, stats,
utils","License":"GPL","NeedsCompilation":"no","Package":"fpc","Repository":"http:\
/\/cran.csiro.au\/src\/contrib","Title":"Flexible Procedures for
Clustering","URL":"http:\/\/www.homepages.ucl.ac.uk\/~ucakche\/","Version":"2.1-
10"},"fpca":{"Author":"Jie Peng <jie@wald.ucdavis.edu> , Debashis
Paul\n<debashis@wald.ucdavis.edu>","Depends":"sm,splines","Description":"A
geometric approach to MLE for functional principal\ncomponents","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"fpca","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Restricted MLE for Functional Principal Components
Analysis","URL":"anson.ucdavis.edu\/~jie\/software.html","Version":"0.2-1"},"fpow":
{"Author":"Ali Baharev <ali.baharev@gmail.com>","Depends":"R (>=
2.14.1)","Description":"Returns the noncentrality parameter of the noncentral
F\ndistribution if probability of type I and type II error,\ndegrees of freedom of
the numerator and the denominator are\ngiven. It may be useful for computing
minimal detectable\ndifferences for general ANOVA models. This program
is\ndocumented in the paper of A. Baharev, S. Kemeny, On the\ncomputation of the
noncentral F and noncentral beta\ndistribution; Statistics and Computing, 2008, 18
(3), 333-
340.","License":"CC0","NeedsCompilation":"yes","Package":"fpow","Repository":"http:
\/\/cran.csiro.au\/src\/contrib","Title":"Computing the noncentrality parameter of
the noncentral F\ndistribution","URL":"http:\/\/dx.doi.org\/10.1007\/s11222-008-
9061-3,\nhttp:\/\/reliablecomputing.eu\/ncbeta.html","Version":"0.0-2"},"fpp":
{"Author":"Rob J Hyndman <Rob.Hyndman@monash.edu>","Depends":"R (>= 2.0.0),
graphics, stats, forecast, fma, expsmooth,\nlmtest, tseries","Description":"All
data sets required for the examples and exercises in\nthe book \"Forecasting:
principles and practice\" by Rob J\nHyndman and George Athanasopoulos. All packages
required to run\nthe examples are also loaded.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"fpp","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Data for \"Forecasting: principles and
practice\"","URL":"http:\/\/otexts.com\/fpp\/","Version":"0.5"},"fptdApprox":
{"Author":"Patricia Román-Román, Juan J. Serrano-Pérez and Francisco Torres-
Ruiz.","Description":"Efficient approximation of first-passage-time densities for
diffusion processes based on the First-Passage-Time Location (FPTL)
function.","License":"GPL-
2","NeedsCompilation":"no","Package":"fptdApprox","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Approximation of First-Passage-Time Densities for
Diffusion\nProcesses","Version":"2.1"},"fracdiff":{"Author":"S original by Chris
Fraley, U.Washington, Seattle. R port by\nFritz Leisch at TU Wien; since 2003-12:
Martin Maechler;\nfdGPH(), fdSperio(), etc by Valderio Reisen and Artur
Lemonte.","Description":"Maximum likelihood estimation of the parameters of
a\nfractionally differenced ARIMA(p,d,q) model (Haslett and\nRaftery,
Appl.Statistics, 1989).","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"fracdiff","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"longmemo, urca","Title":"Fractionally differenced
ARIMA aka ARFIMA(p,d,q) models","Version":"1.4-2"},"fracprolif":{"Author":"Shawn
Garbett, Darren Tyson","Depends":"emg (>= 1.0.5), numDeriv, methods,
stats4","Description":"Functions for fitting data to a quiescent growth
model,\ni.e. a growth process that involves members of the population\nwho stop
dividing or propagating.","License":"GPL-2 | file
LICENSE","NeedsCompilation":"no","Package":"fracprolif","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Fraction Proliferation via a Quiescent Growth
Model","Version":"1.0.6"},"fractal":{"Author":"William Constantine and Donald
Percival (Applied Physics\nLaboratory, University of Washington)","Depends":"R (>=
3.0.2), splus2R (>= 1.2-0), ifultools (>= 2.0-0)","Description":"Stochastic fractal
and deterministic chaotic time series\nanalysis.","Imports":"sapa(>= 2.0-0), wmtsa
(>= 2.0-0), scatterplot3d","License":"GPL-
2","NeedsCompilation":"no","Package":"fractal","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"akima","Title":"Fractal Time Series Modeling and
Analysis","Version":"2.0-0"},"fractaldim":{"Author":"Hana Sevcikova
<hanas@uw.edu>,\nDon
Percival <dbp@apl.washington.edu>,\nTilmann Gneiting
<tilmann@stat.washington.edu>","Depends":"R (>= 2.11.0),
abind","Description":"Implements various methods for estimating fractal dimension
of time series and 2-dimensional data.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"fractaldim","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"wavelets, pcaPP, RandomFields,
snowFT","Title":"Estimation of fractal dimensions","Version":"0.8-
4"},"fractalrock":{"Author":"Brian Lee Yung Rowe","Depends":"futile.any (>= 1.3.0),
futile.logger (>= 1.3.0), timeDate,\nquantmod","Description":"The basic principle
driving fractal generation of time\nseries is that data is generated iteratively
based on\nincreasing levels of resolution. The initial series is defined\nby a so-
called initiator pattern and then generators are used\nto replace each segment of
the initial pattern. Regular,\nrepeatable patterns can be produced by using the
same seed and\ngenerators. By using a set of generators, non-repeatable
time\nseries can be produced. This technique is the basis of the\nfractal time
series process in this package.","License":"GPL-
3","NeedsCompilation":"no","Package":"fractalrock","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Generate fractal time series with non-normal
returns\ndistribution","Version":"1.1.0"},"fractional":{"Author":"Bill
Venables","Description":"The main function of this package allows numerical vector
objects to\nbe displayed with their values in vulgar fractional form. This is
convenient if\npatterns can then be more easily detected. In some cases replacing
the components\nof a numeric vector by a rational approximation can also be
expected to remove\nsome component of round-off error. The main functions form a
re-implementation\nof the functions 'fractions' and 'rational' of the MASS package,
but using a\nradically improved programming
strategy.","Imports":"Rcpp","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"fractional","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"stats, MASS, knitr, rmarkdown, ggplot2,
dplyr","Title":"Vulgar Fractions in R","Version":"0.1.3"},"frailtyHL":{"Author":"Il
Do HA, Maengseok Noh, Youngjo Lee","Depends":"R (>= 2.10.0),
Matrix,numDeriv,survival","Description":"The frailtyHL package implements the h-
likelihood\nestimation procedures for frailty models. The package fits\nCox's
proportional hazards models with random effects (or\nfrailties). For the frailty
distribution lognormal and gamma\nare allowed. The h-likelihood uses the Laplace
approximation\nwhen the numerical integration is intractable, giving
a\nstatistically efficient estimation in frailty
models.","License":"Unlimited","NeedsCompilation":"no","Package":"frailtyHL","Repos
itory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Frailty Models via H-
likelihood","Version":"1.1"},"frailtySurv":{"Author":"John V. Monaco [aut,
cre],\nMalka Gorfine [aut],\nLi Hsu [aut]","Depends":"R (>= 3.0.0),
survival","Description":"Simulates and fits semiparametric shared frailty models
under a\nwide range of frailty distributions using a consistent
and\nasymptotically-normal estimator. Currently supports: gamma, power
variance\nfunction, log-normal, and inverse Gaussian frailty
models.","Imports":"stats, nleqslv, reshape2, ggplot2, numDeriv","License":"LGPL-
2","NeedsCompilation":"yes","Package":"frailtySurv","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"knitr, testthat, parallel,
gridExtra","Title":"General Semiparametric Shared Frailty
Model","URL":"https:\/\/github.com\/vmonaco\/frailtySurv\/","Version":"1.2.2"},"fra
iltypack":{"Author":"Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui,
Audrey\nMauguen, Agnieszka Krol, Amadou Diakite and Alexandre Laurent","Depends":"R
(>= 2.10), survival, boot, MASS, survC1, nlme","Description":"The following several
classes of frailty models using a penalized likelihood estimation on the hazard
function but also a parametric estimation can be fit using this R package:\n1) A
shared frailty model (with gamma or log-normal frailty distribution) and Cox
proportional hazard model. Clustered and recurrent survival times can be
studied.\n2) Additive frailty models for proportional hazard models with two
correlated random effects (intercept random effect with random slope).\n3) Nested
frailty models for hierarchically clustered data (with 2 levels of clustering) by
including two iid gamma random effects.\n4) Joint frailty models in the context of
joint modelling for recurrent events with terminal event for clustered data or not.
A joint frailty model for two semi-competing risks and clustered data is also
proposed.\n5) Joint general frailty models in the context of a joint modelling for
recurrent events with terminal event data with two independent frailty terms.\n6)
Multivariate joint frailty models for two types of recurrent events and a terminal
event.\n7) Joint models for longitudinal data and a terminal event.\n8) Trivariate
joint models for longitudinal data, recurrent events and a terminal
event.\nPrediction values are available. Left-truncated (not for Joint model),
right-censored data, interval-censored data (only for Cox proportional hazard and
shared frailty model) and strata are allowed. In each model, the random effects
have the gamma or normal distribution. Now, you can also consider time-varying
covariates effects in Cox, shared and joint frailty models (1-5). The package
includes concordance measures for Cox proportional hazards models and for shared
frailty models.","License":"GPL (>=
2.0)","NeedsCompilation":"yes","Package":"frailtypack","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"knitr, rmarkdown","Title":"General Frailty
Models: Shared, Joint and Nested Frailty Models\nwith
Prediction","URL":"\nhttp:\/\/virginierondeau.com\/BiostatisticalConsulting\/Liste_
of_examples.html","Version":"2.8.3"},"frair":{"Author":"Daniel
Pritchard","Depends":"R (>= 3.0.0), stats4, bbmle","Description":"A package for
functional response analysis.","Imports":"emdbook, boot, parallel","License":"GPL-
2","NeedsCompilation":"no","Package":"frair","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Functional response analysis in R","Version":"0.4"},"franc":
{"Author":"Gabor Csardi, Titus Wormer, Maciej Ceglowski, Jacob R. Rideout,\nand
Kent S. Johnson","Description":"With no external dependencies and\nsupport for 335
languages; all languages spoken by\nmore than one million speakers. 'Franc' is a
port\nof the 'JavaScript' project of the same name,\nsee
<https:\/\/github.com\/wooorm\/franc>.","Imports":"jsonlite","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"franc","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat","Title":"Detect the Language of
Text","URL":"https:\/\/github.com\/mangothecat\/franc","Version":"1.1.1"},"frbs":
{"Author":"Lala Septem Riza, Christoph Bergmeir, Francisco Herrera, and\nJose
Manuel Benitez","Description":"An implementation of various learning algorithms
based on fuzzy rule-based systems (FRBSs) for dealing with classification and
regression tasks. Moreover, it allows to construct an FRBS model defined by human
experts.\nFRBSs are based on the concept of fuzzy sets, proposed by Zadeh in 1965,
which aims at\nrepresenting the reasoning of human experts in a set of IF-THEN
rules, to\nhandle real-life problems in, e.g., control, prediction and inference,
data\nmining, bioinformatics data processing, and robotics. FRBSs are also
known\nas fuzzy inference systems and fuzzy models. During the modeling of
an\nFRBS, there are two important steps that need to be conducted:
structure\nidentification and parameter estimation. Nowadays, there exists a
wide\nvariety of algorithms to generate fuzzy IF-THEN rules automatically
from\nnumerical data, covering both steps. Approaches that have been used in
the\npast are, e.g., heuristic procedures, neuro-fuzzy techniques,
clustering\nmethods, genetic algorithms, squares methods, etc. Furthermore, in
this\nversion we provide a universal framework named 'frbsPMML', which is
adopted\nfrom the Predictive Model Markup Language (PMML), for representing
FRBS\nmodels. PMML is an XML-based language to provide a standard for
describing\nmodels produced by data mining and machine learning algorithms.
Therefore,\nwe are allowed to export and import an FRBS model to\/from
'frbsPMML'.\nFinally, this package aims to implement the most widely used
standard\nprocedures, thus offering a standard package for FRBS modeling to the
R\ncommunity.","License":"GPL (>= 2) | file
LICENSE","NeedsCompilation":"no","Package":"frbs","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"class, e1071, XML","Title":"Fuzzy Rule-Based Systems
for Classification and Regression
Tasks","URL":"http:\/\/sci2s.ugr.es\/dicits\/software\/FRBS","Version":"3.1-
0"},"freeknotsplines":{"Author":"Steven Spiriti <puzzlesteven@gmail.com>, Philip
Smith\n<philip.smith@ttu.edu>, Pierre
Lecuyer\n<lecuyer@iro.UMontreal.ca>,","Depends":"R (>= 2.14.2), splines,
methods","Description":"This package is for fitting free-knot splines for
data\nwith one independent variable and one dependent variable. Four\nfree-knot
spline algorithms are provided for the case where the\nnumber of knots is known in
advance. A knot-search algorithm\nis provided for the case where the number of
knots is not known\nin advance. In addition, methods are available to compute
the\nfitted values, the residuals, and the coefficients of the\nsplines, and to
plot the results, along with a method to\nsummarize the results.","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"freeknotsplines","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Free-Knot Splines","Version":"1.0"},"freestats":
{"Author":"Xiaoyao Yang","Description":"A collections of useful statistical
functions used in Columbia\ncourse W4240\/W4400.","Imports":"MASS,
mvtnorm","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"freestats","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Statistical algorithms used in common data mining
course","Version":"0.0.3"},"freqMAP":{"Author":"Colin McCulloch","Description":"A
frequency moving average plot (MAP) is estimated from a\nmultinomial data and a
continuous covariate. The frequency MAP\nis a moving average estimate of category
frequencies, where\nfrequency means and posterior bounds are estimated.
Comparisons\nof two frequency MAPs as well as odds ratios can be
plotted.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"freqMAP","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Frequency Moving Average Plots (MAP) of Multinomial Data
by a\nContinuous Covariate","Version":"0.2"},"freqdom":{"Author":"Hormann S.,
Kidzinski L.","Depends":"R (>= 2.15.0), mvtnorm, stats, graphics,
base","Description":"Methods for the analysis of multivariate time series using
frequency domain techniques. Implementations of dynamic principle components
analysis (DPCA) and estimators of operators in lagged regression. Examples of usage
in functional data analysis setup.","License":"GPL-
3","NeedsCompilation":"no","Package":"freqdom","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"fda, MASS, MARSS","Title":"Frequency Domain Analysis
for Multivariate Time Series","Version":"1.0.4"},"freqparcoord":{"Author":"Norm
Matloff <normmatloff@gmail.com> and Yingkang
Xie\n<yingkang.xie@gmail.com>","Depends":"parallel, ggplot2, GGally, FNN,
mvtnorm","Description":"New approaches to parallel coordinates plots
for\nmultivariate data visualization, including applications to
clustering,\noutlier hunting and regression diagnostics. Includes general
functions\nfor multivariate nonparametric density and regression estimation,\nusing
parallel computation.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"freqparcoord","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"mgcv","Title":"Novel Methods for Parallel
Coordinates","Version":"1.0.1"},"freqweights":{"Author":"Emilio Torres-
Manzanera","Description":"The frequency of a particular data value is the number of
times it\noccurs. A frequency table is a table of values with their
corresponding\nfrequencies. Frequency weights are integer numbers that indicate how
many\ncases each case represents. This package provides some functions to
work\nwith such type of collected data.","Imports":"plyr, dplyr (>= 0.3),
data.table, biglm, fastcluster,\nFactoMineR, stats","License":"GPL-
3","NeedsCompilation":"no","Package":"freqweights","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"MASS, hflights, cluster, ggplot2, testthat,
RSQLite","Title":"Working with Frequency Tables","Version":"1.0.2"},"frm":
{"Author":"Joaquim J.S. Ramalho","Description":"Estimation and specification
analysis of one- and two-part fractional regression models and calculation of
partial effects.","License":"GPL-
2","NeedsCompilation":"no","Package":"frm","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Regression Analysis of Fractional
Responses","Version":"1.2.2"},"frmhet":{"Author":"Joaquim J.S.
Ramalho","Description":"Estimation and specification analysis of fractional
regression models with neglected heterogeneity and\/or endogenous
2","NeedsCompilation":"no","Package":"frmhet","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Regression Analysis of Fractional Responses Under
Unobserved\nHeterogeneity","Version":"1.1.2"},"frmpd":{"Author":"Joaquim J.S.
Ramalho","Description":"Estimation of panel data regression models for fractional
responses.","License":"GPL-
2","NeedsCompilation":"no","Package":"frmpd","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Regression Analysis of Panel Fractional
Responses","Version":"1.0.1"},"frmqa":{"Author":"Thanh T.
Tran","Depends":"partitions, Rmpfr","Description":"A collection of R and C++
functions to work with the\ngeneralized hyperbolic distribution, related
distributions and\ntheir applications in financial risk management
and\nquantitative analysis.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"frmqa","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"The Generalized Hyperbolic Distribution, Related
Distributions\nand Their Applications in Finance","Version":"0.1-5"},"fromo":
{"Author":"Steven E. Pav [aut, cre]","Description":"Fast computation of moments via
'Rcpp'. Supports computation on\nvectors and matrices, and Monoidal append of
moments.","Imports":"Rcpp (>= 0.12.3), methods","License":"LGPL-
3","NeedsCompilation":"yes","Package":"fromo","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat, moments, PDQutils,
microbenchmark","Title":"Fast Robust
Moments","URL":"https:\/\/github.com\/shabbychef\/fromo","Version":"0.1.3"},"fronti
er":{"Author":"Tim Coelli, Arne Henningsen","Depends":"R (>= 2.15.0), micEcon (>=
0.6-1), lmtest (>= 0.9-24)","Description":"Maximum Likelihood Estimation
of\nStochastic Frontier Production and Cost Functions.\nTwo specifications are
available:\nthe error components specification with time-varying
efficiencies\n(Battese and Coelli, 1992)\nand a model specification in which the
firm effects are directly\ninfluenced by a number of variables (Battese and Coelli,
1995).","Imports":"moments (>= 0.11), stats (>= 2.15.0), Formula (>= 0.2-
0),\nmiscTools (>= 0.6-1)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"frontier","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"plm (>= 1.0-1), MCMCpack (>= 1.0-8), fdrtool (>=
1.2.6)","Title":"Stochastic Frontier Analysis","URL":"http:\/\/frontier.r-forge.r-
project.org\/","Version":"1.1-0"},"frontiles":{"Author":"Abdelaati Daouia, Thibault
Laurent","Depends":"R (>= 2.8.1), classInt, colorspace, methods, rgl,
sp","Description":"It calculates the alpha-quantile and order-m efficiency score in
multi-dimension and computes several summaries and representation of the associated
frontiers in 2d and 3d.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"frontiles","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"ggplot2","Title":"Partial Frontier Efficiency
Analysis","Version":"1.2"},"frt":{"Author":"Giangiacomo Bravo
<giangiacomo.bravo@unito.it>, Lucia
Tamburino\n<lucia.tamburino@alice.it>.","Description":"Perform full randomization
tests.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"frt","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Full Randomization Test","URL":"http:\/\/www.r-
project.org","Version":"0.1"},"fscaret":{"Author":"Jakub Szlek [aut,
cre],\nAleksander Mendyk [ctb]","Depends":"R (>= 3.1.0), caret, gsubfn, hmeasure,
utils, parallel","Description":"Automated feature selection using variety of
models\nprovided by 'caret' package.\nThis work was funded by Poland-Singapore
bilateral cooperation\nproject no 2\/3\/POL-SIN\/2012.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"fscaret","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"ada, arm, Boruta, bst, C50, car, caTools, class,
Cubist,\ne1071, earth (>= 2.2-3), elasticnet, ellipse, evtree,\nextraTrees,
fastICA, foba, gam, gbm (>= 2.1), glmnet (>= 1.8),\nhda, HDclassif, Hmisc, ipred,
kernlab, kknn, klaR, kohonen,\nKRLS, lars, leaps, LogicReg, MASS, mboost, mda,
mgcv, mlbench,\nneuralnet, nnet, nodeHarvest, obliqueRF, pamr, partDSA, party\n(>=
0.9-99992), penalized, penalizedLDA, pls, pROC, proxy,\nqrnn, quantregForest,
randomForest, RANN, relaxo, rFerns, rocc,\nrpart, rrcov, RRF, rrlda, RSNNS, RWeka
(>= 0.4-1), sda,\nsparseLDA (>= 0.1-1), spls, stepPlr, superpc","Title":"Automated
Feature Selection from 'caret'","Version":"0.9.4"},"fsia":{"Author":"Michela
Battauz","Description":"Import data of tests and questionnaires from FormScanner.
FormScanner is an open source software that converts scanned images to data using
optical mark recognition (OMR) and it can be downloaded from
http:\/\/sourceforge.net\/projects\/formscanner\/. The spreadsheet file created by
FormScanner is imported in a convenient format to perform the analyses provided by
the package. These analyses include the conversion of multiple responses to binary
(correct\/incorrect) data, the computation of the number of corrected responses for
each subject or item, the computation and the graphical representation of the
frequencies of the responses to each item and the report of the responses of one or
a few persons.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"fsia","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Import and Analysis of OMR Data from
FormScanner","Version":"1.0"},"fslr":{"Author":"John Muschelli
<muschellij2@gmail.com>","Depends":"stringr, oro.nifti (>=
0.5.0)","Description":"Wrapper functions that interface with
FSL\n(http:\/\/fsl.fmrib.ox.ac.uk\/fsl\/fslwiki\/), a powerful and commonly-
used\nneuroimaging software, using system commands. The goal is to be able
to\ninterface with FSL completely in R, where you pass R objects of
class \"nifti\",\nimplemented by package 'oro.nifti', and the function executes an
FSL command\nand returns an R object of class \"nifti\" if
desired.","Imports":"methods, matrixStats, R.utils, scales, graphics,
grDevices,\nstats","License":"GPL-
3","NeedsCompilation":"no","Package":"fslr","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"knitr","Title":"Wrapper Functions for FSL (FMRIB Software
Library) from\nFunctional MRI of the Brain (FMRIB)","Version":"1.5.0"},"fso":
{"Author":"David W. Roberts
<droberts@montana.edu>","Depends":"labdsv,rgl","Description":"Fuzzy set ordination
is a multivariate analysis used in\necology to relate the composition of samples to
possible\nexplanatory variables.
While differing in theory and method,\nin practice, the use is similar to
'constrained ordination.'\nThe package contains plotting and summary functions as
well as\nthe analyses","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"fso","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Fuzzy Set
Ordination","URL":"http:\/\/ecology.msu.montana.edu\/labdsv\/R\/labs\/lab11\/lab11.
html","Version":"2.0-1"},"ftnonpar":{"Author":"Laurie Davies <Laurie.Davies@uni-
essen.de> Arne Kovac\n<A.Kovac@bristol.ac.uk>","Description":"The package contains
R-functions to perform the methods in\nnonparametric regression and density
estimation, described in\nDavies, P. L. and Kovac, A. (2001) Local Extremes,
Runs,\nStrings and Multiresolution (with discussion) Annals of\nStatistics. 29. p1-
65 Davies, P. L. and Kovac, A. (2004)\nDensities, Spectral Densities and Modality
Annals of\nStatistics. Annals of Statistics. 32. p1093-1136 Kovac, A.\n(2006)
Smooth functions and local extreme values. Computational\nStatistics and Data
Analysis (to appear) D\\\"umbgen, L. and\nKovac, A. (2006) Extensions of smoothing
via taut strings\nDavies, P. L. (1995) Data features. Statistica
Neerlandica\n49,185-245.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ftnonpar","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Features and Strings for Nonparametric
Regression","URL":"http:\/\/www.maths.bris.ac.uk\/~maxak\/ftnonpar.html","Version":
"0.1-88"},"fts":{"Author":"Whit Armstrong
<armstrong.whit@gmail.com>","Depends":"utils, stats, zoo","Description":"fast
operations for time series objects","License":"GPL-
3","NeedsCompilation":"yes","Package":"fts","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"R interface to tslib (a time series library in c+
+)","Version":"0.9.9"},"ftsspec":{"Author":"Shahin Tavakoli [aut,
cre]","Depends":"R (>= 3.2.0)","Description":"Functions for estimating spectral
density operator of functional\ntime series (FTS) and comparing the spectral
density operator of two\nfunctional time series, in a way that allows detection of
differences of\nthe spectral density operator in frequencies and along the curve
length.","Imports":"sna (>= 2.3-2)","License":"GPL-
2","NeedsCompilation":"no","Package":"ftsspec","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Spectral Density Estimation and Comparison for Functional
Time\nSeries","Version":"1.0.0"},"fueleconomy":{"Author":"'Hadley Wickham' [aut,
cre]","Depends":"R (>= 3.1.0)","Description":"Fuel economy data from the EPA, 1985-
2015, conveniently\npackaged for consumption by R
users.","License":"CC0","NeedsCompilation":"no","Package":"fueleconomy","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"dplyr","Title":"EPA fuel
economy
data","URL":"http:\/\/github.com\/hadley\/fueleconomy","Version":"0.1"},"fugeR":
{"Author":"Alexandre Bujard <alexandre.bujard@gmail.com>","Depends":"R (>= 2.15.1),
snowfall, Rcpp (>= 0.9.12)","Description":"This is an evolutionary algorithm for
fuzzy systems, a\ngenetic algorithm is used to construct a fuzzy system able
to\nfit the given training data. This fuzzy system can then be\nused as a
prediction model, it's composed of fuzzy logic rules\nthat provide a good lingustic
representation.","License":"GPL (>=
2.0)","NeedsCompilation":"yes","Package":"fugeR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"FUzzy GEnetic, a machine learning algorithm to
construct\nprediction model based on fuzzy logic","Version":"0.1.2"},"fullfact":
{"Author":"Aimee Lee Houde [aut, cre], Trevor Pitcher [aut]","Depends":"R (>=
3.2.2), lme4, afex","Description":"Package for the analysis of full factorial
breeding designs.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"fullfact","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Full Factorial Breeding Analysis","URL":"http:\/\/www.r-
project.org","Version":"1.0"},"fulltext":{"Author":"Scott Chamberlain [aut,
cre]","Description":"Provides a single interface to many sources of full
text\n'scholarly' data, including 'Biomed Central', Public Library of\nScience,
'Pubmed Central', 'eLife', 'F1000Research', 'PeerJ',\n'Pensoft', 'Hindawi', 'arXiv'
'preprints', and more. Functionality\nincluded for searching for articles,
downloading full or partial\ntext, downloading supplementary materials, converting
to various\ndata formats used in and outside of R.","Imports":"methods, utils,
stats, httr (>= 1.0.0), magrittr, xml2,\njsonlite, rplos (>= 0.5.2), rcrossref,
aRxiv, rentrez, tm,\nrredis, R.cache, digest, whisker","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"fulltext","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat, knitr","Title":"Full Text of
'Scholarly' Articles Across Many Data
Sources","URL":"https:\/\/github.com\/ropensci\/fulltext","Version":"0.1.6"},"fun":
{"Author":"Yihui Xie, Taiyun Wei and Yixuan Qiu","Description":"This is a
collection of R games and other funny stuff,\nsuch as the classical Mine sweeper
and sliding
puzzles.","License":"GPL","NeedsCompilation":"no","Package":"fun","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Title":"Use R for
Fun","URL":"https:\/\/github.com\/yihui\/fun","Version":"0.1-0"},"funFEM":
{"Author":"Charles Bouveyron","Depends":"R (>= 2.10), MASS, fda,
elasticnet","Description":"The funFEM algorithm (Bouveyron et al., 2014) allows to
cluster functional data by modeling the curves within a common and discriminative
functional subspace.","License":"GPL-
2","NeedsCompilation":"no","Package":"funFEM","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Clustering in the Discriminative Functional
Subspace","Version":"1.1"},"funHDDC":{"Author":"C. Bouveyron & J.
Jacques","Depends":"fda","Description":"The package provides the funHDDC algorithm
(Bouveyron & Jacques, 2011) which allows to cluster functional data by modeling
each group within a specific functional subspace.","License":"GPL-
2","NeedsCompilation":"no","Package":"funHDDC","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Model-based clustering in group-specific functional
subspaces","Version":"1.0"},"funModeling":{"Author":"Pablo Casas","Depends":"R (>=
3.2.1), Hmisc (>= 3.17.1)","Description":"Learn data cleaning, visual data analysis
and model performance assessment (KS, AUC and ROC), package core is in the vignette
documentation explaining last topics as a tutorial.","Imports":"ROCR, ggplot2,
gridExtra, pander, plyr, reshape2, scales","License":"GPL-
2","NeedsCompilation":"no","Package":"funModeling","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr","Title":"Learning Data Cleaning, Visual
Analysis and Model Performance","Version":"1.1"},"functional":{"Author":"Peter
Danenberg <pcd@roxygen.org>","Description":"Curry, Compose, and other higher-order
functions","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"functional","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Curry, Compose, and other higher-order
functions","Version":"0.6"},"functools":{"Author":"Paul Hendricks [aut,
cre]","Depends":"R (>= 3.1.2)","Description":"Extends functional programming in R
by\nproviding support to the usual higher order functional\nsuspects (Map, Reduce,
Filter, etc.).","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"functools","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat, memoise, pryr","Title":"Functional
Programming in
R","URL":"https:\/\/github.com\/paulhendricks\/functools","Version":"0.2.0"},"funcy
":{"Author":"Christina Yassouridis [aut, cre],\nDominik Ernst [ctb],\nMadison
Giacofci [ctb],\nSophie Lambert-Lacroix [ctb],\nGuillemette Marot [ctb],\nFranck
Picard [ctb],\nNicoleta Serban [ctb],\nHuijing Jiang [ctb],\nGareth James
[ctb],\nCatherine Sugar [ctb],\nHans-Georg Mueller [ctb],\nJie Peng [ctb],\nChiou
Jeng-Min [ctb],\nPai-Ling Li [ctb]","Depends":"flexclust,
splines","Description":"Unified framework to cluster functional data according to
one of seven models. All models are based on the projection of the curves onto a
basis. The main function funcit() calls wrapper functions for the existing
algorithms, so that input parameters are the same. A list is returned with each
entry representing the same or extended output for the corresponding method. Method
specific as well as general visualization tools are available.","Imports":"MASS,
Matrix, fda, methods, wavethresh, kernlab, parallel,\ncar, fields, calibrate,
cluster, sm, caTools, plyr","License":"GPL-
2","NeedsCompilation":"yes","Package":"funcy","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"scatterplot3d, Funclustering,
funHDDC","Title":"Functional Clustering Algorithms","Version":"0.8.4"},"fungible":
{"Author":"Niels G. Waller <nwaller@umn.edu> and Jeff Jones
<jeff.jones@kornferry.com>","Depends":"R (>= 3.0)","Description":"Functions for
computing fungible coefficients and Monte Carlo data.","Imports":"e1071, lattice,
MASS, mvtnorm, R2Cuba, stringr, nleqslv,\nmethods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"fungible","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Fungible Coefficients and Monte Carlo
Functions","Version":"1.3"},"funr":{"Author":"Sahil Seth [aut,
cre]","Description":"A small utility which wraps Rscript and provides access to all
R\nfunctions from the shell.","Imports":"utils","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"funr","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Simple Utility Providing Terminal Access to all R
Functions","URL":"https:\/\/github.com\/sahilseth\/funr","Version":"0.2.0"},"funreg
":{"Author":"John Dziak [aut, cre],\nMariya Shiyko [aut]","Depends":"R (>=
2.15.0)","Description":"This package performs functional regression, and some
related\napproaches, for intensive longitudinal data (see Walls & Schafer,
2006)\nwhich is not
necessarily observed on an equally spaced grid of times. The\napproach generally
follows the ideas of Goldsmith, Bobb, Crainiceanu,\nCaffo, and Reich (2011) and the
approach taken in their sample code, but\nwith some modifications to make it more
feasible to use with long rather\nthan wide, non-rectangular longitudinal datasets
with unequal and\npotentially random measurement times. It also allows easy
plotting of the\ncorrelation between the smoothed covariate and the outcome as a
function of\ntime, which can add additional insights on how to interpret a
functional\nregression. Additionally, it also provides several permutation tests
for\nthe significance of the functional predictor. The heuristic
interpretation\nof ``time'' is used to describe the index of the functional
predictor, but\nthe same methods can equally be used for another unidimensional
continuous\nindex, such as space along a north-south axis. The development of
this\npackage was part of a research project supported by Award R03 CA171809-
01\nfrom the National Cancer Institute and Award P50 DA010075 from the
National\nInstitute on Drug Abuse. The content is solely the responsibility of
the\nauthors and does not necessarily represent the official views of the\nNational
Institute on Drug Abuse, the National Cancer Institute, or the\nNational Institutes
of Health.","Imports":"MASS, mgcv, mvtnorm, splines","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"funreg","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"funreg (Functional Regression for Irregularly Timed
Data)","Version":"1.1"},"funtimes":{"Author":"Vyacheslav Lyubchich;\nYulia R.
Gel;\nXingyu Wang;\nCalvin Chu","Depends":"Jmisc, R (>=
3.0.0)","Description":"Includes non-parametric estimators and tests for time series
analysis. The functions are to test for presence of possibly non-monotonic trends
and for synchronism of trends in multiple time series, using modern bootstrap
techniques and robust non-parametric difference-based estimators.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"funtimes","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Functions for Time Series
Analysis","Version":"2.1"},"futile.any":{"Author":"Brian Lee Yung
Rowe","Depends":"lambda.r (>= 1.1.0)","Description":"This utility package provides
polymorphism over common operations and is now subsumed by
lambda.tools.","License":"LGPL-
3","NeedsCompilation":"no","Package":"futile.any","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat","Title":"A Tiny Utility Providing
Polymorphic Operations","Version":"1.3.2"},"futile.logger":{"Author":"Brian Lee
Yung Rowe","Depends":"R (>= 3.0.0)","Description":"Provides a simple yet powerful
logging utility. Based loosely on\nlog4j, futile.logger takes advantage of R idioms
to make logging a\nconvenient and easy to use replacement for cat and print
statements.","Imports":"lambda.r (>= 1.1.0), futile.options","License":"LGPL-
3","NeedsCompilation":"no","Package":"futile.logger","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat, jsonlite","Title":"A Logging Utility
for R","Version":"1.4.1"},"futile.matrix":{"Author":"Brian Lee Yung
Rowe","Depends":"R (>= 3.0.0)","Description":"A collection of functions for
manipulating matrices and generating ensembles of random
matrices","Imports":"lambda.r (>= 1.1.6), lambda.tools, futile.logger (>=
1.3.0),\nRMTstat","License":"LGPL-
3","NeedsCompilation":"no","Package":"futile.matrix","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"RUnit","Title":"Random matrix generation and
manipulation","Version":"1.2.2"},"futile.options":{"Author":"Brian Lee Yung
Rowe","Depends":"R (>= 2.8.0)","Description":"A scoped options management
framework","License":"LGPL-
3","NeedsCompilation":"no","Package":"futile.options","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Futile options
management","Version":"1.0.0"},"futile.paradigm":{"Author":"Brian Lee Yung
Rowe","Depends":"futile.options, RUnit","Description":"Provides dispatching
implementations suitable for\nfunctional programming paradigms. The framework
provides a\nmechanism for attaching guards to functions similar to Erlang,\nwhile
also providing the safety of assertions reminiscent of\nEiffel.","License":"LGPL-
3","NeedsCompilation":"no","Package":"futile.paradigm","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"A framework for working in a functional
programming paradigm in\nR","Version":"2.0.4"},"future":{"Author":"Henrik Bengtsson
[aut, cre, cph]","Description":"A Future API for R is provided. In programming, a
future is an\nabstraction for a value that may be available at some point in the
future.\nThe state of a future can either be unresolved or resolved. As soon as it
is\nresolved, the value is available. Futures are useful constructs in for
instance\nconcurrent evaluation, e.g. parallel processing and distributed
processing on\ncompute clusters. The purpose of this package is to provide a
lightweight\ninterface for using futures in R. Functions 'future()' and 'value()'
exist for\ncreating futures and requesting their values, e.g.\n'f <-
future({ mandelbrot(c(0.28,0), side=2) })' and 'v <- value(f)'.\nThe 'resolve()'
function can be used to check if a future is resolved or not.\nAn infix assignment
operator '%<=%' exists for creating futures whose values\nare accessible by the
assigned variables (as promises), e.g.\n'v %<=% { mandelbrot(c(0.28,0),
side=2) }'.\nThis package implements synchronous \"lazy\" and \"eager\" futures,
and asynchronous\n\"multicore\", \"multisession\" and ad hoc \"cluster\"
futures.\nGlobals variables and functions are automatically identified and
exported.\nRequired packages are attached in external R sessions whenever
needed.\nAll types of futures are designed to behave the same such that the
exact\nsame code work regardless of futures used or number of cores,
background\nsessions or cluster nodes available.\nAdditional types of futures are
provided by other packages enhancing\nthis package.","Imports":"digest, globals (>=
0.6.1), listenv (>= 0.6.0), parallel","License":"LGPL (>=
2.1)","NeedsCompilation":"no","Package":"future","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"R.rsp","Title":"A Future API for
R","URL":"https:\/\/github.com\/HenrikBengtsson\/future","Version":"0.12.0"},"futur
eheatwaves":{"Author":"Brooke Anderson [aut, cre],\nColin Eason [aut],\nElizabeth
Barnes [aut]","Depends":"R (>= 2.10)","Description":"Inputs a directory of climate
projection files and, for each,\nidentifies and characterizes heat waves for
specified study locations. The\ndefinition used to identify heat waves can be
customized. Heat wave\ncharacterizations include several metrics of heat wave
length, intensity,\nand timing in the year. The heat waves that are identified can
be\nexplored using a function to apply user-created functions across all\ngenerated
heat wave files.This work was supported in part by grants from\nthe National
Institute of Environmental Health Sciences (R00ES022631), the\nNational Science
Foundation (1331399), and the Colorado State University\nVice President for
Research.","Imports":"dplyr (>= 0.4.3), ggplot2 (>= 2.0.0), ggthemes (>=
3.0.0),\nRcpp (>= 0.12.3)","License":"GPL-
2","NeedsCompilation":"yes","Package":"futureheatwaves","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"gridExtra (>= 2.0.0), knitr (>= 1.10.5),
mapproj (>= 1.2.4),\nmaps (>= 3.0.2), rmarkdown (>= 0.7.0), testthat (>=
0.11.0)","Title":"Find, Characterize, and Explore Heat Waves in
Climate\nProjections","Version":"1.0.0"},"fuzzyFDR":{"Author":"Alex
Lewin","Description":"Exact calculation of fuzzy decision rules for
multiple\ntesting. Choose to control FDR (false discovery rate) using
the\nBenjamini and Hochberg method, or FWER (family wise error rate)\nusing the
Bonferroni method. Kulinsakaya and Lewin
(2007).","License":"GPL","NeedsCompilation":"no","Package":"fuzzyFDR","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Title":"Exact calculation of fuzzy decision
rules for multiple testing","Version":"1.0"},"fuzzyRankTests":{"Author":"Charles J.
Geyer <charlie@stat.umn.edu>","Depends":"R (>= 2.10.0)","Description":"Does fuzzy
tests and confidence intervals (following Geyer\nand Meeden, Statistical Science,
2005) for sign test and Wilcoxon\nsigned rank and rank sum
tests.","Imports":"stats, graphics","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"fuzzyRankTests","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Title":"Fuzzy Rank Tests and Confidence
Intervals","URL":"http:\/\/www.stat.umn.edu\/geyer\/fuzz\/","Version":"0.3-
7"},"fuzzyforest":{"Author":"Daniel Conn [aut, cre],\nTuck Ngun [aut],\nChristina
M. Ramirez [aut]","Depends":"R (>= 3.2.3)","Description":"Fuzzy forests, a new
algorithm based on random forests,\nis designed to reduce the bias seen in random
forest feature selection\ncaused by the presence of correlated features. Fuzzy
forests uses\nrecursive feature elimination random forests to select\nfeatures from
separate blocks of correlated features where the\ncorrelation within each block of
features is high\nand the correlation between blocks of features is low.\nOne final
random forest is fit using the surviving features.\nThis package fits random
forests using the 'randomForest' package and\nallows for easy use of 'WGCNA' to
split features into distinct blocks.","Imports":"randomForest, foreach, doRNG,
doParallel, parallel, ggplot2","License":"GPL-
3","NeedsCompilation":"no","Package":"fuzzyforest","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"WGCNA,","Title":"Fuzzy
Forests","Version":"1.0.1"},"fuzzyjoin":
{"Author":"c(person(\"David\", \"Robinson\", email
= \"drobinson@stackoverflow.com\",\nrole = c(\"aut\", \"cre\")),\nperson(\"Joran\",
\"Elias\", email = \"statisticalskier@gmail.com\",\nrole
= \"ctb\"))","Depends":"R (>= 2.10)","Description":"Join tables together based not
on whether columns\nmatch exactly, but whether they are similar by some
comparison.\nImplementations include string distance and regular
expression\nmatching.","Imports":"stringdist, stringr, dplyr, tidyr (>= 0.4.0),
purrr, geosphere","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"fuzzyjoin","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat, knitr, ggplot2, qdapDictionaries,
readr, rvest,\nrmarkdown, maps","Title":"Join Tables Together on Inexact
Matching","Version":"0.1"},"fwdmsa":{"Author":"Wobbe P. Zijlstra
<w.p.zijlstra@uvt.nl>","Depends":"R (>= 2.10.0)","Description":"fwdmsa performs the
Forward Search for Mokken scale\nanalysis. It detects outliers, it produces several
types of\ndiagnostic plots.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"fwdmsa","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Forward search for Mokken scale
analysis","URL":"http:\/\/www.tilburguniversity.edu\/webwijs\/show\/?
uid=w.p.zijlstra","Version":"0.2"},"fwi.fbp":{"Author":"Xianli Wang, Alan Cantin,
Marc-Andre Parisien, Mike Wotton, Kerry Anderson, and Mike Flannigan","Depends":"R
(>= 2.15.1)","Description":"Provides three functions to calculate the outputs of
the two main components of the Canadian Forest Fire Danger Rating System (CFFDRS):
the Fire Weather Index (FWI) System and the Fire Behaviour Prediction (FBP)
System.","License":"GPL-
2","NeedsCompilation":"no","Package":"fwi.fbp","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Fire Weather Index System and Fire Behaviour Prediction
System\nCalculations","URL":"https:\/\/r-forge.r-project.org\/projects\/fwi-
fbp\/","Version":"1.7"},"fwsim":{"Author":"Mikkel Meyer Andersen and Poul Svante
Eriksen","Depends":"R (>= 3.1.0)","Description":"Simulates a population under the
Fisher-Wright model (fixed or stochastic population size) with a one-step neutral
mutation process (stepwise mutation model, logistic mutation model and exponential
mutation model supported). The stochastic population sizes are random Poisson
distributed and different kinds of population growth are supported. For the
stepwise mutation model, it is possible to specify locus and direction specific
mutation rate (in terms of upwards and downwards mutation rate). Intermediate
generations can be saved in order to study e.g. drift.","Imports":"Rcpp (>=
2","NeedsCompilation":"yes","Package":"fwsim","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Fisher-Wright Population
Simulation","Version":"0.3.3"},"fxregime":{"Author":"Achim Zeileis [aut,
cre],\nAjay Shah [ctb],\nIla Patnaik [ctb],\nAnmol Sethy [ctb]","Depends":"R (>=
2.14.0), zoo, strucchange","Description":"Exchange rate regression and structural
change tools\nfor estimating, testing, dating, and monitoring\n(de facto) exchange
rate regimes.","Imports":"graphics, stats, car, sandwich","License":"GPL-
2","NeedsCompilation":"no","Package":"fxregime","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"lmtest, foreach","Title":"Exchange Rate Regime
Analysis","Version":"1.0-3"},"g.data":{"Author":"David Brahm
<brahm@alum.mit.edu>","Description":"Create and maintain delayed-data packages
(ddp's). Data stored in\na ddp are available on demand, but do not take up memory
until requested.\nYou attach a ddp with g.data.attach(), then read from it and
assign to it in\na manner similar to S-PLUS, except that you must run g.data.save()
to\nactually commit to
disk.","License":"GPL","NeedsCompilation":"no","Package":"g.data","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Title":"Delayed-Data
Packages","Version":"2.4"},"gCat":{"Author":"Hao Chen and Nancy R.
Zhang","Depends":"R (>= 3.0.1)","Description":"These are two-sample tests for
categorical data utilizing similarity information among the categories. They are
useful when there is underlying structure on the categories.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"gCat","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Graph-based two-sample tests for categorical
data","Version":"0.1"},"gIPFrm":{"Author":"Anna Klimova, Tamas
Rudas","Description":"Maximum likelihood estimation under relational models, with
or without the overall effect.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gIPFrm","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Generalized Iterative Proportional Fitting for Relational
Models","Version":"2.0"},"gMCP":{"Author":"Kornelius Rohmeyer [aut, cre],\nFlorian
Klinglmueller [aut]","Depends":"R (>= 3.0.0), rJava (>= 0.6-3), JavaGD, methods,
xlsxjars (>=\n0.6.1)","Description":"Functions and a graphical user interface for
graphical described multiple test procedures.","Imports":"MASS, PolynomF, multcomp
(>= 1.1), mvtnorm, Matrix,\nCommonJavaJars (>= 1.0.5), stats4","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"gMCP","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"RUnit, Deducer, knitr, graph (>= 1.20), mutoss, boot,
coin","Title":"Graph Based Multiple Comparison
Procedures","URL":"http:\/\/gsrmtp.r-forge.r-project.org\/","Version":"0.8-
10"},"gMWT":{"Author":"Daniel Fischer , Hannu Oja","Depends":"R (>= 2.15.2),
clinfun, Rcpp (>= 0.9.13)","Description":"Generalized Mann-Whitney type tests based
on probabilistic\nindices and new diagnostic plots.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"gMWT","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Generalized Mann-Whitney Type
Tests","Version":"1.0"},"gPCA":{"Author":"Sarah Reese","Description":"This package
implements guided principal components analysis for the detection of batch effects
in high-throughput data.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gPCA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Batch Effect Detection via Guided Principal Components
Analysis","Version":"1.0"},"gPdtest":{"Author":"Elizabeth Gonzalez Estrada, Jose A.
Villasenor Alva","Description":"This package computes the bootstrap goodness-of-fit
test\nfor the generalized Pareto distribution by Villasenor-Alva and\nGonzalez-
Estrada (2009). The null hypothesis includes heavy and\nnon-heavy tailed gPd's. A
function for fitting the gPd to data\nusing the parameter estimation methods
proposed in the same\narticle is also provided.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gPdtest","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Bootstrap goodness-of-fit test for the generalized
Pareto\ndistribution","Version":"0.4"},"gProfileR":{"Author":"Juri Reimand
<juri.reimand@ut.ee>, Raivo Kolde\n<rkolde@gmail.com>, Tambet Arak
<tambet.arak@gmail.com>","Depends":"R (>= 2.10)","Description":"Functional
enrichment analysis, gene identifier conversion\nand mapping homologous genes
across related organisms via the\n'g:Profiler' toolkit
(http:\/\/biit.cs.ut.ee\/gprofiler\/).","Imports":"RCurl, plyr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gProfileR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Interface to the 'g:Profiler'
Toolkit","Version":"0.5.3"},"gRain":{"Author":"Søren Højsgaard
<sorenh@math.aau.dk>","Depends":"R (>= 3.0.2), methods, gRbase (>= 1.7-
2)","Description":"Probability propagation in graphical independence networks, also
known as Bayesian networks or probabilistic expert systems.","Imports":"igraph,
graph, Rcpp (>= 0.11.1)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"gRain","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"Rgraphviz, microbenchmark","Title":"Graphical
Independence
Networks","URL":"http:\/\/people.math.aau.dk\/~sorenh\/software\/gR\/","Version":"1
.2-5"},"gRapHD":{"Author":"Gabriel Coelho Goncalves de Abreu
<abreu_ga@yahoo.com.br>,\nRodrigo Labouriau <Rodrigo.Labouriau@agrsci.dk>,\nDavid
Edwards <David.Edwards@agrsci.dk>.","Depends":"R (>= 2.9.0), methods,
graph","Description":"gRapHD is designed for efficient selection of high-
dimensional undirected\ngraphical models. The package provides tools for selecting
trees, forests\nand decomposable models minimizing information criteria such as AIC
or BIC,\nand for displaying the independence graphs of the models. It has also
some\nuseful tools for analysing graphical structures. It supports the use
of\ndiscrete, continuous, or both types of variables.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"gRapHD","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Efficient selection of undirected graphical models
for\nhigh-dimensional datasets","Version":"0.2.4"},"gRapfa":{"Author":"Smitha
Ankinakatte <Smitha.AA@agrsci.dk> and David Edwards
<David.Edwards@agrsci.dk>","Depends":"R (>= 3.0.2), igraph","Description":"gRapfa
is for modelling discrete longitudinal data using acyclic probabilistic finite
automata (APFA). The package contains functions for constructing APFA models from a
given data using penalized likelihood methods. For graphical display of APFA
models, gRapfa depends on 'igraph package'. gRapfa also contains an interface
function to Beagle software that implements an efficient model selection
2)","NeedsCompilation":"no","Package":"gRapfa","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Acyclic Probabilistic Finite
Automata","Version":"1.0"},"gRbase":{"Author":"Søren Højsgaard
<sorenh@math.aau.dk>","Depends":"R (>= 3.0.2), methods","Description":"The 'gRbase'
package provides general features\nwhich are used by other graphical modelling
packages, in particular\nby the packages 'gRain', 'gRim' and 'gRc'.\n\n'gRbase'
contains several datasets relevant for use in connection with\ngraphical models.
Almost all datasets used in the book Graphical\nModels with R (2012) are contained
in 'gRbase'.\n\n'gRbase' implements several graph
algorithms (based mainly on\nrepresenting graphs as adjacency matrices - either in
the form\nof a standard matrix or a sparse matrix). Some graph\nalgorithms
are:\n(i) maximum cardinality search (for marked and unmarked graphs).\n(ii)
moralize.\n(iii) triangulate.\n(iv) junction tree.\n\n'gRbase' facilitates array
operations,\n\n'gRbase' implements functions for testing for conditional
independence.\n\n'gRbase' illustrates how hierarchical log-linear models may
be\nimplemented and describes concept of graphical meta\ndata. These features,
however, are not maintained anymore and\nremains in 'gRbase' only because there
exists a paper describing\nthese facilities: A Common Platform for Graphical Models
in R:\nThe 'gRbase' Package, Journal of Statistical Software, Vol 14,\nNo 17,
2005.\n\nNOTICE Proper functionality of 'gRbase' requires that the packages
graph,\n'Rgraphviz' and 'RBGL' are installed from 'bioconductor'; for\ninstallation
instructions please refer to the webpage given below.","Imports":"Matrix, RBGL,
igraph, graph, Rcpp (>= 0.11.1)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"gRbase","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"Rgraphviz, microbenchmark","Title":"A Package for
Graphical Modelling in
R","URL":"http:\/\/people.math.aau.dk\/~sorenh\/software\/gR\/","Version":"1.7-
5"},"gRc":{"Author":"Søren Højsgaard <sorenh@math.aau.dk>, Steffen L.
Lauritzen\n<steffen@stats.ox.ac.uk>","Depends":"gRbase,graph,Rgraphviz","Descriptio
n":"Estimation, model selection and other aspects of\nstatistical inference in
Graphical Gaussian models with edge\nand vertex symmetries (Graphical Gaussian
models with
colours)","License":"GPL","NeedsCompilation":"yes","Package":"gRc","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"Inference in Graphical Gaussian Models
with Edge and Vertex\nSymmetries","Version":"0.4-1"},"gRim":{"Author":"Søren
Højsgaard <sorenh@math.aau.dk>","Depends":"R (>=
2.15.2),methods,gRbase,gRain","Description":"gRaphical Interaction
Models:\n\nModels for for contingency tables (i.e. log-linear models)\n\nGraphical
Gaussian models for multivariate normal data (i.e. covariance
selection\nmodels)\n\nMixed interaction models","Imports":"igraph","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"gRim","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"Rgraphviz","Title":"Graphical Interaction
Models","URL":"http:\/\/people.math.aau.dk\/~sorenh\/software\/gR\/","Version":"0.1
-17"},"gSEM":{"Author":"Junheng Ma <jxm216@case.edu>, Nicholas Wheeler
<nrw16@case.edu>, Yifan Xu <ethan.yifanxu@case.edu>, Wenyu Du <wxd97@case.edu>,
Abdulkerim Gok <axg515@case.edu>, Jiayang Sun <jiayang.sun@case.edu>","Depends":"R
(>= 2.14.0)","Description":"Conducts a semi-gSEM statistical analysis (semi-
supervised generalized structural equation modeling) on a data frame of coincident
observations of multiple predictive or intermediate variables and a final
continuous, outcome variable, via two functions sgSEMp1() and sgSEMp2(),
representing fittings based on two statistical principles. Principle 1 determines
all sensible univariate relationships in the spirit of the Markovian process. The
relationship between each pair of variables, including predictors and the final
outcome variable, is determined with the Markovian property that the value of the
current predictor is sufficient in relating to the next level variable, i.e., the
relationship is independent of the specific value of the preceding-level variables
to the current predictor, given the current value. Principle 2 resembles the
multiple regression principle in the way multiple predictors are considered
simultaneously. Specifically, the relationship of the first-level predictors (such
as Time and irradiance etc) to the outcome variable (such as, module degradation or
yellowing) is fit by a supervised additive model. Then each significant
intermediate variable is taken as the new outcome variable and the other variables
(except the final outcome variable) as the predictors in investigating the next-
level multivariate relationship by a supervised additive model. This fitting
process is continued until all sensible models are investigated.","Imports":"knitr,
MASS, htmlwidgets, DiagrammeR","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gSEM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Semi-Supervised Generalized Structural Equation
Modeling","Version":"0.4.3.4"},"gSeg":{"Author":"Hao Chen and Nancy R.
Zhang","Depends":"R (>= 3.0.1)","Description":"Using an approach based on
similarity graph to estimate change-point(s) and the corresponding p-values. Can
be applied to any type of data (high-dimensional, non-Euclidean, etc.) as long as a
reasonable similarity measure is available.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gSeg","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Graph-Based Change-Point Detection (g-
Segmentation)","Version":"0.3"},"gWidgets":{"Author":"John Verzani. Based on the
iwidgets code of Simon Urbanek and suggestions by Simon Urbanek, Philippe Grosjean
and Michael Lawrence","Depends":"methods, utils","Description":"gWidgets provides a
toolkit-independent API for building interactive GUIs. At least one of the
'gWidgetsXXX packages', such as gWidgetstcltk, needs to be installed. Some icons
are on loan from the scigraphica project
http:\/\/scigraphica.sourceforge.net.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gWidgets","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"gWidgetstcltk","Title":"gWidgets API for building
toolkit-independent, interactive GUIs","URL":"https:\/\/r-forge.r-project.org\/R\/?
group_id=761","Version":"0.0-54"},"gWidgets2":{"Author":"John
Verzani","Depends":"methods, digest","Description":"Re-implementation of gWidgets
API. The API is defined in this\npackage. A second, toolkit-specific package is
required to use it. There\nare three in development: 'gWidgets2RGtk2',
'gWidgets2Qt', and 'gWidgets2tcltk'.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"gWidgets2","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Rewrite of gWidgets API for Simplified GUI
Construction","URL":"https:\/\/github.com\/jverzani\/gWidgets2","Version":"1.0-
6"},"gWidgets2RGtk2":{"Author":"John Verzani","Depends":"methods, memoise, RGtk2,
gWidgets2","Description":"Implements the 'gWidgets2' API for
'RGtk2.'","License":"GPL-
3","NeedsCompilation":"no","Package":"gWidgets2RGtk2","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat, cairoDevice","Title":"Implementation
of gWidgets2 for the RGtk2
Package","URL":"https:\/\/github.com\/jverzani\/gWidgets2RGtk2","Version":"1.0-
4"},"gWidgets2tcltk":{"Author":"John Verzani","Depends":"R (>= 2.12.0), methods,
digest, memoise, tcltk(>= 2.7.0),\ngWidgets2","Description":"Port of the gWidgets2
API for the tcltk\npackage.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gWidgets2tcltk","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat","Title":"Toolkit Implementation of
gWidgets2 for
tcltk","URL":"https:\/\/github.com\/jverzani\/gWidgets2tcltk","Version":"1.0-
4"},"gWidgetsRGtk2":{"Author":"Michael Lawrence, John Verzani","Depends":"methods,
RGtk2, gWidgets, cairoDevice","Description":"Port of gWidgets API to
RGtk2","Enhances":"RGtk2Extras","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gWidgetsRGtk2","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Toolkit implementation of gWidgets for
RGtk2","URL":"http:\/\/gwidgets.r-forge.r-project.org\/","Version":"0.0-
83"},"gWidgetstcltk":{"Author":"John Verzani","Depends":"R (>= 2.14.0), methods,
gWidgets(>= 0.0.51), tcltk(>= 2.7.0),\ndigest","Description":"Port of the gWidgets
API to the tcltk package. Requires Tk 8.5 or greater.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gWidgetstcltk","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Toolkit implementation of gWidgets for tcltk
package","URL":"http:\/\/gwidgets.r-forge.r-project.org\/","Version":"0.0-
55"},"gains":{"Author":"Craig A. Rolling <crolling@umn.edu>","Depends":"R (>=
3.0.0)","Description":"This package constructs gains tables and lift charts for
prediction algorithms. Gains tables and lift charts are commonly used in direct
marketing applications.","License":"GPL-
3","NeedsCompilation":"no","Package":"gains","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Gains Table Package","Version":"1.1"},"galts":
{"Author":"Mehmet Hakan Satman","Depends":"genalg, DEoptim","Description":"This
package includes the ga.lts function that estimates\nLTS (Least Trimmed Squares)
parameters using genetic algorithms\nand C-steps. ga.lts() constructs a genetic
algorithm to form a\nbasic subset and iterates C-steps as defined in Rousseeuw
and\nvan-Driessen (2006) to calculate the cost value of the LTS\ncriterion.
OLS(Ordinary Least Squares) regression is known to\nbe sensitive to outliers. A
single outlying observation can\nchange the values of estimated parameters. LTS is
a resistant\nestimator even the number of outliers is up to half of the\ndata. This
package is for estimating the LTS parameters with\nlower bias and variance in a
reasonable time. Version 1.3\nincluded the function medmad for fast outlier
detection in\nlinear
regression.","License":"GPL","NeedsCompilation":"no","Package":"galts","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Title":"Genetic algorithms and C-steps
based LTS (Least Trimmed Squares)\nestimation","Version":"1.3"},"gam":
{"Author":"Trevor Hastie","Depends":"stats, splines,
foreach","Description":"Functions for fitting and working with
generalized\nadditive models, as described in chapter 7 of \"Statistical Models
in\nS\" (Chambers and Hastie (eds), 1991), and \"Generalized Additive\nModels\"
(Hastie and Tibshirani, 1990).","License":"GPL-
2","NeedsCompilation":"yes","Package":"gam","Repository":"http:\/\/cran.csiro.au\/s
rc\/
contrib","Suggests":"akima","Title":"Generalized Additive
Models","Version":"1.12"},"gamair":{"Author":"Simon Wood <simon.wood@r-
project.org>","Depends":"R (>= 2.10)","Description":"Data sets and scripts used in
the book \"Generalized\nAdditive Models: An Introduction with R\", Wood (2006)
CRC.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gamair","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Data for \"GAMs: An Introduction with R\"","Version":"0.0-
9"},"gambin":{"Author":"Michael Krabbe Borregaard, Thomas Matthews & Karl
Ugland","Depends":"stats","Description":"Fits the gambin distribution to species-
abundance distributions from\necological data. 'gambin' is short for 'gamma-
binomial'. The main function is\nfitGambin, which estimates the 'alpha' parameter
of the gambin distribution using\nmaximum likelihood. Functions are also provided
to generate the gambin distribution\nand for calculating likelihood
2","NeedsCompilation":"no","Package":"gambin","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Fit the GamBin Model to Species Abundance
Distributions","Version":"1.3"},"gamboostLSS":{"Author":"Benjamin Hofner, Andreas
Mayr, Nora Fenske, Matthias Schmid","Depends":"R (>= 2.10.0), mboost (>= 2.3-0),
parallel","Description":"Boosting models for fitting generalized additive models
for\nlocation, shape and scale ('GAMLSS') to potentially high
dimensional\ndata.","Imports":"graphics, grDevices, stats, utils","License":"GPL-
2","NeedsCompilation":"no","Package":"gamboostLSS","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"gamlss, BayesX, gamlss.dist, survival,
R2BayesX","Title":"Boosting Methods for 'GAMLSS'","URL":"For source code,
development versions and issue tracker
see\nhttps:\/\/github.com\/hofnerb\/gamboostLSS","Version":"1.2-1"},"gamboostMSM":
{"Author":"Holger Reulen","Description":"Provides features to use function
gamboost() from package mboost for estimation of multistate
models","Imports":"mboost (>= 2.2-2)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gamboostMSM","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Estimating multistate models using
gamboost()","Version":"1.1.87"},"gamclass":{"Author":"John Maindonald","Depends":"R
(>= 3.0.0)","Description":"Functions and data are provided that support a course
that emphasizes statistical\nissues of inference and generalizability. Attention
is restricted to a relatively small\nnumber of methods, often (misleadingly in my
view) referred to as algorithms.","Imports":"car, mgcv, DAAG, MASS, rpart,
randomForest, lattice,\nlatticeExtra, ape, KernSmooth, methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gamclass","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"leaps, quantreg, sp, diagram, oz, forecast, SMIR,
kernlab,\nEcdat, mlbench, DAAGbio, knitr","Title":"Functions and Data for a Course
on Modern Regression and\nClassification","Version":"0.56"},"games":
{"Author":"Curtis S. Signorino [aut],\nBrenton Kenkel [aut, cre]","Depends":"maxLik
(>= 0.7-0), Formula (>= 0.2-0), MASS","Description":"Provides estimation and
analysis functions for\nstrategic statistical
models.","Imports":"stringr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"games","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat","Title":"Statistical Estimation of Game-
Theoretic Models","Version":"1.1.2"},"gamlr":{"Author":"Matt Taddy
<taddy@chicagobooth.edu>","Depends":"R (>= 2.15), Matrix, methods, graphics,
stats","Description":"The gamma lasso algorithm provides regularization paths
corresponding to a range of non-convex cost functions between L0 and L1 norms. As
much as possible, usage for this package is analogous to that for the glmnet
package (which does the same thing for penalization between L1 and L2 norms). For
details see: Taddy (2015), One-Step Estimator Paths for Concave Regularization,
http:\/\/arxiv.org\/abs\/1308.5623.","License":"GPL-
3","NeedsCompilation":"yes","Package":"gamlr","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"parallel","Title":"Gamma Lasso
Regression","URL":"http:\/\/github.com\/TaddyLab\/gamlr,\nhttp:\/\/faculty.chicagob
ooth.edu\/matt.taddy\/index.html","Version":"1.13-3"},"gamlss":{"Author":"Mikis
Stasinopoulos [aut, cre, cph],\nBob Rigby [aut],\nVlasios Voudouris
[ctb],\nCalliope Akantziliotou [ctb],\nMarco Enea [ctb],\nDaniil Kiose
[ctb]","Depends":"R (>= 3.2.0), graphics, stats, splines, utils,
grDevices,\ngamlss.data, gamlss.dist (>= 4.3.1), nlme,
parallel","Description":"Functions for fitting, displaying and checking GAMLSS
Models.","Imports":"MASS, survival, methods","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"gamlss","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Generalised Additive Models for Location Scale and
Shape","URL":"http:\/\/www.gamlss.org\/","Version":"4.3-8"},"gamlss.add":
{"Author":"Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>, Bob Rigby
<r.rigby@londonmet.ac.uk>","Depends":"R (>= 2.15.0), gamlss.dist, gamlss (>=
2.4.0), mgcv, nnet,\nrpart, graphics, stats, utils, grDevices,
methods","Description":"Interfaces for extra smooth functions including tensor
products, neural networks and decision trees.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"gamlss.add","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"lattice","Title":"Extra Additive Terms for GAMLSS
Models","URL":"http:\/\/www.gamlss.org\/","Version":"4.3-4"},"gamlss.cens":
{"Author":"Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>, Bob\nRigby
<r.rigby@londonmet.ac.uk>, Nicoleta Mortan","Depends":"R (>= 2.2.1), gamlss.dist,
gamlss, survival","Description":"This is an add-on package to GAMLSS. The purpose
of this\npackage is to allow users to fit interval response variables in\nGAMLSS
models. The main function gen.cens() generates a\ncensored version of an existing
GAMLSS family distribution.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"gamlss.cens","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Fitting an Interval Response Variable Using
gamlss.family\nDistributions","URL":"http:\/\/www.gamlss.org\/","Version":"4.3-
2"},"gamlss.data":{"Author":"Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>,
Bob\nRigby <r.rigby@londonmet.ac.uk>","Depends":"R (>= 2.10)","Description":"Data
for GAMLSS models.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"gamlss.data","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"GAMLSS
Data","URL":"http:\/\/www.gamlss.org\/","Version":"4.3-2"},"gamlss.demo":
<r.rigby@londonmet.ac.uk>, Paul Eilers <p.eilers@erasmusmc.nl>, Brian Marx
\\email{bmarx@LSU.EDU}, Konstantinos Pateras <kostas.pateras@gmail.com> with
contributions from Larisa Kosidou.","Depends":"R (>= 2.4.0), rpanel (>= 1.1-1),
gamlss.dist, gamlss.tr,\ntcltk, graphics, stats, grDevices","Description":"Demos
for smoothing and gamlss.family distributions.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"gamlss.demo","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"MASS","Title":"Demos for
GAMLSS","URL":"http:\/\/www.gamlss.org\/","Version":"4.3-3"},"gamlss.dist":
<r.rigby@londonmet.ac.uk> with contributions from\nCalliope Akantziliotou, Gillian
Heller, Raydonal Ospina\n<rospina@ime.usp.br>, Nicoletta Motpan, Fiona McElduff,
Vlasios\nVoudouris, Majid Djennad, Marco Enea and Alexios Ghalanos.","Depends":"R
(>= 2.15.0), MASS, graphics, stats","Description":"The different distributions used
for the response variables in GAMLSS\nmodelling.","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"gamlss.dist","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Distributions to be Used for GAMLSS
Modelling","URL":"http:\/\/www.gamlss.org\/","Version":"4.3-5"},"gamlss.mx":
<r.rigby@londonmet.ac.uk>","Depends":"R (>= 2.2.1), gamlss.dist, gamlss, nnet,
stats, graphics","Description":"The main purpose of this package is to allow
fitting of\nmixture distributions with GAMLSS models.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"gamlss.mx","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"MASS","Title":"Fitting Mixture Distributions with
GAMLSS","URL":"http:\/\/www.gamlss.org\/","Version":"4.3-2"},"gamlss.nl":
<r.rigby@londonmet.ac.uk> with contributions from\nPhilippe Lambert.","Depends":"R
(>= 2.2.1), gamlss, survival","Description":"This is an add on package to GAMLSS.
It allows one extra\nmethod for fitting GAMLSS models. The main function
nlgamlss()\ncan fit any parametric (up to four parameter)
GAMLSS\ndistribution.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"gamlss.nl","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Fitting non linear parametric GAMLSS
models","URL":"http:\/\/www.gamlss.org\/","Version":"4.1-0"},"gamlss.spatial":
{"Author":"Fernanda De Bastiani [aut, cre, cph],\nMikis Stasinopoulos [aut],\nBob
Rigby [aut]","Depends":"R (>= 2.15.0), gamlss.dist, gamlss (>= 4.2-7), spam,
mgcv","Description":"It allows us to fit Markov Random Field (MRF) within the
GAMLSS algorithms.","Imports":"stats, grDevices, graphics, methods","License":"GPL-
2 | GPL-
3","NeedsCompilation":"no","Package":"gamlss.spatial","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"spdep, maptools","Title":"Spatial Terms in
GAMLSS Models","URL":"http:\/\/www.gamlss.org\/","Version":"1.3"},"gamlss.tr":
<r.rigby@londonmet.ac.uk>","Depends":"R
(>= 2.2.1), gamlss.dist, gamlss (>= 4.2-7)","Description":"This is an add on
package to GAMLSS. The purpose of this\npackage is to allow users to defined
truncated distributions in\nGAMLSS models. The main function gen.trun() generates
truncated\nversion of an existing GAMLSS family distribution.","License":"GPL-2 |
GPL-
3","NeedsCompilation":"no","Package":"gamlss.tr","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Generating and fitting truncated (gamlss.family)
distributions","URL":"http:\/\/www.gamlss.org\/","Version":"4.3-1"},"gamlss.util":
<r.rigby@londonmet.ac.uk>, Paul Eilers <p.eilers@erasmusmc.nl>","Depends":"R (>=
2.15.0), gamlss.dist, gamlss (>= 4.3.3), zoo","Description":"Extra Functions For
GAMLSS And Others Models","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"gamlss.util","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"colorspace","Title":"GAMLSS
Utilities","URL":"http:\/\/www.gamlss.org\/","Version":"4.3-2"},"gamm4":
{"Author":"Simon Wood, Fabian Scheipl","Depends":"R (>= 2.9.0), methods, Matrix,
lme4 (>= 0.999375-31), mgcv (>=\n1.7-23)","Description":"Fit generalized additive
mixed models via a version of\nmgcv's gamm function, using lme4 for
2)","NeedsCompilation":"no","Package":"gamm4","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Generalized additive mixed models using mgcv and
lme4","Version":"0.2-3"},"gammSlice":{"Author":"Tung Pham and Matt
Wand","Depends":"R(>= 2.13), KernSmooth, lattice, mgcv","Description":"Uses a slice
sampling-based Markov chain Monte Carlo to\nconduct Bayesian fitting and inference
for generalized additive\nmixed models (GAMM). Generalized linear mixed models
and\ngeneralized additive models are also handled as special cases\nof
GAMM.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"gammSlice","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Generalized additive mixed model analysis via slice
sampling","Version":"1.3"},"gamsel":{"Author":"Alexandra Chouldechova and Trevor
Hastie","Depends":"mda, foreach","Description":"Using overlap grouped lasso
penalties, gamsel selects whether a term in a gam is nonzero, linear, or a non-
linear spline (up to a specified max df per variable). It fits the entire
regularization path on a grid of values for the overall penalty lambda, both for
gaussian and binomial families.","License":"GPL-
2","NeedsCompilation":"yes","Package":"gamsel","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Fit Regularization Path for Generalized Additive
Models","URL":"http:\/\/arxiv.org\/abs\/1506.03850","Version":"1.7-3"},"gaoptim":
{"Author":"Fernando Tenorio","Description":"Performs a Genetic Algorithm
Optimization, given a\nreal-based or permutation-based function and the
associated\nsearch space.","License":"GPL-
2","NeedsCompilation":"no","Package":"gaoptim","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Genetic Algorithm optimization for real-based
and\npermutation-based problems","Version":"1.1"},"gap":{"Author":"Jing Hua Zhao
and colleagues with inputs from Kurt Hornik and\nBrian Ripley","Depends":"R (>=
2.10)","Description":"It is designed as an integrated package for genetic
data\nanalysis of both population and family data. Currently, it\ncontains
functions for sample size calculations of both\npopulation-based and family-based
designs, probability of\nfamilial disease aggregation, kinship calculation,
statistics\nin linkage analysis, and association analysis involving
genetic\nmarkers including haplotype analysis with or without
environmental\ncovariates.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"gap","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"BradleyTerry2, MASS, Matrix, MCMCglmm, R2jags,
bdsmatrix,\ncoda, coxme, foreign, grid, haplo.stats, kinship2, lattice,\nmagic,
mets, nlme, pedigree, pedigreemm, regress, rms, survival","Title":"Genetic Analysis
Package","URL":"http:\/\/www.mrc-epid.cam.ac.uk\/people\/jing-hua-
zhao\/","Version":"1.1-16"},"gapmap":{"Author":"Ryo Sakai","Depends":"ggplot2,
reshape2","Description":"The gap encodes the distance between clusters and
improves\ninterpretation of cluster heatmaps. The gaps can be of the same\ndistance
based on a height threshold to cut the dendrogram. Another\noption is to vary the
size of gaps based on the distance
between\nclusters.","Imports":"grid","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"gapmap","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"knitr, dendsort, RColorBrewer","Title":"Functions for
Drawing Gapped Cluster Heatmap with ggplot2","URL":"https:\/\/bitbucket.org\/vda-
lab\/gapmap","Version":"0.0.4"},"gapminder":{"Author":"Jennifer Bryan [aut,
cre]","Depends":"R (>= 3.1.0)","Description":"An excerpt of the data available at
Gapminder.org. For each of 142\ncountries, the package provides values for life
expectancy, GDP per capita,\nand population, every five years, from 1952 to
2007.","License":"CC0","NeedsCompilation":"no","Package":"gapminder","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Suggests":"dplyr, ggplot2,
testthat","Title":"Data from
Gapminder","URL":"https:\/\/github.com\/jennybc\/gapminder,\nhttp:\/\/www.gapminder
.org\/data\/","Version":"0.2.0"},"gaselect":{"Author":"David
Kepplinger","Depends":"R (>= 3.0.2), methods (>= 2.10.0)","Description":"Provides a
genetic algorithm for finding variable\nsubsets in high dimensional data with high
prediction performance. The\ngenetic algorithm can use ordinary least squares (OLS)
regression models or\npartial least squares (PLS) regression models to evaluate the
prediction\npower of variable subsets. By supporting different cross-
validation\nschemes, the user can fine-tune the tradeoff between speed and quality
of\nthe solution.","Imports":"Rcpp (>= 0.10.5)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"gaselect","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"chemometrics","Title":"Genetic Algorithm (GA) for
Variable Selection from\nHigh-Dimensional Data","Version":"1.0.5"},"gaston":
{"Author":"HervÃ© Perdry & Claire Dandine-
Roulland","Depends":"Rcpp,RcppParallel,methods,WhopGenome,LDheatmap","Description":
"Manipulation of genetic data (SNPs), computation of Genetic Relationship Matrix,
Linkage Disequilibrium, etc. Efficient algorithms for Linear Mixed Model (AIREML,
diagonalization trick).","License":"GPL-
3","NeedsCompilation":"yes","Package":"gaston","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Genetic Data Manipulation (Quality Control, GRM and
LD\nComputations, PCA), Linear Mixed Models (AIREML Algorithm),\nAssociation
Testing","Version":"1.4.5"},"gaussDiff":{"Author":"Henning Rust
<henning.rust@met.fu-berlin.de>","Depends":"R (>= 1.8.0)","Description":"A
collection difference measures for multivariate Gaussian\nprobability density
functions, such as the Euclidea mean, the\nMahalanobis distance, the Kullback-
Leibler divergence, the\nJ-Coefficient, the Minkowski L2-distance, the Chi-
square\ndivergence and the Hellinger Coefficient.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gaussDiff","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Difference measures for multivariate Gaussian
probability\ndensity functions","URL":"www.geo.fu-
berlin.de\/met\/ag\/clidia\/Mitarbeiter\/HenningRust\/","Version":"1.1"},"gaussquad
":{"Author":"Frederick Novomestky <fnovomes@poly.edu>","Depends":"R (>= 2.0.1),
polynom, orthopolynom","Description":"A collection of functions to perform Gaussian
quadrature\nwith different weight functions corresponding to the
orthogonal\npolynomials in package orthopolynom. Examples verify
the\northogonality and inner products of the polynomials.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gaussquad","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Collection of functions for Gaussian
quadrature","Version":"1.0-2"},"gazepath":{"Author":"Daan van
Renswoude","Depends":"R (>= 2.10)","Description":"Eye-tracking data must be
transformed into fixations and saccades before it can be analyzed. This package
provides a non-parametric speed-based approach to do this on a trial basis. The
method is especially useful when there are large differences in data quality, as
the thresholds are adjusted accordingly. The same pre-processing procedure can be
applied to all participants, while accounting for individual differences in data
quality.","License":"GPL-
2","NeedsCompilation":"no","Package":"gazepath","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Gazepath Transforms Eye-Tracking Data into Fixations
and\nSaccades","Version":"1.0"},"gb":{"Author":"Bin
Wang\n<bwang@southalabama.edu>.","Depends":"R (>= 2.5.0), boot","Description":"This
package collects algorithms and functions for fitting data to a generalized lambda
distribution via moment matching methods, and generalized
bootstrapping.","License":"Unlimited","NeedsCompilation":"yes","Package":"gb","Repo
sitory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Generalize Lambda
Distribution and Generalized Bootstrapping","Version":"1.1.8-8"},"gbRd":
{"Author":"Georgi N. Boshnakov","Depends":"tools","Description":"Provides utilities
for processing Rd objects and files.\nExtract argument descriptions and other parts
of the help pages\nof functions.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gbRd","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Utilities for processing Rd objects and
files","Version":"0.4-11"},"gbm":{"Author":"Greg Ridgeway <gregridgeway@gmail.com>
with contributions from\nothers","Depends":"R (>= 2.9.0), survival, lattice,
splines, parallel","Description":"An implementation of extensions to Freund
and\nSchapire's AdaBoost algorithm and Friedman's
gradient boosting\nmachine. Includes regression methods for least
squares,\nabsolute loss, t-distribution loss, quantile regression,\nlogistic,
multinomial logistic, Poisson, Cox proportional\nhazards partial likelihood,
AdaBoost exponential loss,\nHuberized hinge loss, and Learning to Rank
measures\n(LambdaMart).","License":"GPL (>= 2) | file
LICENSE","NeedsCompilation":"yes","Package":"gbm","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"RUnit","Title":"Generalized Boosted Regression
Models","URL":"http:\/\/code.google.com\/p\/gradientboostedmodels\/","Version":"2.1
.1"},"gbm2sas":{"Author":"John R. Dixon","Depends":"gbm","Description":"Writes SAS
code to get predicted values from every tree of a gbm.object.","License":"GPL-
3","NeedsCompilation":"no","Package":"gbm2sas","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Convert GBM Object Trees to SAS
Code","Version":"2.1"},"gbutils":{"Author":"Georgi N.
Boshnakov","Depends":"methods","Description":"Simulate real and complex numbers
from distributions of\ntheir magnitude and arguments. Optionally, the magnitudes
and\/or\narguments may be fixed in almost arbitrary ways. Small\nprogramming
utilities: check if an object is identical to NA,\ncount positional arguments in a
call, set intersection of more\nthan two sets, check if an argument is
unnamed.","Imports":"stats, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gbutils","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Simulation of Real and Complex Numbers and Small
Programming\nUtilities","Version":"0.2-0"},"gcdnet":{"Author":"Yi Yang
<yiyang@umn.edu>, Hui Zou
<hzou@stat.umn.edu>","Depends":"Matrix","Description":"This package implements a
generalized coordinate descent (GCD) algorithm for computing the solution path of
the hybrid Huberized support vector machine (HHSVM) and its generalization,
including the elastic net penalized least squares, the elastic net penalized SVM
with the squared hinge loss and the elastic net penalized logistic
regression.","License":"GPL-
2","NeedsCompilation":"yes","Package":"gcdnet","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"LASSO and (adaptive) Elastic-Net penalized least
squares,\nlogistic regression, HHSVM and squared hinge loss SVM using a\nfast GCD
algorithm","URL":"http:\/\/code.google.com\/p\/gcdnet\/","Version":"1.0.4"},"gceris
k":{"Author":"Hanjie Shen <has072@ucsd.edu>, Ruben
Carmona\n<ruben.carmona13@gmail.com>, Loren Mell
<lmell@ucsd.edu>","Depends":"survival, cmprsk, ggplot2,","Description":"Generalized
competing event model based on Cox PH model and Fine-Gray model.\nThis function is
designed to develop optimized risk-stratification methods for competing\nrisks
data, such as described in:\n1. Carmona R, Gulaya S, Murphy JD, Rose BS, Wu J,
Noticewala S,McHale MT, Yashar CM, Vaida F,\nand Mell LK.(2014) Validated competing
event model for thestage I-II endometrial cancer\npopulation. Int J Radiat Oncol
Biol Phys.89:888-98. <DOI:10.1016\/j.ijrobp.2014.03.047>.\n2. Carmona R, Zakeri K,
Green G, Hwang L, Gulaya S, Xu B, Verma R, Williamson CW, Triplett DP, Rose\nBS,
Shen H, Vaida F, Murphy JD, and Mell LK. (2016) Improved method to stratify
elderly\ncancer patients at risk for competing events. J Clin Oncol.in press.
<DOI:10.1200\/JCO.2015.65.0739>.","Imports":"stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gcerisk","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Generalized Competing Event
Model","Version":"16.1.2"},"gclus":{"Author":"Catherine Hurley","Depends":"R (>=
2.10), cluster","Description":"Orders panels in scatterplot matrices and
parallel\ncoordinate displays by some merit index. Package contains\nvarious
indices of merit, ordering functions, and enhanced\nversions of pairs and parcoord
which color panels according to\ntheir merit level.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gclus","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Clustering Graphics","Version":"1.3.1"},"gcmr":
{"Author":"Guido Masarotto and Cristiano Varin","Depends":"R (>=
2.10.0)","Description":"Likelihood inference in Gaussian copula
marginal\nregression models.","Imports":"betareg, car, Formula, geoR, lmtest, nlme,
sandwich, sp","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"gcmr","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Gaussian Copula Marginal
Regression","Version":"0.7.5"},"gconcord":{"Author":"Sang-Yun Oh
<sang.oh@stanford.edu>\nKshitij Khare <kdkhare@stat.ufl.edu>\nBala Rajaratnam
<brajarat@stanford.edu>","Description":"Estimates a sparse inverse covariance
matrix from a convex\npseudo-likelihood function with L1 penalty","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"gconcord","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"mvtnorm","Title":"Concord method for Graphical Model
Selection","Version":"0.41"},"gcookbook":{"Author":"Winston Chang","Depends":"R (>=
2.10)","Description":"This package contains data sets used in the
book \"R\nGraphics Cookbook\" by Winston Chang, published by
O'Reilly\nMedia.","License":"GPL-
2","NeedsCompilation":"no","Package":"gcookbook","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"ggplot2, plyr, MASS","Title":"Data for \"R Graphics
Cookbook\"","Version":"1.0"},"gdalUtils":{"Author":"Jonathan Asher Greenberg and
Matteo Mattiuzzi","Depends":"R (>= 2.14.0)","Description":"Wrappers for the
Geospatial Data Abstraction Library (GDAL)\nUtilities.","Imports":"sp, foreach,
R.utils, raster, rgdal","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gdalUtils","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Wrappers for the Geospatial Data Abstraction Library
(GDAL)\nUtilities","Version":"2.0.1.7"},"gdata":{"Author":"Gregory R. Warnes, Ben
Bolker, Gregor Gorjanc, Gabor\nGrothendieck, Ales Korosec, Thomas Lumley, Don
MacQueen, Arni\nMagnusson, Jim Rogers, and others","Depends":"R (>=
2.3.0)","Description":"Various R programming tools for data manipulation,
including:\n- medical unit conversions ('ConvertMedUnits', 'MedUnits'),\n-
combining objects ('bindData', 'cbindX', 'combine', 'interleave'),\n- character
vector operations ('centerText', 'startsWith', 'trim'),\n- factor manipulation
('levels', 'reorder.factor', 'mapLevels'),\n- obtaining information about R objects
('object.size', 'elem', 'env',\n'humanReadable', 'is.what', 'll', 'keep',
'ls.funs',\n'Args','nPairs', 'nobs'),\n- manipulating MS-Excel formatted files
('read.xls',\n'installXLSXsupport', 'sheetCount', 'xlsFormats'),\n- generating
fixed-width format files ('write.fwf'),\n- extricating components of date & time
objects ('getYear', 'getMonth',\n'getDay', 'getHour', 'getMin', 'getSec'),\n-
operations on columns of data frames ('matchcols', 'rename.vars'),\n- matrix
operations ('unmatrix', 'upperTriangle', 'lowerTriangle'),\n- operations on vectors
('case', 'unknownToNA', 'duplicated2', 'trimSum'),\n- operations on data frames
('frameApply', 'wideByFactor'),\n- value of last evaluated expression ('ans'),
and\n- wrapper for 'sample' that ensures consistent behavior for both\nscalar and
vector arguments ('resample').","Imports":"gtools, stats, methods,
2","NeedsCompilation":"no","Package":"gdata","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"RUnit","Title":"Various R Programming Tools for Data
Manipulation","Version":"2.17.0"},"gdimap":{"Author":"Adelino Ferreira da Silva
<afs@fct.unl.pt>","Depends":"R (>= 3.0.0), rgl","Description":"Diffusion anisotropy
has been used to characterize\nwhite matter neuronal pathways in the human brain,
and infer global\nconnectivity in the central nervous system. The package
implements\nalgorithms to estimate and visualize the orientation of
neuronal\npathways in model-free methods (q-space imaging methods).\nFor estimating
fibre orientations two methods have been\nimplemented. One method implements fibre
orientation detection\nthrough local maxima extraction. A second more robust
method\nis based on directional statistical clustering of ODF voxel data.\nFibre
orientations in multiple fibre voxels are estimated using\na mixture of von Mises-
Fisher (vMF) distributions. This statistical\nestimation procedure is used to
resolve crossing fibre\nconfigurations.\nReconstruction of orientation distribution
function (ODF)\nprofiles may be performed using the standard generalized\nq-
sampling imaging (GQI) approach, Garyfallidis' GQI (GQI2)\napproach, or Aganj's
variant of the Q-ball imaging (CSA-QBI)\napproach. Procedures for the visualization
of RGB-maps,\nline-maps and glyph-maps of real diffusion magnetic
resonance\nimaging (dMRI) data-sets are included in the
package.","Imports":"oro.nifti, movMF, grid, gridExtra, colorspace, geometry,
gsl,\nabind","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gdimap","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Generalized Diffusion Magnetic Resonance
Imaging","URL":"http:\/\/www.r-project.org","Version":"0.1-9"},"gdistance":
{"Author":"Jacob van Etten","Depends":"R (>= 2.8.0), raster (>= 1.9-19), methods,
igraph (>= 0.7.0),\nMatrix","Description":"Calculate distances and routes on
geographic grids.","Imports":"sp, stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gdistance","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Distances and Routes on Geographical
Grids","Version":"1.1-9"},"gdm":{"Author":"Glenn Manion, Matthew Lisk, Simon
Ferrier, Diego Nieto-Lugilde, Matthew C. Fitzpatrick","Depends":"R (>= 2.15.2),
raster, foreach, doParallel, parallel","Description":"A toolkit with functions to
fit, plot, and summarize Generalized Dissimilarity Models.","Imports":"Rcpp (>=
0.10.4), reshape2, vegan","License":"GPL-
2","NeedsCompilation":"yes","Package":"gdm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"R.rsp","Title":"Functions
for Generalized Dissimilarity Modeling","Version":"1.2.2"},"gds":{"Author":"Partha
Sarathi Bishnu <psbishnu@gmail.com>","Description":"Contains a function called
gds() which accepts three input\nparameters like lower limits, upper limits and the
frequencies of the\ncorresponding classes. The gds() function calculate and return
the values\nof mean ('gmean'), median ('gmedian'), mode ('gmode'), variance
('gvar'), standard\ndeviation ('gstdev'), coefficient of variance ('gcv'),
quartiles ('gq1', 'gq2', 'gq3'),\ninter-quartile range ('gIQR'), skewness ('g1'),
and kurtosis ('g2') which facilitate\neffective data analysis. For skewness and
kurtosis calculations we use moments.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gds","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Descriptive Statistics of Grouped
Data","Version":"0.1.0"},"gdtools":{"Author":"David Gohel [aut, cre],\nHadley
Wickham [aut],\nJeroen Ooms [ctb],\nYixuan Qiu [ctb],\nRStudio
[cph]","Description":"Useful tools for writing vector graphics
devices.","Imports":"Rcpp (>= 0.12.0)","License":"GPL-
3","NeedsCompilation":"yes","Package":"gdtools","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"htmltools, testthat","Title":"Utilities for Graphical
Rendering","Version":"0.0.7"},"gear":{"Author":"Joshua
French","Description":"Implements common geostatistical methods in a
clean,\nstraightforward, efficient manner. A quasi reboot of the SpatialTools R
package.","Imports":"sp, parallel, lattice, stats, optimx","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gear","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat, gstat, geoR, spam,
Matrix","Title":"Geostatistical Analysis in R","Version":"0.1.1"},"gee":
{"Author":"Vincent J Carey. Ported to R by Thomas Lumley (versions 3.13 and
4.4)\nand Brian Ripley <ripley@stats.ox.ac.uk> (version 4.13).\nNote that
maintainers are not available to give advice on using a\npackage they did not
author.","Depends":"stats","Description":"Generalized Estimation Equation
solver.","License":"GPL-
2","NeedsCompilation":"yes","Package":"gee","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"MASS","Title":"Generalized Estimation Equation
Solver","Version":"4.13-19"},"geeM":{"Author":"Lee S. McDaniel and Nick
Henderson","Depends":"Matrix","Description":"GEE estimation of the parameters in
mean structures with possible correlation between the outcomes. User-specified mean
link and variance functions are allowed, along with observation weighting.
The \"M\" in the name \"geeM\" is meant to emphasize the use of the Matrix package,
which allows for an implementation based fully in R.","Imports":"stats,
2)","NeedsCompilation":"no","Package":"geeM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"geepack","Title":"Solve Generalized Estimating
Equations","Version":"0.8.0"},"geepack":{"Author":"Søren Højsgaard,
<sorenh@math.aau.dk>, Ulrich Halekoh <Ulrich.Halekoh@agrsci.dk>, Jun Yan
<jun.yan@uconn.edu>,","Description":"Generalized estimating equations solver for
parameters in\nmean, scale, and correlation structures, through mean link,\nscale
link, and correlation link. Can also handle clustered\ncategorical
responses.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"geepack","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Generalized Estimating Equation Package","Version":"1.2-
0.1"},"geesmv":{"Author":"Ming Wang <mwang@phs.psu.edu>","Depends":"R (>=
3.0.2)","Description":"Generalized estimating equations with the original sandwich
variance estimator proposed by Liang and Zeger (1986), and eight types of more
recent modified variance estimators for improving the finite small-sample
performance.","Imports":"stats, nlme, gee, matrixcalc, MASS","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"geesmv","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Modified Variance Estimators for Generalized
Estimating\nEquations","Version":"1.3"},"geigen":{"Author":"Berend Hasselman [cre,
aut],\nLapack authors [aut, cph]","Description":"Functions to compute generalized
eigenvalues and eigenvectors,\nthe generalized Schur decomposition and\nthe
generalized Singular Value Decomposition of a matrix pair,\nusing Lapack
routines.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"geigen","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Calculate Generalized Eigenvalues, the Generalized
Schur\nDecomposition and the Generalized Singular Value Decomposition\nof a Matrix
Pair with Lapack","Version":"1.9"},"geiger":{"Author":"Luke Harmon
<lukeh@uidaho.edu>, Jason Weir, Chad Brock, Rich\nGlor, Wendell Challenger, Gene
Hunt, Rich FitzJohn, Matt Pennell, Graham Slater, Joseph Brown, Josef Uyeda, and
Jon Eastman <jonathan.eastman@gmail.com>","Depends":"ape (>= 3.0-6), R (>=
2.15.0)","Description":"Methods for fitting macroevolutionary models to
phylogenetic trees.","Imports":"MASS, mvtnorm, subplex, deSolve (>= 1.7), digest,
Rcpp (>=\n0.9.0), coda, ncbit, colorspace, methods","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"geiger","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Analysis of Evolutionary
Diversification","URL":"http:\/\/www.webpages.uidaho.edu\/~lukeh\/software.html","V
ersion":"2.0.6"},"gelnet":{"Author":"Artem Sokolov","Depends":"R (>=
3.1.0)","Description":"Implements several extensions of the elastic net
regularization\nscheme. These extensions include individual feature penalties for
the L1 term,\nfeature-feature penalties for the L2 term, as well as translation
coefficients\nfor the latter.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"gelnet","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr, rmarkdown","Title":"Generalized Elastic
Nets","Version":"1.2.1"},"gems":{"Author":"Luisa Salazar Vizcaya, Nello Blaser,
Thomas Gsponer","Description":"Simulate and analyze multistate models with general
hazard functions. gems provides functionality for the preparation of hazard
functions and parameters, simulation from a general multistate model and predicting
future events. The multistate model is not required to be a Markov model and may
take the history of previous events into account. In the basic version, it allows
to simulate from transition-specific hazard function, whose parameters are
multivariable normally distributed.","Imports":"MASS, methods, msm, plyr, graphics,
stats, utils, data.table","License":"GPL-
2","NeedsCompilation":"no","Package":"gems","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"muhaz","Title":"Generalized Multistate Simulation
Model","Version":"1.0.0"},"gemtc":{"Author":"Gert van Valkenhoef, Joel
Kuiper","Depends":"coda (>= 0.13)","Description":"Network meta-analyses (mixed
treatment comparisons) in the Bayesian\nframework using JAGS. Includes methods to
assess heterogeneity and\ninconsistency, and a number of standard
visualizations.","Imports":"igraph (>= 1.0), meta (>= 2.1), plyr (>= 1.8),
graphics,\ngrDevices, stats, utils, grid, rjags (>= 3-0), truncnorm,
Rglpk","License":"GPL-
3","NeedsCompilation":"yes","Package":"gemtc","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat (>= 0.8), Matrix, XML (>=
3.6)","Title":"Network Meta-Analysis Using Bayesian
Methods","URL":"http:\/\/github.com\/gertvv\/gemtc","Version":"0.8"},"gemtc.jar":
{"Author":"Gert van Valkenhoef, Joel Kuiper","Depends":"R (>= 2.7.0), rJava (>=
0.8-0)","Description":"An R package providing the Java JAR for the gemtc
3","NeedsCompilation":"no","Package":"gemtc.jar","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"GeMTC Java binary","Version":"0.14.3"},"genMOSS":
{"Author":"Matthew Friedlander, Adrian Dobra, Helene Massam, and Laurent
Briollais","Depends":"R (>= 2.10), ROCR","Description":"Implements the Mode
Oriented Stochastic Search (MOSS) algorithm as well as a simple moving window
approach to look for combinations of SNPs that are associated with a
response.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"genMOSS","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Functions for the Bayesian Analysis of GWAS
Data","Version":"1.2"},"genSurv":{"Author":"Artur Araujo, Luis Meira-
Machado\n<lmachado@math.uminho.pt> and Susana
Faria\n<sfaria@math.uminho.pt>","Depends":"R (>= 2.12.0)","Description":"Generation
of survival data with one (binary)\ntime-dependent covariate. Generation of
survival data arising\nfrom a progressive illness-death model.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"genSurv","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"survival","Title":"Generating Multi-State Survival
Data","Version":"1.0.3"},"genalg":{"Author":"Egon Willighagen and Michel
Ballings","Description":"R based genetic algorithm for binary and floating
point\nchromosomes.","License":"GPL-
2","NeedsCompilation":"no","Package":"genalg","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"R Based Genetic
Algorithm","URL":"https:\/\/github.com\/egonw\/genalg","Version":"0.2.0"},"genasis"
:{"Author":"Jiri Kalina, Jana Klanova, Ladislav Dusek, Tom Harner, Jana Boruvkova,
Jiri Jarkovsky","Depends":"R (>= 2.0.1), Kendall,
fitdistrplus","Description":"genasis package contains methods for air pollution
assessment. Concerned on persistent organic pollutants, the package allows to
compute trends of their concentrations, compare different datasets and estimate
relations between values from active and passive air samplers.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"genasis","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Global ENvironmental ASsessment Information System
(GENASIS)\ncomputational tools","Version":"1.0"},"gendata":{"Author":"Francis Huang
<flh3@hotmail.com>","Description":"Set of
functions to create datasets using a correlation matrix.","License":"GPL-
3","NeedsCompilation":"no","Package":"gendata","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Generate and Modify Synthetic
Datasets","Version":"1.1"},"gender":{"Author":"Lincoln Mullen [aut, cre],\nCameron
Blevins [ctb],\nBen Schmidt [ctb]","Depends":"R (>= 3.0.0), utils,
stats","Description":"Encodes gender based on names and dates of birth using
historical\ndatasets. By using these datasets instead of lists of male and female
names,\nthis package is able to more accurately guess the gender of a name, and
it\nis able to report the probability that a name was male or
female.","Imports":"dplyr (>= 0.4.2), httr (>= 1.0.0), jsonlite (>=
LICENSE","NeedsCompilation":"no","Package":"gender","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"genderdata (>= 0.5.0), ggplot2 (>= 1.0.0), knitr
(>= 1.11),\ntestthat (>= 0.10.0)","Title":"Predict Gender from Names Using
Historical
Data","URL":"https:\/\/github.com\/ropensci\/gender","Version":"0.5.1"},"genderizeR
":{"Author":"Kamil Wais [aut, cre]","Depends":"R (>=
3.1.1)","Description":"Utilizes the 'genderize.io' API to predict gender from
first\nnames extracted from a text vector. The accuracy of prediction could
be\ncontrolled by two parameters: counts of a first name in the database
and\nprobability of prediction.","Imports":"stringr, httr, tm, data.table,
magrittr, parallel, utils","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"genderizeR","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Gender Prediction Based on
First
Names","URL":"https:\/\/github.com\/kalimu\/genderizeR,\nhttp:\/\/www.wais.kamil.rz
eszow.pl\/genderizeR","Version":"1.2.0"},"gendist":{"Author":"Shaiful Anuar Abu
Bakar","Description":"Computes the probability density function (pdf), cumulative
distribution function (cdf), quantile function (qf) and generates random values
(rg) for the following general models : mixture models, composite models, folded
models, skewed symmetric models and arc tan models.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gendist","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Generated Probability Distribution
Models","Version":"1.0"},"geneListPie":{"Author":"Xutao Deng","Depends":"R (>=
2.10)","Description":"\"geneListPie\" package is for mapping a gene list
to\nfunction categories defined in GOSlim or Kegg. The results can\nbe plotted as a
pie chart to provide a quick view of the genes\ndistribution of the gene list among
the function categories.\nThe gene list must contain a list of gene symbols. The
package\ncontains a set of pre-processed gene sets obtained from Gene\nOntology and
MSigDB including human, mouse, rat and yeast. To\nprovide a high level concise
view, only GO slim and kegg are\nprovided. The gene sets are regulared updated.
User can also\nuse customized gene sets. User can use the R Pie() or
Pie3D()\nfunction for plotting the pie chart. Users can also choose to\noutput the
gene function mapping results and use external\nsoftware such as Excel(R) for
ploting.","License":"GPL-
3","NeedsCompilation":"no","Package":"geneListPie","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"plotrix","Title":"Profiling a gene list into GOslim
or KEGG function pie","Version":"1.0"},"geneNetBP":{"Author":"Janhavi Moharil
<janhavim@buffalo.edu>","Depends":"R (>= 3.1.0),scales (>= 0.2.4),Rgraphviz (>=
2.8.1), graph (>=\n1.42.0)","Description":"Belief propagation methods in genotype-
phenotype networks (Conditional Gaussian Bayesian Networks) to propagate phenotypic
evidence through the network.","License":"GPL-
2","NeedsCompilation":"no","Package":"geneNetBP","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"RHugin","Title":"Belief Propagation in Genotype-
Phenotype Networks","Version":"1.0.0"},"geneSLOPE":{"Author":"Damian Brzyski
[aut],\nChristine Peterson [aut],\nMalgorzata Bogdan [aut],\nChiara Sabatti
[aut],\nPiotr Sobczyk [cre, aut]","Depends":"R (>= 3.1.3),
SLOPE","Description":"Genome-wide association study (GWAS) performed with
SLOPE,\nshort for Sorted L-One Penalized Estimation, a\nmethod for estimating the
vector of coefficients in linear model.\nIn the first step of GWAS, SNPs are
clumped according to their correlations and\ndistances. Then, SLOPE is performed on
data where each clump has\none representative.","Imports":"ggplot2, bigmemory,
grid, utils, stats","License":"GPL-
3","NeedsCompilation":"no","Package":"geneSLOPE","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"shiny, knitr, rmarkdown, testthat","Title":"Genome-
Wide Association Study with
SLOPE","URL":"https:\/\/github.com\/psobczyk\/geneSLOPE","Version":"0.36.6"},"geneS
ignatureFinder":{"Author":"Stefano M. Pagnotta, Michele Ceccarelli","Depends":"R
(>= 3.0.0), survival, cluster, class, parallel","Description":"A tool for finding
an ensemble gene-signature by a steepest ascending algorithm partially supervised
by survival time data.","License":"GPL-
2","NeedsCompilation":"no","Package":"geneSignatureFinder","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Title":"A Gene-signatures finder
tools","URL":"http:\/\/www.bioinformatics.unisannio.it\/gsf","Version":"2014.02.17"
},"genepi":{"Author":"Venkatraman E. Seshan","Depends":"R (>= 2.0.0),
stats","Description":"Functions for Genetic Epi Methods Developed at
MSKCC","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"genepi","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Genetic Epidemiology Design and
Inference","Version":"1.0.1"},"generator":{"Author":"Paul Hendricks [aut,
cre]","Depends":"R (>= 3.1.2)","Description":"Allows users to quickly and easily
generate fake data containing\nPersonally Identifiable Information (PII) through
convenience functions.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"generator","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat","Title":"Generate Data Containing
Fake Personally
Identifiable\nInformation","URL":"https:\/\/github.com\/paulhendricks\/generator","
Version":"0.1.0"},"genetics":{"Author":"Gregory Warnes, with contributions from
Gregor Gorjanc,\nFriedrich Leisch, and Michael Man.","Depends":"combinat, gdata,
gtools, MASS, mvtnorm","Description":"Classes and methods for handling genetic
data. Includes\nclasses to represent genotypes and haplotypes at single markers\nup
to multiple markers on multiple chromosomes. Function\ninclude allele frequencies,
flagging homo\/heterozygotes,\nflagging carriers of certain alleles, estimating and
testing\nfor Hardy-Weinberg disequilibrium, estimating and testing for\nlinkage
disequilibrium, ...","License":"GPL","NeedsCompilation":"no","Package":"genetics","
Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Population
Genetics","Version":"1.3.8.1"},"genie":{"Author":"Marek Gagolewski [aut,
cre],\nMaciej Bartoszuk [aut],\nAnna Cena [aut]","Depends":"R (>= 3.1.0),
stats","Description":"A new hierarchical clustering linkage criterion:\nthe Genie
algorithm links two clusters in such a way that a chosen\neconomic inequity measure
(e.g., the Gini index) of the cluster\nsizes does not increase drastically above a
given threshold. Benchmarks\nindicate a high practical usefulness of the introduced
method:\nit most often outperforms the Ward or average linkage in terms of\nthe
clustering quality while retaining the single linkage speed.","Imports":"Rcpp (>=
0.12.0)","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"genie","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"datasets, testthat, stringi","Title":"A New, Fast, and
Outlier Resistant Hierarchical
Clustering\nAlgorithm","Version":"1.0.0"},"genlasso":{"Author":"Taylor B. Arnold
and Ryan J. Tibshirani","Depends":"MASS, Matrix, igraph","Description":"This
package computes the solution path for generalized lasso problems. Important use
cases are the fused lasso over an arbitrary graph, and trend fitting of any given
polynomial order. Specialized implementations for the latter two subproblems are
given to improve stability and speed.","License":"GPL (>=
2.0)","NeedsCompilation":"yes","Package":"genlasso","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Path algorithm for generalized lasso
problems","URL":"https:\/\/github.com\/statsmaths\/genlasso","Version":"1.3"},"geno
PlotR":{"Author":"Lionel Guy <lionel.guy@imbim.uu.se>","Depends":"R (>= 2.10.0),
ade4, grid","Description":"Draws gene or genome maps and comparisons between these,
in a\npublication-grade manner. Starting from simple, common files, it will\ndraw
postscript or pdf files that can be sent as such to
journals.","Imports":"methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"genoPlotR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Plot Publication-Grade Gene and Genome
Maps","URL":"http:\/\/genoplotr.r-forge.r-
project.org\/","Version":"0.8.4"},"genpathmox":{"Author":"\"Giuseppe Lamberti\"
[aut, cre]","Depends":"R (>= 3.1.1),plspm, quantreg,mice,diagram,
methods","Description":"genpathmox provides a very interesting solution for
handling\nsegmentation variables in complex statistical methodology. It contains
en\nextended version of the PATHMOX algorithm in the context of partial
least\nsquare path modeling (Sanchez, 2009) including the F-block test (to
detect\nthe responsible latent endogenous equations of the difference), the\nF-
coefficient (to detect the path coefficients responsible of the\ndifference) and
the invariance test (to realize a comparison between the\nsub-models' latent
variables). Furthermore, the package contains a\ngeneralized version of the PATHMOX
algorithm to approach different\nmethodologies: linear regression and least
absolute regression models.","License":"GPL-
3","NeedsCompilation":"no","Package":"genpathmox","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"
Generalized PATHMOX Algorithm for PLS-PM, LS and LAD
Regression","Version":"0.2"},"genridge":{"Author":"Michael Friendly [aut,
cre]","Depends":"R (>= 2.11.1), car","Description":"\nThe genridge package
introduces generalizations of the standard univariate\nridge trace plot used in
ridge regression and related methods. These graphical methods\nshow both bias
(actually, shrinkage) and precision, by plotting the covariance ellipsoids of the
estimated\ncoefficients, rather than just the estimates themselves. 2D and 3D
plotting methods are provided,\nboth in the space of the predictor variables and in
the transformed space of the PCA\/SVD of the\npredictors.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"genridge","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"MASS, ElemStatLearn, rgl,
bestglm","Title":"Generalized Ridge Trace Plots for Ridge
Regression","Version":"0.6-5"},"gensemble":{"Author":"Peter Werner, Eugene
Dubossarsky","Depends":"methods","Description":"Generalized ensemble methods
allowing arbitrary underlying\nmodels to be used. Currently only bagging is
supported.","License":"GPL-
2","NeedsCompilation":"no","Package":"gensemble","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"generalized ensemble methods","Version":"1.0"},"geo":
{"Author":"Hoskuldur Bjornsson, Sigurdur Thor Jonsson, Arni Magnusson, and
Bjarki\nThor Elvarsson","Depends":"maps, mapdata, R (>=
2.10.0)","Description":"Used by Hafro staff to draw maps showing the distribution
of\nfishing intensity and catches, and of survey data for Icelandic fish
stocks.\nPotentially useful for others.","Imports":"splines, methods, utils,
grDevices, graphics, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"geo","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Draw and Annotate Maps, Especially Charts of the North
Atlantic","Version":"1.4-3"},"geoBayes":{"Author":"Evangelos Evangelou
<e.evangelou@maths.bath.ac.uk>, Vivekananda\nRoy <vroy@iastate.edu>","Depends":"R
(>= 2.0.0)","Description":"Functions to fit geostatistical data. The data can
be\ncontinuous, binary or count data and the models implemented are\nflexible.
Conjugate priors are assumed on some parameters while\ninference on the other
parameters can be done through a full\nBayesian analysis of by empirical Bayes
methods.","Imports":"stats, coda, sp","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"geoBayes","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"geoR, geoRglm","Title":"Analysis of Geostatistical
Data using Bayes and Empirical Bayes\nMethods","Version":"0.3.3"},"geoCount":
{"Author":"Liang Jing","Depends":"R (>= 2.12.0)","Description":"This package
provides a variety of functions to analyze and model geostatistical count data with
generalized linear spatial models, including\n1) simulate and visualize the
data;\n2) posterior sampling with robust MCMC algorithms (in serial or parallel
way);\n3) perform prediction for unsampled locations;\n4) conduct Bayesian model
checking procedure to evaluate the goodness of fitting;\n5) conduct transformed
residual checking procedure.\nIn the package, seamlessly embedded C++ programs and
parallel computing techniques are implemented to speed up the computing
processes.","Imports":"Rcpp (>= 0.9.4)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"geoCount","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"coda, distr, distrEx, reldist, rlecuyer,
snowfall","Title":"Analysis and Modeling for Geostatistical Count
Data","Version":"1.150120"},"geoR":{"Author":"Paulo J. Ribeiro Jr
<paulojus@ufpr.br> and\nPeter J. Diggle <p.diggle@lancaster.ac.uk>","Depends":"R
(>= 2.10), stats, methods","Description":"Geostatistical analysis including
traditional, likelihood-based and Bayesian methods.","Imports":"MASS, sp, splancs,
RandomFields, graphics","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"geoR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"scatterplot3d, lattice, tcltk,
geoRglm","Title":"Analysis of Geostatistical
Data","URL":"http:\/\/www.leg.ufpr.br\/geoR","Version":"1.7-5.1"},"geoRglm":
{"Author":"Ole F. Christensen [aut, cre],\nPaulo J. Ribeiro Jr [aut]","Depends":"R
(>= 2.2.0), geoR (>= 1.7-5), stats","Description":"Functions for inference in
generalised linear spatial models. The posterior and predictive inference is based
on Markov chain Monte Carlo methods. Package geoRglm is an extension to the package
geoR, which must be installed first.","Imports":"sp","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"geoRglm","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"coda","Title":"A Package for Generalised Linear
Spatial Models","URL":"http:\/\/gbi.agrsci.dk\/~ofch\/geoRglm","Version":"0.9-
8"},"geoaxe":{"Author":"Scott Chamberlain [aut, cre]","Description":"Split
'geospatial' objects into pieces. Includes\nsupport for some spatial object inputs,
'Well-Known Text', and\n'GeoJSON'.","Imports":"methods, sp, rgeos,
LICENSE","NeedsCompilation":"no","Package":"geoaxe","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat, knitr","Title":"Split 'Geospatial'
Objects into
Pieces","URL":"https:\/\/github.com\/ropenscilabs\/geoaxe","Version":"0.1.0"},"geoc
odeHERE":{"Author":"Cory Nissen <corynissen@gmail.com> [aut, cre]","Depends":"R (>=
3.0.0)","Description":"Wrapper for Nokia's HERE geocoding API. See
http:\/\/here.com\/ for\nmore information on HERE and
https:\/\/developer.here.com\/geocoder for more\ninformation on the HERE geocoding
API.","Imports":"httr, utils","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"geocodeHERE","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Wrapper for Nokia's HERE Geocoding
API","URL":"https:\/\/github.com\/corynissen\/geocodeHERE","Version":"0.1.3"},"geoe
lectrics":{"Author":"Anja Kleebaum <anja.kleebaum@stmail.uni-
bayreuth.de>","Depends":"R (>= 2.10), lattice, rgl,
fields","Description":"Visualizes two-dimensional geoelectric resistivity
measurement profiles in three
dimensions.","Imports":"methods","License":"GPL","NeedsCompilation":"no","Package":
"geoelectrics","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"3D-
Visualization of Geoelectric Resistivity Measurement
Profiles","Version":"0.1.5"},"geofd":{"Author":"Ramon Giraldo
<rgiraldoh@unal.edu.co>, Pedro Delicado\n<pedro.delicado@upc.edu>, Jorge Mateu
<mateu@mat.uji.es>","Depends":"fda, geoR","Description":"Kriging based methods are
used for predicting functional data\n(curves) with spatial
dependence.","License":"GPL-
2","NeedsCompilation":"no","Package":"geofd","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Spatial Prediction for Function Value
Data","Version":"1.0"},"geojsonio":{"Author":"Scott Chamberlain [aut, cre],\nAndy
Teucher [aut]","Depends":"R (>= 2.10)","Description":"Convert data to 'geoJSON' or
'topoJSON' from various R classes,\nincluding vectors, lists, data frames, shape
files, and spatial classes.\n'geojsonio' does not aim to replace packages like
'sp', 'rgdal', 'rgeos', but\nrather aims to be a high level client to simplify
conversions of data from and\nto 'geoJSON' and
'topoJSON'.","Enhances":"RColorBrewer","Imports":"methods, stats, utils, sp, rgdal,
rgeos, httr, maptools,\njsonlite, magrittr, V8","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"geojsonio","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"gistr, testthat, knitr,
leaflet","Title":"Convert Data from and to 'geoJSON' or
'topoJSON'","URL":"https:\/\/github.com\/ropensci\/geojsonio","Version":"0.1.8"},"g
eoknife":{"Author":"Jordan Read [aut, cre],\nJordan Walker [aut],\nAlison Appling
[aut],\nDavid Blodgett [aut],\nEmily Read [aut],\nLuke Winslow [aut]","Depends":"R
(>= 3.0)","Description":"Processes gridded datasets found on the U.S. Geological
Survey\nGeo Data Portal web application or elsewhere, using a web-enabled
workflow\nthat eliminates the need to download and store large datasets that are
reliably\nhosted on the Internet. The package provides access to several data
subset and\nsummarization algorithms that are available on remote web processing
servers.","Imports":"XML, methods, httr (>= 1.0.0), curl, sp,
utils","License":"CC0","NeedsCompilation":"no","Package":"geoknife","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Suggests":"testthat, xtable, knitr,
rmarkdown, ggmap, rasterVis,\nggplot2, rgdal, maps","Title":"Web-Processing of
Large Gridded Datasets","URL":"https:\/\/github.com\/USGS-
R\/geoknife","Version":"1.3.0"},"geomapdata":{"Author":"Jonathan M.
Lees","Depends":"R (>= 2.10)","Description":"Set of data for use in package GEOmap.
Includes world\nmap, USA map, Coso map, Japan Map,
ETOPO5","License":"GPL","NeedsCompilation":"no","Package":"geomapdata","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"GEOmap","Title":"Data for
topographic and Geologic Mapping","Version":"1.0-4"},"geometry":{"Author":"C. B.
Barber [cph],\nKai Habel [cph, aut],\nRaoul Grasman [cph, aut],\nRobert B. Gramacy
[cph, aut],\nAndreas Stahel [cph, aut],\nDavid C. Sterratt [cph, aut,
cre]","Depends":"R (>= 2.5.0), magic","Description":"Makes the qhull library
(www.qhull.org)\navailable in R, in a similar manner as in Octave and MATLAB.
Qhull\ncomputes convex hulls, Delaunay triangulations, halfspace\nintersections
about a point, Voronoi diagrams, furthest-site\nDelaunay triangulations, and
furthest-site Voronoi diagrams. It\nruns in 2-d, 3-d, 4-d, and higher dimensions.
It implements the\nQuickhull algorithm for computing the convex hull. Qhull does
not\nsupport constrained Delaunay triangulations, or mesh generation of\nnon-convex
objects, but the package does include some R functions\nthat allow for this.
Currently the package only gives access to\nDelaunay triangulation and convex hull
computation.","License":"GPL
(>= 3) + file
LICENSE","NeedsCompilation":"yes","Package":"geometry","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat, rgl, R.matlab, tripack","Title":"Mesh
Generation and Surface Tesselation","URL":"http:\/\/geometry.r-forge.r-
project.org\/","Version":"0.3-6"},"geomnet":{"Author":"Samantha Tyner, Heike
Hofmann","Depends":"R (>= 2.14), ggplot2 (>= 1.0.1.9003)","Description":"Network
visualization in the 'ggplot2' framework. Network\nfunctionality is provided in a
single 'ggplot2' layer by calling the geom 'net'.\nLayouts are calculated using the
'sna' package, example networks are included.","Imports":"sna,
network","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"geomnet","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"dplyr","Title":"Network Visualization in the 'ggplot2'
Framework","Version":"0.0.1"},"geomorph":{"Author":"Dean Adams, Michael Collyer,
Emma Sherratt","Depends":"rgl, ape, R(>= 3.1.0)","Description":"Read, manipulate,
and digitize landmark data, generate shape\nvariables via Procrustes analysis for
points, curves and surfaces, perform\nshape analyses, and provide graphical
depictions of shapes and patterns of\nshape variation.","Imports":"graphics,
grDevices, stats, utils, jpeg, geiger, Matrix","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"geomorph","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Geometric Morphometric Analyses of 2D\/3D Landmark
Data","Version":"3.0.1"},"geonames":{"Author":"Barry Rowlingson","Depends":"R (>=
2.2.0)","Description":"Code for querying the web service at
www.geonames.org","Imports":"rjson","License":"GPL-
3","NeedsCompilation":"no","Package":"geonames","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Interface to www.geonames.org web
service","Version":"0.998"},"geophys":{"Author":"Jonathan M. Lees","Depends":"R (>=
2.15)","Description":"Codes for analyzing various problems of Geophysics, Continuum
Mechanics and Mogi Models.","Imports":"RPMG, RSEIS, RFOC, GEOmap,
cluster","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"geophys","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"stats","Title":"Geophysics, Continuum Mechanics, Mogi
Models, Gravity","Version":"1.3-8"},"georob":{"Author":"Andreas Papritz [cre,
aut],\nCornelia Schwierz [ctb]","Depends":"R(>= 2.14.0), sp(>= 0.9-
60)","Description":"Provides functions for efficiently fitting linear models
with\nspatially correlated errors by robust and Gaussian (Restricted)\nMaximum
Likelihood and for computing robust and customary point\nand block external-drift
kriging predictions, along with utility\nfunctions for variogram modelling in ad-
hoc geostatistical analyses,\nmodel building, model evaluation by cross-validation
and for\nunbiased back-transformation of kriging predictions of\nlog-transformed
data.","Imports":"constrainedKriging(>= 0.2-1), lmtest, methods, nlme,
nleqslv,\nquantreg, RandomFields(>= 3.0.10), robustbase(>= 0.90-2),\nsnowfall(>=
1.84-6)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"georob","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"geoR, gstat","Title":"Robust Geostatistical Analysis of
Spatial Data","Version":"0.2-3"},"geoscale":{"Author":"Mark A. Bell
<mark.bell521@gmail.com>.","Description":"Function for adding the geological
timescale to bivariate plots.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"geoscale","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Geological Time Scale
Plotting","Version":"2.0"},"geospacom":{"Author":"Davide Morselli [aut,
cre],\nMathieu Cossuta [aut],\nTill Junge [aut],\nSandra Penic [aut],\nGuy
Elcheroth [ctb],\nStephanie Glaeser [ctb]","Depends":"R(>= 2.15-0), rgeos,
classInt, sp, maptools, geosphere","Description":"Generates distance matrices from
shape files and represents spatially weighted multilevel analysis results (see
'spacom')","Enhances":"spacom","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"geospacom","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Facilitate Generating of Distance Matrices Used in
Package\n'spacom' and Plotting Data on Maps","Version":"0.5-8"},"geosphere":
{"Author":"Robert J. Hijmans [cre, aut],\nEd Williams [ctb],\nChris Vennes
[ctb]","Depends":"sp, R (>= 2.10.0)","Description":"Spherical trigonometry for
geographic applications. That is, compute distances and related measures for
angular (longitude\/latitude) locations.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"geosphere","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"methods, raster","Title":"Spherical
Trigonometry","Version":"1.5-1"},"geospt":{"Author":"Carlos Melo
<cmelo@udistrital.edu.co>, Alí Santacruz, Oscar\nMelo
<oomelom@unal.edu.co>","Depends":"R (>= 2.15.0), gstat, genalg, MASS, sp,
minqa","Description":"Estimation of the variogram through trimmed mean, radial
basis\nfunctions (optimization, prediction and cross-validation),
summary\nstatistics from cross-validation, pocket plot, and design of\noptimal
sampling networks through sequential and simultaneous\npoints
methods.","Imports":"limSolve, fields, gsl, plyr, TeachingDemos,
sgeostat,\ngrDevices, stats, methods, graphics, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"geospt","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Geostatistical Analysis and Design of Optimal Spatial
Sampling\nNetworks","Version":"1.0-2"},"geosptdb":{"Author":"Carlos Melo, Oscar
Melo <oomelom@unal.edu.co>","Depends":"R (>= 2.15.0), FD, StatMatch, fields,
sp","Description":"Spatio-temporal: Inverse Distance Weighting (IDW) and radial
basis functions; optimization, prediction, summary statistics from leave-one-out
cross-validation, adjusting distance-based linear regression model and generation
of the principal coordinates of a new individual from Gower's
distance.","Imports":"minqa, limSolve, gsl, geospt","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"geosptdb","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Spatio-Temporal; Inverse Distance Weighting and Radial
Basis\nFunctions with Distance-Based Regression","Version":"0.5-0"},"geostatsp":
{"Author":"Patrick Brown <patrick.brown@utoronto.ca>[aut, cre], Robert Hijmans
[ctb]","Depends":"Matrix (>= 1.2.0), raster, sp, R (>=
3.0.0)","Description":"Geostatistical modelling facilities using Raster and
SpatialPoints objects are provided. Non-Gaussian models are fit using INLA, and
Gaussian geostatistical models use Maximum Likelihood
Estimation.","Enhances":"spatstat, INLA, diseasemapping","Imports":"abind,
numDeriv, methods,
stats","License":"GPL","NeedsCompilation":"yes","Package":"geostatsp","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"geoR, RandomFields, rgdal,
parallel, mapmisc, ellipse,\npracma, knitr","Title":"Geostatistical Modelling with
Likelihood and Bayes","URL":"http:\/\/r-forge.r-
project.org\/projects\/diseasemapping\/","Version":"1.4.0"},"geotech":
{"Author":"James Kaklamanos <kaklamanosj@merrimack.edu> and\nKyle Elmy
<elmyk@merrimack.edu>","Description":"A compilation of functions for performing
calculations and\ncreating plots that commonly arise in geotechnical engineering
and soil\nmechanics. The types of calculations that are currently included
are:\n(1) phase diagrams and index parameters, (2) grain-size distributions,\n(3)
plasticity, (4) soil classification, (5) compaction, (6) groundwater,\n(7)
subsurface stresses (geostatic and induced), (8) Mohr circle analyses,\n(9)
consolidation settlement and rate, (10) shear strength, (11) bearing\ncapacity,
(12) lateral earth pressures, (13) slope stability, and (14)\nsubsurface
explorations. Geotechnical engineering students, educators,\nresearchers, and
practitioners will find this package useful.","Imports":"graphics,
3","NeedsCompilation":"no","Package":"geotech","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Geotechnical Engineering","Version":"1.0"},"geotools":
{"Author":"Antoine
Lucas","Description":"Tools","License":"GPL","NeedsCompilation":"no","Package":"geo
tools","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Geo
tools","Version":"0.1"},"geotopbricks":{"Author":"Emanuele Cordano, Daniele
Andreis, Fabio Zottele","Depends":"R (>=
2.10),methods,raster,stringr,zoo","Description":"It analyzes raster maps and other
information as input\/output\nfiles from the Hydrological Distributed Model GEOtop.
It contains functions\nand methods to import maps and other keywords from
geotop.inpts file. Some\nexamples with simulation cases of GEOtop 2.0 are presented
in the package.\nAny information about the GEOtop Distributed Hydrological Model
source code\nis available on http:\/\/code.google.com\/p\/geotop\/
or\nhttps:\/\/github.com\/se27xx\/GEOtop. Technical details about the model
are\navailable in Endrizzi et al, 2014\n(http:\/\/www.geosci-model-
dev.net\/7\/2831\/2014\/gmd-7-2831-2014.html).","Imports":"rgdal","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"geotopbricks","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"soilwater","Title":"An R Plug-in for the
Distributed Hydrological Model
GEOtop","URL":"\nhttps:\/\/github.com\/ecor\/geotopbricks,http:\/\/code.google.com\
/p\/geotop\/,https:\/\/github.com\/se27xx\/GEOtop,http:\/\/www.geosci-model-
dev.net\/7\/2831\/2014\/gmd-7-2831-2014.html","Version":"1.3.7.2"},"geozoo":
{"Author":"Barret Schloerke [aut, cre],\nDi Cook [ths],\nHadley Wickham
[ths]","Depends":"R (>= 1.8.0)","Description":"Geometric objects defined in geozoo
can be simulated or displayed in the R package tourr.","Imports":"bitops,
2","NeedsCompilation":"no","Package":"geozoo","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"tourr, roxygen2 (>= 5.0.0), testthat","Title":"Zoo of
Geometric Objects","URL":"http:\/\/schloerke.github.io\/geozoo\/,
http:\/\/www.ggobi.org,\nhttps:\/\/github.com\/schloerke\/geozoo","Version":"0.5.0"
},"gesca":{"Author":"Heungsun Hwang, Sunmee Kim, Sungyoung Lee, Taesung
Park","Description":"Fit a variety of component-based structural equation
2)","NeedsCompilation":"no","Package":"gesca","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Generalized Structured Component Analysis
(GSCA)","Version":"1.0.1"},"gesis":{"Author":"Eric Persson [aut,
cre]","Description":"Provides programmatic access to the GESIS - Leibniz-Institute
for\nthe Social Sciences Data Catalogue\/Datenbestandkatalog (DBK),
which\nmaintains a large repository of data sets related to the social
sciences.","Imports":"RSelenium","License":"CC0","NeedsCompilation":"no","Package":
"gesis","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"knitr,
rmarkdown, xml2","Title":"R Client for GESIS Data Catalogue
(DBK)","Version":"0.1"},"getMet":{"Author":"Andrew Sommerlot [aut, cre],\nDaniel
Fuka [aut],\nZachary Easton [aut]","Depends":"R (>=
3.0.0)","Description":"Hydrologic models often require users to collect and format
input meteorological data. This package contains functions for sourcing,
formatting, and\nediting meteorological data for hydrologic
models.","Imports":"EcoHydRology, jsonlite","License":"GPL-
3","NeedsCompilation":"no","Package":"getMet","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Get Meteorological Data for Hydrologic
Models","Version":"0.3.2"},"getPass":{"Author":"Drew Schmidt [aut, cre],\nWei-Chen
Chen [aut],\nGabor Csardi [ctb] (Improved terminal detection)","Depends":"R (>=
3.0.0)","Description":"A micro-package for reading \"passwords\", i.e.
reading\nuser input with masking, so that the input is not displayed as it\nis
typed. Currently we have support for 'RStudio', the command line\n(every OS), and
any platform where 'tcltk' is present.","Imports":"utils, rstudioapi (>=
0.5)","License":"BSD 2-clause License + file
LICENSE","NeedsCompilation":"yes","Package":"getPass","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"tcltk","Title":"Masked User
Input","URL":"https:\/\/github.com\/wrathematics\/getPass","Version":"0.1-
0"},"getopt":{"Author":"Allen Day.\nContributions from Trevor L
Davis.","Description":"Package designed to be used with Rscript to write\n``#!''
shebang scripts that accept short and long flags\/options.\nMany users will prefer
using instead the packages optparse or argparse\nwhich add extra features like
automatically generated help option and usage,\nsupport for default values,
positional argument support, etc.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"getopt","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat","Title":"C-like getopt
behavior","URL":"https:\/\/github.com\/trevorld\/getopt","Version":"1.20.0"},"gets"
:{"Author":"Genaro Sucarrat [aut, cre], Felix Pretis [aut], James Reade
[aut]","Depends":"R (>= 2.10.0), zoo","Description":"Automated General-to-Specific
(GETS) modelling of the mean and variance of a regression, and indicator saturation
methods for detecting and testing for structural breaks in the
mean.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gets","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"lgarch, xtable","Title":"General-to-Specific (GETS)
Modelling and Indicator Saturation\nMethods","URL":"https:\/\/cran.r-
project.org\/package=gets,\nhttp:\/\/www.sucarrat.net\/R\/gets","Version":"0.7"},"g
ettingtothebottom":{"Author":"Jocelyn T. Chi
<jocelynchi@alum.berkeley.edu>","Depends":"R (>= 3.0.2), ggplot2, grid,
Matrix","Description":"Getting to the Bottom accompanies the \"Getting to\nthe
Bottom\" optimization methods series at Statisticsviews.com. It\ncontains data and
code to reproduce the examples in the articles.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"gettingtothebottom","Repository":"http:
\/\/cran.csiro.au\/src\/contrib","Title":"Learning Optimization and Machine
Learning for
Statistics","URL":"http:\/\/jocelynchi.com\/gettingtothebottom","Version":"3.2"},"g
fcanalysis":{"Author":"Alex Zvoleff [aut, cre]","Depends":"R (>= 2.10.0), raster,
methods","Description":"The gfcanalysis package supports analyses using the
Global\nForest Change dataset released by Hansen et al. gfcanalysis was\nwritten
for the Tropical Ecology Assessment and Monitoring (TEAM)
Network\n(http:\/\/www.teamnetwork.org). For additional details on the Global
Forest\nChange dataset, see: Hansen, M. et al. 2013. \"High-Resolution Global
Maps\nof 21st-Century Forest Cover Change.\" Science 342 (15 November): 850-
53.\nThe forest change data and more information on the product is available
at\nhttp:\/\/earthenginepartners.appspot.com.","Imports":"rgdal, geosphere, RCurl,
rgeos, plyr, ggplot2, grid, sp,\nstringr, animation, rasterVis","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"gfcanalysis","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Tools for Working with Hansen et al. Global Forest
Change\nDataset","URL":"http:\/\/azvoleff.com\/gfcanalysis","Version":"1.4"},"ggExt
ra":{"Author":"Dean Attali [aut, cre]","Depends":"R (>=
3.1.0)","Description":"Collection of functions and layers to enhance 'ggplot2'. The
main\nfunction is ggMarginal(), which can be used to add
marginal\nhistograms\/boxplots\/density plots to 'ggplot2'
scatterplots.","Imports":"ggplot2 (>= 1.0.0), grid (>= 3.1.3), gridExtra (>=
0.9.1),\nmethods, miniUI (>= 0.1.1), shiny (>= 0.11.0), shinyjs (>=\n0.5.2),
LICENSE","NeedsCompilation":"no","Package":"ggExtra","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"knitr (>= 1.7), rmarkdown, rstudioapi (>=
0.5)","Title":"Add Marginal Histograms to 'ggplot2', and More
'ggplot2'\nEnhancements","URL":"https:\/\/github.com\/daattali\/ggExtra","Version":
"0.4.0"},"ggROC":{"Author":"Honglong Wu","Depends":"R (>= 2.14.0),
ggplot2","Description":"package for roc curve plot with ggplot2","License":"GPL (>
2)","NeedsCompilation":"no","Package":"ggROC","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"ggplot2","Title":"package for roc curve plot with
ggplot2","Version":"1.0"},"ggRandomForests":{"Author":"John Ehrlinger
<john.ehrlinger@gmail.com>","Depends":"R (>= 3.1.0)","Description":"Graphic
elements for exploring Random Forests using the\nrandomForestSRC package for
survival, regression and classification forests and\nggplot2 package
plotting.","Imports":"randomForestSRC (>= 1.5.5), ggplot2, survival, parallel,
tidyr","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"ggRandomForests","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"testthat, knitr, RColorBrewer, MASS, dplyr,
plot3D","Title":"Visually Exploring Random
Forests","URL":"https:\/\/github.com\/ehrlinger\/ggRandomForests","Version":"1.2.1"
},"ggThemeAssist":{"Author":"Calli Gross [aut, cre],\nPhilipp Ottolinger [aut,
ctb]","Depends":"R (>= 3.0.0)","Description":"Rstudio add-in that delivers a
graphical interface for editing 'ggplot2' theme elements.","Imports":"shiny (>=
0.13), miniUI (>= 0.1.1), rstudioapi (>= 0.5),\nggplot2, formatR","License":"GPL-
3","NeedsCompilation":"no","Package":"ggThemeAssist","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Add-in to Customize 'ggplot2'
Themes","URL":"https:\/\/github.com\/calligross\/ggthemeassist","Version":"0.1.0"},
"ggalt":{"Author":"Bob Rudis [aut, cre]","Depends":"R (>= 3.0.0), ggplot2 (>=
2.0.0)","Description":"A compendium of 'geoms', 'coords' and 'stats' for 'ggplot2',
including\nsplines, 1d and 2d densities, univariate average shifted histograms
and\na new map coordinate system based on the 'PROJ.4'-
library.","Imports":"graphics, grDevices, dplyr, RColorBrewer, KernSmooth,
proj4,\nscales, grid, gtable, ash, maps, MASS","License":"AGPL + file
LICENSE","NeedsCompilation":"no","Package":"ggalt","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat, gridExtra, knitr, rmarkdown,
ggthemes","Title":"Extra Coordinate Systems, Geoms and Statistical
Transformations\nfor
'ggplot2'","URL":"http:\/\/github.com\/hrbrmstr\/ggalt","Version":"0.1.1"},"ggbeesw
arm":{"Author":"Erik Clarke [aut, cre],\nScott Sherrill-Mix [aut]","Depends":"R (>=
3.0.0), ggplot2 (>= 2.0)","Description":"Provides two methods of plotting
categorical scatter plots such\nthat the arrangement of points within a category
reflects the density of\ndata at that region, and avoids over-
plotting.","Imports":"beeswarm, vipor","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ggbeeswarm","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Categorical Scatter (Violin Point)
Plots","Version":"0.5.0"},"ggcorrplot":{"Author":"Alboukadel Kassambara [aut,
cre]","Depends":"ggplot2","Description":"The 'ggcorrplot' package can be used to
visualize easily a\ncorrelation matrix using 'ggplot2'. It provides a solution for
reordering the\ncorrelation matrix and displays the significance level on the plot.
It also\nincludes a function for computing a matrix of correlation p-
values.","Imports":"reshape2, stats","License":"GPL-
2","NeedsCompilation":"no","Package":"ggcorrplot","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr","Title":"Visualization of a Correlation
Matrix using
'ggplot2'","URL":"http:\/\/www.sthda.com","Version":"0.1.1"},"ggdendro":
{"Author":"Andrie de Vries [aut, cre],\nBrian D. Ripley [aut] (author of package
tree)","Description":"This is a set of tools for dendrograms and\ntree plots using
'ggplot2'. The 'ggplot2' philosophy is to\nclearly separate data from the
presentation.\nUnfortunately the plot method for dendrograms plots\ndirectly to a
plot device without exposing the data.\nThe 'ggdendro' package resolves this by
making available\nfunctions that extract the dendrogram plot data. The
package\nprovides implementations for tree, rpart,
as well as diana and agnes\ncluster diagrams.","Imports":"MASS, ggplot2(>=
0.9.2)","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"ggdendro","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"rpart(>= 4.0-0), tree, testthat, knitr,
cluster","Title":"Create Dendrograms and Tree Diagrams Using
'ggplot2'","URL":"https:\/\/github.com\/andrie\/ggdendro","Version":"0.1-
18"},"gge":{"Author":"Kevin Wright [aut, cre],\nJean-Louis Laffont
[aut]","Description":"Create biplots for GGE (genotype plus genotype-by-
environment) and\nGGB (genotype plus genotype-by-block-of-environments)
models.","Imports":"reshape2","License":"GPL-
2","NeedsCompilation":"no","Package":"gge","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"agridat, knitr","Title":"Genotype Plus Genotype-by-
Environment
Biplots","URL":"https:\/\/github.com\/kwstat\/gge","Version":"1.0"},"ggenealogy":
{"Author":"Lindsay Rutter, Susan Vanderplas, Di Cook","Depends":"R (>=
3.0.2)","Description":"Methods for searching through genealogical data and
displaying the results. Plotting algorithms assist with data exploration and
publication-quality image generation. Uses the Grammar of
Graphics.","Imports":"ggplot2 (>= 1.0.0), igraph (>= 0.7.1), plyr (>=
1.8.1),\nreshape2 (>=
1.4)","License":"GPL","NeedsCompilation":"no","Package":"ggenealogy","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Suggests":"stringr (>= 0.6.2), knitr,
roxygen2 (>= 3.0.0)","Title":"Visualization Tools for Genealogical
Data","Version":"0.1.0"},"ggfortify":{"Author":"Masaaki Horikoshi
<sinhrks@gmail.com> and Yuan Tang\n<terrytangyuan@gmail.com>","Depends":"methods,
proto, ggplot2","Description":"Unified plotting tools for statistics commonly used,
such as GLM,\ntime series, PCA families, clustering and survival analysis. The
package offers\na single plotting interface for these analysis results and plots in
a unified\nstyle using 'ggplot2'.","Imports":"dplyr (>= 0.3), tidyr, gridExtra,
scales","License":"GPL-
2","NeedsCompilation":"no","Package":"ggfortify","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat, cluster, changepoint, dlm, fGarch,
forecast,\nglmnet, grDevices, KFAS, knitr, MASS, MSwM, nlme, stats,\nstrucchange,
survival, timeSeries, tseries, utils, vars, xts,\nzoo, lfda","Title":"Data
Visualization Tools for Statistical Analysis Results","Version":"0.1.0"},"ggiraph":
{"Author":"David Gohel [aut, cre],\nMike Bostock [cph] (d3.js)","Depends":"ggplot2
(>= 2.0.0)","Description":"Create interactive 'ggplot2' graphics that are usable in
the 'RStudio'\nviewer pane, in 'R Markdown' documents and in 'Shiny'
apps.","Imports":"grid, htmlwidgets (>= 0.6), htmltools, stats, plyr, rvg
(>=\n0.0.7), xml2","License":"GPL-
3","NeedsCompilation":"no","Package":"ggiraph","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr, rmarkdown, maps, shiny","Title":"Make 'ggplot2'
Graphics Interactive Using 'htmlwidgets'","Version":"0.2.0"},"gglasso":
{"Author":"Yi Yang <yiyang@umn.edu>, Hui Zou
<hzou@stat.umn.edu>","Description":"This package implements a unified algorithm,
blockwise-majorization-decent (BMD), for efficiently computing the solution paths
of the group-lasso penalized least squares, logistic regression, Huberized SVM and
squared SVM.","License":"GPL-
2","NeedsCompilation":"yes","Package":"gglasso","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Group Lasso Penalized Learning Using A Unified BMD
Algorithm","URL":"http:\/\/code.google.com\/p\/gglasso\/","Version":"1.3"},"ggm":
{"Author":"Giovanni M. Marchetti, Mathias Drton, Kayvan
Sadeghi","Depends":"igraph","Description":"Functions and datasets for maximum
likelihood fitting of some classes of graphical Markov models.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ggm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Functions for graphical Markov
models","Version":"2.3"},"ggmap":{"Author":"David Kahle [aut, cre],\nHadley Wickham
[aut]","Depends":"R (>= 2.14.0), ggplot2 (>= 2.0.0)","Description":"A collection of
functions to visualize spatial data and models\non top of static maps from various
online sources (e.g Google Maps and Stamen\nMaps). It includes tools common to
those tasks, including functions for\ngeolocation and routing.","Imports":"proto,
RgoogleMaps, png, plyr, reshape2, rjson, mapproj, jpeg,\ngeosphere, digest,
scales","License":"GPL-
2","NeedsCompilation":"no","Package":"ggmap","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"MASS, stringr, hexbin, dplyr","Title":"Spatial
Visualization with
ggplot2","URL":"https:\/\/github.com\/dkahle\/ggmap","Version":"2.6.1"},"ggmcmc":
{"Author":"Xavier FernÃ¡ndez i MarÃn <xavier.fim@gmail.com>","Depends":"dplyr,
tidyr (>= 0.3.1), ggplot2","Description":"Tools for assessing and diagnosing
convergence of\nMarkov Chain Monte Carlo simulations, as well as for graphically
display\nresults from full MCMC analysis. The package also facilitates the
graphical\ninterpretation of models by providing flexible functions to plot
the\nresults against observed variables.","Imports":"GGally (>=
2","NeedsCompilation":"no","Package":"ggmcmc","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"coda, knitr, rmarkdown, ggthemes, gridExtra, Cairo,
extrafont","Title":"Tools for Analyzing MCMC Simulations from Bayesian
Inference","URL":"http:\/\/xavier-
fim.net\/packages\/ggmcmc,\nhttps:\/\/github.com\/xfim\/ggmcmc","Version":"0.8"},"g
gnetwork":{"Author":"Francois Briatte","Depends":"ggplot2 (>= 2.0.0), R (>=
3.1),","Description":"Geometries to plot network objects with
'ggplot2'.","Imports":"ggrepel (>= 0.5), network, sna","License":"GPL-
3","NeedsCompilation":"no","Package":"ggnetwork","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"intergraph, knitr, testthat","Title":"Geometries to
Plot Networks with 'ggplot2'","Version":"0.5.1"},"ggparallel":{"Author":"Heike
Hofmann, Marie Vendettuoli","Depends":"R (>= 2.10.0),","Description":"Create
hammock plots, parallel sets, and common angle plots\nwith
ggplot2.","Imports":"ggplot2 (>= 0.9.2), reshape2, plyr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"ggparallel","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"RColorBrewer","Title":"Variations of Parallel
Coordinate Plots for Categorical
Data","URL":"http:\/\/github.com\/heike\/ggparallel","Version":"0.1.2"},"ggplot2":
{"Author":"Hadley Wickham [aut, cre],\nWinston Chang [aut],\nRStudio
[cph]","Depends":"R (>= 3.1)","Description":"An implementation of the grammar of
graphics in R. It combines the\nadvantages of both base and lattice graphics:
conditioning and shared axes\nare handled automatically, and you can still build up
a plot step by step\nfrom multiple data sources. It also implements a
sophisticated\nmultidimensional conditioning system and a consistent interface to
map\ndata to aesthetic attributes. See http:\/\/ggplot2.org for more
information,\ndocumentation and examples.","Enhances":"sp","Imports":"digest, grid,
gtable (>= 0.1.1), MASS, plyr (>= 1.7.1),\nreshape2, scales (>= 0.3.0),
2","NeedsCompilation":"no","Package":"ggplot2","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"covr, ggplot2movies, hexbin, Hmisc, lattice, mapproj,
maps,\nmaptools, mgcv, multcomp, nlme, testthat (>= 0.11.0), quantreg,\nknitr,
rpart, rmarkdown, svglite","Title":"An Implementation of the Grammar of
Graphics","URL":"http:\/\/ggplot2.org,
https:\/\/github.com\/hadley\/ggplot2","Version":"2.1.0"},"ggplot2movies":
{"Author":"Hadley Wickham [aut, cre],\nRStudio [cph]","Depends":"R (>=
2.10.0)","Description":"A dataset about movies. This was previously contained in
ggplot2,\nbut has been moved its own package to reduce the download size of
ggplot2.","License":"GPL-
3","NeedsCompilation":"no","Package":"ggplot2movies","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Movies Data","Version":"0.0.1"},"ggpmisc":
{"Author":"Pedro J. Aphalo [aut, cre]","Depends":"R (>=
3.2.0)","Description":"Extensions to 'ggplot2' respecting the grammar of
graphics\nparadigm. Provides new statistics to locate and tag peaks and valleys in
2D\nplots, a statistics to add a label with the equation of a polynomial
fitted\nwith lm(), or R^2 or adjusted R^2 or information criteria for any
model\nfitted with function lm(). Provides a function for flexibly converting
time\nseries to data frames suitable for plotting with ggplot(). In
addition\nprovides two statistics and two geometry useful for diagnosing what data
are\npassed to compute_group() and compute_panel() functions and to
geometries.","Imports":"ggplot2 (>= 2.0.0), polynom (>= 1.3-8), splus2R (>= 1.2-
0),\ndplyr (>= 0.4.3), xts (>= 0.9-7), zoo (>= 1.7-12), lubridate\n(>=
1.5.0)","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"ggpmisc","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr (>= 1.12.3), rmarkdown (>=
0.9.2)","Title":"Miscellaneous Extensions to
'ggplot2'","URL":"http:\/\/www.r4photobiology.info","Version":"0.2.7"},"ggraptR":
{"Author":"Eugene Dubossarsky [aut, cph, cre],\nJulius Neggo [ctb] (Lead
Developer),\nHoward Song [aut] (Developer),\nSusan Wang [ctb] (Project
Manager),\nJason Widjaja [ctb] (Vignette),\nJose Magana [ctb] (Package Manager and
Developer)","Depends":"R (>= 3.1.0), ggplot2 (>= 1.0.1), ggthemes (>= 2.2.1),
shinyjs\n(>= 0.2.0), shinyBS(>= 0.61)","Description":"Intended for both technical
and non-technical users to create\ninteractive data visualizations through a web
browser GUI without writing any\ncode.","Imports":"shiny (>= 0.12.2), dplyr(>=
0.4.3), DT (>= 0.1), futile.logger\n(>= 1.4.1)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ggraptR","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr","Title":"Allows Interactive Visualization of
Data Through a Web Browser\nGUI","Version":"0.1"},"ggrepel":{"Author":"Kamil
Slowikowski [aut, cre]","Depends":"R (>= 3.0.0), ggplot2 (>=
2.0.0)","Description":"\nProvides text and label geoms for 'ggplot2' that help to
avoid overlapping\ntext labels. Labels repel away from each other and away from the
data\npoints.","Imports":"grid, Rcpp","License":"GPL-
2","NeedsCompilation":"yes","Package":"ggrepel","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr, rmarkdown","Title":"Repulsive Text and Label
Geoms for
'ggplot2'","URL":"http:\/\/github.com\/slowkow\/ggrepel","Version":"0.5"},"ggsci":
{"Author":"Nan Xiao <nanx@uchicago.edu>, Miaozhu Li
<miaozhu.li@duke.edu>","Depends":"R (>= 3.0.2)","Description":"A collection of
'ggplot2' color palettes inspired by scientific journals and science fiction TV
shows.","Imports":"grDevices, scales, ggplot2 (>=
2.0.0)","License":"GPL","NeedsCompilation":"no","Package":"ggsci","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Suggests":"knitr, rmarkdown,
gridExtra","Title":"Scientific Journal and Sci-Fi Themed Color Palettes
for\n'ggplot2'","URL":"http:\/\/ggsci.net","Version":"1.1"},"ggseas":
{"Author":"Peter Ellis [aut, cre],\nChristophe Sax [ctb]","Depends":"R (>= 3.1.2),
seasonal, ggplot2 (>= 2.0.0), stats, zoo","Description":"Provides 'ggplot2' 'stats'
that estimate seasonally adjusted series\nand rolling summaries such as rolling
average on the fly for time series.","License":"GPL-
3","NeedsCompilation":"no","Package":"ggseas","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat","Title":"'stats' for Seasonal Adjustment on
the Fly with 'ggplot2'","Version":"0.4.0"},"ggsn":{"Author":"Oswaldo Santos Baquero
[aut, cre]","Depends":"R (>= 3.2.1), ggplot2","Description":"Adds north symbols (18
options) and scale bars in kilometers to\nmaps in geographic or metric coordinates
created with 'ggplot2' or 'ggmap'.","Imports":"png, grid, maptools,
2)","NeedsCompilation":"no","Package":"ggsn","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"rgdal, ggmap, rgeos","Title":"North Symbols and Scale
Bars for Maps Created with 'ggplot2'
or\n'ggmap'","URL":"https:\/\/github.com\/oswaldosantos\/ggsn","Version":"0.3.0"},"
ggspectra":{"Author":"Pedro J. Aphalo [aut, cre]","Depends":"R (>=
3.2.0)","Description":"Additional annotations, stats and scales for
plotting \"light\"\nspectra with 'ggplot2', together with specializations of
ggplot()\nand plot() methods for spectral data stored in objects of the
classes\ndefined in package 'photobiology' and a plot() method for objects
of\nclass \"waveband\", also defined in package
'photobiology'.","Imports":"photobiology (>= 0.9.5), photobiologyWavebands (>=
0.3.5),\nggplot2 (>= 2.0.0), scales (>= 0.3.0), dplyr (>= 0.4.3),\nlubridate (>=
1.5.0), tidyr (>= 0.4.0)","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"ggspectra","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr, rmarkdown","Title":"Extensions to 'ggplot2'
for Radiation
Spectra","URL":"http:\/\/www.r4photobiology.info,\nhttps:\/\/bitbucket.org\/aphalo\
/ggspectra","Version":"0.1.6"},"ggswissmaps":{"Author":"Sandro Petrillo Burri [aut,
cre],\nEric Stephani [aut],\nLisa Bottinelli [ctb]","Depends":"R (>= 2.14), ggplot2
(>= 2.0.0)","Description":"Offers various swiss maps as ggplot2 objects and gives
the\npossibility to add layers of data on the maps. Data are publicly
available\nfrom the swiss federal statistical office.","License":"GPL-
2","NeedsCompilation":"no","Package":"ggswissmaps","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"plyr, reshape2, testthat, data.table,
knitr","Title":"Offers Various Swiss Maps as ggplot2
Objects","Version":"0.0.8"},"ggtern":{"Author":"Nicholas Hamilton [aut,
cre]","Depends":"ggplot2 (>= 2.1.0)","Description":"Extends the functionality of
'ggplot2', providing the capability\nto plot ternary diagrams for (subset of) the
'ggplot2' geometries. Additionally,\n'ggtern' has implemented several NEW
geometries which are unavailable to the\nstandard 'ggplot2' release. For further
examples and documentation, please\nproceed to the 'ggtern'
website.","Enhances":"sp","Imports":"compositions, grid, gridExtra, gtable (>=
0.1.1), latex2exp\n(>= 0.3.3), MASS, plyr (>= 1.7.1), scales (>= 0.3.0),
stats,\nproto, utils, lattice","License":"GPL-
2","NeedsCompilation":"no","Package":"ggtern","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"An Extension to 'ggplot2', for the Creation of Ternary
Diagrams","URL":"http:\/\/www.ggtern.com","Version":"2.1.1"},"ggthemes":
{"Author":"Jeffrey B. Arnold [aut, cre],\nGergely Daroczi [ctb],\nBo Werth
[ctb],\nBrian Weitzner [ctb],\nJoshua Kunst [ctb],\nBaptise Auguie [ctb],\nBob
Rudis [ctb],\nHadley Wickham [ctb, cph] (Code from the ggplot2 package.),\nJustin
Talbot [ctb] (Code from the labeling package)","Depends":"R (>=
3.0.0),","Description":"Some extra themes, geoms, and scales for
'ggplot2'.\nProvides 'ggplot2' themes and scales that replicate the look of
plots\nby Edward Tufte, Stephen Few, 'Fivethirtyeight', 'The Economist',
'Stata',\n'Excel', and 'The Wall Street Journal', among others.\nProvides 'geoms'
for Tufte's box plot and range frame.","Imports":"assertthat, colorspace, ggplot2
(>= 2.0.0), graphics, grid,\nmethods, scales","License":"GPL-
2","NeedsCompilation":"no","Package":"ggthemes","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"extrafont, knitr, lintr, maps, mapproj, pander,
plyr,\nreshape2, rmarkdown, testthat","Title":"Extra Themes, Scales and Geoms for
'ggplot2'","URL":"http:\/\/github.com\/jrnold\/ggthemes","Version":"3.0.3"},"ggvis"
:{"Author":"Winston Chang [aut, cre],\nHadley Wickham [aut],\nRStudio
[cph],\njQuery Foundation [cph] (jQuery library and jQuery UI library),\njQuery
contributors [ctb, cph] (jQuery library; authors listed
in\ninst\/www\/lib\/jquery\/AUTHORS.txt),\njQuery UI contributors [ctb, cph]
(jQuery UI library; authors listed in\ninst\/www\/lib\/jquery-
ui\/AUTHORS.txt),\nMike Bostock [ctb, cph] (D3 library),\nD3 contributors [ctb] (D3
library; authors listed
at\nhttps:\/\/github.com\/mbostock\/d3\/graphs\/contributors),\nTrifacta Inc. [cph]
(Vega library),\nVega contributors [ctb] (Vega library; authors listed
at\nhttps:\/\/github.com\/trifacta\/vega\/graphs\/contributors),\nSebasti<c3><a1>n
D<c3><a9>cima [ctb, cph]\n(javascript-detect-element-resize library)","Depends":"R
(>= 3.0)","Description":"An implementation of an interactive grammar of graphics,
taking the\nbest parts of 'ggplot2', combining them with the reactive framework
from\n'shiny' and web graphics from 'vega'.","Imports":"assertthat, jsonlite (>=
0.9.11), shiny (>= 0.11.1), magrittr,\ndplyr (>= 0.4.0), lazyeval, htmltools (>=
0.2.4)","License":"GPL-2 | file
LICENSE","NeedsCompilation":"no","Package":"ggvis","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"MASS, mgcv, lubridate, testthat (>= 0.8.1), knitr
(>= 1.6),\nrmarkdown","Title":"Interactive Grammar of
Graphics","URL":"http:\/\/ggvis.rstudio.com\/","Version":"0.4.2"},"ghit":
{"Author":"Thomas J. Leeper [aut, cre]","Description":"A lightweight, vectorized
drop-in replacement for 'devtools::install_github()' that uses native git and R
methods to clone and install a package from GitHub.","Imports":"utils, tools,
git2r","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"ghit","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat","Title":"Lightweight GitHub Package
Installer","URL":"https:\/\/github.com\/leeper\/ghit","Version":"0.2.5"},"ghyp":
{"Author":"David Luethi, Wolfgang Breymann","Depends":"R(>= 2.7), methods,
numDeriv, graphics, stats, gplots","Description":"This package provides detailed
functionality for working\nwith the univariate and multivariate Generalized
Hyperbolic\ndistribution and its special cases (Hyperbolic (hyp), Normal\nInverse
Gaussian (NIG), Variance Gamma (VG), skewed Student-t\nand Gaussian distribution).
Especially, it contains fitting\nprocedures, an AIC-based model selection routine,
and functions\nfor the computation of density, quantile, probability,
random\nvariates, expected shortfall and some portfolio optimization\nand plotting
routines as well as the likelihood ratio test. In\naddition, it contains the
Generalized Inverse Gaussian\ndistribution.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ghyp","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"A package on the generalized hyperbolic distribution and
its\nspecial cases","Version":"1.5.6"},"giRaph":{"Author":"Jens Henrik Badsberg,
Claus Dethlefsen, Luca La Rocca","Depends":"R (>= 2.4.0), graphics,
methods","Description":"Supply classes and methods to represent and
manipulate\ngraphs","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"giRaph","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"mathgraph, dynamicGraph","Title":"The giRaph package
for graph representation in
R","URL":"http:\/\/r.kvfc.dk\/giRaph","Version":"0.1.2"},"gibbs.met":
{"Author":"Longhai Li <longhai@math.usask.ca>","Depends":"R (>=
2.5.1)","Description":"This package provides two generic functions for
performing\nMarkov chain sampling in a naive way for a user-defined
target\ndistribution, which involves only continuous variables.
The\nfunction \"gibbs_met\" performs Gibbs sampling with each\n1-dimensional
distribution sampled with Metropolis update using\nGaussian proposal distribution
centered at the previous state.\nThe function \"met_gaussian\" updates the whole
state with\nMetropolis method using independent Gaussian proposal\ndistribution
centered at the previous state. The sampling is\ncarried out without considering
any special tricks for\nimproving efficiency. This package is aimed at only
routine\napplications of MCMC in moderate-dimensional problems.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gibbs.met","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Naive
Gibbs Sampling with Metropolis Steps","URL":"\\url{http:\/\/www.r-
project.org},\n\\url{http:\/\/math.usask.ca\/~longhai}","Version":"1.1-3"},"gimme":
{"Author":"Stephanie Lane [aut, cre, trl],\nKathleen Gates [aut],\nPeter Molenaar
[aut],\nMichael Hallquist [ctb],\nHallie Pike [ctb]","Depends":"R (>=
3.0.2)","Description":"Automated identification and estimation of group-
and\nindividual-level relations in time series data from within a
structural\nequation modeling framework.","Imports":"lavaan (>= 0.5-19), MASS,
doSNOW, foreach, snow, igraph,\nqgraph, parallel, doParallel,
gWidgets2","License":"GPL-
2","NeedsCompilation":"no","Package":"gimme","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"gWidgets2RGtk2","Title":"Group Iterative Multiple Model
Estimation","Version":"0.1-6"},"gimms":{"Author":"Florian Detsch [cre,
aut]","Depends":"raster, methods","Description":"We provide a set of functions to
retrieve information about GIMMS NDVI3g files currently available online; download
and re-arrange the bi-monthly datasets according to creation time; import
downloaded files from native binary (ENVI) format directly into R based on the
widely applied 'raster' package; extract accompanying quality flags and perform
quality control; calculate monthly value composites (e.g. maximum value composites,
MVC) from the bi-monthly input data; and derive long-term monotonous trends from
the Mann-Kendall trend test, optionally featuring pre-whitening to account for lag-
1 autocorrelation.","Imports":"parallel, doParallel, foreach, Kendall,
zyp","License":"GPL (>= 3) | file
LICENSE","NeedsCompilation":"no","Package":"gimms","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Download and Process GIMMS NDVI3g
Data","Version":"0.5.1"},"gistr":{"Author":"Ramnath Vaidyanathan [aut],\nKarthik
Ram [aut],\nScott Chamberlain [aut, cre]","Description":"Work with 'GitHub' 'gists'
from 'R' (e.g., http:\/\/en.wikipedia.org\/\nwiki\/GitHub#Gist,
https:\/\/help.github.com\/articles\/about-gists\/). A 'gist'\nis simply one or
more files with code\/text\/images\/etc. This package allows\nthe user to create
new 'gists', update 'gists' with new files, rename files,\ndelete files, get and
delete 'gists', star and 'un-star' 'gists', fork 'gists',\nopen a 'gist' in your
default browser, get embed code for a 'gist', list\n'gist' 'commits', and get rate
limit information when 'authenticated'. Some\nrequests require authentication and
some do not. 'Gists' website: https:\/\/\ngist.github.com\/.","Imports":"utils,
methods, stats, jsonlite, httr (>= 1.0.0), magrittr,\nassertthat, knitr, rmarkdown,
dplyr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"gistr","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"git2r, testthat","Title":"Work with 'GitHub'
'Gists'","URL":"https:\/\/github.com\/ropensci\/gistr","Version":"0.3.6"},"git2r":
{"Author":"See AUTHORS file.","Depends":"R (>= 3.0.2),
methods","Description":"Interface to the 'libgit2' library, which is a pure
C\nimplementation of the 'Git' core methods. Provides access to 'Git'\nrepositories
to extract data and running some basic 'Git'\ncommands.","Imports":"graphics,
2","NeedsCompilation":"yes","Package":"git2r","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Provides Access to Git
Repositories","URL":"https:\/\/github.com\/ropensci\/git2r","Version":"0.14.0"},"gi
tlabr":{"Author":"Jirka Lewandowski [aut, cre]","Depends":"R (>= 3.1.2),
magrittr","Description":"Provides R functions to access the API of the project
and\nrepository management web application gitlab. For many common tasks
(repository\nfile access, issue assignment and status, commenting) convenience
wrappers\nare provided, and in addition the full API can be used by specifying
request\nlocations. Gitlab is open-source software and can be self-hosted or used
on\ngitlab.com.","Imports":"dplyr (>= 0.4.3), stringr, base64enc, httr (>=
1.1.0),\nfunctional","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"gitlabr","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"devtools (>= 1.8.0), roxygen2, testthat, R.rsp,
knitr","Title":"Access to the Gitlab API","URL":"http:\/\/blog.points-of-
interest.cc\/post\/gitlabr\/\nhttp:\/\/doc.gitlab.com\/ce\/
api\/","Version":"0.6.4"},"gitter":{"Author":"Omar Wagih, Leopold
Parts","Description":"The goal of this package is to allow users to robustly\nand
quickly grid and quantify sizes of pinned colonies in plate images.\ngitter works
by first finding the grid of colonies from a preprocessed image and then locating
the bounds of each colony separately.\nIt includes several image pre-processing
techniques, such\nas autorotation of plates, noise removal, contrast adjustment and
image\nresizing.","Imports":"jpeg, tiff, logging, PET, ggplot2, EBImage (>=
4.11.24)","License":"LGPL","NeedsCompilation":"no","Package":"gitter","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Title":"Quantification of Pinned Microbial
Cultures","Version":"1.1.1"},"gjam":{"Author":"James S. Clark","Depends":"R (>=
2.10)","Description":"Analyzes joint attribute data (e.g., species abundance) that
are combinations of continuous and discrete data with Gibbs
sampling.","Imports":"Rcpp (>= 0.11.5)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"gjam","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"knitr","Title":"Generalized Joint Attribute
Modeling","Version":"1.0"},"gkmSVM":{"Author":"Mahmoud
Ghandi","Description":"Imports the 'gkmSVM' v2.0 functionalities into R
(www.beerlab.org\/gkmsvm). It also uses the 'kernlab' library (separate R package
by different authors) for various SVM algorithms.","Imports":"Rcpp, kernlab,
seqinr, utils, ROCR","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"gkmSVM","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Gapped-Kmer Support Vector
Machine","Version":"0.65"},"glamlasso":{"Author":"Adam
Lund","Description":"Efficient design matrix free procedure for Lasso regularized
estimation in large scale 3-dimensional generalized linear array models. The
Gaussian model with identity link, the Binomial model with logit link, the Poisson
model with log link and the Gamma model with log link is currently
implemented.","Imports":"Rcpp (>= 0.11.2)","License":"GPL-
3","NeedsCompilation":"yes","Package":"glamlasso","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Lasso Penalization in Large Scale Generalized Linear
Array\nModels","Version":"1.0"},"glarma":{"Author":"William T.M. Dunsmuir
<w.dunsmuir@unsw.edu.au>, Cenanning Li\n<cli113@aucklanduni.ac.nz>, and David J.
Scott\n<d.scott@auckland.ac.nz>","Depends":"R (>= 2.3.0)","Description":"Functions
are provided for estimation, testing, diagnostic checking and forecasting of
generalized linear autoregressive moving average (GLARMA) models for discrete
valued time series with regression variables. These are a class of observation
driven non-linear non-Gaussian state space models. The state vector consists of a
linear regression component plus an observation driven component consisting of an
autoregressive-moving average (ARMA) filter of past predictive residuals. Currently
three distributions (Poisson, negative binomial and binomial) can be used for the
response series. Three options (Pearson, score-type and unscaled) for the residuals
in the observation driven component are available. Estimation is via maximum
likelihood (conditional on initializing values for the ARMA process) optimized
using Fisher scoring or Newton Raphson iterative methods. Likelihood ratio and Wald
tests for the observation driven component allow testing for serial dependence in
generalized linear model settings. Graphical diagnostics including model fits,
autocorrelation functions and probability integral transform residuals are included
in the package. Several standard data sets are included in the
package.","Imports":"MASS","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"glarma","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"RUnit, knitr, zoo","Title":"Generalized Linear
Autoregressive Moving Average Models","Version":"1.4-0"},"glasso":{"Author":"Jerome
Friedman, Trevor Hastie and Rob Tibshirani","Description":"Graphical
lasso","License":"GPL-
2","NeedsCompilation":"yes","Package":"glasso","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Graphical lasso- estimation of Gaussian graphical
models","URL":"http:\/\/www-
stat.stanford.edu\/~tibs\/glasso","Version":"1.8"},"glba":{"Author":"Ingmar
Visser","Depends":"R (>= 3.1.2)","Description":"Analyses response times and
accuracies from psychological experiments with the linear ballistic accumulator
(LBA) model from Brown and Heathcote (2008). The LBA model is optionally fitted
with explanatory variables on the parameters such as the drift rate, the boundary
and the starting point parameters. A log-link function on the linear predictors can
be used to ensure that parameters remain positive when
needed.","License":"GPL","NeedsCompilation":"no","Package":"glba","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Title":"General Linear Ballistic Accumulator
Models","Version":"0.2"},"glcm":{"Author":"Alex Zvoleff [aut, cre]","Depends":"R
(>= 2.10.0)","Description":"Enables calculation of image textures derived from
grey-level\nco-occurrence matrices (GLCMs). Supports processing images that
cannot\nfit in memory.","Imports":"Rcpp (>= 0.11.0)","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"glcm","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"raster, testthat (>= 0.8.0)","Title":"Calculate Textures
from Grey-Level Co-Occurrence
Matrices\n(GLCMs)","URL":"http:\/\/www.azvoleff.com\/glcm","Version":"1.6.1"},"gld"
:{"Author":"Robert King <Robert.King@newcastle.edu.au>,\nBenjamin Dean
<Benjamin.Dean@uon.edu.au>, Sigbert Klinke","Description":"The
generalised lambda distribution, or Tukey lambda distribution, provides a wide
variety of shapes with one functional form.\nThis package provides random numbers,
quantiles, probabilities, densities and density quantiles for four different
parameterisations of the distribution.\nIt provides the density function,
distribution function, and Quantile-Quantile plots.\nIt implements a variety of
estimation methods for the distribution, including diagnostic plots.\nEstimation
methods include the starship (all 4 parameterisations) and a number of methods for
only the FKML parameterisation.\nThese include maximum likelihood, maximum product
of spacings, Titterington's method, Moments, L-Moments, Trimmed L-Moments and
Distributional Least Absolutes.","Imports":"stats, graphics, e1071","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"gld","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"lmom","Title":"Estimation and Use of the Generalised
(Tukey)
Lambda\nDistribution","URL":"\nhttp:\/\/tolstoy.newcastle.edu.au\/~rking\/publ\/rpr
ogs\/information.html","Version":"2.3.2"},"gldist":{"Author":"Yohan Chalabi and
Diethelm Wuertz","Depends":"R (>= 2.14.0)","Description":"The generalized lambda
distribution (GLD) is a versatile\ndistribution that can accommodate a wide range
of shapes,\nincluding fat-tailed and asymmetric distributions. This
package\nimplements a more intuitive parameterization of the GLD that\nexpresses
the location and scale parameters directly as the\nmedian and inter-quartile range
of the distribution. The\nremaining two shape parameters characterize the asymmetry
and\nsteepness of the distribution respectively. The fitting of the\nGLD to
empirical data can be reduced to a two-parameter\nestimation problem where the
location and scale parameters are\nestimated by their robust sample estimators.
Moreover, the\nparameterization can be used to compare data sets in a\nconvenient
asymmetry and steepness shape plot. The underline C\nroutines are written such that
compilers that support\nvectorized mathematical operations can automatically
vectorize\nthe most time consuming loops (tested with icc 12.1.0). The\npackage
includes the usual distribution functions, fitting\nroutines and a shape plot
function.","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"gldist","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"RUnit","Title":"An Asymmetry-Steepness Parameterization
of the Generalized\nLambda Distribution","Version":"2160.2"},"glinternet":
{"Author":"Michael Lim, Trevor Hastie","Description":"Group-Lasso INTERaction-NET.
Fits linear pairwise-interaction models that satisfy strong hierarchy: if an
interaction coefficient is estimated to be nonzero, then its two associated main
effects also have nonzero estimated coefficients. Accommodates categorical
variables (factors) with arbitrary numbers of levels, continuous variables, and
combinations thereof. Implements the machinery described in the paper \"Learning
interactions via hierarchical group-lasso regularization\" (JCGS
2014).","License":"GPL-
2","NeedsCompilation":"yes","Package":"glinternet","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"ggplot2","Title":"Learning Interactions via
Hierarchical Group-
Lasso\nRegularization","URL":"http:\/\/web.stanford.edu\/~hastie\/Papers\/glinterne
t_jcgs.pdf","Version":"1.0.0"},"gllm":{"Author":"David Duffy
<David.Duffy@qimr.edu.au>.\nC code in emgllmfitter by Andreas Borg <borg@imbei.uni-
mainz.de>","Depends":"R (>= 0.99)","Description":"Routines for log-linear models of
incomplete contingency tables,\nincluding some latent class models, via EM and
Fisher scoring\napproaches. Allows bootstrapping.","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"gllm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Generalised log-linear
model","URL":"http:\/\/www.qimr.edu.au\/davidD","Version":"0.35"},"glm.ddR":
{"Author":"Vishrut Gupta, Arash Fard","Depends":"R (>=
3.0.0)","Description":"Distributed training and prediction of generalized linear
models using 'ddR' (Distributed Data Structures) API in the 'ddR'
package.","Imports":"ddR, stats, Matrix","License":"GPL (>= 2) | file
LICENSE","NeedsCompilation":"no","Package":"glm.ddR","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat","Title":"Distributed 'glm' for Big Data
using 'ddR' API","Version":"0.1.0"},"glm2":{"Author":"Ian Marschner (using code
from glm and glm.fit in the stats package)","Depends":"R (>= 2.12.1),
stats","Description":"Fits generalized linear models using the same model
specification as glm in the stats package, but with a modified default fitting
method that provides greater stability for models that may fail to converge using
glm","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"glm2","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Fitting Generalized Linear
Models","Version":"1.1.2"},"glmc":{"Author":"Sanjay Chaudhuri
<sanjay@stat.nus.edu.sg>, Mark S. Handcock\n<handcock@stat.ucla.edu>, Michael S.
Rendall\n<mrendall@rand.org>.","Depends":"emplik","Description":"Fits generalized
linear models where the parameters are\nsubject to linear constraints. The model is
specified by giving\na symbolic description of the linear predictor, a
description\nof the error distribution, and a matrix of constraints on
the\nparameters.","License":"GPL-
2","NeedsCompilation":"no","Package":"glmc","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Fitting Generalized Linear Models Subject to
Constraints","Version":"0.2-4"},"glmdm":{"Author":"Jeff Gill, George Casella,
Minjung Kyung, and Jonathan Rapkin","Depends":"R (>= 2.10.0)","Description":"This
package contains functions to perform generalized\nlinear mixed Dirichlet models
using posterior
simulation.","License":"GPL","NeedsCompilation":"no","Package":"glmdm","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Title":"R Code for Simulation of
GLMDM","Version":"2.60"},"glmgraph":{"Author":"Li Chen, Jun Chen","Depends":"Rcpp
(>= 0.11.0)","Description":"We propose to use sparse regression model to achieve
variable selection while accounting for graph-constraints among coefficients.
Different linear combination of a sparsity penalty(L1) and a smoothness(MCP)
penalty has been used, which induces both sparsity of the solution and certain
smoothness on the linear coefficients.","License":"GPL-
2","NeedsCompilation":"yes","Package":"glmgraph","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Graph-Constrained Regularization for Sparse Generalized
Linear\nModels","Version":"1.0.3"},"glmlep":{"Author":"Canhong Wen, Hao
Lin","Description":"Efficient algorithms for fitting regularization paths
for\nlinear or logistic regression models penalized by LEP.","License":"GPL-
2","NeedsCompilation":"yes","Package":"glmlep","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"mvtnorm","Title":"Fit GLM with LEP-based penalized
maximum likelihood","Version":"0.1"},"glmm":{"Author":"Christina
Knudson","Depends":"R (>= 3.1.1), trust, mvtnorm,
Matrix","Description":"Approximates the likelihood of a generalized linear mixed
model using Monte Carlo likelihood approximation. Then maximizes the likelihood
approximation to return maximum likelihood estimates, observed Fisher information,
and other model information.","Imports":"stats","License":"GPL-
2","NeedsCompilation":"yes","Package":"glmm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr","Title":"Generalized Linear Mixed Models via Monte
Carlo Likelihood\nApproximation","Version":"1.0.4"},"glmmBUGS":{"Author":"Patrick
Brown","Depends":"R (>= 3.0.0)","Description":"Write bugs model files for
hierarchical and spatial models, arranges unbalanced data in ragged arrays, and
creates starting values.","Enhances":"R2WinBUGS, R2OpenBUGS, BRugs, R2jags, sp,
nlme","Imports":"MASS,
abind,","License":"GPL","NeedsCompilation":"no","Package":"glmmBUGS","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Suggests":"spdep","Title":"Generalised
Linear Mixed Models and Spatial Models with WinBUGS,\nBRugs, or
OpenBUGS","Version":"2.3"},"glmmGS":{"Author":"Michele Morara, Louise Ryan,
Subharup Guha, Christopher\nPaciorek","Description":"Solve Generalized Linear Mixed
Models using Gauss-
Seidel\nalgorithm","License":"GPL","NeedsCompilation":"yes","Package":"glmmGS","Rep
ository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Gauss-Seidel Generalized
Linear Mixed Model solver","URL":"http:\/\/r-forge.r-
project.org\/projects\/glmmgs\/","Version":"0.5-1"},"glmmLasso":{"Author":"Andreas
Groll","Description":"A variable selection approach for generalized linear mixed
models by L1-penalized estimation is provided.","Imports":"minqa,
Matrix","License":"GPL-
2","NeedsCompilation":"no","Package":"glmmLasso","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Variable Selection for Generalized Linear Mixed Models
by\nL1-Penalized Estimation","Version":"1.4.1"},"glmmML":{"Author":"GÃ¶ran
BrostrÃ¶m","Depends":"R (>= 2.13.0), stats","Description":"Binomial and Poisson
regression for clustered data, fixed\nand random effects with
bootstrapping.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"glmmML","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Generalized linear models with
clustering","Version":"1.0"},"glmmsr":{"Author":"Helen Ogden [aut,
cre]","Depends":"R (>= 3.1.2)","Description":"Conduct inference about generalized
linear mixed models, with a\nchoice about which method to use to approximate the
likelihood. In addition\nto the Laplace and adaptive Gaussian quadrature
approximations, which are\nborrowed from 'lme4', the likelihood may be approximated
by the sequential\nreduction approximation, or an importance sampling
approximation. These\nmethods provide an accurate approximation to the likelihood
in some\nsituations where it
is not possible to use adaptive Gaussian quadrature.","Imports":"lme4 (>= 1.1-8),
Matrix, R6, Rcpp, methods, stats, utils","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"glmmsr","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"BradleyTerry2, hglm.data, knitr, rmarkdown,
testthat","Title":"Fit a Generalized Linear Mixed
Model","URL":"http:\/\/github.com\/heogden\/glmmsr","Version":"0.1.1"},"glmnet":
{"Author":"Jerome Friedman, Trevor Hastie, Noah Simon, Rob
Tibshirani","Depends":"Matrix (>= 1.0-6), utils, foreach","Description":"Extremely
efficient procedures for fitting the entire lasso or elastic-net regularization
path for linear regression, logistic and multinomial regression models, Poisson
regression and the Cox model. Two recent additions are the multiple-response
Gaussian, and the grouped multinomial. The algorithm uses cyclical coordinate
descent in a path-wise fashion, as described in the paper linked to via the URL
below.","Imports":"methods","License":"GPL-
2","NeedsCompilation":"yes","Package":"glmnet","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"survival, knitr, lars","Title":"Lasso and Elastic-Net
Regularized Generalized Linear
Models","URL":"http:\/\/www.jstatsoft.org\/v33\/i01\/.","Version":"2.0-
5"},"glmnetcr":{"Author":"Kellie J. Archer","Depends":"R (>= 2.10),
glmnet","Description":"This packages includes functions for restructuring an
ordinal response dataset for fitting continuation ratio models for datasets\nwhere
the number of covariates exceeds the sample size or when there is collinearity
among the covariates. This package uses the glmnet package\nfitting
2","NeedsCompilation":"no","Package":"glmnetcr","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"tools","Title":"Fit a penalized constrained
continuation ratio model for\npredicting an ordinal
response","Version":"1.0.2"},"glmpath":{"Author":"Mee Young Park, Trevor
Hastie","Depends":"survival, R (>= 2.0)","Description":"A path-following algorithm
for L1 regularized generalized\nlinear models and Cox proportional hazards
2)","NeedsCompilation":"yes","Package":"glmpath","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"L1 Regularization Path for Generalized Linear Models and
Cox\nProportional Hazards Model","Version":"0.97"},"glmpathcr":{"Author":"Kellie J.
Archer","Depends":"R (>= 2.10), glmpath, mvtnorm","Description":"Provides a
function for fitting a penalized constrained continuation ratio model using the
glmpath algorithm and methods for extracting coefficient estimates, predicted
class, class probabilities, and plots.","License":"GPL-
2","NeedsCompilation":"no","Package":"glmpathcr","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"tools","Title":"Fit a penalized continuation ratio
model for predicting an\nordinal response","Version":"1.0.3"},"glmulti":
{"Author":"Vincent Calcagno <vincent.calcagno@sophia.inra.fr>","Depends":"R (>=
2.13.0), rJava (>= 0.5-0), methods","Description":"Automated model selection and
model-averaging. Provides a\nwrapper for glm and other functions, automatically
generating\nall possible models (under constraints set by the user) with\nthe
specified response and explanatory variables, and finding\nthe best models in terms
of some Information Criterion (AIC,\nAICc or BIC). Can handle very large numbers of
candidate\nmodels. Features a Genetic Algorithm to find the best models\nwhen an
exhaustive screening of the candidates is not feasible.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"glmulti","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"MASS, aod, lme4, pscl, leaps, survival,
nnet","Title":"Model selection and multimodel inference made
easy","Version":"1.0.7"},"glmvsd":{"Author":"Ying Nan <nanx0006@gmail.com>, Yanjia
Yu <yuxxx748@umn.edu>, Yuhong Yang <yyang@stat.umn.edu>, Yi Yang
<yi.yang6@mcgill.ca>","Depends":"stats, glmnet, ncvreg, MASS, parallel,
brglm","Description":"Variable selection deviation (VSD) measures and instability
tests for high-dimensional model selection methods such as LASSO, SCAD and MCP,
etc., to decide whether the sparse patterns identified by those methods are
reliable.","License":"GPL-
2","NeedsCompilation":"no","Package":"glmvsd","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Variable Selection Deviation Measures and Instability Tests
for\nHigh-Dimensional Generalized Linear
Models","URL":"https:\/\/github.com\/emeryyi\/glmvsd","Version":"1.4"},"glmx":
{"Author":"Achim Zeileis [aut, cre],\nRoger Koenker [aut],\nPhilipp Doebler
[aut]","Depends":"R (>= 2.14.0)","Description":"Extended techniques for generalized
linear models (GLMs), especially for binary responses,\nincluding parametric links
and heteroskedastic latent variables.","Imports":"stats, MASS, Formula, lmtest,
sandwich","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"glmx","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"AER, gld, numDeriv, pscl","Title":"Generalized Linear
Models Extended","Version":"0.1-1"},"globalGSA":{"Author":"Natalia Vilor, M.Luz
Calle","Description":"Implementation of three different Gene set analysis (GSA)
algorithms for combining the individual pvalues of a set of genetic variats (SNPs)
in a gene level pvalue. The implementation includes the selection of the best
inheritance model for each SNP.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"globalGSA","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Global Gene-Set Analysis for Association
Studies","Version":"1.0"},"globalOptTests":{"Author":"Katharine
Mullen","Description":"This package makes available 50 objective functions for
benchmarking the performance of global optimization algorithms","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"globalOptTests","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Objective functions for benchmarking the
performance of global\noptimization algorithms","Version":"1.1"},"globalboosttest":
{"Author":"Anne-Laure Boulesteix <boulesteix@ibe.med.uni-muenchen.de>,\nTorsten
Hothorn <torsten.hothorn@stat.uni-muenchen.de>.","Depends":"R (>= 2.8), mboost (>=
2.0-0), survival","Description":"'globalboosttest' implements a permutation-based
testing\nprocedure to globally test the (additional) predictive value of\na large
set of predictors given that a small set of predictors\nis already available.
Currently, 'globalboosttest' supports\nbinary outcomes (via logistic regression)
and survival outcomes\n(via Cox regression). It is based on boosting regression
as\nimplemented in the package 'mboost'.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"globalboosttest","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Testing the additional predictive value of high-
dimensional data","Version":"1.1-0"},"globals":{"Author":"Henrik Bengtsson [aut,
cre, cph]","Depends":"R (>= 3.1.2)","Description":"Identifies global (\"unknown\")
objects in R expressions by code\ninspection using various strategies, e.g.
conservative or liberal. The objective\nof this package is to make it as simple as
possible to identify global objects\nfor the purpose of exporting them in
distributed compute environments.","Imports":"codetools","License":"LGPL (>=
2.1)","NeedsCompilation":"no","Package":"globals","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Identify Global Objects in R
Expressions","URL":"https:\/\/github.com\/HenrikBengtsson\/globals","Version":"0.6.
1"},"globe":{"Author":"Adrian Baddeley [aut, cre],\nThomas Lawrence
[aut]","Depends":"graphics, stats","Description":"Basic functions for plotting 2D
and 3D views of a sphere, by default the Earth with its major coastline, and
additional lines and points.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"globe","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Plot 2D and 3D Views of the Earth, Including Major
Coastline","Version":"1.1-2"},"glogis":{"Author":"Achim Zeileis [aut, cre],\nThomas
Windberger [aut]","Depends":"R (>= 2.10.0), zoo","Description":"Tools for the
generalized logistic distribution (Type I,\nalso known as skew-logistic
distribution), encompassing\nbasic distribution functions (p, q, d, r, score),
maximum\nlikelihood estimation, and structural change
methods.","Imports":"graphics, stats, sandwich","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"glogis","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"strucchange, fxregime, lattice","Title":"Fitting and
Testing Generalized Logistic Distributions","Version":"1.0-0"},"glpkAPI":
{"Author":"Claus Jonathan Fritzemeier [cre],\nGabriel Gelius-Dietrich [aut],\nLouis
Luangkesorn [ctb]","Depends":"R (>= 2.6.0)","Description":"R Interface to C API of
GLPK, needs GLPK Version >= 4.42","Imports":"methods","License":"GPL-
3","NeedsCompilation":"yes","Package":"glpkAPI","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"R Interface to C API of GLPK","Version":"1.3.0"},"glrt":
{"Author":"Qiang Zhao and Jianguo Sun","Depends":"R (>= 3.1.1), survival,
stats","Description":"Functions to conduct four generalized logrank tests and a
score test under a proportional hazards model","License":"GPL-
2","NeedsCompilation":"no","Package":"glrt","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Generalized Logrank Tests for Interval-censored Failure
Time\nData","Version":"2.0"},"glycanr":{"Author":"Ivo Ugrina [aut, cre,
cph],\nLucija Klaric [aut],\nFrano Vuckovic [aut]","Depends":"R (>=
3.1.2)","Description":"Useful utilities in N-glycan data analysis. This package
tries\nto fill the gap in N-glycan data analysis by providing easy\nto use
functions for basic operations on data\n(see
https:\/\/en.wikipedia.org\/wiki\/Glycomics for more\ndetails on Glycomics). At the
moment glycanr is mostly oriented\nto data obtained
by UPLC and LCMS analysis of Plasma and IgG glycome.","Imports":"ggplot2, tidyr
(>= 0.3.1), dplyr (>= 0.4.3), coin","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"glycanr","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"knitr, preprocessCore, testthat","Title":"Tools
for Analysing N-Glycan
Data","URL":"https:\/\/github.com\/iugrina\/glycanr","Version":"0.3.0"},"gmailr":
{"Author":"Jim Hester","Depends":"R (>= 3.0.0)","Description":"An interface to the
Gmail RESTful API. Allows access to your\nGmail messages, threads, drafts and
labels.","Imports":"httr, base64enc, magrittr, jsonlite, mime","License":"MIT +
file
LICENSE","NeedsCompilation":"no","Package":"gmailr","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat, knitr","Title":"Access the Gmail RESTful
API","URL":"https:\/\/github.com\/jimhester\/gmailr","Version":"0.6.0"},"gmapsdista
nce":{"Author":"Rodrigo Azuero Melo","Description":"Get distance and travel time
between two points from Google Maps. Four possible modes of transportation
(bicycling, walking, driving and public transportation).","Imports":"RCurl, XML,
2)","NeedsCompilation":"no","Package":"gmapsdistance","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Distance and Travel Time Between Two Points from
Google
Maps","URL":"https:\/\/github.com\/rodazuero\/gmapsdistance","Version":"1.0"},"gmet
a":{"Author":"Guang Yang <gyang.rutgers@gmail.com>, Jerry Q. Cheng
<jcheng1@rwjms.rutgers.edu>,\nand Minge Xie
<mxie@stat.rutgers.edu>","Depends":"stats, BiasedUrn, binom","Description":"An
implementation of an all-in-one function for a wide range of meta-analysis
problems. It contains a single function gmeta() that unifies all standard meta-
analysis methods and also several newly developed ones under a framework of
combining confidence distributions (CDs). Specifically, the package can perform
classical p-value combination methods (such as methods of Fisher, Stouffer,
Tippett, etc.), fit meta-analysis fixed-effect and random-effects models, and
synthesizes 2x2 tables. Furthermore, it can perform robust meta-analysis, which
provides protection against model-misspecifications, and limits the impact of any
unknown outlying studies. In addition, the package implements two exact meta-
analysis methods from synthesizing 2x2 tables with rare events (e.g., zero total
event). A plot function to visualize individual and combined CDs through extended
forest plots is also available.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"gmeta","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Meta-Analysis via a Unified Framework of Confidence
Distribution","Version":"2.2-6"},"gmm":{"Author":"Pierre Chausse
<pchausse@uwaterloo.ca>","Depends":"R (>= 2.10.0), sandwich","Description":"It is a
complete suite to estimate models based on moment\nconditions. It includes the two
step Generalized method of\nmoments (GMM) of Hansen(1982), the iterated GMM and
continuous\nupdated estimator (CUE) of Hansen-Eaton-Yaron(1996) and
several\nmethods that belong to the Generalized Empirical Likelihood\n(GEL) family
of estimators, as presented by Smith(1997),\nKitamura(1997), Newey-Smith(2004) and
Anatolyev(2005).","Imports":"stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gmm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"mvtnorm, car, stabledist, MASS, timeDate,
timeSeries","Title":"Generalized Method of Moments and Generalized
Empirical\nLikelihood","Version":"1.5-2"},"gmnl":{"Author":"Mauricio Sarrias [aut,
cre],\nRicardo Daziano [aut],\nYves Croissant [ctb]","Depends":"R (>= 3.2.1),
maxLik, Formula","Description":"An implementation of maximum simulated likelihood
method for the\nestimation of multinomial logit models with random
coefficients.\nSpecifically, it allows estimating models with continuous
heterogeneity\nsuch as the mixed multinomial logit and the generalized multinomial
logit.\nIt also allows estimating models with discrete heterogeneity such as
the\nlatent class and the mixed-mixed multinomial logit model.","Imports":"plotrix,
msm, mlogit, truncnorm, stats, graphics, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gmnl","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"AER, lmtest, car, memisc","Title":"Multinomial Logit
Models with Random Parameters","URL":"http:\/\/msarrias.weebly.com\/gmnl-package-
in-r.html","Version":"1.1-1"},"gmodels":{"Author":"Gregory R. Warnes, Ben Bolker,
Thomas Lumley, and Randall C\nJohnson. Contributions from Randall C. Johnson are
Copyright\n(2005) SAIC-Frederick, Inc. Funded by the Intramural Research\nProgram,
of the NIH, National Cancer Institute, Center for\nCancer Research under NCI
Contract NO1-CO-12400.","Depends":"R (>= 1.9.0)","Description":"Various R
programming tools for model fitting.","Imports":"MASS, gdata","License":"GPL-
2","NeedsCompilation":"no","Package":"gmodels","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"gplots, gtools, Matrix, nlme, lme4 (>= 0.999999-
0)","Title":"Various R Programming Tools for Model
Fitting","URL":"http:\/\/www.sf.net\/projects\/r-
gregmisc","Version":"2.16.2"},"gmp":{"Author":"Antoine Lucas, Immanuel Scholz,
Rainer Boehme <rb-gmp@reflex-studio.de>,\nSylvain Jasson
<jasson@toulouse.inra.fr>,\nMartin Maechler
<maechler@stat.math.ethz.ch>","Description":"Multiple Precision Arithmetic (big
integers and rationals,\nprime number tests, matrix computation), \"arithmetic
without limitations\"\nusing the C library GMP (GNU Multiple Precision
Arithmetic).","Imports":"methods","License":"GPL","NeedsCompilation":"yes","Package
":"gmp","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"Rmpfr","Tit
le":"Multiple Precision
Arithmetic","URL":"http:\/\/mulcyber.toulouse.inra.fr\/projects\/gmp","Version":"0.
5-12"},"gmt":{"Author":"Arni Magnusson","Description":"Interface between the GMT
map-making software and R,\nenabling the user to manipulate geographic data within
R and call GMT commands\nto draw and annotate maps in postscript format. The 'gmt'
package is about\ninteractive data analysis, rapidly visualizing subsets and
summaries of\ngeographic data, while performing statistical analysis in the R
console.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gmt","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Interface between GMT Map-Making Software and
R","URL":"http:\/\/gmt.soest.hawaii.edu","Version":"1.2-0"},"gmum.r":
{"Author":"Wojciech Czarnecki, Stanislaw Jastrzebski, Marcin Data, Igor Sieradzki,
Mateusz Bruno-Kaminski, Karol Jurek, Piotr Kowenzowski, Michal Pletty, Konrad
Talik, Maciej Zgliczynski","Description":"Direct R interface to Support Vector
Machine libraries ('LIBSVM' and 'SVMLight') and efficient C++ implementations of
Growing Neural Gas and models developed by 'GMUM' group (Cross Entropy Clustering
and 2eSVM).","Imports":"ggplot2 (>= 1.0.0), stats, igraph, SparseM, Matrix, httr,
Rcpp\n(>= 0.11.6), methods, grid","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"gmum.r","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"car, caret, e1071, klaR, testthat,
mlbench","Title":"GMUM Machine Learning Group
Package","URL":"https:\/\/github.com\/gmum\/gmum.r","Version":"0.2.1"},"gmwm":
{"Author":"James Balamuta [aut, cph],\nStephane Guerrier [ctb, cre, cph],\nRoberto
Molinari [ctb, cph],\nWenchao Yang [ctb]","Depends":"R (>= 3.2),
ggplot2","Description":"Generalized Method of Wavelet Moments (GMWM) is an
estimation\ntechnique for the parameters of time series models. It uses the wavelet
variance\nin a moment matching approach that makes it particularly suitable for
the\nestimation of certain state-space models. Furthermore, there exists a
robust\nimplementation of GMWM, which allows the robust estimation of some state-
space\nmodels and ARIMA models. Lastly, the package provides the ability to
quickly\ngenerate time series data, perform different wavelet decompositions,
and\nvisualizations.","Imports":"Rcpp (>= 0.12.2), scales, grid, reshape2, utils,
stats,\nmethods, graphics, grDevices","License":"CC BY-NC-SA
4.0","NeedsCompilation":"yes","Package":"gmwm","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat, knitr, rmarkdown,
imudata","Title":"Generalized Method of Wavelet
Moments","URL":"https:\/\/github.com\/SMAC-Group\/gmwm","Version":"2.0.0"},"gnm":
{"Author":"Heather Turner [aut, cre],\nDavid Firth [aut],\nBrian Ripley
[ctb],\nBill Venables [ctb],\nDouglas M. Bates [ctb],\nMartin Maechler
[ctb]","Depends":"R (>= 2.3.0)","Description":"Functions to specify and fit
generalized nonlinear models, including models with multiplicative interaction
terms such as the UNIDIFF model from sociology and the AMMI model from crop
science, and many others. Over-parameterized representations of models are used
throughout; functions are provided for inference on estimable parameter
combinations, as well as standard methods for diagnostics etc.","Imports":"MASS,
stats, graphics, Matrix, nnet, qvcalc (>= 0.8-3), relimp","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"gnm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"vcdExtra","Title":"Generalized Nonlinear
Models","URL":"http:\/\/go.warwick.ac.uk\/gnm","Version":"1.0-8"},"gnmf":
{"Author":"Jose M. Maisog, Guoli Wang, Karthik Devarajan","Depends":"R (>=
2.10)","Description":"This package performs generalized non-negative matrix
factorization based on Renyi divergence.","License":"GPL-
2","NeedsCompilation":"yes","Package":"gnmf","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Generalized Non-negative Matrix Factorization Based on
Renyi\nDivergence","URL":"http:\/\/devarajan.fccc.edu","Version":"0.7"},"gnumeric":
{"Author":"Karoly Antal <antalk2@gmail.com>.","Depends":"R (>= 2.8.1),
XML","Description":"Read data
files readable by gnumeric into R. Can read\nwhole sheet or a range, from several
file formats, including\nthe native format of gnumeric. Reading is done by
using\nssconvert (a file converter utility included in the gnumeric\ndistribution
http:\/\/projects.gnome.org\/gnumeric\/) to convert\nthe requested part to CSV.
From gnumeric files (but not other\nformats) can list sheet names and sheet sizes
or read all\nsheets.","Imports":"utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gnumeric","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Read Data from Files Readable by
Gnumeric","Version":"0.7-4"},"goalprog":{"Author":"Frederick Novomestky
<fnovomes@poly.edu>","Depends":"R (>= 2.0.1), lpSolve","Description":"A collection
of functions to solve weighted and lexicographical\ngoal programming problems as
specified by Lee (1972) and Ignizio (1976).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"goalprog","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Weighted and lexicographical goal programming and
optimization","Version":"1.0-2"},"gof":{"Author":"Klaus K. Holst","Depends":"R (>=
2.15)","Description":"Implementation of model-checking techniques for generalized
linear\nmodels and linear structural equation models based on cumulative
residuals","License":"GPL","NeedsCompilation":"yes","Package":"gof","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Suggests":"numDeriv, survival, lava (>=
1.2.5)","Title":"Model-diagnostics based on cumulative
residuals","Version":"0.9.1"},"gofCopula":{"Author":"Ostap Okhrin <ostap.okhrin@tu-
dresden.de>,\nSimon Trimborn <simon.trimborn@wiwi.hu-berlin.de>,\nShulin Zhang
<slzhang@swufe.edu.cn>,\nQian M. Zhou <qmzhou@sfu.ca>","Depends":"R (>= 1.9.0),
copula","Description":"Several GoF tests for Copulae are provided. A new hybrid
test is implemented which supports all of the individual tests. Estimation methods
for the margins are provided. All the tests support parameter estimation and
predefined values. The parameters are estimated by pseudo maximum likelihood but if
it fails the estimation switches automatically to inversion of Kendall's
tau.","Imports":"SparseGrid, numDeriv, VineCopula, methods, stats","License":"GPL
(>=
3)","NeedsCompilation":"yes","Package":"gofCopula","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Goodness-of-Fit Tests for Copulae","Version":"0.1-
2"},"goft":{"Author":"Elizabeth Gonzalez-Estrada, Jose A. Villasenor-
Alva","Depends":"R (>= 2.10), stats, gPdtest, mvShapiroTest","Description":"Tests
of fit for Gamma, inverse Gaussian, normal, multivariate normal and generalized
Pareto distributions. Parameter estimators for the Gamma, inverse Gaussian and
generalized Pareto distributions.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"goft","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Tests of Fit for some Probability
Distributions","Version":"1.2"},"goftest":{"Author":"Julian Faraway [aut],\nGeorge
Marsaglia [aut],\nJohn Marsaglia [aut],\nAdrian Baddeley [aut, cre]","Depends":"R
(>= 3.1)","Description":"Cramer-Von Mises and Anderson-Darling tests of goodness-
of-fit\nfor continuous univariate distributions, using\nefficient
algorithms.","Imports":"stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"goftest","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Classical Goodness-of-Fit Tests for Univariate
Distributions","Version":"1.0-3"},"gogarch":{"Author":"Bernhard Pfaff [aut,
cre]","Depends":"R (>= 2.10.0), methods, stats, graphics, fGarch,
fastICA","Description":"Implementation of the GO-GARCH model class","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"gogarch","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Generalized Orthogonal GARCH (GO-GARCH)
models","Version":"0.7-2"},"googleAuthR":{"Author":"Mark Edmondson [aut,
cre],\nJennifer Bryan [ctb],\nJohann deBoer [ctb]","Depends":"R (>=
3.2.0)","Description":"Create R functions that interact with OAuth2 Google APIs
easily,\nwith auto-refresh and Shiny compatibility.","Imports":"httr (>= 1.1.0),
jsonlite (>= 0.9.16), R6 (>= 2.1.0)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"googleAuthR","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"shiny (>= 0.12.1), knitr","Title":"Easy
Authentication with Google OAuth2
APIs","URL":"https:\/\/github.com\/MarkEdmondson1234\/googleAuthR","Version":"0.2.0
"},"googlePublicData":{"Author":"George Vega Yon [aut, cre]","Depends":"R (>=
3.2.0)","Description":"Provides a collection of functions designed for working with
'Google Public Data Explorer'. Automatically builds up the corresponding DSPL (XML)
metadata files and CSV files; compressing all the files and leaving them ready to
be published on the 'Public Data Explorer'.","Imports":"XLConnect, XML,
LICENSE","NeedsCompilation":"no","Package":"googlePublicData","Repository":"http:\/
\/cran.csiro.au\/src\/contrib","Title":"Working with Google Public Data Explorer
DSPL Metadata
Files","URL":"http:\/\/github.com\/gvegayon\/googlePublicData\/","Version":"0.15.7.
28"},"googleVis":{"Author":"Markus Gesmann [aut, cre],\nDiego de Castillo
[aut],\nJoe Cheng [ctb]","Depends":"R (>= 3.0.2)","Description":"R interface to
Google Charts API, allowing users\nto create interactive charts based on data
frames. Charts\nare displayed locally via the R HTTP help server. A modern\nbrowser
with Internet connection is required and for some\ncharts a Flash player. The data
remains local and is not\nuploaded to Google.","Imports":"methods, RJSONIO,
2)","NeedsCompilation":"no","Package":"googleVis","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"shiny (>= 0.4.0), httpuv (>= 1.2.0), knitr (>=
1.5)","Title":"R Interface to Google
Charts","URL":"https:\/\/github.com\/mages\/googleVis#googlevis","Version":"0.5.10"
},"googleformr":{"Author":"Steve Simpson [aut, cre]","Depends":"R (>=
3.2.2)","Description":"GET and POST data to Google Forms; more secure than having
to\nexpose Google Sheets in order to POST data.","Imports":"httr, rvest, xml2,
2","NeedsCompilation":"no","Package":"googleformr","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat","Title":"Collect Data Programmatically by
POST Methods to Google Forms","Version":"0.0.2"},"googlesheets":{"Author":"Jennifer
Bryan [aut, cre],\nJoanna Zhao [aut]","Depends":"R (>=
3.2.0)","Description":"Interact with Google Sheets from R.","Imports":"cellranger
(>= 1.0.0), dplyr (>= 0.4.2), httr (>= 1.1.0),\njsonlite, purrr, readr (>= 0.2.2),
stats, stringr, tidyr,\nutils, XML, xml2","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"googlesheets","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"covr, ggplot2, knitr, testthat,
rmarkdown","Title":"Manage Google Spreadsheets from
R","URL":"https:\/\/github.com\/jennybc\/googlesheets","Version":"0.2.0"},"goric":
{"Author":"Daniel Gerhard [aut, cre],\nRebecca M. Kuiper
[aut]","Depends":"nlme","Description":"Generalized Order-Restricted Information
Criterion (GORIC) value for a set of hypotheses in multivariate regression
models","Imports":"quadprog, mvtnorm, MASS, Matrix, parallel","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"goric","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Generalized Order-Restricted Information
Criterion","Version":"0.0-8"},"govStatJPN":{"Author":"Yuichiro
Otani","Description":"This package purposes to deal with public survey data
of\nJapanese government via their Application Programming
Interface\n(http:\/\/statdb.nstac.go.jp\/)","License":"GPL","NeedsCompilation":"no"
,"Package":"govStatJPN","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title"
:"functions to get public survey data in Japan","Version":"0.1"},"gpDDE":
{"Author":"Ziqian Zhou [aut, cre],\nKung-Sik Chan [aut]","Depends":"R (>= 3.2.1),
fda, CollocInfer (>= 1.0.2)","Description":"Functions implement collocation-
inference for\nstochastic process driven by distributed delay differential
equations.\nThey also provide tools for selecting the lags for distributed
delay\nusing shrinkage methods, estimating time-varying coefficients,\nand tools
for inference and prediction.","Imports":"penalized, nnls, deSolve, MASS, TSA,
lars, limSolve, forecast,\ntrustOptim, methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gpDDE","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"General Profiling Method for Delay Differential
Equation","Version":"0.8.2"},"gpairs":{"Author":"John W. Emerson and Walton A.
Green","Description":"Produces a generalized pairs (gpairs)
plot.","Enhances":"YaleToolkit","Imports":"grid, barcode, lattice, vcd, MASS,
colorspace","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gpairs","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"gpairs: The Generalized Pairs
Plot","Version":"1.2"},"gpclib":{"Author":"Roger D. Peng <rpeng@jhsph.edu> with
contributions from Duncan\nMurdoch and Barry Rowlingson; GPC library by Alan
Murta","Depends":"R (>= 2.14.0), methods","Description":"General polygon clipping
routines for R based on Alan\nMurta's C
library","Imports":"graphics","License":"file
LICENSE","NeedsCompilation":"yes","Package":"gpclib","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"General Polygon Clipping Library for
R","URL":"http:\/\/www.cs.man.ac.uk\/~toby\/gpc\/,\nhttp:\/\/github.com\/rdpeng\/gp
clib","Version":"1.5-5"},"gpk":{"Author":"Prabhanjan
Tattar","Description":"Collection of datasets as prepared by Profs. A.P. Gore, S.A.
Paranjape, and M.B. Kulkarni of Department of Statistics, Poona University, India.
With their permission, first letter of their names forms the name of this package,
the package has been built by me and made available for the benefit of R users.
This collection
requires a rich class of models and can be a very useful building block for a
beginner.","License":"GPL-
2","NeedsCompilation":"no","Package":"gpk","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"100 Data Sets for Statistics
Education","Version":"1.0"},"gplm":{"Author":"Marlene
Mueller","Depends":"AER","Description":"Functions for estimating generalized
partial linear models","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"gplm","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Generalized partial linear models (GPLM)","Version":"0.7-
2"},"gplots":{"Author":"Gregory R. Warnes, Ben Bolker, Lodewijk Bonebakker,
Robert\nGentleman, Wolfgang Huber Andy Liaw, Thomas Lumley, Martin\nMaechler, Arni
Magnusson, Steffen Moeller, Marc Schwartz, Bill\nVenables","Depends":"R (>=
3.0)","Description":"Various R programming tools for plotting data, including:\n-
calculating and plotting locally smoothed summary function as\n('bandplot',
'wapply'),\n- enhanced versions of standard plots ('barplot2',
'boxplot2',\n'heatmap.2', 'smartlegend'),\n- manipulating colors ('col2hex',
'colorpanel', 'redgreen',\n'greenred', 'bluered', 'redblue', 'rich.colors'),\n-
calculating and plotting two-dimensional data summaries ('ci2d',\n'hist2d'),\n-
enhanced regression diagnostic plots ('lmplot2', 'residplot'),\n- formula-enabled
interface to 'stats::lowess' function ('lowess'),\n- displaying textual data in
plots ('textplot', 'sinkplot'),\n- plotting a matrix where each cell contains a dot
whose size\nreflects the relative magnitude of the elements ('balloonplot'),\n-
plotting \"Venn\" diagrams ('venn'),\n- displaying Open-Office style plots
('ooplot'),\n- plotting multiple data on same region, with separate
axes\n('overplot'),\n- plotting means and confidence intervals ('plotCI',
'plotmeans'),\n- spacing points in an x-y plot so they don't overlap
('space').","Imports":"gtools, gdata, stats, caTools, KernSmooth","License":"GPL-
2","NeedsCompilation":"no","Package":"gplots","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"grid, MASS","Title":"Various R Programming Tools for
Plotting Data","Version":"3.0.1"},"gpmap":{"Author":"\nArne B. Gjuvsland
<arne.gjuvsland@nmbu.no> and Yunpeng Wang
<yunpeng.wng@gmail.com>","Depends":"isotone, plyr, ggplot2,
foreach","Description":"This package contains tools for studying genotype-phenotype
(GP) maps for bi-allelic loci underlying quantitative phenotypes. The 0.1 version
is released in connection with the publication of Gjuvsland et al. (2003) and
implements basic line plots and the monotonicity measures for GP maps presented in
the paper. Reference: Gjuvsland AB, Wang Y, Plahte E and Omholt SW (2013)
Monotonicity is a key feature of genotype-phenotype maps. Front. Genet. 4:216. doi:
10.3389\/fgene.2013.00216
[\\href{http:\/\/www.frontiersin.org\/Journal\/10.3389\/fgene.2013.00216\/full}
{link}]","License":"GPL-
3","NeedsCompilation":"no","Package":"gpmap","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Analysing and plotting genotype-phenotype
maps","Version":"0.1.1"},"gpr":{"Author":"Afshin Sadeghi","Depends":"R (>=
2.13)","Description":"This package provides a minimalistic functionality necessary
to apply Gaussian Process in R. They provide a selection of functionalities of GPML
Matlab library.","License":"GPL-
3","NeedsCompilation":"no","Package":"gpr","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"A Minimalistic package to apply Gaussian Process in
R","Version":"1.1"},"gptk":{"Author":"Alfredo Kalaitzis
<alkalait@gmail.com>,\nAntti Honkela <antti.honkela@tkk.fi>,\nPei Gao
<pg349@medschl.cam.ac.uk>,\nNeil D. Lawrence
<N.Lawrence@dcs.shef.ac.uk>","Depends":"R (>= 2.8.0), Matrix,
fields","Description":"The gptk package implements a general-purpose toolkit for
Gaussian\nprocess regression with a variety of covariance functions (e.g. RBF,
Mattern, polynomial, etc).\nBased on a MATLAB implementation by Neil D. Lawrence.
See inst\/doc\/index.html for more details.","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"gptk","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"spam","Title":"Gaussian Processes Tool-
Kit","Version":"1.08"},"gpuR":{"Author":"Charles Determan
Jr.","Description":"Provides GPU enabled functions for R objects in a simple
and\napproachable manner. New gpu* and vcl* classes have been provided to\nwrap
typical R objects (e.g. vector, matrix), in both host and device\nspaces, to mirror
typical R syntax without the need to know OpenCL.","Imports":"Rcpp (>= 0.11.5),
assertive, methods","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"gpuR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat, knitr","Title":"GPU Functions for R
Objects","URL":"http:\/\/github.com\/cdeterman\/gpuR","Version":"1.1.2"},"gputools"
:{"Author":"Josh Buckner [aut, cre],\nMark Seligman [aut],\nJustin Wilson
[ctb]","Depends":"R (>= 3.0.0)","Description":"Provides R interfaces to a handful
of common\nfunctions implemented using the Nvidia CUDA toolkit. Some of
the\nfunctions require at least GPU Compute Capability 1.3.\nThanks to Craig Stark
at UC Irvine for donating time on his lab's Mac.","License":"GPL-
3","NeedsCompilation":"yes","Package":"gputools","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"A Few GPU Enabled
Functions","URL":"https:\/\/github.com\/nullsatz\/gputools\/wiki","Version":"1.0"},
"gquad":{"Author":"Hannah O. Ajoge","Description":"Nucleic acid sequences that are
rich in guanine are capable of forming highly stable four-stranded structures known
as G quadruplex motifs. This package provide functions for predicting G quadruplex
motif(s) in nucleotide sequences.","Imports":"ape, seqinr","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"gquad","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"G Quadruplex Motif Prediction Tool","Version":"1.0-
0"},"grImport":{"Author":"Paul Murrell [aut, cre],\nRichard Walton [aut],\nSimon
Potter [ctb]","Depends":"R (>= 3.0.0), methods, grid, XML","Description":"Functions
for converting, importing, and drawing PostScript\npictures in R
plots.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"grImport","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"lattice, cluster, colorspace,
survival","Title":"Importing Vector Graphics","Version":"0.9-0"},"grade":
{"Author":"Leif Johnson <leif.t.johnson@gmail.com>","Depends":"R (>=
2.4.1)","Description":"Provides functions for matching student-answers to teacher
answers for a variety of data types.","License":"GPL-
2","NeedsCompilation":"no","Package":"grade","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Binary Grading functions for
R","URL":"https:\/\/github.com\/ltjohnson\/grade","Version":"0.2-1"},"gramEvol":
{"Author":"Farzad Noorian, Anthony Mihirana de Silva","Description":"A native R
implementation of grammatical evolution (GE). GE facilitates the discovery of
programs that can achieve a desired goal. This is done by performing an
evolutionary optimisation over a population of R expressions generated via a user-
defined context-free grammar (CFG) and cost function.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gramEvol","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"rex","Title":"Grammatical Evolution for
R","URL":"https:\/\/github.com\/fnoorian\/gramEvol\/","Version":"2.1-2"},"granova":
{"Author":"Robert M. Pruzek <RMPruzek@yahoo.com> and James E. Helmreich
<James.Helmreich@Marist.edu>","Depends":"R (>= 3.1.1), car (>= 2.0-
21)","Description":"This small collection of functions provides what we call
elemental graphics for display of anova\nresults. The term elemental derives from
the fact that each function is aimed at construction of\ngraphical displays that
afford direct visualizations of data with respect to the fundamental\nquestions
that drive the particular anova methods. The two main functions are granova.1w\n(a
graphic for one way anova) and granova.2w (a corresponding graphic for two way
anova). These\nfunctions were written to display data for any number of groups,
regardless of their sizes\n(however, very large data sets or numbers of groups can
be problematic). For these two functions\na specialized approach is used to
construct data-based contrast vectors for which anova data are\ndisplayed. The
result is that the graphics use straight lines, and when appropriate flat
surfaces,\nto facilitate clear interpretations while being faithful to the standard
effect tests in anova.\nThe graphic results are complementary to standard summary
tables for these two basic kinds of\nanalysis of variance; numerical summary
results of analyses are also provided as side effects.\nTwo additional functions
are granova.ds (for comparing two dependent samples), and granova.contr\n(which
provides graphic displays for a priori contrasts). All functions provide
relevant\nnumerical results to supplement the graphic displays of anova data.\nThe
graphics based on these functions should be especially helpful for learning how the
methods have\nbeen applied to answer the question(s) posed. This means they can
be\nparticularly helpful for students and non-statistician analysts. But these
methods should be\nquite generally helpful for work-a-day applications of all
kinds, as they can help to identify\noutliers, clusters or patterns, as well as
highlight the role of non-linear transformations of data. In the case\nof
granova.1w and granova.ds especially, several arguments are provided to facilitate
flexibility\nin the construction of graphics that accommodate diverse features of
data, according to their\ncorresponding display requirements. See the help files
for individual functions.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"granova","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"mgcv, rgl,
tcltk, MASS","Title":"Graphical Analysis of
Variance","Version":"2.1"},"granovaGG":{"Author":"Brian A. Danielak
<brian@briandk.com>,\nRobert M. Pruzek <RMPruzek@yahoo.com>,\nwith contributions
from:\nWilliam E. J. Doane <wil@DrDoane.com>,\nJames E. Helmreich
<James.Helmreich@Marist.edu>,\nJason Bryer <jason@bryer.org>","Depends":"R (>=
2.14.0), ggplot2 (>= 0.9.2)","Description":"This collection of functions in
'granovaGG'\nprovides what we call elemental graphics for display of\nanova
results. The term elemental derives from the fact\nthat each function is aimed at
construction of\ngraphical displays that afford direct visualizations of\ndata with
respect to the fundamental questions that\ndrive the particular anova methods. This
package\nrepresents a modification of the original granova\npackage; the key change
is to use 'ggplot2', Hadley\nWickham's package based on Grammar of Graphics
concepts\n(due to Wilkinson). The main function is granovagg.1w()\n(a graphic for
one way ANOVA); two other functions\n(granovagg.ds() and granovagg.contr()) are to
construct\ngraphics for dependent sample analyses and\ncontrast-based analyses
respectively. (The function\ngranova.2w(), which entails dynamic displays of data,
is\nnot currently part of 'granovaGG'.) The 'granovaGG'\nfunctions are to display
data for any number of groups,\nregardless of their sizes (however, very large
data\nsets or numbers of groups can be problematic). For\ngranovagg.1w() a
specialized approach is used to\nconstruct data-based contrast vectors for which
anova\ndata are displayed. The result is that the graphics use\na straight line to
facilitate clear interpretations\nwhile being faithful to the standard effect test
in\nanova. The graphic results are complementary to\nstandard summary tables;
indeed, numerical summary\nstatistics are provided as side effects of the
graphic\nconstructions. granovagg.ds() and granovagg.contr() provide\ngraphic
displays and numerical outputs for a dependent\nsample and contrast-based analyses.
The graphics based\non these functions can be especially helpful for\nlearning how
the respective methods work to answer the\nbasic question(s) that drive the
analyses. This means\nthey can be particularly helpful for students and\nnon-
statistician analysts. But these methods can be of\nassistance for work-a-day
applications of many kinds,\nas they can help to identify outliers, clusters
or\npatterns, as well as highlight the role of non-linear\ntransformations of data.
In the case of granovagg.1w()\nand granovagg.ds() several arguments are provided
to\nfacilitate flexibility in the construction of graphics\nthat accommodate
diverse features of data, according to\ntheir corresponding display requirements.
See the help\nfiles for individual functions.","Imports":"gridExtra (>= 0.9.1),
plyr, RColorBrewer, reshape2","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"granovaGG","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Graphical Analysis of Variance Using
ggplot2","Version":"1.4.0"},"graphTweets":{"Author":"John Coene [aut,
cre]","Depends":"R (>= 3.2.0)","Description":"Allows building an edge table from
data frame of tweets,\nalso provides function to build nodes and another create a
temporal graph.","Imports":"reshape2, dplyr, igraph, methods","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"graphTweets","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"testthat, twitteR","Title":"Visualise Twitter
Interactions","URL":"https:\/\/github.com\/JohnCoene\/graphTweets","Version":"0.3.1
"},"graphicalVAR":{"Author":"Sacha Epskamp","Depends":"R (>=
3.1.0)","Description":"Estimates within and between time point interactions in
experience sampling data, using the Graphical VAR model in combination with LASSO
and EBIC.","Imports":"Rcpp (>= 0.11.3), Matrix, glasso, glmnet, mvtnorm, qgraph
(>=\n1.3.1)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"graphicalVAR","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Graphical VAR for Experience Sampling
Data","Version":"0.1.3"},"graphicsQC":{"Author":"Stephen Gardiner and Paul
Murrell","Description":"Functions to generate\ngraphics files, compare them with
``model'' files,\nand report the results, including visual and textual\ndiffs of
any differences.","Imports":"XML","License":"GPL-
2","NeedsCompilation":"no","Package":"graphicsQC","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"Sxslt","Title":"Quality Control for Graphics in
R","URL":"http:\/\/graphicsqc.r-forge.r-project.org","Version":"1.0-
7"},"graphscan":{"Author":"Robin Loche, Benoit Giron, David Abrial, Lionel Cucala,
Myriam Charras-Garrido, Jocelyn De-Goer","Depends":"R (>= 3.0.2), snowfall (>=
1.84-6)","Description":"Multiple scan statistic with variable window for one
dimension data and scan statistic based on connected components in 2D or
3D.","Imports":"ape, sp, methods, rgl, utils, graphics, grDevices,
stats","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"graphscan","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Cluster Detection with Hypothesis Free Scan
Statistic","Version":"1.1"},"graticule":{"Author":"Michael D. Sumner [aut,
cre]","Depends":"sp","Description":"Create graticule lines and labels for maps.
Control the creation\nof lines by setting their placement (at particular meridians
and parallels)\nand extent (along parallels and meridians). Labels are created
independently of\nlines.","Imports":"raster","License":"GPL-
3","NeedsCompilation":"no","Package":"graticule","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"devtools, knitr, maptools, oce, rgdal, rworldmap,
testthat","Title":"Meridional and Parallel Lines for
Maps","URL":"https:\/\/github.com\/mdsumner\/graticule","Version":"0.1.2"},"greport
":{"Author":"Frank E Harrell Jr <f.harrell@vanderbilt.edu>","Depends":"Hmisc (>=
3.17-0), data.table","Description":"Contains many functions useful for\nmonitoring
and reporting the results of clinical trials and other\nexperiments in which
treatments are compared. LaTeX is\nused to typeset the resulting reports,
recommended to be in the\ncontext of 'knitr'. The 'Hmisc', 'ggplot2', and 'lattice'
packages are used\nby 'greport' for high-level graphics.","Imports":"rms (>= 4.4-
1), lattice, latticeExtra, ggplot2, Formula,\nsurvival, methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"greport","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Graphical Reporting for Clinical
Trials","URL":"http:\/\/biostat.mc.vanderbilt.edu\/Greport,\nhttps:\/\/github.com\/
harrelfe\/greport","Version":"0.7-1"},"greyzoneSurv":{"Author":"Pingping Qu and
John Crowley","Depends":"stats4, survival, Hmisc, survAUC","Description":"Allows
one to classify patients into low, intermediate, and high risk groups for disease
progression based on a continuous marker that is associated with progression-free
survival. It uses a latent class model to link the marker and survival outcome and
produces two cutoffs for the marker to divide patients into three groups. See the
References section for more details.","License":"GPL-
3","NeedsCompilation":"no","Package":"greyzoneSurv","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Fit a Grey-Zone Model with Survival
Data","Version":"1.0"},"gridBase":{"Author":"Paul Murrell","Depends":"R (>=
2.3.0)","Description":"Integration of base and grid graphics","Imports":"graphics,
grid","License":"GPL","NeedsCompilation":"no","Package":"gridBase","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Suggests":"lattice","Title":"Integration of
base and grid graphics","Version":"0.4-7"},"gridDebug":{"Author":"Paul Murrell and
Velvet Ly.","Depends":"R (>= 3.0.0)","Description":"Functions for drawing scene
trees representing\nscenes that have been drawn using grid
graphics.","Imports":"methods, grid, graph, gridGraphviz, gridSVG (>=
2)","NeedsCompilation":"no","Package":"gridDebug","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"lattice, ggplot2","Title":"Debugging 'grid'
Graphics","Version":"0.5-0"},"gridExtra":{"Author":"Baptiste Auguie [aut,
cre],\nAnton Antonov [ctb]","Description":"Provides a number of user-level
functions to work with \"grid\" graphics, notably to arrange multiple grid-based
plots on a page, and draw tables.","Imports":"gtable, grid, grDevices, graphics,
2)","NeedsCompilation":"no","Package":"gridExtra","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"ggplot2, lattice, knitr,
testthat","Title":"Miscellaneous Functions for \"Grid\"
Graphics","URL":"https:\/\/github.com\/baptiste\/gridextra","Version":"2.2.1"},"gri
dGraphics":{"Author":"Paul Murrell [cre, aut]","Depends":"grid,
graphics","Description":"Functions to convert a page of plots drawn with
the\ngraphics package into identical output drawn with the grid package.\nThe
result looks like the original graphics-based plot, but consists\nof grid grobs and
viewports that can then be manipulated with\ngrid functions (e.g., edit grobs and
revisit viewports).","Imports":"grDevices","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gridGraphics","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"KernSmooth","Title":"Redraw Base Graphics Using
'grid'
Graphics","URL":"https:\/\/github.com\/pmur002\/gridgraphics","Version":"0.1-
5"},"gridGraphviz":{"Author":"Paul Murrell [cre, aut],\nAshley Noel Hinton
[aut]","Depends":"R (>= 2.15.0), grid, graph, Rgraphviz","Description":"Functions
for drawing node-and-edge graphs that have been\nlaid out by graphviz. This
provides an alternative\nrendering to that provided by the 'Rgraphviz' package,
with\ntwo main advantages: the rendering provided by 'gridGraphviz'\nshould be
more similar to what 'graphviz' itself would draw;\nand rendering with 'grid'
allows for post-hoc
customisations\nusing the named viewports and grobs that
'gridGraphviz'\nproduces.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gridGraphviz","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"gridSVG","Title":"Drawing Graphs with
'grid'","URL":"http:\/\/r-forge.r-
project.org\/projects\/gridgraph\/","Version":"0.3"},"gridSVG":{"Author":"Paul
Murrell [cre, aut],\nSimon Potter [aut]","Depends":"R (>=
3.1)","Description":"Functions to export graphics drawn with package grid to
SVG\nformat. Additional functions provide access to SVG features that\nare not
available in standard R graphics, such as hyperlinks,\nanimation, filters, masks,
clipping paths, and gradient and pattern fills.","Imports":"grDevices, graphics,
utils, methods, grid, RJSONIO,
XML","License":"GPL","NeedsCompilation":"yes","Package":"gridSVG","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Suggests":"lattice","Title":"Export 'grid'
Graphics as SVG","Version":"1.5-0"},"grnn":{"Author":"Pierre-Olivier
Chasset","Description":"The program GRNN implements the algorithm proposed
by\nSpecht
(1991).","License":"AGPL","NeedsCompilation":"no","Package":"grnn","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"General regression neural
network","URL":"http:\/\/flow.chasset.net\/r-grnn\/","Version":"0.1.0"},"groc":
{"Author":"M. Bilodeau and P. Lafaye de
Micheaux","Depends":"rrcov","Description":"Robust multiple or multivariate linear
regression, nonparametric regression on orthogonal components, classical or robust
partial least squares models.","Imports":"pls, mgcv, robust, robustbase,
2)","NeedsCompilation":"yes","Package":"groc","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"ppls","Title":"Generalized Regression on Orthogonal
Components","Version":"1.0.5"},"grofit":{"Author":"Matthias Kahm, Maik
Kschischo","Description":"The package was developed to fit fit many growth
curves\nobtained under different conditions in order to derive a\nconclusive dose-
response curve, for instance for a compound\nthat potentially affects growth.
grofit fits data to different\nparametric models (function gcFitModel) and in
addition\nprovides a model free spline fit (function gcFitSpline) to\ncircumvent
systematic errors that might occur within\napplication of parametric
methods.","License":"GPL-
2","NeedsCompilation":"no","Package":"grofit","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"The package was developed to fit fit many growth curves
obtained\nunder different conditions","Version":"1.1.1-1"},"gromovlab":
{"Author":"Volkmar Liebscher","Depends":"R (>= 2.15.1)","Description":"Computing
Gromov-Hausdorff type l^p distances for labeled metric spaces. These distances were
introduced in V.Liebscher, Gromov meets Phylogenetics - new Animals for the Zoo of
Metrics on Tree Space. preprint arXiv:1504.05795, for phylogenetic trees but may
apply to much more situations.","Imports":"methods,igraph, ape, glpkAPI , quadprog,
cluster, stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gromovlab","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Gromov-Hausdorff Type Distances for Labeled Metric
Spaces","Version":"0.7-6"},"groupRemMap":{"Author":"Xianlong Wang
<xwan2@fhcrc.org>, Li Qin, Hexin Zhang, Yuzheng Zhang, Li Hsu, Pei Wang
<pei.wang@mssm.edu>","Description":"An implementation of the GroupRemMap penalty
for fitting regularized multivariate response regression models under the high-
dimension-low-sample-size setting. When the predictors naturally fall into groups,
the GroupRemMap penalty encourages procedure to select groups of predictors, while
control for the overall sparsity of the final model.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"groupRemMap","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Regularized Multivariate Regression for Identifying
Master\nPredictors Using the GroupRemMap Penalty","Version":"0.1-0"},"grouped":
{"Author":"Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl> and Spyridoula\nTsonaka
<s.tsonaka@lumc.nl>","Depends":"R(>= 2.0.0), MASS","Description":"Regression models
for grouped and coarse data, under the\nCoarsened At Random
assumption.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"grouped","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Regression Analysis of Grouped and Coarse
Data","Version":"0.6-0"},"growcurves":{"Author":"Terrance Savitsky","Depends":"R
(>= 3.2.2), Rcpp (>= 0.11.6)","Description":"Employs a non-parametric formulation
for by-subject random effect\nparameters to borrow strength over a constrained
number of repeated\nmeasurement waves in a fashion that permits multiple effects
per subject.\nOne class of models employs a Dirichlet process (DP) prior for the
subject\nrandom effects and includes an additional set of random effects
that\nutilize a different grouping factor and are mapped back to clients through\na
multiple membership weight matrix; e.g. treatment(s) exposure or dosage.\nA second
class of models employs a dependent DP (DDP) prior for the subject\nrandom effects
that directly incorporates the multiple membership pattern.","Imports":"reshape2
(>= 1.2.1), Formula (>= 1.0-0), ggplot2 (>= 1.0.1)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"growcurves","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat (>= 0.9.1)","Title":"Bayesian Semi and
Nonparametric Growth Curve Models that\nAdditionally Include Multiple Membership
Random Effects","Version":"0.2.4.0"},"growfunctions":{"Author":"Terrance
Savitsky","Depends":"R (>= 3.2.2), Rcpp (>= 0.11.6)","Description":"Estimates a
collection of time-indexed functions under\neither of Gaussian process (GP) or
intrinsic Gaussian Markov\nrandom field (iGMRF) prior formulations where a
Dirichlet process\nmixture allows sub-groupings of the functions to share the
same\ncovariance or precision parameters. The GP and iGMRF formulations\nboth
support any number of additive covariance or precision terms,\nrespectively,
expressing either or both of multiple trend and\nseasonality.","Imports":"Matrix(>=
1.1), spam(>= 0.41-0), mvtnorm(>= 1.0-0), ggplot2(>=\n1.0.1), reshape2(>=
1.2.2)","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"growfunctions","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat(>= 0.8.1)","Title":"Bayesian Non-
Parametric Dependent Models for Time-Indexed\nFunctional
Data","Version":"0.12"},"growthcurver":{"Author":"Kathleen sprouffske [aut,
cre]","Depends":"R (>= 2.10)","Description":"This is a simple package that fits the
logistic equation to\nmicrobial growth curve data (e.g., repeated absorbance
measurements\ntaken from a plate reader over time). From this fit, a variety
of\nmetrics are provided, including the maximum growth rate,\nthe doubling time,
the carrying capacity, the area under the logistic\ncurve, and the time to the
inflection point.","Imports":"caTools (>= 1.17.1), minpack.lm (>= 1.1), stats (>=
3.2.2),\ngraphics (>= 3.2.2), grDevices (>= 3.2.2)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"growthcurver","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat, knitr, dplyr, ggplot2","Title":"Simple
Metrics to Summarize Growth
Curves","URL":"https:\/\/github.com\/sprouffske\/growthcurver","Version":"0.2.1"},"
growthmodels":{"Author":"Daniel Rodriguez Perez","Description":"A compilation of
nonlinear growth models used in many areas","License":"GPL-
3","NeedsCompilation":"no","Package":"growthmodels","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Nonlinear Growth
Models","URL":"https:\/\/github.com\/drodriguezperez\/growthmodels","Version":"1.2.
0"},"growthrate":{"Author":"Sara Lopez-Pintado and Ian W.
McKeague","Depends":"Matrix, clime, mvtnorm","Description":"A nonparametric
empirical Bayes method for recovering\ngradients (or growth velocities) from
observations of smooth\nfunctions (e.g., growth curves) at isolated time
points.","License":"GPL-3 | file
LICENSE","NeedsCompilation":"no","Package":"growthrate","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Bayesian reconstruction of growth
velocity","Version":"1.3"},"growthrates":{"Author":"Thomas
Petzoldt","Depends":"lattice, deSolve","Description":"A collection of methods to
determine growth rates from\nexperimental data, in particular from batch
experiments and\nplate reader trials.","Imports":"stats, graphics, methods,
parallel, utils, FME","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"growthrates","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"knitr","Title":"Estimate Growth Rates from
Experimental
Data","URL":"https:\/\/github.com\/tpetzoldt\/growthrates","Version":"0.6.5"},"grpl
asso":{"Author":"Lukas Meier","Depends":"methods","Description":"Fits user
specified (GLM-) models with Group Lasso
penalty","License":"GPL","NeedsCompilation":"no","Package":"grplasso","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Title":"Fitting user specified models with
Group Lasso penalty","Version":"0.4-5"},"grppenalty":{"Author":"Dingfeng Jiang
<dingfengjiang at gmail.com>","Depends":"R (>= 2.9.0)","Description":"The package
implements the concave 1-norm and 2-norm group penalty in linear and logistic
regression.\nThe concave 1-norm group penalty includes 1-norm group SCAD and 1-norm
group MCP.\nThe concave 1-norm group penalty has bi-level selection features. That
is it selects variables at group and individual levels with proper tuning
parameters.\nThe concave 1-norm group penalty is robust to mis-specified group
information.\nThe concave 2-norm group penalty includes 2-norm group SCAD and 2-
norm group MCP. The concave 2-norm group penalty select variable at group level
only.\nThe package can also fit group Lasso, which is a special case of concave 2-
norm group penalty when the regularization parameter
kappa equals zero.\nThe highly efficient (block) coordinate descent algorithm
(CDA) is used to compute the solutions for both penalties in linear models.\nThe
highly stable and efficient (block) CDA and minimization-majorization approach are
used to compute the solution for both penalties in logistic models.\nIn the
computation of solution surface, the solution path along kappa is
implemented.\nThis provides a better solution path compared to the solution path
along lambda.\nThe package also provides a tuning parameter selection method based
on cross-validation for both linear and logistic models.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"grppenalty","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Concave 1-norm and 2-norm group penalty in linear and
logistic\nregression","URL":"http:\/\/www.r-project.org","Version":"2.1-
0"},"grpreg":{"Author":"Patrick Breheny","Depends":"R (>= 2.13.0),
Matrix","Description":"Efficient algorithms for fitting the regularization path
of\nlinear or logistic regression models with grouped penalties. This\nincludes
group selection methods such as group lasso, group MCP, and\ngroup SCAD as well as
bi-level selection methods such as the group\nexponential lasso, the composite MCP,
and the group bridge.","License":"GPL-
2","NeedsCompilation":"yes","Package":"grpreg","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Regularization Paths for Regression Models with
Grouped\nCovariates","Version":"2.8-1"},"grpregOverlap":{"Author":"Yaohui Zeng,
Patrick Breheny","Depends":"R (>= 3.1.0), Matrix, grpreg","Description":"Fit the
regularization path of linear, logistic or poisson models with\noverlapping grouped
covariates based on the latent group lasso approach. Latent\ngroup MCP\/SCAD as
well as bi-level selection methods, namely the group exponential\nlasso and the
composite MCP are also available. This package serves as an\nextension of R package
'grpreg' (by Dr. Patrick Breheny <patrick-breheny@uiowa.edu>)\nfor grouped variable
selection involving overlaps between groups.","License":"GPL-
2","NeedsCompilation":"no","Package":"grpregOverlap","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat","Title":"Penalized Regression Models
with Overlapping Grouped Covariates","Version":"1.0-1"},"grpss":{"Author":"Debin
Qiu, Jeongyoun Ahn","Description":"Contains the tools to screen grouped variables,
and select screened grouped variables afterwards. The main function grpss() can
perform the grouped variables screening as well as selection for ultra-high
dimensional data with group structure. The screening step is primarily used to
reduce the dimensions of data so that the selection procedure can easily handle the
moderate or low dimensions instead of ultra-high dimensions.","Imports":"MASS,
doParallel, foreach, grpreg","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"grpss","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Group Screening and Selection","Version":"3.0.1"},"grr":
{"Author":"Craig Varrichio <canthony427@gmail.com>","Depends":"R (>=
3.0.0)","Description":"Alternative implementations of some base R functions,
including sort, order, and match. Functions are simplified but can be faster or
have other advantages.","License":"GPL-
3","NeedsCompilation":"yes","Package":"grr","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Alternative Implementations of Base R
Functions","Version":"0.9.2"},"grt":{"Author":"Kazunaga Matsuki","Depends":"R (>=
2.10.1), grDevices, graphics, stats, utils, MASS,
rgl,\nmisc3d","Description":"Functions to generate and analyze data for
psychology\nexperiments based on the General Recognition Theory.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"grt","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"General Recognition Theory","Version":"0.2"},"gsDesign":
{"Author":"Keaven Anderson","Depends":"R (>= 3.0.0), xtable,
ggplot2","Description":"Derives group sequential designs and describes their
properties.","Imports":"plyr, methods","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"gsDesign","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr, scales","Title":"Group Sequential
Design","Version":"3.0-1"},"gsEasy":{"Author":"Daniel Greene","Depends":"R (>=
3.0.0)","Description":"R-interface to C++ implementation of the rank\/score
permutation based GSEA test (Subramanian et al 2005).","Imports":"Rcpp (>= 0.11.2),
ontologyIndex","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"gsEasy","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr","Title":"Gene Set Enrichment Analysis in
R","Version":"1.0"},"gsalib":{"Author":"Kiran Garimella","Description":"This
package contains utility functions used by the Genome Analysis Toolkit (GATK) to
load tables and plot data. The GATK is a toolkit for variant discovery in high-
throughput sequencing data.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"gsalib","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Utility Functions For
GATK","Version":"2.1"},"gsarima":{"Author":"Olivier Briet
<o.briet@gmail.com>","Depends":"R (>= 2.4.0)","Description":"Write SARIMA models in
(finite) AR representation and simulate\ngeneralized multiplicative seasonal
autoregressive moving average (time) series\nwith Normal \/ Gaussian, Poisson or
negative binomial distribution.","Imports":"MASS","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gsarima","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"gamlss.util (>= 4.2-0)","Title":"Two functions for
Generalized SARIMA time series simulation","URL":"http:\/\/www.r-
project.org","Version":"0.1-4"},"gsbDesign":{"Author":"Florian Gerber, Thomas
Gsponer","Depends":"gsDesign, lattice, grid,","Description":"Group Sequential
Operating Characteristics for Clinical,\nBayesian two-arm Trials with known Sigma
and Normal Endpoints.","Imports":"stats, graphics, grDevices,
3","NeedsCompilation":"no","Package":"gsbDesign","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Group Sequential Bayes Design","Version":"1.00"},"gset":
{"Author":"Fang Liu [aut, cre]","Depends":"R (>= 3.0.2), Hmisc, mvtnorm, MCMCpack,
graphics","Description":"calculate equivalence and futility boundaries based on the
exact bivariate $t$ test statistics for group sequential designs in studies with
equivalence hypotheses.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gset","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Group Sequential Design in Equivalence
Studies","URL":"http:\/\/www.r-project.org,
http:\/\/www3.nd.edu\/~fliu2\/","Version":"1.1.0"},"gsg":{"Author":"Michael
Morrissey, Krzysztof Sakrejda","Description":"gsg (gam selection gradients)
provides a unified approach to the regression analysis of selection from
longitudinal data collected from natural populations.","Imports":"mgcv, mvtnorm,
boot, numDeriv","License":"GPL-
2","NeedsCompilation":"no","Package":"gsg","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Calculation of selection
coefficients","Version":"2.0"},"gsheet":{"Author":"Max Conway [aut,
cre]","Description":"Simple package to download Google Sheets using just the
sharing\nlink. Spreadsheets can be downloaded as a data frame, or as plain text to
parse\nmanually. Google Sheets is the new name for Google Docs
Spreadsheets.","Imports":"rvest, stringr, magrittr, xml2","License":"GPL-
3","NeedsCompilation":"no","Package":"gsheet","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat","Title":"Download Google Sheets Using Just the
URL","URL":"https:\/\/github.com\/maxconway\/gsheet","Version":"0.2.1"},"gskat":
{"Author":"Xuefeng Wang","Depends":"R (>= 2.10), CompQuadForm, e1071, gee, geepack,
Matrix","Description":"Family based association test via GEE Kernel Machine score
test","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gskat","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"GEE_KM","Version":"1.0"},"gsl":{"Author":"Robin K. S.
Hankin; qrng functions by Duncan Murdoch and\nmultimin by Andrew
Clausen","Depends":"R (>= 2.10.0)","Description":"\nAn R wrapper for the special
functions and quasi random number\ngenerators of the Gnu Scientific
Library\n(http:\/\/www.gnu.org\/software\/gsl\/). See gsl-package.Rd for details
of\noverall package organization, and Misc.Rd for some functions that are\nwidely
used in the package, and some tips on installation.","License":"GPL-
2","NeedsCompilation":"yes","Package":"gsl","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"wrapper for the Gnu Scientific Library","Version":"1.9-
10.1"},"gsmoothr":{"Author":"Mark Robinson
<mark.robinson@imls.uzh.ch>","Depends":"R (>= 2.8.0), methods","Description":"Tools
rewritten in C for various smoothing tasks","License":"LGPL (>=
2.0)","NeedsCompilation":"yes","Package":"gsmoothr","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Smoothing tools","Version":"0.1.7"},"gss":
{"Author":"Chong Gu <chong@purdue.edu>","Depends":"R (>= 2.14.0),
stats","Description":"A comprehensive package for structural multivariate\nfunction
estimation using smoothing splines.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"gss","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"General Smoothing Splines","Version":"2.1-5"},"gsscopu":
{"Author":"Chong Gu <chong@purdue.edu>","Depends":"R (>= 2.14.0), stats, gss (>=
2.1-0)","Description":"A collection of routines for the estimation of copula
density\nand 2-D hazard function using smoothing splines.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"gsscopu","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Copula Density and 2-D Hazard Estimation using Smoothing
Splines","Version":"0.9-3"},"gstat":{"Author":"Edzer Pebesma [aut, cre],\nBenedikt
Graeler
[aut]","Depends":"R (>= 2.10)","Description":"Variogram modelling; simple,
ordinary and universal point or block (co)kriging; spatio-temporal kriging;
sequential Gaussian or indicator (co)simulation; variogram and variogram map
plotting utility functions.","Imports":"utils, stats, graphics, methods, lattice,
sp (>= 0.9-72), zoo,\nspacetime (>= 1.0-0), FNN","License":"GPL (>=
2.0)","NeedsCompilation":"yes","Package":"gstat","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"rgdal (>= 0.5.2), rgeos, fields, maps, mapdata,
maptools, xts","Title":"Spatial and Spatio-Temporal Geostatistical Modelling,
Prediction\nand
Simulation","URL":"https:\/\/github.com\/edzer\/gstat\/","Version":"1.1-
3"},"gsubfn":{"Author":"G. Grothendieck","Depends":"R (>= 2.15.0),
proto","Description":"gsubfn is like gsub but can take a replacement function\nor
certain other objects instead of the replacement string.\nMatches and back
references are input to the replacement function and\nreplaced by the function
output. gsubfn can be used to split strings\nbased on content rather than
delimiters and for quasi-perl-style string\ninterpolation. The package also has
facilities for translating formulas\nto functions and allowing such formulas in
function calls instead of\nfunctions. This can be used with R functions such as
apply, sapply,\nlapply, optim, integrate, xyplot, Filter and any other function
that\nexpects another function as an input argument or functions like cat\nor sql
calls that may involve strings where substitution is desirable.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gsubfn","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"boot, chron, doBy, grid, lattice, quantreg, reshape,
svUnit,\ntcltk, zoo","Title":"Utilities for strings and function
arguments","URL":"http:\/\/gsubfn.googlecode.com","Version":"0.6-6"},"gsw":
{"Author":"Dan Kelley [aut, cre, cph] (C wrapper plus R code, tests,
and\ndocumentation),\nClark Richards [aut, cph] (C wrapper plus R code, tests,
and\ndocumentation),\nWG127 SCOR\/IAPSO [aut, cph] (Original Matlab and derived
code)","Depends":"R (>= 2.15)","Description":"Provides an interface to the Gibbs
SeaWater (TEOS-10) C library, which derives from Matlab and other code written by
WG127 (Working Group 127) of SCOR\/IAPSO (Scientific Committee on Oceanic
Research \/ International Association for the Physical Sciences of the
Oceans).","Imports":"utils","License":"GPL (>= 2) | file
LICENSE","NeedsCompilation":"yes","Package":"gsw","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Gibbs Sea Water Functions","URL":"http:\/\/teos-
10.github.io\/GSW-R\/index.html","Version":"1.0-3"},"gtable":{"Author":"Hadley
Wickham [aut, cre]","Depends":"R (>= 2.14)","Description":"Tools to make it easier
to work with \"tables\" of 'grobs'.","Imports":"grid","License":"GPL-
2","NeedsCompilation":"no","Package":"gtable","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat, covr","Title":"Arrange 'Grobs' in
Tables","Version":"0.2.0"},"gtcorr":{"Author":"Sam Lendle
<lendle@stat.berkeley.edu>","Description":"This package provides functions to
calculate the\nefficiencies (expected tests per unit) of hierarchical and\nmatrix
group testing procedures. Efficiencies can be\ncalculated in the presense of
correlated responses under\nmultiple arrangements of clustesrs. Efficiencies can
also be\nevaluated in the presense of test error.","License":"GPL-
3","NeedsCompilation":"no","Package":"gtcorr","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Calculate efficiencies of group testing algorithms
with\ncorrelated responses","Version":"0.2-1"},"gte":{"Author":"Mohammad Hossein
Dehghan, Thierry Duchesne and Sophie
Baillargeon","Depends":"survival","Description":"Generalized Turnbull's estimator
proposed by Dehghan and Duchesne\n(2011).","License":"GPL-
2","NeedsCompilation":"yes","Package":"gte","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"interval","Title":"Generalized Turnbull's
Estimator","Version":"1.2-2"},"gtools":{"Author":"Gregory R. Warnes, Ben Bolker,
and Thomas Lumley","Depends":"R (>= 2.10)","Description":"Functions to assist in R
programming, including:\n- assist in developing, updating, and maintaining R and R
packages ('ask', 'checkRVersion',\n'getDependencies', 'keywords', 'scat'),\n-
calculate the logit and inverse logit transformations ('logit', 'inv.logit'),\n-
test if a value is missing, empty or contains only NA and NULL values
('invalid'),\n- manipulate R's .Last function ('addLast'),\n- define macros
('defmacro'),\n- detect odd and even integers ('odd', 'even'),\n- convert strings
containing non-ASCII characters (like single quotes) to plain ASCII ('ASCIIfy'),\n-
perform a binary search ('binsearch'),\n- sort strings containing both numeric and
character components ('mixedsort'),\n- create a factor variable from the quantiles
of a continuous variable ('quantcut'),\n- enumerate permutations and combinations
('combinations', 'permutation'),\n- calculate and convert between fold-change and
log-ratio ('foldchange',\n'logratio2foldchange', 'foldchange2logratio'),\n-
calculate probabilities and generate random numbers from Dirichlet
distributions\n('rdirichlet', 'ddirichlet'),\n- apply a function over adjacent
subsets of a vector ('running'),\n- modify the TCP\\_NODELAY ('de-Nagle') flag for
socket objects,\n- efficient 'rbind' of data frames, even if the column names don't
match ('smartbind'),\n- generate significance stars from p-values
('stars.pval'),\n- convert characters to\/from ASCII codes.","License":"GPL-
2","NeedsCompilation":"yes","Package":"gtools","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Various R Programming Tools","Version":"3.5.0"},"gtop":
{"Author":"Jairo Cugliari, Tim van Erven","Depends":"hts, quadprog,
lassoshooting","Description":"In hierarchical time series (HTS) forecasting, the
hierarchical relation between multiple time series is exploited to make better
forecasts. This hierarchical relation implies one or more aggregate consistency
constraints that the series are known to satisfy. Many existing approaches, like
for example bottom-up or top-down forecasting, therefore attempt to achieve this
goal in a way that guarantees that the forecasts will also be aggregate consistent.
This package provides with an implementation of the Game-Theoretically OPtimal
(GTOP) reconciliation method proposed in van Erven and Cugliari (2015), which is
guaranteed to only improve any given set of forecasts. This opens up new
possibilities for constructing the forecasts. For example, it is not necessary to
assume that bottom-level forecasts are unbiased, and aggregate forecasts may be
constructed by regressing both on bottom-level forecasts and on other covariates
that may only be available at the aggregate level.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"gtop","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Game-Theoretically OPtimal (GTOP) Reconciliation
Method","Version":"0.2.0"},"gtrendsR":{"Author":"Philippe Massicotte [aut,
cre],\nDirk Eddelbuettel [aut]","Depends":"R (>= 3.0)","Description":"An interface
for retrieving and displaying the information returned\nonline by Google Trends is
provided. Trends (number of hits) over the time as\nwell as geographic
representation of the results can be displayed.","Imports":"RCurl, googleVis, zoo,
2)","NeedsCompilation":"no","Package":"gtrendsR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"R Functions to Perform and Display Google Trends
Queries","URL":"https:\/\/github.com\/PMassicotte\/gtrendsR","Version":"1.3.3"},"gt
x":{"Author":"Toby Johnson <Toby.x.Johnson@gsk.com>","Depends":"R (>= 2.4.0),
survival","Description":"Assorted tools for genetic association analyses.
The\ncurrent focus is on implementing (either exactly or\napproximately) regression
analyses using summary statistics\ninstead of using subject-specific data. So far,
functions\nexist to support multi-SNP risk score analyses, multi-SNP\nconditional
regression analyses, and multi-phenotype analyses,\nusing summary statistics.
There are helper functions for\nreading and manipulating subject-specific genotype
data, which\nprovide a platform for calculating the summary statistics, or\nfor
using R to conduct other analyses not supported by specific\nGWAS analysis
tools.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gtx","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Genetics ToolboX","Version":"0.0.8"},"guess":
{"Author":"Gaurav Sood [aut, cre],\nKen Cor [aut]","Depends":"R (>=
3.2.1)","Description":"Adjust Estimates of Learning for Guessing. The package
provides\nstandard guessing correction, and a latent class model that
leverages\ninformative pre-post transitions. For details of the latent class
model,\nsee
<http:\/\/gsood.com\/research\/papers\/guess.pdf>.","Imports":"Rsolnp","License":"M
IT + file
LICENSE","NeedsCompilation":"no","Package":"guess","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr (>= 1.11), rmarkdown,
testthat","Title":"Adjust Estimates of Learning for
Guessing","URL":"http:\/\/github.com\/soodoku\/guess","Version":"0.1"},"gumbel":
{"Author":"Anne-Lise Caillat [ctb], Christophe Dutang [aut,cre], Veronique Larrieu
[ctb] and Triet Nguyen [ctb]","Depends":"R (>= 2.10.0)","Description":"Provides
probability functions (cumulative distribution and density functions), simulation
function (Gumbel copula multivariate simulation) and estimation functions (Maximum
Likelihood Estimation, Inference For Margins, Moment Based Estimation and Canonical
Maximum Likelihood).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gumbel","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"The Gumbel-Hougaard Copula","Version":"1.10-
1"},"gunsales":{"Author":"Gregor Aisch,
Josh Keller and Dirk Eddelbuettel","Depends":"R (>=
2.10)","Description":"Statistical analysis of monthly background checks of gun
purchases for the New York Times\nstory \"What Drives Gun Sales: Terrorism, Obama
and Calls for Restrictions\"
at\n<http:\/\/www.nytimes.com\/interactive\/2015\/12\/10\/us\/gun-sales-terrorism-
obama-restrictions.html?> is provided.","Imports":"readr, dplyr, stringr, seasonal,
ggplot2, data.table, zoo,\nx13binary","License":"Apache License (==
2)","NeedsCompilation":"no","Package":"gunsales","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr","Title":"Statistical Analysis of Monthly
Background Checks of Gun\nPurchases","Version":"0.1.1"},"gvc":{"Author":"Bastiaan
Quast [aut, cre],\nVictor Kummritz [aut]","Depends":"R (>=
2.10)","Description":"Several tools for Global Value Chain ('GVC') analysis
are\nimplemented.","Imports":"decompr, diagonals","License":"GPL-
3","NeedsCompilation":"no","Package":"gvc","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"testthat, knitr","Title":"Global Value Chains
Tools","URL":"http:\/\/qua.st\/gvc,
https:\/\/github.com\/bquast\/gvc","Version":"0.5.2"},"gvcm.cat":{"Author":"Margret
Oelker","Depends":"R (>= 2.10.0), Matrix, MASS, splines,
mgcv","Description":"Generalized structured regression models with regularized
categorical effects, categorical effect modifiers, continuous effects and smooth
effects.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gvcm.cat","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Regularized Categorical Effects\/Categorical
Effect\nModifiers\/Continuous\/Smooth Effects in GLMs","Version":"1.9"},"gvlma":
{"Author":"Edsel A. Pena <pena@stat.sc.edu> and Elizabeth H. Slate
<slateeh@musc.edu>","Depends":"R (>= 2.1.1)","Description":"Methods from the paper:
Pena, EA and Slate, EH, \"Global Validation of Linear Model Assumptions,\" J.
American Statistical Association, 101(473):341-354,
2006.","License":"GPL","NeedsCompilation":"no","Package":"gvlma","Repository":"http
:\/\/cran.csiro.au\/src\/contrib","Title":"Global Validation of Linear Models
Assumptions","Version":"1.0.0.2"},"gwerAM":{"Author":"Benjamin Stich
<stich@mpipz.mpg.de>, Bettina Mueller\n<b.mueller@uni-hohenheim.de>, Hans-Peter
Piepho\n<piepho@uni-hohenheim.de>","Depends":"R (>= 2.10.0), MASS,
Matrix","Description":"This package provides functions to calculate
the\nsignificance threshold for controlling the type I error rate in\nmixed-model
association mapping analyses.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gwerAM","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Controlling the genome-wide type I error rate in
association\nmapping experiments","URL":"http:\/\/www.r-
project.org","Version":"1.0"},"gwrr":{"Author":"David Wheeler","Depends":"fields,
lars","Description":"Fits geographically weighted regression (GWR) models and\nhas
tools to diagnose and remediate collinearity in the GWR\nmodels. Also fits
geographically weighted ridge regression\n(GWRR) and geographically weighted lasso
(GWL) models.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"gwrr","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Fits geographically weighted regression models with
diagnostic\ntools","Version":"0.2-1"},"gyriq":{"Author":"Martin Leclerc and Lajmi
Lakhal Chaieb","Depends":"R (>= 2.10)","Description":"SNP-set association testing
for censored phenotypes in the presence of intrafamilial
correlation.","Imports":"CompQuadForm, irlba, mvtnorm, survival","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"gyriq","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"snowfall","Title":"Kinship-Adjusted Survival SNP-Set
Analysis","Version":"1.0.2"},"h2o":{"Author":"Spencer Aiello, Tom Kraljevic and
Petr Maj, with contributions from the\nH2O.ai team","Depends":"R (>= 2.13.0),
methods, statmod, stats","Description":"R scripting functionality for H2O, the open
source\nmath engine for big data that computes parallel distributed\nmachine
learning algorithms such as generalized linear models,\ngradient boosting machines,
random forests, and neural networks\n(deep learning) within various cluster
environments.","Imports":"graphics, RCurl, jsonlite, tools,
utils","License":"Apache License (==
2.0)","NeedsCompilation":"no","Package":"h2o","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"devtools, roxygen2, testthat, ggplot2,
mlbench","Title":"R Interface for
H2O","URL":"http:\/\/www.h2o.ai","Version":"3.8.1.3"},"h5":{"Author":"Mario Annau
[aut, cre]","Depends":"R (>= 3.2)","Description":"S4 Interface to the 'HDF5'
library supporting fast storage and\nretrieval of R-objects like vectors, matrices
and arrays to binary files in\na language independent format. The 'HDF5' format can
therefore be used as\nan alternative to R's save\/load mechanism. Since h5 is able
to access only\nsubsets of stored data it can also handle data sets which do not
fit into\nmemory.","Imports":"Rcpp (>= 0.11.5), methods","License":"BSD_2_clause +
file
LICENSE","NeedsCompilation":"yes","Package":"h5","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat, roxygen2, RCurl,
highlight","Title":"Interface to the 'HDF5'
Library","URL":"http:\/\/h5.predictingdaemon.com
https:\/\/github.com\/mannau\/h5","Version":"0.9.5"},"hBayesDM":{"Author":"Woo-
Young Ahn [aut, cre],\nNate Haines [aut],\nLei Zhang [aut]","Depends":"rstan, loo,
R (>= 3.0.2)","Description":"Fit an array of decision-making tasks with
computational models in a hierarchical Bayesian framework. Can perform hierarchical
Bayesian analysis of various computational models with a single line of
coding.","Imports":"grid, parallel, mail, modeest, ggplot2","License":"GPL-
3","NeedsCompilation":"no","Package":"hBayesDM","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Hierarchical Bayesian Modeling of Decision-Making
Tasks","URL":"http:\/\/u.osu.edu\/ccsl\/codedata\/hbayesdm\/","Version":"0.2.1"},"h
SDM":{"Author":"Ghislain Vieilledent, Cory Merow, JÃ©rÃ´me GuÃ©lat, Andrew M.
Latimer, Marc KÃ©ry, Alan E. Gelfand, Adam M. Wilson, FrÃ©dÃ©ric Mortier and John
A. Silander Jr.","Description":"hSDM is an R package for estimating parameters of
hierarchical Bayesian species distribution models. Such models allow interpreting
the observations (occurrence and abundance of a species) as a result of several
hierarchical processes including ecological processes (habitat suitability, spatial
dependence and anthropogenic disturbance) and observation processes (species
detectability). Hierarchical species distribution models are essential for
accurately characterizing the environmental response of species, predicting their
probability of occurrence, and assessing uncertainty in the model
results.","Imports":"coda","License":"GPL-3 | file
LICENSE","NeedsCompilation":"yes","Package":"hSDM","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr, raster, sp","Title":"hierarchical Bayesian
species distribution
models","URL":"http:\/\/hSDM.sf.net","Version":"1.4"},"haarfisz":{"Author":"Piotr
Fryzlewicz <P.Fryzlewicz@lse.ac.uk>","Depends":"R (>= 2.0),
wavethresh","Description":"A Haar-Fisz algorithm for Poisson intensity
estimation","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"haarfisz","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Software to perform Haar Fisz
transforms","Version":"4.5"},"hail":{"Author":"Oliver Keyes","Description":"Read
data from the City of Portland's 'HYDRA' (http:\/\/or.water.usgs.gov\/precip\/)
rainfall datasets within R.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"hail","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat","Title":"Read HYDRA Rainfall
Data","URL":"https:\/\/github.com\/ironholds\/hail","Version":"0.1.0"},"hamlet":
{"Author":"Teemu Daniel Laajala <teelaa@utu.fi>","Depends":"R (>=
3.0.0)","Description":"Various functions and algorithms are provided here for
solving optimal matching tasks in the context of preclinical cancer studies.
Further, various helper and plotting functions are provided for unsupervised and
supervised machine learning as well as longitudinal mixed-effects modeling of tumor
growth response patterns.","Imports":"grDevices, graphics, stats,
2)","NeedsCompilation":"no","Package":"hamlet","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"lme4, nlme, amap, nbpMatching, lattice, lmerTest,
xtable","Title":"Hierarchical Optimal Matching and Machine Learning
Toolbox","Version":"0.9.4-2"},"hapassoc":{"Author":"K. Burkett
<kburkett@uottawa.ca>, B. McNeney <mcneney@sfu.ca>, J.\nGraham
<jgraham@stat.sfu.ca>, with code for case-control data\ncontributed by Zhijian Chen
<z11chen@math.uwaterloo.ca>","Depends":"R (>= 2.6.0), stats","Description":"The
following R functions are used for inference of trait\nassociations with haplotypes
and other covariates in\ngeneralized linear models. The functions are
developed\nprimarily for data collected in cohort or cross-sectional\nstudies. They
can accommodate uncertain haplotype phase and\nhandle missing genotypes at some
SNPs.","License":"GPL-
2","NeedsCompilation":"yes","Package":"hapassoc","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Inference of Trait Associations with SNP Haplotypes and
Other\nAttributes using the EM
Algorithm","URL":"http:\/\/stat.sfu.ca\/statgen\/research\/hapassoc.html","Version"
:"1.2-8"},"haplo.ccs":{"Author":"Benjamin French and Thomas Lumley","Depends":"R
(>= 2.13.0), haplo.stats, survival","Description":"'haplo.ccs' estimates haplotype
and covariate relative\nrisks in case-control data by weighted logistic
regression.\nDiplotype probabilities, which are estimated by EM computation\nwith
progressive insertion of loci, are utilized as weights.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"haplo.ccs","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Estimate
Haplotype Relative Risks in Case-Control Data","Version":"1.3.1"},"haplo.stats":
{"Author":"Sinnwell JP, Schaid DJ","Depends":"R (>= 3.0.0), methods, stats,
graphics","Description":"Routines for the analysis of indirectly measured
haplotypes. The statistical methods assume that all subjects are unrelated and that
haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The
main functions are: haplo.em(), haplo.glm(), haplo.score(), and haplo.power(); all
of which have detailed examples in the vignette.","Imports":"rms","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"haplo.stats","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"R.rsp","Title":"Statistical Analysis of
Haplotypes with Traits and Covariates\nwhen Linkage Phase is
Ambiguous","URL":"\nhttp:\/\/www.mayo.edu\/research\/labs\/statistical-genetics-
genetic-epidemiology\/software","Version":"1.7.7"},"haplotyper":
{"Author":"Sebastian Simondi <sebastian.simondi@gmail.com> and Gaston Quero,
with\ncontributions from Victoria Bonnecarrere and Lucia Gutierrez","Depends":"R
(>= 2.10)","Description":"Function to identify haplotypes\nwithin QTL
(Quantitative Trait Loci). One haplotype is a combination of SNP\n(Single
Nucleotide Polymorphisms) within the QTL. This function groups\ntogether all
individuals of a population with the same haplotype.\nEach group contains
individual with the same allele in each SNP,\nwhether or not missing data. Thus,
haplotyper groups individuals,\nthat to be imputed, have a non-zero probability of
having the same alleles\nin the entire sequence of SNP's. Moreover, haplotyper
calculates such\nprobability from relative frequencies.","Imports":"graphics,
3","NeedsCompilation":"no","Package":"haplotyper","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr, rmarkdown, testthat","Title":"Tool for
Clustering Genotypes in Haplotypes","Version":"0.1"},"haplotypes":{"Author":"Caner
Aktas","Depends":"R (>= 3.1.1), methods, network","Description":"Provides S4
classes and methods for reading and manipulating aligned DNA sequences, supporting
an indel coding methods (only simple indel coding method is available in the
current version), showing base substitutions and indels, calculating absolute
pairwise distances between DNA sequences, and inferring haplotypes from DNA
sequences or user provided absolute character difference matrix. This package also
includes S4 classes and methods for estimating genealogical relationships among
haplotypes using statistical parsimony.","License":"GPL-
2","NeedsCompilation":"no","Package":"haplotypes","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"sna","Title":"Haplotype Inference and Statistical
Analysis of Genetic\nVariation","URL":"http:\/\/cran.r-
project.org,\nhttps:\/\/biolsystematics.wordpress.com\/r\/","Version":"1.0"},"harve
str":{"Author":"Andrew Redd","Description":"Functions for easy simulation and
reproducability.","Imports":"parallel, plyr, digest","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"harvestr","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat, dostats, doParallel, foreach, MCMCpack,
boot","Title":"A Parallel Simulation Framework","Version":"0.6.0"},"hash":
{"Author":"Christopher Brown","Depends":"R (>= 2.12.0), methods,
utils","Description":"This package implements a data structure similar to
hashes\nin Perl and dictionaries in Python but with a purposefully R\nflavor. For
objects of appreciable size, access using hashes\noutperforms native named lists
and vectors.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hash","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat","Title":"Full feature implementation of
hash\/associated\narrays\/dictionaries","Version":"2.2.6"},"hashFunction":
{"Author":"Xiaowei Zhan","Description":"This package provides common non-
cryptographic hash\nfunctions for R. For example, SpookyHash, Murmur3Hash,
Google\nCityHash.","License":"GPL","NeedsCompilation":"yes","Package":"hashFunction
","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"R.utils,
bitops","Title":"A collection of non-cryptographic hash
functions","Version":"1.0"},"hashids":{"Author":"Alex Shum [aut, cre],\nIvan Akimov
[aut] (original author of hashids -- implemented in\njavascript),\nDavid Aurelio
[ctb] (implemented hashids in python 2 and 3)","Depends":"R (>=
3.2.2)","Description":"An R port of the hashids library. hashids generates
YouTube-like hashes from integers or vector of integers. Hashes generated from
integers are relatively short, unique and non-seqential. hashids can be used to
generate unique ids for URLs and hide database row numbers from the user. By
default hashids will avoid generating common English cursewords by preventing
certain letters being next to each other. hashids are not one-way: it is easy to
encode an integer to a hashid and decode a hashid back into an
integer.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"hashids","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat","Title":"Generate Short Unique YouTube-
Like IDs (Hashes) from Integers","URL":"https:\/\/github.com\/ALShum\/hashids-r\/,
http:\/\/hashids.org","Version":"0.9.0"},"hashmap":{"Author":"Nathan Russell [aut,
cre]","Depends":"methods","Description":"Provides a hash table class for fast\nkey-
value storage of atomic vector types.\nInternally, hashmap makes extensive use of
Rcpp, boost::variant,\nand boost::unordered_map to achieve high performance, type-
safety,\nand versatility, while maintaining compliance with the C++98
standard.","Imports":"Rcpp (>= 0.12.4)","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"hashmap","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"devtools, microbenchmark, testthat","Title":"The
Faster Hash Map","URL":"https:\/\/github.com\/nathan-
russell\/hashmap","Version":"0.1.0"},"hashr":{"Author":"Mark van der Loo [aut,
cre],\nPaul Hsieh [ctb]","Description":"Apply the SuperFastHash algorithm to any R
object. Hash whole R objects or,\nfor vectors or lists, hash R objects to obtain a
set of hash values that is stored\nin a structure equivalent to the
input.","License":"GPL-
3","NeedsCompilation":"yes","Package":"hashr","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat","Title":"Hash R Objects to Integers
Fast","URL":"https:\/\/github.com\/markvanderloo\/hashr","Version":"0.1.0"},"hasseD
iagram":{"Author":"Krzysztof Ciomek","Depends":"Rgraphviz (>= 2.6.0), grid (>=
3.0.2)","Description":"Drawing Hasse diagram - visualization of transitive
reduction of a finite partially ordered set.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"hasseDiagram","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Drawing Hasse
diagram","Version":"0.1.1"},"haven":{"Author":"Hadley Wickham [aut, cre],\nEvan
Miller [aut, cph] (Author of included ReadStat code),\nRStudio [cph]","Depends":"R
(>= 3.1.0)","Description":"Import foreign statistical formats into R via the
embedded\nReadStat C library (https:\/\/github.com\/WizardMac\/ReadStat). Package
includes\npreliminary support for writing Stata and SPSS formats.","Imports":"Rcpp
LICENSE","NeedsCompilation":"yes","Package":"haven","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"dplyr, testthat, knitr","Title":"Import SPSS,
Stata and SAS
Files","URL":"https:\/\/github.com\/hadley\/haven,\nhttps:\/\/github.com\/WizardMac
\/ReadStat","Version":"0.2.0"},"hawkes":{"Author":"Riadh Zaatour
<zaatour_riadh@yahoo.fr>","Depends":"R (>= 3.0.2)","Description":"The package
allows to simulate Hawkes process both in univariate and multivariate settings. It
gives functions to compute different moments of the number of jumps of the process
on a given interval, such as mean, variance or autocorrelation of process jumps on
time intervals separated by a lag.","Imports":"Rcpp (>= 0.11.1)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"hawkes","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Hawkes process simulation and calibration
toolkit","Version":"0.0-4"},"hazus":{"Author":"Gopi Goteti
<my.ration.shop@gmail.com>","Depends":"R (>= 3.0.2)","Description":"Damage
Functions (DFs), also known as\nVulnerability Functions, associate the physical
damage\nto a building or a structure (and also its contents and\ninventory) from
natural disasters to financial damage.\nThe Federal Emergency Management Agency
(FEMA) in USA\ndeveloped several thousand DFs and these serve as a\nbenchmark in
natural catastrophe modeling, both in\nacademia and industry. However, these DFs
and their\ndocumentation are buried within the HAZUS software are\nnot easily
accessible for analysis and visualization.\nThis package provides more than 1300
raw DFs used by FEMA's\nHAZUS software and also functionality to extract
and\nvisualize DFs specific to the flood hazard. The vignette\nincluded with this
package demonstrates its use.","Imports":"reshape2","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hazus","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"ggplot2, knitr","Title":"Damage functions from FEMA's
HAZUS software for use in modeling\nfinancial losses from natural
disasters","Version":"0.1"},"hbim":{"Author":"Michael P. Fay","Depends":"R (>=
2.5.0), stats, mvtnorm","Description":"Calculate expected relative risk and
proportion protected assuming normally distributed log10 transformed antibody dose
for several component vaccine. Uses Hill models for each component which are
combined under Bliss independence.","License":"GPL-
2","NeedsCompilation":"no","Package":"hbim","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Hill\/Bliss Independence Model for Combination
Vaccines","Version":"1.0.3"},"hbm":{"Author":"Yoli
Shavit","Depends":"R (>= 3.0.2)","Description":"A package for building
hierarchical block matrices from association matrices and for performing multi-
scale analysis. It specifically targets chromatin contact maps, generated from
high-throughput chromosome conformation capture data, such as 5C and Hi-C, and
provides methods for detecting movements and for computing chain hierarchy and
region communicability across scales.","Imports":"Matrix, foreach,
2)","NeedsCompilation":"no","Package":"hbm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Hierarchical Block Matrix Analysis","Version":"1.0"},"hbmem":
{"Author":"Michael S. Pratte","Depends":"R (>= 1.8.0),
methods","Description":"Contains functions for fitting hierarchical versions
of\nEVSD, UVSD, DPSD, DPSD with d' restricted to be positive, and\nour gamma signal
detection model to recognition memory\nconfidence-ratings data.","License":"LGPL
(>=
2.0)","NeedsCompilation":"yes","Package":"hbmem","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Hierarchical Bayesian Analysis of Recognition
Memory","URL":"http:\/\/pcl.missouri.edu","Version":"0.3"},"hbsae":{"Author":"Harm
Jan Boonstra","Depends":"R (>= 2.10)","Description":"Functions to compute small
area estimates based on a basic\narea or unit-level model. The model is fit using
restricted\nmaximum likelihood, or in a hierarchical Bayesian way. In the\nlatter
case numerical integration is used to average over the\nposterior density for the
between-area variance. The output\nincludes the model fit, small area estimates
and corresponding\nMSEs, as well as some model selection measures.
Additional\nfunctions provide means to compute aggregate estimates and\nMSEs, to
minimally adjust the small area estimates to\nbenchmarks at a higher aggregation
level, and to graphically\ncompare different sets of small area
estimates.","Imports":"Matrix, arm","License":"GPL-
3","NeedsCompilation":"no","Package":"hbsae","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Hierarchical Bayesian Small Area
Estimation","Version":"1.0"},"hcc":{"Author":"Yun Shi and A. I.
McLeod","Depends":"R (>= 2.1.0)","Description":"A new diagnostic check for model
adequacy in regression\nand generalized linear models is
implemented.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hcc","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Hidden correlation
check","URL":"http:\/\/www.stats.uwo.ca\/faculty\/aim","Version":"0.54"},"hcci":
{"Author":"Pedro Rafael Diniz Marinho [aut, cre], Francisco Cribari Neto [aut,
ctb]","Depends":"R (>= 2.10.0)","Description":"This package calculates the interval
estimates for the parameters of\nlinear models heteroscedastic regression using
bootstrap - (Wild Bootstrap) and double\nbootstrap-t (Wild Bootstrap). It is also
possible to calculate confidence intervals using\nthe percentile bootstrap and
percentile bootstrap double. It is possible to calculate\nconsistent estimates of
the covariance matrix of the parameters of linear regression models\nwith
heteroskedasticity of unknown form. The package also provides function to
calculate\nconsistently the covariance matrix of the parameters of linear models
with heteroskedasticity\nof unknown form.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hcci","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Interval estimation for the parameters of linear models
with\nheteroskedasticity (Wild Bootstrap)","URL":"http:\/\/www.r-
project.org","Version":"1.0.0"},"hcp":{"Author":"Stephen J.Ganocy, Jiayang Sun, and
Yulei Wang","Description":"Estimation of parameters in 3-segment (i.e. 2 change-
point)\nregression models with heteroscedastic variances is provided based on
both\nlikelihood and hybrid Bayesian approaches, with and without
continuity\nconstraints at the change points.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"hcp","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Change Point Estimation for Regression with Heteroscedastic
Data","Version":"0.1"},"hda":{"Author":"Gero Szepannek","Description":"Functions to
perform dimensionality reduction for classification if the covariance matrices of
the classes are unequal.","Imports":"e1071","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hda","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"mvtnorm, klaR, MASS","Title":"Heteroscedastic Discriminant
Analysis","Version":"0.2-14"},"hddplot":{"Author":"John Maindonald","Depends":"R
(>= 3.0.0)","Description":"Cross-validated linear discriminant calculations
determine\nthe optimum number of features. Test and training scores
from\nsuccessive cross-validation steps determine, via a principal\ncomponents
calculation, a low-dimensional global space onto which test\nscores are projected,
in order to plot them. Further functions are\nincluded that serve didactic
purposes.","Imports":"MASS, multtest","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hddplot","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr","Title":"Use known groups in high-dimensional
data to derive scores
for\nplots","URL":"http:\/\/www.maths.anu.edu.au\/~johnm","Version":"0.56"},"hddtoo
ls":{"Author":"Claudia Vitolo [aut, cre], Simon Moulds [aut]","Depends":"R (>=
3.0.2)","Description":"Facilitates discovery and handling of hydrological
data,\nnon-programmatic access to catalogues and databases.","Imports":"sp, rgdal,
raster, RCurl, XML, zoo","License":"GPL-
3","NeedsCompilation":"no","Package":"hddtools","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Hydrological Data Discovery
Tools","URL":"http:\/\/cvitolo.github.io\/r_hddtools\/","Version":"0.2.4"},"hdeco":
{"Author":"Tarmo K. Remmel, Sandor Kabos, and Ferenc (Ferko)
Csillag","Depends":"R(>= 2.0.1)","Description":"A flexible and hierarchical
framework for comparing categorical map composition and configuration (spatial
pattern) along spatial, thematic, or external grouping variables. Comparisons are
based on measures of mutual information between thematic classes (colours) and
location (spatial partitioning). Results are returned in textual, tabular, and
graphical forms.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hdeco","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Hierarchical DECOmposition of Entropy for Categorical
Map\nComparisons","Version":"0.4.1"},"hdi":{"Author":"Lukas Meier [aut, cre], Ruben
Dezeure [aut], Nicolai Meinshausen [aut], Martin Maechler [aut], Peter Buehlmann
[aut]","Depends":"scalreg","Description":"Implementation of multiple approaches to
perform inference in high-dimensional models.","Imports":"grDevices, graphics,
stats, parallel, MASS, glmnet,
linprog","License":"GPL","NeedsCompilation":"no","Package":"hdi","Repository":"http
:\/\/cran.csiro.au\/src\/contrib","Suggests":"Matrix","Title":"High-Dimensional
Inference","Version":"0.1-6"},"hdlm":{"Author":"Taylor B. Arnold","Depends":"R (>=
3.0), glmnet, foreach, MASS, iterators","Description":"Mimics the lm function found
in the package stats to fit\nhigh dimensional regression models with point
estimates,\nstandard errors, and p-values. Methods for printing and\nsummarizing
the results are given.","License":"GPL (>=
2.0)","NeedsCompilation":"yes","Package":"hdlm","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Fitting High Dimensional Linear
Models","Version":"1.2"},"hdm":{"Author":"Martin Spindler [cre, aut],\nVictor
Chernozhukov [aut],\nChristian Hansen [aut]","Depends":"R (>=
3.0.0)","Description":"Implementation of selected high-dimensional statistical and
econometric methods for estimation and inference. Efficient estimators and
uniformly valid confidence intervals for various low-dimensional causal\/structural
parameters are provided which appear in high-dimensional approximately sparse
models. Including functions for fitting heteroscedastic robust Lasso regressions
with non-Gaussian errors and for instrumental variable (IV) and treatment effect
estimation in a high-dimensional setting. Moreover, the methods enable valid post-
selection inference and rely on a theoretically grounded, data-driven choice of the
penalty.","Imports":"MASS, glmnet, ggplot2, checkmate","License":"GPL-
3","NeedsCompilation":"no","Package":"hdm","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"testthat, knitr, xtable","Title":"High-Dimensional
Metrics","Version":"0.1.0"},"hdnom":{"Author":"Miaozhu Li <miaozhu.li@duke.edu>,
Nan Xiao <nanx@uchicago.edu>","Depends":"R (>= 3.0.2)","Description":"Build
nomograms for high-dimensional Cox models, with support for\nreproducible model
validation, calibration, and comparison.","Imports":"survival, glmnet, penalized,
ncvreg, rms, foreach, survAUC,\nggplot2,
gridExtra","License":"GPL","NeedsCompilation":"no","Package":"hdnom","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Suggests":"knitr, doParallel, Hmisc,
mice","Title":"Nomograms for High-Dimensional Cox
Models","URL":"http:\/\/hdnom.org","Version":"3.6"},"hdr":{"Author":"Eric Persson
[aut, cre]","Depends":"R (>= 3.2.3)","Description":"Provides a complete interface
to the United Nations\nDevelopment Programme Human Development Report API
(<http:\/\/hdr.undp.org>). The API\nincludes a large amount of human development
data, including all the series used\nto compute the Human Development Index (HDI),
as well as the HDI
itself.","Imports":"httr","License":"CC0","NeedsCompilation":"no","Package":"hdr","
Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"ggplot2, dplyr,
tidyr, knitr, rmarkdown","Title":"Interface to the UNDR Human Development Report
API","URL":"http:\/\/hdr.undp.org ;
https:\/\/github.com\/expersso\/hdr","Version":"0.1"},"hdrcde":{"Author":"Rob J
Hyndman <Rob.Hyndman@monash.edu> with contributions from Jochen Einbeck and Matt
Wand","Depends":"R (>=
2.15), mvtnorm","Description":"Computation of highest density regions in one and
two dimensions,\nkernel estimation of univariate density functions conditional on
one covariate,\nand multimodal regression.","Imports":"locfit, ash, ks,
KernSmooth","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"hdrcde","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Highest density regions and conditional density
estimation","URL":"http:\/\/www.robjhyndman.com\/software\/hdrcde","Version":"3.1"}
,"heatex":{"Author":"Kerry Atkins","Description":"The heatex package calculates
heat storage in the body and\nthe components of heat exchange (conductive,
convective,\nradiative, and evaporative) between the body and the\nenvironment
during physical activity based on the principles of\npartitional calorimetry. The
program enables heat exchange\ncalculations for a range of environmental conditions
when\nwearing various clothing ensembles.","License":"GPL-
3","NeedsCompilation":"no","Package":"heatex","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Heat exchange calculations during physical
activity","Version":"1.0"},"heatmap.plus":{"Author":"Allen Day
<allenday@ucla.edu>","Description":"Allows heatmap matrix to have non-identical X-
and\nY-dimensions. Allows multiple tracks of annotation for\nRowSideColors and
ColSideColors.","License":"GPL","NeedsCompilation":"no","Package":"heatmap.plus","R
epository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Heatmap with more
sensible behavior","Version":"1.3"},"heatmap3":{"Author":"Shilin Zhao, Yan Guo,
Quanhu Sheng, Yu Shyr","Description":"An improved heatmap package.
Completely\ncompatible with the original R function 'heatmap',\nand provides more
powerful and convenient features.","Imports":"fastcluster","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"heatmap3","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr","Title":"An Improved Heatmap
Package","Version":"1.1.1"},"heatmapFit":{"Author":"Justin Esarey [aut,
cre],\nAndrew Pierce [aut],\nJericho Du [aut]","Depends":"R (>=
3.1.1)","Description":"Generates a fit plot for diagnosing misspecification in
models of\nbinary dependent variables, and calculates the related heatmap
fit\nstatistic (Esarey and Pierce, 2012).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"heatmapFit","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Fit statistic for binary dependent variable
models","Version":"2.0.2"},"heavy":{"Author":"Felipe
Osorio","Description":"Functions to perform robust estimation considering heavy-
tailed distributions.\nCurrently, the package includes linear regression, linear
mixed-effect models, multivariate\nlocation and scatter estimation, multivariate
regression, penalized splines and random\nvariate generation.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"heavy","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Robust Estimation Using Heavy-Tailed
Distributions","URL":"http:\/\/www.ies.ucv.cl\/heavy\/","Version":"0.3"},"heemod":
{"Author":"Kevin Zarca [aut], Antoine Filipovic-Pierucci [aut,cre]","Depends":"R
(>= 3.2.2)","Description":"Health Economic Evaluation Modelling.\nMarkov models
(homogeneous and non-homogeneous)\nfor health economic evaluation. Model
comparison,\nsensitivity and probabilistic analysis.","Imports":"lazyeval (>= 0.1),
dplyr (>= 0.4), diagram (>= 1.6), mvnfast\n(>= 0.1), logitnorm (>= 0.8), ggplot2
(>= 2.0), tidyr (>= 0.3),\nDT (>= 0.1), memoise (>= 1.0.0), rgho","License":"GPL
(>=
3)","NeedsCompilation":"no","Package":"heemod","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat, knitr, rmarkdown","Title":"Models for Health
Economic Evaluation","URL":"https:\/\/github.com\/pierucci\/heemod,
https:\/\/pierucci.github.io","Version":"0.3.1"},"hellno":{"Author":"Peter
Meissner","Description":"Base R's default setting for 'stringsAsFactors'
within\n'data.frame()' and 'as.data.frame()' is supposedly the most often
complained\nabout piece of code in the R infrastructure. The 'hellno' package
provides\nan explicit solution without changing R itself or having to mess around
with\noptions. It tries to solve this problem by providing
alternative\n'data.frame()' and 'as.data.frame()' functions that are in fact
simple\nwrappers around base R's 'data.frame()' and 'as.data.frame()'
with\n'stringsAsFactors' option set to 'HELLNO' ( which in turn equals FALSE )\nby
default.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"hellno","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat","Title":"Providing
'stringsAsFactors=FALSE' Variants of 'data.frame()'\nand
'as.data.frame()'","URL":"https:\/\/github.com\/petermeissner\/hellno","Version":"0
.0.1"},"helloJavaWorld":{"Author":"Tobias Verbeke","Depends":"R (>= 2.7.0), rJava
(>= 0.5-0)","Description":"A dummy package to demonstrate how to interface to a
jar\nfile that resides inside an R package.","License":"GPL-
3","NeedsCompilation":"no","Package":"helloJavaWorld","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Hello Java World","Version":"0.0-9"},"helsinki":
{"Author":"Juuso Parkkinen, Leo Lahti, Joona Lehtomaki","Depends":"R (>= 3.1.0),
maptools, RCurl","Description":"Tools for accessing various open data sources in
the Helsinki\nregion in Finland. Current data sources include\nthe Real Estate
Department (district maps),\nthe Environmental Services Authority,\nService Map
API,\nLinked Events API and\nHelsinki Region Infoshare statistics
API.","Imports":"rjson, sp","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"helsinki","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"R Tools for Helsinki Open
Data","URL":"https:\/\/github.com\/rOpenGov\/helsinki","Version":"0.9.27"},"heplots
":{"Author":"John Fox [aut], Michael Friendly [aut, cre], Georges Monette
[ctb]","Depends":"R (>= 2.10), car","Description":"Provides HE plot and other
functions for visualizing hypothesis tests in multivariate linear models.\nHE plots
represent sums-of-squares-and-products matrices for linear hypotheses and for error
using ellipses\n(in two dimensions) and ellipsoids (in three dimensions). The
related \"candisc\" package provides visualizations\nin a reduced-rank canonical
discriminant space when there are more than a few response
variables.","Imports":"MASS, graphics, grDevices, stats, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"heplots","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"rgl, candisc, effects, reshape, gplots, nlme,
lattice,\nreshape2, corrgram, FRB, animation","Title":"Visualizing Hypothesis Tests
in Multivariate Linear
Models","URL":"http:\/\/datavis.ca\/R\/index.php#heplots","Version":"1.1-
0"},"hergm":{"Author":"Michael Schweinberger <michael.schweinberger@rice.edu> [aut,
cre], Mark S. Handcock <handcock@ucla.edu> [ctb], Pamela Luna
<pamela.luna@rice.edu> [ctb]","Depends":"ergm, latentnet, network, parallel,
sna","Description":"Estimate and simulate hierarchical exponential-family random
graph models with local dependence.","License":"GPL-
3","NeedsCompilation":"yes","Package":"hergm","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Hierarchical Exponential-Family Random Graph
project.org\/web\/packages\/hergm\/index.html","Version":"2.2-2"},"heritability":
{"Author":"Willem Kruijer, with a contribution from Ian White (the internal
function pin). Contains data collected by Padraic Flood and Rik
Kooke.","Depends":"R (>= 2.10), MASS (>= 3.1.20)","Description":"Implements marker-
based estimation of heritability when observations on genetically identical
replicates are available. These can be either observations on individual plants or
plot-level data in a field trial. Heritability can then be estimated using a mixed
model for the individual plant or plot data. For comparison, also mixed-model based
estimation using genotypic means and estimation of repeatability with ANOVA are
implemented. For illustration the package contains several datasets for the model
species Arabidopsis thaliana.","License":"GPL-
3","NeedsCompilation":"no","Package":"heritability","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"synbreed","Title":"Marker-Based Estimation of
Heritability Using Individual Plant\nor Plot
Data","URL":"https:\/\/sites.google.com\/site\/wkruijer\/","Version":"1.1"},"hermit
e":{"Author":"David MoriÃ±a, Manuel Higueras, Pedro Puig and MarÃa
Oliveira","Depends":"R (>= 2.15.0), maxLik","Description":"Probability functions
and other utilities for the generalized Hermite distribution.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hermite","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Generalized Hermite
Distribution","Version":"1.1.1"},"het.test":{"Author":"Sebastian
Andersson","Depends":"vars, methods","Description":"An implementation of White's
Test for Heteroskedasticity\nas outlined in Doornik (1996).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"het.test","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"White's Test for
Heteroskedasticity","Version":"0.1"},"hett":{"Author":"Julian Taylor
<julian.taylor@adelaide.edu.au>","Depends":"R (>= 2.0.0), MASS,
lattice","Description":"Functions for the fitting and summarizing of
heteroscedastic t-regression.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hett","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Heteroscedastic t-regression","Version":"0.3-1"},"hexView":
{"Author":"Paul Murrell <paul@stat.auckland.ac.nz>","Depends":"R (>=
1.8.0)","Description":"Functions to view files in raw binary form like in a hex
editor. Additional functions to specify and read arbitrary binary
formats.","License":"GPL-
2","NeedsCompilation":"no","Package":"hexView","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Viewing
Binary Files","Version":"0.3-3"},"hexbin":{"Author":"Dan Carr
<dcarr@voxel.galaxy.gmu.edu>, ported by Nicholas\nLewin-Koh and Martin Maechler
<maechler@stat.math.ethz.ch>,\ncontains copies of lattice functions written by
Deepayan Sarkar\n<deepayan.sarkar@r-project.org>","Depends":"R (>= 2.0.1),
methods","Description":"Binning and plotting functions for hexagonal bins.
Now\nuses and relies on grid graphics and formal (S4) classes
and\nmethods.","Imports":"lattice, grid, graphics, grDevices, stats,
2","NeedsCompilation":"yes","Package":"hexbin","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"marray, affy, Biobase, limma","Title":"Hexagonal
Binning
Routines","URL":"http:\/\/github.com\/edzer\/hexbin","Version":"1.27.1"},"hflights"
:{"Author":"Hadley Wickham <h.wickham@gmail.com>","Depends":"R (>=
2.10)","Description":"A data only package containing commercial domestic flights
that\ndeparted Houston (IAH and HOU) in
2011.","License":"CC0","NeedsCompilation":"no","Package":"hflights","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Title":"Flights that departed Houston in
2011","Version":"0.1"},"hgam":{"Author":"The students of the Àdvanced R
Programming Course' Hannah\nFrick, Ivan Kondofersky, Oliver S. Kuehnle,
Christian\nLindenlaub, Georg Pfundstein, Matthias Speidel, Martin\nSpindler, Ariane
Straub, Florian Wickler, Katharina Zink under\nthe supervision of Manuel Eugster
and Torsten Hothorn","Depends":"grplasso, splines, lattice,
rgl","Description":"High-dimensional additive models as introduced by Meier,\nvan
der Geer and Buehlmann (2009).","License":"GPL-
2","NeedsCompilation":"no","Package":"hgam","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"parallel","Title":"High-dimensional Additive
Modelling","Version":"0.1-2"},"hglasso":{"Author":"Kean Ming
Tan","Depends":"glasso, mvtnorm, igraph","Description":"Implements the hub
graphical lasso and hub covariance graph proposal by Tan, KM., London, P., Mohan,
K., Lee, S-I., Fazel, M., and Witten, D. (2014). Learning graphical models with
hubs. To appear in Journal of Machine Learning Research.
arXiv.org\/pdf\/1402.7349.pdf.","Imports":"fields","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hglasso","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Learning graphical models with
hubs","Version":"1.2"},"hglm":{"Author":"Moudud Alam, Lars Ronnegard, Xia
Shen","Depends":"R (>= 2.10), utils, Matrix, MASS,
hglm.data","Description":"Procedures for fitting hierarchical generalized linear
models (HGLM). It can be used for linear mixed models and generalized linear mixed
models with random effects for a variety of links and a variety of distributions
for both the outcomes and the random effects. Fixed effects can also be fitted in
the dispersion part of the mean model.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hglm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Hierarchical Generalized Linear Models","Version":"2.1-
1"},"hglm.data":{"Author":"Xia Shen, Moudud Alam, Lars Ronnegard","Depends":"R (>=
2.10), utils, Matrix, MASS","Description":"This data-only package was created for
distributing data used in the examples of the hglm package.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hglm.data","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Data for The hglm Package","Version":"1.0-0"},"hgm":
{"Author":"Nobuki Takayama, Tamio Koyama, Tomonari Sei, Hiromasa Nakayama, Kenta
Nishiyama","Depends":"R (>= 2.6.0), deSolve","Description":"The holonomic gradient
method (HGM, hgm) gives a way to evaluate normalization\nconstants of unnormalized
probability distributions by utilizing holonomic\nsystems of differential or
difference equations. The holonomic gradient descent (HGD, hgd) gives a method\nto
find maximal likelihood estimates by utilizing the HGM.","License":"GPL-
2","NeedsCompilation":"yes","Package":"hgm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Holonomic Gradient Method and Gradient
Descent","URL":"http:\/\/www.openxm.org","Version":"1.11"},"hht":{"Author":"Daniel
C. Bowman [aut, cre],\nJonathan M. Lees [ctb]","Depends":"R (>=
3.1.1)","Description":"This package builds on the EMD package to provide additional
tools for empirical mode decomposition (EMD) and Hilbert spectral analysis. It also
implements the ensemble empirical decomposition (EEMD) and the complete ensemble
empirical mode decomposition (CEEMD) methods to avoid mode mixing and intermittency
problems found in EMD analysis. The package comes with several plotting methods
that can be used to view intrinsic mode functions, the HHT spectrum, and the
Fourier spectrum. To see the version history and download the bleeding-edge version
(at your own risk!), see the project website at code.google.com below. See the
other links for PDF files describing numerical and exact analytical methods for
determining instantaneous frequency, some examples of signals processed with this
package, and some examples of the ensemble empirical mode decomposition
method.","Imports":"EMD (>= 1.5.5), fields (>= 6.7.6), spatstat (>=
1.38.1)","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"hht","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"The Hilbert-Huang Transform: Tools and
Methods","URL":"https:\/\/code.google.com\/p\/r-
hht\/\nhttp:\/\/www.unc.edu\/~haksaeng\/hht\/analytic_instantaneous_freq.pdf\nhttp:
\/\/www.unc.edu\/~haksaeng\/hht\/interesting_signals.pdf\nhttp:\/\/www.unc.edu\/~ha
ksaeng\/hht\/eemd_examples.pdf","Version":"2.1.2"},"hiPOD":{"Author":"Wei E.
Liang","Depends":"rgl","Description":"Based on hierarchical modeling, this package
provides a\nfew practical functions to find and present the optimal designs\nfor a
pooled NGS design.","License":"GPL-
3","NeedsCompilation":"no","Package":"hiPOD","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"hierarchical Pooled Optimal
Design","Version":"1.0"},"hiddenf":{"Author":"Jason A. Osborne, Christopher T.
Franck and Bongseog Choi","Description":"Computes the ACMIF test and Bonferroni-
adjusted p-value of interaction in two-factor studies. Produces corresponding
interaction plot and analysis of variance tables and p-values from several other
tests of non-additivity.","Imports":"graphics, stats, utils","License":"GPL-
2","NeedsCompilation":"no","Package":"hiddenf","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"The All-Configurations, Maximum-Interaction F-Test for
Hidden\nAdditivity","Version":"2.0"},"hier.part":{"Author":"Chris Walsh and Ralph
Mac Nally","Depends":"gtools","Description":"Variance partition of a multivariate
data
set","License":"GPL","NeedsCompilation":"yes","Package":"hier.part","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Title":"Hierarchical
Partitioning","Version":"1.0-4"},"hierDiversity":{"Author":"Zachary Marion, James
Fordyce, and Benjamin Fitzpatrick","Description":"Hierarchical group-wise
partitioning of phenotypic diversity into\nwithin-group (alpha), among-group
(beta), and pooled-total (gamma)\ncomponents using Hill numbers.\nTurnover and
overlap are also calculated as standardized alternatives to\nbeta diversity.
Hierarchical bootstrapping is used to approximate\nuncertainty around each
diversity component.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hierDiversity","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Hierarchical Multiplicative Partitioning of Complex
Phenotypes","Version":"0.1"},"hierNet":{"Author":"Jacob Bien and Rob
Tibshirani","Description":"Fits sparse interaction models for continuous and binary
responses subject to the strong (or weak) hierarchy restriction that an interaction
between two variables only be included if both (or at least one of) the variables
is included as a main effect. For more details, see Bien, J., Taylor, J.,
Tibshirani, R., (2013) \"A Lasso for Hierarchical Interactions.\" Annals of
Statistics. 41(3). 1111-1141.","License":"GPL-
2","NeedsCompilation":"yes","Package":"hierNet","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"A Lasso for Hierarchical
Interactions","Version":"1.6"},"hierarchicalDS":{"Author":"P.B. Conn
\\email{paul.conn@@noaa.gov}","Depends":"R (>= 2.10)","Description":"Functions for
performing hierarchical analysis of distance\nsampling data, with ability to use an
areal spatial ICAR model on\ntop of user supplied covariates to get at variation in
abundance\nintensity. The detection model can be specified as a function
of\nobserver and individual covariates, where a parametric model is\nsupposed for
the population level distribution of covariate values.\nThe model uses data
augmentation and a reversible jump MCMC\nalgorithm to sample animals that were
never observed. Also\nincluded is the ability to include point independence
(increasing\ncorrelation multiple observer's observations as a function
of\ndistance, with independence assumed for distance=0 or first\ndistance bin), as
well as the ability to model species\nmisclassification rates using a multinomial
logit formulation on data\nfrom double observers. New in version 2.1 is the
ability to\ninclude zero inflation, but this is only recommended for cases
where\nsample sizes and spatial coverage of the survey are
high.","Imports":"truncnorm, mvtnorm, Matrix, coda, xtable, mc2d, ggplot2,
rgeos","License":"Unlimited","NeedsCompilation":"no","Package":"hierarchicalDS","Re
pository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Functions For Performing
Hierarchical Analysis of Distance\nSampling
Data","Version":"2.9"},"hierarchicalSets":{"Author":"Thomas Lin
Pedersen","Depends":"R (>= 3.2.0)","Description":"Pure set data visualization
approaches are often limited in\nscalability due to the combinatorial explosion of
distinct set families as\nthe number of sets under investigation increases.
hierarchicalSets applies\na
set centric hierarchical clustering of the sets under investigation and\nuses this
hierarchy as a basis for a range of scalable visual\nrepresentations.
hierarchicalSets is especially well suited for collections\nof sets that describe
comparable comparable entities as it relies on the\nsets to have a meaningful
relational structure.","Imports":"ggdendro, ggplot2 (>= 2.0.0), stats, Rcpp,
scales, Matrix,\nMASS, RColorBrewer, gtable, grDevices, methods,
2)","NeedsCompilation":"yes","Package":"hierarchicalSets","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Set Data Visualization Using
Hierarchies","Version":"1.0.1"},"hierband":{"Author":"Jacob Bien
<jbien@cornell.edu>, Florentina Bunea, and Luo Xiao","Depends":"R (>=
3.2.0)","Description":"Implementation of the convex banding procedure (using
a\nhierarchical group lasso penalty) for covariance estimation that is\nintroduced
in Bien, Bunea, Xiao (2015) Convex Banding of the Covariance\nMatrix. Accepted for
publication in JASA.","License":"GPL-
3","NeedsCompilation":"yes","Package":"hierband","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr","Title":"Convex Banding of the Covariance
Matrix","Version":"1.0"},"hierfstat":{"Author":"Jerome Goudet [aut, cre],\nThibaut
Jombart [aut]","Depends":"R (>= 2.10)","Description":"Allows the estimation of
hierarchical F-statistics from haploid or diploid genetic data\nwith any numbers
of levels in the hierarchy, following the algorithm of Yang (Evolution, 1998,
52(4):950-956;\n<DOI:10.2307\/2411227>. Functions are also given to test via
randomisations the significance of each F and variance components,\nusing the
likelihood-ratio statistics G.","Imports":"gtools,ade4,adegenet","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hierfstat","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"ape,pegas, knitr","Title":"Estimation and Tests of
Hierarchical F-Statistics","URL":"http:\/\/www.r-project.org,
http:\/\/github.com\/jgx65\/hierfstat","Version":"0.04-22"},"hiertest":
{"Author":"Jacob Bien, Noah Simon, and Rob Tibshirani","Depends":"R (>=
3.0.2)","Description":"Implementation of the convex hierarchical testing (CHT)
procedure\nintroduced in Bien, Simon, and Tibshirani (2015) Convex Hierarchical
Testing\nof Interactions. Annals of Applied Statistics. Vol. 9, No. 1, 27-
3","NeedsCompilation":"no","Package":"hiertest","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Convex Hierarchical Testing of
Interactions","Version":"1.1"},"highD2pop":{"Author":"Karl
Gregory","Depends":"fastclime","Description":"Performs the generalized component
test from Gregory et al (2015), as well as the tests from Chen and Qin (2010),
Srivastava and Kubokawa (2013), and Cai, Liu, and Xia (2014) for equality of two
population mean vectors when the length of the vectors exceeds the sample
size.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"highD2pop","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Two-Sample Tests for Equality of Means in High
Dimension","Version":"1.0"},"highTtest":{"Author":"Hongyuan Cao [aut],\nMichael
Kosorok [aut],\nShannon Holloway [aut,
cre]","Depends":"methods","Description":"Implements the method developed by Cao and
Kosorok (2011) for the significance analysis of thousands of features in high-
dimensional biological studies. It is an asymptotically valid data-driven procedure
to find critical values for rejection regions controlling the k-familywise error
rate, false discovery rate, and the tail probability of false discovery
proportion.","License":"GPL-
2","NeedsCompilation":"no","Package":"highTtest","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"colorfulVennPlot","Title":"Simultaneous Critical
Values for t-Tests in Very High Dimensions","Version":"1.1"},"highcharter":
{"Author":"Joshua Kunst <jbkunst@gmail.com>","Depends":"R (>=
2.10)","Description":"A wrapper for the 'Highcharts' library including\nshortcut
functions to plot R objects. 'Highcharts'\n<http:\/\/www.highcharts.com\/> is a
charting library offering\nnumerous chart types with a simple configuration
syntax.","Imports":"htmlwidgets, magrittr, purrr, rlist, assertthat, zoo,
dplyr,\nstringr, viridisLite, xts, quantmod, tidyr, htmltools,\njsonlite,
igraph","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"highcharter","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"knitr, rmarkdown","Title":"A Wrapper for the
'Highcharts'
Library","URL":"http:\/\/jkunst.com\/highcharter","Version":"0.3.0"},"highfrequency
":{"Author":"Kris Boudt [aut, cre], Jonathan Cornelissen [aut], Scott Payseur
[aut],\nGiang Nguyen [ctb], Maarten Schermer [ctb]","Depends":"R (>= 2.12.0), xts,
zoo","Description":"Provide functionality to manage, clean and match
highfrequency\ntrades and quotes data, calculate various liquidity measures,
estimate and\nforecast volatility, and investigate microstructure noise and
intraday\nperiodicity.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"highfrequency","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"robustbase, cubature, mvtnorm, chron, timeDate,
quantmod,\nMASS, sandwich, numDeriv, FKF, BMS, rugarch","Title":"Tools For
Highfrequency Data Analysis","Version":"0.4"},"highlight":{"Author":"Romain
Francois [aut, cre],\nAndre Simon [ctb]","Depends":"R (>=
3.1.3)","Description":"Syntax highlighter for R code based\non the results of the R
parser. Rendering in HTML and latex\nmarkup. Custom Sweave driver performing syntax
highlighting\nof R code chunks.","Imports":"grDevices, tools","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"highlight","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Syntax
Highlighter","URL":"https:\/\/github.com\/romainfrancois\/highlight","Version":"0.4
.7"},"highmean":{"Author":"Lifeng Lin and Wei Pan","Depends":"R (>= 1.9.0), mvtnorm
(>= 1.0-0)","Description":"Provides various tests for comparing high-dimensional
mean vectors in two sample populations.","Imports":"MASS, mnormt","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"highmean","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Two-Sample Tests for High-Dimensional Mean
Vectors","Version":"2.0"},"highr":{"Author":"Christopher Gandrud [ctb],\nQiang Li
[ctb],\nYixuan Qiu [aut],\nYihui Xie [aut, cre]","Depends":"R (>=
3.0.2)","Description":"Provides syntax highlighting for R source code. Currently
it\nsupports LaTeX and HTML output. Source code of other languages is
supported\nvia Andre Simon's highlight package (http:\/\/www.andre-
simon.de).","License":"GPL","NeedsCompilation":"no","Package":"highr","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"knitr, testit","Title":"Syntax
Highlighting for R Source
Code","URL":"https:\/\/github.com\/yihui\/highr","Version":"0.5.1"},"highriskzone":
{"Author":"Heidi Seibold <Heidi.Seibold@uzh.ch>, Monia
Mahling\n<monia.mahling@stat.uni-muenchen.de>, Sebastian
Linne\n<Sebastian.Linne@campus.lmu.de>","Depends":"ks, fields, rgeos, deldir,
Matrix","Description":"Functions for determining and evaluating high-risk zones
and\nsimulating and thinning point process data, as described in 'Determining\nhigh
risk zones using point process methodology - Realization by building\nan R package'
(Seibold, 2012) and 'Determining high-risk zones for\nunexploded World War II bombs
by using point process methodology' (Mahling\net al., 2013).","Imports":"spatstat
(>= 1.42-2), methods, stats, utils","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"highriskzone","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"INLA","Title":"Determining and Evaluating
High-Risk Zones","Version":"1.3-1"},"hillmakeR":{"Author":"David Gilinson
<dgilinson@reefpointgroup.com>","Depends":"R (>= 2.10)","Description":"Generate
occupancy patterns based on arrival and departure timestamps","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"hillmakeR","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"plyr","Title":"Perform occupancy
analysis","URL":"https:\/\/github.com\/gilinson\/hillmakeR","Version":"0.2"},"hinde
xcalculator":{"Author":"Sepand Alavifard [aut, cre]","Depends":"R (>=
3.2.0)","Description":"H(x) is the h-index for the past x years. Here, the h(x) of
a scientist\/department\/etc. can be calculated using the exported excel file from
a Web of Science citation report of a search. Also calculated is the year of first
publication, total number of publications, and sum of times cited for the specified
period. Therefore, for h-10: the date of first publication, total number of
publications, and sum of times cited in the past 10 years are calculated. Note: the
excel file has to first be saved in a .csv
format.","License":"AGPL","NeedsCompilation":"no","Package":"hindexcalculator","Rep
ository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"H-Index Calculator using
Data from a Web of Science (WoS)\nCitation Report","Version":"1.0.0"},"hint":
{"Author":"Alex T. Kalinka","Description":"Hypergeometric Intersection
distributions are a broad group of distributions that describe the probability of
picking intersections when drawing independently from two (or more) urns containing
variable numbers of balls belonging to the same n categories.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"hint","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Tools for hypothesis testing based on
Hypergeometric\nIntersection distributions","Version":"0.1-1"},"hisemi":
{"Author":"Long Qu","Depends":"R (>= 2.12)","Description":"This package implements
methods for hierarchical semiparametric regression models for test statistics.
Specifically, test statistics given the null\/alternative hypotheses are modeled
parametrically, whereas the unobservable status of null\/alternative
hypotheses are modeled using nonparametric additive logistic regression over
covariates.","Enhances":"stats, graphics","Imports":"Matrix , Iso(>= 0.0-5),
splines, fda","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hisemi","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"multtest, qvalue, pi0","Title":"Hierarchical
Semiparametric Regression of Test Statistics","Version":"1.0-319"},"hisse":
{"Author":"Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Brian O'Meara
<bomeara@utk.edu>","Depends":"ape, deSolve, GenSA, subplex,
data.table","Description":"Sets up and executes a HiSSE model (Hidden State
Speciation and Extinction) on a phylogeny and character sets to test for hidden
shifts in trait dependent rates of diversification.","Imports":"parallel, phytools,
2)","NeedsCompilation":"yes","Package":"hisse","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"diversitree, knitr","Title":"Hidden State Speciation
and Extinction","Version":"1.6"},"histmdl":{"Author":"Jouke
Witteveen","Description":"Using the MDL principle, it is possible to
estimate\nparameters for a histogram-like model. The package contains\nthe
implementation of such an estimation method.","Imports":"graphics","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"histmdl","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"A Most Informative Histogram-Like Model","Version":"0.5-
1"},"histogram":{"Author":"Thoralf Mildenberger, Yves Rozenholc, David
Zasada.","Description":"Automatic construction of regular and irregular
histograms\nas described in Rozenholc\/Mildenberger\/Gather (2009).","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"histogram","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Construction of regular and irregular histograms with
different\noptions for automatic choice of bins","Version":"0.0-23"},"historydata":
{"Author":"Lincoln Mullen [aut, cre]","Depends":"R (>= 3.0.2)","Description":"These
sample data sets are intended for historians\nlearning R. They include population,
institutional, religious,\nmilitary, and prosopographical data suitable for
mapping,\nquantitative analysis, and network analysis.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"historydata","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"ggplot2 (>= 1.0.0)","Title":"Data Sets for
Historians","URL":"https:\/\/github.com\/ropensci\/historydata","Version":"0.1"},"h
it":{"Author":"Jonas Klasen [aut, cre]","Depends":"R (>=
3.0.0)","Description":"Hierarchical inference testing (HIT) for (generalized)
linear\nmodels with correlated covariates applicable to high-dimensional
settings.","Imports":"stats, parallel, Rcpp (>= 0.11.0), glmnet,
speedglm","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"hit","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat","Title":"Hierarchical Inference
Testing","URL":"https:\/\/github.com\/QTCAT\/hit","Version":"0.2-1"},"hitandrun":
{"Author":"Gert van Valkenhoef, Tommi Tervonen","Description":"The \"Hit and Run\"
Markov Chain Monte Carlo method for sampling uniformly from convex shapes defined
by linear constraints, and the \"Shake and Bake\" method for sampling from the
boundary of such shapes. Includes specialized functions for sampling normalized
weights with arbitrary linear constraints.","Imports":"rcdd (>= 1.1),
3","NeedsCompilation":"yes","Package":"hitandrun","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat (>= 0.8)","Title":"\"Hit and Run\"
and \"Shake and Bake\" for Sampling Uniformly from\nConvex
Shapes","URL":"http:\/\/github.com\/gertvv\/hitandrun","Version":"0.5-2"},"hive":
{"Author":"Ingo Feinerer [aut],\nStefan Theussl [aut, cre]","Depends":"R (>=
2.9.0)","Description":"Hadoop InteractiVE facilitates distributed\ncomputing via
the MapReduce paradigm through R and Hadoop. An easy to use\ninterface to Hadoop,
the Hadoop Distributed File System (HDFS),\nand Hadoop Streaming is
provided.","Enhances":"HadoopStreaming","Imports":"methods, rJava (>= 0.9-3),
tools, XML","License":"GPL-
3","NeedsCompilation":"no","Package":"hive","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Hadoop InteractiVE","Version":"0.2-0"},"hkevp":
{"Author":"Quentin Sebille","Depends":"Rcpp (>= 0.11.0)","Description":"Simulation
and fitting procedures for a particular hierarchical max-stable model: the HKEVP of
Reich and Shaby (2012) <DOI:10.1214\/12-AOAS591>. Spatial prediction and marginal
distribution extrapolation are also available, which allows a risk estimation at an
ungauged
site.","License":"GPL","NeedsCompilation":"yes","Package":"hkevp","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Title":"Spatial Extreme Value Analysis with the
Hierarchical Model of\nReich and Shaby (2012)","Version":"1.0"},"hmeasure":
{"Author":"Christoforos
Anagnostopoulos\n<christoforos.anagnostopoulos06@imperial.ac.uk> and David J.\nHand
<d.j.hand@imperial.ac.uk>","Depends":"R (>= 2.10)","Description":"Scalar
performance metrics, including the H-measure, based\non classification scores for
several classifiers applied to the\nsame dataset.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hmeasure","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"MASS, class","Title":"The H-measure and other scalar
classification
performance\nmetrics","URL":"http:\/\/www.hmeasure.net","Version":"1.0"},"hmm.discn
p":{"Author":"Rolf Turner","Depends":"R (>= 0.99)","Description":"Fits hidden
Markov models with discrete non-parametric\nobservation distributions to data sets.
Simulates data\nfrom such models. Finds most probable underlying hidden\nstates,
the most probable sequences of such states, and the\nlog likelihood of a collection
of observations given the\nparameters of the model.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"hmm.discnp","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Hidden Markov Models with Discrete Non-Parametric
Observation\nDistributions","Version":"0.2-4"},"hmmm":{"Author":"Colombi Roberto
and Sabrina Giordano and Manuela Cazzaro, with contributions from Joseph
Lang","Description":"Functions for specifying and fitting marginal models for
contingency tables proposed\nby Bergsma and Rudas (2002) here called hierarchical
multinomial marginal models (hmmm) and their extensions presented by Bartolucci et
al.\n(2007); multinomial Poisson homogeneous (mph) models and homogeneous linear
predictor (hlp) models for contingency\ntables proposed by Lang (2004) and (2005);
hidden Markov models where the distribution of the observed variables\nis described
by a marginal model.\nInequality constraints on the parameters are allowed and can
be tested.","Imports":"quadprog, MASS, mvtnorm","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hmmm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"hierarchical multinomial marginal
models","URL":"http:\/\/www.r-project.org","Version":"1.0-3"},"hnp":
{"Author":"Rafael de Andrade Moral [aut, cre], John Hinde [aut], Clarice Garcia
Borges Demetrio [aut]","Depends":"R (>= 3.0.0), MASS (>= 7.3-35), methods,
graphics, stats","Description":"Generates (half-)normal plots with simulation
envelopes using different diagnostics from a range of different fitted models. A
few example datasets are included.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hnp","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"lme4, gamlss, gamlss.dist, pscl, nnet, aods3, VGAM,
glmmADMB,\nlatticeExtra","Title":"Half-Normal Plots with Simulation
Envelopes","Version":"1.2"},"hoa":{"Author":"R port by Alessandra R. Brazzale
<alessandra.brazzale@unipd.it>, following\nearlier work by Douglas Bates. The
function tem is based on work by Anthony Davison
<Anthony.Davison@epfl.ch>","Depends":"R (>= 3.0.0)","Description":"Performs
likelihood-based inference for a wide range of regression models. Provides higher-
order approximations for inference based on extensions of saddlepoint type
arguments as discussed in the book Applied Asymptotics: Case Studies in Small-
Sample Statistics by Brazzale, Davison, and Reid (2007).","Imports":"graphics,
statmod, stats, survival, utils","License":"GPL (>= 2) | file
LICENCE","NeedsCompilation":"no","Package":"hoa","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"boot, csampling","Title":"Higher Order Likelihood
Inference","URL":"http:\/\/www.r-project.org,
http:\/\/statwww.epfl.ch\/AA\/","Version":"2.1.4"},"hoardeR":{"Author":"Daniel
Fischer [aut, cre],\nAnu Sironen [aut]","Depends":"R (>=
3.2.0)","Description":"Information retrieval from National Center for Biotechnology
Information (NCBI) databases, with main focus on identifying genes in unannotated
organisms via Blast similarity search in annotated organisms.","Imports":"httr (>=
0.2), XML (>= 3.98-1.1), stringr (>= 0.6.2), MASS (>=\n7.3-31), R.utils (>=
1.32.4), stats (>= 3.2.0), utils (>=\n3.2.0), graphics (>= 3.2.0)","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"hoardeR","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Information Retrieval for Genetic
Datasets","Version":"0.1"},"holdem":{"Author":"Frederic Paik
Schoenberg","Description":"Simulates hands and tournaments of Texas
Holdem.","License":"GPL-
2","NeedsCompilation":"no","Package":"holdem","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Texas Holdem simulator","Version":"1.1"},"homals":
{"Author":"Patrick Mair [aut, cre], Jan De Leeuw [aut]","Depends":"R (>=
3.0.2)","Description":"Performs a homogeneity analysis (multiple correspondence
analysis) and various extensions. Rank restrictions on the category quantifications
can be imposed (nonlinear PCA). The categories are transformed by means of optimal
scaling with options for nominal, ordinal, and numerical scale levels (for
rank-1 restrictions). Variables can be grouped into sets, in order to emulate
regression analysis and canonical correlation analysis.","Imports":"graphics,
stats, rgl, ape, scatterplot3d,
grDevices","License":"GPL","NeedsCompilation":"no","Package":"homals","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Title":"Gifi Methods for Optimal
Scaling","URL":"http:\/\/r-forge.r-
project.org\/projects\/psychor\/","Version":"1.0-6"},"homeR":{"Author":"Neurobat
AG","Description":"A collection of functions useful for the analysis of\nbuilding
physics experiments.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"homeR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Functions useful for building
physics","Version":"0.1"},"homomorpheR":{"Author":"Balasubramanian Narasimhan [aut,
cre]","Description":"Homomorphic computations in R for privacy-preserving
applications. Currently only\nthe Paillier Scheme is implemented.","Imports":"R6,
gmp, sodium","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"homomorpheR","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"distcomp, knitr,
rmarkdown","Title":"Homomorphic Computations in
R","URL":"http:\/\/github.com\/bnaras\/homomorpheR","Version":"0.1-1"},"homtest":
{"Author":"Alberto Viglione","Depends":"stats","Description":"A collection of
homogeneity tests described in: Viglione\nA., Laio F., Claps P. (2007) `À
comparison of homogeneity\ntests for regional frequency analysis'', Water
Resources\nResearch, 43, W03428, doi:10.1029\/2006WR005095. More on\nRegional
Frequency Analysis can be found in package nsRFA.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"homtest","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Homogeneity tests for Regional Frequency
Analysis","URL":"http:\/\/www.idrologia.polito.it\/~alviglio","Version":"1.0-
5"},"hopbyhop":{"Author":"Christian E. Galarza, Jonathan M.
Olate","Description":"Computes the expectation of the number of transmissions and
receptions considering a Hop-by-Hop transport model with limited number of
retransmissions per packet. It provides the theoretical results shown in Palma et.
al.(2015) <DOI:10.1109\/APCASE.2015.59> and also estimated values based on Monte
Carlo simulations.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hopbyhop","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Transmissions and Receptions in a Hop by Hop
Network","Version":"1.0"},"hornpa":{"Author":"Francis Huang","Description":"A
stand-alone function that generates a user specified number of random datasets and
computes eigenvalues using the random datasets (i.e., implements Horn's [1965,
Psychometrika] parallel analysis). Users then compare the resulting eigenvalues
(the mean or the specified percentile) from the random datasets (i.e., eigenvalues
resulting from noise) to the eigenvalues generated with the user's data. Can be
used for both principal components analysis (PCA) and common\/exploratory factor
analysis (EFA). The output table shows how large eigenvalues can be as a result of
merely using randomly generated datasets. If the user's own dataset has actual
eigenvalues greater than the corresponding eigenvalues, that lends support to
retain that factor\/component. In other words, if the i(th) eigenvalue from the
actual data was larger than the percentile of the (i)th eigenvalue generated using
randomly generated data, empirical support is provided to retain that
factor\/component.\nHorn, J. (1965). A rationale and test for the number of factors
in factor analysis. Psychometrika, 32, 179-185.","License":"GPL-
3","NeedsCompilation":"no","Package":"hornpa","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Horn's (1965) Test to Determine the Number of
Components\/Factors","Version":"1.0"},"hot.deck":{"Author":"Skyler Cranmer, Jeff
Gill, Natalie Jackson, Andreas Murr, Dave Armstrong","Depends":"R (>= 3.0),
mice","Description":"Performs multiple hot-deck imputation of categorical and
continuous variables in a data frame.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hot.deck","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr, mitools, miceadds, Zelig","Title":"Multiple
Hot-Deck Imputation","Version":"1.1"},"hotspot":{"Author":"Csaba
Farago","Description":"Contains data for software hotspot analysis, along with a
function performing the analysis itself.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hotspot","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Software Hotspot Analysis","Version":"1.0"},"hotspots":
{"Author":"Anthony Darrouzet-Nardi","Depends":"lattice,
ineq","Description":"Calculates a hot spot cutoff and associated analyses
for\nstatistical populations","License":"GPL-
2","NeedsCompilation":"no","Package":"hotspots","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Hot spots","Version":"1.0.2"},"housingData":
{"Author":"Ryan Hafen <rhafen@gmail.com>","Depends":"R (>=
2.15)","Description":"Monthly median home listing, sale price per square foot, and
number of units sold for 2984 counties in the contiguous United States From 2008 to
January 2016. Additional data sets containing geographical information and links
to Wikipedia are also
included.","License":"CC0","NeedsCompilation":"no","Package":"housingData","Reposit
ory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"U.S. Housing Data from 2008 to
2016","URL":"http:\/\/github.com\/hafen\/housingData","Version":"0.3.0"},"howmany":
{"Author":"Nicolai Meinshausen","Description":"When testing multiple hypotheses
simultaneously, this\npackage provides functionality to calculate a lower bound
for\nthe number of correct rejections (as a function of the number\nof rejected
hypotheses), which holds simultaneously -with high\nprobability- for all possible
number of rejections. As a\nspecial case, a lower bound for the total number of
false null\nhypotheses can be inferred. Dependent test statistics can be\nhandled
for multiple tests of associations. For independent\ntest statistics, it is
sufficient to provide a list of\np-values.","Imports":"graphics,
stats","License":"GPL","NeedsCompilation":"no","Package":"howmany","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"A lower bound for the number of
correct
rejections","URL":"http:\/\/www.stats.ox.ac.uk\/~meinshau\/","Version":"0.3-
1"},"hpcwld":{"Author":"Alexander Rumyantsev [aut, cre]","Depends":"R (>= 2.10),
multicool, partitions","Description":"Probabilistic models describing the
behavior\nof workload and queue on a High Performance Cluster and computing
GRID\nunder FIFO service discipline basing on modified Kiefer-Wolfowitz\nrecursion.
Also sample data for inter-arrival times, service times,\nnumber of cores per task
and waiting times of HPC of Karelian\nResearch Centre are included, measurements
took place from 06\/03\/2009 to 02\/30\/2011.\nFunctions provided to import\/export
workload traces in Standard Workload Format (swf).\nStability condition of the
model may be verified either exactly, or approximately.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hpcwld","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"High Performance Cluster Models Based on Kiefer-
Wolfowitz\nRecursion","URL":"http:\/\/www.r-project.org,
http:\/\/cluster.krc.karelia.ru","Version":"0.5"},"hpoPlot":{"Author":"Daniel
Greene <dg333@cam.ac.uk>","Depends":"R (>= 3.0.0)","Description":"Collection of
functions for manipulating sets of HPO terms and\nplotting them with a various
options.","Imports":"methods, Rgraphviz, functional, magrittr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hpoPlot","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr","Title":"Functions for Plotting HPO
Terms","Version":"2.4"},"hqmisc":{"Author":"Hugo QuenÃ© [aut, cre]","Depends":"R
(>= 3.0.0)","Description":"This package contains some miscellaneous convenience
functions,\nto create a matrix of dummy columns from a factor,\nto determine
whether x lies in range [a,b],\nto add a rectangular bracket to an existing
plot,\nand to convert frequencies between Hz, semitones, mel and Bark.\nThis
package also contains an example data set of a stratified sample\nof 80 talkers of
Dutch.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hqmisc","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Miscellaneous convenience functions and
dataset","Version":"0.1-1"},"hqreg":{"Author":"Congrui Yi","Description":"Efficient
algorithms for fitting entire regularization paths for Huber loss regression and
quantile regression penalized by lasso or elastic-net.","License":"GPL-
2","NeedsCompilation":"yes","Package":"hqreg","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Regularization Paths for Huber Loss Regression and
Quantile\nRegression Penalized by Lasso or Elastic-Net","Version":"1.2"},"hrr":
{"Author":"Leonardo Di Donato <leodidonato@gmail.com>","Depends":"R (>=
3.0.0)","Description":"Print beautiful horizontal rules in your R
scripts.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"hrr","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Horizontal rule for the R
language","URL":"https:\/\/github.com\/leodido\/hrr","Version":"1.1.1"},"hsdar":
{"Author":"Lukas W. Lehnert [cre, aut],\nHanna Meyer [aut],\nJoerg Bendix
[aut]","Depends":"R (>= 2.10.0), raster, rgdal, rootSolve, signal,
methods,\ncaret","Description":"Transformation of reflectance spectra, calculation
of vegetation indices and red edge parameters, spectral resampling for
hyperspectral remote sensing, simulation of reflectance and transmittance using the
leaf reflectance model PROSPECT and the canopy reflectance model
PROSAIL.","License":"GPL","NeedsCompilation":"yes","Package":"hsdar","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Suggests":"rgl, RCurl,
pracma","Title":"Manage,
Analyse and Simulate Hyperspectral Data","URL":"http:\/\/lcrs.geographie.uni-
marburg.de,\nhttp:\/\/teledetection.ipgp.jussieu.fr\/prosail\/","Version":"0.4.1"},
"hsicCCA":{"Author":"Billy Chang","Description":"Canonical correlation analysis
that extracts nonlinear\ncorrelation through the use of Hilbert Schmidt
Independence\nCriterion and Centered Kernel Target Alignment.","License":"GPL-
2","NeedsCompilation":"no","Package":"hsicCCA","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Canonical Correlation Analysis based on Kernel
Independence\nMeasures","Version":"1.0"},"hsmm":{"Author":"Jan Bulla
<bulla@math.unicaen.fr>, Ingo Bulla\n<ingobulla@googlemail.com>","Depends":"R (>=
2.0.0), mvtnorm","Description":"A package for computation of hidden semi markov
models","License":"GPL","NeedsCompilation":"yes","Package":"hsmm","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Title":"Hidden Semi Markov
Models","Version":"0.4"},"hsphase":{"Author":"Mohammad Ferdosi
<mferdosi@myune.edu.au>, Cedric Gondro <cgondro2@une.edu.au>","Depends":"snowfall,
R (>= 3.1.0)","Description":"Identification of recombination events, haplotype
reconstruction, sire imputation and pedigree reconstruction using half-sib family
SNP data","Imports":"Rcpp","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"hsphase","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Phasing, Pedigree Reconstruction, Sire Imputation
and\nRecombination Events Identification of Half-sib Families Using\nSNP
Data","Version":"2.0.1"},"htmlTable":{"Author":"Max Gordon
<max@gforge.se>","Description":"Tables with state-of-the-art layout elements such
as row spanners,\ncolumn spanners, table spanners, zebra striping, and more. While
allowing\nadvanced layout, the underlying css-structure is simple in order to
maximize\ncompatibility with word processors such as 'MS Word' or 'LibreOffice'.
The package\nalso contains a few text formatting functions that help outputting
text\ncompatible with HTML\/'LaTeX'.","Imports":"stringr, knitr (>= 1.6), magrittr
(>= 1.5), methods","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"htmlTable","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat, XML, xtable, ztable, Hmisc, reshape,
rmarkdown","Title":"Advanced Tables for
Markdown\/HTML","URL":"http:\/\/gforge.se\/packages\/","Version":"1.5"},"htmltab":
{"Author":"Christian Rubba [aut, cre]","Depends":"R (>= 3.0.0)","Description":"HTML
tables are a valuable data source but extracting and recasting\nthese data into a
useful format can be tedious. htmltab is a package for\nextracting structured
information from HTML tables. It is similar to\nreadHTMLTable() of the XML package
but provides two major advantages. First,\nthe function automatically expands row
and column spans in the header and\nbody cells. Second, users are given more
control over the identification of\nheader and body rows which will end up in the R
table. Additionally, the\nfunction preprocesses table code, removes unneeded parts
and so helps to\nalleviate the need for tedious post-processing.","Imports":"XML
(>= 3.98.1.3), httr (>= 1.0.0)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"htmltab","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat, knitr, magrittr (>= 1.5),
tidyr","Title":"Assemble Data Frames from HTML
Tables","URL":"https:\/\/github.com\/crubba\/htmltab","Version":"0.6.0"},"htmltools
":{"Author":"RStudio, Inc.","Depends":"R (>= 2.14.1)","Description":"Tools for HTML
generation and output.","Enhances":"knitr","Imports":"utils, digest,
2)","NeedsCompilation":"yes","Package":"htmltools","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"markdown, testthat","Title":"Tools for
HTML","URL":"https:\/\/github.com\/rstudio\/htmltools","Version":"0.3.5"},"htmlwidg
ets":{"Author":"Ramnath Vaidyanathan [aut, cph],\nYihui Xie [aut],\nJJ Allaire
[aut, cre],\nJoe Cheng [aut],\nKenton Russell [aut, cph],\nRStudio
[cph]","Description":"A framework for creating HTML widgets that render in
various\ncontexts including the R console, 'R Markdown' documents, and 'Shiny'\nweb
applications.","Enhances":"shiny (>= 0.12)","Imports":"htmltools (>= 0.3), jsonlite
(>= 0.9.16), yaml","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"htmlwidgets","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"knitr (>= 1.8)","Title":"HTML Widgets for
R","URL":"https:\/\/github.com\/ramnathv\/htmlwidgets","Version":"0.6"},"hts":
{"Author":"Rob J Hyndman, Earo Wang, Alan Lee, Shanika Wickramasuriya","Depends":"R
(>= 3.0.2), forecast (>= 5.0), SparseM, Matrix, matrixcalc","Description":"Methods
for analysing and forecasting hierarchical and grouped time
series.","Imports":"parallel, utils, methods, graphics, grDevices,
2)","NeedsCompilation":"yes","Package":"hts","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat","Title":"Hierarchical and Grouped Time
Series","Version":"5.0"},"httk":{"Author":"John Wambaugh and Robert Pearce, Schmitt
method implementation by Jimena Davis, dynamic model adapted from code by R.
Woodrow Setzer, Rabbit parameters from Nisha Sipes","Depends":"R (>=
2.10)","Description":"Functions and data tables for simulation and statistical
analysis of chemical toxicokinetics (\"TK\") using data obtained from relatively
high throughput, in vitro studies. Both physiologically-based (\"PBTK\") and
empirical (e.g., one compartment) \"TK\" models can be parameterized for several
hundred chemicals and multiple species. These models are solved efficiently, often
using compiled (C-based) code. A Monte Carlo sampler is included for simulating
biological variability and measurement limitations. Functions are also provided for
exporting \"PBTK\" models to \"SBML\" and \"JARNAC\" for use with other simulation
software. These functions and data provide a set of tools for in vitro-in vivo
extrapolation (\"IVIVE\") of high throughput screening data (e.g., ToxCast) to
real-world exposures via reverse dosimetry (also known
as \"RTK\").","Imports":"deSolve, msm","License":"GPL-
3","NeedsCompilation":"yes","Package":"httk","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"ggplot2","Title":"High-Throughput
Toxicokinetics","Version":"1.4"},"httpRequest":{"Author":"Eryk Witold Wolski,
Andreas Westfeld","Description":"HTTP Request protocols. Implements the GET, POST
and multipart POST request.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"httpRequest","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Basic HTTP Request","Version":"0.0.10"},"httpcache":
{"Author":"Neal Richardson [aut, cre]","Depends":"R (>= 3.0.0)","Description":"In
order to improve performance for HTTP API clients, 'httpcache'\nprovides simple
tools for caching and invalidating cache. It includes the\nHTTP verb functions GET,
PUT, PATCH, POST, and DELETE, which are drop-in\nreplacements for those in the
'httr' package. These functions are cache-aware\nand provide default settings for
cache invalidation suitable for RESTful\nAPIs; the package also enables custom
cache-management strategies.\nFinally, 'httpcache' includes a basic logging
framework to facilitate the\nmeasurement of HTTP request time and cache
performance.","Imports":"httr (>= 1.0.0), digest","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"httpcache","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat","Title":"Query Cache for HTTP
Clients","URL":"https:\/\/github.com\/nealrichardson\/httpcache","Version":"0.1.4"}
,"httpcode":{"Author":"Scott Chamberlain [aut, cre]","Description":"Find and
explain the meaning of 'HTTP' status codes.\nFunctions included for searching for
codes by full or partial number,\nby message, and get appropriate dog and cat
images for many\nstatus codes.","Imports":"utils","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"httpcode","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"'HTTP' Status Code
Helper","Version":"0.1.0"},"httping":{"Author":"Scott Chamberlain [aut,
cre]","Depends":"httr (>= 1.0.0)","Description":"A suite of functions to ping
'URLs' and to time\n'HTTP' 'requests'. Designed to work with
'httr'.","Imports":"methods, stats, jsonlite (>= 0.9.19), pryr (>=
0.1.2),\nmagrittr (>= 1.5), httpcode (>= 0.1.0)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"httping","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat","Title":"'Ping' 'URLs' to Time
'Requests'","URL":"https:\/\/github.com\/sckott\/httping","Version":"0.1.0"},"httpu
v":{"Author":"RStudio, Inc.","Depends":"R (>= 2.15.1),
methods","Description":"Provides low-level socket and protocol support for
handling\nHTTP and WebSocket requests directly from within R. It is
primarily\nintended as a building block for other packages, rather than making
it\nparticularly easy to create complete web applications using httpuv
alone.\nhttpuv is built on top of the libuv and http-parser C libraries, both
of\nwhich were developed by Joyent, Inc. (See LICENSE file for libuv and\nhttp-
parser license information.)","Imports":"Rcpp (>= 0.11.0), utils","License":"GPL-3
| file
LICENSE","NeedsCompilation":"yes","Package":"httpuv","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"HTTP and WebSocket Server
Library","URL":"https:\/\/github.com\/rstudio\/httpuv","Version":"1.3.3"},"httr":
{"Author":"Hadley Wickham [aut, cre],\nRStudio [cph]","Depends":"R (>=
3.0.0)","Description":"Useful tools for working with HTTP organised by HTTP
verbs\n(GET(), POST(), etc). Configuration functions make it easy to
control\nadditional request components (authenticate(), add_headers() and so
on).","Imports":"jsonlite, mime, curl (>= 0.9.1), openssl (>= 0.8),
R6","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"httr","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"httpuv,
jpeg, knitr, png, testthat (>= 0.8.0), readr, xml2","Title":"Tools for Working
with URLs and
HTTP","URL":"https:\/\/github.com\/hadley\/httr","Version":"1.1.0"},"huge":
{"Author":"Tuo Zhao, Xingguo Li, Han Liu, Kathryn Roeder, John Lafferty,
Larry\nWasserman","Depends":"R (>= 3.0.0), Matrix, lattice, igraph,
MASS","Description":"Provides a general framework for\nhigh-dimensional undirected
graph estimation. It integrates\ndata preprocessing, neighborhood screening, graph
estimation,\nand model selection techniques into a pipeline. In\npreprocessing
stage, the nonparanormal(npn) transformation is\napplied to help relax the
normality assumption. In the graph\nestimation stage, the graph structure is
estimated by\nMeinshausen-Buhlmann graph estimation or the graphical lasso,\nand
both methods can be further accelerated by the lossy\nscreening rule preselecting
the neighborhood of each variable\nby correlation thresholding. We target on high-
dimensional data\nanalysis usually d >> n, and the computation is\nmemory-optimized
using the sparse matrix output. We also\nprovide a computationally efficient
approach, correlation\nthresholding graph estimation.
Three\nregularization\/thresholding parameter selection methods are\nincluded in
this package: (1)stability approach for\nregularization selection (2) rotation
information criterion (3)\nextended Bayesian information criterion which is only
available\nfor the graphical lasso.","Imports":"grDevices, graphics, methods,
2","NeedsCompilation":"yes","Package":"huge","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"High-Dimensional Undirected Graph
Estimation","Version":"1.2.7"},"humanFormat":{"Author":"Dustin
Sallings","Depends":"testthat","Description":"Format quantities of time or bytes
into human-friendly strings.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"humanFormat","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Human-friendly formatting
functions","URL":"https:\/\/github.com\/dustin\/humanFormat","Version":"1.0"},"huma
niformat":{"Author":"Oliver Keyes","Description":"Human names are complicated and
nonstandard things. Humaniformat, which is based on Anthony Ettinger's
'humanparser'\nproject (https:\/\/github.com\/chovy\/humanparser) provides
functions for parsing human names,\nmaking a best-guess attempt to distinguish sub-
components such as prefixes, suffixes, middle names and
salutations.","Imports":"Rcpp, methods","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"humaniformat","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Suggests":"testthat, knitr","Title":"A Parser for
Human
Names","URL":"https:\/\/github.com\/ironholds\/humaniformat\/","Version":"0.5.0"},"
humarray":{"Author":"Nicholas Cooper","Depends":"R (>= 3.2), NCmisc (>= 1.1.4),
BiocGenerics (>= 0.10.0),\nIRanges (>= 1.22.10), GenomicRanges (>= 1.16.4),
S4Vectors","Description":"Utilises GRanges, data.frame or IRanges objects.
Integrates gene annotation for ImmunoChip (or your custom chip) with function
calls. Intuitive wrappers for annotation lookup (gene lists, exon ranges, etc) and
conversion (e.g, between build 36 and 37 coordinates). Conversion between ensembl
and HGNC gene ids, chip ids to rs-ids for SNP-arrays. Retrieval of chromosome and
position for gene, band or SNP-ids, or reverse lookup. Simulation functions for
ranges objects.","Imports":"Rcpp, methods, parallel, GenomicFeatures (>=
1.22.10),\nGenomeInfoDb, rtracklayer, biomaRt, BiocInstaller (>= 1.20.1),\ngenoset
(>= 1.16.2), reader (>= 1.0.1), utils, stats, graphics","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"humarray","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Simplify Analysis and Annotation of Human Microarray
Datasets","Version":"1.0.0"},"hunspell":{"Author":"Jeroen Ooms","Description":"A
spell checker and morphological analyzer library designed for\nlanguages with rich
morphology and complex word compounding or character\nencoding. The package can
check and analyze individual words as well as\nsearch for incorrect words within a
text, latex or manual document.","Imports":"Rcpp","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"hunspell","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat","Title":"Morphological Analysis and
Spell Checker for R","URL":"https:\/\/github.com\/jeroenooms\/hunspell
https:\/\/hunspell.github.io","Version":"1.2"},"hwde":{"Author":"John Maindonald,
with \\code{hwexact()} from Randall Johnson.","Depends":"R (>=
2.0)","Description":"Fits models for genotypic disequilibria, as described
in\nHuttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986).\nContrast
terms are available that account for first order interactions\nbetween loci. Also
implements, for a single locus in a single\npopulation, a conditional exact test
for Hardy-Weinberg equilibrium.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hwde","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Models and Tests for Departure from Hardy-Weinberg
Equilibrium\nand Independence Between Loci","URL":"http:\/\/maths-
people.anu.edu.au\/~johnm","Version":"0.67"},"hwriter":{"Author":"Gregoire Pau
<gregoire.pau@gmail.com>","Depends":"R (>= 2.6.0)","Description":"Easy-to-use and
versatile functions to output R objects in\nHTML format","License":"LGPL-
2.1","NeedsCompilation":"no","Package":"hwriter","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"HTML Writer - Outputs R objects in HTML
format","Version":"1.3.2"},"hwriterPlus":{"Author":"David Scott
<d.scott@auckland.ac.nz>","Depends":"R (>= 2.10.0), hwriter","Description":"This
package extends the package hwriter providing\nfacilities such as the inclusion of
output from R, the\nresults of an R session, the display of
mathematical\nexpressions using LaTeX notation and the incorporation of\nSVG
graphical objects. It uses MathJax to display\nmathematical expressions, in
contrast to R2HTML which\nuses
ASCIIMathML.","Imports":"TeachingDemos","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hwriterPlus","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"xtable, RUnit","Title":"hwriterPlus: Extending the
hwriter Package","Version":"1.0-3"},"hwwntest":{"Author":"Delyan Savchev
[aut],\nGuy Nason [aut, cre]","Depends":"R(>= 3.0)","Description":"Provides methods
to test whether time series is consistent\nwith white noise.","Imports":"parallel,
polynom, wavethresh","License":"GPL-
2","NeedsCompilation":"no","Package":"hwwntest","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Tests of White Noise using
Wavelets","Version":"1.3"},"hybridEnsemble":{"Author":"Michel Ballings, Dauwe
Vercamer, and Dirk Van den Poel","Description":"Functions to build and deploy a
hybrid ensemble consisting of eight different sub-ensembles: bagged logistic
regressions, random forest, stochastic boosting, kernel factory, bagged neural
networks, bagged support vector machines, rotation forest, and bagged k-nearest
neighbors. Functions to cross-validate the hybrid ensemble and plot and summarize
the results are also provided. There is also a function to assess the importance of
the predictors.","Imports":"randomForest, kernelFactory, ada, rpart, ROCR, nnet,
e1071,\nNMOF, GenSA, Rmalschains, pso, AUC, soma, genalg, reportr,\nnnls, quadprog,
tabuSearch, rotationForest, FNN, glmnet","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hybridEnsemble","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat","Title":"Build, Deploy and Evaluate
Hybrid Ensembles","Version":"1.0.0"},"hybridHclust":{"Author":"Hugh Chipman, Rob
Tibshirani, with tsvq code originally from Trevor Hastie","Description":"Hybrid
hierarchical clustering via mutual clusters. A mutual cluster is a set of points
closer to each other than to all other points. Mutual clusters are used to enrich
top-down hierarchical clustering.","Imports":"cluster, stats","License":"GPL-
2","NeedsCompilation":"no","Package":"hybridHclust","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Hybrid Hierarchical Clustering","Version":"1.0-
5"},"hybridModels":{"Author":"Fernando S. Marques [aut, cre],\nJose H. H. Grisi-
Filho [aut],\nMarcos Amaku [aut]","Depends":"R (>=
3.2.3),","Description":"Simulates stochastic hybrid models for transmission of
infectious\ndiseases in dynamic networks.","Imports":"doParallel, foreach, ggplot2,
GillespieSSA, parallel,\nreshape2, stats, stringr, grid","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hybridModels","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Stochastic Hybrid Models in Dynamic
Networks","URL":"https:\/\/github.com\/fernandosm\/hybridModels","Version":"0.2.6"}
,"hydroApps":{"Author":"Daniele Ganora","Depends":"nsRFA","Description":"Package
providing tools for hydrological applications and models developed for regional
analysis in Northwestern Italy.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hydroApps","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Tools and models for hydrological
applications","Version":"0.1-1"},"hydroGOF":{"Author":"Mauricio Zambrano-Bigiarini
[aut, cre]","Depends":"R (>= 2.10.0), zoo (>= 1.7-2)","Description":"S3 functions
implementing both statistical and graphical goodness-of-fit measures between
observed and simulated values, mainly oriented to be used during the calibration,
validation, and application of hydrological models. Missing values in observed
and\/or simulated values can be removed before computations. Comments \/
questions \/ collaboration of any kind are very welcomed.","Imports":"hydroTSM (>=
0.3-6), xts (>= 0.8-2), methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hydroGOF","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Goodness-of-fit functions for comparison of simulated
and\nobserved hydrological time
series","URL":"http:\/\/www.rforge.net\/hydroGOF\/,\nhttp:\/\/cran.r-
project.org\/web\/packages\/hydroGOF\/","Version":"0.3-8"},"hydroPSO":
{"Author":"Mauricio Zambrano-Bigiarini [aut, cre], Rodrigo Rojas
[ctb]","Depends":"R (>= 2.13.0)","Description":"This package implements a state-of-
the-art version of the Particle Swarm Optimisation (PSO) algorithm (SPSO-2011 and
SPSO-2007 capable). hydroPSO can be used as a replacement of the 'optim' R function
for (global) optimization of non-smooth and non-linear functions. However, the main
focus of hydroPSO is the calibration of environmental and other real-world models
that need to be executed from the system console. hydroPSO is model-independent,
allowing the user to easily interface any computer simulation model with the
calibration engine (PSO). hydroPSO communicates with the model through the model's
own input and output files, without requiring access to the model's source code.
Several PSO variants and controlling options are included to fine-tune the
performance of the calibration engine to different calibration problems. An
advanced sensitivity analysis function together with user-friendly plotting
summaries facilitate the interpretation and assessment of the calibration results.
hydroPSO is parallel-capable, to alleviate the computational burden of complex
models with \"long\" execution time. Bugs reports\/comments\/questions are very
welcomed (in English, Spanish or Italian).","Imports":"Hmisc, sp, lattice, zoo(>=
1.7-2), grid, lhs","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hydroPSO","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"hydroGOF(>= 0.3-5), hydroTSM(>= 0.3-6), xts(>= 0.8-
2),\nparallel, scatterplot3d, vioplot, SWAT2R","Title":"Particle Swarm
Optimisation, with focus on Environmental
Models","URL":"http:\/\/www.rforge.net\/hydroPSO,\nhttp:\/\/cran.r-
project.org\/web\/packages\/hydroPSO","Version":"0.3-4"},"hydroTSM":
{"Author":"Mauricio Zambrano-Bigiarini [aut, cre, cph]","Depends":"R (>= 2.10.0),
zoo (>= 1.7-2), xts (>= 0.8-2)","Description":"S3 functions for management,
analysis, interpolation and plotting of time series used in hydrology and related
environmental sciences. In particular, this package is highly oriented to
hydrological modelling tasks. The focus of this package has been put in providing a
collection of tools useful for the daily work of hydrologists (although an effort
was made to optimise each function as much as possible, functionality has had
priority over speed). Bugs \/ comments \/ questions \/ collaboration of any kind
are very welcomed, and in particular, datasets that can be included in this package
for academic purposes.","Imports":"e1071, gstat, automap, sp","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hydroTSM","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"rgdal, maptools, lattice","Title":"Time series
management, analysis and interpolation for\nhydrological
modelling","URL":"http:\/\/www.rforge.net\/hydroTSM\/,\nhttp:\/\/cran.r-
project.org\/web\/packages\/hydroTSM\/","Version":"0.4-2-1"},"hydrogeo":
{"Author":"Myles English <myles@rockhead.biz>","Depends":"R (>= 2.6.0),
methods","Description":"Contains one function for drawing Piper diagrams
(also\ncalled Piper-Hill diagrams) of water analyses for major
ions.","License":"BSD_2_clause + file
LICENCE","NeedsCompilation":"no","Package":"hydrogeo","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Groundwater data presentation and
interpretation","URL":"http:\/\/rockhead.biz","Version":"0.2-3"},"hydrostats":
{"Author":"Nick Bond","Description":"Calculates a suite of hydrologic indices for
daily time series data that are widely used in hydrology and stream
ecology.","Imports":"stats, utils, graphics","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hydrostats","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"dplyr, plyr","Title":"Hydrologic Indices for Daily
Time Series
Data","URL":"https:\/\/github.com\/nickbond\/hydrostats","Version":"0.2.4"},"hyfo":
{"Author":"Yuanchao Xu [aut, cre]","Depends":"R (>= 3.1.0), stats (>= 3.1.3),
utils(>= 3.1.3),","Description":"Focuses on data processing and visualization in
hydrology and\nclimate forecasting. Main function includes data extraction, data
downscaling, data\nresampling, gap filler of precipitation, bias correction of
forecasting data, flexible\ntime series plot, and spatial map generation. It is a
good pre-processing and\npost-processing tool for hydrological and hydraulic
modellers.","Imports":"ggplot2 (>= 1.0.1), reshape2 (>= 1.4.1), zoo (>= 1.7-
12),\nrgdal (>= 0.8-16), plyr (>= 1.8.3), moments (>= 0.14), lmom (>=\n2.5),
maps(>= 2.3-9), maptools (>= 0.8-36), rgeos (>= 0.3-8),\nncdf4 (>= 1.14.1), MASS
(>= 7.3-39), methods","License":"GPL-
2","NeedsCompilation":"no","Package":"hyfo","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"gridExtra, knitr, rmarkdown","Title":"Hydrology and
Climate Forecasting","URL":"http:\/\/yuanchao-
xu.github.io\/hyfo\/","Version":"1.3.6"},"hyperSpec":{"Author":"Claudia
Beleites","Depends":"R (>= 2.15), methods, utils, lattice, grid, ggplot2
(>=\n0.9.2), mvtnorm","Description":"Comfortable ways to work with hyperspectral
data sets.\nI.e. spatially or time-resolved spectra, or spectra with any other
kind\nof information associated with each of the spectra. The spectra can be
data\nas obtained in XRF, UV\/VIS, Fluorescence, AES, NIR, IR, Raman, NMR,
MS,\netc. More generally, any data that is recorded over a discretized
variable,\ne.g. absorbance = f (wavelength), stored as a vector of absorbance
values\nfor discrete wavelengths is suitable.","Imports":"latticeExtra,
svUnit","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"hyperSpec","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"R.matlab, tripack, deldir, rgl, plotrix, testthat,
sp,\nbaseline, compiler, inline, Rcpp, MASS, fastcluster, pls","Title":"Work with
Hyperspectral Data, i.e. Spectra + Meta Information\n(Spatial, Time, Concentration,
...)","URL":"http:\/\/hyperSpec.r-forge.r-project.org\/","Version":"0.98-
20150304"},"hyperdirichlet":{"Author":"Robin K.S. Hankin","Depends":"R (>= 2.10),
aylmer (>= 1.0.11), abind","Description":"A suite of routines for the
hyperdirichlet distribution","Imports":"methods, mvtnorm, cubature","License":"GPL-
2","NeedsCompilation":"no","Package":"hyperdirichlet","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"A generalization of the Dirichlet
distribution","Version":"1.4-9"},"hypergea":{"Author":"Markus Boenn","Depends":"R
(>= 3.0.0)","Description":"Performs (exact) hypergeometric tests on IxJ and 2x2x2
contingency tables using parallelised C code.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"hypergea","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Hypergeometric Tests","Version":"1.3.1"},"hypergeo":
{"Author":"Robin K. S. Hankin","Depends":"R (>= 3.1.0),","Description":"The
Gaussian hypergeometric function for complex numbers.","Imports":"elliptic (>= 1.3-
5), contfrac (>= 1.1-9), deSolve","License":"GPL-
2","NeedsCompilation":"no","Package":"hypergeo","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"The Gauss Hypergeometric Function","Version":"1.2-
13"},"hypervolume":{"Author":"Benjamin Blonder","Depends":"Rcpp, rgl, methods, R
(>= 3.0.0)","Description":"Estimates the shape and volume of high-dimensional
datasets and performs set operations: intersection \/ overlap, union, unique
components, inclusion test, and hole detection. Uses stochastic geometry approach
to high-dimensional kernel density estimation. Builds n-dimensional convex hulls
(polytopes). Can measure the n-dimensional ecological hypervolume and perform
species distribution modeling.","Imports":"MASS, geometry, ks, fastcluster,
compiler","License":"GPL-
3","NeedsCompilation":"yes","Package":"hypervolume","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"High-Dimensional Kernel Density Estimation and
Geometry\nOperations","Version":"1.4.1"},"hyphenatr":{"Author":"Bob Rudis [aut,
cre],\nRaph Levien [aut, cph] (original libhnj),\nRene Engelhard [aut, cph] (libhnj
maintainer),\nChris Halls [aut, cph] (libhnj maintainer),\nPeter Novodvorsky [aut,
cph] (libhnj OOo integration),\nLÃ¡szlÃ³ NÃ©meth [aut, cph] (libhnj non-standard
and compound hyphenation\nwith Unicode support),\nNanning Buitenhuis [aut, cph]
(libhnj substrings.c),\nEdwin de Jonge [ctb] (Language testing),\nGergely DarÃ³czi
[ctb] (Language testing)","Depends":"R (>= 3.1.0)","Description":"Identifying
hyphenation points in strings can be useful for both\ntext processing and display
functions. The 'Hunspell' hyphenation
library\n<https:\/\/github.com\/hunspell\/hyphen> provides tools to perform
hyphenation\nusing custom language rule dictionaries. Many hyphenation
rules\ndictionaries are included. Words can be hyphenated directly or split
into\nhyphenated component strings for further processing.","Imports":"Rcpp,
stringi","License":"GPL-3 + file
LICENSE","NeedsCompilation":"yes","Package":"hyphenatr","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Tools to Hyphenate Strings
Using the 'Hunspell' Hyphenation\nLibrary","Version":"0.3.0"},"hypothesestest":
{"Author":"Chengfeng Liu,Huiqing Liu,Yingyan Liang,Ruibin
Feng","Description":"Compute the confidence interval of the population mean\nwith
one sample or of the difference of population means of two\nsamples from normal
distributions or t-distributions.Compute\nthe confidence interval of population
variance with one sample\nor of the difference of population variances of two
samples by\nchi-square tests.Test for population mean or the differences of\ntwo
normal samples under normality with the given null\nhypothesis H0,which depends on
the user,so that he can know if\nhe can reject H0 or not
at the significance level alpha.Do the\nchi-square tests with one or two samples
which have multinomial\ndistributions by using an approximate chi-square
distribution\nwhen n is large enough.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hypothesestest","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Confidence Intervals and Tests of Statistical
Hypotheses","Version":"1.0"},"hysteresis":{"Author":"Spencer Maynes, Fan Yang, and
Anne Parkhurst","Depends":"car, msm, MASS","Description":"Fit, summarize and plot
sinusoidal hysteretic processes using:\ntwo-step simple harmonic least squares,
ellipse-specific non-linear least\nsquares, the direct method, geometric least
squares or linear least squares.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"hysteresis","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr","Title":"Tools for Modeling Rate-Dependent
Hysteretic Processes and\nEllipses","Version":"2.5"},"hzar":{"Author":"Graham
Derryberry","Depends":"R (>= 2.10.0), MCMCpack, foreach, coda","Description":"A
collection of tools for modeling the shape of 1 dimensional clines.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"hzar","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Hybrid Zone Analysis using R","Version":"0.2-5"},"iBATCGH":
{"Author":"Alberto Cassese","Depends":"R (>= 2.10)","Description":"Bayesian
integrative models of gene expression and comparative genomic hybridization data.
The package provides inference on copy number variations and their association with
gene expression.","Imports":"Rcpp (>= 0.11.2), msm","License":"GPL-
2","NeedsCompilation":"yes","Package":"iBATCGH","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Integrative Bayesian Analysis of Transcriptomic and CGH
Data","URL":"http:\/\/www.r-project.org","Version":"1.3"},"iBUGS":{"Author":"Yihui
Xie and Jiebiao Wang","Depends":"R2WinBUGS, gWidgetsRGtk2","Description":"This
package has provided an interface to WinBUGS\/OpenBUGS\/JAGS\nvia R2WinBUGS and
R2jags. Some options will be intelligently guessed, e.g.\nthe path to
WinBUGS\/OpenBUGS\/JAGS and the data\/parameter list. Users can\nspecify all the
options in a GUI.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"iBUGS","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"R2jags, knitr","Title":"An Interface to
WinBUGS\/OpenBUGS\/JAGS by gWidgets","Version":"0.1.4"},"iC10":{"Author":"Oscar M
Rueda","Depends":"pamr, iC10TrainingData","Description":"Implementation of the
classifier described in the paper 'Genome-driven integrated classification of
breast cancer validated in over 7,500 samples' (Ali HR et al., Genome Biology
2014). It uses copy number and\/or expression form breast cancer data, trains a
pamr classifier (Tibshirani et al.) with the features available and predicts the
iC10 group.","License":"GPL-
3","NeedsCompilation":"no","Package":"iC10","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"A Copy Number and Expression-Based Classifier for Breast
Tumours","Version":"1.1.3"},"iC10TrainingData":{"Author":"Oscar M
Rueda","Description":"Training datasets for iC10; which implements the classifier
described in the paper 'Genome-driven integrated classification of breast cancer
validated in over 7,500 samples' (Ali HR et al., Genome Biology 2014). It uses copy
number and\/or expression form breast cancer data, trains a pamr classifier
(Tibshirani et al.) with the features available and predicts the iC10 group.
Genomic annotation for the training dataset has been obtained from Mark Dunning's
lluminaHumanv3.db package.","License":"GPL-
3","NeedsCompilation":"no","Package":"iC10TrainingData","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Training datasets for iC10
package","Version":"1.0.1"},"iClick":{"Author":"Ho Tsung-
wu","Depends":"lattice,rugarch,tcltk","Description":"A GUI designed to support the
analysis of financial-economic time\nseries data.","Imports":"fBasics, forecast,
grid, lubridate, openair, timeDate,\ntimeSeries","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"iClick","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"A Button-Based GUI for Financial and Economic Data
Analysis","Version":"1.2"},"iCluster":{"Author":"Ronglai Shen","Depends":"R (>=
2.15.0), lattice, caTools, gdata, gtools,
gplots,\nparallel","Description":"Integrative clustering of multiple genomic data
types\nusing a joint latent variable model.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"iCluster","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Integrative clustering of multiple genomic data
types","Version":"2.1.0"},"iDynoR":{"Author":"Kieran Alden, Jan-Ulrich
Kreft","Depends":"XML, vegan","Description":"iDynoMiCS is a computer program,
developed by an international team of researchers, whose purpose is to model and
simulate microbial communities in an individual-based way. It is described in
detail in the paper \"iDynoMiCS: next-generation individual-based modelling of
biofilms\" by Lardon et al, published in Environmental Microbiology in 2011. The
simulation produces results in XML file format, describing the state of each
species in each timestep (agent_State), a summary of the species statistics for a
timepoint (agent_Sum), the state of each solute grid in each timestep (env_State)
and a summary of the solutes for a timestep (env_Sum). This R package provides a
means of reading this XML data into R such that the simulation response can be
statistically analysed. iDynoMiCS is available from the website iDynoMiCS.org,
where a full tutorial on using both the simulation and this R package is
provided.","License":"CeCILL","NeedsCompilation":"no","Package":"iDynoR","Repositor
y":"http:\/\/cran.csiro.au\/src\/contrib","Title":"R Analysis package for iDynoMiCS
Simulation Results","Version":"1.0"},"iFad":{"Author":"Haisu Ma
<haisu.ma.pku.2008@gmail.com>","Depends":"R (>=
2.12.1),Rlab,MASS,coda,ROCR","Description":"This package implements a Bayesian
sparse factor model for the joint analysis of paired datasets, one is the gene
expression dataset and the other is the drug sensitivity profiles, measured across
the same panel of samples, e.g., cell lines. Prior knowledge about gene-pathway
associations can be easily incorporated in the model to aid the inference of drug-
pathway associations.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"iFad","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"An integrative factor analysis model for drug-
pathway\nassociation inference","Version":"3.0"},"iGasso":{"Author":"Dr. Kai
Wang","Depends":"lattice, CompQuadForm","Description":"A collection of statistical
tests for genetic association studies.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"iGasso","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Statistical Tests and Utilities for Genetic
Association","Version":"1.3"},"iLaplace":{"Author":"Erlis Ruli [aut, cre], Nicola
Sartori [aut], Laura Ventura [aut]","Depends":"R (>=
3.2.2)","Description":"Improved Laplace approximation for integrals of unimodal
functions. The method requires user-supplied R functions for: the integrand, its
gradient and its Hessian matrix. The computations are run in
parallel.","Imports":"doParallel, foreach, iterators, Rcpp, stats","License":"GPL-
2","NeedsCompilation":"yes","Package":"iLaplace","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"devtools","Title":"Improved Laplace Approximation for
Integrals of
Unimodal\nFunctions","URL":"https:\/\/github.com\/erlisR\/iLaplace","Version":"1.0.
0"},"iNEXT":{"Author":"T. C. Hsieh, K. H. Ma and Anne Chao","Depends":"R (>=
2.14)","Description":"Provides simple functions to compute and plot two\ntypes
(sample-size- and coverage-based) rarefaction and extrapolation of
species\ndiversity (Hill numbers) for individual-based (abundance) data or
sampling-unit-\nbased (incidence) data.","Imports":"stats, graphics,
3)","NeedsCompilation":"no","Package":"iNEXT","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat, knitr, rmarkdown, gridExtra,
ggthemes","Title":"Interpolation and Extrapolation for Species
Diversity","URL":"http:\/\/chao.stat.nthu.edu.tw\/blog\/software-
download\/","Version":"2.0.8"},"iRafNet":{"Author":"Francesca Petralia Developer
[aut, cre],\nPei Wang Developer [aut],\nZhidong Tu Developer [aut],\nJialiang Yang
Developer [aut],\nAdele Cutler Developer [ctb],\nLeo Breiman Developer [ctb],\nAndy
Liaw Developer [ctb],\nMatthew Wiener Developer [ctb]","Depends":"R (>=
3.0.0)","Description":"Provides a flexible integrative algorithm that allows
information from prior data, such as protein protein interactions and gene knock-
down, to be jointly considered for gene regulatory network
inference.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"iRafNet","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Integrative Random Forest for Gene Regulatory Network
Inference","URL":"https:\/\/www.r-project.org","Version":"0.1-1"},"iRefR":
{"Author":"Antonio Mora <antoniocmora@gmail.com>, Ian Donaldson
<ian.oslo@gmail.com>","Depends":"R (>= 2.12.1), igraph (>= 0.6), graph,
RBGL","Description":"\"iRefR\" allows the user to load any version of the
consolidated protein interaction database \"iRefIndex\" and perform tasks such as:
selecting databases, pmids, experimental methods, searching for specific proteins,
separate binary interactions from complexes and polymers, generate complexes
according to an algorithm that looks after possible binary-represented complexes,
make general database statistics and create network graphs, among
2)","NeedsCompilation":"no","Package":"iRefR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"iRefIndex
Manager","URL":"http:\/\/irefindex.org\/wiki\/index.php?
title=iRefR","Version":"1.13"},"iRegression":{"Author":"Eufrasio
de A. Lima Neto with contribution from Claudio
A.\nVasconcelos","Depends":"mgcv","Description":"This package contains some
important regression methods\nfor interval-valued variables. For each method, it is
available\nthe fitted values, residuals and some goodness-of-fit
measures.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"iRegression","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Regression methods for interval-valued
variables","Version":"1.2"},"iRepro":{"Author":"Jelena Kovacic","Description":"This
package calculates intraclass correlation coefficient (ICC) for assessing
reproducibility of interval-censored data with two repeated measurements. ICC is
estimated by maximum likelihood from model with one fixed and one random effect
(both intercepts). Help in model checking (normality of subjects' means and
residuals) is provided.","License":"GPL-
3","NeedsCompilation":"no","Package":"iRepro","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Reproducibility for Interval-Censored
Data","Version":"1.0"},"iWISA":{"Author":"Inga Maslova [aut],\nWen Xiao [aut,
cre]","Depends":"R (>= 2.10.0), stats","Description":"A powerful system for
estimating an improved wavelet-based index\nof magnetic storm activity, storm
activity preindex (from individual station) and SQ variations.\nIt also serves as a
flexible visualization tool.","Imports":"waveslim, fda, ggplot2, splines,
3","NeedsCompilation":"no","Package":"iWISA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Wavelet-Based Index of Storm Activity","Version":"1.0-
2"},"iWeigReg":{"Author":"Zhiqiang Tan and Heng Shu","Depends":"R (>= 2.9.1), MASS
(>= 7.2-1), trust","Description":"Improved methods based on inverse probability
weighting\nand outcome regression for causal inference and missing
data\nproblems","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"iWeigReg","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Improved methods for causal inference and missing data
problems","URL":"http:\/\/www.stat.rutgers.edu\/~ztan","Version":"1.0"},"ibd":
{"Author":"B N Mandal <mandal.stat@gmail.com>","Depends":"R (>= 3.1.1), lpSolve,
MASS, car, lsmeans, multcompView","Description":"This package contains several
utility functions related to incomplete block designs. The package contains
function to generate efficient incomplete block designs with given numbers of
treatments, blocks and block size. The package also contains function to generate
an incomplete block design with specified concurrence matrix. There are functions
to generate balanced treatment incomplete block designs and incomplete block
designs for test versus control treatments comparisons with specified concurrence
matrix. Package also allows performing analysis of variance of data and computing
least square means of factors from experiments using a connected incomplete block
design. Tests of hypothesis of treatment contrasts in incomplete block design set
up is supported.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ibd","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"INCOMPLETE BLOCK DESIGNS","Version":"1.2"},"ibdreg":
{"Author":"Jason P. Sinnwell and Daniel J. Schaid","Depends":"R (>=
2.15.0)","Description":"A method to test genetic linkage with covariates
by\nregression methods with response IBD sharing for relative\npairs. Account for
correlations of IBD statistics and\ncovariates for relative pairs within the same
pedigree.","License":"GPL-2 | file
LICENSE","NeedsCompilation":"yes","Package":"ibdreg","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Regression Methods for IBD Linkage With
Covariates","URL":"http:\/\/mayoresearch.mayo.edu\/mayo\/research\/schaid_lab\/soft
ware.cfm","Version":"0.2.5"},"ibeemd":{"Author":"Maogui Hu","Depends":"R (>=
2.11.0), fields, deldir, rgeos, sp, spdep","Description":"A data-driven and
adaptive hierarchical-scale decomposition method for irregular-lattice field
(represented by polygons).","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"ibeemd","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"rgdal","Title":"Irregular-lattice based ensemble
empirical mode decomposition","Version":"1.0.1"},"ibelief":{"Author":"Kuang Zhou
<kzhoumath@163.com>; Arnaud Martin\n<arnaud.martin@univ-rennes1.fr>","Depends":"R
(>= 2.15.1)","Description":"Some basic functions to implement belief functions
including:\ntransformation between belief functions using the method introduced
by\nPhilippe Smets (arXiv:1304.1122 [cs.AI]), evidence combination,
evidence\ndiscounting, decision-making, and constructing masses. Currently,
thirteen\ncombination rules and five decision rules are supported. It can also
be\nused to generate different types of random masses when working on
belief\ncombination and conflict management.","Imports":"stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ibelief","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Belief Function
Implementation","Version":"1.2"},"ibmdbR":{"Author":"IBM Corporation","Depends":"R
(>= 2.15.1), methods, RODBC, Matrix, arules","Description":"Functionality required
to efficiently use R with\nIBM DB2(C) for Linux, Unix and Windows as well as IBM
dashDB(C).\nMany basic and complex R operations are pushed down into the database,
which removes\nthe main memory boundary of R and allows to make full use of
parallel processing in\nthe underlying database.","Imports":"MASS,rpart,
rpart.plot, ggplot2","License":"GPL-
3","NeedsCompilation":"no","Package":"ibmdbR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"IBM in-Database Analytics for R","Version":"1.47.1"},"ibr":
{"Author":"Pierre-Andre Cornillon, Nicolas Hengartner, Eric Matzner-
Lober","Depends":"R (>= 2.11.1), mgcv","Description":"Multivariate smoothing using
iterative bias reduction with kernel, thin plate splines, Duchon splines or low
rank splines.","Imports":"stats, graphics","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ibr","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat","Title":"Iterative Bias
Reduction","Version":"2.0-2"},"ic.infer":{"Author":"Ulrike
Groemping","Depends":"R(>= 2.5.0)","Description":"This package implements parameter
estimation in normal (linear) models under linear equality and inequality
constraints and implements normal likelihood ratio tests involving inequality-
constrained hypotheses. For inequality-constrained linear models, averaging over R-
squared for different orderings of regressors is also
included.","Imports":"quadprog, mvtnorm, boot, kappalab","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ic.infer","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"relaimpo","Title":"Inequality constrained inference
in linear normal situations","URL":"http:\/\/prof.beuth-
hochschule.de\/groemping\/","Version":"1.1-5"},"ic50":{"Author":"Peter
Frommolt","Depends":"tcltk","Description":"Calculation of IC50 values, automatic
drawing of\ndose-response curves and validation of compound screens on 96-\nand
384-well
plates.","License":"GPL","NeedsCompilation":"no","Package":"ic50","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Title":"Standardized high-throughput evaluation
of cell-based compound\nscreens","URL":"http:\/\/portal.ccg.uni-
koeln.de\/","Version":"1.4.2"},"icRSF":{"Author":"Hui Xu and Raji
Balasubramanian","Description":"Implements a modification to the Random Survival
Forests algorithm for obtaining variable importance in high dimensional datasets.
The proposed algorithm is appropriate for settings in which a silent event is
observed through sequentially administered, error-prone self-reports or laboratory
based diagnostic tests. The modified algorithm incorporates a formal likelihood
framework that accommodates sequentially administered, error-prone self-reports or
laboratory based diagnostic tests. The original Random Survival Forests algorithm
is modified by the introduction of a new splitting criterion based on a likelihood
ratio test statistic.","Imports":"Rcpp (>= 0.11.3), icensmis,
2)","NeedsCompilation":"yes","Package":"icRSF","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"A Modified Random Survival Forest
Algorithm","Version":"1.0"},"ica":{"Author":"Nathaniel E. Helwig
<helwig@umn.edu>","Description":"Independent Component Analysis (ICA) using various
algorithms: FastICA, Information-Maximization (Infomax), and Joint Approximate
Diagonalization of Eigenmatrices (JADE).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ica","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Independent Component Analysis","Version":"1.0-
1"},"icaOcularCorrection":{"Author":"Antoine Tremblay, NeuroCognitive Imaging Lab,
Dalhousie University","Depends":"fastICA, mgcv","Description":"Removes eye-movement
and other types of known (i.e., recorded) or unknown (i.e., not recorded) artifacts
using the fastICA package. The correction method proposed in this package is
largely based on the method described in on Flexer, Bauer, Pripfl, and Dorffner
(2005). The process of correcting electro- and magneto-encephalographic data
(EEG\/MEG) begins by running function `ìcac'', which first performs independent
components analysis (ICA) to decompose the data frame into independent components
(ICs) using function ``fastICA'' from the package of the same name. It then
calculates for each trial the correlation between each IC and each one of the noise
signals -- there can be one or more, e.g., vertical and horizontal electro-
oculograms (VEOG and HEOG), electro-myograms (EMG), electro-cardiograms (ECG),
galvanic skin responses (GSR), and other noise signals. Subsequently, portions of
an IC corresponding to trials at which the correlation between it and a noise
signal was at or above threshold
(set to 0.4 by default; Flexer et al., 2005, p. 1001) are zeroed-out in the source
matrix, ``S''. The user can then identify which ICs correlate with the noise
signals the most by looking at the summary of the `ìcac'' object (using function
``summary.icac''), the scalp topography of the ICs (using function ``topo_ic''),
the time courses of the ICs (using functions ``plot_tric'' and ``plot_nic''), and
other diagnostic plots. Once these ICs have been identified, they can be completely
zeroed-out using function `ùpdate.icac'' and the resulting correction checked
using functions ``plot_avgba'' and ``plot_trba''. Some worked-out examples with R
code are provided in the package vignette.","License":"GPL-
2","NeedsCompilation":"no","Package":"icaOcularCorrection","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Suggests":"wavethresh","Title":"Independent Components
Analysis (ICA) based artifact correction","Version":"3.0.0"},"icamix":
{"Author":"Xiaotian Zhu, David R. Hunter","Description":"The icamix package
provides R functions as well as a C++ library which facilitate the estimation of
ICA mixture models. We have developed and implemented the NSMM-ICA algorithm that
currently integrates npEM and Fast-ICA for non-parametric estimation of ICA mixture
models. We will continue to build in algorithms that interweave the EM step with
other types of ICA techniques.","Imports":"Rcpp (>= 0.11.5)","License":"GPL-2 |
GPL-
3","NeedsCompilation":"yes","Package":"icamix","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"mixtools","Title":"Estimation of ICA Mixture
Models","Version":"1.0.4"},"icapca":{"Author":"Roger Woods
<rwoods@ucla.edu>","Description":"Implements mixed ICA\/PCA model for blind source
separation, potentially with inclusion of Gaussian
sources","License":"Unlimited","NeedsCompilation":"yes","Package":"icapca","Reposit
ory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Mixed
ICA\/PCA","Version":"1.1"},"icarus":{"Author":"Antoine Rebecq [aut,
cre]","Depends":"R (>= 3.1.1)","Description":"Provides user-friendly tools for
calibration in survey sampling. The package is production-oriented, and its
interface is inspired by the famous popular macro 'Calmar' for SAS, so that
'Calmar' users can quickly get used to 'icarus'. In addition to calibration (with
linear, raking and logit methods), 'icarus' features functions for calibration on
tight bounds and penalized calibration.","License":"GPL-
3","NeedsCompilation":"no","Package":"icarus","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat, ggplot2, Rglpk, slam,
xtable","Title":"Calibrates and Reweights Units in
Samples","Version":"0.2.0"},"iccbeta":{"Author":"Steven Andrew Culpepper [aut, cph,
cre],\nHerman Aguinis [aut, cph]","Depends":"R (>= 3.0.2), lme4","Description":"A
function and vignettes for computing an intraclass correlation described in Aguinis
& Culpepper (in press). iccbeta quantifies the share of variance in a dependent
variable that is attributed to group heterogeneity in slopes.","Imports":"Rcpp (>=
0.11.1)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"iccbeta","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Multilevel model intraclass correlation for slope
heterogeneity","Version":"1.0"},"icd":{"Author":"Jack O. Wasey [aut, cre,
cph],\nWilliam Murphy [ctb] (Van Walraven scores),\nR Core Team [ctb, cph] (m4
macro for OpenMP detection in configure),\nKevin Ushey [ctb, cph] (Fast factor
creation, adapted from GPL-2\npackage fastmatch)","Depends":"R (>=
3.1.0)","Description":"Calculate comorbidities, Charlson scores, perform fast and
accurate\nvalidation, conversion, manipulation, filtering and comparison of ICD-9
and\nICD-10 codes. Common ambiguities and code formats are handled. This\npackage
enables a work flow from raw lists of ICD codes in hospital\nbilling databases to
comorbidities. ICD-9 and ICD-10 comorbidity mappings\nfrom Quan (Deyo and
Elixhauser versions), Elixhauser and AHRQ included.","Imports":"checkmate (>=
1.5.1), magrittr, stats, Rcpp (>= 0.12.3),\nstringr, utils","License":"GPL-
3","NeedsCompilation":"yes","Package":"icd","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"knitr, RODBC, roxygen2 (>= 5.0.0), rmarkdown, testthat,
xml2","Title":"Tools for Working with ICD-9 and ICD-10 Codes, and
Finding\nComorbidities","URL":"https:\/\/github.com\/jackwasey\/icd","Version":"2.0
"},"icd9":{"Author":"Jack O. Wasey [aut, cre, cph],\nWilliam Murphy [ctb],\nR Core
Team [ctb, cph]","Depends":"R (>= 3.1.0)","Description":"Calculate comorbidities,
Charlson scores, perform fast and accurate\nvalidation, conversion, manipulation,
filtering and comparison of ICD-9-CM\n(clinical modification) codes. ICD-9 codes
appear numeric but leading and\ntrailing zeroes, and both decimal and non-
decimal \"short\" format codes\nexist. The package enables a work flow from raw
lists of ICD-9 codes from\nhospital billing databases to comorbidities. ICD-9 to
comorbidity mappings\nfrom Quan (Deyo and Elixhauser versions), Elixhauser and AHRQ
included. Any\nother mapping of codes, such as ICD-10, to comorbidities can be
used.","Imports":"Rcpp (>= 0.12.0), checkmate (>= 1.5.1), stats,
utils,\nfastmatch","License":"GPL-
3","NeedsCompilation":"yes","Package":"icd9","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat, devtools, knitr, microbenchmark, magrittr,
XML,\nmemoise, profr, ggplot2, digest, xtable, rmarkdown","Title":"Tools for
Working with ICD-9 Codes, and Finding
Comorbidities","URL":"https:\/\/github.com\/jackwasey\/icd9","Version":"1.3"},"icen
Reg":{"Author":"Clifford Anderson-Bergman; uses Marloes Maathuis's HeightMap
algorithm (MLEcens::reduc)","Depends":"survival","Description":"Regression models
for interval censored data. Currently supports Cox-PH and proportional odds models.
Allows for both semi and fully parametric models. Includes functions for easy
visual diagnostics of model fits and imputation of censored data. Includes fast
algorithm for computing non-parametric maximum likelihood
estimator.","Imports":"foreach, methods, MLEcens","License":"LGPL (>= 2.0, <
3)","NeedsCompilation":"yes","Package":"icenReg","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Regression Models for Interval Censored
Data","Version":"1.3.4"},"icensmis":{"Author":"Xiangdong Gu and Raji
Balasubramanian","Description":"We consider studies in which information from
error-prone\ndiagnostic tests or self-reports are gathered sequentially to
determine the\noccurrence of a silent event. Using a likelihood-based
approach\nincorporating the proportional hazards assumption, we provide functions
to\nestimate the survival distribution and covariate effects. We also
provide\nfunctions for power and sample size calculations for this
setting.","Imports":"Rcpp (>= 0.11.0)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"icensmis","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat","Title":"Study Design and Data Analysis in
the Presence of Error-Prone\nDiagnostic Tests and Self-Reported
Outcomes","Version":"1.3.1"},"icsw":{"Author":"Peter M. Aronow
<peter.aronow@yale.edu>, Dean Eckles <icsw@deaneckles.com> and Kyle Peyton
<kyle.peyton@yale.edu>","Depends":"R (>= 3.0.0)","Description":"Provides the
necessary tools to estimate average treatment effects with an instrumental variable
by re-weighting observations using a model of
compliance.","Imports":"stats","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"icsw","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"rgenoud, minqa","Title":"Inverse Compliance Score
Weighting","Version":"0.9"},"idbg":{"Author":"Ronen Kimchi","Description":"An
interactive R debugger","License":"GPL-
2","NeedsCompilation":"no","Package":"idbg","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"R debugger","Version":"1.0"},"idbr":{"Author":"Kyle Walker
[aut, cre]","Depends":"R (>= 3.0.0)","Description":"Use R to make requests to the
US Census Bureau's International Data Base API.\nResults are returned as R data
frames. For more information about the IDB API,
visit\nhttp:\/\/www.census.gov\/data\/developers\/data-sets\/international-
database.html.","Imports":"jsonlite, dplyr, httr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"idbr","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"tidyr, plotly, countrycode","Title":"R Interface to
the US Census Bureau International Data Base API","Version":"0.1.2"},"idendr0":
{"Author":"Tomas Sieger","Description":"Interactive dendrogram that enables the
user to select and\ncolor clusters, to zoom and pan the dendrogram, and to
visualize\nthe clustered data not only in a built-in heat map, but also in\n'GGobi'
interactive plots and user-supplied plots.\nThis is a backport of Qt-based
'idendro'\n(https:\/\/github.com\/tsieger\/idendro) to base R graphics and Tcl\/Tk
GUI.","Imports":"tcltk, tkrplot, grDevices, graphics, stats","License":"GPL-
2","NeedsCompilation":"no","Package":"idendr0","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"rggobi, DendSer, cluster, RColorBrewer,
datasets","Title":"Interactive
Dendrograms","URL":"http:\/\/github.com\/tsieger\/idendr0","Version":"1.5.2"},"iden
tifyr":{"Author":"George Miranda [aut, cre]","Depends":"R (>=
2.10)","Description":"A fast way to clean and obtain unique identifiers used by the
Los Angeles County Probation Department.","Imports":"stringr (>= 1.0.0), magrittr
(>=
1.5)","License":"GPL","NeedsCompilation":"no","Package":"identifyr","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Clean Unique
Identifiers","URL":"https:\/\/github.com\/georgemirandajr\/identifyr","Version":"0.
1.3"},"identity":{"Author":"Na (Michael) Li <wuolong@gmail.com>","Depends":"R (>=
2.0.0)","Description":"Calculate identity coefficients, based on Mark Abney's
C\ncode.","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"identity","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Jacquard Condensed Coefficients of
Identity","Version":"0.2-1"},"idm":{"Author":"Alfonso Iodice D' Enza [aut], Angelos
Markos [aut, cre], Davide\nButtarazzi [ctb]","Depends":"corpcor, ggplot2, dummies,
animation, ca","Description":"Incremental Multiple Correspondence Analysis and
Principal\nComponent Analysis.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"idm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Incremental Decomposition Methods","Version":"1.3.1"},"idr":
{"Author":"Qunhua Li","Description":"This is a package for estimating the copula
mixture model and plotting correspondence curves in \"Measuring reproducibility of
high-throughput experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3,
1752-1779, by Li, Brown, Huang, and Bickel","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"idr","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Irreproducible discovery rate","Version":"1.2"},"iemisc":
{"Author":"Irucka Embry [aut, cre]. Includes R source code and\/or
documentation\npreviously published by: Felix Andrews (zoo) and Hans Werner
Borchers\n(pracma). [Borrowed from DescTools description.]","Depends":"R (>=
3.0.0), stats, data.table (>= 1.9.4)","Description":"A collection of Irucka Embry's
miscellaneous functions\n(Engineering Economics, Environmental\/Water Resources
Engineering,\nGeometry, Statistics, GNU Octave length functions,
etc.).","Imports":"zoo, pracma","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"iemisc","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"iemiscdata, Rcpp (>= 0.11.5), RcppOctave, rSymPy,
NISTunits,\nimport, financial, optiRum","Title":"Irucka Embry's Miscellaneous
Functions","URL":"https:\/\/gitlab.com\/iembry\/iemisc","Version":"0.5.0"},"iemiscd
ata":{"Author":"Irucka Embry [aut, cre]","Depends":"R (>=
2.14.0)","Description":"Miscellaneous data sets (Environmental\/Water
Resources\nEngineering).","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"iemiscdata","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"rivr","Title":"Irucka Embry's Miscellaneous Data
Collection","URL":"https:\/\/gitlab.com\/iembry\/iemiscdata","Version":"0.5.0"},"if
a":{"Author":"Cinzia Viroli","Depends":"R(>= 1.9.0)","Description":"The package
performes Independent Factor Analysis","Imports":"mvtnorm","License":"GPL-
2","NeedsCompilation":"yes","Package":"ifa","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Independent Factor
Analysis","URL":"www2.stat.unibo.it\/viroli","Version":"7.0"},"ifaTools":
{"Author":"Joshua N. Pritikin [cre, aut]","Depends":"shiny (>= 0.10), ggplot2,
reshape2, rpf (>= 0.48), OpenMx (>=\n2.3.1), R (>= 2.14.0)","Description":"Tools,
tutorials, and demos of Item Factor Analysis using
OpenMx.","Imports":"methods","License":"AGPL (>=
3)","NeedsCompilation":"no","Package":"ifaTools","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat, roxygen2, knitr (>= 1.8)","Title":"Toolkit
for Item Factor Analysis with
OpenMx","URL":"https:\/\/github.com\/jpritikin\/ifaTools","Version":"0.8"},"ifctool
s":{"Author":"Luca Braglia [aut, cre]","Depends":"R (>=
3.1.1)","Description":"Provides utility functions to deal with Italian fiscal\ncode
('codice fiscale').","License":"GPL-
3","NeedsCompilation":"yes","Package":"ifctools","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat","Title":"Italian Fiscal Code ('Codice
Fiscale')
Utilities","URL":"http:\/\/github.com\/lbraglia\/ifctools","Version":"0.3.2"},"ifs"
:{"Author":"S. M. Iacus","Description":"Iterated Function Systems
Estimator.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ifs","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Iterated Function Systems","Version":"0.1.5"},"ifultools":
{"Author":"William Constantine and Donald Percival (Applied Physics\nLaboratory,
University of Washington)","Depends":"R (>= 3.0.2), splus2R (>= 1.2-0),
MASS","Description":"Insightful Research Tools.","License":"GPL-
2","NeedsCompilation":"yes","Package":"ifultools","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Insightful Research Tools","Version":"2.0-
1"},"ig.vancouver.2014.topcolour":{"Author":"Roland Tanglao [aut,
cre]","Depends":"R (>= 2.10)","Description":"A dataset of the top colours of photos
from Instagram\ntaken in 2014 in the city of Vancouver, British Columbia,
Canada.\nIt consists of: top colour and counts data. This data was\nobtained using
the Instagram API. Instagram is a web photo\nsharing service. It can be found at:
<https:\/\/instagram.com>.\nThe Instagram API is documented at:
<https:\/\/instagram.com\/developer\/>.","License":"CC0","NeedsCompilation":"no","P
ackage":"ig.vancouver.2014.topcolour","Repository":"http:\/\/cran.csiro.au\/src\/co
ntrib","Title":"Instagram 2014 Vancouver Top Colour
Dataset","Version":"0.1.2.0"},"igraph":{"Author":"See AUTHORS
file.","Depends":"methods","Description":"Routines for simple graphs and network
analysis. It can\nhandle large graphs very well and provides functions for
generating random\nand regular graphs, graph visualization, centrality methods and
much more.","Imports":"Matrix, magrittr, NMF, irlba","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"igraph","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"igraphdata, stats4, rgl, tcltk, graph, ape,
scales","Title":"Network Analysis and
Visualization","URL":"http:\/\/igraph.org","Version":"1.0.1"},"igraphdata":
{"Author":"Gabor Csardi <csardi.gabor@gmail.com>","Depends":"R (>=
2.10)","Description":"A small collection of various network data sets,\nto use with
the 'igraph' package: the Enron email network, various food webs,\ninteractions in
the immunoglobulin protein, the karate club network,\nKoenigsberg's bridges,
visuotactile brain areas of the macaque monkey,\nUK faculty friendship network,
domestic US flights network, etc.","License":"CC BY-SA 4.0 + file
LICENSE","NeedsCompilation":"no","Package":"igraphdata","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"igraph (>= 1.0.0)","Title":"A Collection of
Network Data Sets for the 'igraph'
Package","URL":"http:\/\/igraph.org","Version":"1.0.1"},"igraphinshiny":
{"Author":"Ming-Jer Lee [aut, cre]","Depends":"R (>= 3.2.0)","Description":"Using
'shiny' to demo 'igraph' package makes learning graph theory easy and
fun.","Imports":"shiny, igraph","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"igraphinshiny","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Use 'shiny' to Demo
'igraph'","Version":"0.1"},"igraphtosonia":{"Author":"Sean J Westwood
<seanjw@stanford.edu>","Depends":"igraph","Description":"This program facilitates
exporting igraph graphs to the\nSoNIA file format","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"igraphtosonia","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Convert iGraph graps to SoNIA .son
files","Version":"1.0"},"ihs":{"Author":"Carter Davis","Depends":"R (>= 2.4.0),
maxLik (>= 1.2-4)","Description":"Density, distribution function, quantile function
and random generation for the inverse hyperbolic sine distribution. This package
also provides a function that can fit data to the inverse hyperbolic sine
distribution using maximum likelihood estimation.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"ihs","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Inverse Hyperbolic Sine
Distribution","Version":"1.0"},"iki.dataclim":{"Author":"Boris
Orlowsky","Depends":"R (>= 3.0.0)","Description":"The package offers an S4
infrastructure to store climatological\nstation data of various temporal
aggregation scales. In-built quality\ncontrol and homogeneity tests follow the
methodology from the European\nClimate Assessment & Dataset project. Wrappers for
climate indices\ndefined by the Expert Team on Climate Change Detection and
Indices\n(ETCCDI), a quick summary of important climate statistics and
climate\ndiagram plots provide a fast overview of climatological\ncharacteristics
of the station.","Imports":"methods, zoo, lubridate, climdex.pcic (>= 1.1-1),
PCICt","License":"GPL-
3","NeedsCompilation":"no","Package":"iki.dataclim","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Consistency, Homogeneity and Summary Statistics
of\nClimatological Data","URL":"www.climate-babel.org","Version":"1.0"},"ilc":
{"Author":"Zoltan Butt, Steven Haberman and Han Lin Shang","Depends":"R (>= 3.0.3),
demography, rainbow, forecast, date","Description":"Fitting a class of Lee-Carter
mortality models using iterative fitting
algorithm.","Imports":"survival","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ilc","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Lee-Carter Mortality Models using Iterative Fitting
Algorithms","Version":"1.0"},"imPois":{"Author":"Chel Hee Lee [aut, cre, cph],
Mikelis Bickis [aut, ths, cph]","Depends":"R (>= 2.7.0)","Description":"A
collection of tools for conducting an imprecise inference is provided. Imprecise
prior is used for this inference, and imprecise probability theory introduced by
Peter Walley (1991) is its underlying theoretical foundation. The package is
developed based on the PhD thesis work of Lee (2014). Poisson and zero-truncated
Poisson sampling models are mainly studied with two types of prior
distributions.","Imports":"geometry, grDevices, graphics, stats, utils,
rgl","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"imPois","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Imprecise Inferential Framework for Poisson Sampling
Model","URL":"http:\/\/r-forge.r-
project.org\/projects\/ipeglim\/","Version":"0.0.7.5"},"imager":{"Author":"Simon
Barthelme [aut, cre],\nAntoine Cecchi [ctb]","Depends":"R (>=
2.10.0),plyr,magrittr,stringr,grDevices,png,jpeg","Description":"Fast
image processing for images in up to 4 dimensions (two spatial\ndimensions, one
time\/depth dimension, one colour dimension). Provides most\ntraditional image
processing tools (filtering, morphology, transformations,\netc.) as well as various
functions for easily analysing image data using
R.","Enhances":"spatstat","Imports":"Rcpp (>=
0.11.5),methods","License":"LGPL","NeedsCompilation":"yes","Package":"imager","Repo
sitory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Image Processing Library
Based on CImg","Version":"0.15"},"imguR":{"Author":"Thomas J. Leeper [aut,
cre],\nAaron Statham [ctb],\nYihui Xie [ctb]","Description":"A complete API client
for the image hosting service Imgur.com, including the an imgur graphics device,
enabling the easy upload and sharing of plots.","Imports":"httr, png, jpeg,
3","NeedsCompilation":"no","Package":"imguR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"An Imgur.com API Client
Package","URL":"https:\/\/github.com\/leeper\/imguR","Version":"1.0.3"},"immer":
{"Author":"\nAlexander Robitzsch [aut, cre], Jan Steinfeld [aut]","Depends":"R (>=
3.0-0)","Description":"\nImplements some item response models for
multiple\nratings, including the hierarchical rater model,\nconditional maximum
likelihood estimation of linear\nlogistic partial credit model and a wrapper
function\nto the commercial FACETS program.","Imports":"CDM, coda, graphics,
methods, psychotools, Rcpp, sirt, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"immer","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"eRm, irr, TAM","Title":"Item Response Models for
Multiple Ratings","Version":"0.4-0"},"import":{"Author":"Stefan Milton
Bache","Description":"This is an alternative mechanism for importing\nobjects from
packages. The syntax allows for importing multiple objects\nfrom a package with a
single command in an expressive way. The import\npackage bridges some of the gap
between using library (or require) and\ndirect (single-object) imports. Furthermore
the imported objects are not\nplaced in the current environment. It is also
possible to import\nobjects from stand-alone .R files. For more information, refer
to\nthe package vignette.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"import","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"knitr","Title":"An Import Mechanism for
R","URL":"https:\/\/github.com\/smbache\/import","Version":"1.1.0"},"imprProbEst":
{"Author":"Robert Hable","Depends":"R(>= 2.7.0), inline, lpSolve","Description":"A
minimum distance estimator is calculated for an\nimprecise probability model. The
imprecise probability model\nconsists of upper coherent previsions whose credal
sets are\ngiven by a finite number of constraints on the expectations.\nThe
parameter set is finite. The estimator chooses that\nparameter such that the
empirical measure lies next to the\ncorresponding credal set with respect to the
total variation\nnorm.","License":"LGPL-
3","NeedsCompilation":"no","Package":"imprProbEst","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Minimum distance estimation in an imprecise
probability model","Version":"1.0.1"},"imputeLCMD":{"Author":"Cosmin
Lazar","Depends":"R (>= 2.10), tmvtnorm, norm, pcaMethods,
impute","Description":"The package contains a collection of functions for left-
censored missing data imputation. Left-censoring is a special case of missing not
at random (MNAR) mechanism that generates non-responses in proteomics experiments.
The package also contains functions to artificially generate peptide\/protein
expression data (log-transformed) as random draws from a multivariate Gaussian
distribution as well as a function to generate missing data (both randomly and non-
randomly). For comparison reasons, the package also contains several wrapper
functions for the imputation of non-responses that are missing at random. * New
functionality has been added: a hybrid method that allows the imputation of missing
values in a more complex scenario where the missing data are both MAR and
MNAR.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"imputeLCMD","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"A collection of methods for left-censored missing
data\nimputation","Version":"2.0"},"imputeMDR":{"Author":"Junghyun Namkung,
Taeyoung Hwang, MinSeok Kwon, Sunggon Yi and\nWonil Chung","Description":"This
package provides various approaches to handling\nmissing values for the MDR
analysis to identify gene-gene\ninteractions using biallelic marker data in genetic
association\nstudies","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"imputeMDR","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"The Multifactor Dimensionality Reduction (MDR)
Analysis for\nIncomplete Data","Version":"1.1.2"},"imputeMissings":
{"Author":"Matthijs Meire, Michel Ballings, Dirk Van den
Poel","Description":"Compute missing values on a training data set and impute them
on a new data set. Current available options are median\/mode and random
forest.","Imports":"randomForest,stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"imputeMissings","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Impute Missing Values in a Predictive
Context","Version":"0.0.1"},"imputeTS":{"Author":"Steffen Moritz","Depends":"R (>=
3.0.1)","Description":"Imputation (replacement) of missing values in univariate
time\nseries.","Imports":"stats, datasets, stinepack, graphics","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"imputeTS","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Time Series Missing Value
Imputation","Version":"0.4"},"imputeYn":{"Author":"Hasinur Rahaman Khan and Ewart
Shaw","Depends":"quadprog, emplik, mvtnorm, survival, boot","Description":"Method
brings less bias and more efficient estimates for AFT models.","License":"GPL-
2","NeedsCompilation":"no","Package":"imputeYn","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Imputing the Last Largest Censored Observation(s) Under
Weighted\nLeast Squares","Version":"1.3"},"in2extRemes":{"Author":"Eric
Gilleland","Depends":"R (>= 2.15.1), tcltk, extRemes (>=
2.0)","Description":"Graphical User Interface (GUI) to some of the functions in the
package extRemes version >= 2.0 are included.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"in2extRemes","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Into the extRemes
Package","URL":"http:\/\/www.assessment.ucar.edu\/toolkit\/","Version":"1.0-
2"},"inTrees":{"Author":"Houtao Deng","Description":"For tree ensembles such as
random forests, regularized random forests and gradient boosted trees, this package
provides functions for: extracting, measuring and pruning rules; selecting a
compact rule set; summarizing rules into a learner; calculating frequent variable
interactions; formatting rules in latex code.","Imports":"RRF, arules, gbm,
3)","NeedsCompilation":"no","Package":"inTrees","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Interpret Tree
Ensembles","URL":"https:\/\/sites.google.com\/site\/houtaodeng\/intrees","Version":
"1.1"},"inarmix":{"Author":"Nicholas Henderson and Paul
Rathouz","Depends":"Matrix","Description":"Fits mixtures models for longitudinal
data. Appropriate when the data are counts and when the correlation structure is
assumed to be AR(1).","Imports":"Rcpp (>= 0.10.3)","License":"GPL-
2","NeedsCompilation":"yes","Package":"inarmix","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Mixture models for longitudinal count
data","Version":"0.4"},"inbreedR":{"Author":"Martin A. Stoffel [aut, cre],\nMareike
Esser [aut],\nJoseph Hoffman [aut],\nMarty Kardos [aut]","Depends":"R (>=
3.2.1)","Description":"A framework for analysing inbreeding and heterozygosity-
fitness\ncorrelations (HFCs) based on microsatellite and SNP
markers.","Imports":"data.table (>= 1.9.6), parallel, stats,
2","NeedsCompilation":"no","Package":"inbreedR","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"testthat (>= 0.10.0), knitr,
rmarkdown","Title":"Analysing Inbreeding Based on Genetic
Markers","Version":"0.3.1"},"indicspecies":{"Author":"Miquel De Caceres, Florian
Jansen","Depends":"permute","Description":"Functions to assess the strength and
statistical significance of the relationship between species occurrence\/abundance
and groups of sites. Also includes functions to measure species niche breadth using
resource categories.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"indicspecies","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"sp, rgeos","Title":"Relationship Between Species
and Groups of Sites","Version":"1.7.5"},"inegiR":{"Author":"Eduardo
Flores","Description":"Provides functions to download and parse information from
INEGI\n(Official Mexican statistics agency).","Imports":"zoo, XML, plyr,
jsonlite","License":"CC0","NeedsCompilation":"no","Package":"inegiR","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Title":"Integrate INEGIâ€™s (Mexican Stats
Office) API with R","Version":"1.2.0"},"ineq":{"Author":"Achim Zeileis [aut,
cre],\nChristian Kleiber [ctb]","Depends":"R (>=
2.10.0)","Description":"Inequality, concentration, and poverty measures. Lorenz
curves (empirical and theoretical).","Imports":"stats, graphics,
grDevices","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"ineq","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Measuring Inequality, Concentration, and
Poverty","Version":"0.2-13"},"inference":{"Author":"Vinh Nguyen
<vinhdizzo@gmail.com>","Depends":"sandwich, methods","Description":"Collection of
functions to extract inferential values\n(point estimates, confidence intervals, p-
values, etc) of a\nfitted model object into a matrix-like object that can be
used\nfor
table\/report generation; transform point estimates via the\ndelta
2)","NeedsCompilation":"no","Package":"inference","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Functions to extract inferential values of a fitted
model object","URL":"http:\/\/r-forge.r-
project.org\/projects\/inference\/","Version":"0.1.0"},"inferference":
{"Author":"Bradley Saul","Depends":"R (>= 3.1)","Description":"Provides methods for
estimating causal effects in the presence of interference. Currently it implements
the IPW estimators proposed by E.J. Tchetgen Tchetgen and T.J. Vanderweele in \"On
causal inference in the presence of interference\" (Statistical Methods in Medical
Research, 21(1) 55-75).","Imports":"numDeriv (>= 2012.9-1), lme4 (>= 1.1-6),
Formula (>= 1.1-2)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"inferference","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat, knitr","Title":"Methods for Causal
Inference with Interference","Version":"0.4.62"},"inflection":{"Author":"Demetris
T. Christopoulos","Description":"Implementation of methods Extremum Surface
Estimator and\nExtremum Distance Estimator for identifying the inflection\npoint of
a convex\/concave curve.","License":"GPL-
2","NeedsCompilation":"no","Package":"inflection","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Finds the inflection point of a
curve","Version":"1.1"},"influence.ME":{"Author":"Rense Nieuwenhuis, Ben Pelzer,
Manfred te Grotenhuis","Depends":"R(>= 2.15.0), lme4(>=
1.0)","Description":"Provides a collection of tools for\ndetecting influential
cases in generalized mixed effects\nmodels. It analyses models that were estimated
using lme4. The\nbasic rationale behind identifying influential data is that\nwhen
iteratively single units are omitted from the data, models\nbased on these data
should not produce substantially different\nestimates. To standardize the
assessment of how influential a\n(single group of) observation(s) is, several
measures of\ninfluence are common practice, such as DFBETAS and Cook's
Distance.\nIn addition, we provide a measure of percentage change of the fixed
point\nestimates and a simple procedure to detect changing levels of
significance.","Imports":"Matrix(>= 1.0), lattice","License":"GPL-
3","NeedsCompilation":"no","Package":"influence.ME","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Tools for Detecting Influential Data in Mixed Effects
Models","URL":"http:\/\/www.rensenieuwenhuis.nl\/r-
project\/influenceme\/","Version":"0.9-6"},"influence.SEM":{"Author":"Massimiliano
Pastore & Gianmarco Altoe'","Depends":"lavaan","Description":"Influence measures in
Structural Equation Models: a set of tools for evaluating several measures of case
influence for Structural Equation Models following the approach of Pek and
MacCallum (2011).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"influence.SEM","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"tcltk","Title":"Case Influence in Structural
Equation Models","Version":"1.5"},"influenceR":{"Author":"Jacobs Simon
[aut],\nKhanna Aditya [aut, cre],\nMadduri Kamesh [ctb],\nBader David
[ctb]","Depends":"R (>= 3.2.0)","Description":"Provides functionality to compute
various node centrality measures on networks.\nIncluded are functions to compute
betweenness centrality (by utilizing Madduri and Bader's\nSNAP library),
implementations of Burt's constraint and effective\nnetwork size (ENS) metrics,
Borgatti's algorithm to identify key players, and Valente's\nbridging metric. On
Unix systems, the betweenness, Key Players, and\nbridging implementations are
parallelized with OpenMP, which may run\nfaster on systems which have OpenMP
configured.","Imports":"igraph (>= 1.0.1), Matrix (>= 1.1-4), methods,
2","NeedsCompilation":"yes","Package":"influenceR","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat","Title":"Software Tools to Quantify
Structural Importance of Nodes in a\nNetwork","URL":"https:\/\/github.com\/rcc-
uchicago\/influenceR","Version":"0.1.0"},"infoDecompuTE":{"Author":"Kevin Chang and
Katya Ruggiero","Depends":"R (>= 2.10.0), MASS","Description":"InfoDecompuTE is
capable of generating the structure of\nthe analysis of variance (ANOVA) table of
the two-phase\nexperiments. By inputting the design and the relationships of\nthe
random and fixed factors using the Wilkinson-Rogers'\nsyntax, infoDecompuTE can
generate the structure of the ANOVA\ntable with the coefficients of the variance
components for the\nexpected mean squares. This package can also study the
balanced\nincomplete block design and provides the efficiency factors of\nthe fixed
effects.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"infoDecompuTE","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Information Decomposition of Two-phase
Experiments","Version":"0.5.1"},"informR":{"Author":"Christopher Steven Marcum
<cmarcum@uci.edu>","Depends":"R (>= 2.12), abind, relevent","Description":"Aids in
creating sequence statistics for Butts's 'relevent' software.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"informR","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Sequence Statistics for Relational Event
Models","Version":"1.0-5"},"infotheo":{"Author":"Patrick E.
Meyer","Description":"This package implements various measures of information
theory based on several entropy estimators.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"infotheo","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Information-Theoretic
Measures","URL":"http:\/\/homepage.meyerp.com\/software","Version":"1.2.0"},"infra"
:{"Author":"Steve Pickering <pickering@penguin.kobe-u.ac.jp>","Depends":"R (>=
3.0.2)","Description":"Takes a data frame containing latitude and longitude
coordinates and downloads images from map servers to determine their file size as a
proxy of infrastructure","License":"GPL-
2","NeedsCompilation":"no","Package":"infra","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"An Infrastructure Proxy
Function","Version":"0.1.2"},"infuser":{"Author":"Bart
Smeets","Description":"Replace parameters in strings and\/or text files with
specified\nvalues.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"infuser","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat","Title":"A Very Basic Templating
Engine","URL":"https:\/\/github.com\/bart6114\/infuser\/","Version":"0.2.3"},"infut
il":{"Author":"Kristian E. Markon","Depends":"ltm","Description":"Calculation of
information utility (i.e., Lindley\ninformation) quantities for item response
models.","Enhances":"MASS","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"infutil","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Information Utility","URL":"http:\/\/www.r-
project.org,\nhttp:\/\/www.psychology.uiowa.edu\/faculty\/markon","Version":"1.0"},
"ini":{"Author":"David Valentim Dias","Description":"Parse simple '.ini'
configuration files to an structured list. Users\ncan manipulate this resulting
list with lapply() functions. This same\nstructured list can be used to write back
to file after modifications.","License":"GPL-
3","NeedsCompilation":"no","Package":"ini","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Read and Write '.ini' Files","Version":"0.2"},"injectoR":
{"Author":"Lev Kuznetsov","Depends":"R (>= 3.1.0)","Description":"R dependency
injection framework. Dependency injection allows\na program design to follow the
dependency inversion principle. The user\ndelegates to external code (the injector)
the responsibility of providing its\ndependencies. This separates the
responsibilities of use and construction.","License":"LGPL (>=
3)","NeedsCompilation":"no","Package":"injectoR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat","Title":"R Dependency
Injection","URL":"https:\/\/github.com\/dfci-
cccb\/injectoR","Version":"0.2.4"},"inline":{"Author":"Oleg Sklyar, Duncan Murdoch,
Mike Smith, Dirk Eddelbuettel,\nRomain Francois, Karline Soetaert","Depends":"R (>=
2.4.0), methods","Description":"Functionality to dynamically define R functions and
S4 methods\nwith inlined C, C++ or Fortran code supporting .C and .Call calling
conventions.","License":"LGPL","NeedsCompilation":"no","Package":"inline","Reposito
ry":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"Rcpp (>=
0.11.0)","Title":"Functions to Inline C, C++, Fortran Function Calls from
R","Version":"0.3.14"},"inlinedocs":{"Author":"Toby Dylan Hocking [aut,
cre],\nKeith Ponting [aut],\nThomas Wutzler [aut],\nPhilippe Grosjean
[aut],\nMarkus MÃ¼ller [aut],\nR Core Team [ctb, cph]","Depends":"methods, utils, R
(>= 2.9)","Description":"Generates Rd files from R source code with comments.\nThe
main features of the default syntax are that\n(1) docs are defined in comments near
the relevant code,\n(2) function argument names are not repeated in comments,
and\n(3) examples are defined in R code, not comments.\nIt is also easy to define a
new syntax.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"inlinedocs","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Convert inline comments to
documentation","URL":"http:\/\/inlinedocs.r-forge.r-
project.org","Version":"2013.9.3"},"inpdfr":{"Author":"Rebaudo Francois (IRD, UMR
EGCE, Univ.ParisSud-CNRS-IRD-\nUniv.ParisSaclay)","Description":"A set of functions
and a graphical user interface\nto analyse and compare texts, using classical text
mining\nfunctions, as well as those from theoretical ecology.","Imports":"wordcloud
(>= 2.5), RColorBrewer (>= 1.1-2), tm (>= 0.6-2),\nSnowballC (>= 0.5.1), ca (>=
0.58), cluster (>= 2.0.1),\nentropart (>= 1.4.1), metacom (>= 1.4.3), RGtk2 (>=
2.20.31),\nparallel (>= 3.1.3), stringi (>= 1.0-1), R.devices (>=
2","NeedsCompilation":"no","Package":"inpdfr","Repository":"http:\/\/cran.csiro.au\
/src\/c
ontrib","Suggests":"knitr, rmarkdown, testthat","Title":"Analyse Text Documents
Using Ecological Tools","Version":"0.1.2"},"insideRODE":{"Author":"YUZHUO PAN,
XIAOYU YAN","Depends":"R (>= 2.13.0), deSolve, nlme, lattice,
compiler","Description":"insideRODE package includes buildin functions
from\ndeSolve, compiled functions from compiler, and C\/FORTRAN code\ninterfaces to
nlme. It includes nlmLSODA, nlmODE,\nnlmVODE,nlmLSODE for general purpose;
cfLSODA,cfLSODE, cfODE,\ncfVODE call C\/FORTRAN compiled dll functions.ver2.0
add\nsink()function into example it helps to directly combine\nc\/fortran source
code in R files. Finally, with new compiler\npackage, we generated compiled
functions: nlmODEcp, nlmVODEcp,\nnlmLSODEcp,nlmLSODAcp and cpODE, cpLSODA, cpLSODE,
cpVODE. They\nwill help to increase speed.","License":"LGPL (>
2.0)","NeedsCompilation":"no","Package":"insideRODE","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"insideRODE includes buildin functions with deSolve
solver and\nC\/FORTRAN interfaces to nlme, together with compiled
codes","Version":"2.0"},"insol":{"Author":"Javier G.
Corripio","Depends":"methods","Description":"Functions to compute insolation on
complex terrain.","License":"GPL-
2","NeedsCompilation":"yes","Package":"insol","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"datasets,graphics,raster,rgl,stats","Title":"Solar
Radiation","URL":"http:\/\/www.meteoexploration.com\/R\/insol\/index.html","Version
":"1.1.1"},"instaR":{"Author":"Pablo Barbera [aut, cre], Tiago Dantas [ctb], Jonne
Guyt [ctb]","Depends":"R (>= 2.12.0), httr, rjson","Description":"Provides an
interface to the Instagram API <https:\/\/instagram.com\/developer\/>, which allows
R users to download public pictures filtered by hashtag, popularity, user or
location, and to access public users' profile data.","License":"GPL-
2","NeedsCompilation":"no","Package":"instaR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Access to Instagram API via
R","URL":"https:\/\/github.com\/pablobarbera\/instaR","Version":"0.2.2"},"install.l
oad":{"Author":"Original install_load function written by maloneypatr as a
contribution\nto Stack Overflow on February 28 2014
(http:\/\/stackoverflow.com\/questions\/\n15155814\/check-if-r-package-is-
installed-then-load-library). Irucka Embry has\nrevised the original
function.","Depends":"R (>= 2.14.0)","Description":"Checks the local R library(ies)
to see if the required\npackage(s) is\/are installed or not. If the package(s)
is\/are\nnot installed, then the package(s) will be installed along with\nthe
required dependency(ies). This function pulls source or\nbinary packages from the
Revolution Analytics CRAN mirror and\/or\nthe USGS GRAN Repository. Lastly, the
chosen package(s)\nis\/are loaded.","Imports":"utils","License":"CC BY-SA
4.0","NeedsCompilation":"no","Package":"install.load","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"needs, easypackages","Title":"Check, Install and
Load CRAN & USGS GRAN
Packages","URL":"https:\/\/gitlab.com\/iembry\/install.load","Version":"1.0.4"},"in
stallr":{"Author":"Tal Galili [aut, cre, cph] (http:\/\/www.r-
statistics.com),\nBarry Rowlingson [ctb],\nBoris Hejblum [ctb],\nDason
[ctb],\nFelix Schonbrodt [ctb],\nG. Grothendieck [ctb],\nGERGELY DAROCZI
[ctb],\nHeuristic Andrew [ctb],\nJames [ctb]
(http:\/\/stackoverflow.com\/users\/269476\/james),\nThomas Leeper [ctb]
(http:\/\/thomasleeper.com\/),\nVitoshKa [ctb],\nYihui Xie [ctb]
(http:\/\/yihui.name),\nMichael Friendly [ctb] (http:\/\/datavis.ca\/),\nKornelius
Rohmeyer [ctb] (http:\/\/algorithm-forge.com\/techblog\/),\nDieter Menne
[ctb],\nTyler Hunt [ctb] (https:\/\/github.com\/JackStat),\nTakekatsu Hiramura
[ctb] (https:\/\/github.com\/hiratake55),\nBerry Boessenkool [ctb]
(https:\/\/github.com\/BerryBoessenkool)","Depends":"R (>= 2.11.0),
utils","Description":"R is great for installing software. Through the
'installr'\npackage you can automate the updating of R (on Windows, using
updateR())\nand install new software. Software installation is initiated through
a\nGUI (just run installr()), or through functions such as:
install.Rtools(),\ninstall.pandoc(), install.git(), and many more. The updateR()
command\nperforms the following: finding the latest R version, downloading
it,\nrunning the installer, deleting the installation file, copy and updating\nold
packages to the new R installation.","Imports":"curl, stringr","License":"GPL-
2","NeedsCompilation":"no","Package":"installr","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"XML, devtools, rjson, data.table, plyr, ggplot2, sp,
tools","Title":"Using R to Install Stuff (Such As: R, Rtools, RStudio, Git,
and\nMore!)","URL":"https:\/\/github.com\/talgalili\/installr\/,\nhttp:\/\/www.r-
statistics.com\/tag\/installr\/","Version":"0.17.5"},"insuranceData":
{"Author":"Alicja Wolny--Dominiak and Michal Trzesiok","Depends":"R (>=
2.10)","Description":"Insurance datasets, which are often used in claims severity
and claims frequency modelling. It helps testing new regression models in those
problems, such as GLM, GLMM, HGLM, non-linear mixed models etc. Most of the data
sets are applied in the project \"Mixed models in ratemaking\" supported by grant
NN 111461540 from Polish National Science Center.","License":"GPL-
2","NeedsCompilation":"no","Package":"insuranceData","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"A Collection of Insurance Datasets Useful in Risk
Classification\nin Non-life Insurance","Version":"1.0"},"intReg":{"Author":"Ott
Toomet <otoomet@gmail.com>","Depends":"R (>= 2.7.0), miscTools, maxLik (>= 1.0-
3)","Description":"Estimating interval regression models. Supports both common and
observation-specific boundaries.","Imports":"sets","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"intReg","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"Ecdat","Title":"Interval
Regression","URL":"http:\/\/www.sampleSelection.org","Version":"0.2-
8"},"intRegGOF":{"Author":"Jorge Luis Ojeda Cabrera,
<jojeda@unizar.es>","Depends":"R (>= 2.5.0)","Description":"Performs Goodness of
Fit for regression models
using","License":"GPL","NeedsCompilation":"no","Package":"intRegGOF","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Title":"Integrated Regression Goodness of
Fit","Version":"0.85-1"},"intamap":{"Author":"Edzer Pebesma <edzer.pebesma@uni-
muenster.de>, Jon Olav Skoien <jon.skoien@gmail.com> with contributions from
Olivier Baume, A.Chorti, D.T. Hristopulos, H. Kazianka, S.J. Melles, G.
Spiliopoulos","Depends":"R (>= 2.14.0), sp (>= 0.9-0)","Description":"A package
that provides classes and methods for automated\nspatial
interpolation.","Enhances":"psgp","Imports":"gstat (>= 0.9-36), automap, mvtnorm,
MASS, evd","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"intamap","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"doParallel, rgdal","Title":"procedures for automated
interpolation","URL":"http:\/\/www.intamap.org\/","Version":"1.3-
37"},"intamapInteractive":{"Author":"Edzer Pebesma <edzer.pebesma@uni-muenster.de>,
Jon Skoien <jon.skoien@gmail.com> with contributions from Olivier Baume, A.Chorti,
D.T. Hristopulos, S.J. Melles, G.
Spiliopoulos","Depends":"intamap","Description":"A package that provides
additional functionality for spatial interpolation in the intamap
package.","Imports":"spcosa, spatstat, automap, gstat","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"intamapInteractive","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Suggests":"rgdal","Title":"procedures for automated
interpolation - methods only to be used\ninteractively, not included in intamap
package","URL":"http:\/\/www.intamap.org\/","Version":"1.1-10"},"intcox":
{"Author":"Volkmar Henschel [aut, cre], Ulrich Mansmann [aut], Christiane\nHeiss
[ctb]","Depends":"R (>= 2.14.0), survival","Description":"Implementation of ICM-
Algorithm by Wei Pan, J. Comp. & Gr.\nStat. 78: 109-120, 1999 Algorithm for the Cox
proportional\nhazard model for interval censored data","License":"GPL-
2","NeedsCompilation":"yes","Package":"intcox","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Iterated Convex Minorant Algorithm for interval censored
event\ndata","Version":"0.9.3"},"interAdapt":{"Author":"Aaron Fisher
<afisher@jhsph.edu>, Michael Rosenblum\n<mrosenbl@jhsph.edu>, Harris
Jaffee<hj@jhu.edu>","Depends":"R (>= 3.0.1)","Description":"A shiny application for
designing adaptive clinical trials. For\nmore details, see:
http:\/\/arxiv.org\/abs\/1404.0734","Imports":"shiny, knitcitations, RCurl,
mvtnorm, knitr","License":"GPL-
2","NeedsCompilation":"no","Package":"interAdapt","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"interAdapt","Version":"0.1"},"interactionTest":
{"Author":"Justin Esarey and Jane Lawrence Sumner","Depends":"stats, R (>=
3.2.1)","Description":"Implements the procedures suggested in Esarey and Sumner
(2015) for controlling the false discovery rate or familywise error rate when
constructing marginal effects plots for models with interaction
terms.","License":"GPL","NeedsCompilation":"no","Package":"interactionTest","Reposi
tory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Calculates Critical Test
Statistics to Control False Discovery\nand Familywise Error Rates in Marginal
Effects Plots","Version":"1.0"},"intercure":{"Author":"Julio Brettas [aut,
cre]","Depends":"R (>= 2.10)","Description":"Implementations of semiparametric cure
rate estimators for interval\ncensored data in R. The algorithms are based on the
promotion time and\nfrailty models, all for interval censoring. For the frailty
model,\nthere is also a implementation contemplating clustered
data.","Imports":"foreach, survival, MASS, stats4, Matrix, iterators,
parallel","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"intercure","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat,
knitr, rmarkdown, doParallel","Title":"Cure Rate Estimators for Interval Censored
Data","URL":"https:\/\/github.com\/JBrettas\/intercure","Version":"0.1.0"},"interfe
renceCI":{"Author":"Joseph Rigdon","Depends":"compiler,
gtools","Description":"Computes large sample confidence intervals of Liu and
Hudgens (2014), exact confidence intervals of Tchetgen Tchetgen and VanderWeele
(2012), and exact confidence intervals of Rigdon and Hudgens (2014) for treatment
effects on a binary outcome in two-stage randomized experiments with
interference.","License":"GPL-
3","NeedsCompilation":"no","Package":"interferenceCI","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Exact Confidence Intervals in the Presence of
Interference","Version":"1.1"},"intergraph":{"Author":"Michal
Bojanowski","Description":"Functions implemented in this package allow to coerce
(i.e.\nconvert) network data between classes provided by other R
packages.\nCurrently supported classes are those defined in packages: network
and\nigraph.","Imports":"network (>= 1.4-1-1), igraph (>= 0.6-0),
3","NeedsCompilation":"no","Package":"intergraph","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat, roxygen2, knitr","Title":"Coercion
Routines for Network Data
Objects","URL":"http:\/\/mbojan.github.io\/intergraph","Version":"2.0-
2"},"internetarchive":{"Author":"Lincoln Mullen [aut, cre]","Depends":"R (>=
3.1.0)","Description":"Search the Internet Archive, retrieve metadata, and
download\nfiles.","Imports":"httr (>= 1.1.0), dplyr (>= 0.4.3)","License":"MIT +
file
LICENSE","NeedsCompilation":"no","Package":"internetarchive","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Suggests":"knitr, testthat, rmarkdown","Title":"An
API Client for the Internet
Archive","URL":"https:\/\/github.com\/ropensci\/internetarchive","Version":"0.1.5"}
,"interplot":{"Author":"Frederick Solt <frederick-solt@uiowa.edu>, Yue Hu <yue-hu-
1@uiowa.edu>","Depends":"R (>= 3.1.1), ggplot2, abind, arm","Description":"Plots
the conditional coefficients (\"marginal effects\") of\nvariables included in
multiplicative interaction terms.","Imports":"stats","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"interplot","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"knitr","Title":"Plot the Effects of Variables
in Interaction Terms","Version":"0.1.2.1"},"interpretR":{"Author":"Michel Ballings
and Dirk Van den Poel","Depends":"randomForest","Description":"Compute permutation-
based performance measures and create partial\ndependence plots for (cross-
validated) 'randomForest' and 'ada' models.","Imports":"AUC, stats,
2)","NeedsCompilation":"no","Package":"interpretR","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Binary Classifier and Regression Model Interpretation
Functions","Version":"0.2.4"},"interval":{"Author":"Michael P. Fay","Depends":"R
(>= 2.2.1), stats, survival, perm (>= 1.0), Icens,
MLEcens","Description":"Functions to fit nonparametric survival curves, plot them,
and perform logrank or Wilcoxon type tests.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"interval","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"coin","Title":"Weighted Logrank Tests and NPMLE for
interval censored data","Version":"1.1-0.1"},"intervals":{"Author":"Richard Bourgon
<bourgon.richard@gene.com>","Depends":"R (>= 2.9.0)","Description":"Tools for
working with and comparing sets of points and intervals.","Imports":"utils,
graphics, methods","License":"Artistic-
2.0","NeedsCompilation":"yes","Package":"intervals","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Tools for Working with Points and
Intervals","URL":"http:\/\/github.com\/edzer\/intervals","Version":"0.15.1"},"inter
ventionalDBN":{"Author":"Simon Spencer","Description":"This package allows a
dynamic Bayesian network to be inferred from microarray timecourse data with
interventions (inhibitors).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"interventionalDBN","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Interventional Inference for Dynamic Bayesian
Networks","Version":"1.2.2"},"intpoint":{"Author":"Alejandro Quintela del
Rio","Description":"Solves linear programming problems by the interior
point\nmethod, and plots the graphical solution of a linear\nprogramming problem of
two dimensions.","License":"GPL-
2","NeedsCompilation":"no","Package":"intpoint","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"linear programming solver by the interior point method
and\ngraphically (two dimensions)","Version":"1.0"},"introgress":
{"Author":"Zachariah Gompert, C. Alex Buerkle","Depends":"nnet, genetics,
RColorBrewer","Description":"introgress provides functions for analyzing
introgression\nof genotypes between divergent, hybridizing lineages,
including\nestimating genomic clines from multi-locus genotype data and\ntesting
for deviations from neutral expectations. Functions are\nalso provided for maximum
likelihood estimation of molecular\nhybrid index and graphical
2)","NeedsCompilation":"no","Package":"introgress","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"methods for analyzing introgression between divergent
lineages","URL":"http:\/\/www.uwyo.edu\/buerkle\/software\/introgress\/","Version":
"1.2.3"},"intsvy":{"Author":"Daniel Caro <daniel.caro@education.ox.ac.uk>,
Przemyslaw Biecek <przemyslaw.biecek@gmail.com>","Description":"\nProvides tools
for importing, merging, and analysing data from\ninternational assessment studies
(TIMSS, PIRLS, PISA. ICILS, and PIAAC).","Imports":"foreign, ggplot2, Hmisc,
memisc, plyr, reshape, stats, utils","License":"GPL-
2","NeedsCompilation":"no","Package":"intsvy","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"International Assessment Data
Manager","URL":"http:\/\/users.ox.ac.uk\/~educ0279,\nhttps:\/\/github.com\/eldafani
\/intsvy","Version":"1.8"},"invGauss":{"Author":"Hakon K.
Gjessing","Depends":"survival","Description":"invGauss fits the (randomized drift)
inverse Gaussian distribution to survival data. The model is described in Aalen OO,
Borgan O, Gjessing HK. Survival and Event History Analysis. A Process Point of
View. Springer, 2008. It is based on describing time to event as the barrier
hitting time of a Wiener process, where drift towards the barrier has been
randomized with a Gaussian distribution. The model allows covariates to influence
starting values of the Wiener process and\/or average drift towards a barrier, with
a user-defined choice of link functions.","Imports":"optimx","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"invGauss","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Threshold regression that fits the (randomized drift)
inverse\nGaussian distribution to survival
data","URL":"http:\/\/www.uib.no\/smis\/gjessing\/projects\/invgauss\/","Version":"
1.1"},"invLT":{"Author":"Christopher Barry","Description":"Provides two functions
for the numerical inversion of Laplace-Transformed functions, returning the value
of the standard (time) domain function at a specified value. The first algorithm
is the first optimum contour algorithm described by Evans and Chung (2000)[1].\nThe
second algorithm uses the Bromwich contour as per the definition of the inverse
Laplace Transform. The latter is unstable for numerical inversion and mainly
included for comparison or interest. There are also some additional functions
provided for utility, including plotting and some simple Laplace Transform
examples, for which there are known analytical solutions. Polar-cartesian
conversion functions are included in this package and are used by the inversion
functions.\n[1] Evans & Chung, 2000: Laplace transform inversions using optimal
contours in the complex plane; International Journal of Computer Mathematics v73
pp531-543.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"invLT","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Inversion of Laplace-Transformed
Functions","Version":"0.2.1"},"investr":{"Author":"Brandon M.
Greenwell","Depends":"base,","Description":"Functions to facilitate inverse
estimation (e.g., calibration) in\nlinear, generalized linear, nonlinear, and
(linear) mixed-effects models. A\ngeneric function is also provided for plotting
fitted regression models with\nor without confidence\/prediction bands that may be
of use to the general\nuser.","Imports":"graphics, nlme, stats,
utils,","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"investr","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"boot, datasets, knitr, MASS,
testthat,","Title":"Inverse Estimation\/Calibration
Functions","URL":"https:\/\/github.com\/bgreenwell\/investr","Version":"1.4.0"},"io
":{"Author":"David J. H. Shih","Depends":"filenamer","Description":"One function to
read files. One function to write files. One\nfunction to direct plots to screen or
file. Automatic file format inference\nand directory structure
creation.","Imports":"stringr","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"io","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"XML (>= 3.98-1.1), rhdf5 (>= 2.10.0), yaml (>=
2.1.13),\njsonlite (>= 0.9.14), testthat","Title":"A Unified Framework for Input-
Output Operations in
R","URL":"https:\/\/bitbucket.org\/djhshih\/io","Version":"0.2.3"},"ioncopy":
{"Author":"Jan Budczies","Description":"Method for the calculation of copy numbers
and calling of copy number alterations. The algorithm uses coverage data from
amplicon sequencing of a sample cohort as input. The method includes significance
assessment, correction for multiple testing and does not depend on normal DNA
controls.","Imports":"stats, multtest","License":"GPL-
3","NeedsCompilation":"no","Package":"ioncopy","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Calling
Copy Number Alterations in Amplicon Sequencing Data","Version":"1.0"},"ionflows":
{"Author":"Michael Bockmayr and Jan
Budczies","Depends":"Biostrings","Description":"Two methods for calculation of the
number of required flows for semiconductor sequencing: 1. Using a simulation, the
number of flows can be calculated for a concrete list of amplicons. 2. An exact
combinatorial model is evaluated to calculate the number of flows for a random
ensemble of sequences.","License":"GPL-
3","NeedsCompilation":"no","Package":"ionflows","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Calculate the Number of Required Flows for
Semiconductor\nSequencing","Version":"1.1"},"ionr":{"Author":"Uku Vainik
<ukuvainik@gmail.com>, Rene Mottus <rene.mottus@ed.ac.uk>","Depends":"R (>=
3.0)","Description":"Provides item exclusion procedure, which is a formal method
to\ntest 'Indifference Of iNdicator' (ION). When a latent personality\ntrait-
outcome association is assumed, then the association strength\nshould not depend on
which subset of indicators (i.e. items) has been\nchosen to reflect the trait.
Personality traits are often measured\n(reflected) by a sum-score of a certain
set of indicators.\nItem exclusion procedure randomly excludes items from a sum-
score and\ntests, whether the sum-score - outcome correlation changes. ION has
been\nachieved, when any item can be excluded from the sum-score without the\nsum-
score - outcome correlation substantially changing . For more details,\nsee Vainik,
Mottus et. al, (2015) \"Are Trait-Outcome Associations Caused\nby Scales or
Particular Items? Example Analysis of Personality Facets and\nBMI\",European
Journal of Personality DOI: <10.1002\/per.2009> .","Imports":"gplots,
psych","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ionr","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"lavaan","Title":"Test for Indifference of
Indicator","URL":"www.ut.ee\/uku.vainik\/ion\/","Version":"0.3.0"},"iopsych":
{"Author":"Allen Goebl <goebl005@umn.edu>, Jeff Jones <jone1087@umn.ed>, and Adam
Beatty <abeatty@humrro.org>","Depends":"R (>= 3.0)","Description":"Collection of
functions for IO Psychologists.","Imports":"mvtnorm (>= 1.0), mco (>= 1.0), stats
(>= 1.0)","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"iopsych","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Methods for Industrial\/Organizational
Psychology","Version":"0.90.1"},"iosmooth":{"Author":"Timothy L. McMurry, Dimitris
N. Politis","Description":"Density, spectral density, and regression estimation
using infinite order
kernels.","License":"GPL","NeedsCompilation":"no","Package":"iosmooth","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Title":"Functions for smoothing with
infinite order flat-top kernels","Version":"0.91"},"iotools":{"Author":"Simon
Urbanek <Simon.Urbanek@r-project.org>, Taylor Arnold
<taylor.arnold@acm.org>","Depends":"R (>= 2.9.0)","Description":"Basic I\/O tools
for streaming.","Imports":"methods, parallel, utils","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"iotools","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"testthat","Title":"I\/O Tools for
Streaming","URL":"http:\/\/www.rforge.net\/iotools","Version":"0.1-12"},"ipdmeta":
{"Author":"S. Kovalchik","Depends":"nlme, methods","Description":"This package
provides functions to estimate an IPD linear\nmixed effects model for a continuous
outcome and any\ncategorical covariate from study summary statistics. There
are\nalso functions for estimating the power of a\ntreatment-covariate interaction
test in an individual patient\ndata meta-analysis from aggregate
2","NeedsCompilation":"no","Package":"ipdmeta","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Tools for subgroup analyses with multiple trial data
using\naggregate statistics","Version":"2.4"},"ipdw":{"Author":"Joseph Stachelek
<jstachel@sfwmd.gov>","Depends":"R (>= 3.0.2),gdistance","Description":"Functions
are provided to interpolate georeferenced point data via\nInverse Path Distance
Weighting. Useful for coastal marine applications where\nbarriers in the landscape
preclude interpolation with Euclidean
distances.","Imports":"sp,raster","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ipdw","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"geoR,gstat,gdata,spatstat,rgdal,
testthat","Title":"Spatial Interpolation by Inverse Path Distance
Weighting","URL":"http:\/\/www.github.com\/jsta\/ipdw","Version":"0.2-
4"},"ipflasso":{"Author":"Anne-Laure Boulesteix, Mathias Fuchs","Depends":"glmnet,
survival","Description":"The core of the package is cvr2.ipflasso(), an extension
of glmnet to be used when the (large) set of available predictors is partitioned
into several modalities which potentially differ with respect to their information
content in terms of prediction. For example, in biomedical applications patient
outcome such as survival time or response to therapy may have to be predicted based
on, say, mRNA data, miRNA data, methylation data, CNV data, clinical data, etc. The
clinical predictors are on average often much more important for outcome prediction
than the mRNA data. The ipflasso method takes this problem into account by using
different penalty parameters for predictors from different modalities. The ratio
between the different penalty parameters can be chosen by cross-
validation.","License":"GPL","NeedsCompilation":"no","Package":"ipflasso","Reposito
ry":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Integrative Lasso with Penalty
Factors","Version":"0.1"},"ipfp":{"Author":"Alexander W Blocker","Description":"A
fast (C) implementation of the iterative proportional fitting\nprocedure. Based on
corresponding code from the networkTomography package.","License":"Apache License
(==
2.0)","NeedsCompilation":"yes","Package":"ipfp","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Fast Implementation of the Iterative Proportional
Fitting\nProcedure in
C","URL":"https:\/\/github.com\/awblocker\/ipfp","Version":"1.0.1"},"iplots":
{"Author":"Simon Urbanek <simon.urbanek@r-project.org>, Tobias Wichtrey
<tobias@tarphos.de>","Depends":"R (>= 1.5.0), methods, rJava (>= 0.5-
0)","Description":"Interactive plots for R","Imports":"grDevices,
png","License":"GPL-
2","NeedsCompilation":"no","Package":"iplots","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"maps, MASS","Title":"iPlots - interactive graphics for
R","URL":"http:\/\/www.iPlots.org\/","Version":"1.1-7"},"ipred":{"Author":"Andrea
Peters [aut],\nTorsten Hothorn [aut, cre],\nBrian D. Ripley [ctb],\nTerry Therneau
[ctb],\nBeth Atkinson [ctb]","Depends":"R (>= 2.10)","Description":"Improved
predictive models by indirect classification and\nbagging for classification,
regression and survival problems\nas well as resampling based estimators of
prediction error.","Imports":"rpart (>= 3.1-8), MASS, survival, nnet, class,
prodlim","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ipred","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"mvtnorm, mlbench, TH.data","Title":"Improved
Predictors","Version":"0.9-5"},"ips":{"Author":"Christoph Heibl
<christoph.heibl@gmx.net>","Depends":"ape, colorspace, XML","Description":"This
package provides functions that wrap popular phylogenetic software for sequence
alignment, masking of sequence alignments, and estimation of phylogenies and
ancestral character states.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ips","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Interfaces to Phylogenetic Software in R","Version":"0.0-
7"},"iptools":{"Author":"Bob Rudis <bob@rudis.net> [aut, cre],\nOliver Keyes
<ironholds@gmail.com> [aut],\nTim Smith [ctb]","Depends":"R (>=
3.0.0)","Description":"A toolkit for manipulating, validating and testing 'IP'
addresses and\nranges, along with datasets relating to 'IP' addresses. Tools are
also provided\nto map 'IPv4' blocks to country codes. While it primarily has
support for the 'IPv4'\naddress space, more extensive 'IPv6' support is
intended.","Imports":"Rcpp (>= 0.11.2), utils, stats, AsioHeaders,
ISOcodes","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"iptools","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat, knitr, rmarkdown","Title":"Manipulate,
Validate and Resolve 'IP'
Addresses","URL":"http:\/\/github.com\/hrbrmstr\/iptools","Version":"0.4.0"},"ipw":
{"Author":"Ronald B. Geskus [aut, cre],\nWillem M. van der Wal [aut] (maintainer
until 2010)","Depends":"R (>= 3.0.0)","Description":"Functions to estimate the
probability to receive the observed treatment, based on\nindividual
characteristics. The inverse of these probabilities can be used as weights
when\nestimating causal effects from observational data via marginal structural
models. Both point\ntreatment situations and longitudinal studies can be analysed.
The same functions can be used to\ncorrect for informative
censoring.","Imports":"MASS, nnet, survival, geepack, graphics, methods,
2)","NeedsCompilation":"no","Package":"ipw","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"nlme, survey, boot","Title":"Estimate Inverse Probability
Weights","Version":"1.0-11"},"iqLearn":{"Author":"Kristin A. Linn, Eric B. Laber,
Leonard A. Stefanski","Description":"Estimate an optimal dynamic treatment regime
using Interactive Q-learning.","License":"GPL-
2","NeedsCompilation":"no","Package":"iqLearn","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Interactive Q-Learning","Version":"1.4"},"irace":
{"Author":"Manuel LÃ³pez-IbÃ¡Ã±ez, JÃ©rÃ©mie Dubois-Lacoste, Leslie PÃ©rez
CÃ¡ceres,\nThomas StÃ¼tzle, Mauro Birattari, Eric Yuan and Prasanna
Balaprakash","Depends":"R (>= 2.14.0)","Description":"Iterated racing for automatic
algorithm configuration.","Imports":"stats,
2)","NeedsCompilation":"no","Package":"irace","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"Rmpi (>= 0.6.0), parallel","Title":"Iterated Racing
Procedures","URL":"http:\/\/iridia.ulb.ac.be\/irace","Version":"1.07"},"irlba":
{"Author":"Jim Baglama and Lothar Reichel","Depends":"Matrix","Description":"Fast
and memory efficient methods for truncated singular and eigenvalue decompositions
and principal component analysis of large sparse or dense
matrices.","Imports":"stats","License":"GPL","NeedsCompilation":"no","Package":"irl
ba","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Fast Truncated
SVD, PCA and Symmetric Eigendecomposition for\nLarge Dense and Sparse
Matrices","Version":"2.0.0"},"irr":{"Author":"Matthias Gamer <m.gamer@uke.uni-
hamburg.de>, Jim Lemon\n<jim@bitwrit.com.au>, Ian Fellows <ifellows@uscd.edu>
Puspendra\nSingh
<puspendra.pusp22@gmail.com>","Depends":"lpSolve","Description":"Coefficients of
Interrater Reliability and Agreement for\nquantitative, ordinal and nominal data:
ICC, Finn-Coefficient,\nRobinson'A, Kendall's W, Cohen's Kappa, ...","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"irr","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Various Coefficients of Interrater Reliability and
Agreement","URL":"http:\/\/www.r-project.org","Version":"0.84"},"irtProb":
{"Author":"Gilles Raiche","Depends":"R (>= 3.0.0), stats, lattice, moments,
methods","Description":"Multidimensional Person Item Response Theory probability
distributions","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"irtProb","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Utilities and Probability Distributions Related
to\nMultidimensional Person Item Response Models","Version":"1.2"},"irtoys":
{"Author":"Ivailo Partchev","Depends":"sm, ltm","Description":"Provides a simple
common interface to the estimation of item\nparameters in IRT models for binary
responses with three different programs\n(ICL, BILOG-MG, and ltm, and a variety of
functions useful with IRT models.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"irtoys","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"MASS","Title":"Simple interface to the estimation and
plotting of IRT models","Version":"0.1.7"},"irtrees":{"Author":"Ivailo Partchev and
Paul De Boeck","Depends":"R(>= 2.10)","Description":"Helper functions and example
data sets accompanying De\nBoeck, P. and Partchev, I. (2012) IRTrees: Tree-Based
Item\nResponse Models of the GLMM Family, Journal of Statistical\nSoftware - Code
Snippets, 48(1), 1-28.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"irtrees","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"lme4","Title":"Estimation of Tree-Based Item Response
Models","Version":"0.1.0"},"isa2":{"Author":"Gabor Csardi
<csardi.gabor@gmail.com>","Depends":"methods","Description":"The ISA is a
biclustering algorithm that finds modules\nin an input matrix. A module or
bicluster is a block of the\nreordered input
matrix.","Imports":"lattice","License":"CC BY-NC-SA
4.0","NeedsCompilation":"yes","Package":"isa2","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"igraph (>= 0.5.5), biclust","Title":"The Iterative
Signature
Algorithm","URL":"https:\/\/github.com\/gaborcsardi\/ISA","Version":"0.3.4"},"isdal
s":{"Author":"Claus Ekstrom <ekstrom@sund.ku.dk> and Helle Sorensen
<helle@math.ku.dk>","Description":"Provides datasets for Introduction to
Statistical Data Analysis for the Life Sciences","License":"GPL-
2","NeedsCompilation":"no","Package":"isdals","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"VGAM","Title":"Provides datasets for Introduction to
Statistical Data Analysis\nfor the Life Sciences","Version":"2.0-4"},"isingLenzMC":
{"Author":"Mehmet Suzen","Depends":"R (>= 3.0)","Description":"Classical Ising
Model is a land mark system in statistical physics. Model explains physics of spin
glasses and magnetic materials, but used in many different context for example
phase transitions and neural systems. This package provides utilities to simulate
one dimensional Ising Model with Metropolis and Glauber Monte Carlo with single
flip dynamics in periodic boundary conditions.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"isingLenzMC","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Monte Carlo for Classical Ising
Model","Version":"0.2.3"},"island":{"Author":"Vicente Jimenez [aut, cre],\nDavid
Alonso [aut]","Depends":"R (>= 3.0.0), stats, utils","Description":"Tools to
develop stochastic models based on the Theory of Island\nBiogeography (TIB) of
MacArthur and Wilson (1967) <DOI:10.1023\/A:1016393430551>\nand extensions. The
package implements methods to estimate colonization and\nextinction rates
(including environmental variables) given presence-absence\ndata, simulate
community assembly, and perform model selection.","License":"GPL-
3","NeedsCompilation":"no","Package":"island","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Stochastic Island Biogeography Theory Made
Easy","Version":"0.1.2"},"ismev":{"Author":"Original S functions written by Janet
E. Heffernan with R port and R\ndocumentation provided by Alec G.
Stephenson.","Depends":"R (>= 2.10.0), mgcv","Description":"Functions to support
the computations carried out in\nÀn Introduction to Statistical Modeling of
Extreme Values' by\nStuart Coles. The functions may be divided into the
following\ngroups; maxima\/minima, order statistics, peaks over thresholds\nand
point processes.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ismev","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"An Introduction to Statistical Modeling of Extreme
Values","URL":"http:\/\/www.ral.ucar.edu\/~ericg\/softextreme.php","Version":"1.40"
},"isocir":{"Author":"Sandra Barragán, Miguel A. Fernández and Cristina
Rueda.","Depends":"circular(>= 0.4-3)","Description":"This is a package to draw
isotonic inference for circular data.","Imports":"combinat(>= 0.0-
8)","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"isocir","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Isotonic Inference for Circular data","Version":"1.1-
3"},"isopam":{"Author":"\nSebastian Schmidtlein","Depends":"vegan,
cluster","Description":"Isopam clustering algorithm and utilities.\nIsopam
optimizes clusters and optionally cluster numbers in\na brute force style and aims
at an optimum separation\nby all or some descriptors (typically
species).","License":"GPL-
2","NeedsCompilation":"no","Package":"isopam","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"proxy","Title":"Isopam (Clustering)","Version":"0.9-
13"},"isopat":{"Author":"Martin Loos","Description":"The function calculates the
isotopic pattern (fine\nstructures) for a given chemical formula.","License":"GPL-
2","NeedsCompilation":"no","Package":"isopat","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Calculation of isotopic pattern for a given molecular
formula","Version":"1.0"},"isoph":{"Author":"Yunro Chung [cre], Anastasia Ivanova,
Michael G. Hudgens and Jason P. Fine","Depends":"R (>= 3.0.2), Iso,
survival","Description":"Nonparametric estimation of an isotonic covariate effect
for proprotional hazards model.","Imports":"Rcpp (>= 0.12.1)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"isoph","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Isotonic Proportional Hazards
Model","Version":"0.5"},"isotone":{"Author":"Patrick Mair [aut, cre], Jan De Leeuw
[aut], Kurt Hornik [aut]","Depends":"R (>= 3.0.2)","Description":"Contains two main
functions: one for\nsolving general isotone regression problems using the\npool-
adjacent-violators algorithm (PAVA); another one provides\na framework for active
set methods for isotone optimization\nproblems with arbitrary order restrictions.
Various types of\nloss functions are prespecified.","Imports":"graphics, stats,
nnls","License":"GPL-
2","NeedsCompilation":"yes","Package":"isotone","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Active Set and Generalized PAVA for Isotone
Optimization","URL":"http:\/\/r-forge.r-
project.org\/projects\/psychor\/","Version":"1.1-0"},"isotonic.pen":{"Author":"Mary
C Meyer, Jiwen Wu, and Jean D. Opsomer","Depends":"graphics, grDevices, stats,
utils, coneproj, Matrix","Description":"Given a response y and a one- or two-
dimensional predictor, the isotonic regression estimator is calculated with the
usual orderings.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"isotonic.pen","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Penalized Isotonic Regression in one and two
dimensions","Version":"1.0"},"isva":{"Author":"Andrew E
Teschendorff","Depends":"qvalue, fastICA","Description":"Independent Surrogate
Variable Analysis is an algorithm\nfor feature selection in the presence of
potential confounding\nfactors.","License":"GPL-
2","NeedsCompilation":"no","Package":"isva","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Independent Surrogate Variable
Analysis","Version":"1.8"},"itcSegment":{"Author":"Michele Dalponte","Depends":"R
(>= 3.2.0),sp,raster,maptools,rgeos,methods,grDevices","Description":"Two methods
for Individual Tree Crowns (ITCs) delineation on remote sensing data: one is based
on LiDAR data in x,y,z format and one on imagery data in raster
format.","License":"GPL","NeedsCompilation":"no","Package":"itcSegment","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Individual Tree Crowns
Segmentation","Version":"0.1"},"iteRates":{"Author":"Premal Shah, Benjamin
Fitzpatrick, James Fordyce","Depends":"partitions, stats, VGAM, MASS, ape,
apTreeshape, geiger,\ngtools","Description":"Iterates through a phylogenetic tree
to identify regions\nof rate variation using the parametric rate comparison
test.","License":"GPL
(>=
3)","NeedsCompilation":"no","Package":"iteRates","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Parametric rate comparison","Version":"3.1"},"iterLap":
{"Author":"Bjoern Bornkamp","Depends":"quadprog, randtoolbox, parallel, R (>=
2.15)","Description":"The iterLap (iterated Laplace approximation)
algorithm\napproximates a general (possibly non-normalized) probability\ndensity on
R^p, by repeated Laplace approximations to the\ndifference between current
approximation and true density (on\nlog scale). The final approximation is a
mixture of\nmultivariate normal distributions and might be used for example\nas a
proposal distribution for importance sampling (eg in\nBayesian applications). The
algorithm can be seen as a\ncomputational generalization of the Laplace
approximation\nsuitable for skew or multimodal
densities.","License":"GPL","NeedsCompilation":"yes","Package":"iterLap","Repositor
y":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Approximate probability
densities by iterated Laplace\nApproximations","Version":"1.1-2"},"iterators":
{"Author":"Rich Calaway [cre],\nRevolution Analytics [aut, cph],\nSteve Weston
[aut]","Depends":"R (>= 2.5.0), utils","Description":"Support for iterators, which
allow a programmer to traverse\nthrough all the elements of a vector, list, or
other collection\nof data.","License":"Apache License (==
2.0)","NeedsCompilation":"no","Package":"iterators","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"RUnit","Title":"Provides Iterator Construct for
R","Version":"1.0.8"},"iterpc":{"Author":"Randy Lai [aut, cre], Martin Broadhurst
[aut]","Depends":"R (>= 3.0.0)","Description":"A collection of iterators for
generating permutations and combinations with or\nwithout replacement; with
distinct items or non-distinct items (multiset).\nThe generated sequences are in
lexicographical order (dictionary order). The\nalgorithms to generate permutations
and combinations are memory efficient. These\niterative algorithms enable users to
process all sequences without putting all\nresults in the memory at the same time.
The algorithms are written in C\/C++ for\nfaster
performances.","Imports":"iterators, Rcpp (>= 0.11.0), polynom","License":"GPL-
2","NeedsCompilation":"yes","Package":"iterpc","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"foreach, testthat","Title":"Efficient Iterator for
Permutations and
Combinations","URL":"http:\/\/randy.city\/iterpc","Version":"0.2.9"},"itertools":
{"Author":"Steve Weston, Hadley Wickham","Depends":"R (>= 2.14.0), iterators(>=
1.0.0)","Description":"Various tools for creating iterators, many patterned
after\nfunctions in the Python itertools module, and others patterned\nafter
functions in the 'snow' package.","Imports":"parallel","License":"GPL-
2","NeedsCompilation":"no","Package":"itertools","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"foreach","Title":"Iterator Tools","Version":"0.1-
3"},"itertools2":{"Author":"John A. Ramey <johnramey@gmail.com>,\nKayla Schaefer
<kschaefer.tx@gmail.com>","Depends":"R (>= 3.0.2)","Description":"A port of
Python's excellent itertools module to R for
efficient\nlooping.","Imports":"iterators (>= 1.0.7)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"itertools2","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"testthat (>= 0.8.1)","Title":"itertools2:
Functions creating iterators for efficient
looping","URL":"https:\/\/github.com\/ramhiser\/itertools2,
http:\/\/ramhiser.com","Version":"0.1.1"},"itree":{"Author":"Alex Goldstein (itree
modifications) Terry Therneau, Beth\nAtkinson, Brian Ripley (rpart)","Depends":"R
(>= 2.13.0), graphics, stats, grDevices","Description":"This package is based on
the code of the rpart package.\nIt extends rpart by adding additional splitting
methods\nemphasizing interpretable\/parsimonious trees. Unless
indicated\notherwise, it is safe to assume that all functions herein
are\nextensions of or copied directly from similar or nearly\nidentical rpart
methods. As such, the authors of rpart are\nauthors of this package as well.
However, please direct any\nerror reports or other questions about itree to the
maintainer\nof this package; they are welcome and appreciated.","License":"GPL-2 |
GPL-
3","NeedsCompilation":"yes","Package":"itree","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"survival, mlbench","Title":"Tools for classification and
regression trees, with an emphasis\non interpretability","Version":"0.1"},"its":
{"Author":"Portfolio & Risk Advisory Group, Commerzbank Securities","Depends":"R
(>= 2.0.0), methods, stats, Hmisc","Description":"The its package contains an S4
class for handling\nirregular time series","License":"GPL-
2","NeedsCompilation":"no","Package":"its","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Irregular Time Series","Version":"1.1.8"},"itsadug":
{"Author":"Jacolien van Rij [aut, cre],\nMartijn Wieling [aut],\nR. Harald Baayen
[aut],\nHedderik van Rijn [ctb]","Depends":"R (>= 2.14.0), mgcv (>=
1.8)","Description":"GAMM (Generalized Additive Mixed Modeling; Lin & Zhang,
1999)\nas implemented in the R package mgcv (Wood, S.N., 2006; 2011) is a
nonlinear\nregression analysis which is particularly useful for time course data
such as\nEEG, pupil dilation, gaze data (eye tracking), and articulography
recordings,\nbut also for behavioral data such as reaction times and response data.
As time\ncourse measures are sensitive to autocorrelation problems, GAMMs
implements\nmethods to reduce the autocorrelation problems. This package includes
functions\nfor the evaluation of GAMM models (e.g., model comparisons, determining
regions\nof significance, inspection of autocorrelational structure in
residuals)\nand interpreting of GAMMs (e.g., visualization of complex interactions,
and\ncontrasts).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"itsadug","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr, xtable, sp, data.table","Title":"Interpreting
Time Series and Autocorrelated Data Using GAMMs","Version":"2.0"},"itsmr":
{"Author":"George Weigt","Description":"This package provides a subset of the
functionality found in the Windows-based program ITSM. The intended audience is
students using the textbook \"Introduction to Time Series and Forecasting\" by
Peter J. Brockwell and Richard A.
Davis.","License":"Unlimited","NeedsCompilation":"no","Package":"itsmr","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Time series analysis package for
students","Version":"1.5"},"ivbma":{"Author":"Alex Lenkoski, Anna Karl, Andreas
Neudecker","Description":"This package allows one incorporate instrument and
covariate uncertainty into instrumental variable regression.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ivbma","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Bayesian Instrumental Variable Estimation and
Model\nDetermination via Conditional Bayes Factors","Version":"1.05"},"ivfixed":
{"Author":"Zaghdoudi Taha","Description":"Fit an Instrumental least square dummy
variable model","Imports":"Formula","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"ivfixed","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Instrumental fixed effect panel data
model","Version":"1.0"},"ivlewbel":{"Author":"Alan Fernihough","Depends":"stats,
gmm, plyr, lmtest","Description":"GMM estimation of triangular systems using
heteroscedasticity based instrumental variables as in Lewbel
(2012)","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"ivlewbel","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Uses heteroscedasticity to estimate mismeasured and
endogenous\nregressor models","Version":"1.1"},"ivmodel":{"Author":"Yang Jiang,
Hyunseung Kang, and Dylan Small","Depends":"Matrix","Description":"Contains
functions for carrying out instrumental variable estimation of causal effects,
including power analysis, sensitivity analysis, and diagnostics.","License":"GPL-
2","NeedsCompilation":"no","Package":"ivmodel","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Statistical Inference and Sensitivity Analysis for
Instrumental\nVariables Model","Version":"1.1"},"ivpack":{"Author":"Yang Jiang and
Dylan Small","Depends":"AER, sandwich, lmtest","Description":"This package contains
functions for carrying out instrumental variable estimation of causal effects and
power analyses for instrumental variable studies.","License":"GPL-
2","NeedsCompilation":"no","Package":"ivpack","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Instrumental Variable
Estimation","Version":"1.2"},"ivpanel":{"Author":"Zaghdoudi
Taha","Description":"Fit the instrumental panel data models: the fixed effects,
random\neffects and between models.","Imports":"Formula","License":"GPL-
3","NeedsCompilation":"no","Package":"ivpanel","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Instrumental Panel Data
Models","Version":"1.0"},"ivprobit":{"Author":"Zaghdoudi
Taha","Description":"ivprobit fit an Instrumental variables probit model using
the\ngeneralized least squares estimator","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"ivprobit","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Instrumental variables probit
model","Version":"1.0"},"jSonarR":{"Author":"jSonar Inc.","Depends":"R (>= 2.12.1),
RCurl, jsonlite, methods","Description":"This package enables users to access
MongoDB by running queries\nand returning their results in R data frames. Usually,
data in MongoDB is\nonly available in the form of a JSON document. jSonarR uses
data\nprocessing and conversion capabilities in the jSonar Analytics Platform\nand
the JSON Studio Gateway (http:\/\/www.jsonstudio.com), to convert it to\na tabular
format which is easy to use with existing R packages.","License":"AGPL-
3","NeedsCompilation":"no","Package":"jSonarR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"jSonar
Analytics Platform API for
R","URL":"http:\/\/www.jsonstudio.com\/","Version":"1.1.1"},"jaatha":
{"Author":"Paul Staab [aut, cre],\nLisha Mathew [aut],\nDirk Metzler [aut,
ths]","Depends":"R (>= 3.0)","Description":"An estimation method that can use
computer simulations to\napproximate maximum-likelihood estimates even when the
likelihood function can not\nbe evaluated directly. It can be applied whenever it
is feasible to conduct many\nsimulations, but works best when the data is
approximately Poisson distributed.\nIt was originally designed for demographic
inference in evolutionary\nbiology. It has optional support for conducting
coalescent simulation using\nthe 'coala' package.","Imports":"assertthat (>= 0.1),
R6 (>= 2.1.1), parallel, stats, utils","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"jaatha","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"boot (>= 1.3-10), coala (>= 0.2.1), knitr,
rmarkdown,\ntestthat (>= 0.11.0)","Title":"Simulation-Based Maximum Likelihood
Parameter
Estimation","URL":"https:\/\/github.com\/statgenlmu\/jaatha","Version":"3.1.1"},"ja
ckknifeKME":{"Author":"Hasinur Rahaman Khan and Ewart
Shaw","Depends":"imputeYn","Description":"Computing the original and modified
jackknife estimates of Kaplan-Meier estimators.","License":"GPL-
2","NeedsCompilation":"no","Package":"jackknifeKME","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Jackknife Estimates of Kaplan-Meier Estimators or
Integrals","Version":"1.2"},"jackstraw":{"Author":"Neo Christopher Chung
<nchchung@gmail.com>, Wei Hao <whao@princeton.edu>, John D. Storey
<jstorey@princeton.edu>","Description":"Significance test for association between
variables\nand their estimated latent variables.\nLatent variables may be estimated
by principal component analysis (PCA),\nlogistic factor analysis (LFA), and other
techniques.","Imports":"corpcor, lfa, stats","License":"GPL-
2","NeedsCompilation":"no","Package":"jackstraw","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"parallel","Title":"Statistical Inference of Variables
Driving Systematic Variation","Version":"1.1"},"jagsUI":{"Author":"Ken Kellner
<ken@kenkellner.com>","Depends":"R (>= 2.14.0), lattice","Description":"A set of
wrappers around 'rjags' functions to run Bayesian analyses in 'JAGS' (specifically,
via 'libjags'). A single function call can control adaptive, burn-in, and sampling
MCMC phases, with MCMC chains run in sequence or in parallel. Posterior
distributions are automatically summarized (with the ability to exclude some
monitored nodes if desired) and functions are available to generate figures based
on the posteriors (e.g., predictive check plots, traceplots). Function inputs,
argument syntax, and output format are nearly identical to the
'R2WinBUGS'\/'R2OpenBUGS' packages to allow easy switching between MCMC
samplers.","Imports":"rjags (>= 3-13), coda (>= 0.13), parallel, methods,
stats,\ngrDevices, graphics, utils","License":"GPL-
2","NeedsCompilation":"no","Package":"jagsUI","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"A Wrapper Around 'rjags' to Streamline 'JAGS'
Analyses","URL":"https:\/\/github.com\/kenkellner\/jagsUI","Version":"1.4.2"},"jame
s.analysis":{"Author":"Herman De Beukelaer","Depends":"R (>= 2.10), graphics (>=
2.15.3)","Description":"Analyze and visualize results of studies performed with
the\nanalysis tools in 'JAMES', a modern object-oriented Java\nframework for
discrete optimization using local search\nmetaheuristics (see
http:\/\/www.jamesframework.org).","Imports":"rjson (>= 0.2.14), naturalsort (>=
LICENSE","NeedsCompilation":"no","Package":"james.analysis","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Suggests":"testthat (>= 0.9.1)","Title":"Analysis
Tools for the 'JAMES' Framework","Version":"1.0.1"},"jetset":{"Author":"Qiyuan Li,
Aron Eklund","Depends":"R (>= 2.10)","Description":"On Affymetrix gene expression
microarrays, a single gene may be measured by multiple probe sets. This can present
a mild conundrum when attempting to evaluate a gene \"signature\" that is defined
by gene names rather than by specific probe sets. This package provides a one-to-
one mapping from gene to \"best\" probe set for four Affymetrix human gene
expression microarrays: hgu95av2, hgu133a, hgu133plus2, and u133x3p. This package
also includes the pre-calculated probe set quality scores that were used to define
the mapping.","Imports":"org.Hs.eg.db, AnnotationDbi","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"jetset","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"One-to-One Gene-Probeset Mapping for Affymetrix
Human\nMicroarrays","URL":"http:\/\/www.cbs.dtu.dk\/biotools\/jetset\/","Version":"
3.1.3"},"jiebaR":{"Author":"Qin Wenfeng, and the authors of CppJieba for the
included version of\nCppJieba","Depends":"R (>= 3.1),
jiebaRD","Description":"Chinese text segmentation, keyword extraction and speech
tagging\nFor R.","Imports":"Rcpp (>= 0.12.1)","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"jiebaR","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"knitr,testthat,devtools,rmarkdown,roxygen2","Titl
e":"Chinese Text
Segmentation","URL":"https:\/\/github.com\/qinwf\/jiebaR\/","Version":"0.8"},"jieba
RD":{"Author":"Qin Wenfeng","Description":"jiebaR is a package for Chinese text
segmentation, keyword extraction\nand speech tagging. This package provides the
data files required by jiebaR.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"jiebaRD","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"jiebaR","Title":"Chinese Text Segmentation Data
for jiebaR
Package","URL":"https:\/\/github.com\/qinwf\/jiebaRD\/","Version":"0.1"},"jmcm":
{"Author":"Jianxin Pan [aut, cre],\nYi Pan [aut]","Depends":"R (>=
3.2.2)","Description":"Fit joint mean-covariance models for longitudinal data. The
models\nand their components are represented using S4 classes and methods. The
core\ncomputational algorithms are implemented using the 'Armadillo' C++
library\nfor numerical linear algebra and 'RcppArmadillo'
glue.","Imports":"Formula, methods, Rcpp (>= 0.11.6)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"jmcm","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Joint Mean-Covariance Models using 'Armadillo' and
S4","Version":"0.1.1.0"},"jmetrik":{"Author":"J. Patrick Meyer
<support@itemanalysis.com>","Description":"The main purpose of this package is to
make it easy for userR's to interact with 'jMetrik' an open source application for
psychometric analysis. For example it allows useR's to write data frames to file in
a format that can be used by 'jMetrik'. It also allows useR's to read *.jmetrik
files (e.g. output from an analysis) for follow-up analysis in R. The *.jmetrik
format is a flat file that includes a multiline header and the data as comma
separated values. The header includes metadata about the file and one row per
variable with the following information in each row: variable name, data type, item
scoring, special data codes, and variable label.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"jmetrik","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Tools for Interacting with
'jMetrik'","Version":"1.0"},"jmotif":{"Author":"Pavel Senin [aut,
cre]","Depends":"R (>= 3.1.0), Rcpp (>= 0.11.1)","Description":"Implements z-
normalization, SAX, HOT-SAX, VSM, and SAX-VSM algorithms\nfacilitating time series
motif (i.e., recurrent pattern), discord (i.e., anomaly),\nand characteristic
pattern discovery along with interpretable time series
classification.","Imports":"stats","License":"GPL-
2","NeedsCompilation":"yes","Package":"jmotif","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat","Title":"Tools for Time Series Analysis Based
on Symbolic Aggregate\nDicretization","URL":"https:\/\/github.com\/jMotif\/jmotif-
R","Version":"1.0.2"},"jmuOutlier":{"Author":"Steven T. Garren [aut,
cre]","Depends":"R (>= 2.0)","Description":"Performs a permutation test on the
difference between two location parameters, a permutation correlation test, a
permutation F-test, the Siegel-Tukey test, a ratio mean deviance test. Also
performs some graphing techniques, such as for confidence intervals, vector
addition, and Fourier analysis; and includes functions related to the Laplace
(double exponential) and triangular distributions. Performs power calculations for
the binomial test.","License":"GPL-
3","NeedsCompilation":"no","Package":"jmuOutlier","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Permutation Tests for Nonparametric
Statistics","Version":"1.1"},"joineR":{"Author":"Pete Philipson, Ines Sousa, Peter
Diggle, Paula Williamson,\nRuwanthi Kolamunnage-Dona, Robin Henderson","Depends":"R
(>= 2.13.0), nlme, MASS, boot, survival, lattice,
statmod,\ngdata","Description":"Analysis of repeated measurements and time-to-event
data\nvia random effects joint models. Some plotting functions and\nthe variogram
are also
included.","License":"Unlimited","NeedsCompilation":"no","Package":"joineR","Reposi
tory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Joint modelling of repeated
measurements and time-to-event data","URL":"http:\/\/www.r-
project.org","Version":"1.0-3"},"joint.Cox":{"Author":"Takeshi
Emura","Description":"Perform regression analyses under the joint Cox proportional
hazards model between tumour progression and death for meta-analysis.\nThe method
is applicable for meta-analysis combining several studies or for cluster survival
2","NeedsCompilation":"no","Package":"joint.Cox","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Penalized Likelihood Estimation and Prediction under the
Joint\nCox Models Between Tumour Progression and Death for\nMeta-
Analysis","Version":"2.4"},"jointDiag":{"Author":"Cedric Gouy-Pailler
<cedric.gouypailler@gmail.com>","Description":"Different algorithms to perform
approximate joint\ndiagonalization of a finite set of square matrices.
Depending\non the algorithm, orthogonal or non-orthogonal diagonalizer is\nfound.
These algorithms are particularly useful in the context\nof blind source
separation.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"jointDiag","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Joint Approximate Diagonalization of a set of square
matrices","URL":"http:\/\/www.r-
project.org\nhttp:\/\/www.lis.inpg.fr\/pages_perso\/gouypailler\/","Version":"0.2"}
,"jointPm":{"Author":"Feifei Zheng, Michael Leonard, Seth Westra","Depends":"R (>=
3.0.1)","Description":"A bivariate integration method to estimate risk caused by
two extreme and dependent forcing variables.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"jointPm","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Risk estimation using the joint probability
method","Version":"2.3.1"},"jomo":{"Author":"Matteo Quartagno, James
Carpenter","Description":"Similarly to Schafer's package pan, jomo is a package for
multilevel joint modelling multiple imputation.\nNovel aspects of jomo are the
possibility of handling binary and categorical data through latent normal variables
and the option to use cluster-specific covariance matrices.","License":"GPL-
2","NeedsCompilation":"yes","Package":"jomo","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"BaBooN","Title":"Multilevel Joint Modelling Multiple
Imputation","Version":"2.1-2"},"jpeg":{"Author":"Simon Urbanek <Simon.Urbanek@r-
project.org>","Depends":"R (>= 2.9.0)","Description":"This package provides an easy
and simple way to read, write and display bitmap images stored in the JPEG format.
It can read and write both files and in-memory raw vectors.","License":"GPL-2 |
GPL-
3","NeedsCompilation":"yes","Package":"jpeg","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Read and write JPEG
images","URL":"http:\/\/www.rforge.net\/jpeg\/","Version":"0.1-8"},"jqr":
{"Author":"Rich FitzJohn [aut],\nScott Chamberlain [aut, cre],\nStefan Milton Bache
[aut],\nStephen Dolan [aut, cph] (jq library),\njq contributors [ctb] (jq library;
authors listed in inst\/AUTHORS.jq),\nFree Software Foundation [ctb, cph] (parser
code in src\/parser.c),\nDavid M Gay [ctb, cph] (code in
src\/jv_dtoa.c)","Depends":"R (>= 3.1.2)","Description":"Client for 'jq', a JSON
processor (<http:\/\/stedolan.github.io\/jq\/>), written\nin C. 'jq' allows the
following with JSON data: index into, parse, do calculations,\ncut up and filter,
change key names and values, perform conditionals and comparisons,\nand
more.","Imports":"Rcpp, lazyeval, magrittr","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"jqr","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"jsonlite, testthat, knitr, covr","Title":"Client for
'jq', a JSON
Processor","URL":"https:\/\/github.com\/ropensci\/jqr","Version":"0.2.0"},"jrich":
{"Author":"Daniel R. Miranda-Esquivel","Depends":"ape","Description":"These
functions calculate the taxonomic measures presented in Miranda-Esquivel
(2016).\nThe package introduces Jack-knife resampling in evolutionary
distinctiveness prioritization analysis,\nas a way to evaluate the support of the
ranking in area prioritization, and the persistence of a given area\nin a
conservation analysis.\nThe algorithm is described in: Miranda-Esquivel, D (2016)
<DOI:10.1007\/978-3-319-22461-9_11>.","License":"GPL-
3","NeedsCompilation":"no","Package":"jrich","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Jack-Knife Support for Evolutionary Distinctiveness Indices
I\nand W","URL":"https:\/\/github.com\/Dmirandae\/jrich","Version":"0.60-
35"},"jrvFinance":{"Author":"Jayanth Varma [aut, cre]","Depends":"R (>=
3.0.0)","Description":"Implements the basic financial analysis\nfunctions similar
to (but not identical to) what\nis available in most spreadsheet software.
This\nincludes finding the IRR and NPV of regularly\nspaced cash flows and
annuities. Bond pricing and\nYTM calculations are included. In addition,
Black\nScholes option pricing and Greeks are also\nprovided.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"jrvFinance","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr","Title":"Basic Finance;
NPV\/IRR\/Annuities\/Bond-Pricing; Black
Scholes","URL":"http:\/\/github.com\/jrvarma\/jrvFinance","Version":"1.03"},"js":
{"Author":"Jeroen Ooms","Description":"A set of utility functions for working with
JavaScript in R.\nCurrently includes functions to compile, validate, reformat,
optimize\nand analyze JavaScript code.","Imports":"V8 (>= 0.5)","License":"MIT +
file
LICENSE","NeedsCompilation":"no","Package":"js","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr","Title":"Tools for Working with JavaScript in
R","URL":"https:\/\/github.com\/jeroenooms\/js","Version":"0.2"},"jsonlite":
{"Author":"Jeroen Ooms, Duncan Temple Lang, Lloyd
Hilaiel","Depends":"methods","Description":"A fast JSON parser and generator
optimized for statistical data\nand the web. Started out as a fork of 'RJSONIO',
but has been completely\nrewritten in recent versions. The package offers flexible,
robust, high\nperformance tools for working with JSON in R and is particularly
powerful\nfor building pipelines and interacting with a web API. The implementation
is\nbased on the mapping described in the vignette (Ooms, 2014). In addition
to\nconverting JSON data from\/to R objects, 'jsonlite' contains functions
to\nstream, validate, and prettify JSON data. The unit tests included with
the\npackage verify that all edge cases are encoded and decoded consistently
for\nuse with dynamic data in systems and applications.","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"jsonlite","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"curl (>= 0.5), plyr, testthat, knitr,
rmarkdown, R.rsp","Title":"A Robust, High Performance JSON Parser and Generator for
R","URL":"http:\/\/arxiv.org\/abs\/1403.2805,\nhttps:\/\/www.opencpu.org\/posts\/js
onlite-a-smarter-json-encoder","Version":"0.9.19"},"jtrans":{"Author":"Yuchen Wang
[aut, cre]","Depends":"R (>= 3.1.0)","Description":"Transforming univariate non-
normal data to normality using Johnson\nfamilies of distributions. Johnson family
is a comprehensive distribution\nfamily that accommodates many kinds of non-normal
distributions. A bunch of\ndistributions with various parameters will be fit and
the corresponding\np-values under a user-specified normality test will be given.
The final\ntransformation will be the one with the largest p-value under the
given\nnormality test.","License":"GPL-
2","NeedsCompilation":"no","Package":"jtrans","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"nortest, knitr","Title":"Johnson Transformation for
Normality","Version":"0.2.1"},"jug":{"Author":"Bart Smeets","Depends":"R (>=
3.1.0), magrittr, R6","Description":"A set of convenience functions to build simple
APIs.","Imports":"mime, httpuv, stringi, infuser, jsonlite,
base64enc","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"jug","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat, knitr, rmarkdown","Title":"Create a Simple
Web API for your R Functions","Version":"0.1.1"},"junr":{"Author":"Frans van DunnÃ©
[aut, cre]","Depends":"R (>= 3.0.0)","Description":"\nThe Junar API is a commercial
platform to organize and publish data\n<http:\/\/junar.com>. It has been used in a
number of national and local\ngovernment Open Data initiatives in Latin America and
the USA. This package\nis a wrapper to make it easier to access data made public
through the Junar\nAPI.","Imports":"httr, jsonlite","License":"MIT + file
LICENCE","NeedsCompilation":"no","Package":"junr","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr, rmarkdown, testthat (>=
0.8.0)","Title":"Access Open Data Through the Junar
API","URL":"https:\/\/github.com\/fvd\/junr","Version":"0.1.0"},"jvnVaR":
{"Author":"Hung Vu","Depends":"R(>= 2.10.0), stats, utils","Description":"Many
method to compute, predict and back-test VaR. For more detail, see the report:
Value at Risk <researchgate.net>.","License":"GPL-
3","NeedsCompilation":"no","Package":"jvnVaR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Value at Risk","Version":"1.0"},"kSamples":{"Author":"Fritz
Scholz [aut, cre],\nAngie Zhu [aut]","Depends":"SuppDists","Description":"Compares
k samples using the Anderson-Darling test, Kruskal-Wallis type tests\nwith
different rank score criteria, Steel's multiple comparison test, and
the\nJonckheere-Terpstra (JT) test. It computes asymptotic, simulated or (limited)
exact\nP-values, all valid under randomization, with or without ties, or
conditionally\nunder random sampling from populations, given the observed tie
pattern. Except for\nSteel's test and the JT test it also combines these tests
across several blocks of\nsamples. Also analyzed are 2 x t contingency tables and
their blocked combinations\nusing the Kruskal-Wallis criterion. Steel's test is
inverted to provide simultaneous\nconfidence bounds for shift parameters. A
plotting function compares tail probabilities\nobtained under asymptotic
approximation with those obtained via simulation or
exact\ncalculations.","Imports":"methods, graphics, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"kSamples","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"K-Sample Rank Tests and their
Combinations","Version":"1.2-3"},"kantorovich":{"Author":"StÃ©phane
Laurent","Depends":"R (>= 2.5.3)","Description":"Computes the Kantorovich distance
between two probability measures on a finite set.","Imports":"rcdd, gmp,
2","NeedsCompilation":"no","Package":"kantorovich","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat,
knitr, rmarkdown","Title":"Kantorovich Distance Between Probability
Measures","Version":"1.1.0"},"kappaSize":{"Author":"Michael A Rotondi
<mrotondi@yorku.ca>","Depends":"R (>= 2.10)","Description":"This package contains
basic tools for the purpose of\nsample size estimation in studies of
interobserver\/interrater\nagreement (reliability). This package contains sample
size\nestimation functions for both the power-based and confidence\ninterval-based
methods, with binary or multinomial outcomes and\ntwo through six
raters.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"kappaSize","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Sample Size Estimation Functions for Studies of
Interobserver\nAgreement","Version":"1.1"},"kappalab":{"Author":"Michel Grabisch,
Ivan Kojadinovic, Patrick Meyer.","Depends":"R(>= 2.1.0), methods, lpSolve,
quadprog, kernlab","Description":"S4 tool box for capacity (or non-additive
measure, fuzzy measure) and integral manipulation in a finite setting. It contains
routines for handling various types of set functions such as games or capacities.
It can be used to compute several non-additive integrals: the Choquet integral, the
Sugeno integral, and the symmetric and asymmetric Choquet integrals. An analysis of
capacities in terms of decision behavior can be performed through the computation
of various indices such as the Shapley value, the interaction index, the orness
degree, etc. The well-known Möbius transform, as well as other equivalent
representations of set functions can also be computed. Kappalab further contains
seven capacity identification routines: three least squares based approaches, a
method based on linear programming, a maximum entropy like method based on variance
minimization, a minimum distance approach and an unsupervised approach based on
parametric entropies. The functions contained in Kappalab can for instance be used
in the framework of multicriteria decision making or cooperative game
theory.","License":"CeCILL","NeedsCompilation":"yes","Package":"kappalab","Reposito
ry":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Non-Additive Measure and
Integral Manipulation Functions","Version":"0.4-7"},"kaps":{"Author":"Soo-Heang Eo
[aut, cre],\nSeung-Mo Hong [ctb],\nHyungJun Cho [aut]","Depends":"R (>= 3.0.0),
methods, graphics, survival, Formula, coin","Description":"This package provides
some routines to conduct the K-adaptive parititioning (kaps) algorithm for survival
data. A function kaps is an implementation version of our
3","NeedsCompilation":"yes","Package":"kaps","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"locfit","Title":"K-Adaptive Partitioning for Survival
data","Version":"1.0.2"},"karaoke":{"Author":"John R. Dixon","Depends":"tuneR,
seewave","Description":"Attempts to remove vocals from a stereo '.wav' recording of
a song.","License":"GPL-
3","NeedsCompilation":"no","Package":"karaoke","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Remove Vocals from a Song","Version":"1.0"},"kcirt":
{"Author":"Dave Zes, Jimmy Lewis, Dana Landis @ Korn\/Ferry
International","Depends":"R (>= 3.0.0), mvtnorm, snowfall,
corpcor","Description":"Create, Simulate, Fit, Solve k-Cube Thurstonian IRT
Models","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"kcirt","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"k-Cube Thurstonian IRT
Models","Version":"0.6.0"},"kdecopula":{"Author":"Thomas Nagler [aut,
cre]","Depends":"R (>= 3.0.0)","Description":"Provides fast implementations of
kernel smoothing techniques for\nbivariate copula densities, in particular density
estimation and resampling.","Imports":"lattice, cubature, locfit, qrng, Rcpp (>=
0.11.2), VineCopula\n(>= 1.6), graphics, grDevices, stats, utils","License":"GPL-
3","NeedsCompilation":"yes","Package":"kdecopula","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"R.rsp","Title":"Kernel Smoothing for Bivariate
Copula
Densities","URL":"https:\/\/github.com\/tnagler\/kdecopula","Version":"0.5.0"},"kde
trees":{"Author":"Grady Weyenberg and Ruriko Yoshida","Depends":"R (>=
2.15.1)","Description":"A non-parametric method for identifying potential\noutlying
observations in a collection of phylogenetic trees based\non the methods of Owen
and Provan (2011). Such discordant trees\nmay indicate problems with sequence
annotation or tree\nreconstruction, or they may represent interesting
biological\nphenomena, such as horizontal gene transfers.","Imports":"ape, distory,
ggplot2","License":"GPL-
2","NeedsCompilation":"no","Package":"kdetrees","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Nonparametric method for identifying discordant
phylogenetic\ntrees","URL":"http:\/\/github.com\/grady\/kdetrees","Version":"0.1.5"
},"kedd":{"Author":"Arsalane Chouaib Guidoum","Depends":"R (>=
2.15.0)","Description":"Smoothing techniques and computing bandwidth selectors of
the nth derivative of a probability density for one-dimensional
2)","NeedsCompilation":"no","Package":"kedd","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Kernel Estimator and Bandwidth Selection for Density and
Its\nDerivatives","Version":"1.0.3"},"keep":{"Author":"Paavo
Jumppanen","Depends":"methods","Description":"Provides arrays with flexible control
over dimension dropping when
subscripting.","License":"GPL","NeedsCompilation":"no","Package":"keep","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"Oarray","Title":"Arrays with
Better Control over Dimension Dropping","Version":"1.0"},"kelvin":{"Author":"Andrew
J Barbour","Depends":"R (>= 2.10.1)","Description":"Uses Bessel functions to
calculate the\nfundamental and complementary analytic solutions to the\nKelvin
differential equation.","Imports":"Bessel (>= 0.5-4)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"kelvin","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr, testthat","Title":"Calculate Solutions to the
Kelvin Differential Equation using\nBessel
Functions","URL":"https:\/\/github.com\/abarbour\/kelvin","Version":"2.0-
0"},"kequate":{"Author":"Bjorn Andersson, Kenny Branberg and Marie
Wiberg","Depends":"R(>= 2.11.0), methods, stats, graphics,
ltm","Description":"Implements the kernel method of test equating using the CB, EG,
SG, NEAT CE\/PSE and NEC designs, supporting gaussian, logistic and uniform kernels
and unsmoothed and pre-smoothed input data.","Imports":"equateIRT, mirt,
utils","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"kequate","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"The Kernel Method of Test
Equating","Version":"1.5.0"},"kerdiest":{"Author":"Alejandro Quintela del Rio and
Graciela Estevez Perez","Depends":"date, chron, evir","Description":"Nonparametric
kernel distribution function estimation is\nperformed. Three automatic bandwidth
selection methods for\nnonparametric kernel distribution function estimation
are\nimplemented: the plug-in of Altman and Leger, the plug-in of\nPolansky and
Baker, and the modified cross-validation of\nBowman, Hall and Prvan. The exceedance
function, the mean\nreturn period and the return level are also
computed.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"kerdiest","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Nonparametric kernel estimation of the distribution
function.\nBandwidth selection and estimation of related
functions","Version":"1.2"},"kergp":{"Author":"Yves Deville, David Ginsbourger,
Olivier Roustant. Contributors: Nicolas Durrande.","Depends":"Rcpp (>= 0.10.5),
methods, testthat","Description":"Gaussian Process models with customised
covariance kernels.","Imports":"MASS, numDeriv, stats4, doParallel","License":"GPL-
3","NeedsCompilation":"yes","Package":"kergp","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"DiceKriging, DiceDesign, lhs, inline,
foreach","Title":"Gaussian Process
Laboratory","Version":"0.2.0"},"kernDeepStackNet":{"Author":"Thomas Welchowski
<welchow@imbie.meb.uni-bonn.de> and Matthias Schmid\n<matthias.schmid@imbie.uni-
bonn.de>","Description":"Contains functions for estimation and model selection of
kernel\ndeep stacking networks. The model selection includes direct optimization
or\nmodel based alternatives with arbitrary loss functions.","Imports":"methods,
Rcpp, glmnet, mvtnorm, lhs, DiceKriging, parallel,\nglobalOptTests","License":"GPL-
3","NeedsCompilation":"yes","Package":"kernDeepStackNet","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"caret, pROC, mgcv","Title":"Kernel Deep
Stacking Networks","Version":"1.0.1"},"kerndwd":{"Author":"Boxiang Wang
<boxiang@umn.edu>, Hui Zou
<hzou@stat.umn.edu>","Depends":"methods","Description":"A novel implementation that
solves the DWD and the kernel DWD which can be hundred times faster than the
existing implementation of DWD based on the second-order-cone programming (SOCP).
The package also handles some other general loss functions including large-margin
unified machines (LUM).","Imports":"graphics, grDevices, stats,
2","NeedsCompilation":"yes","Package":"kerndwd","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Distance Weighted Discrimination (DWD) and Kernel
Methods","Version":"1.1.2"},"kernelFactory":{"Author":"Michel Ballings, Dirk Van
den Poel","Description":"Binary classification based on an ensemble of kernel
machines (\"Ballings, M. and Van den Poel, D. (2013), Kernel Factory: An Ensemble
of Kernel Machines. Expert Systems With Applications, 40(8), 2904-2913\"). Kernel
factory is an ensemble method where each base classifier (random forest) is fit on
the kernel matrix of a subset of the training data.","Imports":"randomForest, AUC,
genalg, kernlab, stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"kernelFactory","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Kernel
Factory: An Ensemble of Kernel Machines","Version":"0.3.0"},"kernlab":
{"Author":"Alexandros Karatzoglou [aut, cre],\nAlex Smola [aut],\nKurt Hornik
[aut]","Depends":"R (>= 2.10)","Description":"Kernel-based machine learning methods
for classification,\nregression, clustering, novelty detection, quantile
regression\nand dimensionality reduction. Among other methods 'kernlab'\nincludes
Support Vector Machines, Spectral Clustering, Kernel\nPCA, Gaussian Processes and a
QP solver.","Imports":"methods, stats, grDevices, graphics","License":"GPL-
2","NeedsCompilation":"yes","Package":"kernlab","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Kernel-Based Machine Learning Lab","Version":"0.9-
24"},"keyplayer":{"Author":"Weihua An; Yu-Hsin Liu","Description":"Provides group
centrality measures and identifies the most central group of players in a
network.","Imports":"sna, matpow","License":"GPL-
3","NeedsCompilation":"no","Package":"keyplayer","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Locating Key Players in Social
Networks","Version":"1.0.1"},"keypress":{"Author":"Gabor Csardi [aut,
cre]","Description":"Wait for a single key press at the 'R' prompt.\nThis works in
terminals, but does not currently work\nin the 'Windows' 'GUI', the 'OS X' 'GUI'
('R.app'),\nin 'Emacs' 'ESS', in an 'Emacs' shell buffer or in\n'R Studio'. In
these cases 'keypress' stops with an\nerror message.","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"keypress","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Wait for a Key Press in a
Terminal","URL":"https:\/\/github.com\/gaborcsardi\/keypress","Version":"1.0.0"},"k
figr":{"Author":"Michael C Koohafkan [aut, cre]","Depends":"R (>=
3.1.0)","Description":"A streamlined cross-referencing system for R Markdown
documents\ngenerated with 'knitr'. R Markdown is an authoring format for
generating\ndynamic content from R. 'kfigr' provides a hook for anchoring
code\nchunks and a function to cross-reference document elements generated
from\nsaid chunks, e.g. figures and tables.","Imports":"knitr (>= 1.6),
3)","NeedsCompilation":"no","Package":"kfigr","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"ggplot2","Title":"Integrated Code Chunk Anchoring and
Referencing for R
Markdown\nDocuments","URL":"https:\/\/github.com\/mkoohafkan\/kfigr","Version":"1.2
"},"kimisc":{"Author":"Kirill MÃ¼ller [aut, cre]","Description":"A collection of
useful functions not found anywhere else,\nmainly for programming: Pretty
intervals, generalized lagged\ndifferences, checking containment in an interval,
creating a\nfactor where the levels maintain the order of appearance,\nsampling
rows from a data frame, converting seconds from\nmidnight to and from H:M:S format,
choosing the first non-NA\nvalue, transposing lists of lists, returning the name of
the\nfile currently sourced, smart named lists and vectors, and an\nalternative
interface to assign().","Enhances":"knitr","Imports":"plyr, pryr","License":"GPL-
3","NeedsCompilation":"no","Package":"kimisc","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat (>= 0.10.0)","Title":"Kirill's Miscellaneous
Functions","URL":"http:\/\/krlmlr.github.io\/kimisc","Version":"0.3"},"kin.cohort":
{"Author":"Victor Moreno, Nilanjan Chatterjee, Bhramar
Mukherjee","Depends":"survival","Description":"Analysis of kin-cohort studies.
kin.cohort provides estimates of age-specific\ncumulative risk of a disease for
carriers and noncarriers of a mutation. The cohorts are\nretrospectively built from
relatives of probands for whom the genotype is known. Currently\nthe method of
moments and marginal maximum likelihood are implemented. Confidence intervals\nare
calculated from bootstrap samples.\nMost of the code is a translation from previous
'MATLAB' code by N. Chatterjee.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"kin.cohort","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Analysis of Kin-Cohort
Studies","Version":"0.7"},"kineticF":{"Author":"Dipesh E Patel & Mario Cortina-
Borja","Depends":"R(> 3.1.0)","Description":"Data cleaning, processing,
visualisation and analysis for manual (Goldmann) and automated (Octopus 900)
kinetic visual field data.","Imports":"circular, lqmm, splancs, sp, plotrix,
2)","NeedsCompilation":"no","Package":"kineticF","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Framework for the Analysis of Kinetic Visual Field
Data","Version":"1.0"},"kinfit":{"Author":"Johannes Ranke [aut, cre, cph],\nKatrin
Lindenberger [ctb]","Description":"\nThe FOCUS Kinetics Report first published in
2006 describes mathematical\nmodels and recommends statistical methods for the
evaluation of\nchemical degradation data. This package implements fitting the
kinetic\nmodels suitable for observations of the decline of a single
chemical\ncompound (no metabolite formation\/decline or multi-compartment
kinetics).\nPlease note that no warranty is implied for correctness of results
or\nfitness for a particular purpose. 'kinfit' is maintained, but not\nactively
developed at the moment. Please check the 'mkin' package for an\nactively developed
package for kinetic evaluations of degradation data.","Imports":"graphics, stats,
utils","License":"GPL","NeedsCompilation":"no","Package":"kinfit","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Title":"Routines for Fitting Kinetic Models to
Chemical Degradation Data","URL":"http:\/\/cran.r-project.org, http:\/\/kinfit.r-
forge.r-project.org","Version":"1.1.14"},"kinship2":{"Author":"Terry M Therneau
[aut],\nSchaid Daniel [ctb],\nJason Sinnwell [aut, cre],\nElizabeth Atkinson
[ctb]","Depends":"R (>= 3.1.0), Matrix, quadprog","Description":"Routines to handle
family data with a pedigree object. The initial purpose was to create correlation
structures that describe\nfamily relationships such as kinship and identity-by-
descent, which\ncan be used to model family data in mixed effects models, such as
in the\ncoxme function. Also includes a tool for pedigree drawing which
is\nfocused on producing compact layouts without intervention. Recent
additions\ninclude utilities to trim the pedigree object with various criteria,
and\nkinship for the X chromosome.","Imports":"graphics, stats,
2)","NeedsCompilation":"no","Package":"kinship2","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Pedigree Functions","URL":"http:\/\/r-forge.r-
project.org","Version":"1.6.4"},"kissmig":{"Author":"Michael P. Nobis [cre, aut],
Signe Normand [ctb]","Depends":"raster, R (>= 2.15.0)","Description":"Simulating
species migration and range dynamics under stable or changing environmental
conditions based on a simple, raster-based, stochastic migration model. Providing
accessibility for considering species migration in niche-based species distribution
3)","NeedsCompilation":"yes","Package":"kissmig","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"a Keep It Simple Species Migration
Model","URL":"http:\/\/purl.oclc.org\/wsl\/kissmig","Version":"1.0-3"},"kitagawa":
{"Author":"Andrew J Barbour","Depends":"R (>= 2.10.1), kelvin (>= 1.2-
0)","Description":"Provides tools to calculate the theoretical hydrodynamic
response\nof an aquifer undergoing harmonic straining or pressurization. There
are\ntwo classes of models here: (1) for sealed wells, based on the model
of\nKitagawa et al (2011), and (2) for open wells, based on the models of\nCooper
et al (1965), Hsieh et al (1987), Rojstaczer (1988), and Liu et al\n(1989). These
models treat strain (or aquifer head) as an input to the\nphysical system, and
fluid-pressure (or water height) as the output. The\napplicable frequency band of
these models is characteristic of seismic\nwaves, atmospheric pressure
fluctuations, and solid earth
tides.","License":"GPL","NeedsCompilation":"no","Package":"kitagawa","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Suggests":"knitr, RColorBrewer,
signal","Title":"Spectral response of water wells to harmonic strain and
pressure","URL":"http:\/\/abarbour.github.io\/kitagawa\/","Version":"2.1-
0"},"kknn":{"Author":"Klaus Schliep [aut, cre],\nKlaus Hechenbichler
[aut],\nAntoine Lizee [ctb]","Depends":"R (>= 2.10)","Description":"Weighted k-
Nearest Neighbors for Classification, Regression and Clustering.","Imports":"igraph
(>= 1.0), Matrix, stats, graphics","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"kknn","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Weighted k-Nearest
Neighbors","URL":"https:\/\/github.com\/KlausVigo\/kknn","Version":"1.3.1"},"klaR":
{"Author":"Christian Roever, Nils Raabe, Karsten Luebke, Uwe Ligges, Gero
Szepannek, Marc Zentgraf","Depends":"R (>= 2.10.0),
MASS","Description":"Miscellaneous functions for classification and
visualization\ndeveloped at the Fakultaet Statistik, Technische Universitaet
Dortmund","Imports":"combinat","License":"GPL-
2","NeedsCompilation":"no","Package":"klaR","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"scatterplot3d (>= 0.3-22), som, mlbench, rpart,
e1071","Title":"Classification and visualization","URL":"http:\/\/www.statistik.tu-
dortmund.de","Version":"0.6-12"},"klausuR":{"Author":"m.eik michalke [aut,
cre]","Depends":"R (>= 2.9.0), xtable, psychometric, polycor, methods,\ngraphics,
tools","Description":"A set of functions designed to quickly generate results of
a\nmultiple choice test. Generates detailed global results, lists for\nanonymous
feedback and personalised result feedback (in LaTeX and\/or PDF\nformat), as well
as item statistics like Cronbach's alpha or disciminatory\npower. klausuR also
includes a plugin for the R GUI and IDE RKWard,\nproviding dialogs for its basic
features. To use them, install RKWard from\nhttp:\/\/rkward.sf.net (plugins are
detected automatically).
Due to some\nrestrictions on CRAN, the full package sources are only available
from the\nproject homepage.","Enhances":"rkward","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"klausuR","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Multiple Choice Test Evaluation","URL":"http:\/\/r-
forge.r-project.org\/projects\/klausur","Version":"0.12-10"},"klin":
{"Author":"Tamas K Papp <tpapp@princeton.edu>","Depends":"R (>= 2.0.0), Matrix (>=
0.9975-8)","Description":"The package implements efficient ways to evaluate
and\nsolve equations of the form Ax=b, where A is a kronecker\nproduct of matrices.
Functions to solve least squares problems\nof this type are also
2)","NeedsCompilation":"no","Package":"klin","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Linear equations with Kronecker structure","Version":"2007-
02-05"},"km.ci":{"Author":"Ralf Strobl <rstrobl@ibe.med.uni-
muenchen.de>","Depends":"R (>= 1.8.0), survival, stats","Description":"Computes
various confidence intervals for the Kaplan-Meier\nestimator, namely: Petos CI,
Rothman CI, CI's based on\nGreenwoods variance, Thomas and Grunkemeier CI and
the\nsimultaneous confidence bands by Nair and Hall and Wellner.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"km.ci","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Confidence intervals for the Kaplan-Meier
estimator","Version":"0.5-2"},"kmc":{"Author":"Yifan Yang [aut,cre], Mai Zhou
[aut]","Depends":"R (>= 2.13.1), compiler, rootSolve,
emplik","Description":"Linearly constrained Kaplan-Meier estimator for right
censored data. This version does empirical likelihood ratio test with right
censored data with linear type constraint and hypothesis testing for coefficients
in accelerated failure time model.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"kmc","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Kaplan-Meier Estimator with Constraints for Right Censored
Data\n-- a Recursive Computational
Algorithm","URL":"https:\/\/github.com\/yfyang86\/kmc","Version":"0.2-
2"},"kmconfband":{"Author":"David E. Matthews
<dematthews@uwaterloo.ca>","Depends":"R (>= 2.14.0), graphics,
survival","Description":"Computes and plots an exact nonparametric band for any
user-specified level of confidence from a single-sample survfit
object","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"kmconfband","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Kaplan-Meier Simultaneous Confidence Band for the
Survivor\nFunction","Version":"0.1"},"kmeans.ddR":{"Author":"Vishrut Gupta, Arash
Fard","Depends":"R (>= 3.0.0)","Description":"Distributed k-means clustering
algorithm written using 'ddR' (Distributed Data Structures) API in the 'ddR'
package.","Imports":"ddR, Rcpp (>= 0.11.0)","License":"GPL (>= 2) | file
LICENSE","NeedsCompilation":"yes","Package":"kmeans.ddR","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Distributed k-Means for
Big Data using 'ddR' API","Version":"0.1.0"},"kmi":{"Author":"Arthur Allignol
<arthur.allignol@uni-ulm.de>","Depends":"survival","Description":"The package
performs a Kaplan-Meier multiple imputation to recover the missing potential
censoring information from competing risks events, so that standard right-censored
methods could be applied to the imputed data sets to perform analyses of the
cumulative incidence functions.","Imports":"mitools","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"kmi","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Kaplan-Meier multiple imputation for the analysis of
cumulative\nincidence functions in the competing risks
setting","Version":"0.5.1"},"kml":{"Author":"Christophe Genolini [cre, aut],\nBruno
Falissard [ctb]","Depends":"methods,clv,longitudinalData (>=
2.4)","Description":"An implementation of k-means specifically design\nto cluster
longitudinal data. It provides facilities to deal with missing\nvalue, compute
several quality criterion (Calinski and Harabatz,\nRay and Turie, Davies and
Bouldin, BIC, ...) and propose a graphical\ninterface for choosing the 'best'
number of clusters.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"kml","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"K-Means for Longitudinal Data","URL":"http:www.r-
project.org","Version":"2.4.1"},"kml3d":{"Author":"Christophe Genolini [cre,
aut],\nBruno Falissard [ctb],\nJean-Baptiste Pingault
[ctb]","Depends":"methods,clv,rgl,misc3d,longitudinalData(>= 2.4), kml(>=
2.4)","Description":"An implementation of k-means specifically design\nto cluster
joint trajectories (longitudinal data on\nseveral variable-trajectories).\nLike
'kml', it provides facilities to deal with missing\nvalue, compute several quality
criterion (Calinski and Harabatz,\nRay and Turie, Davies and Bouldin, BIC,...) and
propose a graphical\ninterface for choosing the 'best' number of clusters. In
addition, the 3D graph\nrepresenting the mean joint-trajectories of each cluster
can be exported through\nLaTeX in a 3D dynamic rotating PDF graph.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"kml3d","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"K-Means for Joint Longitudinal Data","URL":"http:www.r-
project.org","Version":"2.4.1"},"kmlShape":{"Author":"Christophe Genolini [cre,
aut],\nElie Guichard
[ctb]","Depends":"methods,class,longitudinalData,kml,lattice","Description":"K-
means for longitudinal data using shape-respecting distance and shape-respecting
means.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"kmlShape","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"K-Means for Longitudinal Data using Shape-Respecting
Distance","URL":"http:www.r-project.org","Version":"0.9.5"},"kmlcov":
{"Author":"Mamoun O. Benghezal [aut, cre],\nChristophe Genolini
[ctb]","Depends":"methods","Description":"'kmlcov' Cluster longitudinal data using
the likelihood as a\nmetric of distance. The generalised linear model allow the
user to\nintroduce covariates with different level effects (2
levels).","License":"GPL-
2","NeedsCompilation":"no","Package":"kmlcov","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Clustering longitudinal data using the likelihood as a
metric of\ndistance","Version":"1.0.1"},"kmodR":{"Author":"David Charles Howe [aut,
cre]","Description":"An implementation of the 'k-means--' algorithm proposed by
Chawla and Gionis, 2013 in their paper, \"k-means-- : A unified approach to
clustering and outlier detection. SIAM International Conference on Data Mining
(SDM13)\", and using 'ordering' described by Howe, 2013 in the thesis, \"Clustering
and anomaly detection in tropical cyclones\". Useful for creating (potentially)
tighter clusters than standard k-means and simultaneously finding outliers
inexpensively in multidimensional space.","License":"GPL-
3","NeedsCompilation":"no","Package":"kmodR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat","Title":"K-Means with Simultaneous Outlier
Detection","Version":"0.1.0"},"knitLatex":{"Author":"John Shea [aut,
cre]","Depends":"R (>= 3.2.0)","Description":"Provides several helper functions for
working with 'knitr' and 'LaTeX'.\nIt includes 'xTab' for creating traditional
'LaTeX' tables, 'lTab' for generating\n'longtable' environments, and 'sTab' for
generating a 'supertabular' environment.\nAdditionally, this package contains a
knitr_setup() function which fixes a\nwell-known bug in 'knitr', which distorts the
'results=\"asis\"' command when used\nin conjunction with user-defined commands;
and a com command (<<com=TRUE>>=)\nwhich renders the output from 'knitr' as a
'LaTeX' command.","Imports":"knitr (>= 1.10.5)","License":"GPL-
3","NeedsCompilation":"no","Package":"knitLatex","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"'Knitr' Helpers - Mostly
Tables","Version":"0.9.0"},"knitcitations":{"Author":"Carl Boettiger [aut,
cre]","Depends":"R (>= 3.0)","Description":"Provides the ability to create dynamic
citations\nin which the bibliographic information is pulled from the web
rather\nthan having to be entered into a local database such as 'bibtex' ahead
of\ntime. The package is primarily aimed at authoring in the R 'markdown'\nformat,
and can provide outputs for web-based authoring such as linked\ntext for inline
citations. Cite using a 'DOI', URL, or\n'bibtex' file key. See the package URL
for details.","Imports":"RefManageR (>= 0.8.2), digest, httr (>= 0.3), methods,
LICENSE","NeedsCompilation":"no","Package":"knitcitations","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Suggests":"testthat, knitr (>=
1.6)","Title":"Citations for 'Knitr' Markdown
Files","URL":"https:\/\/github.com\/cboettig\/knitcitations","Version":"1.0.7"},"kn
itr":{"Author":"Yihui Xie [aut, cre],\nAdam Vogt [ctb],\nAlastair Andrew
[ctb],\nAlex Zvoleff [ctb],\nAndre Simon [ctb] (the CSS files under inst\/themes\/
were derived from\nthe Highlight package http:\/\/www.andre-simon.de),\nAron Atkins
[ctb],\nAaron Wolen [ctb],\nAshley Manton [ctb],\nBen Baumer [ctb],\nBrian Diggs
[ctb],\nCassio Pereira [ctb],\nDavid Robinson [ctb],\nDonald Arseneau [ctb, cph]
(the framed package at inst\/misc\/framed.sty),\nDoug Hemken [ctb],\nDuncan Murdoch
[ctb],\nFabian Hirschmann [ctb],\nFitch Simeon [ctb],\nFrank E Harrell Jr [ctb]
(the Sweavel package at inst\/misc\/Sweavel.sty),\nGregoire Detrez [ctb],\nHadley
Wickham [ctb],\nHeewon Jeon [ctb],\nHenrik Bengtsson [ctb],\nHiroaki Yutani
[ctb],\nJake Burkhead [ctb],\nJames Manton [ctb],\nJared Lander [ctb],\nJason
Punyon [ctb],\nJeff Arnold [ctb],\nJeremy Ashkenas [ctb, cph] (the CSS file
at\ninst\/misc\/docco-classic.css),\nJeremy Stephens [ctb],\nJim Hester [ctb],\nJoe
Cheng [ctb],\nJohannes Ranke [ctb],\nJohn Honaker [ctb],\nJohn Muschelli
[ctb],\nJonathan Keane [ctb],\nJJ
Allaire [ctb],\nJohan Toloe [ctb],\nJoseph Larmarange [ctb],\nJulien Barnier
[ctb],\nKaiyin Zhong [ctb],\nKevin K. Smith [ctb],\nKirill Mueller [ctb],\nKohske
Takahashi [ctb],\nMichael Friendly [ctb],\nMichal Bojanowski [ctb],\nMichel
Kuhlmann [ctb],\nNacho Caballero [ctb],\nNick Salkowski [ctb],\nNoam Ross
[ctb],\nQiang Li [ctb],\nRamnath Vaidyanathan [ctb],\nRichard Cotton [ctb],\nRobert
Krzyzanowski [ctb],\nRomain Francois [ctb],\nScott Kostyshak [ctb],\nSebastian
Meyer [ctb],\nSietse Brouwer [ctb],\nSimon de Bernard [ctb],\nTaiyun Wei
[ctb],\nThibaut Assus [ctb],\nThibaut Lamadon [ctb],\nThomas Leeper [ctb],\nTom
Torsney-Weir [ctb],\nTrevor Davis [ctb],\nViktoras Veitas [ctb],\nWeicheng Zhu
[ctb],\nWush Wu [ctb],\nZachary Foster [ctb]","Depends":"R (>=
3.0.2)","Description":"Provides a general-purpose tool for dynamic report
generation in R\nusing Literate Programming techniques.","Imports":"evaluate (>=
0.8), digest, formatR, highr, markdown, stringr\n(>= 0.6), yaml (>= 2.1.5),
methods,
tools","License":"GPL","NeedsCompilation":"no","Package":"knitr","Repository":"http
:\/\/cran.csiro.au\/src\/contrib","Suggests":"testit, rgl (>= 0.95.1201),
codetools, rmarkdown, tikzDevice\n(>= 0.9), XML, RCurl","Title":"A General-Purpose
Package for Dynamic Report Generation in
R","URL":"http:\/\/yihui.name\/knitr\/","Version":"1.12.3"},"knitrBootstrap":
{"Author":"Jim Hester","Depends":"R (>= 3.0.0)","Description":"A framework to
create Bootstrap 3 HTML reports from knitr\nRmarkdown.","Imports":"knitr (>=
1.5.25), rmarkdown, markdown","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"knitrBootstrap","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Suggests":"testthat, roxygen2, corrplot, ggplot2,
igraph, maps, mapproj,\nmaptools, plyr, reshape2, xtable","Title":"Knitr Bootstrap
Framework","URL":"https:\/\/github.com\/jimhester\/","Version":"1.0.0"},"knnGarden"
:{"Author":"Boxian Wei & Fan Yang & Xinmiao Wang & Yanni
Ge","Depends":"cluster","Description":"Multi-distance based k-Nearest Neighbors
Classification\nwith K Threshold Value Check and Same K_i Problem Dealing,\nMissing
Observations Filling","Imports":"stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"knnGarden","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Multi-distance based k-Nearest
Neighbors","Version":"1.0.1"},"knnIndep":{"Author":"Sebastian DÃ¼mcke
<duemcke@mpipz.mpg.de>","Description":"This package provides the implementation of
an exact formula of the\nith nearest neighbour distance distribution and
implementations of tests of\nindependence based on that formula. Furthermore the
package provides a\ngeneral framework to benchmark tests of
independence.","Imports":"parallel","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"knnIndep","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Independence tests and
benchmarks","Version":"2.0"},"knncat":{"Author":"Sam Buttrey","Description":"Scale
categorical variables in such a way as\nto make NN classification as accurate as
possible. The code also\nhandles continuous variables and prior probabilities, and
does\nintelligent variable selection and estimation of both error rates\nand the
right number of NN's.","License":"GPL-
2","NeedsCompilation":"yes","Package":"knncat","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Nearest-neighbor Classification with Categorical
Variables","Version":"1.2.2"},"knockoff":{"Author":"Rina Foygel Barber, Emmanuel
Candes, Evan Patterson","Description":"The knockoff filter is a procedure for
controlling the false\ndiscovery rate (FDR) when performing variable selection. For
more information,\nsee the website below and the accompanying
paper.","Imports":"glmnet, RJSONIO","License":"GPL-
3","NeedsCompilation":"no","Package":"knockoff","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"lars, knitr, testthat","Title":"Knockoff Filter for
Controlling the False Discovery
Rate","URL":"http:\/\/statweb.stanford.edu\/~candes\/Knockoffs","Version":"0.2.1"},
"koRpus":{"Author":"m.eik michalke [aut, cre],\nEarl Brown [ctb],\nAlberto Mirisola
[ctb],\nAlexandre Brulet [ctb],\nLaura Hauser [ctb]","Depends":"R (>=
2.10.0),methods","Description":"A set of tools to analyze texts. Includes, amongst
others,\nfunctions for automatic language detection, hyphenation, several indices
of\nlexical diversity (e.g., type token ratio, HD-D\/vocd-D, MTLD) and
readability\n(e.g., Flesch, SMOG, LIX, Dale-Chall). Basic import functions for
language\ncorpora are also provided, to enable frequency analyses (supports Celex
and\nLeipzig Corpora Collection file formats) and measures like tf-idf. Support
for\nadditional languages can be added on-the-fly or by plugin packages. Note:
For\nfull functionality a local installation of TreeTagger is recommended.
'koRpus'\nalso includes a plugin for the R GUI and IDE RKWard, providing graphical
dialogs\nfor its basic features. The respective R package 'rkward' cannot be
installed\ndirectly from a repository, as it is a part of RKWard. To make full use
of this\nfeature, please install RKWard from https:\/\/rkward.kde.org (plugins are
detected\nautomatically). Due to some restrictions on CRAN, the full package
sources are\nonly available from the project homepage. To ask for help, report
bugs, suggest\nfeature improvements, or discuss the global development of the
package, please\nsubscribe to the koRpus-dev mailing list
(https:\/\/ml06.ispgateway.de\/mailman\/\nlistinfo\/korpus-
dev_r.reaktanz.de).","Enhances":"rkward","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"koRpus","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat,tm,SnowballC,shiny","Title":"An R Package for
Text Analysis","URL":"http:\/\/reaktanz.de\/?c=hacking&s=koRpus","Version":"0.06-
4"},"kobe":{"Author":"Laurence Kell","Depends":"R(>= 3.0.2),
methods","Description":"The tuna Regional Fisheries Management Organisations
(tRFMOs) use a common framework for providing scientific advice, i.e. the Kobe II
Framework. This is based on maintaining fishing mortality below FMSY and stock
biomass above BMSY. This package provides methods for summarising results from
stock assessments and Management Strategy Evaluations in the Kobe
format.","Imports":"plyr, reshape, ggplot2, MASS, emdbook, coda","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"kobe","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"akima,","Title":"Tools for the provision of scientific
fisheries management\nadvice","Version":"1.3.2"},"kofnGA":{"Author":"Mark A.
Wolters","Description":"Function kofnGA uses a genetic algorithm to choose a subset
of a\nfixed size k from the integers 1:n, such that a user-supplied objective
function\nis minimized at that subset. The selection step is done by tournament
selection\nbased on ranks, and elitism may be used to retain a portion of the best
solutions\nfrom one generation to the next.","License":"GPL-
2","NeedsCompilation":"no","Package":"kofnGA","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"A Genetic Algorithm for Fixed-Size Subset
Selection","Version":"1.2"},"kohonen":{"Author":"Ron Wehrens","Depends":"R (>=
2.6.0), class, MASS","Description":"Functions to train supervised and self-
organising maps (SOMs). Also interrogation of the maps and prediction using trained
maps are supported. The name of the package refers to Teuvo Kohonen, the inventor
of the SOM.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"kohonen","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Supervised and Unsupervised Self-Organising
Maps","Version":"2.0.19"},"kolmim":{"Author":"Luis
Carvalho","Description":"Provides an alternative, more efficient evaluation of
extreme\nprobabilities of Kolmogorov's goodness-of-fit measure, Dn, when compared
to\nthe original implementation of Wang, Marsaglia, and Tsang. These\nprobabilities
are used in Kolmogorov-Smirnov tests when comparing two\nsamples.","License":"GPL-
2","NeedsCompilation":"yes","Package":"kolmim","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"An Improved Evaluation of Kolmogorov's
Distribution","Version":"1.0"},"kpodclustr":{"Author":"Jocelyn T. Chi [aut,
cre],\nEric C. Chi [ctb]","Depends":"R (>= 3.1.0), clues","Description":"The
kpodclustr package implements the k-POD method for clustering\npartially observed
data.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"kpodclustr","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Method for Clustering Partially Observed
Data","URL":"http:\/\/jocelynchi.com\/kpodclustr","Version":"1.0"},"kriens":
{"Author":"Matteo Provenzano","Description":"Provides basic functions for
Continuation-Passing Style development.","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"kriens","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat","Title":"Continuation Passing Style
Development","URL":"http:\/\/www.alephdue.com","Version":"0.1"},"kriging":
{"Author":"Omar E. Olmedo","Description":"Simple and highly optimized ordinary
kriging algorithm to plot geographical data","License":"GPL-
2","NeedsCompilation":"yes","Package":"kriging","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"maps","Title":"Ordinary
Kriging","Version":"1.1"},"krm":{"Author":"Youyi Fong <youyifong@gmail.com>, Saheli
Datta, Krisztian Sebestyen","Depends":"R (>= 3.0.0),
kyotil","Description":"Implements several methods for testing the variance
component parameter in regression models that contain kernel-based random effects,
including a maximum of adjusted scores test. Several kernels are supported,
including a profile hidden Markov model mutual information kernel for protein
sequence.","License":"GPL-
2","NeedsCompilation":"yes","Package":"krm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"RUnit, MASS","Title":"Kernel
Based Regression Models","Version":"2015.3-4"},"ks":{"Author":"Tarn Duong
<tarn.duong@gmail.com>","Depends":"R (>= 1.4.0), KernSmooth (>= 2.22), misc3d (>=
0.4-0), mvtnorm\n(>= 1.0-0), rgl (>= 0.66)","Description":"Kernel smoothers for
univariate and multivariate data.","Imports":"grDevices, graphics, multicool,
stats, utils","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"ks","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"MASS","Title":"Kernel
Smoothing","URL":"http:\/\/www.mvstat.net\/tduong","Version":"1.10.3"},"kselection"
:{"Author":"Daniel Rodriguez","Description":"Selection of k in k-means clustering
based on Pham et al. paper\n``Selection of k in k-means
clustering''.","Imports":"tools","License":"GPL-
3","NeedsCompilation":"no","Package":"kselection","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"amap, FactoClass, foreach, LICORS,
testthat","Title":"Selection of K in K-Means
Clustering","URL":"https:\/\/github.com\/drodriguezperez\/kselection","Version":"0.
2.0"},"ksrlive":{"Author":"Westa Domanova","Depends":"R (>=
3.0.0)","Description":"Using this package you can combine known kinase substrate
relationships with experimental data and determine active kinases and their
substrates.","Imports":"tightClust, stats","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"ksrlive","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Identify Kinase Substrate Relationships Using Dynamic
Data","Version":"1.0"},"kst":{"Author":"Christina Stahl [aut, cre],\nDavid Meyer
[aut]","Depends":"R (>= 2.7.0), proxy, relations (>= 0.4-0), sets (>= 0.3-
2)","Description":"Knowledge Space Theory is a set-theoretical framework,
which\nproposes mathematical formalisms to operationalize knowledge structures in
a\nparticular domain. The kst-package provides basic functionalities to\ngenerate,
handle, and manipulate knowledge structures and knowledge spaces.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"kst","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"Rgraphviz","Title":"Knowledge Space
Theory","Version":"0.2-1"},"ktsolve":{"Author":"Carl Witthoft","Description":"This
function is designed for use with an arbitrary set of equations with\nan arbitrary
set of unknowns.\nThe user selects \"fixed\" values for enough unknowns to leave as
many variables as\nthere are equations, which in most cases means the system is
properly\ndefined and a unique solution exists. The function, the fixed values\nand
initial values for the remaining unknowns are fed to a nonlinear backsolver.\nThe
original version of \"TK!Solver\" was the inspiration for this
function.","License":"LGPL-
3","NeedsCompilation":"no","Package":"ktsolve","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"BB, nleqslv","Title":"Configurable function for solving
families of nonlinear\nequations","Version":"1.1"},"ktspair":{"Author":"Julien
Damond <julien.damond@gmail.com>","Depends":"R (>= 2.2.1), Biobase (>=
2.4.0)","Description":"These functions compute the k best pairs of genes used to
classify samples based on the relative rank of the genes expression within each
profile. A score based on the sensitivity and the specificity is calculated for
every possible pair. The k pairs with the highest score will be selected with the
restriction that a gene can appear in at most one pair. The value of k is either
set as a parameter chosen by the user or computed through crossvalidation. Other
functions related to the k-TSP are also available, for example the functions
prediction, summary, plot, etc. can be found in the package.","License":"GPL-
2","NeedsCompilation":"yes","Package":"ktspair","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"k-Top Scoring Pairs for Microarray
Classification","Version":"1.0"},"kulife":{"Author":"Claus Ekstrom
<ekstrom@sund.ku.dk>, Ib M. Skovgaard <ims@life.ku.dk>, Torben Martinussen
<tma@sund.ku.dk>","Description":"Provides various functions and data sets from
experiments at the Faculty of Life Sciences, University of Copenhagen. This package
will be discontinued and archived, and the functions and datasets will be
maintained and updated in the MESS package","License":"GPL-
2","NeedsCompilation":"no","Package":"kulife","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"lme4, XML","Title":"Datasets and functions from the (now
non-existing) Faculty of\nLife Sciences, University of Copenhagen","Version":"0.1-
14"},"kwb.hantush":{"Author":"Michael Rustler","Depends":"R (>= 3.0.0),
lattice","Description":"Calculation groundwater mounding beneath an infiltration
basin based on the Hantush (1967) equation
(http:\/\/doi.org\/10.1029\/WR003i001p00227). The correct implementation is shown
with a verification example based on a USGS report (page 25,
http:\/\/pubs.usgs.gov\/sir\/2010\/5102\/support\/sir2010-
5102.pdf).","Imports":"hydroGOF","License":"GPL-
2","NeedsCompilation":"no","Package":"kwb.hantush","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Calculation of Groundwater Mounding Beneath an
Infiltration\nBasin","URL":"http:\/\/kwb-
r.github.io\/kwb.hantush\/","Version":"0.2.1"},"kyotil":{"Author":"Youyi Fong
<yfong@fhcrc.org>, Krisztian Sebestyen <ksebestyen@gmail.com>","Depends":"R (>=
3.0.0)","Description":"A miscellaneous set of functions for printing, plotting,
kernels, etc. Additional contributors are acknowledged on individual function help
pages.","Imports":"methods","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"kyotil","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"RUnit, knitr, lme4, nlme, xtable, MASS, splines,
survival,\nabind","Title":"Utility Functions by Youyi, Krisz and
Others","Version":"2015.11-13"},"kza":{"Author":"Brian Close
<brian.close@gmail.com> and Igor Zurbenko
<IZurbenko@albany.edu>","Description":"Time Series Analysis including break
detection, spectral analysis, KZ Fourier Transforms.","License":"GPL-
3","NeedsCompilation":"yes","Package":"kza","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"polynom","Title":"Kolmogorov-Zurbenko Adaptive
Filters","Version":"4.0.0"},"kzft":{"Author":"Wei Yang <peterwyang@gmail.com> and
Igor Zurbenko\n<igorg.zurbenko@gmail.com>","Depends":"polynom","Description":"A
colletion of functions to implement Kolmogorov-Zurbenko\nFourier transform based
periodograms and smoothing methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"kzft","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"graphics","Title":"Kolmogorov-Zurbenko Fourier Transform
and Applications","Version":"0.17"},"kzs":{"Author":"Derek Cyr
<cyr.derek@gmail.com> and Igor Zurbenko <igorg.zurbenko@gmail.com>.","Depends":"R
(>= 2.8.0), graphics, lattice, stats","Description":"A spatial smoothing algorithm
based on convolutions of finite rectangular kernels that provides sharp resolution
in the presence of high levels of noise.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"kzs","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Kolmogorov-Zurbenko Spatial Smoothing and
Applications","Version":"1.4"},"l2boost":{"Author":"John Ehrlinger [aut, cre],
Hemant Ishwaran [aut]","Depends":"R (>= 2.14.0), MASS,
parallel","Description":"Efficient implementation of Friedman's boosting
algorithm\nwith l2-loss function and coordinate direction (design matrix\ncolumns)
basis functions.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"l2boost","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"l2boost - Friedman's boosting algorithm for regularized
linear\nregression","Version":"1.0"},"laGP":{"Author":"Robert B. Gramacy
<rbgramacy@chicagobooth.edu>","Depends":"R (>= 2.14)","Description":"Performs
approximate GP regression for large computer experiments and spatial datasets. The
approximation is based on finding small local designs for prediction
(independently) at particular inputs. OpenMP and SNOW parallelization are supported
for prediction over a vast out-of-sample testing set; GPU acceleration is also
supported for an important subroutine. OpenMP and GPU features may require special
compilation. An interface to lower-level (full) GP inference and prediction is
also provided, as are associated wrapper routines for blackbox optimization under
constraints via an augmented Lagrangian scheme, and large scale computer model
calibration.","Imports":"tgp,
parallel","License":"LGPL","NeedsCompilation":"yes","Package":"laGP","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Suggests":"mvtnorm, MASS, akima, lhs,
crs","Title":"Local Approximate Gaussian Process
Regression","URL":"http:\/\/bobby.gramacy.com\/r_packages\/laGP","Version":"1.2-
1"},"labdsv":{"Author":"David W. Roberts <droberts@montana.edu>","Depends":"R (>=
2.10), mgcv, MASS, cluster","Description":"A variety of ordination and community
analyses\nuseful in analysis of data sets in community ecology.\nIncludes many of
the common ordination methods, with\ngraphical routines to facilitate their
interpretation,\nas well as several novel analyses.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"labdsv","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"optpart","Title":"Ordination and Multivariate Analysis
for Ecology","URL":"http:\/\/ecology.msu.montana.edu\/labdsv\/R","Version":"1.8-
0"},"label.switching":{"Author":"Panagiotis Papastamoulis","Description":"The
Bayesian estimation of mixture models (and more general hidden Markov models)
suffers from the label switching phenomenon, making the MCMC output non-
identifiable. This package can be used in order to deal with this problem using
various relabelling algorithms.","Imports":"combinat, lpSolve","License":"GPL-
2","NeedsCompilation":"no","Package":"label.switching","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Relabelling MCMC Outputs of Mixture
Models","Version":"1.5"},"labeledLoop":{"Author":"Kohske
Takahashi","Depends":"R (>= 2.14)","Description":"Support labeled loop and escape
from nested
loop","License":"MIT","NeedsCompilation":"no","Package":"labeledLoop","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Title":"Labeled
Loop","Version":"0.1"},"labeling":{"Author":"Justin Talbot","Description":"Provides
a range of axis labeling algorithms","License":"MIT + file LICENSE |
Unlimited","NeedsCompilation":"no","Package":"labeling","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Axis Labeling","Version":"0.3"},"labelled":
{"Author":"Joseph Larmarange [aut, cre],\nDaniel Ludecke [ctb],\nHadley Wickham
[ctb]","Description":"Work with labelled data imported from\n'SPSS' or 'Stata' with
'haven' or 'foreign'.","Enhances":"memisc","License":"GPL-
3","NeedsCompilation":"no","Package":"labelled","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"haven, dplyr, testthat, knitr","Title":"Manipulating
Labelled
Data","URL":"https:\/\/github.com\/larmarange\/labelled","Version":"0.1.2"},"labelr
ank":{"Author":"Artur Aiguzhinov [cre],\nCarlos Soares [aut]","Depends":"R (>=
2.10)","Description":"An implementation of distance-based ranking algorithms to
predict rankings of labels. Two common algorithms are included: the naive Bayes
and the nearest neighbor algorithms.","Imports":"pdist","License":"GPL-
3","NeedsCompilation":"no","Package":"labelrank","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr","Title":"Predicting Rankings of
Labels","Version":"0.1"},"labeltodendro":{"Author":"Vahid PARTOVI NIA, Anthony
Davison, and Arpit Chaudhary","Depends":"R (>= 2.15.2)","Description":"The package
offers a dendrogram representation of series\nof labels, this is specially needed
in Markov chain Monte Carlo\nclustering. If you have a dendrogram in your mind you
can\neasily put series of meaningful labels in a matrix and heights\nin a vector,
then convert them to a dendrogram abject.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"labeltodendro","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Convert labels or tables to a
dendrogram","URL":"http:\/\/labeltodendro.r-forge.r-
project.org\/","Version":"1.3"},"labstatR":{"Author":"Stefano M.Iacus
<stefano.iacus@unimi.it> and Guido
Masarotto\n<guido@sirio.stat.unipd.it>","Depends":"R (>=
2.10)","Description":"Insieme di funzioni di supporto al volume \"Laboratorio
di\nStatistica con R\", Iacus-Masarotto, MacGraw-Hill Italia, 2006.\nThis package
contains sets of functions defined in \"Laboratorio\ndi Statistica con R\", Iacus-
Masarotto, MacGraw-Hill Italia,\n2006. Function names and docs are in italian as
2)","NeedsCompilation":"no","Package":"labstatR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Libreria Del Laboratorio Di Statistica Con
R","URL":"http:\/\/www.catalogo.mcgraw-hill.it\/catLibro.asp?
item_id=2958","Version":"1.0.8"},"labstats":{"Author":"Stanley E.
Lazic","Depends":"R (>= 2.10)","Description":"Contains data sets to accompany the
book \"Experimental Design for\nLaboratory Biologists: Maximising Information and
Improving Reproducibility\"\n(available mid 2016 from Cambridge University
Press).","License":"GPL-
3","NeedsCompilation":"no","Package":"labstats","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Data Sets for the Book \"Experimental Design for
Laboratory\nBiologists\"","URL":"https:\/\/github.com\/stanlazic\/labstats","Versio
n":"1.0"},"laeken":{"Author":"Andreas Alfons [aut, cre],\nJosef Holzer
[aut],\nMatthias Templ [aut]","Depends":"R (>= 2.10.0), boot,
MASS","Description":"Estimation of indicators on social exclusion and poverty, as
well\nas Pareto tail modeling for empirical income distributions.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"laeken","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Estimation of indicators on social exclusion and
poverty","Version":"0.4.6"},"laercio":{"Author":"Laercio Junio da Silva
<laerciojunio@yahoo.com.br>","Description":"The package contains functions to
compare and group means.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"laercio","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Duncan test, Tukey test and Scott-Knott
test","Version":"1.0-1"},"lakemorpho":{"Author":"Jeffrey W. Hollister [aut,
cre]","Depends":"R (>= 2.10), maptools","Description":"Lake morphometry metrics are
used by limnologists to understand,\namong other things, the ecological processes
in a lake. This\npackage provides the tools to calculate a typical suite of
these\nmetrics from an input elevation model and lake polygon.","Imports":"rgdal,
raster, rgeos, sp,
geosphere","License":"CC0","NeedsCompilation":"no","Package":"lakemorpho","Reposito
ry":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Lake morphometry in
R","URL":"http:\/\/www.github.com\/USEPA\/lakemorpho","Version":"1.0"},"laketemps":
{"Author":"Jordan S Read","Depends":"R (>= 3.0),","Description":"Lake temperature
records, metadata, and climate drivers for 291 global lakes during the time period
1985-2009. Temperature observations were collected using satellite and in situ
methods. Climatic drivers and geomorphometric characteristics were also compiled
and are included for each lake. Data are part of the associated publication from
the Global Lake Temperature Collaboration project
(http:\/\/www.laketemperature.org). See citation('laketemps') for dataset
attribution.","Imports":"dplyr,
reshape2","License":"CC0","NeedsCompilation":"no","Package":"laketemps","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Lake Temperatures Collected by
Situ and Satellite Methods from\n1985-2009","Version":"0.5.1"},"lamW":
{"Author":"Avraham Adler [aut, cph, cre]","Description":"Implements both real-
valued branches of the Lambert-W function, also known as the product logarithm,
without the need for installing the entire GSL.","Imports":"Rcpp (>=
LICENSE","NeedsCompilation":"yes","Package":"lamW","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat","Title":"Lambert-W
Function","URL":"https:\/\/bitbucket.org\/aadler\/lamw","Version":"1.1.0"},"lambda.
r":{"Author":"Brian Lee Yung Rowe","Depends":"R (>= 3.0.0)","Description":"A
language extension to efficiently write functional programs in R. Syntax extensions
include multi-part function definitions, pattern matching, guard statements, built-
in (optional) type safety.","License":"LGPL-
3","NeedsCompilation":"no","Package":"lambda.r","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"RUnit","Title":"Modeling Data with Functional
Programming","Version":"1.1.7"},"lambda.tools":{"Author":"Brian Lee Yung
Rowe","Depends":"R (>= 3.0.0)","Description":"Provides tools that manipulate and
transform data using methods\nand techniques consistent with functional
programming. The idea is that\nthrough the use of these tools, a program can be
reasoned about insomuch\nthat the implementation can be proven to be equivalent to
the mathematical\nmodel.","Imports":"lambda.r (>= 1.1.6)","License":"LGPL-
3","NeedsCompilation":"no","Package":"lambda.tools","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat (>= 0.2)","Title":"Tools for Modeling
Data with Functional Programming","Version":"1.0.7"},"landest":{"Author":"Layla
Parast","Description":"Provides functions to estimate survival and a treatment
effect using a landmark estimation approach.","Imports":"stats,
survival","License":"GPL","NeedsCompilation":"no","Package":"landest","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Title":"Landmark Estimation of Survival and
Treatment Effect","Version":"1.0"},"landpred":{"Author":"Layla
Parast","Description":"This package includes functions for landmark prediction of a
survival outcome incorporating covariate and short-term event information. For more
information about landmark prediction please see: Parast, Layla, Su-Chun Cheng, and
Tianxi Cai. Incorporating short-term outcome information to predict long-term
survival with discrete markers. Biometrical Journal 53.2 (2011): 294-
307.","Imports":"survival","License":"GPL","NeedsCompilation":"no","Package":"landp
red","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Landmark
Prediction of a Survival Outcome","Version":"1.0"},"landsat":{"Author":"Sarah
Goslee","Depends":"R (>= 2.15.0), rgdal, sp (>= 1.0)","Description":"Processing of
Landsat or other multispectral satellite\nimagery. Includes relative normalization,
image-based\nradiometric correction, and topographic correction
options.","Imports":"lmodel2, mgcv","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"landsat","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Radiometric and topographic correction of satellite
imagery","Version":"1.0.8"},"landsat8":{"Author":"Alexandre dos
Santos","Depends":"R (>= 3.1.2)","Description":"Functions for converted Landsat 8
multispectral satellite imagery\nrescaled to the top of atmosphere (TOA)
reflectance, radiance\nand\/or at satellite brightness temperature using
radiometric\nrescaling coefficients provided in the metadata file (MTL
file).","Imports":"rgdal, sp","License":"GPL-
2","NeedsCompilation":"no","Package":"landsat8","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Landsat 8 Imagery Rescaled to Reflectance, Radiance
and\/or\nTemperature","Version":"0.1-9"},"languageR":{"Author":"R. H.
Baayen","Depends":"R(>= 3.0.2)","Description":"Data sets exemplifying statistical
methods, and some\nfacilitatory utility functions used in \"Analyzing
Linguistic\nData: A practical introduction to statistics using R\",\nCambridge
University Press, 2008.","Imports":"methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"languageR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"cluster, e1071, rms, Hmisc, MASS, rpart, lattice,
zipfR,\nlme4, multcomp, lmerTest, optimx","Title":"Data sets and functions
with \"Analyzing Linguistic Data: A\npractical introduction to
statistics\"","Version":"1.4.1"},"lar":{"Author":"Richard Zijdeman [aut,
cre],\nJosemiguel Lana-Berasain [ctb]","Description":"This package is intended for
researchers studying historical labour relations (see
http:\/\/www.historyoflabourrelations.org). The package allows for easy access of
excel files in the standard defined by the Global Collaboratory on the History of
Labour Relations. The package also allows for visualisation of labour relations
according to the Collaboratory's format.","Imports":"data.table, grid, treemap,
xlsx","License":"GPL-
3","NeedsCompilation":"no","Package":"lar","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"History of labour relations package","Version":"0.1-
2"},"lars":{"Author":"Trevor Hastie <hastie@stanford.edu> and Brad
Efron\n<brad@stat.stanford.edu>","Depends":"R (>= 2.10)","Description":"Efficient
procedures for fitting an entire lasso sequence\nwith the cost of a single least
squares fit. Least angle\nregression and infinitesimal forward stagewise regression
are\nrelated to the lasso, as described in the paper below.","License":"GPL-
2","NeedsCompilation":"yes","Package":"lars","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Least Angle Regression, Lasso and Forward
Stagewise","URL":"http:\/\/www-
stat.stanford.edu\/~hastie\/Papers\/#LARS","Version":"1.2"},"laser":{"Author":"Dan
Rabosky, Klaus Schliep","Depends":"R(>= 2.6), ape, geiger (>= 1.99-
3)","Description":"laser implements maximum likelihood methods based on the\nbirth-
death process to test whether diversification rates have\nchanged over time and
whether rates vary among lineages.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"laser","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Likelihood Analysis of Speciation\/Extinction Rates
from\nPhylogenies","Version":"2.4-1"},"lasso2":{"Author":"Justin Lokhorst, Bill
Venables and Berwin Turlach;\nport to R, tests etc: Martin Maechler
<maechler@stat.math.ethz.ch>","Depends":"R (>= 2.15.0)","Description":"Routines and
documentation for solving regression problems\nwhile imposing an L1 constraint on
the estimates, based on\nthe algorithm of Osborne et al. (1998)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"lasso2","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"L1 constrained estimation aka
`lasso'","URL":"http:\/\/www.maths.uwa.edu.au\/~berwin\/software\/lasso.html","Vers
ion":"1.2-19"},"lassoscore":{"Author":"Arie Voorman
<arie.voorman@gmail.com>","Depends":"R (>= 2.10), glasso, glmnet,
Matrix","Description":"Use the lasso regression method to perform approximate
inference\nin high dimensions, by penalizing the effects of nuisance
2)","NeedsCompilation":"no","Package":"lassoscore","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"covTest, lars","Title":"High-Dimensional Inference
with the Penalized Score Test","Version":"0.6"},"lassoshooting":{"Author":"Tobias
Abenius <Tobias.Abenius@Chalmers.se>","Depends":"R (>= 2.12.0)","Description":"L1
regularized regression (Lasso) solver using the Cyclic\nCoordinate Descent
algorithm aka Lasso Shooting is fast. This\nimplementation can choose which
coefficients to penalize. It\nsupport coefficient-specific penalities and it can
take X'X and\nX'y instead of X and y.","License":"LGPL-
3","NeedsCompilation":"yes","Package":"lassoshooting","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"L1 regularized regression (Lasso) solver using the
Cyclic\nCoordinate Descent algorithm aka Lasso Shooting","Version":"0.1.5-
1"},"lasvmR":{"Author":"Aydin Demircioglu","Description":"This is a simple wrapper
for the LASVM Solver (see http:\/\/leon.bottou.org\/projects\/lasvm). LASVM is
basically an online variant of the SMO solver.","Imports":"Rcpp (>= 0.11.6),
checkmate (>= 1.5.1)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"lasvmR","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr, testthat","Title":"A Simple Wrapper for the
LASVM
Solver","URL":"http:\/\/github.com\/aydindemircioglu\/lasvmR","Version":"0.1.2"},"l
atdiag":{"Author":"Michael Dewey","Description":"A graph\nproposed by Rosenbaum is
useful\nfor checking some properties of various\nsorts of latent scale, this
program generates commands\nto obtain the graph using 'dot' from
'graphviz'.","License":"GPL-
2","NeedsCompilation":"no","Package":"latdiag","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Draws Diagrams Useful for Checking Latent
Scales","Version":"0.2-2"},"latentnet":{"Author":"Pavel N. Krivitsky [aut,
cre],\nMark S. Handcock [aut],\nSusan M. Shortreed [ctb],\nJeremy Tantrum
[ctb],\nPeter D. Hoff [ctb],\nLi Wang [ctb],\nKirk Li [ctb]","Depends":"R (>=
2.8.0), statnet.common, network, ergm (>= 3.2.0)","Description":"Fit and simulate
latent position and cluster models for statistical networks.","Imports":"sna,
mvtnorm, abind, coda (>= 0.17.1), tools","License":"GPL-3 + file
LICENSE","NeedsCompilation":"yes","Package":"latentnet","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"KernSmooth, snowFT, rgl, heplots, rlecuyer,
ergm.userterms","Title":"Latent Position and Cluster Models for Statistical
Networks","URL":"http:\/\/www.statnet.org","Version":"2.7.1"},"latex2exp":
{"Author":"Stefano Meschiari [aut, cre]","Description":"Parses and converts LaTeX
math formulas to R's plotmath\nexpressions, used to enter mathematical formulas and
symbols to be rendered as\ntext, axis labels, etc. throughout R's plotting
system.","Imports":"stringr, magrittr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"latex2exp","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat, knitr, ggplot2, plyr,
rmarkdown","Title":"Use LaTeX Expressions in
Plots","URL":"http:\/\/github.com\/stefano-
meschiari\/latex2exp","Version":"0.4.0"},"lattice":{"Author":"Deepayan Sarkar
<deepayan.sarkar@r-project.org>","Depends":"R (>= 3.0.0)","Description":"A powerful
and elegant high-level data visualization\nsystem inspired by Trellis graphics,
with an emphasis on\nmultivariate data. Lattice is sufficient for typical graphics
needs,\nand is also flexible enough to handle most nonstandard requirements.\nSee ?
Lattice for an introduction.","Enhances":"chron","Imports":"grid, grDevices,
2)","NeedsCompilation":"yes","Package":"lattice","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"KernSmooth, MASS","Title":"Trellis Graphics for
R","URL":"http:\/\/lattice.r-forge.r-project.org\/","Version":"0.20-
33"},"latticeDensity":{"Author":"Ronald Barry
<rpbarry@alaska.edu>","Depends":"splancs, spdep, spatstat,
spam","Description":"This package contains functions that compute the\nlattice-
based density estimator of Barry and McIntyre, which\naccounts for point processes
in two-dimensional regions with\nirregular boundaries and holes. The package also
implements\ntwo-dimensional non-parametric regression for similar
regions.","License":"GPL-
2","NeedsCompilation":"no","Package":"latticeDensity","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Density estimation and nonparametric regression on
irregular\nregions","URL":"www.r-project.org","Version":"1.0.7"},"latticeExtra":
{"Author":"Deepayan Sarkar <deepayan.sarkar@r-project.org>, Felix Andrews
<felix@nfrac.org>","Depends":"R (>= 2.10.0), lattice,
RColorBrewer","Description":"Building on the infrastructure provided by the
lattice\npackage, this package provides several new high-level\nfunctions and
methods, as well as additional utilities\nsuch as panel and axis annotation
functions.","Imports":"grid, stats, utils, grDevices","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"latticeExtra","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"maps, mapproj, deldir, tripack, zoo, MASS,
quantreg, mgcv","Title":"Extra Graphical Utilities Based on
Lattice","URL":"http:\/\/latticeextra.r-forge.r-project.org\/","Version":"0.6-
28"},"lava":{"Author":"Klaus K. Holst","Depends":"R (>=
2.15)","Description":"Estimation and simulation of latent variable
models.","Imports":"numDeriv, methods, graphics, grDevices, utils,
3","NeedsCompilation":"no","Package":"lava","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"mets (>= 1.1), graph, data.table, Rgraphviz, igraph (>=
0.6),\nMatrix, KernSmooth, lme4, geepack, gof (>= 0.9), foreach,\nquantreg, rgl,
fields, survival, testthat (>= 0.11), ascii, zoo","Title":"Latent Variable
Models","URL":"https:\/\/github.com\/kkholst\/lava","Version":"1.4.3"},"lava.tobit"
:{"Author":"Klaus K. Holst","Depends":"R (>= 2.14), lava (>= 1.1), mvtnorm,
survival","Description":"lava plugin allowing combinations of left and
right\ncensored and binary outcomes","License":"GPL-
3","NeedsCompilation":"no","Package":"lava.tobit","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"LVM with censored and binary outcomes","Version":"0.4-
7"},"lavaan":{"Author":"Yves Rosseel [aut, cre],\nDaniel Oberski [ctb],\nJarrett
Byrnes [ctb],\nLeonard Vanbrabant [ctb],\nVictoria Savalei [ctb],\nEd Merkle
[ctb],\nMichael Hallquist [ctb],\nMijke Rhemtulla [ctb],\nMyrsini Katsikatsou
[ctb],\nMariska Barendse [ctb]","Depends":"R(>= 3.1.0), methods","Description":"Fit
a variety of latent variable models, including confirmatory\nfactor analysis,
structural equation modeling and latent growth curve models.","Imports":"stats4,
stats, utils, graphics, MASS, mnormt, pbivnorm,\nquadprog","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"lavaan","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"lavaan.survey, semPlot, semTools,
simsem","Title":"Latent Variable
Analysis","URL":"http:\/\/lavaan.org","Version":"0.5-20"},"lavaan.shiny":
{"Author":"William
Kyle Hamilton <kyle.hamilton@gmail.com>","Depends":"R (>=
3.0.3)","Description":"Interactive shiny application for working with different
kinds of\nlatent variable analysis, with the 'lavaan' package. Graphical output for
models\nare provided and different estimators are supported.","Imports":"shiny,
shinyAce, psych, lavaan, semPlot","License":"GPL-
3","NeedsCompilation":"no","Package":"lavaan.shiny","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Latent Variable Analysis with
Shiny","URL":"https:\/\/github.com\/kylehamilton\/lavaan.shiny","Version":"1.0"},"l
avaan.survey":{"Author":"Daniel Oberski","Depends":"R(>= 2.14.0), lavaan(>= 0.5-
20), survey(>= 3.30-3)","Description":"Fit structural equation models (SEM)
including factor analysis,\nmultivariate regression models with latent variables
and many other latent\nvariable models while correcting estimates, standard errors,
and\nchi-square-derived fit measures for a complex sampling design.\nIncorporate
clustering, stratification, sampling weights, and\nfinite population corrections
into a SEM analysis.\nWrapper around packages lavaan and
survey.","Imports":"MASS","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"lavaan.survey","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat, mice, mitools","Title":"Complex Survey
Structural Equation Modeling
(SEM)","URL":"http:\/\/daob.nl\/","Version":"1.1.3"},"lawn":{"Author":"Scott
Chamberlain [aut, cre],\nJeff Hollister [aut]","Description":"Client for 'Turfjs'
(http:\/\/turfjs.org\/) for\n'geospatial' analysis. The package revolves around
using 'GeoJSON'\ndata. Functions are included for creating 'GeoJSON' data
objects,\nmeasuring aspects of 'GeoJSON', and combining, transforming,\nand
creating random 'GeoJSON' data objects.","Enhances":"maps,
geojsonio","Imports":"methods, stats, utils, V8, jsonlite, magrittr","License":"MIT
+ file
LICENSE","NeedsCompilation":"no","Package":"lawn","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat, knitr, leaflet","Title":"Client for
'Turfjs' for 'Geospatial'
Analysis","URL":"https:\/\/github.com\/ropensci\/lawn","Version":"0.1.6"},"lawstat"
:{"Author":"(in alphabetical order)\nJoseph L. Gastwirth <jlgast@gwu.edu>;\nYulia
R. Gel <ygl@utdallas.edu>;\nW. L. Wallace Hui <wlwhui@uwaterloo.ca>;\nVyacheslav
Lyubchich <lyubchic@cbl.umces.edu>;\nWeiwen Miao <miao@macalester.edu>;\nKimihiro
Noguchi <kinoguchi@ucdavis.edu>","Depends":"R (>= 2.6.0), Hmisc, Kendall, mvtnorm,
VGAM","Description":"Statistical tests widely utilized in biostatistics, public
policy, and law. Along with the well-known tests for equality of means and
variances, randomness,\nmeasures of relative variability etc, the package contains
new robust tests of symmetry,\nomnibus and directional tests of normality, and
their graphical counterparts such as\nRobust QQ plot; a robust trend tests for
variances etc. All implemented tests and methods\nare illustrated by simulations
and real-life examples from legal statistics, economics,\nand
biostatistics.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"lawstat","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"fBasics","Title":"Tools for Biostatistics, Public
Policy, and Law","Version":"3.0"},"lazy":{"Author":"Mauro Birattari
<mbiro@ulb.ac.be> and Gianluca Bontempi\n<gbonte@ulb.ac.be>","Description":"By
combining constant, linear, and quadratic local models,\nlazy estimates the value
of an unknown multivariate function on\nthe basis of a set of possibly noisy
samples of the function\nitself. This implementation of lazy learning
automatically\nadjusts the bandwidth on a query-by-query basis through a\nleave-
one-out cross-validation.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"lazy","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Lazy Learning for Local
Regression","URL":"http:\/\/iridia.ulb.ac.be\/~lazy","Version":"1.2-
15"},"lazyData":{"Author":"Bill Venables","Depends":"R (>=
2.15.0)","Description":"Supplies a LazyData facility for packages which have
data\nsets but do not provide LazyData. A single function is\nis included,
requireData, which is a drop-in replacement for\nbase::require, but carrying the
additional\nfunctionality. By default, it suppresses package\nstartup messages as
well. See argument 'reallyQuitely'.","Imports":"utils","License":"GPL-
2","NeedsCompilation":"no","Package":"lazyData","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"mgcv","Title":"A LazyData
Facility","Version":"1.0.3"},"lazyWeave":{"Author":"Benjamin Nutter","Depends":"R
(>= 2.10.0)","Description":"Provides the functionality to write LaTeX code from
within R\nwithout having to learn LaTeX. Functionality also exists to create
HTML\nand Markdown code. While the functionality still exists to write\ncomplete
documents with lazyWeave, it is generally easier to do so with\nwith markdown and
knitr. lazyWeave's main strength now is the ability\nto design custom and complex
tables for reporting results.","Imports":"Hmisc (>= 3.14-
6)","License":"GPL","NeedsCompilation":"no","Package":"lazyWeave","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Suggests":"testthat","Title":"LaTeX Wrappers
for R Users","Version":"3.0.1"},"lazyeval":{"Author":"Hadley Wickham [aut,
cre],\nRStudio [cph]","Depends":"R (>= 3.1.0)","Description":"A disciplined
approach to non-standard evaluation.","License":"GPL-
3","NeedsCompilation":"yes","Package":"lazyeval","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr, rmarkdown (>= 0.2.65), microbenchmark,
testthat","Title":"Lazy (Non-Standard) Evaluation","Version":"0.1.10"},"lazysql":
{"Author":"Uwe Block [aut, cre]","Description":"\nHelper functions to build SQL
statements\nfor dbGetQuery or dbSendQuery under program control.\nThey are intended
to increase speed of coding and\nto reduce coding errors. Arguments are carefully
checked,\nin particular SQL identifiers such as names of tables or columns.\nMore
patterns will be added as required.","Imports":"checkmate (>= 1.7.2), magrittr,
plyr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"lazysql","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat","Title":"Lazy SQL
Programming","URL":"https:\/\/github.com\/UweBlock\/lazysql","Version":"0.1.3"},"lb
a":{"Author":"Enio G. Jelihovschi <eniojelihovs@gmail.com> and\nIvan Bezerra
Allaman <ivanalaman@gmail.com>","Depends":"R (>= 3.1.2), MASS, alabama, plotrix,
ca","Description":"Latent budget analysis is a method for the analysis of a two-way
contingency table with an exploratory variable and a response variable. It is
specially designed for compositional data.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"lba","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Latent Budget Analysis for Compositional
Data","Version":"1.2"},"lbfgs":{"Author":"Antonio Coppola [aut, cre, cph],\nBrandon
Stewart [aut, cph],\nNaoaki Okazaki [aut, cph],\nDavid Ardia [ctb, cph],\nDirk
Eddelbuettel [ctb, cph],\nKatharine Mullen [ctb, cph],\nJorge Nocedal [ctb,
cph]","Description":"A wrapper built around the libLBFGS optimization library by
Naoaki Okazaki. The lbfgs package implements both the Limited-memory Broyden-
Fletcher-Goldfarb-Shanno (L-BFGS) and the Orthant-Wise Quasi-Newton Limited-Memory
(OWL-QN) optimization algorithms. The L-BFGS algorithm solves the problem of
minimizing an objective, given its gradient, by iteratively computing
approximations of the inverse Hessian matrix. The OWL-QN algorithm finds the
optimum of an objective plus the L1-norm of the problem's parameters. The package
offers a fast and memory-efficient implementation of these optimization routines,
which is particularly suited for high-dimensional problems.","Imports":"Rcpp (>=
0.11.2)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"lbfgs","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Limited-memory BFGS
Optimization","Version":"1.2.1"},"lbfgsb3":{"Author":"John C Nash [aut,
cre],\nCiyou Zhu [aut],\nRichard Byrd [aut],\nJorge Nocedal [aut],\nJose Luis
Morales [aut]","Depends":"R (>= 2.15.0), numDeriv","Description":"Interfacing to
Nocedal et al. L-BFGS-B.3.0 (2011) limited\nmemory BFGS minimizer with bounds on
parameters.","License":"GPL-
2","NeedsCompilation":"yes","Package":"lbfgsb3","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Limited Memory BFGS Minimizer with Bounds on
Parameters","Version":"2015-2.13"},"lbiassurv":{"Author":"Pierre-Jerome Bergeron
and Vahid Partovi Nia","Depends":"R (>= 2.15.0), actuar","Description":"The package
offers various length-bias corrections to\nsurvival curve
2)","NeedsCompilation":"yes","Package":"lbiassurv","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Length-biased correction to survival curve
estimation","URL":"http:\/\/lbiassurv.r-forge.r-
project.org\/","Version":"1.1"},"lcda":{"Author":"Michael Buecker","Depends":"R (>=
2.6.0), poLCA","Description":"Local Discrimination via Latent Class
Models","License":"GPL","NeedsCompilation":"no","Package":"lcda","Repository":"http
:\/\/cran.csiro.au\/src\/contrib","Title":"Latent Class Discriminant
Analysis","Version":"0.3"},"lcmm":{"Author":"Cecile Proust-Lima, Viviane Philipps,
Amadou Diakite and Benoit Liquet","Depends":"R (>= 2.14.0), survival (>= 2.37-
2)","Description":"Estimation of various extensions of the mixed models including
latent class mixed models, joint latent latent class mixed models and mixed models
for curvilinear univariate or multivariate longitudinal outcomes using a maximum
likelihood estimation method.","License":"GPL (>=
2.0)","NeedsCompilation":"yes","Package":"lcmm","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Extended Mixed Models Using Latent Classes and Latent
Processes","Version":"1.7.5"},"lcopula":{"Author":"Leo Belzile
[aut, cre],\nChristian Genest [aut, ctb],\nAlexander J. McNeil [ctb],\nJohanna G.
Neslehova [ctb]","Depends":"copula (>= 0.999-12), R (>=
2.12.0)","Description":"Collections of functions allowing random number generations
and estimation of Liouville copulas.","Imports":"Rcpp (>= 0.11.4), pcaPP, utils,
3","NeedsCompilation":"yes","Package":"lcopula","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Liouville Copulas","Version":"0.205"},"lctools":
{"Author":"Stamatis Kalogirou [aut, cre]","Depends":"R (>= 3.2.1), reshape (>=
0.8.5), weights (>= 0.80), pscl (>=\n1.4.9), MASS (>= 7.3-43)","Description":"The
main purpose of lctools is to provide researchers and educators with easy-to-
learn\nuser friendly tools for calculating key spatial statistics and to apply
simple as well as\nadvanced methods of spatial analysis in real data. These
include: Local Pearson and\nGeographically Weighted Pearson Correlation
Coefficients, Spatial Inequality Measures\n(Gini, Spatial Gini, LQ, Focal LQ),
Spatial Autocorrelation (Global and Local Moran's I),\nseveral Geographically
Weighted Regression techniques and other Spatial Analysis tools\n(other
geographically weighted statistics). This package also contains functions
for\nmeasuring the significance of each statistic calculated, mainly based on Monte
Carlo simulations.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"lctools","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr, sp","Title":"Local Correlation, Spatial
Inequalities, Geographically Weighted\nRegression and Other
Tools","URL":"http:\/\/gisc.gr","Version":"0.2-4"},"lda":{"Author":"Jonathan
Chang","Depends":"R (>= 2.10)","Description":"Implements latent Dirichlet
allocation (LDA)\nand related models. This includes (but is not limited\nto) sLDA,
corrLDA, and the mixed-membership stochastic\nblockmodel. Inference for all of
these models is\nimplemented via a fast collapsed Gibbs sampler written\nin C.
Utility functions for reading\/writing data\ntypically used in topic models, as
well as tools for\nexamining posterior distributions are also
included.","License":"LGPL","NeedsCompilation":"yes","Package":"lda","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Suggests":"Matrix, reshape2, ggplot2 (>=
1.0.0), penalized, nnet","Title":"Collapsed Gibbs Sampling Methods for Topic
Models","Version":"1.4.2"},"ldamatch":{"Author":"Kyle Gorman [aut, cre],\nGeza Kiss
[ctb]","Depends":"R (>= 3.0.0)","Description":"Performs group matching by backward
elimination using linear discriminant analysis.","Imports":"RUnit, data.table,
foreach, kSamples, MASS, entropy,\niterators, iterpc","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"ldamatch","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"knitr","Title":"Multivariate Condition Matching
by Backwards Elimination Using\nLinear Discriminant
Analysis","Version":"0.6.3"},"ldatuning":{"Author":"Murzintcev Nikita [aut,
cre]","Description":"For this first version only metrics to estimate the best
fitting\nnumber of topics are implemented.","Imports":"parallel, topicmodels, slam,
Rmpfr, ggplot2, reshape2, scales,\ngrid","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"ldatuning","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"knitr","Title":"Tuning of the LDA Models
Parameters","URL":"https:\/\/github.com\/nikita-
moor\/ldatuning","Version":"0.1.0"},"ldbounds":{"Author":"Charlie Casper and Oscar
A. Perez. Based on FORTRAN\nprogram ld98.","Description":"Computations related to
group sequential boundaries.\nIncludes calculation of bounds using the Lan-
DeMets\nalpha spending function approach.","Imports":"lattice","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ldbounds","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Lan-DeMets Method for Group Sequential
Boundaries","Version":"1.1-1"},"ldlasso":{"Author":"Samuel G. Younkin","Depends":"R
(>= 2.6.0), GenABEL, quadprog","Description":"ldlasso requires data be of class
gwaa.data from the the\npackage GenABEL","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ldlasso","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"LD LASSO Regression for SNP Association
Study","Version":"3.2"},"ldr":{"Author":"Kofi Placid Adragni, Andrew
Raim","Depends":"R (>= 2.10), GrassmannOptim, Matrix","Description":"Functions,
methods, and data sets for fitting likelihood-based dimension reduction in
regression, using principal fitted components (pfc), likelihood acquired directions
(lad), covariance reducing models (core).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ldr","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Methods for likelihood-based dimension reduction in
regression","URL":"http:\/\/www.jstatsoft.org\/v61\/i03\/","Version":"1.3.3"},"lead
erCluster":{"Author":"Taylor B. Arnold","Description":"The leader clustering
algorithm provides\na means for clustering a set of data points. Unlike many other
clustering\nalgorithms it does not require the user to specify the number of
clusters,\nbut instead requires the approximate radius of a cluster as its
primary\ntuning parameter. The package provides a fast implementation of
this\nalgorithm in n-dimensions using Lp-distances (with special cases for
p=1,2,\nand infinity) as well as for spatial data using the Haversine\nformula,
which takes latitude\/longitude pairs as inputs and clusters\nbased on great circle
distances.","License":"LGPL-
2","NeedsCompilation":"yes","Package":"leaderCluster","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Leader Clustering
Algorithm","Version":"1.2"},"leaflet":{"Author":"Joe Cheng [aut, cre],\nYihui Xie
[aut],\nHadley Wickham [ctb],\njQuery Foundation and contributors [ctb, cph]
(jQuery library),\nVladimir Agafonkin [ctb, cph] (Leaflet library),\nCloudMade
[cph] (Leaflet library),\nLeaflet contributors [ctb] (Leaflet library),\nLeaflet
Providers contributors [ctb, cph] (Leaflet Providers plugin),\nRStudio
[cph]","Description":"Create and customize interactive maps using the 'Leaflet'
JavaScript\nlibrary and the 'htmlwidgets' package. These maps can be used directly
from\nthe R console, from 'RStudio', in Shiny apps and R Markdown
documents.","Imports":"base64enc, grDevices, htmlwidgets, htmltools,
magrittr,\nmarkdown, methods, png, RColorBrewer, raster, scales (>=\n0.2.5), sp,
stats, utils","License":"GPL-3 | file
LICENSE","NeedsCompilation":"no","Package":"leaflet","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"knitr, maps, shiny, testit (>= 0.4), rgdal, R6,
RJSONIO","Title":"Create Interactive Web Maps with the JavaScript
'Leaflet'\nLibrary","URL":"http:\/\/rstudio.github.io\/leaflet\/","Version":"1.0.1"
},"leafletR":{"Author":"Christian Graul, with contributions from Francois
Guillem","Depends":"R (>= 3.0.0)","Description":"Display your spatial data on
interactive web-maps using the open-source JavaScript library Leaflet. 'leafletR'
provides basic web-mapping functionality to combine vector data and online map
tiles from different sources. See <http:\/\/leafletjs.com> for more information on
Leaflet.","Imports":"brew, grDevices, jsonlite, methods, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"leafletR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"httr, rgdal, sp","Title":"Interactive Web-Maps Based
on the Leaflet JavaScript
Library","URL":"https:\/\/github.com\/chgrl\/leafletR","Version":"0.4-0"},"leapp":
{"Author":"Yunting Sun <yunting.sun@gmail.com> , Nancy
R.Zhang\n<nzhang@stanford.edu>, Art B.Owen <owen@stanford.edu>","Depends":"R (>=
3.1.1), sva, MASS, corpcor","Description":"These functions take a gene expression
value matrix, a\nprimary covariate vector, an additional known covariates\nmatrix.
A two stage analysis is applied to counter the effects\nof latent variables on the
rankings of hypotheses. The\nestimation and adjustment of latent effects are
proposed by\nSun, Zhang and Owen (2011). \"leapp\" is developed in the\ncontext of
microarray experiments, but may be used as a general\ntool for high throughput data
sets where dependence may be\ninvolved.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"leapp","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"latent effect adjustment after primary
projection","Version":"1.2"},"leaps":{"Author":"Thomas Lumley
<tlumley@u.washington.edu> using Fortran code by\nAlan
Miller","Description":"Regression subset selection including exhaustive
search","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"leaps","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"biglm","Title":"regression subset
selection","Version":"2.9"},"learNN":{"Author":"Bastiaan Quast [aut,
cre]","Depends":"R (>= 2.10.0)","Description":"Implementations of several basic
neural network concepts in R, as based on posts on
\\url{http:\/\/qua.st\/}.","License":"GPL-
3","NeedsCompilation":"no","Package":"learNN","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat","Title":"Examples of Neural
Networks","Version":"0.2.0"},"learningr":{"Author":"Richie
Cotton","Description":"Crabs in the English channel, deer skulls,
English\nmonarchs, half-caste Manga characters, Jamaican cities,\nShakespeare's The
Tempest, drugged up cyclists and sexually\ntransmitted
diseases.","Imports":"plyr","License":"Unlimited","NeedsCompilation":"no","Package"
:"learningr","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"knitr"
,"Title":"Data and functions to accompany the book \"Learning
R\"","Version":"0.29"},"learnstats":{"Author":"Daniel Walter [aut,
cre]","Depends":"R (>= 3.1.0), ggplot2","Description":"Allows students to use R as
an interactive educational environment\nfor statistical concepts, ranging from p-
values to confidence intervals\nto stability
in time series.","Imports":"shiny,
Rcmdr","License":"GPL","NeedsCompilation":"no","Package":"learnstats","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Title":"An Interactive Environment for
Learning Statistics","Version":"0.1.1"},"lefse":{"Author":"Nathan G.
Swenson","Depends":"R (>= 2.10)","Description":"Utilizing phylogenetic and
functional information for the analyses of ecological datasets. The analyses
include methods for quantifying the phylogenetic and functional diversity of
assemblages.","Imports":"ape, picante, geiger, fBasics, SDMTools,
vegan","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"lefse","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Phylogenetic and Functional Analyses for
Ecology","Version":"0.1"},"leiv":{"Author":"David Leonard [aut, cre]","Depends":"R
(>= 2.9.0)","Description":"Estimate the slope and intercept of a bivariate\nlinear
relationship by calculating a posterior density\nthat is invariant to interchange
and scaling of the\ncoordinates.","Imports":"methods, stats,
2)","NeedsCompilation":"no","Package":"leiv","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"grDevices","Title":"Bivariate Linear Errors-In-Variables
Estimation","URL":"http:\/\/www.r-project.org","Version":"2.0-7"},"lessR":
{"Author":"David W. Gerbing, School of Business Administration, Portland State
University","Depends":"R (>= 2.15.0)","Description":"Each function accomplishes the
work of several or more standard R functions. For example, two function calls,
Read() and CountAll(), read the data and generate summary statistics for all
variables in the data frame, plus histograms and bar charts as appropriate. Other
functions provide for descriptive statistics, a comprehensive regression analysis,
analysis of variance and t-test, plotting, bar chart, histogram, box plot, density
curves, calibrated power curve, reading multiple data formats with the same
function call, variable labels, color themes, and a built-in help system. A
confirmatory factor analysis of multiple indicator measurement models is available,
as are pedagogical routines for data simulation such as for the Central Limit
Theorem. Compatible with 'RStudio' and 'knitr' including generation of R markdown
instructions for interpretative output.","Imports":"graphics, grDevices, stats,
utils, ellipse, leaps, MBESS,\nforeign, sas7bdat, readxl, triangle","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"lessR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Less Code, More Results","Version":"3.4.6"},"lestat":
{"Author":"Petter Mostad <mostad@chalmers.se>","Depends":"R (>= 1.8.0), stats,
MASS","Description":"This package contains some simple objects and functions to
do\nstatistics using linear models and a Bayesian framework.","License":"GPL-
2","NeedsCompilation":"no","Package":"lestat","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"A package for LEarning
STATistics","Version":"1.8"},"letsR":{"Author":"Bruno Vilela & Fabricio
Villalobos","Depends":"R (>= 2.10), raster, maps","Description":"R functions for
handling, processing, and analyzing geographic\ndata on species' distributions and
environmental variables as well as species'\ndescription and conservation
information.","Imports":"XML, geosphere, fields, maptools, sp, rgdal, rgeos,
2","NeedsCompilation":"no","Package":"letsR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat","Title":"Tools for Data Handling and Analysis
in Macroecology","URL":"\nhttp:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/2041-
210X.12401\/abstract,\nhttps:\/\/github.com\/macroecology\/letsR","Version":"2.4"},
"lettercase":{"Author":"Christopher Brown [aut, cre],\nDecision Patterns
[cph]","Depends":"R (>= 3.1.0), stringr (>= 1.0.0)","Description":"Utilities for
formatting strings and character\nvectors to for capitalization, word break and
white space. Supported formats\nare: snake_case, spine-case, camelCase, PascalCase,
Title Case, UPPERCASE,\nlowercase, Sentence case or combinations thereof.
'lettercase' strives to\nprovide a simple, consistent, intuitive and high
performing interface.","License":"GPL-2 | file
LICENSE","NeedsCompilation":"no","Package":"lettercase","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"testthat, knitr, magrittr (>=
1.5)","Title":"Utilities for Formatting Strings with Consistent
Capitalization,\nWord Breaks and White Space","Version":"0.13.1"},"lfactors":
{"Author":"Paul Bailey [aut, cre]","Depends":"R (>= 3.1.0)","Description":"Provides
an extension to factors called 'lfactor' that are similar\nto factors but allow
users to refer to 'lfactor' levels by either the level or\nthe
label.","Imports":"methods, stats, utils","License":"GPL-
2","NeedsCompilation":"no","Package":"lfactors","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"testthat, Matrix","Title":"Factors with
Levels","Version":"0.9.2"},"lfda":{"Author":"Yuan Tang <terrytangyuan@gmail.com>
and Zachary Deane-Mayer with contributions from Nan Xiao.","Depends":"R (>=
3.1.0)","Description":"Functions for performing and visualizing Local Fisher
Discriminant Analysis(LFDA), Kernel Fisher Discriminant Analysis(KLFDA), and Semi-
supervised Local Fisher Discriminant Analysis(SELF).","Imports":"plyr, grDevices,
rARPACK","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"lfda","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat, rgl","Title":"Local Fisher Discriminant
Analysis","URL":"https:\/\/github.com\/terrytangyuan\/lfda","Version":"1.1.1"},"lfe
":{"Author":"Simen Gaure, Ragnar Frisch Centre for Economic Research","Depends":"R
(>= 2.15.2), Matrix (>= 1.1-2)","Description":"Transforms away factors with many
levels prior to doing an OLS.\nUseful for estimating linear models with multiple
group fixed effects, and for\nestimating linear models which uses factors with many
levels as pure control variables.\nIncludes support for instrumental variables,
conditional F statistics for weak instruments,\nrobust and multi-way clustered
standard errors, as well as limited mobility bias correction.","Imports":"Formula,
xtable, compiler, utils, methods, sandwich, numDeriv","License":"Artistic-
2.0","NeedsCompilation":"yes","Package":"lfe","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"knitr, igraph, plm, R2Cuba","Title":"Linear Group Fixed
Effects","Version":"2.5-1968"},"lfl":{"Author":"Michal Burda","Depends":"R (>=
3.1.1)","Description":"Various algorithms related to linguistic fuzzy logic: mining
for linguistic fuzzy association\nrules, performing perception-based logical
deduction (PbLD), and forecasting time-series using fuzzy\nrule-based ensemble
(FRBE).","Imports":"Rcpp (>= 0.11.0), foreach, forecast (>= 5.5), plyr,
tseries,\ne1071, zoo, utils","License":"GPL (>=
3.0)","NeedsCompilation":"yes","Package":"lfl","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat, doMC","Title":"Linguistic Fuzzy
Logic","Version":"1.2"},"lfstat":{"Author":"Daniel Koffler, Tobias Gauster and
Gregor Laaha","Depends":"R (>= 2.10), xts, lmom","Description":"The \"Manual on
Low-flow Estimation and Prediction\", published by the World Meteorological
Organisation (WMO), gives a comprehensive summary on how to analyse stream flow
data focusing on low-flows. This packages provides functions to compute the
described statistics and produces plots similar to the ones in the
manual.","Imports":"lmomRFA, dygraphs, zoo, lattice, latticeExtra","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"lfstat","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat","Title":"Calculation of Low Flow Statistics
for Daily Stream Flow Data","Version":"0.8.0"},"lga":{"Author":"Justin
Harrington","Depends":"R (>= 2.2.1)","Description":"Tools for linear grouping
analysis. Three user-level\nfunctions: gap, rlga and lga.","Imports":"boot,
lattice","License":"GPL","NeedsCompilation":"no","Package":"lga","Repository":"http
:\/\/cran.csiro.au\/src\/contrib","Suggests":"snow, MASS, maps","Title":"Tools for
linear grouping analysis (LGA)","Version":"1.1-1"},"lgarch":{"Author":"Genaro
Sucarrat","Depends":"R (>= 2.15.0), zoo","Description":"Simulation and estimation
of univariate and multivariate log-GARCH models. The main functions of the package
are: lgarchSim(), mlgarchSim(), lgarch() and mlgarch(). The first two functions
simulate from a univariate and a multivariate log-GARCH model, respectively,
whereas the latter two estimate a univariate and multivariate log-GARCH model,
respectively.","License":"GPL-
2","NeedsCompilation":"yes","Package":"lgarch","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Simulation and Estimation of Log-GARCH
Models","URL":"http:\/\/www.sucarrat.net\/","Version":"0.6-2"},"lgcp":
{"Author":"Benjamin M. Taylor, Tilman M. Davies, Barry S. Rowlingson, Peter J.
Diggle. Additional\ncode contributions from Edzer Pebesma.","Depends":"R (>=
2.10)","Description":"Spatial and spatio-temporal modelling of point patterns using
the\nlog-Gaussian Cox process. Bayesian inference for spatial,
spatiotemporal,\nmultivariate and aggregated point processes using Markov chain
Monte Carlo.","Imports":"spatstat (>= 1.40-0), sp, raster, tcltk,
RandomFields,\niterators, ncdf4, methods, rpanel (>= 1.1-3), fields,
maptools,\nMatrix, rgeos","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"lgcp","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"sparr, rgdal, gpclib","Title":"Log-Gaussian Cox
Process","Version":"1.3-14"},"lgtdl":{"Author":"R. Gentleman","Depends":"R(>=
1.2)","Description":"A very simple implementation of a class for\nlongitudinal
2)","NeedsCompilation":"no","Package":"lgtdl","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"A set of methods for longitudinal
data objects","Version":"1.1.3"},"lhs":{"Author":"Rob Carnell [aut,
cre]","Depends":"R (>= 2.14.2)","Description":"Provides a number of methods for
creating and augmenting Latin Hypercube Samples.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"lhs","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"RUnit","Title":"Latin Hypercube
Samples","URL":"http:\/\/lhs.r-forge.r-project.org","Version":"0.13"},"libamtrack":
{"Author":"Steffen Greilich and the libamtrack team","Depends":"R (>=
2.11.0)","Description":"R interface to the open-source, ANSI C library 'libamtrack'
(http:\/\/libamtrack.dkfz.org). 'libamtrack' provides computational routines for
the prediction of detector response and radiobiological efficiency in heavy charged
particle beams. It is designed for research in proton and ion dosimetry and
radiotherapy. 'libamtrack' also includes many auxiliary physics routines for proton
and ion beams. Original package and C-to-R conversion routines developed by Felix
A. Klein.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"libamtrack","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"lattice","Title":"Computational Routines for
Proton and Ion
Radiotherapy","URL":"libamtrack.dkfz.org","Version":"0.6.3"},"lifecontingencies":
{"Author":"Giorgio Alfredo Spedicato [cre,aut], Reinhold Kainhofer [ctb], Kevin J.
Owens [ctb], Christophe Dutang [ctb]","Depends":"R (>= 3.0.0),
methods","Description":"Classes and methods that allow the user to manage life
table, actuarial tables (also multiple decrement tables). Moreover, functions to
easily perform demographic, financial and actuarial mathematics on life
contingencies insurances calculations are contained therein.","Imports":"parallel,
utils, markovchain, Rcpp, stats","License":"GPL-
2","NeedsCompilation":"yes","Package":"lifecontingencies","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"demography, forecast, testthat, knitr,
rmarkdown","Title":"Financial and Actuarial Mathematics for Life
Contingencies","URL":"http:\/\/github.com\/spedygiorgio\/lifecontingencies","Versio
n":"1.1.10"},"lift":{"Author":"Steven Hoornaert, Michel Ballings, Dirk Van den
Poel","Description":"Compute the top decile lift and plot the lift curve.
Cumulative lift curves are also supported.","Imports":"stats,
2)","NeedsCompilation":"no","Package":"lift","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Compute the Top Decile Lift and Plot the Lift
Curve","Version":"0.0.2"},"liftr":{"Author":"Miaozhu Li [ctb],\nTengfei Yin
[ctb],\nNan Xiao [aut, cre]","Depends":"R (>= 3.0.2)","Description":"Dockerize R
Markdown documents with support for Rabix.","Imports":"yaml, knitr, rmarkdown,
stringr","License":"GPL","NeedsCompilation":"no","Package":"liftr","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"Dockerize R Markdown
Documents","URL":"http:\/\/liftr.me","Version":"0.3"},"lightsout":{"Author":"Dean
Attali [aut, cre]","Depends":"R (>= 3.0.0)","Description":"Lights Out is a puzzle
game consisting of a grid of lights\nthat are either on or off. Pressing any light
will toggle it and its\nadjacent lights. The goal of the game is to switch all the
lights off. This\npackage provides an interface to play the game on different board
sizes,\nboth through the command line or with a visual application. Puzzles
can\nalso be solved using the automatic solver included. View a demo\nonline at
http:\/\/daattali.com\/shiny\/lightsout\/.","Imports":"magrittr (>= 1.5), shiny (>=
0.10.0), shinyjs (>= 0.3.0),\nstats, utils","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"lightsout","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"knitr (>= 1.7), testthat (>= 0.9.1),
rmarkdown","Title":"Implementation of the 'Lights Out' Puzzle
Game","URL":"https:\/\/github.com\/daattali\/lightsout","Version":"0.2.1"},"likeLTD
":{"Author":"David Balding, Adrian Timpson, Christopher Steele, Mayeul d'Avezac,
James Hetherington.","Depends":"R (>= 2.10), DEoptim, ggplot2, gtools,
rtf","Description":"Tools to determine DNA profile Weight of Evidence.\nFor further
information see the likeLTD guide provided,\nor Balding, D.J. (2013)
<DOI:10.1073\/pnas.1219739110>.","Imports":"gdata, tools, tcltk","License":"GPL-
3","NeedsCompilation":"yes","Package":"likeLTD","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"svUnit, scales","Title":"Tools to Evaluate DNA Profile
Evidence","URL":"https:\/\/sites.google.com\/site\/baldingstatisticalgenetics\/","V
ersion":"6.0.4"},"likelihood":{"Author":"Lora Murphy
<murphyl@caryinstitute.org>","Depends":"R (>= 2.1.1), nlme","Description":"Tools
for maximum likelihood estimation of parameters\nof scientific
2","NeedsCompilation":"no","Package":"likelihood","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Methods for Maximum Likelihood
Estimation","Version":"1.7"},"likelihoodAsy":{"Author":"Ruggero Bellio and Donald
Pierce","Depends":"nleqslv, Rsolnp, alabama, pracma, cond","Description":"Functions
for computing the r and r* statistics for inference on an arbitrary scalar function
of model parameters, plus some code for the (modified) profile
likelihood.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"likelihoodAsy","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"MASS, lme4, knitr","Title":"Functions for
Likelihood Asymptotics","Version":"0.40"},"likert":{"Author":"Jason Bryer
<jason@bryer.org>, Kimberly Speerschneider\n<kimkspeer@gmail.com>","Depends":"R (>=
3.0),ggplot2,xtable","Description":"Functions to analyze and visualize likert type
items.","Imports":"psych,reshape2,gridExtra,grid,plyr","License":"GPL","NeedsCompil
ation":"no","Package":"likert","Repository":"http:\/\/cran.csiro.au\/src\/contrib",
"Suggests":"devtools,shiny","Title":"Functions to Analyze and Visualize Likert Type
Items","URL":"http:\/\/jason.bryer.org\/likert,
http:\/\/github.com\/jbryer\/likert","Version":"1.3.3"},"limSolve":
{"Author":"Karline Soetaert [aut, cre],\nKarel Van den Meersche [aut],\nDick van
Oevelen [aut],\nLAPACK authors [cph]","Depends":"R (>=
2.10)","Description":"Functions that (1.) Find the minimum\/maximum of a linear or
quadratic function:\nmin or max (f(x)), where f(x) = ||Ax-b||^2 or f(x) =
sum(ai*xi)\nsubject to equality constraints Ex=f and\/or inequality constraints
Gx>=h.\n(2.) Sample an underdetermined- or overdetermined system Ex=f subject to
Gx>=h, and if applicable Ax~=b.\n(3.) Solve a linear system Ax=B for the unknown x.
Includes banded and tridiagonal linear systems.\nThe package calls Fortran
functions from LINPACK","Imports":"quadprog, lpSolve,
MASS","License":"GPL","NeedsCompilation":"yes","Package":"limSolve","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Title":"Solving Linear Inverse
Models","Version":"1.5.5.1"},"limitplot":{"Author":"Omar E. Olmedo","Depends":"R
(>= 2.9.0)","Description":"Values below a specified limit of detection are stacked
in\nrows in order to reduce overplotting and create a clear\ngraphical
representation of your data.","License":"GPL-
2","NeedsCompilation":"no","Package":"limitplot","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Jitter\/CI Plot with Ordered Points Below the Limit of
Detection","Version":"1.2"},"linERR":{"Author":"David MoriÃ±a (ISGlobal, Centre for
Research in Environmental Epidemiology)","Depends":"R (>= 3.1.1), survival,
stats4","Description":"Fits a linear excess relative risk model by maximum
likelihood, possibly including several variables and allowing for lagged
exposures.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"linERR","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Linear Excess Relative Risk
Model","Version":"1.0"},"linLIR":{"Author":"Andrea Wiencierz","Description":"This
package implements the methodology of\nLikelihood-based Imprecise Regression (LIR)
for the case of\nlinear regression with interval data.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"linLIR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"linear Likelihood-based Imprecise
Regression","Version":"1.1"},"linbin":{"Author":"Ethan Z. Welty [aut,
cre],\nChristian E. Torgersen [ctb] (author support and guidance),\nSamuel J.
Brenkman [ctb] (elwha and quinault datasets),\nJeffrey J. Duda [ctb] (elwha
dataset),\nJonathan B. Armstrong [ctb] (fishmotion dataset)","Depends":"R (>=
3.0.1)","Description":"Short for 'linear binning', the linbin package provides
functions\nfor manipulating, binning, and plotting linearly referenced data.
Although\ndeveloped for data collected on river networks, it can be used with any
interval\nor point data referenced to a 1-dimensional coordinate system. Flexible
bin\ngeneration and batch processing makes it easy to compute and visualize
variables\nat multiple scales, useful for identifying patterns within and between
variables\nand investigating the influence of scale of observation on data
interpretation.","Imports":"stats, utils, graphics, grDevices","License":"AGPL-
3","NeedsCompilation":"no","Package":"linbin","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"knitr","Title":"Binning and Plotting of Linearly
Referenced
Data","URL":"https:\/\/github.com\/ezwelty\/linbin","Version":"0.1.1"},"lineup":
{"Author":"Karl W Broman <kbroman@biostat.wisc.edu>","Depends":"R (>=
2.10.1)","Description":"Tools for detecting and correcting sample mix-ups between
two sets\nof measurements, such as between gene expression data on two
tissues.","Imports":"qtl (>= 1.20-15), class, graphics, grDevices, utils,
stats,\nparallel","License":"GPL-
3","NeedsCompilation":"yes","Package":"lineup","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"roxygen2, knitr, rmarkdown, devtools,
testthat","Title":"Lining Up Two Sets of
Measurements","URL":"https:\/\/github.com\/kbroman\/lineup","Version":"0.37-
6"},"linkR":{"Author":"Aaron
Olsen","Depends":"R (>= 2.11.0), svgViewR","Description":"Creates kinematic and
static force models of 3D levers and linkage mechanisms, with particular
application to the fields of engineering and biomechanics.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"linkR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"3D Lever and Linkage Mechanism
Modeling","URL":"http:\/\/home.uchicago.edu\/~aolsen\/software\/linkr.shtml","Versi
on":"1.0.1"},"linkcomm":{"Author":"Alex T. Kalinka <alex.t.kalinka@gmail.com>, with
contributions from Alain Guenoche","Depends":"igraph,
RColorBrewer","Description":"Link communities reveal the nested and overlapping
structure in networks, and uncover the key nodes that form connections to multiple
communities. linkcomm provides a set of tools for generating, visualizing, and
analysing link communities in networks of arbitrary size and type. The linkcomm
package also includes tools for generating, visualizing, and analysing Overlapping
Cluster Generator (OCG) communities.","Imports":"dynamicTreeCut, grid,
2)","NeedsCompilation":"yes","Package":"linkcomm","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"fastcluster","Title":"Tools for Generating,
Visualizing, and Analysing Link\nCommunities in Networks","Version":"1.0-
11"},"linkim":{"Author":"Yi Xu <statxy@gmail.com> and Jixiang Wu
<jixiang.wu@sdstate.edu>","Depends":"R(>= 2.10)","Description":"A linkage
information based method for imputing missing diploid genotypes","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"linkim","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Linkage information based genotype imputation
method","Version":"0.1"},"linprog":{"Author":"Arne Henningsen","Depends":"R (>=
2.4.0), lpSolve","Description":"This package can be used to solve Linear
Programming \/\nLinear Optimization problems by using the simplex
2)","NeedsCompilation":"no","Package":"linprog","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Linear Programming \/
Optimization","URL":"http:\/\/linprog.r-forge.r-project.org\/","Version":"0.9-
2"},"lint":{"Author":"Andrew Redd <andrew.redd@hsc.utah.edu>","Depends":"R (>=
3.0)","Description":"Tools for checking R code for style compliance. Tools
for\ncreating style compliance tests. A suite of pre-built tests
is\nprovided.","Imports":"plyr, harvestr, stringr, dostats, foreach","License":"GPL
(>=
3)","NeedsCompilation":"no","Package":"lint","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat, roxygen2","Title":"Tools to check R code
style","Version":"0.3"},"lintools":{"Author":"Mark van der Loo [aut, cre],\nEdwin
de Jonge [aut]","Description":"Variable elimination (Gaussian elimination, Fourier-
Motzkin elimination),\nMoore-Penrose pseudoinverse, reduction to reduced row
echelon form, value substitution,\nprojecting a vector on the convex polytope
described by a system of (in)equations,\nsimplify systems by removing spurious
columns and rows and collapse implied equalities,\ntest if a matrix is totally
unimodilar, compute variable ranges implied by
linear\n(in)equalities.","Imports":"utils","License":"GPL-
3","NeedsCompilation":"yes","Package":"lintools","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat, knitr","Title":"Manipulation of Linear
Systems of (in)Equalities","URL":"https:\/\/github.com\/data-
cleaning\/lintools","Version":"0.1.1.1"},"lintr":{"Author":"Jim Hester [aut,
cre]","Depends":"R (>= 3.1.1)","Description":"Checks adherence to a given style,
syntax errors and possible\nsemantic issues. Supports on the fly checking of R
code edited with Emacs,\nVim and Sublime Text.","Imports":"rex, crayon, codetools,
stringdist, testthat, digest, igraph,\nrstudioapi (>= 0.2), httr, jsonlite, knitr,
stats, utils","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"lintr","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Static R Code
Analysis","URL":"https:\/\/github.com\/jimhester\/lintr","Version":"0.3.3"},"lira":
{"Author":"Mauro Sereno","Depends":"R (>= 2.14.0), coda,
rjags","Description":"Performs Bayesian linear regression in astronomy. The method
accounts for heteroscedastic errors in both the independent and the dependent
variables, intrinsic scatters (in both variables), time evolution of slopes,
normalization and scatters, Malmquist and Eddington bias, and break of linearity.
The posterior distribution of the regression parameters is sampled with a Gibbs
method exploiting the JAGS library.","License":"GPL-
2","NeedsCompilation":"no","Package":"lira","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"LInear Regression in Astronomy","Version":"1.2.0"},"liso":
{"Author":"Zhou Fang","Depends":"MASS, Iso","Description":"Fits lasso (total
variation) penalised additive isotone
models","License":"GPL","NeedsCompilation":"no","Package":"liso","Repository":"http
:\/\/cran.csiro.au\/src\/contrib","Title":"Fitting lasso penalised additive isotone
models","Version":"0.2"},"lisp":{"Author":"Peter Danenberg
<pcd@roxygen.org>","Description":"Though SRFI-1 scopes both list-processing and
higher-order\nprogramming, we'll save some list-orthogonal functions for
the\n`functional' package; this is freely a mixture of\nimplementation and
API.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"lisp","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"RUnit","Title":"List-processing Ã la SRFI-
1","Version":"0.1"},"lisrelToR":{"Author":"Sacha Epskamp","Depends":"R (>=
2.15.0)","Description":"This is an unofficial package aimed at automating
the\nimport of LISREL output in R. This package or its maintainer\nis not in any
way affiliated with the creators of LISREL and\nSSI, Inc.","License":"GPL-
2","NeedsCompilation":"no","Package":"lisrelToR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Import output from LISREL into
R","Version":"0.1.4"},"list":{"Author":"Graeme Blair [aut, cre], Kosuke Imai [aut,
cre], Bethany Park [ctb],\nAlexander Coppock [ctb]","Depends":"R (>= 3.2.0), utils,
sandwich (>= 2.3-3)","Description":"Allows researchers to conduct multivariate
statistical analyses of survey data with list experiments. This survey methodology
is also known as the item count technique or the unmatched count technique and is
an alternative to the commonly used randomized response method. The package
implements the methods developed by Imai (2011), Blair and Imai (2012), Blair,
Imai, and Lyall (2013), Imai, Park, and Greene (2014), and Aronow, Coppock,
Crawford, and Green (2015). This includes a Bayesian MCMC implementation of
regression for the standard and multiple sensitive item list experiment designs and
a random effects setup, a Bayesian MCMC hierarchical regression model with up to
three hierarchical groups, the combined list experiment and endorsement experiment
regression model, a joint model of the list experiment that enables the analysis of
the list experiment as a predictor in outcome regression models, and a method for
combining list experiments with direct questions. In addition, the package
implements the statistical test that is designed to detect certain failures of list
experiments, and a placebo test for the list experiment using data from direct
questions.","Imports":"VGAM (>= 0.9-8), magic (>= 1.5-6), gamlss.dist (>= 4.3-
4),\nMASS (>= 7.3-40), quadprog (>= 1.5-5), corpcor (>= 1.6.7),\nmvtnorm (>= 1.0-
2), coda (>= 0.17-1)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"list","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat (>= 0.9.1), knitr (>=
1.10.5)","Title":"Statistical Methods for the Item Count Technique and
List\nExperiment","Version":"8.0"},"listWithDefaults":{"Author":"Russell S.
Pierce","Description":"Provides a function that, as an alternative to base::list,
allows default values to be inherited from another
list.","Imports":"assertthat","License":"GPL-
2","NeedsCompilation":"no","Package":"listWithDefaults","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"testthat","Title":"List with
Defaults","Version":"1.0.0"},"listenv":{"Author":"Henrik Bengtsson [aut, cre,
cph]","Depends":"R (>= 3.1.2)","Description":"List environments are environments
that have list-like properties. For instance, the elements of a list environment
are ordered and can be accessed and iterated over using index subsetting, e.g. 'x
<- listenv(a=1, b=2); for (i in seq_along(x)) x[[i]] <- x[[i]]^2; y <-
as.list(x)'.","License":"LGPL (>=
2.1)","NeedsCompilation":"no","Package":"listenv","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"R.utils, R.rsp","Title":"Environments Behaving
(Almost) as
Lists","URL":"https:\/\/github.com\/HenrikBengtsson\/listenv","Version":"0.6.0"},"l
ivechatR":{"Author":"Lawrence Wu","Description":"Provides a wrapper around
LiveChat's API. The R functions allow for\none to extract chat sessions, raw text
of chats between agents and customers and\nevents.","Imports":"dplyr, purrr,
jsonlite, data.table, magrittr","License":"GPL-
2","NeedsCompilation":"no","Package":"livechatR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"R Wrapper for LiveChat REST
API","URL":"https:\/\/github.com\/lawwu\/livechatR","Version":"0.1.0"},"llama":
{"Author":"Lars Kotthoff [aut,cre],\nBernd Bischl [aut],\nBarry Hurley
[ctb],\nTalal Rahwan [ctb]","Depends":"R (>= 2.10), mlr (>=
2.5)","Description":"Provides functionality to train and evaluate algorithm
selection models for portfolios.","Imports":"rJava, parallelMap, ggplot2,
checkmate, BBmisc, plyr","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"llama","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat, ParamHelpers","Title":"Leveraging
Learning to Automatically Manage
Algorithms","URL":"https:\/\/bitbucket.org\/lkotthoff\/llama","Version":"0.9.1"},"l
le":{"Author":"Holger
Diedrich, Dr. Markus Abel (Department of Physics,\nUniversity
Potsdam)","Depends":"scatterplot3d, MASS, snowfall","Description":"LLE is a non-
linear algorithm for mapping high-dimensional\ndata into a lower dimensional
(intrinsic) space. This package\nprovides the main functions to performs the LLE
alogrithm\nincluding some enhancements like subset selection, calculation\nof the
intrinsic dimension etc.","License":"GPL-
3","NeedsCompilation":"no","Package":"lle","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"rgl","Title":"Locally linear
embedding","Version":"1.1"},"lllcrc":{"Author":"Zach Kurtz","Description":"Applies
local log-linear capture-recapture models (LLLMs) for\nclosed populations, as
described in the doctoral thesis of Zachary Kurtz.\nThe method is relevant when
there are 3-5 capture occasions, with auxiliary\ncovariates available for all
capture occasions. As part of estimating the\nnumber of missing population units,
the method estimates the \"rate of\nmissingness\" as it varies over the covariate
space. In addition,\nuser-friendly functions are provided to recreate
(approximately) the method\nof Zwane and van der Heijden (2004), which applied the
VGAM package\nin a way that is closely related to LLLMs.","Imports":"data.table,
combinat, VGAM, plyr","License":"GPL-
2","NeedsCompilation":"no","Package":"lllcrc","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Local Log-linear Models for Capture-
Recapture","Version":"1.2"},"lm.beta":{"Author":"Stefan Behrendt [aut,
cre]","Description":"Adds standardized regression coefficients to objects created
by lm. Also extends the S3 methods print, summary and coef with additional boolean
argument standardized.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"lm.beta","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Add Standardized Regression Coefficients to lm-
Objects","Version":"1.5-1"},"lm.br":{"Author":"Marc Adams [aut, cre],\nauthors of R
function 'lm' [ctb] (general interface),\nauthors of 'lm.gls' [ctb] (interface and
R code for covariate weights),\nU.S. NIST [ctb] (C++ code for TNT::Vector
template)","Depends":"R(>= 3.0.1), Rcpp (>= 0.11.0)","Description":"Exact
significance tests for a changepoint in linear or multiple linear
regression.\nConfidence regions with exact coverage probabilities for the
changepoint.","Imports":"stats, methods, graphics, datasets","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"lm.br","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Linear Model with
Breakpoint","Version":"2.8"},"lmSupport":{"Author":"John Curtin
<jjcurtin@wisc.edu>","Depends":"car","Description":"Accompanies Markus Brauer, Bas
Rokers, and John Curtin's two-course graduate series in\nGeneral, Generalized, and
Multi-level Linear Models (PSY 610\/710).","Imports":"psych, gvlma, AICcmodavg,
lme4, pbkrtest","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"lmSupport","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Support for Linear
Models","URL":"http:\/\/dionysus.psych.wisc.edu\/","Version":"2.9.2"},"lme4":
{"Author":"Douglas Bates [aut],\nMartin Maechler [aut],\nBen Bolker [aut,
cre],\nSteven Walker [aut],\nRune Haubo Bojesen Christensen [ctb],\nHenrik Singmann
[ctb],\nBin Dai [ctb],\nGabor Grothendieck [ctb],\nPeter Green [ctb]","Depends":"R
(>= 3.0.2), Matrix (>= 1.1.1), methods, stats","Description":"Fit linear and
generalized linear mixed-effects models.\nThe models and their components are
represented using S4 classes and\nmethods. The core computational algorithms are
implemented using the\n'Eigen' C++ library for numerical linear algebra and
'RcppEigen' \"glue\".","Imports":"graphics, grid, splines, utils, parallel, MASS,
lattice, nlme\n(>= 3.1-123), minqa (>= 1.1.15), nloptr (>= 1.0.4)","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"lme4","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"knitr, boot, PKPDmodels, MEMSS, testthat (>= 0.8.1),
ggplot2,\nmlmRev, optimx (>= 2013.8.6), gamm4, pbkrtest, HSAUR2,
numDeriv","Title":"Linear Mixed-Effects Models using 'Eigen' and
S4","URL":"https:\/\/github.com\/lme4\/lme4\/ http:\/\/lme4.r-forge.r-
project.org\/","Version":"1.1-11"},"lmeNB":{"Author":"Yinshan Zhao and Yumi Kondo
(with contributions from Steven G. Johnson, Rudolf Schuerer and Brian Gough on the
integration
subroutines)","Depends":"numDeriv,statmod,lmeNBBayes","Description":"The functions
in this package implement the safety monitoring procedures proposed in the paper
titled \"Detection of unusual increases in MRI lesion counts in individual multiple
sclerosis patients\" by Zhao, Y., Li, D.K.B., Petkau, A.J., Riddehough, A.,
Traboulsee, A., published in Journal of the American Statistical Association in
2013. The procedure first models longitudinally collected count variables with a
negative binomial mixed-effect regression model. To account for the correlation
among repeated measures from the same patient, the model has subject-specific
random intercept, which can be modelled with a gamma or log-normal distributions.
One can also choose the semi-parametric option which does not assume any
distribution for the random effect. These mixed-effect models could be useful
beyond the application of the safety monitoring. The maximum likelihood methods are
used to estimate the unknown fixed effect parameters of the model. Based on the
fitted model, the personalized activity index is computed for each patient. Lastly,
this package is companion to R package lmeNBBayes, which contains the functions to
compute the Personalized Activity Index in Bayesian framework.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"lmeNB","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Compute the Personalized Activity Index Based on a
Negative\nBinomial Model","Version":"1.3"},"lmeNBBayes":{"Author":"Yumi
Kondo","Description":"The functions in this package implement the safety monitoring
procedures proposed in the paper titled \"A flexible mixed effect negative binomial
regression model for detecting unusual increases in MRI lesion counts in individual
multiple sclerosis patients\" by Kondo, Y., Zhao, Y. and Petkau, A.J. The procedure
first models longitudinally collected count variables with a negative binomial
mixed-effect regression model. To account for the correlation among repeated
measures from the same patient, the model has subject-specific random intercept,
which is modelled with the infinite mixture of Beta distributions, very flexible
distribution that theoretically allows any form. The package also has the option of
a single beta distribution for random effects. These mixed-effect models could be
useful beyond the application of the safety monitoring. The inference is based on
MCMC samples and this package contains a Gibbs sampler to sample from the posterior
distribution of the negative binomial mixed-effect regression model. Based on the
fitted model, the personalized activity index is computed for each patient. Lastly,
this package is companion to R package lmeNB, which contains the functions to
compute the Personalized Activity Index in the frequentist
framework.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"lmeNBBayes","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Compute the Personalized Activity Index Based on a
Flexible\nBayesian Negative Binomial Model","Version":"1.3.1"},"lmeSplines":
{"Author":"Rod Ball <rod.ball@scionresearch.com>","Depends":"nlme(>= 3.1-
29)","Description":"Add smoothing spline modelling capability to nlme.
Fit\nsmoothing spline terms in Gaussian linear and nonlinear\nmixed-effects
2)","NeedsCompilation":"no","Package":"lmeSplines","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Add smoothing spline modelling capability to
nlme","Version":"1.1-10"},"lmeVarComp":{"Author":"Yichi Zhang","Description":"Test
zero variance components in linear mixed models and\ntest additivity in
nonparametric regression\nusing the restricted likelihood ratio test and the
generalized F-test.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"lmeVarComp","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"RLRsim, varComp","Title":"Testing for a subset of
variance components in linear mixed\nmodels","Version":"1.0"},"lmec":
{"Author":"Florin Vaida and Lin Liu","Depends":"mvtnorm","Description":"This
package includes a function to fit a linear\nmixed-effects model in the formulation
described in Laird and\nWare (1982) but allowing for censored normal responses. In
this\nversion, the with-in group errors are assumed independent and\nidentically
distributed.","License":"GPL-
2","NeedsCompilation":"no","Package":"lmec","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Linear Mixed-Effects Models with Censored
Responses","Version":"1.0"},"lmenssp":{"Author":"Ozgur Asar, Peter J.
Diggle","Depends":"MASS, nlme, mvtnorm, geoR,","Description":"Contains functions to
estimate model parameters and filter, smooth and forecast random effects
coefficients for mixed models with stationary and non-stationary stochastic
processes under multivariate normal and t response distributions, diagnostic
checks, bootstrap standard error calculation, etc.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"lmenssp","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Linear Mixed Effects Models with Non-Stationary
Stochastic\nProcesses","Version":"1.1"},"lmerTest":{"Author":"Alexandra Kuznetsova
[aut, cre],\nPer Bruun Brockhoff [aut, ths],\nRune Haubo Bojesen Christensen
[aut]","Depends":"R (>= 3.0.0), Matrix, stats, methods, lme4 (>=
1.0)","Description":"Different kinds of tests for linear mixed effects models as
implemented\nin 'lme4' package are provided. The tests comprise types I - III F
tests\nfor fixed effects, LR tests for random
effects.\nThe package also provides the calculation of population means for fixed
factors\nwith confidence intervals and corresponding plots. Finally the
backward\nelimination of non-significant effects is implemented.","Imports":"plyr,
MASS, Hmisc, ggplot2","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"lmerTest","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"pbkrtest","Title":"Tests in Linear Mixed Effects
Models","Version":"2.0-30"},"lmf":{"Author":"Thomas Kvalnes","Description":"This R
package provide methods for estimation and statistical\ninference on directional
and fluctuating selection in age-structured\npopulations.","License":"GPL-
2","NeedsCompilation":"no","Package":"lmf","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Functions for estimation and inference of selection in\nage-
structured populations","Version":"1.2"},"lmfor":{"Author":"Lauri
Mehtatalo","Depends":"stats4, nlme, MASS","Description":"Functions related to
forest biometrics, including illustrative graphics, numerical computation, modeling
height-diameter relationships, prediction of tree volumes, and recovery of tree
diameter distributions. Datasets on tree height-diameter relationship and light
response of moss photosynthesis are included.","License":"GPL-
2","NeedsCompilation":"no","Package":"lmfor","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Functions for Forest Biometrics","Version":"1.1"},"lmm":
{"Author":"Original by Joseph L. Schafer","Depends":"R (>=
2.0.0)","Description":"Some improved procedures for linear mixed
models.","License":"Unlimited","NeedsCompilation":"yes","Package":"lmm","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Linear Mixed
Models","URL":"http:\/\/www.stat.psu.edu\/~jls\/misoftwa.html","Version":"1.0"},"lm
mlasso":{"Author":"Juerg Schelldorfer","Depends":"methods, emulator, miscTools,
penalized","Description":"This package fits (gaussian) linear mixed-effects
models\nfor high-dimensional data (n<<p) using a Lasso-type approach\nfor the
fixed-effects
parameter.","License":"GPL","NeedsCompilation":"no","Package":"lmmlasso","Repositor
y":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Linear mixed-effects models with
Lasso","Version":"0.1-2"},"lmmot":{"Author":"Marvin N. Wright","Depends":"maxLik,
MASS","Description":"Fit right censored Multiple Ordinal Tobit (MOT)
3","NeedsCompilation":"no","Package":"lmmot","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Multiple Ordinal Tobit (MOT)
Model","Version":"0.1.3"},"lmms":{"Author":"Jasmin Straube [aut, cre],\nKim-Anh Le
Cao [aut],\nEmma Huang [aut],\nDominique Gorse [ctb]","Depends":"R (>= 3.0.0),
ggplot2","Description":"Linear Mixed effect Model Splines ('lmms') implements
linear mixed\neffect model splines for modelling and differential expression for
highly\ndimensional data sets: investNoise() for quality control and filterNoise()
for\nremoving non-informative trajectories; lmmSpline() to model time course
expression\nprofiles and lmmsDE() performs differential expression analysis to
identify\ndifferential expression between groups, time and\/or group x time
interaction.","Imports":"stats, methods, nlme, lmeSplines, parallel, reshape2,
gdata,\ngplots, gridExtra","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"lmms","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Linear Mixed Effect Model Splines for Modelling and Analysis
of\nTime Course Data","Version":"1.3.3"},"lmodel2":{"Author":"Pierre
Legendre","Depends":"R (>= 2.14.0)","Description":"Computes model II simple linear
regression using ordinary\nleast squares (OLS), major axis (MA), standard major
axis (SMA), and\nranged major axis (RMA).","License":"GPL-
2","NeedsCompilation":"no","Package":"lmodel2","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Model II Regression","Version":"1.7-2"},"lmom":
{"Author":"J. R. M. Hosking","Description":"Functions related to L-moments:
computation of L-moments\nand trimmed L-moments of distributions and data samples;
parameter\nestimation; L-moment ratio diagram; plot vs. quantiles of an\nextreme-
value distribution.","Imports":"stats, graphics","License":"Common Public License
Version
1.0","NeedsCompilation":"yes","Package":"lmom","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"L-moments","Version":"2.5"},"lmomRFA":{"Author":"J. R. M.
Hosking","Depends":"lmom (>= 2.0)","Description":"Functions for regional frequency
analysis using the methods\nof J. R. M. Hosking and J. R. Wallis (1997), \"Regional
frequency analysis:\nan approach based on L-moments\".","Imports":"stats,
graphics","License":"Common Public License Version
1.0","NeedsCompilation":"yes","Package":"lmomRFA","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Regional frequency analysis using L-
moments","Version":"3.0-1"},"lmomco":{"Author":"William Asquith","Depends":"R (>=
2.10.0), utils","Description":"Extensive functions for the theory of L-moments
(LMs) in addition to probability-weighted moments (PWMs), and parameter (p)
estimation for numerous familiar and not-so-familiar distributions. Estimation of
LMs for the same distributions is provided as are L-moment ratio diagrams.
Estimation of LMs for right-tail and left-tail censoring by known or unknown
threshold and also by indicator variable is available. Asymmetric trimmed LMs (TL-
moments, TLMs) are supported as are numerical integrations to dynamically compute
trajectories of select TLM ratios for TL-moment ratio diagram construction. LMs of
residual (resid.) and reversed (rev.) resid. life are implemented along with 13
operators on quantile functions that are useful in reliability, lifetime, and
survival analysis. Exact analytical bootstrap estimates of order statistics, LMs,
and variances-covariances of LMs are provided. The Harri-Coble Tau34-squared Test
for Normality is available. Distribution support with \"L\" (LMs), \"TL\" (TLMs)
and added (+) support for right-tail censoring (RC) encompasses: Asymmetric (Asy.)
Exponential (Exp.) Power [L], Asy. Triangular [L], Cauchy [TL], Eta-Mu [L], Exp.
[L], Gamma [L], Generalized (Gen.) Exp. Poisson [L], Gen. Extreme Value [L], Gen.
Lambda [L,TL], Gen. Logistic [L), Gen. Normal [L], Gen. Pareto [L+RC, TL],
Govindarajulu [L], Gumbel [L], Kappa [L], Kappa-Mu [L], Kumaraswamy [L], Laplace
[L], Linear Mean Residual Quantile Function [L], Normal [L], 3-p log-Normal [L],
Pearson Type III [L], Rayleigh [L], Rev. Gumbel [L+RC], Rice\/Rician (L), Slash
[TL], 3-p Student t [L], Truncated Exponential [L], Wakeby [L], and Weibull [L].
LMs have multivariate analogs; the sample L-comoments (LCMs) are implemented and
might have considerable application with copulas because LCMs measure asymmetric
association and higher comoments or comovements of variables.","Imports":"Lmoments,
MASS","License":"GPL","NeedsCompilation":"no","Package":"lmomco","Repository":"http
:\/\/cran.csiro.au\/src\/contrib","Suggests":"copBasic","Title":"L-Moments,
Censored L-Moments, Trimmed L-Moments, L-Comoments,\nand Many
Distributions","URL":"http:\/\/www.amazon.com\/dp\/1463508417\/","Version":"2.2.2"}
,"lmtest":{"Author":"Torsten Hothorn [aut],\nAchim Zeileis [aut, cre],\nRichard W.
Farebrother [aut] (pan.f),\nClint Cummins [aut] (pan.f),\nGiovanni Millo
[ctb],\nDavid Mitchell [ctb]","Depends":"R (>= 2.10.0), stats,
zoo","Description":"A collection of tests, data sets, and examples\nfor diagnostic
checking in linear regression models. Furthermore,\nsome generic tools for
inference in parametric models are provided.","Imports":"graphics","License":"GPL-2
| GPL-
3","NeedsCompilation":"yes","Package":"lmtest","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"car, strucchange, sandwich, dynlm, stats4, survival,
AER","Title":"Testing Linear Regression Models","Version":"0.9-34"},"loa":
{"Author":"Karl Ropkins","Depends":"R (>= 3.0.0), lattice","Description":"Various
plots and functions that make use of the lattice\/trellis plotting framework.\nThe
plots (which include 'loaPlot', 'GoogleMap' and 'trianglePlot') use panelPal(), a
function that\nextends 'lattice' and 'hexbin' package methods to automate plot
subscript and panel-to-panel\nand panel-to-key
synchronization\/management.","Imports":"methods, MASS, grid, png, RgoogleMaps,
RColorBrewer, mgcv","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"loa","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Lattice Options and Add-
Ins","Version":"0.2.38"},"localdepth":{"Author":"Claudio Agostinelli
<claudio@unive.it>, Mario Romanazzi <romanaz@unive.it> and SLATEC Common
Mathematical Library <www.netlib.org\/slatec>","Depends":"R (>= 3.0.0),
circular","Description":"Simplicial, Mahalanobis and Ellipsoid Local and Global
Depth","License":"GPL-
2","NeedsCompilation":"yes","Package":"localdepth","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Local Depth","Version":"0.5-7"},"localgauss":
{"Author":"Tore Selland Kleppe <tore.kleppe@uis.no>","Depends":"ggplot2, MASS,
foreach, matrixStats","Description":"Computational routines for estimating and
visualizing local Gaussian parameters. Local Gaussian parameters are useful for
characterizing and testing for non-linear dependence within bivariate data. See
e.g. Tjostheim and Hufthammer, Local Gaussian correlation: A new measure of
dependence, Journal of Econometrics, 2013, Volume 172 (1), pages 33-
2","NeedsCompilation":"yes","Package":"localgauss","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Estimating Local Gaussian
Parameters","Version":"0.35"},"localsolver":{"Author":"Walerian Sokolowski [aut,
cre, cph],\nWit Jakuczun [aut, cph],\nNatalia Okinczyc [aut],\nBogumil Kaminski
[aut]","Depends":"R (>= 3.0.1)","Description":"The package converts R data onto
input and data for LocalSolver,\nexecutes optimization and exposes optimization
results
as R data.\nLocalSolver (http:\/\/www.localsolver.com\/) is an optimization
engine\ndeveloped by Innovation24 (http:\/\/www.innovation24.fr\/). It is designed
to\nsolve large-scale mixed-variable non-convex optimization problems.
The\nlocalsolver package is developed and maintained by WLOG
Solutions\n(http:\/\/www.wlogsolutions.com\/en\/) in collaboration with Decision
Support\nand Analysis Division at Warsaw School of
Economics\n(http:\/\/www.sgh.waw.pl\/en\/).","License":"LGPL-
2.1","NeedsCompilation":"no","Package":"localsolver","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"knitr","Title":"R API to
LocalSolver","Version":"2.3"},"locfdr":{"Author":"Bradley Efron [aut],\nBrit
Turnbull [aut],\nBalasubramanian Narasimhan [aut, cre],\nKorbinian Strimmer
[ctb]","Description":"Computation of local false discovery
rates.","Imports":"stats, splines, graphics","License":"GPL-
2","NeedsCompilation":"no","Package":"locfdr","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Computes Local False Discovery Rates","Version":"1.1-
8"},"locfit":{"Author":"Catherine Loader","Depends":"R (>=
2.0.1)","Description":"Local regression, likelihood and density
estimation.","Imports":"lattice","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"locfit","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"akima, gam","Title":"Local Regression, Likelihood and
Density Estimation","Version":"1.5-9.1"},"locits":{"Author":"Guy Nason [aut,
cre]","Depends":"R (>= 2.0), wavethresh, igraph","Description":"Provides test of
second-order stationarity for time\nseries (for dyadic and arbitrary-n length
data). Provides\nlocalized autocovariance, with confidence intervals,\nfor locally
stationary (nonstationary) time series.","License":"GPL-
2","NeedsCompilation":"yes","Package":"locits","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Test of Stationarity and Localized
Autocovariance","URL":"http:\/\/www.stats.bris.ac.uk\/~guy","Version":"1.7.1"},"loc
pol":{"Author":"Jorge Luis Ojeda Cabrera, <jojeda@unizar.es>","Depends":"R (>=
2.5.0)","Description":"Computes local polynomial estimators.","License":"GPL-
2","NeedsCompilation":"yes","Package":"locpol","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Kernel local polynomial regression","Version":"0.6-
0"},"lodGWAS":{"Author":"Ahmad Vaez, Ilja M. Nolte, Peter J. van der
Most","Depends":"R (>= 3.0.0)","Description":"Genome-wide association (GWAS)
analyses\nof a biomarker that account for the limit of
detection.","Imports":"survival, rms, stats, utils","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"lodGWAS","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Genome-Wide Association Analysis of a Biomarker
Accounting for\nLimit of Detection","Version":"1.0-7"},"loe":{"Author":"Yoshikazu
Terada, Ulrike von Luxburg","Depends":"R (>= 3.2.3), MASS","Description":"Local
Ordinal embedding (LOE) is one of graph embedding methods for unweighted
graphs.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"loe","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"igraph, Matrix, vegan","Title":"Local Ordinal
Embedding","Version":"1.1"},"log4r":{"Author":"John Myles White [aut, cph],\nKenton
White [ctb],\nKirill MÃ¼ller [ctb, cre]","Description":"logr4 provides an object-
oriented logging system that uses an API\nroughly equivalent to log4j and its
related variants.","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"log4r","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat","Title":"A simple logging system for R, based
on
log4j","URL":"https:\/\/github.com\/johnmyleswhite\/log4r","Version":"0.2"},"logbin
":{"Author":"Mark W. Donoghoe <mark.donoghoe@mq.edu.au>","Depends":"R (>=
3.0.1)","Description":"Methods for fitting log-link GLMs and GAMs to binomial
data,\nusing EM-type algorithms with more stable convergence properties than
standard methods.","Imports":"splines, glm2","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"logbin","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Relative Risk Regression Using the Log-Binomial
Model","Version":"1.2"},"logconPH":{"Author":"Clifford Anderson-
Bergman","Description":"Computes a cox PH model with a log concave baseline
distribution. If no covariates are provided, estimates the log concave NPMLE. Built
specifically for interval censored data, where data is a n by 2 matrix with [i, 1]
as the left side of the interval for subject i and [i,2] as right side. Uncensored
data can be entered by setting [i,1] = [i,2]. Alternatively, this can also handle
uncensored data. If all the data is uncensored, you may enter data as a length(n)
vector.","License":"GPL-
2","NeedsCompilation":"yes","Package":"logconPH","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"CoxPH Model with Log Concave Baseline
Distribution","Version":"1.5"},"logconcens":{"Author":"Dominic Schuhmacher
<dominic.schuhmacher@mathematik.uni-goettingen.de>, Kaspar Rufibach
<kaspar.rufibach@gmail.com>, Lutz Duembgen <duembgen@stat.unibe.ch>","Depends":"R
(>= 2.15.0), base, methods, utils, grDevices,
graphics,\nstats","Description":"Based on right or interval censored data, compute
the maximum likelihood estimator of a (sub)probability density under the assumption
that it is log-concave. For further information see Duembgen, Rufibach, and
Schuhmacher (2011, preprint).","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"logconcens","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"logcondens","Title":"Maximum likelihood estimation
of a log-concave density based on\ncensored
data","URL":"http:\/\/www.dominic.schuhmacher.name,
http:\/\/www.kasparrufibach.ch,\nhttp:\/\/www.staff.unibe.ch\/duembgen","Version":"
0.16-4"},"logcondens":{"Author":"Kaspar Rufibach <kaspar.rufibach@gmail.com> and
Lutz Duembgen <duembgen@stat.unibe.ch>","Depends":"R (>=
2.10)","Description":"Given independent and identically distributed observations
X(1), ..., X(n), compute the maximum likelihood estimator (MLE) of a density as
well as a smoothed version of it under the assumption that the density is log-
concave, see Rufibach (2007) and Duembgen and Rufibach (2009). The main function of
the package is 'logConDens' that allows computation of the log-concave MLE and its
smoothed version. In addition, we provide functions to compute (1) the value of the
density and distribution function estimates (MLE and smoothed) at a given point (2)
the characterizing functions of the estimator, (3) to sample from the estimated
distribution, (5) to compute a two-sample permutation test based on log-concave
densities, (6) the ROC curve based on log-concave estimates within cases and
controls, including confidence intervals for given values of false positive
fractions (7) computation of a confidence interval for the value of the true
density at a fixed point. Finally, three datasets that have been used to illustrate
log-concave density estimation are made available.","Imports":"ks, graphics,
2)","NeedsCompilation":"no","Package":"logcondens","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Estimate a Log-Concave Probability Density from iid
Observations","URL":"http:\/\/www.kasparrufibach.ch
,\nhttp:\/\/www.imsv.unibe.ch\/content\/staff\/personalhomepages\/duembgen\/index_e
ng.html","Version":"2.1.4"},"logcondens.mode":{"Author":"Charles
Doss","Depends":"logcondens","Description":"Computes maximum likelihood estimate of
a log-concave density with fixed and known location of the mode. Performs
inference about the mode via a likelihood ratio test. Extension of the logcondens
package.","Imports":"distr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"logcondens.mode","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Compute MLE of Log-Concave Density on R with
Fixed Mode, and\nPerform Inference for the Mode","Version":"1.0.1"},"logcondiscr":
{"Author":"Kaspar Rufibach <kaspar.rufibach@gmail.com> and Fadoua Balabdaoui
<fadoua@ceremade.dauphine.fr> and Hanna Jankowski <hkj@mathstat.yorku.ca> and
Kathrin Weyermann <kathrin.weyermann@bkw-fmb.ch>","Depends":"Matrix, mvtnorm,
cobs","Description":"Given independent and identically distributed observations
X(1), ..., X(n), allows to compute the maximum likelihood estimator (MLE) of
probability mass function (pmf) under the assumption that it is log-concave, see
Weyermann (2007) and Balabdaoui, Jankowski, Rufibach, and Pavlides (2012). The main
functions of the package are 'logConDiscrMLE' that allows computation of the log-
concave MLE, 'logConDiscrCI' that computes pointwise confidence bands for the MLE,
and 'kInflatedLogConDiscr' that computes a mixture of a log-concave PMF and a point
mass at k.","Imports":"stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"logcondiscr","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Estimate a Log-Concave Probability Mass Function from
Discrete\ni.i.d. Observations","URL":"http:\/\/www.kasparrufibach.ch
,\nhttp:\/\/www.ceremade.dauphine.fr\/~fadoua
,\nhttp:\/\/www.math.yorku.ca\/~hkj","Version":"1.0.6"},"logging":{"Author":"Mario
Frasca <mariotomo@gmail.com>","Depends":"R (>= 2.12.0),
methods","Description":"logging is a pure R package that implements the
ubiquitous\nlog4j package.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"logging","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"svUnit, XML","Title":"R logging
package","Version":"0.7-103"},"logistf":{"Author":"Georg Heinze
<georg.heinze@meduniwien.ac.at>, Meinhard Ploner,\nDaniela Dunkler (former
versions), Harry Southworth (former\nversions)","Depends":"R (>= 3.0.0), mice,
mgcv","Description":"Firth's bias reduced logistic regression approach
with\npenalized profile likelihood based confidence intervals for\nparameter
estimates.","License":"GPL","NeedsCompilation":"yes","Package":"logistf","Repositor
y":"http:\/\/cran.csiro.au\/src\/contrib","Ti
tle":"Firth's bias reduced logistic
regression","URL":"\nhttp:\/\/cemsiis.meduniwien.ac.at\/en\/kb\/science-
research\/software\/statistical-
software\/fllogistf\/","Version":"1.21"},"logisticPCA":{"Author":"Andrew J.
Landgraf","Description":"Dimensionality reduction techniques for binary data
including\nlogistic PCA.","Imports":"ggplot2","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"logisticPCA","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"rARPACK (>= 0.10-0), testthat (>= 0.11.0),
knitr, rmarkdown","Title":"Binary Dimensionality
Reduction","URL":"https:\/\/github.com\/andland\/logisticPCA","Version":"0.2"},"log
itchoice":{"Author":"Michael Lim","Description":"Fits linear discrete logit choice
models with l2 regularization. To handle reasonably sized datasets, we employ an
accelerated version of generalized gradient descent.","License":"GPL-
2","NeedsCompilation":"yes","Package":"logitchoice","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Fitting l2-regularized logit choice models via
generalized\ngradient descent","Version":"0.9.4"},"logitnorm":{"Author":"Thomas
Wutzler","Description":"Density, distribution, quantile and random
generation\nfunction for the logitnormal distribution. Estimation of the\nmode and
the first two moments. Estimation of distribution\nparameters.","License":"GPL-
2","NeedsCompilation":"no","Package":"logitnorm","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"RUnit","Title":"Functions for the logitnormal
distribution","Version":"0.8.29"},"loglognorm":{"Author":"Heike Trautmann, Detlef
Steuer and Olaf Mersmann","Depends":"R (>= 2.7.0)","Description":"r,d,p,q functions
for the double log normal distribution","License":"GPL-
2","NeedsCompilation":"yes","Package":"loglognorm","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Double log normal distribution
functions","Version":"1.0.1"},"logmult":{"Author":"Milan Bouchet-Valat [aut,
cre],\nHeather Turner [ctb]","Depends":"gnm (>= 1.0-5)","Description":"Functions to
fit log-multiplicative models using gnm, with\nsupport for convenient printing,
plots, and jackknife\/bootstrap\nstandard errors. For complex survey data, models
can be fitted from\ndesign objects from the 'survey' package. Currently supported
models\ninclude UNIDIFF (Erikson & Goldthorpe), a.k.a. log-multiplicative\nlayer
effect model (Xie), and several association models: Goodman's\nrow-column
association models of the RC(M) and RC(M)-L families\nwith one or several
dimensions; two skew-symmetric association\nmodels proposed by Yamaguchi and by van
der Heijden & Mooijaart.","Imports":"stats, utils, graphics, grDevices,
qvcalc","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"logmult","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"survey, boot, ellipse, parallel","Title":"Log-
Multiplicative Models, Including Association
Models","URL":"https:\/\/github.com\/nalimilan\/logmult","Version":"0.6.3"},"logspl
ine":{"Author":"Charles Kooperberg <clk@fredhutch.org>","Description":"Routines for
the logspline density estimation. oldlogspline()\nuses the same algorithm as the
logspline 1.0.x package - the Kooperberg\nand Stone (1992) <DOI: 10.2307\/1390786>
algorithm (with an improved interface).\nThe recommended routine logspline() uses
an algorithm from Stone et al (1997).\n<DOI:
10.1214\/aos\/1031594728>","Imports":"stats, graphics","License":"Apache License
2.0","NeedsCompilation":"yes","Package":"logspline","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Logspline Density Estimation
Routines","Version":"2.1.9"},"lokern":{"Author":"Eva Herrmann
<eherrmann@mathematik.tu-darmstadt.de> (F77 & S original);\nPackaged for R and
enhanced by Martin Maechler","Description":"Kernel regression smoothing with
adaptive local or global plug-in\nbandwidth selection.","Imports":"sfsmisc (>= 1.0-
2)","NeedsCompilation":"yes","Package":"lokern","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Kernel Regression Smoothing with Local or Global Plug-
in\nBandwidth","Version":"1.1-6"},"lomb":{"Author":"Thomas Ruf, partially based on
C original by Press et al. (Numerical Recipes)","Description":"Computes the Lomb-
Scargle Periodogram for unevenly sampled time series. Includes a randomization
procedure to obtain reliable p-values.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"lomb","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Lomb-Scargle Periodogram","Version":"1.0"},"longCatEDA":
{"Author":"Stephen Tueller. Funded by the National Institute on Drug Abuse (NIDA)
Award number 1R03DA030850 and the National Institute on Alcohol Abuse and
Alcoholism (NIAAA) Award Number R03
AA019775.","Depends":"methods","Description":"Package for Plotting Categorical
Longitudinal and Time-Series Data","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"longCatEDA","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Package for Plotting Categorical Longitudinal and
Time-Series\nData","Version":"0.17"},"longclust":{"Author":"Paul D. McNicholas
[aut, cre], K. Raju Jampani [aut] (May to Dec 2012), Sanjeena Subedi
[aut]","Description":"Clustering or classification of longitudinal data based on a
mixture of multivariate t or Gaussian distributions with a Cholesky-decomposed
covariance structure.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"longclust","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"mvtnorm","Title":"Model-Based Clustering and
Classification for Longitudinal Data","Version":"1.2"},"longitudinal":
{"Author":"Rainer Opgen-Rhein and Korbinian Strimmer.","Depends":"R (>= 3.0.2),
corpcor (>= 1.6.8)","Description":"Contains general data structures and\nfunctions
for longitudinal data with multiple variables,\nrepeated measurements, and
irregularly spaced time points.\nAlso implements a shrinkage estimator of dynamical
correlation\nand dynamical covariance.","Imports":"graphics, grDevices,
3)","NeedsCompilation":"no","Package":"longitudinal","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Analysis of Multiple Time Course
Data","URL":"http:\/\/strimmerlab.org\/software\/longitudinal\/","Version":"1.1.12"
},"longitudinalData":{"Author":"Christophe Genolini [cre, aut],\nBruno Falissard
[ctb],\nDai Fang [ctb],\nLuke Tierney
[ctb]","Depends":"methods,clv,class,rgl,utils,misc3d","Description":"Tools for
longitudinal data and joint longitudinal data (used by packages kml and
kml3d).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"longitudinalData","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Longitudinal Data","URL":"http:www.r-
project.org","Version":"2.4.1"},"longmemo":{"Author":"S scripts originally by Jan
Beran <jan.beran@uni-konstanz.de>;\nDatasets via Brandon Whitcher
<brandon@stat.washington.edu>.\nToplevel R functions and much more by Martin
Maechler.","Depends":"stats","Description":"Datasets and Functionality from the
textbook Jan Beran\n(1994). Statistics for Long-Memory Processes; Chapman &
Hall.","Enhances":"fracdiff","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"longmemo","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"sfsmisc","Title":"Statistics for Long-Memory
Processes (Jan Beran) -- Data and\nFunctions","Version":"1.0-0"},"longpower":
{"Author":"Michael C. Donohue, Anthony C. Gamst, Steven D. Edland","Depends":"R (>=
3.0.0), Matrix, lme4 (>= 1.0), nlme, methods","Description":"The longpower package
contains functions for computing\npower and sample size for linear models of
longitudinal data\nbased on the formula due to Liu and Liang (1997) and Diggle
et\nal (2002). Either formula is expressed in terms of marginal\nmodel or
Generalized Estimating Equations (GEE) parameters.\nThis package contains functions
which translate pilot mixed\neffect model parameters (e.g. random intercept and\/or
slope)\ninto marginal model parameters so that the formulas of Diggle\net al or Liu
and Liang formula can be applied to produce sample\nsize calculations for two
sample longitudinal designs assuming\nknown variance.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"longpower","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr, gee","Title":"Sample size calculations for
longitudinal
data","URL":"https:\/\/bitbucket.org\/mdonohue\/longpower","Version":"1.0-
11"},"longurl":{"Author":"Bob Rudis [aut, cre]","Depends":"R (>=
3.1.0)","Description":"Interface to the 'LongURL' API to identify known URL
shortener services\nand expand vectors of short URLs with optional error checking
and\nURL validation. See <http:\/\/longurl.org\/> for more information
about\n'LongURL'.","Imports":"httr, dplyr, pbapply","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"longurl","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat","Title":"Expand Short URLs Using the
'LongURL' API","Version":"0.1.1"},"loo":{"Author":"Aki Vehtari [aut],\nAndrew
Gelman [aut],\nJonah Gabry [cre, aut],\nJuho Piironen [ctb],\nBen Goodrich
[ctb]","Depends":"R (>= 3.1.2)","Description":"Efficient approximate leave-one-out
cross-validation (LOO)\nusing Pareto smoothed importance sampling (PSIS), a new
procedure for\nregularizing importance weights. As a byproduct of the calculations,
we also\nobtain approximate standard errors for estimated predictive errors and
for\nthe comparison of predictive errors between models. We also compute
the\nwidely applicable information criterion (WAIC).","Imports":"graphics,
matrixStats (>= 0.14.1), parallel, stats","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"loo","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"covr, knitr, rmarkdown, testthat","Title":"Efficient
Leave-One-Out Cross-Validation and WAIC for
Bayesian\nModels","URL":"https:\/\/github.com\/stan-
dev\/loo","Version":"0.1.6"},"lookupTable":{"Author":"Enzo
Jia [aut, cre],\nMarc Maier [aut]","Depends":"data.table","Description":"Fits
look-up tables by filling entries with the mean or median values of
observations\nfall in partitions of the feature space. Partitions can be determined
by user of the\npackage using input argument feature.boundaries, and dimensions of
the feature space\ncan be any combination of continuous and categorical features
provided by the data set.\nA Predict function directly fetches corresponding entry
value, and a default value is\ndefined as the mean or median of all available
observations.\nThe table and other components are represented using the S4 class
lookupTable.","Imports":"dplyr, methods","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"lookupTable","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Look-Up Tables using
S4","Version":"0.1"},"loop":{"Author":"Youhua
Chen","Depends":"grid,MASS","Description":"The program can perform loop analysis
and plot network\nstructure (especially for food webs),including minimum
spanning\ntree, loop decomposition of weighted directed graphs, and other\nnetwork
properties which may be related to food chain\nproperties in
ecology.","License":"GPL-
2","NeedsCompilation":"no","Package":"loop","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"loop decomposition of weighted directed graphs for life
cycle\nanalysis, providing flexbile network plotting methods, and\nanalyzing food
chain properties in ecology","Version":"1.1"},"loopr":{"Author":"Brandon
Taylor","Depends":"R (>= 3.1.3)","Description":"Remedies a common problem in
piping: not having access to\nintermediate outputs of the pipe. Within a \"loop\",
a piping intermediate\nis stored in a stack archive, data is processed, and then
both the\nstored intermediate and the current output are reintegrated using
an\n\"ending\" function. Two special ending functions are provided: amend
and\ninsert. However, any ending function can be specified, including
merge\nfunctions, join functions, setNames(), etc. This framework allows
the\nfollowing work-flow: focus on a particular aspect or section of a\ndata set,
conduct specific operations, and then reintegrate changes into\nthe
whole.","Imports":"plyr (>= 1.8.1), dplyr (>= 0.4.1), magrittr (>= 1.5),
lazyeval\n(>= 0.1.10), R6 (>= 2.0.1)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"loopr","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr (>= 1.9)","Title":"Uses an Archive to Amend
Previous Stages of a Pipe using Current\nOutput","Version":"1.0.1"},"lordif":
{"Author":"Seung W. Choi, with contributions from Laura E. Gibbons and\nPaul K.
Crane","Depends":"R (>= 2.7.0), mirt, rms","Description":"Analysis of Differential
Item Functioning (DIF) for\ndichotomous and polytomous items using an iterative
hybrid of\nordinal logistic regression and item response theory
(IRT).","Imports":"stats4","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"lordif","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Logistic Ordinal Regression Differential Item Functioning
using\nIRT","Version":"0.3-3"},"lorec":{"Author":"Xi (Rossi)
LUO","Description":"Estimate covariance matrices that contain low rank and sparse
components","License":"GPL-
2","NeedsCompilation":"yes","Package":"lorec","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"clime, scio","Title":"LOw Rand and sparsE Covariance
matrix estimation","Version":"0.6.1"},"lpSolve":{"Author":"Michel Berkelaar and
others","Description":"Lp_solve is freely available (under LGPL 2) software
for\nsolving linear, integer and mixed integer programs. In this\nimplementation we
supply a \"wrapper\" function in C and some R\nfunctions that solve general
linear\/integer problems,\nassignment problems, and transportation problems. This
version\ncalls lp_solve version 5.5.","License":"LGPL-
2","NeedsCompilation":"yes","Package":"lpSolve","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Interface to 'Lp_solve' v. 5.5 to Solve Linear\/Integer
Programs","Version":"5.6.13"},"lpSolveAPI":{"Author":"lp_solve
<http:\/\/lpsolve.sourceforge.net\/>,\nKjell Konis
<kjell.konis@me.com>.","Description":"The lpSolveAPI package provides an R
interface to 'lp_solve',\na Mixed Integer Linear Programming (MILP) solver with
support for pure\nlinear, (mixed) integer\/binary, semi-continuous and special
ordered sets\n(SOS) models.","License":"LGPL-
2","NeedsCompilation":"yes","Package":"lpSolveAPI","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"R Interface to 'lp_solve' Version
5.5.2.0","Version":"5.5.2.0-17"},"lpbrim":{"Author":"Timothee Poisot
<tim@poisotlab.io>, Daniel B Stouffer
<daniel.stouffer@canterbury.ac.nz>","Depends":"R (>=
2.12.0)","Description":"Optimization of bipartite modularity using LP-BRIM (Label
propagation\nfollowed by Bipartite Recursively Induced
Modularity).","Imports":"Matrix, plyr, RColorBrewer","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"lpbrim","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"doMC","Title":"LP-BRIM Bipartite
Modularity","URL":"http:\/\/poisotlab.io\/software","Version":"1.0.0"},"lpc":
{"Author":"Daniela M Witten and Robert Tibshirani","Description":"Implements the
LPC method of Witten&Tibshirani(Annals of Applied Statistics 2008) for
identification of significant genes in a microarray experiment.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"lpc","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Lassoed principal components for testing significance
of\nfeatures","Version":"1.0.2"},"lpint":{"Author":"Feng Chen
<feng.chen@unsw.edu.au>","Description":"Estimates the intensity function, or its
derivative of a given order, of a multiplicative counting process using the local
polynomial method","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"lpint","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Local polynomial estimators of intensity function or
its\nderivatives","Version":"2.0"},"lpme":{"Author":"Haiming Zhou
<zhouh@email.sc.edu> and Xianzheng Huang <huang@stat.sc.edu>","Depends":"R (>=
3.0.2)","Description":"Two local polynomial estimators for solving the errors-in-
variables problem: one is in Delaigle, Fan, and Carroll (2009), and one is in Huang
and Zhou (2014+). The SIMEX bandwidth selection method is also provided for both
estimators.","Imports":"Rcpp (>= 0.11.1)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"lpme","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Local Polynomial Estimator in Measurement Error
Models","Version":"1.0.1"},"lpmodeler":{"Author":"Cyrille Szymanski
<cnszym@gmail.com> [aut]","Depends":"R (>= 2.15.0)","Description":"lpmodeler is a
set of user-friendly functions to simplify the modelling of linear programs (LP)
and mixed integer programs (MIP). It provides a unified interface compatible with
optimization packages: Rsymphony.","Imports":"slam (>= 0.1-31)","License":"GPL (>=
2) | BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"lpmodeler","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"Rsymphony (>= 0.1-17)","Title":"Modeler for
linear programs (LP) and mixed integer linear\nprograms (MILP)","Version":"0.2-
1"},"lpridge":{"Author":"Burkhardt Seifert <seifert@ifspm.unizh.ch> (S
original);\nPackaged for R by Martin
Maechler","Depends":"stats","Description":"Local Polynomial Regression with
Ridging.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"lpridge","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Local Polynomial (Ridge) Regression","Version":"1.0-
7"},"lqa":{"Author":"Jan Ulbricht","Description":"This package provides some basic
infrastructure and tools\nto fit Generalized Linear Models (GLMs) via
penalized\nlikelihood inference. Estimating procedures already implemented\nare the
LQA algorithm (that is where its name come from),\nP-IRLS, RidgeBoost, GBlockBoost
and ForwardBoost.","License":"GPL-
2","NeedsCompilation":"no","Package":"lqa","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Penalized Likelihood Inference for GLMs","Version":"1.0-
3"},"lqmm":{"Author":"Marco Geraci","Depends":"R (>= 3.0.0)","Description":"This is
a collection of functions to fit quantile regression models for independent and
hierarchical data.","Imports":"stats, utils, nlme (>= 3.1-124),
SparseGrid","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"lqmm","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"R.rsp","Title":"Linear Quantile Mixed
Models","URL":"http:\/\/CRAN.R-project.org\/package=lqmm","Version":"1.5.3"},"lqr":
{"Author":"Christian E. Galarza, Luis Benites, Victor H. Lachos","Description":"It
fits a robust linear quantile regression model using a new family of zero-quantile
distributions for the error term.\nThis family of distribution includes skewed
versions of the Normal, Student's t, Laplace, Slash and Contaminated Normal
distribution.\nIt provides estimates and full inference. It also provides envelopes
plots for assessing the fit and confidences bands when several quantiles are
provided simultaneously.","Imports":"graphics, stats, ghyp,
spatstat","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"lqr","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"ald, qrLMM, qrNLMM","Title":"Robust Linear Quantile
Regression","Version":"1.1"},"lrequire":{"Author":"Rick Wargo
<lrequire@rickwargo.com>","Depends":"R (>= 3.0.1)","Description":"In the fashion of
'node.js' <https:\/\/nodejs.org\/>, requires a file,\nsourcing into the current
environment only the variables explicitly specified\nin the module.exports or
exports list variable. If the file was already sourced,\nthe result of the earlier
sourcing is returned to the caller.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"lrequire","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat","Tit
le":"Sources an R \"Module\" with Caching & Encapsulation, Returning\nExported
Vars","URL":"https:\/\/github.com\/rickwargo\/lrequire","Version":"0.1.3"},"lrgs":
{"Author":"Adam Mantz","Description":"Implements a Gibbs sampler to do linear
regression with multiple covariates, multiple responses, Gaussian measurement
errors on covariates and responses, Gaussian intrinsic scatter, and a covariate
prior distribution which is given by either a Gaussian mixture of specified size or
a Dirichlet process with a Gaussian base
distribution.","Imports":"mvtnorm","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"lrgs","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Linear Regression by Gibbs
Sampling","URL":"https:\/\/github.com\/abmantz\/lrgs","Version":"0.4.2"},"lrmest":
{"Author":"Ajith Dissanayake [aut, cre],\nP. Wijekoon [aut],\nR-core
[cph]","Depends":"MASS","Description":"When multicollinearity exists among
predictor variables of the linear model, least square estimators does not provide a
better solution for estimating parameters. To deal with multicollinearity several
estimators are proposed in the literature. Some of these estimators are Ordinary
Least Square Estimator (OLSE), Ordinary Ridge Regression Estimator (ORRE),
Restricted Least Square Estimator (RLSE), Ordinary Mixed Regression Estimator
(OMRE), Liu Estimator (LE), Restricted Liu Estimator (RLE), Stochastic Restricted
Liu Estimator (SRLE), Type (1) Liu Estimator (Type-1 LTE), Type (2) Liu Estimator
(Type-2 LTE), Type (3) Liu Estimator (Type-3 LTE), Type (1) Adjusted Liu Estimator
(Type-1 ALTE), Type (2) Adjusted Liu Estimator (Type-2 ALTE), Type (3) Adjusted Liu
Estimator (Type-3 ALTE), Almost Unbiased Ridge Estimator (AURE), Almost Unbiased
Liu Estimator (AULE), Stochastic Restricted Ridge Estimator (SRRE) and Restricted
Ridge Regression Estimator (RRRE). To select the best estimator in a practical
situation the Mean Square Error (MSE) is used. Using this package scalar MSE value
of all the above estimators and Prediction Sum of Square (PRESS) values of some of
the estimators can be obtained, and the variation of the MSE and PRESS values for
the relevant estimators can be shown graphically.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"lrmest","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Different types of estimators to deal with
multicollinearity","Version":"1.0"},"lsa":{"Author":"Fridolin
Wild","Depends":"SnowballC","Description":"The basic idea of latent semantic
analysis (LSA) is,\nthat text do have a higher order (=latent semantic) structure
which,\nhowever, is obscured by word usage (e.g. through the use of synonyms\nor
polysemy). By using conceptual indices that are derived statistically\nvia a
truncated singular value decomposition (a two-mode factor analysis)\nover a given
document-term matrix, this variability problem can be overcome.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"lsa","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"tm","Title":"Latent Semantic
Analysis","Version":"0.73.1"},"lsbclust":{"Author":"Pieter Schoonees [aut, cre],
Patrick Groenen [ctb]","Depends":"R (>= 3.2.2), stats, parallel,
ggplot2","Description":"Functions for performing least-squares bilinear clustering
of\nthree-way data. The method uses the bilinear decomposition (or
biadditive\nmodel) to model two-way matrix slices while clustering over the third
way.\nUp to four different types of clusters are included, one for each term of
the\nbilinear decomposition. In this way, matrices are clustered simultaneously
on\n(a subset of) their overall means, row margins, column margins and row-
column\ninteractions. The orthogonality of the bilinear model results in
separability of\nthe joint clustering problem into four separate ones. Three of
these subproblems\nare specific k-means problems, while a special algorithm is
implemented for the\ninteractions. Plotting methods are provided, including biplots
for the low-rank\napproximations of the interactions.","Imports":"plyr, clue, grid,
gridExtra, reshape2, Rcpp, graphics, methods","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"lsbclust","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat","Title":"Least-Squares Bilinear Clustering
for Three-Way Data","Version":"1.0.4"},"lsdv":{"Author":"Zaghdoudi
Taha","Description":"Fit a least square dummy variable
regression","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"lsdv","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Least square dummy variable
regression","Version":"1.1"},"lsei":{"Author":"Yong Wang [aut, cre],\nCharles L.
Lawson [aut],\nRichard J. Hanson [aut]","Description":"It contains functions that
solve least squares linear\nregression problems under linear
equality\/inequality\nconstraints. It is developed based on the 'Fortran' program
of\nLawson and Hanson (1974, 1995), which is public domain and\navailable at
http:\/\/www.netlib.org\/lawson-hanson.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"lsei","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Solving Least Squares Problems under
Equality\/Inequality\nConstraints","URL":"https:\/\/www.stat.auckland.ac.nz\/~yongw
ang","Version":"1.1-1"},"lsgl":{"Author":"Martin Vincent","Depends":"R (>= 3.0.0),
sglOptim (== 1.2.0), Matrix","Description":"Linear multiple output using sparse
group lasso. The algorithm finds the sparse group lasso penalized maximum
likelihood estimator. This result in feature and parameter selection, and parameter
estimation. Use of multiple processors for cross validation and subsampling is
supported through OpenMP. Development version is on github.","Imports":"methods,
utils, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"lsgl","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Linear Sparse Group
Lasso","URL":"https:\/\/github.com\/vincent-dk\/lsgl","Version":"1.2.0"},"lshorth":
{"Author":"G. Sawitzki","Description":"Calculates the (localised) length of the
shorth and\nsupplies corresponding diagnostic
plots.","License":"LGPL","NeedsCompilation":"no","Package":"lshorth","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Title":"The Length of the
Shorth","URL":"http:\/\/lshorth.r-forge.r-project.org\/","Version":"0.1-6"},"lsl":
{"Author":"Po-Hsien Huang [aut, cre]","Depends":"R (>=
3.2.0)","Description":"Conduct structural equation modeling via penalized
likelihood.","Imports":"ggplot2, reshape2, methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"lsl","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Latent Structure Learning","Version":"0.5.1"},"lsmeans":
{"Author":"Russell Lenth [aut, cre]","Depends":"estimability, methods, R (>=
3.2)","Description":"Obtain least-squares means for many linear, generalized
linear,\nand mixed models. Compute contrasts or linear functions of least-
squares\nmeans, and comparisons of slopes. Plots and compact letter
displays.","Imports":"graphics, stats, utils, nlme, coda (>= 0.17), multcomp,
plyr,\nmvtnorm, xtable (>= 1.8-2)","License":"GPL-
2","NeedsCompilation":"no","Package":"lsmeans","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"car, lattice, MCMCpack, mediation, multcompView,
ordinal,\npbkrtest (>= 0.4-1), CARBayes, coxme, gee, geepack, glmmADMB,\nlme4.0,
lme4, MASS, MCMCglmm, nnet, pscl, survival","Title":"Least-Squares
Means","Version":"2.23"},"lspls":{"Author":"Bjørn-Helge Mevik","Depends":"pls (>=
2.2.0)","Description":"Implements the LS-PLS (least squares - partial
least\nsquares) method described in for instance Jørgensen, K.,\nSegtnan, V. H.,
Thyholt, K., Næs, T. (2004) A Comparison of\nMethods for Analysing Regression
Models with Both Spectral and\nDesigned Variables. Journal of Chemometrics,
18(10), 451--464.","License":"GPL-
2","NeedsCompilation":"no","Package":"lspls","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"LS-PLS
Models","URL":"http:\/\/mevik.net\/work\/software\/lspls.html","Version":"0.2-
1"},"lsr":{"Author":"Daniel Navarro","Description":"A collection of tools intended
to make introductory statistics easier to teach, including wrappers for common
hypothesis tests and basic data manipulation. It accompanies Navarro, D. J. (2015).
Learning Statistics with R: A Tutorial for Psychology Students and Other Beginners,
Version 0.5. [Lecture notes] School of Psychology, University of Adelaide,
Adelaide, Australia. ISBN: 978-1-326-18972-3. URL:
http:\/\/health.adelaide.edu.au\/psychology\/ccs\/teaching\/lsr\/.","License":"GPL-
3","NeedsCompilation":"no","Package":"lsr","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Companion to \"Learning Statistics with
R\"","URL":"http:\/\/health.adelaide.edu.au\/psychology\/ccs\/teaching\/lsr\/","Ver
sion":"0.5"},"lss":{"Author":"Lin Huang <lh2123@columbia.edu>, Zhezhen Jin
<zj7@columbia.edu>","Depends":"R(>= 2.1.0), quantreg","Description":"Due to lack of
proper inference procedure and software,\nthe ordinary linear regression model is
seldom used in practice\nfor the analysis of right censored data. This paper
presents an\nS-Plus\/R program that implements a recently developed
inference\nprocedure (Jin, Lin and Ying, 2006)\\cite{Jin} for the\naccelerated
failure time model based on the least-squares\nprinciple.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"lss","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"survival","Title":"the accelerated failure time model to
right censored data based\non least-squares principle","Version":"0.52"},"ltbayes":
{"Author":"Timothy R. Johnson","Depends":"R (>= 3.1.1), mcmc (>= 0.9-3), MHadaptive
(>= 1.1-8), numDeriv\n(>= 2012.9-1)","Description":"Functions for simulating
realizations from the posterior distribution of\na latent trait of an item response
model. Distributions are conditional on
one or\na subset of response patterns (e.g., sum scores). Functions for computing
likelihoods,\nFisher and observed information, posterior modes, and profile
likelihood confidence\nintervals are also included. These functions are designed to
be easily amenable to\nuser-specified models.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ltbayes","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"coda, mcmcplots, ggmcmc, knitr, ggplot2, gridExtra,
reshape2","Title":"Simulation-Based Bayesian Inference for Latent Traits of
Item\nResponse Models","Version":"0.3"},"ltm":{"Author":"Dimitris Rizopoulos
<d.rizopoulos@erasmusmc.nl>","Depends":"R (>= 2.14.0), MASS, msm,
polycor","Description":"Analysis of multivariate dichotomous and polytomous data
using latent trait models under the Item Response Theory approach. It includes the
Rasch, the Two-Parameter Logistic, the Birnbaum's Three-Parameter, the Graded
Response, and the Generalized Partial Credit Models.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ltm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Latent Trait Models under
IRT","URL":"http:\/\/rwiki.sciviews.org\/doku.php?
id=packages:cran:ltm","Version":"1.0-0"},"ltmle":{"Author":"Joshua Schwab [aut,
cre],\nSamuel Lendle [aut],\nMaya Petersen [aut],\nMark van der Laan [aut],\nSusan
Gruber [ctb]","Depends":"R(>= 3.0.0)","Description":"Targeted Maximum Likelihood
Estimation (TMLE) of\ntreatment\/censoring specific mean outcome or marginal
structural model for\npoint-treatment and longitudinal
data.","Imports":"Matrix","License":"GPL-
2","NeedsCompilation":"no","Package":"ltmle","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"SuperLearner, memoise, testthat","Title":"Longitudinal
Targeted Maximum Likelihood
Estimation","URL":"https:\/\/github.com\/joshuaschwab\/ltmle","Version":"0.9-
7"},"ltsa":{"Author":"A.I. McLeod, Hao Yu, Zinovi Krougly","Depends":"R (>=
2.1.0)","Description":"Methods of developing linear time series modelling.\nMethods
are given for loglikelihood computation, forecasting\nand
simulation.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ltsa","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Linear Time Series
Analysis","URL":"http:\/\/www.stats.uwo.ca\/faculty\/aim","Version":"1.4.6"},"ltsba
se":{"Author":"Betul Kan Kilinc [aut, cre], Ozlem Alpu [aut, cre]","Depends":"MASS,
robustbase","Description":"This is a new tool to estimate Ridge and Liu estimators
based on LTS method in multiple linear regression analysis.","License":"GPL-
3","NeedsCompilation":"no","Package":"ltsbase","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Ridge and Liu Estimates based on LTS (Least Trimmed
Squares)\nMethod","Version":"1.0.1"},"ltsk":{"Author":"Naresh Kumar, Dong Liang,
Jin Chen, Jun Chen","Depends":"parallel,R (>= 2.10)","Description":"Implements
local spatial and local spatiotemporal Kriging based on local spatial and local
spatiotemporal variograms,
respectively.","Imports":"fields,gstat,sp","License":"GPL-
2","NeedsCompilation":"yes","Package":"ltsk","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Local Time Space Kriging","Version":"1.0.4"},"lubridate":
{"Author":"Garrett Grolemund [aut],\nVitalie Spinu [aut, cre],\nHadley Wickham
[aut],\nJan Lyttle [ctb],\nImanuel Constigan [ctb],\nJason Law [ctb],\nDoug
Mitarotonda [ctb],\nJoseph Larmarange [ctb],\nJonathan Boiser [ctb],\nChel Hee Lee
[ctb]","Depends":"methods, R (>= 3.0.0)","Description":"Functions to work with
date-times and timespans: fast and user\nfriendly parsing of date-time data,
extraction and updating of components of\na date-time (years, months, days, hours,
minutes, and seconds), algebraic\nmanipulation on date-time and timespan objects.
The 'lubridate' package has\na consistent and memorable syntax that makes working
with dates easy and\nfun.","Enhances":"chron, timeDate, zoo, xts, its, tis,
timeSeries, fts, tseries","Imports":"stringr","License":"GPL-
2","NeedsCompilation":"yes","Package":"lubridate","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat, knitr, covr","Title":"Make Dealing with
Dates a Little Easier","Version":"1.5.6"},"luca":{"Author":"Ji-Hyung Shin
<shin@sfu.ca>, Brad McNeney\n<mcneney@stat.sfu.ca>, Jinko Graham
<jgraham@stat.sfu.ca>","Depends":"R (>= 2.0.0), survival,
genetics","Description":"Likelihood inference in case-control studies of a
rare\ndisease under independence or simple dependence of genetic and\nnon-genetic
covariates","License":"GPL-
2","NeedsCompilation":"no","Package":"luca","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Likelihood inference from case-control data Under
Covariate\nAssumptions (LUCA)","URL":"http:\/\/stat-
db.stat.sfu.ca:8080\/statgen\/research\/luca","Version":"1.0-5"},"lucid":
{"Author":"Kevin Wright [aut, cre]","Description":"Print vectors (and data frames)
of floating point numbers\nusing a non-scientific format optimized for human
readers. Vectors\nof numbers are rounded using significant digits, aligned at
the\ndecimal point, and all zeros trailing the decimal point are
dropped.","Imports":"nlme","License":"GPL-
2","NeedsCompilation":"no","Package":"lucid","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr, lattice, lme4, rjags","Title":"Printing Floating
Point Numbers in a Human-Friendly
Format","URL":"https:\/\/github.com\/kwstat\/lucid","Version":"1.3"},"lucr":
{"Author":"Oliver Keyes","Description":"Reformat currency-based data as numeric
values (or numeric values as currency-based data) and convert between
currencies.","Imports":"Rcpp, httr","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"lucr","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat","Title":"Currency Formatting and
Conversion","URL":"https:\/\/github.com\/ironholds\/lucr","Version":"0.1.1"},"lulcc
":{"Author":"Simon Moulds <simon.moulds10@imperial.ac.uk>","Depends":"methods,
raster, R (>= 3.1.0)","Description":"Classes and methods for spatially explicit
land use change\nmodelling in R.","Imports":"ROCR, lattice,
rasterVis","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"lulcc","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"caret, rpart, randomForest, gsubfn, Hmisc,
plyr,\nRColorBrewer,","Title":"Land Use Change Modelling in
R","Version":"1.0.1"},"lumendb":{"Author":"Thomas J. Leeper [aut,
cre]","Description":"A simple client for the Lumen Database
<https:\/\/lumendatabase.org\/> (formerly Chilling Effects)
API.","Imports":"httr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"lumendb","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"testthat","Title":"Lumen Database API
Client","URL":"https:\/\/github.com\/leeper\/lumendb","Version":"0.2.0"},"lunar":
{"Author":"Emmanuel Lazaridis [aut, cre]","Depends":"R (>=
2.10.0)","Description":"Provides functions to calculate lunar and other
environmental\ncovariates.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"lunar","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Lunar Phase & Distance, Seasons and Other
Environmental Factors","URL":"http:\/\/statistics.lazaridis.eu","Version":"0.1-
04"},"luzlogr":{"Author":"Ben Bond-Lamberty [aut, cre]","Depends":"R (>=
3.0)","Description":"Provides flexible but lightweight logging facilities for R
scripts.\nSupports priority levels for logs and messages, flagging messages,
capturing\nscript output, switching logs, and logging to files or
connections.","Imports":"assertthat (>= 0.1)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"luzlogr","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat, knitr, rmarkdown","Title":"Lightweight
Logging for R Scripts","Version":"0.2.0"},"lvm4net":{"Author":"Isabella Gollini
[aut, cre]","Depends":"R (>= 3.1.1), MASS, ergm, network,
ellipse","Description":"Latent variable models for network data using fast
inferential\nprocedures.","Imports":"igraph","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"lvm4net","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Latent Variable Models for
Networks","URL":"http:\/\/github.com\/igollini\/lvm4net","Version":"0.2"},"lxb":
{"Author":"BjÃ¶rn Winckler [aut, cre],\nJames K. Lawless [ctb, cph]","Depends":"R
(>= 2.8.0)","Description":"Functions to quickly read LXB parameter
data.","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"lxb","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Fast LXB File Reader","Version":"1.5"},"lymphclon":
{"Author":"Yi Liu [aut, cre],\nRichard A. Olshen [aut],\nAndrew Z. Fire
[ctb],\nScott D. Boyd [ctb]","Depends":"R (>= 2.15.0)","Description":"We provide a
clonality score estimator that takes full advantage of the multi-biological-
replicate structure of modern sequencing experiments; it specifically takes into
account the reality that, typically, the clonal coverage is well below
0.1%.","Imports":"MASS, expm, corpcor","License":"LGPL-
2","NeedsCompilation":"no","Package":"lymphclon","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Accurate Estimation of Clonal Coincidences and
Abundances from\nBiological Replicates","Version":"1.3.0"},"m4fe":{"Author":"Nathan
Esau <nesau@sfu.ca>","Depends":"R (>= 3.1.0)","Description":"Provides binomial tree
models for European, American and Asian\nOptions as well as Interest Rates. Monte
Carlo Simulation and Methods for\nSolving Differential Equations are also
2","NeedsCompilation":"no","Package":"m4fe","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Models for Financial Economics","Version":"0.1"},"mAr":
{"Author":"S. M. Barbosa","Depends":"MASS","Description":"R functions for
multivariate autoregressive analysis","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mAr","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Multivariate
AutoRegressive analysis","Version":"1.1-2"},"mBvs":{"Author":"Kyu Ha Lee, Mahlet
G. Tadesse, Brent A. Coull","Depends":"R (>= 3.1.3)","Description":"Bayesian
variable selection methods for data with continuous multivariate responses and
multiple covariates.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"mBvs","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Multivariate Bayesian Variable Selection Method
Exploiting\nDependence among Outcomes","Version":"1.0"},"mFilter":{"Author":"Mehmet
Balcilar <mbalcilar@yahoo.com>","Depends":"R (>= 2.2.0), stats","Description":"The
package implements several time series filters useful\nfor smoothing and extracting
trend and cyclical components of a\ntime series. The routines are commonly used in
economics and\nfinance, however they should also be interest to other
areas.\nCurrently, Christiano-Fitzgerald, Baxter-King,\nHodrick-Prescott,
Butterworth, and trigonometric regression\nfilters are included in the
2)","NeedsCompilation":"no","Package":"mFilter","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"tseries, pastecs, locfit, tseriesChaos, RTisean,
tsDyn,\nforecast","Title":"Miscellaneous time series
filters","URL":"http:\/\/www.mbalcilar.net\/mFilter, http:\/\/www.r-
project.org","Version":"0.1-3"},"mGSZ":{"Author":"Pashupati Mishra, Petri
Toronen","Depends":"R(>= 3.0.0),
Biobase,GSA,limma,MASS,ismev","Description":"Performs gene set analysis based on
GSZ scoring function and asymptotic p-value. It is different from GSZ in that it
implements asymptotic p-values instead of empirical p-values. Asymptotic p-values
are calculated by fitting suitable distribution model to the null distribution.
Unlike empirical p-values, resolution of asymptotic p-values are independent of the
number of permutations and hence requires considerably fewer permutations. In
addition, this package allows gene set analysis with seven other popular gene set
analysis methods.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mGSZ","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Gene set analysis based on GSZ-scoring function and
asymptotic\np-value","Version":"1.0"},"mHG":{"Author":"Kobi
Perl","Depends":"methods","Description":"Runs a minimum-hypergeometric (mHG) test
as described in: Eden, E. (2007). Discovering Motifs in Ranked Lists of DNA
Sequences. Haifa.","License":"GPL-
2","NeedsCompilation":"no","Package":"mHG","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"testthat","Title":"Minimum-Hypergeometric
Test","Version":"1.0"},"mQTL":{"Author":"Lyamine Hedjazi and Jean-Baptiste
Cazier","Depends":"R (>= 2.15.0), qtl, MASS, outliers","Description":"mQTL provides
a complete QTL analysis pipeline for metabolomic data.\nDistinctive features
include normalisation using PQN approach, peak alignment\nusing RSPA approach,
dimensionality reduction using SRV approach and finally\nQTL mapping using R\/qtl
package.","License":"GPL","NeedsCompilation":"yes","Package":"mQTL","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Title":"Metabolomic Quantitative Trait Locus
Mapping","Version":"1.0"},"mRMRe":{"Author":"Nicolas De Jay, Simon Papillon-
Cavanagh, Catharina Olsen, Gianluca Bontempi, Benjamin Haibe-Kains","Depends":"R
(>= 2.10), survival, igraph, methods","Description":"This package contains a set of
function to compute mutual information matrices from continuous, categorical and
survival variables. It also contains function to perform feature selection with
mRMR and a new ensemble mRMR technique.","License":"Artistic-
2.0","NeedsCompilation":"yes","Package":"mRMRe","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"R package for parallelized mRMR ensemble feature
selection","URL":"http:\/\/www.pmgenomics.ca\/bhklab\/","Version":"2.0.5"},"mRm":
{"Author":"David Preinerstorfer","Description":"Conditional maximum likelihood
estimation via the EM\nalgorithm and information-criterion-based model selection
in\nbinary mixed Rasch models.","License":"GPL-
2","NeedsCompilation":"yes","Package":"mRm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"An R package for conditional maximum likelihood estimation
in\nmixed Rasch models","Version":"1.1.5"},"maGUI":{"Author":"Dhammapal Bharne,
Praveen Kant, Vaibhav Vindal","Description":"Provides a Graphical User Interface
for Microarray Data Analysis. Protein protein interactions can also be predicted
from two normalized microarray data.","Imports":"Biobase, Biostrings,
BiocInstaller, RSQLite, pdInfoBuilder,\nconvert, marray, GEOquery, GEOmetadb,
annotate, RGtk2,\ngWidgets, gWidgetsRGtk2, tcltk, RBGL, grDevices, stats,
utils,\nlimma, affy, genefilter, simpleaffy, impute, oligo, beadarray,\nlumi,
GOstats, globaltest, WGCNA, ssize, graph, Rgraphviz","License":"GPL-
2","NeedsCompilation":"no","Package":"maGUI","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"A Graphical User Interface for Microarray Data
Analysis","Version":"1.0"},"maRketSim":{"Author":"Ari Friedman","Depends":"R (>=
2.15.1)","Description":"maRketSim is a market simulator for R. It was initially
designed\naround the bond market, with plans to expand to stocks. maRketSim
is\nbuilt around the idea of portfolios of fundamental objects. Therefore\nit is
slow in its current incarnation, but allows you the flexibility of\nseeing exactly
what is in your final results, since the objects are retained.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"maRketSim","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"taRifx, gsl","Title":"Market simulator for
R","Version":"0.9.2"},"maSAE":{"Author":"Andreas Dominik Cullmann [aut,
cre],\nDaniel Mandallaz [ctb],\nAlexander Francis Massey [ctb]","Depends":"methods,
stats","Description":"An S4 implementation of the unbiased extension of the
model-\nassisted synthetic-regression estimator proposed by\nMandallaz (2013)
<DOI:10.1139\/cjfr-2012-0381>,\nMandallaz et al. (2013) <DOI:10.1139\/cjfr-2013-
0181> and\nMandallaz (2014) <DOI:10.1139\/cjfr-2013-0449>.\nIt yields smaller
variances than the standard bias correction,\nthe generalised regression
estimator.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"maSAE","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"nlme","Title":"Mandallaz' Model-Assisted Small Area
Estimators","URL":"https:\/\/github.com\/fvafrCU\/maSAE","Version":"0.1-
4"},"maboost":{"Author":"Tofigh Naghibi","Depends":"R(>=
2.10),rpart,C50","Description":"Performs binary and multiclass boosting in maximum-
margin, sparse, smooth and normal settings\nas described in \"A Boosting Framework
on Grounds of Online Learning\" by T. Naghibi and B. Pfister, (2014).\nFor further
information regarding the algorithms, please refer to
http:\/\/arxiv.org\/abs\/1409.7202","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"maboost","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Binary and Multiclass Boosting
Algorithms","Version":"1.0-0"},"machina":{"Author":"Nelson Mark [aut],\nGursky
Michael [aut],\nKamal Akram [ctb],\nNorton Tim [cre]","Description":"Connects to
<https:\/\/machi.na\/>. and allows the creation\nof time series, and running
backtests on selected portfolio if requested.","Imports":"httr, jsonlite,
lubridate, xts, rhandsontable,
DT","License":"GPL","NeedsCompilation":"no","Package":"machina","Repository":"http:
\/\/cran.csiro.au\/src\/contrib","Title":"Machina Time Series Generation and
Backtesting","Version":"0.1.3"},"mada":{"Author":"Philipp
Doebler","Depends":"stats, mvtnorm, ellipse, mvmeta","Description":"Provides
functions for diagnostic meta-analysis. Next to basic analysis and visualization
the bivariate Model of Reitsma et al. (2005) that is equivalent to the HSROC of
Rutter&Gatsonis (2001) can be fitted. A new approach based to diagnostic meta-
analysis of Holling et al. (2012) is also available. Standard methods like summary,
plot and so on are provided.","License":"GPL-
2","NeedsCompilation":"no","Package":"mada","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Meta-Analysis of Diagnostic Accuracy","URL":"r-forge.r-
project.org\/projects\/mada\/","Version":"0.5.7"},"maddison":{"Author":"Eric
Persson [aut, cre]","Depends":"R(>= 2.10.0)","Description":"Contains the Maddison
Project database, which provides estimates of\nGDP per capita for all countries in
the world between AD 1 and 2010. See\nhttp:\/\/www.ggdc.net\/maddison for more
information.","License":"CC0","NeedsCompilation":"no","Package":"maddison","Reposit
ory":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"knitr, rmarkdown,
ggplot2","Title":"Maddison Project Database","URL":"http:\/\/www.ggdc.net\/maddison
https:\/\/github.com\/expersso\/maddison","Version":"0.1"},"madness":
{"Author":"Steven E. Pav [aut, cre]","Depends":"R (>= 3.2.0)","Description":"An
object that supports automatic differentiation\nof matrix- and multidimensional-
valued functions with\nrespect to multidimensional independent
variables.\nAutomatic differentiation is via 'forward
accumulation'.","Imports":"matrixcalc, expm, methods","License":"LGPL-
3","NeedsCompilation":"no","Package":"madness","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat, R.rsp, knitr","Title":"Automatic
Differentiation of Multivariate
Operations","URL":"https:\/\/github.com\/shabbychef\/madness","Version":"0.2.0"},"m
ads":{"Author":"Laura Marshall","Depends":"mrds, stats","Description":"Performs
distance sampling analyses on a number of species\naccounting for unidentified
sightings, model uncertainty and covariate\nuncertainty.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mads","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat","Title":"Multi-Analysis Distance
Sampling","Version":"0.1.3"},"madsim":{"Author":"Doulaye
Dembele","Description":"This function allows to generate two biological
conditions\nsynthetic
microarray dataset which has similar behavior to\nthose currently observed with
common platforms. User provides a\nsubset of parameters. Available default
parameters settings\ncan be modified.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"madsim","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"A Flexible Microarray Data Simulation
Model","Version":"1.1"},"magclass":{"Author":"Jan Philipp Dietrich,\nBenjamin
Bodirsky,\nMisko Stevanovic,\nLavinia Baumstark,\nChristoph Bertram,\nMarkus
Bonsch,\nAnastasis Giannousakis,\nFlorian Humpenoeder,\nDavid Klein,\nIna
Neher,\nMichaja Pehl,\nAnselm Schultes","Depends":"R(>=
2.10.0)","Description":"Data class for increased interoperability working with
spatial-temporal data together with corresponding functions and methods
(conversions, basic calculations and basic data manipulation). The class
distinguishes between spatial, temporal and other dimensions to facilitate the
development and interoperability of tools build for it. Additional features are
name-based addressing of data and internal consistency checks (e.g. checking for
the right data order in calculations).","Imports":"methods, sp, maptools, abind,
ncdf4, reshape2","License":"LGPL-3 | file
LICENSE","NeedsCompilation":"no","Package":"magclass","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Data Class and Tools for Handling Spatial-Temporal
Data","Version":"3.74"},"magic":{"Author":"Robin K. S. Hankin","Depends":"R (>=
2.10), abind","Description":"a collection of efficient, vectorized algorithms for
the\ncreation and investigation of magic squares and hypercubes, including\na
variety of functions for the manipulation and analysis of\narbitrarily dimensioned
arrays. The package includes methods for\ncreating normal magic squares of any
order greater than 2. The\nultimate intention is for the package to be a
computerized embodiment\nall magic square knowledge, including direct numerical
verification\nof properties of magic squares (such as recent results on
the\ndeterminant of odd-ordered semimagic squares). Some antimagic\nfunctionality
is included. The package also\nserves as a rebuttal to the often-heard comment \"I
thought R\nwas just for statistics\".","License":"GPL-
2","NeedsCompilation":"no","Package":"magic","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"create and investigate magic squares","Version":"1.5-
6"},"magicaxis":{"Author":"Aaron Robotham","Depends":"R (>= 2.13), MASS, plotrix,
sm","Description":"Functions to make useful (and pretty) plots for scientific
plotting. Additional plotting features are added for base plotting, with particular
emphasis on making attractive log axis plots.","License":"GPL-
3","NeedsCompilation":"no","Package":"magicaxis","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Pretty Scientific Plotting with Minor-Tick and log
Minor-Tick\nSupport","Version":"1.9.4"},"magrittr":{"Author":"Stefan Milton Bache
<stefan@stefanbache.dk> and\nHadley Wickham
<h.wickham@gmail.com>","Description":"Provides a mechanism for chaining commands
with a\nnew forward-pipe operator, %>%. This operator will forward a\nvalue, or the
result of an expression, into the next function\ncall\/expression. There is
flexible support for the type\nof right-hand side expressions. For more
information, see\npackage vignette.\nTo quote Rene Magritte, \"Ceci n'est pas un
pipe.\"","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"magrittr","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat, knitr","Title":"A Forward-Pipe
Operator for R","Version":"1.5"},"mail":{"Author":"Statistical Consulting -
intelligent data analysis, stochastic modelling and statistical inference, Dr. Lin
Himmelmann","Depends":"R (>= 2.0.0)","Description":"Easy to use package for sending
email notifications with status information from R","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mail","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Sending Email Notifications from
R","URL":"www.linhi.com","Version":"1.0"},"mailR":{"Author":"Rahul
Premraj","Description":"Interface to Apache Commons Email to send emails\nfrom
R.","Imports":"rJava, stringr, R.utils","License":"GPL-
3","NeedsCompilation":"no","Package":"mailR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"A Utility to Send Emails from
R","URL":"https:\/\/github.com\/rpremraj\/mailR","Version":"0.4.1"},"makeProject":
{"Author":"Noah Silverman","Description":"This package creates an empty framework
of files and\ndirectories for the \"Load, Clean, Func, Do\" structure described\nby
Josh Reich.","License":"GPL-
3","NeedsCompilation":"no","Package":"makeProject","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Creates an empty package framework for the LCFD
format","Version":"1.0"},"mallet":{"Author":"David
Mimno","Depends":"rJava","Description":"This package allows you to train topic
models in mallet and load results directly into R.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"mallet","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"A wrapper around the Java machine learning tool
MALLET","Version":"1.0"},"managelocalrepo":{"Author":"Imanuel Costigan
<i.costigan@me.com>","Depends":"R (>= 3.0)","Description":"This will allow easier
management of a CRAN-style repository on\nlocal networks (i.e. not on CRAN). This
might be necessary where hosted\npackages contain intellectual property owned by a
corporation.","Imports":"stringr (>= 0.6.2), assertthat (>= 0.1), tools (>=
2","NeedsCompilation":"no","Package":"managelocalrepo","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Manage a CRAN-Style Local
Repository","Version":"0.1.5"},"mangoTraining":{"Author":"Mango Solutions
<rin24hours@mango-solutions.com>","Depends":"R (>= 2.10.0)","Description":"Datasets
designed to be used in conjunction with Mango Solutions\ntraining materials and the
book SAMS Teach Yourself R in 24 Hours (ISBN: 978-0-672-33848-9).","License":"GPL-
2","NeedsCompilation":"no","Package":"mangoTraining","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Mango Solutions Training
Datasets","URL":"http:\/\/www.mango-solutions.com","Version":"1.0-6"},"manifestoR":
{"Author":"Jirka Lewandowski [aut, cre],\nNicolas Merz [aut],\nSven Regel
[ctb],\nPola Lehmann [ctb]","Depends":"R (>= 3.1.0), NLP (>= 0.1-3), tm (>= 0.6),
dplyr (>= 0.4.3)","Description":"Provides access to coded election programmes from
the Manifesto\nCorpus and to the Manifesto Project's Main Dataset and routines to
analyse this\ndata. The Manifesto Project (https:\/\/manifesto-project.wzb.eu)
collects and\nanalyses election programmes across time and space to measure the
political\npreferences of parties. The Manifesto Corpus contains the collected
and\nannotated election programmes in the Corpus format of the package 'tm' to
enable\neasy use of text processing and text mining functionality. Specific
functions\nfor scaling of coded political texts are included.","Imports":"utils,
stats, magrittr, httr (>= 1.0.0), jsonlite (>= 0.9.12),\nfunctional (>= 0.6), zoo
(>= 1.7-11), psych, base64enc","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"manifestoR","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr, rmarkdown, testthat, R.rsp, haven, readxl,
devtools\n(>= 1.7.0)","Title":"Access and Process Data and Documents of the
Manifesto
Project","URL":"https:\/\/github.com\/ManifestoProject\/manifestoR,\nhttps:\/\/mani
festo-project.wzb.eu\/","Version":"1.2"},"manipulate":{"Author":"JJ Allaire [aut,
cre] (R interface),\nRStudio [cph]","Depends":"R (>=
2.11.1)","Description":"Interactive plotting functions for use within RStudio.\nThe
manipulate function accepts a plotting expression and a set of\ncontrols (e.g.
slider, picker, checkbox, or button) which are used\nto dynamically change values
within the expression. When a value is\nchanged using its corresponding control the
expression is\nautomatically re-executed and the plot is redrawn.","License":"GPL-
2","NeedsCompilation":"no","Package":"manipulate","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Interactive Plots for
RStudio","Version":"1.0.1"},"mapStats":{"Author":"Samuel Ackerman","Depends":"R (>=
3.0.2), survey, lattice, maptools","Description":"Automated calculation and
visualization of survey data statistics on a color-coded
map.","Imports":"RColorBrewer, Hmisc, classInt, sp, colorspace,
2)","NeedsCompilation":"no","Package":"mapStats","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Geographic Display of Survey Data
Statistics","Version":"2.4"},"mapdata":{"Author":"Original S code by Richard A.
Becker and Allan R. Wilks.\nR version by Ray Brownrigg
<Ray.Brownrigg@ecs.vuw.ac.nz>.","Depends":"R (>= 2.14.0), maps (>= 2.0-
7)","Description":"Supplement to maps package, providing the larger
and\/or\nhigher-resolution databases.","License":"GPL-
2","NeedsCompilation":"yes","Package":"mapdata","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Extra Map Databases","Version":"2.2-6"},"mapfit":
{"Author":"Hiroyuki Okamura","Depends":"methods, Matrix","Description":"Estimation
methods for phase-type\ndistribution (PH) and Markovian arrival process (MAP)
from\nempirical data (point and grouped data) and density function.","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"mapfit","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"A Tool for PH\/MAP Parameter
Estimation","Version":"0.9.7"},"mapmisc":{"Author":"Patrick Brown
<patrick.brown@utoronto.ca>","Depends":"sp, raster, R (>= 3.0.0)","Description":"A
minimal, light-weight set of tools for producing nice looking maps in R, with
support for map projections.","Enhances":"maptools","Imports":"methods, grDevices,
stats, utils,
graphics","License":"GPL","NeedsCompilation":"no","Package":"mapmisc","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Sugg
ests":"RColorBrewer, geonames, classInt, rgdal, rgeos, geosphere,\nknitr,
dismo","Title":"Utilities for Producing Maps","Version":"1.4.6"},"mapplots":
{"Author":"Hans Gerritsen","Depends":"R (>= 2.10.0)","Description":"Create simple
maps; add sub-plots like pie plots to a map or any other plot; format, plot and
export gridded data. The package was developed for displaying fisheries data but
most functions can be used for more generic data visualisation.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mapplots","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"shapefiles","Title":"Data Visualisation on
Maps","Version":"1.5"},"mapproj":{"Author":"Doug McIlroy. Packaged for R by Ray
Brownrigg and Thomas P\nMinka, transition to Plan 9 codebase by Roger
Bivand.","Depends":"maps (>= 2.3-0)","Description":"Converts latitude\/longitude
into projected coordinates.","Imports":"stats, graphics","License":"Lucent Public
License","NeedsCompilation":"yes","Package":"mapproj","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Map Projections","Version":"1.2-4"},"mapr":
{"Author":"Scott Chamberlain [aut, cre]","Description":"Utilities for 'vizualizing'
species occurrence data. Includes\nfunctions to 'vizualize' occurrence data from
'spocc', 'rgbif',\nand other packages. Mapping options included for base R plots,
'ggplot2',\nand various interactive maps.","Imports":"methods, utils, stats,
graphics, ggplot2, leaflet, spocc (>=\n0.4.5), sp, rworldmap, RColorBrewer, httr
(>= 1.0.0), gistr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"mapr","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat, ggmap, knitr, taxize,
maptools","Title":"'Visualize' Species Occurrence
Data","URL":"https:\/\/github.com\/ropensci\/mapr","Version":"0.2.0"},"maps":
{"Author":"Original S code by Richard A. Becker and Allan R. Wilks.\nR version by
Ray Brownrigg.\nEnhancements by Thomas P Minka and Alex Deckmyn.","Depends":"R (>=
2.14.0)","Description":"Display of maps. Projection code and larger maps are
in\nseparate packages ('mapproj' and 'mapdata').","Imports":"graphics,
2","NeedsCompilation":"yes","Package":"maps","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"mapproj (>= 1.2-0), mapdata (>= 2.2-4), sp,
maptools","Title":"Draw Geographical Maps","Version":"3.1.0"},"maptools":
{"Author":"Roger Bivand [cre, aut],\nNicholas Lewin-Koh [aut],\nEdzer Pebesma
[ctb],\nEric Archer [ctb],\nAdrian Baddeley [ctb],\nNick Bearman [ctb],\nHans-JÃ¶rg
Bibiko [ctb],\nSteven Brey [ctb],\nJonathan Callahan [ctb],\nGerman Carrillo
[ctb],\nStÃ©phane Dray [ctb],\nDavid Forrest [ctb],\nMichael Friendly
[ctb],\nPatrick Giraudoux [ctb],\nDuncan Golicher [ctb],\nVirgilio GÃ³mez Rubio
[ctb],\nPatrick Hausmann [ctb],\nKarl Ove Hufthammer [ctb],\nThomas Jagger
[ctb],\nKent Johnson [ctb],\nSebastian Luque [ctb],\nDon MacQueen [ctb],\nAndrew
Niccolai [ctb],\nEdzer Pebesma [ctb],\nOscar PerpiÃ±Ã¡n Lamigueiro [ctb],\nTom
Short [ctb],\nGreg Snow [ctb],\nBen Stabler [ctb],\nMurray Stokely [ctb],\nRolf
Turner [ctb]","Depends":"R (>= 2.10), sp (>= 1.0-11)","Description":"Set of tools
for manipulating and reading geographic data, in particular ESRI shapefiles; C code
used from shapelib. It includes binary access to GSHHG shoreline files. The package
also provides interface wrappers for exchanging spatial objects with packages such
as PBSmapping, spatstat, maps, RArcInfo, Stata tmap, WinBUGS, Mondrian, and
others.","Enhances":"gpclib, RArcInfo","Imports":"foreign (>= 0.8), methods, grid,
lattice, stats, utils,\ngrDevices","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"maptools","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"rgeos (>= 0.1-8), spatstat (>= 1.18), PBSmapping,
maps,\nRColorBrewer, raster, polyclip","Title":"Tools for Reading and Handling
Spatial Objects","URL":"http:\/\/r-forge.r-
project.org\/projects\/maptools\/","Version":"0.8-39"},"maptpx":{"Author":"Matt
Taddy <taddy@chicagobooth.edu>","Depends":"R (>= 2.10),
slam","Description":"Posterior maximization for topic models (LDA) in text
analysis,\nas described in Taddy (2012) òn estimation and selection for topic
models'. Previous versions of this code were included as part of the textir
package. If you want to take advantage of openmp parallelization, uncomment the
relevant flags in src\/MAKEVARS before compiling.","License":"GPL-
3","NeedsCompilation":"yes","Package":"maptpx","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"MASS","Title":"MAP Estimation of Topic
Models","URL":"http:\/\/faculty.chicagobooth.edu\/matt.taddy\/index.html","Version"
:"1.9-2"},"maptree":{"Author":"Denis White, Robert B. Gramacy
<rbgramacy@chicagobooth.edu>","Depends":"R (>= 2.14), cluster,
rpart","Description":"Functions with example data for graphing, pruning,
and\nmapping models from hierarchical clustering, and classification\nand
regression
trees.","License":"Unlimited","NeedsCompilation":"no","Package":"maptree","Reposito
ry":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Mapping, pruning, and graphing
tree models","Version":"1.4-7"},"mapview":{"Author":"Tim Appelhans [cre,
aut],\nFlorian Detsch [aut],\nChristoph Reudenbach [aut],\nStefan Woellauer
[aut],\nSpaska Forteva [ctb],\nThomas Nauss [ctb],\nEnvironmental Informatics
Marburg [ctb]","Depends":"R (>= 2.10), leaflet, methods","Description":"Methods to
view spatial objects interactively.","Imports":"sp, raster, satellite, scales (>=
0.2.5), brew, htmlwidgets,\nhtmltools, png, Rcpp (>= 0.11.3), lattice,
latticeExtra, rgdal,\ngdalUtils, data.table, rasterVis,
OpenStreetMap","License":"GPL (>= 3) | file
LICENSE","NeedsCompilation":"yes","Package":"mapview","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Interactive Viewing of Spatial Objects in
R","Version":"1.0.0"},"mar1s":{"Author":"Andrey Paramonov","Depends":"cmrutils,
fda, zoo","Description":"Multiplicative AR(1) with Seasonal is a
stochastic\nprocess model built on top of AR(1). The package provides
the\nfollowing procedures for MAR(1)S processes: fit, compose, decompose,\nadvanced
simulate and predict.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"mar1s","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Multiplicative AR(1) with Seasonal
Processes","URL":"http:\/\/aparamon.msk.ru\/svn\/study\/R-
packages\/mar1s\/","Version":"2.1"},"marelac":{"Author":"Karline Soetaert
<karline.soetaert@nioz.nl>,\nThomas Petzoldt <thomas.petzoldt@tu-
dresden.de>,\nFilip Meysman <filip.meysman@nioz.nl>","Depends":"R (>= 2.10), shape,
seacarb","Description":"Datasets, constants, conversion factors, utilities for
MArine, Riverine,\nEstuarine, LAcustrine and Coastal science.\nThe package contains
among others: (1) chemical and\nphysical constants and datasets, e.g. atomic
weights, gas\nconstants, the earths bathymetry; (2) conversion factors\n(e.g. gram
to mol to liter, barometric units,\ntemperature, salinity); (3) physical functions,
e.g. to\nestimate concentrations of conservative substances, gas\ntransfer and
diffusion coefficients, the Coriolis force\nand gravity; (4) thermophysical
properties of the\nseawater, as from the UNESCO polynomial or from the more\nrecent
derivation based on a Gibbs function.","Imports":"stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"marelac","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Tools for Aquatic Sciences","Version":"2.1.5"},"marg":
{"Author":"S original by Alessandra R. Brazzale <alessandra.brazzale@unipd.it>.\nR
port by Alessandra R. Brazzale <alessandra.brazzale@unipd.it>, following\nearlier
work by Douglas Bates.","Depends":"R (>= 3.0.0), statmod,
survival","Description":"Likelihood inference based on higher order
approximations\nfor linear nonnormal regression models","License":"GPL (>= 2) |
file
LICENCE","NeedsCompilation":"no","Package":"marg","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"boot, cond, csampling, nlreg","Title":"Approximate
marginal inference for regression-scale models","URL":"http:\/\/www.r-project.org,
http:\/\/statwww.epfl.ch\/AA\/","Version":"1.2-2"},"marima":{"Author":"Henrik
Spliid","Description":"Multivariate time series estimation using Spliid's
2","NeedsCompilation":"no","Package":"marima","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Multivariate ARIMA Analysis","Version":"1.3"},"markdown":
{"Author":"JJ Allaire, Jeffrey Horner, Vicent Marti, and Natacha
Porte","Depends":"R (>= 2.11.1)","Description":"Provides R bindings to the
'Sundown' 'Markdown' rendering library\n(https:\/\/github.com\/vmg\/sundown).
'Markdown' is a plain-text formatting\nsyntax that can be converted to 'XHTML' or
other formats. See\nhttp:\/\/en.wikipedia.org\/wiki\/Markdown for more information
about 'Markdown'.","Imports":"mime (>= 0.3)","License":"GPL-
2","NeedsCompilation":"yes","Package":"markdown","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr, RCurl","Title":"'Markdown' Rendering for
R","URL":"https:\/\/github.com\/rstudio\/markdown","Version":"0.7.7"},"marked":
{"Author":"Jeff Laake <jeff.laake@noaa.gov>, Devin
Johnson\n<devin.johnson@noaa.gov>, Paul Conn <paul.conn@noaa.gov>","Depends":"R (>=
2.15.0), lme4, methods, parallel","Description":"Functions for fitting various
models to capture-recapture data\nincluding fixed and mixed-effects Cormack-Jolly-
Seber(CJS) for survival\nestimation and POPAN structured Jolly-Seber models for
abundance\nestimation. Includes a CJS models that concurrently estimates and
corrects\nfor tag loss. Hidden Markov model (HMM) implementations of CJS
and\nmultistate models with and without state uncertainty.","Imports":"graphics,
stats, utils, R2admb, truncnorm, coda, Matrix,\nnumDeriv, expm, Rcpp (>= 0.9.13),
optimx (>= 2013.8.6)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"marked","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"ggplot2","Title":"M
ark-Recapture Analysis for Survival and Abundance
Estimation","Version":"1.1.11"},"markmyassignment":{"Author":"Mans Magnusson, Oscar
Pettersson","Depends":"R (>= 3.1.0), methods, yaml, testthat (>= 0.11.0), httr
(>=\n1.0.0)","Description":"Automatic marking of R assignments for students and
teachers based\non 'testthat' test
suites.","Imports":"codetools","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"markmyassignment","Repository":"http:\/
\/cran.csiro.au\/src\/contrib","Suggests":"knitr, rmarkdown","Title":"Automatic
Marking of R Assignments","Version":"0.5.0"},"markophylo":{"Author":"Utkarsh J.
Dang and G. Brian Golding","Depends":"R (>= 2.10)","Description":"Allows for
fitting of maximum likelihood models using Markov chains\non phylogenetic trees for
analysis of discrete character data. Examples of such\ndiscrete character data
include restriction sites, gene family presence\/absence,\nintron
presence\/absence, and gene family size data. Hypothesis-driven user-\nspecified
substitution rate matrices can be estimated. Allows for biologically\nrealistic
models combining constrained substitution rate matrices, site rate\nvariation, site
partitioning, branch-specific rates, allowing for non-stationary\nprior root
probabilities, correcting for sampling bias, etc.","Imports":"Rcpp (>= 0.11.4), ape
(>= 3.2), numDeriv (>= 2012.9.1),\nphangorn (>= 1.99.13)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"markophylo","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"knitr (>= 1.10), testthat (>=
0.9.1)","Title":"Markov Chain Models for Phylogenetic
Trees","Version":"1.0.4"},"markovchain":{"Author":"Giorgio Alfredo Spedicato
[aut,cre], Tae Seung Kang [aut], Sai Bhargav Yalamanchi [aut], Mildenberger Thoralf
[ctb]","Depends":"R (>= 3.0.0), methods","Description":"Functions and S4 methods to
create and manage discrete time Markov chains (DTMC) more easily. In addition
functions to perform statistical (fitting and drawing random variates) and
probabilistic (analysis of DTMC proprieties) analysis are
provided.","Imports":"igraph, Matrix, matlab, expm, stats4, parallel, Rcpp
(>=\n0.11.5), RcppParallel, utils, stats","License":"GPL-
2","NeedsCompilation":"yes","Package":"markovchain","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"knitr, testthat, diagram, DiagrammeR, msm, etm,
Rsolnp,\nknitcitations, rmarkdown","Title":"Easy Handling Discrete Time Markov
Chains","URL":"http:\/\/github.com\/spedygiorgio\/markovchain\/","Version":"0.4.3.1
"},"marl":{"Author":"Milan Bimali","Description":"Functions provided allow data
simulation; construction of weighted relative likelihood functions; clustering and
principal component analysis based on weighted relative likelihood
functions.","License":"GPL-
2","NeedsCompilation":"no","Package":"marl","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Multivariate Analysis Based on Relative
Likelihoods","Version":"1.0"},"marmap":{"Author":"Eric Pante, Benoit Simon-Bouhet,
and Jean-Olivier Irisson","Depends":"R (>= 2.10)","Description":"Import xyz data
from the NOAA, GEBCO and other sources, plot xyz data to prepare publication-ready
figures, analyze xyz data to extract transects, get depth \/ altitude based on
geographical coordinates, or calculate z-constrained least-cost
paths.","Imports":"DBI, RSQLite, gdistance, geosphere, sp, raster, ncdf4,\nplotrix,
shape, reshape2, adehabitatMA, ggplot2, methods","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"marmap","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"maps, mapdata, lattice, mapproj,
R.rsp","Title":"Import, Plot and Analyze Bathymetric and Topographic
Data","Version":"0.9.5"},"marqLevAlg":{"Author":"D. Commenges
<Daniel.Commenges@isped.u-bordeaux2.fr>, M. Prague\n<Melanie.Prague@isped.u-
bordeaux2.fr> and A. Diakite","Depends":"R (>= 2.0.0)","Description":"This
algorithm provides a numerical solution to the\nproblem of minimizing a function.
This is more efficient than\nthe Gauss-Newton-like algorithm when starting from
points very\nfar from the final minimum. A new convergence test is\nimplemented
(RDM) in addition to the usual stopping criterion :\nstopping rule is when the
gradients are small enough in the\nparameters metric (GH-1G).","License":"GPL (>=
2.0)","NeedsCompilation":"yes","Package":"marqLevAlg","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"An algorithm for least-squares curve
fitting","URL":"http:\/\/www.r-project.org","Version":"1.1"},"matR":
{"Author":"Daniel Braithwaite [aut, cre],\nKevin Keegan [aut],\nUniversity of
Chicago [cph]","Depends":"R (>= 2.10), MGRASTer, BIOM.utils, graphics, stats,
utils","Description":"An analysis platform for metagenomics combining\nspecialized
tools and workflows, easy handling of the BIOM\nformat, and transparent access to
MG-RAST resources. matR integrates\neasily with other R packages and non-R
software.","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"matR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"RJSONIO, qvalue, ecodist, gplots,
scatterplot3d","Title":"Metagenomics Analysis Tools for
R","URL":"https:\/\/github.com\/MG-RAST\/matR\/","Version":"0.9"},"matchMulti":
{"Author":"Luke Keele and Sam Pimentel","Depends":"R (>=
3.2.3)","Description":"Performs multilevel matches for data with cluster-level
treatments and individual-level outcomes using a network optimization algorithm.
Functions for checking balance at the cluster and individual levels are also
provided, as are methods for permutation-inference-based outcome
analysis.","Imports":"rcbsubset, plyr, coin, weights, mvtnorm,
MASS,Hmisc","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"matchMulti","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"optmatch, testthat","Title":"Optimal
Multilevel Matching using a Network Algorithm","Version":"1.1"},"matchingMarkets":
{"Author":"Thilo Klein","Depends":"R (>= 3.0.2)","Description":"Implements
structural estimators to correct for\nthe sample selection bias from observed
outcomes in matching\nmarkets. This includes one-sided matching of agents
into\ngroups as well as two-sided matching of students to schools.\nThe package
also contains R code for three matching algorithms:\nthe deferred-acceptance (or
Gale-Shapley) algorithm for\nstable marriage and college admissions problems,
the\ntop-trading-cycles algorithm for house allocation and a\npartitioning linear
programme for the roommates problem.","Imports":"Rcpp (>= 0.11.2), lpSolve (>=
5.6.6), partitions, stats","License":"GPL (>= 2) | file
LICENSE","NeedsCompilation":"yes","Package":"matchingMarkets","Repository":"http:\/
\/cran.csiro.au\/src\/contrib","Suggests":"knitr, testthat","Title":"Analysis of
Stable
Matchings","URL":"https:\/\/github.com\/thiloklein\/matchingMarkets,\nhttp:\/\/matc
hingmarkets.r-forge.r-project.org, http:\/\/klein.uk","Version":"0.2-
1"},"matchingR":{"Author":"Jan Tilly, Nick
Janetos","Depends":"Rcpp","Description":"Computes matching algorithms quickly using
Rcpp.\nImplements the Gale-Shapley Algorithm to compute the stable\nmatching for
two-sided markets, such as the stable marriage\nproblem and the college-admissions
problem. Implements Irving's\nAlgorithm for the stable roommate problem. Implements
the top\ntrading cycle algorithm for the indivisible goods trading
problem.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"matchingR","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat, knitr, microbenchmark","Title":"Matching
Algorithms in R and C+
+","URL":"https:\/\/github.com\/jtilly\/matchingR\/","Version":"1.2.1"},"matconv":
{"Author":"Siddarta Jairam [aut, cre],\nDavid Hiebeler
[ctb]","Description":"Transferring over a code base from Matlab to R is often a
repetitive\nand inefficient use of time. This package provides a translator for
Matlab \/\nOctave code into R code. It does some syntax changes, but most of the
heavy\nlifting is in the function changes since the languages are so
similar.\nOptions for different data structures and the functions that can be
changed\nare given. The Matlab code should be mostly in adherence to the
standard\nstyle guide but some effort has been made to accommodate different number
of\nspaces and other small syntax issues. This will not make the code more
R\nfriendly and may not even run afterwards. However, the rudimentary syntax,\nbase
function and data structure conversion is done quickly so that the\nmaintainer can
focus on changes to the design structure.","Imports":"methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"matconv","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr, testthat","Title":"A Code Converter from the
Matlab\/Octave Language to R","Version":"0.3.0"},"mateable":{"Author":"Stuart
Wagenius [cre, aut],\nDanny Hanson [aut],\nAmy Waananen [aut]","Description":"Tools
to simulate, manage, visualize, and analyze\nspatially and temporally explicit
datasets of mating potential.\nImplements methods to calculate synchrony,
proximity, and compatibility.","Imports":"FNN, graphics, grDevices, Rcpp, sn,
stats","License":"GPL","NeedsCompilation":"yes","Package":"mateable","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Suggests":"knitr, rmarkdown","Title":"Tools
to Assess Mating Potential in Space and
Time","URL":"https:\/\/github.com\/stuartWagenius\/mateable","Version":"0.3.1"},"ma
thgraph":{"Author":"Original S code by Patrick J. Burns. Ported to R by
Nick\nEfthymiou. Adapted to new R releases by Claus Dethlefsen.","Depends":"R (>=
2.1.1)","Description":"Simple tools for constructing and manipulating objects
of\nclass mathgraph from the book \"S Poetry\", available at\nhttp:\/\/www.burns-
stat.com\/pages\/spoetry.html","License":"file
LICENSE","NeedsCompilation":"no","Package":"mathgraph","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Directed
and undirected graphs","Version":"0.9-11"},"matie":{"Author":"Ben Murrell, Dan
Murrell & Hugh Murrell.","Description":"Uses a ratio of weighted distributions to
estimate association between variables in a data set.","Imports":"dfoptim, mvtnorm,
seriation, igraph, gplots, cba","License":"GPL-
3","NeedsCompilation":"yes","Package":"matie","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Measuring Association and Testing Independence
Efficiently","Version":"1.2"},"matlab":{"Author":"P. Roebuck","Depends":"R (>=
2.15)","Description":"Emulate MATLAB code using
R","Imports":"methods","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"matlab","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"MATLAB emulation package","URL":"http:\/\/cran.r-
project.org\/package=matlab","Version":"1.0.2"},"matlabr":{"Author":"John Muschelli
<muschellij2@gmail.com>","Description":"Provides users to call MATLAB from using
the \"system\" command.\nAllows users to submit lines of code or MATLAB m
files.\nThis is in comparison to 'R.matlab', which creates a MATLAB
server.","Imports":"stringr","License":"GPL-
3","NeedsCompilation":"no","Package":"matlabr","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"An Interface for MATLAB using System
Calls","Version":"1.1"},"matlib":{"Author":"Michael Friendly [aut, cre], John Fox
[aut], Georges Monette [ctb], Gaston Sanchez [ctb]","Description":"A collection of
matrix functions for teaching and learning matrix\nlinear algebra as used in
multivariate statistical methods. These functions are\nmainly for tutorial purposes
in learning matrix algebra ideas using R. In some\ncases, functions are provided
for concepts available elsewhere in R, but where\nthe function call or name is not
obvious. In other cases, functions are provided\nto show or demonstrate an
algorithm. In addition, a collection of functions are\nprovided for drawing vector
diagrams in 2D and 3D.","Imports":"rgl","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"matlib","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"MASS, knitr, rglwidget, rmarkdown, car","Title":"Matrix
Functions for Teaching and Learning Linear Algebra and\nMultivariate
Statistics","URL":"https:\/\/github.com\/friendly\/matlib","Version":"0.7.2"},"matp
ow":{"Author":"Norm Matloff, Jack Norman","Description":"A general framework for
computing powers of matrices. A\nkey feature is the capability for users to write
callback functions,\ncalled after each iteration, thus enabling customization for
specific\napplications. Diverse types of matrix classes\/matrix
multiplication\nare accommodated. If the multiplication type computes in
parallel,\nthen the package computation is also parallel.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"matpow","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"bigmemory, gputools","Title":"matrix
powers","Version":"0.1.1"},"matrixStats":{"Author":"Henrik Bengtsson [aut, cre,
cph], Hector Corrada Bravo [ctb], Robert Gentleman [ctb], Ola Hossjer [ctb], Harris
Jaffee [ctb], Dongcan Jiang [ctb], Peter Langfelder [ctb]","Depends":"R (>=
2.12.0)","Description":"High-performing functions operating on rows and columns of
matrices, e.g. col \/ rowMedians(), col \/ rowRanks(), and col \/ rowSds().
Functions optimized per data type and for subsetted calculations such that both
memory usage and processing time is minimized. There are also optimized vector-
based methods, e.g. binMeans(), madDiff() and
weightedMedians().","Imports":"methods","License":"Artistic-
2.0","NeedsCompilation":"yes","Package":"matrixStats","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"base64enc, ggplot2, knitr, microbenchmark,
R.devices, R.rsp","Title":"Functions that Apply to Rows and Columns of Matrices
(and
to\nVectors)","URL":"https:\/\/github.com\/HenrikBengtsson\/matrixStats","Version":
"0.50.1"},"matrixcalc":{"Author":"Frederick Novomestky
<fnovomes@poly.edu>","Depends":"R (>= 2.0.1)","Description":"A collection of
functions to support matrix calculations\nfor probability, econometric and
numerical analysis. There are\nadditional functions that are comparable to APL
functions which\nare useful for actuarial models such as pension mathematics.\nThis
package is used for teaching and research purposes at the\nDepartment of Finance
and Risk Engineering, New York\nUniversity, Polytechnic Institute, Brooklyn, NY
11201.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"matrixcalc","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Collection of functions for matrix
calculations","Version":"1.0-3"},"matrixpls":{"Author":"Mikko RÃ¶nkkÃ¶ [aut,
cre]","Description":"Partial Least Squares Path Modeling\nalgorithm and related
algorithms. The algorithm implementations aim for\ncomputational efficiency using
matrix algebra and covariance data. The\npackage is designed toward Monte Carlo
simulations and includes functions\nto perform simple Monte Carlo
simulations.","Imports":"assertive, matrixcalc, lavaan, psych, MASS,
3","NeedsCompilation":"no","Package":"matrixpls","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"plspm, simsem, RUnit, parallel, semPLS, boot, Matrix,
ASGSCA","Title":"Matrix-Based Partial Least Squares
Estimation","URL":"https:\/\/github.com\/mronkko\/matrixpls","Version":"0.7.0"},"ma
xLik":{"Author":"Ott Toomet <otoomet@gmail.com>,\nArne Henningsen
<arne.henningsen@gmail.com>,\nwith contributions from Spencer Graves and Yves
Croissant","Depends":"R (>= 2.4.0), miscTools (>= 0.6-8),
methods","Description":"Functions for Maximum Likelihood (ML) estimation and non-
linear\noptimization, and related tools. It includes a unified way to
call\ndifferent optimizers, and classes and methods to handle the results from\nthe
ML viewpoint. It also includes a number of convenience tools for testing\nand
developing your own models.","Imports":"sandwich","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"maxLik","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Maximum Likelihood Estimation and Related
Tools","URL":"http:\/\/www.maxLik.org","Version":"1.3-4"},"maxent":
{"Author":"Timothy P. Jurka, Yoshimasa Tsuruoka","Depends":"R (>= 2.13.0), methods,
SparseM, tm","Description":"maxent is an R package with tools for low-
memory\nmultinomial logistic regression, also known as maximum entropy.\nThe focus
of this maximum entropy classifier is to minimize\nmemory consumption on very large
datasets, particularly sparse\ndocument-term matrices represented by the tm
package. The\nclassifier is based on an efficient C++ implementation written\nby
Dr. Yoshimasa Tsuruoka.","Imports":"Rcpp","License":"GPL-
3","NeedsCompilation":"yes","Package":"maxent","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Low-memory Multinomial Logistic Regression with Support
for Text\nClassification","Version":"1.3.3.1"},"maxlike":{"Author":"Richard
Chandler and Andy Royle","Depends":"R (>= 2.10.0), raster","Description":"Provides
a likelihood-based approach to modeling species distributions using presence-only
data. In contrast to the popular software program MAXENT, this approach yields
estimates of the probability of occurrence, which is a natural descriptor of a
species' distribution.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"maxlike","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Model species distributions by estimating the probability
of\noccurrence using presence-only data","Version":"0.1-5"},"maxstat":
{"Author":"Torsten Hothorn","Depends":"R (>= 1.7.0)","Description":"Maximally
selected rank statistics with\nseveral p-value
approximations.","Imports":"exactRankTests(>= 0.8-23), mvtnorm(>= 0.5-10), stats,
2)","NeedsCompilation":"yes","Package":"maxstat","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"TH.data, survival","Title":"Maximally Selected Rank
Statistics","Version":"0.7-24"},"mbbefd":{"Author":"Giorgio Spedicato [aut,
cre],\nChristophe Dutang [aut],\nMarkus Gesmann [ctb]","Depends":"R (>= 2.14),
fitdistrplus (>= 1.0-5), alabama","Description":"Distributions that are typically
used for exposure rating in\ngeneral insurance, in particular to price reinsurance
contracts.\nThe vignettes show code snippets to fit the distribution to\nempirical
data.","Imports":"Rcpp, utils, actuar, gsl, MASS","License":"GPL-
2","NeedsCompilation":"yes","Package":"mbbefd","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat, copula, pander, knitcitations, rmarkdown,
knitr,\nlattice","Title":"Maxwell Boltzmann Bose Einstein Fermi Dirac Distribution
and\nDestruction Rate
Modelling","URL":"http:\/\/github.com\/spedygiorgio\/mbbefd","Version":"0.8-
0"},"mbest":{"Author":"Patrick O. Perry [aut, cre],\nTimothy Sweetser
[ctb]","Depends":"nlme (>= 3.1-124)","Description":"Implements methods from the
paper\n\"Fast Moment-Based Estimation for Hierarchical Models,\" by Perry
(2016).","Imports":"lme4, bigmemory, foreach, logging","License":"Apache License
(== 2.0) | file
LICENSE","NeedsCompilation":"yes","Package":"mbest","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat","Title":"Moment-Based Estimation for
Hierarchical Models","URL":"https:\/\/github.com\/patperry\/r-
mbest","Version":"0.5"},"mblm":{"Author":"Lukasz Komsta
<lukasz.komsta@umlub.pl>","Description":"This package provides linear models based
on Theil-Sen\nsingle median and Siegel repeated medians. They are very robust\n(29
or 50 percent breakdown point, respectively), and if no\noutliers are present, the
estimators are very similar to OLS.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mblm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Median-Based Linear Models","URL":"http:\/\/www.r-
project.org, http:\/\/www.komsta.net\/","Version":"0.12"},"mbmdr":{"Author":"Victor
Urrea, Malu Calle, Kristel Van Steen, Nuria Malats","Depends":"R (>= 2.10),
logistf","Description":"Model Based Multifactor Dimension Reduction proposed
by\nCalle et al. (2008) as a dimension reduction method for\nexploring gene-gene
interactions.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mbmdr","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Model Based Multifactor Dimensionality
Reduction","Version":"2.6"},"mboost":{"Author":"Torsten Hothorn [aut],\nPeter
Buehlmann [aut],\nThomas Kneib [aut],\nMatthias Schmid [aut],\nBenjamin Hofner
[aut, cre],\nFabian Sobotka [ctb],\nFabian Scheipl [ctb]","Depends":"R (>= 2.14.0),
methods, stats, parallel, stabs (>= 0.5-0)","Description":"Functional gradient
descent algorithm\n(boosting) for optimizing general risk functions
utilizing\ncomponent-wise (penalised) least squares estimates or regression\ntrees
as base-learners for fitting generalized linear, additive\nand interaction models
to potentially high-dimensional data.","Imports":"Matrix, survival, splines,
lattice, nnls, quadprog, utils,\ngraphics, grDevices, party (>= 1.0-
2","NeedsCompilation":"yes","Package":"mboost","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"TH.data, MASS, fields, BayesX, gbm, mlbench,
RColorBrewer,\nrpart (>= 4.0-3), randomForest, nnet, testthat (>=
0.10.0)","Title":"Model-Based Boosting","URL":"https:\/\/github.com\/boost-
R\/mboost,\nhttp:\/\/mboost.r-forge.r-project.org","Version":"2.6-0"},"mc2d":
{"Author":"Regis Pouillot [aut, cre],\nMarie-Laure Delignette-Muller [ctb],\nJean-
Baptiste Denis [ctb]","Depends":"R (>= 2.10.0), mvtnorm","Description":"A complete
framework to build and study Two-Dimensional Monte-Carlo simulations, aka Second-
Order Monte-Carlo simulations. Also includes various distributions (pert,
triangular, Bernoulli, empirical discrete and continuous).","Imports":"stats,
grDevices, graphics, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mc2d","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"fitdistrplus, survival","Title":"Tools for Two-
Dimensional Monte-Carlo Simulations","Version":"0.1-16"},"mcGlobaloptim":
{"Author":"Thierry Moudiki","Depends":"R (>= 2.12.1), utils","Description":"The
package performs global optimization combining Monte Carlo and Quasi Monte Carlo
simulation with a local search. \\n The local searches can be easily speeded-
up by using a network of local workstations.","Imports":"randtoolbox,
snow","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mcGlobaloptim","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Global optimization using Monte Carlo and Quasi
Monte Carlo\nsimulation","URL":"http:\/\/www.r-
project.org","Version":"0.1"},"mcIRT":{"Author":"Manuel Reif","Depends":"R (>=
2.14)","Description":"This package provides functions to estimate two popular IRT-
models: The Nominal Response Model (Bock 1972) and the quite recently developed
Nested Logit Model (Suh & Bolt 2010). These are two models to examine multiple-
choice items and other multicategorial response formats.","Imports":"Rcpp (>=
3","NeedsCompilation":"yes","Package":"mcIRT","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat","Title":"IRT models for multiple choice items
(mcIRT)","URL":"https:\/\/github.com\/manuelreif\/mcIRT","Version":"0.41"},"mcbiopi
":{"Author":"Holger Schwender","Description":"Computes the prime implicants or a
minimal disjunctive normal form for a\nlogic expression presented by a truth table
or a logic tree. Has been particularly\ndeveloped for logic expressions resulting
from a logic regression analysis, i.e.\nlogic expressions typically consisting of
up to 16 literals, where the prime implicants\nare typically composed of a maximum
of 4 or 5 literals.","License":"LGPL (>=
2)","NeedsCompilation":"no","Package":"mcbiopi","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Matrix Computation Based Identification Of Prime
Implicants","Version":"1.1.2"},"mcc":{"Author":"Yi-Hui Zhou","Description":"A
number of biomedical problems involve performing many hypothesis tests, with an
attendant need to apply stringent thresholds. Often the data take the form of a
series of predictor vectors, each of which must be compared with a single response
vector, perhaps with nuisance covariates. Parametric tests of association are often
used, but can result in inaccurate type I error at the extreme thresholds, even for
large sample sizes. Furthermore, standard two-sided testing can reduce power
compared to the doubled p-value, due to asymmetry in the null distribution. Exact
(permutation) testing approaches are attractive, but can be computationally
intensive and cumbersome. MCC is an approximation to exact association testing of
two vectors that is accurate and fast enough for standard use in high-throughput
settings, and can easily provide standard two-sided or doubled p-
values.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mcc","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Moment Corrected Correlation","Version":"1.0"},"mcclust":
{"Author":"Arno Fritsch","Depends":"R (>= 2.10), lpSolve","Description":"Implements
methods for processing a sample of (hard)\nclusterings, e.g. the MCMC output of a
Bayesian clustering\nmodel. Among them are methods that find a single
best\nclustering to represent the sample, which are based on the\nposterior
similarity matrix or a relabelling algorithm.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"mcclust","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Process an MCMC Sample of
Clusterings","Version":"1.0"},"mcemGLM":{"Author":"Felipe Acosta
Archila","Depends":"trust, stats","Description":"Maximum likelihood estimation for
generalized linear mixed models via Monte Carlo EM.","Imports":"Rcpp (>=
0.11.3)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"mcemGLM","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Maximum Likelihood Estimation for Generalized Linear
Mixed\nModels","Version":"1.1"},"mcga":{"Author":"Mehmet Hakan
Satman","Depends":"GA","Description":"Machine coded genetic algorithm (MCGA) is a
fast tool for\nreal-valued optimization problems. It uses the byte\nrepresentation
of variables rather than real-values. It\nperforms the classical crossover
operations (uniform) on these\nbyte representations. Mutation operator is also
similar to\nclassical mutation operator, which is to say, it changes a\nrandomly
selected byte value of a chromosome by +1 or -1 with\nprobability 1\/2. In MCGAs
there is no need for\nencoding-decoding process and the classical operators
are\ndirectly applicable on real-values. It is fast and can handle a\nwide range of
a search space with high precision. Using a\n256-unary alphabet is the main
disadvantage of this algorithm\nbut a moderate size population is convenient for
many problems.\nPackage also includes multi_mcga function for multi
objective\noptimization problems. This function sorts the chromosomes\nusing their
ranks calculated from the non-dominated sorting\nalgorithm.","Imports":"Rcpp (>=
0.11.4)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"mcga","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Machine Coded Genetic Algorithms for Real-Valued
Optimization\nProblems","Version":"3.0"},"mcgibbsit":{"Author":"Gregory R. Warnes
<greg@warnes.net>, Robert Burrows","Depends":"coda","Description":"\n'mcgibbsit'
provides an implementation of Warnes & Raftery's\nMCGibbsit run-length diagnostic
for a set of (not-necessarily\nindependent) MCMC samplers. It combines the
estimate error-bounding\napproach of the Raftery and Lewis MCMC run length
diagnostic with\nthe between verses within chain approach of the Gelman and\nRubin
MCMC convergence
diagnostic.","License":"GPL","NeedsCompilation":"no","Package":"mcgibbsit","Reposit
ory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Warnes and Raftery's MCGibbsit
MCMC diagnostic","Version":"1.1.0"},"mcheatmaps":{"Author":"Thierry Chenard
[aut],\nRafael Najmanovich [aut, cre]","Depends":"gridBase,
grid","Description":"mcheatmaps serves to visualize multiple different symmetric
matrices and matrix clusters in a single figure using a dendogram, two half
matrices and various color labels.","License":"GPL-
3","NeedsCompilation":"no","Package":"mcheatmaps","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Multiple matrices heatmap
visualization","URL":"\"bcb.med.usherbrooke.ca\"","Version":"1.0.0"},"mcll":
{"Author":"Minjeong Jeon, Cari Kaufman, and Sophia Rabe-Hesketh","Depends":"R (>=
2.13.0),statmod, locfit","Description":"Maximum likelihood estimation using a Monte
Carlo local likelihood (MCLL) method","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mcll","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Monte Carlo Local Likelihood
Estimation","Version":"1.2"},"mclogit":{"Author":"Martin Elff","Depends":"stats,
Matrix","Description":"This packages provides a function to estimate parameters
for\nthe conditional logit model (also with multinomial counts), and for the\nmixed
conditional logit model, or conditional logit with random effects\n(random
intercepts only, no random slopes yet).\nThe current implementation of random
effects is limited to\nthe PQL technique, which requires large cluster
sizes.","Enhances":"memisc","License":"GPL-
2","NeedsCompilation":"no","Package":"mclogit","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Mixed Conditional Logit","Version":"0.3-1"},"mclust":
{"Author":"Chris Fraley [aut],\nAdrian E. Raftery [aut],\nLuca Scrucca [aut,
cre],\nThomas Brendan Murphy [ctb],\nMichael Fop [ctb]","Depends":"R (>=
3.0)","Description":"Gaussian finite mixture models fitted via EM algorithm for
model-based clustering, classification, and density estimation, including
Bayesian regularization, dimension reduction for visualisation, and resampling-
based inference.","Imports":"stats, utils, graphics, grDevices","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"mclust","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr (>= 1.12), rmarkdown (>= 0.9), mix (>=
1.0)","Title":"Gaussian Mixture Modelling for Model-Based
Clustering,\nClassification, and Density
Estimation","URL":"http:\/\/www.stat.washington.edu\/mclust\/","Version":"5.2"},"mc
mc":{"Author":"Charles J. Geyer <charlie@stat.umn.edu> and Leif T.
Johnson\n<ltjohnson@google.com>","Depends":"R (>= 2.10.0)","Description":"Simulates
continuous distributions of random vectors using\nMarkov chain Monte Carlo (MCMC).
Users specify the distribution by an\nR function that evaluates the log
unnormalized density. Algorithms\nare random walk Metropolis algorithm (function
metrop), simulated\ntempering (function temper), and morphometric random walk
Metropolis\n(Johnson and Geyer, Annals of Statistics, 2012, function
morph.metrop),\nwhich achieves geometric ergodicity by change of
variable.","Imports":"stats","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"mcmc","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"xtable, Iso","Title":"Markov Chain Monte
Carlo","URL":"http:\/\/www.stat.umn.edu\/geyer\/mcmc\/,\nhttps:\/\/github.com\/cjge
yer\/mcmc","Version":"0.9-4"},"mcmcplots":{"Author":"S. McKay Curtis [aut,
cre],\nIlya Goldin [ctb],\nEvangelos Evangelou [ctb],\n'sumtxt' from GitHub
[ctb]","Depends":"coda (>= 0.17.1)","Description":"Functions for convenient
plotting and viewing of MCMC output.","Imports":"sfsmisc, colorspace,
denstrip","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mcmcplots","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Create Plots from MCMC
Output","Version":"0.4.2"},"mcmcse":{"Author":"James M. Flegal <jflegal@ucr.edu>,
John Hughes\n<hughesj@umn.edu> and Dootika Vats
<vatsx007@umn.edu>","Description":"Provides tools for computing Monte Carlo
standard\nerrors (MCSE) in Markov chain Monte Carlo (MCMC) settings.
MCSE\ncomputation for expectation and quantile estimators is\nsupported as well as
multivariate estimations. The package also provides\nfunctions for computing
effective sample size and for plotting\nMonte Carlo estimates versus sample
size.","Imports":"utils, ellipse, Rcpp (>= 0.11.3)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"mcmcse","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"testthat, mAr, knitr","Title":"Monte Carlo Standard
Errors for MCMC","URL":"http:\/\/faculty.ucr.edu\/~jflegal
,\nhttp:\/\/www.biostat.umn.edu\/~johnh,\nhttp:\/\/www.stat.umn.edu\/~vatsx007","Ve
rsion":"1.2-1"},"mco":{"Author":"Olaf Mersmann [aut, cre],\nHeike Trautmann
[ctb],\nDetlef Steuer [ctb],\nBernd Bischl [ctb],\nKalyanmoy Deb
[cph]","Depends":"R (>= 3.0.0)","Description":"Functions for multiple criteria
optimization using genetic\nalgorithms and related test problems","License":"GPL-
2","NeedsCompilation":"yes","Package":"mco","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"scatterplot3d, testthat","Title":"Multiple Criteria
Optimization Algorithms and Related Functions","URL":"http:\/\/git.p-
value.net\/p\/mco.git","Version":"1.0-15.1"},"mcparallelDo":{"Author":"Russell S.
Pierce","Description":"Provides a function that wraps\nmcparallel() and mccollect()
from 'parallel' with temporary variables and a\ntask handler. Wrapped in this way
the results of an mcparallel() call\ncan be returned to the R session when the fork
is complete\nwithout explicitly issuing a specific mccollect() to retrieve the
value.\nOutside of top-level tasks, multiple mcparallel() jobs can be retrieved
with\na single call to mcparallelDoCheck().","Imports":"parallel, R.utils,
ArgumentCheck, R6","License":"GPL-
2","NeedsCompilation":"no","Package":"mcparallelDo","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat","Title":"A Simplified Interface for
Running Commands on Parallel\nProcesses","Version":"1.0.0"},"mcprofile":
{"Author":"Daniel Gerhard","Depends":"ggplot2","Description":"Calculation of signed
root deviance profiles for linear combinations of parameters in a generalized
linear model. Multiple tests and simultaneous confidence intervals are
provided.","Imports":"quadprog, mvtnorm, splines","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mcprofile","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr, multcomp, MASS","Title":"Multiple Contrast
Profiles","Version":"0.2-1"},"mcr":{"Author":"Ekaterina Manuilova
<ekaterina.manuilova@roche.com> Andre Schuetzenmeister
<andre.schuetzenmeister@roche.com> Fabian Model
<fabian.model@roche.com>","Depends":"R (>= 3.0.0), methods","Description":"This
package provides regression methods to quantify the relation between two
measurement methods. In particular it addresses regression problems with errors in
both variables and without repeated measurements. The package provides
implementations of Deming regression, weighted Deming regression, and Passing-
Bablok regression following the CLSI EP09-A3 recommendations for analytical method
comparison and bias estimation using patient samples.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"mcr","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"RUnit, XML","Title":"Method Comparison
Regression","Version":"1.2.1"},"mcsm":{"Author":"Christian P. Robert, Universite
Paris Dauphine","Depends":"stats, MASS, coda","Description":"mcsm contains a
collection of functions that allows the\nreenactment of the R programs used in the
book EnteR Monte\nCarlo Methods without further programming. Programs
being\navailable as well, they can be modified by the user to conduct\none's own
2)","NeedsCompilation":"no","Package":"mcsm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Functions for Monte Carlo Methods with
R","Version":"1.0"},"md":{"Author":"Genzo Kaga","Description":"Selects bandwidth
for the kernel density estimator with minimum distance method as proposed by
Devroye and Lugosi (1996). The minimum distance method directly selects the optimal
kernel density estimator from countably infinite kernel density estimators and
indirectly selects the optimal bandwidth. This package selects the optimal
bandwidth from finite kernel density estimators.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"md","Repository":"http:\/\/cran.csiro.au\/src
\/contrib","Title":"Selecting Bandwidth for Kernel Density Estimator with
Minimum\nDistance Method","Version":"1.0.4"},"mda":{"Author":"S original by Trevor
Hastie & Robert Tibshirani. Original R port by Friedrich Leisch, Kurt Hornik and
Brian D. Ripley.","Depends":"R (>= 1.9.0), stats, class","Description":"Mixture and
flexible discriminant analysis, multivariate\nadaptive regression splines (MARS),
BRUTO, ...","License":"GPL-
2","NeedsCompilation":"yes","Package":"mda","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"earth","Title":"Mixture and Flexible Discriminant
Analysis","Version":"0.4-8"},"mdatools":{"Author":"Sergey
Kucheryavskiy","Description":"Package implements projection based methods for
preprocessing,\nexploring and analysis of multivariate data used in
chemometrics.","Imports":"methods","License":"GPL-
3","NeedsCompilation":"no","Package":"mdatools","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Multivariate Data Analysis for
Chemometrics","Version":"0.7.0"},"mded":{"Author":"Hideo
Aizaki","Description":"Provides a function for measuring the difference between two
independent or non-independent empirical distributions and returning a significance
level of the
difference.","License":"CC0","NeedsCompilation":"no","Package":"mded","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Title":"Measuring the Difference Between
Two Empirical Distributions","Version":"0.1-2"},"mdhglm":{"Author":"Youngjo Lee,
Maengseok Noh","Depends":"R (>= 3.2.0), methods, Matrix, numDeriv, boot,
mvtnorm","Description":"Allows different models for multivariate response variables
where each response is assumed to follow double hierarchical generalized linear
models. In double hierarchical generalized linear models, the mean, dispersion
parameters for variance of random effects, and residual variance (overdispersion)
can be further modeled as random-effect
models.","License":"Unlimited","NeedsCompilation":"no","Package":"mdhglm","Reposito
ry":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Multivariate Double
Hierarchical Generalized Linear Models","Version":"1.2"},"mdscore":
{"Author":"Antonio Hermes M. da Silva-Junior [aut, cre], Damiao N. da Silva [aut],
Silvia L. P. Ferrari [ctb]","Depends":"R (>= 3.1.1), MASS","Description":"A set of
functions to obtain modified score test for generalized linear
2)","NeedsCompilation":"no","Package":"mdscore","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"Sleuth3","Title":"Improved Score Tests for Generalized
Linear Models","Version":"0.1-2"},"mdsdt":{"Author":"Robert X.D. Hawkins
<rxdh@stanford.edu>, Joe Houpt\n<joseph.houpt@wright.edu>, Noah Silbert
<noahpoah@gmail.com>, Leslie\nBlaha <Leslie.Blaha@wpafb.af.mil>, Thomas D.
Wickens\n<twickens@socrates.berkeley.edu>","Depends":"R (>= 1.8.0), ellipse,
mnormt, polycor","Description":"Tools associated with General\nRecognition Theory
(Townsend & Ashby, 1986), including Gaussian model fitting of 2x2 and more\ngeneral
designs, associated plotting and model comparison tools,\nand tests of marginal
response invariance and report independence.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mdsdt","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Functions for Analysis of Data with General Recognition
Theory","Version":"1.2"},"measuRing":{"Author":"Wilson
Lara, Carlos Sierra, Felipe Bravo","Depends":"pastecs, png,
tiff","Description":"Identification of ring borders on scanned image sections from
dendrochronological samples. Processesing of image reflectances to produce gray
matrices and a time series of smoothed gray values. Luminance data is plotted on
segmented images for users to perform both: visual identification of ring borders,
or control of automatic detection. Routines to visually include\/exclude ring
borders on the R graphical device, or automatically detect ring borders using a
linear detection algorithm. This algorithm detects ring borders according to
positive\/negative extreme values in the smoothed time-series of gray
values.","License":"GPL-
3","NeedsCompilation":"no","Package":"measuRing","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Detection and Control of Tree-Ring Widths on Scanned
Image\nSections","Version":"0.3"},"meboot":{"Author":"Hrishikesh D. Vinod
<Vinod@fordham.edu> and Javier\nLÃ³pez-de-Lacalle","Depends":"R (>= 3.0.0), dynlm,
nlme","Description":"This package performs maximum entropy density based\ndependent
data bootstrap. An algorithm is provided to create a\npopulation of time series
(ensemble) without assuming\nstationarity. The reference paper (Vinod, H.D., 2004)
explains\nhow the algorithm satisfies the ergodic theorem and the central\nlimit
theorem.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"meboot","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"boot, car, ConvergenceConcepts, geepack, lmtest,
strucchange,\nplm, zoo","Title":"Maximum Entropy Bootstrap for Time
Series","Version":"1.4-6"},"medSTC":{"Author":"Jun Zhu <junzhu@cs.cmu.edu>, Aykut
FIRAT <aykut@mit.edu>","Depends":"R (>= 2.10)","Description":"This is a C++
implementation of Sparse Topical Coding\n(STC), a model of discrete data which is
fully described in Zhu\net al. (2011)
(http:\/\/www.cs.cmu.edu\/~junzhu\/stc\/stc.pdf). It\ncan be used for multi-class
classification and describing\ndocuments with underlying sparse
topics.","License":"file
LICENSE","NeedsCompilation":"yes","Package":"medSTC","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"A max-margin supervised Sparse Topical Coding
Model","Version":"1.0.0"},"mederrRank":{"Author":"Sergio Venturini, Jessica
Myers","Depends":"BB, methods, numDeriv, utils","Description":"Two distinct but
related statistical approaches to the problem of identifying the combinations of
medication error characteristics that are more likely to result in harm are
implemented in this package: 1) a Bayesian hierarchical model with optimal Bayesian
ranking on the log odds of harm, and 2) an empirical Bayes model that estimates the
ratio of the observed count of harm to the count that would be expected if error
characteristics and harm were independent. In addition, for the Bayesian
hierarchical model, the package provides functions to assess the sensitivity of
results to different specifications of the random effects
distributions.","Imports":"graphics, stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mederrRank","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Bayesian Methods for Identifying the Most Harmful
Medication\nErrors","Version":"0.0.8"},"medflex":{"Author":"Johan Steen [aut,
cre],\nTom Loeys [aut],\nBeatrijs Moerkerke [aut],\nStijn Vansteelandt
[aut],\nJoris Meys [ctb] (technical support),\nTheis Lange [ctb] (valuable
suggestions)","Depends":"R (>= 3.1.2), multcomp (>= 1.3-6)","Description":"Run
flexible mediation analyses using natural\neffect models as described in Lange,
Vansteelandt and Bekaert (2012),\nVansteelandt, Bekaert and Lange (2012) and Loeys,
Moerkerke, De Smet,\nBuysse, Steen and Vansteelandt (2013).","Imports":"boot (>=
1.3-8), car (>= 2.0-21), Matrix (>= 1.1-4), graphics\n(>= 3.1.2), sandwich (>= 2.3-
2), stats (>= 3.1.2), utils (>=\n3.1.2)","License":"GPL-
2","NeedsCompilation":"no","Package":"medflex","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"arm (>= 1.7-05), gam (>= 1.09.1), glmnet (>= 1.9-8),
mice (>=\n2.22), mitools (>= 2.3), rpart (>= 4.1-8), SuperLearner (>=\n2.0-15),
VGAM (>= 0.9-5)","Title":"Flexible Mediation Analysis Using Natural Effect
Models","URL":"https:\/\/github.com\/jmpsteen\/medflex","Version":"0.6-
0"},"mediation":{"Author":"Dustin Tingley <dtingley@gov.harvard.edu>,\nTeppei
Yamamoto <teppei@mit.edu>,\nKentaro Hirose <hirose@princeton.edu>,\nLuke Keele
<ljk20@psu.edu>,\nKosuke Imai <kimai@princeton.edu>","Depends":"R (>= 2.15.1),
MASS, Matrix, mvtnorm, sandwich","Description":"We implement parametric and non
parametric mediation analysis. This package performs the methods and suggestions in
Imai, Keele and Yamamoto (2010), Imai, Keele and Tingley (2010), Imai, Tingley and
Yamamoto (2013), Imai and Yamamoto (2013) and Yamamoto (2013). In addition to the
estimation of causal mediation effects, the software also allows researchers to
conduct sensitivity analysis for certain parametric models.","Imports":"lpSolve,
Hmisc, lme4 (>= 1.0), stats, graphics, grDevices,\nutils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mediation","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"mgcv, quantreg, VGAM, SuppDists, survival,
parallel","Title":"Causal Mediation
Analysis","URL":"http:\/\/imai.princeton.edu\/projects\/mechanisms.html","Version":
"4.4.5"},"medicalrisk":{"Author":"Patrick McCormick [aut, cre],\nThomas Joseph
[aut]","Depends":"R (>= 3.0.0)","Description":"Generates risk estimates and
comorbidity flags from ICD-9-CM\ncodes available in administrative medical
datasets. The package supports\nthe Charlson Comorbidity Index, the Elixhauser
Comorbidity\nclassification, the Revised Cardiac Risk Index, and the Risk
Stratification\nIndex. Methods are table-based, fast, and use the 'plyr' package,
so\nparallelization is possible for large jobs. Also includes a sample of\nreal
ICD-9 data for 100 patients from a publicly available dataset.","Imports":"plyr (>=
1.5), reshape2, hash","License":"GPL-3 | file
LICENSE","NeedsCompilation":"no","Package":"medicalrisk","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"testthat, knitr, ggplot2,
gridExtra","Title":"Medical Risk and Comorbidity Tools for ICD-9-CM
Data","URL":"https:\/\/github.com\/patrickmdnet\/medicalrisk","Version":"1.2"},"mef
a":{"Author":"Peter Solymos","Depends":"R (>= 2.14.0)","Description":"A framework
package aimed to provide standardized computational environment for specialist work
via object classes to represent the data coded by samples, taxa and segments (i.e.
subpopulations, repeated measures). It supports easy processing of the data along
with cross tabulation and relational data tables for samples and taxa. An object of
class `mefa' is a project specific compendium of the data and can be easily used in
further analyses. Methods are provided for extraction, aggregation, conversion,
plotting, summary and reporting of `mefa' objects. Reports can be generated in
plain text or LaTeX format. Vignette contains worked
examples.","Imports":"methods","License":"GPL-
2","NeedsCompilation":"no","Package":"mefa","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"MASS, vegan, mefa4, Matrix","Title":"Multivariate Data
Handling in Ecology and
Biogeography","URL":"https:\/\/github.com\/psolymos\/mefa","Version":"3.2-
7"},"mefa4":{"Author":"Peter Solymos","Depends":"R (>= 2.14.0), methods, Matrix,
pbapply","Description":"An S4 update of the 'mefa' package\nusing sparse matrices
for enhanced efficiency.\nSparse array-like objects are supported via\nlists of
sparse matrices.","License":"GPL-
2","NeedsCompilation":"no","Package":"mefa4","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"mefa","Title":"Multivariate Data Handling with S4 Classes
and Sparse Matrices","URL":"https:\/\/github.com\/psolymos\/mefa4","Version":"0.3-
3"},"megaptera":{"Author":"Christoph Heibl","Depends":"R (>= 2.10), snowfall,
ips","Description":"Given a set of taxa and marker, the goal is build a complete
and correct sequence alignment for phylogenetic analysis.","Imports":"ape, seqinr,
methods, RPostgreSQL, XML","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"megaptera","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr","Title":"MEGAPhylogeny Techniques in
R","Version":"1.0-0"},"meifly":{"Author":"Hadley Wickham
<h.wickham@gmail.com>","Description":"Exploratory model analysis. Fit and
graphical\nexplore ensembles of linear models.","Imports":"plyr, leaps,
MASS,","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"meifly","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Interactive model exploration using
GGobi","URL":"https:\/\/github.com\/hadley\/meifly","Version":"0.3"},"mem":
{"Author":"Jose E. Lozano Alonso <lozalojo@jcyl.es>","Depends":"R (>= 3.1.0), sm,
boot","Description":"Modelization of influenza epidemics in order to monitor future
activity.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mem","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Moving Epidemic Method R Package","Version":"1.4"},"memgene":
{"Author":"Pedro Peres-Neto, Paul Galpern","Description":"Memgene can detect
relatively weak spatial genetic patterns by using Moran's Eigenvector Maps (MEM) to
extract only the spatial component of genetic variation. Memgene has applications
in landscape genetics where the movement and dispersal of organisms are studied
using neutral genetic variation.","Imports":"ade4, raster, gdistance,
vegan","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"memgene","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"adegenet, geosphere, knitr","Title":"Spatial pattern
detection in genetic distance data using Moran's\nEigenvector
Maps","Version":"1.0"},"memisc":{"Author":"Martin Elff (with contributions from
Christopher
N. Lawrence, Dave Atkins, Jason W. Morgan, Achim Zeileis)","Depends":"R (>=
3.0.0), lattice, stats, methods, utils, MASS","Description":"One of the aims of
this package is to make life easier for\nuseRs who deal with survey data sets. It
provides an\ninfrastructure for the management of survey data including\nvalue
labels, definable missing values, recoding of variables,\nproduction of code books,
and import of (subsets of) SPSS and\nStata files. Further, it provides
functionality to produce\ntables and data frames of arbitrary descriptive
statistics and\n(almost) publication-ready tables of regression model\nestimates,
which can be exported to LaTeX and HTML.","Enhances":"AER, car, eha, lme4, ordinal,
simex","Imports":"grid","License":"GPL-
2","NeedsCompilation":"yes","Package":"memisc","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"splines, knitr","Title":"Tools for Management of Survey
Data and the Presentation of\nAnalysis
Results","URL":"\nhttp:\/\/www.elff.eu\/software\/memisc\/,http:\/\/github.com\/mel
ff\/memisc\/","Version":"0.99.6"},"memoise":{"Author":"Hadley Wickham [aut],\nJim
Hester [aut, cre],\nKirill MÃ¼ller [aut]","Description":"Cache the results of a
function so that when you call it\nagain with the same arguments it returns the
pre-computed value.","Imports":"digest (>= 0.6.3)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"memoise","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat","Title":"Memoisation of
Functions","URL":"https:\/\/github.com\/hadley\/memoise","Version":"1.0.0"},"memuse
":{"Author":"Drew Schmidt [aut, cre],\nChristian Heckendorf [ctb],\nWei-Chen Chen
[ctb]","Depends":"R (>= 2.15.1)","Description":"How much ram do you need to store a
100,000 by 100,000 matrix?\nHow much ram is your current R session using? How much
ram do you even have?\nLearn the scintillating answer to these and many more such
questions with\nthe 'memuse' package.","Imports":"methods","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"memuse","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Memory Estimation
Utilities","URL":"https:\/\/github.com\/shinra-
dev\/memuse","Version":"2.5"},"merTools":{"Author":"Jared E. Knowles [aut,
cre],\nCarl Frederick [aut]","Depends":"R (>= 3.0.2), arm, lme4 (>= 1.1-11),
methods, plyr","Description":"Provides methods for extracting results from mixed-
effect model\nobjects fit with the 'lme4' package. Allows construction of
prediction intervals\nefficiently from large scale linear and generalized linear
mixed-effects models.","Imports":"mvtnorm, DT, shiny, abind, ggplot2, blme,
broom","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"merTools","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat, knitr, rmarkdown, dplyr, foreach,
parallel","Title":"Tools for Analyzing Mixed Effect Regression
Models","Version":"0.2.1"},"merror":{"Author":"Richard A. Bilonick
<rabilonick@gmail.com>","Description":"N>=3 methods are used to measure each of n
items.\nThe data are used to estimate simultaneously systematic error (bias)\nand
random error (imprecision). Observed measurements for each method\nor device are
assumed to be linear functions of the unknown true values\nand the errors are
assumed normally distributed. Maximum likelihood\nestimation is used for the
imprecision standard deviation estimates.\nPairwise calibration curves and plots
can be easily generated.","Imports":"graphics, grDevices, stats,
2)","NeedsCompilation":"no","Package":"merror","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Accuracy and Precision of
Measurements","Version":"2.0.2"},"metRology":{"Author":"Stephen L R Ellison
<s.ellison@lgc.co.uk>.","Depends":"R (>= 2.14.0), base,
stats","Description":"metRology provides classes and calculation and plotting
functions\nfor metrology applications, including measurement uncertainty
estimation\nand inter-laboratory metrology comparison
studies.","Imports":"graphics, MASS, numDeriv","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"metRology","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Support for metrological
applications","URL":"http:\/\/metrology.sourceforge.net","Version":"0.9-
17"},"meta":{"Author":"Guido Schwarzer [cre, aut]","Depends":"R (>=
2.9.1)","Description":"User-friendly general package providing standard methods for
meta-analysis:\n- fixed effect and random effects meta-analysis;\n- several plots
(forest, funnel, Galbraith \/ radial, L'Abbe, Baujat, bubble);\n- statistical tests
and trim-and-fill method to evaluate bias in meta-analysis;\n- import data from
RevMan 5;\n- prediction interval, Hartung-Knapp and Paule-Mandel method for random
effects model;\n- cumulative meta-analysis and leave-one-out meta-analysis;\n-
meta-regression (if R package 'metafor' is
installed).","Imports":"grid","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"meta","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"metafor","Title":"General Package for Meta-
Analysis","Version":"4.3-2"},"meta4diag":{"Author":"Jingyi Guo
<jingyi.guo@math.ntnu.no> and Andrea Riebler
<andrea.riebler@math.ntnu.no>","Depends":"R (>= 2.10), RGtk2, cairoDevice, methods,
grid","Description":"Bayesian inference analysis for bivariate meta-analysis of
diagnostic test studies using integrated nested Laplace approximation with INLA. A
purpose built graphic user interface is available. The installation of R package
INLA is compulsory for successful usage. The INLA package can be obtained from
<http:\/\/www.r-inla.org>. We recommend the testing version, which can be
downloaded by running: install.packages(\"INLA\",
repos=\"http:\/\/www.math.ntnu.no\/inla\/R\/testing\").","License":"GPL","NeedsComp
ilation":"no","Package":"meta4diag","Repository":"http:\/\/cran.csiro.au\/src\/cont
rib","Suggests":"INLA","Title":"Meta-Analysis for Diagnostic Test
Studies","Version":"1.0.20"},"metaLik":{"Author":"Annamaria Guolo and Cristiano
Varin","Depends":"R (>= 3.0.0)","Description":"First- and higher-order likelihood
inference in\nmeta-analysis and meta-regression models.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"metaLik","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Likelihood Inference in Meta-Analysis and Meta-Regression
Models","Version":"0.42.0"},"metaMA":{"Author":"Guillemette Marot","Depends":"R (>=
3.1.2),","Description":"Combines either p-values or modified effect sizes from
different\nstudies to find differentially expressed genes","Imports":"limma,
SMVar","License":"GPL","NeedsCompilation":"no","Package":"metaMA","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Suggests":"GEOquery, org.Hs.eg.db, VennDiagram,
annaffy, hgu133plus2.db,\nhgu133a.db, hgu95av2.db","Title":"Meta-analysis for
MicroArrays","Version":"3.1.2"},"metaMix":{"Author":"Sofia Morfopoulou
<sofia.morfopoulou.10@ucl.ac.uk>","Depends":"R (>= 3.0.1)","Description":"Resolves
complex metagenomic mixtures by analysing\ndeep sequencing data, using a mixture
model based approach.\nThe use of parallel Monte Carlo Markov chains for the
exploration\nof the species space enables the identification of the set\nof species
more likely to contribute to the mixture.","Imports":"data.table (>= 1.9.2),
Matrix, gtools, Rmpi, ggplot2","License":"GPL-
3","NeedsCompilation":"yes","Package":"metaMix","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr","Title":"Bayesian Mixture Analysis for
Metagenomic Community Profiling","Version":"0.2"},"metaRNASeq":
{"Author":"Guillemette Marot, Florence Jaffrezic, Andrea Rau","Depends":"R (>=
2.15.0)","Description":"Implementation of two p-value combination techniques
(inverse normal and Fisher methods). A vignette is provided to explain how to
perform a meta-analysis from two independent RNA-seq
experiments.","License":"GPL","NeedsCompilation":"no","Package":"metaRNASeq","Repos
itory":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"HTSFilter (>= 0.1.1),
DESeq (>= 1.8.3), DESeq2 (>= 1.0.17),\nVennDiagram (<= 1.6.7)","Title":"Meta-
analysis of RNA-seq data","Version":"1.0.2"},"metaSEM":{"Author":"Mike W.-L. Cheung
<mikewlcheung@nus.edu.sg>","Depends":"R (>= 3.2.0), OpenMx (>=
2.3.1)","Description":"A collection of functions for conducting meta-analysis using
a\nstructural equation modeling (SEM) approach via the 'OpenMx' package.\nIt also
implements the two-stage SEM approach to conduct meta-analytic\nstructural equation
modeling on correlation and covariance matrices.","Imports":"Matrix, MASS, ellipse,
2)","NeedsCompilation":"no","Package":"metaSEM","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"metafor, semPlot","Title":"Meta-Analysis using
Structural Equation
Modeling","URL":"https:\/\/github.com\/mikewlcheung\/metasem","Version":"0.9.6"},"m
etabolomics":{"Author":"Alysha M De Livera and Jairus B Bowne","Depends":"limma,
crmn, gplots, R (>= 3.1.0)","Description":"A collection of functions to aid in the
statistical analysis of metabolomic data","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"metabolomics","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Analysis of Metabolomics
Data","Version":"0.1.4"},"metacom":{"Author":"Tad Dallas","Description":"Functions
to analyze coherence, boundary clumping, and turnover following the pattern-based
metacommunity analysis of Leibold and Mikkelson 2002. The package also includes
functions to visualize ecological networks, and to calculate modularity as a
replacement to boundary clumping.","Imports":"devtools, vegan,
2","NeedsCompilation":"no","Package":"metacom","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Analysis of the \"Elements of Metacommunity
Structure\"","Version":"1.4.3"},"metacor":{"Author":"Etienne
Laliberté","Depends":"R (>=
2.8.0), rmeta, gsl","Description":"Implement the DerSimonian-Laird (DSL) and
Olkin-Pratt (OP)\nmeta-analytical approaches with correlation coefficients
as\neffect sizes.","License":"GPL-
2","NeedsCompilation":"no","Package":"metacor","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Meta-analysis of correlation coefficients","Version":"1.0-
2"},"metafolio":{"Author":"Sean C. Anderson [aut, cre],\nJonathan W. Moore
[ctb],\nMichelle M. McClure [ctb],\nNicholas K. Dulvy [ctb],\nAndrew B. Cooper
[ctb]","Depends":"R (>= 3.1.0)","Description":"The metafolio R package is a tool to
simulate salmon\nmetapopulations and apply financial portfolio optimization
concepts. The\npackage accompanies the paper 'Portfolio conservation of
metapopulations\nunder climate change'. See
citation(\"metafolio\").","Imports":"Rcpp (>= 0.11.2), plyr, colorspace,
2","NeedsCompilation":"yes","Package":"metafolio","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr, devtools, TeachingDemos, RColorBrewer,
reshape2","Title":"Metapopulation simulations for conserving salmon
through\nportfolio
optimization","URL":"http:\/\/github.com\/seananderson\/metafolio","Version":"0.1.0
"},"metafor":{"Author":"Wolfgang Viechtbauer [aut, cre]","Depends":"R (>= 3.2.2),
Matrix","Description":"A comprehensive collection of functions for conducting meta-
analyses in R. The package includes functions to calculate various effect sizes or
outcome measures, fit fixed-, random-, and mixed-effects models to such data, carry
out moderator and meta-regression analyses, and create various types of meta-
analytical plots (e.g., forest, funnel, radial, L'Abbe, Baujat plots). For meta-
analyses of binomial and person-time data, the package also provides functions that
implement specialized methods, including the Mantel-Haenszel method, Peto's method,
and a variety of suitable generalized linear (mixed-effects) models (i.e., mixed-
effects logistic and Poisson regression models). Finally, the package provides
functionality for fitting meta-analytic multivariate\/multilevel models that
account for non-independent sampling errors and\/or true effects (e.g., due to the
inclusion of multiple treatment studies, multiple endpoints, or other forms of
clustering). Network meta-analyses and meta-analyses accounting for known
correlation structures (e.g., due to phylogenetic relatedness) can also be
conducted.","Imports":"stats, utils, graphics, grDevices, methods","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"metafor","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"lme4, numDeriv, minqa, nloptr, dfoptim, ucminf,
CompQuadForm,\nmvtnorm, Formula, R.rsp, testthat, BiasedUrn, survival,
Epi,\nigraph, multcomp, plyr","Title":"Meta-Analysis Package for
R","URL":"http:\/\/www.metafor-project.org
http:\/\/www.wvbauer.com","Version":"1.9-8"},"metafuse":{"Author":"Lu Tang, Peter
X.K. Song","Description":"For each covariate, cluster its coefficient effects
across different data sets during\ndata integration. Supports Gaussian, binomial
and Poisson regression models.","Imports":"glmnet, Matrix, MASS","License":"GPL-
2","NeedsCompilation":"no","Package":"metafuse","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Fused Lasso Approach in Regression Coefficient
Clustering","Version":"1.0-1"},"metagear":{"Author":"Marc J. Lajeunesse [aut,
cre]","Depends":"R (>= 3.0.1)","Description":"Functionalities for facilitating
systematic reviews, data extractions, and meta-analyses. It includes a GUI
(graphical user interface) to help screen the abstracts and titles of bibliographic
data; tools to assign screening effort across multiple collaborators\/reviewers and
to assess inter-reviewer reliability; tools to help automate the download and
retrieval of journal PDF articles from online databases; automated and manual data
extraction from scatter-plot and bar-plot images; PRISMA (Preferred Reporting Items
for Systematic Reviews and Meta-Analyses) flow diagrams; simple imputation tools to
fill gaps in incomplete or missing study parameters; generation of random effects
sizes for Hedges' d, log response ratio, odds ratio, and correlation coefficients
for Monte Carlo experiments; covariance equations for modelling dependencies among
multiple effect sizes (e.g., effect sizes with a common control); and finally
summaries that replicate analyses and outputs from widely used but no longer
updated meta-analysis software. Funding for this package was supported by National
Science Foundation (NSF) grants DBI-1262545 and DEB-1451031.","Imports":"EBImage
(>= 4.4.0), gWidgetsRGtk2 (>= 0.0-83), gWidgets (>=\n0.0-54), stringr (>= 0.6.2),
metafor (>= 1.9-4), MASS (>=\n7.3-29), Matrix (>= 1.1-3)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"metagear","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Comprehensive Research Synthesis Tools for Systematic
Reviews\nand Meta-
Analysis","URL":"http:\/\/lajeunesse.myweb.usf.edu","Version":"0.2"},"metagen":
{"Author":"Thomas W. D. MÃ¶bius <kontakt@thomasmoebius.de>","Description":"Provides
methods for making inference in the random effects meta\nregression model such as
point estimates and confidence intervals for the\nheterogeneity parameter and the
regression coefficients vector. Inference\nmethods are based on different
approaches to statistical inference.\nMethods from three different schools are
included: methods based on the\nmethod of moments approach, methods based on
likelihood, and methods based\non generalised inference. The package also includes
tools to run extensive\nsimulation studies in parallel on high performance clusters
in a modular\nway. This allows extensive testing of custom inferential methods
with all\nimplemented state-of-the-art methods in a standardised way. Tools
for\nevaluating the performance of both point and interval estimates are\nprovided.
Also, a large collection of different pre-defined plotting\nfunctions is
implemented in a ready-to-use fashion.","Imports":"MASS, lhs, plyr, BBmisc,
ParamHelpers, BatchJobs,\nBatchExperiments, ggplot2, metafor","License":"GPL-
3","NeedsCompilation":"no","Package":"metagen","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Inference in Meta Analysis and Meta
Regression","URL":"http:\/\/00tau.github.io\/metagen\/","Version":"1.0"},"metaheur"
:{"Author":"Markus Vattulainen","Depends":"R (>= 2.10)","Description":"Automation
of preprocessing often requires computationally costly\npreprocessing combinations.
This package helps to find near-best combinations\nfaster. Sub heuristics supported
are random and grid restarts, taboo list,\ndecreasing probability for accepting
inferior solutions and location of\npreviously best solution candidate is compared
to. The package is intended\nto be used with package 'preprocomb' and takes its
'GridClass' object as input.","Imports":"utils, reshape2, ggplot2,
preprocomb","License":"GPL-
2","NeedsCompilation":"no","Package":"metaheur","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"testthat","Title":"Metaheuristic Optimization
Framework for Preprocessing\nCombinations","Version":"0.1.0"},"metamisc":
{"Author":"Thomas Debray","Depends":"stats, mvtnorm, ellipse, bbmle, rjags,
coda","Description":"This package provides functions for diagnostic and\nprognostic
meta-analyses. It estimates univariate, bivariate\nand multivariate models, and
allows the aggregation of\npreviously published prediction models with new
2","NeedsCompilation":"no","Package":"metamisc","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Diagnostic and prognostic meta analysis
(metamisc)","URL":"http:\/\/r-forge.r-
project.org\/projects\/metamisc\/","Version":"0.1.1"},"metansue":{"Author":"Joaquim
Radua","Description":"A novel meta-analytic method that allows an unbiased
inclusion of studies with Non Statistically-Significant Unreported Effects (NSUEs).
Briefly, the method first calculates the interval where the unreported effects
(e.g. t-values) should be according to the threshold of statistical significance
used in each study. Afterwards, maximizing likelihood techniques are used to impute
the expected effect size of each study with NSUEs, accounting for between-study
heterogeneity and potential covariates. Multiple imputations of the NSUEs are then
randomly created based on the expected value, variance and statistical significance
bounds. Finally, a restricted-maximum likelihood random-effects meta-analysis is
separately conducted for each set of imputations, and estimations from these meta-
analyses are pooled. Please read the reference in 'meta.nsue' for details of the
procedure.","License":"GPL-
3","NeedsCompilation":"no","Package":"metansue","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Meta-Analysis of Studies with Non Statistically-
Significant\nUnreported Effects","Version":"1.0"},"metap":{"Author":"Michael
Dewey","Description":"The canonical way to perform meta-analysis\ninvolves using
effect sizes. When they are not available\nthis package provides a number of
methods for\nmeta-analysis of significance values, a\nnumber of data-sets to
replicate published results, and a\nroutine for graphical display.","License":"GPL-
2","NeedsCompilation":"no","Package":"metap","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Meta-Analysis of Significance
Values","URL":"http:\/\/www.dewey.myzen.co.uk\/meta\/meta.html","Version":"0.7"},"m
etaplus":{"Author":"Ken Beath [aut, cre], Ben Bolker [aut], R Development Core Team
[aut]","Depends":"R(>= 3.2.0)","Description":"Performs meta-analysis and meta-
regression using standard and robust methods with confidence intervals based on the
profile likelihood. Robust methods are based on alternative distributions for the
random effect, either the t-distribution (Lee and Thompson, 2008
<doi:10.1002\/sim.2897>
or Baker and Jackson, 2008 <doi:10.1007\/s10729-007-9041-8>) or mixtures of
normals (Beath, 2014 <doi:10.1002\/jrsm.1114>).","Imports":"bbmle, metafor, boot,
methods, numDeriv, lme4, MASS, graphics,\nstats, fastGHQuad","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"metaplus","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Robust Meta-Analysis and Meta-
Regression","Version":"0.7-7"},"metasens":{"Author":"Guido Schwarzer [aut,
cre],\nJames Carpenter [aut],\nGerta RÃ¼cker [aut]","Depends":"meta (>= 4.0-
0)","Description":"The following methods are implemented to evaluate how sensitive
the results of a meta-analysis are to potential bias in meta-analysis:\n- Copas
selection model;\n- limit meta-analysis;\n- upper bound for outcome reporting
bias.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"metasens","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Advanced Statistical Methods to Model and Adjust for
Bias in\nMeta-Analysis","Version":"0.3-0"},"metatest":{"Author":"Hilde M. Huizenga
& Ingmar Visser","Depends":"R (>= 2.15.2)","Description":"This package fits meta
regression models and generates a\nnumber of statistics: next to t- and z-tests,
the likelihood\nratio, bartlett corrected likelihood ratio and permutation\ntests
are performed on the model
coefficients.","License":"GPL","NeedsCompilation":"no","Package":"metatest","Reposi
tory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Fit and test metaregression
models","Version":"1.0-4"},"meteR":{"Author":"Andy Rominger, Cory
Merow","Depends":"R (>= 2.10)","Description":"Fit and plot macroecological patterns
predicted by the Maximum\nEntropy Theory of Ecology (METE).","Imports":"nleqslv,
distr","License":"GPL-
2","NeedsCompilation":"no","Package":"meteR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat","Title":"Fitting and Plotting Tools for the
Maximum Entropy Theory of\nEcology
(METE)","URL":"https:\/\/github.com\/cmerow\/meteR","Version":"1.1"},"meteo":
{"Author":"Milan Kilibarda, Aleksandar Sekulic, Tomislav Hengl, Edzer Pebesma,
Benedikt Graeler","Depends":"R (>= 3.0.0)","Description":"Spatio-temporal
geostatistical mapping of meteorological data. Global spatio-temporal models
calculated using publicly available data are stored in
package.","Imports":"methods, utils, stats, sp, spacetime, rgdal, gstat,
raster,\nsnowfall, plyr","License":"GPL (>= 2.0) | file
LICENCE","NeedsCompilation":"no","Package":"meteo","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Spatio-Temporal Analysis and Mapping of
Meteorological\nObservations","URL":"http:\/\/meteo.r-forge.r-
project.org\/","Version":"0.1-5"},"meteoForecast":{"Author":"Oscar Perpinan
Lamigueiro [cre, aut],\nMarcelo Pinho Almeida [ctb]","Depends":"raster, sp,
zoo","Description":"Access to several Numerical Weather Prediction services both in
raster format and as a time series for a location. Currently it works with GFS,
MeteoGalicia, NAM, and RAP.","Imports":"methods, stats, utils, XML","License":"GPL-
3","NeedsCompilation":"no","Package":"meteoForecast","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"ncdf4, rgdal, lattice,
rasterVis","Title":"Numerical Weather
Predictions","URL":"http:\/\/github.com\/oscarperpinan\/meteoForecast","Version":"0
.49"},"meteogRam":{"Author":"Bogdan Bochenek","Depends":"ggplot2,
RadioSonde","Description":"meteogram is a collection of programs for
plotting\nmeteograms for meteorological data such as atmospheric cross\nsection,
temperatures plots.","License":"GPL-
2","NeedsCompilation":"no","Package":"meteogRam","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Tools for plotting
meteograms","Version":"1.0"},"metricTester":{"Author":"Eliot Miller, Chris Trisos &
Damien Farine","Depends":"R (>= 3.1.1), ape","Description":"Explore the behavior
and performance of phylogenetic metrics and\nnull models.","Imports":"methods,
geiger, spacodiR, dplyr, picante, foreach,\ndoParallel, colorRamps","License":"GPL-
3","NeedsCompilation":"no","Package":"metricTester","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat","Title":"Test Metric and Null Model
Statistical
Performance","URL":"https:\/\/github.com\/eliotmiller\/metricTester","Version":"1.0
.0"},"metricsgraphics":{"Author":"Bob Rudis [aut, cre],\nAli Almossawi [ctb, cph]
(MetricsGraphics library),\nHamilton Ulmer [ctb, cph] (MetricsGraphics
library),\nMozilla [cph] (MetricsGraphics library),\njQuery Foundation and
contributors [ctb, cph] (jQuery library)","Depends":"R (>=
3.0.0)","Description":"Provides an 'htmlwidgets' interface to
the\n'MetricsGraphics.js' ('D3'-based) charting library which is geared
towards\ndisplaying time-series data. Chart types include line charts,
scatterplots,\nhistograms and rudimentary bar charts. Support for laying out
multiple charts\ninto a grid layout is also provided. All charts are interactive
and many\nhave an option for line, label and region
annotations.","Imports":"magrittr, htmlwidgets, htmltools","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"metricsgraphics","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Suggests":"testthat, RColorBrewer, ggplot2,
ggplot2movies, jsonlite (>=\n0.9.16), knitr (>= 1.8), shiny (>= 0.12.0), binom,
dplyr,\ngrDevices","Title":"Create Interactive Charts with the JavaScript
'MetricsGraphics'\nLibrary","URL":"http:\/\/github.com\/hrbrmstr\/metricsgraphics",
"Version":"0.9.0"},"mets":{"Author":"Klaus K. Holst and Thomas
Scheike","Depends":"R (>= 2.15), timereg (>= 1.8.9), lava (>=
1.4)","Description":"Implementation of various statistical models for
multivariate\nevent history data. Including multivariate cumulative incidence
models, and\nbivariate random effects probit models (Liability models). Also
contains\ntwo-stage binomial modelling that can do pairwise odds-ratio
dependence\nmodelling based marginal logistic regression models. This is an
alternative\nto the alternating logistic regression approach
(ALR).","Imports":"numDeriv, compiler, Rcpp, splines, survival","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"mets","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"lava.tobit (>= 0.4-7), prodlim, testthat,
ucminf","Title":"Analysis of Multivariate Event Times","URL":"http:\/\/lava.r-
forge.r-project.org\/","Version":"1.1.1"},"mev":{"Author":"Leo Belzile [aut,
cre],\nJennifer L. Wadsworth [aut],\nPaul J. Northrop [aut],\nClaire L. Coleman
[aut],\nJin. Zhang [ctb],\nMichael A. Newton [ctb],\nArt Owen
[ctb]","Description":"Exact simulation from max-stable processes and multivariate
extreme value distributions for various parametric models. Threshold selection
methods.","Imports":"stats, Rcpp (>= 0.11.6), ismev, evd","License":"GPL-
3","NeedsCompilation":"yes","Package":"mev","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Multivariate Extreme Value
Distributions","Version":"1.6.1"},"mewAvg":{"Author":"Adam L. Pintar and Zachary H.
Levine","Depends":"methods","Description":"Computes the average of a sequence of
random vectors\nin a moving expanding window using a fixed amount of
storage","License":"GPL (>=
2.0)","NeedsCompilation":"yes","Package":"mewAvg","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"A Fixed Memeory Moving Expanding Window
Average","Version":"0.3.0"},"mfp":{"Author":"original by Gareth Ambler
<gareth@stats.ucl.ac.uk>, modified by Axel Benner
<benner@dkfz.de>","Depends":"survival","Description":"Fractional polynomials are
used to represent curvature in regression models. A key reference is Royston and
Altman, 1994.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mfp","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Multivariable Fractional
Polynomials","Version":"1.5.2"},"mfx":{"Author":"Alan Fernihough","Depends":"stats,
sandwich, lmtest, MASS, betareg","Description":"Estimates probit, logit, Poisson,
negative binomial, and beta regression models, returning their marginal effects,
odds ratios, or incidence rate ratios as an output.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"mfx","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Marginal Effects, Odds Ratios and Incidence Rate Ratios for
GLMs","Version":"1.1"},"mgarchBEKK":{"Author":"Harald Schmidbauer [aut],\nAngi
Roesch [aut],\nVehbi Sinan Tunalioglu [cre, aut]","Depends":"R (>= 3.2.3), tseries,
mvtnorm","Description":"Procedures to simulate, estimate and diagnose
MGARCH\nprocesses of BEKK and multivariate GJR (bivariate asymmetric GARCH\nmodel)
specification.","License":"GPL-
3","NeedsCompilation":"yes","Package":"mgarchBEKK","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat, devtools, roxygen2","Title":"Simulating,
Estimating and Diagnosing MGARCH (BEKK and
mGJR)\nProcesses","URL":"https:\/\/github.com\/vst\/mgarchBEKK\/","Version":"0.0.2"
},"mgcv":{"Author":"Simon Wood <simon.wood@r-project.org>","Depends":"R (>=
2.14.0), nlme (>= 3.1-64)","Description":"GAMs, GAMMs and other generalized ridge
regression with\nmultiple smoothing parameter estimation by GCV, REML or
UBRE\/AIC.\nIncludes a gam() function, a wide variety of smoothers, JAGS\nsupport
and distributions beyond the exponential family.","Imports":"methods, stats,
graphics, Matrix","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"mgcv","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"splines, parallel, survival, MASS","Title":"Mixed GAM
Computation Vehicle with GCV\/AIC\/REML Smoothness\nEstimation","Version":"1.8-
12"},"mglmn":{"Author":"Masatoshi Katabuchi and Akihiro Nakamura","Depends":"R (>=
2.10), mvabund, snowfall","Description":"Tools for univariate and multivariate
generalized linear models with model averaging and null model
technique.","License":"GPL-
2","NeedsCompilation":"no","Package":"mglmn","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Model
Averaging for Multivariate GLM with Null Models","Version":"0.0.2"},"mgm":
{"Author":"Jonas Haslbeck","Description":"Estimation of Mixed Graphical model using
L1-regularized neighborhood regression.","Imports":"Rcpp (>= 0.11.4), matrixcalc,
glmnet","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"mgm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Estimating Mixed Graphical
Models","URL":"http:\/\/arxiv.org\/abs\/1510.06871","Version":"1.1-4"},"mgpd":
{"Author":"Pal Rakonczai","Depends":"R (>= 2.10.1), evd, numDeriv, corpcor,
fields","Description":"Extends distribution and density functions to
parametric\nmultivariate generalized Pareto distributions (MGPD of Type\nII), and
provides fitting functions which calculate maximum\nlikelihood estimates for
bivariate and trivariate models. (Help\nis under progress)","License":"GPL-
3","NeedsCompilation":"no","Package":"mgpd","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"mgpd: Functions for multivariate generalized Pareto
distribution\n(MGPD of Type II)","Version":"1.99"},"mgraph":{"Author":"George Owusu
<owusugeorge@ug.edu.gh>","Depends":"rgdal (>= 0.5.2)","Description":"Each function
in the package performs three main functions\ni) it reads spatial data and produces
basic graphs including\npie chart, bar chart, box plots, histogram, scatter plots,
and\nlines ii)it reads non-spatial data such as \"csv\", \"txt\", \"dat\"\ndata and
produces basic graphs and iii) it plots map(s) of the\ninput attribute(s) of
spatial data by setting \"type\" parameter\nto \"map\"","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"mgraph","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"gstat,MASS","Title":"Graphing map attributes and non-
map variables in R","URL":"http:\/\/www.ug.edu.gh\/index1.php?
linkid=616&sectionid=919&page=2","Version":"1.03"},"mhde":{"Author":"Paul W.
Eslinger [aut, cre],\nHeather Orr [aut, ctb]","Description":"Implementation of a
goodness-of-fit test for normality using the Minimum Hellinger
Distance.","Imports":"graphics, stats","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"mhde","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Minimum Hellinger Distance Test for
Normality","URL":"\"https:\/\/cran.r-project.org\/package=mhde\"","Version":"1.0-
1"},"mhsmm":{"Author":"Jared O'Connell <jaredoconnell@gmail.com>, Søren
Højsgaard\n<sorenh@math.aau.dk>","Depends":"mvtnorm","Description":"Parameter
estimation and prediction for hidden Markov and semi-Markov models for data with
multiple observation sequences. Suitable for equidistant time series data, with
multivariate and\/or missing data. Allows user defined emission
2)","NeedsCompilation":"yes","Package":"mhsmm","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Inference for Hidden Markov and Semi-Markov
Models","Version":"0.4.14"},"mht":{"Author":"Florian Rohart","Depends":"glmnet,
Matrix","Description":"Multiple Hypothesis Testing For Variable Selection in high
dimensional linear models. This package performs variable selection with multiple
hypothesis testing, either for ordered variable selection or non-ordered variable
selection. In both cases, a sequential procedure is performed. It starts to test
the null hypothesis \"no variable is relevant\"; if this hypothesis is rejected, it
then tests \"only the first variable is relevant\", and so on until the null
hypothesis is accepted.","License":"GPL-
3","NeedsCompilation":"yes","Package":"mht","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Multiple Hypothesis Testing for Variable Selection in\nHigh-
Dimensional Linear Models","Version":"3.1.2"},"mhurdle":{"Author":"Yves Croissant
[aut, cre],\nFabrizio Carlevaro [aut],\nStephane Hoareau [aut]","Depends":"R (>=
2.10), Formula, truncreg, maxLik, pbivnorm","Description":"Estimation of models
with zero left-censored variables.\nNull values may be caused by a selection
process, insufficient\nresources or infrequency of purchase.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mhurdle","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"survival","Title":"Multiple hurdle Tobit
models","URL":"http:\/\/www.r-project.org","Version":"1.0-1"},"mi":
{"Author":"Andrew Gelman [ctb],\nJennifer Hill [ctb],\nYu-Sung Su [aut],\nMasanao
Yajima [ctb],\nMaria Pittau [ctb],\nBen Goodrich [cre, aut],\nYajuan Si [ctb],\nJon
Kropko [aut]","Depends":"R (>= 3.0.0), methods, Matrix, stats4","Description":"The
mi package provides functions for data manipulation, imputing missing values in an
approximate Bayesian framework, diagnostics of the models used to generate the
imputations, confidence-building mechanisms to validate some of the assumptions of
the imputation algorithm, and functions to analyze multiply imputed data sets with
the appropriate degree of sampling uncertainty.","Imports":"arm (>= 1.4-
2)","NeedsCompilation":"no","Package":"mi","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"betareg, lattice, knitr, MASS, nnet, parallel, sn,
survival,\ntruncnorm, foreign","Title":"Missing Data Imputation and Model
Checking","URL":"http:\/\/www.stat.columbia.edu\/~gelman\/","Version":"1.0"},"miCoP
TCM":{"Author":"Aurelie Bertrand, Catherine Legrand, Ingrid Van
Keilegom","Description":"Fits Semiparametric Promotion Time Cure Models, taking
into account (using a\ncorrected score approach or the SIMEX algorithm) or not the
measurement error\nin the covariates, using a backfitting approach to maximize the
likelihood.","Imports":"MASS, nleqslv, survival, compiler, distr","License":"GPL-
2","NeedsCompilation":"no","Package":"miCoPTCM","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Promotion Time Cure Model with Mis-Measured
Covariates","Version":"1.0"},"miRada":{"Author":"Bin Wang
<bwang@southalabama.edu>.","Depends":"R (>= 2.10.0), stats","Description":"This
package collects algorithms\/functions developed for\nmicroRNA profiling data
analyses. Analytical platforms include\ntraditional hybridization microarray, CGH,
beads-based\nmicroarray, and qRT-PCR array.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"miRada","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"MicroRNA Microarray Data Analysis","Version":"1.13.8-
8"},"miRtest":{"Author":"Stephan Artmann, Klaus Jung, Tim
Beissbarth","Depends":"corpcor, MASS","Description":"combined miRNA- and mRNA-
testing","Imports":"globaltest, GlobalAncova, limma,
RepeatedHighDim","License":"GPL","NeedsCompilation":"no","Package":"miRtest","Repos
itory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"combined miRNA- and mRNA-
testing","URL":"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/22723856","Version":"1.8"},"
micEcon":{"Author":"Arne Henningsen","Depends":"R (>= 2.4.0)","Description":"Tools
for microeconomic analysis and microeconomic modelling","Imports":"miscTools (>=
0.6-1)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"micEcon","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"plm (>= 1.1-0), Ecdat (>= 0.1-5), systemfit (>= 1.0-
0)","Title":"Microeconomic Analysis and
Modelling","URL":"http:\/\/www.micEcon.org","Version":"0.6-12"},"micEconAids":
{"Author":"Arne Henningsen","Depends":"R (>= 2.14.0), lmtest, micEcon (>= 0.6-
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(AIDS)\nsuggested by Deaton and Muellbauer (1980)","Imports":"stats, systemfit (>=
1.1-12), miscTools (>= 0.6-0)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"micEconAids","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Demand Analysis with the Almost Ideal Demand System
(AIDS)","URL":"http:\/\/www.micEcon.org","Version":"0.6-16"},"micEconCES":
{"Author":"Arne Henningsen and Geraldine Henningsen","Depends":"R (>= 2.4.0),
minpack.lm (>= 1.1-4), DEoptim (>= 2.0-4)","Description":"Tools for economic
analysis and economic modelling\nwith a Constant Elasticity of Substitution (CES)
function","Imports":"systemfit (>= 1.0-0), car (>= 2.0-0), micEcon (>= 0.6-
1),\nmiscTools (>= 0.6-1)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"micEconCES","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"maxLik (>= 0.8-0), xtable (>= 1.5-6), AER (>= 1.1-
9)","Title":"Analysis with the Constant Elasticity of Substitution
(CES)\nfunction","URL":"http:\/\/www.micEcon.org","Version":"0.9-8"},"micEconSNQP":
{"Author":"Arne Henningsen","Depends":"R (>= 2.4.0)","Description":"Production
analysis with the Symmetric Normalized Quadratic (SNQ) profit
function","Imports":"miscTools (>= 0.6-1), systemfit (>= 1.0-0),
2)","NeedsCompilation":"no","Package":"micEconSNQP","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"micEcon (>= 0.6-1)","Title":"Symmetric Normalized
Quadratic Profit Function","URL":"http:\/\/www.micEcon.org","Version":"0.6-
6"},"mice":{"Author":"Stef van Buuren [aut, cre],\nKarin Groothuis-Oudshoorn
[aut],\nAlexander Robitzsch [ctb],\nGerko Vink [ctb],\nLisa Doove [ctb],\nShahab
Jolani [ctb]","Depends":"methods, R (>= 2.10.0), Rcpp (>=
0.10.6)","Description":"Multiple imputation using Fully Conditional Specification
(FCS)\nimplemented by the MICE algorithm. Each variable has its own
imputation\nmodel. Built-in imputation models are provided for continuous
data\n(predictive mean matching, normal), binary data (logistic
regression),\nunordered categorical data (polytomous logistic regression) and
ordered\ncategorical data (proportional odds). MICE can also impute
continuous\ntwo-level data (normal model, pan, second-level variables).
Passive\nimputation can be used to maintain consistency between variables.
Various\ndiagnostic plots are available to inspect the quality of the
imputations.","Imports":"lattice, grDevices, graphics, MASS, nnet, rpart,
splines,\nstats, survival, utils","License":"GPL-2 |
GPL-
3","NeedsCompilation":"yes","Package":"mice","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"AGD, CALIBERrfimpute, gamlss, lme4, mitools, nlme,
pan,\nrandomForest, Zelig","Title":"Multivariate Imputation by Chained
Equations","URL":"http:\/\/www.stefvanbuuren.nl , http:\/\/www.multiple-
imputation.com","Version":"2.25"},"miceadds":{"Author":"\nAlexander Robitzsch [aut,
cre], Simon Grund [ctb],\nThorsten Henke [ctb]","Depends":"R (>= 2.15.0),
mice","Description":"\nContains some auxiliary functions for multiple\nimputation
which complements existing functionality\nin R.\nIn addition to some utility
functions, main features\ninclude plausible value imputation,
multilevel\nimputation functions, imputation using partial least\nsquares (PLS) for
high dimensional predictors, nested\nmultiple imputation, and two-way
imputation.","Imports":"bayesm, car, foreign, graphics, grouped, Hmisc, inline,
lme4,\nMASS, MBESS, MCMCglmm, methods, mitools, multiwayvcov, mvtnorm,\npls, Rcpp,
sirt, sjmisc, stats, TAM, utils","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"miceadds","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"Amelia, BIFIEsurvey, haven, jomo, mitml, pan,
Zelig","Title":"Some Additional Multiple Imputation Functions, Especially
for\n'mice'","Version":"1.7-8"},"microbats":{"Author":"Seong Hyun Hwang with
contributions from Rachel Myoung Moon","Depends":"R (>= 3.2.1)","Description":"A
nature-inspired metaheuristic algorithm based on the echolocation behavior of
microbats that uses frequency tuning to optimize problems in both continuous and
discrete dimensions. This R package makes it easy to implement the standard bat
algorithm on any user-supplied function. The algorithm was first developed by Xin-
She Yang in 2010 (<DOI:10.1007\/978-3-642-12538-6_6>,
<DOI:10.1109\/CINTI.2014.7028669>).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"microbats","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"An Implementation of Bat Algorithm in
R","URL":"https:\/\/github.com\/stathwang\/microbats","Version":"0.1-
1"},"microbenchmark":{"Author":"Olaf Mersmann [aut, cre],\nClaudia Beleites
[ctb],\nRainer Hurling [ctb],\nAri Friedman [ctb]","Description":"Provides
infrastructure to accurately measure and compare\nthe execution time of R
expressions.","Imports":"graphics, ggplot2, stats","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"yes","Package":"microbenchmark","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Suggests":"multcomp","Title":"Accurate Timing
Functions","Version":"1.4-2.1"},"micromap":{"Author":"Quinn Payton [aut],\nTony
Olsen [aut],\nMarc Weber [ctb],\nMichael McManus [ctb],\nTom Kincaid [cre,
ctb]","Depends":"R (>= 2.10), maptools, RColorBrewer, rgdal,
sp","Description":"This group of functions simplifies the creation of linked
micromap\nplots.","Imports":"ggplot2, grid","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"micromap","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Linked Micromap
Plots","URL":"http:\/\/www.jstatsoft.org\/v63\/i02\/","Version":"1.9.2"},"micromapS
T":{"Author":"Dan Carr <dcarr@gmu.edu> and James B Pearson
<jpearson@statnetconsulting.com>,\nwith contributions from Linda Pickle
<linda@statnetconsulting.com>.","Depends":"R (>= 3.0.0)","Description":"This
package provides the user with the ability to quickly create Linked\nMicromap plots
of the 50 U.S. states and District of Columbia (51 areas).\nLinked Micromap plots
are visualizations of geo-referenced data that link statistical\ngraphics to an
organized series of small maps.\nThe Help description contains examples of how to
use the micromapST function.\nThis package contains the US and State boundary files
and U. S. FIPS code to State conversion tables\nused by the micromapST function and
several data sets used in the micromapST examples.\nCopyrighted 2013, 2014 and 2015
by Carr, Pearson and Pickle.","Imports":"graphics, RColorBrewer, grDevices,
2)","NeedsCompilation":"no","Package":"micromapST","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"R.rsp","Title":"Linked Micromap Plots for U. S.
States","Version":"1.0.5"},"micropan":{"Author":"Lars Snipen and Kristian Hovde
Liland","Depends":"R (>= 2.15.0), igraph","Description":"A collection of functions
for computations and visualizations of microbial pan-genomes.","License":"GPL-
2","NeedsCompilation":"no","Package":"micropan","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Microbial Pan-genome Analysis","Version":"1.0"},"midasr":
{"Author":"Virmantas Kvedaras <virmantas.kvedaras@mif.vu.lt>, Vaidotas
Zemlys\n<vaidotas.zemlys@mif.vu.lt>","Depends":"R (>= 2.11.0), sandwich,
optimx","Description":"Methods and tools for mixed frequency time series data
analysis. Allows estimation, model selection and forecasting for MIDAS
regressions.","Imports":"MASS, numDeriv, Matrix, forecast, stats, graphics,
utils","License":"GPL-2 | MIT + file
LICENCE","NeedsCompilation":"no","Package":"midasr","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat","Title":"Mixed Data Sampling
Regression","URL":"http:\/\/mpiktas.github.io\/midasr\/","Version":"0.5"},"midastou
ch":{"Author":"Philipp Gaffert [aut, cre],\nFlorian Meinfelder [aut],\nVolker Bosch
[aut]","Depends":"R (>= 3.2.0)","Description":"Contains the function
mice.impute.midastouch(). Technically this function is to be run from within the
'mice' package (van Buuren et al. 2011), type ??mice. It substitutes the method
'pmm' within mice by 'midastouch'. The authors have shown that 'midastouch' is
superior to default 'pmm'. Many ideas are based on Siddique \/ Belin 2008's
MIDAS.","Imports":"utils","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"midastouch","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"mice","Title":"Multiple Imputation by Distance Aided
Donor Selection","URL":"\nhttps:\/\/www.uni-
bamberg.de\/fileadmin\/uni\/fakultaeten\/sowi_lehrstuehle\/statistik\/Personen\/Dat
eien_Florian\/properPMM.pdf","Version":"1.3"},"midrangeMCP":{"Author":"Ben Deivide
[aut, cre],\nDaniel Furtado [aut]","Description":"Apply tests of multiple
comparisons based on studentized midrange\nand range distributions. The tests are:
Tukey Midrange test, Student-Newman-\nKeuls Midrange test, Skott-Knott Midrange
test and Skott-Knott Range test.","Imports":"stats, utils, graphics, grDevices,
SMR, WriteXLS, xtable","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"midrangeMCP","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Multiple Comparisons Procedures Based on Studentized
Midrange\nand Range Distributions","Version":"1.1"},"migest":{"Author":"Guy J.
Abel","Description":"Indirect methods for estimating bilateral migration flows in
the presence of partial or missing data. Methods might be relevant to other
categorical data situations on non-migration data, where for example, marginal
totals are known and only auxiliary bilateral data is available.","License":"GPL-
2","NeedsCompilation":"no","Package":"migest","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Methods for the Indirect Estimation of Bilateral
Migration","URL":"http:\/\/gjabel.wordpress.com\/category\/r\/migest\/","Version":"
1.7.1"},"migration.indices":{"Author":"Lajos BÃ¡lint <balint@demografia.hu> and
Gergely DarÃ³czi\n<daroczig@rapporter.net>","Description":"This package provides
various indices, like Crude Migration Rate,\ndifferent Gini indices or the
Coefficient of Variation among others, to\nshow the (un)equality of
migration.","Imports":"calibrate","License":"AGPL-
3","NeedsCompilation":"no","Package":"migration.indices","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Migration
indices","URL":"http:\/\/github.com\/daroczig\/migration.indices","Version":"0.3.0"
},"migui":{"Author":"Bob Carpenter [ctb],\nBen Goodrich [cre, aut],\nYu-Sung Su
[ctb]","Depends":"gWidgets2","Description":"This GUI for the mi package walks the
user through the steps of multiple imputation and the analysis of completed
data.","Imports":"mi (>= 1.0), arm","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"migui","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"foreign, gWidgets2RGtk2","Title":"Graphical User
Interface to the 'mi' Package","Version":"1.1"},"mime":{"Author":"Jeffrey Horner
[ctb],\nYihui Xie [aut, cre]","Description":"Guesses the MIME type from a filename
extension using the data\nderived from \/etc\/mime.types in UNIX-type
systems.","Imports":"tools","License":"GPL-
2","NeedsCompilation":"yes","Package":"mime","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Map Filenames to MIME
Types","URL":"https:\/\/github.com\/yihui\/mime","Version":"0.4"},"minPtest":
{"Author":"Stefanie Hieke","Depends":"scrime, Epi","Description":"Package minPtest
is designed for estimating a gene region-level summary for SNP data from case-
control studies using a permutation-based resampling method, called min P test,
allowing execution on a compute cluster or multicore computer.","License":"GPL (>=
2.14)","NeedsCompilation":"no","Package":"minPtest","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"parallel, snowfall","Title":"Gene region-level
testing procedure for SNP data, using the min\nP test resampling
approach","Version":"1.7"},"minerva":{"Author":"Michele Filosi [aut, cre], Roberto
Visintainer [aut], Davide\nAlbanese [aut], Samantha Riccadonna [ctb], Giuseppe
Jurman\n[ctb], Cesare Furlanello [ctb]","Depends":"R (>= 2.14.0)","Description":"R
wrapper for 'cmine' implementation of Maximal\nInformation-based Nonparametric
Exploration statistics (MIC and\nMINE family). Detailed information of the ANSI C
implementation 'cmine'\ncan be found at
'http:\/\/mpba.fbk.eu\/cmine'.","Imports":"parallel","License":"GPL-
3","NeedsCompilation":"yes","Package":"minerva","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Maximal
Information-Based Nonparametric Exploration R Package\nfor Variable
Analysis","URL":"http:\/\/mpba.fbk.eu\/cmine,
http:\/\/minepy.sourceforge.net,\nhttp:\/\/www.exploredata.net, http:\/\/www.r-
project.org","Version":"1.4.5"},"miniCRAN":{"Author":"Revolution Analytics
[aut],\nAndrie de Vries [aut, cre],\nAlex Chubaty [ctb]","Description":"Makes it
possible to create an internally consistent\nrepository consisting of selected
packages from CRAN-like repositories.\nThe user specifies a set of desired
packages, and miniCRAN recursively\nreads the dependency tree for these packages,
then downloads only this\nsubset. The user can then install packages from this
repository directly,\nrather than from CRAN. This is useful in production
settings, e.g. server\nbehind a firewall, or remote locations with slow broadband
access.","Imports":"tools, XML, httr, methods, utils","License":"GPL-
2","NeedsCompilation":"no","Package":"miniCRAN","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"testthat(>= 0.9), knitr, igraph","Title":"Create a
Mini Version of CRAN Containing Only Selected
Packages","URL":"https:\/\/github.com\/RevolutionAnalytics\/miniCRAN","Version":"0.
2.4"},"miniGUI":{"Author":"Jorge Luis Ojeda Cabrera","Depends":"R (>= 2.5.0),
tcltk","Description":"quick and simple tktcl miniGUI to call
functions.","License":"GPL","NeedsCompilation":"no","Package":"miniGUI","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Title":"tktcl quick and simple function
GUI","Version":"0.8.0"},"miniUI":{"Author":"Joe Cheng [cre, aut],\nRStudio
[cph]","Description":"Provides UI widget and layout functions for writing Shiny
apps\nthat work well on small screens.","Imports":"shiny (>= 0.13), htmltools (>=
0.3), utils","License":"GPL-
3","NeedsCompilation":"no","Package":"miniUI","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Shiny UI Widgets for Small
Screens","Version":"0.1.1"},"minimap":{"Author":"Sean Kross [aut,
cre]","Depends":"R (>= 3.1.0), graphics","Description":"Create tile grid maps,
which are like choropleth maps except each\nregion is represented with equal visual
space.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"minimap","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat","Title":"Create Tile Grid
Maps","URL":"http:\/\/github.com\/seankross\/minimap","Version":"0.1.0"},"minimax":
{"Author":"Bill Venables","Description":"The minimax family of distributions is a
two-parameter\nfamily like the beta family, but computationally a lot
more\ntractible.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"minimax","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Minimax distribution family","Version":"1.0"},"minimist":
{"Author":"Jeroen Ooms, James Halliday","Description":"A binding to the minimist
JavaScript library. This module implements\nthe guts of optimist's argument parser
without all the fanciful decoration.","Imports":"V8","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"minimist","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Parse Argument
Options","URL":"https:\/\/github.com\/jeroenooms\/minimist,\nhttps:\/\/www.npmjs.co
m\/package\/minimist","Version":"0.1"},"minpack.lm":{"Author":"Timur V. Elzhov,
Katharine M. Mullen, Andrej-Nikolai Spiess, Ben Bolker","Description":"The nls.lm
function provides an R interface to lmder and lmdif from the MINPACK library, for
solving nonlinear least-squares problems by a modification of the Levenberg-
Marquardt algorithm, with support for lower and upper parameter bounds. The
implementation can be used via nls-like calls using the nlsLM
function.","License":"GPL-3 + file
LICENSE","NeedsCompilation":"yes","Package":"minpack.lm","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"MASS","Title":"R Interface to the Levenberg-
Marquardt Nonlinear Least-Squares\nAlgorithm Found in MINPACK, Plus Support for
Bounds","Version":"1.2-0"},"minqa":{"Author":"Douglas Bates, Katharine M. Mullen,
John C. Nash, Ravi Varadhan","Description":"Derivative-free optimization by
quadratic approximation\nbased on an interface to Fortran implementations by M. J.
D.\nPowell.","Imports":"Rcpp (>= 0.9.10)","License":"GPL-
2","NeedsCompilation":"yes","Package":"minqa","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Derivative-free optimization algorithms by
quadratic\napproximation","URL":"http:\/\/optimizer.r-forge.r-
project.org","Version":"1.2.4"},"minque":{"Author":"Jixiang Wu","Depends":"klaR,
stats,utils,Matrix","Description":"This package offers three important components:
(1) to construct a use-defined linear mixed model, (2) to employ one of linear
mixed model approaches: minimum norm quadratic unbiased estimation (MINQUE) (Rao,
1971) for variance component estimation and random effect prediction; and (3) to
employ a jackknife resampling technique to conduct various statistical tests. In
addition, this package provides the function for model or data evaluations.This R
package offers fast computations for large data sets analyses for various irregular
data structures.","License":"GPL-
2","NeedsCompilation":"no","Package":"minque","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"An R Package for Linear Mixed Model
Analyses","Version":"1.1"},"minval":{"Author":"Daniel Osorio [aut,cre], Janneth
Gonzalez [aut], Andres Pinzon-Velasco\n[aut]","Depends":"R (>=
2.10)","Description":"For a given set of stoichiometric reactions, this package
evaluates the mass balance and extracts all reactants, products, orphan
metabolites, metabolite names and compartments. Also are included some options to
check the compound names associated to Chemical Entities of Biological Interest
(ChEBI) database <https:\/\/www.ebi.ac.uk\/chebi>.","License":"GPL-
2","NeedsCompilation":"no","Package":"minval","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"RUnit","Title":"MINimal VALidation for Stoichiometric
Reactions","Version":"0.2"},"minxent":{"Author":"Senay Asma
<senayyolacan@anadolu.edu.tr>","Depends":"R (>= 1.6.0)","Description":"This package
implements entropy optimization distribution\nunder specified constraints. It also
offers an R interface to\nthe MinxEnt and MaxEnt distributions.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"minxent","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Entropy Optimization
Distributions","URL":"http:\/\/www.r-project.org","Version":"0.01"},"mipfp":
{"Author":"Johan Barthelemy [aut, cre], Thomas Suesse [aut], Mohammad Namazi-Rad
[ctb]","Depends":"cmm, Rsolnp, numDeriv, R(>= 2.10.0)","Description":"An
implementation of the iterative proportional fitting (IPFP),\nmaximum likelihood,
minimum chi-square and weighted least squares procedures\nfor updating a N-
dimensional array with respect to given target marginal\ndistributions (which, in
turn can be multi-dimensional). The package also\nprovides an application of the
IPFP to simulate multivariate Bernoulli\ndistributions.","License":"GPL-
2","NeedsCompilation":"no","Package":"mipfp","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Multidimensional Iterative Proportional Fitting and
Alternative\nModels","URL":"https:\/\/github.com\/jojo-\/mipfp","Version":"2.2.1"},
"mirt":{"Author":"Phil Chalmers [aut, cre, cph],\nJoshua Pritikin [ctb],\nAlexander
Robitzsch [ctb],\nMateusz Zoltak [ctb],\nKwonHyun Kim [ctb],\nCarl F. Falk
[ctb]","Depends":"stats, R (>= 3.1.0), stats4, lattice,
methods","Description":"Analysis of dichotomous and polytomous response data
using\nunidimensional and multidimensional latent trait models under the
Item\nResponse Theory paradigm. Exploratory and confirmatory models can
be\nestimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory\nbi-
factor and two-tier analyses are available for modeling item testlets.\nMultiple
group analysis and mixed effects designs also are available for\ndetecting
differential item and test functioning as well as modelling\nitem and person
covariates.","Imports":"GPArotation, Rcpp, sfsmisc, mgcv, numDeriv","License":"GPL
(>=
3)","NeedsCompilation":"yes","Package":"mirt","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"boot, latticeExtra, directlabels, shiny, knitr,
Rsolnp,\nalabama, sirt, mirtCAT","Title":"Multidimensional Item Response
Theory","URL":"https:\/\/github.com\/philchalmers\/mirt,\nhttps:\/\/github.com\/phi
lchalmers\/mirt\/wiki","Version":"1.16"},"mirtCAT":{"Author":"Phil Chalmers [aut,
cre, cph]","Depends":"mirt (>= 1.14), shiny (>= 0.13.0)","Description":"Provides
tools to generate an HTML interface for creating adaptive\nand non-adaptive
educational and psychological tests using the shiny\npackage. Suitable for applying
unidimensional and multidimensional\ncomputerized adaptive tests using item
response theory methodology and for\ncreating simple questionnaires forms to
collect response data directly in R.\nPackage also contains tools useful for
performing Monte Carlo simulations\nfor studying the behaviour of computerized
adaptive test banks.","Imports":"lattice, stats, Rcpp, methods,
markdown","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"mirtCAT","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"parallel, SimDesign, knitr,
testthat","Title":"Computerized Adaptive Testing with Multidimensional
Item\nResponse
Theory","URL":"https:\/\/github.com\/philchalmers\/mirtCAT,\nhttps:\/\/github.com\/
philchalmers\/mirtCAT\/wiki","Version":"0.8"},"misc3d":{"Author":"Dai Feng and Luke
Tierney","Description":"A collection of miscellaneous 3d plots,
including\nisosurfaces.","License":"GPL","NeedsCompilation":"no","Package":"misc3d"
,"Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"rgl, tkrplot,
MASS","Title":"Miscellaneous 3D Plots","Version":"0.8-4"},"miscF":{"Author":"Dai
Feng","Depends":"R (>= 2.15.0), MCMCpack (>= 1.2-4), mvtnorm(>=
0.9-9992), Rcpp\n(>= 0.10.3), RcppArmadillo (>= 0.3.810.2)","Description":"Various
functions for random number generation, density\nestimation, classification, curve
fitting, and spatial
data\nanalysis.","License":"GPL","NeedsCompilation":"yes","Package":"miscF","Reposi
tory":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"mixAK (>=
2.6)","Title":"Miscellaneous Functions","Version":"0.1-2"},"miscFuncs":
{"Author":"Benjamin M. Taylor","Depends":"roxygen2, mvtnorm","Description":"LaTeX
tables, Kalman filter, web scraping, development tools,\nrelative risk, odds
ratio","License":"GPL-
3","NeedsCompilation":"no","Package":"miscFuncs","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Miscellaneous Useful Functions","Version":"1.2-
7"},"miscTools":{"Author":"Arne Henningsen, Ott Toomet","Depends":"R (>=
2.14.0)","Description":"Miscellaneous small tools and utilities","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"miscTools","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"Ecdat (>= 0.1-5)","Title":"Miscellaneous Tools and
Utilities","URL":"http:\/\/www.micEcon.org","Version":"0.6-16"},"miscset":
{"Author":"Sven E. Templer","Description":"A collection of miscellaneous methods to
simplify various tasks,\nincluding plotting, data.frame and matrix transformations,
environment\nfunctions, regular expression methods, and string and logical
operations, as\nwell as numerical and statistical tools. Most of the methods are
simple but\nuseful wrappers of common base R functions, which extend S3 generics
or\nprovide default values for important parameters.","Imports":"ggplot2,
gridExtra, parallel, Rcpp (>= 0.11.1), xtable","License":"GPL-
3","NeedsCompilation":"yes","Package":"miscset","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr, rmarkdown","Title":"Miscellaneous Tools
Set","URL":"https:\/\/github.com\/setempler\/miscset","Version":"1.0.0"},"missDeath
s":{"Author":"Tomaz Stupnik [aut, cre],\nMaja Pohar Perme
[aut]","Depends":"survival, rms, relsurv, cmprsk","Description":"Implements two
methods: a nonparametric risk adjustment and a data imputation method that use
general population mortality tables to allow a correct analysis of time to disease
recurrence.","Imports":"Rcpp (>= 0.11.1), mitools","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"missDeaths","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"'Correctly Analyse Disease Recurrence with Missing at
Risk\nInformation using Population Mortality'","Version":"1.2"},"missForest":
{"Author":"Daniel J. Stekhoven
<stekhoven@stat.math.ethz.ch>","Depends":"randomForest,foreach,itertools","Descript
ion":"The function 'missForest' in this package is used to\nimpute missing values
particularly in the case of mixed-type\ndata. It uses a random forest trained on
the observed values of\na data matrix to predict the missing values. It can be used
to\nimpute continuous and\/or categorical data including complex\ninteractions and
non-linear relations. It yields an out-of-bag\n(OOB) imputation error estimate
without the need of a test set\nor elaborate cross-validation. It can be run in
parallel to\nsave computation time.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"missForest","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Nonparametric Missing Value Imputation using Random
Forest","URL":"http:\/\/www.r-project.org,
https:\/\/github.com\/stekhoven\/missForest","Version":"1.4"},"missMDA":
{"Author":"Francois Husson, Julie Josse","Depends":"R (>=
3.2.0)","Description":"Imputation of incomplete continuous or categorical datasets;
Missing values are imputed with a principal component analysis (PCA), a multiple
correspondence analysis (MCA) model or a multiple factor analysis (MFA) model;
Perform multiple imputation with and in PCA.","Imports":"FactoMineR
(>=\n1.32),graphics,grDevices,mice,mvtnorm,stats,utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"missMDA","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Handling Missing Values with Multivariate Data
Analysis","URL":"http:\/\/www.agrocampus-ouest.fr\/math\/husson,
http:\/\/juliejosse.com\/","Version":"1.10"},"mistat":{"Author":"Daniele
Amberti","Depends":"R (>= 2.14), graphics, grDevices, methods, stats,
utils","Description":"This R package is providing all the data sets and statistical
analysis applications used in \"Modern Industrial Statistics: with applications in
R, MINITAB and JMP\" by R.S. Kenett and S. Zacks with contributions by D. Amberti,
John Wiley and Sons, 2013, which is a second revised and expanded revision
of \"Modern Industrial Statistics: Design and Control of Quality and Reliability\",
R. Kenett and S. Zacks, Duxbury\/Wadsworth Publishing, 1998.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mistat","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"e1071, mvtnorm, AcceptanceSampling, boot, car,
Dodge,\ntseries, qcc, DoE.base, FrF2, rsm, LearnBayes, ggplot2, grid,\nDiceEval,
DiceKriging, DiceDesign, DiceView, lhs, survival","Title":"Data Sets, Functions and
Examples from the Book: \"Modern\nIndustrial Statistics\" by Kenett, Zacks and
Amberti","Version":"1.0-3"},"mistral":{"Author":"Clement WALTER, Gilles DEFAUX,
Bertrand IOOSS and Vincent MOUTOUSSAMY, with contributions from Nicolas BOUSQUET,
Claire CANNAMELA and Paul LEMAITRE","Depends":"R (>= 3.0.0)","Description":"Various
reliability analysis methods for rare event inference:\n1) computing failure
probability (probability that the output of a numerical model exceeds a
threshold),\n2) computing quantiles of low or high-order,\n3) Wilks formula to
compute quantile(s) from a sample or the size of the required i.i.d.
sample.","Imports":"e1071, Matrix, mvtnorm, ggplot2, doParallel,
foreach,\niterators, DiceKriging, emoa,
quadprog","License":"CeCILL","NeedsCompilation":"no","Package":"mistral","Repositor
y":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"microbenchmark,
kernlab","Title":"Methods in Structural Reliability
Analysis","Version":"2.1.0"},"mitml":{"Author":"Simon Grund [aut,cre], Alexander
Robitzsch [aut], Oliver Luedtke [aut]","Description":"Provides tools for multiple
imputation of missing data in multilevel\nmodeling. Includes a user-friendly
interface to the packages 'pan' and 'jomo',\nand several functions for
visualization, data management and the analysis\nof multiply imputed data
sets.","Imports":"pan, jomo, haven, grDevices, graphics, stats,
2)","NeedsCompilation":"no","Package":"mitml","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"lme4, nlme, mice","Title":"Tools for Multiple Imputation
in Multilevel Modeling","Version":"0.3-0"},"mitools":{"Author":"Thomas
Lumley","Depends":"R (>= 2.10)","Description":"Tools to perform analyses and
combine results from\nmultiple-imputation datasets.","License":"GPL-
2","NeedsCompilation":"no","Package":"mitools","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"RODBC, DBI, foreign","Title":"Tools for multiple
imputation of missing data","Version":"2.3"},"mix":{"Author":"Original by Joseph L.
Schafer <jls@stat.psu.edu>.","Depends":"stats","Description":"Estimation\/multiple
imputation programs for mixed categorical\nand continuous
data.","License":"Unlimited","NeedsCompilation":"yes","Package":"mix","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Title":"Estimation\/Multiple Imputation for
Mixed Categorical and\nContinuous
Data","URL":"http:\/\/www.stat.psu.edu\/~jls\/misoftwa.html","Version":"1.0-
9"},"mixAK":{"Author":"ArnoÅ¡t KomÃ¡rek <arnost.komarek@mff.cuni.cz>","Depends":"R
(>= 3.0.0), colorspace, lme4 (>= 1.0)","Description":"Contains a mixture of
statistical methods including the MCMC methods to analyze normal mixtures.
Additionally, model based clustering methods are implemented to perform
classification based on (multivariate) longitudinal (or otherwise correlated) data.
The basis for such clustering is a mixture of multivariate generalized linear mixed
models.","Imports":"graphics, stats, splines, fastGHQuad, mnormt, parallel,
coda","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"mixAK","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Multivariate Normal Mixture Models and Mixtures of
Generalized\nLinear Mixed Models Including Model Based
Clustering","URL":"http:\/\/msekce.karlin.mff.cuni.cz\/~komarek","Version":"4.2"},"
mixOmics":{"Author":"Kim-Anh Le Cao, Ignacio Gonzalez, Sebastien Dejean with key
contributors Florian Rohart, Benoit Gautier\nand contributions from Pierre Monget,
Jeff Coquery, FangZou Yao, Benoit Liquet.","Depends":"R (>= 2.10), MASS, lattice,
ggplot2","Description":"We provide statistical integrative techniques and\nvariants
to analyse highly dimensional data sets: regularized\nCanonical Correlation
Analysis ('rCCA') and sparse Partial Least Squares variants ('sPLS')\nto unravel
relationships between two heterogeneous data sets of size (n times p) and (n times
q) where the p and\nq variables are measured on the same samples or individuals n.
These data may come from high throughput\ntechnologies, such as 'omics' data (e.g.
transcriptomics, metabolomics or proteomics\ndata) that require an integrative or
joint analysis. However, 'mixOmics' can also be applied to any other\nlarge data
sets where p + q >> n. 'rCCA' is a regularized version of Canonical Correlation
Analysis to deal with\nthe large number of variables. 'sPLS' allows variable
selection in a one step procedure and two frameworks\nare proposed: regression and
canonical analysis. Numerous graphical outputs are provided to help
interpreting\nthe results. Recent methodological developments include: sparse PLS-
Discriminant Analysis ('sPLS-DA'), Independent\nPrincipal Component Analysis
('IPCA'), multilevel analysis using variance decomposition of the data and
integration\nof multiple data sets
with regularized Generalised Canonical Correlation Analysis ('rGCCA') and variants
(sparse 'GCCA'). More details can be found\non our website.","Imports":"igraph,
rgl, ellipse, corpcor","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mixOmics","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Omics Data Integration
Project","URL":"http:\/\/www.mixOmics.org","Version":"5.2.0"},"mixPHM":
{"Author":"Patrick Mair [cre, aut],\nMarcus Hudec [aut]","Depends":"R (>=
3.0.0)","Description":"Fits multiple variable mixtures of various parametric
proportional hazard models using the EM-Algorithm. Proportionality restrictions can
be imposed on the latent groups and\/or on the variables. Several survival
distributions can be specified. Missing values and censored values are allowed.
Independence is assumed over the single variables.","Imports":"graphics, stats,
survival, lattice","License":"GPL-
2","NeedsCompilation":"no","Package":"mixPHM","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Mixtures of Proportional Hazard Models","Version":"0.7-
2"},"mixRasch":{"Author":"John T. Willse","Description":"Estimates Rasch models and
mixture Rasch models, including the dichotomous Rasch model, the rating scale
model, and the partial credit model.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mixRasch","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Mixture Rasch Models with
JMLE","Version":"1.1"},"mixcat":{"Author":"Georgios Papageorgiou and John
Hinde","Depends":"R (>= 2.8.1), statmod","Description":"Mixed effects cumulative
and baseline logit link models\nfor the analysis of ordinal or nominal responses,
with\nnon-parametric distribution for the random effects","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"mixcat","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Mixed effects cumulative link and logistic regression
models","Version":"1.0-3"},"mixdist":{"Author":"Peter Macdonald
<pdmmac@mcmaster.ca>, with contributions from\nJuan Du
<duduyy@hotmail.com>","Depends":"R (>= 1.4.0)","Description":"This package contains
functions for fitting finite mixture\ndistribution models to grouped data and
conditional data by the\nmethod of maximum likelihood using a combination of
a\nNewton-type algorithm and the EM algorithm.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mixdist","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Finite Mixture Distribution
Models","URL":"http:\/\/www.r-
project.org,\nhttp:\/\/www.math.mcmaster.ca\/peter\/mix\/mix.html","Version":"0.5-
4"},"mixedMem":{"Author":"Y. Samuel Wang [aut, cre],\nElena A. Erosheva
[aut]","Depends":"R (>= 3.0.2)","Description":"Fits mixed membership models with
discrete multivariate data (with\nor without repeated measures) following the
general framework of Erosheva et al\n(2004). This package uses a Variational EM
approach by approximating the\nposterior distribution of latent memberships and
selecting hyperparameters\nthrough a pseudo-MLE procedure. Currently supported data
types are\nBernoulli, multinomial and rank (Plackett-Luce). The extended GoM model
with fixed stayers from Erosheva et al (2007) is now also supported. See
Airoldi et al (2014) for other examples of mixed membership
models.","Imports":"Rcpp (>= 0.11.3), gtools","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"mixedMem","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr, xtable,","Title":"Tools for Discrete
Multivariate Mixed Membership Models","Version":"1.1.0"},"mixer":
{"Author":"Christophe Ambroise [aut],\nGilles Grasseau [aut],\nMark Hoebeke
[aut],\nPierre Latouche [aut, cre],\nVincent Miele [aut],\nFranck Picard
[aut],\nLAPACK authors [aut] (copyrights apply to src\/*.f)","Depends":"R (>=
2.5.0), methods","Description":"Routines for the analysis (unsupervised clustering)
of\nnetworks using MIXtures of Erdos-Renyi random graphs","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"mixer","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Random graph
clustering","URL":"http:\/\/ssbgroup.fr\/mixnet\/mixer.html,
http:\/\/ssbgroup.fr","Version":"1.8"},"mixexp":{"Author":"John Lawson [aut,
cre],\nCameron Willden [aut],\nGreg Piepel [ctb]","Depends":"gdata, lattice, grid,
daewr","Description":"Functions for creating designs for mixture experiments,
making ternary contour plots, and making mixture effect plots.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"mixexp","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Design and Analysis of Mixture
Experiments","Version":"1.2.3"},"mixlm":{"Author":"Kristian Hovde Liland [aut,
cre],\nSolve Sæbø [ctb],\nR-Core [ctb]","Description":"The main functions perform
mixed models analysis by least squares or REML by adding the function r() to
formulas of lm and glm. A collection of text-book statistics for higher education
is also included, e.g. modifications of the functions lm, glm and associated
summaries from the package stats.","Imports":"lme4, car, pls, multcomp, pracma,
leaps","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mixlm","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Mixed Model ANOVA and Statistics for
Education","Version":"1.1.1"},"mixor":{"Author":"Donald Hedeker
<DHedeker@health.bsd.uchicago.edu>, Kellie J. Archer, Rachel Nordgren, Robert D.
Gibbons","Depends":"R (>= 2.10)","Description":"Provides the function 'mixord' for
fitting a mixed-effects ordinal and binary response models and associated methods
for printing, summarizing, extracting estimated coefficients and variance-
covariance matrix, and estimating contrasts for the fitted models.","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"mixor","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"survival","Title":"Mixed-Effects Ordinal Regression
Analysis","Version":"1.0.3"},"mixpack":{"Author":"Marc Comas-CufÃ [aut,
cre],\nJosep Antoni MartÃn-FernÃ¡ndez [aut],\nGlÃ²ria Mateu-Figueras
[aut]","Depends":"R (>= 3.0.2)","Description":"A collection of tools implemented to
facilitate the analysis of the components of a finite mixture distributions. The
package has some functions to generate random samples coming from a finite mixture.
The package provides a C++ implementation for the construction of a hierarchy over
the components of a given finite mixture.","Imports":"Rcpp (>= 0.11.5), mvtnorm,
methods,
stats","License":"GPL","NeedsCompilation":"yes","Package":"mixpack","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Suggests":"mclust, Rmixmod,
knitr","Title":"Tools to Work with Mixture
Components","URL":"http:\/\/mcomas.net\/software\/mixpack","Version":"0.3.4"},"mixr
eg":{"Author":"Rolf Turner <r.turner@auckland.ac.nz>","Depends":"R (>=
0.99)","Description":"Fits mixtures of (possibly multivariate) regressions\n(which
has been described as doing ANCOVA when you don't\nknow the
levels).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mixreg","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Functions to fit mixtures of
regressions","URL":"http:\/\/www.stat.auckland.ac.nz\/~rolf\/","Version":"0.0-
5"},"mixsep":{"Author":"Torben Tvedebrink <tvede@math.aau.dk>","Depends":"R (>=
2.0.0), tcltk, tcltk2, MASS, RODBC","Description":"Separates DNA mixtures using a
statistical model within a\ngreedy algorithm with a useful tcl\/tk
GUI.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mixsep","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Forensic Genetics DNA Mixture
Separation","URL":"http:\/\/people.math.aau.dk\/~tvede\/mixsep","Version":"0.2.1-
2"},"mixsmsn":{"Author":"Marcos Prates [aut, cre, trl], Victor Lachos [aut], Celso
Cabral [aut]","Depends":"R (>= 1.9.0), mvtnorm (>= 0.9-9)","Description":"Functions
to fit finite mixture of scale mixture of\nskew-normal (FM-SMSN)
2.0)","NeedsCompilation":"no","Package":"mixsmsn","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Fitting Finite Mixture of Scale Mixture of Skew-
Normal\nDistributions","Version":"1.1-1"},"mixtNB":{"Author":"Elisabetta Bonafede,
Cinzia Viroli","Description":"Differential expression analysis of RNA-Seq data when
replicates under two conditions are available is performed. First, mixtures of
Negative Binomial distributions are fitted on the data in order to estimate the
dispersions, then the Wald test is computed.","License":"GPL-
3","NeedsCompilation":"no","Package":"mixtNB","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"DE Analysis of RNA-Seq Data by Mixtures of
NB","Version":"1.0"},"mixtools":{"Author":"Derek Young [aut, cre],\nTatiana
Benaglia [aut],\nDidier Chauveau [aut],\nDavid Hunter [aut],\nRyan Elmore
[ctb],\nThomas Hettmansperger [ctb],\nHoben Thomas [ctb],\nFengjuan Xuan
[ctb]","Depends":"R (>= 3.2.2)","Description":"A collection of R functions for
analyzing finite mixture models. This package is based upon work supported by the
National Science Foundation under Grant No. SES-0518772.","Imports":"boot, MASS,
segmented, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"mixtools","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Tools for Analyzing Finite Mixture
Models","Version":"1.0.4"},"mixtox":{"Author":"Xiangwei Zhu","Depends":"R (>=
3.0.2)","Description":"Curve Fitting for monotonic(sigmoidal) & non-monotonic(J-
shaped)\nconcentration-response data. Toxicity prediction of chemical mixtures
using reference\nmodels such as 'concentration addition' and 'independent action'
(Backhaus, T., Faust,\nM., Environmental Science and Technology. 2012, 46, 2564-
2573. doi:10.1021\/es2034125).","Imports":"nls2","License":"GPL-
2","NeedsCompilation":"no","Package":"mixtox","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Curve Fitting and Mixture Toxicity
Assessment","Version":"1.2"},"mixture":{"Author":"Ryan
P. Browne, Aisha ElSherbiny and Paul D. McNicholas","Description":"An
implementation of all 14 Gaussian parsimonious\nclustering models (GPCMs) for
model-based clustering and\nmodel-based classification.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mixture","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Mixture Models for Clustering and
Classification","Version":"1.4"},"mizer":{"Author":"Finlay Scott (JRC, IT) and
Julia Blanchard (Sheffield University, UK)\nand Ken Andersen (DTU Aqua, Copenhagen,
DK)","Depends":"R (>= 3.0)","Description":"A set of classes and methods to set up
and run multispecies, trait\nbased and community size spectrum ecological models,
focussed on the marine\nenvironment.","Imports":"methods, plyr, reshape2,
3","NeedsCompilation":"no","Package":"mizer","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat, roxygen2","Title":"Multi-species sIZE spectrum
modelling in R","Version":"0.2"},"mkde":{"Author":"Jeff A. Tracey, James Sheppard,
Jun Zhu, Robert Sinkovts, Amit Chourasia, Glenn Lockwood, and Robert N.
Fisher","Depends":"R (>= 2.10)","Description":"Provides functions to compute and
visualize movement-based kernel density estimates (MKDEs) for animal utilization
distributions in 2 or 3 spatial dimensions.","Imports":"Rcpp (>= 0.9.6), raster,
3)","NeedsCompilation":"yes","Package":"mkde","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"2D and 3D movement-based kernel density estimates
(MKDEs)","Version":"0.1"},"mkin":{"Author":"Johannes Ranke [aut, cre, cph],\nKatrin
Lindenberger [ctb],\nRenÃ© Lehmann [ctb],\nEurofins Regulatory AG
[cph]","Depends":"minpack.lm, rootSolve, inline,
parallel","Description":"Calculation routines based on the FOCUS Kinetics Report
(2006).\nIncludes a function for conveniently defining differential equation
models,\nmodel solution based on eigenvalues if possible or using numerical
solvers\nand a choice of the optimisation methods made available by the 'FME'
package.\nIf a C compiler (on windows: 'Rtools') is installed,
differential\nequation models are solved using compiled C functions.\nPlease note
that no warranty is implied for correctness of results or fitness\nfor a particular
purpose.","Imports":"stats, graphics, methods, FME, deSolve,
R6","License":"GPL","NeedsCompilation":"no","Package":"mkin","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Suggests":"knitr, testthat, microbenchmark,
ggplot2","Title":"Routines for Fitting Kinetic Models with One or More
State\nVariables to Chemical Degradation Data","URL":"http:\/\/kinfit.r-forge.r-
project.org\/mkin_static\nhttp:\/\/github.com\/jranke\/mkin","Version":"0.9.42"},"m
kssd":{"Author":"B N Mandal <mandal.stat@gmail.com>","Depends":"R(>=
2.13.0)","Description":"mkssd is a package that generates efficient balanced\nnon-
aliased multi-level k-circulant supersaturated designs by\ninterchanging the
elements of the generator vector. The package\ntries to generate a supersaturated
design that has chisquare\nefficiency more than user specified efficiency level
(mef). The\npackage also displays the progress of generation of an\nefficient
multi-level k-circulant design through a progress\nbar. The progress of 100% means
that one full round of\ninterchange is completed. More than one full round
(typically\n4-5 rounds) of interchange may be required for larger
2)","NeedsCompilation":"no","Package":"mkssd","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Efficient multi-level k-circulant supersaturated
designs","Version":"1.1"},"mlDNA":{"Author":"Chuang Ma and Xiangfeng
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necessary to perform the machine learning-based\ndifferential network analysis of
transcriptome data.","Imports":"pROC (>= 1.5.4), ROCR(>= 1.0-5)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mlDNA","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"bigmemory, GeneSelector, gplots, nnet, cairoDevice,
fBasics","Title":"Machine Learning-based Differential Network Analysis
of\nTranscriptome
Data","URL":"http:\/\/www.cmbb.arizona.edu\/mlDNA","Version":"1.1"},"mlPhaser":
{"Author":"Dave T. Gerrard","Description":"Phase haplotypes from genotypes based on
a list of known\nhaplotypes. Suited to highly diverse loci such as
HLA.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mlPhaser","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Multi-Locus Haplotype
Phasing","URL":"https:\/\/github.com\/davetgerrard\/mlPhaser","Version":"0.01"},"ml
VAR":{"Author":"Sacha Epskamp, Marie K. Deserno and Laura F.
Bringmann","Depends":"R (>= 3.0.0)","Description":"Compute estimates of the
multivariate vector autoregression model as\nused to (but not limited to) analyze
experience sampling method data in\nclinical psychology. The model can be extended
through treatment effects,\ncovariates and pre- and post-assessment
effects.","Imports":"plyr, lme4, arm, qgraph","License":"GPL-
2","NeedsCompilation":"no","Package":"mlVAR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Multi-Level Vector
Autoregression","Version":"0.1.0"},"mlbench":{"Author":"Friedrich Leisch and
Evgenia Dimitriadou.","Depends":"R (>= 2.10)","Description":"A collection of
artificial and real-world machine learning\nbenchmark problems, including, e.g.,
several data sets from the\nUCI repository.","License":"GPL-
2","NeedsCompilation":"yes","Package":"mlbench","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"lattice","Title":"Machine Learning Benchmark
Problems","Version":"2.1-1"},"mldr":{"Author":"David Charte [cre],\nFrancisco
Charte [aut]","Depends":"R (>= 3.0.0)","Description":"Exploratory data analysis and
manipulation functions for multi-\nlabel data sets along with an interactive Shiny
application to ease their use.","Imports":"shiny (>= 0.11), XML, circlize,
graphics, grDevices, stats,\nmethods","License":"LGPL (>= 3) | file
LICENSE","NeedsCompilation":"no","Package":"mldr","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"pROC, knitr, mldr.datasets","Title":"Exploratory
Data Analysis and Manipulation of Multi-Label
Data\nSets","URL":"https:\/\/github.com\/fcharte\/mldr","Version":"0.3.22"},"mldr.d
atasets":{"Author":"David Charte [cre],\nFrancisco Charte [aut]","Depends":"R (>=
3.0.0)","Description":"Large collection of multilabel datasets along with the
functions\nneeded to export them to several formats, to make partitions, and to
obtain\nbibliographic information.","Imports":"utils","License":"LGPL (>= 3) | file
LICENSE","NeedsCompilation":"no","Package":"mldr.datasets","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Suggests":"mldr","Title":"R Ultimate Multilabel
Dataset
Repository","URL":"https:\/\/github.com\/fcharte\/mldr.datasets","Version":"0.3.15"
},"mlearning":{"Author":"Ph. Grosjean & K. Denis","Depends":"R (>=
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various\nmachine learning algorithms. Confusion matrices are
provided\ntoo.","Imports":"stats, grDevices, class, nnet, MASS, e1071,
randomForest,\nipred","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mlearning","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"mlbench, datasets, RColorBrewer","Title":"Machine
learning algorithms with unified interface and
confusion\nmatrices","URL":"http:\/\/www.sciviews.org\/zooimage","Version":"1.0-
0"},"mlegp":{"Author":"Garrett M. Dancik","Description":"Maximum likelihood
Gaussian process modeling for\nunivariate and multi-dimensional outputs with
diagnostic plots.\nContact the maintainer for a package version that
implements\nsensitivity analysis functionality.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"mlegp","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"snowfall","Title":"Maximum Likelihood Estimates of
Gaussian Processes","Version":"3.1.4"},"mleur":{"Author":"A. I. McLeod, Hao Yu and
Ying Zhang","Depends":"R (>= 2.0.0), urca, stabledist, fGarch,
lattice","Description":"Provides functions for unit root testing using MLE
method","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mleur","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Maximum likelihood unit root test","Version":"1.0-
6"},"mlgt":{"Author":"Dave T. Gerrard","Depends":"R (>= 2.13.0), methods,
seqinr","Description":"Processing and analysis of high throughput (Roche
454)\nsequences generated from multiple loci and multiple biological\nsamples.
Sequences are assigned to their locus and sample of\norigin, aligned and trimmed.
Where possible, genotypes are\ncalled and variants mapped to known
alleles.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mlgt","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"snowfall","Title":"Multi-Locus Geno-
Typing","URL":"http:\/\/personalpages.manchester.ac.uk\/staff\/David.Gerrard\/","Ve
rsion":"0.16"},"mlica2":{"Author":"Andrew Teschendorff","Depends":"R (>=
2.10)","Description":"An R code implementation of the maximum likelihood
(fixed\npoint) algorithm of Hyvaerinen, Karhuna, and Oja for\nindependent component
2","NeedsCompilation":"no","Package":"mlica2","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Independent Component Analysis using Maximum
Likelihood","Version":"2.1"},"mlmRev":{"Author":"Douglas Bates
<bates@stat.wisc.edu>,\nMartin Maechler <maechler@R-project.org> and\nBen Bolker
<bolker@mcmaster.ca>","Depends":"lme4, R (>= 2.10)","Description":"Data and
examples from a multilevel modelling software review\nas well as other well-known
data sets from the multilevel modelling\nliterature.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mlmRev","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"lattice","Title":"Examples
from Multilevel Modelling Software Review","Version":"1.0-6"},"mlma":
{"Author":"Qingzhao Yu, Bin Li","Depends":"R (>= 2.14.1), lme4","Description":"Used
for mediation analysis with generalized multilevel models.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mlma","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Multilevel Mediation Analysis","URL":"http:\/\/www.r-
project.org,\nhttp:\/\/publichealth.lsuhsc.edu\/Faculty_pages\/qyu\/index.html","Ve
rsion":"2.0-0"},"mlmmm":{"Author":"Recai Yucel
<ryucel@albany.edu>.","Description":"Computational strategies for multivariate
linear\nmixed-effects models with missing values, Schafer and Yucel\n(2002),
Journal of Computational and Graphical Statistics, 11,\n421-442.","License":"GPL-
2","NeedsCompilation":"yes","Package":"mlmmm","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"ML estimation under multivariate linear mixed models
with\nmissing values","URL":"http:\/\/www.albany.edu\/~ry491374","Version":"0.3-
1.2"},"mlogit":{"Author":"Yves Croissant [aut, cre]","Depends":"R (>= 2.10),
Formula, maxLik","Description":"Estimation of the multinomial logit
model","Imports":"statmod, zoo, MASS, lmtest","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mlogit","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"car, nnet, lattice, AER","Title":"multinomial logit
model","URL":"http:\/\/www.r-project.org","Version":"0.2-4"},"mlogitBMA":
{"Author":"Hana Sevcikova, Adrian Raftery","Depends":"R (>= 2.9.0), BMA, abind,
maxLik","Description":"Provides a modified function bic.glm of the BMA package that
can be applied to multinomial logit (MNL) data. The data is converted to binary
logit using the Begg & Gray approximation. The package also contains functions for
maximum likelihood estimation of MNL.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"mlogitBMA","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"mlogit","Title":"Bayesian Model Averaging for
Multinomial Logit Models","Version":"0.1-6"},"mlr":{"Author":"Bernd Bischl [aut,
cre],\nMichel Lang [aut],\nJakob Richter [aut],\nJakob Bossek [aut],\nLeonard Judt
[aut],\nTobias Kuehn [aut],\nErich Studerus [aut],\nLars Kotthoff [aut],\nZachary
Jones [ctb],\nSchiffner Julia [aut]","Depends":"R (>= 3.0.2), BBmisc (>= 1.9),
ggplot2, ParamHelpers (>= 1.7),\nstats","Description":"Interface to a large number
of classification and regression\ntechniques, including machine-readable parameter
descriptions. There is\nalso an experimental extension for survival analysis,
clustering and\ngeneral, example-specific cost-sensitive learning. Generic
resampling,\nincluding cross-validation, bootstrapping and subsampling.
Hyperparameter\ntuning with modern optimization techniques, for single- and multi-
objective\nproblems. Filter and wrapper methods for feature selection. Extension
of\nbasic learners with additional operations common in machine learning,
also\nallowing for easy nested resampling. Most operations can be
parallelized.","Imports":"checkmate (>= 1.7.1), ggvis, methods, parallelMap (>=
1.3),\nplyr, reshape2, shiny, survival","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"yes","Package":"mlr","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"ada, adabag, bartMachine, brnn, bst, care, caret (>=
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deepnet, DiceKriging, DiceOptim, DiscriMiner,\ne1071, earth, elasticnet, elmNN,
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lqa, MASS, mboost, mco, mda, mlbench, modeltools,\nmRMRe, nnet, nodeHarvest (>=
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rFerns,\nrjson, rknn, rmarkdown, robustbase, ROCR, rotationForest,\nrpart, rrlda,
rsm, RSNNS, RWeka, sda, sparsediscrim, sparseLDA,\nstepPlr, SwarmSVM, testthat,
tgp, TH.data, xgboost, XML","Title":"Machine Learning in
R","URL":"https:\/\/github.com\/mlr-org\/mlr","Version":"2.8"},"mlsjunkgen":
{"Author":"Steve Myles [aut, cre]","Depends":"R (>= 3.1.3)","Description":"Generate
a stream of pseudo-random numbers generated using the MLS\nJunk Generator
algorithm. Functions exist to generate single pseudo-random\nnumbers as well as a
vector, data frame, or matrix of pseudo-random numbers.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"mlsjunkgen","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"knitr, testthat","Title":"Use the MLS Junk
Generator Algorithm to Generate a Stream of\nPseudo-Random
Numbers","URL":"http:\/\/steve.mylesandmyles.info\/projects\/mls-junk-
generator\/,\nhttps:\/\/github.com\/scumdogsteev\/mlsjunkgen","Version":"0.1.1"},"m
lt":{"Author":"Torsten Hothorn [aut, cre]","Depends":"basefun (>= 0.0-30),
variables (>= 0.0-30)","Description":"Likelihood-based estimation of conditional
transformation\nmodels via the most likely transformation approach.","Imports":"BB,
stats, quadprog, graphics, methods, grDevices, sandwich,\nnumDeriv","License":"GPL-
2","NeedsCompilation":"no","Package":"mlt","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"MASS, nnet, TH.data, survival, multcomp","Title":"Most
Likely Transformations","Version":"0.0-30"},"mlt.docreg":{"Author":"Torsten Hothorn
[aut, cre]","Depends":"mlt (>= 0.0-30)","Description":"Additional documentation, a
package vignette and\nregression tests for package mlt.","Imports":"numDeriv,
2","NeedsCompilation":"no","Package":"mlt.docreg","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"variables, basefun, np, eha, truncreg, lattice,
MASS,\nTH.data, multcomp (>= 1.4-4), knitr, survival, prodlim,\ngridExtra, nnet,
HSAUR3, sandwich, flexsurv, grid,\nlatticeExtra, colorspace, mgcv, intcox,
coxinterval, ICsurv,\npolspline, logspline, bshazard, gss, MIICD,
TransModel,\ndynsurv, timereg, survivalMPL, gamlss, Matrix, muhaz, ICE,\nordinal,
VGAM, AER, coin, gamlss.data, mlbench","Title":"Most Likely Transformations:
Documentation and Regression Tests","Version":"0.0-30"},"mlxR":{"Author":"Marc
Lavielle [aut, cre],\nRaphael Kuate [ctb]","Depends":"R (>= 3.0.1),
ggplot2","Description":"Simulation and visualization of complex\nmodels for
longitudinal data. The models are encoded using the model coding\nlanguage
'Mlxtran', automatically converted into C++ codes, compiled on the\nfly and linked
to R using the 'Rcpp' package. That allows one to implement\nvery easily complex
ODE-based models and complex statistical models,\nincluding mixed effects models,
for continuous, count, categorical, and\ntime-to-event data.","Imports":"XML, Rcpp
(>= 0.11.3), tools, tcltk, methods, graphics,\ngrDevices, utils,
stats","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"mlxR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"reshape2, gridExtra, shiny","Title":"Simulation of
Longitudinal Data","URL":"http:\/\/simulx.webpopix.org","Version":"3.0.0"},"mma":
{"Author":"Qingzhao Yu","Depends":"R (>= 2.14.1), gbm","Description":"Used for
general multiple mediation analysis.\nThe analysis method is described in Yu et al.
2014, \"General Multiple Mediation Analysis With an Application to Explore Racial
Disparity in Breast Cancer Survival\", published on Journal of Biometrics &
Biostatistics, 5(2):189.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mma","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Multiple Mediation Analysis","URL":"http:\/\/www.r-
project.org,\nhttp:\/\/publichealth.lsuhsc.edu\/Faculty_pages\/qyu\/index.html","Ve
rsion":"2.0-4"},"mmand":{"Author":"Jon Clayden","Description":"Provides tools for
performing mathematical morphology operations,\nsuch as erosion and dilation, on
data of arbitrary dimensionality. Can also\nbe used for finding connected
components, resampling, filtering, smoothing\nand other image processing-style
operations.","Imports":"stats, methods, graphics, grDevices, reportr,
2","NeedsCompilation":"yes","Package":"mmand","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"png, testthat (>= 0.9)","Title":"Mathematical Morphology
in Any Number of
Dimensions","URL":"https:\/\/github.com\/jonclayden\/mmand","Version":"1.3.0"},"mma
p":{"Author":"Jeffrey A. Ryan","Description":"R interface to POSIX mmap and
Window's MapViewOfFile","License":"GPL-
3","NeedsCompilation":"yes","Package":"mmap","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Map Pages of Memory","Version":"0.6-12"},"mmc":
{"Author":"Jaejoon Song <jjsong2@mdanderson.org>","Depends":"R (>= 2.10), survival
(>= 2.38-1), MASS (>= 7.3), stats (>=\n2.5.0)","Description":"Provides routines for
multivariate measurement error correction. Includes procedures for linear, logistic
and Cox regression models. Bootstrapped standard errors and confidence intervals
can be obtained for corrected estimates.","License":"GNU General Public License (>=
3)","NeedsCompilation":"no","Package":"mmc","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Multivariate Measurement Error
Correction","Version":"0.0.3"},"mmcm":{"Author":"Kengo NAGASHIMA and Yasunori
SATO","Depends":"mvtnorm","Description":"An implementation of modified maximum
contrast methods\nand the maximum contrast method: Functions 'mmcm.mvt'
and\n'mcm.mvt' give P-value by using randomized quasi-Monte Carlo\nmethod with
'pmvt' function of package 'mvtnorm', and\n'mmcm.resamp' gives P-value by using a
permutation method.","License":"GPL-
3","NeedsCompilation":"yes","Package":"mmcm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Modified Maximum Contrast Method","Version":"1.2-6"},"mmds":
{"Author":"David Lawrence Miller <dave@ninepointeightone.net>","Depends":"R
(>= 2.8.0)","Description":"This library implements mixture model distance
sampling\nmethods. See Miller and Thomas (in prep.).","License":"GPL-
2","NeedsCompilation":"no","Package":"mmds","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Mixture Model Distance Sampling
(mmds)","Version":"1.1"},"mme":{"Author":"E. Lopez-Vizcaino, M.J. Lombardia and D.
Morales","Depends":"R (>= 1.8.0), MASS","Description":"mme fit Gaussian Multinomial
mixed-effects models for small area estimation: Model 1, with one\nrandom effect in
each category of the response variable; Model 2, introducing\nindependent time
effect; Model 3, introducing correlated time effect.\nmme calculates analytical and
parametric bootstrap MSE estimators.","Imports":"Matrix","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mme","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Multinomial Mixed Effects Models","Version":"0.1-5"},"mmeln":
{"Author":"Charles-Edouard Giguere","Description":"Fit multivariate mixture of
normal distribution using\ncovariance structure.","License":"GPL-
3","NeedsCompilation":"no","Package":"mmeln","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Estimation of Multinormal Mixture
Distribution","Version":"1.2"},"mmeta":{"Author":"Sheng Luo, Yong Chen, Xiao Su,
Haitao Chu","Depends":"R (>= 2.10.0)","Description":"This package implements a
novel multivariate meta-analysis.","Imports":"aod,HI","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"mmeta","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Multivariate Meta-Analysis","Version":"2.2"},"mmm":
{"Author":"Ozgur Asar, Ozlem Ilk","Depends":"gee","Description":"fits multivariate
marginal models for multivariate longitudinal data for both continuous and discrete
responses","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mmm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"an R package for analyzing multivariate longitudinal data
with\nmultivariate marginal models","Version":"1.4"},"mmm2":{"Author":"Ozgur Asar,
Ozlem Ilk","Depends":"gee","Description":"Fits multivariate marginal models with
shared regression parameters for discrete and continuous responses","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"mmm2","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Multivariate marginal models with shared regression
parameters","Version":"1.2"},"mmod":{"Author":"David Winter [aut, cre],\nPeter
Green [ctb],\nZhian Kamvar [ctb],\nThierry Gosselin [ctb]","Depends":"R (>= 2.6.0),
adegenet (>= 2.0),","Description":"Provides functions for measuring\npopulation
divergence from genotypic data.","Imports":"stats, pegas","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"mmod","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Modern Measures of Population
Differentiation","URL":"https:\/\/github.com\/dwinter\/mmod","Version":"1.3.1"},"mm
pp":{"Author":"Hideitsu Hino, Ken Takano, Yuki Yoshikawa, and Noboru
Murata","Description":"Compute similarities and distances between marked point
2","NeedsCompilation":"no","Package":"mmpp","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Various Similarity and Distance Metrics for Marked
Point\nProcesses","Version":"0.4"},"mmppr":{"Author":"Graham Mueller [aut,
cre]","Depends":"R (>= 3.0.2), expm, reshape2, stats, methods","Description":"Time-
series of count data occur in many different contexts. A\nMarkov-modulated Poisson
process provides a framework for detecting\nanomalous events using an unsupervised
learning approach.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mmppr","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Markov Modulated Poisson Process for Unsupervised
Event\nDetection in Time Series of Counts","Version":"0.1"},"mmtfa":
{"Author":"Jeffrey L. Andrews, Paul D. McNicholas, and Mathieu
Chalifour","Description":"Fits a family of mixtures of multivariate t-distributions
under a continuous t-distributed latent variable structure for the purpose of
clustering or classification. The alternating expectation-conditional maximization
algorithm is used for parameter estimation.","Imports":"parallel, mvnfast,
matrixStats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mmtfa","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Model-Based Clustering and Classification with Mixtures
of\nModified t Factor Analyzers","Version":"0.1"},"mnlogit":{"Author":"Asad Hasan,
Wang Zhiyu, Alireza S. Mahani","Description":"Time and memory efficient estimation
of multinomial logit models using maximum likelihood method. Numerical optimization
performed by Newton-Raphson method using an optimized, parallel C++ library to
achieve fast computation of Hessian matrices. Motivated by large scale multiclass
classification problems in econometrics and machine learning.","Imports":"mlogit,
lmtest, Formula, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"mnlogit","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"VGAM, nnet","Title":"Multinomial Logit
Model","Version":"1.2.4"},"mnormpow":{"Author":"Alan Genz [ctb],\nAdelchi Azzalini
[ctb],\nAlexis BienvenÃ¼e [aut, cre],\nChristian Robert [aut]","Depends":"R (>=
2.2.0)","Description":"Computes integral of f(x)*x_i^k on a product of
intervals,\nwhere f is the density of a gaussian law.\nThis a is small alteration
of the mnormt code from A. Genz and A. Azzalini.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"mnormpow","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Multivariate Normal Distributions with Power
Integrand","Version":"0.1.1"},"mnormt":{"Author":"Fortran code by Alan Genz, R code
by Adelchi Azzalini","Depends":"R (>= 2.2.0)","Description":"Functions are provided
for computing the density and the\ndistribution function of multivariate normal and
\"t\" random variables,\nand for generating random vectors sampled from these
distributions.\nProbabilities are computed via non-Monte Carlo methods; different
routines\nare used in the case d=1, d=2, d>2, if d denotes the number of
dimensions.","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"mnormt","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"The Multivariate Normal and t
Distributions","URL":"http:\/\/azzalini.stat.unipd.it\/SW\/Pkg-
mnormt","Version":"1.5-4"},"modMax":{"Author":"Maria Schelling, Cang
Hui","Depends":"gtools, igraph","Description":"The algorithms implemented here are
used to detect the community structure of a network.\nThese algorithms follow
different approaches, but are all based on the concept of modularity
maximization.","License":"GPL-
2","NeedsCompilation":"no","Package":"modMax","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Community Structure Detection via Modularity
Maximization","Version":"1.1"},"modQR":{"Author":"Miroslav Å iman [aut], Pavel
BoÄek [aut, cre]","Depends":"R (>= 2.5.0), lpSolve (>= 5.6.1), geometry (>= 0.3-
1)","Description":"Contains basic tools for performing\nmultiple-output quantile
regression and computing\nregression quantile contours by means of
directional\nregression quantiles. In the location case, one can thus\nobtain
halfspace depth contours in two to six dimensions.","License":"LGPL-
2","NeedsCompilation":"no","Package":"modQR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"rgl","Title":"Multiple-Output Directional Quantile
Regression","Version":"0.1.1"},"modTempEff":{"Author":"Vito M.R.
Muggeo","Depends":"mgcv, splines","Description":"Fits a Constrained Segmented
Distributed Lag regression model\nto epidemiological time series of mortality,
temperature, and other
confounders.","License":"GPL","NeedsCompilation":"no","Package":"modTempEff","Repos
itory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Modelling temperature
effects using time series data","Version":"1.5.2"},"modeest":{"Author":"P.
PONCET","Depends":"R (>= 2.12.0)","Description":"This package provides estimators
of the mode of univariate\nunimodal data or univariate unimodal
distributions","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"modeest","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"stats, evd, fBasics, stabledist, VGAM","Title":"Mode
Estimation","Version":"2.1"},"modehunt":{"Author":"Kaspar Rufibach
<kaspar.rufibach@gmail.com> and Guenther Walther
<gwalther@stanford.edu>","Description":"Given independent and identically
distributed observations X(1), ..., X(n) from a density f,\nprovides five methods
to perform a multiscale analysis about f as well as the necessary critical\nvalues.
The first method, introduced in Duembgen and Walther (2008), provides simultaneous
confidence statements\nfor the existence and location of local increases (or
decreases) of f, based on all intervals I(all) spanned by\nany two observations
X(j), X(k). The second method approximates the latter approach by using only a
subset of\nI(all) and is therefore computationally much more efficient, but
asymptotically equivalent. Omitting the additive\ncorrection term Gamma in either
method offers another two approaches which are more powerful on small scales
and\nless powerful on large scales, however, not asymptotically minimax optimal
anymore. Finally, the block procedure is a\ncompromise between adding Gamma or not,
having intermediate power properties. The latter is again
asymptotically\nequivalent to the first and was introduced in Rufibach and Walther
(2010).","Imports":"stats, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"modehunt","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Multiscale Analysis for Density
Functions","URL":"http:\/\/www.kasparrufibach.ch,\nhttp:\/\/www-
stat.stanford.edu\/~gwalther","Version":"1.0.7"},"modelObj":{"Author":"Shannon T.
Holloway","Depends":"methods","Description":"A
utility library to facilitate the generalization of statistical methods built on a
regression framework. Package developers can use 'modelObj' methods to initiate a
regression analysis without concern for the details of the regression model and the
method to be used to obtain parameter estimates. The specifics of the regression
step are left to the user to define when calling the function. The user of a
function developed within the 'modelObj' framework creates as input a 'modelObj'
that contains the model and the R methods to be used to obtain parameter estimates
and to obtain predictions. In this way, a user can easily go from linear to non-
linear models within the same package.","License":"GPL-
2","NeedsCompilation":"no","Package":"modelObj","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"A Model Object Framework for Regression
Analysis","Version":"1.0"},"modelfree":{"Author":"Ivan Marin-Franch
<imarinfr@indiana.edu>, Kamila Zychaluk\n<kamila.zychaluk@liverpool.ac.uk>, and
David H. Foster\n<d.h.foster@manchester.ac.uk>","Depends":"R (>= 2.8.1), PolynomF
(>= 0.93), SparseM (>= 0.79), stats,\nutils, base","Description":"Local linear
estimation of psychometric functions.\nProvides functions for nonparametric
estimation of a\npsychometric function and for estimation of a derived
threshold\nand slope, and their standard deviations and
confidence\nintervals","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"modelfree","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Model-free estimation of a psychometric
function","URL":"http:\/\/www.modelfree.manchester.ac.uk,\nhttp:\/\/www.modelfree.l
iv.ac.uk,\nhttp:\/\/modelfree.r-forge.r-project.org\/","Version":"1.1-
1"},"modeltools":{"Author":"Torsten Hothorn, Friedrich Leisch, Achim
Zeileis","Depends":"stats, stats4","Description":"A collection of tools to deal
with statistical models.\nThe functionality is experimental and the user interface
is likely to\nchange in the future. The documentation is rather terse, but packages
`coin'\nand `party' have some working examples. However, if you find
the\nimplemented ideas interesting we would be very interested in a discussion\nof
this proposal. Contributions are more than
welcome!","Imports":"methods","License":"GPL-
2","NeedsCompilation":"no","Package":"modeltools","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Tools and Classes for Statistical
Models","Version":"0.2-21"},"modes":{"Author":"Sathish Deevi [aut, cre],\n4D
Strategies [aut,own]","Depends":"R (>= 3.2.2)","Description":"Designed with a dual
purpose of\naccurately estimating the mode (or modes) as well as
characterizing\nthe modality of data. The specific application area includes
complex\nor mixture distributions particularly in a big data environment.\nThe
heterogeneous nature of (big) data may require deep introspective\nstatistical and
machine learning techniques, but these statistical tools\noften fail when applied
without first understanding the data. In small\ndatasets, this often isn't a big
issue, but when dealing with large scale\ndata analysis or big data thoroughly
inspecting each dimension\ntypically yields an O(n^n-1) problem. As such, dealing
with big data\nrequire an alternative toolkit. This package not only identifies
the\nmode or modes for various data types, it also provides a programmatic\nway of
understanding the modality (i.e. unimodal, bimodal, etc.) of\na dataset (whether
it's big data or not). See\n<http:\/\/www.sdeevi.com\/modes_package> for examples
and discussion.","License":"CC BY-NC-SA
4.0","NeedsCompilation":"no","Package":"modes","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Find the Modes and Assess the Modality of Complex and
Mixture\nDistributions, Especially with Big
Datasets","URL":"http:\/\/www.sdeevi.com\/modes_package\nhttps:\/\/github.com\/sath
ish-deevi\/modes-Package\/","Version":"0.7.0"},"modiscloud":{"Author":"Nicholas J.
Matzke, Dept. of Integrative Biology, U.C. Berkeley","Depends":"date, sp, sfsmisc,
raster, rgdal","Description":"Package for processing downloaded MODIS Cloud Product
HDF\nfiles and derived files. Specifically, MOD35_L2 cloud product\nfiles, and the
associated MOD03 geolocation files (for\nMODIS-TERRA); and MYD35_L2 cloud product
files, and the\nassociated MYD03 geolocation files (for MODIS-AQUA). The\npackage
will be most effective if the user installs MRTSwath\n(MODIS Reprojection Tool for
swath
products;\nhttps:\/\/lpdaac.usgs.gov\/tools\/modis_reprojection_tool_swath),\nand
adds the directory with the MRTSwath executable to the\ndefault R PATH by editing
~\/.Rprofile.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"modiscloud","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"R tools for processing Level 2 Cloud Mask products
from
MODIS","URL":"http:\/\/phylo.wikidot.com\/modiscloud","Version":"0.14"},"moduleColo
r":{"Author":"Peter Langfelder <Peter.Langfelder@gmail.com> and Steve Horvath
<SHorvath@mednet.ucla.edu>","Depends":"R (>= 2.3.0), stats, impute, grDevices,
dynamicTreeCut","Description":"Methods for color labeling, calculation of
eigengenes, merging of closely related modules.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"moduleColor","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Basic Module
Functions","URL":"\nhttp:\/\/www.genetics.ucla.edu\/labs\/horvath\/CoexpressionNetw
ork\/BranchCutting\/","Version":"1.08-3"},"modules":{"Author":"Sebastian Warnholz
[aut, cre]","Depends":"R (>= 3.2.0), aoos, methods","Description":"Provides modules
as an organizational unit for source code. Modules\nenforce to be more rigorous
when defining dependencies and have\na local search path. They can be used as a sub
unit within packages\nor in scripts.","Imports":"stringr, utils","License":"MIT +
file
LICENSE","NeedsCompilation":"no","Package":"modules","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"disposables, testthat, devtools, knitr,
rmarkdown, parallel","Title":"Self Contained Units of Source
Code","URL":"https:\/\/github.com\/wahani\/modules","Version":"0.4.0"},"mogavs":
{"Author":"Tommi Pajala [aut, cre],\nPekka Malo [aut],\nAnkur Sinha [aut],\nTimo
Kuosmanen [ctb]","Depends":"R (>= 2.10)","Description":"Functions for exploring the
best subsets in regression with a genetic algorithm. The package is much faster
than methods relying on complete enumeration, and is suitable for datasets with
large number of variables.","Imports":"cvTools, graphics, stats","License":"GPL-
2","NeedsCompilation":"no","Package":"mogavs","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Multiobjective Genetic Algorithm for Variable Selection
in\nRegression","Version":"1.0.1"},"mokken":{"Author":"L. Andries van der Ark
<L.A.vanderArk@uva.nl>","Depends":"R (>= 2.8.1), graphics,
poLCA","Description":"mokken contains functions for performing Mokken\nscale
analysis on test and questionnaire data. It includes an automated\nitem selection
algorithm, and various checks of model assumptions.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"mokken","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"MASS","Title":"Mokken Scale Analysis in
R","URL":"https:\/\/sites.google.com\/a\/tilburguniversity.edu\/avdrark\/mokken","V
ersion":"2.7.7"},"molaR":{"Author":"James D. Pampush [aut, cre, cph],\nJulia M.
Winchester [aut, cph],\nPaul E. Morse [aut, cph],\nAlexander Q. Vining [aut,
cph]","Depends":"R (>= 2.10), alphahull, rgl, Rvcg","Description":"Surface
topography calculations of Dirichlet's normal energy,\nrelief index, and
orientation patch count for teeth using scans of enamel caps.\nImportantly, for the
relief index and orientation patch count calculations to\nwork, the scanned tooth
files must be oriented with the occlusal plane parallel\nto the x and y axes, and
perpendicular to the z axis. The files should also be\nsimplified, and smoothed in
some other software prior to uploading into
R.","License":"ACM","NeedsCompilation":"no","Package":"molaR","Repository":"http:\/
\/cran.csiro.au\/src\/contrib","Suggests":"knitr, rmarkdown,
rglwidget","Title":"Dental Surface Complexity Measurement
Tools","Version":"3.0"},"mombf":{"Author":"David Rossell, John D. Cook, Donatello
Telesca, P. Roebuck","Depends":"R (>= 2.14.0), methods, mvtnorm, ncvreg, actuar,
mgcv","Description":"Model selection and parameter estimation based on non-local
priors. Routines are provided to compute Bayes factors, marginal densities and to
perform variable selection in regression setups. Routines to evaluate prior
densities, distribution functions, quantiles and modes are
included.","Imports":"survival","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"mombf","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"parallel","Title":"Moment and Inverse Moment Bayes
Factors","URL":"http:\/\/mombf.r-forge.r-
project.org\/","Version":"1.6.1"},"momentchi2":{"Author":"Dean
Bodenham","Depends":"R (>= 3.1.2)","Description":"A collection of moment-matching
methods for computing the cumulative distribution function of a positively-weighted
sum of chi-squared random variables. Methods include the Satterthwaite-Welch
method, Hall-Buckley-Eagleson method, Wood's F method, and the Lindsay-Pilla-Basak
method.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"momentchi2","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Moment-Matching Methods for Weighted Sums of Chi-
Squared Random\nVariables","Version":"0.1.0"},"moments":{"Author":"Lukasz Komsta
<lukasz.komsta@umlub.pl>, Frederick
Novomestky\n<fnovomes@poly.edu>","Description":"Functions to calculate: moments,
Pearson's kurtosis,\nGeary's kurtosis and skewness; tests related to
them\n(Anscombe-Glynn, D'Agostino, Bonett-Seier).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"moments","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Moments,
cumulants, skewness, kurtosis and related tests","URL":"http:\/\/www.r-
project.org, http:\/\/www.komsta.net\/","Version":"0.14"},"momr":{"Author":"Edi
Prifti, Emmanuelle Le Chatelier","Depends":"R (>=
2.10)","Description":"'MetaOMineR' suite is a set of R packages that offers many
functions and modules needed for the analyses\nof quantitative metagenomics data.
'momr' is the core package and contains routines for biomarker identification and
exploration.\nDeveloped since the beginning of field, 'momr' has evolved and is
structured around the different modules\nsuch as preprocessing, analysis,
vizualisation, etc. See package help for more information.","Imports":"Hmisc,
gplots, nortest","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"momr","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Mining Metaomics Data
(MetaOMineR)","Version":"1.1"},"mondate":{"Author":"Dan Murphy","Depends":"utils,
methods, R (>= 3.0.0)","Description":"Keep track of dates in terms of
months.\nModel dates as at close of business.\nPerform date arithmetic in units
of \"months\" and \"years\" (multiples of months).\nAllow \"infinite\" dates to
model \"ultimate\" time spans.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mondate","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"zoo","Title":"Keep track of dates in terms of
months","URL":"http:\/\/www.r-project.org,
http:\/\/code.google.com\/p\/mondate\/","Version":"0.10.01.02"},"mongolite":
{"Author":"Jeroen Ooms [aut, cre],\nMongoDB, Inc [cph] (Author of mongo-c-
driver)","Description":"High-level, high-performance MongoDB client based on
libmongoc and\njsonlite. Includes support for aggregation, indexing, map-reduce,
streaming,\nSSL encryption and SASL authentication. The vignette gives a brief
overview\nof the available methods in the package.","Imports":"jsonlite (>=
0.9.16)","License":"Apache License
2.0","NeedsCompilation":"yes","Package":"mongolite","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"knitr, rmarkdown","Title":"Fast and Simple MongoDB
Client for
R","URL":"https:\/\/github.com\/jeroenooms\/mongolite\nhttps:\/\/github.com\/mongod
b\/mongo-c-driver","Version":"0.8.1"},"monitoR":{"Author":"Sasha D. Hafner
<sdh11@cornell.edu> and Jon Katz <jonkatz4@gmail.com>, with code for the Fourier
transform from the seewave package (by Jerome Sueur, Thierry Aubin, and Caroline
Simonis), and code for the readMP3 function from the tuneR package (by Uwe Ligges).
Therese Donovan provided creative direction and database design
support.","Depends":"R (>= 2.10), tuneR, methods","Description":"Acoustic template
detection and monitoring database interface. Create, modify, save, and use
templates for detection of animal vocalizations. View, verify, and extract results.
Upload a MySQL schema to a existing instance, manage survey metadata, write and
read templates and detections locally or to the database.","Imports":"graphics,
2","NeedsCompilation":"no","Package":"monitoR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"fftw, parallel, RODBC, knitr","Title":"Acoustic
Template Detection in R","URL":"http:\/\/www.uvm.edu\/rsenr\/vtcfwru\/R\/?
Page=monitoR\/monitoR.htm","Version":"1.0.4"},"monmlp":{"Author":"Alex J.
Cannon","Description":"Train and make predictions from a multi-layer perceptron
neural\nnetwork with partial monotonicity constraints.","License":"GPL-
2","NeedsCompilation":"no","Package":"monmlp","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Monotone Multi-Layer Perceptron Neural
Network","Version":"1.1.3"},"monogeneaGM":{"Author":"Tsung Fei Khang","Depends":"R
(>= 3.0.3)","Description":"Geometric morphometric and evolutionary biology analyses
of anchor shape from four-anchored monogeneans.","Imports":"ape, cluster, circular,
geomorph, gplots, phytools, rgl","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"monogeneaGM","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Geometric Morphometric Analysis of Monogenean
Anchors","Version":"1.1"},"monographaR":{"Author":"Marcelo Reginato","Depends":"R
(>= 3.0.0), maptools","Description":"Contains functions intended to facilitate the
production of plant taxonomic monographs. The package includes functions to convert
tables into taxonomic descriptions, lists of collectors, examined specimens, and
can generate a monograph skeleton. Additionally, wrapper functions to batch the
production of phenology charts and distributional and diversity maps are also
available.","Imports":"circular, png, raster, rmarkdown, sp","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"monographaR","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"knitr","Title":"Taxonomic Monographs
Tools","Version":"1.01"},"monomvn":{"Author":"Robert B. Gramacy
<rbgramacy@chicagobooth.edu>","Depends":"R (>= 2.14.0), pls, lars,
MASS","Description":"Estimation of multivariate normal and student-t data
of\narbitrary dimension where the pattern of missing data is monotone.\nThrough the
use of parsimonious\/shrinkage regressions\n(plsr, pcr, lasso, ridge, etc.), where
standard regressions fail,\nthe package can handle a nearly arbitrary amount of
missing data.\nThe current version supports maximum likelihood inference and\na
full Bayesian approach employing scale-mixtures for Gibbs sampling.\nMonotone data
augmentation extends this\nBayesian approach to arbitrary missingness patterns.\nA
fully functional standalone interface to the Bayesian lasso\n(from Park & Casella),
Normal-Gamma (from Griffin & Brown),\nHorseshoe (from Carvalho, Polson, & Scott),
and ridge regression\nwith model selection via Reversible Jump, and student-t
errors\n(from Geweke) is also provided.","Imports":"quadprog,
mvtnorm","License":"LGPL","NeedsCompilation":"yes","Package":"monomvn","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Title":"Estimation for Multivariate Normal
and Student-t Data with\nMonotone
Missingness","URL":"http:\/\/bobby.gramacy.com\/r_packages\/monomvn","Version":"1.9
-6"},"monreg":{"Author":"This version Kay Pilz and Steffanie Titoff.
Earlier\ndevelopements by Holger Dette and Kay Pilz.","Depends":"R (>=
2.0.0)","Description":"Estimates monotone regression and variance functions in
a\nnonparametric model.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"monreg","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Nonparametric Monotone
Regression","Version":"0.1.3"},"moonBook":{"Author":"Keon-Woong Moon [aut,
cre]","Depends":"R (>= 3.1.2)","Description":"Several analysis-related functions
for the book entitled \"R\nstatistics and graph for medical articles\" (written in
Korean), version 1,\nby Keon-Woong Moon with Korean demographic data with several
plot\nfunctions.","Imports":"nortest, survival","License":"GPL-
2","NeedsCompilation":"no","Package":"moonBook","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"testthat, knitr, ggplot2","Title":"Functions and
Datasets for the Book by Keon-Woong Moon","Version":"0.1.3"},"moonsun":
{"Author":"Lukasz Komsta <lukasz.komsta@umlub.pl>","Description":"A collection of
basic astronomical routines for R based on\n\"Practical astronomy with your
calculator\" by Peter\nDuffet-Smith.","License":"GPL-
2","NeedsCompilation":"no","Package":"moonsun","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Basic astronomical calculations with
R","Version":"0.1.3"},"mopsocd":{"Author":"Pros Naval","Description":"A multi-
objective optimization solver based on particle\nswarm optimization with crowding
distance.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mopsocd","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"scatterplot3d","Title":"MOPSOCD: Multi-objective
Particle Swarm Optimization with\nCrowding
Distance","Version":"0.5.1"},"morgenstemning":{"Author":"Matthias Geissbuehler
<matthias.geissbuehler@a3.epfl.ch>, James
Manton\n<ajd.manton@googlemail.com>","Depends":"R (>= 2.15.0)","Description":"This
package is a port of the MATLAB colourmap functions\naccompanying the paper M.
Geissbuehler and T. Lasser, \"How to display data\nby color schemes compatible with
red-green color perception deficiencies,\"\nOpt. Express 21, 9862-9874 (2013) to
R.","License":"GPL-
3","NeedsCompilation":"no","Package":"morgenstemning","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat","Title":"Color schemes compatible with
red-green color
perception\ndifficulties","URL":"https:\/\/github.com\/ajdm\/morgenstemning","Versi
on":"1.0"},"morse":{"Author":"Marie Laure Delignette-Muller [aut], Philippe Ruiz
[aut], Sandrine\nCharles [aut], Wandrille Duchemin [ctb], Christelle Lopes [ctb],
Guillaume Kon-\nKam-king [ctb], Philippe Veber [aut]","Depends":"R (>=
3.0.0)","Description":"Tools for ecotoxicologists and regulators dedicated to
the\nmathematical and statistical modelling of bioassay data. They use advanced
and\ninnovative methods for a valuable quantitative environmental risk
assessment.","Imports":"coda, dplyr, graphics, grDevices, ggplot2, grid,
gridExtra,\nmethods, rjags, stats, stringr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"morse","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"knitr, rmarkdown, testthat","Title":"MOdelling Tools for
Reproduction and Survival Data in\nEcotoxicology","Version":"2.1.1"},"mosaic":
{"Author":"Randall Pruim <rpruim@calvin.edu>, Daniel
Kaplan\n<kaplan@macalester.edu>, Nicholas Horton
<nhorton@amherst.edu>","Depends":"R (>= 3.0.0), dplyr, lattice (>= 0.20-21),
ggplot2, car,\nmosaicData","Description":"Data sets and utilities from Project
MOSAIC (mosaic-web.org) used\nto teach mathematics, statistics, computation and
modeling. Funded by the\nNSF, Project MOSAIC is a community of educators working
to tie together\naspects of quantitative work that students in science,
technology,\nengineering and mathematics will need in their professional lives,
but\nwhich are usually taught in isolation, if at
all.","Enhances":"manipulate","Imports":"lazyeval, MASS, grid, reshape2, readr,
methods, utils,\nsplines, latticeExtra, ggdendro, gridExtra","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mosaic","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"lubridate, fastR, magrittr, NHANES, RCurl, sp,
maptools, vcd,\ntestthat, tidyr, knitr, tools, parallel, mapproj,
rgl","Title":"Project MOSAIC Statistics and Mathematics Teaching
Utilities","URL":"https:\/\/github.com\/ProjectMOSAIC\/mosaic","Version":"0.13.0"},
"mosaicData":{"Author":"Randall Pruim <rpruim@calvin.edu>, Daniel
Kaplan\n<kaplan@macalester.edu>, Nicholas Horton
<nhorton@amherst.edu>","Depends":"R (>= 3.0.0)","Description":"Data sets from
Project MOSAIC (mosaic-web.org) used\nto teach mathematics, statistics, computation
and modeling. Funded by the\nNSF, Project MOSAIC is a community of educators
working to tie together\naspects of quantitative work that students in science,
technology,\nengineering and mathematics will need in their professional lives,
but\nwhich are usually taught in isolation, if at all.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mosaicData","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"lattice, mosaic, reshape2","Title":"Project MOSAIC
(mosaic-web.org) data sets","Version":"0.13.0"},"moult":{"Author":"Birgit Erni
<birgit.erni@uct.ac.za>. Based on models\ndeveloped by Underhill and Zucchini
(1988, 1990).","Description":"Functions to estimate start and duration of moult
from moult\ndata (of types 1 to 5), based on models developed in Underhill\nand
Zucchini (1988, 1990). Allows modelling parameters as\nfunctions of
covariates.","Imports":"Formula, Matrix","License":"GPL-
2","NeedsCompilation":"no","Package":"moult","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Models for analysing moult in
birds","Version":"1.4"},"mountainplot":{"Author":"Kevin Wright [aut,
cre]","Description":"Lattice functions for drawing folded empirical
cumulative\ndistribution plots, or mountain plots. A mountain plot is similar\nto
an empirical CDF plot, except that the curve increases from\n0 to 0.5, then
decreases from 0.5 to 1 using an inverted scale at\nthe right side. See: Monti
(1995), Folded empirical distribution\nfunction curves-mountain plots. The
American Statistician, 49, 342-345.","Imports":"lattice, stats","License":"GPL-
2","NeedsCompilation":"no","Package":"mountainplot","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"knitr, latticeExtra","Title":"Mountain Plots,
Folded Empirical Cumulative Distribution
Plots","URL":"https:\/\/github.com\/kwstat\/mountainplot","Version":"1.1"},"mousetr
ack":{"Author":"Moreno I. Coco and Nicholas D. Duran with contributions of Rick
Dale, Denis O'Hora and Michael J. Spivey.","Depends":"R (>= 3.0.0),
pracma","Description":"Extract from two-dimensional x-y coordinates of an arm-
reaching trajectory, several dependent measures such as area under the curve,
latency to start the movement, x-flips, etc.; which characterize the action-
dynamics of the response. Mainly developed to analyze data coming from mouse-
tracking experiments.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mousetrack","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Mouse-Tracking Measures from Trajectory
Data","Version":"1.0.0"},"mousetrap":{"Author":"Pascal J. Kieslich [aut,
cre],\nFelix Henninger [aut]","Depends":"R (>= 3.1.0)","Description":"Mouse-
tracking, the analysis of mouse movements in computerized\nexperiments, is a method
that is becoming increasingly popular in the\ncognitive sciences. The mousetrap
package offers functions for importing,\npreprocessing, analyzing, aggregating, and
visualizing mouse-tracking data.","Imports":"utils, stats, pracma, reshape2,
graphics, grDevices, ggplot2,\nscales, psych (>= 1.2.4), diptest","License":"GPL-
3","NeedsCompilation":"no","Package":"mousetrap","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"readbulk, testthat","Title":"Process and Analyze
Mouse-Tracking
Data","URL":"https:\/\/github.com\/pascalkieslich\/mousetrap","Version":"1.0.0"},"m
ovMF":{"Author":"Kurt Hornik [aut, cre],\nBettina GrÃ¼n [aut]","Depends":"R (>=
3.0.0)","Description":"Fit and simulate mixtures of von Mises-Fisher
distributions.","Imports":"skmeans (>= 0.2-2), clue, slam (>= 0.1-30),
2","NeedsCompilation":"yes","Package":"movMF","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"lattice, tm (>= 0.5-8.5), vcd, SnowballC, HSAUR2,
colorspace,\ncorpus.useR.2008.abstracts","Title":"Mixtures of von Mises-Fisher
Distributions","Version":"0.2-0"},"move":{"Author":"Bart Kranstauber
<bart.kranstauber@uni-konstanz.de>, Marco Smolla
<marco.smolla@postgrad.manchester.ac.uk>","Depends":"geosphere (>= 1.4-3), methods,
sp, raster (>= 2.4-15), rgdal,\nR (>= 2.15.0)","Description":"Contains functions to
access movement data stored in movebank.org as well as tools to visualize and
statistically analyze animal movement data, among others functions to calculate
dynamic Brownian Bridge Movement Models. Move helps addressing movement ecology
questions.","Imports":"httr","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"move","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"adehabitatHR, adehabitatLT, circular, ggmap,
mapproj,\nmaptools, testthat","Title":"Visualizing and Analyzing Animal Track
Data","URL":"http:\/\/computational-ecology.com\/main-
move.html","Version":"1.6.541"},"moveHMM":{"Author":"Theo Michelot, Roland
Langrock, Toby Patterson, Eric Rexstad","Depends":"CircStats, boot, MASS,
sp","Description":"Provides tools for animal movement modelling using hidden Markov
models.\nThese include processing of tracking data, fitting HMMs to movement data,
visualization of\ndata and fitted model, decoding of the state
process...","Imports":"Rcpp","License":"GPL-
3","NeedsCompilation":"yes","Package":"moveHMM","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"testthat, knitr","Title":"Animal Movement Modelling
using Hidden Markov
Models","URL":"https:\/\/github.com\/TheoMichelot\/moveHMM,\nhttps:\/\/cran.r-
project.org\/package=moveHMM","Version":"1.1"},"mp":{"Author":"Francisco M.
Fatore,\nSamuel G. Fadel","Depends":"R (>= 1.8.0)","Description":"Multidimensional
projection techniques are used to create two dimensional representations of
multidimensional data sets.","Imports":"Rcpp (>=
0.11.0)","License":"GPL","NeedsCompilation":"yes","Package":"mp","Repository":"http
:\/\/cran.csiro.au\/src\/contrib","Title":"Multidimensional Projection
Techniques","Version":"0.3.1"},"mpMap":{"Author":"Emma Huang","Depends":"gdata,
seriation, qtl, wgaim","Description":"Tools for constructing linkage maps,
reconstructing\nhaplotypes, estimating linkage disequilibrium and QTL mapping\nin
multi-parent RIL designs (e.g. MAGIC)","License":"GPL-
2","NeedsCompilation":"yes","Package":"mpMap","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"aod, asreml, happy.hbrem, Heatplus, MASS, VPdtw,
lattice","Title":"Multi-parent RIL genetic analysis","Version":"1.14"},"mpa":
{"Author":"Daniel Hernando Rodriguez <dhrodriguezt@unal.edu.co> & Campo\nElias
Pardo <cepardot@unal.edu.co>","Depends":"R (>= 2.5.1),
network","Description":"CoWords Method","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mpa","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"CoWords Method","Version":"0.7.3"},"mpath":{"Author":"Zhu
Wang, with contributions from Achim Zeileis, Simon Jackman, Brian Ripley, Trevor
Hastie, Rob Tibshirani, Balasubramanian Narasimhan, Gil Chu and Patrick
Breheny","Depends":"methods","Description":"Algorithms for fitting model-based
penalized coefficient paths. Currently the models include penalized Poisson,
negative binomial, zero-inflated Poisson and zero-inflated negative binomial
regression models. The penalties include least absolute shrinkage and selection
operator (LASSO), smoothly clipped absolute deviation (SCAD) and minimax concave
penalty (MCP), and each possibly combining with L_2
penalty.","Imports":"MASS,glmnet,pscl,numDeriv, foreach,
doParallel","License":"GPL-
2","NeedsCompilation":"yes","Package":"mpath","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"zic, R.rsp","Title":"Regularized Linear
Models","Version":"0.2-1"},"mpbart":{"Author":"Bereket Kindo [aut,
cre]","Depends":"R (>= 3.2.2), mlbench, bayesm, cvTools,
mlogit","Description":"Fits Multinomial Probit Bayesian Additive Regression
Trees.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"mpbart","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Multinomial Probit Bayesian Additive Regression
Trees","Version":"0.2"},"mpcv":{"Author":"Krzysztof Ciupke
<krzysztof.ciupke@polsl.pl>","Depends":"lpSolve","Description":"Multivariate
process capability analysis using the multivariate process capability vector.
Allows to analyze a multivariate process with both normally and non-normally
distributed and also with dependent and independent quality
characteristics.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"mpcv","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Multivariate Process Capability
Vector","Version":"1.1"},"mph":{"Author":"Samuel Gerber
<sgerber@math.duke.edu>","Depends":"R (>= 2.10)","Description":"A fast approach to
compute approximate persistent homology using a multiscale
approach","License":"GPL-
2","NeedsCompilation":"yes","Package":"mph","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Multiscale persistent homology","Version":"0.9"},"mplot":
{"Author":"Garth Tarr [aut, cre],\nSamuel Mueller [aut],\nAlan Welsh
[aut]","Description":"Model stability and variable inclusion plots [Mueller and
Welsh\n(2010, <doi:10.1111\/j.1751-5823.2010.00108.x>); Murray, Heritier and
Mueller\n(2013, <doi:10.1002\/sim.5855>)] as well as the adaptive fence [Jiang et
al.\n(2008, <doi:10.1214\/07-AOS517>); Jiang et al.\n(2009,
<doi:10.1016\/j.spl.2008.10.014>)] for linear and generalised linear
models.","Imports":"leaps, foreach, parallel, bestglm, doParallel,
plyr,\nshinydashboard, shiny, glmnet, graphics, stats, googleVis","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"mplot","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"knitr, mvoutlier","Title":"Graphical Model Stability and
Variable Selection
Procedures","URL":"https:\/\/github.com\/garthtarr\/mplot","Version":"0.7.7"},"mpm"
:{"Author":"Luc Wouters <wouters_luc@telenet.be>","Depends":"R (>= 2.10), MASS,
KernSmooth","Description":"Exploratory graphical analysis of multivariate
data,\nspecifically gene expression data with different projection\nmethods:
principal component analysis, correspondence analysis,\nspectral map
2)","NeedsCompilation":"no","Package":"mpm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Multivariate Projection Methods","URL":"http:\/\/mpm.r-
forge.r-project.org","Version":"1.0-22"},"mpmcorrelogram":{"Author":"Marcelino de
la Cruz","Depends":"vegan","Description":"Functions to compute and plot
multivariate (partial)\nMantel correlograms.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mpmcorrelogram","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Multivariate Partial Mantel
Correlogram","Version":"0.1-3"},"mpmi":{"Author":"Chris
Pardy","Depends":"KernSmooth","Description":"Uses a kernel smoothing approach to
calculate Mutual Information\nfor comparisons between all types of variables
including continuous vs\ncontinuous, continuous vs discrete and discrete vs
discrete. Uses a\nnonparametric bias correction giving Bias Corrected Mutual
Information\n(BCMI). Implemented efficiently in Fortran 95 with OpenMP and suited
to\nlarge genomic datasets.","License":"GPL-
3","NeedsCompilation":"yes","Package":"mpmi","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Mixed-pair mutual information estimators","URL":"http:\/\/r-
forge.r-project.org\/projects\/mpmi\/","Version":"0.41"},"mpoly":{"Author":"David
Kahle [aut, cre]","Depends":"stringr (>= 1.0.0)","Description":"Symbolic computing
with multivariate polynomials in R.","Imports":"rSymPy, rJython, rJava, rjson,
partitions, plyr, stats,\nggplot2, polynom, orthopolynom, reshape2","License":"GPL-
2","NeedsCompilation":"no","Package":"mpoly","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat","Title":"Symbolic Computation and More with
Multivariate
Polynomials","URL":"https:\/\/github.com\/dkahle\/mpoly","Version":"1.0.0"},"mppa":
{"Author":"Patrick Rubin-Delanchy <patrick.rubin-delanchy@bristol.ac.uk> and
Nicholas A Heard <n.heard@imperial.ac.uk>","Depends":"R (>= 2.2.0), methods,
stats","Description":"A procedure to test for dependence between point processes on
the real line, e.g. causal dependence, correlation, inhibition or anti-correlation.
The package also provides a number of utilities for plotting simultaneous point
processes, and combining p-values.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mppa","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Statistics for analysing multiple simultaneous point
processes\non the real line","Version":"1.0"},"mpt":{"Author":"Florian Wickelmaier
[aut, cre],\nAchim Zeileis [aut]","Depends":"R (>= 3.0.0), stats,
graphics","Description":"Fitting and testing multinomial processing tree (MPT)
models, a\nclass of statistical models for categorical data. The parameters are
the\nlink probabilities of a tree-like graph and represent the latent
cognitive\nprocessing steps executed to arrive at observable response
categories\n(Batchelder & Riefer, 1999; Erdfelder et al., 2009; Riefer
&\nBatchelder, 1988).","Imports":"utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mpt","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Multinomial Processing Tree
Models","URL":"http:\/\/homepages.uni-
tuebingen.de\/florian.wickelmaier","Version":"0.5-2"},"mptools":{"Author":"John
Baumgartner [aut, cre]","Depends":"R (>= 3.2.0)","Description":"'RAMAS Metapop'
<https:\/\/www.ramas.com\/ramas.htm#metapop> is a\npopular software package for
performing spatially-explicit population\nviability analysis. It is primarily GUI-
driven, but can benefit from\nintegration into an R workflow, wherein model results
can be subjected to\nfurther analysis. 'RAMAS Metapop' stores metapopulation model
parameter\nsettings and population dynamics simulation results in plain text
files\n(.mp files). This package facilitates access, summary and visualisation
of\n'RAMAS Metapop 5' outputs in order to better integrate 'RAMAS' analyses
into\nan R workflow.","Imports":"methods, utils, grDevices, graphics, stats,
raster, sp,\nanimation, lattice, zoo, rasterVis, latticeExtra,
viridis","License":"GPL-
3","NeedsCompilation":"no","Package":"mptools","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr, rmarkdown, rgdal, devtools","Title":"RAMAS
Metapop
Tools","URL":"https:\/\/github.com\/johnbaums\/mptools","Version":"1.0.1"},"mrMLM":
{"Author":"Wenlong Ren,Shibo Wang,Bo Huang and Yuanming
Zhang","Depends":"gWidgets,gWidgetsRGtk2,RGtk2Extras,qqman","Description":"Conduct
multi-locus random-SNP-effect mixed linear model analysis for genome-wide
association study. First, each marker is scanned using random-SNP-effect mixed
linear model method. Then, all the markers selected from the first step are
included in the multi-locus model and their effects are estimated by an EM
empirical Bayes method. No multiple test correction is
needed.","Imports":"RGtk2,methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mrMLM","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Multilocus Random Mixed Linear Model for Genome-Wide
Association\nStudy","Version":"1.2"},"mra":{"Author":"Trent McDonald [cre,
aut],\nEric Regehr [ctb],\nJeff Bromaghin [ctb]","Description":"Analysis of mark-
recapture data using covariates. Models: CJS open population; Huggin's closed
population. Link functions: logit, sine, hazard. Model selection and model
averaging routines. Plot methods. Simulation routine. CJS methods produce estimates
of population size using the Horvitz-Thompson estimator.","License":"GNU General
Public
License","NeedsCompilation":"yes","Package":"mra","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Analysis of Mark-Recapture
Data","Version":"2.16.4"},"mratios":{"Author":"Gemechis Dilba Djira, Mario Hasler,
Daniel Gerhard, Frank\nSchaarschmidt","Depends":"R (>= 2.12.0)","Description":"With
this package, it is possible to perform\n(simultaneous) inferences for ratios of
linear combinations of\ncoefficients in the general linear model. In particular,
tests\nand confidence interval estimations for ratios of treatment\nmeans in the
normal one-way layout and confidence interval\nestimations like in (multiple) slope
ratio and parallel line\nassays can be carried out. Moreover, it is possible
to\ncalculate the sample sizes required in comparisons with a\ncontrol based on
relative margins. For the simple two-sample\nproblem, functions for a t-test for
ratio-formatted hypotheses\nand the corresponding Fieller-type confidence interval
are\nprovided assuming homogeneous or heterogeneous group
variances.","Imports":"mvtnorm","License":"GPL","NeedsCompilation":"no","Package":"
mratios","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"multcomp,
nlme","Title":"Inferences for ratios of coefficients in the general
linear\nmodel","Version":"1.3.17"},"mrds":{"Author":"Jeff Laake
<jeff.laake@noaa.gov>, David Borchers\n<dlb@st-and.ac.uk>, Len Thomas
<len.thomas@st-and.ac.uk>, David\nMiller <dave@ninepointeightone.net> and Jon
Bishop","Depends":"R (>= 3.0)","Description":"Animal abundance estimation via
conventional, multiple covariate\nand mark-recapture distance sampling
(CDS\/MCDS\/MRDS). Detection function\nfitting is performed via maximum likelihood.
Also included are diagnostics\nand plotting for fitted detection functions.
Abundance estimation is via a\nHorvitz-Thompson-like estimator.","Imports":"optimx
(>= 2013.8.6), mgcv, numDeriv, Rsolnp","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mrds","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat","Title":"Mark-Recapture Distance
Sampling","Version":"2.1.14"},"mreg":{"Author":"Simon
Bond","Description":"Implements the methods described in Bond S, Farewell V, 2006,
Exact Likelihood Estimation for a Negative Binomial Regression Model with Missing
Outcomes,
Biometrics","License":"GPL","NeedsCompilation":"no","Package":"mreg","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Title":"Fits regression models when the
outcome is partially missing","Version":"1.1"},"mri":{"Author":"Marjan
Cugmas","Description":"Provides three Modified Rand Indices and three Modified
Adjusted Rand Indices for comparing two partitions, which are usually obtained on
two different sets of units, where one is a subset of another set of units.
Splitting and merging of clusters have a different affects on the value of the
indices.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mri","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Modified Rand Index (1 and 2.1 and 2.2) and Modified
Adjusted\nRand Index (1 and 2.1 and 2.2)","Version":"0.1.1"},"mritc":{"Author":"Dai
Feng and Luke Tierney","Depends":"R (>= 2.14.0), lattice (>= 0.18-8), misc3d (>=
0.8-1),\noro.nifti(>= 0.4.0)","Description":"Various methods for MRI tissue
classification.","License":"GPL","NeedsCompilation":"yes","Package":"mritc","Reposi
tory":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"tkrplot
(>= 0.0-23)","Title":"MRI Tissue Classification","Version":"0.5-0"},"ms.sev":
{"Author":"Helga Westerlind, Ali Manouchehrinia","Description":"Calculates ARMSS
(age related multiple sclerosis severity), and both local and global MSSS (multiple
sclerosis severity score).","License":"GPL-
2","NeedsCompilation":"no","Package":"ms.sev","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Package for Calculation of ARMSS, Local MSSS and Global
MSSS","Version":"1.0.3"},"msBP":{"Author":"Antonio
Canale","Depends":"DPpackage","Description":"Performs Bayesian nonparametric
multiscale density estimation and multiscale testing of group differences with
multiscale Bernstein polynomials (msBP) mixtures as in Canale and Dunson
2","NeedsCompilation":"yes","Package":"msBP","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Multiscale Bernstein Polynomials for
Densities","Version":"1.0-2.1"},"msSurv":{"Author":"Nicole Ferguson
<nicole.ferguson@kennesaw.edu>, Somnath Datta <somnath.datta@louisville.edu>, Guy
Brock <guy.brock@louisville.edu>","Depends":"R (>= 2.0),
graph","Description":"Nonparametric estimation for right censored, left truncated
time to event data in multistate models.","Imports":"methods, class,
2","NeedsCompilation":"no","Package":"msSurv","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"KMsurv, Rgraphviz","Title":"Nonparametric Estimation for
Multistate Models","Version":"1.2-2"},"msap":{"Author":"Andres Perez-Figueroa [aut,
cre]","Depends":"R (>= 2.14.0)","Description":"Statistical Analyses of Methylation-
sensitive Amplification Polymorphism (MSAP) assays.","Imports":"ade4,
ape","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"msap","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Statistical analysis for Methylation-sensitive
Amplification\nPolymorphism data","URL":"http:\/\/msap.r-forge.r-
project.org\/","Version":"1.1.8"},"msarc":{"Author":"Gord Brown, Hisham
Mohammed","Depends":"R (>= 3.1.0)","Description":"The output of an affinity-
purification mass spectrometry\nexperiment is typically a list of proteins that
were observed\nin the experiment, identified by UniProt
identifiers\n(http:\/\/www.uniprot.org\/). This package takes as input a list
of\nUniProt identifiers, and the associated Mascot scores from the\nexperiment
(which indicate the likelihood that the protein has\nbeen correctly identified),
clusters them by gene ontology\ncategory (http:\/\/geneontology.org\/), then draws
diagrams\nshowing the results in hierarchical clusters by category, with lines\nfor
individual proteins representing the associated Mascot score.\nThe results are in
general not publication-ready, but will rather\nrequire editing via a graphics
editor that can interpret SVG (scalable\nvector graphics) format. As an
alternative representation, the\npackage will also generate tag clouds based on the
Mascot scores.","Imports":"AnnotationDbi, gplots, XLConnect, wordcloud,
RColorBrewer","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"msarc","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"GO.db, org.Hs.eg.db, org.Mm.eg.db","Title":"Draw
Diagrams (mis)Representing the Results of Mass
Spec\nExperiments","Version":"1.4.5"},"msda":{"Author":"Qing Mai
<mai@stat.fsu.edu>, Yi Yang <yiyang@umn.edu>, Hui Zou
<hzou@stat.umn.edu>","Depends":"Matrix, MASS","Description":"Efficient procedures
for computing a new Multi-Class Sparse Discriminant Analysis method that estimates
all discriminant directions simultaneously.","License":"GPL-
2","NeedsCompilation":"yes","Package":"msda","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Multi-Class Sparse Discriminant
Analysis","URL":"https:\/\/github.com\/emeryyi\/msda","Version":"1.0.2"},"mseapca":
{"Author":"Hiroyuki Yamamoto","Depends":"XML","Description":"This package provides
functions for metabolite set\nenrichment analysis (MSEA) and principal component
analysis\n(PCA), and converting metabolite set list from your own csv\nfiles or
KEGG's tar.gz files to XML documents. This package is\nsuitable for computation of
MSEA for factor loading in
PCA.","License":"BSD","NeedsCompilation":"no","Package":"mseapca","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Title":"Metabolite set enrichment analysis for
factor loading in\nprincipal component analysis","Version":"1.0"},"msgl":
{"Author":"Martin Vincent","Depends":"R (>= 3.0.0), Matrix, sglOptim (==
1.2.0)","Description":"Multinomial logistic regression with sparse group lasso
penalty. Suitable for high dimensional multiclass classification with many classes.
The algorithm finds the sparse group lasso penalized maximum likelihood estimator.
This result in feature and parameter selection, and parameter estimation. Use of
multiple processors for cross validation and subsampling is supported through
OpenMP. Development version is on github.","Imports":"methods, utils,
2)","NeedsCompilation":"yes","Package":"msgl","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"High Dimensional Multiclass Classification Using Sparse
Group\nLasso","URL":"http:\/\/dx.doi.org\/10.1016\/j.csda.2013.06.004\nhttps:\/\/gi
thub.com\/vincent-dk\/msgl","Version":"2.2.0"},"msgpackR":{"Author":"Mikiya
TANIZAWA","Description":"This is the library that can serialize or unserialize
MessagePack format data.","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"msgpackR","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"A library to serialize or unserialize data in
MessagePack format","Version":"1.1"},"msgps":{"Author":"Kei
Hirose","Description":"This package computes the degrees of freedom of the
lasso,\nelastic net, generalized elastic net and adaptive lasso based\non the
generalized path seeking algorithm. The optimal model\ncan be selected by model
selection criteria including Mallows'\nCp, bias-corrected AIC (AICc), generalized
cross validation\n(GCV) and BIC.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"msgps","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Degrees of freedom of elastic net, adaptive lasso
and\ngeneralized elastic
net","URL":"http:\/\/www.keihirose.com\/.","Version":"1.3"},"msir":{"Author":"Luca
Scrucca <luca@stat.unipg.it>","Depends":"R (>= 3.0), mclust (>=
5.0)","Description":"An R package for dimension reduction based on finite Gaussian
mixture modeling of inverse regression.","Imports":"stats, utils, graphics,
grDevices, rgl","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"msir","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Model-Based Sliced Inverse
Regression","Version":"1.3.1"},"msltrend":{"Author":"Phil J Watson
<philwatson.slr@gmail.com>","Depends":"R (>= 3.2.2)","Description":"Analysis of
annual average ocean water level time series\nfrom long (minimum length 80 years)
individual records, providing improved\nestimates of trend (mean sea level) and
associated real-time velocities and\naccelerations. Improved trend estimates are
based on Singular Spectrum Analysis\nmethods. Various gap-filling options are
included to accommodate incomplete time\nseries records. The package also contains
a forecasting module to consider the\nimplication of user defined quantum of sea
level rise between the end of the\navailable historical record and the year 2100. A
wide range of screen and pdf\nplotting options are available in the
package.","Imports":"changepoint (>= 2.1.1), forecast (>= 6.2), plyr (>=
1.8.3),\nRssa (>= 0.13-1), tseries (>= 0.10-34), zoo (>= 1.7-12)","License":"GPL
(>=
3)","NeedsCompilation":"no","Package":"msltrend","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Improved Techniques to Estimate Trend, Velocity and
Acceleration\nfrom Sea Level Records","Version":"1.0"},"msm":{"Author":"Christopher
Jackson <chris.jackson@mrc-bsu.cam.ac.uk>","Description":"Functions for fitting
continuous-time Markov and hidden\nMarkov multi-state models to longitudinal data.
Designed for\nprocesses observed at arbitrary times in continuous time (panel
data)\nbut some other observation schemes are supported. Both Markov\ntransition
rates and the hidden Markov output process can be modelled\nin terms of covariates,
which may be constant or piecewise-constant\nin
time.","Imports":"survival,mvtnorm,expm","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"msm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"mstate,minqa,doParallel,foreach,numDeriv,testthat,flexsur
v","Title":"Multi-State Markov and Hidden Markov Models in Continuous
Time","Version":"1.6.1"},"msma":{"Author":"Atsushi
Kawaguchi","Depends":"mvtnorm","Description":"There are several functions to
implement the method for analysis in a multiblock multivariable data. If the input
is only a matrix, then the principal components analysis (PCA) is implemented. If
the input is a list of matrices, then the multiblock PCA is implemented. If the
input is two matrices for exploratory and objective variables, then the partial
least squares (PLS) analysis is implemented. If the input is two list of matrices
for exploratory and objective variables, then the multiblock PLS analysis is
implemented. Moreover, if the extra outcome variable is specified, then the
supervised version for the methods above is implemented. For each methods, the
sparse modeling is also incorporated. Functions to select the number of components
and the regularized parameters are also provided.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"msma","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Multiblock Sparse Multivariable
Analysis","Version":"0.7"},"msme":{"Author":"Joseph Hilbe and Andrew
Robinson","Depends":"R (>= 2.10), MASS, lattice","Description":"This package
provides functions and datasets from the book \"Methods of Statistical Model
Estimation\".","License":"GPL-
3","NeedsCompilation":"no","Package":"msme","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Functions and Datasets for \"Methods of Statistical
Model\nEstimation\"","Version":"0.5.1"},"msos":{"Author":"John Marden [aut, cph]
and James Balamuta [cre, ctb, com]","Depends":"R (>= 3.0.0), mclust,
tree","Description":"Contains necessary Multivariate Analysis methods and Datasets
used in STAT 571 at the University of Illinois at Urbana-Champaign","License":"MIT
+ file
LICENSE","NeedsCompilation":"no","Package":"msos","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Datasets and Functions used in Multivariate Statistics:
Old\nSchool by John Marden","Version":"1.0.1"},"msr":{"Author":"Samuel Gerber
<sgerber@uoregon.edu>,\nKristi Potter <kpotter@sci.utah.edu>,\nOliver Ruebel
<ruebel1@llnl.gov>","Depends":"R (>= 2.10)","Description":"Discrete Morse-Smale
complex approximation based on kNN graph. The Morse-Smale complex provides a
decomposition of the domain. This package provides methods to compute a
hierarchical sequence of Morse-Smale complicies and tools that exploit this domain
decomposition for regression and visualization of scalar
functions.","Imports":"glmnet, e1071, rgl, RColorBrewer, colorspace, stats,
2","NeedsCompilation":"yes","Package":"msr","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Morse-Smale Approximation, Regression and
Visualization","Version":"0.4.4"},"mstate":{"Author":"Hein Putter, Liesbeth de
Wreede, Marta Fiocco, with contributions by\nRonald
Geskus","Depends":"survival","Description":"The mstate packages contains functions
for data preparation, descriptives, hazard estimation and prediction with Aalen-
Johansen or simulation in competing risks and multi-state
models.","Imports":"RColorBrewer","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"mstate","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"cmprsk","Title":"Data Preparation, Estimation and
Prediction in Multi-
State\nModels","URL":"http:\/\/www.msbi.nl\/putter","Version":"0.2.9"},"mtconnectR"
:{"Author":"Alex Joseph [aut, cre],\nSainath Adapa [aut],\nNitin Madasu
[aut]","Depends":"R (>= 3.0.0)","Description":"Read data in the
'MTConnect'<http:\/\/www.mtconnect.org\/> standard.\nYou can use the package to
read data from historical 'MTConnect logs' along\nwith the 'devices.xml'
describing\nthe device. The data is organised into a 'MTConnectDevice' S4 data
structure\nand some convenience methods are also provided for basic read\/view
operations.","Imports":"methods, data.table (>= 1.9.6), XML (>= 3.98), stringr
(>=\n1.0), plyr (>= 1.8.3), dplyr (>= 0.4.3)","License":"AGPL-
3","NeedsCompilation":"no","Package":"mtconnectR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr, rmarkdown, testthat, roxygen2","Title":"Read
Data from Delimited MTConnect Data Files","Version":"0.2.0"},"mtk":{"Author":"Juhui
WANG [aut, cre] (Software and Engineering), HervÃ© MONOD [aut] (Applications and
Statistical Methods), Robert FAIVRE [ctb] (Applications and Statistical Methods),
HervÃ© RICHARD [ctb] (Software and Engineering)","Depends":"R (>= 2.15.0), base,
stringr, graphics, methods, XML,\nsensitivity, lhs, rgl","Description":"MTK (Mexico
ToolKit) is a generic platform for the sensitivity and uncertainty analysis of
complex models. It provides functions and facilities for experimental design, model
simulation, sensitivity and uncertainty analysis, methods integration and data
reporting, etc.","License":"GPL-
3","NeedsCompilation":"no","Package":"mtk","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"MASS","Title":"Mexico ToolKit library
(MTK)","Version":"1.0"},"mtsdi":{"Author":"Washington Junger <wjunger@ims.uerj.br>
and Antonio Ponce de\nLeon <ponce@ims.uerj.br>","Depends":"R (>=
2.15.0),utils,stats,gam,splines","Description":"This is an EM algorithm based
method for imputation of\nmissing values in multivariate normal time series.
The\nimputation algorithm accounts for both spatial and temporal\ncorrelation
structures. Temporal patterns can be modelled using\nan ARIMA(p,d,q), optionally
with seasonal components, a\nnon-parametric cubic spline or generalised additive
models with\nexogenous covariates. This algorithm is specially tailored
for\nclimate data with missing measurements from several monitors\nalong a given
region.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mtsdi","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Multivariate time series data
imputation","Version":"0.3.3"},"muRL":{"Author":"Ryan T. Moore <rtm@american.edu>
and Andrew Reeves <reeves@wustl.edu>","Depends":"utils,
maps","Description":"Provides mailmerge methods for reading spreadsheets of
addresses and other relevant information to create standardized but customizable
letters. Provides a method for mapping US ZIP codes, including those of letter
recipients. Provides a method for parsing and processing html code from online job
postings of the American Political Science
Association.","Imports":"graphics","License":"GPL-2 | file
LICENSE","NeedsCompilation":"no","Package":"muRL","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Mailmerge using R, LaTeX, and the
Web","URL":"http:\/\/nw18.american.edu\/~rtm\/software.muRL.htm","Version":"0.1-
10"},"muStat":{"Author":"Knut M. Wittkowski <kmw@rockefeller.edu> and Tingting
Song\n<ttsong@gmail.com>","Depends":"R (>= 2.11.1), stats","Description":"Performs
Wilcox rank sum test, Kruskal rank sum test,\nFriedman rank sum test and McNemar
test.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"muStat","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Prentice Rank Sum Test and McNemar
Test","URL":"http:\/\/mustat.rockefeller.edu","Version":"1.7.0"},"muhaz":
{"Author":"S original by Kenneth Hess, <khess@odin.mdacc.tmc.edu> R port\nby R.
Gentleman","Depends":"R(>= 2.3)","Description":"A package for producing a smooth
estimate of the hazard\nfunction for censored
data.","Imports":"survival","License":"GPL","NeedsCompilation":"yes","Package":"muh
az","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Hazard Function
Estimation in Survival Analysis","Version":"1.2.6"},"muir":{"Author":"Justin Alford
[aut, cre]","Depends":"R (>= 3.1.2)","Description":"A simple tool allowing users to
easily and dynamically explore or document a data set using a tree
structure.","Imports":"DiagrammeR (>= 0.6), dplyr (>= 0.4.1), stringr (>=
0.6.2)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"muir","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"htmlwidgets (>= 0.3.2)","Title":"Exploring Data with Tree
Data
Structures","URL":"https:\/\/github.com\/alforj\/muir","Version":"0.1.0"},"multcomp
":{"Author":"Torsten Hothorn [aut, cre],\nFrank Bretz [aut],\nPeter Westfall
[aut],\nRichard M. Heiberger [ctb],\nAndre Schuetzenmeister [ctb],\nSusan Scheibe
[ctb]","Depends":"stats, graphics, mvtnorm (>= 1.0-3), survival (>= 2.35-
7),\nTH.data (>= 1.0-2)","Description":"Simultaneous tests and confidence
intervals\nfor general linear hypotheses in parametric models, including\nlinear,
generalized linear, linear mixed effects, and survival models.\nThe package
includes demos reproducing analyzes presented\nin the book \"Multiple Comparisons
Using R\" (Bretz, Hothorn,\nWestfall, 2010, CRC Press).","Imports":"sandwich (>=
2.3-0), codetools","License":"GPL-
2","NeedsCompilation":"no","Package":"multcomp","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"lme4 (>= 0.999375-16), nlme, robustbase, coin, MASS,
car,\nforeign, xtable, lmtest, coxme (>= 2.2-1), SimComp,
ISwR","Title":"Simultaneous Inference in General Parametric
Models","URL":"http:\/\/multcomp.R-forge.R-project.org The publishers web page
is\nhttp:\/\/www.crcpress.com\/product\/isbn\/9781584885740","Version":"1.4-
4"},"multcompView":{"Author":"Spencer Graves, Hans-Peter Piepho and Luciano Selzer
with\nhelp from Sundar Dorai-Raj","Description":"Convert a logical vector or a
vector of\np-values or a correlation, difference, or distance\nmatrix into a
display identifying the pairs for\nwhich the differences were not
significantly\ndifferent. Designed for use in conjunction with\nthe output of
functions like TukeyHSD, dist{stats},\nsimint, simtest, csimint,
csimtest{multcomp},\nfriedmanmc,
kruskalmc{pgirmess}.","Imports":"grid","License":"GPL","NeedsCompilation":"no","Pac
kage":"multcompView","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests"
:"multcomp, pgirmess, MASS","Title":"Visualizations of Paired
Comparisons","Version":"0.1-7"},"multgee":{"Author":"Anestis Touloumis
<A.Touloumis@brighton.ac.uk>","Depends":"R (>= 2.15.0), gnm,
VGAM","Description":"GEE solver for correlated nominal or ordinal multinomial
responses using a local odds ratios parameterization.","Imports":"utils,
3","NeedsCompilation":"no","Package":"multgee","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"GEE Solver for Correlated Nominal or Ordinal
Multinomial\nResponses","Version":"1.5.3"},"multiAssetOptions":{"Author":"Michael
Eichenberger and Carlo Rosa","Depends":"Matrix","Description":"Efficient finite
difference method for valuing European and American multi-asset
options.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"multiAssetOptions","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Finite Difference Method for Multi-Asset Option
Valuation","Version":"0.1-1"},"multiPIM":{"Author":"Stephan Ritter
<sritter@berkeley.edu>, Alan Hubbard <hubbard@berkeley.edu>, Nicholas Jewell
<jewell@berkeley.edu>","Depends":"lars (>= 0.9-8), penalized, polspline,
rpart","Description":"Performs variable importance analysis using a causal
inference approach. This is done by fitting Population Intervention Models. The
default is to use a Targeted
Maximum Likelihood Estimator (TMLE). The other available estimators are Inverse
Probability of Censoring Weighted (IPCW), Double-Robust IPCW (DR-IPCW), and
Graphical Computation (G-COMP) estimators. Inference can be obtained from the
influence curve (plug-in) or by bootstrapping.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"multiPIM","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"parallel","Title":"Variable Importance Analysis with
Population Intervention
Models","URL":"http:\/\/www.jstatsoft.org\/v57\/i08\/","Version":"1.4-
3"},"multiband":{"Author":"Eric C. Chi, James P. Long","Depends":"R (>=
3.0.2)","Description":"Algorithms for performing joint parameter estimation
in\nastronomical survey data acquired in multiple bands.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"multiband","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Period Estimation for Multiple
Bands","Version":"0.1.0"},"multibiplotGUI":{"Author":"Ana Belen Nieto Librero
<ananieto@usal.es>, Nora Baccala\n<norabaccala@gmail.com>, Purificacion Vicente
Galindo\n<purivg@usal.es>, Purificacion Galindo
Villardon\n<pgalindo@usal.es>","Depends":"R (>= 3.1.1)","Description":"A GUI with
which users can construct and interact\nwith Multibiplot Analysis and provides
inferential results by using Bootstrap Methods.","Imports":"rgl, tkrplot, tcltk,
tcltk2, shapes, cluster, dendroextras,\nMatrix","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"multibiplotGUI","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Multibiplot Analysis in
R","Version":"1.0"},"multicon":{"Author":"Ryne A. Sherman","Depends":"R (>= 3.0.0),
psych, abind, foreach","Description":"Includes functions designed to examine
relationships among multivariate constructs (e.g., personality). This includes
functions for profile (within-person) analysis, dealing with large numbers of
analyses, lens model analyses, and structural summary methods for data with
circumplex structure. The package also includes functions for graphically comparing
and displaying group means.","Imports":"mvtnorm, sciplot,","License":"GPL-
2","NeedsCompilation":"no","Package":"multicon","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Multivariate Constructs","Version":"1.6"},"multicool":
{"Author":"James Curran, Aaron Williams, Jerome Kelleher, Dave
Barber","Depends":"methods, Rcpp (>= 0.11.2)","Description":"A set of tools to
permute multisets without loops or hash tables and to generate integer partitions.
The permutation functions are based on C code from Aaron Williams. Cool-lex order
is similar to colexicographical order. The algorithm is described in Williams, A.
Loopless Generation of Multiset Permutations by Prefix Shifts. SODA 2009, Symposium
on Discrete Algorithms, New York, United States. The permutation code is
distributed without restrictions. The code for stable and efficient computation of
multinomial coefficients comes from Dave Barber. The code can be download from
http:\/\/home.comcast.net\/~tamivox\/dave\/multinomial\/index.html and is
distributed without conditions. The package also generates the integer partitions
of a positive, non-zero integer n. The C++ code for this is based on Python code
from Jerome Kelleher which can be found here
http:\/\/jeromekelleher.net\/partitions.php. The C++ code and Python code are
distributed without conditions.","License":"GPL-
2","NeedsCompilation":"yes","Package":"multicool","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Permutations of Multisets in Cool-Lex
Order","Version":"0.1-9"},"multifwf":{"Author":"Panos Rontogiannis","Depends":"R
(>= 3.1.1)","Description":"Read a table of fixed width formatted data of different
types into\na data.frame for each type.","Imports":"utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"multifwf","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat","Title":"Read Fixed Width Format Files
Containing Lines of Different
Type","URL":"https:\/\/github.com\/prontog\/multifwf","Version":"0.2.2"},"multigrou
p":{"Author":"Aida Eslami, El Mostafa Qannari, Stephanie Bougeard, Gaston
Sanchez\nQuestions and comments go to Aida Eslami <aida.eslami@yahoo.fr>
and\nStephanie Bougeard <stephanie.bougeard@anses.fr>","Depends":"R (>=
2.15.0)","Description":"Several functions are presented in order to study data in a
group structure,\nwhere the same set of variables are measured on different groups
of\nindividuals.","Imports":"MASS","License":"GPL-
3","NeedsCompilation":"no","Package":"multigroup","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Multigroup Data
Analysis","Version":"0.4.4"},"multilevel":{"Author":"Paul Bliese","Depends":"R (>=
2.10), nlme, MASS","Description":"The functions in this package are designed to be
used in\nthe analysis of multilevel data by applied psychologists. The\npackage
includes functions for estimating common within-group\nagreement and reliability
indices. The package also contains\nbasic data manipulation functions that
facilitate the analysis\nof multilevel and longitudinal data.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"multilevel","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Multilevel
Functions","Version":"2.5"},"multilevelPSA":{"Author":"Jason Bryer
<jason@bryer.org>","Depends":"ggplot2, xtable, R (>= 3.0)","Description":"Functions
to estimate and visualize propensity\nscore analysis for multilevel, or clustered,
data.","Imports":"PSAgraphics, plyr, psych, reshape, grid, party,
2)","NeedsCompilation":"no","Package":"multilevelPSA","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat","Title":"Multilevel Propensity Score
Analysis","URL":"http:\/\/jason.bryer.org\/multilevelPSA\/,\nhttp:\/\/github.com\/j
bryer\/multilevelPSA","Version":"1.2.4"},"multimark":{"Author":"Brett T. McClintock
[aut, cre],\nAcho Arnold [ctb, cph] (C original matrix
library,\nhttps:\/\/github.com\/najela\/matrix.h),\nBarry Brown [ctb] (Fortran
original ranlib library),\nJames Lovato [ctb] (Fortran original ranlib
library),\nJohn Burkardt [ctb] (C original ranlib
library,\nhttp:\/\/people.sc.fsu.edu\/~jburkardt\/c_src\/ranlib),\nCleve Moler
[ctb] (C original linpack
library,\nhttp:\/\/www.kkant.net\/geist\/ranlib\/)","Depends":"R (>=
3.2.1)","Description":"Capture-mark-recapture analysis with multiple non-invasive
marks. The models implemented in 'multimark' combine encounter history data arising
from two different non-invasive ``marks'', such as images of left-sided and right-
sided pelage patterns of bilaterally asymmetrical species, to estimate abundance
and related demographic parameters while accounting for imperfect detection.
Bayesian models are specified using simple formulae and fitted using Markov chain
Monte Carlo. Addressing deficiencies in currently available software, 'multimark'
also provides a user-friendly interface for performing Bayesian multimodel
inference using capture-recapture data consisting of a single conventional mark or
multiple non-invasive marks.","Imports":"parallel, Matrix, coda, statmod, RMark,
Brobdingnag, mvtnorm,\ngraphics, methods, stats, utils","License":"GPL-
2","NeedsCompilation":"yes","Package":"multimark","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Capture-Mark-Recapture Analysis using Multiple Non-
Invasive\nMarks","Version":"1.3.2"},"multinbmod":{"Author":"Ivonne Solis-
Trapala","Description":"This is a likelihood approach for the regression analysis
of overdispersed correlated count data with cluster varying covariates. The
approach fits a multivariate negative binomial model by maximum likelihood and
provides robust estimates of the regression coefficients.","License":"GPL-
2","NeedsCompilation":"no","Package":"multinbmod","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Regression analysis of overdispersed correlated count
data","Version":"1.0"},"multinomRob":{"Author":"Walter R. Mebane, Jr.
<wrm1@cornell.edu>, Jasjeet Singh Sekhon\n<sekhon@berkeley.edu>","Depends":"R (>=
1.7.1), rgenoud (>= 2.9), MASS (>= 7.1-8), mvtnorm (>=\n0.6-3)","Description":"MNL
and overdispersed multinomial regression using robust\n(LQD and tanh)
2)","NeedsCompilation":"yes","Package":"multinomRob","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Robust Estimation of Overdispersed Multinomial
Regression Models","URL":"http:\/\/sekhon.berkeley.edu\/","Version":"1.8-
6.1"},"multipleNCC":{"Author":"Nathalie C. Stoer, Sven Ove
Samuelsen","Depends":"survival, mgcv","Description":"Fit Cox proportional hazard
models with a weighted\npartial likelihood. It handles one or multiple endpoints,
additional matching\nand makes it possible to reuse controls for other
endpoints.","License":"GPL-
2","NeedsCompilation":"no","Package":"multipleNCC","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Weighted Cox-regression for Nested Case-Control
Data","Version":"1.2"},"multiplex":{"Author":"Antonio Rivero Ostoic [aut,
cre]","Depends":"R (>= 3.2.3)","Description":"Algebraic procedures for the analysis
of multiple social networks are delivered with\nthis package. Among other things,
it is possible to create and manipulate multivariate network\ndata with different
formats, and there are effective ways available to treat multiple networks\nwith
routines that combine algebraic systems like the partially ordered semigroup or
the\nsemiring structure together with the relational bundles occurring in different
types of\nmultivariate network data sets. As well an algebraic approach for two-
mode networks is made\nthrough Galois derivations between families of the pair of
subsets.","Imports":"methods","License":"GPL-
3","NeedsCompilation":"no","Package":"multiplex","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"Rgraphviz, knitr","Title":"Algebraic
Tools for the Analysis of Multiple Social Networks","Version":"1.8.2"},"multipol":
{"Author":"Robin K. S. Hankin","Depends":"abind","Description":"Various utilities
to manipulate multivariate
polynomials","License":"GPL","NeedsCompilation":"no","Package":"multipol","Reposito
ry":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"polynom","Title":"multivaria
te polynomials","Version":"1.0-6"},"multirich":{"Author":"Alexander
Keyel","Description":"Functions to calculate Unique Trait Combinations (UTC) and
scaled\nUnique Trait Combinations (sUTC) as measures of multivariate richness.
The\npackage can also calculate beta-diversity for trait richness and
can\npartition this into nestedness-related and turnover components. The code\nwill
also calculate several measures of overlap.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"multirich","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr","Title":"Calculate Multivariate Richness via
UTC and sUTC","Version":"2.1.1"},"multisensi":{"Author":"Matieyendou LAMBONI
<clamboni@yahoo.fr>, Herve MONOD\n<herve.monod@jouy.inra.fr>, Caroline
BIDOT\n<caroline.bidot@jouy.inra.fr>","Depends":"R (>=
2.8.0)","Description":"Functions to perform sensitivity analysis on a model with
multivariate output.","License":"CeCILL-
2","NeedsCompilation":"no","Package":"multisensi","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"MASS","Title":"Multivariate Sensitivity
Analysis","Version":"1.0-8"},"multisom":{"Author":"Sarra Chair and Malika
Charrad","Depends":"R (>= 3.1.3),class, kohonen","Description":"Implements two
version of Multi-SOM algorithm namely stochastic Multi-SOM and batch Multi-SOM. The
package determines also the best number of clusters and offers to the user the best
clustering scheme from different results.","License":"GPL-
2","NeedsCompilation":"no","Package":"multisom","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Clustering a Dataset using Multi-SOM
Algorithm","URL":"\nhttps:\/\/sites.google.com\/site\/malikacharrad\/research\/mult
isom-package","Version":"1.0"},"multispatialCCM":{"Author":"Adam
Clark","Depends":"R (>= 3.0.2)","Description":"The multispatial convergent cross
mapping algorithm can be used as a test for causal associations between pairs of
processes represented by time series. This is a combination of convergent cross
mapping (CCM), described in Sugihara et al., 2012, Science, 338, 496-500, and dew-
drop regression, described in Hsieh et al., 2008, American Naturalist, 171,
71â€“80. The algorithm allows CCM to be implemented on data that are not from a
single long time series. Instead, data can come from many short time series, which
are stitched together using bootstrapping.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"multispatialCCM","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Multispatial Convergent Cross
Mapping","Version":"1.0"},"multitable":{"Author":"Steve C
Walker","Description":"Data frames are integral to R. They provide a standard
format for passing data to model-fitting and plotting functions, and this standard
makes it easier for experienced users to learn new functions that accept data as a
single data frame. Still, many data sets do not easily fit into a single data
frame; data sets in ecology with a so-called fourth-corner problem provide
important examples. Manipulating such inherently multiple-table data using several
data frames can result in long and difficult-to-read work-flows. This package
provides new data storage objects called data.list objects, which extend the
data.frame concept to explicitly multiple-table settings. Like data frames, data
lists are lists of variables stored as vectors; what is new is that these vectors
have dimension attributes that make accessing and manipulating them easier. As
data.list objects can be coerced to data.frame objects, they can be used with all R
functions that accept an object that can be coerced to a
data.frame.","License":"GPL-
2","NeedsCompilation":"no","Package":"multitable","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"MASS, lattice, testthat, arm, ggplot2, rbenchmark,
scales,\nvegan","Title":"Simultaneous manipulation of multiple arrays of data,
with\ndata.list objects","URL":"http:\/\/multitable.r-forge.r-
project.org\/","Version":"1.6"},"multitaper":{"Author":"Karim Rahim
<karim.rahim@queensu.ca>, Wesley S. Burr <wesley.burr@gmail.com>","Depends":"R (>=
3.0)","Description":"Implements multitaper spectral analysis using discrete prolate
spheroidal sequences (Slepians) and sine tapers. It includes an adaptive weighted
multitaper spectral estimate, a coherence estimate, Thomson's Harmonic F-test, and
complex demodulation. The Slepians sequences are generated efficiently using a
tridiagonal matrix solution, and jackknifed confidence intervals are available for
most estimates.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"multitaper","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"psd, astrochron, fftwtools","Title":"Multitaper
Spectral Analysis
Tools","URL":"http:\/\/github.com\/wesleyburr\/multitaper\/","Version":"1.0-
11"},"multivator":{"Author":"Robin K. S. Hankin","Depends":"R(>=
2.10.0)","Description":"A multivariate generalization of the emulator
package","Imports":"utils, emulator (>= 1.2-13), mvtnorm, methods","License":"GPL-
2","NeedsCompilation":"no","Package":"multivator","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"abind","Title":"A multivariate
emulator","Version":"1.1-4"},"multiwave":{"Author":"Sophie Achard [aut,
cre],\nIrene Gannaz [aut]","Description":"Computation of an estimation of the long-
memory parameters and\nthe long-run covariance matrix using a multivariate
model\n(Lobato, 1999; Shimotsu 2007). Two semi-parametric methods are\nimplemented:
a Fourier based approach (Shimotsu 2007) and a wavelet based\napproach (Achard and
Gannaz 2014).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"multiwave","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Estimation of Multivariate Long-Memory Models
Parameters","Version":"1.0"},"multiway":{"Author":"Nathaniel E. Helwig
<helwig@umn.edu>","Depends":"parallel","Description":"Fits multi-way component
models via alternating least squares algorithms with optional constraints
(orthogonality, non-negativity, and structural). Fit models include Individual
Differences Scaling, Parallel Factor Analysis (1 and 2), Simultaneous Component
Analysis, and Tucker Factor Analysis.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"multiway","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Component Models for Multi-Way Data","Version":"1.0-
2"},"multiwayvcov":{"Author":"Nathaniel Graham and Mahmood Arai and BjÃ¶rn
HagstrÃ¶mer","Depends":"R (>= 3.0.0)","Description":"Exports two functions
implementing\nmulti-way clustering using the method suggested by Cameron, Gelbach,
&\nMiller (2011) and cluster (or block)\nbootstrapping for estimating variance-
covariance matrices. Normal one and\ntwo-way clustering matches the results of
other common statistical\npackages. Missing values are handled transparently and
rudimentary\nparallelization support is provided.","Imports":"sandwich, boot,
compiler, parallel, stats, utils","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"multiwayvcov","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"lmtest","Title":"Multi-way Standard Error
Clustering","URL":"http:\/\/sites.google.com\/site\/npgraham1\/research\/code","Ver
sion":"1.2.2"},"multxpert":{"Author":"Alex Dmitrienko, Eric Nantz, and Gautier
Paux, with\ncontributions by Thomas Brechenmacher","Depends":"R (>= 2.1.0), stats,
mvtnorm (>= 0.9)","Description":"Implementation of commonly used p-value-based
and\nparametric multiple testing procedures (computation of adjusted\np-values and
simultaneous confidence intervals) and parallel\ngatekeeping procedures based on
the methodology presented in\nthe book \"Multiple Testing Problems in
Pharmaceutical\nStatistics\" (edited by Alex Dmitrienko, Ajit C. Tamhane and\nFrank
Bretz) published by Chapman and Hall\/CRC Press 2009.","License":"GPL-
2","NeedsCompilation":"no","Package":"multxpert","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Common Multiple Testing Procedures and Gatekeeping
Procedures","URL":"http:\/\/multxpert.com\/wiki\/MultXpert_package","Version":"0.1"
},"muma":{"Author":"Edoardo Gaude, Francesca Chignola, Dimitrios
Spiliotopoulos,\nSilvia Mari, Andrea Spitaleri and Michela Ghitti","Depends":"car,
pdist, pls, gplots, mvtnorm, robustbase, gtools, bitops,\ncaTools, pcaPP,
rrcov","Description":"Preprocessing of high-throughput data (normalization
and\nscalings); Principal Component Analysis with help tool for\nchoosing best-
separating principal components and automatic\ntesting for outliers; automatic
univariate analysis for\nparametric and non-parametric data, with generation of
specific\nreports (volcano and box plots); partial least square\ndiscriminant
analysis (PLS-DA); orthogonal partial least square\ndiscriminant analysis (OPLS-
DA); Statistical Total Correlation\nSpectroscopy (STOCSY); Ratio Analysis Nuclear
Magnetic\nResonance (NMR) Spectroscopy (RANSY).","License":"GPL-
2","NeedsCompilation":"no","Package":"muma","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Metabolomics Univariate and Multivariate
Analysis","Version":"1.4"},"munfold":{"Author":"Martin
Elff","Description":"Multidimensional unfolding using Schoenemann's algorithm for
metric\nand Procrustes rotation of unfolding results.","Imports":"memisc, MASS,
stats, graphics","License":"GPL-
2","NeedsCompilation":"no","Package":"munfold","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Metric
Unfolding","URL":"\nhttp:\/\/www.elff.eu\/software\/munfold\/,http:\/\/github.com\/
melff\/munfold\/","Version":"0.3.5"},"munsell":{"Author":"Charlotte
Wickham <cwickham@gmail.com>","Description":"Provides easy access to, and
manipulation of, the Munsell\ncolours. Provides a mapping between
Munsell's\noriginal notation (e.g. \"5R 5\/10\") and hexadecimal strings
suitable\nfor use directly in R graphics. Also provides utilities\nto explore
slices through the Munsell colour tree, to transform\nMunsell colours and display
colour palettes.","Imports":"colorspace, methods","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"munsell","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"ggplot2, testthat","Title":"Utilities for Using
Munsell Colours","Version":"0.4.3"},"munsellinterpol":{"Author":"Jose Gama [aut,
cre, trl],\nPaul Centore [aut, cph]","Depends":"R (>= 2.10),
geometry","Description":"Methods for interpolating data in the Munsell color system
following the ASTM D-1535 standard. Hues and chromas with decimal values can be
interpolated and converted to\/from the Munsell color system and CIE xyY, CIE XYZ,
sRGB, CIE Lab or CIE Luv. Chromas can be odd and hue steps can be real numbers.
Based on the work by Paul Centore, \"The Munsell and Kubelka-Munk
Toolbox\".","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"munsellinterpol","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Interpolate Munsell Renotation Data from
Hue\/Chroma to CIE\/sRGB","Version":"1.0.2"},"murphydiagram":{"Author":"Alexander
Jordan, Fabian Krueger","Description":"Data and code for the paper by Ehm,
Gneiting, Jordan and Krueger ('Of Quantiles and Expectiles: Consistent Scoring
Functions, Choquet Representations, and Forecast Rankings', 2015).","License":"GPL-
3","NeedsCompilation":"no","Package":"murphydiagram","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Murphy Diagrams for Forecast
Comparisons","URL":"https:\/\/sites.google.com\/site\/fk83research\/code","Version"
:"0.11"},"musicNMR":{"Author":"Stefano Cacciatore, Edoardo Saccenti, Mario
Piccioli","Depends":"R (>= 2.10.0), seewave","Description":"This package is a
collection of function for converting and modifying mono dimensional nuclear
magnetic resonance spectra.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"musicNMR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"plsgenomics","Title":"Conversion of Nuclear Magnetic
Resonance spectrum in audio file","Version":"0.0.2"},"mutoss":{"Author":"MuToss
Coding Team (Berlin 2010), Gilles Blanchard, Thorsten Dickhaus,\nNiklas Hack, Frank
Konietschke, Kornelius Rohmeyer,\nJonathan Rosenblatt, Marsel Scheer, Wiebke
Werft","Depends":"R (>= 2.10.0), mvtnorm","Description":"The Mutoss package and
accompanying mutossGUI package are\ndesigned to ease the application and comparison
of multiple\nhypothesis testing procedures.","Imports":"plotrix, multtest (>=
2.2.0), multcomp (>= 1.1-0),
methods","License":"GPL","NeedsCompilation":"no","Package":"mutoss","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Suggests":"fdrtool, qvalue, RUnit,
lattice","Title":"Unified Multiple Testing Procedures","URL":"http:\/\/mutoss.r-
forge.r-project.org\/","Version":"0.1-10"},"mutossGUI":{"Author":"MuToss Coding
Team (Berlin 2010), Gilles Blanchard, Thorsten Dickhaus,\nNiklas Hack, Frank
Konietschke, Kornelius Rohmeyer,\nJonathan Rosenblatt, Marsel Scheer, Wiebke
Werft","Depends":"R (>= 2.8.0), mutoss (>= 0.1-6), multcomp,
plotrix","Description":"The mutossGUI package provides a graphical user interface
for the MuToss Project.","Imports":"rJava (>= 0.8-0), JavaGD (>= 0.5-2),
CommonJavaJars (>=\n1.0.4),
JGR","License":"GPL","NeedsCompilation":"no","Package":"mutossGUI","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"A Graphical User Interface for the
MuToss Project","URL":"http:\/\/mutoss.r-forge.r-project.org\/","Version":"0.1-
10"},"mvMORPH":{"Author":"Julien Clavel, with contributions from Aaron King, and
Emmanuel Paradis","Depends":"R(>= 2.9.1), phytools, ape, corpcor, subplex,
spam","Description":"Fits multivariate (Brownian Motion, Early Burst, ACDC,
Ornstein-Uhlenbeck and Shifts) models of continuous traits evolution on
trees.","Imports":"stats","License":"GPL (>=
2.0)","NeedsCompilation":"yes","Package":"mvMORPH","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr","Title":"Multivariate Comparative Tools for
Fitting Evolutionary Models\nto Morphometric
Data","URL":"https:\/\/github.com\/JClavel\/mvMORPH","Version":"1.0.6"},"mvProbit":
{"Author":"Arne Henningsen <arne.henningsen@gmail.com>","Depends":"R (>= 2.4.0),
mvtnorm (>= 0.9-9994), maxLik (>= 1.0-0), abind\n(>= 1.3-0)","Description":"Tools
for estimating multivariate probit models,\ncalculating conditional and
unconditional expectations,\nand calculating marginal effects on conditional and
unconditional\nexpectations.","Imports":"bayesm (>= 2.2-4), miscTools (>= 0.6-
2)","NeedsCompilation":"no","Package":"mvProbit","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Multivariate Probit
Models","URL":"http:\/\/www.sampleSelection.org","Version":"0.1-8"},"mvQuad":
{"Author":"Constantin Weiser (HHU of Duesseldorf \/ Germany)","Depends":"R (>=
3.0)","Description":"Provides methods to construct multivariate grids, which can be
used\nfor multivariate quadrature. This grids can be based on different
quadrature\nrules like Newton-Cotes formulas (trapezoidal-, Simpson's- rule, ...)
or Gauss\nquadrature (Gauss-Hermite, Gauss-Legendre, ...). For the construction of
the\nmultidimensional grid the product-rule or the combination- technique can
be\napplied.","Imports":"rgl, data.table, statmod, methods","License":"GPL-
3","NeedsCompilation":"no","Package":"mvQuad","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"knitr, rmarkdown","Title":"Methods for Multivariate
Quadrature","Version":"1.0-5"},"mvSLOUCH":{"Author":"Krzysztof Bartoszek
<bartoszekkj@gmail.com>","Depends":"R(>= 2.9.1), ouch, ape, numDeriv, mvtnorm,
corpcor","Description":"Fits multivariate Ornstein-Uhlenbeck types of models to
continues trait data from species related by a common evolutionary
history.","Imports":"methods","License":"GPL (>= 2) | file
LICENCE","NeedsCompilation":"no","Package":"mvSLOUCH","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Multivariate Stochastic Linear Ornstein-Uhlenbeck
Models for\nPhylogenetic Comparative Hypotheses","Version":"1.3"},"mvShapiroTest":
{"Author":"Elizabeth Gonzalez-Estrada, Jose A. Villasenor-Alva","Depends":"stats,
datasets","Description":"This package implements the generalization of the Shapiro-
Wilk test\nfor multivariate normality proposed by Villasenor-Alva and\nGonzalez-
Estrada (2009).","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"mvShapiroTest","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Generalized Shapiro-Wilk test for multivariate
normality","Version":"1.0"},"mvabund":{"Author":"Yi Wang, Ulrike Naumann, Stephen
Wright, Dirk Eddelbuettel and David Warton","Depends":"R (>=
3.0.0)","Description":"A set of tools for displaying, modeling and
analysing\nmultivariate abundance data in community ecology. See\n'mvabund-
package.Rd' for details of overall package organization.\nThe package is
implemented with the Gnu Scientific
Library\n(http:\/\/www.gnu.org\/software\/gsl\/) and
Rcpp\n(http:\/\/dirk.eddelbuettel.com\/code\/rcpp.html) R \/ C++
classes.","Imports":"Rcpp, MASS, methods, stats, tweedie, statmod,
parallel","License":"LGPL (>=
2.1)","NeedsCompilation":"yes","Package":"mvabund","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Statistical Methods for Analysing Multivariate
Abundance Data","Version":"3.11.7"},"mvbutils":{"Author":"Mark V. Bravington
<mark.bravington@csiro.au>","Depends":"R (>= 2.13), utils, tools,
stats","Description":"Hierarchical workspace tree, code editing and backup,
easy\npackage prep, editing of packages while loaded, per-object\nlazy-loading,
easy documentation, macro functions, and\nmiscellaneous utilities. Needed by debug
2)","NeedsCompilation":"no","Package":"mvbutils","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Workspace organization, code and documentation editing,
package\nprep and editing, etc","Version":"2.7.4.1"},"mvc":{"Author":"Andreas Maunz
<andreas@maunz.de>","Depends":"R (>= 2.14.1), rattle (>= 2.6.18)","Description":"An
implementation of Multi-View Clustering (Bickel and Scheffer, 2004). Documents are
generated by drawing word values from a categorical distribution for each word,
given the cluster. This means words are not counted (multinomial, as in the paper),
but words take on different values from a finite set of values (categorical). Thus,
it implements Mixture of Categoricals EM (as opposed to Mixture of Multinomials
developed in the paper), and Spherical k-Means. The latter represents documents as
vectors in the categorical space.","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"mvc","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Multi-View
Clustering","URL":"http:\/\/cs.maunz.de","Version":"1.3"},"mvcluster":
{"Author":"Jiangwen Sun, Jin Lu, Tingyang Xu, Joseph Muller, Jinbo
Bi","Depends":"Rcpp (>= 0.12.0)","Description":"Implementation of multi-view bi-
clustering algorithms. When a sample is characterized by two or more sets of input
features, it creates multiple data matrices for the same set of examples, each
corresponding to a view. For instance, individuals who are diagnosed with a
disorder can be described by their clinical symptoms (one view) and their genomic
markers (another view). Rows of a data matrix correspond to examples and columns
correspond to features. A multi-view bi-clustering algorithm groups examples (rows)
consistently across the views and simultaneously identifies the subset of features
(columns) in each view that are associated with the row groups. This mvcluster
package includes three
such methods. (1) MVSVDL1: multi-view bi-clustering based on singular value
decomposition where the left singular vectors are used to identify row clusters and
the right singular vectors are used to identify features (columns) for each row
cluster. Each singular vector is regularized by the L1 vector norm. (2) MVLRRL0:
multi-view bi-clustering based on sparse low rank representation (i.e., matrix
approximation) where the decomposed components are regularized by the so-called L0
vector norm (which is not really a vector norm). (3) MVLRRL1: multi-view bi-
clustering based on sparse low rank representation (i.e., matrix approximation)
where the decomposed components are regularized by the L1 vector
norm.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"mvcluster","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Multi-View
Clustering","URL":"http:\/\/www.labhealthinfo.uconn.edu\/multi-view-
analytics\/","Version":"1.0"},"mvctm":{"Author":"Denis Larocque","Depends":"R (>=
3.1.0), Formula, nlme, MNM, quantreg, Rfit","Description":"Permutation tests for
variance components for 2-level, 3-level and 4-level data with univariate or
multivariate responses.","License":"GPL-
2","NeedsCompilation":"no","Package":"mvctm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Multivariate Variance Components Tests for Multilevel
Data","Version":"1.0"},"mvcwt":{"Author":"Timothy H. Keitt","Description":"This
package computes the continuous wavelet transform of\nirregularly sampled time
series.","Imports":"foreach, RColorBrewer,
grDevices","License":"GPL","NeedsCompilation":"no","Package":"mvcwt","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Title":"Wavelet analysis of multiple time
series","URL":"https:\/\/bitbucket.org\/tkeitt\/mvcwt\/overview,\nhttp:\/\/www.keit
tlab.org","Version":"1.3"},"mvdalab":{"Author":"Nelson Lee Afanador, Thanh Tran,
and Lionel Blanchet","Description":"Implementation of latent variable methods and
multivariate modeling tools. The focus is on exploratory analyses using
dimensionality reduction methods and classical multivariate statistical
tools.","Imports":"car, dummies, ggplot2, MASS, moments, parallel,
penalized,\nplyr, reshape2, sn","License":"GPL-
3","NeedsCompilation":"no","Package":"mvdalab","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Multivariate Data Analysis
Laboratory","Version":"1.0"},"mvglmmRank":{"Author":"Andrew T. Karl (Adsurgo LLC),
Jennifer Broatch (Arizona State University)","Depends":"Matrix, numDeriv, methods,
stats, utils","Description":"Maximum likelihood estimates are obtained via an EM
algorithm with either a first-order or a fully exponential Laplace
approximation.","License":"GPL-
2","NeedsCompilation":"no","Package":"mvglmmRank","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Multivariate Generalized Linear Mixed Models for
Ranking Sports\nTeams","Version":"1.1-2"},"mvinfluence":{"Author":"Michael
Friendly","Depends":"car, heplots","Description":"This package computes regression
deletion diagnostics for\nmultivariate linear models and provides some
associated\ndiagnostic plots.","License":"GPL-
2","NeedsCompilation":"no","Package":"mvinfluence","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Influence Measures and Diagnostic Plots for
Multivariate
Linear\nModels","URL":"http:\/\/datavis.ca\/R","Version":"0.6"},"mvmesh":
{"Author":"John P. Nolan","Depends":"R (>= 3.0), rcdd, rgl, geometry, abind,
SimplicialCubature","Description":"Define, manipulate and plot meshes on simplices,
spheres, balls, rectangles and tubes.\nDirectional and other multivariate
histograms are provided.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"mvmesh","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Multivariate Meshes and Histograms in Arbitrary
Dimensions","Version":"1.2"},"mvmeta":{"Author":"Antonio Gasparrini","Depends":"R
(>= 2.13.0)","Description":"Collection of functions to perform fixed and random-
effects multivariate and univariate meta-analysis and meta-
regression.","Imports":"stats, graphics, grDevices, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mvmeta","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"metafor, meta, rmeta, nlme, MASS,
dlnm","Title":"Multivariate and Univariate Meta-Analysis and Meta-
Regression","URL":"http:\/\/www.ag-myresearch.com\/package-
mvmeta","Version":"0.4.7"},"mvnTest":{"Author":"Natalya Pya [aut, cre], Vassilly
Voinov [aut], Rashid Makarov [aut], Yevgeniy Voinov [aut]","Depends":"R (>=
2.15.0), mvtnorm","Description":"Routines for assessing multivariate normality.
Implements three Wald's type chi-squared tests; non-parametric Anderson-Darling and
Cramer-von Mises tests; Doornik-Hansen test, Royston test and Henze-Zirkler
test.","Imports":"methods, stats, graphics, MASS","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mvnTest","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Goodness of Fit Tests for Multivariate
Normality","Version":"1.1-0"},"mvna":{"Author":"Arthur
Allignol","Description":"This package computes the Nelson-Aalen estimator of the
cumulative transition hazard for multistate
models.","Imports":"lattice","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"mvna","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"Rgraphviz, gridBase","Title":"Nelson-Aalen estimator of
the cumulative hazard in multistate\nmodels","Version":"1.2-3"},"mvnfast":
{"Author":"Matteo Fasiolo, using the C++ parallel RNG of Thijs van den Berg
and\nZiggurat algorithm of Jens Maurer and Steven Watanabe
(boost)","Description":"Provides computationally efficient tools related to\nthe
multivariate normal distribution. The main functionalities are:\nsimulating
multivariate normal random vectors, evaluating multivariate\nnormal densities and
Mahalanobis distances. These tools are very efficient\nthanks to the use of C++
code and of the OpenMP API.","Imports":"Rcpp (>= 0.10.4)","License":"GPL (>=
2.0)","NeedsCompilation":"yes","Package":"mvnfast","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr, testthat, mvtnorm, microbenchmark, MASS,
plyr","Title":"Fast Multivariate Normal
Methods","URL":"https:\/\/github.com\/mfasiolo\/mvnfast,
www.sitmo.com","Version":"0.1.4"},"mvngGrAd":{"Author":"Frank
Technow","Depends":"methods, stats","Description":"Package for moving grid
adjustment\nin plant breeding field trials.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mvngGrAd","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Moving Grid Adjustment in Plant Breeding Field
Trials","Version":"0.1.5"},"mvnmle":{"Author":"Kevin Gross, with help from Douglas
Bates","Depends":"R (>= 1.2.0)","Description":"Finds the maximum likelihood
estimate of the mean vector\nand variance-covariance matrix for multivariate normal
data\nwith missing values.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"mvnmle","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"ML estimation for multivariate normal data with missing
values","Version":"0.1-11"},"mvnormtest":{"Author":"Slawomir
Jarek","Depends":"stats","Description":"Generalization of shapiro-wilk test for
multivariate\nvariables.","License":"GPL","NeedsCompilation":"no","Package":"mvnorm
test","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Normality test
for multivariate variables","Version":"0.1-9"},"mvnpermute":{"Author":"Mark
Abney","Description":"Given a vector of multivariate normal data, a matrix
of\ncovariates and the data covariance matrix, generate new multivariate
normal\nsamples that have the same covariance matrix based on permutations of\nthe
transformed data residuals.","License":"GPL (>=
3.0)","NeedsCompilation":"no","Package":"mvnpermute","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Generate New Multivariate Normal Samples from
Permutations","Version":"1.0.0"},"mvoutlier":{"Author":"Peter Filzmoser
<P.Filzmoser@tuwien.ac.at> and\nMoritz Gschwandtner
<e0125439@student.tuwien.ac.at>","Depends":"sgeostat, R (>=
2.14)","Description":"various methods for multivariate outlier
detection.","Imports":"robCompositions, robustbase","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"mvoutlier","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Multivariate outlier detection based on robust
methods","URL":"http:\/\/www.statistik.tuwien.ac.at\/public\/filz\/","Version":"2.0
.6"},"mvprpb":{"Author":"Noboru Nomura","Description":"Computes orthant
probabilities multivariate normal distribution.","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"mvprpb","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Orthant Probability of the Multivariate Normal
Distribution","Version":"1.0.4"},"mvrtn":{"Author":"Matthew
McLeod","Description":"Mean, variance, and random variates for left\/right
truncated normal distributions.","License":"LGPL (>= 2.0, < 3) | Mozilla Public
License","NeedsCompilation":"yes","Package":"mvrtn","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Mean and Variance of Truncated Normal
Distribution","Version":"1.0"},"mvsf":{"Author":"David
Delmail","Depends":"nortest,mvnormtest","Description":"Generalization of the
Shapiro-Francia test for\nmultivariate variables.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mvsf","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Shapiro-Francia Multivariate Normality
Test","Version":"1.0"},"mvtboost":{"Author":"Patrick Miller [aut,
cre]","Depends":"R (>= 3.0.0)","Description":"Fits a multivariate model of decision
trees for multiple, continuous outcome variables. A model for each outcome variable
is fit separately, selecting predictors that explain covariance in the outcomes.
Built on top of 'gbm', which fits an ensemble of decision trees to univariate
outcomes.","Imports":"gbm,
RColorBrewer, stats, graphics, grDevices, utils,","License":"GPL (>= 2) | file
LICENSE","NeedsCompilation":"no","Package":"mvtboost","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat, plyr, MASS, parallel, lars, ggplot2,
knitr,\nrmarkdown","Title":"Tree Boosting for Multivariate
Outcomes","URL":"https:\/\/github.com\/patr1ckm\/mvtboost","Version":"0.4.1"},"mvtm
eta":{"Author":"Han Chen","Depends":"gtools","Description":"This package contains
functions to run fixed effects or\nrandom effects multivariate meta-
2)","NeedsCompilation":"no","Package":"mvtmeta","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Multivariate meta-analysis","Version":"1.0"},"mvtnorm":
{"Author":"Alan Genz [aut],\nFrank Bretz [aut],\nTetsuhisa Miwa [aut],\nXuefei Mi
[aut],\nFriedrich Leisch [ctb],\nFabian Scheipl [ctb],\nBjoern Bornkamp
[ctb],\nMartin Maechler [ctb],\nTorsten Hothorn [aut, cre]","Depends":"R(>=
1.9.0)","Description":"Computes multivariate normal and t probabilities,
quantiles,\nrandom deviates and densities.","Imports":"stats,
2","NeedsCompilation":"yes","Package":"mvtnorm","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Multivariate Normal and t
Distributions","URL":"http:\/\/mvtnorm.R-forge.R-project.org","Version":"1.0-
5"},"mvtsplot":{"Author":"Roger D. Peng <rpeng@jhsph.edu>","Depends":"R (>=
2.14.0), RColorBrewer","Description":"A function for plotting multivariate time
series data","Imports":"splines, graphics","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"mvtsplot","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Multivariate Time Series
Plot","URL":"http:\/\/github.com\/rdpeng\/mvtsplot","Version":"1.0-1"},"mwa":
{"Author":"Sebastian Schutte and Karsten Donnay","Depends":"R (>= 2.6), cem (>=
0.3), rJava (>= 0.9), MASS (>= 7.0)","Description":"Matched Wake Analysis (mwa)
grants insights into causal relationships in spatiotemporal event
data.","License":"LGPL-
3","NeedsCompilation":"no","Package":"mwa","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Causal Inference in Spatiotemporal Event
Data","Version":"0.4.1"},"mwaved":{"Author":"Justin Rory
Wishart","Description":"Computes the Wavelet deconvolution estimate of a common
signal\npresent in multiple channels that have possible different levels of
blur\nand long memory additive error.","Imports":"Rcpp (>= 0.11.1), shiny,
grid","License":"GPL","NeedsCompilation":"yes","Package":"mwaved","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Suggests":"fracdiff, ggplot2, testthat,
knitr","Title":"Multichannel Wavelet Deconvolution with Additive Long
Memory\nNoise","URL":"https:\/\/github.com\/jrwishart\/mwaved","Version":"1.1.4"},"
mxkssd":{"Author":"B N Mandal <mandal.stat@gmail.com>","Depends":"R(>=
2.13.0)","Description":"mxkssd is a package that generates efficient
balanced\nmixed-level k-circulant supersaturated designs by interchanging\nthe
elements of the generator vector. The package tries to\ngenerate a supersaturated
design that has EfNOD efficiency more\nthan user specified efficiency level (mef).
The package also\ndisplays the progress of generation of an efficient mixed-
level\nk-circulant design through a progress bar. The progress of 100\nper cent
means that one full round of interchange is completed.\nMore than one full round
(typically 4-5 rounds) of interchange\nmay be required for larger
2)","NeedsCompilation":"no","Package":"mxkssd","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Efficient mixed-level k-circulant supersaturated
designs","Version":"1.1"},"myTAI":{"Author":"Hajk-Georg Drost","Depends":"R (>=
3.1.1)","Description":"A statistical framework allowing users interested in the
evolution of biological processes to capture evolutionary signals in
transcriptomes.","Imports":"Rcpp (>= 0.11.3), nortest (>= 1.0-2), fitdistrplus (>=
1.0-2),\nparallel (>= 3.1.1), foreach (>= 1.4.2), doParallel (>= 1.0.8),\ndplyr (>=
0.3.0), RColorBrewer (>= 1.1-2), taxize (>= 0.6.0),\nedgeR, methods (>= 3.1.1),
graphics (>= 3.1.1), stats (>=\n3.1.1), grDevices (>= 3.1.1), utils (>= 3.1.1),
reshape2 (>=\n1.4.1), ggplot2 (>= 1.0.1)","License":"GPL-
3","NeedsCompilation":"yes","Package":"myTAI","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"knitr (>= 1.6), rmarkdown (>= 0.3.3), devtools (>=
1.6.1),\ntestthat (>= 0.9.1)","Title":"Performing Phylotranscriptomics with
R","URL":"https:\/\/github.com\/HajkD\/myTAI","Version":"0.3.0"},"mycobacrvR":
{"Author":"Deepika Kulshreshtha, Rupanjali Chaudhuri, S. Ramachandran","Depends":"R
(>= 2.15), methods","Description":"The mycobacrvR package contains utilities to
provide detailed information for B cell and T cell epitopes for predicted adhesins
from various servers such as ABCpred, Bcepred, Bimas, Propred, NetMHC and IEDB.
Please refer the URL below to download data files (data_mycobacrvR.zip) used in
functions of this package.","License":"GPL-
2","NeedsCompilation":"no","Package":"mycobacrvR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Integrative immunoinformatics for Mycobacterial
diseases in
R\nplatform","URL":"http:\/\/mycobacteriarv.igib.res.in\/download.html","Version":"
1.0"},"mycor":{"Author":"Keon-Woong Moon [aut, cre]","Depends":"R (>=
3.1.1)","Description":"Perform correlation and linear regression test\namong the
numeric columns in a data frame automatically\nand make plots using pairs or
lattice::parallelplot.","Imports":"lattice","License":"CC0","NeedsCompilation":"no"
,"Package":"mycor","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"
knitr, testthat","Title":"Automatic Correlation and Regression Test in a Data
Frame","Version":"0.1"},"myepisodes":{"Author":"Matt Malin
<email@mattmalin.co.uk>","Description":"Useful functions for accessing MyEpisodes
feeds and\nepisode information as well as other tv episode related actions\nthrough
www.myepisodes.com","Imports":"XML","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"myepisodes","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"MyEpisodes RSS\/API
functions","Version":"1.1.1"},"mztwinreg":{"Author":"Aldo Cordova-
Palomera","Description":"Linear and logistic regression models for quantitative
genetic analysis of data from monozygotic twins.","Imports":"rms,
mclogit","License":"GPL-
3","NeedsCompilation":"no","Package":"mztwinreg","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"lme4","Title":"Regression Models for Monozygotic Twin
Data","URL":"https:\/\/github.com\/AldoCP\/mztwinreg","Version":"1.0-
1"},"nCDunnett":{"Author":"Siomara Cristina Broch, Daniel Furtado
Ferreira","Depends":"R (>= 2.15.0)","Description":"Computes the noncentral
Dunnett's test distribution (pdf, cdf and quantile) and generates random
numbers.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"nCDunnett","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Noncentral Dunnett's Test
Distribution","URL":"www.dex.ufla.br\/~danielff\/r_resources.html","Version":"1.1.0
"},"nCal":{"Author":"Youyi Fong <yfong@fhcrc.org>, Krisztian Sebestyen
<ksebestyen@gmail.com>, Xuesong Yu <xyu@scharp.org>","Depends":"R (>= 3.0.0), drc,
gdata, gWidgets, kyotil","Description":"Performs nonlinear calibration and curve
fitting for data from Luminex, RT-PCR, ELISA, RPPA etc. Its precursor is
Ruminex.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"nCal","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr, RUnit, rjags, gWidgetstcltk,
nlme","Title":"Nonlinear Calibration","Version":"2015.3-3"},"nFCA":
{"Author":"Junheng Ma, Jiayang Sun, and Guo-Qiang Zhang","Description":"Numerical
Formal Concept Analysis (nFCA) is a modern unsupervised learning tool for analyzing
general numerical data. Given input data, this R package nFCA outputs two nFCA
graphs: a H-graph and an I-graph that reveal systematic, hierarchical clustering
and inherent structure of the data.","License":"GPL-
2","NeedsCompilation":"no","Package":"nFCA","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Numerical Formal Concept Analysis for Systematic
Clustering","Version":"0.3"},"nFactors":{"Author":"Gilles Raiche (Universite du
Quebec a Montreal) and David Magis (Universite de Liege)","Depends":"R (>= 2.9.2),
MASS, psych, boot, lattice","Description":"Indices, heuristics and strategies to
help determine the number of factors\/components to retain:\n1. Acceleration factor
(af with or without Parallel Analysis);\n2. Optimal Coordinates (noc with or
without Parallel Analysis);\n3. Parallel analysis (components, factors and
bootstrap);\n4. lambda > mean(lambda) (Kaiser, CFA and related);\n5. Cattell-
Nelson-Gorsuch (CNG);\n6. Zoski and Jurs multiple regression (b, t and p);\n7.
Zoski and Jurs standard error of the regression coeffcient (sescree);\n8. Nelson
R2;\n9. Bartlett khi-2;\n10. Anderson khi-2;\n11. Lawley khi-2 and\n12. Bentler-
Yuan khi-2.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"nFactors","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"xtable","Title":"Parallel Analysis and Non Graphical
Solutions to the Cattell\nScree Test","Version":"2.3.3"},"nLTT":{"Author":"Thijs
Janzen","Description":"Provides functions to calculate the normalised Lineage-
Through-Time (nLTT) statistic, given two phylogenetic trees. The nLTT statistic
measures the difference between two Lineage-Through-Time curves, where each curve
is normalised both in time and in number of lineages.","Imports":"deSolve, coda,
ape","License":"GPL-
2","NeedsCompilation":"no","Package":"nLTT","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"TESS","Title":"Calculate the NLTT
Statistic","Version":"1.1.1"},"nabor":{"Author":"Stephane Mangenat (for 'libnabo'),
Gregory Jefferis","Depends":"R (>= 3.0.2)","Description":"An R wrapper for
'libnabo', an exact or
approximate k nearest\nneighbour library which is optimised for low dimensional
spaces (e.g. 3D).\n'libnabo' has speed and space advantages over the 'ANN' library
wrapped by\npackage 'RANN'. 'nabor' includes a knn function that is designed as
a\ndrop-in replacement for 'RANN' function nn2. In addition, objects which\ninclude
the k-d tree search structure can be returned to speed up repeated\nqueries of the
same set of target points.","Imports":"Rcpp (>= 0.11.2),
LICENSE","NeedsCompilation":"yes","Package":"nabor","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat, RANN","Title":"Wraps 'libnabo', a Fast K
Nearest Neighbour Library for
Low\nDimensions","URL":"https:\/\/github.com\/jefferis\/nabor\nhttps:\/\/github.com
\/ethz-asl\/libnabo","Version":"0.4.6"},"nadiv":{"Author":"Matthew Wolak [cre,
aut]","Depends":"Matrix","Description":"Constructs (non)additive genetic
relationship matrices, and their inverses, from a pedigree to be used in linear
mixed effect models (A.K.A. the 'animal model'). Also includes other functions to
facilitate the use of animal models. Some functions have been created to be used in
conjunction with the R package 'asreml' for the 'ASReml' software, which can be
obtained upon purchase from 'VSN' international
(http:\/\/www.vsni.co.uk\/software\/asreml).","Enhances":"MCMCglmm,
asreml","Imports":"graphics, methods, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"nadiv","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"parallel","Title":"(Non)Additive Genetic Relatedness
Matrices","URL":"http:\/\/github.com\/matthewwolak\/nadiv","Version":"2.14.2"},"nam
espace":{"Author":"Winston Chang, Daniel Adler, Hadley Wickham, Gregory R.
Warnes,\nR Core Team","Description":"This package provides user-level functions to
manage\nnamespaces not (yet) available in base R:
'registerNamespace',\n'unregisterNamespace', 'makeNamespace',
and\n'getRegisteredNamespace'\n\n('makeNamespaces' is extracted from the R 'base'
package source code:\nsrc\/library\/base\/R\/namespace.R)","License":"GPL-
2","NeedsCompilation":"yes","Package":"namespace","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Provide namespace managment functions not (yet) present
in base\nR","Version":"0.9.1"},"nanop":{"Author":"Anton Gagin, Katharine Mullen,
Igor Levin","Description":"This software package implements functions to simulate
spherical, ellipsoid and cubic polyatomic nanoparticles with arbitrary crystal
structures and to calculate the associated pair-distribution function and X-
ray\/neutron total-scattering signals. It also provides a target function that can
be used for simultaneous fitting of small- and wide-angle total scattering data in
real and reciprocal spaces. The target function can be generated either as a sum of
weighted residuals for individual datasets or as a vector of residuals suitable for
optimization using multi-criteria algorithms (e.g. Pareto
methods).","Imports":"distrEx, rgl","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"nanop","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"DEoptim, mco","Title":"Tools for Nanoparticle
Simulation and Calculation of PDF and\nTotal Scattering Structure
Function","URL":"http:\/\/scripts.iucr.org\/cgi-bin\/paper?
S1600576714001046","Version":"2.0-6"},"nasaweather":{"Author":"'Hadley Wickham'
[aut, cre]","Depends":"R (>= 3.1.0)","Description":"This package contains tidied
data from the ASA 2006 data expo,\nas well as a number of useful other related data
sets.","License":"GPL-
3","NeedsCompilation":"no","Package":"nasaweather","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Collection of datasets from the ASA 2006 data
expo","URL":"http:\/\/github.com\/hadley\/nasaweather,\nhttp:\/\/stat-
computing.org\/dataexpo\/2006\/","Version":"0.1"},"nat":{"Author":"Greg Jefferis
and James Manton","Depends":"R (>= 2.15.1), rgl","Description":"NeuroAnatomy
Toolbox (nat) enables analysis and visualisation of 3D\nbiological image data,
especially traced neurons. Reads and writes 3D images\nin NRRD and 'Amira'
AmiraMesh formats and reads surfaces in 'Amira' hxsurf\nformat. Traced neurons can
be imported from and written to SWC and 'Amira'\nLineSet and SkeletonGraph formats.
These data can then be visualised in 3D\nvia 'rgl', manipulated including applying
calculated registrations, e.g.\nusing the 'CMTK' registration suite, and analysed.
There is also a simple\nrepresentation for neurons that have been subjected to 3D
skeletonisation\nbut not formally traced; this allows morphological comparison
between\nneurons including searches and clustering (via the 'nat.nblast'
extension\npackage).","Imports":"nabor, igraph, methods, filehash, digest,
nat.utils (>=\n0.4.2), plyr, yaml","License":"GPL-
3","NeedsCompilation":"no","Package":"nat","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"Rvcg, testthat, httr, XML","Title":"NeuroAnatomy Toolbox
for Analysis of 3D Image Data","URL":"https:\/\/github.com\/jefferis\/nat
http:\/\/jefferislab.org","Version":"1.8.1"},"nat.nblast":{"Author":"Greg Jefferis
and James Manton","Depends":"R (>= 2.15.1), rgl, methods, nat (>=
1.5.12)","Description":"Extends package nat (NeuroAnatomy Toolbox) by providing
a\ncollection of NBLAST-related functions.","Imports":"nabor, dendroextras, plyr,
spam","License":"GPL-
3","NeedsCompilation":"no","Package":"nat.nblast","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"bigmemory, ff, testthat","Title":"NeuroAnatomy
Toolbox (nat) Extension for Assessing Neuron\nSimilarity and
Clustering","Version":"1.5"},"nat.templatebrains":{"Author":"James Manton and
Gregory Jefferis","Depends":"R (>= 2.10), rgl, nat (>=
1.7.0)","Description":"Extends package 'nat' (NeuroAnatomy Toolbox) by providing
objects\nand functions for handling template brains.","Imports":"igraph, digest,
rappdirs","License":"GPL-
3","NeedsCompilation":"no","Package":"nat.templatebrains","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"testthat (>= 0.10),
git2r","Title":"NeuroAnatomy Toolbox ('nat') Extension for Handling
Template\nBrains","Version":"0.6.2"},"nat.utils":{"Author":"Gregory
Jefferis","Description":"Utility functions that may be of general interest but
are\nspecifically required by the 'NeuroAnatomy Toolbox' ('nat').
Includes\nfunctions to provide a basic make style system to update files based
on\ntimestamp information, file locking and 'touch' utility. Convenience\nfunctions
for working with file paths include 'abs2rel', 'split_path'\nand 'common_path'.
Finally there are utility functions for working with\n'zip' and 'gzip' files
including integrity tests.","License":"GPL-
3","NeedsCompilation":"no","Package":"nat.utils","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat (>= 0.9), roxygen2","Title":"File System
Utility Functions for 'NeuroAnatomy Toolbox'","Version":"0.5.1"},"naturalsort":
{"Author":"Kosei Abe","Description":"\nThe package provides functions related to
human natural ordering.\nIt handles adjacent digits in a character sequence as a
number\nso that natural sort function arranges a character vector by their numbers,
not digit characters.\nIt is typically seen when operating systems lists file
names.\nFor example, a sequence a-1.png, a-2.png, a-10.png looks naturally
ordered\nbecause 1 < 2 < 10 and natural sort algorithm arranges so whereas general
sort algorithms arrange\nit into a-1.png, a-10.png, a-2.png owing to their third
and fourth characters.","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"naturalsort","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Natural
Ordering","Version":"0.1.2"},"nbconvertR":{"Author":"Philipp
Angerer","Description":"\nCalls the 'Jupyter'\/'IPython' script 'nbconvert' to
create vignettes from notebooks.\nThose notebooks ('.ipynb' files) are files
containing rich text, code, and its output.\nCode cells can be edited and evaluated
interactively.\nSee <http:\/\/ipython.org\/notebook.html> for more
information.","License":"GPL-
3","NeedsCompilation":"no","Package":"nbconvertR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Vignette Engine Wrapping IPython
Notebooks","Version":"1.0.2"},"nbpMatching":{"Author":"Cole Beck [aut, cre], Bo Lu
[aut], Robert Greevy [aut]","Description":"Perform non-bipartite matching and
matched randomization. A\n\"bipartite\" matching utilizes two separate groups, e.g.
smokers being\nmatched to nonsmokers or cases being matched to controls. A \"non-
bipartite\"\nmatching creates mates from one big group, e.g. 100 hospitals
being\nrandomized for a two-arm cluster randomized trial or 5000 children who\nhave
been exposed to various levels of secondhand smoke and are being\npaired to form a
greater exposure vs. lesser exposure comparison. At the\ncore of a non-bipartite
matching is a N x N distance matrix for N potential\nmates. The distance between
two units expresses a measure of similarity or\nquality as mates (the lower the
better). The 'gendistance()' and\n'distancematrix()' functions assist in creating
this. The 'nonbimatch()'\nfunction creates the matching that minimizes the total
sum of distances\nbetween mates; hence, it is referred to as an \"optimal\"
matching. The\n'assign.grp()' function aids in performing a matched randomization.
Note\nbipartite matching can be performed using the prevent option
in\n'gendistance()'.","Imports":"methods, stats, Hmisc, MASS, utils","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"nbpMatching","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat","Title":"Functions for Optimal Non-
Bipartite
Matching","URL":"http:\/\/biostat.mc.vanderbilt.edu\/wiki\/Main\/MatchedRandomizati
on","Version":"1.5.0"},"ncappc":{"Author":"Chayan Acharya [aut, cre],\nAndrew C.
Hooker [aut],\nSiv Jonsson [aut],\nMats O. Karlsson [aut]","Depends":"R (>=
2.15.3), ggplot2, grid, gridExtra","Description":"A flexible tool is presented here
that can perform\n(i) traditional non-compartmental analysis (NCA) and\n(ii)
simulation-based posterior predictive checks for a population\npharmacokinetic (PK)
model using NCA metrics.","Imports":"scales, gtable, knitr, xtable, reshape2,
testthat, dplyr,\nreadr (>= 0.2.2), lazyeval","License":"GPL-
3","NeedsCompilation":"no","Package":"ncappc","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"NCA Calculation and Population PK Model
Diagnosis","Version":"0.2.1.1"},"ncbit":{"Author":"Jon Eastman","Depends":"R (>=
2.10)","Description":"making NCBI taxonomic data locally available and\nsearchable
as an R object","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ncbit","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"retrieve and build NBCI taxonomic
data","Version":"2013.03.29"},"ncdf.tools":{"Author":"Jannis v.
Buttlar","Depends":"R (>= 2.10.0)","Description":"Set of tools to simplify the
handling of 'NetCDF' files with the 'RNetCDF' package.\nMost functions are wrappers
of basic functions from the 'RNetCDF' package to easily run combinations of
these\nfunctions for frequently encountered tasks.","Imports":"RNetCDF, chron,
parallel, abind, plotrix, raster,\nRColorBrewer, JBTools","License":"GPL-
2","NeedsCompilation":"no","Package":"ncdf.tools","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Easier 'NetCDF' File
Handling","Version":"0.7.1.295"},"ncdf4":{"Author":"David Pierce
<dpierce@ucsd.edu>","Description":"Provides a high-level R interface to\ndata files
written using Unidata's\nnetCDF library (version 4 or earlier), which are binary
data files that are portable\nacross platforms and include metadata information in
addition to the data sets.\nUsing this package, netCDF files (either version
4\nor \"classic\" version 3) can be opened and data sets read in easily.\nIt is
also easy to create new netCDF dimensions, variables, and files,\nin either version
3 or 4 format, and manipulate existing netCDF files.\nThis package replaces the
former ncdf package, which only worked with\nnetcdf version 3 files. For various
reasons the names of the functions\nhave had to be changed from the names in the
ncdf package. The old ncdf package is still\navailable at the URL given below, if
you need to have backward compatibility.\nIt should be possible to have both the
ncdf and ncdf4 packages installed\nsimultaneously without a problem.\nHowever, the
ncdf package does not provide an interface for netcdf version 4
3)","NeedsCompilation":"yes","Package":"ncdf4","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Interface to Unidata netCDF (Version 4 or Earlier) Format
Data\nFiles","URL":"http:\/\/cirrus.ucsd.edu\/~pierce\/ncdf","Version":"1.15"},"ncd
f4.helpers":{"Author":"David Bronaugh <bronaugh@uvic.ca> for the Pacific Climate
Impacts\nConsortium (PCIC)","Depends":"R (>= 2.12.0)","Description":"This package
contains a collection of helper functions for dealing\nwith NetCDF files opened
using ncdf4.","Imports":"ncdf4, PCICt, abind","License":"LGPL-
2.1","NeedsCompilation":"no","Package":"ncdf4.helpers","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"RUnit, proj4","Title":"Helper functions for use
with the ncdf4 package","URL":"http:\/\/www.r-project.org","Version":"0.3-
3"},"ncf":{"Author":"Ottar N. Bjornstad <onb1@psu.edu>","Depends":"R (>=
2.8.0)","Description":"R functions for analyzing spatial (cross-)covariance:
the\nnonparametric (cross-)covariance, the spline correlogram, the\nnonparametric
phase coherence function, and related.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ncf","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Spatial Nonparametric Covariance
Functions","URL":"http:\/\/www.cidd.psu.edu\/people\/onb1","Version":"1.1-
6"},"ncg":{"Author":"Daniel Furtado Ferreira, Izabela Regina Cardoso de Oliveira
and\nFernando Henrique Toledo","Description":"Computes the noncentral gamma
function: pdf, cdf, quantile\nfunction and inverse for the noncentrality
parameter.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ncg","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Computes the noncentral gamma
function","URL":"www.dex.ufla.br\/~danielff\/r_resources.html","Version":"0.1.1"},"
ncvreg":{"Author":"Patrick Breheny [aut,cre], Sangin Lee
[ctb]","Description":"Efficient algorithms for fitting regularization paths for
linear or logistic regression models penalized by MCP or SCAD, with optional
additional L2 penalty.","License":"GPL-
2","NeedsCompilation":"yes","Package":"ncvreg","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"survival, parallel","Title":"Regularization Paths for
SCAD and MCP Penalized
Regression\nModels","URL":"http:\/\/myweb.uiowa.edu\/pbreheny\/publications\/Brehen
y2011.pdf","Version":"3.5-2"},"ndl":{"Author":"Antti Arppe [aut],\nPeter Hendrix
[aut],\nPetar Milin [aut],\nR. Harald Baayen [aut],\nTino Sering [aut, cre],\nCyrus
Shaoul [aut]","Depends":"R (>= 3.0.2)","Description":"Naive discriminative learning
implements learning and\nclassification models based on the Rescorla-Wagner
equations and their\nequilibrium equations.","Imports":"Rcpp (>= 0.11.0), MASS,
Hmisc","License":"GPL-
3","NeedsCompilation":"yes","Package":"ndl","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Naive Discriminative Learning","Version":"0.2.17"},"ndtv":
{"Author":"Skye Bender-deMoll [cre, aut],\nMartina Morris [ctb]","Depends":"R (>=
3.0), network (>= 1.13),networkDynamic (>=\n0.8),animation (>=
2.4),sna","Description":"Renders dynamic network data from 'networkDynamic' objects
as movies, interactive animations, or other representations of changing relational
structures and attributes.","Imports":"MASS, statnet.common, jsonlite,
base64","License":"GPL-3 + file
LICENSE","NeedsCompilation":"no","Package":"ndtv","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"tergm (>= 3.1), tsna, testthat, knitr,
htmlwidgets,\nscatterplot3d","Title":"Network Dynamic Temporal
Visualizations","URL":"http:\/\/statnet.org","Version":"0.9.0"},"neariso":
{"Author":"Holger Hoefling, Ryan Tibshirani, Robert Tibshirani","Depends":"R (>=
2.0.0)","Description":"This package implements a path algorithm for Near-
Isotonic\nRegression. For more details see the help files","License":"GPL-
2","NeedsCompilation":"yes","Package":"neariso","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Near-Isotonic Regression","Version":"1.0"},"needs":
{"Author":"Josh Katz [aut, cre]","Depends":"R (>= 3.2.0)","Description":"A simple
function for easier package loading and auto-
installation.","Imports":"utils","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"needs","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Attaches and Installs
Packages","URL":"https:\/\/github.com\/joshkatz\/needs","Version":"0.0.3"},"needy":
{"Author":"Ryan Grannell","Depends":"R (>= 2.14.0)","Description":"needy is a small
utility library designed to make testing function\ninputs less difficult. R is a
dynamically typed language, but larger\nprojects need input checking for scalabity.
needy offers a single\nfunction, require_a( ), which lets you specify the traits an
input object\nshould have, such as class, size, numerical properties or number
of\nparameters, while reducing boilerplate code and aiding
debugging.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"needy","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat,
combinat","Title":"needy","Version":"0.2"},"negenes":{"Author":"Karl W Broman
<kbroman@biostat.wisc.edu>","Depends":"R (>= 2.10.1),
stats","Description":"Estimating the number of essential genes in a genome on the
basis of data from a random transposon mutagenesis experiment, through the use of a
Gibbs sampler.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"negenes","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Estimating the Number of Essential Genes in a
Genome","URL":"https:\/\/github.com\/kbroman\/negenes","Version":"1.0-
3"},"neldermead":{"Author":"Sebastien Bihorel, Michael Baudin (author of the
original\nmodule)","Depends":"optimbase (>= 1.0-9), optimsimplex (>= 1.0-5),
methods","Description":"Provides several direct search optimization algorithms
based on the\nsimplex method. The provided algorithms are direct search algorithms,
i.e.\nalgorithms which do not use the derivative of the cost function. They
are\nbased on the update of a simplex. The following algorithms are available:
the\nfixed shape simplex method of Spendley, Hext and Himsworth
(unconstrained\noptimization with a fixed shape simplex), the variable shape
simplex method of\nNelder and Mead (unconstrained optimization with a variable
shape simplex\nmade), and Box's complex method (constrained optimization with a
variable\nshape simplex).","License":"CeCILL-
2","NeedsCompilation":"no","Package":"neldermead","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"R port of the Scilab neldermead module","Version":"1.0-
10"},"neotoma":{"Author":"Simon J. Goring [aut, cre], Gavin L. Simpson [aut],
Jeremiah P. Marsicek\n[ctb], Karthik Ram [aut], Luke Sosalla [ctb]","Depends":"R
(>= 2.10)","Description":"Access paleoecological datasets from the Neotoma
Paleoecological\nDatabase using the published API (http:\/\/api.neotomadb.org\/).
The functions\nin this package access various pre-built API functions and attempt
to return\nthe results from Neotoma in a usable format for researchers and the
public.","Imports":"plyr, reshape2, jsonlite, httr, xml2","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"neotoma","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat,
knitr","Title":"Access to the Neotoma Paleoecological Database Through
R","URL":"https:\/\/github.com\/ropensci\/neotoma","Version":"1.5.0"},"nephro":
{"Author":"Cristian Pattaro","Description":"Set of functions to estimate the
Glomerular Filtration Rate (GFR) using different biomarkers and other phenotypes of
interest for nephrology.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"nephro","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Biostatistics Utilities for
Nephrology","Version":"1.1"},"nestedRanksTest":{"Author":"Douglas G. Scofield [aut,
cre]","Depends":"R (>= 3.2.0)","Description":"Calculate a Mann-Whitney-Wilcoxon
test for a difference between treatment levels using nested ranks. This test can
be used when observations are structured into several groups and each group has
received both treatment levels. The p-value is determined via bootstrapping. The
nested ranks test is intended to be one possible mixed-model extension of the Mann-
Whitney-Wilcoxon test, for which treatment is a fixed effect and group membership
is a random effect.","License":"LGPL-3 | file
LICENSE","NeedsCompilation":"no","Package":"nestedRanksTest","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Suggests":"knitr (>= 0.5), testthat","Title":"Mann-
Whitney-Wilcoxon Test for Nested
Ranks","URL":"https:\/\/github.com\/douglasgscofield\/nestedRanksTest","Version":"0
.2"},"netClass":{"Author":"Yupeng Cun","Depends":"R (>= 2.14),
kernlab","Description":"netClass is an R package for network-based feature
(gene)\nselection for biomarkers discovery via integrating biological\ninformation.
This package adapts the following 5 algorithms\nfor classifying and predicting gene
expression data using prior\nknowledge: 1) average gene expression of pathway
(aep); 2)\npathway activities classification (PAC); 3) Hub network\nClassification
(hubc); 4) filter via top ranked genes (FrSVM);\n5) network smoothed t-statistic
(stSVM).","Imports":"AnnotationDbi, Matrix, ROCR, graph, igraph,
samr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"netClass","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"parallel, Biobase, KEGG.db,
pathClass","Title":"netClass: An R Package for Network-Based Biomarker
Discovery","Version":"1.2.1"},"netassoc":{"Author":"Benjamin Blonder, Naia Morueta-
Holme","Depends":"igraph, infotheo","Description":"Infers species associations from
community matrices. Uses local and (optional) regional-scale co-occurrence data by
comparing observed partial correlation coefficients between species to those
estimated from regional species distributions. Extends Gaussian graphical models to
a null modeling framework. Provides interface to a variety of inverse covariance
matrix estimation methods.","Imports":"rags2ridges, corpcor, huge,
vegan","License":"GPL-
3","NeedsCompilation":"no","Package":"netassoc","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Inference of Species Associations from Co-Occurrence
Data","Version":"0.6.2"},"netcoh":{"Author":"Tianxi Li, Elizaveta Levina, Ji
Zhu","Depends":"methods,Matrix","Description":"Model fitting procedures for
regression with network cohesion effects, when a network connecting sample
individuals is available in a regression problem. In the future, other commonly
used statistical models will be added, such as gaussian graphical
model.","Imports":"Rcpp (>= 0.11.5)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"netcoh","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Statistical Modeling with Network
Cohesion","Version":"0.1"},"netdiffuseR":{"Author":"George Vega Yon [aut, cre]
(Rewrite functions with Rcpp, plus new\nfeatures),\nStephanie Dyal [aut] (Package's
first version),\nTim Hayes [aut] (Package's first version),\nThomas Valente [aut,
cph] (R original code)","Depends":"R (>= 3.1.1)","Description":"Empirical
statistical analysis, visualization and simulation\nof network models of the
diffusion of innovations. The package implements\nalgorithms for calculating
network diffusion statistics such as transmission\nrate, hazard rates, exposure
models, network threshold levels, infectiousness\n(contagion), and susceptibility.
The package is inspired by work published\nin Valente, et al., (2015)
<DOI:10.1016\/j.socscimed.2015.10.001>;\nValente (1995) <ISBN:9781881303213>, Myers
(2000) <DOI:10.1086\/303110>,\nIyengar and others (2011)
<DOI:10.1287\/mksc.1100.0566>,\nBurt (1987) <DOI:10.1086\/228667>; among
others.","Imports":"Rcpp (>= 0.12.1), sna, Matrix, SparseM, methods,
grDevices,\ngraphics, stats, utils, boot","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"netdiffuseR","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"testthat, knitr, ape, RSiena, igraph,
survival","Title":"Network Analysis for Diffusion of
Innovations","URL":"https:\/\/github.com\/USCCANA\/netdiffuseR","Version":"1.16.2"}
,"netgen":{"Author":"Jakob Bossek [aut, cre]","Depends":"BBmisc (>= 1.6), mvtnorm
(>= 1.0-2), lhs (>= 0.10), checkmate\n(>= 1.5.1)","Description":"Methods for the
generation of a wide range of network geographies,\ne.g., grid networks or
clustered networks. Useful for the generation of\nbenchmarking instances for the
investigation of, e.g., Vehicle-Routing-Problems\nor Travelling Salesperson
Problems.","Imports":"ggplot2, lpSolve, igraph (>= 0.7.1), stringr (>=
LICENSE","NeedsCompilation":"no","Package":"netgen","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat","Title":"Network Generator for
Combinatorial Graph
Problems","URL":"https:\/\/github.com\/jakobbossek\/netgen","Version":"1.3"},"netgs
a":{"Author":"Ali Shojaie and Jing Ma","Depends":"cvTools, corpcor, glasso, glmnet,
igraph","Description":"The netgsa-package contains functions for carrying out
Network-based Gene Set Analysis by incorporating external information about
interactions among genes, as well as novel interactions learned from
2)","NeedsCompilation":"no","Package":"netgsa","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"MASS","Title":"Network-Based Gene Set
Analysis","URL":"http:\/\/arxiv.org\/abs\/1411.7919","Version":"2.0"},"netmeta":
{"Author":"Gerta RÃ¼cker [aut],\nGuido Schwarzer [aut, cre],\nUlrike Krahn
[aut],\nJochem KÃ¶nig [aut]","Depends":"meta (>= 4.0-0)","Description":"Network
meta-analysis following methods by RÃ¼cker (2012) and Krahn et al.
(2013).","Imports":"magic","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"netmeta","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"colorspace","Title":"Network Meta-Analysis using
Frequentist Methods","Version":"0.8-0"},"nets":{"Author":"Christian
Brownlees","Description":"Sparse VAR estimation based on LASSO.","Imports":"stats,
igraph","License":"GPL","NeedsCompilation":"yes","Package":"nets","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Title":"Network Estimation for Time
Series","URL":"https:\/\/github.com\/ctbrownlees\/R-Package-
nets","Version":"0.8"},"nettools":{"Author":"Michele Filosi [aut, cre], Roberto
Visintainer [aut], Samantha Riccadonna [aut], Giuseppe Jurman [ctb], Cesare
Furlanello [ctb]","Depends":"R (>= 2.14.1), methods","Description":"A collection of
network inference methods for co-expression networks, quantitative network
distances and a novel framework for network stability
analysis.","Imports":"parallel, rootSolve, dtw, WGCNA, minet, Matrix,
minerva,\ncombinat, igraph","License":"CC BY-NC-SA
4.0","NeedsCompilation":"no","Package":"nettools","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"A Network Comparison
Framework","Version":"1.0.1"},"network":{"Author":"Carter T. Butts [aut,
cre],\nDavid Hunter [ctb],\nMark Handcock [ctb],\nSkye Bender-deMoll
[ctb],\nJeffrey Horner [ctb]","Depends":"R (>= 2.10), utils","Description":"Tools
to create and modify network objects. The network class can represent a range of
relational data types, and supports arbitrary vertex\/edge\/graph
attributes.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"network","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"sna, statnet.common, testthat","Title":"Classes for
Relational Data","URL":"http:\/\/statnet.org\/","Version":"1.13.0"},"networkD3":
{"Author":"Christopher Gandrud [aut, cre],\nJ.J. Allaire [aut],\nKenton Russell
[aut],\nB.W. Lewis [ctb],\nKevin Kuo [ctb],\nCharles Sese [ctb],\nPeter Ellis
[ctb],\nJonathan Owen [ctb],\nJennifer Rogers [ctb]","Depends":"R (>=
3.0.0)","Description":"Creates 'D3' 'JavaScript' network, tree, dendrogram, and
Sankey\ngraphs from 'R'.","Enhances":"knitr, shiny","Imports":"htmlwidgets (>=
0.3.2)","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"networkD3","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"htmltools (>= 0.2.6), jsonlite","Title":"D3
JavaScript Network Graphs from R","URL":"http:\/\/cran.r-
project.org\/package=networkD3","Version":"0.2.8"},"networkDynamic":
{"Author":"Carter T. Butts [aut],\nAyn Leslie-Cook [aut],\nPavel N. Krivitsky
[aut],\nSkye Bender-deMoll [aut, cre],\nZack Almquist [ctb],\nDavid R. Hunter
[ctb],\nLi Wang [ctb],\nKirk Li [ctb],\nSteven M. Goodreau [ctb],\nJeffrey Horner
[ctb],\nMartina Morris [ctb]","Depends":"R (>= 3.0.0), network (>=
1.13)","Description":"Simple interface routines to facilitate the handling of
network objects with complex intertemporal data. This is a part of the \"statnet\"
suite of packages for network analysis.","Imports":"statnet.common,
3","NeedsCompilation":"yes","Package":"networkDynamic","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat","Title":"Dynamic Extensions for
Network
Objects","URL":"http:\/\/statnet.org","Version":"0.9.0"},"networkDynamicData":
{"Author":"Skye Bender-deMoll [cre],\nMartina Morris [ctb],\nLi Wang
[ctb],\nGerhard van de Bunt
[ctb],\nGoele Bossaert [ctb],\nNadine Meidert [ctb],\nSocioPatterns.org
[ctb],\nTore Opsahi [ctb],\nRadoslaw Michalski, (et al) [ctb],\nAllison Davis, (et.
al.) [ctb],\nC.E. Priebe, (et. al.) [ctb]","Depends":"R (>= 3.0),networkDynamic (>=
0.6), network (>= 1.9)","Description":"A collection of dynamic network data sets
from various sources and multiple authors represented as 'networkDynamic'-formatted
objects.","License":"GPL-3 + file
LICENSE","NeedsCompilation":"no","Package":"networkDynamicData","Repository":"http:
\/\/cran.csiro.au\/src\/contrib","Title":"Dynamic (Longitudinal) Network
Datasets","URL":"http:\/\/statnet.org","Version":"0.2.1"},"networkTomography":
{"Author":"Alexander W Blocker, Paul Koullick, Edoardo Airoldi","Depends":"R (>=
2.10.0),","Description":"networkTomography implements the methods developed and
evaluated in\nBlocker and Airoldi (2011) and Airoldi and Blocker (2012). These
include the\nauthors' own dynamic multilevel model with calibration based upon a
Gaussian\nstate-space model in addition to implementations of the methods of
Tebaldi &\nWest (1998; Poisson-Gamma model with MCMC sampling), Zhang et al.
(2002;\ntomogravity), Cao et al. (2000; Gaussian model with mean-variance
relation),\nand Vardi (1996; method of moments). Data from the 1router network of
Cao et\nal. (2000), the Abilene network of Fang et al. (2007), and the CMU
network\nof Blocker and Airoldi (2011) are included for testing and
reproducibility.","Imports":"coda (>= 0.11-3), igraph (>= 0.5), KFAS (>= 1.0),
limSolve (>=\n1.4), plyr, Rglpk (>= 0.3),","License":"LGPL-
2","NeedsCompilation":"yes","Package":"networkTomography","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Tools for network
tomography","URL":"https:\/\/github.com\/awblocker\/networkTomography","Version":"0
.3"},"networkreporting":{"Author":"Dennis Feehan, Matthew
Salganik","Description":"networkreporting has a collection of functions useful\nfor
producing estimates from data that were collected using network\nreporting
techniques like network scale-up, indirect sampling,\nnetwork reporting, and
sibling history.","Imports":"functional, ggplot2, plyr, reshape2,
stringr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"networkreporting","Repository":"http:\/
\/cran.csiro.au\/src\/contrib","Suggests":"knitr","Title":"Tools for using network
reporting
estimators","URL":"http:\/\/dfeehan.github.io\/networkreporting","Version":"0.0.1"}
,"networksis":{"Author":"Ryan Admiraal <R.Admiraal@murdoch.edu.au> and Mark S.
Handcock\n<handcock@ucla.edu>","Depends":"network","Description":"Tools to simulate
bipartite networks\/graphs with the\ndegrees of the nodes fixed and specified.
'networksis' is part\nof the 'statnet' suite of packages for network
2)","NeedsCompilation":"yes","Package":"networksis","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Simulate Bipartite Graphs with Fixed Marginals
Through\nSequential Importance
Sampling","URL":"http:\/\/statnet.org","Version":"2.1-3"},"neuRosim":
{"Author":"Marijke Welvaert with contributions from Joke Durnez,
Beatrijs\nMoerkerke, Yves Rosseel and Geert Verdoolaege","Depends":"R (>= 3.1.1),
deSolve","Description":"The package allows users to generate fMRI time series or 4D
data. Some high-level functions are created for fast data generation with only a
few arguments and a diversity of functions to define activation and noise. For more
advanced users it is possible to use the low-level functions and manipulate the
arguments.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"neuRosim","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Functions to Generate fMRI Data Including Activated
Data, Noise\nData and Resting State Data","Version":"0.2-12"},"neural":
{"Author":"Adam Nagy","Description":"RBF and MLP neural networks with graphical
user interface","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"neural","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Neural Networks","Version":"1.4.2.2"},"neuralnet":
{"Author":"Stefan Fritsch, Frauke Guenther <guenther@bips.uni-
bremen.de>,\nfollowing earlier work by Marc Suling","Depends":"R (>= 2.9.0),grid,
MASS","Description":"Training of neural networks using backpropagation,\nresilient
backpropagation with (Riedmiller, 1994) or without\nweight backtracking (Riedmiller
and Braun, 1993) or the\nmodified globally convergent version by Anastasiadis et
al.\n(2005). The package allows flexible settings through\ncustom-choice of error
and activation function. Furthermore,\nthe calculation of generalized weights
(Intrator O & Intrator\nN, 1993) is implemented.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"neuralnet","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Training of neural
networks","Version":"1.32"},"neuroblastoma":{"Author":"Toby Dylan
Hocking","Depends":"R (>= 2.10)","Description":"Annotated neuroblastoma copy number
profiles,\na benchmark data set for change-point detection
algorithms.","License":"GPL-
3","NeedsCompilation":"no","Package":"neuroblastoma","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Neuroblastoma copy number
profiles","Version":"1.0"},"neuroim":{"Author":"Bradley R. Buchsbaum","Depends":"R
(>= 3.0.0), stringr, hash, methods, stats, grDevices,
grid,\nutils","Description":"A collection of data structures that
represent\nvolumetric brain imaging data. The focus is on basic data handling for
3D\nand 4D neuroimaging data. In addition, there are function to read and
write\nNIFTI files and limited support for reading AFNI files.","Imports":"Matrix,
yaImpute, Rcpp, iterators, abind, assertthat, readr,\nrgl","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"neuroim","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"foreach, testthat, knitr","Title":"Data Structures
and Handling for Neuroimaging Data","Version":"0.0.6"},"ngram":{"Author":"Drew
Schmidt [aut, cre], Christian Heckendorf [aut]","Depends":"R (>= 2.14.0),
methods","Description":"This package offers utilities for creating,
displaying,\nand \"babbling\" n-grams. The babbler is a simple
Markov\nprocess.","License":"BSD 2-clause License + file
LICENSE","NeedsCompilation":"yes","Package":"ngram","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"An n-gram Babbler","Version":"1.1"},"ngramrr":
{"Author":"Chung-hong Chan <chainsawtiney@gmail.com>","Depends":"R (>=
3.0.0)","Description":"A simple n-gram (contiguous sequences of n items from
a\ngiven sequence of text) tokenizer to be used with the 'tm' package with
no\n'rJava'\/'RWeka' dependency.","Imports":"tm, tau","License":"GPL-
2","NeedsCompilation":"no","Package":"ngramrr","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat, magrittr","Title":"A Simple General Purpose
N-Gram
Tokenizer","URL":"https:\/\/github.com\/chainsawriot\/ngramrr","Version":"0.2.0"},"
ngspatial":{"Author":"John Hughes <hughesj@umn.edu> and Xiaohui Cui
<cuixx132@umn.edu>","Depends":"Rcpp, utils, batchmeans","Description":"ngspatial
provides tools for analyzing spatial data, especially\nnon-Gaussian areal data. The
current version supports the sparse spatial\ngeneralized linear mixed model of
Hughes and Haran (2013) and the centered\nautologistic model of Caragea and Kaiser
(2009).","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ngspatial","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"parallel","Title":"Fitting the centered
autologistic and sparse spatial generalized\nlinear mixed models for areal
data","URL":"http:\/\/www.biostat.umn.edu\/~johnh","Version":"1.0-5"},"nhanesA":
{"Author":"Christopher Endres","Depends":"R (>= 3.0.0)","Description":"Utility to
retrieve data from the National Health and Nutrition\nExamination Survey
(NHANES).","Imports":"stringr, Hmisc (>= 3.17-1), rvest, magrittr, xml2,
2)","NeedsCompilation":"no","Package":"nhanesA","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr, rmarkdown","Title":"NHANES Data
Retrieval","URL":"https:\/\/github.com\/cjendres1\/nhanes","Version":"0.6.3.1"},"nh
lscrapr":{"Author":"A.C. Thomas, Samuel L. Ventura","Depends":"R (>=
2.15.0)","Description":"Compiling the NHL Real Time Scoring System Database for
easy use in R","Imports":"RCurl, rjson, biglm, bitops","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"nhlscrapr","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Compiling the NHL Real Time Scoring System Database
for easy use\nin R","Version":"1.8"},"nicheROVER":{"Author":"Martin Lysy [aut,
cre],\nAshley D. Stasko [aut, ctb],\nHeidi K. Swanson [aut, ctb]","Depends":"R (>=
1.9.0), mvtnorm","Description":"This package uses a probabilistic method to
calculate niche\nregions and pairwise niche overlap using multidimensional niche
indicator\ndata (e.g., stable isotopes, environmental variables, etc.). The
niche\nregion is defined as the joint probability density function of
the\nmultidimensional niche indicators at a user-defined probability alpha\n(e.g.,
95%). Uncertainty is accounted for in a Bayesian framework, and the\nmethod can be
extended to three or more indicator dimensions. It provides\ndirectional estimates
of niche overlap, accounts for species-specific\ndistributions in multivariate
niche space, and produces unique and\nconsistent bivariate projections of the
multivariate niche region. A\nforthcoming article by Swanson et al. (Ecology,
2014) provides a detailed\ndescription of the methodology. See the package
vignette for a worked\nexample using fish stable isotope data.","License":"GPL-
2","NeedsCompilation":"no","Package":"nicheROVER","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr","Title":"(Niche) (R)egion and Niche (Over)lap
Metrics for\nMultidimensional Ecological Niches","Version":"1.0"},"nima":
{"Author":"Nima
Hejazi [aut, cre]","Depends":"R (>= 3.2.3)","Description":"Miscellaneous R
functions developed over the course of statistical\nresearch. These include
utilities that supplement the existing\nidiosyncrasies of R; extend plotting
functionality and aesthetics;\nprovide alternative presentations of matrix
decompositions; extend\ntypes of random variables supported for simulation; extend
access\nto command line tools and system information, making work on
remote\nsystems easier.","Imports":"plyr, utils, stats, survival, gridExtra,
assertthat, ggplot2,\ngrid","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"nima","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"devtools, roxygen2, testthat","Title":"Nima Hejazi's
Miscellaneous R
Code","URL":"https:\/\/github.com\/nhejazi\/nima","Version":"0.3.0"},"nivm":
{"Author":"Michael P. Fay","Depends":"stats, bpcp,
ssanv","Description":"Noninferiority tests for difference in failure rates at a
prespecified control rate or prespecified time.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"nivm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Noninferiority Tests with Variable
Margins","Version":"0.3"},"nlWaldTest":{"Author":"Oleh Komashko","Depends":"R (>=
3.0.2)","Description":"Wald Test for nonlinear restrictions on model parameters and
confidence\nintervals for nonlinear functions of parameters using delta-method.
Applicable\nafter ANY model, provided parameters estimates and their covariance
matrix are\navailable.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"nlWaldTest","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Wald Test of Nonlinear Restrictions and Nonlinear
CI","Version":"1.1.3"},"nleqslv":{"Author":"Berend Hasselman","Description":"Solve
a system of nonlinear equations using a Broyden or a Newton method\nwith a choice
of global strategies such as line search and trust region.\nThere are options for
using a numerical or user supplied Jacobian,\nfor specifying a banded numerical
Jacobian and for allowing\na singular or ill-conditioned Jacobian.","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"nleqslv","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Solve Systems of Nonlinear
Equations","Version":"3.0"},"nlme":{"Author":"JosÃ© Pinheiro [aut] (S
version),\nDouglas Bates [aut] (up to 2007),\nSaikat DebRoy [ctb] (up to
2002),\nDeepayan Sarkar [ctb] (up to 2005),\nEISPACK authors [ctb]
(src\/rs.f),\nSiem Heisterkamp [ctb] (Author fixed sigma),\nBert Van Willigen [ctb]
(Programmer fixed sigma),\nR-core [aut, cre]","Depends":"graphics, stats, R (>=
3.0.2)","Description":"Fit and compare Gaussian linear and nonlinear mixed-effects
models.","Imports":"utils, lattice","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"nlme","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"Hmisc, MASS","Title":"Linear and Nonlinear Mixed Effects
Models","Version":"3.1-126"},"nlmeODE":{"Author":"Christoffer W. Tornoe
<ctornoe@gmail.com>","Depends":"R (>= 2.6.0), deSolve, nlme,
lattice","Description":"This package combines the odesolve and nlme packages
for\nmixed-effects modelling using differential equations.","License":"LGPL (>=
2.1)","NeedsCompilation":"no","Package":"nlmeODE","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Non-linear mixed-effects modelling in nlme using
differential\nequations","URL":"http:\/\/www.cran.r-
project.org","Version":"1.1"},"nlmeU":{"Author":"Andrzej Galecki
<agalecki@umich.edu>, Tomasz
Burzykowski\n<tomasz.burzykowski@uhasselt.be>","Depends":"R (>=
2.14.2)","Description":"nlmeU: Datasets and utility functions enhancing
functionality of nlme package. Datasets, functions and scripts are described in
book titled 'Linear Mixed-Effects Models:\nA Step-by-Step Approach' by Galecki and
Burzykowski (2013). Package is under development.","Imports":"nlme","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"nlmeU","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"reshape, WWGbook, lattice, ellipse, roxygen2,
testthat","Title":"Datasets and utility functions enhancing functionality of
nlme\npackage","URL":"http:\/\/www-
personal.umich.edu\/~agalecki\/","Version":"0.70-3"},"nlmrt":{"Author":"John C.
Nash [aut, cre]","Depends":"R (>= 2.15.0)","Description":"Replacement for nls()
tools for working with nonlinear least squares problems.\nThe calling structure is
similar to, but much simpler than, that of the nls()\nfunction. Moreover, where
nls() specifically does NOT deal with small or zero\nresidual problems, nlmrt is
quite happy to solve them. It also attempts to be\nmore robust in finding
solutions, thereby avoiding 'singular gradient' messages\nthat arise in the Gauss-
Newton method within nls(). The Marquardt-Nash approach\nin nlmrt generally works
more reliably to get a solution, though this may be\none of a set of possibilities,
and may also be statistically unsatisfactory.\nAdded print and summary as of August
28, 2012.","License":"GPL-
2","NeedsCompilation":"no","Package":"nlmrt","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"minpack.lm, optimx, Rvmmin, Rcgmin,
numDeriv","Title":"Functions for Nonlinear Least Squares
Solutions","Version":"2016.3.2"},"nlnet":{"Author":"Haodong Liu, Tianwei
Yu","Description":"It includes three methods: K-profiles clustering, non-linear
network reconstruction, and non-linear hierarchical clustering.","Imports":"TSP,
igraph, fdrtool, coin, methods, graphics, stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"nlnet","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Nonlinear Network Reconstruction and Clustering Based on
DCOL\n(Distance Based on Conditional Ordered List)","Version":"1.0"},"nloptr":
{"Author":"Jelmer Ypma <uctpjyy@ucl.ac.uk>, with contributions by\nHans W. Borchers
<hwborchers@googlemail.com> and\nDirk Eddelbuettel
<edd@debian.org>","Description":"\nnloptr is an R interface to NLopt. NLopt is a
free\/open-source library for\nnonlinear optimization, providing a common interface
for a number of\ndifferent free optimization routines available online as well as
original\nimplementations of various other algorithms.\nSee http:\/\/ab-
initio.mit.edu\/wiki\/index.php\/NLopt_Introduction for more\ninformation on the
available algorithms. During installation on Unix the\nNLopt code is downloaded and
compiled from the NLopt website.","License":"LGPL-
3","NeedsCompilation":"yes","Package":"nloptr","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat (>= 0.8.1)","Title":"R interface to
NLopt","Version":"1.0.4"},"nlreg":{"Author":"S original by Alessandra R. Brazzale
<alessandra.brazzale@unipd.it>\nand Ruggero Bellio <ruggero.bellio@uniud.it>. R
port by Alessandra R.\nBrazzale <alessandra.brazzale@unipd.it>, following earlier
work by\nDouglas Bates.","Depends":"R (>= 3.0.0), statmod,
survival","Description":"Likelihood inference based on higher order
approximations\nfor nonlinear models with possibly non constant
variance","License":"GPL (>= 2) | file
LICENCE","NeedsCompilation":"no","Package":"nlreg","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"boot, cond, csampling, marg","Title":"Higher Order
Inference for Nonlinear Heteroscedastic Models","URL":"http:\/\/www.r-project.org,
http:\/\/statwww.epfl.ch\/AA\/","Version":"1.2-2"},"nlrr":{"Author":"Yiqiang Zhan
[aut, cre]","Depends":"R (>= 3.2.2)","Description":"Estimate the non-linear odds
ratio and plot it against a continuous exposure.","Imports":"rms,
Hmisc","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"nlrr","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Non-Linear Relative Risk Estimation and
Plotting","Version":"0.1"},"nls2":{"Author":"G.
Grothendieck","Depends":"proto","Description":"Adds brute force and multiple
starting values to nls.","License":"GPL-
2","NeedsCompilation":"no","Package":"nls2","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"nlstools","Title":"Non-linear regression with brute
force","URL":"http:\/\/nls2.googlecode.com","Version":"0.2"},"nlsMicrobio":
{"Author":"Florent Baty <florent.baty@gmail.com> and Marie-Laure\nDelignette-Muller
<marielaure.delignettemuller@vetagro-sup.fr>","Depends":"stats,
nlstools","Description":"Data sets and nonlinear regression models dedicated to
predictive microbiology","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"nlsMicrobio","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Nonlinear regression in predictive
microbiology","Version":"0.0-1"},"nlsem":{"Author":"Nora Umbach [aut,
cre],\nKatharina Naumann [aut],\nDavid Hoppe [aut],\nHolger Brandt [aut],\nAugustin
Kelava [ctb],\nBernhard Schmitz [ctb]","Depends":"R (>= 3.1.0), gaussquad,
mvtnorm","Description":"Estimation of structural equation models with nonlinear
effects\nand underlying nonnormal distributions.","Imports":"nlme","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"nlsem","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"lavaan","Title":"Fitting Structural Equation Mixture
Models","Version":"0.6"},"nlsmsn":{"Author":"Aldo Garay <amedina@ime.usp.br>,
Marcos Prates\n<marcosop@est.ufmg.br> and Victor
Lachos\n<hlachos@ime.unicamp.br>","Depends":"R (>= 2.10.0)","Description":"Fit
univariate non-linear scale mixture of\nskew-normal(NL-SMSN)
regression.","License":"GPL (>=
3.0)","NeedsCompilation":"no","Package":"nlsmsn","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Fitting nonlinear models with scale mixture of skew-
normal\ndistributions","Version":"0.0-4"},"nlstools":{"Author":"Florent Baty
<florent.baty@gmail.com> and Marie-Laure\nDelignette-Muller
<marielaure.delignettemuller@vetagro-sup.fr>,\nwith contributions from Sandrine
Charles, Jean-Pierre Flandrois,\nand Christian
Ritz","Depends":"stats","Description":"Several tools for assessing the
quality of fit of a\ngaussian nonlinear model are provided.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"nlstools","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Tools for Nonlinear Regression Analysis","Version":"1.0-
2"},"nlt":{"Author":"Marina Knight, Matt Nunes","Depends":"EbayesThresh, adlift (>=
1.3)","Description":"Uses a modified lifting algorithm on which it builds
the\nnondecimated lifting transform. It has applications in
wavelet\nshrinkage.","License":"GPL","NeedsCompilation":"no","Package":"nlt","Repos
itory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"A nondecimated lifting
transform for signal denoising","Version":"2.1-3"},"nlts":{"Author":"Ottar N.
Bjornstad <onb1@psu.edu>","Depends":"R (>= 2.2.0), locfit (>= 1.5.3),
acepack","Description":"R functions for (non)linear time series analysis. A
core\ntopic is order estimation through cross-
validation.","License":"GPL","NeedsCompilation":"no","Package":"nlts","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Title":"(non)linear time series
analysis","URL":"http:\/\/onb.ent.psu.edu\/onb1\/R","Version":"0.2-0"},"nmcdr":
{"Author":"Changliang Zou, Lancezhange","Depends":"CDFt","Description":"Without the
need to know the true number of change-points in advance,\nthis package provides a
function for detecting multiple change-points\nusing a non-parametric maximum
likelihood approach.","License":"GPL-
2","NeedsCompilation":"yes","Package":"nmcdr","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Non-parametric Multiple Change-points
Detection","Version":"0.3.0"},"nnet":{"Author":"Brian Ripley [aut, cre,
cph],\nWilliam Venables [cph]","Depends":"R (>= 2.14.0), stats,
utils","Description":"Software for feed-forward neural networks with a
single\nhidden layer, and for multinomial log-linear models.","License":"GPL-2 |
GPL-
3","NeedsCompilation":"yes","Package":"nnet","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"MASS","Title":"Feed-Forward Neural Networks and
Multinomial Log-Linear
Models","URL":"http:\/\/www.stats.ox.ac.uk\/pub\/MASS4\/","Version":"7.3-
12"},"nnetpredint":{"Author":"Xichen Ding
<rockingdingo@gmail.com>","Description":"Computing prediction intervals of neural
network models (e.g.backpropagation) at certain confidence level. It can take the
output from models trained by other packages like 'nnet', 'neuralnet', 'RSNNS',
etc.","Imports":"stats, RSNNS","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"nnetpredint","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"MASS, nnet, neuralnet","Title":"Prediction
Intervals of Multi-Layer Neural Networks","Version":"1.2"},"nnlasso":
{"Author":"Baidya Nath Mandal <mandal.stat@gmail.com> and Jun Ma
<jun.ma@mq.edu.au>","Depends":"R (>= 3.2.2)","Description":"Estimates of
coefficients of lasso penalized linear regression and generalized linear models
subject to non-negativity constraints on the parameters using multiplicative
iterative algorithm. Entire regularization path for a sequence of lambda values can
be obtained. Functions are available for creating plots of regularization path,
cross validation and estimating coefficients at a given lambda value. There is also
provision for obtaining standard error of coefficient estimates.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"nnlasso","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Non-Negative Lasso and Elastic Net Penalized Generalized
Linear\nModels","Version":"0.3"},"nnls":{"Author":"Katharine M. Mullen and Ivo H.
M. van Stokkum","Description":"An R interface to the Lawson-Hanson implementation
of an\nalgorithm for non-negative least squares (NNLS). Also allows\nthe
combination of non-negative and non-positive constraints.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"nnls","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"The Lawson-Hanson algorithm for non-negative least
squares\n(NNLS)","Version":"1.4"},"nodeHarvest":{"Author":"Nicolai
Meinshausen","Description":"Node harvest is a simple interpretable tree-like
estimator for high-dimensional regression and classification. A few nodes are
selected from an initially large ensemble of nodes, each associated with a positive
weight. New observations can fall into one or several nodes and predictions are the
weighted average response across all these groups. The package offers visualization
of the estimator. Predictions can return the nodes a new observation fell into,
along with the mean response of training observations in each node, offering a
simple explanation of the prediction.","Imports":"graphics,
quadprog,randomForest","License":"GPL-
3","NeedsCompilation":"no","Package":"nodeHarvest","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Node Harvest for Regression and
Classification","URL":"http:\/\/stat.ethz.ch\/~nicolai","Version":"0.7-3"},"nodiv":
{"Author":"Michael Krabbe Borregaard","Depends":"R (>= 3.0)","Description":"An
implementation of the nodiv algorithm, see Borregaard, M.K., Rahbek, C., Fjeldsaa,
J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of
species distributions. Methods in Ecology and Evolution 5(11): 1225-1235.
<DOI:10.1111\/2041-210X.12283>. Package for phylogenetic analysis of species
distributions. The main function goes through each node in the phylogeny, compares
the distributions of the two descendant nodes, and compares the result to a null
model. This highlights nodes where major distributional divergence have occurred.
The distributional divergence for these nodes is mapped using the SOS
statistic.","Imports":"picante, raster, ape, sp, vegan, utils","License":"GPL-
3","NeedsCompilation":"no","Package":"nodiv","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"RColorBrewer, parallel, testthat,
colorspace","Title":"Compares the Distribution of Sister Clades Through a
Phylogeny","Version":"1.1.4"},"noia":{"Author":"Arnaud Le Rouzic (2007-2014), Arne
B. Gjuvsland (2010), Olivier Ariste (2010)","Depends":"stats","Description":"The
NOIA model, as described extensively in Alvarez-Castro & Carlborg (2007), is a
framework facilitating the estimation of genetic effects and genotype-to-phenotype
maps. This package provides the basic tools to perform linear and multilinear
regressions from real populations (provided the phenotype and the genotype of every
individuals), estimating the genetic effects from different reference points, the
genotypic values, and the decomposition of genetic variances in a multi-locus, 2
alleles system. This package is presented in Le Rouzic & Alvarez-Castro
2","NeedsCompilation":"no","Package":"noia","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Implementation of the Natural and Orthogonal InterAction
(NOIA)\nmodel","Version":"0.97.1"},"nomclust":{"Author":"Sulc Zdenek
<zdenek.sulc@vse.cz>, Rezankova Hana <hana.rezankova@vse.cz>","Depends":"cluster,
dummies","Description":"Package for hierarchical clustering of objects
characterized by nominal variables.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"nomclust","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Hierarchical Nominal Clustering
Package","Version":"0.91.1010"},"noncensus":{"Author":"John A. Ramey
<johnramey@gmail.com>","Depends":"R (>= 2.14)","Description":"A collection of
various regional information determined by the\nU.S. Census Bureau along with
demographic data.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"noncensus","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"U.S. Census Regional and Demographic
Data","URL":"https:\/\/github.com\/ramey\/noncensus,
http:\/\/ramhiser.com","Version":"0.1"},"noncompliance":{"Author":"Wen Wei Loh
[aut, cre],\nThomas S. Richardson [aut]","Description":"A finite-population
significance test of the 'sharp' causal null hypothesis that\ntreatment exposure X
has no effect on final outcome Y, within the principal stratum of Compliers.\nA
generalized likelihood ratio test statistic is used, and the resulting p-value is
exact.\nCurrently, it is assumed that there are only Compliers and Never Takers in
the population.","Imports":"data.table (>= 1.9.4), Rcpp (>= 0.12.1)","License":"GPL
(>=
3)","NeedsCompilation":"yes","Package":"noncompliance","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat","Title":"Causal Inference in the
Presence of Treatment Noncompliance\nUnder the Binary Instrumental Variable
Model","URL":"https:\/\/www.stat.washington.edu\/~wloh\/","Version":"0.2.2"},"nonli
nearTseries":{"Author":"Constantino A. Garcia [aut, cre],\nGunther Sawitzki
[ctb]","Depends":"Matrix, rgl, tseries, TSA, Rcpp (>= 0.10.5), graphics,
stats","Description":"Functions for nonlinear time series analysis. This package
permits\nthe computation of the most-used nonlinear
statistics\/algorithms\nincluding generalized correlation dimension, information
dimension,\nlargest Lyapunov exponent, sample entropy and
Recurrence\nQuantification Analysis (RQA), among others. Basic routines\nfor
surrogate data testing are also included. Part of this work\nwas based on the book
\"Nonlinear time series analysis\" by\nHolger Kantz and Thomas Schreiber (ISBN:
9780521529020).","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"nonlinearTseries","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"plot3D, knitr,","Title":"Nonlinear Time
Series Analysis","Version":"0.2.3"},"nonnest2":{"Author":"Edgar Merkle and Dongjun
You","Depends":"R (>= 3.0.0)","Description":"Testing non-nested models via theory
supplied by Vuong (1989).\nIncludes tests of model distinguishability and of model
fit that can be applied\nto both nested and non-nested models. Also includes
functionality to obtain\nconfidence intervals associated with AIC and BIC. This
material is based on work\nsupported by the National
Science Foundation under Grant Number SES-1061334.","Imports":"CompQuadForm,
mvtnorm, lavaan (>= 0.5-20), sandwich","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"nonnest2","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr, testthat","Title":"Tests of Non-Nested
Models","Version":"0.3"},"nonparaeff":{"Author":"Dong-hyun Oh
<oh.donghyun77@gmail.com>, with Dukrok Suh","Depends":"R (>= 1.8.0), lpSolve,
gdata, Hmisc, rms, geometry, psych, pwt","Description":"This package contains
functions for measuring efficiency\nand productivity of decision making units
(DMUs) under the\nframework of Data Envelopment Analysis (DEA) and
its\nvariations.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"nonparaeff","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"gtools","Title":"Nonparametric Methods for
Measuring Efficiency and Productivity","URL":"http:\/\/www.r-
project.org","Version":"0.5-8"},"nonrandom":{"Author":"Susanne Stampf [cre,
aut]","Depends":"lme4","Description":"This package offers a comprehensive data
analysis if\nstratification and matching by the propensity score is done.\nSeveral
functions are implemented, starting from the selection\nof the propensity score
model up to estimating propensity score\nbased treatment or exposure effects. All
functions can be\napplied separately as well as
combined.","License":"GPL","NeedsCompilation":"no","Package":"nonrandom","Repositor
y":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"colorspace","Title":"Stratifi
cation and matching by the propensity score","Version":"1.42"},"nontarget":
{"Author":"Martin Loos","Depends":"enviPat(>= 1.9), nontargetData(>= 1.1), mgcv(>=
1.7-22)","Description":"Screening a HRMS data set for peaks related by (1) isotope
patterns, (2) different adducts of the same molecule and\/or (3) homologue series.
The resulting isotopic pattern and adduct groups can then be combined to so-called
components, with homologue series information attached. Also allows plotting and
filtering HRMS data for mass defects, frequent m\/z distances and components vs.
non-components.","License":"GPL-
3","NeedsCompilation":"yes","Package":"nontarget","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Detecting Isotope, Adduct and Homologue Relations in
LC-MS Data","Version":"1.8"},"nontargetData":{"Author":"Martin Loos, Francesco
Corona","Depends":"R (>= 2.10)","Description":"Data sets for isotope pattern
grouping of LC-HRMS peaks with package nontarget. Based on a vast set of unique
PubChem molecular formulas, quantized (a) m\/z, (b) m\/z differences, (c) intensity
ratios and (d) marker centroids of simulated centroid pairs are listed for
different instrument resolutions.","License":"GPL-
3","NeedsCompilation":"no","Package":"nontargetData","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Quantized simulation data of isotope pattern
centroids","Version":"1.1"},"nopp":{"Author":"Luigi Curini, Stefano M.
Iacus","Depends":"R (>= 2.10), mlogit","Description":"Estimation of
party\/candidate ideological positions\nthat correspond to a Nash equilibrium along
a\none-dimensional space.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"nopp","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Nash Optimal Party Positions","Version":"1.0.6"},"nor1mix":
{"Author":"Martin Mächler","Description":"Onedimensional Normal Mixture Models
Classes, for, e.g.,\ndensity estimation or clustering algorithms research and
teaching;\nproviding the widely used Marron-Wand densities. Now fitting to
data\nby ML (Maximum Likelihood) or EM estimation.","Imports":"stats,
2)","NeedsCompilation":"no","Package":"nor1mix","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"cluster","Title":"Normal (1-d) Mixture Models (S3
Classes and Methods)","Version":"1.2-1"},"nordklimdata1":{"Author":"Heikki
Tuomenvirta [aut],\nAchim Drebs [aut],\nEirik FÃ¸rland [aut],\nOle Einar Tveito
[aut],\nHans Alexandersson [aut],\nEllen Vaarby Laursen [aut],\nTrausti JÃ³nsson
[aut],\nJose Gama [cre]","Depends":"R (>= 2.10)","Description":"The Nordklim
dataset 1.0 is a unique and useful achievement for climate\nanalysis. It includes
observations of twelve different climate elements from\nmore than 100 stations in
the Nordic region, in time span over 100 years.\nThe project contractors were
NORDKLIM\/NORDMET on behalf of the National\nmeteorological services in Denmark
(DMI), Finland (FMI), Iceland (VI),\nNorway (DNMI) and Sweden
(SMHI).","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"nordklimdata1","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Dataset for Climate Analysis with Data from the
Nordic Region","Version":"1.2"},"norm":{"Author":"Ported to R by Alvaro A. Novo
<alvaro@novo-online.net>.\nOriginal by Joseph L. Schafer
<jls@stat.psu.edu>.","Description":"Analysis of multivariate normal datasets with
missing\nvalues","License":"file
LICENSE","NeedsCompilation":"yes","Package":"norm","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Analysis of multivariate normal datasets with missing
values","URL":"http:\/\/www.stat.psu.edu\/~jls\/misoftwa.html#aut","Version":"1.0-
9.5"},"normalp":{"Author":"Angelo M. Mineo <angelo.mineo@unipa.it>","Depends":"R
(>= 1.5.0)","Description":"Collection of utilities referred to Exponential Power
distribution,\nalso known as General Error Distribution (see Mineo, A.M. and
Ruggieri, M. (2005), A software Tool for the Exponential Power Distribution: The
normalp package. In Journal of Statistical Software, Vol. 12, Issue
4)","License":"GPL","NeedsCompilation":"no","Package":"normalp","Repository":"http:
\/\/cran.csiro.au\/src\/contrib","Title":"Routines for Exponential Power
Distribution","URL":"http:\/\/www.r-project.org,
http:\/\/dssm.unipa.it\/elio","Version":"0.7.0"},"normtest":{"Author":"Ilya
Gavrilov, Ruslan Pusev","Description":"Tests for the composite hypothesis of
normality","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"normtest","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Tests for Normality","Version":"1.1"},"normwhn.test":
{"Author":"Peter Wickham","Description":"Includes Omnibus Univariate and
Multivariate Normality\nTests (See Doornik and Hansen (1994)). One variation allows
for\nthe possibility of weak dependence rather than independence in\nthe
variable(s). Also included is an univariate white noise\ntest where the null
hypothesis is \"white noise\" rather than\nstrict \"white noise\".","License":"GPL-
3","NeedsCompilation":"no","Package":"normwhn.test","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Normality and White Noise
Testing","Version":"1.0"},"nortest":{"Author":"Juergen Gross [aut],\nUwe Ligges
[aut, cre]","Description":"Five omnibus tests for testing the composite hypothesis
of\nnormality.","Imports":"stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"nortest","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Tests for Normality","Version":"1.0-4"},"nose":
{"Author":"originally written by Subbiah M <sisufive@gmail.com> packaged\nby
Sumathi R with considerable contributions by Srinivasan M R","Description":"The
nose package consists of a collection of three\nfunctions for classifying
sparseness in typical 2 x 2 data sets\nwith at least one cell should have zero
count. These functions\nare based on the three widely applied summary measures for
2 x\n2 categorical data viz, Risk Difference (RD), Relative Risk\n(RR), Odds Ratio
(OR). This package helps to identify suitable\ncontinuity correction for zero cells
when a multi centre\nanalysis or a meta analysis is carried out. Further, it can
be\nconsidered as a tool for sensitivity analysis for adding a\ncontinuity
correction and to identify the presence of Simpson's\nparadox.","License":"GPL-
2","NeedsCompilation":"no","Package":"nose","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"nose Package for R","Version":"1.0"},"notifyR":
{"Author":"Torben Engelmeyer","Depends":"R (>= 2.15.0), RCurl,
rjson","Description":"This Package provides a connection to the pushover.net
API\nto send push notification to your smartphone directly from R.\n(ACCOUNT
REQUIRED!)","License":"GPL-
2","NeedsCompilation":"no","Package":"notifyR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Send push notifications to your smartphone via
pushover.net\n(ACCOUNT
REQUIRED!)","URL":"http:\/\/www.engelmeyer.de\/notifyR","Version":"1.02"},"novelist
":{"Author":"Na Huang and Piotr Fryzlewicz","Depends":"R (>=
3.0.2)","Description":"Estimate Large correlation and covariance matrices and their
inverses using\nintegration of the sample and thresholded correlation and
covariance estimators.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"novelist","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"NOVEL Integration of the Sample and Thresholded
(NOVELIST)\nCorrelation and Covariance Estimators","Version":"1.0"},"noweb":
{"Author":"Terry Therneau","Depends":"R (>= 3.0.0)","Description":"The noweb system
for source code, implemented in R.","License":"LGPL-
2","NeedsCompilation":"no","Package":"noweb","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Noweb system for R","Version":"1.0-4"},"np":
{"Author":"Jeffrey S. Racine [aut, cre],\nTristen Hayfield
[aut]","Description":"This package provides a variety of nonparametric (and
semiparametric) kernel methods that seamlessly handle a mix of continuous,
unordered, and ordered factor data types. We would like to gratefully acknowledge
support from the Natural Sciences and Engineering Research Council of Canada
(NSERC:www.nserc.ca), the Social Sciences and Humanities Research Council of Canada
(SSHRC:www.sshrc.ca), and the Shared Hierarchical Academic Research Computing
Network (SHARCNET:www.sharcnet.ca).","Imports":"boot, cubature,
stats","License":"GPL","NeedsCompilation":"yes","Package":"np","Repository":"http:\
/\/cran.csiro.au\/src\/contrib"
,"Suggests":"quantreg, MASS","Title":"Nonparametric kernel smoothing methods for
mixed data types","URL":"https:\/\/github.com\/JeffreyRacine\/R-Package-
np\/","Version":"0.60-2"},"npIntFactRep":{"Author":"Jos
Feys","Depends":"ez","Description":"Returns nonparametric aligned rank tests for
the interaction in two-way factorial designs, on R data sets with repeated measures
in 'wide' format. Five ANOVAs tables are reported. A PARAMETRIC one on the original
data, one for a CHECK upon the interaction alignments, and three aligned rank
tests: one on the aligned REGULAR, one on the FRIEDMAN, and one on the KOCH ranks.
In these rank tests, only the resulting values for the interaction are
relevant.","Imports":"plyr, stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"npIntFactRep","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Nonparametric Interaction Tests for Factorial
Designs with\nRepeated Measures","Version":"1.5"},"nparACT":{"Author":"Christine
Blume <christine.blume@sbg.ac.at>\nNayantara Santhi <n.santhi@surrey.ac.uk>\nManuel
Schabus <manuel.schabus@sbg.ac.at>","Description":"Computes interday stability
(IS), intraday variability (IV) & the relative amplitude (RA) from actigraphy data
as described in van Someren et al. (1999). Additionally, it also computes L5 (i.e.
the 5 hours with lowest average actigraphy amplitude) and M10 (the 10 hours with
highest average amplitude) as well as the respective start times. The flex versions
will also compute the L-value for a user-defined number of minutes. IS describes
the strength of coupling of a rhythm to supposedly stable zeitgebers. It varies
between 0 (Gaussian Noise) and 1 for perfect IS. IV describes the fragmentation of
a rhythm, i.e. the frequency and extent of transitions between rest and activity.
It is near 0 for a perfect sine wave, about 2 for Gaussian noise and may be even
higher when a definite ultradian period of about 2 hrs is present. RA is the
relative amplitude of a rhythm. Note that to obtain reliable results, actigraphy
data should cover a reasonable number of days.","Imports":"ggplot2, grid, stringr,
2","NeedsCompilation":"no","Package":"nparACT","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Non-Parametric Measures of Actigraphy
Data","URL":"http:\/\/www.r-project.org","Version":"0.3"},"nparLD":
{"Author":"Kimihiro Noguchi <kinoguchi@ucdavis.edu>, Mahbub
Latif\n<mlatif@gwdg.de>, Karthinathan Thangavelu <kthanga@gwdg.de>,\nFrank
Konietschke <fkoniet@gwdg.de>, Yulia R. Gel\n<ygl@math.uwaterloo.ca>, Edgar
Brunner\n<brunner@ams.med.uni-goettingen.de>","Depends":"R (>= 2.6.0),
MASS","Description":"The package \"nparLD\" is designed to perform
nonparametric\nanalysis of longitudinal data in factorial
experiments.\nLongitudinal data are those which are collected from the
same\nsubjects over time, and they frequently arise in biological\nsciences.
Nonparametric methods do not require distributional\nassumptions, and are
applicable to a variety of data types\n(continuous, discrete, purely ordinal, and
dichotomous). Such\nmethods are also robust with respect to outliers and for
small\nsample sizes.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"nparLD","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Nonparametric Analysis of Longitudinal Data in
Factorial\nExperiments","Version":"2.1"},"nparcomp":{"Author":"Frank
Konietschke","Depends":"multcomp, mvtnorm","Description":"With this package, it is
possible to compute nonparametric simultaneous confidence intervals for relative
contrast effects in the unbalanced one way layout. Moreover, it computes
simultaneous p-values. The simultaneous confidence intervals can be computed using
multivariate normal distribution, multivariate t-distribution with a Satterthwaite
Approximation of the degree of freedom or using multivariate range preserving
transformations with Logit or Probit as transformation function. 2 sample
comparisons can be performed with the same methods described above. There is no
assumption on the underlying distribution function, only that the data have to be
at least ordinal
numbers.","License":"GPL","NeedsCompilation":"no","Package":"nparcomp","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Title":"Multiple Comparisons and
Simultaneous Confidence Intervals","Version":"2.6"},"npbr":{"Author":"Abdelaati
Daouia <Abdelaati.Daouia@tse-fr.eu>, Thibault Laurent <thibault.laurent@univ-
tlse1.fr>, Hohsuk Noh <word5810@gmail.com>","Depends":"R (>= 2.9.1), graphics,
stats, utils","Description":"A variety of functions for the best known and most
innovative approaches to nonparametric boundary estimation. The selected methods
are concerned with empirical, smoothed, unrestricted as well as constrained fits
under both separate and multiple shape constraints. They cover robust approaches to
outliers as well as data envelopment techniques based on piecewise polynomials,
splines, local linear fitting, extreme values and kernel smoothing. The package
also seamlessly allows for Monte Carlo comparisons among these different estimation
methods. Its use is illustrated via a number of empirical applications and
simulated examples.","Imports":"Benchmarking, np, quadprog, Rglpk,
splines","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"npbr","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Nonparametric Boundary Regression","Version":"1.2"},"npcp":
{"Author":"Ivan Kojadinovic","Description":"Provides nonparametric tests for
assessing whether possibly serially dependent univariate or multivariate
observations have the same c.d.f. or not. In addition to tests focusing directly on
the c.d.f., the package contains tests designed to be particularly sensitive to
changes in the underlying copula, Spearman's rho or certain quantities that can be
estimated using one-sample U-statistics of order two such as the variance, Gini's
mean difference or Kendall's tau. The latest addition is a nonparametric test for
detecting changes in the distribution of independent block
maxima.","Imports":"stats","License":"GPL (>= 3) | file
LICENCE","NeedsCompilation":"yes","Package":"npcp","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"copula","Title":"Some Nonparametric Tests for
Change-Point Detection in Possibly\nMultivariate Observations","Version":"0.1-
6"},"npde":{"Author":"Emmanuelle Comets, Karl Brendel, Thi Huyen Tram Nguyen,
France\nMentre.","Depends":"methods, mclust","Description":"Routines to compute
normalised prediction distribution\nerrors, a metric designed to evaluate non-
linear mixed effect\nmodels such as those used in pharmacokinetics
and\npharmacodynamics","Imports":"graphics, stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"npde","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Normalised prediction distribution errors for
nonlinear\nmixed-effect models","Version":"2.0"},"nplplot":{"Author":"Robert V
Baron <rvb5@pitt.edu>, Nandita Mukhopadhyay,\nXinyu Tang, Daniel E. Weeks
<weeks@pitt.edu>","Description":"This package provides routines for
plotting\nlinkage and association results along a chromosome,\nwith marker names
displayed along the top border.\nThere are also routines for generating BED and
BedGraph\ncustom tracks for viewing in the UCSC genome browser.\nThe data
reformatting program Mega2 uses this\npackage to plot output from a variety
of\nprograms.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"nplplot","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Plotting linkage and association
results","URL":"http:\/\/watson.hgen.pitt.edu\/register","Version":"4.5"},"nplr":
{"Author":"Frederic Commo [aut, cre],\nBrian M. Bot
[aut]","Depends":"methods","Description":"Performing drug response analyses and
IC50 estimations using n-Parameter logistic regression. nplr can also be applied to
proliferation
analyses.","Imports":"stats,graphics","License":"GPL","NeedsCompilation":"no","Pack
age":"nplr","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"RUnit,k
nitr","Title":"N-Parameter Logistic
Regression","URL":"https:\/\/github.com\/fredcommo\/nplr","Version":"0.1-
4"},"npmlreg":{"Author":"Jochen Einbeck, Ross Darnell and John Hinde","Depends":"R
(>= 2.3.1)","Description":"Nonparametric maximum likelihood estimation or
Gaussian\nquadrature for overdispersed generalized linear models and\nvariance
component models","Imports":"statmod (>= 1.4.20)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"npmlreg","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"MASS, forward, nlme, lattice","Title":"Nonparametric
maximum likelihood estimation for random effect\nmodels","Version":"0.46-
1"},"npmr":{"Author":"Scott Powers, Trevor Hastie, Robert
Tibshirani","Description":"Fit multinomial logistic regression with a penalty on
the nuclear\nnorm of the estimated regression coefficient matrix, using
proximal\ngradient descent.","License":"GPL-
2","NeedsCompilation":"no","Package":"npmr","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Nuclear Penalized Multinomial
Regression","Version":"1.0"},"npmv":{"Author":"Woodrow Burchett and Amanda
Ellis","Description":"Performs analysis of one-way multivariate data, for small
samples using Nonparametric techniques. Using approximations for ANOVA Type, Wilks'
Lambda, Lawley Hotelling, and Bartlett Nanda Pillai Test statics, the package
compares the multivariate distributions for a single explanatory variable. The
comparison is also performed using a permutation test for each of the four test
statistics. The package also performs an all-subsets algorithm regarding variables
and regarding factor levels.","Imports":"Formula, methods","License":"GPL-
2","NeedsCompilation":"no","Package":"npmv","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Nonparametric Comparison of Multivariate
Samples","Version":"2.3.0"},"nppbib":{"Author":"David
Allingham, D.J. Best","Description":"Implements a nonparametric statistical test
for rank or\nscore data from partially-balanced incomplete block-
design\nexperiments.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"nppbib","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Nonparametric Partially-Balanced Incomplete Block
Design\nAnalysis","URL":"http:\/\/carma.newcastle.edu.au\/davida\/","Version":"1.0-
0"},"npregfast":{"Author":"Marta Sestelo [aut, cre],\nNora M. Villanueva
[aut],\nJavier Roca-Pardinas [aut]","Depends":"R (>= 3.2.0)","Description":"A
method for obtain nonparametric estimates of regression models\nwith or without
factor-by-curve interactions using local polynomial\nkernel smoothers.
Additionally, a parametric model (allometric model)\ncan be
estimated.","Imports":"graphics, stats, utils, shiny, ggplot2,
gridExtra","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"npregfast","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Nonparametric Estimation of Regression Models
with\nFactor-by-Curve Interactions","Version":"1.2.1"},"nproc":{"Author":"Yang
Feng, Jessica Li and Xin Tong","Description":"Given a sample of class 0 and class 1
and a classification method, the package generates the corresponding Neyman-Pearson
classifier with a pre-specified type-I error control and Neyman-Pearson Receiver
Operator Curve.","Imports":"glmnet, e1071, randomForest, MASS, parallel, ada,
stats,\ngraphics","License":"GPL-
2","NeedsCompilation":"no","Package":"nproc","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Neyman-Pearson Receiver Operator
Curve","Version":"0.1"},"npsf":{"Author":"Oleg Badunenko [aut, cre],\nYaryna
Kolomiytseva [aut],\nPavlo Mozharovskyi
[aut]","Depends":"Formula","Description":"Provides a variety of tools for
nonparametric and parametric efficiency measurement.","License":"GPL-2 | file
LICENSE","NeedsCompilation":"yes","Package":"npsf","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"snowFT, Rmpi","Title":"Nonparametric and Stochastic
Efficiency and Productivity\nAnalysis","Version":"0.1.6"},"npsm":{"Author":"John
Kloke, Joseph McKean","Depends":"Rfit","Description":"Functions and datasets used
in the book Nonparametric Statistical Methods Using
R.","Imports":"plyr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"npsm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"boot, survival, sm, HSAUR2, devtools","Title":"Package
for Nonparametric Statistical Methods using R","Version":"0.5"},"npsp":
{"Author":"Ruben Fernandez-Casal","Depends":"R (>= 2.14.0),
graphics","Description":"Multidimensional nonparametric spatio-temporal
geostatistics.\nS3 classes and methods for multidimensional: gridded data, linear
binning,\nlocal polynomial kernel regression, density and variogram
estimation.\nNonparametric methods for trend and\/or variogram
inferences.","Imports":"quadprog","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"npsp","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"sp, gstat, geoR, fields, DEoptim","Title":"Nonparametric
spatial (geo)statistics","Version":"0.3-6"},"npst":{"Author":"Roland
Rau","Description":"Package 'npst' generalizes Hewitt's (1971) test for seasonality
and\nRogerson's (1996) extension based on Monte-Carlo simulation.","License":"GPL-
2","NeedsCompilation":"yes","Package":"npst","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"parallel","Title":"Generalization of Hewitt's Seasonality
Test","Version":"2.0"},"npsurv":{"Author":"Yong
Wang","Depends":"lsei","Description":"Contains functions for non-parametric
survival analysis of\nexact and interval-censored
observations.","Imports":"methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"npsurv","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Non-Parametric Survival
Analysis","URL":"https:\/\/www.stat.auckland.ac.nz\/~yongwang","Version":"0.3-
4"},"nsRFA":{"Author":"Alberto Viglione [aut, cre],\nJonathan R. M. Hosking
[ctb],\nFrancesco Laio [ctb],\nAlan Miller [ctb],\nEric Gaume [ctb],\nOlivier
Payrastre [ctb],\nJose Luis Salinas [ctb],\nChi Cong N'guyen [ctb],\nKarine Halbert
[ctb]","Depends":"R (>= 3.0.0), stats, graphics","Description":"A collection of
statistical tools for objective (non-supervised) applications\nof the Regional
Frequency Analysis methods in hydrology.\nThe package refers to the index-value
method and, more precisely, helps the\nhydrologist to: (1) regionalize the index-
value; (2) form homogeneous regions\nwith similar growth curves; (3) fit
distribution functions to the\nempirical regional growth curves.","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"nsRFA","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Non-supervised Regional Frequency
Analysis","URL":"http:\/\/www.idrologia.polito.it\/~alviglio\/index_en.htm","Versio
n":"0.7-12"},"nscancor":{"Author":"Christian Sigg [aut, cre],\nR Core team
[aut]","Description":"This package implements two algorithms for canonical
correlation\nanalysis (CCA) that are based on iterated regression\nsteps. By
choosing the appropriate regression algorithm for each data\nmodality, it is
possible to enforce sparsity, non-negativity or other kinds\nof constraints on the
projection vectors. Multiple canonical variables are\ncomputed sequentially using a
generalized deflation scheme, where the\nadditional correlation not explained by
previous variables is maximized.\n'nscancor' is used to analyze paired data from
two domains, and has the same\ninterface as the 'cancor' function from the 'stats'
package (plus some extra\nparameters). 'mcancor' is appropriate for analyzing data
from three or more\ndomains.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"nscancor","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"CCA, glmnet, MASS, PMA, testthat (>= 0.8),
roxygen2","Title":"Non-Negative and Sparse CCA","URL":"http:\/\/sigg-
iten.ch\/research\/","Version":"0.6"},"nsga2R":{"Author":"Ching-Shih (Vince) Tsou
<cstsou@mail.ntcb.edu.tw>","Depends":"mco","Description":"This package provide
functions for box-constrained\nmultiobjective optimization using the elitist non-
dominated\nsorting genetic algorithm - NSGA-II. Fast non-dominated\nsorting,
crowding distance, tournament selection, simulated\nbinary crossover, and
polynomial mutation are called in the\nmain program, nsga2R, to complete the
search.","License":"LGPL-
3","NeedsCompilation":"no","Package":"nsga2R","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Elitist Non-dominated Sorting Genetic Algorithm based on
R","Version":"1.0"},"nsgp":{"Author":"Markus Heinonen","Depends":"R (>=
3.0.0)","Description":"A Gaussian process regression using a Gaussian kernel for
both\none-sample and two-sample cases. Includes non-stationary Gaussian
kernel\n(exponential decay function) and several likelihood ratio tests
for\ndifferential testing along target points.","Imports":"MASS","License":"GPL-
2","NeedsCompilation":"no","Package":"nsgp","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Non-Stationary Gaussian Process
Regression","URL":"http:\/\/amis-
group.fr\/software\/nsgp","Version":"1.0.5"},"nsprcomp":{"Author":"Christian Sigg
[aut, cre],\nR Core team [aut]","Description":"This package implements two methods
for performing a constrained\nprincipal component analysis (PCA), where non-
negativity and\/or sparsity\nconstraints are enforced on the principal axes (PAs).
The function\n'nsprcomp' computes one principal component (PC) after the other.
Each PA\nis optimized such that the corresponding PC has maximum additional
variance\nnot explained by the previous components. In contrast, the
function\n'nscumcomp' jointly computes all PCs such that the cumulative variance
is\nmaximal. Both functions have the same interface as the 'prcomp' function\nfrom
the 'stats' package (plus some extra parameters), and both return the\nresult of
the analysis as an object of class 'nsprcomp', which inherits\nfrom
'prcomp'.","Imports":"stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"nsprcomp","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"MASS, testthat (>= 0.8), roxygen2","Title":"Non-
Negative and Sparse PCA","URL":"http:\/\/sigg-
iten.ch\/research\/","Version":"0.5"},"nullabor":{"Author":"Hadley Wickham
<h.wickham@gmail.com>, Niladri Roy Chowdhury\n<niladri.ia@gmail.com>, Di Cook
<dicook@iastate.edu>","Depends":"ggplot2","Description":"Tools for visual
inference. Generate null data sets\nand null plots using permutation and
simulation. Calculate distance metrics\nfor a lineup, and examine the distributions
of metrics.","Imports":"MASS, plyr, dplyr, moments,
fpc","License":"GPL","NeedsCompilation":"no","Package":"nullabor","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Suggests":"reshape2, knitr","Title":"Tools for
Graphical Inference","Version":"0.3.1"},"numDeriv":{"Author":"Paul Gilbert and Ravi
Varadhan","Depends":"R (>= 2.11.1)","Description":"Methods for calculating
(usually) accurate\nnumerical first and second order derivatives. Accurate
calculations\nare done using Richardson's extrapolation or, when applicable, a
complex\nstep derivative is available. A simple difference\nmethod is also
provided. Simple difference is (usually) less accurate\nbut is much quicker than
Richardson's extrapolation and provides a\nuseful cross-check.\nMethods are
provided for real scalar and vector valued functions.","License":"GPL-
2","NeedsCompilation":"no","Package":"numDeriv","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Accurate Numerical
Derivatives","URL":"http:\/\/optimizer.r-forge.r-project.org\/","Version":"2014.2-
1"},"numOSL":{"Author":"Jun Peng [aut, cre], Jorge More [ctb], Burton Garbow [ctb],
Kenneth Hillstrom [ctb], John Burkardt [ctb], Paul Gilbert [ctb], Ravi Varadhan
[ctb]","Depends":"R
(>= 2.15.3)","Description":"Package for optimizing regular numeric problems in
optically stimulated luminescence\ndating, such as: equivalent dose calculation,
annual dose rate determination, growth curve\nfitting, decay curve decomposition,
fast-component equivalent dose estimation, statistical\nage model optimization, and
statistical plot visualization.","Imports":"graphics, stats, utils","License":"GPL-
3","NeedsCompilation":"yes","Package":"numOSL","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Numeric Routines for Optically Stimulated Luminescence
Dating","URL":"http:\/\/CRAN.R-
project.org\/package=numOSL","Version":"1.9"},"numbers":{"Author":"Hans Werner
Borchers","Depends":"R (>= 3.0.0)","Description":"\nProvides some number-theoretic
functions for R.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"numbers","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"gmp (>= 0.5-1)","Title":"Number-Theoretic
Functions","Version":"0.6-1"},"nutshell":{"Author":"Joseph Adler","Depends":"R (>=
2.10), nutshell.bbdb, nutshell.audioscrobbler","Description":"This package contains
data sets used as examples in the\nbook \"R in a Nutshell\" from O'Reilly Media.
For more\ninformation on this book,
see\nhttp:\/\/shop.oreilly.com\/product\/0636920022008.do","License":"CC BY-NC-ND
3.0
US","NeedsCompilation":"no","Package":"nutshell","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"MASS, RSQLite, arules, lattice,
survival","Title":"Data for \"R in a
Nutshell\"","Version":"2.0"},"nutshell.audioscrobbler":{"Author":"Joseph
Adler","Depends":"R (>= 2.10)","Description":"This package contains the Audio
Scrobbler data set used as\nan example in the book \"R in a Nutshell\" from
O'Reilly Media.\nFor more information about this book,
see\nhttp:\/\/shop.oreilly.com\/product\/0636920022008.do","License":"CC BY-NC-SA
3.0","NeedsCompilation":"no","Package":"nutshell.audioscrobbler","Repository":"http
:\/\/cran.csiro.au\/src\/contrib","Suggests":"arules","Title":"Audioscrobbler data
for \"R in a Nutshell\"","Version":"1.0"},"nutshell.bbdb":{"Author":"Joseph
Adler","Depends":"R (>= 2.10)","Description":"This package contains the baseball
databank data set used\nas an example in the book \"R in a Nutshell\" from
O'Reilly\nMedia. For more information about this book,
see\nhttp:\/\/shop.oreilly.com\/product\/0636920022008.do","License":"CC BY-NC-ND
3.0
US","NeedsCompilation":"no","Package":"nutshell.bbdb","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"RSQLite","Title":"Baseball Database for \"R in a
Nutshell\"","Version":"1.0"},"nws":{"Author":"REvolution Computing
<packages@revolution-computing.com> with\nsupport and contributions from Pfizer,
Inc.","Depends":"R (>= 2.1), methods","Description":"Provides coordination and
parallel execution facilities,\nas well as limited cross-language data exchange,
using the\nnetWorkSpaces server developed by REvolution Computing","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"nws","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"R functions for NetWorkSpaces and
Sleigh","URL":"http:\/\/nws-
r.sourceforge.net\/","Version":"1.7.0.1"},"nycflights13":{"Author":"'Hadley
Wickham' [aut, cre]","Depends":"R (>= 3.1.0)","Description":"Airline on-time data
for all flights departing NYC in 2013.\nAlso includes useful metadata on airlines,
airports, weather, and
planes.","License":"CC0","NeedsCompilation":"no","Package":"nycflights13","Reposito
ry":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"dplyr","Title":"Data about
flights departing NYC in
2013","URL":"http:\/\/github.com\/hadley\/nycflights13","Version":"0.1"},"oaColors"
:{"Author":"Jason Waddell","Description":"Provides carefully chosen color palettes
as used a.o. at OpenAnalytics <http:\/\/www.openanalytics.eu>.","Imports":"MASS,
grid, RColorBrewer","License":"GPL-3 + file
LICENSE","NeedsCompilation":"no","Package":"oaColors","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"OpenAnalytics Colors
Package","URL":"http:\/\/www.openanalytics.eu","Version":"0.0.4"},"oaPlots":
{"Author":"Jason Waddell, Willem
Ligtenberg","Depends":"oaColors","Description":"Offers a suite of functions for
enhancing R plots.","Imports":"ggplot2","License":"GPL-3 + file
LICENSE","NeedsCompilation":"no","Package":"oaPlots","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"RColorBrewer","Title":"OpenAnalytics Plots
Package","URL":"http:\/\/www.openanalytics.eu","Version":"0.0.25"},"oai":
{"Author":"Scott Chamberlain [aut, cre],\nMichal Bojanowski [aut]","Description":"A
general purpose client to work with any 'OAI-PMH'\n(Open Archives Initiative
Protocol for 'Metadata' Harvesting) service.\nThe 'OAI-PMH' protocol is described
at\nhttp:\/\/www.openarchives.org\/OAI\/openarchivesprotocol.html.\nFunctions are
provided to work with the 'OAI-PMH' verbs: 'GetRecord',\n'Identify',
'ListIdentifiers', 'ListMetadataFormats', 'ListRecords',
and\n'ListSets'.","Imports":"methods, stats, utils, xml2 (>= 0.1.2), httr (>=
1.0.0), plyr\n(>= 1.8.3), stringr (>= 1.0.0)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"oai","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"DBI, knitr, RSQLite, testthat","Title":"General
Purpose 'Oai-PMH' Services
Client","URL":"https:\/\/github.com\/sckott\/oai","Version":"0.2.0"},"oapackage":
{"Author":"Pieter Thijs Eendebak","Description":"Interface to D-optimal design
generation code of the Orthogonal Array package. Can generate D-optimal designs
with specified number of runs and factors. The optimality of the designs is defined
in terms of a user specified optimization function based on the D-efficiency and
Ds-efficiency.","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"yes","Package":"oapackage","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"reshape2, ggplot2","Title":"Orthogonal Array
Package","URL":"http:\/\/www.pietereendebak.nl\/oapackage","Version":"2.0.23"},"oas
is":{"Author":"Elizabeth M. Sweeney [aut, cre],\nJohn Muschelli [aut],\nR. Taki
Shinohara [aut]","Depends":"fslr (>= 1.5.0)","Description":"Trains and makes
predictions from the OASIS method, described in\ndetail in the paper \"OASIS is
Automated Statistical Inference for Segmentation,\nwith applications to multiple
sclerosis lesion segmentation in MRI\"\n<doi:10.1016\/j.nicl.2013.03.002>. OASIS is
a method\nfor multiple sclerosis (MS) lesion segmentation on structural magnetic
resonance\nimage (MRI) studies. OASIS creates probability maps of lesion presence
using the\nFLAIR, T2, T1, and PD structural MRI volumes. This packages allows for
training\nof the OASIS model and prediction of OASIS probability maps from a
trained model\nwith user supplied studies that have a gold standard lesion
segmentation masks.\nThe package will also create OASIS probability maps for MRI
studies using the\nOASIS model from the OASIS paper if no gold standard lesion
segmentation masks\nare available.","Imports":"stats, parallel,
oro.nifti","License":"GPL-
2","NeedsCompilation":"no","Package":"oasis","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"downloader","Title":"Multiple Sclerosis Lesion
Segmentation using Magnetic Resonance\nImaging (MRI)","Version":"0.99.5"},"oaxaca":
{"Author":"Marek Hlavac <hlavac@fas.harvard.edu>","Description":"An implementation
of the Blinder-Oaxaca decomposition for linear regression
models.","Imports":"Formula, ggplot2, reshape2, methods, stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"oaxaca","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Blinder-Oaxaca
Decomposition","Version":"0.1.3"},"obAnalytics":{"Author":"Philip
Stubbings","Depends":"R (>= 3.1.1)","Description":"Data processing, visualisation
and analysis of Limit Order Book\nevent data.","Imports":"zoo, ggplot2, reshape2,
2)","NeedsCompilation":"no","Package":"obAnalytics","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"grid, rmarkdown, knitr, testthat","Title":"Limit
Order Book Analytics","URL":"https:\/\/github.com\/phil8192\/ob-
analytics","Version":"0.1.0"},"objectProperties":{"Author":"Tengfei Yin, Michael
Lawrence","Depends":"R (>= 2.12), methods, objectSignals","Description":"Supports
the definition of sets of properties on objects. Observers can listen to changes on
individual properties or the set as a whole. The properties are meant to be fully
self-describing. In support of this, there is a framework for defining enumerated
types, as well as other bounded types, as S4 classes.","Imports":"methods,
objectSignals (>= 0.10.2)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"objectProperties","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"A factory of self-describing
properties","Version":"0.6.5"},"objectSignals":{"Author":"Michael Lawrence, Tengfei
Yin","Depends":"R (>= 2.12), methods","Description":"A mutable Signal object can
report changes to its state,\nclients could register functions so that they are
called whenever\nthe signal is emited. The signal could be emited,
disconnected,\nblocked, unblocked, and
buffered.","Imports":"methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"objectSignals","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"objectSignals","Version":"0.10.2"},"obliclus":
{"Author":"Michio Yamamoto","Description":"This package conducts factor rotation
techniques which\nintentd to identify a simple and well-clustered structure in
a\nfactor loading matrix.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"obliclus","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Cluster-based factor
rotation","URL":"http:\/\/michioyamamoto.com","Version":"0.9"},"oblique.tree":
{"Author":"Alfred Truong","Depends":"tree, glmnet","Description":"Grows Oblique
Trees to Classification Data.","Imports":"nnet","License":"GPL-
3","NeedsCompilation":"yes","Package":"oblique.tree","Repository":"http:\/\/cran.cs
iro.
au\/src\/contrib","Suggests":"MASS","Title":"Oblique Trees for Classification
Data","Version":"1.1.1"},"obliqueRF":{"Author":"Bjoern Menze and Nico
Splitthoff","Depends":"R (>= 2.0.0), stats, ROCR, pls, mda,
e1071","Description":"Random forest with oblique decision trees for
binary\nclassification tasks. Discriminative node models in the tree\nare based on:
ridge regression, partial least squares\nregression, logistic regression, linear
support vector\nmachines, or random coefficients.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"obliqueRF","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Oblique Random Forests from Recursive Linear Model
Splits","Version":"0.3"},"obs.agree":{"Author":"Teresa Henriques, Luis Antunes and
Cristina Costa-Santos","Description":"The package includes two functions for
measuring agreement. Raw Agreement Indices (RAI) to categorical data and
Information-Based Measure of Disagreement (IBMD) to continuous data. It can be used
for multiple raters and multiple readings cases.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"obs.agree","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"An R package to assess agreement between
observers","URL":"http:\/\/www.r-project.org,
http:\/\/disagreement.med.up.pt\/","Version":"1.0"},"obsSens":{"Author":"Greg Snow
<greg.snow@imail.org>","Description":"Observational studies are limited in that
there could be\nan unmeasured variable related to both the response variable\nand
the primary predictor. If this unmeasured variable were\nincluded in the analysis
it would change the relationship\n(possibly changing the conclusions). Sensitivity
analysis is a\nway to see how much of a relationship needs to exist with
the\nunmeasured variable before the conclusions change. This\npackage provides
tools for doing a sensitivity analysis for\nregression (linear, logistic, and cox)
style models.","License":"GPL-
2","NeedsCompilation":"no","Package":"obsSens","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Sensitivity analysis for Observational
studies","Version":"1.3"},"oc":{"Author":"Keith Poole <ktpoole@uga.edu>, Jeffrey
Lewis\n<jblewis@ucla.edu>, James Lo <jameslo@princeton.edu> and Royce\nCarroll
<rcarroll@rice.edu>","Depends":"R (>= 2.3.1), pscl (>=
0.59)","Description":"Estimates Optimal Classification scores from roll call\nvotes
supplied though a 'rollcall' object from package 'pscl'.","License":"GPL-
2","NeedsCompilation":"yes","Package":"oc","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"OC Roll Call Analysis Software","Version":"0.95"},"occ":
{"Author":"Joaquim Radua","Description":"This package provides a generic function
for estimating\npositron emission tomography (PET) neuroreceptor occupancies\nfrom
the total volumes of distribution of a set of regions of\ninterest. Fittings
methods include the simple 'reference\nregion' and 'ordinary least squares'
(sometimes known as\noccupancy plot) methods, as well as the more
efficient\n'restricted maximum likelihood
estimation'.","License":"GPL","NeedsCompilation":"no","Package":"occ","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Title":"Estimates PET neuroreceptor
occupancies","Version":"1.0"},"oce":{"Author":"Dan Kelley [aut, cre],\nClark
Richards [aut],\nChantelle Layton [ctb, cph] (curl() coauthor),\nBritish Geological
Survey [ctb, cph] (magnetic-field fortran\nsubroutine)","Depends":"R (>= 2.15),
utils, methods, gsw","Description":"Supports the analysis of Oceanographic data,
including 'ADCP'\nmeasurements, measurements made with 'argo' floats, 'CTD'
measurements, sectional\ndata, sea-level time series, coastline and topographic
data, etc. Provides\nspecialized functions for calculating seawater properties such
as potential\ntemperature in either the 'UNESCO' or 'TEOS-10' equation of state.
Produces\ngraphical displays that conform to the conventions of the Oceanographic
literature.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"oce","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"ocedata, foreign, mapproj, ncdf4, tiff, akima, RSQLite,
DBI,\nrgdal, R.utils, testthat, knitr","Title":"Analysis of Oceanographic
Data","URL":"http:\/\/dankelley.github.com\/oce\/","Version":"0.9-18"},"ocean":
{"Author":"Benjamin Jones [aut, cre]","Depends":"R (>= 3.0.2), graphics, methods,
ncdf4, proj4","Description":"This package contains a set of functions for
manipulating and\nvisualizing output from numerical ocean models. Many of the
routines are\ntargeted towards Lagrangian particle-tracking models with the data
stored\nin NetCDF files. This package may be useful to spatial marine
ecologists\nand biological or physical oceanographers.","License":"GPL-
3","NeedsCompilation":"yes","Package":"ocean","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Biophysical Oceanography
Tools","URL":"https:\/\/github.com\/btjones16\/ocean","Version":"0.2-4"},"ocedata":
{"Author":"Dan Kelley <Dan.Kelley@Dal.Ca>","Depends":"R (>= 2.15),
methods","Description":"Several important and Oceanographic datasets are provided.
These are particularly useful to the Oce package, but can be helpful in a general
context, as well.","Enhances":"oce","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ocedata","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Oceanographic Datasets for
Oce","URL":"http:\/\/dankelley.github.com\/ocedata\/","Version":"0.1.3"},"ocomposit
ion":{"Author":"Arturas Rozenas, New York University","Depends":"R (>= 3.2.1),
coda, bayesm","Description":"Regression model where the response variable is a
rank-indexed compositional vector (non-negative values that sum up to one and are
ordered from the largest to the smallest). Parameters are estimated in the Bayesian
framework using MCMC methods.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ocomposition","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Regression for Rank-Indexed Compositional
Data","Version":"1.1"},"odds.converter":{"Author":"Marco
Blume","Description":"Conversion between the most common odds types for sports
betting. Hong Kong odds, US odds, Decimal odds, Indonesian odds, Malaysian odds,
and raw Probability are covered in this package.","License":"GPL-
2","NeedsCompilation":"no","Package":"odds.converter","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Betting Odds
Conversion","Version":"1.3"},"odeintr":{"Author":"Timothy H.
Keitt","Description":"Wraps the Boost 'odeint' library for integration of
differential equations.","Imports":"Rcpp (>= 0.10.0)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"odeintr","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"C++ ODE Solvers Compiled on-
Demand","URL":"https:\/\/github.com\/thk686\/odeintr","Version":"1.3"},"odfWeave":
{"Author":"Max Kuhn. Contributions from Steve Weston, Nathan Coulter, Patrick
Lenon, Zekai Otles and the R Core Team","Depends":"R (>= 2.13.1), lattice, XML (>=
3.9-4)","Description":"Sweave processing of Open Document Format (ODF)
files","License":"GPL-
2","NeedsCompilation":"no","Package":"odfWeave","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"MASS","Title":"Sweave processing of Open Document
Format (ODF) files","Version":"0.8.4"},"odfWeave.survey":{"Author":"Thomas
Lumley","Depends":"odfWeave, survey","Description":"Provides methods for odfTable()
for objects in the survey\npackage.","License":"GPL-
2","NeedsCompilation":"no","Package":"odfWeave.survey","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Support for odfWeave on the survey
package","Version":"1.0"},"oem":{"Author":"Bin Dai","Depends":"R (>= 3.0.2), Rcpp
(>= 0.0.9)","Description":"Fit penalized regression with orthogonalizing EM
algorithm","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"oem","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Orthogonalizing Expectation
maximization","Version":"1.02.1"},"oglmx":{"Author":"Nathan
Carroll","Depends":"maxLik","Description":"Ordered models such as ordered probit
and ordered logit presume that the error variance is constant across observations.
In the case that this assumption does not hold estimates of marginal effects are
typically biased. This package allows for generalization of ordered probit and
ordered logit models by allowing the user to specify a model for the variance.
Furthermore, the package includes functions to calculate the marginal
effects.","Imports":"stats","License":"GPL-
2","NeedsCompilation":"no","Package":"oglmx","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"glmx, lmtest","Title":"Estimation of Ordered Generalized
Linear Models","Version":"1.0.3"},"okmesonet":{"Author":"Brady Allred, Torre
Hovick, Samuel Fuhlendorf","Depends":"R (>= 2.14.0),
utils","Description":"okmesonet retrieves and summarizes Oklahoma (USA)
Mesonet\nclimatological data provided by the Oklahoma Climatological
Survey.\nMeasurements are recorded every five minutes at approximately 120
stations\nthroughout Oklahoma and are available in near real-
time.","Imports":"plyr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"okmesonet","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Retrieve Oklahoma Mesonet climatological
data","Version":"0.1.5"},"omd":{"Author":"Bin Ma","Description":"This package
including two useful function, which can be\nused for filter the molecular
descriptors matrix for QSAR.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"omd","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"filter the molecular descriptors for
QSAR","Version":"1.0"},"omics":{"Author":"Gianluca Campanella [aut,
cre]","Depends":"R (>= 3.0.0), methods","Description":"A collection of functions to
analyse '--omics' datasets such as DNA\nmethylation and gene expression
profiles.","Imports":"lme4, pheatmap","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"omics","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"t
estthat","Title":"'--omics' Data Analysis Toolbox","Version":"0.1-4"},"oncomodel":
{"Author":"Anja von Heydebreck <anja.von.heydebreck@merck.de>,\ncontributions from
Christiane Heiss <christiane.heiss@web.de>","Depends":"R (>= 2.5.1),
ade4","Description":"Computing probabilistic tree models for oncogenesis based\non
genetic data using maximum likelihood.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"oncomodel","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Maximum likelihood tree models for
oncogenesis","Version":"1.0"},"onemap":{"Author":"Gabriel Margarido [aut], Marcelo
Mollinari [aut, cre], Karl\nBroman [ctb], Augusto Garcia [ctb]","Depends":"tcltk,
tkrplot, R (>= 2.12.0)","Description":"Analysis of molecular marker data from model
(backcrosses,\nF2 and recombinant inbred lines) and non-model systems (i.
e.\noutcrossing species). For the later, it allows statistical\nanalysis by
simultaneously estimating linkage and linkage\nphases (genetic map construction).
All analysis are based on\nmultipoint approaches using hidden Markov
3","NeedsCompilation":"yes","Package":"onemap","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"qtl","Title":"Software for constructing genetic maps in
experimental crosses:\nfull-sib, RILs, F2 and backcrosses","Version":"2.0-
4"},"onewaytests":{"Author":"Osman Dag, Anil Dolgun, N. Meric Konar","Depends":"R
(>= 3.1.1)","Description":"Two or more samples in one-way independent groups design
are compared via different tests.","Imports":"stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"onewaytests","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"One-Way Independent Groups
Design","Version":"1.1"},"onion":{"Author":"Robin K. S. Hankin","Depends":"R (>=
2.10)","Description":"\nA collection of routines to manipulate and visualize
quaternions
and\noctonions.","License":"GPL","NeedsCompilation":"yes","Package":"onion","Reposi
tory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"octonions and
quaternions","Version":"1.2-4"},"onlinePCA":{"Author":"David Degras [aut, cre],
Herve Cardot [ctb]","Depends":"R (>= 3.0.2), rARPACK","Description":"Online PCA for
multivariate and functional data using perturbation methods, low-rank incremental
methods, and stochastic optimization methods.","Imports":"Rcpp (>= 0.11.4),
splines, stats","License":"GPL-
3","NeedsCompilation":"yes","Package":"onlinePCA","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Online Principal Component
Analysis","URL":"http:\/\/cran.r-
project.org\/package=onlinePCA","Version":"1.3"},"onls":{"Author":"Andrej-Nikolai
Spiess <a.spiess@uke.uni-hamburg.de>","Depends":"R (>= 2.13.0),
minpack.lm","Description":"Orthogonal Nonlinear Least-Squares Regression using
Levenberg-Marquardt Minimization.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"onls","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Orthogonal Nonlinear Least-Squares
Regression","Version":"0.1-1"},"ontologyIndex":{"Author":"Daniel Greene
<dg333@cam.ac.uk>","Depends":"R (>= 3.0.0)","Description":"Functions for reading
ontologies into R as lists and handling sets of ontological terms.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"ontologyIndex","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"knitr","Title":"Functions for Reading Ontologies
into R","Version":"1.0"},"ontologyPlot":{"Author":"Daniel Greene
<dg333@cam.ac.uk>","Depends":"R (>= 3.0.0)","Description":"Functions for
visualising sets of ontological terms using the graphviz layout
system.","Imports":"ontologyIndex, Rgraphviz, methods, functional,
magrittr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ontologyPlot","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"knitr","Title":"Functions for Visualising Sets of
Ontological Terms","Version":"1.0"},"ontologySimilarity":{"Author":"Daniel
Greene","Depends":"R (>= 3.0.0)","Description":"Functions for calculating semantic
similarities between ontological terms or sets of ontological terms based on term
information content and assessing statistical significance of similarity in the
context of a collection of sets of ontological terms.","Imports":"Rcpp (>= 0.11.2),
ontologyIndex","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ontologySimilarity","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Suggests":"knitr","Title":"Functions for Calculating
Ontological Similarities","Version":"1.0"},"opefimor":{"Author":"Stefano Maria
Iacus","Description":"Companion package to the book Option Pricing and\nEstimation
of Financial Models in R, Wiley, Chichester. ISBN:\n978-0-470-74584-
2)","NeedsCompilation":"no","Package":"opefimor","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Option Pricing and Estimation of Financial Models in
R","Version":"1.2"},"openNLP":{"Author":"Kurt Hornik [aut, cre]","Description":"An
interface to the Apache OpenNLP tools (version 1.5.3).\nThe Apache OpenNLP library
is a machine learning based toolkit for the\nprocessing of natural language text
written in Java.\nIt supports the most common NLP tasks, such as tokenization,
sentence\nsegmentation, part-of-speech tagging, named entity extraction,
chunking,\nparsing, and coreference resolution.\nSee
<http:\/\/opennlp.apache.org\/> for more information.","Imports":"NLP (>= 0.1-6.3),
openNLPdata (>= 1.5.3-1), rJava (>= 0.6-3)","License":"GPL-
3","NeedsCompilation":"no","Package":"openNLP","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"openNLPmodels.en","Title":"Apache OpenNLP Tools
Interface","Version":"0.2-6"},"openNLPdata":{"Author":"Kurt Hornik [aut, cre],\nThe
Apache Software Foundation [ctb, cph] (Apache OpenNLP Java\nlibraries),\nJWNL
development team [ctb, cph] (JWNL Java WordNet Library)","Description":"Apache
OpenNLP jars and basic English language models.","Imports":"rJava (>= 0.6-
3)","License":"GPL-
3","NeedsCompilation":"no","Package":"openNLPdata","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Apache OpenNLP Jars and Basic English Language
Models","URL":"http:\/\/opennlp.apache.org\/,\nhttp:\/\/opennlp.sourceforge.net\/mo
dels-1.5\/","Version":"1.5.3-2"},"openVA":{"Author":"Zehang Li, Tyler McCormick,
Sam Clark","Depends":"R (>= 2.15.0), InSilicoVA (>= 1.1.1), InterVA4 (>=
1.7.1),\nTariff (>= 1.0.1), ggplot2","Description":"Implements multiple existing
open-source algorithms for coding cause of death from verbal autopsies. It also
provides tools for data manipulation tasks commonly used in Verbal Autopsy analysis
and implements easy graphical visualization of individual and population level
2","NeedsCompilation":"no","Package":"openVA","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Automated Method for Verbal
Autopsy","Version":"1.0.1"},"openair":{"Author":"David Carslaw [aut, cre],\nKarl
Ropkins [aut]","Depends":"R (>= 2.15.1), maps,","Description":"Tools to analyse,
interpret and understand air\npollution data. Data are typically hourly time
series\nand both monitoring data and dispersion model output\ncan be analysed.
Many functions can also be applied to\nother data, including meteorological and
traffic data.","Imports":"grid, plyr, lazyeval, dplyr, reshape2, mgcv,
lattice,\nlatticeExtra, lubridate, cluster, RColorBrewer, mapproj,\nhexbin,
mapdata, RgoogleMaps, Rcpp, grDevices, graphics,\nmethods, stats,
2)","NeedsCompilation":"yes","Package":"openair","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"png, KernSmooth","Title":"Tools for the Analysis of
Air Pollution Data","URL":"http:\/\/www.openair-
project.org\/,\nhttps:\/\/github.com\/davidcarslaw\/openair","Version":"1.8-
0"},"opencpu":{"Author":"Jeroen Ooms","Depends":"R (>= 3.0.0)","Description":"The
OpenCPU system exposes an HTTP API for embedded scientific\ncomputing with R. This
provides scalable foundations for integrating R\nbased analysis and visualization
modules into pipelines, web applications\nor big data infrastructures. The OpenCPU
server can run either as a\nsingle-user development server within the interactive R
session, or as a\nhigh performance multi-user cloud server that builds on Linux,
Nginx and\nrApache. The current R package forms the core of the system. When
loaded\nin R, it automatically initiates the single-user server and displays
the\nweb address in the console. Visit the OpenCPU website for
detailed\ninformation and documentation on the API.","Imports":"parallel, tools,
stats, evaluate (>= 0.5.1), httpuv (>= 1.3),\nknitr (>= 1.6), jsonlite (>= 0.9.14),
devtools (>= 1.9.1), httr\n(>= 0.3), brew, openssl","License":"Apache License
2.0","NeedsCompilation":"no","Package":"opencpu","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"RAppArmor, sendmailR, RProtoBuf (>= 0.4.2), pander,
R.rsp","Title":"A System for Embedded Scientific Computing and
Reproducible\nResearch with R","URL":"https:\/\/www.opencpu.org,
http:\/\/arxiv.org\/abs\/1406.4806","Version":"1.5.4"},"openintro":{"Author":"David
M Diez, Christopher D Barr, and Mine Cetinkaya-Rundel","Depends":"graphics,
grDevices, stats, utils, R (>= 2.10)","Description":"This package is a supplement
to OpenIntro Statistics,\nwhich is a free textbook available at openintro.org (at
cost\npaperbacks are also available for under $10 on Amazon). The\npackage contains
data sets used in the textbook along with\ncustom plotting functions for
reproducing book figures. Note\nthat many functions and examples include color
transparency.\nSome plotting elements may not show up properly (or at all) in\nsome
Windows versions.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"openintro","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"OpenIntro data sets and supplemental
functions","URL":"http:\/\/www.openintro.org\/","Version":"1.4"},"openssl":
{"Author":"Jeroen
Ooms [cre, aut],\nOliver Keyes [ctb]","Description":"Bindings to OpenSSL libssl
and libcrypto, plus custom SSH\npubkey parsers. Supports RSA, DSA and NIST curves
P-256, P-384 and P-521.\nCryptographic signatures can either be created and
verified manually or via x509\ncertificates. AES block cipher is used in CBC mode
for symmetric encryption; RSA\nfor asymmetric (public key) encryption. High-level
envelope functions combine\nRSA and AES for encrypting arbitrary sized data. Other
utilities include key\ngenerators, hash functions (md5, sha1, sha256, etc), base64
encoder, a secure\nrandom number generator, and 'bignum' math methods for manually
performing\ncrypto calculations on large multibyte integers.","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"openssl","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat, digest, knitr,
jsonlite","Title":"Toolkit for Encryption, Signatures and Certificates Based
on\nOpenSSL","URL":"https:\/\/github.com\/jeroenooms\/openssl","Version":"0.9.2"},"
opentraj":{"Author":"Thalles Santos Silva","Depends":"R (>=
2.10)","Description":"opentraj uses the Hybrid Single Particle Lagrangian
Integrated Trajectory Model (HYSPLIT) for computing simple air parcel trajectories.
The functions in this package allow users to run HYSPLIT for trajectory
calculations, as well as get its results, directly from R without using any GUI
interface.","Imports":"plyr, maptools, openair, raster, rgdal, reshape,
doParallel,\nparallel, foreach, sp","License":"GPL-
2","NeedsCompilation":"no","Package":"opentraj","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Tools for Creating and Analysing Air Trajectory
Data","Version":"1.0"},"openxlsx":{"Author":"Alexander Walker [aut, cre],\nLuca
Braglia [ctb]","Description":"Simplifies the creation of Excel .xlsx files by
providing a\nhigh level interface to writing, styling and editing worksheets.
Through\nthe use of Rcpp, read\/write times are comparable to the xlsx and
XLConnect\npackages with the added benefit of removing the dependency on
Java.","Imports":"methods, Rcpp (>= 0.11.1), grDevices, stats,
3","NeedsCompilation":"yes","Package":"openxlsx","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr, testthat","Title":"Read, Write and Edit XLSX
Files","URL":"https:\/\/github.com\/awalker89\/openxlsx","Version":"3.0.0"},"operat
or.tools":{"Author":"Decision Patterns","Depends":"utils","Description":"These
utilities allow for programatically working with\nR's operators: translating
between an operator and its underlying\nfunction, inverting an operator,
determining an operator's type, etc.","License":"GPL-2 | file
LICENSE","NeedsCompilation":"no","Package":"operator.tools","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Suggests":"operators, magrittr,
testthat","Title":"Utilities for Working with R's
Operators","URL":"https:\/\/github.com\/decisionpatterns\/operator.tools","Version"
:"1.4.4"},"operators":{"Author":"Romain Francois <romain@r-
enthusiasts.com>","Depends":"R (>= 3.1.0)","Description":"A set of binary operators
for common tasks such as regex\nmanipulation.","Imports":"utils","License":"MIT +
file
LICENSE","NeedsCompilation":"no","Package":"operators","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat","Title":"Additional Binary
Operators","URL":"https:\/\/github.com\/romainfrancois\/operators","Version":"0.1-
8"},"ops":{"Author":"Micha Sammeth","Description":"Comparison of data by Pearson
product-moment correlation\ncoefficients is prone to outliers. The problem can
be\nalleviated by normalizing data with outliers before computing\nthe Pearson
correlation coefficient. The sample provides such\nnormalization by optimal power
space transformation.","License":"Apache License
2.0","NeedsCompilation":"no","Package":"ops","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Optimal Power Space
Transformation","Version":"1.0"},"optAUC":{"Author":"Xin Huang, Gengsheng Qin,
Yixin Fang","Depends":"R (>= 2.15.2), MASS","Description":"Searches for optimal
linear combination of multiple\ndiagnostic tests (markers) that maximizes the area
under the\nreceiver operating characteristic curve (AUC); performs an\napproximated
cross-validation for estimating the AUC associated\nwith the estimated
coefficients.","License":"GPL-
2","NeedsCompilation":"no","Package":"optAUC","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Optimal Combinations of Diagnostic Tests Based on
AUC","Version":"1.0"},"optBiomarker":{"Author":"Mizanur Khondoker
<mizanur.khondoker@gmail.com>","Depends":"R (>= 2.10), rpanel,
rgl","Description":"Estimates optimal number of biomarkers for two-
group\nclassification based on microarray data","Imports":"MASS, randomForest,
e1071,ipred, msm, Matrix","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"optBiomarker","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Estimation of optimal number of biomarkers for two-
group\nmicroarray based classifications at a given error tolerance\nlevel for
various classification rules","Version":"1.0-27"},"optCluster":{"Author":"Michael
Sekula <michael.sekula@louisville.edu>,\nSomnath Datta
<somnath.datta@louisville.edu>,\nand Susmita Datta
<susmita.datta@louisville.edu>","Depends":"R (>= 3.0)","Description":"Cluster
analysis using statistical and biological\nvalidation measures for both continuous
and count data.","Imports":"grDevices, graphics, stats, utils, clValid,
RankAggreg,\nmclust, methods, cluster, gplots, kohonen,
MBCluster.Seq","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"optCluster","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"Biobase, annotate, GO.db,
org.At.tair.db","Title":"Determine Optimal Clustering Algorithm and Number of
Clusters","Version":"1.1.0"},"optR":{"Author":"Prakash (PKS Prakash)
<prakash2@uwalumni.com>","Description":"The optR function provides an option to
solve the linear system\nusing numeric computation approach. The current packages
supports Gauss\nElimination, LU decomposition, Gauss-Sideil, CGM and Cholesky
methods to\nsolve equations having relationships of Ax=b form. The package can be
used\nto build linear and non-linear models by defining them in linear
system.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"optR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Optimization Toolbox for solving linear
systems","Version":"1.1.1"},"optextras":{"Author":"John C. Nash [aut,
cre]","Depends":"numDeriv","Description":"Tools to assist in safely applying user-
generated objective and\nderivative functions to optimization
programs. \"Optimization\" at the\ntime of writing refers primarily to function
minimization methods with at most\nbounds and masks on the parameters.\nTools are
provided to check the basic computation of objective functions that\nthe user
provides, along with proposed gradient and Hessian functions,\nas well as to wrap
such functions to avoid failures when inadmissible parameters\nare provided. Checks
on bounds and masks (fixed parameters) are available, as\nare a check on scaling or
optimality conditions. An axial search to seek lower\npoints on the objective
function surface is included. Though numDeriv is\nused as the primary tool for
numerical derivative approximations, forward,\ncentral and backward gradient
approximation codes for convenience.","License":"GPL-
2","NeedsCompilation":"no","Package":"optextras","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Tools to Support Optimization Methods","Version":"2013-
10.28"},"optiRum":{"Author":"Stephanie Locke [aut, cre]","Depends":"R (>=
3.0.2)","Description":"This fills the gaps credit analysts and loan modellers
at\nOptimum Credit identify in the existing R code body.\nIt allows for the
production of documentation with less coding,\nreplicates a number of Microsoft
Excel functions useful for\nmodelling loans (without rounding), and other helpful
functions\nfor producing charts and tables. It also has some additional scales
for\nuse, including a GBP scale.","Imports":"data.table (>= 1.9.6), ggplot2, AUC,
grid, knitr, plyr,\nscales, stringr, XML","License":"GPL-
3","NeedsCompilation":"no","Package":"optiRum","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat, covr","Title":"Financial Functions &
More","Version":"0.37.3"},"optifunset":{"Author":"Nicholas
Hamilton","Description":"A single function 'options.ifunset(...)' is contained
herewith, which allows the user to set a global option ONLY if it is not already
set. By this token, for package maintainers this function can be used in preference
to the standard 'options(...)' function, making provision for THEIR end user to
place 'options(...)' directives within their '.Rprofile' file, which will not be
overridden at the point when a package is loaded.","License":"GPL-
2","NeedsCompilation":"no","Package":"optifunset","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Set Options if Unset","Version":"1.0"},"optigrab":
{"Author":"Christopher Brown","Depends":"R (>= 3.0.0),
methods","Description":"Parse options from the command-line using a simple, clean
syntax.\nIt requires little or no specification and supports short and long
options,\nGNU-, Java- or Microsoft- style syntaxes, verb commands and
more.","Imports":"stringi (>= 0.4.1), magrittr (>= 1.5)","License":"GPL (>= 2) |
file
LICENSE","NeedsCompilation":"no","Package":"optigrab","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat (>= 0.9.1), knitr (>= 1.9),
rmarkdown","Title":"Command-Line Parsing for an R
World","URL":"https:\/\/github.com\/decisionpatterns\/optigrab","Version":"0.7.3"},
"optimbase":{"Author":"Sebastien Bihorel, Michael Baudin (author of the
original\nmodule)","Depends":"Matrix, methods","Description":"Provides a set of
commands to manage an abstract\noptimization
method. The goal is to provide a building block\nfor a large class of specialized
optimization methods. This\npackage manages: the number of variables, the minimum
and\nmaximum bounds, the number of non linear inequality\nconstraints, the cost
function, the logging system, various\ntermination criteria,
etc...","License":"CeCILL-
2","NeedsCompilation":"no","Package":"optimbase","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"R port of the Scilab optimbase module","Version":"1.0-
9"},"optimsimplex":{"Author":"Sebastien Bihorel, Michael Baudin (author of the
original\nmodule)","Depends":"optimbase (>= 1.0-8),methods","Description":"Provides
a building block for optimization algorithms\nbased on a simplex. The optimsimplex
package may be used in the\nfollowing optimization methods: the simplex method of
Spendley\net al., the method of Nelder and Mead, Box's algorithm for\nconstrained
optimization, the multi-dimensional search by\nTorczon, etc...","License":"CeCILL-
2","NeedsCompilation":"no","Package":"optimsimplex","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"R port of the Scilab optimsimplex
module","Version":"1.0-5"},"optimx":{"Author":"John C Nash [aut, cre], Ravi
Varadhan [aut], Gabor Grothendieck [ctb]","Description":"Provides a replacement and
extension of the optim()\nfunction to unify and streamline optimization
capabilities in R\nfor smooth, possibly box constrained functions of several
or\nmany parameters. This is the CRAN version of the package.","Imports":"numDeriv,
ucminf, BB, Rcgmin, Rvmmin, minqa, setRNG, dfoptim,\nsvUnit","License":"GPL-
2","NeedsCompilation":"no","Package":"optimx","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"A Replacement and Extension of the optim()
Function","Version":"2013.8.7"},"optiscale":{"Author":"William G.
Jacoby","Depends":"lattice","Description":"Tools for performing an optimal scaling
transformation on a data\nvector","License":"GPL-
2","NeedsCompilation":"no","Package":"optiscale","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Optimal scaling","Version":"1.1"},"optismixture":
{"Author":"Hera Y. He, Art B. Owen","Depends":"R (>= 3.0.2)","Description":"Code
for optimal mixture weights in importance sampling. Workhorse\nfunctions
penoptpersp() and penoptpersp.alpha.only() minimize estimated\nvariances with and
without control variates respectively. It can be used in\nadaptive mixture
importance sampling, for example, function batch.estimation() does\ntwo stages, a
pilot estimate of mixing alpha and a following
importance\nsampling.","Imports":"mvtnorm, Matrix","License":"GPL-
2","NeedsCompilation":"no","Package":"optismixture","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Optimal Mixture Weights in Multiple Importance
Sampling","Version":"0.1"},"optmatch":{"Author":"Ben B. Hansen
<ben.hansen@umich.edu>, Mark Fredrickson\n<mark.m.fredrickson@gmail.com>, Josh
Buckner, Josh Errickson, and Peter\nSolenberger, with embedded Fortran code due to
Dimitri P. Bertsekas\n<dimitrib@mit.edu> and Paul Tseng","Depends":"R (>= 2.15.1),
stats, methods, graphics, survival","Description":"Provides routines for distance
based bipartite matching to reduce\ncovariate imbalance between treatment and
control groups in observational\nstudies. Routines are provided to generate
distances from GLM models (propensity\nscore matching) and formulas (Euclidean and
Mahalanobis matching), stratified\nmatching (exact matching), and calipers. Results
of the fullmatch routine are\nguaranteed to provide minimum average within matched
set distance.","Imports":"Rcpp, RItools, digest","License":"file
LICENSE","NeedsCompilation":"yes","Package":"optmatch","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"boot, biglm, testthat, brglm,
arm","Title":"Functions for Optimal Matching","URL":"http:\/\/www.r-
project.org,\nhttps:\/\/github.com\/markmfredrickson\/optmatch","Version":"0.9-
5"},"optparse":{"Author":"Trevor L Davis. Some documentation and examples ported
from Allen Day's\ngetopt package. Some documentation from the optparse Python
module by the\nPython Software Foundation. Contributions from Steve Lianoglou,
Jim\nNikelski, Kirill MÃ¼ller, Peter Humburg, and Rich FitzJohn.","Depends":"R (>=
2.9.0)","Description":"A command line parser inspired by Python's 'optparse'
library to\nbe used with Rscript to write \"#!\" shebang scripts that accept short
and\nlong flag\/options.","Imports":"methods, getopt (>= 1.19)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"optparse","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr, stringr, testthat","Title":"Command Line
Option
Parser","URL":"https:\/\/github.com\/trevorld\/optparse","Version":"1.3.2"},"optpar
t":{"Author":"David W. Roberts <droberts@montana.edu>","Depends":"cluster, labdsv,
MASS, plotrix","Description":"Contains a set of algorithms for creating\npartitions
and coverings of objects largely based on operations\non (dis)similarity relations
(or matrices). There are several\niterative re-assignment algorithms optimizing
different\ngoodness-of-clustering criteria. In addition, there are\ncovering
algorithms 'clique' which derives maximal cliques, and\n'maxpact' which creates a
covering of maximally compact sets.\nGraphical analyses and conversion routines are
also included.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"optpart","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"tree","Title":"Optimal Partitioning of Similarity
Relations","URL":"http:\/\/ecology.msu.montana.edu\/labdsv\/R","Version":"2.2-
0"},"optrees":{"Author":"Manuel Fontenla [aut, cre]","Depends":"R (>= 2.7.0),
igraph (>= 0.7.1)","Description":"Finds optimal trees in weighted graphs.
In\nparticular, this package provides solving tools for minimum cost spanning\ntree
problems, minimum cost arborescence problems, shortest path tree\nproblems and
minimum cut tree problem.","License":"GPL-
3","NeedsCompilation":"no","Package":"optrees","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Optimal Trees in Weighted Graphs","Version":"1.0"},"orQA":
{"Author":"Florian Klinglmueller","Depends":"Rcpp (>= 0.8.9), gtools (>= 2.6.1),
genefilter (>= 1.24.3),\nnlme (>= 3.1-96)","Description":"Assess repeatability,
accuracy and corss-platform\nagreement of titration microarray data based on
order\nrestricted inference procedures","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"orQA","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Order Restricted Assessment Of Microarray Titration
Experiments","Version":"0.2.1"},"ora":{"Author":"Arni Magnusson","Depends":"DBI,
ROracle","Description":"Easy-to-use functions to explore Oracle databases and
import data\ninto R. User interface for the ROracle package.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ora","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Convenient Tools for Working with Oracle
Databases","Version":"2.0-1"},"orca":{"Author":"Tomaz Hocevar, Janez
Demsar","Depends":"R (>= 3.1)","Description":"Implements orbit counting using a
fast combinatorial approach.\nCounts orbits of nodes and edges from edge matrix or
data frame, or a\ngraph object from the graph
package.","Enhances":"graph","License":"LGPL-
3","NeedsCompilation":"yes","Package":"orca","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Computation of Graphlet Orbit Counts in Sparse
Graphs","Version":"1.1"},"orclus":{"Author":"Gero
Szepannek","Description":"Functions to perform subspace clustering
and\nclassification.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"orclus","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"ORCLUS subspace clustering","Version":"0.2-5"},"orcutt":
{"Author":"Stefano Spada, Matteo Quartagno, Marco Tamburini","Description":"This
package has been implemented to solve first order\nautocorrelation problems using
an iterative method. This\nprocedure estimates both autocorrelation and beta
coefficients\nrecursively until we reach the convergence (8th decimal).
The\nresiduals are computed after estimating Beta using EGLS\napproach and Rho is
estimated using the previous residuals.","License":"GPL-
2","NeedsCompilation":"no","Package":"orcutt","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Estimate procedure in case of first order
autocorrelation","Version":"1.1"},"ordBTL":{"Author":"Giuseppe
Casalicchio","Depends":"caret, VGAM, wikibooks, gtools","Description":"This package
extends the Bradley-Terry-Luce model for fitting pair\ncomparison models with an
ordinal response. It is also possible to\nincorporate an order effect, or,
equivalently, an effect for the home\nadvantage.","License":"GPL-
3","NeedsCompilation":"no","Package":"ordBTL","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"BradleyTerry2, prefmod, psychotree, psychotools,
psychomix","Title":"Modelling comparison data with ordinal
response","Version":"0.8"},"ordPens":{"Author":"Jan Gertheiss","Depends":"grplasso,
mgcv, RLRsim, tcltk","Description":"Selection and\/or smoothing of ordinally scaled
independent variables using a group lasso or generalized ridge
penalty.","License":"GPL-
2","NeedsCompilation":"no","Package":"ordPens","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"IsoGene, Biobase","Title":"Selection and\/or Smoothing
of Ordinal Predictors","Version":"0.3-1"},"orddom":{"Author":"Jens J. Rogmann,
University of Hamburg, Department of\nPsychology,
Germany","Depends":"psych","Description":"Computes ordinal, statistics and effect
sizes as an\nalternative to mean comparison: Cliff's delta or success
rate\ndifference (SRD), Vargha and Delaney's A or the Area Under a\nReceiver
Operating Characteristic Curve (AUC), the discrete\ntype of McGraw & Wong's Common
Language Effect Size (CLES) or\nGrissom & Kim's Probability of Superiority (PS),
and the Number\nneeded
to treat (NNT) effect size. Moreover, comparisons to\nCohen's d are offered based
on Huberty & Lowman's Percentage of\nGroup (Non-)Overlap
considerations.","License":"GPL-
2","NeedsCompilation":"no","Package":"orddom","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Ordinal Dominance Statistics","Version":"3.1"},"orderbook":
{"Author":"Andrew Liu, Khanh Nguyen, David Kane","Depends":"R (>= 2.15.0), methods,
graphics, lattice, hash, grid","Description":"Functions for visualizing and
retrieving data for the\nstate of an orderbook at a particular period in
time.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"orderbook","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Orderbook visualization\/Charting
software","Version":"1.03"},"orderedLasso":{"Author":"Jerome Friedman, Xiaotong Suo
and Robert Tibshirani","Depends":"R (>= 3.0.0), Matrix","Description":"Ordered
lasso and time-lag sparse regression. Ordered Lasso fits a\nlinear model and
imposes an order constraint on the coefficients. It writes\nthe coefficients as
positive and negative parts, and requires positive\nparts and negative parts are
non-increasing and positive. Time-Lag Lasso\ngeneralizes the ordered Lasso to a
general data matrix with multiple\npredictors. For more details, see Suo,
X.,Tibshirani, R., (2014) 'An\nOrdered Lasso and Sparse Time-lagged
Regression'.","Imports":"Iso,quadprog,ggplot2,reshape2","License":"GPL-
2","NeedsCompilation":"yes","Package":"orderedLasso","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Ordered Lasso and Time-lag Sparse
Regression","Version":"1.7"},"ordiBreadth":{"Author":"James
Fordyce","Depends":"vegan","Description":"Calculates ordinated diet breadth with
some plotting functions.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"ordiBreadth","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Ordinated Diet Breadth","Version":"1.0"},"ordinal":
{"Author":"Rune Haubo Bojesen Christensen [aut, cre]","Depends":"R (>= 2.13.0),
methods","Description":"Implementation of cumulative link (mixed) models also
known\nas ordered regression models, proportional odds models,
proportional\nhazards models for grouped survival times and ordered
logit\/probit\/...\nmodels. Estimation is via maximum likelihood and mixed models
are fitted\nwith the Laplace approximation and adaptive Gauss-Hermite
quadrature.\nMultiple random effect terms are allowed and they may be nested,
crossed or\npartially nested\/crossed. Restrictions of symmetry and equidistance
can be\nimposed on the thresholds (cut-points\/intercepts). Standard model\nmethods
are available (summary, anova, drop-methods, step,\nconfint, predict etc.) in
addition to profile methods and slice\nmethods for visualizing the likelihood
function and checking\nconvergence.","Imports":"ucminf, MASS,
2)","NeedsCompilation":"yes","Package":"ordinal","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"lme4, nnet, xtable, testthat (>=
0.8)","Title":"Regression Models for Ordinal Data","Version":"2015.6-
28"},"ordinalCont":{"Author":"Maurizio Manuguerra [aut, cre],\nGillian Heller
[aut]","Depends":"R (>= 3.1.1), fastGHQuad, boot, ucminf","Description":"A
regression framework for response variables which are continuous self-rating scales
such as the Visual Analog Scale (VAS) used in pain assessment, or the Linear Analog
Self-Assessment (LASA) scales in quality of life studies. These scales measure
subjects' perception of an intangible quantity, and cannot be handled as ratio
variables because of their inherent nonlinearity. We treat them as ordinal
variables, measured on a continuous scale. A function (the g function, currently
the generalized logistic function) connects the scale with an underlying continuous
latent variable. The link function is the inverse of the CDF of the assumed
underlying distribution of the latent variable. Currently the logit link, which
corresponds to a standard logistic distribution, is implemented.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"ordinalCont","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Ordinal Regression Analysis for Continuous
Scales","Version":"0.4"},"ordinalNet":{"Author":"Mike Wurm [aut,
cre]","Description":"Fits ordinal regression models with elastic net penalty.
Supported\nmodels include cumulative logit, probit, cauchit, and complementary log-
log.\nThe algorithm uses Fisher Scoring with Coordinate Descent
updates.","Imports":"stats","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"ordinalNet","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Penalized Ordinal
Regression","Version":"1.4"},"ordinalgmifs":{"Author":"Kellie J. Archer, Jiayi Hou,
Qing Zhou, Kyle Ferber, John G. Layne, Amanda Gentry","Depends":"R (>=
2.10)","Description":"This package provides a function for fitting cumulative link,
adjacent category, forward and backward continuation ratio, and stereotype ordinal
response models when the number of parameters exceeds the sample size, using the
the generalized monotone incremental forward stagewise method.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ordinalgmifs","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"Biobase","Title":"Ordinal Regression for High-
dimensional Data","Version":"1.0.2"},"ore":{"Author":"Jon Clayden, based on Onigmo
by K. Kosako and K. Takata","Description":"Provides an alternative to R's built-in
functionality for handling\nregular expressions, based on the Oniguruma library.
Offers first-class\ncompiled regex objects, partial matching and function-based
substitutions,\namongst other features.","License":"BSD_3_clause + file
LICENCE","NeedsCompilation":"yes","Package":"ore","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"crayon, rex, testthat","Title":"An R Interface to
the Oniguruma Regular Expression
Library","URL":"https:\/\/github.com\/jonclayden\/ore","Version":"1.3.0"},"ores":
{"Author":"Oliver Keyes [aut, cre], Aaron Halfaker [ctb], Yuvi Panda
[ctb]","Depends":"R (>= 3.1.2), httr","Description":"A connector to ORES
(<http:\/\/ores.wmflabs.org\/>), an AI project to provide edit scoring for
content\non Wikipedia and other Wikimedia projects. This lets a researcher
identify\nif edits are likely to be reverted, damaging, or made in good
faith.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"ores","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat, knitr, rmarkdown","Title":"Connector to
the Objective Revision Evaluation Service
(ORES)","URL":"https:\/\/github.com\/Ironholds\/ores","Version":"0.1.0"},"orgR":
{"Author":"Yi Tang","Depends":"ggthemes (>= 1.7.0), ggplot2 (>= 1.0.0),
lubridate(>= 1.3.3),\ndata.table (>= 1.9.4), stringr (>=
0.6.2)","Description":"Provides functionality to process text files created by
Emacs' Org mode, and decompose the content to the smallest components (headlines,
body, tag, clock entries etc). Emacs is an extensible, customizable text editor
and Org mode is for keeping notes, maintaining TODO lists, planning projects.
Allows users to analyze org files as data frames in R, e.g., to convieniently group
tasks by tag into project and calculate total working hours. Also provides some
help functions like search.parent, gg.pie (visualise working hours in ggplot2) and
tree.headlines (visualise headline stricture in tree format) to help user managing
their complex org files.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"orgR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Analyse Text Files Created by Emacs' Org
mode","Version":"0.9.0"},"orientlib":{"Author":"Duncan Murdoch","Depends":"R (>=
2.13.0), methods","Description":"Representations, conversions and display of
orientation\nSO(3) data. See the orientlib help topic for
details.","License":"GPL","NeedsCompilation":"no","Package":"orientlib","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"rgl,
scatterplot3d","Title":"Support for orientation data","Version":"0.10.3"},"orloca":
{"Author":"Fernando Fernandez-Palacin <fernando.fernandez@uca.es> and
Manuel\nMunoz-Marquez
<manuel.munoz@uca.es>","Depends":"methods","Description":"This version of the
package deals with the min-sum location\nproblem, also known as Fermat--Weber
problem. The min-sum location problem\nsearch for a point such that the weighted
sum of the distances to the\ndemand points are minimized.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"orloca","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"grDevices, graphics, png, ucminf","Title":"The package
deals with Operations Research LOCational
Analysis\nmodels","URL":"http:\/\/knuth.uca.es\/orloca","Version":"4.2"},"orloca.es
":{"Author":"Fernando Fernandez-Palacin <fernando.fernandez@uca.es> and\nManuel
Munoz-Marquez <manuel.munoz@uca.es>","Depends":"orloca (>=
4.1)","Description":"Version espanola del paquete orloca que trata el problema\nde
localizacion min-sum, tambien conocido como problema de\nFermat--Weber. El problema
de localizacion min-sum busca un\npunto tal que la suma ponderada de las distancias
a los puntos\nde demanda sea minima.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"orloca.es","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Spanish version of orloca
package","URL":"http:\/\/knuth.uca.es\/orloca","Version":"4.1"},"oro.dicom":
{"Author":"Brandon Whitcher [aut, cre]","Depends":"R (>=
2.14.0)","Description":"Data input\/output functions for data that conform to
the\nDigital Imaging and Communications in Medicine (DICOM) standard, part\nof the
Rigorous Analytics bundle.","Imports":"utils, oro.nifti (>=
LICENSE","NeedsCompilation":"no","Package":"oro.dicom","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat,
hwriter","Title":"Rigorous - DICOM Input \/
Output","URL":"http:\/\/rig.oro.us.com,
http:\/\/rigorousanalytics.blogspot.com","Version":"0.5.0"},"oro.nifti":
{"Author":"Brandon Whitcher [aut, cre],\nVolker Schmid [aut],\nAndrew Thornton
[aut],\nKarsten Tabelow [ctb],\nJon Clayden [ctb],\nJohn Muschelli
[ctb]","Depends":"R (>= 2.14.0)","Description":"Functions for the input\/output and
visualization of\nmedical imaging data that follow either the ANALYZE, NIfTI or
AFNI\nformats. This package is part of the Rigorous Analytics
bundle.","Enhances":"dcemriS4, fmri, oro.dicom","Imports":"bitops, splines,
graphics, grDevices, methods, utils, abind","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"oro.nifti","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"XML, testthat","Title":"Rigorous - NIfTI +
ANALYZE + AFNI : Input \/ Output","URL":"http:\/\/rig.oro.us.com,
http:\/\/rigorousanalytics.blogspot.com","Version":"0.5.2"},"oro.pet":
{"Author":"Brandon Whitcher","Depends":"R (>= 2.14.0)","Description":"Image
analysis techniques for positron emission tomography\n(PET) that form part of the
Rigorous Analytics bundle.","Imports":"grDevices, methods, oro.dicom (>= 0.3.7),
oro.nifti (>=\n0.3.9), utils","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"oro.pet","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"minpack.lm, msm","Title":"Rigorous - Positron
Emission Tomography","URL":"http:\/\/rig.oro.us.com,
http:\/\/rigorousanalytics.blogspot.com","Version":"0.2.3"},"orsifronts":
{"Author":"Michael D. Sumner [aut, cre]","Depends":"sp","Description":"A data set
package with the \"Orsi\" fronts as a\n'SpatialLinesDataFrame' object. The Orsi et
al. (1995) fronts are published at\nthe Southern Ocean Atlas Database Page, please
see package CITATION for details.","License":"GPL-
3","NeedsCompilation":"no","Package":"orsifronts","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr","Title":"Southern Ocean Frontal Distributions
(Orsi)","Version":"0.1.1"},"orsk":{"Author":"Zhu Wang","Description":"Convert the
Odds Ratio to the Relative Risk in Cohort Studies with Partial Data
Information.","Imports":"BB, BHH2","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"orsk","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"setRNG","Title":"Converting Odds Ratio to Relative Risk
in Cohort Studies with\nPartial Data Information","Version":"1.0-
2"},"orthogonalsplinebasis":{"Author":"Andrew Redd","Depends":"methods, stats,
graphics","Description":"Represents the basis functions for B-splines in a simple
matrix\nformulation that facilitates, taking integrals, derivatives, and\nmaking
orthogonal the basis functions.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"orthogonalsplinebasis","Repository":"http:\/
\/cran.csiro.au\/src\/contrib","Title":"Orthogonal B-Spline Basis
Functions","URL":"https:\/\/github.com\/halpo\/obsplines","Version":"0.1.6"},"ortho
polynom":{"Author":"Frederick Novomestky <fnovomes@poly.edu>","Depends":"R (>=
2.0.1), polynom","Description":"A collection of functions to construct sets of
orthogonal\npolynomials and their recurrence relations. Additional\nfunctions are
provided to calculate the derivative, integral,\nvalue and roots of lists of
polynomial objects.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"orthopolynom","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Collection of functions for orthogonal and
orthonormal\npolynomials","Version":"1.0-5"},"osDesign":{"Author":"Sebastien
Haneuse, Takumi Saegusa, Nilanjan Chaterjee, Norman Breslow, Elizabeth
Smoot","Depends":"R (>= 2.10)","Description":"The osDesign serves for planning an
observational study. Currently, functionality is focused on the two-phase and case-
control designs. Functions in this packages provides Monte Carlo based evaluation
of operating characteristics such as powers for estimators of the components of a
logistic regression model.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"osDesign","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Design and analysis of observational
studies","Version":"1.7"},"osd":{"Author":"Xavier Domingo-
Almenara","Description":"Compound deconvolution for chromatographic data, including
gas chromatography - mass spectrometry (GC-MS) and comprehensive gas chromatography
- mass spectrometry (GCxGC-MS). The package includes functions to perform
independent component analysis - orthogonal signal deconvolution (ICA-OSD),
independent component regression (ICR), multivariate curve resolution (MCR-ALS) and
orthogonal signal deconvolution (OSD) alone.","Imports":"JADE, nnls","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"osd","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Orthogonal Signal Deconvolution for Spectra Deconvolution
in\nGC-MS and GCxGC-MS Data","Version":"0.1"},"osmar":{"Author":"Thomas Schlesinger
and Manuel J. A. Eugster","Depends":"R (>= 2.10), methods, XML, RCurl,
geosphere","Description":"This package provides infrastructure to
access\nOpenStreetMap data from different sources, to work with the data\nin common
R manner, and to convert data into available\ninfrastructure provided by existing R
packages (e.g., into sp and\nigraph objects).","License":"GPL-
2","NeedsCompilation":"no","Package":"osmar","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"igraph, sp (>= 0.9-93)","Title":"OpenStreetMap and
R","URL":"http:\/\/osmar.r-forge.r-project.org\/","Version":"1.1-7"},"osmplotr":
{"Author":"Mark Padgham [aut, cre]","Depends":"R (>=
3.2.3)","Description":"Produces customisable images of OpenStreetMap (OSM) data and
enables data visualisation using OSM objects.","Imports":"ggm, igraph, httr,
methods, osmar, rgeos, sp, spatstat, XML,","License":"GPL-
3","NeedsCompilation":"no","Package":"osmplotr","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr, roxygen2, rmarkdown, devtools, maptools,
RColorBrewer,\nwesanderson","Title":"Customisable Images of OpenStreetMap
Data","URL":"https:\/\/github.com\/mpadge\/osmplotr","Version":"0.1-3"},"osrm":
{"Author":"TimothÃ©e Giraud [cre, aut]","Depends":"R (>= 2.10)","Description":"An
interface between R and the OSRM API. OSRM is a routing\nservice based on
OpenStreetMap data. See <http:\/\/project-osrm.org\/> for more\ninformation. A
public API exists but one can run its own instance. This package\nallows to compute
distances (travel time and kilometric distance) between points\nand travel time
matrices.","Imports":"jsonlite, sp, RCurl, utils","License":"GPL-
3","NeedsCompilation":"no","Package":"osrm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Interface Between R and the OpenStreetMap-Based Routing
Service\nOSRM","URL":"https:\/\/github.com\/rCarto\/osrm","Version":"2.0.0"},"ouch"
:{"Author":"Aaron A. King <kingaa@umich.edu> and Marguerite A. Butler
<mbutler@hawaii.edu>","Depends":"R(>= 3.0.0), methods, stats, graphics,
subplex","Description":"Fit and compare Ornstein-Uhlenbeck models for evolution
along a phylogenetic tree.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"ouch","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"ape, geiger","Title":"Ornstein-Uhlenbeck Models for
Phylogenetic
Comparative\nHypotheses","URL":"http:\/\/kingaa.github.io\/ouch\/","Version":"2.9-
2"},"outbreaker":{"Author":"Thibaut Jombart <thibautjombart@gmail.com>, Anne Cori,
Joel Hellewell","Depends":"R (>= 3.0.0), parallel","Description":"Bayesian
reconstruction of disease outbreaks using epidemiological\nand genetic
information.","Imports":"utils, graphics, ape, igraph, adegenet","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"outbreaker","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"EpiEstim, OutbreakTools","Title":"Bayesian
Reconstruction of Disease Outbreaks by Combining\nEpidemiologic and Genomic
Data","URL":"http:\/\/sites.google.com\/site\/therepiproject\/r-
pac\/outbreaker","Version":"1.1-7"},"outliers":{"Author":"Lukasz Komsta
<lukasz.komsta@umlub.pl>","Depends":"R (>= 2.0)","Description":"A collection of
some tests commonly used for identifying\noutliers.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"outliers","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Tests for outliers","URL":"http:\/\/www.r-project.org,
http:\/\/www.komsta.net\/","Version":"0.14"},"overlap":{"Author":"Mike Meredith and
Martin Ridout","Description":"Provides functions to fit kernel density functions
to\ndata on temporal activity patterns of animals; estimate coefficients\nof
overlapping of densities for two species; and calculate bootstrap\nestimates of
confidence intervals.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"overlap","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Estimates of Coefficient of Overlapping for Animal
Activity\nPatterns","Version":"0.2.6"},"overlapping":{"Author":"Massimiliano
Pastore","Depends":"R (>= 3.2.0), lattice","Description":"Functions for estimating
the overlapping area of two or more empirical distributions.","License":"GPL-
2","NeedsCompilation":"no","Package":"overlapping","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Estimation of Overlapping in Empirical
Distributions","Version":"1.2"},"oz":{"Author":"Bill Venables [aut] (S
original),\nKurt Hornik [aut, cre] (R port)","Description":"Functions for plotting
Australia's coastline and state\nboundaries.","Imports":"graphics","License":"GPL-
2","NeedsCompilation":"no","Package":"oz","Repository":"http:\/\/cran.csiro.au\/src
\/contrib","Title":"Plot the Australian Coastline and States","Version":"1.0-
20"},"p2distance":{"Author":"A.J. Perez-Luque; R. Moreno; R. Perez-Perez and F.J.
Bonet","Description":"The welfare's synthetic indicator provides an ideal tool\nfor
measuring multi-dimensional
concepts such as welfare,\ndevelopment, living standards, etc. It enables
information from\nthe various indicators to be aggregated into a single
synthetic\nmeasure.","License":"GPL","NeedsCompilation":"no","Package":"p2distance"
,"Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Welfare's Synthetic
Indicator","Version":"1.0.1"},"p3state.msm":{"Author":"Luis Meira-Machado and
Javier Roca-Pardinas <roca@uvigo.es>","Depends":"R (>=
2.8.1),survival,base","Description":"Analyzing survival data from illness-death
model","License":"GPL","NeedsCompilation":"no","Package":"p3state.msm","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Title":"Analyzing survival
data","Version":"1.3"},"pAnalysis":{"Author":"Joseph G Kreke, PhD; Harris,
Inc.\nSangeet Khemlani, PhD; Naval Research Laboratory.\nGreg Trafton, PhD; Naval
Research Laboratory.","Depends":"ggplot2, coin, grDevices, graphics,
stats","Description":"Provides the tools needed to benchmark the R2 value
corresponding to a certain acceptable noise level while also providing a rescaling
function based on that noise level yielding a new value of R2 we refer to as R2k
which is independent of both the number of degrees of freedom and the noise
distribution function.","License":"GPL-
2","NeedsCompilation":"no","Package":"pAnalysis","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Benchmarking and Rescaling R2 using Noise Percentile
Analysis","Version":"2.0"},"pBrackets":{"Author":"Andreas Schulz","Depends":"R (>=
3.0.0)","Description":"Adds different kinds of brackets to a plot, including
braces, chevrons, parentheses or square brackets.","Imports":"grid","License":"GPL
(>=
2.0)","NeedsCompilation":"no","Package":"pBrackets","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Plot Brackets","Version":"1.0"},"pGLS":
{"Author":"Xianyun Mao <xianyunmao@gmail.com> and Timothy
Ryan\n<tmr21@psu.edu>","Depends":"MASS","Description":"Based on the Generalized
Least Square model for\ncomparative Phylogenetics (ref).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pGLS","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Generalized Least Square in comparative
Phylogenetics","Version":"0.0-1"},"pRF":{"Author":"Ankur
Chakravarthy","Depends":"R(>= 3.1.0)","Description":"Estimate False Discovery Rates
(FDRs) for importance metrics from\nrandom forest runs.","Imports":"ggplot2,
permute, randomForest, reshape2, dplyr(>= 0.4.1),\nmulttest(>=
3","NeedsCompilation":"no","Package":"pRF","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Permutation Significance for Random
Forests","Version":"1.2"},"pROC":{"Author":"Xavier Robin, Natacha Turck, Alexandre
Hainard, Natalia Tiberti, FrÃ©dÃ©rique Lisacek, Jean-Charles Sanchez and Markus
MÃ¼ller.","Depends":"R (>= 2.14)","Description":"Tools for visualizing, smoothing
and comparing receiver operating characteristic (ROC curves). (Partial) area under
the curve (AUC) can be compared with statistical tests based on U-statistics or
bootstrap. Confidence intervals can be computed for (p)AUC or ROC
curves.","Imports":"plyr, utils, methods, Rcpp (>= 0.11.1)","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"pROC","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"microbenchmark, tcltk, MASS, logcondens,
doParallel","Title":"Display and Analyze ROC
Curves","URL":"http:\/\/expasy.org\/tools\/pROC\/","Version":"1.8"},"pRSR":
{"Author":"M. S. Islam","Depends":"R (>= 2.10)","Description":"Test of periodicity
in short time series using response surface regression","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"pRSR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Test of periodicity using response surface
regression","Version":"3.0.2"},"pSI":{"Author":"Xiaoxiao Xu, Alan B. Wells, David
OBrien, Arye Nehorai, Joseph D. Dougherty","Depends":"R (>= 2.10),
gdata","Description":"This package contains functions to calculate the Specificity
Index statistic, which can be used for comparative quantitative analysis to
identify genes enriched in specific cell populations across a large number of
profiles, as well as perform numerous post-processing operations.
NOTE:Supplementary data (human & mouse expression sets, calculated pSI datasets,
etc.) can be found in pSI.data package located at the following URL:
http:\/\/genetics.wustl.edu\/jdlab\/psi_package\/","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pSI","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Specificity Index Statistic","Version":"1.1"},"pa":
{"Author":"Yang Lu [aut, cre],\nDavid Kane [aut]","Depends":"grid, R (>=
2.10)","Description":"A package that provides tools for conducting performance
attribution for equity portfolios. The package uses two methods: the Brinson method
and a regression-based analysis.","Imports":"ggplot2, methods","License":"GPL-
2","NeedsCompilation":"no","Package":"pa","Repository":"http:\/\/cran.csiro.au\/src
\/contrib","Title":"Performance Attribution for Equity Portfolios","Version":"1.2-
1"},"pacbpred":{"Author":"Benjamin Guedj","Description":"This package is intended
to perform estimation and\nprediction in high-dimensional additive models, using a
sparse\nPAC-Bayesian point of view and a MCMC algorithm. The method is\nfully
described in Guedj and Alquier (2013), 'PAC-Bayesian\nEstimation and Prediction in
Sparse Additive Models',\nElectronic Journal of Statistics, 7, 264--
2)","NeedsCompilation":"no","Package":"pacbpred","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"PAC-Bayesian Estimation and Prediction in Sparse
Additive\nModels","URL":"http:\/\/www.lsta.upmc.fr\/doct\/guedj\/index.html","Versi
on":"0.92.2"},"pack":{"Author":"Josh Ulrich","Description":"Functions to easily
convert data to binary formats other programs\/machines can
understand.","License":"GPL-
3","NeedsCompilation":"no","Package":"pack","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Convert values to\/from raw vectors","Version":"0.1-
1"},"packClassic":{"Author":"Christophe
Genolini","Depends":"graphics","Description":"This package comes to illustrate the
book \"Petit Manuel de\nProgrammation Orientee Objet sous R\"","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"packClassic","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Toy example of Pack Classic","URL":"www.r-
project.org","Version":"0.5.2"},"packHV":{"Author":"Hugo
Varet","Depends":"survival","Description":"Various useful functions for
statisticians: describe data, plot Kaplan-Meier curves with numbers of subjects at
risk, compare data sets, display spaghetti-plot, build multi-contingency
tables...","Imports":"WriteXLS (>= 2.3.0)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"packHV","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"A few useful functions for
statisticians","Version":"1.8"},"packS4":{"Author":"Christophe
Genolini","Depends":"methods, graphics, codetools","Description":"Illustration of
the book \"Petit Manuel de Programmation Orientee Objet sous R\". The english
version \"A (Not so) Short Introduction to S4\" is on CRAN, 'Contributed
documentation'.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"packS4","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Toy Example of S4 Package","URL":"www.r-
project.org,christophe.genolini.free.fr\/webTutorial","Version":"0.9.3"},"packagetr
ackr":{"Author":"Jirka Lewandowski","Depends":"magrittr","Description":"Allows to
get and cache R package download log files\nfrom RStudio's CRAN mirror for
analyzing package usage.","Imports":"rappdirs, utils, httr (>= 1.0.0), dplyr (>=
0.4.3)","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"packagetrackr","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Track R Package Downloads from RStudio's CRAN
Mirror","URL":"\nhttp:\/\/gitlab.points-of-interest.cc\/points-of-
interest\/packagetrackr\nhttp:\/\/cran-
logs.rstudio.com\/","Version":"0.1.1"},"packcircles":{"Author":"Michael Bedward
[aut, cre],\nDavid Eppstein [aut] (Original author of Python code for graph-
based\ncircle packing ported to C++ for this package)","Description":"Simple
algorithm to arrange non-overlapping circles within a rectangle.","Imports":"Rcpp
LICENSE","NeedsCompilation":"yes","Package":"packcircles","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"ggplot2, gridExtra, knitr","Title":"Circle
Packing","URL":"https:\/\/github.com\/mbedward\/packcircles","Version":"0.1.1"},"pa
ckrat":{"Author":"Kevin Ushey, Jonathan McPherson, Joe Cheng, Aron Atkins, JJ
Allaire","Depends":"R (>= 3.0.0)","Description":"Manage the R packages your project
depends\non in an isolated, portable, and reproducible
way.","Enhances":"BiocInstaller","Imports":"tools, utils","License":"GPL-
2","NeedsCompilation":"no","Package":"packrat","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat (>= 0.7), devtools, httr, knitr,
rmarkdown","Title":"A Dependency Management System for Projects and their R
Package\nDependencies","URL":"https:\/\/github.com\/rstudio\/packrat\/","Version":"
0.4.7-1"},"pacman":{"Author":"Tyler Rinker [aut, cre, ctb], Dason Kurkiewicz [aut,
ctb],\nKeith Hughitt [ctb]","Depends":"R (>= 3.0.2)","Description":"Tools to more
conveniently perform tasks associated with\nadd-on packages. pacman conveniently
wraps library and package\nrelated functions and names them in an intuitive and
consistent\nfashion. It seeks to combine functionality from lower level\nfunctions
which can speed up workflow.","Imports":"devtools, methods, stats,
2","NeedsCompilation":"no","Package":"pacman","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"knitr, lattice, testthat (>= 0.9.0),
XML","Title":"Package Management
Tool","URL":"https:\/\/github.com\/trinker\/pacman","Version":"0.4.1"},"paco":
{"Author":"Juan
Antonio Balbuena <j.a.balbuena@uv.es>, Timothee Poisot\n<tim@poisotlab.io>,
Matthew Hutchinson <matthewhutchinson15@gmail.com>,\nFernando Cagua
<fernando@cagua.co>","Depends":"R (>= 3.0.0)","Description":"Procrustes analyses to
infer co-phylogenetic\nmatching between pairs of (ultrametric) phylogenetic
trees.","Imports":"vegan (>= 2.2-0), plyr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"paco","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"ape, doMC","Title":"Procrustes Application to
Cophylogenetic
Analysis","URL":"http:\/\/www.uv.es\/cophylpaco\/","Version":"0.2.3"},"paf":
{"Author":"Li Chen","Depends":"R(>= 2.13.0), survival","Description":"Calculate
unadjusted\/adjusted attributable fraction function of a set of covariates for a
censored survival outcome from a Cox model using the method proposed by Chen, Lin
and Zeng (Biometrika 97, 713-726., 2010).","License":"GPL-
2","NeedsCompilation":"no","Package":"paf","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Attributable Fraction Function for Censored Survival
Data","Version":"1.0"},"pagenum":{"Author":"Kevin Wright [aut,
cre]","Description":"A simple way to add page numbers to base\/ggplot\/lattice
graphics.","Imports":"grid","License":"GPL-
2","NeedsCompilation":"no","Package":"pagenum","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"ggplot2, knitr, lattice","Title":"Put Page Numbers on
Graphics","URL":"https:\/\/github.com\/kwstat\/pagenum","Version":"1.0"},"pageviews
":{"Author":"Oliver Keyes","Description":"Pageview data from the 'Wikimedia' sites,
such as\n'Wikipedia' (https:\/\/www.wikipedia.org\/), from entire projects to per-
article\nlevels of granularity, through the new RESTful API and data source
(https:\/\/\nwikimedia.org\/api\/rest_v1\/?doc).","Imports":"jsonlite,
httr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"pageviews","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat, knitr, rmarkdown, WikipediR,
WikidataR","Title":"An API Client for Wikimedia Traffic
Data","URL":"https:\/\/github.com\/ironholds\/pageviews","Version":"0.2.0"},"paired
CI":{"Author":"Cornelia Froemke, Ludwig Hothorn and Michael
Schneider","Description":"The package contains two functions: paired.Loc
and\npaired.Scale. A parametric and nonparametric confidence\ninterval can be
computed for the ratio of locations\n(paired.Loc) and the ratio of scales
(paired.Scale). The\nsamples must be paired and expected values must be
positive.","License":"GPL-
2","NeedsCompilation":"no","Package":"pairedCI","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Confidence intervals for the ratio of locations and for
the\nratio of scales of two paired samples","Version":"0.5-4"},"pairheatmap":
{"Author":"Xiaoyong Sun","Depends":"R (>= 2.10.0), grid","Description":"A tool to
compare two heatmaps and discover patterns\nwithin and across groups. In the
context of biology, group can\nbe defined based on gene ontology.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"pairheatmap","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"A tool for comparing
heatmaps","Version":"1.0.1"},"pairsD3":{"Author":"Garth Tarr [aut,
cre]","Depends":"R (>= 3.1.2)","Description":"Creates an interactive scatterplot
matrix using the D3 JavaScript library. See <http:\/\/d3js.org\/> for more
information on D3.","Imports":"htmlwidgets (>= 0.3.2), shiny","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"pairsD3","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr","Title":"D3 Scatterplot
Matrices","URL":"http:\/\/github.com\/garthtarr\/pairsD3\/","Version":"0.1.0"},"pai
rwise":{"Author":"Joerg-Henrik Heine <jhheine@googlemail.com>","Depends":"R (>=
2.10.1)","Description":"Performs the explicit calculation\n-- not estimation! -- of
the Rasch item parameters for dichotomous and\npolytomous item responses, using a
pairwise comparison approach. Person\nparameters (WLE) are calculated according to
Warm's weighted likelihood\napproach.","Imports":"graphics, stats,
3","NeedsCompilation":"no","Package":"pairwise","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"psych","Title":"Rasch Model Parameters by Pairwise
Algorithm","Version":"0.3.1"},"pairwiseCI":{"Author":"Frank Schaarschmidt [aut,
cre], Daniel Gerhard [aut]","Depends":"MCPAN","Description":"Calculation of the
parametric, nonparametric confidence intervals\nfor the difference or ratio of
location parameters, nonparametric confidence interval\nfor the Behrens-Fisher
problem and for the difference, ratio and odds-ratio of binomial\nproportions for
comparison of independent samples. Common wrapper functions to split\ndata sets and
apply confidence intervals or tests to these subsets.\nA by-statement allows
calculation of CI separately for the levels of further factors.\nCI are not
adjusted for multiplicity.","Imports":"graphics, stats, coin, boot, mratios,
binMto, MASS, mcprofile","License":"GPL-
2","NeedsCompilation":"no","Package":"pairwiseCI","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Confidence Intervals for Two Sample
Comparisons","Version":"0.1-25"},"palaeoSig":{"Author":"Richard Telford, Mathias
Trachsel","Depends":"vegan","Description":"Tests if quantitative
palaeoenvironmental reconstructions are statistically
significant.","Imports":"TeachingDemos, rioja, mgcv, MASS","License":"GPL-
3","NeedsCompilation":"no","Package":"palaeoSig","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"fields","Title":"Significance Tests for
Palaeoenvironmental Reconstructions","Version":"1.1-3"},"paleoMAS":
{"Author":"Alexander Correa-Metrio, Dunia H. Urrego, Kenneth R. Cabrera,\nMark B.
Bush","Depends":"MASS, vegan, lattice","Description":"Transfer functions and
statistical operations for\npaleoecology","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"paleoMAS","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Paleoecological Analysis","Version":"2.0-1"},"paleoTS":
{"Author":"Gene Hunt","Description":"Facilitates analysis of paleontological
sequences of trait values from an evolving lineage. Functions are provided to fit,
using maximum likelihood, evolutionary models including unbiased random walks,
directional evolution, stasis, Ornstein-Uhlenbeck, punctuated change, and
evolutionary models in which traits track some measured
covariate.","Imports":"mnormt, doParallel, parallel, foreach,
iterators","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"paleoTS","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Analyze Paleontological Time-Series","Version":"0.5-
1"},"paleobioDB":{"Author":"Sara Varela [aut, cre],\nJavier GonzÃ¡lez HernÃ¡ndez
[aut],\nLuciano Fabris Sgarbi [aut]","Depends":"raster, maps","Description":"19
functions to wrap each endpoint of\nthe PaleobioDB API, plus 8 functions to
visualize and process the fossil\ndata. The API documentation for the Paleobiology
Database can be found in\n<http:\/\/paleobiodb.org\/data1.1\/>","Imports":"rjson,
gtools, RCurl, plyr, scales","License":"GPL-
2","NeedsCompilation":"no","Package":"paleobioDB","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"roxygen2, testthat","Title":"Download and Process
Data from the Paleobiology
Database","URL":"https:\/\/github.com\/ropensci\/paleobioDB","Version":"0.3"},"pale
ofire":{"Author":"Global Paleofire Working Group <paleofire@univ-
fcomte.fr>","Depends":"R(>= 2.10.0), methods, GCD","Description":"Tools to extract
and analyse charcoal sedimentary data stored in\nthe Global Charcoal Database. Main
functionalities includes data extraction\nand sites selection, transformation and
interpolation of the charcoal\nrecords as well as compositing.","Imports":"locfit,
raster, ggplot2, plyr, rgdal, lattice","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"paleofire","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"gtools,caTools,pscl,agricolae,Imap,sp,rworldmap,RCol
orBrewer","Title":"Analysis of Charcoal Records from the Global Charcoal
Database","URL":"http:\/\/gpwg.paleofire.org","Version":"1.1.8"},"paleotree":
{"Author":"David W. Bapst","Depends":"R (>= 3.0.0), ape (>=
3.2)","Description":"Provides tools for transforming, time-scaling, and\nmodifying
phylogenies containing extinct (i.e. fossil) lineages. In particular,\nmost users
are interested in the functions timePaleoPhy, bin_timePaleoPhy,\ncal3TimePaleoPhy
and bin_cal3TimePaleoPhy, which time-scale cladograms of\nfossil taxa into dated
phylogenies. This package also contains a large number\nof likelihood functions for
estimating sampling and diversification rates from\ndifferent types of data
available from the fossil record (e.g. range data,\noccurrence data, etc).
paleotree users can also simulate diversification and\nsampling in the fossil
record using the function simFossilRecord, which is a\ndetailed simulator for
branching birth-death-sampling processes composed of\ndiscrete taxonomic units
arranged in ancestor-descendant relationships. Users\ncan use simFossilRecord to
simulate diversification in incompletely sampled\nfossil records, under various
models of morphological differentiation (i.e.\nthe various patterns by which
morphotaxa originate from one another), and\nwith time-dependent, longevity-
dependent and\/or diversity-dependent rates of\ndiversification, extinction and
sampling. Additional functions allow users to\ntranslate simulated ancestor-
descendant data from simFossilRecord into standard\ntime-scaled phylogenies or
unscaled cladograms that reflect the relationships\namong taxon
units.","Imports":"phangorn (>= 1.99.12), stats, phytools, graphics,
grDevices,\nmethods,
utils","License":"CC0","NeedsCompilation":"no","Package":"paleotree","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Title":"Paleontological and Phylogenetic
Analyses of Evolution","URL":"https:\/\/github.com\/dwbapst\/paleotree
,\nhttp:\/\/webpages.sdsmt.edu\/~dbapst\/","Version":"2.6"},"palettetown":
{"Author":"Tim Lucas","Description":"Use Pokemon(R) inspired palettes with
additional 'ggplot2' scales.\nPalettes are the colours in each Pokemon's sprite,
ordered by how common\nthey are in the image. The first 386 Pokemon are currently
provided.","Imports":"grDevices, stats, graphics","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"palettetown","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"ggplot2, magrittr","Title":"Use Pokemon
Inspired Colour
Palettes","URL":"https:\/\/github.com\/timcdlucas\/palettetown","Version":"0.1.1"},
"palinsol":{"Author":"Michel Crucifix","Depends":"R (>= 2.10), stats,
gsl,","Description":"R package to compute Incoming Solar Radiation (insolation) for
palaeoclimate studies. Features three solutions: Berger (1978), Berger and Loutre
(1991) and Laskar et al. (2004). Computes daily-mean, season-averaged and annual
means for all latitudes.","License":"file
LICENSE","NeedsCompilation":"no","Package":"palinsol","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Insolation for Palaeoclimate
Studies","URL":"https:\/\/bitbucket.org\/mcrucifix\/insol","Version":"0.93"},"palr"
:{"Author":"Michael D. Sumner [aut, cre]","Depends":"R (>=
2.10)","Description":"Colour palettes for data, based on some well known public
data sets.","License":"GPL-
3","NeedsCompilation":"no","Package":"palr","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"knitr, raster","Title":"Colour Palettes for
Data","Version":"0.0-4"},"pamctdp":{"Author":"Campo Elias Pardo
<cepardot@unal.edu.co>","Depends":"R (>= 2.7.0), ade4,
xtable,FactoClass","Description":"Correspondence Analysis of Contingency Tables
with Simple\nand Double Structures Superimposed Representations, Intra\nBlocks
Correspondence Analysis (IBCA), Weighted Intra Blocks\nCorrespondence Analysis
(WIBCA).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pamctdp","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Principal Axes Methods for Contingency Tables with
Partition\nStructures on Rows and Columns","Version":"0.3.1"},"pamm":
{"Author":"Julien Martin [aut, cre]","Depends":"R (>=
3.0.0)","Description":"Simulation functions to assess or explore the power of a
dataset to estimates significant random effects (intercept or slope) in a mixed
model. The functions are based on the \"lme4\" package.","Imports":"lmerTest,
gmodels, lattice, mvtnorm, lme4","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"pamm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"rgl","Title":"Power Analysis for Random Effects in Mixed
Models","URL":"https:\/\/github.com\/JulienGAMartin\/pamm_R","Version":"0.9"},"pamp
e":{"Author":"Ainhoa Vega-Bayo","Depends":"leaps","Description":"Implements the
Panel Data Approach Method for program evaluation as developed in Hsiao, Ching and
Ki Wan (2012). pampe estimates the effect of an intervention by comparing the
evolution of the outcome for a unit affected by an intervention or treatment to the
evolution of the unit had it not been affected by the
intervention.","Enhances":"xtable","License":"GPL-
2","NeedsCompilation":"no","Package":"pampe","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Implementation of the Panel Data Approach Method for
Program\nEvaluation","Version":"1.1.2"},"pamr":{"Author":"T. Hastie, R. Tibshirani,
Balasubramanian Narasimhan, Gil Chu","Depends":"R (>= 2.10), cluster,
survival","Description":"Some functions for sample classification in
microarrays","License":"GPL-
2","NeedsCompilation":"yes","Package":"pamr","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Pam: prediction analysis for
microarrays","Version":"1.55"},"pan":{"Author":"Original by Joseph L.
Schafer","Description":"Multiple imputation for multivariate panel or clustered
3","NeedsCompilation":"yes","Package":"pan","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"mitools, lme4","Title":"Multiple Imputation for
Multivariate Panel or Clustered Data","Version":"1.4"},"pander":{"Author":"Gergely
DarÃ³czi <daroczig@rapporter.net>, Roman
Tsegelskyi\n<roman.tsegelskyi@gmail.com>","Depends":"R (>=
2.15.0)","Description":"Contains some functions catching all messages, stdout and
other\nuseful information while evaluating R code and other helpers to return
user\nspecified text elements (like: header, paragraph, table, image, lists
etc.)\nin pandoc's markdown or several type of R objects similarly
automatically\ntransformed to markdown format. Also capable of
exporting\/converting (the\nresulting) complex pandoc documents to e.g. HTML, PDF,
docx or odt. This\nlatter reporting feature is supported in brew syntax or with a
custom\nreference class with a smarty caching backend.","Imports":"grDevices,
graphics, methods, utils, stats, digest, tools,\nRcpp","License":"AGPL-3 | file
LICENSE","NeedsCompilation":"yes","Package":"pander","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"grid, lattice, ggplot2 (>= 0.9.2), koRpus,
futile.logger,\nsurvival, microbenchmark, zoo, nlme, descr, MASS, knitr,\ntables,
reshape, memisc, Epi, randomForest, tseries, gtable,\nrms","Title":"An R Pandoc
Writer","URL":"http:\/\/rapporter.github.io\/pander","Version":"0.6.0"},"panelAR":
{"Author":"Konstantin Kashin <kkashin@fas.harvard.edu>","Depends":"R (>=
2.15.0)","Description":"The package estimates linear models on panel data
structures in the presence of AR(1)-type autocorrelation as well as panel
heteroskedasticity and\/or contemporaneous correlation. First, AR(1)-type
autocorrelation is addressed via a two-step Prais-Winsten feasible generalized
least squares (FGLS) procedure, where the autocorrelation coefficients may be
panel-specific. A number of common estimators for the autocorrelation coefficient
are supported. In case of panel heteroskedasticty, one can choose to use a
sandwich-type robust standard error estimator with OLS or a panel weighted least
squares estimator after the two-step Prais-Winsten estimator. Alternatively, if
panels are both heteroskedastic and contemporaneously correlated, the package
supports panel-corrected standard errors (PCSEs) as well as the Parks-Kmenta FGLS
estimator.","Imports":"car","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"panelAR","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Estimation of Linear AR(1) Panel Data Models with\nCross-
Sectional Heteroskedasticity and\/or
Correlation","Version":"0.1"},"panelaggregation":{"Author":"Matthias Bannert [aut,
cre], Gabriel Bucur [aut]","Depends":"R (>= 3.0.0), data.table (>=
1.9.4)","Description":"Aggregate Business Tendency Survey Data (and other
qualitative\nsurveys) to time series at various aggregation levels. Run aggregation
of\nsurvey data in a speedy, re-traceable and a easily deployable way.\nAggregation
is substantially accelerated by use of data.table.\nPanelaggregation aims at
providing an interface that is more geared towards\nsurvey
researchers.","License":"GPL-
2","NeedsCompilation":"no","Package":"panelaggregation","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Aggregate Longitudinal Survey
Data","Version":"0.1"},"pangaear":{"Author":"Scott Chamberlain [aut, cre],\nKara
Woo [aut],\nAndrew MacDonald [aut],\nNaupaka Zimmerman [aut],\nGavin Simpson
[aut]","Description":"Tools to interact with the 'Pangaea' Database
(http:\/\/\nwww.pangaea.de\/), including functions for searching for data, fetching
'datasets'\nby 'dataset' 'ID', and working with the 'Pangaea' 'OAI-PMH'
service.","Imports":"methods, stats, utils, httr (>= 1.0.0), XML,
oai","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"pangaear","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Client for the 'Pangaea'
Database","URL":"https:\/\/github.com\/ropensci\/pangaear","Version":"0.1.0"},"pape
R":{"Author":"Benjamin Hofner, with contributions by many others (see
inst\/CONTRIBUTIONS)","Depends":"car, xtable","Description":"A toolbox for writing
'knitr', 'Sweave' or other 'LaTeX'- or 'markdown'-based\nreports and to prettify
the output of various estimated models.","Enhances":"nlme, lme4,
survival","Imports":"utils, gmodels, graphics, stats","License":"GPL-
2","NeedsCompilation":"no","Package":"papeR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr, testthat (>= 0.10.0), foreign","Title":"A Toolbox
for Writing Pretty Papers and
Reports","URL":"http:\/\/github.com\/hofnerb\/papeR","Version":"1.0-
1"},"parallelMCMCcombine":{"Author":"Alexey Miroshnikov, Erin
Conlon","Depends":"mvtnorm","Description":"Recent Bayesian Markov chain Monto Carlo
(MCMC) methods have been developed for big data sets that are too large to be
analyzed using traditional statistical methods. These methods partition the data
into non-overlapping subsets, and perform parallel independent Bayesian MCMC
analyses on the data subsets, creating independent subposterior samples for each
data subset. These independent subposterior samples are combined through four
functions in this package, including averaging across subset samples, weighted
averaging across subsets samples, and kernel smoothing across subset samples. The
four functions assume the user has previously run the Bayesian analysis and has
produced the independent subposterior samples outside of the package; the functions
use as input the array of subposterior samples. The methods have been demonstrated
to be useful for Bayesian MCMC models including Bayesian logistic regression,
Bayesian Gaussian mixture models and Bayesian hierarchical Poisson-Gamma models.
The methods are appropriate for Bayesian hierarchical models with hyperparameters,
as long as data values in a single level of the hierarchy are not split into
subsets.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"parallelMCMCcombine","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Title":"Methods
for combining independent subset Markov chain Monte\nCarlo (MCMC) posterior
samples to estimate a posterior density\ngiven the full data
set","Version":"1.0"},"parallelML":{"Author":"Wannes Rosiers
(InfoFarm)","Depends":"R (>= 2.14.0)","Description":"By sampling your data, running
the provided classifier on these samples in parallel on your own machine and
letting your models vote on a prediction, we return much faster predictions than
the regular machine learning algorithm and possibly even more accurate
predictions.","Imports":"parallel (>= 3.1.1), foreach (>= 1.2.0), doParallel (>=
2","NeedsCompilation":"no","Package":"parallelML","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"A Parallel-Voting Algorithm for many
Classifiers","URL":"www.infofarm.be","Version":"1.2"},"parallelMap":
{"Author":"Bernd Bischl <bernd_bischl@gmx.net>, Michel
Lang\n<michellang@gmail.com>","Depends":"R (>= 3.0.0)","Description":"Unified
parallelization framework for multiple back-end,\ndesigned for internal package and
interactive usage.\nThe main operation is a parallel \"map\" over lists.\nSupports
local, multicore, mpi and BatchJobs mode.\nAllows \"tagging\" of the parallel
operation\nwith a level name that can be later selected by the user to\nswitch on
parallel execution for exactly this operation.","Imports":"BBmisc (>= 1.8),
checkmate (>= 1.5.1), parallel","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"parallelMap","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"testthat, Rmpi, BatchJobs (>=
1.5)","Title":"Unified Interface to Parallelization Back-
Ends","URL":"https:\/\/github.com\/berndbischl\/parallelMap","Version":"1.3"},"para
llelSVM":{"Author":"Wannes Rosiers (InfoFarm)","Depends":"R (>= 2.14.0), e1071 (>=
1.6-3)","Description":"By sampling your data, running the Support-Vector-Machine
algorithm on these samples in parallel on your own machine and letting your models
vote on a prediction, we return much faster predictions than the regular Support-
Vector-Machine and possibly even more accurate predictions.","Imports":"parallel
(>= 3.1.1), foreach (>= 1.2.0), doParallel (>= 1.0.8)","License":"GPL-
2","NeedsCompilation":"no","Package":"parallelSVM","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"A Parallel-Voting Version of the Support-Vector-
Machine\nAlgorithm","URL":"www.infofarm.be","Version":"0.1-
9"},"parallelize.dynamic":{"Author":"Stefan Boehringer <r-packages@s-
boehringer.org>","Depends":"methods, tools, parallel","Description":"Passing a
given function name or a call to the\nparallelize\/parallelize_call functions
analyses and executes\nthe code, if possible in parallel. Parallel code execution
can\nbe performed locally or on remote batch queuing
systems.","License":"LGPL","NeedsCompilation":"no","Package":"parallelize.dynamic",
"Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Automate
parallelization of function calls by means of dynamic\ncode
analysis","Version":"0.9-1"},"paramlink":{"Author":"Magnus Dehli
Vigeland","Depends":"R (>= 3.2), kinship2","Description":"Parametric linkage
analysis and other likelihood-based pedigree analyses based on the Elston-Stewart
algorithm, including singlepoint LOD scores, power analysis and computation of
marker genotype distributions. Multipoint analysis is provided through a convenient
MERLIN wrapper. Includes many utility functions for creating, manipulating and
plotting pedigrees, markers and linkage results.","Imports":"graphics, maxLik,
2)","NeedsCompilation":"no","Package":"paramlink","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Parametric Linkage Analysis in R","Version":"0.9-
7"},"params":{"Author":"Sahil Seth [aut, cre],\nYihui Xie [ctb] (kable from knitr
R\/table.R)","Depends":"R (>= 3.0.2), whisker","Description":"An interface to
simplify organizing parameters used in a package,\nusing external configuration
files. This attempts to provide a cleaner\nalternative to
options().","Imports":"utils","License":"GPL-
2","NeedsCompilation":"no","Package":"params","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"openxlsx, testthat","Title":"Simplify
Parameters","URL":"https:\/\/github.com\/sahilseth\/params","Version":"0.5.0"},"par
an":{"Author":"Alexis Dinno <adinno@post.harvard.edu>","Depends":"R (>= 1.8.0),
MASS","Description":"paran is an implementation of Horn's technique
for\nnumerically and graphically evaluating the components or\nfactors retained in
a principle components analysis (PCA) or\ncommon factor analysis (FA). Horn's
method contrasts\neigenvalues produced through a PCA or FA on a number of
random\ndata sets of uncorrelated variables with the same number of\nvariables and
observations as the experimental or observational\ndata set to produce eigenvalues
for components or factors that\nare adjusted for the sample error-induced
inflation. Components\nwith adjusted eigenvalues greater than one are retained.
paran\nmay also be used to conduct parallel analysis following\nGlorfeld's (1995)
suggestions to reduce the likelihood of\nover-retention.","License":"GPL-
2","NeedsCompilation":"no","Package":"paran","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Horn's Test of Principal
Components\/Factors","URL":"http:\/\/doyenne.com\/Software\/files\/PA_for_PCA_vs_FA
.pdf","Version":"1.5.1"},"parboost":{"Author":"Ronert Obst
<ronert.obst@gmail.com>","Depends":"R (>= 3.0.1), parallel, mboost, party,
iterators","Description":"Distributed gradient boosting based on the mboost
package. The\nparboost package is designed to scale up component-wise
functional\ngradient boosting in a distributed memory environment by splitting
the\nobservations into disjoint subsets, or alternatively using bootstrap\nsamples
(bagging). Each cluster node then fits a boosting model to its\nsubset of the data.
These boosting models are combined in an ensemble,\neither with equal weights, or
by fitting a (penalized) regression\nmodel on the predictions of the individual
models on the complete\ndata.","Imports":"plyr, caret, glmnet,
doParallel","License":"GPL-
2","NeedsCompilation":"no","Package":"parboost","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Distributed Model-Based
Boosting","Version":"0.1.4"},"parcor":{"Author":"Nicole Kraemer, Juliane
Schaefer","Depends":"MASS, glmnet, ppls, Epi, GeneNet","Description":"The package
estimates the matrix of partial correlations\nbased on different regularized
regression methods: lasso,\nadaptive lasso, PLS, and Ridge Regression. In addition,
the\npackage provides model selection for lasso, adaptive lasso and\nRidge
regression based on cross-validation.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"parcor","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Regularized estimation of partial correlation
matrices","Version":"0.2-6"},"parfm":{"Author":"Federico Rotolo
<federico.rotolo@gustaveroussy.fr>\nand Marco Munda
<marco.munda@arlenda.com>","Depends":"R (>= 2.10), survival","Description":"Fits
Parametric Frailty Models by maximum marginal likelihood.\nPossible baseline
hazards: Weibull, inverse Weibull, exponential, Gompertz, lognormal and
loglogistic.\nPossible Frailty distributions: gamma, inverse Gaussian, positive
stable and lognormal.","Imports":"eha, msm, graphics","License":"GPL-
2","NeedsCompilation":"no","Package":"parfm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Parametric Frailty Models","Version":"2.5.10"},"parfossil":
{"Author":"Matthew Vavrek <matthew@matthewvavrek.com>","Depends":"fossil,
foreach","Description":"The package provides a number of easily
parallelized\nfunctions from the fossil package. This package is designed to\nbe
used with some type of parallel computing backend, such as\nmulticore, snow or
MPI.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"parfossil","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Parallelized functions for palaeoecological
and\npalaeogeographical
analysis","URL":"http:\/\/matthewvavrek.com","Version":"0.2.0"},"parma":
{"Author":"Alexios Ghalanos and Bernhard Pfaff","Depends":"R (>= 2.10), methods,
nloptr","Description":"Methods for Portfolio Optimization and Risk
Management.","Imports":"slam, Rglpk, quadprog, FRAPO, corpcor, parallel,
stats,\nutils,truncnorm","License":"GPL-
3","NeedsCompilation":"no","Package":"parma","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"xts, Rsymphony","Title":"Portfolio Allocation and Risk
Management Applications","Version":"1.5-2"},"parmigene":{"Author":"Gabriele Sales
<gabriele.sales@unipd.it>, Chiara
Romualdi\n<chiara.romualdi@unipd.it>","Description":"The package provides a
parallel estimation of the mutual\ninformation based on entropy estimates from k-
nearest neighbors\ndistances and algorithms for the reconstruction of
gene\nregulatory networks.","License":"AGPL-
3","NeedsCompilation":"yes","Package":"parmigene","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Parallel Mutual Information estimation for Gene
Network\nreconstruction","Version":"1.0.2"},"parsec":{"Author":"Alberto Arcagni
[aut, cre], Marco Fattore [ctb]","Description":"Implements basic partial order
tools for multidimensional poverty evaluation with ordinal variables. Its main goal
is to provide socio-economic scholars with an integrated set of elementary
functions for multidimensional poverty evaluation, based on ordinal information.
The package is organized in four main parts. The first two comprise functions for
data management and basic partial order analysis; the third and the fourth are
devoted to evaluation and implement both the poset-based approach and a more
classical counting procedure.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"parsec","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Partial
Orders in Socio-Economics","Version":"1.1"},"parsedate":{"Author":"Gabor Csardi,
Linus Torvalds","Depends":"methods","Description":"Parse dates automatically,
without the need of\nspecifying a format. Currently it includes the git date
parser.\nIt can also recognize and parse all ISO 8601 formats.","License":"GPL-
2","NeedsCompilation":"yes","Package":"parsedate","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat","Title":"Recognize and Parse Dates in
Various Formats, Including All ISO\n8601
Formats","URL":"https:\/\/github.com\/gaborcsardi\/parsedate","Version":"1.1.1"},"p
artDSA":{"Author":"Annette Molinaro <annette.molinaro@ucsf.edu>,\nAdam Olshen
<olshena@biostat.ucsf.edu>,\nKaren Lostritto <karen.lostritto@yale.edu>,\nGregory
Ryslik <gregory.ryslik@yale.edu>,\nSteve Weston
<stephen.weston@yale.com>","Depends":"R (>= 2.5), survival","Description":"A novel
tool for generating a piecewise\nconstant estimation list of increasingly complex
predictors\nbased on an intensive and comprehensive search over the
entire\ncovariate space.","License":"GPL-
2","NeedsCompilation":"no","Package":"partDSA","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"parallel, MASS, TH.data, VGAM","Title":"Partitioning
Using Deletion, Substitution, and Addition Moves","Version":"0.9.10"},"partialAR":
{"Author":"Matthew Clegg [aut, cre, cph]","Description":"Fits time series models
which consist of a sum of a permanent and a transient component.","Imports":"Rcpp
(>= 0.11.2), zoo, parallel, ggplot2, grid, MASS, tseries,\ndata.table, FKF, urca,
plot3D","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"partialAR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"egcm, TTR","Title":"Partial
Autoregression","Version":"1.0.5"},"partialOR":{"Author":"Vaclav Fidler and Nico
Nagelkerke","Depends":"nnet","Description":"Computes Odds Ratio adjusted for a
vector of possibly\ncontinuous covariates","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"partialOR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Partial Odds Ratio","Version":"0.9"},"partitionMap":
{"Author":"Nicolai Meinshausen","Depends":"randomForest","Description":"Low-
dimensional embedding, using Random Forests for\nmulticlass
classification","Imports":"stats,
graphics","License":"GPL","NeedsCompilation":"no","Package":"partitionMap","Reposit
ory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Partition
Maps","URL":"http:\/\/www.stats.ox.ac.uk\/~meinshau","Version":"0.5"},"partitionMet
ric":{"Author":"David Weisman, Dan Simovici","Depends":"R (>=
2.10.1)","Description":"partitionMetric computes a distance between two
partitions\nof a set.","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"partitionMetric","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Title":"Compute a distance metric between two
partitions of a set","Version":"1.1"},"partitions":{"Author":"Robin K. S.
Hankin","Description":"Additive partitions of integers. Enumerates
the\npartitions, unequal partitions, and restricted partitions of an\ninteger; the
three corresponding partition functions are also\ngiven. Set partitions are now
included.","Imports":"gmp,
polynom","License":"GPL","NeedsCompilation":"yes","Package":"partitions","Repositor
y":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Additive Partitions of
Integers","Version":"1.9-18"},"partools":{"Author":"Norm Matloff
<normmatloff@gmail.com> [aut],\nAlex Rumbaugh <aprumbaugh@ucdavis.edu>
[ctb]","Depends":"parallel,stats,utils","Description":"Miscellaneous utilities for
the 'parallel' package,\ncluster-oriented section; \"Snowdoop\" alternative to
MapReduce;\nfile splitting and distributed operations such as sort and
aggregate.\n\"Software Alchemy\" method for parallelizing most statistical
methods,\npresented in N. Matloff, Parallel Computation for Data Science,\nChapman
and Hall, 2015. Includes a debugging aid.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"partools","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"data.table","Title":"Tools for the 'Parallel'
Package","Version":"1.1.3"},"partsm":{"Author":"Javier Lopez-de-
Lacalle","Depends":"R (>= 2.0.0)","Description":"This package performs basic
functions to fit and predict periodic autoregressive time series models. These
models are discussed in the book P.H. Franses (1996) \"Periodicity and Stochastic
Trends in Economic Time Series\", Oxford University Press. Data set analyzed in
that book is also provided. NOTE: the package was orphaned during several years. It
is now only maintained, but no major enhancement are expected, and the maintainer
cannot provide any support.","Imports":"methods","License":"GPL-
2","NeedsCompilation":"no","Package":"partsm","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Periodic Autoregressive Time Series
Models","URL":"http:\/\/github.com\/MatthieuStigler\/partsm","Version":"1.1-
2"},"party":{"Author":"Torsten Hothorn [aut, cre],\nKurt Hornik [aut],\nCarolin
Strobl [aut],\nAchim Zeileis [aut]","Depends":"R (>= 2.14.0), methods, grid, stats,
mvtnorm (>= 1.0-2),\nmodeltools (>= 0.2-21), strucchange","Description":"A
computational toolbox for recursive partitioning.\nThe core of the package is
ctree(), an implementation of\nconditional inference trees which embed tree-
structured\nregression models into a well defined theory of conditional\ninference
procedures. This non-parametric class of regression\ntrees is applicable to all
kinds of regression problems, including\nnominal, ordinal, numeric, censored as
well as multivariate response\nvariables and arbitrary measurement scales of the
covariates.\nBased on conditional inference trees, cforest() provides
an\nimplementation of Breiman's random forests. The function mob()\nimplements an
algorithm for recursive partitioning based on\nparametric models (e.g. linear
models, GLMs or survival\nregression) employing parameter instability tests for
split\nselection. Extensible functionality for visualizing tree-
structured\nregression models is available.","Imports":"survival (>= 2.37-7), coin
(>= 1.1-0), zoo, sandwich (>=\n1.1-1)","License":"GPL-
2","NeedsCompilation":"yes","Package":"party","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"TH.data (>= 1.0-3), mlbench, colorspace, MASS, vcd,
ipred","Title":"A Laboratory for Recursive Partytioning","URL":"http:\/\/party.R-
forge.R-project.org","Version":"1.0-25"},"partykit":{"Author":"Torsten Hothorn
[aut, cre],\nAchim Zeileis [aut]","Depends":"R (>= 3.1.0), graphics,
grid","Description":"A toolkit with infrastructure for representing, summarizing,
and\nvisualizing tree-structured regression and classification models.
This\nunified infrastructure can be used for reading\/coercing tree models
from\ndifferent sources (rpart, RWeka, PMML) yielding objects that
share\nfunctionality for print\/plot\/predict methods. Furthermore, new and
improved\nreimplementations of conditional inference trees (ctree) and model-
based\nrecursive partitioning (mob) from the party package are provided based\non
the new infrastructure.","Imports":"stats, survival","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"partykit","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"XML, pmml, rJava, rpart, mvtnorm, Formula (>= 1.2-
1),\nsandwich, strucchange, vcd, AER, mlbench, TH.data (>= 1.0-3),\ncoin (>= 1.1-
0), RWeka (>= 0.4-19), datasets, parallel,\npsychotools, psychotree","Title":"A
Toolkit for Recursive Partytioning","URL":"http:\/\/partykit.R-forge.R-
project.org\/partykit","Version":"1.0-5"},"parviol":{"Author":"Jaroslav Myslivec
<jaroslav.myslivec@upce.cz>","Depends":"R (>= 2.9.1),
vioplot","Description":"Parviol combines parallel coordinates and violin
plot","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"parviol","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Parviol","Version":"1.1"},"pass":{"Author":"Yixin Fang,
Wei Sun, Junhui Wang","Depends":"R (>= 2.10.0), MASS, lars,
ncvreg","Description":"To implement two methods, Kappa and PASS, for
selecting\ntuning parameters in regularized procedures such as LASSO,\nSCAD,
adaptive LASSO, aiming for variable selection in\nregularized
regression","License":"GPL-
2","NeedsCompilation":"no","Package":"pass","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Prediction and Stability Selection of Tuning
Parameters","Version":"1.0"},"password":{"Author":"Enrico
Schumann","Description":"Create random passwords of letters, numbers and
punctuation.","License":"GPL-
3","NeedsCompilation":"no","Package":"password","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Create Random Passwords","Version":"1.0-0"},"pastecs":
{"Author":"Philippe Grosjean [aut, cre],\nFrederic Ibanez [aut],\nMichele Etienne
[ctb]","Depends":"boot, stats","Description":"Regulation, decomposition and
analysis of space-time series. The pastecs library is a PNEC-Art4 and IFREMER
(Benoit Beliaeff <Benoit.Beliaeff@ifremer.fr>) initiative to bring PASSTEC 2000
(http:\/\/www.obs-vlfr.fr\/~enseigne\/anado\/passtec\/passtec.htm) functionalities
to R.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pastecs","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Package for Analysis of Space-Time Ecological
Series","URL":"http:\/\/www.sciviews.org\/pastecs","Version":"1.3-18"},"pastis":
{"Author":"Klaas Hartmann, Gavin Thomas, Arne Mooers, Jeffrey Joy, Walter
Jetz","Depends":"R (>= 2.10), caper (>= 0.5.0), ape (>= 3.0.0)","Description":"A
pre-processor for mrBayes that assimilates sequences, taxonomic\ninformation and
tree constraints as per xxx. The main functions of\ninterest for most users will
be pastis_simple, pastis_main and conch. The\nmain analysis is conducted with
pastis_simple or pastis_main followed by a\nmanual execution of mrBayes (>3.2). The
placement of taxa not contained
in\nthe tree constraint can be investigated using conch.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"pastis","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Phylogenetic Assembly with Soft Taxonomic
Inferences","URL":"http:\/\/cran.r-
project.org\/web\/packages\/pastis\/","Version":"0.1-2"},"patPRO":
{"Author":"Hannigan GD, Loesche MA, Hodkinson BP, Mehta S, Grice
EA","Description":"Quickly and easily visualize longitudinal microbiome profiles
using standard output from the QIIME microbiome analysis toolkit (see
<http:\/\/qiime.org> for more information).","Imports":"reshape2, ggplot2, grid,
gridExtra, plyr, RColorBrewer","License":"GPL-
3","NeedsCompilation":"no","Package":"patPRO","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Visualizing Temporal Microbiome
Data","Version":"1.1.0"},"patchDVI":{"Author":"Duncan Murdoch","Depends":"R (>=
2.10.0)","Description":"Functions to patch specials in .dvi files,\nor entries
in .synctex files. Works with \"concordance=TRUE\"\nin Sweave or knitr to link
sources to previews.","Imports":"utils, tools","License":"GPL-
2","NeedsCompilation":"yes","Package":"patchDVI","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr","Title":"Package to Patch .dvi or .synctex
Files","Version":"1.9.1616"},"patchPlot":{"Author":"Pierrick Bruneau","Depends":"R
(>= 2.10.0), grid, datautils","Description":"Functions to generate scatterplots
with images patches\ninstead of usual glyphs, with associated
utilities.","License":"LGPL-
3","NeedsCompilation":"no","Package":"patchPlot","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Scatterplots of image
patches","Version":"0.1.5"},"patchSynctex":{"Author":"Jan Gleixner [aut],\nDaniel
Hicks [ctb],\nEmmanuel Charpentier [aut, cre]","Depends":"tools,
stringr","Description":"This utility eases the debugging of literate
documents\n('noweb' files) by patching the synchronization information\n(the
'.synctex(.gz)' file) produced by 'pdflatex' with\nconcordance information produced
by 'Sweave' or 'knitr' and\n'Sweave' or 'knitr' ; this allows for bilateral
communication\nbetween a text editor (visualizing the 'noweb' source) and\na viewer
(visualizing the resultant 'PDF'), thus bypassing\nthe intermediate 'TeX'
file.","Enhances":"knitr, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"patchSynctex","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Communication Between Editor and Viewer for Literate
Programs","URL":"https:\/\/github.com\/EmmanuelCharpentier\/patchSynctex","Version"
:"0.1-3"},"pathClass":{"Author":"Marc Johannes","Depends":"R (>= 2.14), svmpath,
kernlab, affy, Biobase, ROCR, igraph,\nlpSolve","Description":"pathClass is a
collection of classification methods that\nuse information about feature
connectivity in a biological\nnetwork as an additional source of information. This
additional\nknowledge is incorporated into the classification a priori.\nSeveral
authors have shown that this approach significantly\nincreases the classification
performance.","Enhances":"parallel","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pathClass","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"hu6800.db, golubEsets","Title":"Classification using
biological pathways as prior knowledge","Version":"0.9.4"},"pathdiagram":
{"Author":"Gaston Sanchez","Depends":"R (>= 3.0),
shape","Description":"Implementation of simple functions to draw\nbasic path
diagrams just for visualization purposes.","License":"GPL-
3","NeedsCompilation":"no","Package":"pathdiagram","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr","Title":"Basic functions for drawing path
diagrams","URL":"http:\/\/www.gastonsanchez.com","Version":"0.1.9"},"pathmox":
{"Author":"Gaston Sanchez [aut, cre],\nTomas Aluja [aut, ths]","Depends":"R (>=
3.0.1), plspm, tester","Description":"pathmox, the cousin package of plspm,
provides a very\ninteresting solution for handling segmentation variables\nin PLS
Path Modeling: segmentation trees in PLS Path Modeling.","License":"GPL-
3","NeedsCompilation":"no","Package":"pathmox","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"plsdepot","Title":"Pathmox Approach of Segmentation
Trees in Partial Least Squares\nPath
Modeling","URL":"http:\/\/www.gastonsanchez.com","Version":"0.2.0"},"pathological":
{"Author":"Richard Cotton [aut, cre], Janko Thyson [ctb]","Depends":"R (>=
2.15.0)","Description":"Utilities for paths, files and
directories.","Imports":"assertive.base (>= 0.0-3),
assertive.properties,\nassertive.types, assertive.files,
assertive.reflection,\nassertive.strings, plyr, stringr (>= 1.0.0),
utils","License":"Unlimited","NeedsCompilation":"no","Package":"pathological","Repo
sitory":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Path
Manipulation
Utilities","URL":"https:\/\/github.com\/richierocks\/pathological","Version":"0.0-
7"},"pauwels2014":{"Author":"Edouard Pauwels","Depends":"deSolve, ggplot2, R (>=
2.10)","Description":"Implementation of a Bayesian active learning strategy to
carry out sequential experimental design in the context of biochemical network
kinetic parameter estimation. This package gathers functions and pre-computed data
sets to reproduce results presented in Pauwels E. et. al published in BMC Systems
Biology, 2014. Scripts are given to compute all results from scratch or to draw
pictures based on pre-computed data sets.","License":"GPL-
3","NeedsCompilation":"yes","Package":"pauwels2014","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Bayesian Experimental Design for Systems
Biology","Version":"1.0"},"pavo":{"Author":"Rafael Maia [aut, cre],\nChad Eliason
[aut],\nPierre-Paul Bitton [aut]","Depends":"rgl","Description":"A cohesive
framework for parsing, analyzing and organizing color\nfrom spectral
data.","Imports":"geometry, mapproj, rcdd","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pavo","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Perceptual Analysis, Visualization and Organization of
Spectral\nColor Data in R","URL":"www.rafaelmaia.net\/r-
packages\/pavo","Version":"0.5-5"},"pawacc":{"Author":"Marco Geraci","Depends":"R
(>= 3.0.0)","Description":"Process, format and store accelerometer
data","Imports":"SparseM","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pawacc","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Physical activity with
accelerometers","URL":"http:\/\/CRAN.R-
project.org\/package=pawacc","Version":"1.2.1"},"pbapply":{"Author":"Peter Solymos
[aut, cre], Zygmunt Zawadzki [aut]","Depends":"R (>= 3.2.0)","Description":"A
lightweight package that adds\nprogress bar to vectorized R functions\n('*apply').
The implementation can easily be added\nto functions where showing the progress
is\nuseful (e.g. bootstrap). The type and style of the\nprogress bar (with
percentages or remaining time)\ncan be set through options.","License":"GPL-
2","NeedsCompilation":"no","Package":"pbapply","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Adding Progress Bar to '*apply'
Functions","URL":"https:\/\/github.com\/psolymos\/pbapply","Version":"1.2-
0"},"pbatR":{"Author":"Thomas Hoffmann <tjhoffm@gmail.com>, with contributions
from\nChristoph Lange <clange@hsph.harvard.edu>","Depends":"R (>= 2.0.0), survival,
rootSolve","Description":"This package provides data analysis via the pbat
program,\nand an alternative internal implementation of the power\ncalculations via
simulation only. For analysis, this package\nprovides a frontend to the PBAT
software, automatically reading\nin the output from the pbat program and displaying
the\ncorresponding figure when appropriate (i.e. PBAT-logrank). It\nincludes
support for multiple processes and clusters. For\nanalysis, users must download
PBAT (developed by Christoph\nLange) and accept it's license, available on the PBAT
webpage.\nBoth the data analysis and power calculations have command line\nand
graphical interfaces using
tcltk.","Imports":"tcltk","License":"GPL","NeedsCompilation":"yes","Package":"pbatR
","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"kinship2,
tcltk","Title":"P2BAT","URL":"http:\/\/sites.google.com\/site\/thomashoffmannprojec
t\/\nhttp:\/\/www.biostat.harvard.edu\/~clange\/default.htm\nhttp:\/\/bioinformatic
s.oxfordjournals.org\/cgi\/content\/short\/22\/24\/3103","Version":"2.2-
9"},"pbdBASE":{"Author":"Drew Schmidt [aut, cre],\nWei-Chen Chen [aut],\nGeorge
Ostrouchov [aut],\nPragneshkumar Patel [aut],\nEwan Higgs [ctb]","Depends":"R (>=
3.0.0), methods","Description":"An interface to and extensions for the 'PBLAS'
and\n'ScaLAPACK' numerical libraries. This enables R to utilize\ndistributed
linear algebra for codes written in the 'SPMD' fashion.\nThis interface is
deliberately low-level and mimics the style of\nthe native libraries it wraps. For
a much higher level way of\nmanaging distributed matrices, see the 'pbdDMAT'
package.","Imports":"pbdMPI (>= 0.3-1), pbdSLAP(>= 0.2-1)","License":"Mozilla
Public License
2.0","NeedsCompilation":"yes","Package":"pbdBASE","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Programming with Big Data -- Base Wrappers for
Distributed\nMatrices","URL":"http:\/\/r-pbd.org\/","Version":"0.4-3"},"pbdDEMO":
{"Author":"Drew Schmidt [aut, cre],\nWei-Chen Chen [aut],\nGeorge Ostrouchov
[aut],\nPragneshkumar Patel [aut]","Depends":"R (>= 3.0.0), methods, pbdMPI (>=
0.3-0), pbdBASE(>= 0.4-3),\npbdDMAT(>= 0.4-0)","Description":"A set of demos of
'pbdR' packages, together with a useful,\nunifying vignette.","Enhances":"maps,
RColorBrewer, pbdNCDF4 (>= 0.1-2), pmclust, MixSim,\nEMCluster, phyclust,
MASS","License":"Mozilla Public License
2.0","NeedsCompilation":"yes","Package":"pbdDEMO","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Programming with Big Data -- Demonstrations and
Examples
Using\n'pbdR' Packages","URL":"http:\/\/r-pbd.org\/","Version":"0.3-0"},"pbdDMAT":
{"Author":"Drew Schmidt [aut, cre],\nWei-Chen Chen [aut],\nGeorge Ostrouchov
[aut],\nPragneshkumar Patel [aut],\nZhaoKang Wang [ctb],\nMichael Lawrence
[ctb],\nR Core team [ctb] (some wrappers taken from the base and
stats\npackages)","Depends":"R (>= 3.0.0), pbdMPI (>= 0.3-1), pbdBASE (>= 0.4-
3)","Description":"A set of classes for managing distributed matrices, and\na
collection of methods for computing linear algebra and\nstatistics. Computation is
handled mostly by routines from the\n'pbdBASE' package, which itself relies on the
'ScaLAPACK' and\n'PBLAS' numerical libraries for distributed
computing.","Imports":"utils, stats, methods","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"pbdDMAT","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Programming with Big Data -- Distributed Matrix
Methods","URL":"http:\/\/r-pbd.org\/","Version":"0.4-0"},"pbdMPI":{"Author":"Wei-
Chen Chen [aut, cre],\nGeorge Ostrouchov [aut],\nDrew Schmidt [aut],\nPragneshkumar
Patel [aut],\nHao Yu [aut],\nChristian Heckendorf [ctb] (FreeBSD),\nBrian Ripley
[ctb] (Windows HPC Pack 2012),\nR Core team [ctb] (some functions are modified from
the base packages)","Depends":"R (>= 3.0.0), methods, rlecuyer","Description":"An
efficient interface to MPI by utilizing S4\nclasses and methods with a focus on
Single Program\/Multiple Data ('SPMD')\nparallel programming style, which is
intended for batch parallel\nexecution.","Enhances":"pbdPROF,
pbdZMQ","License":"Mozilla Public License
2.0","NeedsCompilation":"yes","Package":"pbdMPI","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Programming with Big Data -- Interface to
MPI","URL":"http:\/\/r-pbd.org\/","Version":"0.3-1"},"pbdNCDF4":
{"Author":"Pragneshkumar Patel [aut, cre],\nGeorge Ostrouchov [aut],\nWei-Chen Chen
[aut],\nDrew Schmidt [aut],\nDavid Pierce [aut]","Depends":"R (>=
3.0.0)","Description":"This package adds collective parallel read and write
capability\nto the R package ncdf4 version 1.8. Typical use is as a\nparallel
NetCDF4 file reader in SPMD style programming. Each R\nprocess reads and writes its
own data in a synchronized\ncollective mode, resulting in faster parallel
performance.\nPerformance improvement is conditional on a parallel file
system.","Enhances":"pbdMPI","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"pbdNCDF4","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Programming with Big Data -- Interface to Parallel
Unidata\nNetCDF4 Format Data Files","URL":"http:\/\/r-pbd.org\/","Version":"0.1-
4"},"pbdPROF":{"Author":"Wei-Chen Chen [aut, cre],\nDrew Schmidt [aut],\nGaurav
Sehrawat [aut],\nPragneshkumar Patel [aut],\nGeorge Ostrouchov [aut]","Depends":"R
(>= 3.0.0)","Description":"MPI profiling tools.","Imports":"methods, stats,
utils","License":"Mozilla Public License
2.0","NeedsCompilation":"yes","Package":"pbdPROF","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Programming with Big Data --- MPI Profiling
Tools","URL":"http:\/\/r-pbd.org\/","Version":"0.3-0"},"pbdSLAP":{"Author":"Wei-
Chen Chen [aut, cre],\nDrew Schmidt [aut],\nGeorge Ostrouchov [aut],\nPragneshkumar
Patel [aut],\nBrian Ripley [ctb] (Solaris & Mac)","Depends":"R (>= 3.0.0), methods,
rlecuyer, pbdMPI (>= 0.3-1)","Description":"Utilizing scalable linear algebra
packages mainly\nincluding BLACS, PBLAS, and ScaLAPACK in double precision
via\npbdMPI based on ScaLAPACK version 2.0.2.","License":"Mozilla Public License
2.0","NeedsCompilation":"yes","Package":"pbdSLAP","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Programming with Big Data -- Scalable Linear Algebra
Packages","URL":"http:\/\/r-pbd.org\/","Version":"0.2-1"},"pbdZMQ":{"Author":"Wei-
Chen Chen [aut, cre],\nDrew Schmidt [aut],\nChristian Heckendorf [aut] (file
transfer),\nGeorge Ostrouchov [aut] (Mac OSX),\nWhit Armstrong [ctb] (some
functions are modified from the rzmq package\nfor backwards compatibility),\nBrian
Ripley [ctb] (C code of shellexec, and Solaris),\nR Core team [ctb] (some functions
are modified from the R source code)","Depends":"R (>=
3.0.0)","Description":"'ZeroMQ' is a well-known library for high-
performance\nasynchronous messaging in scalable, distributed applications.
This\npackage provides high level R wrapper functions to easily utilize\n'ZeroMQ'.
We mainly focus on interactive client\/server programming\nframeworks. For
convenience, a minimal 'ZeroMQ' library (4.1.0 rc1)\nis shipped with 'pbdZMQ',
which can be used if no system installation\nof 'ZeroMQ' is available. A few
wrapper functions compatible with\n'rzmq' are also
provided.","Imports":"R6","License":"GPL-
3","NeedsCompilation":"yes","Package":"pbdZMQ","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Programming with Big Data -- Interface to
ZeroMQ","URL":"http:\/\/r-pbd.org\/","Version":"0.2-1"},"pbivnorm":
{"Author":"Fortran code by Alan Genz. R code by Brenton Kenkel,\nbased on Adelchi
Azzalini's 'mnormt' package.","Description":"Provides a vectorized R function for
calculating\nprobabilities from a standard bivariate normal CDF.","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"pbivnorm","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Vectorized Bivariate Normal
CDF","URL":"https:\/\/github.com\/brentonk\/pbivnorm","Version":"0.6.0"},"pbkrtest"
:{"Author":"Ulrich Halekoh <uhalekoh@health.sdu.dk> Søren Højsgaard
<sorenh@math.aau.dk>","Depends":"R (>= 3.2.3), lme4 (>=
1.1.10)","Description":"Test in mixed effects models.\n\nAttention is on mixed
effects models as implemented in the\n'lme4' package.\n\nThis package implements a
parametric bootstrap test and a Kenward Roger\nmodification of F-tests for linear
mixed effects models and a parametric bootstrap\ntest for generalized linear mixed
models.","Imports":"Matrix (>= 1.2.3), parallel, MASS, methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pbkrtest","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"gplots","Title":"Parametric Bootstrap and Kenward
Roger Based Methods for Mixed\nModel
Comparison","URL":"http:\/\/people.math.aau.dk\/~sorenh\/software\/pbkrtest\/","Ver
sion":"0.4-6"},"pbo":{"Author":"Matt Barry <mrb@softisms.com>","Depends":"utils,
lattice","Description":"Following the method of Bailey et al., computes for a
collection\nof candidate models the probability of backtest overfitting,
the\nperformance degradation and probability of loss, and the
stochastic\ndominance.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"pbo","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"PerformanceAnalytics, foreach, grid, latticeExtra,
testthat,\ndoParallel, knitr","Title":"Probability of Backtest
Overfitting","URL":"https:\/\/github.com\/mrbcuda\/pbo","Version":"1.3.4"},"pbs":
{"Author":"Shuangcai Wang","Description":"Periodic B Splines
Basis","Imports":"graphics, stats, splines","License":"GPL-
2","NeedsCompilation":"no","Package":"pbs","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Periodic B Splines","Version":"1.1"},"pcIRT":
{"Author":"Christine Hohensinn","Depends":"R (>= 2.15)","Description":"pcIRT
estimates the multidimensional polytomous Rasch model\n(Rasch, 1961) and the
Continous Rating Scale model (Mueller, 1987).","Imports":"Rcpp, combinat, stats,
graphics, grDevices, utils, methods","License":"GPL-
3","NeedsCompilation":"yes","Package":"pcIRT","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"roxygen2","Title":"IRT Models for Polytomous and
Continuous Item
Responses","URL":"https:\/\/github.com\/christinehohensinn\/pcIRT","Version":"0.2"}
,"pca3d":{"Author":"January Weiner","Description":"Functions simplifying
presentation of PCA models in a 3D interactive representation using
'rgl'.","Imports":"rgl,ellipse","License":"GPL-
2","NeedsCompilation":"no","Package":"pca3d","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr","Title":"Three Dimensional PCA
Plots","URL":"http:\/\/logfc.wordpress.com","Version":"0.8"},"pcaBootPlot":
{"Author":"Joshua Starmer","Depends":"R (>= 3.0.2)","Description":"Draws a 2D
principal component plot using the first 2 principal\ncomponents from the original
and bootstrapped data to give some sense of\nvariability.","Imports":"FactoMineR,
RColorBrewer","License":"GPL-
2","NeedsCompilation":"no","Package":"pcaBootPlot","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr","Title":"Create 2D Principal Component Plots
with
Bootstrapping","URL":"https:\/\/github.com\/starmerj\/pcaBootPlot","Version":"0.2.0
"},"pcaL1":{"Author":"Sapan Jot <sapan.madaan@gmail.com> and Paul
Brooks\n<jpbrooks@vcu.edu>","Description":"Three implementations of principal
component analysis methods\nusing the L1 norm. The package depends on COIN-OR Clp
version >=\n1.12.0. The methods implemented are PCA-L1 (Kwak 2008), L1-PCA (Ke
and\nKanade 2003, 2005), and L1-PCA* (Brooks, Dula, and Boone
2013).","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"pcaL1","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Three L1-Norm PCA
Methods","URL":"http:\/\/www.optimization-
online.org\/DB_HTML\/2012\/04\/3436.html,\nhttp:\/\/www.coin-
or.org","Version":"1.3"},"pcaPP":{"Author":"Peter Filzmoser, Heinrich Fritz,
Klaudius Kalcher","Description":"Robust PCA by Projection
Pursuit","Imports":"mvtnorm","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"pcaPP","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Robust PCA by Projection Pursuit","Version":"1.9-
60"},"pcadapt":{"Author":"Keurcien Luu, Michael G.B. Blum","Depends":"robust, MASS,
stats,","Description":"Methods to detect genetic markers involved in
biological\nadaptation. 'pcadapt' provides statistical tools for outlier detection
based on\nPrincipal Component Analysis.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pcadapt","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr,
qvalue, rmarkdown","Title":"Principal Component Analysis for Outlier
Detection","Version":"2.2"},"pcalg":{"Author":"Markus Kalisch [aut, cre], Alain
Hauser [aut], Martin Maechler [aut],\nDiego Colombo [ctb], Doris Entner [ctb],
Patrik Hoyer [ctb],\nAntti Hyttinen [ctb], Jonas Peters [ctb]","Depends":"R (>=
3.0.2)","Description":"Functions for causal structure\nlearning and causal
inference using graphical models. The main algorithms\nfor causal structure
learning are PC (for observational data without hidden\nvariables), FCI and RFCI
(for observational data with hidden variables),\nand GIES (for a mix of data from
observational studies\n(i.e. observational data) and data from
experiments\ninvolving interventions (i.e. interventional data) without
hidden\nvariables). For causal inference the IDA algorithm, the
Generalized\nBackdoor Criterion (GBC) and the Generalized Adjustment Criterion
(GAC)\nare implemented.","Imports":"stats, graphics, utils, methods, abind, graph,
RBGL, igraph,\nggm, corpcor, robustbase, vcd, Rcpp, bdsmatrix, sfsmisc (>=\n1.0-
26), fastICA, clue, gmp","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"pcalg","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"MASS, Matrix, Rgraphviz, mvtnorm","Title":"Methods for
Graphical Models and Causal Inference","URL":"http:\/\/pcalg.r-forge.r-
project.org\/","Version":"2.2-4"},"pcev":{"Author":"Maxime Turgeon [aut,
cre],\nAurelie Labbe [aut],\nKarim Oualkacha [aut]","Depends":"R (>=
3.0.0)","Description":"Principal component of explained variance (PCEV) is a
statistical tool for the analysis of a multivariate\nresponse vector. It is a
dimension-reduction technique, similar to Principal\ncomponent analysis (PCA),
which seeks the maximize the proportion of\nvariance (in the response vector) being
explained by a set of covariates.","Imports":"RMTstat, stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pcev","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr","Title":"Principal Component of Explained
Variance","URL":"http:\/\/github.com\/GreenwoodLab\/pcev","Version":"1.1.1"},"pcg":
{"Author":"B N Mandal <mandal.stat@gmail.com> and Jun Ma
<jun.ma@mq.edu.au>","Description":"The package solves linear system of equations
Ax=b by using Preconditioned Conjugate Gradient Algorithm where A is real symmetric
positive definite matrix. A suitable preconditioner matrix may be provided by user.
This can also be used to minimize quadratic function (x'Ax)\/2-bx for unknown
x.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pcg","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Preconditioned Conjugate Gradient Algorithm for solving
Ax=b","Version":"1.1"},"pch":{"Author":"Paolo
Frumento","Depends":"survival","Description":"Using piecewise constant hazards
models is a very flexible approach\nfor the analysis of survival data. The time
line is divided into sub-intervals;\nfor each interval, a different hazard is
estimated using Poisson regression.","Imports":"stats","License":"GPL-
2","NeedsCompilation":"no","Package":"pch","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Piecewise Constant Hazards Models for Censored and
Truncated\nData","Version":"1.1"},"pcnetmeta":{"Author":"Lifeng Lin, Jing Zhang,
and Haitao Chu","Depends":"R (>= 2.14.0), rjags (>= 4-4)","Description":"Provides
functions to perform arm-based network meta-analysis for datasets with binary,
continuous, and count outcomes.","Imports":"coda, grDevices","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pcnetmeta","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Patient-Centered Network Meta-
Analysis","Version":"2.3"},"pco":{"Author":"Georgi
Marinov","Depends":"stats","Description":"Computation of the Pedroni (1999) panel
cointegration test statistics. Reported are the empirical and the standardized
2","NeedsCompilation":"no","Package":"pco","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Panel Cointegration Tests","Version":"1.0.1"},"pcse":
{"Author":"Delia Bailey <delia.bailey@gmail.com> and Jonathan N.
Katz\n<jkatz@caltech.edu>","Description":"This package contains a function to
estimate\npanel-corrected standard errors. Data may contain balanced or\nunbalanced
panels.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"pcse","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Panel-Corrected Standard Error Estimation in
R","Version":"1.9"},"pdR":{"Author":"Ho Tsung-wu","Description":"Threshold model,
panel version of Hylleberg et al. (1990) seasonal unit root tests, and panel unit
root test of Chang (2002).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pdR","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Panel Data Regression: Threshold Model and Unit Root
Tests","Version":"1.3"},"pdc":{"Author":"Andreas M.
Brandmaier","Description":"Permutation Distribution Clustering is a clustering
method for time series. Dissimilarity of time series is formalized as the
divergence between their permutation distributions. The permutation distribution
was proposed as measure of the complexity of a time series.","Imports":"stats,
utils, grDevices, graphics","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"pdc","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"plotrix, lattice","Title":"Permutation Distribution
Clustering","Version":"1.0.3"},"pdfCluster":{"Author":"Adelchi Azzalini, Giovanna
Menardi for the current version;\nAdelchi Azzalini, Giovanna Menardi and Tiziana
Rosolin up to version 0.1-13.","Description":"The package performs cluster analysis
via nonparametric density\nestimation. Operationally, the kernel method is used
throughout to estimate\nthe density. Diagnostics methods for evaluating the quality
of the clustering\nare available. The package includes also a routine to estimate
the\nprobability density function obtained by the kernel method, given a set
of\ndata with arbitrary dimensions.","Imports":"geometry, methods","License":"GPL-
2","NeedsCompilation":"yes","Package":"pdfCluster","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"cluster","Title":"Cluster analysis via
nonparametric density estimation","Version":"1.0-2"},"pdfetch":{"Author":"Abiel
Reinhart <abielr@gmail.com>","Description":"Download economic and financial time
series from public sources.","Imports":"httr, zoo, xts, XML, lubridate, jsonlite,
reshape2","License":"GPL","NeedsCompilation":"no","Package":"pdfetch","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Title":"Fetch Economic and Financial Time
Series Data from Public\nSources","Version":"0.1.7"},"pdftables":{"Author":"Eric
Persson [aut, cre]","Description":"Allows the user to convert PDF tables to formats
more amenable to\nanalysis ('.csv', '.xml', or '.xlsx') by wrapping the PDFTables
API.\nIn order to use the package, the user needs to sign up for an API account\non
the PDFTables website (<https:\/\/pdftables.com\/pdf-to-excel-api>).\nThe package
works by taking a PDF file as input, uploading it to PDFTables,\nand returning a
file with the extracted data.","Imports":"httr,
tools","License":"CC0","NeedsCompilation":"no","Package":"pdftables","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Suggests":"knitr,
rmarkdown","Title":"Programmatic Conversion of PDF
Tables","URL":"https:\/\/www.github.com\/expersso\/pdftables ,
https:\/\/pdftables.com","Version":"0.1"},"pdftools":{"Author":"Jeroen
Ooms","Description":"Utilities based on libpoppler for extracting text,\nfonts,
attachments and metadata from a pdf file. Also implements\nrendering of PDF to
bitmaps on supported platforms.","Imports":"Rcpp (>= 0.12.0)","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"pdftools","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"jpeg, png, webp","Title":"Extract Text and Data
from PDF Documents","URL":"https:\/\/ropensci.org\/blog\/2016\/03\/01\/pdftools-
and-jeroen\nhttps:\/\/github.com\/ropensci\/pdftools","Version":"0.3"},"pdist":
{"Author":"Jeffrey Wong","Depends":"methods","Description":"Computes the euclidean
distance between rows of a matrix X\nand rows of another matrix Y. Previously,
this could be done\nby binding the two matrices together and calling 'dist',
but\nthis creates unnecessary computation by computing the distances\nbetween a row
of X and another row of X, and likewise for Y.\npdist strictly computes distances
across the two matrices, not\nwithin the same matrix, making computations
significantly\nfaster for certain use
cases.","License":"GPL","NeedsCompilation":"yes","Package":"pdist","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"Partitioned Distance
Function","URL":"https:\/\/github.com\/jeffwong\/pdist","Version":"1.2"},"pdmod":
{"Author":"Chloe Bracis","Description":"This package provides a model of Pavlovian
conditioning phenomena, such as response extinction and spontaneous recovery, and
partial reinforcement extinction effects. Competing proximal and distal reward
predictions, computed using fast and slow learning rates, combine according to
their uncertainties and the recency of information. The resulting mean prediction
drives the response rate.","Imports":"mco,stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"pdmod","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"RUnit","Title":"Proximal\/distal modeling framework for
Pavlovian conditioning\nphenomena","Version":"1.0"},"pdolsms":{"Author":"Raad
Khraishi [aut, cre]","Depends":"R (>= 3.2.2)","Description":"Estimates panel data
cointegrating relationships following the estimator of Mark and Sul (2003),
<DOI:10.1111\/j.1468-0084.2003.00066.x>.","Imports":"reshape2,
3)","NeedsCompilation":"no","Package":"pdolsms","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Panel Dynamic OLS Estimation
of Cointegrating Vectors","Version":"0.2"},"peacots":{"Author":"Stilianos
Louca","Depends":"stats,graphics","Description":"Calculates the periodogram of a
time series, maximum-likelihood fits an Ornstein-Uhlenbeck state space (OUSS) null
model and evaluates the statistical significance of periodogram peaks against the
OUSS null hypothesis. The OUSS is a parsimonious model for stochastically
fluctuating variables with linear stabilizing forces, subject to uncorrelated
measurement errors. Contrary to the classical white noise null model for detecting
cyclicity, the OUSS model can account for temporal correlations typically occurring
in ecological and geological time series.","License":"GPL-
3","NeedsCompilation":"no","Package":"peacots","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Periodogram Peaks in Correlated Time
Series","Version":"1.2"},"peakPick":{"Author":"Paal O.
Westermark","Description":"Biologically inspired methods for\ndetecting peaks in
one-dimensional data, such as time series or genomics data.\nThe algorithms were
originally designed by Weber, Ramachandran, and Henikoff,\nsee
documentation.","Imports":"matrixStats, parallel","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"peakPick","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"knitr, rmarkdown","Title":"Peak Picking Methods
Inspired by Biological Data","Version":"0.11"},"pear":{"Author":"A. I. McLeod
<aim@uwo.ca> and Mehmet Balcilar\n<mehmet@mbalcilar.net>.","Depends":"R (>=
2.1.0)","Description":"Package for estimating periodic autoregressive
models.\nDatasets: monthly ozone and Fraser riverflow. Plots: periodic\nversions of
boxplot, auto\/partial correlations, moving-average\nexpansion.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pear","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Package for Periodic Autoregression
Analysis","URL":"http:\/\/www.stats.uwo.ca\/faculty\/aim","Version":"1.2"},"pearson
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maximum likelihood inference for the Pearson VII\ndistribution with shape parameter
3\/2 and free location and scale\nparameters. This distribution is relevant when
estimating the velocity of\nprocessive motor proteins with random
detachment.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pearson7","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Maximum Likelihood Inference for the Pearson VII
Distribution\nwith Shape Parameter
3\/2","URL":"http:\/\/www.biostat.umn.edu\/~johnh","Version":"1.0-1"},"pec":
{"Author":"Thomas A. Gerds","Depends":"R (>= 2.9.0), prodlim (>=
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2)","NeedsCompilation":"yes","Package":"pec","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"timereg, randomForestSRC, party, cmprsk (>= 2.2-7),
rpart,\ndoMC, CoxBoost, crrstep, riskRegression (>= 1.0.8), lava, Hmisc\n(>= 3.14-
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Survival\nAnalysis","Version":"2.4.7"},"pedantics":{"Author":"Michael
Morrissey","Depends":"R (>= 2.4.0), MasterBayes, MCMCglmm, kinship2,
grid","Description":"Contains functions for sensitivity and power analysis, for
calculating statistics describing pedigrees from wild populations, and for viewing
pedigrees","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"pedantics","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Functions to facilitate power and sensitivity analyses
for\ngenetic studies of natural populations","Version":"1.5"},"pedgene":
{"Author":"Schaid Daniel [aut],\nJason Sinnwell [aut, cre]","Depends":"R (>=
3.1.1), stats, Matrix, CompQuadForm, survey, kinship2\n(>=
1.6.0)","Description":"Gene-level association tests with disease status for
pedigree data: kernel and burden association statistics.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pedgene","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Gene-Level Statistics for Pedigree
Data","Version":"2.9"},"pedigree":{"Author":"Albart Coster [aut,
cre]","Depends":"Matrix, HaploSim (>= 1.8.4), reshape","Description":"Pedigree
related functions","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"pedigree","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Pedigree functions","Version":"1.4"},"pedigreemm":
{"Author":"Douglas Bates and Ana Ines Vazquez,","Depends":"R(>= 3.0.0), lme4 (>=
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2)","NeedsCompilation":"yes","Package":"pedigreemm","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Pedigree-based mixed-effects
models","URL":"http:\/\/pedigreemm.r-forge.r-project.org\/","Version":"0.3-
3"},"pedometrics":{"Author":"Alessandro Samuel-Rosa [aut, cre],\nLÃºcia Anjos
[ths],\nGustavo Vasques [ths],\nGerard Heuvelink [ths],\nTony Olsen [ctb],\nTom
Kincaid [ctb],\nJuan Carlos Ruiz Cuetos [ctb],\nMaria Eugenia Polo Garcia
[ctb],\nPablo Garcia Rodriguez [ctb],\nJoshua French [ctb],\nKen Kleinman
[ctb],\nDick Brus [ctb],\nFrank Harrell Jr [ctb],\nRuo Xu [ctb]","Depends":"R (>=
3.2.0)","Description":"Functions to employ many of the tools and techniques used in
the\nfield of pedometrics.","Imports":"lattice, latticeExtra, Rcpp (>=
0.12.0)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"pedometrics","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"car, geoR, georob, grDevices, grid, gstat, MASS,
methods,\nmoments, pbapply, plyr, randomForest, sp, SpatialTools,\nspsurvey,
xtable","Title":"Pedometric Tools and
Techniques","URL":"https:\/\/github.com\/samuel-rosa\/pedometrics","Version":"0.6-
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cph],\nKlaus Schliep [aut, cph],\nAlastair Potts [aut, cph],\nDavid Winter [aut,
cph]","Depends":"R (>= 2.6.0), ape (>= 2.4), adegenet","Description":"Functions for
reading, writing, plotting, analysing, and manipulating allelic and haplotypic
data, and for the analysis of population nucleotide sequences and micro-satellites
including coalescence analyses.","Imports":"graphics, utils","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"pegas","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Population and Evolutionary Genetics Analysis
System","URL":"http:\/\/ape-package.ird.fr\/pegas.html","Version":"0.8-
2"},"pems.utils":{"Author":"Karl Ropkins","Depends":"R (>= 2.10.0), lattice,
loa","Description":"Utility functions for the handling, analysis and
visualisation\nof data from portable emissions measurement systems ('PEMS') and
other\nsimilar mobile activity monitoring devices. The package includes a
dedicated\n'pems' data class that manages many of the quality control, unit
handling\nand data archiving issues that can hinder efforts to standardise
'PEMS'\nresearch.","Imports":"methods, utils, grid, RColorBrewer, latticeExtra,
ggplot2,\nplyr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pems.utils","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Portable Emissions (and Other Mobile) Measurement
System\nUtilities","Version":"0.2.17.8"},"penDvine":{"Author":"Christian Schellhase
<cschellhase@wiwi.uni-bielefeld.de>","Depends":"R (>= 2.15.1), lattice, TSP, fda,
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Bivariate Penalized Splines.","Imports":"quadprog, latticeExtra,
2)","NeedsCompilation":"no","Package":"penDvine","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Flexible Pair-Copula Estimation in D-Vines using
Bivariate\nPenalized Splines","Version":"0.2.4"},"penMSM":{"Author":"Holger
Reulen","Description":"Structured fusion Lasso penalized estimation of multi-state
models with the penalty applied to absolute effects and absolute effect differences
(i.e., effects on transition-type specific hazard rates).","Imports":"Rcpp (>=
0.11.3)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"penMSM","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Estimating Regularized Multi-state Models Using L1
Penalties","Version":"0.99"},"penalized":{"Author":"Jelle Goeman, Rosa Meijer,
Nimisha Chaturvedi","Depends":"R (>= 2.10.0), survival, methods","Description":"A
package for fitting possibly high dimensional penalized\nregression models. The
penalty structure can be any combination\nof an L1 penalty (lasso and fused lasso),
an L2 penalty (ridge) and a\npositivity constraint on the regression coefficients.
The\nsupported regression models are linear, logistic and Poisson\nregression and
the Cox Proportional Hazards model.\nCross-validation routines allow optimization
of the tuning\nparameters.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"penalized","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"globaltest","Title":"L1 (lasso and fused lasso) and
L2 (ridge) penalized estimation\nin GLMs and in the Cox model","Version":"0.9-
45"},"penalizedLDA":{"Author":"Daniela Witten","Depends":"R (>=
1.9.0)","Description":"Implements the penalized LDA proposal of \"Witten and
Tibshirani (2011), Penalized classification using Fisher's linear discriminant, to
appear in Journal of the Royal Statistical Society, Series B\".","Imports":"flsa,
2)","NeedsCompilation":"no","Package":"penalizedLDA","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Penalized Classification using Fisher's Linear
Discriminant","Version":"1.1"},"penalizedSVM":{"Author":"Natalia Becker, Wiebke
Werft, Axel Benner","Depends":"e1071, MASS, corpcor, statmod, tgp, mlegp,
lhs","Description":"This package provides feature selection SVM using
penalty\nfunctions. The smoothly clipped absolute deviation (SCAD),\n'L1-norm',
'Elastic Net' ('L1-norm' and 'L2-norm') and 'Elastic\nSCAD' (SCAD and 'L2-norm')
penalties are availible. The tuning\nparameters can be founf using either a fixed
grid or a interval\nsearch.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"penalizedSVM","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Feature Selection SVM using penalty
functions","Version":"1.1"},"pencopula":{"Author":"Christian Schellhase
<cschellhase@wiwi.uni-bielefeld.de>","Depends":"R (>= 2.15.1), lattice, fda,
quadprog, latticeExtra","Description":"Flexible copula density estimation with
penalized hierarchical B-Splines.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pencopula","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"MASS","Title":"Flexible Copula Density Estimation
with Penalized Hierarchical\nB-Splines","Version":"0.3.5"},"pendensity":
{"Author":"Christian Schellhase","Depends":"R (>= 2.15.1), lattice,
fda","Description":"Estimation of univariate (conditional) densities using
penalized B-splines with automatic selection of optimal smoothing
parameter.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pendensity","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Density Estimation with a Penalized Mixture
Approach","Version":"0.2.10"},"pensim":{"Author":"L. Waldron, M. Pintilie, M.-S.
Tsao, F. A. Shepherd, C. Huttenhower*, I. Jurisica* (*equal
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correlated high-dimensional data with time to event or binary response, and
parallelized functions for Lasso, Ridge, and Elastic Net penalized regression with
repeated starts and two-dimensional tuning of the Elastic
Net.","Imports":"parallel, penalized, MASS","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pensim","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"survivalROC, survival","Title":"Simulation of high-
dimensional data and parallelized repeated\npenalized
regression","Version":"1.2.9"},"peperr":{"Author":"Christine Porzelius, Harald
Binder","Depends":"snowfall, survival","Description":"Package peperr is designed
for prediction error estimation\nthrough resampling techniques, possibly
accelerated by parallel\nexecution on a compute cluster. Newly developed model
fitting\nroutines can be easily incorporated.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"peperr","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"CoxBoost, locfit, penalized,
codetools","Title":"Parallelised Estimation of Prediction Error","Version":"1.1-
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variety of methods for dealing\nwith analysis of peptide library data, including
clustering,\nmotif finding, and QSAR model fitting.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"peplib","Repository":"http:\/\/cran.csiro.au
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[aut, cre],\nGGobi Foundation [aut]","Depends":"R (>=
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NNB,\nNNK\/S, and 20\/20 schemes. Custom encoding schemes can also be
defined.\nMetrics for evaluation include expected coverage, relative efficiency,
and\nthe functional diversity of the library. Peptide-level
inclusion\nprobabilities are computable for both the native and custom
encoding\nschemes.","Imports":"discreteRV (>= 1.2), plyr, dplyr","License":"GPL-
3","NeedsCompilation":"no","Package":"peptider","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"ggplot2","Title":"Evaluation of Diversity in
Nucleotide
Libraries","URL":"https:\/\/github.com\/heike\/peptider","Version":"0.2.2"},"pequod
":{"Author":"Alberto Mirisola & Luciano Seta","Depends":"ggplot2,
car","Description":"Moderated regression with mean and residual centering and
simple slopes analysis.","Imports":"methods","License":"GPL-
2","NeedsCompilation":"no","Package":"pequod","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Moderated Regression Package","Version":"0.0-5"},"perARMA":
{"Author":"Anna Dudek, Harry Hurd and Wioletta
Wojtowicz","Description":"Identification, model fitting and estimation for time
series with periodic structure.\nAdditionally procedures for simulation of periodic
processes\nand real data sets are included.","Imports":"corpcor, gnm, matlab,
Matrix, signal, stats","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"perARMA","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Periodic Time Series
Analysis","Version":"1.6"},"performanceEstimation":{"Author":"Luis Torgo [aut,
cre]","Depends":"R(>= 3.0), methods","Description":"An infra-structure for
estimating the predictive performance\nof predictive models. In this context, it
can also be used to compare and\/or select among\ndifferent alternative ways of
solving one or more predictive tasks. The main goal of the\npackage is to provide a
generic infra-structure to estimate the values of different metrics\nof predictive
performance using different estimation procedures. These estimation tasks can
be\napplied to any solutions (workflows) to the predictive tasks. The package
provides easy to use\nstandard workflows that allow the usage of any available R
modeling algorithm together with\nsome pre-defined data pre-processing steps and
also prediction post-processing methods. It also provides means for addressing
issues related with the statistical significance of the observed
differences.","Imports":"ggplot2 (>= 0.9.3), foreach (>= 1.2.0), doParallel (>=
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2)","NeedsCompilation":"no","Package":"performanceEstimation","Repository":"http:\/
\/cran.csiro.au\/src\/contrib","Title":"An Infra-Structure for Performance
Estimation of
Predictive\nModels","URL":"https:\/\/github.com\/ltorgo\/performanceEstimation","Ve
rsion":"1.0.2"},"pergola":{"Author":"Fabian Grandke [aut, cre],\nDirk Metzler
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implements the method PERGOLA, which is a fast, deterministic method to\ncalculate
the order of markers in a linkage group.","Imports":"seriation, utils,
3","NeedsCompilation":"no","Package":"pergola","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr, gclus, dendextend, dendextendRcpp, Matrix,
rmarkdown,\ngrDevices","Title":"Toolbox for Polyploid Genetic
Data","URL":"http:\/\/github.com\/grafab\/pergola","Version":"1.0"},"perm":
{"Author":"Michael Fay","Depends":"R (>= 2.2.1), stats","Description":"Perform
Exact or Asymptotic permutation
tests","License":"GPL","NeedsCompilation":"no","Package":"perm","Repository":"http:
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permutation tests","Version":"1.0-0.0"},"permubiome":{"Author":"Alfonso Benitez-
Paez","Description":"All the functions compiled in this package were created to
perform permutation-based non-parametric analysis on microbiome data for biomarker
discovery aims. This test executes thousands of comparisons in pairwise manner,
after random shuffling of data into the different groups of
study.","Imports":"ggplot2","License":"GPL-
2","NeedsCompilation":"no","Package":"permubiome","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"A Permutation Based Test for Biomarker Discovery in
Microbiome\nData","Version":"1.1"},"permutations":{"Author":"Robin K. S.
Hankin","Description":"Manipulates invertible functions from a finite set to
itself. Can transform from word form to cycle form and
back.","Imports":"magic,numbers,partitions (>= 1.9-17)","License":"GPL-
2","NeedsCompilation":"no","Package":"permutations","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Permutations of a Finite Set","Version":"1.0-
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[cph],\nDouglas M. Bates [ctb],\nJari Oksanen [ctb]","Depends":"R (>=
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exchangeable, line transects (time series), and spatial grid designs plus
permutation of blocks (groups of samples) is provided. 'permute' also allows split-
plot designs, in which the whole-plots or split-plots or both can be freely-
exchangeable or one of the restricted designs. The 'permute' package is modelled
after the permutation schemes of 'Canoco 3.1' (and later) by Cajo ter
Braak.","Imports":"stats","License":"GPL-
2","NeedsCompilation":"no","Package":"permute","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"vegan (>= 2.0-0), testthat (>= 0.5),
parallel","Title":"Functions for Generating Restricted Permutations of
Data","URL":"https:\/\/github.com\/gavinsimpson\/permute","Version":"0.9-
0"},"perry":{"Author":"Andreas Alfons [aut, cre]","Depends":"R (>= 2.14.1), ggplot2
(>= 0.9.2), parallel, robustbase","Description":"Tools that allow developers to
write functions for\nprediction error estimation with minimal programming effort
and\nassist users with model selection in regression
problems.","Imports":"stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"perry","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Resampling-based prediction error estimation for
regression\nmodels","Version":"0.2.0"},"persiandictionary":{"Author":"Sadegh
Rasoulinejad (R package and database version of the\ndictionary) Manouchehr
Aryanpour (for the original dictionary)","Depends":"R (>=
2.10)","Description":"Translate words from English to Persian (Over
67,000\nwords)","License":"GPL-
2","NeedsCompilation":"no","Package":"persiandictionary","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"English
to Persian dictionary","Version":"1.0"},"personograph":{"Author":"Joel Kuiper
[aut, cre], Iain Marshall [aut]","Depends":"R (>= 3.1.0),
grImport","Description":"Visualizes treatment effects using person icons, similar
to Cates (NNT) charts.","Imports":"stats, grDevices, grid","License":"LGPL (>= 2.0,
< 3) | Mozilla Public
License","NeedsCompilation":"no","Package":"personograph","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"meta","Title":"Pictographic Representation
of Treatment
Effects","URL":"https:\/\/github.com\/joelkuiper\/personograph","Version":"0.1.3"},
"perspectev":{"Author":"Kenneth B. Hoehn [aut, cre],\nGlen A. Sargeant
[ctb]","Depends":"R (>= 2.10), ggplot2, foreach, ape, doParallel,
parallel,\ngrDevices, stats, methods","Description":"Provides a robust framework
for analyzing the extent to which differential survival with respect to higher
level trait variation is reducible to lower level variation. In addition to its
primary test, it also provides functions for simulation-based power analysis,
reading in common data set formats, and visualizing results. Temporarily contains
an edited version of function hr.mcp() from package 'wild1', written by Glen
Sargeant. For tutorial see:
http:\/\/evolve.zoo.ox.ac.uk\/Evolve\/Perspectev.html.","Imports":"mapproj, boot,
sp","License":"GPL-
3","NeedsCompilation":"no","Package":"perspectev","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Permutation of Species During Turnover
Events","Version":"1.1"},"perturb":{"Author":"John
Hendrickx","Description":"\"perturb\" evaluates collinearity by adding random noise
to\nselected variables. \"colldiag\" calculates condition numbers and\nvariance
decomposition proportions to test for collinearity and\nuncover its
sources.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"perturb","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"car, rms","Title":"Tools for evaluating
collinearity","URL":"http:\/\/home.wanadoo.nl\/john.hendrickx\/statres\/","Version"
:"2.05"},"pesticides":{"Author":"David M Diez","Description":"Single item and
composite pesticide residue measurements\nof fifteen commodity-pesticide
combinations plus analytical\ntools.","License":"GPL-
3","NeedsCompilation":"no","Package":"pesticides","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Analysis of single serving and composite pesticide
residue\nmeasurements","Version":"0.1"},"pez":{"Author":"William D. Pearse, Marc W.
Cadotte, Jeannine Cavender-Bares,\nAnthony R. Ives, Caroline Tucker, Steve C.
Walker, Matthew R. Helmus","Depends":"ape (>= 3.1-4)","Description":"Eco-
phylogenetic and community phylogenetic analyses.\nKeeps community ecological and
phylogenetic data matched up and\ncomparable using 'comparative.comm' objects.
Wrappers for common\ncommunity phylogenetic indices ('pez.shape',
'pez.evenness',\n'pez.dispersion', and 'pez.dissimilarity' metrics).
Implementation\nof Cavender-Bares (2004) correlation of phylogenetic
and\necological matrices ('fingerprint.regression'). Phylogenetic\nGeneralised
Linear Mixed Models (PGLMMs; 'pglmm') following Ives &\nHelmus (2011) and Rafferty
& Ives (2013). Simulation of null\nassemblages, traits, and phylogenies ('scape',
'sim.meta.comm').","Imports":"caper (>= 0.5-2), picante (>= 1.6-2), quantreg (>=
5.05),\nmvtnorm (>= 1.0-0), vegan (>= 2.0-10), ade4 (>= 1.6-2),\napTreeshape (>=
1.4-5), FD (>= 1.0-12), Matrix (>= 1.1-4),\nmethods (>= 3.1.0)","License":"GPL-
3","NeedsCompilation":"no","Package":"pez","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"knitr (>= 1.6), lme4 (>= 1.1-7)","Title":"Phylogenetics for
the Environmental Sciences","Version":"1.1-1"},"pgam":{"Author":"Washington Junger
<wjunger@ims.uerj.br> and Antonio Ponce de\nLeon <ponce@ims.uerj.br>","Depends":"R
(>= 2.14.0),stats,utils","Description":"This work is an extension of the state
space model for\nPoisson count data, Poisson-Gamma model, towards a\nsemiparametric
specification. Just like the generalized\nadditive models (GAM), cubic splines are
used for covariate\nsmoothing. The semiparametric models are fitted by an
iterative\nprocess that combines maximization of likelihood and\nbackfitting
2)","NeedsCompilation":"yes","Package":"pgam","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Poisson-Gamma Additive
Models","Version":"0.4.12"},"pgirmess":{"Author":"Patrick Giraudoux
<patrick.giraudoux@univ-fcomte.fr>","Description":"Miscellaneous functions for data
analysis in ecology, with special emphasis on spatial data.","Imports":"boot (>=
1.3-4), maptools (>= 0.8-36), rgdal (>= 0.7-8), rgeos\n(>= 0.3-8), sp (>= 0.9-97),
spdep (>= 0.5-43), splancs (>=\n2.01-31)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pgirmess","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"MASS (>= 7.3-1), nlme (>= 3.1-120)","Title":"Data
Analysis in
Ecology","URL":"http:\/\/perso.orange.fr\/giraudoux","Version":"1.6.4"},"pglm":
{"Author":"Yves Croissant [aut, cre]","Depends":"R (>= 2.10), maxLik,
plm","Description":"Estimation of panel models for glm-like models: this includes
binomial models (logit and probit) count models (poisson and negbin) and ordered
models (logit and probit)","Imports":"statmod","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pglm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"lmtest, car","Title":"panel generalized linear
model","URL":"http:\/\/www.r-project.org","Version":"0.1-2"},"pgmm":{"Author":"Paul
D. McNicholas [aut, cre], Aisha ElSherbiny [aut], K. Raju Jampani [ctb], Aaron F.
McDaid [aut], T. Brendan Murphy [aut], Larry Banks [ctb]","Description":"Carries
out model-based clustering or classification using parsimonious Gaussian mixture
2)","NeedsCompilation":"yes","Package":"pgmm","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Parsimonious Gaussian Mixture
Models","Version":"1.2"},"pgnorm":{"Author":"Steve Kalke","Description":"Evaluation
of the pdf and the cdf of the univariate,\nnoncentral, p-generalized normal
distribution. Sampling from\nthe univariate, noncentral, p-generalized normal
distribution\nusing either the p-generalized polar method, the p-
generalized\nrejecting polar method, the Monty Python method, the Ziggurat\nmethod
or the method of Nardon and Pianca. The package also\nincludes routines for the
simulation of the bivariate,\np-generalized uniform distribution and the simulation
of the\ncorresponding angular distribution.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pgnorm","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"The p-Generalized Normal
Distribution","Version":"2.0"},"pgs":{"Author":"Kien Kieu <Kien.Kieu@jouy.inra.fr>,
Marianne Mora <Marianne.Mora@u-paris10.fr>","Depends":"methods, gsl,
R2Cuba","Description":"Computation of mean squared errors of stereological
predictors.","License":"CeCILL","NeedsCompilation":"no","Package":"pgs","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Precision of Geometric
Sampling","Version":"0.4-0"},"ph2bayes":{"Author":"Kengo
NAGASHIMA","Description":"An implementation of Bayesian single-arm phase II\ndesign
methods for binary outcome based on posterior\nprobability and predictive
probability.","Imports":"stats, Rcpp (>= 0.12.3)","License":"GPL-
3","NeedsCompilation":"yes","Package":"ph2bayes","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Bayesian Single-Arm Phase II
Designs","Version":"0.0.1"},"phalen":{"Author":"Robert P.
Bronaugh","Depends":"graphics, grDevices, stats, utils","Description":"The phalen
package contains (1) clustering and\npartitioning algorithms; (2) penalty functions
for numeric\nvectors; (3) a ranking function; and (4) color palettes
and\nfunctions.","Imports":"sqldf","License":"GPL-
2","NeedsCompilation":"no","Package":"phalen","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Phalen Algorithms and
Functions","Version":"1.0"},"phangorn":{"Author":"Klaus Schliep [aut,
cre],\nEmmanuel Paradis [aut],\nAlastair Potts [aut]","Depends":"R (>= 3.0.0), ape
(>= 3.4)","Description":"Phylogenetic analysis in R: Estimation of
phylogenetic\ntrees and networks using Maximum Likelihood, Maximum
Parsimony,\ndistance methods and Hadamard conjugation.","Imports":"quadprog, igraph
(>= 1.0), Matrix, parallel, nnls, methods,\nutils, stats, graphics,
2)","NeedsCompilation":"yes","Package":"phangorn","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat, seqLogo, seqinr, xtable, flashClust, rgl,
knitr,\nrmarkdown, Biostrings","Title":"Phylogenetic Analysis in
R","URL":"https:\/\/github.com\/KlausVigo\/phangorn","Version":"2.0.2"},"phaseR":
{"Author":"Michael J. Grayling","Depends":"deSolve","Description":"phaseR is an R
package for the qualitative analysis of one and\ntwo dimensional autonomous ODE
systems, using phase plane methods. Programs\nare available to identify and
classify equilibrium points, plot the\ndirection field, and plot trajectories for
multiple initial conditions. In\nthe one dimensional case, a program is also
available to plot the phase\nportrait. Whilst in the two dimensional case,
additionally a program is\navailable to plot nullclines. Many example systems are
provided for the\nuser.","License":"GPL-
3","NeedsCompilation":"no","Package":"phaseR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Phase Plane Analysis of One and Two Dimensional Autonomous
ODE\nSystems","Version":"1.3"},"phcfM":{"Author":"Ghislain Vieilledent
<ghislain.vieilledent@cirad.fr>","Depends":"coda","Description":"phcfM is an R
package for modelling anthropogenic\ndeforestation. It was initially developed to
obtain REDD+\nbaseline scenarios of deforestation for the \"programme\nholistique
de conservation des forets a Madagascar\" (from which\nthe package is named after).
Parameter inference is done in a\nhierarchical Bayesian framework. Markov chains
Monte Carlo\n(MCMC) are coded in C++ using the Scythe statistical library
to\nmaximize computation efficiency.","License":"GPL-3 | file
LICENSE","NeedsCompilation":"yes","Package":"phcfM","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Modelling anthropogenic
deforestation","URL":"http:\/\/phcfM.sf.net","Version":"1.2"},"pheatmap":
{"Author":"Raivo Kolde","Depends":"R (>= 2.0)","Description":"Implementation of
heatmaps that offers more control\nover dimensions and
appearance.","Imports":"grid, RColorBrewer, scales, gtable, stats, grDevices,
2","NeedsCompilation":"no","Package":"pheatmap","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Pretty Heatmaps","Version":"1.0.8"},"phenability":
{"Author":"Leonardo Castelo Branco","Depends":"calibrate, R (>=
2.12.0)","Description":"An alternative to carrying out phenotypic adaptability and
stability analyses, taking into account nonparametric statistics. Can be used as a
robust approach, less sensitive to departures from common genotypic, environmental,
and GxE effects data assumptions (e.g., normal distribution of
errors).","License":"GPL-
3","NeedsCompilation":"no","Package":"phenability","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Nonparametric Stability
Analysis","Version":"2.0"},"phenex":{"Author":"Lange, Maximilian and Doktor,
Daniel","Depends":"R (>= 3.0)","Description":"Provides some easy-to-use functions
for\nspatial analyses of (plant-) phenological data\nsets and satellite
observations of vegetation.","Imports":"methods, foreach","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"phenex","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Auxiliary Functions for Phenological Data
Analysis","Version":"1.1-9"},"phenmod":{"Author":"Maximilian Lange","Depends":"R
(>= 2.14), gstat, RColorBrewer, lattice, pheno","Description":"Provides functions
to preprocess phenological data, for modelling and result handling.","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"phenmod","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Auxiliary functions for phenological data processing,
modelling\nand result handling","Version":"1.2-3"},"pheno":{"Author":"Joerg
Schaber","Depends":"R (>= 2.14), nlme, SparseM, quantreg","Description":"Provides
some easy-to-use functions for time series\nanalyses of (plant-) phenological data
sets. These functions\nmainly deal with the estimation of combined phenological
time\nseries and are usually wrappers for functions that are already\nimplemented
in other R packages adapted to the special\nstructure of phenological data and the
needs of phenologists.\nSome date conversion functions to handle Julian dates are
also\nprovided.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"pheno","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Auxiliary functions for phenological data
analysis","Version":"1.6"},"pheno2geno":{"Author":"Konrad Zych <k.zych@rug.nl> and
Danny Arends <danny.arends@gmail.com>","Depends":"R (>= 2.14.1), graphics, stats,
utils, qtl, VGAM, mixtools","Description":"High-throughput generation of genetic
markers from molecular phenotypes for crosses between inbred strains. These markers
can be use to saturate existing genetic map or creating a new one.","License":"GPL-
3","NeedsCompilation":"no","Package":"pheno2geno","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"RankProd","Title":"High-Throughput Generation of
Genetic Markers and Maps from\nMolecular Phenotypes for Crosses Between Inbred
Strains","Version":"1.3.1"},"phenology":{"Author":"Marc
Girondot","Depends":"fields, zoo, coda, HelpersMG (>= 1.2), shiny, R (>=
2.14.0)","Description":"Functions used to fit and test the phenology of species
based on counts.","License":"GPL-
2","NeedsCompilation":"no","Package":"phenology","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"optimx","Title":"Tools to Manage a Parametric
Function that Describes Phenology","URL":"\nhttp:\/\/max2.ese.u-
psud.fr\/epc\/conservation\/Girondot\/Publications\/Marine_Turtles_Nesting_Season.h
tml","Version":"4.2.4"},"phia":{"Author":"Helios De Rosario-Martinez [aut,
cre],\nJohn Fox [ctb],\nR Core Team [ctb]","Depends":"car, graphics,
stats","Description":"Analysis of terms in linear, generalized and mixed linear
models,\non the basis of multiple comparisons of factor contrasts. Specially
suited\nfor the analysis of interaction terms.","Imports":"Matrix, grDevices,
methods, utils","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"phia","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"nlme, lme4","Title":"Post-Hoc Interaction
Analysis","URL":"https:\/\/github.com\/heliosdrm\/phia","Version":"0.2-1"},"phmm":
{"Author":"Michael Donohue and Ronghui Xu","Depends":"survival, lattice,
Matrix","Description":"Fits proportional hazards model incorporating random effects
using\nan EM algorithm using Markov Chain Monte Carlo at E-step.","License":"GPL-
3","NeedsCompilation":"yes","Package":"phmm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"lme4 (>= 1.0)","Title":"Proportional Hazards Mixed-
effects Model (PHMM)","Version":"0.7-5"},"phonR":{"Author":"Daniel R.
McCloy","Depends":"R (>= 2.10)","Description":"Tools for phoneticians and
phonologists, including functions for normalization and plotting of
vowels.","Imports":"splancs, deldir, plotrix","License":"GPL-
3","NeedsCompilation":"no","Package":"phonR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Tools for Phoneticians and
Phonologists","URL":"http:\/\/drammock.github.io\/phonR\/","Version":"1.0-
3"},"phonTools":{"Author":"Santiago Barreda","Depends":"R (>=
2.15)","Description":"Contains tools for the organization, display, and analysis of
the sorts of data frequently encountered in phonetics research and experimentation,
including the easy creation of IPA vowel plots, and the creation and manipulation
of WAVE audio files.","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"phonTools","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Tools for Phonetic and Acoustic
Analyses","URL":"http:\/\/www.santiagobarreda.com\/rscripts.html","Version":"0.2-
2.1"},"phonenumber":{"Author":"Steve Myles [aut, cre]","Depends":"R (>=
3.1.3)","Description":"Convert English letters to numbers or numbers to English
letters as\non a telephone keypad. When converting letters to numbers, a
character\nvector is returned with \"A,\" \"B,\" or \"C\" becoming 2, \"D,\" \"E\",
or \"F\"\nbecoming 3, etc. When converting numbers to letters, a character vector
is\nreturned with multiple elements (i.e., \"2\" becomes a vector of \"A,\" \"B,\"
and\n\"C\").","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"phonenumber","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"knitr, testthat","Title":"Convert Letters to
Numbers and Back as on a Telephone
Keypad","URL":"http:\/\/steve.mylesandmyles.info\/projects\/phonenumber\/,\nhttps:\
/\/github.com\/scumdogsteev\/phonenumber","Version":"0.2.2"},"phonics":
{"Author":"James P. Howard, II [aut, cre]","Description":"Provides a collection of
phonetic algorithms including\nSoundex, Metaphone, NYSIIS, Caverphone, and
others.","Imports":"Rcpp (>= 0.12.1)","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"yes","Package":"phonics","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat","Title":"Phonetic Spelling
Algorithms","URL":"https:\/\/jameshoward.us\/software\/phonics\/,\nhttps:\/\/github
.com\/howardjp\/phonics","Version":"0.7.3"},"photobiology":{"Author":"Pedro J.
Aphalo [aut, cre]","Depends":"R (>= 3.2.0)","Description":"Definitions of classes,
methods, operators and functions for use in\n'photobiology' and radiation
meteorology and climatology. Calculation of\neffective (weighted) and not-weighted
'irradiances'\/doses, 'fluence' rates,\n'transmittance', 'reflectance',
'absorptance', 'absorbance' and diverse\nratios and other derived quantities from
spectral data. Local 'maxima' and\n'minima'. Conversion between energy- and photon-
based units. Wavelength\ninterpolation. Astronomical calculations related solar
angles and day\nlength. Colours and vision.","Imports":"lubridate (>= 1.5.0), plyr
(>= 1.8.3), dplyr (>= 0.4.3),\nsplus2R (>= 1.2-0), caTools (>=
1.17.1)","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"photobiology","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"knitr (>= 1.12.3), testthat (>= 0.11.0), roxygen2
(>= 5.0.1)","Title":"'Photobiological'
Calculations","URL":"http:\/\/www.r4photobiology.info\/,\nhttps:\/\/bitbucket.org\/
aphalo\/photobiology","Version":"0.9.7"},"photobiologyWavebands":{"Author":"Pedro
J. Aphalo [aut, cre]","Depends":"R (>= 3.2.0), photobiology (>=
0.9.4)","Description":"Constructors of waveband objects for commonly used
biological\nspectral weighting functions (BSWFs) and for different wavebands
describing\nnamed ranges of wavelengths in the ultraviolet (UV), visible (VIS)\nand
infrared (IR) regions of the electromagnetic spectrum.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"photobiologyWavebands","Repository":"http:\/
\/cran.csiro.au\/src\/contrib","Suggests":"knitr (>= 1.12.3)","Title":"Waveband
Definitions for UV, VIS, and IR
Radiation","URL":"http:\/\/www.r4photobiology.info\/,\nhttps:\/\/bitbucket.org\/aph
alo\/photobiologywavebands","Version":"0.4.0"},"phreeqc":{"Author":"S.R. Charlton,
D.L. Parkhurst, and C.A.J. Appelo, with contributions\nfrom D. Gillespie for
Chipmunk BASIC and S.D. Cohen, A.C. Hindmarsh,\nR. Serban, D. Shumaker, and A.G.
Taylor for CVODE\/SUNDIALS","Depends":"R (>= 2.10)","Description":"A geochemical
modeling program developed by the US Geological\nSurvey that is designed to perform
a wide variety of
aqueous geochemical\ncalculations, including speciation, batch-reaction, one-
dimensional\nreactive-transport, and inverse geochemical
calculations.","License":"GPL-3 + file
LICENSE","NeedsCompilation":"yes","Package":"phreeqc","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"R Interface to Geochemical Modeling
Software","URL":"http:\/\/wwwbrr.cr.usgs.gov\/projects\/GWC_coupled\/phreeqc","Vers
ion":"3.3.1"},"phtt":{"Author":"Oualid Bada, Dominik Liebl","Depends":"R(>=
2.10)","Description":"The package provides estimation procedures for panel data
with large dimensions n, T, and general forms of unobservable heterogeneous
effects. Particularly, the estimation procedures are those of Bai (2009) and Kneip,
Sickles, and Song (2012), which complement one another very well: both models
assume the unobservable heterogeneous effects to have a factor structure. The
method of Bai (2009) assumes that the factors are stationary, whereas the method of
Kneip et al. (2012) allows the factors to be non-stationary. Additionally, the
'phtt' package provides a wide range of dimensionality criteria in order to
estimate the number of the unobserved factors simultaneously with the remaining
model parameters.","Imports":"pspline","License":"GPL-
2","NeedsCompilation":"no","Package":"phtt","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Panel Data Analysis with Heterogeneous Time
Trends","Version":"3.1.2"},"phyclust":{"Author":"Wei-Chen Chen [aut, cre],\nKarin
Dorman [aut]","Depends":"R (>= 3.0.0), ape","Description":"Phylogenetic clustering
(phyloclustering) is an evolutionary\nContinuous Time Markov Chain model-based
approach to identify\npopulation structure from molecular data without
assuming\nlinkage equilibrium. The package phyclust (Chen 2011) provides
a\nconvenient implementation of phyloclustering for DNA and SNP data,\ncapable of
clustering individuals into subpopulations and identifying\nmolecular sequences
representative of those subpopulations. It is\ndesigned in C for performance,
interfaced with R for visualization,\nand incorporates other popular open source
programs including\nms (Hudson 2002), seq-gen (Rambaut and Grassly 1997),\nHap-
Clustering (Tzeng 2005) and PAML baseml (Yang 1997, 2007), for\nsimulating data,
additional analyses, and searching the best tree.\nSee the phyclust website for
more information, documentations and\nexamples.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"phyclust","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Phylogenetic Clustering
(Phyloclustering)","URL":"http:\/\/thirteen-
01.stat.iastate.edu\/snoweye\/phyclust\/","Version":"0.1-16"},"phyext2":
{"Author":"J. Conrad Stack","Description":"Based on (but not identical to) the no-
longer-maintained package 'phyext', provides enhancements to 'phylobase' classes,
specifically for use by package 'SigTree'; provides classes and methods which help
users manipulate branch-annotated trees (as in 'SigTree'); also provides support
for a few other extra features.","Imports":"methods, phylobase, ape, grid,
3","NeedsCompilation":"no","Package":"phyext2","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"An Extension (for Package 'SigTree') of Some of the
Classes in\nPackage 'phylobase'","Version":"0.0.4"},"phylin":{"Author":"Pedro
Tarroso, Guillermo Velo-Anton, Silvia Carvalho","Description":"The spatial
interpolation of genetic distances between\nsamples is based on a modified kriging
method that\naccepts a genetic distance matrix and generates a map of\nprobability
of lineage presence. This package also offers\ntools to generate a map of
potential contact zones\nbetween groups with user-defined thresholds in the
tree\nto account for old and recent divergence. Additionally,\nit has functions for
IDW interpolation using genetic data\nand midpoints.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"phylin","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"geometry","Title":"Spatial Interpolation of Genetic
Data","URL":"http:\/\/www.r-
project.org,\nhttp:\/\/webpages.icav.up.pt\/pessoas\/ptarroso\/phylin\/phylin.html,
\nhttps:\/\/github.com\/ptarroso\/phylin","Version":"1.1.1"},"phylobase":
{"Author":"R Hackathon et al. (alphabetically: Ben Bolker, Marguerite
Butler,\nPeter Cowan, Damien de Vienne, Dirk Eddelbuettel, Mark Holder,
Thibaut\nJombart, Steve Kembel, Francois Michonneau, David Orme, Brian
O'Meara,\nEmmanuel Paradis, Jim Regetz, Derrick Zwickl)","Description":"Provides a
base S4 class for comparative methods, incorporating\none or more trees and trait
data.","Imports":"ade4, ape (>= 3.0), Rcpp (>= 0.11.0), rncl (>= 0.6.0),
grid,\nmethods, stats, RNeXML","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"phylobase","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"MASS, testthat (>= 0.8.1), knitr","Title":"Base
Package for Phylogenetic Structures and Comparative
Data","URL":"https:\/\/github.com\/fmichonneau\/phylobase","Version":"0.8.2"},"phyl
oclim":{"Author":"Christoph Heibl, Clement Calenge
(\\code{import.ascii})","Depends":"ape, raster","Description":"This package
implements some recently developed methods in phyloclimatic
modeling.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"phyloclim","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Integrating Phylogenetics and Climatic Niche
Modeling","Version":"0.9-4"},"phylocurve":{"Author":"Eric W.
Goolsby","Description":"Tools for studying the evolution of high-dimensional traits
(morphometric, function-valued, etc.) including ancestral state reconstruction,
estimating phylogenetic signal, and assessing correlated trait evolution. Visit
http:\/\/www.phylocurve.org for more information.","Imports":"Rcpp, ape, drc, dtw,
geiger, geomorph (>= 3.0.0), GPfit,\nMatrix, mvnmle, phylolm, phytools, rgl,
doSNOW, doParallel,\nforeach, parallel, grDevices, graphics, stats,
2)","NeedsCompilation":"yes","Package":"phylocurve","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Phylogenetic Comparative Methods for High-Dimensional
Traits","URL":"http:\/\/www.phylocurve.org","Version":"2.0.2"},"phyloland":
{"Author":"Louis Ranjard, Marie Paturel","Description":"Phyloland package models a
space colonization process mapped onto a phylogeny, it aims at estimating limited
dispersal and ecological competitive exclusion in a Bayesian MCMC statistical
phylogeographic framework (please refer to phyloland-package help for
details.)","Imports":"ape","License":"GPL-
2","NeedsCompilation":"yes","Package":"phyloland","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Modelling Competitive Exclusion and Limited Dispersal
in a\nStatistical Phylogeographic Framework","Version":"1.3"},"phylolm":
{"Author":"Lam Si Tung Ho [aut, cre],\nCecile Ane [aut],\nRobert Lachlan
[ctb],\nKelsey Tarpinian [ctb],\nRachel Feldman [ctb]","Depends":"R (>= 3.0),
ape","Description":"Provides functions for fitting phylogenetic linear models and
phylogenetic generalized linear models. The computation uses an algorithm that is
linear in the number of tips in the tree. The package also provides functions for
simulating continuous or binary traits along the tree. Other tools include
functions to test the adequacy of a population tree.","License":"GPL (>= 2) | file
LICENSE","NeedsCompilation":"yes","Package":"phylolm","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Phylogenetic Linear
Regression","URL":"https:\/\/cran.r-
project.org\/package=phylolm","Version":"2.4"},"phylometrics":{"Author":"Xia Hua
<xia.hua@anu.edu.au>, Lindell Bromham\n<lindell.bromham@anu.edu.au>","Depends":"R
(>= 2.1.1)","Description":"Provides functions to estimate statistical errors of
phylogenetic\nmetrics particularly to detect binary trait influence on
diversification, as\nwell as a function to simulate trees with fixed number of
sampled taxa and trait\nprevalence.","Imports":"mvtnorm","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"phylometrics","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat","Title":"Estimating Statistical Errors
of Phylogenetic Metrics","Version":"0.0.1"},"phylosignal":{"Author":"Francois Keck
<francois.keck@gmail.com>","Description":"A collection of tools to explore the
phylogenetic signal in univariate and multivariate data. The package provides
functions to plot traits data against a phylogenetic tree, different measures and
tests for the phylogenetic signal, methods to describe where the signal is located
and a phylogenetic clustering method.","Imports":"Rcpp (>= 0.11.0), adephylo,
igraph, ape, phylobase, boot,\nRCurl, graphics, grDevices, methods, stats,
3","NeedsCompilation":"yes","Package":"phylosignal","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Exploring the Phylogenetic Signal in Continuous
Traits","Version":"1.1"},"phylotools":{"Author":"Jinlong Zhang, Nancai Pei,
Xiangcheng Mi","Depends":"seqRFLP, ape, picante, spaa,
fields","Description":"Building supermatrix for DNA barcodes using
different\ngenes, calculating the inequality among lineages and\nphylogenetic
similarity for very large dataset using slicing\nmethods by invoking
Phylocom.","License":"GPL-
2","NeedsCompilation":"no","Package":"phylotools","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"vegan","Title":"Phylogenetic tools for Eco-
phylogenetics","Version":"0.1.2"},"phyndr":{"Author":"Rich FitzJohn, Matt Pennell
and Will Cornwell","Depends":"R (>= 3.0)","Description":"Use topological or
taxonomic information to maximize the overlap of phylogenetic and comparative
data.","Imports":"ape","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"yes","Package":"phyndr","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat","Title":"Matches Tip and Trait
Data","Version":"0.1.0"},"phyreg":{"Author":"Alan
Grafen","Description":"Provides general linear model facilities (single y-
variable, multiple x-variables with arbitrary mixture of continuous and categorical
and arbitrary interactions) for cross-species data. The theory is in A. Grafen
(1989, Proc. R. Soc. B 326, 119-157) and aims to cope with both recognised
phylogeny (closely related species tend to be similar) and unrecognised phylogeny
(a polytomy usually indicates ignorance about the true sequence of binary
splits).","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"phyreg","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Implements the Phylogenetic Regression of Grafen
(1989)","Version":"0.7"},"physiology":{"Author":"Jack O. Wasey [aut,
cre]","Depends":"R (>= 3.0.2)","Description":"A variety of formulae are provided
for estimation of height,\nweight and fluid compartments of adults and children.
Each formula is\nreferenced to the original publication. Warnings can be given
for\nestimation based on input data outside of normal ranges. Future
functions\nwill cover more material with a focus on anaesthesia, critical\ncare and
peri-operative medicine.","License":"GPL-
3","NeedsCompilation":"no","Package":"physiology","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"ggplot2, reshape2, testthat,
knitr","Title":"Calculate Physiological Characteristics of Adults and
Children","URL":"https:\/\/github.com\/jackwasey\/physiology","Version":"0.2.2"},"p
hytools":{"Author":"Liam J. Revell","Depends":"R (>= 2.10), ape (>= 3.0-10),
maps","Description":"Package contains various functions for phylogenetic
analysis.\nThis functionality is concentrated in the phylogenetic analysis
of\ncomparative data from species. For example, the package includes\nfunctions for
Bayesian and ML ancestral state estimation; visual\nsimulation of trait evolution;
fitting models of trait evolution\nwith multiple Brownian rates and correlations;
visualizing\ndiscrete and continuous character evolution using colors
or\nprojections into trait space; identifying the location of a change\nin the rate
of character evolution on the tree; fast Brownian motion\nsimulation and simulation
under several other models of\ncontinuous trait evolution; fitting a model of
correlated binary\ntrait evolution; locating the position of a fossil or an
recently\nextinct lineage on a tree using continuous character data with
ML;\nplotting lineage accumulation through time, including across\nmultiple trees
(such as a Bayesian posterior sample); conducting\nan analysis called stochastic
character mapping, in which character\nhistories for a discrete trait are sampled
from their posterior\nprobability distribution under a model; conducting a
multiple\n(i.e., partial) Mantel test; fitting a phylogenetic regression
model\nwith error in predictor and response variables; conducting a\nphylogenetic
principal components analysis, a phylogenetic\nregression, a reduced major axis
regression, a phylogenetic\ncanonical correlation analysis, and a phylogenetic
ANOVA; projecting\na tree onto a geographic map; simulating discrete
character\nhistories on the tree; and fitting a model in which a
discrete\ncharacter evolves under the threshold model. In addition to
this\nphylogenetic comparative method functionality, the package also\ncontains
functions for a wide range of other purposes in\nphylogenetic biology. For
instance, functionality in this package\nincludes (but is not restricted to):
adding taxa to a tree\n(including randomly, everywhere, or automatically to
genera);\ngenerating all bi- and multi-furcating trees for a set of taxa;\nreducing
a phylogeny to its backbone tree; dropping tips or adding\ntips to special types of
phylogenetic trees; exporting a tree as an\nXML file; converting a tree with a
mapped character to a tree with\nsingleton nodes and one character state per edge;
estimating a\nphylogeny using the least squares method; simulating birth-
death\ntrees under a range of conditions; rerooting trees; a wide range\nof
visualizations of trees; and a variety of other manipulations\nand analyses that
phylogenetic biologists may find useful for\ntheir research.","Imports":"animation,
clusterGeneration, graphics, grDevices, methods,\nmnormt, msm, numDeriv, phangorn
(>= 1.6-3), plotrix,\nscatterplot3d, stats, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"phytools","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"geiger, rgl","Title":"Phylogenetic Tools for
Comparative Biology (and Other
Things)","URL":"http:\/\/www.phytools.org","Version":"0.5-20"},"phytotools":
{"Author":"Greg M. Silsbe, Sairah Y. Malkin","Depends":"insol,
FME","Description":"Fits PE and RLC data to one of a four published PE
models.\nSimulates incident irradiance as a function of time and space.\nCalculates
phytoplankton production by transposing modeled PE or RLC data\nto a water column
with a user-defined theoretical in-situ irradiance field.","License":"GPL-
2","NeedsCompilation":"no","Package":"phytotools","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Phytoplankton Production Tools","Version":"1.0"},"pi0":
{"Author":"Long Qu [aut, cre, ctb],\nKun Liang [ctb],\nYudi Pawitan [aut] (The
author(s) of OCplus::tMixture, which was\nmodified slightly leading to discTMix in
this package.),\nAlexander Ploner [aut] (The author(s) of OCplus::tMixture, which
was\nmodified slightly leading to discTMix in this package.),\nEgil Ferkingstad
[aut] (The author(s) of limma::convest, which was\nmodified slightly leading to
convest in this package.),\nMette Langaas [aut] (The author(s) of limma::convest,
which was\nmodified slightly leading to convest in this package.),\nMarcus Davy
[aut] (The author(s) of limma::convest, which was modified\nslightly leading to
convest in this package.)","Depends":"R (>= 2.12.0)","Description":"Methods for
estimating the proportion of true null hypotheses, i.e., the pi0, when a very large
number of hypotheses are simultaneously tested, especially for the purpose of
(local) false discovery rate control for microarray data. It also contains
functions to estimate the distribution of noncentrality parameters from a large
number of parametric tests.","Imports":"Matrix (>= 1.0-0), numDeriv, limSolve (>=
1.5.2), rgl,\nscatterplot3d, qvalue, Iso(>= 0.0-5), quadprog (>= 1.5-3),\nkernlab,
LowRankQP, graphics, grDevices, methods, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"pi0","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"limma, OCplus","Title":"Estimating the Proportion of True
Null Hypotheses for
FDR","URL":"https:\/\/github.com\/gitlongor\/pi0","Version":"1.4-0"},"picante":
{"Author":"Steven W. Kembel <steve.kembel@gmail.com>, David D. Ackerly
<dackerly@berkeley.edu>, Simon P. Blomberg <s.blomberg1@uq.edu.au>, Will K.
Cornwell <cornwell@zoology.ubc.ca>, Peter D. Cowan <pdc@berkeley.edu>, Matthew R.
Helmus <mrhelmus@wisc.edu>, Helene Morlon <morlon.helene@gmail.com>, Campbell O.
Webb <cwebb@oeb.harvard.edu>","Depends":"ape, vegan, nlme","Description":"Phylocom
integration, community analyses, null-models, traits and evolution in
R","License":"GPL-
2","NeedsCompilation":"yes","Package":"picante","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"brglm, circular, corpcor, quantreg","Title":"R tools
for integrating phylogenies and ecology","Version":"1.6-2"},"picasso":
{"Author":"Xingguo Li, Tuo Zhao, Tong Zhang and Han Liu","Depends":"R (>= 2.15.0),
lattice, igraph, MASS, Matrix","Description":"Implements the pathwise calibrated
sparse shooting algorithm (PICASSO) for high dimensional regularized sparse linear
regression, sparse logistic regression, and sparse undirected graphical model
estimation. As a pathwise coordinate optimization algorithm, PICASSO exploits warm
start initialization, active set updating, and strong rule for coordinate
preselection to boost computation, and attains a linear convergence to a unique
sparse local optimum with optimal statistical properties. Moreover, users can
choose different regularizers, including L1, MCP, and SCAD regularizers. The
computation is memory-optimized using the sparse matrix
output.","Imports":"methods","License":"GPL-
2","NeedsCompilation":"yes","Package":"picasso","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Pathwise Calibrated Sparse Shooting
Algorithm","Version":"0.5.0"},"pid":{"Author":"Kevin Dunn [aut, cre]","Depends":"R
(>= 2.15.0), ggplot2, stats, png, FrF2, DoE.base","Description":"A collection of
scripts and data files for the statistics text:\n\"Process Improvement using
Data\". The package contains code for designed\nexperiments, data sets and other
convenience functions used in the book.","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"pid","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"MASS","Title":"Process Improvement using
Data","URL":"http:\/\/learnche.org\/pid","Version":"0.36"},"piecewiseSEM":
{"Author":"Jon Lefcheck","Description":"Implements piecewise structural equation
models.","Imports":"ggm, lavaan, pbkrtest, nlme, lme4, methods","License":"GPL-
3","NeedsCompilation":"no","Package":"piecewiseSEM","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"knitr, rmarkdown","Title":"Piecewise Structural
Equation Modeling","Version":"1.1"},"pinfsc50":{"Author":"Brian J. Knaus [cre,
aut],\nNiklaus J. Grunwald [aut]","Depends":"R (>= 3.2.1)","Description":"Genomic
data for the plant pathogen \"Phytophthora infestans.\" It includes a variant file
(\"vcf\") sequence file (\"fasta\") and an annotation file (\"gff\"). This package
is intended to be used as example data for packages that work with genomic
data.","License":"GPL","NeedsCompilation":"no","Package":"pinfsc50","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Title":"Sequence (\"Fasta\"), Annotation
(\"Gff\") and Variants (\"Vcf\")
for\n17 Samples of \"P. Infestans\" and 1 \"P.
Mirabilis\"","Version":"1.0.0"},"pingr":{"Author":"\"Gabor Csardi\" [aut,
cre]","Description":"Check if a remote computer is up. It can either\njust call the
system ping command, or check a specified\nTCP port.","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"pingr","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat","Title":"Check If a Remote Computer is
Up","URL":"https:\/\/github.com\/gaborcsardi\/pingr","Version":"1.1.0"},"pinnacle.A
PI":{"Author":"Marco Blume, Nicholas Jhirad, Amine Gassem","Description":"An R
interface to the Pinnaclesports.com API.","Imports":"dplyr, uuid, httr, RCurl, XML,
rjson, jsonlite","License":"GPL-
3","NeedsCompilation":"no","Package":"pinnacle.API","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"A Wrapper for the Pinnacle Sports
API","URL":"https:\/\/github.com\/marcoblume\/pinnacle.API","Version":"1.90"},"pipe
.design":{"Author":"Michael Sweeting","Depends":"ggplot2 (>= 0.9.2),
gtools","Description":"Implements the Product of Independent beta Probabilities
dose Escalation (PIPE) design for dual-agent Phase I trials as described in Mander
AP, Sweeting MJ. Statistics in Medicine 2015. doi:
10.1002\/sim.6434.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pipe.design","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Dual-Agent Dose Escalation for Phase I Trials using
the PIPE\nDesign","Version":"0.3"},"pipeR":{"Author":"Kun Ren
<ken@renkun.me>","Depends":"R (>= 2.15)","Description":"Provides various styles of
function chaining methods: Pipe\noperator, Pipe object, and pipeline function, each
representing a distinct\npipeline model yet sharing almost a common set of
features: A value can be\npiped to the first unnamed argument of a function and to
dot symbol in an\nenclosed expression. The syntax is designed to make the pipeline
more\nreadable and friendly to a wide range of operations.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"pipeR","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat","Title":"Multi-Paradigm Pipeline
Implementation","URL":"https:\/\/renkun.me\/pipeR, https:\/\/github.com\/renkun-
ken\/pipeR,\nhttps:\/\/renkun.me\/pipeR-tutorial","Version":"0.6.1.3"},"pitchRx":
{"Author":"Carson Sievert <cpsievert1@gmail.com>","Depends":"R (>= 2.15.1), ggplot2
(>= 0.9.3)","Description":"With 'pitchRx', one can easily obtain Major League
Baseball Advanced\nMedia's 'Gameday' data (as well as store it in a remote
database). The\n'Gameday' website hosts a wealth of data in XML format, but perhaps
most\ninteresting is 'pitchfx'. Among other things, 'pitchfx' data can be used
to\nrecreate a baseball's flight path from a pitcher's hand to home plate.
With\npitchRx, one can easily create animations and interactive 3D
'scatterplots'\nof the baseball's flight path. 'pitchfx' data is also commonly used
to\ngenerate a static plot of baseball locations at the moment they cross
home\nplate. These plots, sometimes called strike-zone plots, can also refer to
a\nplot of event probabilities over the same region. 'pitchRx' provides an
easy\nand robust way to generate strike-zone plots using the 'ggplot2'
package.","Imports":"XML2R (>= 0.0.6), plyr, MASS, hexbin, mgcv","License":"MIT +
file
LICENSE","NeedsCompilation":"no","Package":"pitchRx","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"DBI, dplyr, RSQLite (>= 1.0.0), parallel, knitr,
animation,\nshiny, testthat, ggsubplot, rgl","Title":"Tools for Harnessing 'MLBAM'
'Gameday' Data and
Visualizing\n'pitchfx'","URL":"http:\/\/cpsievert.github.com\/pitchRx","Version":"1
.8.2"},"pixiedust":{"Author":"Benjamin Nutter [aut, cre]","Depends":"R (>=
3.2.1)","Description":"The introduction of the broom package has made converting
model objects into data\nframes as simple as a single function. While the broom
package focuses on providing tidy\ndata frames that can be used in advanced
analysis, it deliberately stops short of providing\nfunctionality for reporting
models in publication-ready tables. pixiedust provides this\nfunctionality with a
programming interface intended to be similar to ggplot2's system of\nlayers with
fine tuned control over each cell of the table. Options for output
include\nprinting to the console and to the common markdown formats (markdown,
HTML, and LaTeX).\nWith a little pixiedust (and happy thoughts) tables can really
fly.","Imports":"ArgumentCheck, broom, dplyr, Hmisc (>= 3.14-6), htmltools,\nknitr,
lazyWeave, magrittr, stringr, tidyr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"pixiedust","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"rmarkdown, testthat","Title":"Tables so
Beautifully Fine-Tuned You Will Believe It's
Magic","URL":"https:\/\/github.com\/nutterb\/pixiedust","Version":"0.6.1"},"pixmap"
:{"Author":"Roger Bivand, Friedrich Leisch and Martin
Maechler","Depends":"methods","Description":"Functions for import, export, plotting
and other\nmanipulations of bitmapped images.","License":"GPL-
2","NeedsCompilation":"no","Package":"pixmap","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Bitmap Images (``Pixel Maps'')","Version":"0.4-
11"},"pkgKitten":{"Author":"Dirk Eddelbuettel","Description":"Provides a function
kitten() which creates cute little\npackages which pass R package checks. This sets
it apart from\npackage.skeleton() which it calls, and which leaves imperfect
files\nbehind. As this is not exactly helpful for beginners, kitten() offers\nan
alternative.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pkgKitten","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"whoami (>= 1.1.0)","Title":"Create Simple Packages
Which Do not Upset R Package Checks","Version":"0.1.3"},"pkgconfig":
{"Author":"Gabor Csardi","Description":"Set configuration options on a per-package
basis.\nOptions set by a given package only apply to that package,\nother packages
are unaffected.","Imports":"utils","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"pkgconfig","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat, disposables","Title":"Private
Configuration for 'R'
Packages","URL":"https:\/\/github.com\/gaborcsardi\/pkgconfig","Version":"2.0.0"},"
pkgmaker":{"Author":"Renaud Gaujoux","Depends":"R (>= 3.0.0), stats,
registry","Description":"This package provides some low-level utilities to use for
package\ndevelopment. It currently provides managers for multiple package
specific\noptions and registries, vignette, unit test and bibtex related
utilities.\nIt serves as a base package for packages like NMF, RcppOctave, doRNG,
and\nas an incubator package for other general purposes utilities, that
will\neventually be packaged separately.\nIt is still under heavy development and
changes in the interface(s) are\nmore than likely to happen.","Imports":"methods,
tools, codetools, digest, stringr, xtable, grDevices","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pkgmaker","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"devtools (>= 0.8), bibtex, RUnit, testthat,
knitr,\nReportingTools, hwriter, argparse","Title":"Package development
utilities","URL":"https:\/\/renozao.github.io\/pkgmaker","Version":"0.22"},"pks":
{"Author":"Florian Wickelmaier [cre, aut], Juergen Heller [aut],\nPasquale Anselmi
[ctb]","Depends":"R (>= 2.14.0), stats, sets","Description":"Fitting and testing
probabilistic knowledge structures,\nespecially the basic local independence model
(BLIM, Doignon & Flamagne,\n1999), using the minimum discrepancy maximum likelihood
(MDML) method.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pks","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Probabilistic Knowledge
Structures","URL":"http:\/\/homepages.uni-
tuebingen.de\/florian.wickelmaier","Version":"0.3-1"},"plRasch":{"Author":"Zhushan
Li & Feng Hong","Depends":"survival","Description":"Fit Log Linear by Linear
Association models and Rasch family models by pseudolikelihood
2)","NeedsCompilation":"no","Package":"plRasch","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Log Linear by Linear Association models and Rasch family
models\nby pseudolikelihood estimation","Version":"1.0"},"pla":{"Author":"Jens
Henrik Badsberg","Depends":"R (>= 3.1.0), methods","Description":"Parallel Line
Assays: Completely randomized design,\nRandomized Block design, and Latin squares
design.\nBalanced data are fitted as described in the Ph.Eur.\nIn the presence of
missing values complete data analysis can be\nperformed (with computation of
Fieller's confidence intervals for\nthe estimated potency), or imputation of values
can be applied.\nThe package contains a script such that a pdf-document with
a\nreport of an analysis of an assay can be produced from an input file\nwith data
of the assay. Here no knowledge of R is needed by the user.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pla","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Parallel Line Assays","Version":"0.2"},"plan":{"Author":"Dan
Kelley <Dan.Kelley@Dal.Ca>","Depends":"R (>= 0.99)","Description":"Supports the
creation of burndown charts and gantt diagrams.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"plan","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Tools for project
planning","URL":"http:\/\/github.com\/dankelley\/plan","Version":"0.4-2"},"planar":
{"Author":"Baptiste Auguie [aut, cre] (Some functions ported from the
original\nMatlab SPLAC code by E.C. Le Ru and P. G. Etchegoin),\nSteven Johnson
[aut, cph] (C code for the cubature library)","Depends":"methods,
dielectric","Description":"Solves the electromagnetic problem of reflection and
transmission at a planar multilayer interface. Also computed are the decay rates
and emission profile for a dipolar emitter.","Imports":"Rcpp, statmod, cubature,
reshape2, plyr, ggplot2","License":"GPL-
3","NeedsCompilation":"yes","Package":"planar","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"Hmisc, grid, gridExtra, lattice, knitr,
testthat","Title":"Multilayer
Optics","URL":"https:\/\/github.com\/baptiste\/planar","Version":"1.6"},"planor":
{"Author":"HervÃ© Monod, Annie Bouvier, AndrÃ© Kobilinsky","Depends":"methods,
conf.design","Description":"Automatic generation of regular factorial designs,
including fractional designs, orthogonal block designs, row-column designs and
split-plots.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"planor","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Generation of Regular Factorial
Designs","URL":"http:\/\/www3.jouy.inra.fr\/miaj\/public\/logiciels\/planor","Versi
on":"0.2-4"},"plantecophys":{"Author":"Remko Duursma [aut,
cre]","Description":"Coupled leaf gas exchange model, A-Ci curve simulation
and\nfitting, leaf energy balance using Penman-Monteith, Cowan-
Farquhar\noptimization, unit
conversions.","License":"GPL","NeedsCompilation":"no","Package":"plantecophys","Rep
ository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"nlstools","Title":"Mode
lling and Analysis of Leaf Gas Exchange
Data","URL":"https:\/\/www.bitbucket.org\/remkoduursma\/plantecophys","Version":"1.
0-3"},"plaqr":{"Author":"Adam Maidman [cre, aut]","Depends":"R (>= 3.0), quantreg,
splines","Description":"Estimation, prediction, thresholding, and plotting for
partially linear additive quantile regression. Intuitive functions for fitting and
plotting partially linear additive quantile regression models. Uses and works with
functions from the 'quantreg' package.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"plaqr","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Partially Linear Additive Quantile
Regression","Version":"1.0"},"playwith":{"Author":"Felix Andrews
<felix@nfrac.org>","Depends":"R (>= 2.7.0), lattice (>= 0.16-3), cairoDevice,
gWidgetsRGtk2\n(>= 0.0-45), grid","Description":"A GTK+ graphical user interface
for editing and\ninteracting with R plots.","Imports":"RGtk2 (>= 2.20.1), gWidgets
(>= 0.0-30), gridBase, grDevices,\ngraphics, stats, utils","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"playwith","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"latticist, zoo, MASS, ggplot2, sp","Title":"A GUI
for interactive plots using
GTK+","URL":"http:\/\/playwith.googlecode.com\/","Version":"0.9-54"},"plfMA":
{"Author":"Dhammapal Bharne, Vaibhav Vindal","Description":"Provides a graphical
user interface for viewing and designing various types of graphs of the data. The
graphs can be saved in different formats of an image.","Imports":"gWidgets, limma,
gWidgetsRGtk2, tcltk, cairoDevice, grDevices,\ngraphics, stats","License":"GPL-
2","NeedsCompilation":"no","Package":"plfMA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"A GUI to View, Design and Export Various Graphs of
Data","Version":"1.0.2"},"plfm":{"Author":"Michel Meulders [aut, cre], Philippe De
Bruecker [ctb]","Depends":"sfsmisc, abind","Description":"Functions for estimating
probabilistic latent feature models with a disjunctive or a conjunctive mapping
rule on (aggregated) binary three-way data.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"plfm","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Probabilistic Latent Feature
Analysis","Version":"2.1"},"plgp":{"Author":"Robert B. Gramacy
<rbgramacy@chicagobooth.edu>","Depends":"R (>= 2.4), mvtnorm,
tgp","Description":"Sequential Monte Carlo inference for fully Bayesian\nGaussian
process (GP) regression and classification models by\nparticle learning (PL). The
sequential nature of inference\nand the active learning (AL) hooks provided
facilitate thrifty\nsequential design (by entropy) and optimization\n(by
improvement) for classification and\nregression models, respectively.\nThis package
essentially provides a generic\nPL interface, and functions (arguments to the
interface) which\nimplement the GP models and AL heuristics. Functions for\na
special, linked, regression\/classification GP model and\nan integrated expected
conditional improvement (IECI) statistic\nis provides for optimization in the
presence of unknown constraints.\nSeparable and isotropic Gaussian, and single-
index correlation\nfunctions are supported.\nSee the examples section of ?plgp and
demo(package=\"plgp\")\nfor an index of
demos","License":"LGPL","NeedsCompilation":"yes","Package":"plgp","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Suggests":"ellipse, splancs,
akima","Title":"Particle Learning of Gaussian
Processes","URL":"http:\/\/faculty.chicagobooth.edu\/robert.gramacy\/plgp.html","Ve
rsion":"1.1-7"},"plm":{"Author":"Yves Croissant [aut, cre],\nGiovanni Millo
[aut],\nOtt Toomet [ctb],\nChristian Kleiber [ctb],\nAchim Zeileis [ctb],\nArne
Henningsen [ctb],\nLiviu Andronic [ctb],\nNina Schoenfelder [ctb],\nKevin Tappe
[ctb]","Depends":"R (>= 2.10), Formula (>= 0.2-0), stats","Description":"A set of
estimators and tests for panel data.","Imports":"MASS, bdsmatrix, zoo, nlme,
sandwich, lattice, car, lmtest","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"plm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"AER","Title":"Linear Models for Panel
Data","URL":"http:\/\/www.R-project.org","Version":"1.5-12"},"plmDE":
{"Author":"Jonas Mueller","Depends":"R (>= 2.14.2), MASS, splines, limma,
R.oo","Description":"A set of tools for identifying genes whose
differential\nexpression is associated with measurements of other covariates\non a
continuous scale. These methods rely on generalized\nadditive partially linear
models which can be fitted\nefficiently using a B-spline basis approximation.
Still under\ndevelopment: methods for interfacing with objects extending the\neSet
class and a function to pass linear models in edgeR and\nDEseq
format.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"plmDE","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"Biobase, edgeR, DESeq","Title":"Additive partially
linear models for differential gene\nexpression analysis","Version":"1.0"},"plmm":
{"Author":"OHINATA Ren","Depends":"sm, Formula, nlme","Description":"This package
fits the partially linear mixed effects model\n(semiparametric random intercept
model) using kernel\nregression, without distributional assumptions for the
random\nterms. Estimation procedure is an iterative generalized least\nsquares
type. A nonparametric heteroskedastic variance function\nis allowed for the
regression error. Bootstrap resampling is\nprovided for inference. The package
implements bandwidth\nselection by an alternative cross validation for
correlated\ndata.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"plmm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Partially Linear Mixed Effects Model","Version":"0.1-
1"},"pln":{"Author":"Carl F. Falk and Harry Joe","Depends":"R (>=
2.9.0)","Description":"Performs bivariate composite likelihood and
full\ninformation maximum likelihood estimation for polytomous\nlogit-normit
(graded logistic) item response theory (IRT)\nmodels.","License":"GPL-
3","NeedsCompilation":"yes","Package":"pln","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Polytomous logit-normit (graded logistic) model
estimation","Version":"0.2-1"},"plot3D":{"Author":"Karline Soetaert
<karline.soetaert@nioz.nl>","Depends":"R (>= 2.15)","Description":"Functions for
viewing 2-D and 3-D data, including perspective plots, slice plots, surface plots,
scatter plots, etc. Includes data sets from oceanography.","Imports":"misc3d,
stats, graphics, grDevices","License":"GPL (>=
3.0)","NeedsCompilation":"no","Package":"plot3D","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Plotting Multi-Dimensional
Data","Version":"1.1"},"plot3Drgl":{"Author":"Karline Soetaert
<karline.soetaert@nioz.nl>","Depends":"rgl, plot3D, R (>=
3.2.3)","Description":"The 'rgl' implementation of plot3D
functions.","Imports":"grDevices","License":"GPL (>=
3.0)","NeedsCompilation":"no","Package":"plot3Drgl","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Plotting Multi-Dimensional Data - Using
'rgl'","Version":"1.0.1"},"plotGoogleMaps":{"Author":"Milan Kilibarda","Depends":"R
(>= 2.15.0), sp, spacetime","Description":"Provides an interactive plot device for
handling the geographic data for web browsers, designed for the automatic creation
of web maps as a combination of users' data and Google Maps
layers.","Imports":"rgdal, maptools,lattice, raster","License":"GPL-
2","NeedsCompilation":"no","Package":"plotGoogleMaps","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Plot Spatial or Spatio-Temporal Data Over Google
Maps","URL":"http:\/\/r-forge.r-
project.org\/projects\/plotgooglemaps\/","Version":"2.2"},"plotKML":
{"Author":"Tomislav Hengl [cre, aut],\nPierre Roudier [ctb],\nDylan Beaudette
[ctb],\nEdzer Pebesma [ctb],\nMichael Blaschek [ctb]","Depends":"R (>=
2.13.0)","Description":"Writes sp-class, spacetime-class, raster-class and similar
spatial and spatio-temporal objects to KML following some basic cartographic
rules.","Imports":"methods, tools, utils, XML, sp, raster, rgdal,
spacetime,\ncolorspace, plotrix, dismo, aqp, pixmap, plyr, stringr,\ncolorRamps,
scales, gstat, zoo, RColorBrewer, RSAGA,
classInt","License":"GPL","NeedsCompilation":"no","Package":"plotKML","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"adehabitat, maptools, fossil,
spcosa, rjson, animation,\nspatstat, RCurl, rgbif, Hmisc, GSIF, uuid, intervals,
reshape,\ngdalUtils, snowfall, parallel","Title":"Visualization of Spatial and
Spatio-Temporal Objects in Google\nEarth","URL":"http:\/\/plotkml.r-forge.r-
project.org\/","Version":"0.5-5"},"plotMCMC":{"Author":"Arni
Magnusson [aut, cre], Ian Stewart [aut]","Depends":"R (>=
2.10)","Description":"Markov chain Monte Carlo diagnostic plots. The purpose of
the\npackage is to combine existing tools from the 'coda' and 'lattice'
packages,\nand make it easy to adjust graphical details.","Imports":"coda, gplots,
lattice","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"plotMCMC","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"gdata","Title":"MCMC Diagnostic
Plots","Version":"2.0-0"},"plotROC":{"Author":"Michael C Sachs","Depends":"R (>=
3.0.0), ggplot2","Description":"Most ROC curve plots obscure the cutoff values and
inhibit\ninterpretation and comparison of multiple curves. This attempts to
address\nthose shortcomings by providing plotting and interactive tools.
Functions\nare provided to generate an interactive ROC curve plot for web use,
and\nprint versions. A Shiny application implementing the functions is
also\nincluded.","Imports":"methods, grid, gridSVG, shiny, plyr","License":"MIT +
file
LICENSE","NeedsCompilation":"no","Package":"plotROC","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"knitr, testthat, stringr,
survivalROC","Title":"Generate Useful ROC Curve Charts for Print and Interactive
Use","URL":"http:\/\/sachsmc.github.io\/plotROC","Version":"2.0.1"},"plotSEMM":
{"Author":"Bethany Kok [ctb],\nJolynn Pek [ctb],\nSonya Sterba [ctb],\nDan Bauer
[ctb],\nPhil Chalmers [cre, ctb]","Depends":"plyr, shiny","Description":"Contains a
graphical user interface to generate the\ndiagnostic plots proposed by Bauer (2005)
and Pek & Chalmers (2015) to investigate\nnonlinear bivariate relationships in
latent regression models using\nstructural equation mixture models
(SEMMs).","Imports":"graphics, methods, stats, MplusAutomation, Rcpp,
plotrix","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"plotSEMM","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Graphing Nonlinear Relations Among Latent Variables
from\nStructural Equation Mixture
Models","URL":"https:\/\/github.com\/philchalmers\/plotSEMM","Version":"2.1"},"plot
ly":{"Author":"Carson Sievert [aut, cre],\nChris Parmer [aut, cph],\nToby Hocking
[aut],\nScott Chamberlain [aut],\nKarthik Ram [aut],\nMarianne Corvellec
[aut],\nPedro Despouy [aut]","Depends":"ggplot2 (>= 2.1.0)","Description":"Easily
translate 'ggplot2' graphs to an interactive web-based version and\/or create
custom web-based visualizations directly from R. Once uploaded to a 'plotly'
account, 'plotly' graphs (and the data behind them) can be viewed and modified in a
web browser.","Imports":"scales, httr, jsonlite, magrittr, digest, viridis,
base64enc,\nhtmlwidgets, tidyr, plyr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"plotly","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"dplyr, maps, ggthemes, GGally, testthat, knitr,
devtools,\nshiny, htmltools, curl, rmarkdown, RColorBrewer, Rserve,\nRSclient,
broom, hexbin","Title":"Create Interactive Web Graphics via
'plotly.js'","URL":"https:\/\/plot.ly\/r,
https:\/\/github.com\/ropensci\/plotly","Version":"3.4.1"},"plotmo":
{"Author":"Stephen Milborrow","Depends":"plotrix,
TeachingDemos","Description":"Plot a model's response when varying one or two
predictors\nwhile holding the other predictors constant. A poor man's\npartial
dependence plot. Also plot model residuals.","License":"GPL-
3","NeedsCompilation":"no","Package":"plotmo","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"earth (>= 4.3.0), MASS, neuralnet, rpart,
rpart.plot","Title":"Plot a Model's Response and
Residuals","URL":"http:\/\/www.milbo.users.sonic.net","Version":"3.1.4"},"plotpc":
{"Author":"Stephen Milborrow","Depends":"grid","Description":"Plot principal
component histograms around a bivariate\nscatter plot.","License":"GPL-
3","NeedsCompilation":"no","Package":"plotpc","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Plot Principal Component Histograms Around a Scatter
Plot","URL":"http:\/\/www.milbo.users.sonic.net","Version":"1.0.4"},"plotrix":
{"Author":"Jim Lemon, Ben Bolker, Sander Oom,\nEduardo Klein, Barry
Rowlingson,\nHadley Wickham, Anupam Tyagi,\nOlivier Eterradossi, Gabor
Grothendieck,\nMichael Toews, John Kane, Rolf Turner,\nCarl Witthoft, Julian
Stander, Thomas Petzoldt,\nRemko Duursma, Elisa Biancotto, Ofir Levy,\nChristophe
Dutang, Peter Solymos, Robby Engelmann,\nMichael Hecker, Felix Steinbeck, Hans
Borchers,\nHenrik Singmann, Ted Toal, Derek Ogle","Description":"Lots of plots,
various labeling, axis and color scaling functions.","Imports":"grDevices,
2)","NeedsCompilation":"no","Package":"plotrix","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Various Plotting Functions","Version":"3.6-1"},"pls":
{"Author":"Bjørn-Helge Mevik, Ron Wehrens and Kristian Hovde Liland","Depends":"R
(>= 2.10)","Description":"Multivariate regression methods\nPartial Least Squares
Regression (PLSR), Principal Component\nRegression (PCR) and Canonical Powered
Partial Least Squares (CPPLS).","Imports":"grDevices, graphics, methods,
2","NeedsCompilation":"no","Package":"pls","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"MASS, parallel, Rmpi","Title":"Partial Least Squares and
Principal Component
Regression","URL":"http:\/\/mevik.net\/work\/software\/pls.html","Version":"2.5-
0"},"plsRbeta":{"Author":"Frederic Bertrand <frederic.bertrand@math.unistra.fr>,
Myriam Maumy-Bertrand <myriam.maumy-bertrand@math.unistra.fr>, Nicolas Meyer
<Nicolas.Meyer@nmeyer@unistra.fr>.","Depends":"R (>=
2.4.0)","Description":"Provides Partial least squares Regression for (weighted)
beta regression models and k-fold cross-validation of such models using various
criteria. It allows for missing data in the explanatory variables. Bootstrap
confidence intervals constructions are also available.","Imports":"mvtnorm, boot,
Formula, plsdof, MASS, betareg, plsRglm","License":"GPL-
3","NeedsCompilation":"no","Package":"plsRbeta","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"pls","Title":"Partial Least Squares Regression for
Beta Regression Models","URL":"http:\/\/www-irma.u-
strasbg.fr\/~fbertran\/","Version":"0.2.0"},"plsRcox":{"Author":"Frederic Bertrand
<frederic.bertrand@math.unistra.fr>, Myriam Maumy-Bertrand <myriam.maumy-
bertrand@math.unistra.fr>, Nicolas Meyer
<Nicolas.Meyer@nmeyer@unistra.fr>.","Depends":"R (>=
2.4.0)","Description":"Provides Partial least squares Regression and various
regular, sparse or kernel, techniques for fitting Cox models in high dimensional
settings.","Imports":"survival, plsRglm, lars, pls, kernlab, mixOmics,
risksetROC,\nsurvcomp, survAUC, rms","License":"GPL-
3","NeedsCompilation":"no","Package":"plsRcox","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"survivalROC, plsdof","Title":"Partial Least Squares
Regression for Cox Models and Related\nTechniques","URL":"http:\/\/www-irma.u-
strasbg.fr\/~fbertran\/","Version":"1.7.2"},"plsRglm":{"Author":"Frederic Bertrand
<frederic.bertrand@math.unistra.fr>, Nicolas Meyer
<Nicolas.Meyer@nmeyer@unistra.fr>, Myriam Maumy-Bertrand <myriam.maumy-
bertrand@math.unistra.fr>.","Depends":"R (>= 2.4.0)","Description":"Provides
(weighted) Partial least squares Regression for generalized linear models and
repeated k-fold cross-validation of such models using various criteria. It allows
for missing data in the explanatory variables. Bootstrap confidence intervals
constructions are also available.","Enhances":"pls","Imports":"mvtnorm, boot,
bipartite, car","License":"GPL-
3","NeedsCompilation":"no","Package":"plsRglm","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"MASS, plsdof, R.rsp, chemometrics,
plsdepot","Title":"Partial Least Squares Regression for Generalized Linear
Models","URL":"http:\/\/www-irma.u-
strasbg.fr\/~fbertran\/","Version":"1.1.1"},"plsVarSel":{"Author":"Kristian Hovde
Liland, Tahir Mehmood, Solve SÃ¦bÃ¸","Description":"Interfaces and methods for
variable selection in Partial Least\nSquares. The methods include filter methods,
wrapper methods and embedded\nmethods.","Imports":"grDevices, graphics, genalg,
mvtnorm, bdsmatrix, pls, MASS,\nprogress, parallel, stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"plsVarSel","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"Rmpi","Title":"Variable Selection in Partial Least
Squares","Version":"0.7"},"plsdepot":{"Author":"Gaston Sanchez","Depends":"R (>=
2.15.1)","Description":"plsdepot contains different methods for PLS analysis
of\none or two data tables such as Tucker's Inter-Battery, NIPALS,\nSIMPLS, SIMPLS-
CA, PLS Regression, and PLS Canonical Analysis.\nThe main reference for this
software is the awesome book (in\nFrench) 'La Regression PLS: Theorie et Pratique'
by Michel\nTenenhaus.","License":"GPL-
3","NeedsCompilation":"no","Package":"plsdepot","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"FactoMineR, plspm","Title":"Partial Least Squares
(PLS) Data Analysis Methods","URL":"http:\/\/www.gastonsanchez.com\/plsdepot,
http:\/\/www.plsmodeling.com","Version":"0.1.17"},"plsdof":{"Author":"Nicole
Kraemer, Mikio L. Braun","Depends":"MASS","Description":"The plsdof package
provides Degrees of Freedom estimates\nfor Partial Least Squares (PLS) Regression.
Model selection for\nPLS is based on various information criteria (aic, bic,
gmdl)\nor on cross-validation. Estimates for the mean and covariance\nof the PLS
regression coefficients are available. They allow\nthe construction of approximate
confidence intervals and the\napplication of test procedures. Further, cross-
validation\nprocedures for Ridge Regression and Principal Components\nRegression
are available.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"plsdof","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Degrees of Freedom and Statistical
Inference for Partial Least\nSquares Regression","Version":"0.2-7"},"plsgenomics":
{"Author":"Anne-Laure Boulesteix <boulesteix@ibe.med.uni-muenchen.de>,\nGhislain
Durif <ghislain.durif@univ-lyon1.fr>,\nSophie Lambert-Lacroix
<Sophie.Lambert@imag.fr>, Julie Peyre\n<Julie.Peyre@imag.fr>, and Korbinian
Strimmer\n<strimmer@uni-leipzig.de>.","Depends":"R (>= 3.0), MASS, boot,
parallel","Description":"Routines for PLS-based genomic analyses,\nimplementing PLS
methods for classification with\nmicroarray data and prediction of transcription
factor\nactivities from combined ChIP-chip analysis. The >=1.2-1\nversions include
two new classification methods for microarray\ndata: GSIM and Ridge PLS. The >=1.3
versions includes a\nnew classification method combining variable selection
and\ncompression in logistic regression context: RIRLS-SPLS; and\nan adaptive
version of the sparse PLS.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"plsgenomics","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"PLS Analyses for Genomics","URL":"http:\/\/cran.r-
project.org\/web\/packages\/plsgenomics\/index.html","Version":"1.3-1"},"plspm":
{"Author":"Gaston Sanchez [aut, cre],\nLaura Trinchera [aut],\nGiorgio Russolillo
[aut]","Depends":"R (>= 3.0.1)","Description":"Partial Least Squares Path Modeling
(PLS-PM)\nanalysis for both metric and\nnon-metric data, as well as REBUS
analysis.","Imports":"tester, turner, diagram, shape, amap","License":"GPL-
3","NeedsCompilation":"no","Package":"plspm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"plsdepot, FactoMineR, ggplot2, reshape, testthat,
knitr","Title":"Tools for Partial Least Squares Path Modeling (PLS-
PM)","URL":"https:\/\/github.com\/gastonstat\/plspm","Version":"0.4.7"},"plspm.form
ula":{"Author":"ACHIEPO Odilon Yapo M. [aut, cre]","Depends":"R (>=
3.0.0)","Description":"The main objective is to make easy the PLS Path Modeling
with R using the package 'plspm'. It compute automatically the inner matrix and the
outer list the 'plspm' function need simply by specify the model using
formulas.","Imports":"plspm","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"plspm.formula","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Formula Based PLS Path
Modeling","Version":"1.0.1"},"plugdensity":{"Author":"Eva Herrmann
<eherrmann@mathematik.tu-darmstadt.de> (C original);\nR interface etc by Martin
Maechler","Description":"Kernel density estimation with global bandwidth
selection\nvia \"plug-in\".","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"plugdensity","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Plug-in Kernel Density Estimation","URL":"originally
from http:\/\/www.unizh.ch\/biostat\/Software\/","Version":"0.8-3"},"plumbr":
{"Author":"Michael Lawrence, Hadley Wickham","Depends":"R (>=
2.10.0)","Description":"The base R data.frame, like any vector, is\ncopied upon
modification. This behavior is at odds with\nthat of GUIs and interactive graphics.
To rectify this,\nplumbr provides a mutable, dynamic tabular data model.\nModels
may be chained together to form the complex\nplumbing necessary for sophisticated
graphical\ninterfaces. Also included is a\ngeneral framework for linking datasets;
an typical\nuse case would be a linked brush.","Imports":"utils, methods,
objectSignals (>= 0.10.2)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"plumbr","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"plyr, testthat, MASS","Title":"Mutable and dynamic data
models","URL":"https:\/\/github.com\/ggobi\/plumbr\/wiki","Version":"0.6.9"},"plus"
:{"Author":"Cun-Hui Zhang and Ofer Melnik, with contributions from Yi Yu\nand
Stephanie Zhang","Depends":"R (>= 2.10), grDevices, graphics, stats,
utils","Description":"Efficient procedures for fitting an entire
regression\nsequences with different model types.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"plus","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Penalized Linear Unbiased
Selection","Version":"1.0"},"plusser":{"Author":"Christoph Waldhauser [aut,
cre]","Depends":"R (>= 3.0.2)","Description":"plusser provides an API interface to
Google+ so that posts,\nprofiles and pages can be automatically
retrieved.","Imports":"RCurl, RJSONIO, lubridate, plyr","License":"GPL-3 | file
LICENSE","NeedsCompilation":"no","Package":"plusser","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"A Google+ Interface for
R","URL":"http:\/\/kdss.at","Version":"0.4-0"},"plyr":{"Author":"Hadley Wickham
[aut, cre]","Depends":"R (>= 3.1.0)","Description":"A set of tools that solves a
common set of problems: you\nneed to break a big problem down into manageable
pieces, operate on each\npiece and then put all the pieces back together. For
example, you might\nwant to fit a model to each spatial location or time point in
your study,\nsummarise data by panels or collapse high-dimensional arrays to
simpler\nsummary statistics. The development of 'plyr' has been generously
supported\nby 'Becton Dickinson'.","Imports":"Rcpp (>= 0.11.0)","License":"MIT +
file
LICENSE","NeedsCompilation":"yes","Package":"plyr","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"abind, testthat, tcltk, foreach, doParallel,
itertools,\niterators","Title":"Tools for Splitting, Applying and Combining
Data","URL":"http:\/\/had.co.nz\/plyr,
https:\/\/github.com\/hadley\/plyr","Version":"1.8.3"},"pmc":{"Author":"Carl
Boettiger [aut, cre]","Description":"Monte Carlo based model choice for applied
phylogenetics of\ncontinuous traits. Method described in Carl Boettiger, Graham
Coop,\nPeter Ralph (2012) Is your phylogeny informative? Measuring\nthe power of
comparative methods, Evolution 66 (7)\n2240-51. doi:10.1111\/j.1558-
5646.2011.01574.x.","Imports":"dplyr, geiger, ggplot2, parallel, ouch,
tidyr","License":"CC0","NeedsCompilation":"no","Package":"pmc","Repository":"http:\
/\/cran.csiro.au\/src\/contrib","Suggests":"covr, gridExtra, knitr,
testthat","Title":"Phylogenetic Monte
Carlo","URL":"https:\/\/github.com\/cboettig\/pmc","Version":"1.0.1"},"pmcgd":
{"Author":"Antonio Punzo and Paul D. McNicholas","Depends":"R (>=
2.15.0)","Description":"Parsimonious Mixtures of Contaminated Gaussian
Distributions","Imports":"mixture, mnormt","License":"GPL-
2","NeedsCompilation":"no","Package":"pmcgd","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"pmcgd","Version":"1.1"},"pmclust":{"Author":"Wei-Chen Chen
[aut, cre],\nGeorge Ostrouchov [aut]","Depends":"R (>= 3.0.0), pbdMPI (>= 0.3-1),
pbdBASE (>= 0.4-3), pbdDMAT\n(>= 0.4-0)","Description":"Aims to utilize model-based
clustering (unsupervised)\nfor high dimensional and ultra large data, especially in
a distributed\nmanner. The code employs pbdMPI to perform a\nexpectation-gathering-
maximization algorithm\nfor finite mixture Gaussian\nmodels. The unstructured
dispersion matrices are assumed in the\nGaussian models. The implementation is
default in the single program\nmultiple data programming model. The code can be
executed\nthrough pbdMPI and independent to most MPI applications.\nSee the High
Performance\nStatistical Computing website for more information, documents\nand
examples.","Enhances":"MixSim","Imports":"methods, MASS","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"pmclust","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Parallel Model-Based Clustering using\nExpectation-
Gathering-Maximization Algorithm for Finite Mixture\nGaussian
Model","URL":"http:\/\/r-pbd.org\/","Version":"0.1-7"},"pmg":{"Author":"John
Verzani with contributions by Yvonnick Noel","Depends":"gWidgets, gWidgetsRGtk2,
proto, lattice","Description":"Simple GUI for R using
gWidgets.","Enhances":"reshape, cairoDevice","Imports":"foreign,
2)","NeedsCompilation":"no","Package":"pmg","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Poor Man's
GUI","URL":"http:\/\/www.math.csi.cuny.edu\/pmg","Version":"0.9-43"},"pmhtutorial":
{"Author":"Johan Dahlin <johan.dahlin@liu.se>","Depends":"R (>=
3.2.3)","Description":"Routines for state estimate in a linear\nGaussian state
space model and a simple stochastic volatility model using\nparticle filtering.
Parameter inference is also carried out in these models\nusing the particle
Metropolis-Hastings algorithm that includes the particle\nfilter to provided an
unbiased estimator of the likelihood. This package is\na collection of minimal
working examples of these algorithms and is only\nmeant for educational use and as
a start for learning to them on your own.","Imports":"mvtnorm, Quandl, grDevices,
2","NeedsCompilation":"no","Package":"pmhtutorial","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Minimal Working Examples for Particle Metropolis-
Hastings","URL":"https:\/\/github.com\/compops\/pmh-
tutorial","Version":"1.0.0"},"pmlr":{"Author":"Sarah Colby <colby@lunenfeld.ca>,
Sophia Lee, Juan Pablo\nLewinger, Shelley Bull
<bull@lunenfeld.ca>","Description":"Extends the approach proposed by Firth (1993)
for bias\nreduction of MLEs in exponential family models to the\nmultinomial
logistic regression model with general covariate\ntypes. Modification of the
logistic regression score function\nto remove first-order bias is equivalent to
penalizing the\nlikelihood by the Jeffreys prior, and yields penalized
maximum\nlikelihood estimates (PLEs) that always exist. Hypothesis\ntesting is
conducted via likelihood ratio statistics. Profile\nconfidence intervals (CI) are
constructed for the PLEs.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pmlr","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Penalized Multinomial Logistic
Regression","Version":"1.0"},"pmml":{"Author":"Graham Williams, Tridivesh Jena, Wen
Ching Lin, Michael Hahsler (arules),\nZementis Inc, Hemant Ishwaran, Udaya B.
Kogalur,
Rajarshi Guha, Dmitriy Bolotov","Depends":"XML","Description":"\nThe Predictive
Model Markup Language (PMML) is an XML-based language\nwhich provides a way for
applications to define statistical and data\nmining models and to share models
between PMML compliant applications.\nMore information about PMML and the Data
Mining Group can be found at\nhttp:\/\/www.dmg.org.\nThe generated PMML can be
imported into any PMML consuming application,\nsuch as the Zementis ADAPA and UPPI
scoring engines which allow for\npredictive models built in R to be deployed and
executed on site, in\nthe cloud (Amazon, IBM, and FICO), in-database (IBM Netezza,
Pivotal,\nSybase IQ, Teradata and Teradata Aster) or Hadoop (Datameer and
Hive).","Imports":"survival, methods, stats, utils","License":"GPL (>=
2.1)","NeedsCompilation":"no","Package":"pmml","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"ada, amap, arules, glmnet, nnet, rpart,
randomForestSRC,\nrandomForest, kernlab, e1071,
pmmlTransformations(>=\n1.3.0),testthat","Title":"Generate PMML for Various
Models","URL":"http:\/\/zementis.com\/","Version":"1.5.0"},"pmmlTransformations":
{"Author":"Tridivesh Jena, Wen Ching Lin, Dmitriy Bolotov (Zementis,
Inc.)","Description":"Allows for data to be transformed before using\nit to
construct models. Builds structures to allow functions in\nthe PMML package to
output transformation details in\naddition to the model in the resulting PMML
file.","License":"GPL (>=
2.1)","NeedsCompilation":"no","Package":"pmmlTransformations","Repository":"http:\/
\/cran.csiro.au\/src\/contrib","Suggests":"pmml (>= 1.5.0), knitr,
testthat","Title":"Transforms Input Data from a PMML
Perspective","Version":"1.3.0"},"pmr":{"Author":"Paul H. Lee and Philip L. H.
Yu","Depends":"stats4","Description":"Descriptive statistics (mean rank, pairwise
frequencies, and marginal matrix), Analytic Hierarchy Process models (with Saaty's
and Koczkodaj's inconsistencies), probability models (Luce models, distance-based
models, and rank-ordered logit models) and visualization with multidimensional
preference analysis for ranking data are provided. Current, only complete rankings
are supported by this package.","License":"GPL-
2","NeedsCompilation":"no","Package":"pmr","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Probability Models for Ranking
Data","Version":"1.2.5"},"pnea":{"Author":"Mirko Signorelli, Veronica Vinciotti and
Ernst C. Wit","Depends":"R (>= 3.2.0)","Description":"Includes functions and
examples to compute Parametric Network Enrichment Analysis.","License":"GPL-
3","NeedsCompilation":"no","Package":"pnea","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"igraph, Matrix","Title":"Parametric Network Enrichment
Analysis","Version":"1.2.4"},"pnf":{"Author":"Abby Rothway","Description":"An R
package for prime number generation, primality testing and integer factorization,
currently, using simple methods.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pnf","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Prime Numbers and Integer
Factorization","Version":"0.1.1"},"png":{"Author":"Simon Urbanek <Simon.Urbanek@r-
project.org>","Depends":"R (>= 2.9.0)","Description":"This package provides an easy
and simple way to read, write and display bitmap images stored in the PNG format.
It can read and write both files and in-memory raw vectors.","License":"GPL-2 |
GPL-
3","NeedsCompilation":"yes","Package":"png","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Read and write PNG
images","URL":"http:\/\/www.rforge.net\/png\/","Version":"0.1-7"},"pnmtrem":
{"Author":"Ozgur Asar, Ozlem Ilk","Depends":"MASS","Description":"An R package for
Probit-Normal Marginalized Transition\nRandom Effects Models","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pnmtrem","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Probit-Normal Marginalized Transition Random Effects
Models","Version":"1.3"},"pnn":{"Author":"Pierre-Olivier
Chasset","Description":"The program pnn implements the algorithm proposed
by\nSpecht (1990). It is written in the R statistical language. It\nsolves a
common problem in automatic learning. Knowing a set of\nobservations described by a
vector of quantitative variables,\nwe classify them in a given number of groups.
Then, the\nalgorithm is trained with this datasets and should guess\nafterwards the
group of any new observation. This neural\nnetwork has the main advantage to begin
generalization\ninstantaneously even with a small set of known observations. It\nis
delivered with four functions (learn, smooth, perf and\nguess) and a dataset. The
functions are documented with\nexamples and provided with unit
tests.","License":"AGPL","NeedsCompilation":"no","Package":"pnn","Repository":"http
:\/\/cran.csiro.au\/src\/contrib","Suggests":"testthat, roxygen2,
rgenoud","Title":"Probabilistic neural
networks","URL":"http:\/\/flow.chasset.net\/pnn\/","Version":"1.0.1"},"poLCA":
{"Author":"Drew Linzer <drew@votamatic.org>,\nJeffrey Lewis
<jblewis@ucla.edu>.","Depends":"scatterplot3d, MASS","Description":"Latent class
analysis and latent class regression models\nfor polytomous outcome variables.
Also known as latent structure analysis.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"poLCA","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Polytomous variable Latent Class
Analysis","URL":"http:\/\/dlinzer.github.com\/poLCA","Version":"1.4.1"},"pocrm":
{"Author":"Nolan A. Wages","Depends":"dfcrm, nnet","Description":"Provides
functions to implement and simulate the partial order continual reassessment method
(PO-CRM) for use in Phase I trials of combinations of agents. Provides a function
for generating a set of initial guesses (skeleton) for the toxicity probabilities
at each combination that correspond to the set of possible orderings of the
toxicity probabilities specified by the user.","License":"GPL-
2","NeedsCompilation":"no","Package":"pocrm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Dose Finding in Drug Combination Phase I Trials Using PO-
CRM","Version":"0.9"},"pogit":{"Author":"Michaela Dvorzak [aut, cre], Helga Wagner
[aut]","Depends":"R(>= 2.10.0)","Description":"Bayesian variable selection for
regression models of under-reported\ncount data as well as for (overdispersed)
Poisson, negative binomal and\nbinomial logit regression models using spike and
slab priors.","Imports":"BayesLogit, ggplot2, logistf, plyr, stats, utils,
2","NeedsCompilation":"no","Package":"pogit","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"COUNT","Title":"Bayesian Variable Selection for a
Poisson-Logistic Model","Version":"1.1.0"},"poibin":{"Author":"Yili
Hong","Description":"This package implements both the exact and
approximation\nmethods for computing the cdf of the Poisson binomial\ndistribution.
It also provides the pmf, quantile function, and\nrandom number generation for the
Poisson binomial distribution.","License":"GPL-
2","NeedsCompilation":"yes","Package":"poibin","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"The Poisson Binomial
Distribution","Version":"1.2"},"poilog":{"Author":"Vidar Grøtan and Steinar
Engen","Description":"Functions for obtaining the density, random deviates\nand
maximum likelihood estimates of the Poisson lognormal\ndistribution and the
bivariate Poisson lognormal distribution.","License":"GPL-
3","NeedsCompilation":"yes","Package":"poilog","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Poisson lognormal and bivariate Poisson lognormal
distribution","Version":"0.4"},"pointRes":{"Author":"Marieke van der Maaten-
Theunissen and Ernst van der Maaten","Depends":"R (>= 3.1.2), stats, graphics,
ggplot2","Description":"Functions to calculate and plot event and pointer years as
well as components of resilience. Designed for dendroecological applications, but
also suitable to analyze patterns in other ecological time
series.","Imports":"gridExtra, plyr, TripleR","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pointRes","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"dplR, knitr, rmarkdown","Title":"Analyzing Pointer
Years and Components of Resilience","Version":"1.1.2"},"pointdensityP":
{"Author":"Paul Evangelista <paul.evangelista@usma.edu> and Dave
Beskow\n<david.beskow@usma.edu>","Depends":"R (>= 3.1.1)","Description":"For every
spatial point in a list, calculates the density\nand temporal tendency (average
age) of points within a user defined\nneighborhood; also supports point density and
temporal tendency\nvisualization using 'ggmap'.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"pointdensityP","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Title":"Point Density for Geospatial
Data","Version":"0.2.1"},"poisDoubleSamp":{"Author":"David Kahle [aut, cre],\nPhil
Young [aut],\nDean Young [aut]","Description":"Functions to create confidence
intervals for ratios of Poisson\nrates under misclassification using double
sampling.","Imports":"Rcpp","License":"GPL-
2","NeedsCompilation":"yes","Package":"poisDoubleSamp","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Confidence Intervals with Poisson Double
Sampling","URL":"https:\/\/github.com\/dkahle\/poisDoubleSamp","Version":"1.1"},"po
isson":{"Author":"Kristian Brock [aut] <kristian.brock@gmail.com>, Daniel Slade
[ctb]","Depends":"methods","Description":"Contains functions and classes for
simulating, plotting and analysing homogenous and non-homogenous Poisson
2","NeedsCompilation":"no","Package":"poisson","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Simulating Homogenous & Non-Homogenous Poisson
Processes","Version":"1.0"},"poisson.glm.mix":{"Author":"Panagiotis Papastamoulis,
Marie-Laure Martin-Magniette, Cathy Maugis-Rabusseau","Description":"High
dimensional mixtures of Poisson Generalized Linear models with three different
parameterizations of Poisson means are considered. Moreover, partitioning the
response variables into a set of blocks is possible. The package estimates
parameters via EM algorithm. For an efficient initialization, a random splitting
small-EM is introduced.","License":"GPL-
2","NeedsCompilation":"no","Package":"poisson.glm.mix","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Fit high dimensional mixtures of Poisson
GLMs","Version":"1.2"},"poistweedie":{"Author":"David Pechel Cactcha, Laure Pauline
Fotso and Celestin C\nKokonendji","Depends":"R (>=
2.10.0)","Description":"Simulation of models Poisson-Tweedie.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"poistweedie","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Poisson-Tweedie exponential family
models","URL":"http:\/\/www.r-
project.org\/package=poistweedie","Version":"1.0"},"polidata":{"Author":"Eunjeong
Park [aut, cre],\nJong Hee Park [aut]","Description":"This package provides easy
access to various political data APIs\ndirectly from R. For example, you can access
Google Civic Information API\n(https:\/\/developers.google.com\/civic-
information\/) or Sunlight Congress
API\n(https:\/\/sunlightlabs.github.io\/congress\/) for US Congress data, and
POPONG\nAPI (http:\/\/data.popong.com\/) for South Korea National Assembly
data.","Imports":"jsonlite, RCurl","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"polidata","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"knitr","Title":"Political Data Interface in
R","URL":"http:\/\/github.com\/e9t\/polidata-r","Version":"0.1.0"},"pollstR":
{"Author":"Jeffrey B. Arnold [aut, cre],\nThomas J. Leeper [aut],\nDrew Linzer
[aut]","Depends":"R (>= 3.0.3)","Description":"Client for the HuffPost Pollster
API, which provides\naccess to U.S. opinion polls since 2004.","Imports":"httr,
plyr, jsonlite","License":"GPL-
2","NeedsCompilation":"no","Package":"pollstR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr, dplyr, ggplot2, rmarkdown,
testthat","Title":"Client for the HuffPost Pollster
API","URL":"https:\/\/github.com\/rOpenGov\/pollstR","Version":"1.2.2"},"polspline"
:{"Author":"Charles Kooperberg <clk@fredhutch.org>","Description":"Routines for the
polynomial spline fitting routines\nhazard regression, hazard estimation with
flexible tails, logspline,\nlspec, polyclass, and polymars, by C. Kooperberg and
co-authors.","Imports":"stats, graphics","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"polspline","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Polynomial Spline
Routines","Version":"1.1.12"},"polyCub":{"Author":"Sebastian Meyer [aut, cre,
trl],\nLeonhard Held [ths],\nMichael Hoehle [ths]","Depends":"R (>= 2.15.0),
methods, sp","Description":"The following methods for cubature (numerical
integration)\nover polygonal domains are currently implemented:\nthe two-
dimensional midpoint rule as a simple wrapper around\nas.im.function() from package
spatstat (Baddeley and Turner, 2005),\nthe product Gauss cubature by Sommariva and
Vianello (2007),\nan adaptive cubature for isotropic functions via line
integrate()\nalong the boundary (Meyer and Held, 2014),\nand quasi-exact methods
specific to the integration of the\nbivariate Gaussian density over polygonal and
circular domains\n(based on formulae from the Abramowitz and Stegun (1972)
handbook).\nFor cubature over simple hypercubes, the packages \"cubature\"
and\n\"R2Cuba\" are more appropriate.","Imports":"grDevices, graphics, stats,
spatstat","License":"GPL-
2","NeedsCompilation":"yes","Package":"polyCub","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"lattice, testthat, mvtnorm, statmod, rgeos,
gpclib","Title":"Cubature over Polygonal
Domains","URL":"https:\/\/github.com\/WastlM\/polyCub","Version":"0.5-
2"},"polySegratio":{"Author":"Peter Baker","Description":"Perform classic chi-
squared tests and Ripol et al(1999)\nbinomial confidence interval approach for
autopolyploid\ndominant markers. Also, dominant markers may be generated\nfor
families of offspring where either one or both of the\nparents possess the marker.
Missing values and\nmisclassified markers may be generated at
random.","Imports":"gdata","License":"GPL-
3","NeedsCompilation":"no","Package":"polySegratio","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Simulate and test marker dosage for dominant markers
in\nautopolyploids","Version":"0.2-4"},"polySegratioMM":{"Author":"Peter
Baker","Depends":"R (>= 2.12.0), polySegratio","Description":"Fits Bayesian mixture
models to estimate marker dosage for dominant markers on autopolyploids using JAGS
(1.0 or greater) as outlined in Baker et al (2010). May be used in conjunction with
polySegratio for simulation studies and comparison with standard
methods.","Imports":"gtools, coda, lattice","License":"GPL-
3","NeedsCompilation":"no","Package":"polySegratioMM","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Bayesian mixture models for marker dosage in
autopolyploids","Version":"0.6-3"},"polyaAeppli":{"Author":"Conrad
Burden","Depends":"R (>= 3.0.0)","Description":"Functions for evaluating the mass
density, cumulative distribution function, quantile function and random variate
generation for the Polya-Aeppli distribution, also known as the geometric compound
Poisson distribution.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"polyaAeppli","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Implementation of the Polya-Aeppli
distribution","Version":"2.0"},"polyapost":{"Author":"Glen Meeden
<glen@stat.umn.edu> and Radu Lazar\n<lazar@stat.umn.edu> and Charles J. Geyer
<charlie@stat.umn.edu>","Depends":"R (>= 3.0.0), rcdd (>= 1.1-
5)","Description":"Simulate via Markov chain Monte Carlo (hit-and-run algorithm)\na
Dirichlet distribution conditioned to satisfy a finite set of linear\nequality and
inequality constraints (hence to lie in a convex polytope\nthat is a subset of the
unit simplex).","Imports":"boot, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"polyapost","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Simulating from the Polya Posterior","Version":"1.4-
2"},"polychaosbasics":{"Author":"A. Bouvier [aut], J.-P. Gauchi [cre], A. Bensadoun
[aut]","Depends":"methods","Description":"Computation of sensitivity indexes by
using a method based on a truncated Polynomial Chaos Expansions of the
response.\nThe necessary condition of the method is: the inputs must be uniformly
and independently sampled. Since the inputs are uniformly distributed, the
truncated Polynomial Chaos Expansion is built from the multivariate Legendre
orthogonal polynomials.","Imports":"utils, lhs, MASS","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"polychaosbasics","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"graphics, stats","Title":"Sensitivity Indexes
Calculated from Polynomial Chaos Expansions","Version":"1.1-0"},"polyclip":
{"Author":"Angus Johnson [aut] (C++
original,\nhttp:\/\/www.angusj.com\/delphi\/clipper.php),\nAdrian Baddeley [aut,
trl, cre],\nBrian D. Ripley [ctb]","Depends":"R (>= 3.0.0)","Description":"R port
of Angus Johnson's open source library Clipper. Performs polygon clipping
operations (intersection, union, set minus, set difference) for polygonal regions
of arbitrary complexity, including holes. Computes offset polygons (spatial buffer
zones, morphological dilations, Minkowski dilations) for polygonal regions and
polygonal lines. Computes Minkowski Sum of general polygons. There is a function
for removing self-intersections from polygon
data.","License":"BSL","NeedsCompilation":"yes","Package":"polyclip","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Title":"Polygon
Clipping","URL":"http:\/\/www.angusj.com\/delphi\/clipper.php,\nhttps:\/\/sourcefor
ge.net\/projects\/polyclipping,\nhttps:\/\/github.com\/baddstats\/polyclip","Versio
n":"1.5-6"},"polycor":{"Author":"John Fox","Depends":"R (>= 1.9.0), mvtnorm,
sfsmisc","Description":"Computes polychoric and polyserial correlations by
quick\n\"two-step\" methods or ML, optionally with standard errors;\ntetrachoric
and biserial correlations are special cases.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"polycor","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Polychoric and Polyserial Correlations","Version":"0.7-
8"},"polyfreqs":{"Author":"Paul Blischak [aut, cre]","Depends":"R (>=
3.0)","Description":"Implements a Gibbs sampling algorithm to perform Bayesian
inference on biallelic SNP frequencies, genotypes and heterozygosity (observed and
expected) in a population of autopolyploids.","Imports":"Rcpp","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"polyfreqs","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr, coda","Title":"Bayesian Population Genomics
in
Autopolyploids","URL":"http:\/\/pblischak.github.io\/polyfreqs\/,\nhttps:\/\/github
.com\/pblischak\/polyfreqs","Version":"1.0.0"},"polynom":{"Author":"Bill Venables
[aut] (S original),\nKurt Hornik [aut, cre] (R port),\nMartin Maechler [aut] (R
port)","Description":"A collection of functions to implement a class for
univariate\npolynomial manipulations.","Imports":"stats, graphics","License":"GPL-
2","NeedsCompilation":"no","Package":"polynom","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"A Collection of Functions to Implement a Class for
Univariate\nPolynomial Manipulations","Version":"1.3-8"},"polysat":
{"Author":"Lindsay V. Clark [aut, cre]","Description":"A collection of tools to
handle microsatellite data of\nany ploidy (and samples of mixed ploidy) where
allele copy number is not\nknown in partially heterozygous genotypes. It can
import and export data in\nABI 'GeneMapper', 'Structure', 'ATetra',
'Tetrasat'\/'Tetra',
'GenoDive', 'SPAGeDi',\n'POPDIST', 'STRand', and binary presence\/absence formats.
It can calculate\npairwise distances between individuals using a stepwise mutation
model or\ninfinite alleles model, with or without taking ploidies and allele
frequencies\ninto account. These distances can be used for the calculation of
clonal\ndiversity statistics or used for further analysis in R. Allelic
diversity\nstatistics are also available. polysat can assist the user in
estimating the\nploidy of samples, and it can estimate allele frequencies
in\npopulations, calculate pairwise Fst values based on those frequencies,
and\nexport allele frequencies to 'SPAGeDi' and 'adegenet'. Functions are
also\nincluded for assigning alleles to isoloci in cases where one pair
of\nmicrosatellite primers amplifies alleles from two or more
independently\nsegregating isoloci.","Imports":"methods, stats,
2","NeedsCompilation":"no","Package":"polysat","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"combinat, ade4, adegenet, ape","Title":"Tools for
Polyploid Microsatellite
Analysis","URL":"http:\/\/openwetware.org\/wiki\/Polysat","Version":"1.4-
1"},"polywog":{"Author":"Brenton Kenkel and Curtis S.
Signorino","Depends":"miscTools (>= 0.6-12)","Description":"Routines for flexible
functional form estimation via basis\nregression, with model selection via the
adaptive LASSO or SCAD to prevent\noverfitting.","Imports":"foreach, Formula,
glmnet (>= 1.9-5), iterators, Matrix, ncvreg\n(>= 2.4-0), Rcpp (>= 0.11.0),
2)","NeedsCompilation":"yes","Package":"polywog","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"car, lattice, rgl","Title":"Bootstrapped Basis
Regression with Oracle Model
Selection","URL":"https:\/\/github.com\/brentonk\/polywog-package","Version":"0.4-
0"},"pom":{"Author":"Fawn Hornsby, Ryan Nielson, and Trent McDonald\n(www.west-
inc.com)","Depends":"matrixcalc","Description":"This package fits a patch occupancy
model","License":"GNU General Public
License","NeedsCompilation":"no","Package":"pom","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"POM - Patch Occupancy Models","Version":"1.1"},"pomp":
{"Author":"Aaron A. King [aut, cre],\nEdward L. Ionides [aut],\nCarles Breto
[aut],\nStephen P. Ellner [ctb],\nMatthew J. Ferrari [ctb],\nBruce E. Kendall
[ctb],\nMichael Lavine [ctb],\nDao Nguyen [ctb],\nDaniel C. Reuman [ctb],\nHelen
Wearing [ctb],\nSimon N. Wood [ctb],\nSebastian Funk [ctb]","Depends":"R(>= 3.1.0),
methods","Description":"Tools for working with partially observed Markov processes
(POMPs, AKA stochastic dynamical systems, state-space models). 'pomp' provides
facilities for implementing POMP models, simulating them, and fitting them to time
series data by a variety of frequentist and Bayesian methods. It is also a
platform for the implementation of new inference methods.","Imports":"stats,
graphics, digest, mvtnorm, deSolve, coda, subplex,\nnloptr","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"pomp","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"magrittr, plyr, reshape2, ggplot2,
knitr","Title":"Statistical Inference for Partially Observed Markov
Processes","URL":"http:\/\/kingaa.github.io\/pomp","Version":"1.4.1.1"},"pooh":
{"Author":"Charles J. Geyer <charlie@stat.umn.edu>.","Depends":"R (>=
2.10.0)","Description":"Finds equivalence classes corresponding to a symmetric
relation\nor undirected graph. Finds total order consistent with partial order\nor
directed graph (so-called topological sort).","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"pooh","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Partial Orders and
Relations","URL":"http:\/\/www.stat.umn.edu\/geyer\/pooh\/","Version":"0.3-
1"},"pop.wolf":{"Author":"Guillaume Chapron [aut, cre],\nCamilla Wikenros
[ctb],\nOlof Liberg [ctb],\nÃ˜ystein Flagstad [ctb],\nCyril Milleret [ctb],\nJohan
MÃ¥nsson [ctb],\nLinn Svensson [ctb],\nBarbara Zimmermann [ctb],\nMikael Ã…kesson
[ctb],\nPetter Wabakken [ctb],\nHÃ¥kan Sand [ctb]","Depends":"parallel,
abind","Description":"Simulate the dynamic of wolf populations using a specific
Individual-Based Model (IBM) compiled in C.","License":"GPL-
3","NeedsCompilation":"yes","Package":"pop.wolf","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Models for Simulating Wolf
Populations","Version":"0.1"},"popEpi":{"Author":"Joonas Miettinen [aut,
cre],\nMatti Rantanen [aut],\nKarri Seppa [ctb]","Depends":"R (>= 3.2.0),
data.table (>= 1.9.6)","Description":"Enables computation of various
epidemiological statistics where the use of population data such as population
counts and hazards is required.\nRelatively high computation speed achieved by
using data.table.","Imports":"Epi, survival","License":"GPL-
3","NeedsCompilation":"no","Package":"popEpi","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"reshape2, methods, testthat, knitr, rmarkdown,
relsurv,\nggplot2, mstate, date, splines, roxygen2","Title":"Functions for
Epidemiological Analysis using Population
Data","URL":"https:\/\/github.com\/WetRobot\/popEpi","Version":"0.3.0"},"popKorn":
{"Author":"Vik Gopal, Claudio Fuentes","Depends":"R (>= 3.0.0),
boot","Description":"Provides a suite of tools for various methods of
estimating\nconfidence intervals for the mean of selected
populations.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"popKorn","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"plotrix","Title":"For interval estimation of mean
of selected populations","Version":"0.3-0"},"popRange":{"Author":"Kimberly F.
McManus","Depends":"findpython","Description":"Runs a forward genetic
simulator","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"popRange","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"popRange: A spatially and temporally explicit
forward
genetic\nsimulator","URL":"http:\/\/stanford.edu\/~kfm\/html\/research.html","Versi
on":"1.1.3"},"popReconstruct":{"Author":"Mark C.
Wheldon","Depends":"coda","Description":"Implements the Bayesian hierarchical model
described by Wheldon, Raftery, Clark and Gerland (see:
http:\/\/www.csss.washington.edu\/Papers\/wp108.pdf) for simultaneously estimating
age-specific population counts, fertility rates, mortality rates and net
international migration flows, at the national level.","License":"GPL-
3","NeedsCompilation":"no","Package":"popReconstruct","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"ggplot2, reshape, gdata","Title":"Reconstruct
Human Populations of the Recent Past","Version":"1.0-4"},"popbio":{"Author":"Chris
Stubben, Brook Milligan, Patrick Nantel","Description":"Construct and analyze
projection matrix models from a demography study of marked individuals classified
by age or stage. The package covers methods described in Matrix Population Models
by Caswell (2001) and Quantitative Conservation Biology by Morris and Doak
3","NeedsCompilation":"no","Package":"popbio","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"quadprog","Title":"Construction and Analysis of Matrix
Population Models","Version":"2.4.3"},"popdemo":{"Author":"Iain Stott
<iainmstott@gmail.com>, Dave Hodgson <D.J.Hodgson@exeter.ac.uk>, Stuart Townley
<S.B.Townley@exeter.ac.uk>","Depends":"R (>= 2.14.1)","Description":"\npopdemo
provides a set of tools designed for modelling population demography\nusing
population projection matrix (PPM) models. The focus is mainly on indices\nof
transient dynamics, and the use of control theory (specifically
transfer\nfunctions). However, popdemo includes a number of tools focussing on
other\nareas of demographic modelling. Some tools may prove useful to anyone
working\nwith projection matrix models of any type, or indeed matrices in
general.\nThe package is designed to build on those tools already available in
popbio.","Imports":"expm","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"popdemo","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Provides Tools For Demographic Modelling Using
Projection\nMatrices","Version":"0.1-4"},"popgraph":{"Author":"Rodney J.
Dyer","Depends":"R (>= 2.15), ggplot2, igraph","Description":"This is a generic
package that produces \"Population Graphs\"\na graph-theoretic topology based upon
conditional genetic covariance. This\nfunctionality used to be within the gstudio
package, but has been taken out\nto focus on spatial integration of graph
topologies with existing packages\nlike sp, raster, and ggplot2.","Imports":"MASS,
sp, Matrix, sampling","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"popgraph","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat, maps, fields, grid","Title":"This is an R
package that constructs and manipulates
population\ngraphs","Version":"1.4"},"poplite":{"Author":"Daniel Bottomly [cre,
aut],\nShannon McWeeney [aut],\nBeth Wilmot [aut]","Depends":"R (>= 3.1), methods,
dplyr (>= 0.3.0.2)","Description":"Provides objects and accompanying methods which
facilitates populating and querying SQLite databases.","Imports":"DBI, igraph,
lazyeval, RSQLite (>= 1.0.0)","License":"GPL-
3","NeedsCompilation":"no","Package":"poplite","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat, Lahman, VariantAnnotation","Title":"Tools for
Simplifying the Population and Querying of
SQLite\nDatabases","URL":"https:\/\/github.com\/dbottomly\/poplite","Version":"0.99
.16"},"poppr":{"Author":"Zhian N. Kamvar [cre, aut],\nJavier F. Tabima
[aut],\nSydney E. Everhart [ctb, dtc],\nJonah C. Brooks [aut],\nStacy A. Krueger-
Hadfield [ctb],\nErik Sotka [ctb],\nNiklaus J. Grunwald [ths]","Depends":"R (>=
2.15.1), adegenet (>= 2.0.0)","Description":"Population genetic analyses for
hierarchical analysis of partially\nclonal populations built upon the architecture
of the 'adegenet' package.","Imports":"stats, graphics, grDevices, utils, vegan,
ggplot2, phangorn,\nape (>= 3.1-1), igraph, methods, ade4, pegas, reshape2,
dplyr\n(>= 0.4), boot, shiny","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"poppr","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat, knitr, rmarkdown, knitcitations, polysat,
poweRlaw,\ncowplot","Title":"Genetic Analysis of Populations with Mixed
Reproduction","URL":"http:\/\/github.com\/grunwaldlab\/poppr,\nhttp:\/\/grunwaldlab
.github.io\/Population_Genetics_in_R\/,\nhttp:\/\/grunwaldlab.cgrb.oregonstate.edu\
/poppr-r-package-population-genetics","Version":"2.1.1"},"popprxl":{"Author":"Zhian
N. Kamvar [cre, aut]","Depends":"poppr (>= 2.0.2)","Description":"GenAlEx is a
popular Excel macro for genetic analysis. The 'poppr'\nR package allows import of
GenAlEx formatted CSV data. This package serves as a\nsmall 'poppr' add on for
those who have trouble or simply do not want to export\ntheir data into CSV
format.","Imports":"readxl, utils","License":"GPL-
3","NeedsCompilation":"no","Package":"popprxl","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat","Title":"Read GenAlEx Files Directly from
Excel","URL":"https:\/\/github.com\/zkamvar\/popprxl","Version":"0.1.1"},"popsom":
{"Author":"Lutz Hamel [aut, cre],\nBenjamin Ott [aut],\nGregory Breard
[aut]","Description":"A set of routines which are useful in constructing\nand
evaluating self-organizing maps (SOMs).","Imports":"som, fields, graphics, stats,
grDevices","License":"GPL","NeedsCompilation":"no","Package":"popsom","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Title":"Routines for Constructing and
Evaluating Self-Organizing
Maps","URL":"http:\/\/homepage.cs.uri.edu\/faculty\/hamel\/","Version":"3.0.1"},"po
pulation":{"Author":"Guillaume Chapron","Depends":"parallel,
abind","Description":"Run population simulations using an Individual-Based Model
(IBM) compiled in C.","License":"GPL-
3","NeedsCompilation":"yes","Package":"population","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Models for Simulating
Populations","Version":"0.1"},"portes":{"Author":"Esam Mahdi, Ken Jinkun Xiao and
A. Ian McLeod","Depends":"R (>= 2.14.0), parallel","Description":"This package
contains a set of portmanteau diagnostic\nchecks for univariate and multivariate
time series.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"portes","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"fGarch, FitAR, FGN, TSA, vars, tseries, forecast,
akima","Title":"Portmanteau Tests for Univariate and Multivariate Time
Series\nModels","URL":"http:\/\/www.stats.uwo.ca\/faculty\/aim
and\nhttp:\/\/site.iugaza.edu.ps\/emahdi","Version":"2.1-3"},"portfolio":
{"Author":"Jeff Enos <jeff@kanecap.com> and David Kane <dave@kanecap.com>,\nwith
contributions from Daniel Gerlanc <daniel@gerlanc.com> and\nKyle Campbell
<Kyle.W.Campbell@williams.edu>","Depends":"R (>= 2.10), methods, graphics, grid,
lattice, nlme","Description":"Classes for analysing and implementing equity
portfolios.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"portfolio","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Analysing equity
portfolios","URL":"https:\/\/github.com\/dgerlanc\/portfolio","Version":"0.4-
7"},"portfolioSim":{"Author":"Jeff Enos <jeff@kanecap.com> and David Kane
<dave@kanecap.com>,\nwith contributions from Kyle
Campbell\n<Kyle.W.Campbell@williams.edu>","Depends":"R (>= 2.10), methods, lattice,
portfolio (>= 0.4.0)","Description":"Classes that serve as a framework for
designing equity\nportfolio simulations.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"portfolioSim","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Framework for simulating equity portfolio
strategies","Version":"0.2-7"},"potts":{"Author":"Charles J. Geyer
<charlie@stat.umn.edu> and Leif Johnson\n<leif@stat.umn.edu>","Depends":"R (>=
2.10.0)","Description":"Does Markov chain Monte Carlo (MCMC) simulation of Potts
models\nand composite likelihood inference for Potts models.","Imports":"stats,
2)","NeedsCompilation":"yes","Package":"potts","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"pooh (>= 0.2)","Title":"Markov Chain Monte Carlo for
Potts Models","URL":"http:\/\/www.stat.umn.edu\/geyer\/mcmc\/","Version":"0.5-
4"},"poweRlaw":{"Author":"Colin Gillespie [aut, cre]","Depends":"R (>=
3.0.0)","Description":"An implementation of maximum likelihood estimators for a
variety\nof heavy tailed distributions, including both the discrete and
continuous\npower law distributions. Additionally, a goodness-of-fit based approach
is\nused to estimate the lower cut-off for the scaling region.","Imports":"VGAM,
parallel, methods, utils, stats","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"poweRlaw","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr, R.matlab, testthat","Title":"Analysis of Heavy
Tailed
Distributions","URL":"https:\/\/github.com\/csgillespie\/poweRlaw","Version":"0.60.
0"},"powell":{"Author":"Sundar Dorai-Raj <sdorairaj@gmail.com>, original Fortran
from Mike Powell <mjdp@cam.ac.uk>","Description":"Optimizes a function using
Powell's UObyQA
algorithm.","License":"GPL","NeedsCompilation":"yes","Package":"powell","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Powell's UObyQA
algorithm","Version":"1.0-0"},"powerAnalysis":{"Author":"Felix Yanhui Fan
<nolanfyh@gmail.com>","Description":"Basic functions for power analysis and effect
size calculation.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"powerAnalysis","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Power analysis in experimental
design","URL":"https:\/\/github.com\/felixfan\/powerAnalysis","Version":"0.2"},"pow
erGWASinteraction":{"Author":"Charles Kooperberg <clk@fredhutch.org> and Li Hsu
<lih@fredhutch.org>","Depends":"R (>= 2.10), mvtnorm,
pwr","Description":"Analytical power calculations for GxE and GxG interactions for
case-control studies of candidate genes and genome-wide association studies (GWAS).
This includes power calculation for four two-step screening and testing procedures.
It can also calculate power for GxE and GxG without any
screening.","Imports":"stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"powerGWASinteraction","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Title":"Power Calculations for GxE and GxG
Interactions for GWAS","Version":"1.1.3"},"powerMediation":{"Author":"Weiliang Qiu
<stwxq@channing.harvard.edu>","Depends":"R (>= 3.1.0),
stats","Description":"Functions to\ncalculate power and sample size for
testing\n(1) mediation effects;\n(2) the slope in a simple linear regression;\n(3)
odds ratio in a simple logistic regression;\n(4) mean change for longitudinal study
with 2 time points;\n(5) interaction effect in 2-way ANOVA; and\n(6) the slope in a
simple Poisson regression.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"powerMediation","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Power\/Sample Size Calculation for Mediation
Analysis","Version":"0.2.4"},"powerSurvEpi":{"Author":"Weiliang Qiu
<stwxq@channing.harvard.edu>, Jorge Chavarro <JCHAVARR@hsph.harvard.edu>, Ross
Lazarus <ross.lazarus@channing.harvard.edu>, Bernard Rosner
<stbar@channing.harvard.edu>, Jing Ma <jing.ma@channing.harvard.edu>.","Depends":"R
(>= 3.1.0)","Description":"Functions to calculate power and\nsample size for
testing main effect or interaction effect in\nthe survival analysis of
epidemiological studies\n(non-randomized studies), taking into account
the\ncorrelation between the covariate of the\ninterest and other covariates. Some
calculations also take\ninto account the competing risks and stratified
analysis.\nThis package also includes\na set of functions to calculate power and
sample size\nfor testing main effect in the survival analysis of\nrandomized
clinical trials.","Imports":"stats, survival","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"powerSurvEpi","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Power and Sample Size Calculation for Survival
Analysis of\nEpidemiological Studies","Version":"0.0.9"},"powerbydesign":
{"Author":"Frank Papenmeier [aut, cre]","Description":"Functions for bootstrapping
the power of ANOVA designs\nbased on estimated means and standard deviations of the
conditions.\nPlease refer to the documentation of the boot.power.anova()
function\nfor further details.","Imports":"lme4, gdata, MASS, reshape2, stringr,
plyr, ggplot2","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"powerbydesign","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat","Title":"Power Estimates for ANOVA
Designs","Version":"1.0.2"},"powerpkg":{"Author":"Daniel E.
Weeks","Depends":"tcltk","Description":"(1) To estimate the power of testing for
linkage using an\naffected sib pair design, as a function of the recurrence
risk\nratios. We will use analytical power formulae as implemented in\nR. These are
based on a Mathematica notebook created by Martin\nFarrall. (2) To examine how the
power of the transmission\ndisequilibrium test (TDT) depends on the disease
allele\nfrequency, the marker allele frequency, the strength of the\nlinkage
disequilibrium, and the magnitude of the genetic\neffect. We will use an R program
that implements the power\nformulae of Abel and Muller-Myhsok (1998). These
formulae allow\none to quickly compute power of the TDT approach under a\nvariety
of different conditions. This R program was modeled on\nMartin Farrall's
Mathematica notebook.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"powerpkg","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Power analyses for the affected sib pair and the TDT
design","Version":"1.5"},"powerplus":{"Author":"Albert
Dorador","Depends":"R (>= 3.1.0)","Description":"Computation of matrix and scalar
exponentiation.","Imports":"phonTools (>= 0.2-2.1), Matrix (>= 1.2-3), expm (>=
0.999-0),\nMASS (>= 7.3-45)","License":"GPL-
2","NeedsCompilation":"no","Package":"powerplus","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Exponentiation Operations","Version":"1.0"},"ppcor":
{"Author":"Seongho Kim","Depends":"R (>= 2.6.0), MASS","Description":"Calculates
partial and semi-partial\n(part) correlations along with p-value.","License":"GPL-
2","NeedsCompilation":"no","Package":"ppcor","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Partial and Semi-Partial (Part)
Correlation","Version":"1.1"},"ppiPre":{"Author":"Yue Deng, Rongjie Shao, Gang Wang
and Yuanjun Sun","Depends":"R (>= 3.1.0)","Description":"Computing similarities
between proteins based on their GO annotation, KEGG annotation and PPI network
topology. It integrates seven features (TCSS, IntelliGO, Wang, KEGG, Jaccard, RA
and AA) to predict PPIs using an SVM classifier. Some internal functions to
calculate GO semantic similarities are re-used from R package GOSemSim authored by
Guangchuang Yu.","Enhances":"KEGG.db, org.Hs.eg.db, org.Sc.sgd.db,
org.Ag.eg.db,\norg.Pt.eg.db, org.Rn.eg.db, org.Ss.eg.db,
org.At.tair.db,\norg.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db,
org.Dm.eg.db,\norg.Dr.eg.db, org.EcK12.eg.db, org.EcSakai.eg.db,
org.Gg.eg.db,\norg.Mm.eg.db, org.Mmu.eg.db, org.Pf.plasmo.db,
org.Xl.eg.db","Imports":"AnnotationDbi, igraph, e1071, GOSemSim, GO.db, stats,
2","NeedsCompilation":"no","Package":"ppiPre","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Predict Protein-Protein Interactions Based on Functional
and\nTopological Similarities","Version":"1.9"},"ppls":{"Author":"Nicole Kraemer
<kraemer_r_packages@yahoo.de> Anne-Laure Boulesteix\n<boulesteix@ibe.med.uni-
muenchen.de>","Depends":"splines, MASS","Description":"This package contains linear
and nonlinear regression\nmethods based on Partial Least Squares and
Penalization\nTechniques. Model parameters are selected via cross-validation,\nand
confidence intervals ans tests for the regression\ncoefficients can be conducted
via jackknifing.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ppls","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Penalized Partial Least Squares","Version":"1.6-
1"},"ppmlasso":{"Author":"Ian Renner","Depends":"R (>= 3.0.0), spatstat (>= 1.40-
0)","Description":"Toolkit for fitting point process models with sequences of LASSO
penalties (\"regularisation paths\"). Regularisation paths of Poisson point process
models or area-interaction models can be fitted with LASSO, adaptive LASSO or
elastic net penalties. A number of criteria are available to judge the bias-
variance tradeoff.","Imports":"methods","License":"GPL-
3","NeedsCompilation":"no","Package":"ppmlasso","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Point Process Models with LASSO
Penalties","Version":"1.1"},"pps":{"Author":"Jack G. Gambino
<jack.gambino@gmail.com>","Description":"The pps package contains functions to
select samples using\nPPS (probability proportional to size) sampling. It
also\nincludes a function for stratified simple random sampling, a\nfunction to
compute joint inclusion probabilities for\nSampford's method of PPS sampling, and a
few utility functions.\nThe user's guide pps-ug.pdf is included.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"pps","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Functions for PPS
sampling","Version":"0.94"},"pqantimalarials":{"Author":"J. Patrick Renschler
<patrick.renschler@gmail.com>","Depends":"R (>= 2.14.1)","Description":"This
package allows users to calculate the number of\nunder-five child deaths caused by
consumption of poor quality\nantimalarials across 39 sub-Saharan nations. The
package supports one\nfunction, that starts an interactive web tool created
using\nthe shiny R package. The web tool runs locally on the user's machine.\nThe
web tool allows users to set input parameters (prevalence of poor\nquality
antimalarials, case fatality rate of children who take poor\nquality antimalarials,
and sample size) which are then used to perform\nan uncertainty analysis following
the Latin hypercube\nsampling scheme. Users can download the output figures as
PDFs, and the\noutput data as CSVs. Users can also download their input
parameters\nfor reference. This package was designed to accompany the
analysis\npresented in:\nJ. Patrick Renschler, Kelsey Walters, Paul Newton, Ramanan
Laxminarayan\n\"Estimated under-five deaths associated with poor-
quality\nantimalarials in sub-Saharan Africa\", 2014. Paper
submitted.","Imports":"reshape2, RColorBrewer, plyr, shiny","License":"GPL-
3","NeedsCompilation":"no","Package":"pqantimalarials","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"web tool for estimating under-five deaths caused
by poor-quality\nantimalarials in sub-Saharan
Africa","Version":"0.2"},"prLogistic":{"Author":"Raydonal Ospina
<raydonal@de.ufpe.br> and Leila D. Amorim <leiladen@ufba.br>.","Depends":"R (>=
2.10.0), boot, methods, stats, stats4, lme4, Hmisc","Description":"Estimation of
prevalence ratios using logistic models and confidence intervals with delta and
bootstrap methods.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"prLogistic","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Estimation of Prevalence Ratios using Logistic
Models","Version":"1.2"},"prabclus":{"Author":"Christian Hennig
<c.hennig@ucl.ac.uk>,\nBernhard Hausdorf <Hausdorf@zoologie.uni-
hamburg.de>","Depends":"R (>= 2.10), MASS, mclust","Description":"Distance-based
parametric bootstrap tests for clustering with\nspatial neighborhood information.
Some distance measures,\nClustering of presence-absence, abundance and multilocus
genetical data\nfor species delimitation, nearest neighbor\nbased noise detection.
Try package?prabclus for on
overview.","License":"GPL","NeedsCompilation":"no","Package":"prabclus","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"spdep, maptools, foreign,
mvtnorm","Title":"Functions for Clustering of Presence-Absence, Abundance
and\nMultilocus Genetic
Data","URL":"http:\/\/www.homepages.ucl.ac.uk\/~ucakche","Version":"2.2-
6"},"pracma":{"Author":"Hans Werner Borchers","Depends":"R (>=
2.11.1)","Description":"\nFunctions from numerical analysis and linear algebra,
numerical\noptimization, differential equations, plus some special functions.\nUses
Matlab function names where appropriate to simplify porting.","Imports":"graphics,
grDevices, stats, utils","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"pracma","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Practical Numerical Math
Functions","Version":"1.8.8"},"pragma":{"Author":"Christopher Brown","Depends":"R
(>= 2.13.0), utils, methods","Description":"pragma allows for the use of pragma
(also sometimes called\ndirectives or keywords. These allow assigning
arbitrary\nfunctionality to a word without requiring the standard function\ncall
syntax i.e. with parens.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pragma","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Provides a pragma \/ directive \/ keyword syntax for
R","URL":"http:\/\/www.decisionpatterns.com","Version":"0.1.3"},"prais":
{"Author":"Franz Mohr","Depends":"base, stats","Description":"The Prais-Winsten
estimation procedure takes into account serial correlation of type AR(1) in a
linear model. The procedure is an iterative method that recursively estimates the
beta coefficients and the error autocorrelation of the specified model until
convergence of rho, i.e. the AR(1) coefficient, is attained. All estimates are
obtained by OLS.","License":"GPL-
2","NeedsCompilation":"no","Package":"prais","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Prais-Winsten Estimation Procedure for AR(1) Serial
Correlation","Version":"0.1.1"},"praise":{"Author":"Gabor Csardi, Sindre
Sorhus","Description":"Build friendly R packages that\npraise their users if they
have done something\ngood, or they just need it to feel better.","License":"MIT +
file
LICENSE","NeedsCompilation":"no","Package":"praise","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat","Title":"Praise
Users","URL":"https:\/\/github.com\/gaborcsardi\/praise","Version":"1.0.0"},"prakti
kum":{"Author":"Kenn Konstabel","Description":"Kasulikud funktsioonid
kvantitatiivsete mudelite kursuse\n(SHPH.00.004) jaoks","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"praktikum","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Kvantitatiivsete meetodite praktikumi asjad \/
Functions used in\nthe course \"Quantitative methods in behavioural
sciences\"\n(SHPH.00.004), University of Tartu","Version":"0.1"},"prc":
{"Author":"Youyi Fong","Depends":"R (>= 3.0.0), kyotil,
nlme","Description":"Estimation, prediction and testing for analyzing serial
dilution assay data using paired response curve.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"prc","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"RUnit, Rmosek, Matrix","Title":"Paired Response
Curve","Version":"2015.6-24"},"prcbench":{"Author":"Takaya Saito [aut, cre],\nMarc
Rehmsmeier [aut]","Depends":"R (>= 3.2.3)","Description":"A testing workbench for
evaluating Precision-Recall curves under various conditions.","Imports":"ROCR (>=
1.0-7), PRROC (>= 1.1), PerfMeas (>= 1.2.1), precrec\n(>= 0.1), rJava (>= 0.9-7),
R6 (>= 2.1.1), assertthat (>= 0.1),\ngrid, gridExtra (>= 2.0.0), graphics, ggplot2
(>= 2.0.0),\nmethods, memoise (>= 1.0.0)","License":"GPL-
3","NeedsCompilation":"no","Package":"prcbench","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"microbenchmark (>= 1.4-2.1), testthat (>= 0.11.0),
knitr
(>=\n1.11), rmarkdown (>= 0.8.1)","Title":"Testing Workbench for Precision-Recall
Curves","URL":"https:\/\/github.com\/takayasaito\/prcbench","Version":"0.3.1"},"prc
lust":{"Author":"Chong Wu, Wei Pan","Depends":"R (>=
3.1.1)","Description":"Clustering is unsupervised and exploratory in nature. Yet,
it can be performed through penalized regression with grouping pursuit. In this
package, we provide two algorithms for fitting the penalized regression-based
clustering (PRclust). One algorithm is based on quadratic penalty and difference
convex method. Another algorithm is based on difference convex and ADMM, called DC-
ADD, which is more efficient. Generalized cross validation was provided to select
the tuning parameters. Rand index, adjusted Rand index and Jaccard index were
provided to estimate the agreement between estimated cluster memberships and the
truth.","Imports":"Rcpp (>= 0.12.1), parallel","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"prclust","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Penalized Regression-Based Clustering
Method","Version":"1.1"},"precintcon":{"Author":"Lucas Venezian Povoa [aut,
cre],\nJonas Teixeira Nery [ctb]","Depends":"R (>= 2.14), ggplot2 (>= 2.0.0),
scales","Description":"Contains functions to analyze the precipitation\nintensity,
concentration and anomaly.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"precintcon","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Precipitation Intensity, Concentration and Anomaly
Analysis","URL":"https:\/\/github.com\/lucasvenez\/precintcon","Version":"2.2.1"},"
precrec":{"Author":"Takaya Saito [aut, cre],\nMarc Rehmsmeier [aut]","Depends":"R
(>= 3.2.1)","Description":"Accurate calculations and visualization of Precision-
Recall and Receiver Operator Characteristics\ncurves.","Imports":"Rcpp (>= 0.12.2),
ggplot2 (>= 1.0.1), assertthat (>= 0.1),\ngrid, gridExtra (>= 2.0.0),
3","NeedsCompilation":"yes","Package":"precrec","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"testthat (>= 0.11.0), knitr (>= 1.11), rmarkdown (>=
0.8.1)","Title":"Calculate Accurate Precision-Recall and Receiver
Operator\nCharacteristics
Curves","URL":"https:\/\/github.com\/takayasaito\/precrec","Version":"0.3.1"},"pred
ictmeans":{"Author":"Dongwen Luo, Siva Ganesh and John Koolaard","Depends":"R (>=
3.0.0), lme4, nlme","Description":"This package provides functions to diagnose\nand
make inferences from various linear models, such as those obtained from
'aov',\n'lm', 'glm', 'gls', 'lme', and 'lmer'. Inferences include predicted\nmeans
and standard errors, contrasts, multiple comparisons, permutation tests and
graphs.","Imports":"ggplot2, lattice, pbkrtest, plyr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"predictmeans","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Calculate Predicted Means for Linear
Models","URL":"http:\/\/www.r-project.org","Version":"0.99"},"predmixcor":
{"Author":"Longhai Li <longhai@math.usask.ca>","Depends":"R (>=
1.5.0)","Description":"\"train_predict_mix\" predicts the binary response
with\nbinary features","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"predmixcor","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Classification rule based on Bayesian mixture models
with\nfeature selection bias corrected","URL":"http:\/\/www.r-project.org,
http:\/\/math.usask.ca\/~longhai","Version":"1.1-1"},"prefmod":{"Author":"Reinhold
Hatzinger [aut],\nMarco Johannes Maier [cre]","Depends":"R (>= 3.0.0), stats,
graphics, gnm (>= 1.0-0), colorspace","Description":"Generates design matrix for
analysing real paired comparisons and derived paired comparison data (Likert type
items\/ratings or rankings) using a loglinear approach. Fits loglinear Bradley-
Terry model (LLBT) exploiting an eliminate feature. Computes pattern models for
paired comparisons, rankings, and ratings. Some treatment of missing values (MCAR
and MNAR). Fits latent class (mixture) models for paired comparison, rating and
ranking patterns using a non-parametric ML approach.","Imports":"grDevices,
2)","NeedsCompilation":"yes","Package":"prefmod","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Utilities to Fit Paired Comparison Models for
Preferences","Version":"0.8-33"},"prepdat":{"Author":"Ayala S. Allon [aut,
cre],\nRoy Luria [aut],\nJames Grange [ctb],\nNachshon Meiran [ctb]","Depends":"R
(>= 3.0.3)","Description":"Prepares data for statistical analysis (e.g., analysis
of variance\n;ANOVA) by enabling the user to easily and quickly merge (using
the\nfile_merge() function) raw data files into one merged table and
then\naggregate the merged table (using the prep() function) into a
finalized\ntable while keeping track and summarizing every step of the
preparation.\nThe finalized table contain several possibilities for dependent
measures of\nthe dependent variable. Most suitable when measuring variables in
an\ninterval or ratio scale (e.g., reaction-times) and\/or discrete values such\nas
accuracy. Main functions included are file_merge() and prep(). The\nfile_merge()
function vertically merges individual data files (in a long\nformat) in which each
line is a single observation to one single dataset.\nThe prep() function aggregates
the single dataset according to any\ncombination of grouping variables (i.e.,
between-subjects and\nwithin-subjects independent variables, respectively), and
returns a data\nframe with a number of dependent measures for further analysis for
each cell\naccording to the combination of provided grouping variables.
Dependent\nmeasures for each cell include among others means before and after
rejecting\nall values according to a flexible standard deviation criteria, number
of\nrejected values according to the flexible standard deviation
criteria,\nproportions of rejected values according to the flexible standard
deviation\ncriteria, number of values before rejection, means after rejecting
values\naccording to procedures described in Van Selst & Jolicoeur (1994;
suitable\nwhen measuring reaction-times), standard deviations, medians, means
according\nto any percentile (e.g., 0.05, 0.25, 0.75, 0.95) and harmonic means. The
data\nframe prep() returns can also be exported as a txt file to be used
for\nstatistical analysis in other statistical programs.","Imports":"dplyr (>=
0.4.2), reshape2 (>= 1.4.1), psych(>= 1.5.4)","License":"GPL-
3","NeedsCompilation":"no","Package":"prepdat","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr, testthat","Title":"Preparing Experimental Data
for Statistical
Analysis","URL":"http:\/\/github.com\/ayalaallon\/prepdat","Version":"1.0.7"},"prep
rocomb":{"Author":"Markus Vattulainen","Description":"Preprocessing is often the
most time-consuming phase in knowledge\ndiscovery and preprocessing transformations
interdependent in unexpected\nways. This package helps to make preprocessing faster
and more effective. It\nprovides an S4 framework for creating and testing
preprocessing combinations\nfor classification, clustering and outlier detection.
The framework supports\nuser-defined and domain-specific preprocessors and
preprocessing phases.\nDefault preprocessors can be used for low variance removal,
missing value\nimputation, scaling, outlier removal, noise smoothing, feature
selection and\nclass imbalance correction.","Imports":"DMwR, randomForest, caret,
clustertend, stats, e1071, methods,\nutils, arules, zoo","License":"GPL-
2","NeedsCompilation":"no","Package":"preprocomb","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"kernlab, testthat","Title":"Tools for Preprocessing
Combinations","URL":"https:\/\/github.com\/mvattulainen\/preprocomb","Version":"0.2
.0"},"preproviz":{"Author":"Markus Vattulainen [aut, cre]","Depends":"R (>=
3.2.2)","Description":"Data quality issues such as missing values and outliers are
often\ninterdependent, which makes preprocessing both time-consuming and leads
to\nsuboptimal performance in knowledge discovery tasks. This package
supports\npreprocessing decision making by visualizing interdependent data quality
issues\nthrough means of feature construction. The user can define his own
application\ndomain specific constructed features that express the quality of a
data point\nsuch as number of missing values in the point or use nine default
features.\nThe outcome can be explored with plot methods and the feature
constructed data\nacquired with get methods.","Imports":"caret, DMwR, randomForest,
ClustOfVar, reshape2, ggplot2,\nggdendro, gridExtra, methods, utils,
2","NeedsCompilation":"no","Package":"preproviz","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat, knitr, preprocomb","Title":"Tools for
Visualization of Interdependent Data Quality
Issues","URL":"https:\/\/github.com\/mvattulainen\/preproviz","Version":"0.1.1"},"p
rereg":{"Author":"Frederik Aust [aut, cre]","Depends":"R (>=
3.2.3)","Description":"The R Markdown template in this package is based on the
Center\nfor Open Science Preregistration Challenge and is, thus, particularly
suited to\ndraft preregistration documents for studies that enter the
challenge.","Imports":"rmarkdown (>= 0.9.2)","License":"GPL-
3","NeedsCompilation":"no","Package":"prereg","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat","Title":"R Markdown Template to Preregister
Scientific
Studies","URL":"https:\/\/github.com\/crsh\/prereg","Version":"0.1.0"},"presens":
{"Author":"Matthew A. Birk","Description":"Makes output files from select PreSens
Fiber Optic Oxygen\nTransmitters easier to work with in R. See
http:\/\/www.presens.de for more\ninformation about PreSens (Precision Sensing
GmbH).","Imports":"birk (>= 2.1.0), marelac (>= 2.1.4), stats","License":"GPL-
3","NeedsCompilation":"no","Package":"presens","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"R
Interface for PreSens Fiber Optic Data","Version":"2.0.0"},"preseqR":
{"Author":"Chao Deng, Timothy Daley and Andrew D. Smith","Description":"Estimating
the number of species represented r or more times in a random
sample.","Imports":"polynom","License":"GPL-
3","NeedsCompilation":"yes","Package":"preseqR","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Predicting Species Accumulation
Curves","Version":"2.0.0"},"prettyGraphs":{"Author":"Derek
Beaton","Description":"prettyGraphs contains simple, crisp graphics. Graphics
produced by prettyGraphs are publication-quality.","License":"GPL-
2","NeedsCompilation":"no","Package":"prettyGraphs","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"publication-quality
graphics","Version":"2.1.5"},"prettyR":{"Author":"Jim Lemon
<drjimlemon@gmail.com>,\nPhilippe Grosjean
<phgrosjean@sciviews.org>","Description":"Functions for conventionally formatting
descriptive stats,\nreshaping data frames and formatting R output as
HTML.","Imports":"grDevices, stats, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"prettyR","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Pretty Descriptive Stats","Version":"2.2"},"prettymapr":
{"Author":"Dewey Dunnington <dewey@fishandwhistle.net>","Description":"Automates
the process of creating a scale bar and north arrow in\nany package that uses base
graphics to plot in R. Bounding box tools help find\nand manipulate extents.
Finally, there is a function to automate the process\nof setting margins, plotting
the map, scale bar, and north arrow, and resetting\ngraphic parameters upon
completion.","Imports":"sp, rgdal, digest, rjson, foreach","License":"GPL-
2","NeedsCompilation":"no","Package":"prettymapr","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"maptools, raster, rosm","Title":"Scale Bar, North
Arrow, and Pretty Margins in
R","URL":"https:\/\/github.com\/paleolimbot\/prettymapr","Version":"0.1.5"},"pretty
units":{"Author":"Gabor Csardi","Description":"Pretty, human readable formatting of
quantities.\nTime intervals: 1337000 -> 15d 11h 23m 20s.\nVague time intervals:
2674000 -> about a month ago.\nBytes: 1337 -> 1.34 kB.","Imports":"magrittr,
assertthat, methods","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"prettyunits","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Pretty, Human Readable
Formatting of
Quantities","URL":"https:\/\/github.com\/gaborcsardi\/prettyunits","Version":"1.0.2
"},"prevR":{"Author":"Joseph Larmarange - IRD CEPED","Depends":"R (>= 2.10), sp,
rgdal (>= 0.7-4), ggplot2, directlabels","Description":"Spatial estimation of a
prevalence surface\nor a relative risks surface, using data from a Demographic and
Health\nSurvey (DHS) or an analog survey.","Imports":"GenKern, fields, gstat,
foreign, maptools,
methods","License":"CeCILL","NeedsCompilation":"no","Package":"prevR","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"tcltk, geoR","Title":"Estimating
Regional Trends of a Prevalence from a DHS","URL":"http:\/\/www.ceped.org\/prevR,
http:\/\/joseph.larmarange.net\/prevR","Version":"3.3"},"prevalence":
{"Author":"Brecht Devleesschauwer [aut, cre], Paul Torgerson [aut],\nJohannes
Charlier [aut], Bruno Levecke [aut], Nicolas Praet [aut],\nSophie Roelandt [aut],
Suzanne Smit [aut], Pierre Dorny [aut],\nDirk Berkvens [aut], Niko Speybroeck
[aut]","Depends":"R (>= 3.0.0), rjags, coda, methods","Description":"The prevalence
package provides Frequentist and Bayesian methods for prevalence assessment
studies. IMPORTANT: the truePrev functions in the prevalence package call on JAGS
(Just Another Gibbs Sampler), which therefore has to be available on the user's
system. JAGS can be downloaded from http:\/\/mcmc-
jags.sourceforge.net\/.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"prevalence","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Tools for Prevalence Assessment
Studies","URL":"http:\/\/prevalence.cbra.be\/","Version":"0.4.0"},"prim":
{"Author":"Tarn Duong <tarn.duong@gmail.com>","Depends":"R (>=
2.10.0)","Description":"Patient Rule Induction Method (PRIM) for bump hunting in
high-dimensional data.","Imports":"grDevices, graphics, misc3d, rgl, stats, tcltk,
utils","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"prim","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"MASS","Title":"Patient Rule Induction Method
(PRIM)","URL":"http:\/\/www.mvstat.net\/tduong","Version":"1.0.16"},"primer":
{"Author":"M Henry H Stevens","Depends":"deSolve, lattice","Description":"Functions
are primarily functions for systems of ordinary\ndifferential equations, difference
equations, and eigenanalysis\nand projection of demographic matrices; data are for
examples.","License":"GPL","NeedsCompilation":"no","Package":"primer","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"bbmle, gdata, nlme,
vegan","Title":"Functions and data for A Primer of Ecology with
R","Version":"1.0"},"primerTree":{"Author":"Jim Hester","Depends":"R (>= 3.0.0),
directlabels, gridExtra","Description":"Identifies potential target sequences for a
given set of primers\nand generates taxonomically annotated phylogenetic trees with
the predicted\namplification products.","Imports":"ggplot2, grid, XML, ape, httr,
lubridate, plyr, scales,\nstringr, foreach","License":"GPL-
2","NeedsCompilation":"yes","Package":"primerTree","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Visually Assessing the Specificity and Informativeness
of Primer\nPairs","Version":"1.0.3"},"primes":{"Author":"Oliver
Keyes","Description":"Functions to test whether a number is prime and generate the
prime numbers within a specified range. Based around\nan implementation of Wilson's
theorem for testing for an integer's primality.","Imports":"Rcpp","License":"MIT +
file
LICENSE","NeedsCompilation":"yes","Package":"primes","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat","Title":"Generate and Test for Prime
Numbers","Version":"0.1.0"},"princurve":{"Author":"S original by Trevor Hastie
<trevor@research.att.com> R port by\nAndreas Weingessel
<Andreas.Weingessel@ci.tuwien.ac.at>","Description":"fits a principal curve to a
data matrix in arbitrary\ndimensions","Imports":"stats, graphics","License":"GPL-
2","NeedsCompilation":"yes","Package":"princurve","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Fits a Principal Curve in Arbitrary
Dimension","Version":"1.1-12"},"prinsimp":{"Author":"Davor Cubranic, Jonathan
Zhang, Nancy Heckman, Travis Gaydos,\nand J.S. Marron","Description":"Provides
capabilities beyond principal components\nanalysis to focus on finding structure in
low variability\nsubspaces. Constructs and plots simple basis vectors for\npre-
defined and user-defined measures of simplicity.","License":"AGPL-
3","NeedsCompilation":"no","Package":"prinsimp","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Finding and plotting simple basis vectors for
multivariate data","Version":"0.8-8"},"prism":{"Author":"Hart Edmund [aut,
cre],\nKendon Bell [aut]","Description":"Allows users to access the Oregon State
Prism climate data. Using the web service API data can easily downloaded in bulk
and loaded into R for spatial analysis. Some user friendly visualizations are also
provided.","Imports":"ggplot2, raster, httr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"prism","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat, knitr","Title":"Access Data from the
Oregon State Prism Climate
Project","URL":"http:\/\/github.com\/ropensci\/prism","Version":"0.0.7"},"pro":
{"Author":"Xi (Rossi) LUO with contributions from Dylan Small and Vikaas
Sohal","Description":"Optogenetics is a new tool to study neuronal circuits that
have been genetically modified to allow stimulation by flashes of light. This
package implements the methodological framework, Point-process Response model for
Optogenetics (PRO), for analyzing data from these experiments. This method
provides explicit nonlinear transformations to link the flash point-process with
the spiking point-process. Such response functions can be used to provide
important and interpretable scientific insights into the properties of the
biophysical process that governs neural spiking in response to optogenetic
stimulation.","License":"GPL-
2","NeedsCompilation":"no","Package":"pro","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"cin","Title":"Point-Process Response Model for
Optogenetics","Version":"0.1.1"},"prob":{"Author":"G. Jay Kerns [aut, cre,
cph]","Depends":"combinat, fAsianOptions, hypergeo, VGAM","Description":"\nThis
package provides a framework for performing elementary probability\ncalculations on
finite sample spaces, which may be represented by data frames\nor lists.
Functionality includes setting up sample spaces, counting tools,\ndefining
probability spaces, performing set algebra, calculating probability\nand
conditional probability, tools for simulation and checking the law of\nlarge
numbers, adding random variables, and finding marginal
distributions.\nCharacteristic functions for all base R distributions are
3)","NeedsCompilation":"no","Package":"prob","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Elementary Probability on Finite Sample
Spaces","URL":"http:\/\/prob.r-forge.r-project.org,
http:\/\/people.ysu.edu\/~gkerns\/","Version":"0.9-5"},"probFDA":{"Author":"Charles
Bouveyron & Camille Brunet","Depends":"MASS","Description":"Probabilistic Fisher
discriminant analysis (pFDA) is a probabilistic version of the popular and powerful
Fisher linear discriminant analysis for dimensionality reduction and
classification.","License":"GPL-
2","NeedsCompilation":"no","Package":"probFDA","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Probabilistic
Fisher Discriminant Analysis","Version":"1.0.1"},"probemod":{"Author":"Jiat Chow
Tan [aut, cre]","Depends":"R (>= 3.1.2)","Description":"Contains functions that are
useful for probing moderation effects (or interactions) including techniques such
as pick-a-point (also known as spotlight analysis) and Johnson-Neyman (also known
as floodlight analysis). Plot function is also provided to facilitate visualization
of results from each of these techniques.","License":"GPL-
3","NeedsCompilation":"no","Package":"probemod","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Statistical Tools for Probing Moderation
Effects","Version":"0.2.1"},"probsvm":{"Author":"Chong Zhang, Seung Jun Shin,
Junhui Wang, Yichao Wu, Hao Helen\nZhang, and Yufeng
Liu","Depends":"kernlab","Description":"This package provides multiclass
conditional probability\nestimation for the SVM, which is distributional
assumption\nfree.","License":"GPL-
2","NeedsCompilation":"no","Package":"probsvm","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"probsvm: Class probability estimation for Support
Vector\nMachines","Version":"1.00"},"processcontrol":{"Author":"Peter P. Lupo [aut,
cre]","Depends":"R (>= 3.1.0)","Description":"Generate time series chart for
individual values with mean and +\/-\n3 standard deviation lines and the
corresponding mR chart with the upper control\nlimit. Also execute the 8 Shewhart
stability run tests and display the violations.","Imports":"plyr","License":"MIT +
file
LICENSE","NeedsCompilation":"no","Package":"processcontrol","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Title":"Statistical Process Control
Charts","Version":"0.1.0"},"prodlim":{"Author":"Thomas A. Gerds","Depends":"R (>=
2.9.0)","Description":"Fast and user friendly implementation of nonparametric
estimators\nfor censored event history (survival) analysis. Kaplan-Meier
and\nAalen-Johansen method.","Imports":"Rcpp (>= 0.11.5), stats, graphics,
survival, KernSmooth, lava","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"prodlim","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Product-Limit Estimation for Censored Event History
Analysis","Version":"1.5.7"},"profdpm":{"Author":"Matt
Shotwell","Description":"This package facilitates profile inference (inference
at\nthe posterior mode) for a class of product partition models\n(PPM). The
Dirichlet process mixture is currently the only\navailable member of this class.
These methods search for the\nmaximum posterior (MAP) estimate for the data
partition in a\nPPM.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"profdpm","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Profile Dirichlet Process
Mixtures","Version":"3.3"},"profileModel":{"Author":"Ioannis Kosmidis
<i.kosmidis@ucl.ac.uk>","Depends":"R (>= 2.6.0)","Description":"profileModel
provides tools that can be used to calculate, evaluate, plot and use for inference
the profiles of *arbitrary* inference functions for *arbitrary* 'glm'-like fitted
models with linear predictors.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"profileModel","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"MASS, gnm","Title":"Tools for profiling inference
functions for various
model\nclasses","URL":"http:\/\/www.ucl.ac.uk\/~ucakiko\/index.html","Version":"0.5
-9"},"profileR":{"Author":"Okan Bulut <okanbulut84@gmail.com>, Christopher David
Desjardins\n<cddesjardins@gmail.com>","Depends":"ggplot2, RColorBrewer, reshape,
lavaan, R (>= 3.0.0)","Description":"A suite of multivariate methods and data
visualization\ntools to implement profile analysis and cross-validation techniques
described in\nDavison & Davenport (2002) <DOI: 10.1037\/1082-989X.7.4.468>, Bulut
(2013), and other published and unpublished resources.\nThe package includes
routines to perform criterion-related profile analysis, profile analysis\nvia
multidimensional scaling, moderated profile analysis, profile analysis by group,
and a\nwithin-person factor model to derive score profiles.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"profileR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Profile Analysis of Multivariate Data in
R","Version":"0.3-3"},"profilr":{"Author":"Paul Hendricks [aut, cre]","Depends":"R
(>= 3.1.2)","Description":"Allows users to quickly and reliably profile data in
R\nusing convenience functions. The profiled data returns as a data.frame\nand
provides a wealth of common and uncommon summary statistics.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"profilr","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat","Title":"Quickly Profile Data in
R","URL":"https:\/\/github.com\/paulhendricks\/profilr","Version":"0.1.0"},"profr":
{"Author":"Hadley Wickham <h.wickham@gmail.com>","Description":"profr provides an
alternative data structure\nand visual rendering for the profiling
information\ngenerated by Rprof.","Imports":"stringr, plyr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"profr","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"ggplot2","Title":"An alternative display for
profiling
information","URL":"https:\/\/github.com\/hadley\/profr","Version":"0.3.1"},"profto
ols":{"Author":"Luke Tierney and Riad Jarjour","Description":"Tools for examining
Rprof profile
output.","License":"GPL","NeedsCompilation":"no","Package":"proftools","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"graph,Rgraphviz,boot,knitr","Ti
tle":"Profile Output Processing Tools for R","Version":"0.99-2"},"progenyClust":
{"Author":"C.W. Hu","Depends":"graphics,stats","Description":"Implementing the
Progeny Clustering algorithm, the progenyClust package assesses the clustering
stability and identifies the optimal clustering number for a given data matrix. It
uses kmeans clustering as default, but can be customized to work with other
clustering algorithms and different parameter settings. The package includes one
main function progenyClust(), plot and summary methods for progenyClust object, and
two example datasets (test and cell) for
testing.","Imports":"Hmisc","License":"AGPL-
3","NeedsCompilation":"no","Package":"progenyClust","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Finding the Optimal Cluster Number Using Progeny
Clustering","Version":"1.1"},"prognosticROC":{"Author":"Y. Foucher
<Yohann.Foucher@univ-nantes.fr> and C. Combescure
<Christophe.Combescure@hcuge.ch>","Depends":"splines,
survival","Description":"Prognostic ROC curve is an alternative graphical approach
to represent the discriminative capacity of the marker: a receiver operating
characteristic (ROC) curve by plotting 1 minus the survival in the high-risk group
against 1 minus the survival in the low-risk group. This package contains functions
to assess prognostic ROC curve. The user can enter the survival according to a
model previously estimated or the user can also enter individual survival data for
estimating the prognostic ROC curve by using Kaplan-Meier estimator. The area under
the curve (AUC) corresponds to the probability that a patient in the low-risk group
has a longer lifetime than a patient in the high-risk group. The prognostic ROC
curve provides complementary information compared to survival curves. The AUC is
assessed by using the trapezoidal rules. When survival curves do not reach 0, the
prognostic ROC curve is incomplete and the extrapolations of the AUC are performed
by assuming pessimist, optimist and non-informative situations.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"prognosticROC","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Prognostic ROC curves for evaluating the predictive
capacity of\na binary test","URL":"www.r-project.org,
www.divat.fr","Version":"0.7"},"progress":{"Author":"Gabor Csardi [aut,
cre]","Description":"Terminal progress bars. They are\nconfigurable, may include
percentage, elapsed time, and\/or\nthe estimated completion time. They work in the
command line,\nin Emacs, R Studio, Windows Rgui and Mac OSX R.app. The
package\nalso provides a C++ API, that works with or without
Rcpp.","Imports":"prettyunits, R6","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"progress","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat","Title":"Terminal Progress
Bars","URL":"https:\/\/github.com\/gaborcsardi\/progress","Version":"1.0.2"},"proj4
":{"Author":"Simon Urbanek <simon.urbanek@r-project.org>","Depends":"R (>=
2.0.0)","Description":"A simple interface to lat\/long projection and
datum\ntransformation of the PROJ.4 cartographic projections library.\nIt allows
transformation of geographic coordinates from one\nprojection and\/or datum to
another.","License":"GPL-
2","NeedsCompilation":"yes","Package":"proj4","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"A simple interface to the PROJ.4 cartographic
projections\nlibrary","URL":"http:\/\/www.rforge.net\/proj4\/","Version":"1.0-
8"},"prop.comb.RR":{"Author":"Maria Alvarez and Javier Roca-
Pardinas","Depends":"rootSolve","Description":"The prop.comb.RR package analyzes
combination of proportions and relative
risk.","License":"GPL","NeedsCompilation":"no","Package":"prop.comb.RR","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Analyzing Combination of
Proportions and Relative Risk","Version":"1.1"},"propOverlap":{"Author":"Osama
Mahmoud, Andrew Harrison, Aris Perperoglou, Asma Gul, Zardad Khan, Berthold
Lausen","Depends":"R (>= 2.10), Biobase","Description":"A package for selecting the
most relevant features (genes) in the high-dimensional binary classification
problems. The discriminative features are identified using analyzing the overlap
between the expression values across both classes. The package includes functions
for measuring the proportional overlapping score for each gene avoiding
the outliers effect. The used measure for the overlap is the one defined in
the \"Proportional Overlapping Score (POS)\" technique for feature selection. A
gene mask which represents a gene's classification power can also be produced for
each gene (feature). The set size of the selected genes might be set by the user.
The minimum set of genes that correctly classify the maximum number of the given
tissue samples (observations) can be also produced.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"propOverlap","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Feature (gene) selection based on the Proportional
Overlapping\nScores","Version":"1.0"},"propagate":{"Author":"Andrej-Nikolai Spiess
<a.spiess@uke.uni-hamburg.de>","Depends":"R (>= 2.13.0), MASS, tmvtnorm, Rcpp (>=
0.10.1), ff,\nminpack.lm","Description":"Propagation of uncertainty using higher-
order Taylor expansion and Monte Carlo simulation.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"propagate","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Propagation of Uncertainty","Version":"1.0-
4"},"properties":{"Author":"Tobias Verbeke, based on read.dcf by R Core Development
Team","Description":"The properties package allows to parse Java properties
files\nin the context of R Service Bus applications.","License":"GPL-
2","NeedsCompilation":"no","Package":"properties","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Parse Java Properties Files for R Service Bus
Applications","URL":"http:\/\/www.openanalytics.eu\/r-service-bus","Version":"0.0-
8"},"proportion":{"Author":"M.Subbiah, V.Rajeswaran","Depends":"R (>=
3.2.2)","Description":"Abundant statistical literature has revealed the importance
of constructing and evaluating various methods for constructing confidence
intervals (CI) for single binomial proportion (p). We comprehensively provide
procedures in frequentist (approximate with or without adding pseudo counts or
continuity correction or exact) and in Bayesian cultures. Evaluation procedures for
CI warrant active computational attention and required summaries pertaining to
four criterion (coverage probability, expected length, p-confidence, p-bias, and
error) are implemented.","Imports":"TeachingDemos, ggplot2","License":"GPL-
2","NeedsCompilation":"no","Package":"proportion","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr, rmarkdown","Title":"Inference on Single
Binomial Proportion and
Bayesian\nComputations","URL":"https:\/\/github.com\/RajeswaranV\/proportion","Vers
ion":"1.2.0"},"prospectr":{"Author":"Antoine Stevens and Leonardo Ramirez-
Lopez","Depends":"R (>= 3.0.0), RcppArmadillo (>= 0.4.000)","Description":"The
package provides functions for pretreatment and sample\nselection of visible and
near infrared diffuse reflectance spectra","Imports":"foreach, iterators, Rcpp (>=
0.11.0)","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"prospectr","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"hyperSpec, knitr","Title":"Miscellaneous functions
for processing and sample selection of\nvis-NIR diffuse reflectance
data","URL":"https:\/\/github.com\/antoinestevens\/prospectr","Version":"0.1.3"},"p
rotViz":{"Author":"Christian Panse <cp@fgcz.ethz.ch>, Jonas Grossmann
<jg@fgcz.ethz.ch>,\nSimon Barkow-Oesterreicher <sb@fgcz.ethz.ch>","Depends":"R (>=
3.0.2), methods","Description":"This R package helps with quality checks,
visualizations\nand analysis of mass spectrometry data, coming from
proteomics\nexperiments. The package is developed, tested and used at the
Functional\nGenomics Center Zurich. We use this package mainly for
prototyping,\nteaching, and having fun with proteomics data. But it can also
be\nused to do data analysis for small scale data sets.","Imports":"Rcpp (>=
3","NeedsCompilation":"yes","Package":"protViz","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"lattice, RUnit, BiocGenerics","Title":"Visualizing and
Analyzing Mass Spectrometry Related Data in\nProteomics","URL":"http:\/\/fgcz-
data.uzh.ch\/~cpanse\/protViz\/","Version":"0.2.9"},"proteomicdesign":
{"Author":"Irene SL Zeng","Depends":"MASS","Description":"This package provides
functions to identify the optimal\nsolution that maximizes numbers of detectable
differentiated\nproteins from a multi-stage clinical proteomic
study.","License":"GPL-
3","NeedsCompilation":"no","Package":"proteomicdesign","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Optimization of a multi-stage proteomic
study","Version":"2.0"},"proteomics":{"Author":"Thomas W. D. MÃ¶bius
<kontakt@thomasmoebius.de>","Description":"Provides methods for making inference in
isobaric labelled\nLC-MS\/MS experiments, i.e. iTRAQ experiments. It provides a
function that\nreasonably parses a CSV-export from Proteome Discoverer(TM) into a
data\nframe that can be easily handled in R. Functions and methods are
provided\nfor quality control, filtering, norming, and the calculation of
response\nvariables for further analysis. The merging of multiple iTRAQ
experiments\nwith respect to a reference is also covered.","Imports":"plyr,
reshape2, ggplot2, foreach","License":"GPL-
3","NeedsCompilation":"no","Package":"proteomics","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Statistical Analysis of High Throughput Proteomics
Data","URL":"http:\/\/00tau.github.io\/proteomics-in-
r\/","Version":"0.2"},"protiq":{"Author":"Sarah Gerster and Peter
Buehlmann","Depends":"methods","Description":"Method for protein quantification
based on identified and\nquantified peptides. protiq can be used for absolute and
relative protein\nquantification. Input peptide abundance scores can come from
various\nsources, including SRM transition areas and intensities or spectral
counts\nderived from shotgun experiments. The package is still being extended
to\nalso include the model for protein identification, MIPGEM, presented
in\nGerster, S., Qeli, E., Ahrens, C.H. and Buehlmann, P. (2010). Protein and\ngene
model inference based on statistical modeling in k-partite graphs.\nProceedings of
the National Academy of Sciences 107(27):12101-12106.","Imports":"graph, RBGL,
mvtnorm","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"protiq","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"gplots","Title":"Protein (identification and)
quantification based on peptide\nevidence","Version":"1.2"},"proto":
{"Author":"Louis Kates, Thomas Petzoldt","Description":"An object oriented system
using object-based, also called\nprototype-based, rather than class-based object
oriented ideas.","License":"GPL-
2","NeedsCompilation":"no","Package":"proto","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"graph, Rgraphviz","Title":"Prototype object-based
programming","URL":"http:\/\/r-proto.googlecode.com","Version":"0.3-
10"},"protoclass":{"Author":"Jacob Bien and Robert
Tibshirani","Depends":"class","Description":"Greedy algorithm described in Bien and
Tibshirani (2011)\nPrototype Selection for Interpretable Classification. Annals
of\nApplied Statistics. 5(4). 2403-2424","License":"GPL-
3","NeedsCompilation":"no","Package":"protoclass","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat, roxygen2","Title":"Interpretable
classification with prototypes","Version":"1.0"},"protoclust":{"Author":"Jacob Bien
and Rob Tibshirani","Description":"Performs minimax linkage hierarchical
clustering. Every cluster\nhas an associated prototype element that represents
that cluster as\ndescribed in Bien, J., and Tibshirani, R. (2011), \"Hierarchical
Clustering\nwith Prototypes via Minimax Linkage,\" accepted for publication in
The\nJournal of the American Statistical Association,
DOI:\n10.1198\/jasa.2011.tm10183.","License":"GPL-
2","NeedsCompilation":"yes","Package":"protoclust","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Hierarchical Clustering with
Prototypes","Version":"1.5"},"proton":{"Author":"PrzemysÅ‚aw Biecek [aut,
cre],\nWitold Chodor [trl],\nFoundation SmarterPoland.pl [cph]","Depends":"R (>=
3.0.0)","Description":"'The Proton Game' is a console-based data-crunching game for
younger and older data scientists.\nAct as a data-hacker and find Slawomir
Pietraszko's credentials to the Proton server.\nYou have to solve four data-based
puzzles to find the login and password.\nThere are many ways to solve these
puzzles. You may use loops, data filtering, ordering, aggregation or other
tools.\nOnly basics knowledge of R is required to play the game, yet the more
functions you know, the more approaches you can try.\nThe knowledge of dplyr is not
required but may be very helpful.\nThis game is linked with the ,,Pietraszko's
Cave'' story available at http:\/\/biecek.pl\/BetaBit\/Warsaw.\nIt's a part of Beta
and Bit series.\nYou will find more about the Beta and Bit series at
http:\/\/biecek.pl\/BetaBit.","Imports":"digest","License":"GPL-
2","NeedsCompilation":"no","Package":"proton","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"The Proton Game","Version":"1.0"},"prototest":
{"Author":"Stephen Reid","Depends":"intervals, MASS,
glmnet","Description":"Procedures for testing for group-wide signal in clusters of
variables. Tests can be performed for single groups in isolation (univariate) or
multiple groups together (multivariate). Specific tests include the exact and
approximate (un)selective likelihood ratio tests described in Reid et al (2015),
the selective F test and marginal screening prototype test of Reid and Tibshirani
(2015). User may pre-specify columns to be included in prototype formation, or
allow the function to select them itself. A mixture of these two is also possible.
Any variable selection is accounted for using the selective inference framework.
Options for non-sampling and hit-and-run null reference
distributions.","Imports":"Rcpp (>= 0.12.1)","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"prototest","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Inference on Prototypes from Clusters of
Features","URL":"http:\/\/arxiv.org\/abs\/1511.07839","Version":"1.1"},"protr":
{"Author":"Nan Xiao <road2stat@gmail.com>, Qingsong Xu
<dasongxu@gmail.com>,\nDongsheng Cao <oriental-
cds@163.com>","Description":"Comprehensive toolkit for generating various
numerical\nrepresentation schemes of protein sequence. The descriptors and
similarity\nscores included are extensively used in bioinformatics and
chemogenomics.\nFor full functionality, the software 'ncbi-blast+' is needed,
see\n<http:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?
CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download>\nfor more
information.","License":"BSD 3-clause License + file
LICENSE","NeedsCompilation":"no","Package":"protr","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"Biostrings, GOSemSim, foreach, doParallel,
org.Hs.eg.db","Title":"Generating Various Numerical Representation Schemes of
Protein\nSequence","URL":"https:\/\/github.com\/road2stat\/protr","Version":"1.1-
1"},"provenance":{"Author":"Pieter Vermeesch [aut, cre]","Depends":"R (>=
3.0.0)","Description":"Bundles a number of established statistical methods to
facilitate\nthe visual interpretation of large datasets in sedimentary geology.
Includes\nfunctionality for adaptive kernel density estimation, multidimensional
scaling,\ngeneralised procrustes analysis and individual differences scaling using
a\nvariety of dissimilarity measures. Univariate provenance proxies, such
as\nsingle-grain ages or (isotopic) compositions are compared with the
Kolmogorov-\nSmirnov dissimilarity and Sircombe-Hazelton L2-norm. Categorical
provenance\nproxies, such as mineralogical, petrographic or chemical compositions
are\ncompared with the Aitchison and Bray-Curtis distances. Also included are
tools\nto plot compositional data on ternary diagrams, to calculate the sample
size\nrequired for specified levels of statistical precision, and to assess
the\neffects of hydraulic sorting on detrital compositions. Includes an
intuitive\nquery-based user interface for users who are not proficient in
R.","Imports":"MASS, methods","License":"GPL-
2","NeedsCompilation":"no","Package":"provenance","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Statistical Toolbox for Sedimentary Provenance
Analysis","Version":"1.4"},"proxy":{"Author":"David Meyer [aut, cre],\nChristian
Buchta [aut]","Depends":"R (>= 2.4.0)","Description":"Provides an extensible
framework for the efficient calculation of auto- and cross-proximities, along with
implementations of the most popular ones.","Imports":"stats, utils","License":"GPL-
2","NeedsCompilation":"yes","Package":"proxy","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"cba","Title":"Distance and Similarity
Measures","Version":"0.4-15"},"prozor":{"Author":"Witold
Wolski","Description":"Determine minimal protein set explaining peptide spectrum
matches.","Imports":"Matrix, doParallel, foreach, seqinr","License":"GPL-
3","NeedsCompilation":"no","Package":"prozor","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Minimal Protein Set Explaining Peptide Spectrum
Matches","URL":"https:\/\/github.com\/wolski\/prozor","Version":"0.1.1"},"pryr":
{"Author":"Hadley Wickham [aut, cre],\nR Core team [ctb] (Some code extracted from
base R)","Depends":"R (>= 3.1.0)","Description":"Useful tools to pry back the
covers of R and understand the\nlanguage at a deeper level.","Imports":"stringr,
codetools, methods, Rcpp (>= 0.11.0)","License":"GPL-
2","NeedsCompilation":"yes","Package":"pryr","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat (>= 0.8.0)","Title":"Tools for Computing on the
Language","URL":"https:\/\/github.com\/hadley\/pryr","Version":"0.1.2"},"psData":
{"Author":"Christopher Gandrud","Depends":"R (>= 3.0.2)","Description":"This R
package includes functions for gathering commonly used and\nregularly maintained
data set in political science. It also includes\nfunctions for combining components
from these data sets into variables that\nhave been suggested in the literature,
but are not regularly maintained.","Imports":"countrycode, DataCombine, reshape2,
rio, xlsx","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"psData","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Download Regularly Maintained Political Science Data
Sets","URL":"http:\/\/cran.r-
project.org\/package=psData","Version":"0.2"},"psbcGroup":{"Author":"Kyu Ha Lee,
Sounak Chakraborty, (Tony) Jianguo Sun","Depends":"LearnBayes, SuppDists, mvtnorm,
R (>= 3.2.3)","Description":"Algorithms for fitting penalized parametric and
semiparametric Bayesian survival models with shrinkage and grouping
priors.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"psbcGroup","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Penalized Parametric and Semiparametric Bayesian
Survival Models\nwith Shrinkage and Grouping Priors","Version":"1.3"},"pscl":
{"Author":"Simon Jackman, with contributions from\nAlex Tahk, Achim Zeileis,
Christina Maimone and Jim Fearon","Depends":"MASS, lattice","Description":"Bayesian
analysis of item-response theory (IRT) models,\nroll call analysis; computing
highest density regions; maximum\nlikelihood estimation of zero-inflated and hurdle
models for count\ndata; goodness-of-fit measures for GLMs; data sets used\nin
writing\tand teaching at the Political Science\nComputational Laboratory; seats-
votes curves.","Enhances":"stats","License":"GPL-
2","NeedsCompilation":"yes","Package":"pscl","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"MCMCpack, car, lmtest, sandwich, zoo, coda, vcd,
mvtnorm,\nmgcv","Title":"Political Science Computational Laboratory, Stanford
University","URL":"http:\/\/pscl.stanford.edu\/","Version":"1.4.9"},"pscore":
{"Author":"Joshua F. Wiley <jwiley.psych@gmail.com>","Depends":"R (>=
3.1.0)","Description":"Provides a number of functions to\nsimplify and automate the
scoring, comparison, and evaluation of\ndifferent ways of creating composites of
data. It is particularly\naimed at facilitating the creation of physiological
composites of\nmetabolic syndrome symptom score (MSSS) and allostatic load
(AL).","Imports":"ggplot2, reshape2, lavaan","License":"LGPL-
3","NeedsCompilation":"no","Package":"pscore","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Standardizing Physiological Composite Risk
Endpoints","URL":"https:\/\/jwiley.github.io\/score-project\/","Version":"0.1-
2"},"psd":{"Author":"Andrew J. Barbour and Robert L. Parker, with contributions
from David\nMyer","Depends":"R (>= 2.14.1), utils, stats, graphics,
grDevices","Description":"Produces power spectral density estimates through
iterative\nrefinement of the optimal number of sine-tapers at each frequency.
This\noptimization procedure is based on the method of Riedel and
Sidorenko\n(1995), which minimizes the Mean Square Error (sum of variance and
bias)\nat each frequency, but modified for computational
stability.","Imports":"Rcpp (>= 0.11.5), RColorBrewer, signal, zoo","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"psd","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"bspec, fftw (>= 1.0.3), ggplot2 (>= 0.9), knitr,
multitaper,\nplyr, RSEIS, rbenchmark, reshape2, testthat","Title":"Adaptive, Sine-
Multitaper Power Spectral Density
Estimation","URL":"https:\/\/github.com\/abarbour\/psd, Barbour and Parker
(2014):\nhttp:\/\/dx.doi.org\/10.1016\/j.cageo.2013.09.015, Riedel and\nSidorenko
(1995): http:\/\/dx.doi.org\/10.1109\/78.365298","Version":"1.0-1"},"pse":
{"Author":"Andre Chalom, Paulo Inacio Knegt Lopez de Prado","Depends":"R (>=
3.0.1), Hmisc","Description":"Functions for creating Latin Hypercubes
with\nprescribed correlations and performing parameter space exploration.\nAlso
implements the PLUE method.\nBased on the package sensitivity, by Gilles
Pujol,\nBertrand Iooss & Alexandre Janon.","Imports":"utils, graphics, stats, boot,
3","NeedsCompilation":"yes","Package":"pse","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"sensitivity, mcmc","Title":"Parameter Space Exploration
with Latin
Hypercubes","URL":"https:\/\/github.com\/andrechalom\/pse","Version":"0.4.5"},"pseu
do":{"Author":"Maja Pohar Perme [aut], Mette Gerster [aut, cre]","Depends":"KMsurv,
geepack","Description":"Various functions for computing pseudo-observations
for\ncensored data regression","License":"GPL-
2","NeedsCompilation":"no","Package":"pseudo","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Pseudo - observations","Version":"1.1"},"pseval":
{"Author":"Michael C Sachs","Description":"Contains the core methods for the
evaluation of principal\nsurrogates in a single clinical trial. Provides a flexible
interface for\ndefining models for the risk given treatment and the surrogate, the
models\nfor integration over the missing counterfactual surrogate responses, and
the\nestimation methods. Estimated maximum likelihood and pseudo-score can be
used\nfor estimation, and the bootstrap for inference. A variety of post-
estimation\nsummary methods are provided, including print, summary, plot, and
testing.","Imports":"survival","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"pseval","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"ggplot2, testthat, knitr, printr","Title":"Methods
for Evaluating Principal Surrogates of
Treatment\nResponse","Version":"1.0.0"},"psgp":{"Author":"Ben Ingram
<bri@utalca.cl>, Remi Barillec <r.barillec@aston.ac.uk>","Depends":"R (>= 3.0.2),
intamap","Description":"Implements projected sparse Gaussian process kriging for
the intamap package","Imports":"automap, gstat","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"psgp","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"doParallel,
rgdal","Title":"Projected Spatial Gaussian Process (psgp) methods","Version":"0.3-
6"},"psidR":{"Author":"Florian Oswald","Depends":"data.table, RCurl, foreign,
SAScii","Description":"Makes it easy to build panel data in wide format from
PSID\ndelivered raw data. Deals with data downloaded and pre-processed by Stata or
SAS,\nor can optionally download directly from the PSID server using the SAScii
package.\n`psidR` takes care of merging data from each wave onto a cross-period
index file,\nso that individuals can be followed over time. The user must specify
which years\nthey are interested in, and the PSID variable names (e.g. ER21003) for
each year\n(they differ in each year). There are different panel data designs
and\nsample subsetting criteria implemented (\"SRC\", \"SEO\", \"immigrant\"
and \"latino\"\nsamples).","License":"GPL-
3","NeedsCompilation":"no","Package":"psidR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat","Title":"Build Panel Data Sets from PSID Raw
Data","URL":"https:\/\/github.com\/floswald\/psidR","Version":"1.3"},"pso":
{"Author":"Claus Bendtsen <papyrus.bendtsen@gmail.com>.","Depends":"R (>= 2.10.0),
methods","Description":"The package provides an implementation of PSO
consistent\nwith the standard PSO 2007\/2011 by Maurice Clerc et al.\nAdditionally
a number of ancillary routines are provided for\neasy testing and
graphics.","License":"LGPL-
3","NeedsCompilation":"no","Package":"pso","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"numDeriv","Title":"Particle Swarm
Optimization","Version":"1.0.3"},"psoptim":{"Author":"Krzysztof Ciupke [aut,
cre]","Depends":"R (>= 2.0.0)","Description":"Particle swarm optimization - a basic
variant.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"psoptim","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Particle Swarm Optimization","URL":"https:\/\/www.r-
project.org","Version":"1.0"},"pspearman":{"Author":"Petr Savicky
<savicky@cs.cas.cz>","Description":"Spearman's rank correlation test with
precomputed exact\nnull distribution for n <= 22.","License":"GPL-
3","NeedsCompilation":"yes","Package":"pspearman","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Spearman's rank correlation test","Version":"0.3-
0"},"pspline":{"Author":"S original by Jim Ramsey <ramsay@psych.mcgill.ca>.\nR port
by Brian Ripley <ripley@stats.ox.ac.uk>.","Depends":"R (>= 2.0.0), stats,
graphics","Description":"Smoothing splines with penalties on order m
derivatives.","License":"Unlimited","NeedsCompilation":"yes","Package":"pspline","R
epository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Penalized Smoothing
Splines","Version":"1.0-17"},"pssm":{"Author":"David A. Schoenfeld [aut,
cre]","Depends":"methods","Description":"Estimates parameters of a piecewise
exponential model for time to progression and time from progression to death with
interval censoring of the time to progression and covariates for each distribution
using proportional hazards.","Imports":"MASS, abind, numDeriv,
MHadaptive","License":"GPL-
2","NeedsCompilation":"no","Package":"pssm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Piecewise Exponential Model for Time to Progression and
Time\nfrom Progression to Death","Version":"1.0"},"psy":{"Author":"Bruno
Falissard","Description":"Kappa, ICC, Cronbach alpha, screeplot,
mtmm","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"psy","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Various procedures used in
psychometry","Version":"1.1"},"psych":{"Author":"William Revelle
<revelle@northwestern.edu>","Depends":"R (>= 2.10)","Description":"A general
purpose toolbox for personality, psychometrics and experimental psychology.
Functions are primarily for multivariate analysis and scale construction using
factor analysis, principal component analysis, cluster analysis and reliability
analysis, although others provide basic descriptive statistics. Item Response
Theory is done using factor analysis of tetrachoric and polychoric correlations.
Functions for analyzing data at multi-levels include within and between group
statistics, including correlations and factor analysis. Functions for simulating
particular item and test structures are included. Several functions serve as a
useful front end for structural equation modeling. Graphical displays of path
diagrams, factor analysis and structural equation models are created using basic
graphics. Some of the functions are written to support a book on psychometrics as
well as publications in personality research. For more information, see the
personality-project.org\/r
webpage.","Imports":"mnormt,parallel,stats,graphics,grDevices,methods","License":"G
PL (>=
2)","NeedsCompilation":"no","Package":"psych","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"GPArotation, sem, lavaan, Rcsdp, graph,
Rgraphviz","Title":"Procedures for Psychological, Psychometric, and
Personality\nResearch","URL":"http:\/\/personality-
project.org\/r\/psych\nhttp:\/\/personality-project.org\/r\/psych-
manual.pdf","Version":"1.5.8"},"psychometric":{"Author":"Thomas D.
Fletcher","Depends":"multilevel, nlme, R(>= 2.11.0)","Description":"Contains
functions useful for correlation theory,\nmeta-analysis (validity-generalization),
reliability, item\nanalysis, inter-rater reliability, and classical
utility","Imports":"multilevel, nlme","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"psychometric","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Applied Psychometric
Theory","Version":"2.2"},"psychomix":{"Author":"Hannah Frick [aut, cre],\nCarolin
Strobl [aut],\nFriedrich Leisch [aut],\nAchim Zeileis [aut]","Depends":"R (>=
2.10.0), flexmix (>= 2.3-7), psychotools (>= 0.3-0)","Description":"Psychometric
mixture models based on 'flexmix' infrastructure. At the moment Rasch mixture
models\nwith different parameterizations of the score distribution (saturated vs.
mean\/variance specification)\nand Bradley-Terry mixture models are implemented.
Both mixture models can be estimated with or without\nconcomitant variables. See
vignette('raschmix', package = 'psychomix') for details on the Rasch
mixture\nmodels.","Imports":"graphics, methods, stats, lattice, Formula (>= 1.1-
0),\nmodeltools","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"psychomix","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"effects, lmtest, mRm, nnet,
numDeriv","Title":"Psychometric Mixture Models","Version":"1.1-3"},"psychotools":
{"Author":"Achim Zeileis [aut, cre],\nCarolin Strobl [aut],\nFlorian Wickelmaier
[aut],\nBasil Abou El-Komboz [aut],\nJulia Kopf [aut]","Depends":"R (>=
2.10.0)","Description":"Infrastructure for psychometric modeling such as data
classes\n(for item response data and paired comparisons), basic model
fitting\nfunctions (for Bradley-Terry, Rasch, partial credit, rating
scale,\nmultinomial processing tree models), extractor functions for different
types\nof parameters (item, person, threshold, discrimination), unified
inference\nand visualizations, and various datasets for illustration. Intended as
a\ncommon lightweight and efficient toolbox for psychometric modeling and a\ncommon
building block for fitting psychometric mixture models in package\n\"psychomix\"
and psychometric tree models in package \"psychotree\".","Imports":"graphics,
3","NeedsCompilation":"yes","Package":"psychotools","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"multcomp, Formula, likert","Title":"Infrastructure
for Psychometric Modeling","Version":"0.4-0"},"psychotree":{"Author":"Achim Zeileis
[aut, cre],\nCarolin Strobl [aut],\nFlorian Wickelmaier [aut],\nBasil Abou El-
Komboz [aut],\nJulia Kopf [aut]","Depends":"R (>= 2.15.0), partykit (>= 0.8-4),
psychotools (>= 0.4-0)","Description":"Recursive partitioning based on psychometric
models,\nemploying the general MOB algorithm (from package partykit) to
obtain\nBradley-Terry trees, Rasch trees, rating scale and partial credit trees,
and\nMPT trees.","Imports":"graphics, grid, stats, Formula","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"psychotree","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"colorspace, strucchange","Title":"Recursive
Partitioning Based on Psychometric Models","Version":"0.15-0"},"psyphy":
{"Author":"Kenneth Knoblauch","Depends":"R (>= 3.0), stats,
graphics","Description":"An assortment of functions that could be useful in
analyzing data from psychophysical experiments. It includes functions for
calculating d' from several different experimental designs, links for m-alternative
forced-choice (mafc) data to be used with the binomial family in glm (and possibly
other contexts) and self-Start functions for estimating gamma values for CRT screen
calibrations.","License":"GPL","NeedsCompilation":"no","Package":"psyphy","Reposito
ry":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"MASS, nlme,
lattice","Title":"Functions for analyzing psychophysical data in R","Version":"0.1-
9"},"psytabs":{"Author":"Johannes Beller, Soeren Kliem","Depends":"psych, plyr,
rtf, R2HTML, mokken, lavaan, semTools","Description":"Psytabs produces well-
formatted tables in .rtf or .html,\nwhich largely conform to \"psychological
style\".","License":"GPL-
2","NeedsCompilation":"no","Package":"psytabs","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Produce well-formatted tables for psychological
research","Version":"0.5"},"ptinpoly":{"Author":"Jose M. Maisog, Yuan Wang, George
Luta, Jianfei Liu","Depends":"R (>= 2.10), misc3d","Description":"Function 'pip3d'
tests whether a point in 3D space is\nwithin, exactly on, or outside an enclosed
surface defined by a triangular mesh.\nFunction 'pip2d' tests whether a point in 2D
space is within, exactly on, or outside a polygon.","License":"GPL-
2","NeedsCompilation":"yes","Package":"ptinpoly","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"rgl,
geometry","Title":"Point-In-Polyhedron Test (2D and
3D)","URL":"http:\/\/ptinpoly.pbworks.com","Version":"2.4"},"ptw":{"Author":"Jan
Gerretzen <j.gerretzen@science.ru.nl>, Paul Eilers\n<p.eilers@erasmusmc.nl>, Hans
Wouters, Tom Bloemberg\n<t.bloemberg@science.ru.nl>, Ron Wehrens
<ron.wehrens@gmail.com>","Description":"Parametric Time Warping aligns patterns,
i.e. it aims to\nput corresponding features at the same locations. The
algorithm\nsearches for an optimal polynomial describing the warping. It\nis
possible to align one sample to a reference, several samples\nto the same
reference, or several samples to several\nreferences. One can choose between
calculating individual\nwarpings, or one global warping for a set of samples and
one\nreference. Two optimization criteria are implemented: RMS (Root\nMean Square
error) and WCC (Weighted Cross Correlation). Both\nwarping of peak profiles and of
peak lists are supported.","Imports":"nloptr, graphics, grDevices,
2)","NeedsCompilation":"yes","Package":"ptw","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Parametric Time Warping","Version":"1.9-11"},"ptycho":
{"Author":"Laurel Stell and Chiara Sabatti","Depends":"R (>=
3.0.0)","Description":"\nBayesian variable selection for linear regression models
using hierarchical\npriors. There is a prior that combines information across
responses and one\nthat combines information across covariates, as well as a
standard spike and\nslab prior for comparison. An MCMC samples from the marginal
posterior\ndistribution for the 0-1 variables indicating if each covariate belongs
to the\nmodel for each response.","Imports":"coda, plyr, reshape2","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"ptycho","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"foreach, doRNG","Title":"Bayesian Variable Selection
with Hierarchical
Priors","URL":"web.stanford.edu\/~lstell\/ptycho\/","Version":"1.1-
4"},"pubmed.mineR":{"Author":"Jyoti Rani, S.Ramachandran, Ab Rauf
Shah","Depends":"R (>= 2.10), methods","Description":"Text mining of PubMed
Abstracts (text and XML) from
http:\/\/www.ncbi.nlm.nih.gov\/pubmed.","Imports":"RCurl, XML, boot,
R2HTML","License":"GPL-
3","NeedsCompilation":"no","Package":"pubmed.mineR","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Text Mining of PubMed
Abstracts","Version":"1.0.5"},"pubprint":{"Author":"Rudolf Siegel [aut,
cre]","Depends":"R (>= 3.0.2)","Description":"Takes the output of statistical tests
and transforms it in a publish-friendly pattern. Currently only APA style is
supported with output to HTML, LaTeX, Markdown and plain text. It is easily
extendable and can be used well with
'knitr'.","Imports":"stringr","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"pubprint","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"knitr, testthat","Title":"Printing Results of
Statistical Computing in a Publishable
Way","URL":"https:\/\/bitbucket.org\/mutluyum\/pubprint\/","Version":"0.1.1"},"pull
word":{"Author":"Tong He <hetong007@gmail.com>","Depends":"R (>=
3.0.2),RCurl","Description":"R interface to pullword service for Natural Language
Processing\nin Chinese. It enables users to extract valuable words from text by
deep learning models.\nFor more details please visit the official site (in Chinese)
http:\/\/pullword.com\/.","License":"LGPL","NeedsCompilation":"yes","Package":"pull
word","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"R Interface to
Pullword Service","Version":"0.1"},"pumilioR":{"Author":"Luis J. Villanueva-
Rivera","Depends":"R(>= 2.14.0), XML, RCurl","Description":"R package to query and
get data out of a Pumilio sound archive system
(http:\/\/ljvillanueva.github.io\/pumilio\/).","License":"GPL-
3","NeedsCompilation":"no","Package":"pumilioR","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr","Title":"Pumilio in
R","URL":"http:\/\/ljvillanueva.github.io\/pumilioR\/","Version":"1.3"},"purge":
{"Author":"Marc Maier [cre],\nChaoqun Jia [ctb],\nMassMutual Advanced Analytics
[aut] (http:\/\/datascience.massmutual.com)","Description":"Enables the removal of
training data from fitted R models while\nretaining predict functionality. The
purged models are more portable as their\nmemory footprints do not scale with the
training sample size.","Imports":"methods","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"purge","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat, survival, lme4 (>= 1.1-8), ranger,
randomForest,\nrpart","Title":"Purge Training Data from
Models","Version":"0.2.0"},"purrr":{"Author":"Hadley Wickham [aut, cre],\nLionel
Henry [ctb],\nRStudio [cph]","Description":"Make your pure functions purr with the
'purrr' package. This\npackage completes R's functional programming tools with
missing features\npresent in other programming languages.","Imports":"magrittr (>=
1.5), dplyr (>= 0.4.3), Rcpp, lazyeval","License":"GPL-3 | file
LICENSE","NeedsCompilation":"yes","Package":"purrr","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat, covr","Title":"Functional Programming
Tools","URL":"https:\/\/github.com\/hadley\/purrr","Version":"0.2.1"},"pushoverr":
{"Author":"Brian Connelly [aut, cre]","Depends":"R (>= 3.0.0)","Description":"A
package for sending push notifications to mobile devices (iOS and\nAndroid) and the
desktop using Pushover","Imports":"httr, methods","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"pushoverr","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Send push notifications using
Pushover","URL":"https:\/\/github.com\/briandconnelly\/pushoverr","Version":"0.1.4"
},"pvar":{"Author":"Vygantas Butkus","Description":"The calculation of p-variation
of the finite sample data","Imports":"Rcpp (>= 0.11.1)","License":"GPL-
2","NeedsCompilation":"yes","Package":"pvar","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"e1071, testthat, knitr, formatR","Title":"Calculation and
Application of p-variation","Version":"2.2"},"pvclass":{"Author":"Niki Zumbrunnen
<niki.zumbrunnen@gmail.com>,\nLutz Duembgen
<lutz.duembgen@stat.unibe.ch>.","Description":"Computes nonparametric p-values for
the potential class\nmemberships of new observations as well as cross-validated\np-
values for the training data. The p-values are based on\npermutation tests applied
to an estimated Bayesian likelihood\nratio, using a plug-in statistic for the
Gaussian model, 'k\nnearest neighbors', 'weighted nearest neighbors' or\n'penalized
logistic regression'.\nAdditionally, it provides graphical displays and
quantitative\nanalyses of the p-values.","Imports":"Matrix","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pvclass","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"P-Values for Classification","Version":"1.3"},"pvclust":
{"Author":"Ryota Suzuki <suzuki@ef-prime.com>, Hidetoshi
Shimodaira\n<shimo@sigmath.es.osaka-u.ac.jp>","Depends":"R (>=
2.10.0)","Description":"An implementation of multiscale bootstrap resampling
for\nassessing the uncertainty in hierarchical cluster analysis.\nIt provides AU
(approximately unbiased) p-value as well as\nBP (bootstrap probability) value for
each cluster in a dendrogram.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pvclust","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"MASS, parallel","Title":"Hierarchical Clustering with
P-Values via Multiscale
Bootstrap\nResampling","URL":"http:\/\/www.sigmath.es.osaka-u.ac.jp\/shimo-
lab\/prog\/pvclust\/","Version":"2.0-0"},"pvrank":{"Author":"Amerise I. L.
<ilaria.amerise@unical.it>, Marozzi M. <marco.marozzi@unical.it>, Tarsitano A.
<agostino.tarsitano@unical.it>","Depends":"R(>= 3.0.1), EnvStats,
Rmpfr","Description":"Computes rank correlations and their p-values with various
options for tied ranks.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"pvrank","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Rank Correlations","Version":"1.1"},"pvsR":
{"Author":"Ulrich Matter","Depends":"R (>= 3.0)","Description":"The pvsR package
facilitates data retrieval from Project\nVote Smart's rich online data base on US
politics via the Project Vote\nSmart application programming interface (PVS API).
The functions in this\npackage cover most PVS API classes and methods and return
the\nrequested data in a data frame.","Imports":"XML, nnet, httr","License":"GPL-
2","NeedsCompilation":"no","Package":"pvsR","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"An R package to interact with the Project Vote Smart API
for\nscientific research","Version":"0.3"},"pweight":{"Author":"Edgar Dobriban
[aut, cre],\nKristen Fortney [aut]","Description":"This R package contains open
source implementations\nof several p-value weighting methods, including Spjotvoll,
exponential\nand Bayes weights. These are methods for improving power in multiple
testing\nvia the use of prior information.","Imports":"qqman","License":"GPL-
3","NeedsCompilation":"no","Package":"pweight","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr","Title":"P-Value
Weighting","URL":"https:\/\/github.com\/dobriban\/pweight","Version":"0.0.1"},"pwr"
:{"Author":"Stephane Champely [aut],\nClaus Ekstrom [ctb],\nPeter Dalgaard
[ctb],\nJeffrey Gill [ctb],\nJan Wunder [ctb],\nHelios De Rosario
[cre]","Description":"Power analysis functions along the lines of Cohen
(1988).","Imports":"stats","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"pwr","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Basic Functions for Power
Analysis","URL":"https:\/\/github.com\/heliosdrm\/pwr","Version":"1.1-
3"},"pwrRasch":{"Author":"Takuya Yanagida [cre, aut],\nJan Steinfeld [aut],\nThomas
Kiefer [ctb]","Depends":"R (>= 3.0)","Description":"Statistical power simulation
for testing the
Rasch Model based on a three-way analysis of variance design with mixed
classification.","License":"GPL-
3","NeedsCompilation":"no","Package":"pwrRasch","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"eRm, roxygen2, utils, testthat","Title":"Statistical
Power Simulation for Testing the Rasch Model","Version":"0.1-2"},"pwt":
{"Author":"Achim Zeileis [aut, cre],\nGuan Yang [aut]","Depends":"R (>=
2.10.0)","Description":"The Penn World Table provides purchasing power parity
and\nnational income accounts converted to international prices for\n189 countries
for some or all of the years 1950-2010.","License":"GPL-
2","NeedsCompilation":"no","Package":"pwt","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Penn World Table (Versions 5.6, 6.x, 7.x)","Version":"7.1-
1"},"pwt8":{"Author":"Achim Zeileis [aut, cre]","Depends":"R (>=
2.10.0)","Description":"The Penn World Table 8.x provides information on relative
levels of\nincome, output, inputs, and productivity for 167 countries\nbetween 1950
and 2011.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"pwt8","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Penn World Table (Version 8.x)","Version":"8.1-0"},"pxR":
{"Author":"Francisco J. Viciana [aut],\nCarlos J. Gil Bellosta [cre, aut],\nOscar
Perpinan Lamigueiro [aut],\nEmilio Torres Manzanera [ctb],\nVicente David Canto
Casasola [ctb],\nJorge Ivan Velez [ctb]","Depends":"stringr, reshape2, RJSONIO,
plyr","Description":"The pxR package provides a set of functions for reading and
writing PC-Axis files, used by different statistical organizations around the globe
for data dissemination.","License":"GPL-
3","NeedsCompilation":"no","Package":"pxR","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"PC-Axis with R","URL":"http:\/\/pxr.r-forge.r-
project.org\/","Version":"0.40.0"},"pxweb":{"Author":"Mans Magnusson, Leo Lahti,
Love Hansson","Depends":"methods","Description":"Generic interface for the PX-
Web\/PC-Axis API. The PX-Web\/PC-Axis\nAPI is used by organizations such as
Statistics Sweden and Statistics\nFinland to disseminate data. The R package can
interact with all\nPX-Web\/PC-Axis APIs to fetch information about the data
hierarchy, extract\nmetadata and extract and parse statistics to R data.frame
format. PX-Web is\na solution to disseminate PC-Axis data files in dynamic tables
on the web.\nSince 2013 PX-Web contains an API to disseminate PC-Axis
files.","Imports":"data.table, plyr, stringr, RJSONIO, httr (>=
1.1)","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"pxweb","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat, ggplot2, knitr, rmarkdown","Title":"R
Interface to the PX-Web\/PC-Axis
API","URL":"https:\/\/github.com\/rOpenGov\/pxweb\/","Version":"0.6.0"},"pycno":
{"Author":"Chris Brunsdon","Depends":"stats, sp, maptools,
rgeos","Description":"Given a SpatialPolygonsDataFrame and a set of populations for
each polygon,\ncompute a population density estimate based on Tobler's
pycnophylactic interpolation\nalgorithm. The result is a
SpatialGridDataFrame.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pycno","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Pycnophylactic Interpolation","Version":"1.2"},"pyramid":
{"Author":"Minato Nakazawa <minato-nakazawa@umin.net>","Depends":"R (>=
2.2.0)","Description":"Drawing population pyramid using (1) data.frame or (2)
vectors.\nThe former is named as pyramid() and the latter pyramids(), as
wrapper\nfunction of pyramid(). pyramidf() is the function to draw
population\npyramid within the specified frame.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"pyramid","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Functions to draw population
pyramid","URL":"http:\/\/minato.sip21c.org\/swtips\/R.html#PYRAMID","Version":"1.4"
},"pystr":{"Author":"Nicole White","Description":"String operations the Python way
- a package for those of us who miss Python's string methods while we're working in
R.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"pystr","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat","Title":"Python String Methods in
R","URL":"https:\/\/github.com\/nicolewhite\/pystr","Version":"1.0.0"},"qLearn":
{"Author":"Jingyi Xin, Bibhas Chakraborty, and Eric B.
Laber","Description":"Functions to implement Q-learning for estimating
optimal\ndynamic treatment regimes from two stage sequentially\nrandomized trials,
and to perform inference via m-out-of-n\nbootstrap for parameters indexing the
optimal regime.","License":"GPL-
2","NeedsCompilation":"no","Package":"qLearn","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Estimation and inference for Q-
learning","Version":"1.0"},"qPCR.CT":{"Author":"Yuzhuo Pan, Xiaoyu Yan, Junxin
Li","Depends":"RColorBrewer","Description":"use 2^ddCT methods calculate the
relative gene expression,\ndata file can be export from bio-rad qpcr machine, the
results\ncan be plot with errorbar. ver 1.1 add GroupPlot function, can\nplot all
the groups once.","License":"GPL-
2","NeedsCompilation":"no","Package":"qPCR.CT","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"qPCR data analysis and plot
package","Version":"1.1"},"qVarSel":{"Author":"Stefano
Benati","Depends":"lpSolveAPI","Description":"For a given data matrix A and cluster
centers\/prototypes collected in the matrix P, the functions described here select
a subset of statistic variables Q that mostly explains\/justifies P as prototypes.
The functions are useful to reduce the data dimension for classification and to
discard masking variables for clustering.","Imports":"Rcpp (>=
2","NeedsCompilation":"yes","Package":"qVarSel","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"clusterGeneration, mclust","Title":"Variables
Selection for Clustering and Classification","Version":"1.0"},"qap":
{"Author":"Michael Hahsler [aut, cre, cph],\nFranz Rendl [ctb,
cph]","Description":"Implements heuristics for the Quadratic Assignment Problem
(QAP). Currently only a simulated annealing heuristic is
available.","License":"GPL-
3","NeedsCompilation":"yes","Package":"qap","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Heuristics for the Quadratic Assignment Problem
(QAP)","Version":"0.1-0"},"qcc":{"Author":"Luca Scrucca
<luca@stat.unipg.it>","Depends":"R (>= 2.11)","Description":"Shewhart quality
control charts for continuous, attribute and count data. Cusum and EWMA charts.
Operating characteristic curves. Process capability analysis. Pareto chart and
cause-and-effect chart. Multivariate control
charts.","Imports":"MASS","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"qcc","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Quality Control Charts","Version":"2.6"},"qclust":
{"Author":"Yichen Qin, Carey E. Priebe","Depends":"mclust,
mvtnorm","Description":"Robust estimation of Gaussian mixture models fitted by
modified EM algorithm, robust clustering and classification.","License":"GPL-
2","NeedsCompilation":"no","Package":"qclust","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Robust Estimation of Gaussian Mixture
Models","URL":"http:\/\/homepages.uc.edu\/~qinyn\/qclust\/","Version":"1.0"},"qcr":
{"Author":"Miguel Flores <mflores@outlook.com>,\nSalvador Naya <salva@udc.es>,
Ruben Fernandez <ruben.fcasal@udc.es>","Depends":"R (>= 1.8.0),
qcc","Description":"This package allows to generate Shewhart-type charts and to
obtain\nnumerical results of interest to the quality control of a
process\n(involving continuous, attribute or count data).\nThis package provides
basic functionality for univariable and multivariable\nquality control analysis,
including: xbar, xbar-one, S, R, ewna, cusum,\nmewna, mcusum and T2
charts.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"qcr","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"IQCC","Title":"Quality control and
reliability","Version":"0.1-18"},"qdap":{"Author":"Bryan Goodrich [ctb],\nDason
Kurkiewicz [ctb],\nTyler Rinker [aut, cre]","Depends":"R (>= 3.1.0),
qdapDictionaries (>= 1.0.2), qdapRegex (>=\n0.1.2), qdapTools (>= 1.3.1),
RColorBrewer","Description":"Automates many of the tasks associated with
quantitative\ndiscourse analysis of transcripts containing discourse\nincluding
frequency counts of sentence types, words, sentences,\nturns of talk, syllables and
other assorted analysis tasks. The\npackage provides parsing tools for preparing
transcript data.\nMany functions enable the user to aggregate data by any
number\nof grouping variables, providing analysis and seamless\nintegration with
other R packages that undertake higher level\nanalysis and visualization of text.
This affords the user a\nmore efficient and targeted analysis. 'qdap' is designed
for\ntranscript analysis, however, many functions are applicable to\nother areas of
Text Mining\/Natural Language Processing.","Imports":"chron, dplyr (>= 0.3), gdata,
gender (>= 0.5.1), ggplot2 (>=\n0.9.3.1), grid, gridExtra, igraph, methods, NLP,
openNLP (>=\n0.2-1), parallel, plotrix, RCurl, reports, reshape2,
scales,\nstringdist, tidyr, tm (>= 0.6.2), tools, venneuler, wordcloud,\nxlsx,
XML","License":"GPL-
2","NeedsCompilation":"no","Package":"qdap","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"koRpus, knitr, lda, proxy, stringi, SnowballC,
testthat","Title":"Bridging the Gap Between Qualitative Data and
Quantitative\nAnalysis","URL":"http:\/\/trinker.github.com\/qdap\/","Version":"2.2.
4"},"qdapDictionaries":{"Author":"Tyler Rinker","Depends":"R (>=
3.0.0)","Description":"A collection of dictionaries and word lists for use
with\nthe 'qdap' package.","License":"GPL-
2","NeedsCompilation":"no","Package":"qdapDictionaries","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Dictionaries and Word
Lists for the 'qdap'
Package","URL":"http:\/\/trinker.github.com\/qdapDictionaries\/","Version":"1.0.6"}
,"qdapRegex":{"Author":"Jason Gray [ctb],\nTyler Rinker [aut, cre]","Depends":"R
(>= 3.1.0)","Description":"A collection of regular expression tools associated with
the 'qdap' package\nthat may be useful outside of the context of discourse
analysis. Tools include\nremoval\/extraction\/replacement of abbreviations, dates,
dollar amounts, email\naddresses, hash tags, numbers, percentages, citations,
person tags, phone\nnumbers, times, and zip codes.","Imports":"stringi (>= 0.5-
5)","License":"GPL-
2","NeedsCompilation":"no","Package":"qdapRegex","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat","Title":"Regular Expression Removal,
Extraction, and Replacement
Tools","URL":"http:\/\/trinker.github.com\/qdapRegex\/","Version":"0.6.0"},"qdapToo
ls":{"Author":"Bryan Goodrich [ctb],\nDason Kurkiewicz [ctb],\nKirill Muller
[ctb],\nTyler Rinker [aut, cre]","Depends":"R (>= 3.0.0)","Description":"A
collection of tools associated with the 'qdap' package\nthat may be useful outside
of the context of text analysis.","Imports":"chron, data.table (>= 1.9.6), methods,
RCurl, XML","License":"GPL-
2","NeedsCompilation":"no","Package":"qdapTools","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat","Title":"Tools for the 'qdap'
Package","URL":"http:\/\/trinker.github.com\/qdapTools\/","Version":"1.3.1"},"qdm":
{"Author":"Nora Umbach [aut, cre],\nFlorian Wickelmaier [aut]","Depends":"R (>=
3.1.0), stats, graphics","Description":"This package provides different
specifications of a Quadrilateral\nDissimilarity Model which can be used to fit
same-different judgments\nin order to get a predicted matrix that satisfies regular
minimality\n[Colonius & Dzhafarov, 2006, Measurement and representations
of\nsensations, Erlbaum]. From such a matrix, Fechnerian distances can
be\ncomputed.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"qdm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Fitting a Quadrilateral Dissimilarity Model to Same-
Different\nJudgments","Version":"0.1-0"},"qgraph":{"Author":"Sacha Epskamp, Giulio
Costantini, Angelique O. J. Cramer, Lourens J. Waldorp, Verena D. Schmittmann and
Denny Borsboom","Depends":"R (>= 3.0.0)","Description":"The qgraph package can be
used to visualize data as networks as well as provides an interface for visualizing
weighted graphical models.","Imports":"methods, grDevices, psych, ellipse, lavaan,
sem, plyr, Hmisc,\nigraph, jpeg, png, colorspace, Matrix, sna, corpcor,
reshape2,\nggplot2, glasso, huge, fdrtool, d3Network, ggm, gtools","License":"GPL-
2","NeedsCompilation":"yes","Package":"qgraph","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"RSVGTipsDevice, sendplot","Title":"Graph Plotting
Methods, Psychometric Data Visualization and\nGraphical Model
Estimation","URL":"http:\/\/sachaepskamp.com\/qgraph","Version":"1.3.2"},"qgtools":
{"Author":"Jixiang Wu (South Dakota State University), Johnie N. Jenkins and Jack
C. McCarty (USDA-ARS)","Depends":"stats,utils,Matrix, MASS","Description":"Two
linear mixed model approaches: REML(restricted maximum likelihood) and MINQUE
(minimum norm quadratic unbiased estimation) approaches and several resampling
techniques are integrated for various quantitative genetics analyses. With these
two types of approaches, various unbalanced data structures, missing data, and any
irregular genetic mating designs can be analyzed and statistically tested. This
package also offers fast computations for many large data sets. Other functions
will be added to this R tool in the future.","License":"GPL-
2","NeedsCompilation":"no","Package":"qgtools","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Tools for Quantitative Genetics Data
Analyses","Version":"1.0"},"qicharts":{"Author":"Jacob Anhoej [aut, cre],\nTimo
Roeder [ctb]","Depends":"R (>= 3.0.0)","Description":"Functions for making run
charts and basic Shewhart control\ncharts for measure and count data.\nThe main
function, qic(), creates run and control charts and has a\nsimple interface with a
rich set of options to control data analysis\nand plotting, including options for
automatic data aggregation by\nsubgroups, easy analysis of before-and-after data,
exclusion of one\nor more data points from analysis, and splitting charts
into\nsequential time periods.\nMissing values and empty subgroups are handled
gracefully.","Imports":"lattice, latticeExtra, graphics, grDevices, stats,
scales,\nggplot2 (>= 2.0.0), ggrepel","License":"GPL-
3","NeedsCompilation":"no","Package":"qicharts","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr","Title":"Quality Improvement
Charts","Version":"0.5.1"},"qiimer":{"Author":"Kyle Bittinger
<kylebittinger@gmail.com>","Description":"Open QIIME output files in R, compute
statistics, and\ncreate plots from the data.","Imports":"grDevices, pheatmap,
2)","NeedsCompilation":"no","Package":"qiimer","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat, biom","Title":"Work with QIIME Output Files
in R","URL":"http:\/\/www.r-project.org","Version":"0.9.4"},"qlcData":
{"Author":"Michael Cyosuw","Description":"This is a collection of functions to
read, recode, and transcode data.","Imports":"stringi (>= 0.2-5), yaml (>=
3","NeedsCompilation":"no","Package":"qlcData","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr","Title":"Processing Data for Quantitative
Language Comparison (QLC)","Version":"0.1.0"},"qlcMatrix":{"Author":"Michael
Cysouw","Depends":"Matrix (>= 1.1-0), R (>= 2.10), slam (>= 0.1-
32)","Description":"Extension of the functionality of the Matrix package for using
sparse matrices. Some of the functions are very general, while other are highly
specific for special data format as used for quantitative language comparison
(QLC).","Imports":"methods","License":"GPL-
3","NeedsCompilation":"no","Package":"qlcMatrix","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"MASS, knitr","Title":"Utility Sparse Matrix Functions
for Quantitative Language\nComparison","Version":"0.9.5"},"qlcVisualize":
{"Author":"Michael Cysouw","Description":"Collection of visualizations as used in
quantitative language comparison.","Imports":"fields, MASS, qlcMatrix, seriation,
spatstat, raster, maps,\nmapdata, maptools, mapplots, methods, sp,
alphahull","License":"ACM | file
LICENSE","NeedsCompilation":"no","Package":"qlcVisualize","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Visualization for Quantitative Language
Comparison (QLC)","Version":"0.1.0"},"qmap":{"Author":"Lukas
Gudmundsson","Depends":"R (>= 2.8.0), fitdistrplus","Description":"Empirical
adjustment of the distribution of variables originating from (regional) climate
model simulations using quantile mapping.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"qmap","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Statistical transformations for post-processing climate
model\noutput","Version":"1.0-3"},"qmethod":{"Author":"Aiora Zabala [aut, cre]
(Main author),\nMaximilian Held [aut] (Author of additional data management
functions)","Description":"Analysis of Q methodology, used to identify distinct
perspectives existing within a group.\nThis methodology is used across social,
health and environmental sciences to understand diversity of attitudes, discourses,
or decision-making styles (for more information, see http:\/\/qmethod.org).\nA
single function runs the full analysis. Each step can be run separately using the
corresponding functions: for automatic flagging of Q-sorts (manual flagging is
optional), for statement scores, for distinguishing and consensus statements, and
for general characteristics of the factors.\nAdditional functions are available to
import and export data, to print and plot, to import raw data from individual *.CSV
files, and to make printable cards.\nThe package also offers functions to print Q
cards and to generate Q distributions for study administration.\nThe package uses
principal components and it allows manual or automatic flagging, a number of
mathematical methods for rotation, and a number of correlation coefficients for the
initial correlation matrix.\nSee further details in the package documentation, and
in the web pages below, which include a cookbook, guidelines for more advanced
analysis (how to perform manual flagging or change the sign of factors), data
management, and a beta graphical user interface for online and offline
use.","Imports":"methods, psych, GPArotation, tools, digest, knitr,
xtable,\nMCMCpack","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"qmethod","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Analysis of Subjective Perspectives Using Q
Methodology","URL":"https:\/\/github.com\/aiorazabala\/qmethod,\nhttps:\/\/github.c
om\/aiorazabala\/qmethod\/wiki","Version":"1.4.1"},"qmrparser":{"Author":"Juan Gea
Rosat, Ramon MartÃnez CoscollÃ .","Depends":"R (>= 2.11.1)","Description":"Basic
functions for building parsers, with an application to PC-AXIS format
3)","NeedsCompilation":"no","Package":"qmrparser","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"RUnit","Title":"Parser combinator in
R","Version":"0.1.5"},"qpcR":{"Author":"Andrej-Nikolai Spiess <a.spiess@uke.uni-
hamburg.de>","Depends":"R (>= 2.13.0), MASS, minpack.lm, rgl, robustbase,
Matrix","Description":"Model fitting, optimal model selection and calculation of
various features that are essential in the analysis of quantitative real-time
polymerase chain reaction (qPCR).","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"qpcR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Modelling and analysis of real-time PCR
data","Version":"1.4-0"},"qqman":{"Author":"Stephen
Turner <vustephen@gmail.com>","Depends":"R (>= 3.0.0)","Description":"Q-Q and
manhattan plots for GWAS data","License":"GPL-
3","NeedsCompilation":"no","Package":"qqman","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr","Title":"Q-Q and manhattan plots for GWAS
data","Version":"0.1.2"},"qqtest":{"Author":"Wayne Oldford [aut, cre]","Depends":"R
(>= 2.10.0)","Description":"Provides the function qqtest which incorporates
uncertainty in its\nqqplot display(s) so that the user might have a better sense of
the\nevidence against the specified distributional hypothesis. qqtest draws
a\nquantile quantile plot for visually assessing whether the data come from a\ntest
distribution that has been defined in one of many ways. The vertical\naxis plots
the data quantiles, the horizontal those of a test distribution.\nThe default
behaviour generates 1000 samples from the test distribution and\noverlays the plot
with shaded pointwise interval estimates for the ordered\nquantiles from the test
distribution. A small number of independently\ngenerated exemplar quantile plots
can also be overlaid. Both the interval\nestimates and the exemplars provide
different comparative information to\nassess the evidence provided by the qqplot
for or against the hypothesis\nthat the data come from the test distribution
(default is normal or\ngaussian). Finally, a visual test of significance (a lineup
plot) can also\nbe displayed to test the null hypothesis that the data come from
the test\ndistribution.","Imports":"grDevices, robust, stats","License":"GPL-
3","NeedsCompilation":"no","Package":"qqtest","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Self Calibrating Quantile-Quantile Plots for Visual
Testing","Version":"1.1.1"},"qrLMM":{"Author":"Christian E. Galarza
<cgalarza88@gmail.com> and Victor H. Lachos
<hlachos@ime.unicamp.br>","Depends":"nlme","Description":"Quantile regression (QR)
for Linear\nMixed-Effects Models via the asymmetric Laplace distribution (ALD).\nIt
uses the Stochastic Approximation of the EM (SAEM) algorithm for\nderiving exact
maximum likelihood estimates and full inference results\nfor the fixed-effects and
variance components.\nIt also provides graphical summaries for assessing the
algorithm\nconvergence and fitting results.","Imports":"matrixcalc, mvtnorm, ghyp,
quantreg, psych, tcltk","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"qrLMM","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Quantile Regression for Linear Mixed-Effects
Models","Version":"1.1"},"qrNLMM":{"Author":"Christian E. Galarza
<cgalarza88@gmail.com> and Victor H. Lachos
<hlachos@ime.unicamp.br>","Description":"Quantile regression (QR) for
Nonlinear\nMixed-Effects Models via the asymmetric Laplace distribution (ALD).\nIt
uses the Stochastic Approximation of the EM (SAEM) algorithm for\nderiving exact
maximum likelihood estimates and full inference results\nfor the fixed-effects and
variance components.\nIt also provides graphical summaries for assessing the
algorithm\nconvergence and fitting results.","Imports":"matrixcalc, mvtnorm, ghyp,
quantreg, psych, tcltk, ald","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"qrNLMM","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Quantile Regression for Nonlinear Mixed-Effects
Models","Version":"1.0"},"qrage":{"Author":"\"Shingo Yamamoto (gloops, Inc.)\"
[aut, cre],\nRStudio, Inc. [cph],\nMichael Bostock [ctb, cph] (D3.js
library),\njQuery Foundation [cph] (jQuery library and jQuery UI library),\njQuery
contributors [ctb, cph] (jQuery library; authors listed in
inst\/htmlwidgets\/lib\/jquery\/jquery-AUTHORS.txt),\njQuery UI contributors [ctb,
cph] (jQuery UI library; authors listed in inst\/htmlwidgets\/lib\/jquery-
ui\/AUTHORS.txt)","Description":"Tools that create D3 JavaScript force directed
graph from R. D3 JavaScript was created by Michael Bostock. See http:\/\/d3js.org\/
and, more specifically for Force Directed Graph
https:\/\/github.com\/mbostock\/d3\/wiki\/Force-
Layout.","Imports":"htmlwidgets","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"qrage","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"shiny","Title":"Tools that Create D3 JavaScript
Force Directed Graph from R","Version":"1.0"},"qrcm":{"Author":"Paolo Frumento
<paolo.frumento@ki.se>","Depends":"survival, pch","Description":"Parametric
modeling of quantile regression coefficient functions.","Imports":"stats, utils,
2","NeedsCompilation":"no","Package":"qrcm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Quantile Regression Coefficients
Modeling","Version":"1.0"},"qrcode":{"Author":"Victor Teh","Depends":"R (>=
3.0.0)","Description":"Create QRcode in R.","Imports":"R.utils, stringr, stats,
3","NeedsCompilation":"no","Package":"qrcode","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"QRcode Generator for R","Version":"0.1.1"},"qrfactor":
{"Author":"George Owusu <owusugeorge@ug.edu.gh>","Depends":"R (>= 2.10),
mvoutlier,mgraph,pvclust,cluster,maptools","Description":"The qrfactor package
simultaneously runs both Q and R mode factor analyses. The package contains only
one function called qrfactor() that can perform PCA, R-mode Factor Analysis, Q-mode
Factor Analysis, Simultaneous R- and Q-mode Factor Analysis, Principal Coordinate
Analysis, as wells as Multidimensional Scaling (MDS). Loadings and scores can
easily be computed from the simulation.The plot.qrfactor() function offers several
annotated biplots for all possible combinations of eigenvectors, loadings, and
scores. Input data includes shapefiles, tables and dataframe","License":"GPL-
2","NeedsCompilation":"no","Package":"qrfactor","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"MASS","Title":"Simultaneous simulation of Q and R mode
factor analyses with\nSpatial
data","URL":"http:\/\/www.openictghana.com\/qrfactor","Version":"1.4"},"qrjoint":
{"Author":"Surya Tokdar <tokdar@stat.duke.edu>","Depends":"R (>= 2.6), stats,
graphics, grDevices, quantreg","Description":"Joint estimation of quantile specific
intercept and slope parameters in a linear regression setting.","Imports":"splines,
coda, Matrix, kernlab","License":"GPL-
2","NeedsCompilation":"yes","Package":"qrjoint","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Joint Estimation in Linear Quantile
Regression","Version":"1.0-0"},"qrmtools":{"Author":"Marius Hofert [aut, cre], Kurt
Hornik [aut]","Depends":"R (>= 3.2.0)","Description":"Functions and data sets for
reproducing selected results from\nthe book \"Quantitative Risk Management:
Concepts, Techniques and Tools\".\nFurthermore, new developments and auxiliary
functions for Quantitative\nRisk Management practice.","Imports":"quantmod, Quandl,
zoo, methods, grDevices, stats","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"qrmtools","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"combinat, copula, knitr, mvtnorm, QRM, rugarch,
sfsmisc","Title":"Tools for Quantitative Risk Management","Version":"0.0-
5"},"qrng":{"Author":"Marius Hofert [aut, cre], Christiane Lemieux
[aut]","Depends":"R (>= 3.0.0)","Description":"Functionality for generating
(randomized) quasi-random numbers in\nhigh dimensions.","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"qrng","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"(Randomized) Quasi-Random Number Generators","Version":"0.0-
2"},"qrnn":{"Author":"Alex J. Cannon","Description":"Fit a quantile regression
neural network with optional\nleft censoring using a variant of the finite
smoothing\nalgorithm.","License":"GPL-
2","NeedsCompilation":"no","Package":"qrnn","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Quantile Regression Neural
Network","Version":"1.1.3"},"qtbase":{"Author":"Michael Lawrence, Deepayan
Sarkar","Depends":"R (>= 2.10.0), methods, utils","Description":"Dynamic bindings
to the Qt library for calling Qt\nmethods and extending Qt classes from R. Other
packages build upon 'qtbase'\nto provide special-purpose high-level interfaces to
specific parts of Qt.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"qtbase","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Interface Between R and
Qt","URL":"http:\/\/qtinterfaces.r-forge.r-project.org","Version":"1.0.11"},"qte":
{"Author":"Brantly Callaway","Depends":"R (>= 2.10)","Description":"Provides
several methods for computing the Quantile Treatment Effect (QTE) and Quantile
Treatment Effect on the Treated (QTET). The main cases covered are (i) Treatment
is randomly assigned, (ii) Treatment is as good as randomly assigned after
conditioning on some covariates (also called conditional independence or selection
on observables), (iii) Identification is based on a Difference in Differences
assumption (several varieties are available in the package).","License":"GPL-
2","NeedsCompilation":"no","Package":"qte","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Quantile Treatment Effects","Version":"1.0.1"},"qtl":
{"Author":"Karl W Broman <kbroman@biostat.wisc.edu> and Hao Wu, with\nideas from
Gary Churchill and Saunak Sen and contributions from\nDanny Arends, Robert Corty,
Timothee Flutre, Ritsert Jansen, Pjotr\nPrins, Lars Ronnegard, Rohan Shah, Laura
Shannon, Quoc Tran, Aaron\nWolen, and Brian Yandell","Depends":"R (>=
2.14.0)","Description":"Analysis of experimental crosses to identify genes\n(called
quantitative trait loci, QTLs) contributing to variation in\nquantitative
traits.","Imports":"parallel, graphics, stats, utils, grDevices","License":"GPL-
3","NeedsCompilation":"yes","Package":"qtl","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"testthat","Title":"Tools for Analyzing QTL
Experiments","URL":"http:\/\/www.rqtl.org","Version":"1.39-5"},"qtlDesign":
{"Author":"Saunak Sen,
Jaya Satagopan, Karl Broman, and Gary Churchill","Description":"Tools for the
design of QTL
experiments","License":"GPL","NeedsCompilation":"no","Package":"qtlDesign","Reposit
ory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Design of QTL
experiments","URL":"http:\/\/www.biostat.ucsf.edu\/sen\/","Version":"0.941"},"qtlbo
ok":{"Author":"Karl W Broman <kbroman@biostat.wisc.edu>","Depends":"R (>= 2.10.1),
qtl","Description":"Datasets for the book, A Guide to QTL Mapping with
R\/qtl.","License":"GPL-
3","NeedsCompilation":"no","Package":"qtlbook","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Datasets for the R\/qtl
Book","URL":"http:\/\/www.rqtl.org\/book","Version":"0.18-3"},"qtlc":
{"Author":"Ivan D. Pavicevic","Depends":"tiff, rgl, plot3D, graphics, grDevices,
stats, utils","Description":"Densitometric evaluation of the photo-archived
quantitative thin-layer chromatography (TLC) plates.","License":"GPL-
2","NeedsCompilation":"no","Package":"qtlc","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Densitometric Analysis of Thin-Layer Chromatography
Plates","Version":"1.0"},"qtlcharts":{"Author":"Karl W Broman [aut, cre],\nMichael
Bostock [ctb, cph] (d3.js library in htmlwidgets\/lib, http:\/\/d3js.org),\nJustin
Palmer [ctb, cph] (d3.tip library in htmlwidgets\/lib,
https:\/\/github.com\/caged\/d3-tip),\nCynthia Brewer [cph] (ColorBrewer library in
htmlwidgets\/lib, http:\/\/colorbrewer2.org),\nMark Harrower [cph] (ColorBrewer
library in htmlwidgets\/lib, http:\/\/colorbrewer2.org),\nThe Pennsylvania State
University [cph] (ColorBrewer library in
htmlwidgets\/lib,\nhttp:\/\/colorbrewer2.org),\njQuery Foundation [cph] (jQuery
library in htmlwidgets\/lib, http:\/\/jquery.com),\njQuery contributors [ctb]
(jQuery library in htmlwidgets\/lib;
see\nhttps:\/\/github.com\/jquery\/jquery\/blob\/master\/AUTHORS.txt),\njQuery UI
contributors [ctb] (jQuery UI library in htmlwidgets\/lib; see
http:\/\/jqueryui.com\/about)","Depends":"R (>= 2.15)","Description":"Web-based
interactive charts (using D3.js) for the analysis of\nexperimental crosses to
identify genetic loci (quantitative trait\nloci, QTL) contributing to variation in
quantitative traits.","Imports":"qtl (>= 1.30-4), htmlwidgets, jsonlite, graphics,
stats, utils","License":"GPL-3 | file
LICENSE","NeedsCompilation":"no","Package":"qtlcharts","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"htmltools, knitr, devtools, roxygen2,
rmarkdown, testthat","Title":"Interactive Graphics for QTL
Experiments","URL":"http:\/\/kbroman.org\/qtlcharts","Version":"0.5-25"},"qtlhot":
{"Author":"Elias Chaibub Neto <echaibub@hotmail.com> and Brian S Yandell
<byandell@wisc.edu>","Depends":"R (>= 2.10), stats, qtl, lattice, corpcor,
mnormt","Description":"Functions to infer co-mapping trait hotspots and causal
2)","NeedsCompilation":"yes","Package":"qtlhot","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Inference for QTL
Hotspots","URL":"http:\/\/www.stat.wisc.edu\/~yandell\/statgen","Version":"0.9.0"},
"qtlmt":{"Author":"Riyan Cheng <riyan.cheng@anu.edu.au>","Depends":"R (>=
2.10)","Description":"Provides tools for joint analysis of multiple traits in a
backcross (BC) or recombinant inbred lines (RIL) population. It can be used to
select an optimal subset of traits for multiple-trait mapping, analyze multiple
traits via the SURE model, which can associate different QTL with different traits,
and perform multiple-trait composite multiple-interval mapping.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"qtlmt","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Tools for Mapping Multiple Complex Traits","Version":"0.1-
4"},"qtlnet":{"Author":"Elias Chaibub Neto <echaibub@hotmail.com> and Brian S.
yandell <byandell@wisc.edu>","Depends":"R (>= 2.10), qtl, igraph, sem, graph,
pcalg","Description":"Functions to Simultaneously Infer Causal Graphs and Genetic
Architecture","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"qtlnet","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Causal Inference of QTL
Networks","URL":"http:\/\/www.stat.wisc.edu\/~yandell\/sysgen","Version":"1.3.6"},"
qtpaint":{"Author":"Michael Lawrence, Deepayan Sarkar","Depends":"R (>= 2.6.0),
utils, qtbase (>= 0.99.2), methods","Description":"Low-level interface to
functionality in Qt for efficiently drawing\ndynamic graphics and handling basic
user input.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"qtpaint","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Qt-Based Painting
Infrastructure","Version":"0.9.1"},"qtutils":{"Author":"Deepayan
Sarkar","Depends":"R (>= 2.14.0), qtbase","Description":"Miscellaneous Qt-based
tools for R","Imports":"qtbase","License":"LGPL (>=
2)","NeedsCompilation":"yes","Package":"qtutils","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"xtable","Title":"Miscellaneous Qt-based
utilities","URL":"http:\/\/qtinterfaces.r-forge.r-project.org","Version":"0.1-
3"},"quad":{"Author":"Yi-Hui Zhou","Description":"This package gives you the exact
first four permutation moments for the most commonly used quadratic form
statistics, which need not be positive definite. The extension of this work to
quadratic forms greatly expands the utility of density approximations for these
problems, including for high-dimensional applications, where the statistics must be
extreme in order to exceed stringent testing thresholds. Approximate p-values are
obtained by matching the exact moments to the Pearson family of distributions using
the PearsonDS package.","Imports":"PearsonDS","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"quad","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Exact permutation moments of quadratic form
statistics","Version":"1.0"},"quadprog":{"Author":"S original by Berwin A. Turlach
<Berwin.Turlach@gmail.com> R\nport by Andreas Weingessel
<Andreas.Weingessel@ci.tuwien.ac.at>","Depends":"R (>= 2.15.0)","Description":"This
package contains routines and documentation for\nsolving quadratic programming
problems.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"quadprog","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Functions to solve Quadratic Programming
Problems","Version":"1.5-5"},"quadrupen":{"Author":"Julien Chiquet","Depends":"R
(>= 3.0.2), Rcpp, ggplot2, Matrix","Description":"This package fits classical
sparse regression models with\nefficient active set algorithms by solving quadratic
problems. Also\nprovides a few methods for model selection purpose (cross-
validation,\nstability selection).","Imports":"reshape2, methods, scales, grid,
2)","NeedsCompilation":"yes","Package":"quadrupen","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat","Title":"Sparsity by Worst-Case Quadratic
Penalties","Version":"0.2-4"},"qualCI":{"Author":"Konstantin Kashin
<kkashin@fas.harvard.edu>, Adam Glynn <aglynn@emory.edu>, Nahomi Ichino
<nichino@umich.edu>","Depends":"R (>= 2.15.0)","Description":"Exact one-sided p-
values and confidence intervals for an outcome variable defined on an interval
measurement scale with only qualitative and ordinal information
available.","Imports":"combinat","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"qualCI","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Causal Inference with Qualitative and Ordinal Information
on\nOutcomes","Version":"0.1"},"qualV":{"Author":"K. Gerald van den Boogaart [aut,
ths],\nStefanie Rost [aut],\nThomas Petzoldt [aut, ths, cre]","Depends":"R (>=
2.0.0), KernSmooth","Description":"Qualitative methods for the validation of
dynamic models.\nIt contains (i) an orthogonal set of deviance measures for
absolute,\nrelative and ordinal scale and (ii) approaches accounting for
time\nshifts. The first approach transforms time to take time delays and
speed\ndifferences into account. The second divides the time series into\ninterval
units according to their main features and finds the longest\ncommon subsequence
(LCS) using a dynamic programming algorithm.","Imports":"graphics, grDevices,
2)","NeedsCompilation":"yes","Package":"qualV","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Qualitative Validation Methods","URL":"http:\/\/qualV.R-
Forge.R-Project.org\/","Version":"0.3-2"},"qualityTools":{"Author":"Thomas
Roth","Depends":"R(>= 2.15.0), graphics, methods, Rsolnp,
MASS","Description":"Contains methods associated with the Define, Measure, Analyze,
Improve and Control (i.e. DMAIC) cycle of the Six Sigma Quality Management
methodology.It covers distribution fitting, normal and non-normal process
capability indices, techniques for Measurement Systems Analysis especially gage
capability indices and Gage Repeatability (i.e Gage RR) and Reproducibility
studies, factorial and fractional factorial designs as well as response surface
methods including the use of desirability functions. Improvement via Six Sigma is
project based strategy that covers 5 phases: Define - Pareto Chart; Measure -
Probability and Quantile-Quantile Plots, Process Capability Indices for various
distributions and Gage RR Analyze i.e. Pareto Chart, Multi-Vari Chart, Dot Plot;
Improve - Full and fractional factorial, response surface and mixture designs as
well as the desirability approach for simultaneous optimization of more than one
response variable. Normal, Pareto and Lenth Plot of effects as well as Interaction
Plots; Control - Quality Control Charts can be found in the 'qcc' package. The
focus is on teaching the statistical methodology used in the Quality
Sciences.","License":"GPL-
2","NeedsCompilation":"no","Package":"qualityTools","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Statistical Methods for Quality
Science","URL":"http:\/\/www.r-qualitytools.org","Version":"1.55"},"qualvar":
{"Author":"Joel
Gombin","Depends":"R (>= 2.10)","Description":"Implements indices of qualitative
variation proposed by Wilcox (1973).","Imports":"stats","License":"GPL-
3","NeedsCompilation":"no","Package":"qualvar","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr,dplyr,tidyr,ggplot2,GGally,DT","Title":"Implement
s Indices of Qualitative Variation Proposed by
Wilcox\n(1973)","Version":"0.1.0"},"quantable":{"Author":"Witold Wolski
<wewolski@gmail.com>","Description":"Methods which streamline the descriptive
analysis of quantitative matrices.","Imports":"scales, gplots,
3","NeedsCompilation":"no","Package":"quantable","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Streamline Descriptive Analysis of Quantitative Data
Matrices","URL":"https:\/\/github.com\/wolski\/quantable","Version":"0.1"},"quantch
em":{"Author":"Lukasz Komsta","Depends":"R (>= 2.0), MASS,
outliers","Description":"Statistical evaluation of calibration curves by
different\nregression techniques: ordinary, weighted, robust (up to 4th\norder
polynomial). Log-log and Box-Cox transform, estimation\nof optimal power and
weighting scheme. Tests for\nheteroscedascity and normality of residuals. Different
kinds of\nplots commonly used in illustrating calibrations.
Easy \"inverse\nprediction\" of concentration by given responses and
statistical\nevaluation of results (comparison of precision and accuracy by\ncommon
tests).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"quantchem","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Quantitative chemical analysis: calibration and
evaluation of\nresults","URL":"http:\/\/www.r-project.org,
http:\/\/www.komsta.net\/","Version":"0.13"},"quanteda":{"Author":"Kenneth Benoit
[aut, cre],\nPaul Nulty [aut],\nPablo BarberÃ¡ [ctb],\nKohei Watanabe
[ctb],\nBenjamin Lauderdale [ctb]","Depends":"R (>= 3.2.2)","Description":"A fast,
flexible toolset for for the management, processing, and\nquantitative analysis of
textual data in R.","Imports":"methods, utils, stats, Matrix (>= 1.2), data.table
(>= 1.9.6),\nSnowballC, wordcloud, proxy, parallel, Rcpp, ca,
stringi","License":"GPL-
3","NeedsCompilation":"yes","Package":"quanteda","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr, lda, topicmodels, jsonlite (>= 0.9.10),
streamR, tm\n(>= 0.6), slam, ggplot2, XML, testthat,
RColorBrewer","Title":"Quantitative Analysis of Textual
Data","URL":"http:\/\/github.com\/kbenoit\/quanteda","Version":"0.9.4"},"quantifica
tion":{"Author":"Joachim Zuckarelli
<joachim@zuckarelli.de>","Depends":"car","Description":"This package provides
different functions for quantifying qualitative survey data. It supports the
Carlson-Parkin method, the regression approach and the balance
approach.","License":"GPL-
3","NeedsCompilation":"no","Package":"quantification","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Quantification of Qualitative Survey
Data","URL":"cran.r-
project.org\/package=quantification","Version":"0.1.0"},"quantileDA":
{"Author":"Christian Hennig, Cinzia Viroli","Description":"Code for centroid,
median and quantile classifiers.","License":"GPL-
3","NeedsCompilation":"no","Package":"quantileDA","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Quantile Classifier","Version":"1.1"},"quantmod":
{"Author":"Jeffrey A. Ryan [aut, cph],\nJoshua M. Ulrich [cre, ctb],\nWouter
Thielen [ctb]","Depends":"xts(>= 0.9-0), zoo, TTR(>= 0.2),
methods","Description":"Specify, build, trade, and analyse quantitative financial
trading strategies.","License":"GPL-
3","NeedsCompilation":"yes","Package":"quantmod","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"DBI,RMySQL,RSQLite,timeSeries,its,XML,downloader","Ti
tle":"Quantitative Financial Modelling Framework","URL":"http:\/\/www.quantmod.com
https:\/\/github.com\/joshuaulrich\/quantmod","Version":"0.4-5"},"quantreg":
{"Author":"Roger Koenker [cre, aut],\nStephen Portnoy [ctb] (Contributions to
Censored QR code),\nPin Tian Ng [ctb] (Contributions to Sparse QR code),\nAchim
Zeileis [ctb] (Contributions to dynrq code essentially identical\nto his dynlm
code),\nPhilip Grosjean [ctb] (Contributions to nlrq code),\nBrian D Ripley [trl,
ctb] (Initial (2001) R port from S (to my\neverlasting shame -- how could I have
been so slow to adopt R!) and\nfor numerous other suggestions and useful
advice)","Depends":"R (>= 2.6), stats, SparseM","Description":"Estimation and
inference methods for models of conditional quantiles:\nLinear and nonlinear
parametric and non-parametric (total variation penalized) models\nfor conditional
quantiles of a univariate response and several methods for handling\ncensored
survival data. Portfolio selection methods based on expected shortfall\nrisk are
also included.","Imports":"methods, graphics, Matrix, MatrixModels","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"quantreg","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"tripack, akima, MASS, survival, rgl, logspline,
nor1mix,\nFormula, zoo","Title":"Quantile Regression","URL":"http:\/\/www.r-
project.org","Version":"5.21"},"quantreg.nonpar":{"Author":"Michael Lipsitz,
Alexandre Belloni, Victor Chernozhukov, Ivan Fernandez-Val","Depends":"R (>= 2.10),
quantreg, mnormt, fda, Rearrangement","Description":"Implements the nonparametric
quantile regression method developed by Belloni, Chernozhukov, and Fernandez-Val
(2011) to partially linear quantile models. Provides point estimates of the
conditional quantile function and its derivatives based on series approximations to
the nonparametric part of the model. Provides pointwise and uniform confidence
intervals using analytic and resampling methods.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"quantreg.nonpar","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Nonparametric Series Quantile
Regression","Version":"1.0"},"quantregForest":{"Author":"Nicolai Meinshausen, Lukas
Schiesser","Depends":"randomForest","Description":"Quantile Regression Forests is a
tree-based ensemble\nmethod for estimation of conditional quantiles. It
is\nparticularly well suited for high-dimensional data. Predictor\nvariables of
mixed classes can be handled. The package is\ndependent on the package
randomForests, written by Andy Liaw.","Imports":"stats, graphics,
grDevices","License":"GPL","NeedsCompilation":"yes","Package":"quantregForest","Rep
ository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"gss","Title":"Quantile
Regression Forests","Version":"1.2"},"quantregGrowth":{"Author":"Vito M. R. Muggeo
[aut, cre]","Depends":"quantreg, splines","Description":"Fits non-crossing
regression quantiles as a function of linear covariates and a smooth terms via B-
splines with difference
penalties.","License":"GPL","NeedsCompilation":"no","Package":"quantregGrowth","Rep
ository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Growth Charts via
Regression Quantiles","Version":"0.3-1"},"quantspec":{"Author":"Tobias Kley [aut,
cre],\nStefan Birr [ctb] (Contributions to lag window estimation)","Depends":"R (>=
3.0.0), stats4","Description":"Methods to determine, smooth and plot quantile
periodograms for\nunivariate and multivariate time series.","Imports":"methods,
graphics, quantreg, abind, zoo, snowfall, Rcpp (>=\n0.11.0)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"quantspec","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat","Title":"Quantile-Based Spectral Analysis
of Time Series","URL":"http:\/\/github.com\/tobiaskley\/quantspec","Version":"1.2-
1"},"questionr":{"Author":"Julien Barnier [aut, cre],\nFranÃ§ois Briatte
[aut],\nJoseph Larmarange [aut]","Depends":"R (>= 2.10)","Description":"Set of
functions to make the processing and analysis of\nsurveys easier : interactive
shiny apps and addins for data recoding,\ncontingency tables, dataset metadata
handling, and several convenience\nfunctions.","Imports":"shiny (>= 0.13), miniUI,
rstudioapi, highr, classInt,\nhtmltools, graphics, stats, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"questionr","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"memisc, testthat, roxygen2,
R2HTML","Title":"Functions to Make Surveys Processing
Easier","URL":"https:\/\/github.com\/juba\/questionr","Version":"0.5"},"queueing":
{"Author":"Pedro Canadilla","Depends":"R (>= 2.11.1)","Description":"It provides
versatile tools for analysis of birth and death based Markovian Queueing
Models\nand Single and Multiclass Product-Form Queueing Networks.\nIt implements
M\/M\/1, M\/M\/c, M\/M\/Infinite, M\/M\/1\/K, M\/M\/c\/K, M\/M\/c\/c,
M\/M\/1\/K\/K, M\/M\/c\/K\/K, M\/M\/c\/K\/m, M\/M\/Infinite\/K\/K,\nMultiple
Channel Open Jackson Networks, Multiple Channel Closed Jackson Networks,\nSingle
Channel Multiple Class Open Networks, Single Channel Multiple Class Closed
Networks\nand Single Channel Multiple Class Mixed Networks.\nAlso it provides a B-
Erlang, C-Erlang and Engset calculators.\nThis work is dedicated to the memory of
D. Sixto Rios Insua.","License":"GPL-
2","NeedsCompilation":"no","Package":"queueing","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Analysis of Queueing Networks and
Models","URL":"http:\/\/www.r-project.org","Version":"0.2.6"},"quickReg":
{"Author":"Xikun Han [aut, cre]","Depends":"R (>= 3.0.0)","Description":"A set of
functions to extract results from regression models and\nplot the effect size using
'ggplot2' seamlessly. While 'broom' is useful to\nconvert statistical analysis
objects into tidy data frames, 'coefplot' is adept at showing\nmultivariate
regression results. With specific outcome, this package could build regression
models\nautomatically, extract results into a data frame and provide a quicker way
to summarize\nmodels' statistical findings using 'ggplot2'.","Imports":"ggplot2 (>=
2.0.0), survival, psych, utils, stats, nortest","License":"GPL-
2","NeedsCompilation":"no","Package":"quickReg","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"ggthemes, knitr, rmarkdown","Title":"Build
Regression Models Quickly and Display the Results
Using\n'ggplot2'","Version":"0.0.2"},"quickmapr":{"Author":"Jeffrey W. Hollister
[aut, cre]","Depends":"R (>= 3.0.0)","Description":"While analyzing geospatial
data, easy visualization is often needed\nthat allows for quick plotting, and
simple, but easy interactivity.\nAdditionally, visualizing geospatial data in
projected coordinates is also\ndesirable. The 'quickmapr' package provides a
simple method to visualize 'sp'\nand 'raster' objects, allows for basic zooming,
panning, identifying, and\nlabeling of spatial objects, and does not require that
the data be in\ngeographic coordinates.","Imports":"rgeos, sp, rgdal, stats,
grDevices, graphics, methods,
httr,\nraster","License":"CC0","NeedsCompilation":"no","Package":"quickmapr","Repos
itory":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"testthat,
knitr","Title":"Quickly Map and Explore Spatial
Data","URL":"https:\/\/www.github.com\/jhollist\/quickmapr","Version":"0.1.1"},"qui
ckpsy":{"Author":"Linares Daniel [aut, cre],\nLÃ³pez-Moliner Joan
[aut]","Depends":"R (>= 3.1.1), boot, DEoptim, dplyr, ggplot2,
tidyr","Description":"Quickly fits and plots psychometric functions (normal,
logistic,\nWeibull or any or any function defined by the user) for multiple
groups.","Imports":"MPDiR","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"quickpsy","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Fits Psychometric Functions for Multiple
Groups","URL":"http:\/\/dlinares.org\/quickpsy.html","Version":"0.1.2"},"quint":
{"Author":"Elise Dusseldorp [aut, cre, cph],\nLisa Doove [aut],\nCor Ninaber [ctb]
(supported with the plot function),\nIven Van Mechelen [aut, cph]","Depends":"R (>=
3.0.2), partykit, Formula, rpart","Description":"Grows a qualitative interaction
tree. Quint is a tool for subgroup analysis, suitable for data from a two-arm
randomized controlled trial.","License":"GPL-
2","NeedsCompilation":"no","Package":"quint","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Qualitative Interaction Trees","Version":"1.0"},"quipu":
{"Author":"Reinhard Simon, Pablo Carhuapoma, Vilma Hualla, Stef de Haan,
Marc\nGhislain, Jorge Nunez, Rene Gomez, Felipe de Mendiburu, William
Roca,\nMerideth Bonierbale","Depends":"R (>= 3.0.0), stats, agricolae, stringr,
pixmap, shiny, xtable","Description":"Gene banks increasingly use molecular markers
for routine\ncharacterization of plant collections and farmer managed diversity.
The\ngene bank of the International Potato Center presently uses a\nmicro-satellite
marker kit to produce molecular profiles for potato\naccessions. We have been
searching for a compact graphical representation\nthat shows both molecular
diversity and accession characteristics - thus\npermitting biologists and
collection curators to have a simple way to\ninterpret molecular data. Inspired by
the ancient Andean data recording\nsystem we devised a graph that allows for
standardized representation while\nleaving room for updates of the marker kit and
the collection of\naccessions. The graph has been used in several catalogs of
potatoes.","License":"GPL-
2","NeedsCompilation":"no","Package":"quipu","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr","Title":"Summary charts of micro satellite
profiles for a set of\nbiological samples","Version":"1.9.0"},"qut":
{"Author":"Jairo Diaz, Sylvain Sardy, Caroline Giacobino, Nick
Hengartner.","Depends":"Matrix, glmnet, lars","Description":"Selection of a
threshold parameter for GLM-lasso to obtain a sparse model\nwith a good compromise
between high true positive rate and low false discovery rate.","License":"GPL-
2","NeedsCompilation":"no","Package":"qut","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Quantile Universal Threshold","Version":"1.0.1"},"qvcalc":
{"Author":"David Firth","Description":"Functions to compute quasi variances and
associated measures of approximation error.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"qvcalc","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"relimp, MASS","Title":"Quasi Variances for Factor
Effects in Statistical
Models","URL":"http:\/\/warwick.ac.uk\/qvcalc","Version":"0.9-0"},"qwraps2":
{"Author":"Peter DeWitt [aut, cre],\nTell Bennett [ctb]","Depends":"R (>=
3.0.2)","Description":"A collection of (wrapper) functions the creator found
useful\nfor quickly placing data summaries and formatted regression results
into\n'.Rnw' or '.Rmd' files. Functions for generating commonly used
graphics,\nsuch as receiver operating curves or Bland-Altman plots, are also
provided\nby 'qwraps2'. 'qwraps2' is a updated version of a package 'qwraps'.
The\noriginal version 'qwraps' was never submitted to CRAN but can be found
at\n<https:\/\/github.com\/dewittpe\/qwraps\/>. The implementation and limited
scope\nof the functions within 'qwraps2'
<https:\/\/github.com\/dewittpe\/qwraps2\/> is\nfundamentally different from
'qwraps'.","Imports":"dplyr, ggplot2, knitr","License":"GPL-
2","NeedsCompilation":"no","Package":"qwraps2","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"survival","Title":"Quick Wraps
2","URL":"https:\/\/github.com\/dewittpe\/qwraps2\/","Version":"0.1.4"},"r.jive":
{"Author":"Michael J. O'Connell and Eric F. Lock","Depends":"R(>=
2.10.0)","Description":"Performs the JIVE decompositions on a list of data sets
when the data share a dimension, returning low-rank matrices that capture the joint
and individual structure of the data. It provides two methods of rank selection
when the rank is unknown, a permutation test and a BIC selection algorithm. Also
included in the package are three plotting functions for visualizing the variance
attributed to each data source: a bar plot that shows the percentages of the
variability attributable to joint and individual structure, a heatmap that shows
the structure of the variability, and principal component
plots.","Imports":"SpatioTemporal, gplots, graphics, stats","License":"GPL-
3","NeedsCompilation":"no","Package":"r.jive","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"knitr, rmarkdown","Title":"Perform JIVE Decompositions
for Multi-Source Data","Version":"1.4"},"r2d2":{"Author":"Arni Magnusson [aut],
Julian Burgos [aut, cre], Gregory R. Warnes [ctb]","Description":"This package
provides generic functions to analyze the distribution\nof two continuous
variables: 'conf2d' to calculate a smooth empirical\nconfidence region, and
'freq2d' to calculate a frequency distribution.","Imports":"KernSmooth, MASS,
2)","NeedsCompilation":"no","Package":"r2d2","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"cluster, lattice","Title":"Bivariate (Two-Dimensional)
Confidence Region and Frequency\nDistribution","Version":"1.0-0"},"r2dRue":
{"Author":"Gabriel del Barrio, Juan Puigdefabregas, Maria E. Sanjuan &\nAlberto
Ruiz","Depends":"rgdal,sp,matrixStats","Description":"2dRUE is a methodology to
make a diagnostic of land\ncondition in a large territory during a given time
period. The\nfollowing projects have funded this package: DeSurvey IP (EC\nFP6
Integrated Project contract No. 003950), DesertWatch (ESA\nDUE contract No.
18487\/04\/I-LG) and MesoTopos (Junta de\nAndalucia PE ref. RNM-
4023).","License":"GPL","NeedsCompilation":"no","Package":"r2dRue","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"2d Rain Use Efficience
model","Version":"1.0.4"},"r2lh":{"Author":"Christophe Genolini, Bernard
Desgraupes, Lionel Riou Franca","Depends":"methods","Description":"generate
univariate and bivariate analyses in LaTeX or\nHTML formats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"r2lh","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"R to LaTeX and HTML","URL":"http:www.r-
project.org","Version":"0.7"},"r2stl":{"Author":"Ian Walker and Jose'
Gama","Depends":"R (>= 2.7.0)","Description":"r2stl, R package for visualizing data
using a 3D printer\nPackage r2stl converts R data to STL (stereolithography)
files\nthat can be used to feed a 3-dimensional printer. The\n3-dimensional output
from an R function can be materialized\ninto a solid surface in a plastic material,
therefore allowing\nmore detailed examination. There are many possible uses
for\nthis new R tool, such as to examine mathematical expressions\nwith very
irregular shapes, to aid teaching people with\nimpaired vision, to create raised
relief maps from digital\nelevation maps (DEMs), to bridge the gap between
mathematical\ntools and rapid prototyping, and many more. Ian Walker created\nthe
function \"r2stl\" and Jose' Gama assembled the package.","License":"CC BY-NC-SA
3.0","NeedsCompilation":"no","Package":"r2stl","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"r2stl, R package for visualizing data using a 3D
printer","Version":"1.0.0"},"r4ss":{"Author":"Ian G. Taylor, Ian J. Stewart, Allan
C. Hicks, Tommy M. Garrison,\nAndre E. Punt, John R. Wallace, Chantel R. Wetzel,
James T. Thorson,\nYukio Takeuchi, Kotaro Ono, Cole C. Monnahan, Christine C.
Stawitz,\nZ. Teresa A'mar, Athol R. Whitten, Kelli F. Johnson, Robbie L.
Emmet,\nSean C. Anderson, and other contributors.","Depends":"R (>=
2.10.0)","Description":"A collection of R functions for use with Stock Synthesis,
a\nfisheries stock assessment modeling platform written in ADMB by Dr. Richard\nD.
Methot at the NOAA Northwest Fisheries Science Center. The functions\ninclude tools
for summarizing and plotting results, manipulating files,\nvisualizing model
parameterizations, and various other common stock\nassessment
tasks.","Imports":"coda, corpcor, gplots, gtools, maps, pso, tcltk,
truncnorm","License":"GPL-
3","NeedsCompilation":"no","Package":"r4ss","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"R Code for Stock
Synthesis","URL":"https:\/\/github.com\/r4ss","Version":"1.24.0"},"rARPACK":
{"Author":"Yixuan Qiu, Jiali Mei and authors of the ARPACK library. See
file\nAUTHORS for details.","Description":"Previously an R wrapper of the 'ARPACK'
library\n<http:\/\/www.caam.rice.edu\/software\/ARPACK\/>, and now a shell of
the\nR package 'RSpectra', an R interface to the 'Spectra'
library\n<http:\/\/yixuan.cos.name\/spectra\/> for solving large
scale\neigenvalue\/vector problems. The current version of 'rARPACK'\nsimply
imports and exports the functions provided by 'RSpectra'.\nNew users of 'rARPACK'
are advised to switch to the 'RSpectra'
package.","Imports":"RSpectra","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"rARPACK","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"Matrix (>= 1.1-0)","Title":"Solvers for Large
Scale Eigenvalue and SVD
Problems","URL":"https:\/\/github.com\/yixuan\/rARPACK","Version":"0.11-
0"},"rAltmetric":{"Author":"Karthik Ram [aut, cre]","Description":"Programmatic
interface to the Altmetric.com API.","Imports":"plyr, RCurl, reshape2, png, ggplot2
(>= 0.9.2.1),
RJSONIO","License":"CC0","NeedsCompilation":"no","Package":"rAltmetric","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Retrieves
Altmerics Data For Any Published Paper
From\nAltmetric.com","URL":"https:\/\/github.com\/ropensci\/rAltmetric","Version":"
0.6"},"rAmCharts":{"Author":"Jeffery Petit [aut, cre],\nAntanas Marcelionis [aut,
cph] ('AmCharts' library in th directory\nhtmlwidgets\/lib\/amcharts, refer to
http:\/\/www.amcharts.com\/),\nBenoit Thieurmel [aut, ctb],\nElena Salette [aut,
ctb],\nTitouan Robert [aut, ctb]","Depends":"R (>= 3.2.0)","Description":"API for
using 'AmCharts' Library. Based on the 'htmlwidgets'\npackage, it provides a global
architecture to generate 'JavaScript' source\ncode for charts. Most of classes in
the library have their equivalent in R\nwith S4 classes; for those classes, not all
properties have been referenced\nbut can easily be added in the constructors.
Complex properties (e.g.\n'JavaScript' object) can be passed as named list. See
examples at <http:\/\/\ndatastorm-open.github.io\/introduction_ramcharts\/>. and
<http:\/\/www.amcharts.com\/> for\nmore information about the library. The package
includes the free version of\n'AmCharts' Library. Its only limitation is that a
small link to the web site\nwill be displayed in your charts. If you enjoy this
library, do not hesitate\nto refer to this page <http:\/\/www.amcharts.com\/online-
store\/> to purchase a\nlicence, and thus support its creators and get a period of
Priority Support.\nSee also <http:\/\/www.amcharts.com\/about\/> for more
information about\n'AmCharts' company.","Imports":"methods, htmlwidgets, htmltools,
rlist, data.table (>= 1.9.6),\ngraphics, utils, pipeR, knitr,
2)","NeedsCompilation":"no","Package":"rAmCharts","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"magrittr, shiny, testthat,
shinydashboard","Title":"JavaScript Charts API Tool","URL":"http:\/\/datastorm-
open.github.io\/introduction_ramcharts\/","Version":"2.0.0"},"rAverage":
{"Author":"Giulio Vidotto <giulio.vidotto@unipd.it>,\nStefano Noventa
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Vicentini <marco.vicentini@gmail.com>","Depends":"R (>= 2.8), methods,
tcltk","Description":"Parameter estimation for averaging models of Anderson's
Information Integration Theory","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"rAverage","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Parameter estimation for the averaging model of
Information\nIntegration
Theory","URL":"http:\/\/qplab.psy.unipd.it\/","Version":"0.4-13"},"rAvis":
{"Author":"Javier GonzÃ¡lez HernÃ¡ndez <javigzz@yahoo.es>, Sara Varela
<svarela@paleobiogeography.org>","Depends":"R (>= 2.10)","Description":"Interface
to <http:\/\/proyectoavis.com> database.\nIt provides means to download data
filtered by species, order,\nfamily, and several other criteria. Provides also
basic functionality to\nplot exploratory maps of the datasets.","Imports":"stringr,
XML, RCurl, scrapeR, gdata, scales, rgdal, maptools,\nraster, sp,
2","NeedsCompilation":"no","Package":"rAvis","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat, roxygen2","Title":"Interface to the Bird-
Watching Dataset Proyecto
AVIS","URL":"https:\/\/github.com\/ropensci\/rAvis","Version":"0.1.4"},"rBeta2009":
{"Author":"Ching-Wei Cheng, Ying-Chao Hung, Narayanaswamy
Balakrishnan","Description":"The package contains functions to generate random
numbers\nfrom the beta distribution and random vectors from the\nDirichlet
2","NeedsCompilation":"yes","Package":"rBeta2009","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"The Beta Random Number and Dirichlet Random Vector
Generating\nFunctions","Version":"1.0"},"rCBA":{"Author":"Jaroslav Kuchar [aut,
cre]","Depends":"R (>= 3.1.3), rJava, arules","Description":"Provides
implementations of rule pruning algorithms based on the \"Classification Based on
Associations\" (CBA). It can be used for building classification models from
association rules. Rules are pruned in the order of precedence given by the sort
criteria and a default rule is added. CBA was originally proposed by Liu, B. Hsu,
W. and Ma, Y (1998). Integrating Classification and Association Rule Mining.
Proceedings KDD-98, New York, 27-31 August. AAAI. pp80-86.","License":"Apache
License (==
2.0)","NeedsCompilation":"no","Package":"rCBA","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"CBA Classifier for
R","URL":"https:\/\/github.com\/jaroslav-kuchar\/rCBA","Version":"0.0.1"},"rCMA":
{"Author":"Wolfgang Konen <wolfgang.konen@fh-koeln.de>, Nikolaus Hansen <hansen
.AT. lri.fr>","Depends":"R (>= 2.14.0),","Description":"Tool for providing access
to the Java version 'CMAEvolutionStrategy' of\nNikolaus Hansen. 'CMA-ES' is the
Covariance Matrix Adaptation Evolution Strategy,\nsee
https:\/\/www.lri.fr\/~hansen\/cmaes_inmatlab.html#java.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"rCMA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"rJava","Title":"R-to-Java Interface for 'CMA-
ES'","Version":"1.1"},"rCUR":{"Author":"Andras Bodor, Norbert
Solymosi","Depends":"R (>= 2.10.0), MASS, methods, Matrix,
lattice","Description":"Functions and objects for CUR matrix
decomposition.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rCUR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"CUR decomposition package","Version":"1.3"},"rCarto":
{"Author":"Timothee Giraud - UMS RIATE
(CNRS)","Depends":"RColorBrewer,maptools,classInt","Description":"This package
makes some maps using shapefiles and\ndataframes. Five kinds of maps are
available : proportionnal\ncircles, proportionnal circles colored by a
discretized\nquantitative variable, proportionnal circles colored by
the\nmodalities of a qualitative variable, choropleth and typology.","License":"GPL
(>=
2.0)","NeedsCompilation":"no","Package":"rCarto","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"This package builds maps with a full cartographic
layout","Version":"0.8"},"rChoiceDialogs":{"Author":"Alex Lisovich [aut,
cre],\nRoger Day [aut],\nSun Microsystems, Inc [cph] (swing-layout-1.0.4.jar,
download
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ds":"rJava, utils","Description":"Collection of portable choice dialog
widgets","Imports":"tcltk","License":"LGPL (>=
2.1)","NeedsCompilation":"no","Package":"rChoiceDialogs","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"rChoiceDialogs
collection","Version":"1.0.6"},"rClinicalCodes":{"Author":"David
Springate","Depends":"R (>= 2.15)","Description":"R tools for integrating with the
www.clinicalcodes.org web\nrepository","Imports":"stringr, RCurl, XML, rjson,
tm","License":"GPL-
2","NeedsCompilation":"no","Package":"rClinicalCodes","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat, roxygen2,","Title":"R tools for
integrating with the www.clinicalcodes.org\nrepository","Version":"1.0.1"},"rDEA":
{"Author":"Jaak Simm [aut, cre],\nGalina Besstremyannaya [aut]","Description":"Data
Envelopment Analysis for R, estimating robust DEA scores without and with
environmental variables and doing returns-to-scale tests.","Imports":"slam (>= 0.1-
9), truncreg(>= 0.2-1), truncnorm(>= 1.0-7),\nmaxLik","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"rDEA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat","Title":"Robust Data Envelopment Analysis (DEA)
for R","URL":"https:\/\/github.com\/jaak-s\/rDEA","Version":"1.2-3"},"rDNA":
{"Author":"Philip Leifeld","Depends":"R (>= 2.14), rJava (>= 0.5-
0)","Description":"A package that controls the Java software Discourse
Network\nAnalyzer (DNA) from within R. Network matrices, statement frequency
time\nseries and attributes of actors can be transferred directly into
R.","License":"GPL-
3","NeedsCompilation":"no","Package":"rDNA","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"network, sna","Title":"R Bindings for the Discourse
Network Analyzer","Version":"1.30.1"},"rDVR":{"Author":"\"John Harrison\" [aut,
cre]","Depends":"R (>= 3.0.0)","Description":"The rDVR package allows you to start
stop and save a video server\nfrom within R. It does this by way of a REST
interface to a JAVA service.\nThe jar binary relies on the screen recorder included
in the Monte Media\nLibrary (CC BY 3.0 licence) developed by Werner
Randelshofer\n(http:\/\/http:\/\/www.randelshofer.ch\/monte\/). The REST interface
was modified\nfrom https:\/\/github.com\/tuenti\/VideoRecorderService which has an
Apache\nlicence.","Imports":"methods,RCurl","License":"AGPL-
3","NeedsCompilation":"no","Package":"rDVR","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Sugge
sts":"knitr,RSelenium","Title":"The rDVR package allows you to start stop and save
a video\nserver from within
R","URL":"http:\/\/johndharrison.github.io\/rDVR\/","Version":"0.1.1"},"rEDM":
{"Author":"Hao Ye, Adam Clark, Ethan Deyle","Description":"Contains C++ compiled
objects that use time delay embedding to perform state-space reconstruction and
nonlinear forecasting and an R interface to those objects using 'Rcpp'. It supports
both the simplex projection method from Sugihara & May (1990)
<DOI:10.1038\/344734a0> and the S-map algorithm in Sugihara (1994)
<DOI:10.1098\/rsta.1994.0106>. In addition, this package implements convergent
cross mapping as described by Sugihara et al. (2012)
<DOI:10.1126\/science.1227079>.","Imports":"Rcpp (>= 0.11.5),
methods","License":"GPL-3 | file
LICENSE","NeedsCompilation":"yes","Package":"rEDM","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr, rmarkdown","Title":"Applications of
Empirical Dynamic Modeling from Time Series","Version":"0.4.7"},"rEMM":
{"Author":"Michael Hahsler [aut, cre, cph],\nMargaret H. Dunham [aut,
cph]","Depends":"R (>= 2.10.0), proxy (>= 0.4-7), igraph","Description":"Implements
TRACDS (Temporal Relationships\nbetween Clusters for Data Streams), a
generalization of\nExtensible Markov Model (EMM). TRACDS adds a temporal or order
model\nto data stream clustering by superimposing a dynamically adapting\nMarkov
Chain. Also provides an implementation of EMM (TRACDS on top of tNN\ndata stream
clustering). Development of this\npackage was supported in part by NSF IIS-0948893
and R21HG005912 from\nthe National Human Genome Research
Institute.","Imports":"methods, stats, cluster, clusterGeneration, MASS,
2","NeedsCompilation":"yes","Package":"rEMM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"graph, Rgraphviz, testthat","Title":"Extensible Markov
Model for Modelling Temporal Relationships\nBetween
Clusters","URL":"http:\/\/lyle.smu.edu\/IDA\/TRACDS\/","Version":"1.0-11"},"rFDSN":
{"Author":"Daniel C. Bowman [aut, cre]","Depends":"R (>= 3.1.1), XML (>=
3.98.1.1)","Description":"This package facilitates searching for and downloading
seismic time series in miniSEED format (a minimalist version of the Standard for
the Exchange of Earthquake Data) from International Federation of Digital
Seismograph Networks repositories. This package can also be used to gather
information about seismic networks (stations, channels, locations, etc) and find
historical earthquake data (origins, magnitudes, etc).","Enhances":"RSEIS (>=
3.3.3)","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"rFDSN","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Get Seismic Data from the International Federation of
Digital\nSeismograph Networks","Version":"0.0.0"},"rFerns":{"Author":"Miron B.
Kursa","Description":"An R implementation of the random ferns classifier by Ozuysal
et al., modified for generic and multi-label classification and featuring OOB error
approximation and importance measure.","License":"GPL-
3","NeedsCompilation":"yes","Package":"rFerns","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Random Ferns Classifier","Version":"2.0.0"},"rGammaGamma":
{"Author":"Tim Triche, Jr.","Depends":"gsl","Description":"This package implements
a Gamma convolution model for\nbackground correction.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"rGammaGamma","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Gamma convolutions for methylation array background
correction","Version":"1.0.12"},"rGroovy":{"Author":"Thomas P. Fuller
<thomas.fuller@coherentlogic.com>","Depends":"rJava","Description":"Integrates the
Groovy scripting language with the R Project for Statistical
Computing.","License":"LGPL-
3","NeedsCompilation":"no","Package":"rGroovy","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat","Title":"Groovy Language
Integration","URL":"http:\/\/www.r-project.org,
http:\/\/groovy.codehaus.org\/,\nhttp:\/\/www.groovy-
lang.org\/indy.html,\nhttp:\/\/docs.groovy-
lang.org\/latest\/html\/api\/index.html,\nhttps:\/\/coherentlogic.com\/middleware-
development\/rgroovy?source=cran","Version":"1.0"},"rHealthDataGov":{"Author":"Erin
LeDell","Depends":"R (>= 3.0.1), bit64, httr, jsonlite","Description":"An R
interface for the HealthData.gov data API. For each data resource, you can filter
results (server-side) to select subsets of data.","License":"GPL-
2","NeedsCompilation":"no","Package":"rHealthDataGov","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Retrieve data sets from the HealthData.gov data
API","Version":"1.0.1"},"rHpcc":{"Author":"Dinesh Shetye","Depends":"R (>= 2.11.0),
methods, RCurl, XML","Description":"rHpcc is an R package providing an Interface
between R and\nHPCC.Familiarity with ECL (Enterprise Control Language) is a\nmust
to use this package.HPCC is a massive parallel-processing\ncomputing platform that
solves Big Data problems.ECL is the\nEnterprise Control Language designed
specifically for huge data\nprojects using the HPCC platform.Its extreme
scalability comes\nfrom a design that allows you to leverage every query
you\ncreate for re-use in subsequent queries as needed. To do this,\nECL takes a
dictionary approach to building queries wherein\neach ECL definition defines an
Attribute. Each previously\ndefined Attribute can then be used in succeeding ECL
Attribute\ndefinitions as the language extends itself as you use
it.","License":"GPL-
2","NeedsCompilation":"no","Package":"rHpcc","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Interface between HPCC and
R","URL":"http:\/\/hpccsystems.com","Version":"1.0"},"rJPSGCS":{"Author":"Sigal
Blay [aut],\nJinko Graham [aut],\nBrad McNeney [aut, cre],\nAnnick Nembot-Simo
[aut],\nAlun Thomas [ctb],\nHin-Tak Leung [ctb]","Depends":"R (>= 2.12.0), rJava
(>= 0.8-4), chopsticks (>= 1.18.0)","Description":"R-interface to gene drop
programs from Alun Thomas' Java Programs for Statistical Genetics and Computational
Statistics (JPSGCS)","License":"GPL-
3","NeedsCompilation":"yes","Package":"rJPSGCS","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"R-interface to Gene Drop Simulation from
JPSGCS","Version":"0.2-7"},"rJava":{"Author":"Simon Urbanek <simon.urbanek@r-
project.org>","Depends":"R (>= 2.5.0), methods","Description":"Low-level interface
to Java VM very much like .C\/.Call and friends. Allows creation of objects,
calling methods and accessing fields.","License":"GPL-
2","NeedsCompilation":"yes","Package":"rJava","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Low-Level R to Java
Interface","URL":"http:\/\/www.rforge.net\/rJava\/","Version":"0.9-8"},"rJython":
{"Author":"G. Grothendieck and Carlos J. Gil Bellosta (authors of Jython\nitself
are Jim Hugunin, Barry Warsaw, Samuele Pedroni, Brian\nZimmer, Frank Wierzbicki and
others; Bob Ippolito is the author\nof the simplejson Python
module)","Depends":"rJava (>= 0.8-1), rjson (>= 0.1.9)","Description":"R interface
to Python via Jython allowing R to call python\ncode.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rJython","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"R interface to Python via Jython","URL":"https:\/\/r-
forge.r-project.org\/projects\/rjython\/","Version":"0.0-4"},"rLTP":{"Author":"Tong
He <hetong007@gmail.com>","Depends":"R (>= 3.0.2),RCurl","Description":"R interface
to LTP-Cloud service for Natural Language Processing\nin Chinese. For more details
please visit http:\/\/www.ltp-cloud.com\/.
Visit\nhttps:\/\/github.com\/hetong007\/rLTP for up-to-date
version.","License":"LGPL","NeedsCompilation":"yes","Package":"rLTP","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Title":"R Interface to LTP-Cloud
Service","Version":"0.1.2"},"rLakeAnalyzer":{"Author":"Luke Winslow, Jordan Read,
Richard Woolway, Jennifer Brentrup, Taylor\nLeach, Jake
Zwart","Description":"Standardized methods for calculating common important
derived\nphysical features of lakes including water density based based
on\ntemperature, thermal layers, thermocline depth, lake number,
Wedderburn\nnumber, Schmidt stability and others.","Imports":"plyr","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"rLakeAnalyzer","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Package for the Analysis of Lake
Physics","Version":"1.7.6"},"rLiDAR":{"Author":"Carlos A. Silva, Nicholas L.
Crookston,\nAndrew T. Hudak, Lee A. Vierling","Depends":"R (>=
3.1.2)","Description":"Set of tools for reading, processing and visualizing small
set\nof LiDAR (Light Detection and Ranging) data for forest inventory
applications.","Imports":"spatstat,sp,deldir,plyr,raster,geometry,rgl,bitops","Lice
nse":"GPL (>=
2)","NeedsCompilation":"no","Package":"rLiDAR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"LiDAR Data Processing and
Visualization","Version":"0.1"},"rLindo":{"Author":"Zhe Liu","Depends":"R (>=
2.14.1), methods","Description":"An interface to LINDO API. Supports Linear,
Integer, Quadratic, Conic, General Nonlinear, Global, and Stochastic Programming
models. To download the trial version LINDO API, please visit
www.lindo.com\/rlindo.","License":"LGPL (>=
2.1)","NeedsCompilation":"yes","Package":"rLindo","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"R Interface to LINDO
API","URL":"www.lindo.com\/rlindo","Version":"8.0.1"},"rNMF":{"Author":"Yifan Ethan
Xu <ethan.yifanxu@gmail.com>, Jiayang Sun <jsun@case.edu>","Depends":"R (>=
2.14.0)","Description":"An implementation of robust nonnegative matrix
factorization (rNMF). The rNMF algorithm decomposes a nonnegative high dimension
data matrix into the product of two low rank nonnegative matrices, while detecting
and trimming outliers. The main function is rnmf(). The package also includes a
visualization tool, see(), that arranges and prints vectorized
images.","Imports":"nnls,
knitr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rNMF","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Robust Nonnegative Matrix
Factorization","Version":"0.5.0"},"rNOMADS":{"Author":"Daniel C. Bowman [aut,
cre]","Depends":"R (>= 3.2.2), rvest (>= 0.3.0)","Description":"An interface to the
National Oceanic and Atmospheric Administration's Operational Model Archive and
Distribution System (NOMADS) that allows R users to quickly and efficiently
download global and regional weather model data for processing. rNOMADS currently
supports a variety of models ranging from global weather data to an altitude of 40
km, to high resolution regional weather models, to wave and sea ice models. It can
also retrieve archived NOMADS models. rNOMADS can retrieve binary data in grib
format as well as import ascii data directly into R by interfacing with the GrADS-
DODS system.","Imports":"scrapeR (>= 0.1.6), stringr (>= 1.0.0), fields (>=
8.2.1),\nGEOmap (>= 2.3-5), MBA, RCurl (>= 1.95-4.7), XML (>= 3.98.1.3),\nxml2 (>=
0.1.2)","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"rNOMADS","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"An Interface to the NOAA Operational Model Archive
and\nDistribution System","URL":"https:\/\/r-forge.r-
project.org\/projects\/rnomads\/
(subversion\nrepository)\nhttp:\/\/www.unc.edu\/~haksaeng\/rNOMADS\/rNOMADS_dods_ex
amples.pdf\n(GrADS-DODS
examples)\nhttp:\/\/www.unc.edu\/~haksaeng\/rNOMADS\/rNOMADS_grib_examples.pdf\n(gr
ib examples)","Version":"2.2.0"},"rPlant":{"Author":"Barb Banbury
<darwinthesun@gmail.com> and Kurt Michels <kamichels@math.arizona.edu>, Jeremy M.
Beaulieu <jeremy.beaulieu@yale.edu>, Brian O'Meara <bomeara@utk.edu>","Depends":"R
(>= 2.13.0), rjson, RCurl, seqinr","Description":"Provides an interface to the the
many computational resources iPlant offers through their RESTful application
programming interface, see <http:\/\/www.iplantcollaborative.org\/> for more
information about iPlant, and <http:\/\/www.iplantcollaborative.org\/ci\/iplant-
science-apis> for its APIs. Currently, 'rPlant' functions interact with the iPlant
Agave API, the Taxonomic Name Resolution Service API, and the Phylotastic
Taxosaurus API. Before using 'rPlant', users will have to register with the iPlant
Collaborative. See <http:\/\/agaveapi.co\/> for more information on the Agave API
and <http:\/\/user.iplantcollaborative.org\/> to register with
iPlant.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rPlant","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Interface to the Agave
API","URL":"http:\/\/www.iplantcollaborative.org\/discover\/discovery-
environment","Version":"2.16"},"rPowerSampleSize":{"Author":"Pierre Lafaye de
Micheaux, Benoit Liquet and Jeremie Riou","Depends":"R (>= 2.10.0), mvtnorm, stats,
ssanv, parallel","Description":"The significance of mean difference tests in
clinical trials is established if at least r null hypotheses are rejected among m
that are simultaneously tested. This package enables one to compute necessary
sample sizes for single-step (Bonferroni) and step-wise procedures (Holm and
Hochberg). These three procedures control the q-generalized family-wise error rate
(probability of making at least q false rejections). Sample size is computed (for
these single-step and step-wise procedures) in a such a way that the r-power
(probability of rejecting at least r false null hypotheses, i.e. at least r
significant endpoints among m) is above some given threshold, in the context of
tests of difference of means for two groups of continuous endpoints (variables).
Various types of structure of correlation are considered. It is also possible to
analyse data (i.e., actually test difference in means) when these are available.
The case r equals 1 is treated in separate functions that were used in Lafaye de
Micheaux et al. (2014) <doi:10.1080\/10543406.2013.860156>.","License":"GPL (>
2)","NeedsCompilation":"no","Package":"rPowerSampleSize","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Sample Size Computations Controlling the Type-II
Generalized\nFamily-Wise Error Rate","Version":"1.0.1"},"rPref":{"Author":"Patrick
Roocks <mail@p-roocks.de>","Depends":"R (>= 3.0.0),
methods","Description":"Routines to select and visualize the maxima for a given
strict\npartial order. This especially includes the computation of the
Pareto\nfrontier, also known as (Top-k) Skyline operator, and some\ngeneralizations
(database preferences).","Imports":"Rcpp (>= 0.11.5), RcppParallel (>= 4.3.6),
dplyr (>= 0.4.1),\nigraph (>= 1.0.1)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"rPref","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat","Title":"Database Preferences and Skyline
Computation","URL":"http:\/\/www.p-roocks.de\/rpref","Version":"0.7"},"rSCA":
{"Author":"Xiuquan Wang","Depends":"R (>= 2.10.0)","Description":"This package
implements a statistical tool for modeling multivariate relationships using a
stepwise cluster analysis (SCA) method.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rSCA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"An R Package for Stepwise Cluster
Analysis","Version":"2.1"},"rSFA":{"Author":"Wolfgang Konen <wolfgang.konen@fh-
koeln.de>, Martin Zaefferer,\nPatrick Koch; Bug hunting and testing by Ayodele
Fasika, Ashwin\nKumar, Prawyn Jebakumar","Depends":"R (>=
2.0.0)","Description":"Slow Feature Analysis in R, ported to R based on the\nmatlab
versions SFA toolkit 1.0 by Pietro Berkes and SFA toolkit\n2.8 by Wolfgang Konen
for matlab.","Imports":"stats, MASS","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rSFA","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Slow Feature Analysis in
R","URL":"http:\/\/gociop.de\/research-projects\/sfa\/","Version":"1.04"},"rSPACE":
{"Author":"Martha Ellis, Jake Ivan, Jody Tucker, Mike
Schwartz","Description":"Conducts a spatially-explicit, simulation-based power
analysis for detecting trends in population abundance through occupancy-based
modeling. Applicable for evaluating monitoring designs in conservation and
ecological settings.","Imports":"raster, RMark, ggplot2, tcltk2, sp, grid, plyr,
tcltk,\ngrDevices, methods, stats, utils","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"rSPACE","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Spatially-Explicit Power Analysis for Conservation and
Ecology","URL":"http:\/\/github.com\/mmellis\/rSPACE","Version":"1.2.0"},"rSymPy":
{"Author":"G Grothendieck (SymPy itself is by Ondrej Certik and
others),\nContributors: Carlos J. Gil
Bellosta","Depends":"rJython","Description":"Access SymPy computer algebra system
from R via
Jython","License":"GPL","NeedsCompilation":"no","Package":"rSymPy","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"R interface to SymPy computer algebra
system","URL":"http:\/\/rsympy.googlecode.com","Version":"0.2-1.1"},"rTableICC":
{"Author":"Haydar Demirhan","Depends":"partitions, aster,
stats","Description":"Contains functions for random generation of R x C and 2 x 2 x
K contingency tables. In addition to the generation of contingency tables over
predetermined intraclass-correlated clusters, it is possible to generate
contingency tables without intraclass correlations under product multinomial,
multinomial, and Poisson sampling plans. It also consists of a function for
generation of random data from a given discrete probability distribution
function.","License":"GPL-
3","NeedsCompilation":"no","Package":"rTableICC","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Random Generation of Contingency
Tables","Version":"1.0.3"},"rTensor":{"Author":"James Li and Jacob Bien and Martin
Wells","Depends":"methods, R (>= 2.10.0)","Description":"A set of tools for
creation, manipulation, and modeling\nof tensors with arbitrary number of modes. A
tensor in the context of data\nanalysis is a multidimensional array. rTensor does
this by providing a S4\nclass 'Tensor' that wraps around the base 'array' class.
rTensor\nprovides common tensor operations as methods, including matrix
unfolding,\nsumming\/averaging across modes, calculating the Frobenius norm, and
taking\nthe inner product between two tensors. Familiar array operations
are\noverloaded, such as index subsetting via '[' and element-wise
operations.\nrTensor also implements various tensor decomposition, including CP,
GLRAM,\nMPCA, PVD, and Tucker. For tensors with 3 modes, rTensor also
implements\ntranspose, t-product, and t-SVD, as defined in Kilmer et al. (2013).
Some\nauxiliary functions include the Khatri-Rao product, Kronecker product,
and\nthe Hamadard product for a list of matrices.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rTensor","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Tools for Tensor Analysis and
Decomposition","URL":"http:\/\/jamesyili.github.io\/rTensor","Version":"1.3"},"rUne
mploymentData":{"Author":"Ari Lamstein
<arilamstein@gmail.com>[cre]","Description":"Contains data and visualization
functions for USA unemployment\ndata. Data comes from the US Bureau of Labor
Statistics (BLS). State data\nis in ?df_state_unemployment and covers 2000-2013.
County data is in\n?df_county_unemployment and covers 1990-2013. Choropleth maps of
the data\ncan be generated with ?state_unemployment_choropleth and\n?
county_unemployment_choropleth respectively. See the vignettes for\nadditional
information.","Imports":"stringr, choroplethr, rvest","License":"BSD_3_clause +
file
LICENSE","NeedsCompilation":"no","Package":"rUnemploymentData","Repository":"http:\
/\/cran.csiro.au\/src\/contrib","Suggests":"choroplethrMaps, knitr,
testthat","Title":"Data and Functions for USA State and County Unemployment
Data","URL":"https:\/\/github.com\/trulia\/rUnemploymentData\/,\nhttps:\/\/groups.g
oogle.com\/forum\/#!forum\/choroplethr","Version":"1.0.0"},"rWBclimate":
{"Author":"Edmund
Hart [aut, cre]","Description":"This package will download model predictions from
15 different global circulation models in 20 year intervals from the world bank.
Users can also access historical data, and create maps at 2 different spatial
scales.","Imports":"ggplot2, httr, plyr, rgdal, jsonlite, reshape2,
sp","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rWBclimate","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"knitr","Title":"A package for accessing World
Bank climate
data","URL":"http:\/\/github.com\/ropensci\/rWBclimate","Version":"0.1.3"},"rYouthe
ria":{"Author":"Tom August","Depends":"R (>= 3.0.0)","Description":"A programmatic
interface to web-services of Youtheria. Youtheria is an online database of
mammalian trait data.","Imports":"plyr, RJSONIO, reshape2, RCurl","License":"MIT +
file
LICENSE","NeedsCompilation":"no","Package":"rYoutheria","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"knitr, testthat, roxygen2","Title":"Access to
the YouTheria mammal trait
database","URL":"https:\/\/github.com\/biologicalrecordscentre\/rYoutheria","Versio
n":"1.0.0"},"race":{"Author":"Mauro Birattari
<mbiro@ulb.ac.be>","Description":"Implementation of some racing methods for the
empirical\nselection of the best. If the R package `rpvm' is installed\n(and if PVM
is available, properly configured, and\ninitialized), the evaluation of the
candidates are performed in\nparallel on different hosts.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"race","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"rpvm, nnet","Title":"Racing methods for the selection of
the best","Version":"0.1.59"},"radar":{"Author":"Jose' Gama [aut, cre],\nNick Guy
[aut]","Depends":"R (>= 2.7.0)","Description":"Fundamental formulas for Radar, for
attenuation, range, velocity,\neffectiveness, power, scatter, doppler, geometry,
radar equations, etc.\nBased on Nick Guy's Python package
PyRadarMet","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"radar","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Fundamental Formulas for
Radar","Version":"1.0.0"},"radarchart":{"Author":"Doug Ashton [aut, cre],\nShane
Porter [aut],\nNick Downie [ctb] (chart.js library),\nTanner Linsley [ctb]
(chart.js library),\nWilliam Entriken [ctb] (chart.js library)","Depends":"R (>=
3.1.2)","Description":"Create interactive radar charts using the 'Chart.js'
JavaScript library\nand the 'htmlwidgets' package. Chart.js
(http:\/\/www.chartjs.org\/) is a\nlightweight library that supports several types
of simple chart using the HTML5\ncanvas element. This package provides an R
interface specifically to the\nradar chart, sometimes called a spider chart, for
visualising multivariate data.","Imports":"htmlwidgets, htmltools,
grDevices","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"radarchart","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"testthat, knitr, rmarkdown,
tidyr","Title":"Radar Chart from
Chart.js","URL":"https:\/\/github.com\/mangothecat\/radarchart","Version":"0.1.2"},
"radiomics":{"Author":"Joel Carlson","Depends":"R (>=
2.10)","Description":"Functions to extract first and second order statistics
from\nimages.","Imports":"spatstat, reshape2, methods,","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"radiomics","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat, knitr, viridis,
devtools","Title":"Radiomic Image Processing Toolbox","Version":"0.1.1"},"radir":
{"Author":"David MoriÃ±a (Centre for Research in Environmental Epidemiology,
CREAL), Manuel Higueras (Universitat AutÃ²noma de Barcelona and Public Health
England) and Pedro Puig (Universitat AutÃ²noma de Barcelona)","Depends":"R (>=
3.1.1), hermite","Description":"Radioactive doses estimation using individual
chromosomal aberrations information. See Higueras M, Puig P, Ainsbury E, Rothkamm
K. (2015). A new inverse regression model applied to radiation biodosimetry.
Proceedings of the Royal Society A, 471.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"radir","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Inverse-Regression Estimation of Radioactive
Doses","Version":"1.0.1"},"rafalib":{"Author":"Rafael A. Irizarry and Michael I.
Love","Description":"A series of shortcuts for routine tasks originally developed
by Rafael A. Irizarry to facilitate data
exploration.","Imports":"RColorBrewer","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"rafalib","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Convenience Functions for Routine Data
Exploration","Version":"1.0.0"},"rags2ridges":{"Author":"Carel F.W. Peeters [cre,
aut], Anders Ellern Bilgrau [aut], Wessel N. van Wieringen [aut]","Depends":"R (>=
2.15.1)","Description":"Proper L2-penalized ML estimators for the\nprecision matrix
as well as supporting functions to employ these estimators\nin a graphical modeling
setting.","Imports":"igraph, stats, methods, expm, reshape, ggplot2,
Hmisc,\nfdrtool, snowfall, sfsmisc, utils, grDevices, graphics","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"rags2ridges","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"KEGGgraph, graph, testthat","Title":"Ridge
Estimation of Precision Matrices from High-
Dimensional\nData","Version":"2.0"},"rainbow":{"Author":"Han Lin Shang and Rob J
Hyndman","Depends":"R (>= 3.2.3), MASS, pcaPP","Description":"Functions and data
sets for functional data display and outlier detection.","Imports":"hdrcde,
cluster, colorspace, ks","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rainbow","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"forecast","Title":"Rainbow Plots, Bagplots and
Boxplots for Functional
Data","URL":"https:\/\/sites.google.com\/site\/hanlinshangswebsite\/","Version":"3.
4"},"raincpc":{"Author":"Gopi Goteti <my.ration.shop@gmail.com>","Depends":"R (>=
3.0.2)","Description":"The Climate Prediction Center's (CPC) rainfall data for
the\nworld (1979 to present, 50 km resolution) and the USA (1948 to\npresent, 25 km
resolution), is one of the few high quality, long\nterm, observation based, daily
rainfall products available for free.\nAlthough raw data is available at CPC's ftp
site, obtaining,\nprocessing and visualizing the data is not straightforward. There
are\nmore than 12,000 files for the world and about 24,000 files for the
USA.\nMoreover, file formats and file extensions have not been consistent.\nThis
package provides functionality to download, process and visualize\nover 35 years of
global rainfall data and over 65 years of USA rainfall\ndata from
CPC.","Imports":"SDMTools","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"raincpc","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"knitr, raster, ggplot2","Title":"Obtain and
Analyze Rainfall Data from the Climate
Prediction\nCenter","Version":"0.4"},"rainfreq":{"Author":"Gopi Goteti
<my.ration.shop@gmail.com>","Depends":"R (>= 3.0.2)","Description":"Estimates of
rainfall at desired frequency (e.g., 1% annual\nchance or 100-year return period)
and desired duration (e.g.,\n24-hour duration) are often required in the design of
dams and other\nhydraulic structures, catastrophe risk modeling,
environmental\nplanning and management. One major source of such estimates for
the\nUSA is the NOAA National Weather Service's (NWS) division
of\nHydrometeorological Design Studies Center (HDSC). Raw data from\nNWS-HDSC is
available at 1-km resolution and comes as a huge number\nof GIS files. This package
provides functionality to easily access\nand analyze the 1-km GIS files provided by
NWS' PF Data Server for\nthe entire USA. This package also comes with datasets on
record point\nrainfall measurements provided by NWS-HDSC.","Imports":"RCurl,
SDMTools","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rainfreq","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"knitr, raster, maps","Title":"Rainfall Frequency
(Design Storm) Estimates from the US National\nWeather
Service","Version":"0.3"},"ramify":{"Author":"Brandon Greenwell [aut,
cre]","Depends":"base,","Description":"Additional matrix functionality for R
including: (1) wrappers\nfor the base matrix function that allows matrices to be
created from character\nstrings and lists (the former is especially useful for
creating block\nmatrices), (ii) better printing of large matrices via a new generic
function\nfor \"pretty\" printing, and (iii) a number of convenience functions for
users\nmore familiar with other scientific languages like 'Julia',
'Matlab'\/'Octave',\nor 'Python'+'NumPy'.","Imports":"stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ramify","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat, knitr","Title":"Additional Matrix
Functionality","URL":"https:\/\/github.com\/bgreenwell\/ramify","Version":"0.3.2"},
"ramps":{"Author":"Brian J Smith [aut, cre],\nJun Yan [aut],\nMary Kathryn Cowles
[aut]","Depends":"coda, maps, Matrix, nlme","Description":"Bayesian geostatistical
modeling of Gaussian processes using a reparameterized and marginalized posterior
sampling (RAMPS) algorithm designed to lower autocorrelation in MCMC samples.
Package performance is tuned for large spatial datasets.","Imports":"fields,
2","NeedsCompilation":"no","Package":"ramps","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Bayesian Geostatistical Modeling with RAMPS","Version":"0.6-
13"},"ramsvm":{"Author":"Chong Zhang, Yufeng Liu, and Shannon
Holloway","Depends":"foreach, doParallel, methods, parallel,
stats","Description":"Provides a solution path for Reinforced Angle-based
Multicategory Support Vector Machines, with linear learning, polynomial learning,
and Gaussian kernel learning.","License":"GPL-
2","NeedsCompilation":"yes","Package":"ramsvm","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Reinforced
Angle-Based Multicategory Support Vector Machines","Version":"2.0"},"randNames":
{"Author":"Karthik Ram [aut, cre]","Depends":"R (>=
3.1.2)","Description":"Generates random names with additional information including
fake SSNs, gender, location, zip, age, address, and nationality.","Imports":"dplyr,
httr, jsonlite","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"randNames","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"gender, testthat","Title":"Package Provides
Access to Fake User
Data","URL":"https:\/\/github.com\/karthik\/randNames","Version":"0.2.1"},"randaes"
:{"Author":"Thomas Lumley","Description":"The deterministic part of the Fortuna
cryptographic\npseudorandom number generator, described by Schneier &
Ferguson\n\"Practical Cryptography\"","License":"GPL-
2","NeedsCompilation":"yes","Package":"randaes","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Random number generator based on AES
cipher","Version":"0.3"},"random":{"Author":"Dirk Eddelbuettel
<edd@debian.org>","Depends":"R (>= 2.8.0)","Description":"The true random number
service provided by the RANDOM.ORG\nwebsite created by Mads Haahr samples
atmospheric noise via radio tuned to\nan unused broadcasting frequency together
with a skew correction algorithm\ndue to John von Neumann. More background is
available in the included\nvignette based on an essay by Mads Haahr. In its
current form, the package\noffers functions to retrieve random integers, randomized
sequences and\nrandom strings.","Imports":"curl, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"random","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"True Random Numbers using
RANDOM.ORG","URL":"https:\/\/www.random.org","Version":"0.2.5"},"random.polychor.pa
":{"Author":"Fabio Presaghi & Marta Desimoni","Depends":"psych, nFactors,
boot","Description":"The Function performs a parallel analysis using simulated
polychoric correlation matrices. The nth-percentile of the eigenvalues distribution
obtained from both the randomly generated and the real data polychoric correlation
matrices is returned. A plot comparing the two types of eigenvalues (real and
simulated) will help determine the number of real eigenvalues that outperform
random data. The function is based on the idea that if real data are non-normal and
the polychoric correlation matrix is needed to perform a Factor Analysis, then the
Parallel Analysis method used to choose a non-random number of factors should also
be based on randomly generated polychoric correlation matrices and not on Pearson
correlation matrices. Random data sets are simulated assuming or a uniform or a
multinomial distribution or via the bootstrap method of resampling (i.e., random
permutations of cases). Also Multigroup Parallel analysis is made available for
random (uniform and multinomial distribution and with or without difficulty factor)
and bootstrap methods. An option to choose between default or full output is also
available as well as a parameter to print Fit Statistics (Chi-squared, TLI, RMSEA,
RMR and BIC) for the factor solutions indicated by the Parallel
Analysis.","Imports":"MASS, mvtnorm, sfsmisc","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"random.polychor.pa","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Title":"A Parallel Analysis With Polychoric
Correlation Matrices","Version":"1.1.4-1"},"randomForest":{"Author":"Fortran
original by Leo Breiman and Adele Cutler, R port by\nAndy Liaw and Matthew
Wiener.","Depends":"R (>= 2.5.0), stats","Description":"Classification and
regression based on a forest of trees\nusing random inputs.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"randomForest","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"RColorBrewer, MASS","Title":"Breiman and
Cutler's Random Forests for Classification
and\nRegression","URL":"https:\/\/www.stat.berkeley.edu\/~breiman\/RandomForests\/"
,"Version":"4.6-12"},"randomForest.ddR":{"Author":"Vishrut Gupta, Arash Fard,
Winston Li, Matthew Saltz","Depends":"R (>= 3.0.0)","Description":"Distributed
training and prediction of random forest models based upon 'randomForest' package
using 'ddR' (Distributed Data Structures) API in the 'ddR'
package.","Imports":"ddR, stats, randomForest (>= 4.6-10), Matrix","License":"GPL
(>= 2) | file
LICENSE","NeedsCompilation":"no","Package":"randomForest.ddR","Repository":"http:\/
\/cran.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Distributed
'randomForest' for Big Data using 'ddR' API","Version":"0.1.1"},"randomForestSRC":
{"Author":"Hemant Ishwaran <hemant.ishwaran@gmail.com>, Udaya B. Kogalur
<ubk@kogalur.com>","Depends":"R (>= 3.1.0),","Description":"A unified treatment of
Breiman's random forests for survival, regression and classification problems based
on Ishwaran and Kogalur's random survival forests (RSF) package. The package runs
in both serial and parallel (OpenMP) modes. Now extended to include multivariate
and unsupervised forests.","Imports":"parallel","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"randomForestSRC","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"glmnet, XML, survival, pec, prodlim, Hmisc,
mlbench","Title":"Random Forests for Survival, Regression and Classification\n(RF-
SRC)","URL":"http:\/\/web.ccs.miami.edu\/~hishwaran
http:\/\/www.kogalur.com","Version":"2.1.0"},"randomGLM":{"Author":"Lin Song, Peter
Langfelder","Depends":"R (>= 2.14.0), MASS, foreach, doParallel","Description":"The
package implements a bagging predictor based on\ngeneral linear
2)","NeedsCompilation":"no","Package":"randomGLM","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Random General Linear Model
Prediction","URL":"http:\/\/www.genetics.ucla.edu\/labs\/horvath\/CoexpressionNetwo
rk\/","Version":"1.02-1"},"randomLCA":{"Author":"Ken Beath [aut,
cre]","Depends":"R(>= 3.0.0), lattice","Description":"Fits standard and random
effects latent class models. The single level random effects model is described in
Qu et al (doi: 10.2307\/2533043) and the two level random effects model in Beath
and Heller (doi: 10.1177\/1471082X0800900302). Examples are given for their use in
diagnostic testing.","Imports":"boot, fastGHQuad, Matrix,
SciencesPo","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"randomLCA","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"xtable","Title":"Random Effects Latent Class
Analysis","Version":"1.0-6"},"randomNames":{"Author":"Damian W. Betebenner
<dbetebenner@nciea.org>","Depends":"R (>= 2.10.0)","Description":"Function for
generating random gender and ethnicity correct first and\/or last names. Names are
chosen proportionally based upon their probability of appearing in a large scale
data base of real names.","Imports":"data.table (>= 1.8.0)","License":"GPL-
3","NeedsCompilation":"no","Package":"randomNames","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Function for Generating Random Names and a
Dataset","URL":"https:\/\/github.com\/CenterForAssessment\/randomNames,\nhttp:\/\/c
ran.r-project.org\/package=randomNames","Version":"0.1-0"},"randomUniformForest":
{"Author":"Saip Ciss","Depends":"R (>= 3.0.0)","Description":"Ensemble model, for
classification, regression\nand unsupervised learning, based on a forest of
unpruned\nand randomized binary decision trees. Each tree is grown\nby sampling,
with replacement, a set of variables at each node.\nEach cut-point is generated
randomly, according to the continuous\nUniform distribution. For each tree, data
are either bootstrapped\nor subsampled. The unsupervised mode introduces
clustering, dimension reduction\nand variable importance, using a three-layer
engine. Random Uniform Forests are mainly\naimed to lower correlation between trees
(or trees residuals), to provide a deep analysis\nof variable importance and to
allow native distributed and incremental learning.","Imports":"methods, Rcpp (>=
0.11.1), parallel, doParallel, iterators,\nforeach (>= 1.4.2), ggplot2, pROC,
gtools, cluster, MASS","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"yes","Package":"randomUniformForest","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Suggests":"R.rsp","Title":"Random Uniform
Forests for Classification, Regression and\nUnsupervised
Learning","Version":"1.1.5"},"randomcoloR":{"Author":"Ron
Ammar","Description":"Simple methods to generate attractive random colors. The
random\ncolors are from a wrapper of
'randomColor.js'\n<https:\/\/github.com\/davidmerfield\/randomColor>. In addition,
it also generates\noptimally distinct colors based on k-means (inspired by
'IWantHue'\n<https:\/\/github.com\/medialab\/iwanthue>).","Imports":"colorspace,
stringr, V8, stats,
methods","License":"CC0","NeedsCompilation":"no","Package":"randomcoloR","Repositor
y":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Generate Attractive Random
Colors","Version":"1.0.0"},"randomizationInference":{"Author":"Joseph J. Lee and
Tirthankar Dasgupta","Description":"Allows the user to conduct randomization-based
inference for a wide variety of experimental scenarios. The package leverages a
potential outcomes framework to output randomization-based p-values and null
intervals for test statistics geared toward any estimands of interest, according to
the specified null and alternative hypotheses. Users can define custom
randomization schemes so that the randomization distributions are accurate for
their experimental settings. The package also creates visualizations of
randomization distributions and can test multiple test statistics
simultaneously.","Imports":"permute (>= 0.7-8), matrixStats","License":"GPL-
2","NeedsCompilation":"no","Package":"randomizationInference","Repository":"http:\/
\/cran.csiro.au\/src\/contrib","Title":"Flexible Randomization-Based
Inference","Version":"1.0.3"},"randomizeBE":{"Author":"D.
Labes","Description":"Contains a function to randomize subjects, patients in
groups of\nsequences (treatment sequences).\nIf a blocksize is given, the
randomization will be done within blocks.\nThe randomization may be controlled by a
Wald-Wolfowitz runs test.\nFunctions to obtain the p-value of that test are
included.\nThe package is mainly intended for randomization of bioequivalence
studies\nbut may be used also for other clinical crossover studies.\nContains two
helper functions sequences() and williams() to get the sequences\nof commonly used
designs in BE studies.","Imports":"stats","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"randomizeBE","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Function to Create a Random List for Crossover
Studies","Version":"0.3-2"},"randomizr":{"Author":"Alexander Coppock [aut,
cre]","Depends":"R (>= 2.10.0)","Description":"Generates random assignments for
common experimental\ndesigns: simple, complete, blocked, and
clustered.","License":"GPL-
3","NeedsCompilation":"no","Package":"randomizr","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr, dplyr, blockTools, testthat","Title":"Easy to
Use Tools for Common Forms of Random Assignment","Version":"0.3.0"},"randstr":
{"Author":"Alan Gu","Description":"Generate random strings of a dictated size of
symbol set and\ndistribution of the lengths of strings.","Imports":"truncnorm,
random, stringi","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"randstr","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Generate Random
Strings","Version":"0.2.0"},"randtests":{"Author":"Frederico Caeiro and Ayana
Mateus","Description":"Several non parametric randomness tests for numeric
sequences","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"randtests","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Testing randomness in
R","Version":"1.0"},"randtoolbox":{"Author":"R port by Yohan Chalabi, Christophe
Dutang, Petr Savicky and Diethelm Wuertz with underlying C codes of (i) the SFMT
algorithm from M. Matsumoto and M. Saito, (ii) the Knuth-TAOCP RNG from D.
Knuth.","Depends":"rngWELL (>= 0.10-1)","Description":"Provides (1) pseudo random
generators - general linear congruential generators, multiple recursive generators
and generalized feedback shift register (SF-Mersenne Twister algorithm and WELL
generators); (2) quasi random generators - the Torus algorithm, the Sobol sequence,
the Halton sequence (including the Van der Corput sequence) and (3) some RNG tests
- the gap test, the serial test, the poker test. The package depends on rngWELL
package but it can be provided without this dependency on demand to the maintainer.
For true random number generation, use the 'random' package, for Latin Hypercube
Sampling (a hybrid QMC method), use the 'lhs' package. A number of RNGs and tests
for RNGs are also provided by 'RDieHarder', all available on CRAN. There is also a
small stand-alone package 'rngwell19937' for the WELL19937a
RNG.","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"yes","Package":"randtoolbox","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Toolbox for Pseudo and Quasi Random Number
Generation and RNG\nTests","Version":"1.17"},"rangeBuilder":{"Author":"Pascal
Title","Depends":"sp, raster, rgdal, R (>= 2.10)","Description":"Provides tools for
filtering occurrence records, generating alpha-hull-derived range polygons and
mapping species richness.","Imports":"alphahull, stringi, rgeos (>= 0.1-4),
methods","License":"ACM","NeedsCompilation":"no","Package":"rangeBuilder","Reposito
ry":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"parallel","Title":"Occurrenc
e Filtering and Generation of Species Range
Polygons","URL":"https:\/\/github.com\/ptitle\/rangeBuilder","Version":"1.1"},"rang
eMapper":{"Author":"Mihai Valcu [aut, cre],\nJames Dale [aut],\nJoan Maspons
[ctb]","Depends":"R (>= 3.0.0)","Description":"Tools for easy generation of (life-
history) traits maps based on\nspecies range (extent-of-occurrence)
maps.","Imports":"methods, sp, rgdal, RSQLite(>= 1.0.0), rgeos, raster,\nmaptools,
gridExtra, lattice, ggplot2, RColorBrewer, classInt,\nmagrittr, data.table,
foreach","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rangeMapper","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"shiny (>= 0.8.0), doParallel, testthat, knitr,
rmarkdown,\nMASS","Title":"A Platform for the Study of Macroecology of Life History
Traits","URL":"https:\/\/github.com\/valcu\/rangeMapper","Version":"0.3-
0"},"rangemodelR":{"Author":"Aniruddha Marathe, ATREE, Bangalore","Depends":"R (>=
2.10)","Description":"Generates expected values of species richness, with
continuous or\nscattered ranges, for data across one or two
dimensions.","Imports":"stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rangemodelR","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"spdep,sp,ggplot2,maptools,plyr,reshape2,rgeos","Ti
tle":"Mid-Domain Effect and Species Richness Patterns","Version":"1.0"},"ranger":
{"Author":"Marvin N. Wright","Depends":"R (>= 3.1)","Description":"A fast
implementation of Random Forests, particularly suited for high dimensional data.
Ensembles\nof classification, regression, survival and probability prediction trees
are supported. Data from\ngenome-wide association studies can be analyzed
efficiently. In addition to data frames, datasets\nof class 'gwaa.data' (R package
'GenABEL') can be directly analyzed.","Imports":"Rcpp (>= 0.11.2)","License":"GPL-
3","NeedsCompilation":"yes","Package":"ranger","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"survival, testthat","Title":"A Fast Implementation of
Random Forests","Version":"0.4.0"},"rankdist":{"Author":"Zhaozhi Qian","Depends":"R
(>= 2.10)","Description":"Implements distance based probability models for ranking
data.\nThe supported distance metrics include Kendall distance, Spearman distance,
Footrule distance, Hamming distance,\n, Weighted-tau distance and Weighted Kendall
distance.\nPhi-component model and mixture models are also
supported.","Imports":"Rcpp (>= 0.11.4), hash, optimx, permute,
2)","NeedsCompilation":"yes","Package":"rankdist","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat","Title":"Distance Based Ranking
Models","Version":"1.1.2"},"rankhazard":{"Author":"Juha Karvanen, Nanni
Koski","Description":"Rank-hazard plots (Karvanen and Harrell, Statistics in
Medicine 2009) visualize the relative importance of covariates in a proportional
hazards model. The key idea is to rank the covariate values and plot the relative
hazard as a function of ranks scaled to interval [0,1]. The relative hazard is
plotted in respect to the reference hazard, which can bee.g. the hazard related to
the median of the covariate.","Imports":"survival","License":"GPL-
2","NeedsCompilation":"no","Package":"rankhazard","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"rms","Title":"Rank-Hazard Plots","Version":"1.0-
2"},"rappdirs":{"Author":"Hadley Wickham [trl, cre, cph],\nRStudio [cph],\nSridhar
Ratnakumar [aut],\nTrent Mick [aut],\nActiveState [cph] (R\/appdir.r, R\/cache.r,
R\/data.r, R\/log.r translated\nfrom appdirs),\nEddy Petrisor [ctb],\nTrevor Davis
[trl, aut],\nGabor Csardi [ctb],\nGregory Jefferis [ctb]","Depends":"R (>= 2.14),
methods","Description":"An easy way to determine which directories on the users
computer\nyou should use to save data, caches and logs. A port of Python's
'Appdirs'\n(\\url{https:\/\/github.com\/ActiveState\/appdirs}) to
R.","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"rappdirs","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat, roxygen2","Title":"Application
Directories: Determine Where to Save Data, Caches,\nand
Logs","URL":"https:\/\/github.com\/hadley\/rappdirs\nhttps:\/\/github.com\/ActiveSt
ate\/appdirs","Version":"0.3.1"},"rapport":{"Author":"Aleksandar BlagotiÄ‡
<alex@rapporter.net> and Gergely DarÃ³czi\n<daroczig@rapporter.net>","Depends":"R
(>= 2.15.0)","Description":"Facilitating the creation of reproducible
statistical\nreport templates. Once created, rapport templates can be exported
to\nvarious external formats (HTML, LaTeX, PDF, ODT etc.) with pandoc as
the\nconverter backend.","Imports":"grDevices, utils, yaml, stringr, rapportools,
pander","License":"AGPL-
3","NeedsCompilation":"no","Package":"rapport","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"A Report Templating System","URL":"http:\/\/rapport-
package.info\/","Version":"1.0"},"rapportools":{"Author":"Aleksandar BlagotiÄ‡
<alex@rapporter.net> and Gergely
DarÃ³czi\n<daroczig@rapporter.net>","Depends":"reshape","Description":"Helper
functions that act as wrappers to more advanced statistical\nmethods with the
advantage of having sane defaults for quick reporting.","Imports":"plyr,
pander","License":"AGPL-
3","NeedsCompilation":"no","Package":"rapportools","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Miscellaneous (stats) helper functions with sane
defaults for\nreporting","Version":"1.0"},"rareGE":{"Author":"Han
Chen","Description":"Tests gene-environment interaction for rare genetic variants
using Sequence Kernel Association Test (SKAT) type gene-based tests. Includes two
tests for the interaction term only, and one joint test for genetic main effects
and gene-environment interaction.","Imports":"MASS, nlme, survey","License":"GPL-
3","NeedsCompilation":"no","Package":"rareGE","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Testing Gene-Environment Interaction for Rare Genetic
Variants","URL":"http:\/\/www.hsph.harvard.edu\/han-
chen\/","Version":"0.1"},"rareNMtests":{"Author":"Luis Cayuela and Nicholas J.
Gotelli","Depends":"vegan","Description":"Randomization tests for the statistical
comparison of \\emph{i}
= two or more individual-based, sample-based or coverage-based rarefaction curves.
The ecological null hypothesis is that the \\emph{i} samples were all drawn
randomly from a single assemblage, with (necessarily) a single underlying species
abundance distribution. The biogeographic null hypothesis is that the \\emph{i}
samples were all drawn from different assemblages that, nonetheless, share similar
species richness and species abundance distributions","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rareNMtests","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Ecological and biogeographical null model tests for
comparing\nrarefaction curves","Version":"1.1"},"rasclass":{"Author":"Daniel
Wiesmann <daniel.wiesmann@ist.utl.pt> and David
Quinn\n<djq@mit.edu>","Description":"This package contains functions to perform
supervised and\npixel based raster image classification. It has been designed\nto
facilitate land-cover analysis. Five classification\nalgorithms can be used:
Maximum Likelihood Classification,\nMultinomial Logistic Regression, Neural
Networks, Random\nForests and Support Vector Machines. The output includes
the\nclassified raster and standard classification accuracy\nassessment such as the
accuracy matrix, the overall accuracy\nand the kappa coefficient. An option for in-
sample verification\nis available.","Imports":"methods, car, nnet, RSNNS, e1071,
randomForest","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rasclass","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Supervised Raster Image
Classification","Version":"0.2.1"},"rase":{"Author":"Ignacio Quintero [aut,
cre],\nForrest W. Crawford [aut],\nPetr Keil [aut]","Depends":"R (>= 2.14.0), ape
(>= 3.1-0)","Description":"The rase package primarily implements the Range
Ancestral State Estimation for phylogeography described in Quintero, I., Keil, P.,
Jetz, W., & Crawford, F. W. (2015). Historical Biogeography Using Species
Geographical Ranges. Systematic biology, 64(6), 1059-1073. It also includes
Bayesian inference of ancestral states under a Brownian Motion model of character
evolution and Maximum Likelihood estimation of rase for n-dimensional data.
Visualizing functions in 3D are implemented using the rgl
package.","Imports":"mvtnorm (>= 1.0-0), polyCub (>= 0.5-0), spatstat (>= 1.36-
0),\nrgl, sm, methods, grDevices, stats,","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rase","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"sp, ggmcmc, rpanel, tcltk","Title":"Range Ancestral State
Estimation for Phylogeography and\nComparative Analyses","Version":"0.2-
22"},"raster":{"Author":"Robert J. Hijmans [cre, aut],\nJacob van Etten [ctb],\nJoe
Cheng [ctb],\nMatteo Mattiuzzi [ctb],\nMichael Sumner [ctb],\nJonathan A. Greenberg
[ctb],\nOscar Perpinan Lamigueiro [ctb],\nAndrew Bevan [ctb],\nEtienne B. Racine
[ctb],\nAshton Shortridge [ctb]","Depends":"methods, sp (>= 1.2-0), R (>=
3.0.0)","Description":"Reading, writing, manipulating, analyzing and modeling of
gridded spatial data. The package implements basic and high-level functions.
Processing of very large files is supported.","Imports":"Rcpp","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"raster","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"rgdal (>= 0.9-1), rgeos (>= 0.3-8), ncdf4, igraph,
tcltk,\nparallel, rasterVis","Title":"Geographic Data Analysis and
Modeling","URL":"http:\/\/cran.r-project.org\/package=raster","Version":"2.5-
2"},"rasterVis":{"Author":"Oscar Perpinan Lamigueiro [cre, aut],\nRobert Hijmans
[aut]","Depends":"R (>= 2.14.0), methods, raster (>= 2.0-12),
lattice,\nlatticeExtra","Description":"Methods for enhanced visualization and
interaction with raster data. It implements visualization methods for quantitative
data and categorical data, both for univariate and multivariate rasters. It also
provides methods to display spatiotemporal rasters, and vector fields. See the
website for examples.","Imports":"stats, utils, parallel, grid, grDevices,
RColorBrewer, hexbin,\nsp (>= 1.0-6), zoo,","License":"GPL-
3","NeedsCompilation":"no","Package":"rasterVis","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"rgl, ggplot2, colorspace,
dichromat","Title":"Visualization Methods for Raster
Data","URL":"http:\/\/oscarperpinan.github.io\/rastervis","Version":"0.37"},"ratera
tio.test":{"Author":"Michael Fay <mfay@niaid.nih.gov>","Depends":"R (>= 2.4.1),
stats","Description":"A function which performs exact rate ratio tests and returns
an object of class
htest.","License":"GPL","NeedsCompilation":"no","Package":"rateratio.test","Reposit
ory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Exact rate ratio
test","Version":"1.0-2"},"raters":{"Author":"Daniele Giardiello [cre],\nPiero
Quatto [aut],\nEnrico Ripamonti [aut],\nStefano Vigliani [ctb]","Description":"The
kappa statistic implemented by Fleiss is a very popular index for assessing the
reliability of agreement among multiple observers. It is used both in the
psychological and in the psychiatric field. Other fields of application are
typically medicine, biology and engineering. Unfortunately,the kappa statistic may
behave inconsistently in case of strong agreement between raters, since this index
assumes lower values than it would have been expected. We propose a modification
kappa implemented by Fleiss in case of nominal and ordinal variables. Monte Carlo
simulations are used both to testing statistical hypotheses and to calculating
percentile bootstrap confidence intervals based on proposed statistic in case of
nominal and ordinal data.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"raters","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"A Modification of Fleiss' Kappa in Case of Nominal and
Ordinal\nVariables","Version":"2.0.1"},"rationalfun":{"Author":"Yixuan Qiu
<yixuan.qiu@cos.name>","Depends":"polynom","Description":"This package provides
several functions to\nmanipulate rational functions, including basic\narithmetic
operators, derivatives and integrals with\nEXPLICIT
forms.","Imports":"stats","License":"GPL","NeedsCompilation":"no","Package":"ration
alfun","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Manipulation of
Rational
Functions","URL":"https:\/\/github.com\/yixuan\/rationalfun","Version":"0.1-
0"},"rattle":{"Author":"Graham Williams [aut, cph, cre],\nMark Vere Culp [cph],\nEd
Cox [ctb],\nAnthony Nolan [ctb],\nDenis White [cph],\nDaniele Medri [ctb],\nAkbar
Waljee [ctb] (OOB AUC for Random Forest),\nBrian Ripley [cph] (Author of original
print.summary.nnet),\nJose Magana [ctb] (Contributed the ggpairs
plots.)","Depends":"R (>= 2.13.0)","Description":"The R Analytic Tool To Learn
Easily (Rattle) provides a\nGnome (RGtk2) based interface to R functionality for
data mining.\nThe aim is to provide a simple and intuitive interface\nthat allows a
user to quickly load data from a CSV file\n(or via ODBC), transform and explore the
data,\nbuild and evaluate models, and export models as PMML (predictive\nmodelling
markup language) or as scores. All of this with knowing little\nabout R. All R
commands are logged and commented through the log tab. Thus they\nare available to
the user as a script file or as an aide for the user to\nlearn R or to copy-and-
paste directly into R itself.\nRattle also exports a number of utility\nfunctions
and the graphical user interface, invoked as rattle(), does\nnot need to be run to
deploy these.","Imports":"stats, utils, grDevices, graphics, methods, RGtk2,
magrittr,\nstringi","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rattle","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"pmml (>= 1.2.13), bitops, colorspace, ada, amap,
arules,\narulesViz, biclust, cairoDevice, cba, cluster, corrplot, descr,\ndoBy,
dplyr, e1071, ellipse, fBasics, foreign, fpc, gdata,\nggdendro, ggplot2, gplots,
graph, grid, gridExtra, gtools,\ngWidgetsRGtk2, hmeasure, Hmisc, kernlab, Matrix,
mice, nnet,\nodfWeave, party, playwith, plyr, psych, randomForest,
RBGL,\nRColorBrewer, readxl, reshape, rggobi, RGtk2Extras, ROCR,\nRODBC, rpart,
rpart.plot, SnowballC, stringr, survival,\ntimeDate, tm, verification, wskm, XML,
pkgDepTools, Rgraphviz","Title":"Graphical User Interface for Data Mining in
R","URL":"http:\/\/rattle.togaware.com\/","Version":"4.1.0"},"rbamtools":
{"Author":"Wolfgang Kaisers","Depends":"methods","Description":"Provides an
interface to functions of the 'SAMtools' C-Library by Heng
Li.","License":"Artistic-
2.0","NeedsCompilation":"yes","Package":"rbamtools","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"xtable","Title":"Read and Write BAM (Binary
Alignment) Files","Version":"2.14.3"},"rbefdata":{"Author":"Claas-Thido Pfaff [cre,
aut],\nKarin Nadrowski [aut],\nXingxing Man [aut]","Description":"Basic R package
to access data structures offered by any\nBEFdata portal instance.","Imports":"XML,
RCurl, rjson, wordcloud, rtematres, RColorBrewer","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rbefdata","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"ggplot2, plyr","Title":"BEFdata R
package","URL":"https:\/\/github.com\/befdata\/rbefdata","Version":"0.3.5"},"rbench
mark":{"Author":"Wacek Kusnierczyk <waku@idi.ntnu.no>","Description":"rbenchmark is
inspired by the Perl module Benchmark, and\nis intended to facilitate benchmarking
of arbitrary R code. The\nlibrary consists of just one function, benchmark, which
is a\nsimple wrapper around system.time. Given a specification of\nthe
benchmarking process (counts of replications, evaluation\nenvironment) and an
arbitrary number of expressions, benchmark\nevaluates each of the expressions in
the specified environment,\nreplicating the evaluation as many times as specified,
and\nreturning the results conveniently wrapped into a data frame.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"rbenchmark","Repository":"http:\/\/cran.csir
o.au\/src\/contrib
","Title":"Benchmarking routine for
R","URL":"http:\/\/rbenchmark.googlecode.com","Version":"1.0.0"},"rbhl":
{"Author":"Scott Chamberlain [aut, cre]","Description":"Interface to 'Biodiversity'
'Heritage' Library ('BHL') 'API'\nmethods. 'BHL' is a repository of 'digitized'
literature on 'biodiversity'\nstudies, including 'floras', research papers, and
more.","Imports":"methods, utils, stats, httr, XML, jsonlite, plyr","License":"MIT
+ file
LICENSE","NeedsCompilation":"no","Package":"rbhl","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat, roxygen2, knitr","Title":"Interface to the
'Biodiversity' 'Heritage'
Library","URL":"https:\/\/github.com\/ropensci\/rbhl","Version":"0.2.0"},"rbiouml":
{"Author":"Ivan Yevshin [aut, cre],\nTagir Valeev [aut]","Depends":"RCurl,
RJSONIO","Description":"Functions for connecting to BioUML server, querying BioUML
repository and launching BioUML analyses.","License":"GPL-
2","NeedsCompilation":"no","Package":"rbiouml","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Interact with BioUML Server","Version":"1.7"},"rbison":
{"Author":"Scott Chamberlain [aut, cre]","Description":"Interface to the 'USGS'
'BISON' 'API', a 'database' for\nspecies occurrence data on the web. Data comes
from species in the\nUnited States from participating data providers. You can
get\ndata via 'taxonomic' and location based queries. A simple function\nis
provided to help visualize data.","Imports":"methods, stats, plyr, httr, ggplot2,
mapproj, grid, sp, dplyr,\njsonlite","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rbison","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"knitr, testthat, taxize","Title":"Interface to the
'USGS' 'BISON'
'API'","URL":"https:\/\/github.com\/ropensci\/rbison","Version":"0.4.8"},"rbitcoinc
hartsapi":{"Author":"Thomas P. Fuller
<thomas.fuller@coherentlogic.com>","Depends":"R (>= 3.0.3), RJSONIO,
RCurl","Description":"An R package for the BitCoinCharts.com API.","License":"LGPL-
3","NeedsCompilation":"no","Package":"rbitcoinchartsapi","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"R Package for the BitCoinCharts.com
API","URL":"http:\/\/www.r-
project.org,\nhttp:\/\/www.coherentlogic.com\/wordpress\/?
page_id=3580&source=cran","Version":"1.0.4"},"rbmn":{"Author":"Jean-Baptiste Denis
<Jean-Baptiste.Denis@jouy.inra.fr>","Depends":"MASS","Description":"Creation,
manipulation, simulation of linear Gaussian Bayesian\nnetworks from text files and
more...","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rbmn","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"bnlearn, igraph","Title":"Handling Linear Gaussian
Bayesian Networks","Version":"0.9-2"},"rbokeh":{"Author":"Ryan Hafen [aut,
cre],\nKenton Russell [ctb],\nJonathan Owen [ctb],\nBarret Schloerkep
[ctb],\nSaptasrhi Guha [ctb],\nContinuum Analytics, Inc. [aut, cph] (Bokeh library
in htmlwidgets\/lib,\nhttp:\/\/bokeh.pydata.org)","Description":"R interface for
creating plots in Bokeh. Bokeh by Continuum\nAnalytics,
\\url{http:\/\/bokeh.pydata.org\/en\/latest\/}.","Enhances":"shiny (>=
0.12)","Imports":"htmlwidgets (>= 0.5), maps, methods, jsonlite, digest,
hexbin,\nlazyeval, pryr, magrittr, ggplot2, scales, gistr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rbokeh","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat, data.table, lattice, roxygen2 (>=
5.0.0)","Title":"R Interface for
Bokeh","URL":"https:\/\/hafen.github.io\/rbokeh","Version":"0.4.2"},"rbounds":
{"Author":"Luke J. Keele","Depends":"R (>= 2.8.1), Matching","Description":"Takes
matched and unmatched data and calculates Rosenbaum bounds for the treatment
effect. Calculates bounds for binary outcome data, Hodges-Lehmann point estimates,
Wilcoxon signed-rank test for matched data and matched IV estimators, Wilcoxon sum
rank test, and for data with multiple matched controls. Package is also designed to
work with the Matching package and operate on Match() objects.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rbounds","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Perform Rosenbaum bounds sensitivity tests for matched
and\nunmatched data","Version":"2.1"},"rbugs":{"Author":"Jun Yan
<jyan@stat.uconn.edu> and Marcos
Prates\n<marcosop@est.ufmg.br>","Description":"Functions to prepare files needed
for running BUGS in\nbatch-mode, and running BUGS from R. Support for Linux
and\nWindows systems with OpenBugs is emphasized.","License":"GPL (>=
3.0)","NeedsCompilation":"no","Package":"rbugs","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"coda (>= 0.13-5)","Title":"Fusing R and OpenBugs and
Beyond","Version":"0.5-9"},"rbundler":{"Author":"Yoni Ben-Meshulam
<yoni.bmesh@gmail.com>","Depends":"R (>= 2.15.1), devtools (>=
1.3)","Description":"Rbundler manages a project-specific library for
dependency\npackage installation. By specifying dependencies in a DESCRIPTION
file\nin a project's root directory, one may install and use dependencies\nin a
repeatable fashion without requiring manual maintenance.\nrbundler creates a
project-specific R library in\n`PROJECT_ROOT\/.Rbundle` (by default) and a project-
specific\n`R_LIBS_USER` value, set in `PROJECT_ROOT\/.Renviron`. It
supports\ndependency management for R
standard \"Depends\", \"Imports\",\n\"Suggests\", and \"LinkingTo\" package
dependencies. rbundler also\nattempts to validate and install versioned
dependencies, such\nas \">=\", \"==\", \"<=\". Note that, due to the way R manages
package\ninstallation, differing nested versioned dependencies are not\nallowed.
For example, if your project depends on packages A (== 1),\nand B (== 2), but
package A depends on B (== 1), then a nested\ndependency violation will cause
rbundler to error out.","License":"GPL-
3","NeedsCompilation":"no","Package":"rbundler","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"testthat (>= 0.8), roxygen2","Title":"Rbundler manages
an application's dependencies systematically\nand
repeatedly","Version":"0.3.7"},"rbvs":{"Author":"Rafal Baranowski, Patrick Breheny,
Isaac Turner","Depends":"stats","Description":"Implements the Ranking-Based
Variable Selection\nalgorithm for variable selection in high-dimensional
2)","NeedsCompilation":"yes","Package":"rbvs","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Ranking-Based Variable
Selection","Version":"1.0.2"},"rcanvec":{"Author":"Dewey Dunnington
<dewey@fishandwhistle.net>","Depends":"R (>= 2.10), sp","Description":"Provides an
interface to the National Topographic System (NTS),\nwhich is the way in which a
number of freely available Canadian datasets are\norganized. CanVec and CanVec+
datasets, which include all data used to create\nCanadian topographic maps, are two
such datasets that are useful in creating\nvector-based maps for locations across
Canada. This packages searches CanVec\ndata by location, plots it using pretty
defaults, and exports it to human-\nreadable shapefiles for use in another
GIS.","Imports":"rgdal","License":"GPL-
2","NeedsCompilation":"no","Package":"rcanvec","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"prettymapr, testthat","Title":"Access and Plot CanVec
and CanVec+ Data for Rapid Basemap\nCreation in
Canada","URL":"https:\/\/github.com\/paleolimbot\/rcanvec","Version":"0.2.0"},"rcba
lance":{"Author":"Samuel D. Pimentel","Depends":"R (>= 3.2.0), MASS,
plyr","Description":"Tools for large, sparse optimal matching of treated units\nand
control units in observational studies. Provisions are\nmade for refined covariate
balance constraints, which include\nfine and near-fine balance as special cases.
Matches are\noptimal in the sense that they are computed as solutions to\nnetwork
optimization problems rather than greedy algorithms.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rcbalance","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"optmatch, testthat","Title":"Large, Sparse
Optimal Matching with Refined Covariate Balance","Version":"1.8.2"},"rcbsubset":
{"Author":"Samuel D. Pimentel","Depends":"R (>= 3.2.0), MASS,
plyr","Description":"Tools for optimal subset matching of treated units\nand
control units in observational studies, with support\nfor refined covariate balance
constraints, (including\nfine and near-fine balance as special cases). A
close\nrelative is the 'rcbalance' package.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rcbsubset","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"rcbalance, optmatch, testthat","Title":"Optimal
Subset Matching with Refined Covariate Balance","Version":"1.1.2"},"rcdd":
{"Author":"Charles J. Geyer <charlie@stat.umn.edu> and\nGlen D. Meeden
<glen@stat.umn.edu>, incorporates code from\ncddlib (ver 0.94f) written by Komei
Fukuda <fukuda@ifor.math.ethz.ch>","Depends":"R (>= 3.0.0)","Description":"R
interface to (some of)
cddlib\n(http:\/\/www.ifor.math.ethz.ch\/~fukuda\/cdd_home\/cdd.html).\nConverts
back and forth between two representations of a convex polytope:\nas solution of a
set of linear equalities and inequalities and as\nconvex hull of set of points and
rays.\nAlso does linear programming and redundant generator elimination\n(for
example, convex hull in n dimensions). All functions can use exact\ninfinite-
precision rational arithmetic.","Imports":"methods","License":"GPL-
2","NeedsCompilation":"yes","Package":"rcdd","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Computational
Geometry","URL":"http:\/\/www.stat.umn.edu\/geyer\/rcdd\/","Version":"1.1-
9"},"rcdk":{"Author":"Rajarshi Guha [aut, cre,
cph]","Depends":"fingerprint","Description":"This package allows the user to access
functionality in the\nCDK, a Java framework for cheminformatics. This allows the
user to load\nmolecules, evaluate fingerprints, calculate molecular
descriptors and so on.\nIn addition the CDK API allows the user to view structures
in 2D.","Imports":"rJava, rcdklibs (>= 1.5.8), methods, png,
iterators","License":"LGPL","NeedsCompilation":"no","Package":"rcdk","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Suggests":"xtable, RUnit","Title":"rcdk -
Interface to the CDK Libraries","Version":"3.3.2"},"rcdklibs":{"Author":"Rajarshi
Guha [aut, cre],\nCDK Project [ctb, cph] (CDK Java library contained in multiple
jar files)","Depends":"R (>= 2.0.0), rJava","Description":"This package provides
the CDK libraries for use\nin the R environment. Given the size of the library
itself,\nthis package is not expected to change very frequently. To make\nuse of
the CDK within R, it is suggested that you use the rcdk\npackage. Note that it is
possible to directly interact with the CDK\nusing rJava. However rcdk exposes
functionality in a more idiomatic way.\nThe CDK library itself is released as LGPL
and the sources can be\nobtained from
https:\/\/github.com\/cdk\/cdk","License":"LGPL","NeedsCompilation":"no","Package":
"rcdklibs","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"rcdklib -
CDK libraries packaged for R","Version":"1.5.8.4"},"rchallenge":{"Author":"Adrien
Todeschini [aut, cre],\nRobin Genuer [ctb]","Depends":"R (>=
3.2.0)","Description":"A simple data science challenge system using R Markdown and
Dropbox <https:\/\/www.dropbox.com\/>.\nIt requires no network configuration, does
not depend on external platforms\nlike e.g. Kaggle <https:\/\/www.kaggle.com\/> and
can be easily installed on a personal computer.","Imports":"rmarkdown (>= 0.5.1),
knitr (>= 1.6)","License":"GPL-
2","NeedsCompilation":"no","Package":"rchallenge","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"A Simple Data Science Challenge
System","URL":"https:\/\/adrtod.github.io\/rchallenge","Version":"1.1.1"},"rchess":
{"Author":"Joshua Kunst <jbkunst@gmail.com>","Description":"R package for chess
validations, pieces movements and check\ndetection. Also integrates functions to
plot chess boards given a\nForsyth Edwards and Portable Game
notations.","Imports":"htmlwidgets, V8, R6, ggplot2, plyr, dplyr,
assertthat","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rchess","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Chess Move, Generation\/Validation, Piece Placement\/
Movement,\nand Check\/Checkmate\/Stalemate
Detection","URL":"https:\/\/github.com\/jbkunst\/rchess","Version":"0.1"},"rcicr":
{"Author":"Ron Dotsch <rdotsch@gmail.com>","Description":"Functions to generate
stimuli and analyze data of reverse correlation image classification experiments
(psychophysical tasks aimed at visualizing cognitive mental representations of
faces).","Imports":"matlab, aspace, jpeg, dplyr","License":"GPL-
2","NeedsCompilation":"no","Package":"rcicr","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Reverse-Correlation Image-Classification
Toolbox","URL":"http:\/\/ron.dotsch.org\/rcicr","Version":"0.3.2.1"},"rclinicaltria
ls":{"Author":"Michael C Sachs <sachsmc@gmail.com>","Depends":"R (>=
3.0.0)","Description":"ClinicalTrials.gov is a registry and results database of
publicly\nand privately supported clinical studies of human participants
conducted\naround the world. Users can search for information about and results
from\nthose trials. This provides a set of functions to interact with the
search\nand download features. Results are downloaded to temporary directories
and\nreturned as R objects.","Imports":"httr, XML, plyr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rclinicaltrials","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Suggests":"devtools, knitr, roxygen2, testthat,
ggplot2","Title":"Download Aggregate Trial Information and Results
from\nClinicalTrials.gov","Version":"1.4.1"},"rcmdcheck":{"Author":"Gabor
Csardi","Description":"Run 'R CMD check' from 'R' programmatically, and capture
the\nresults of the individual checks.","Imports":"clisymbols, crayon,
withr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rcmdcheck","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat","Title":"Run 'R CMD check' from 'R'
and Capture
Results","URL":"https:\/\/github.com\/MangoTheCat\/rcmdcheck","Version":"1.0.0"},"r
corpora":{"Author":"Darius Kazemi, Matthew Rothenberg, Karl Swedberg, Matthew
Hokanson,\nNathan Lachenmyer, Aaron Marriner, Mark Sample, Casey
Kolderup,\nNathaniel Mitchell, Daniel D. Beck, Mike Nowak, Ryan Freebern,\nRoss
Barclay, Ross Binden, Justin Alford, Cole Willsea,\nAndrew Gorman, Javier Arce,
Patrick Rodriguez,\nLiam Cooke, Will Hankinson, K. Adam White, Garrett Miller, Zac
Moody,\nJordan Killpack, Brian Jones, Greg Borenstein, Noah Swartz, Nathan
Black,\nRussell Horton, Mark Wunsch, Kay Belardinelli, Colin Mitchell,\nMichael
Dewberry, Joe Mahoney","Description":"A collection of small text corpora of
interesting data.\nIt contains all data sets from
https:\/\/github.com\/dariusk\/corpora.\nSome examples:\nnames of animals: birds,
dinosaurs, dogs; foods: beer categories,\npizza toppings; geography: English towns,
rivers, oceans;\nhumans: authors, US presidents, occupations; science:
elements,\nplanets; words: adjectives, verbs, proverbs, US president
quotes.","Imports":"jsonlite,
utils","License":"CC0","NeedsCompilation":"no","Package":"rcorpora","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Title":"A Collection of Small Text Corpora of
Interesting
Data","URL":"https:\/\/github.com\/gaborcsardi\/rcorpora","Version":"1.1.1"},"rcppb
ugs":{"Author":"Whit Armstrong <armstrong.whit@gmail.com>","Depends":"Rcpp (>=
0.11)","Description":"R binding for cppbugs","License":"GPL-
3","NeedsCompilation":"yes","Package":"rcppbugs","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"R binding for
cppbugs","URL":"http:\/\/github.com\/armstrtw\/rcppbugs","Version":"0.1.4.2"},"rcro
ssref":{"Author":"Scott Chamberlain [aut, cre],\nCarl Boettiger [aut],\nTed Hart
[aut],\nKarthik Ram [aut]","Description":"Client for various 'CrossRef' 'APIs',
including 'metadata' search\nwith their old and newer search 'APIs', get
'citations' in various formats\n(including 'bibtex', 'citeproc-json', 'rdf-xml',
etc.), convert 'DOIs'\nto 'PMIDs', and 'vice versa', get citations for 'DOIs', and
get links to\nfull text of articles when available.","Imports":"utils, methods,
stats, jsonlite, httr (>= 1.0.0), xml2, plyr,\nbibtex, dplyr, R6","License":"MIT +
file
LICENSE","NeedsCompilation":"no","Package":"rcrossref","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat, knitr","Title":"Client for Various
'CrossRef'
'APIs'","URL":"https:\/\/github.com\/ropensci\/rcrossref","Version":"0.5.2"},"rcryp
t":{"Author":"Brett Klamer [aut, cre]","Depends":"R (>=
3.0.0)","Description":"Provides easy symmetric file encryption using GPG
with\ncryptographically strong defaults. Only symmetric encryption is\nsupported.
GPG is pre-installed with most Linux distributions.\nWindows users will need to
install 'Gpg4win' (http:\/\/www.gpg4win.org\/).\nOS X users will need to install
'GPGTools' (https:\/\/gpgtools.org\/).","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rcrypt","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat","Title":"Symmetric File Encryption Using
GPG","URL":"http:\/\/brettklamer.com\/work\/rcrypt\/","Version":"0.1.1"},"rda":
{"Author":"Yaqian Guo <yaqiang@stat.stanford.edu> Trevor
Hastie\n<hastie@stat.stanford.edu> Robert
Tibshirani\n<tibs@stanford.edu>","Depends":"R (>= 2.10)","Description":"Shrunken
Centroids Regularized Discriminant Analysis for\nthe classification purpose in high
dimensional data.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rda","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Shrunken Centroids Regularized Discriminant
Analysis","URL":"http:\/\/www.r-project.org","Version":"1.0.2-2"},"rdatacite":
{"Author":"Scott Chamberlain [aut, cre]","Description":"Client for the web service
methods provided\nby 'DataCite' (<https:\/\/www.datacite.org\/>), including
functions to interface with\ntheir 'OAI-PMH' 'metadata' service, and a 'RESTful'
search 'API'. The 'API'\nis backed by 'SOLR', allowing expressive queries,
including faceting,\nstatistics on variables, and 'more-like-this'
queries.","Imports":"oai (>= 0.2.0), solrium (>= 0.3.0)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rdatacite","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"knitr, testthat","Title":"'DataCite' Client for
'OAI-PMH' Methods and their Search
'API'","URL":"https:\/\/github.com\/ropensci\/rdatacite","Version":"0.1.0"},"rdatam
arket":{"Author":"Gunnlaugur Thor Briem <gthb@datamarket.com>","Depends":"R (>=
2.10.0), zoo","Description":"Fetches data from DataMarket.com, either
as\ntimeseries in zoo form (dmseries) or as long-form data\nframes (dmlist).
Metadata including dimension structure\nis fetched with dminfo, or just the
dimensions with\ndmdims.","Imports":"RCurl, RJSONIO","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rdatamarket","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Data access API for
DataMarket.com","URL":"http:\/\/datamarket.com\/api\/lib\/rdatamarket","Version":"0
.6.5"},"rdd":{"Author":"Drew Dimmery","Depends":"R (>= 2.15.0), sandwich, lmtest,
AER, Formula","Description":"Provides the tools to undertake estimation
in\nRegression Discontinuity Designs. Both sharp and fuzzy designs are\nsupported.
Estimation is accomplished using local linear regression.\nA provided function will
utilize Imbens-Kalyanaraman optimal\nbandwidth calculation. A function is also
included to test the\nassumption of no-sorting effects.","License":"Apache License
(==
2.0)","NeedsCompilation":"no","Package":"rdd","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Regression
Discontinuity Estimation","Version":"0.57"},"rddtools":{"Author":"Matthieu Stigler
[aut],\nBastiaan Quast [aut, cre]","Depends":"AER, np","Description":"Set of
functions for Regression Discontinuity Design ('RDD'), for\ndata visualisation,
estimation and testing.","Imports":"KernSmooth, ggplot2, rdd, sandwich, lmtest,
Formula, locpol,\nmethods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rddtools","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"stats4, car, knitr, testthat","Title":"Toolbox for
Regression Discontinuity Design
('RDD')","URL":"https:\/\/github.com\/bquast\/RDDtools","Version":"0.4.0"},"rdetool
s":{"Author":"Jan Saputra Mueller","Description":"The package provides functions
for estimating the relevant\ndimension of a data set in feature spaces,
applications to\nmodel selection, graphical illustrations and
prediction.","License":"GPL-
2","NeedsCompilation":"no","Package":"rdetools","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Relevant Dimension Estimation (RDE) in Feature
Spaces","Version":"1.0"},"rdian":{"Author":"Oliver Keyes","Description":"A client
library for 'The Guardian' (https:\/\/www.guardian.com\/)\nand their API, this
package allows users to search for Guardian articles and\nretrieve both the content
and metadata.","Imports":"httr, curl","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rdian","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat","Title":"Client Library for The
Guardian","URL":"https:\/\/github.com\/ironholds\/rdian","Version":"0.1.1"},"rdnb":
{"Author":"Christian Graul","Description":"A wrapper for the Deutsche
Nationalbibliothek (German National Library) API, available at
<http:\/\/www.dnb.de>. The German National Library is the German central archival
library, collecting, archiving, bibliographically classifying all German and
German-language publications from 1913, foreign publications about Germany,
translations of German works, and the works of German-speaking emigrants published
abroad between 1933 and 1945. A personal access token is required for
usage.","Imports":"brew, grDevices, httr, methods, utils, stats,
xml2","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rdnb","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr","Title":"R Interface to the Deutsche
Nationalbibliothek (German National\nLibrary)
API","URL":"https:\/\/github.com\/chgrl\/rdnb","Version":"0.1-0"},"rdrobust":
{"Author":"Sebastian Calonico <scalonico@bus.miami.edu>, Matias D. Cattaneo
<cattaneo@umich.edu>, Rocio Titiunik <titiunik@umich.edu>","Depends":"R (>=
3.0.2)","Description":"Regression-discontinuity (RD) designs are quasi-experimental
research designs popular in social, behavioral and natural sciences. The RD design
is usually employed to study the (local) causal effect of a treatment, intervention
or policy. This package provides tools for data-driven graphical and analytical
statistical inference in RD\tdesigns: rdrobust to construct local-polynomial point
estimators and robust confidence intervals for average treatment effects at the
\tcutoff in Sharp, Fuzzy and Kink RD settings, rdbwselect to perform bandwidth
selection for the different procedures implemented, and rdplot to conduct
exploratory data analysis (RD plots).","License":"GPL-
2","NeedsCompilation":"no","Package":"rdrobust","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Robust Data-Driven Statistical Inference in\nRegression-
Discontinuity Designs","Version":"0.80"},"rdrop2":{"Author":"Karthik Ram [aut,
cre]","Depends":"R (>= 3.1.1)","Description":"Provides full programmatic access to
the Dropbox file hosting platform (dropbox.com), including support for all standard
file operations.","Imports":"assertthat, data.table, dplyr, httr, jsonlite,
magrittr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rdrop2","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat, uuid","Title":"Programmatic Interface to
the 'Dropbox' API","Version":"0.7.0"},"rdryad":{"Author":"Scott Chamberlain [aut,
cre],\nCarl Boettiger [aut],\nKarthik Ram [aut]","Description":"Interface to the
Dryad Solr API, their OAI-PMH service, and\nfetch datasets.","Imports":"utils, httr
(>= 1.0.0), xml2, oai, solr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rdryad","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat","Title":"Access for Dryad Web
Services","URL":"https:\/\/github.com\/ropensci\/rdryad","Version":"0.2.0"},"reGeno
typer":{"Author":"Yang Li <yang.li@rug.nl>","Depends":"R (>= 3.0.1), gplots, zoo,
methods, MatrixEQTL","Description":"Detecting mislabeled samples in genetic
data.","License":"GPL","NeedsCompilation":"no","Package":"reGenotyper","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Title":"Detecting Mislabeled Samples in
Genetic Data","Version":"1.2.0"},"reReg":{"Author":"Sy Han (Steven)
Chiou","Description":"A collection of regression models for recurrent event process
and failure time.","Imports":"BB, MASS, SQUAREM, aftgee, survival","License":"GPL
(>=
3)","NeedsCompilation":"yes","Package":"reReg","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Recurrent Event Regression","Version":"1.0-
0"},"readBrukerFlexData":{"Author":"Sebastian Gibb [aut, cre]","Depends":"R (>=
2.15.0)","Description":"Reads data files acquired by MALDI-TOF MS on Bruker
Daltonics\nmachines of the *flex series.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"readBrukerFlexData","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Title":"Reads Mass Spectrometry Data in Bruker *flex
Format","URL":"http:\/\/strimmerlab.org\/software\/maldiquant\/\nhttps:\/\/github.c
om\/sgibb\/readBrukerFlexData\/","Version":"1.8.2"},"readGenalex":
{"Author":"Douglas G. Scofield [aut, cre]","Depends":"R (>=
3.0.0)","Description":"A collection of R functions to read, write, manipulate,
and\nconvert genotype data in GenAlEx format. GenAlEx is a widely-used
Excel\nplugin for manipulating and analysing genotype data. This package
reads\nGenAlEx data from text or Excel files and creates an annotated data
frame\nof class 'genalex'. Several functions are provided for
accessing,\nmanipulating, printing, writing and converting this data. GenAlEx and
its\ndocumentation are available at http:\/\/biology-
assets.anu.edu.au\/GenAlEx.","Imports":"pegas (>= 0.7)","License":"LGPL-3 | file
LICENSE","NeedsCompilation":"no","Package":"readGenalex","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"XLConnect, testthat, genetics, combinat,
gdata, gtools, MASS,\nmvtnorm, ape (>= 2.4), adegenet","Title":"Read, Write,
Manipulate and Convert GenAlEx-Format
Genotype\nFiles","URL":"https:\/\/github.com\/douglasgscofield\/readGenalex","Versi
on":"1.0"},"readMLData":{"Author":"Petr Savicky","Description":"Functions for
reading data sets in different formats\nfor testing machine learning tools are
provided. This allows to run\na loop over several data sets in their original form,
for example\nif they are downloaded from UCI Machine Learning Repository.\nThe data
are not part of the package and have to be
downloaded\nseparately.","Imports":"XML","License":"GPL-
3","NeedsCompilation":"no","Package":"readMLData","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Reading Machine Learning Benchmark Data Sets in
Different\nFormats","URL":"http:\/\/www.cs.cas.cz\/~savicky\/readMLData","Version":
"0.9-7"},"readMzXmlData":{"Author":"Sebastian Gibb [aut, cre]","Depends":"R (>=
2.15.0)","Description":"Functions for reading mass spectrometry data in mzXML
format.","Imports":"base64enc, digest, XML","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"readMzXmlData","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Reads Mass Spectrometry Data in mzXML
Format","URL":"http:\/\/strimmerlab.org\/software\/maldiquant\/\nhttps:\/\/github.c
om\/sgibb\/readMzXmlData\/","Version":"2.8.1"},"readODS":{"Author":"Gerrit-Jan
Schutten, Chung-hong Chan","Description":"Read ODS (OpenDocument Spreadsheet) and
puts them into data frames.","Imports":"xml2, cellranger, readr","License":"GPL-
3","NeedsCompilation":"no","Package":"readODS","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"dplyr, testthat","Title":"Read ODS
Files","Version":"1.6.2"},"readbitmap":{"Author":"Gregory
Jefferis","Description":"Identifies and reads Windows BMP, JPEG and PNG format
bitmap\nimages. Identification defaults to the use of the magic number embedded
in\nthe file rather than the file extension. Reading of JPEG and PNG image\ndepends
on libjpg and libpng libraries. See file INSTALL for details
if\nnecessary.","Imports":"bmp, jpeg, png","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"readbitmap","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"pixmap, testthat","Title":"Simple Unified Interface
to Read Bitmap Images
(BMP,JPEG,PNG)","URL":"https:\/\/github.com\/jefferis\/readbitmap","Version":"0.1-
4"},"readbulk":{"Author":"Pascal J. Kieslich [aut, cre],\nFelix Henninger
[aut]","Depends":"R (>= 3.1.0)","Description":"Combine multiple data files from a
common directory.\nThe data files will be read into R and bound together, creating
a\nsingle large data.frame. A general function is provided along with\na specific
function for data that was collected using the open-source\nexperiment builder
'OpenSesame' <http:\/\/osdoc.cogsci.nl\/>.","Imports":"utils, plyr","License":"GPL-
3","NeedsCompilation":"no","Package":"readbulk","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Read and Combine Multiple Data
Files","URL":"https:\/\/github.com\/pascalkieslich\/readbulk","Version":"1.0.0"},"r
eader":{"Author":"Nicholas Cooper","Depends":"R (>= 2.10), utils, NCmisc (>=
1.1)","Description":"A set of functions to simplify reading data from files. The
main function, reader(), should
read most common R datafile types without needing any parameters except the
filename. Other functions provide simple ways of handling file paths and
extensions, and automatically detecting file format and
structure.","Imports":"grDevices, graphics, stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"reader","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Suite of Functions to Flexibly Read Data from
Files","Version":"1.0.5"},"readr":{"Author":"Hadley Wickham [aut, cre],\nRomain
Francois [aut],\nR Core Team [ctb] (Date time code adapted from R),\nRStudio
[cph]","Depends":"R (>= 3.0.2)","Description":"Read flat\/tabular text files from
disk (or a connection).","Imports":"Rcpp (>= 0.11.5), curl","License":"GPL (>= 2) |
file
LICENSE","NeedsCompilation":"yes","Package":"readr","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat, knitr, rmarkdown, stringi","Title":"Read
Tabular
Data","URL":"https:\/\/github.com\/hadley\/readr","Version":"0.2.2"},"readstata13":
{"Author":"Jan Marvin Garbuszus [aut],\nSebastian Jeworutzki [aut, cre],\nR Core
Team [cph],\nMagnus Thor Torfason [ctb]","Description":"Function to read and write
the Stata file format.","Imports":"Rcpp (>= 0.11.5)","License":"GPL-2 | file
LICENSE","NeedsCompilation":"yes","Package":"readstata13","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Import Stata Data
Files","URL":"https:\/\/github.com\/sjewo\/readstata13","Version":"0.8.2"},"readxl"
:{"Author":"Hadley Wickham [aut, cre],\nRStudio [cph] (Copyright holder of all R
code and all C\/C++ code\nwithout explicit copyright attribution),\nMarcin
Kalicinski [ctb, cph] (Author of included RapidXML code),\nKomarov Valery [ctb,
cph] (Author of included libxls code),\nChristophe Leitienne [ctb, cph] (Author of
included libxls code),\nBob Colbert [ctb, cph] (Author of included libxls
code),\nDavid Hoerl [ctb, cph] (Author of included libxls
code)","Description":"Import excel files into R. Supports '.xls' via the
embedded\n'libxls' C library (http:\/\/sourceforge.net\/projects\/libxls\/) and
'.xlsx' via\nthe embedded 'RapidXML' C++ library
(http:\/\/rapidxml.sourceforge.net). Works on\nWindows, Mac and Linux without
external dependencies.","Imports":"Rcpp (>= 0.11.5)","License":"GPL-3 + file
LICENSE","NeedsCompilation":"yes","Package":"readxl","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat","Title":"Read Excel
Files","Version":"0.1.1"},"reams":{"Author":"Philip Reiss <phil.reiss@nyumc.org>
and Lei Huang\n<huangracer@gmail.com>","Depends":"R (>= 2.9.0), leaps,
mgcv","Description":"Resampling methods for adaptive linear model selection.\nThese
can be thought of as extensions of the Akaike information\ncriterion that account
for searching among candidate models.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"reams","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Resampling-Based Adaptive Model
Selection","Version":"0.1"},"rebird":{"Author":"Rafael Maia [aut],\nScott
Chamberlain [aut],\nAndy Teucher [aut],\nSebastian Pardo [aut,
cre]","Description":"A programmatic client for the eBird database, including
functions\nfor searching for bird observations by geographic location
(latitude,\nlongitude), eBird hotspots, location identifiers, by notable sightings,
by\nregion, and by taxonomic name.","Imports":"methods, utils, stats, httr (>=
1.0.0), jsonlite, dplyr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rebird","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"knitr, testthat","Title":"R Client for the eBird
Database of Bird
Observations","URL":"http:\/\/github.com\/ropensci\/rebird","Version":"0.3.0"},"reb
mix":{"Author":"Marko Nagode [aut, cre]","Depends":"R (>= 2.10)","Description":"R
functions for random univariate and multivariate finite mixture model generation,
estimation, clustering and classification. Variables can be continuous, discrete,
independent or dependent and may follow normal, lognormal, Weibull, gamma,
binomial, Poisson or Dirac parametric families.","Imports":"methods, stats, utils,
graphics, grDevices, mvtnorm","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"rebmix","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"flexmix, mclust, mixtools","Title":"Finite Mixture
Modeling, Clustering & Classification","Version":"2.8.1"},"rebus":
{"Author":"Richard Cotton [aut, cre]","Depends":"R (>= 3.1.0)","Description":"Build
regular expressions piece by piece using human readable code.\nThis package is
designed for interactive use. For package development, use\nthe rebus.*
dependencies.","Imports":"rebus.base, rebus.datetimes, rebus.numbers,
rebus.unicode","License":"Unlimited","NeedsCompilation":"no","Package":"rebus","Rep
ository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Buil
d Regular Expressions in a Human Readable Way","Version":"0.1-0"},"rebus.base":
regular expressions piece by piece using human readable code.\nThis package
contains core functionality, and is primarily intended to be\nused by package
developers.","Imports":"stats","License":"Unlimited","NeedsCompilation":"no","Packa
ge":"rebus.base","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"st
ringi, testthat","Title":"Core Functionality for the 'rebus'
Package","Version":"0.0-1"},"rebus.datetimes":{"Author":"Richard Cotton [aut,
cre]","Depends":"R (>= 3.1.0)","Description":"Build regular expressions piece by
piece using human readable code.\nThis package contains date and time
functionality, and is primarily intended\nto be used by package
developers.","Imports":"rebus.base","License":"Unlimited","NeedsCompilation":"no","
Package":"rebus.datetimes","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Sug
gests":"stats, testthat","Title":"Date and Time Extensions for the 'rebus'
Package","Version":"0.0-1"},"rebus.numbers":{"Author":"Richard Cotton [aut,
cre]","Depends":"R (>= 3.1.0)","Description":"Build regular expressions piece by
piece using human readable code.\nThis package contains number-related
functionality, and is primarily intended\nto be used by package
developers.","Imports":"rebus.base,
utils","License":"Unlimited","NeedsCompilation":"no","Package":"rebus.numbers","Rep
ository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Nume
ric Extensions for the 'rebus' Package","Version":"0.0-1"},"rebus.unicode":
regular expressions piece by piece using human readable code.\nThis package
contains Unicode functionality, and is primarily intended to be\nused by package
developers.","Imports":"rebus.base","License":"Unlimited","NeedsCompilation":"no","
Package":"rebus.unicode","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title
":"Unicode Extensions for the 'rebus' Package","Version":"0.0-1"},"rechonest":
{"Author":"Mukul Chaware[aut,cre]","Description":"The 'Echo nest'
<http:\/\/the.echonest.com> is the industry's leading\nmusic intelligence company,
providing developer with deepest understanding of\nmusic content and music fans.
This package can be used to access artist's data\nincluding songs, blogs, news,
reviews etc. Song's data including audio summary,\nstyle, danceability, tempo etc
can also be accessed.","Imports":"httr,RCurl,jsonlite","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rechonest","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"R Interface to Echo Nest
API","URL":"https:\/\/github.com\/mukul13\/rechonest","Version":"1.2"},"recluster":
{"Author":"Leonardo Dapporto, Matteo Ramazzotti, Simone Fattorini, Roger\nVila,
Gerard Talavera, Roger H.L. Dennis","Depends":"vegan, ape","Description":"Beta-
diversity indices provide dissimilarity matrices with particular distribution of
data requiring specific treatment. For example the high frequency of ties and zero
values in turnover indices produces hierarchical cluster dendrograms whose topology
and bootstrap supports are affected by the order of rows in the original matrix.
Moreover, biogeographical regionalization can be facilitated by a combination of
hierarchical clustering and multi-dimensional scaling. The recluster package
provides robust techniques to analyze pattern of similarity in species
composition.","Imports":"picante, phangorn, phytools, cluster","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"recluster","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Ordination Methods for the Analysis of Beta-Diversity
Indices","URL":"http:\/\/www.unifi.it\/scibio\/bioinfo\/recluster.html","Version":"
2.8"},"recoder":{"Author":"Ali Sanaei","Depends":"R (>= 3.1), stringr (>=
1.0.0)","Description":"Simple, easy to use, and flexible functionality for recoding
variables. It allows for simple piecewise definition of
transformations.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"recoder","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"A Simple and Flexible
Recoder","Version":"0.1"},"recommenderlab":{"Author":"Michael Hahsler [aut, cre,
cph]","Depends":"R (>= 2.10.0), Matrix, registry, arules (>= 1.0-1),
proxy","Description":"Provides a research infrastructure to test and
develop\nrecommender algorithms.","Imports":"methods, utils, stats,
bcv","License":"GPL-
2","NeedsCompilation":"no","Package":"recommenderlab","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"ROCR","Title":"Lab for Developing and Testing
Recommender Algorithms","URL":"http:\/\/R-Forge.R-
project.org\/projects\/recommenderlab\/,\nhttp:\/\/lyle.smu.edu\/IDA\/recommenderla
b\/","Version":"0.1-8"},"recommenderlabBX":{"Author":"Michael Hahsler","Depends":"R
(>= 2.10), recommenderlab (>= 0.1.3)","Description":"Provides the Book-Crossing
Dataset for the package
recommenderlab.","License":"GPL-
2","NeedsCompilation":"no","Package":"recommenderlabBX","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Book-Crossing Dataset (BX) for
'recommenderlab'","URL":"http:\/\/lyle.smu.edu\/IDA\/recommenderlab\/","Version":"0
.1-1"},"recommenderlabJester":{"Author":"Michael Hahsler","Depends":"R (>= 2.10),
recommenderlab (>= 0.1.3)","Description":"Provides the Jester Dataset for package
recommenderlab.","License":"GPL-
2","NeedsCompilation":"no","Package":"recommenderlabJester","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Title":"Jester Dataset for
'recommenderlab'","URL":"http:\/\/lyle.smu.edu\/IDA\/recommenderlab\/","Version":"0
.1-1"},"reconstructr":{"Author":"Oliver Keyes","Depends":"R (>=
2.10)","Description":"Functions to aid in reconstructing sessions\nand efficiently
calculating an array of metrics from the resulting data,\nincluding bounce rate,
time-on-page, and session length. Although primarily\ndesigned for web data and
analytics, its approach is plausibly applicable\nto other
domains.","Imports":"Rcpp","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"reconstructr","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Suggests":"testthat, knitr","Title":"Session
Reconstruction and Analysis","Version":"1.1.0"},"recosystem":{"Author":"Yixuan Qiu,
Chih-Jen Lin, Yu-Chin Juan, Yong Zhuang,\nWei-Sheng Chin and other contributors.
See file AUTHORS for\ndetails.","Depends":"methods","Description":"R wrapper of the
'libmf' library\n(http:\/\/www.csie.ntu.edu.tw\/~cjlin\/libmf\/) for
recommender\nsystem using matrix factorization. It is typically used
to\napproximate an incomplete matrix using the product of two\nmatrices in a latent
space. Other common names for this task\ninclude \"collaborative
filtering\", \"matrix completion\",\n\"matrix recovery\", etc.","Imports":"Rcpp (>=
LICENSE","NeedsCompilation":"yes","Package":"recosystem","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"knitr","Title":"Recommender System using
Matrix
Factorization","URL":"https:\/\/github.com\/yixuan\/recosystem","Version":"0.3"},"r
eda":{"Author":"Wenjie Wang [aut, cre],\nHaoda Fu [aut],\nJun Yan
[ctb]","Depends":"R (>= 3.2.0)","Description":"Functions that fit gamma frailty
model with spline or piecewise\nconstant baseline rate function for recurrent event
data, compute and\nplot parametric mean cumulative function (MCF) from a fitted
model\nas well as nonparametric sample MCF (Nelson-Aalen estimator) are
provided.\nMost functions are S4 methods that produce S4 class
objects.","Imports":"ggplot2, grDevices, methods, plyr, splines, stats,
3)","NeedsCompilation":"no","Package":"reda","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr","Title":"Recurrent Event Data
Analysis","URL":"https:\/\/github.com\/wenjie2wang\/reda","Version":"0.2.1"},"redca
pAPI":{"Author":"Benjamin Nutter. Initiated by Jeffrey Horner and Will Gray
with\ncontributions from Jeremy Stephens, and Will Beasley","Depends":"R (>=
3.0.0)","Description":"Access data stored in REDCap databases using the
Application\nProgramming Interface (API). REDCap (Research Electronic Data
CAPture) is\na web application for building and managing online surveys and
databases\ndeveloped at Vanderbilt University. The API allows users to access
data\nand project meta data (such as the data dictionary) from the
web\nprogrammatically. The redcapAPI package facilitates the process of\naccessing
data with options to prepare an analysis-ready data set\nconsistent with the
definitions in a database's data dictionary.","Imports":"chron, DBI, Hmisc (>=
3.14-6), httr, stringr","License":"GPL-
2","NeedsCompilation":"yes","Package":"redcapAPI","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"R Interface to
REDCap","URL":"https:\/\/github.com\/nutterb\/redcapAPI\/wiki,\nhttps:\/\/github.co
m\/nutterb\/redcapAPI, http:\/\/project-redcap.org","Version":"1.3"},"reddPrec":
{"Author":"Roberto Serrano-Notivoli","Depends":"snowfall","Description":"Computes
quality control to daily precipitation datasets, reconstructs the original series
by estimating precipitation in missing values, creates new series in a specified
pair of coordinates and creates grids.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"reddPrec","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Reconstruction of Daily Data -
Precipitation","Version":"0.2"},"redist":{"Author":"Ben Fifield
<bfifield@princeton.edu>, Alexander Tarr <atarr@princeton.edu>, Michael Higgins
<mjh5@princeton.edu>, and Kosuke Imai <kimai@princeton.edu>","Depends":"R (>=
3.1.0)","Description":"Enables researchers to sample redistricting plans from a
pre-specified target distribution using a Markov Chain Monte Carlo algorithm. The
package allows for the implementation of various constraints in the redistricting
process such as geographic compactness and population parity requirements. The
algorithm also can be used in combination with efficient simulation methods such as
simulated and parallel tempering algorithms. Tools for analysis such as inverse
probability reweighting and plotting functionality are included. The package
implements methods described in Fifield, Higgins, Imai and Tarr (2015) `À New
Automated Redistricting Simulator Using Markov Chain Monte Carlo,'' working paper
available at
<http:\/\/http:\/\/imai.princeton.edu\/research\/files\/redist.pdf>.","Imports":"Rc
pp (>= 0.11.0), spdep, sp, coda","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"redist","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Markov Chain Monte Carlo Methods for Redistricting
Simulation","Version":"1.2"},"redland":{"Author":"Matthew B. Jones [aut,
cre],\nPeter Slaughter [aut],\nJeroen Ooms [aut],\nCarl Boettiger [aut],\nScott
Chamberlain [aut],\nDavid Beckett [cph],\nUniversity of Bristol [cph],\nRegents of
the University of California [cph]","Depends":"R (>= 3.1.1),
methods","Description":"Provides methods to parse, query and serialize
information\nstored in the Resource Description Framework (RDF). RDF is described
at <http:\/\/www.w3.org\/TR\/rdf-primer>.\nThis package supports RDF by
implementing an R interface to the Redland RDF C library,\ndescribed at
<http:\/\/librdf.org\/docs\/api\/index.html>. In brief, RDF provides a structured
graph\nconsisting of Statements composed of Subject, Predicate, and Object
Nodes.","Imports":"roxygen2","License":"Apache License
2.0","NeedsCompilation":"yes","Package":"redland","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr, testthat","Title":"RDF Library Bindings in
R","Version":"1.0.17-7"},"ref":{"Author":"Jens Oehlschlägel
<jens.oehlschlaegel@truecluster.com>","Depends":"R (>= 1.5.1)","Description":"small
package with functions for creating references,\nreading from and writing to
references and a memory efficient\nrefdata type that transparently encapsulates
matrices and\ndata.frames","License":"GPL-
2","NeedsCompilation":"no","Package":"ref","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"References for R","URL":"http:\/\/cran.r-
project.org\/web\/packages\/ref\/","Version":"0.99"},"refGenome":
{"Author":"Wolfgang
Kaisers","Depends":"methods,doBy,RSQLite","Description":"Contains functionality for
import and managing of downloaded genome annotation Data from Ensembl genome
browser (European Bioinformatics Institute) and from UCSC genome browser
(University of California, Santa Cruz) and annotation routines for genomic
positions and splice site positions.","Imports":"DBI","License":"GPL-
2","NeedsCompilation":"yes","Package":"refGenome","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Gene and Splice Site Annotation Using Annotation Data
from\nEnsembl and UCSC Genome Browsers","Version":"1.6.0"},"referenceIntervals":
{"Author":"Daniel Finnegan","Description":"This is a collection of tools to allow
the medical professional to\ncalculate appropriate reference ranges (intervals)
with confidence intervals around\nthe limits for diagnostic
purposes.","Imports":"boot, extremevalues, car, outliers","License":"GPL-
3","NeedsCompilation":"no","Package":"referenceIntervals","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Reference
Intervals","Version":"1.1.1"},"refset":{"Author":"David Hugh-Jones
<davidhughjones@gmail.com>","Description":"Provides subsets with reference
semantics, i.e. subsets\nwhich automatically reflect changes in the original
object, and which\noptionally update the original object when they are
changed.","License":"GPL-
2","NeedsCompilation":"no","Package":"refset","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"knitr, rmarkdown, testthat","Title":"Subsets with
Reference Semantics","Version":"0.1.0"},"refund":{"Author":"Lei Huang [aut,
cre],\nFabian Scheipl [aut],\nJeff Goldsmith [aut],\nJonathan Gellar
[aut],\nJaroslaw Harezlak [aut],\nMathew W. McLean [aut],\nBruce Swihart
[aut],\nLuo Xiao [aut],\nCiprian Crainiceanu [aut],\nPhilip Reiss [aut],\nYakuan
Chen [ctb],\nSonja Greven [ctb],\nLan Huo [ctb],\nMadan Gopal Kundu [ctb],\nJulia
Wrobel [ctb],\nSo Young Park [ctb]","Depends":"R (>=
2.14.0)","Description":"Methods for regression for functional\ndata, including
function-on-scalar, scalar-on-function, and\nfunction-on-function regression. Some
of the functions are applicable to\nimage data.","Imports":"fda, Matrix, lattice,
boot, mgcv (>= 1.8-4), MASS, magic,\nnlme, gamm4, lme4, RLRsim, splines, grpreg,
ggplot2, stats,\nMCMCpack, pbs, methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"refund","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"RColorBrewer, reshape2","Title":"Regression with
Functional Data","Version":"0.1-14"},"refund.shiny":{"Author":"Julia Wrobel [aut,
cre],\nJeff Goldsmith [aut]","Depends":"R (>=
3.0.1)","Description":"Interactive plotting for functional data
analyses.","Imports":"ggplot2, shiny (>= 0.11), reshape2, dplyr, gridExtra,
lme4,\nrefund","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"refund.shiny","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Interactive Plotting for Functional Data
Analyses","Version":"0.2.0"},"refund.wave":{"Author":"Lan Huo, Philip Reiss and
Yihong Zhao","Depends":"R (>= 2.14.0), glmnet, wavethresh","Description":"Methods
for regressing scalar responses on functional or image predictors, via
transformation to the wavelet domain and back.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"refund.wave","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Wavelet-Domain Regression with Functional
Data","Version":"0.1"},"regRSM":{"Author":"Pawel Teisseyre, Robert A.
Klopotek","Depends":"R (>= 3.0.0)","Description":"Performs Random Subspace Method
(RSM) for high-dimensional linear regression to obtain variable importance
measures. The final model is chosen based on validation set or Generalized
Information Criterion.","Imports":"Rmpi, doParallel, parallel,
foreach","License":"LGPL-2 | LGPL-3 | GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"regRSM","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Random Subspace Method (RSM) for Linear
Regression","URL":"http:\/\/www.ipipan.eu\/~teisseyrep\/SOFTWARE\/","Version":"0.5"
},"regexr":{"Author":"Tyler Rinker [aut, cre]","Depends":"R (>=
3.1.0)","Description":"An R framework for constructing and managing human\nreadable
regular expressions. It aims to provide tools that\nenable the user to write
regular expressions in a way that is\nsimilar to the ways R code is written. The
tools allow the user\nto (1) write in smaller, modular, named, sub-expressions,
(2)\nwrite top to bottom, rather than a single string (3) comment\nindividual
chunks, (4) indent expressions to clearly present\nregular expression groups, (5)
add vertical line spaces and R\ncomments (i.e., #), and (6) test the validity of
the\nconcatenated expression and the modular sub-expressions.","License":"GPL-
2","NeedsCompilation":"no","Package":"regexr","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat, qdapRegex (>= 0.2.0)","Title":"Readable
Regular
Expressions","URL":"http:\/\/trinker.github.com\/regexr\/","Version":"1.1.0"},"regi
stry":{"Author":"David Meyer","Depends":"R (>= 2.6.0)","Description":"Provides a
generic infrastructure for creating and using
registries.","Imports":"utils","License":"GPL-
2","NeedsCompilation":"no","Package":"registry","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Infrastructure for R Package
Registries","Version":"0.3"},"reglogit":{"Author":"Robert B. Gramacy
<rbgramacy@chicagobooth.edu>","Depends":"R (>= 2.14.0), methods, mvtnorm, boot,
Matrix","Description":"Regularized (polychotomous) logistic regression\nby Gibbs
sampling. The package implements subtly different\nMCMC schemes with varying
efficiency depending on the data type\n(binary v. binomial, say) and the desired
estimator (regularized maximum\nlikelihood, or Bayesian maximum a
posteriori\/posterior mean, etc.) through a\nunified
interface.","License":"LGPL","NeedsCompilation":"yes","Package":"reglogit","Reposit
ory":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"plgp","Title":"Simulation-
Based Regularized Logistic
Regression","URL":"http:\/\/faculty.chicagobooth.edu\/robert.gramacy\/reglogit.html
","Version":"1.2-4"},"regpro":{"Author":"Jussi Klemela
<jussi.klemela@gmail.com>","Depends":"denpro (>= 0.9.0)","Description":"\nTools are
provided for\n(1) nonparametric regression (kernel, local linear),\n(2)
semiparametric regression (single index, additive models), and\n(3) quantile
regression (linear, kernel).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"regpro","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Nonparametric
Regression","URL":"http:\/\/jklm.fi\/regpro","Version":"0.1.1"},"regress":
{"Author":"David Clifford and Peter McCullagh. Additional contributions by\nHJ
Auinger.","Description":"Functions to fit Gaussian linear model by maximising
the\nresidual log likelihood where the covariance structure can be\nwritten as a
linear combination of known matrices. Can be used\nfor multivariate models and
random effects models. Easy\nstraight forward manner to specify random effects
models,\nincluding random interactions. Code now optimised to use\nSherman Morrison
Woodbury identities for matrix inversion in\nrandom effects models. We've added the
ability to fit models\nusing any kernel as well as a function to return the mean
and\ncovariance of random effects conditional on the data
(BLUPs).","License":"GPL","NeedsCompilation":"no","Package":"regress","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"nlme, MASS","Title":"Gaussian
linear models with linear covariance
structure","URL":"http:\/\/www.csiro.au","Version":"1.3-14"},"regsel":
{"Author":"Michal Knut","Depends":"glmnet, elasticnet","Description":"Functions for
fitting linear and generalized linear models with variable selection. The functions
can automatically do Stepwise Regression, Lasso or Elastic Net as variable
selection methods. Lasso and Elastic net are improved and handle factors better
(they can either include or exclude all factor levels).","License":"GPL-
2","NeedsCompilation":"no","Package":"regsel","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Variable Selection and
Regression","Version":"0.2"},"regsem":{"Author":"Ross
Jacobucci[aut,cre]","Depends":"lavaan, Rcpp","Description":"Uses both ridge and
lasso penalties (and extensions) to penalize\nspecific parameters in structural
equation models. The package offers additional cost functions, cross validation,
and other extensions beyond traditional SEM.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"regsem","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"snowfall, GA, rgenoud, Rsolnp, numDeriv, optimx,
semPlot","Title":"Performs Regularization on Structural Equation
Models","Version":"0.1.0"},"regsubseq":{"Author":"Yanming Di","Depends":"R (>=
2.10)","Description":"For a sequence of event occurence times, we are interested
in\nfinding subsequences in it that are too \"regular\". We define regular as
being\nsignificantly different from a homogeneous Poisson process. The departure
from\nthe Poisson process is measured using a L1 distance. See Di and Perlman
2007\nfor more details.","License":"GPL-
2","NeedsCompilation":"no","Package":"regsubseq","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Detect and Test Regular Sequences and
Subsequences","Version":"0.12"},"regtest":{"Author":"Jens Oehlschlägel
<Jens_Oehlschlaegel@truecluster.com>","Depends":"R (>=
2.5.1)","Description":"Functions for unary and binary regression
tests","License":"file
LICENSE","NeedsCompilation":"no","Package":"regtest","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Regression testing","Version":"0.05"},"rehh":
{"Author":"Mathieu Gautier and Renaud Vitalis","Depends":"R (>= 2.10), gplots,
methods","Description":"Functions for the detection of footprints of selection
on\ndense SNP data using Extended Homozygosity Haplotype (EHH)\nbased tests. The
package includes computation of EHH, iHS\n(within population) and Rsb (across pairs
of populations)\nstatistics. Various plotting functions are also included
to\nfacilitate visualization and interpretation of the results.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"rehh","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Searching for Footprints of Selection using
Haplotype\nHomozygosity Based Tests","Version":"1.13"},"relMix":{"Author":"Navreet
Kaur and Thore Egeland","Description":"Makes relationship inference involving
mixtures with unknown profiles and unknown number of
contributors.","Imports":"Familias, paramlink","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"relMix","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Relationship Inference Based on
Mixtures","Version":"1.0"},"relSim":{"Author":"James M. Curran","Description":"A
set of tools to explore the behaviour statistics used for forensic DNA
interpretation when close relatives are involved. The package also offers some
useful tools for exploring other forensic DNA situations.","Imports":"Rcpp (>=
0.11.5)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"relSim","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Relative Simulator","Version":"0.2-0"},"rela":
{"Author":"Michael Chajewski <chajewski@fordham.edu>","Description":"Item analysis
with alpha standard error and principal axis\nfactoring for continuous variable
scales (with plots).","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"rela","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Item Analysis Package with Standard
Errors","URL":"http:\/\/www.chajewski.com\/","Version":"4.1"},"relaimpo":
{"Author":"Ulrike Groemping [aut, cre],\nLehrkamp Matthias [ctb]","Depends":"R(>=
2.2.1), MASS, boot, survey, mitools, graphics","Description":"relaimpo provides
several metrics for assessing relative importance in linear models. These can be
printed, plotted and bootstrapped. The recommended metric is lmg, which provides a
decomposition of the model explained variance into non-negative contributions.
There is a version of this package available that additionally provides a new and
also recommended metric called pmvd. If you are a non-US user, you can download
this extended version from Ulrike Groempings web site.","Imports":"methods,
corpcor","License":"GPL-
2","NeedsCompilation":"no","Package":"relaimpo","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Relative importance of regressors in linear
models","URL":"http:\/\/prof.beuth-
hochschule.de\/groemping\/relaimpo\/,\nhttp:\/\/prof.beuth-
hochschule.de\/groemping\/","Version":"2.2-2"},"relations":{"
Author":"David Meyer [aut],\nKurt Hornik [aut, cre],\nChristian Buchta
[ctb]","Depends":"R (>= 2.14.0)","Description":"Data structures and algorithms for
k-ary relations with\narbitrary domains, featuring relational algebra, predicate
functions,\nand fitters for consensus relations.","Enhances":"seriation,
Rcplex","Imports":"cluster, stats, slam, sets (>= 1.0-16), graphics,
2","NeedsCompilation":"no","Package":"relations","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"Rgraphviz, clue (>= 0.3-49), Rglpk (>= 0.3-1),
lpSolve (>=\n5.6.3), Rsymphony (>= 0.1-9), methods","Title":"Data Structures and
Algorithms for Relations","Version":"0.6-6"},"relax":{"Author":"Hans Peter Wolf
<pwolf@wiwi.uni-bielefeld.de>","Depends":"R (>= 3.0.0),
tcltk","Description":"package relax contains some functions for report\nwriting,
presentation, and programming: relax(), tangleR(),\nweaveR(),
(g)slider(). \"relax\" is written in R and Tcl\/Tk.\nrelax creates a new window
(top level Tcl\/Tk widget) that consists\nof two text fields and some buttons and
menus.\nText (chunks) and code (chunks) are inserted in the upper text field
(report field).\nCode chunks are evaluated by clicking on EvalRCode.\nResults are
shown in the lower text field (output field) and\nwill be transferred to the report
field by pressing on Insert.\nIn this way you get correct reports. These reports
can be\nloaded again in cause of presentation, modification and result
checking.\ntangleR() and weaveR() implement a plain kind of tangling\nand weaving.
gslider() and slider() are designed to define sliders for interactive\nexperiments
in a simple way.\nThe syntax rules of code chunks and text chunks are defined
by\nthe noweb system proposed by Norman
Ramsey\n(http:\/\/www.eecs.harvard.edu\/~nr\/noweb\/intro.html).","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"relax","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"tkrplot","Title":"relax -- R Editor for Literate
Analysis and lateX","URL":"http:\/\/www.wiwi.uni-
bielefeld.de\/com\/wolf\/software\/relax.html","Version":"1.3.15"},"relaxnet":
{"Author":"Stephan Ritter, Alan Hubbard","Depends":"glmnet","Description":"Extends
the glmnet package with \"relaxation\", done by running glmnet once on the entire
predictor matrix, then again on each different subset of variables from along the
regularization path. Relaxation may lead to improved prediction accuracy for truly
sparse data generating models, as well as fewer false positives (i.e. fewer
noncontributing predictors in the final model). Penalty may be lasso (alpha = 1) or
elastic net (0 < alpha < 1). For this version, family may be \"gaussian\"
or \"binomial\" only. Takes advantage of fast FORTRAN code from the glmnet
2)","NeedsCompilation":"no","Package":"relaxnet","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"parallel","Title":"Relaxation of glmnet models (as in
relaxed lasso, Meinshausen\n2007)","URL":"http:\/\/cran.r-
project.org\/package=relaxnet","Version":"0.3-2"},"relaxo":{"Author":"Nicolai
Meinshausen","Depends":"lars","Description":"Relaxed Lasso is a generalisation of
the Lasso shrinkage\ntechnique for linear regression. Both variable selection
and\nparameter estimation is achieved by regular Lasso, yet both\nsteps do not
necessarily use the same penalty parameter. The\nresults include all standard Lasso
solutions but allow often\nfor sparser models while having similar or even slightly
better\npredictive performance if many predictor variables are present.\nThe
package depends on the LARS package.","Imports":"graphics, utils,
stats","License":"GPL","NeedsCompilation":"no","Package":"relaxo","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Title":"Relaxed
Lasso","URL":"http:\/\/www.stats.ox.ac.uk\/~meinshau\/","Version":"0.1-
2"},"reldist":{"Author":"Mark S. Handcock
<handcock@stat.ucla.edu>","Description":"R functions for the comparison of
distributions.\nThis includes nonparametric estimation of the relative
distribution\nPDF and CDF and numerical summaries as described in\n\"Relative
Distribution Methods in the Social Sciences\"\nby Mark S. Handcock and Martina
Morris,\nSpringer-Verlag, 1999, Springer-Verlag, ISBN
0387987789","Imports":"mgcv","License":"GPL-3 + file
LICENSE","NeedsCompilation":"no","Package":"reldist","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"locfit","Title":"Relative Distribution
Methods","URL":"http:\/\/www.stat.ucla.edu\/~handcock\/RelDist","Version":"1.6-
4"},"relen":{"Author":"Soeren Braehmer","Description":"This function computes the
relative entropy (H) as an index for qualitative variation of a
factor.","License":"GPL-
2","NeedsCompilation":"no","Package":"relen","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Compute Relative Entropy","Version":"1.0.1"},"relevent":
{"Author":"Carter T. Butts <buttsc@uci.edu>","Depends":"trust, sna (>= 2.0),
coda","Description":"Tools to fit relational event models.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"relevent","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Relational Event Models","Version":"1.0-4"},"reliaR":
{"Author":"Vijay Kumar <vkgkp@rediffmail.com> and Uwe Ligges\n<ligges@statistik.tu-
dortmund.de>","Description":"A collection of utilities for some
reliability\nmodels\/probability distributions.","License":"GPL-
2","NeedsCompilation":"no","Package":"reliaR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Package for some probability
distributions","Version":"0.01"},"relimp":{"Author":"David Firth with contributions
from Heather Turner and John Fox","Depends":"R (>= 2.0.0)","Description":"Functions
to facilitate inference on the relative importance of predictors in a linear or
generalized linear model, and a couple of useful Tcl\/Tk
widgets.","Imports":"stats, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"relimp","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"tcltk, nnet, MASS, Rcmdr","Title":"Relative
Contribution of Effects in a Regression
Model","URL":"http:\/\/warwick.ac.uk\/relimp","Version":"1.0-5"},"relsurv":
{"Author":"Maja Pohar Perme [aut, cre], Klemen Pavlic [ctb]","Depends":"survival,
splines, date","Description":"Various functions for relative survival
analysis.","License":"GPL","NeedsCompilation":"yes","Package":"relsurv","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Relative
Survival","Version":"2.0-7"},"rem":{"Author":"Laurence Brandenberger","Depends":"R
(>= 2.14.0)","Description":"Calculate endogenous network effects in event sequences
and fit relational event models (REM): Using network event sequences (where each
tie between a sender and a target in a network is time-stamped), REMs can measure
how networks form and evolve over time. Endogenous patterns such as popularity
effects, inertia, similarities, cycles or triads can be calculated and analyzed
over time.","Imports":"Rcpp, flexsurv, survival","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"rem","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"xergm, texreg, statnet, ggplot2","Title":"Relational
Event Models (REM)","Version":"1.1.2"},"remMap":{"Author":"Jie Peng
<jie@wald.ucdavis.edu>, Pei Wang <pwang@fhcrc.org>, Ji Zhu
<jizhu@umich.edu>.","Description":"remMap is developed for fitting multivariate
response regression models under the high-dimension-low-sample-size
setting","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"remMap","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Regularized Multivariate Regression for Identifying
Master\nPredictors","Version":"0.2-0"},"remix":{"Author":"David
Hajage","Depends":"R (>= 2.13.0), plyr, survival","Description":"remix provides
remix, a quick and easy function for\ndescribing datasets. It can be view as a mix
of cast (in\npackage reshape) and summary.formula (in package
Hmisc).","Imports":"Hmisc, ascii","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"remix","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Remix your
data","URL":"http:\/\/eusebe.github.com\/remix\/,
http:\/\/github.com\/eusebe\/remix\/","Version":"2.1"},"remote":{"Author":"Tim
Appelhans, Florian Detsch, Thomas Nauss","Depends":"R (>= 2.10), Rcpp (>= 0.10.3),
raster, foreach, methods","Description":"\nEmpirical orthogonal teleconnections in
R.\n'remote' is short for \"R(-based) EMpirical Orthogonal TEleconnections\".\nIt
implements a collection of functions to facilitate empirical\northogonal
teleconnection analysis. Empirical Orthogonal Teleconnections\n(EOTs) denote a
regression based approach to decompose spatio-temporal\nfields into a set of
independent orthogonal patterns. They are quite\nsimilar to Empirical Orthogonal
Functions (EOFs) with EOTs producing\nless abstract results. In contrast to EOFs,
which are orthogonal in both\nspace and time, EOT analysis produces patterns that
are orthogonal in\neither space or time.","License":"GPL (>= 3) | file
LICENSE","NeedsCompilation":"yes","Package":"remote","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"maps, lattice, latticeExtra, grid, gridExtra,
sp","Title":"Empirical Orthogonal Teleconnections in
R","Version":"1.0.0"},"remoter":{"Author":"Drew Schmidt [aut, cre],\nWei-Chen Chen
[aut]","Depends":"R (>= 3.2.0), pbdZMQ (>= 0.2-1)","Description":"A set of
utilities for controlling a remote R session\nfrom a local one. Simply set up a
server (see package vignette\nfor more details) and connect to it from your local R
session,\nincluding 'RStudio'. Network communication is handled\nby the 'ZeroMQ'
library by way of the 'pbdZMQ' package. The\nclient\/server framework is a custom
'REPL'.","Imports":"stats, utils, assertthat (>= 0.1), sodium (>=
0.2)","License":"BSD 2-clause License + file
LICENSE","NeedsCompilation":"no","Package":"remoter","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"knitr,
rmarkdown","Title":"Remote R: Control a Remote R Session from a Local
One","URL":"https:\/\/github.com\/wrathematics\/remoter","Version":"0.2-
0"},"rentrez":{"Author":"David Winter [aut, cre],\nScott Chamberlain [ctb],\nHan
Guangchun [ctb]","Depends":"R (>= 2.6.0)","Description":"Provides an R interface to
the NCBI's EUtils API\nallowing users to search databases like GenBank and PubMed,
process the\nresults of those searches and pull data into their R
sessions.","Imports":"XML, httr (>= 0.5), jsonlite (>= 0.9)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rentrez","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat, knitr, rmarkdown","Title":"Entrez in
R","Version":"1.0.1"},"repfdr":{"Author":"Ruth Heller [cre, aut],\nShachar Kaufman
[aut],\nShay Yaacoby [aut],\nDaniel Yekutieli [aut]","Depends":"R (>=
2.10)","Description":"Estimation of Bayes and local Bayes false discovery rates
for\nreplicability analysis.","Imports":"splines","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"repfdr","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Replicability Analysis for Multiple Studies of High
Dimension","URL":"http:\/\/github.com\/shay-y\/repfdr","Version":"1.1-
3"},"repijson":{"Author":"Andy South [aut, cre],\nThomas Finnie [aut],\nEllie
Sherrard-Smith [aut],\nAna Bento [aut],\nThibaut Jombart [aut]","Depends":"R (>=
3.1.0)","Description":"Supplies classes and routines to convert data to and from
EpiJSON files. This package provides conversion functions for data.frame, sp and
obkData.","Imports":"OutbreakTools, jsonlite, plyr, sp, ggplot2,
geojsonio","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"repijson","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"HistData, knitr, testthat, rgdal,
base64enc","Title":"Tools for Handling EpiJSON (Epidemiology Data)
Files","Version":"0.1.0"},"replicatedpp2w":{"Author":"Marcelino de la Cruz
Rot","Description":"Test for effects of both individual factors and their
interaction on replicated spatial patterns in a two factorial
design.","Imports":"spatstat","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"replicatedpp2w","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Two-Way ANOVA-Like Method to Analyze Replicated
Point Patterns","Version":"0.1-1"},"replicationInterval":{"Author":"David
Stanley","Description":"A common problem faced by journal reviewers and authors is
the\nquestion of whether the results of a replication study are consistent
with\nthe original published study. One solution to this problem is to examine\nthe
effect size from the published study and generate the range of effect\nsizes that
could reasonably be obtained (due to random sampling) in a\nreplication attempt
(i.e., calculate a replication interval). If a\nreplication effect size falls
outside the replication interval then that\nvalue could not have occurred to due
the effects of sampling error alone.\nAlternatively, if a replication effect size
falls within the replication\ninterval then the replication results could have
reasonably occurred due to\nthe effects of sampling error alone. This package has
functions that\ncalculate the replication interval for two different types of
effect sizes,\nnamely correlation (i.e., r) and the standardized mean
difference\n(i.e., d-value).","Imports":"MBESS,
stats","License":"Unlimited","NeedsCompilation":"no","Package":"replicationInterval
","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Replication Interval
Functions","Version":"1.0.0"},"repmis":{"Author":"Christopher Gandrud [aut,
cre]","Depends":"R (>= 3.0.0)","Description":"Tools to load 'R' packages\nand
automatically generate BibTeX files citing them as well as load and\ncache plain-
text and 'Excel' formatted data stored on 'GitHub', and\nfrom other
sources.","Imports":"data.table, digest, httr, plyr, R.cache","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"repmis","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"xlsx","Title":"Miscellaneous Tools for Reproducible
Research","URL":"http:\/\/cran.r-
project.org\/package=repmis","Version":"0.5"},"repo":{"Author":"Francesco
Napolitano <franapoli@gmail.com>","Description":"This is an R data manager meant to
avoid manual storage\/retrieval of R data to\/from the file system. It builds one
(or more) centralized repository where R objects are stored with annotations, tags,
dependency notes, provenance traces. It also provides navigation tools to easily
locate, load and edit previously stored resources.","Imports":"digest,
3","NeedsCompilation":"no","Package":"repo","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"igraph, knitr","Title":"A Resource Manager for R
Objects","Version":"1.0"},"repolr":{"Author":"Nick Parsons","Description":"Fits
linear models to repeated ordinal scores using GEE methodology.","Imports":"Rcpp
(>= 0.11.3), Matrix, methods","License":"GPL-
3","NeedsCompilation":"yes","Package":"repolr","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Repeated Measures Proportional Odds Logistic
Regression","Version":"3.4"},"reportRx":{"Author":"Ryan Del
Bel\n<rdelbel@gmail.com>,\nWei
Xu\n<wxu@uhnres.utoronto.ca>","Depends":"reshape","Description":"reportRx is a set
of tools that integrates with LaTeX and knitr to\nautomatically generate generate
reproducible clinical reports. Fuctions to\nautomatically produce demoraphic
tables, outcome summaries, univariate and\nmultivariate analysis results and more
are included.","Imports":"survival, xtable, aod, cmprsk, geoR,
stringr,","License":"GPL-
3","NeedsCompilation":"no","Package":"reportRx","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Tools for automatically generating reproducible clinical
report","Version":"1.0"},"reportr":{"Author":"Jon Clayden","Description":"Provides
a system for reporting messages, which provides certain useful features over the
standard R system, such as the incorporation of output consolidation, message
filtering, expression substitution, automatic generation of stack traces for
debugging, and conditional reporting based on the current \"output
level\".","Imports":"ore","License":"GPL-
2","NeedsCompilation":"no","Package":"reportr","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat (>= 0.11.0)","Title":"A General Message and
Error Reporting
System","URL":"https:\/\/github.com\/jonclayden\/reportr","Version":"1.2.1"},"repor
ts":{"Author":"Tyler Rinker","Depends":"R (>= 2.15)","Description":"Assists in
writing reports and\npresentations by providing a frame work that brings
together\nexisting R, LaTeX\/.docx and Pandoc tools. The package is\ndesigned to be
used with RStudio, MiKTex\/Tex Live\/LibreOffice,\nknitr, knitcitations, Pandoc and
pander. The user will want to\ndownload these free programs\/packages to maximize
the\neffectiveness of the reports package. Functions with two\nletter names are
general text formatting functions for copying\ntext from articles for inclusion as
a citation.","License":"GPL-
2","NeedsCompilation":"no","Package":"reports","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"pander, knitr, knitcitations,
ProjectTemplate","Title":"Assist the Workflow of Writing Academic Articles and
Other\nReports","URL":"http:\/\/trinker.github.com\/reports\/","Version":"0.1.4"},"
reporttools":{"Author":"Kaspar Rufibach","Depends":"xtable","Description":"These
functions are especially helpful when writing reports of data analysis using
Sweave.","Imports":"stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"reporttools","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"survival","Title":"Generate LaTeX Tables of
Descriptive
Statistics","URL":"http:\/\/www.kasparrufibach.ch","Version":"1.1.2"},"represent":
{"Author":"Harmen Draisma","Description":"Contains workhorse function jrparams(),
as well as two\nhelper functions Mboxtest() and JRsMahaldist(), and four\nexample
data sets.","License":"GPL-
3","NeedsCompilation":"no","Package":"represent","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Determine the representativity of two multidimensional
data sets","Version":"1.0"},"reproducer":{"Author":"Lech Madeyski [cre, aut,
ctb],\nMarian Jureczko [ctb] (Data contributor),\nBarbara Kitchenham [ctb] (Data
contributor),\nDavid Bodgen [ctb] (Data contributor),\nPearl Brereton [ctb] (Data
contributor),\nJacky Keung [ctb] (Data contributor),\nStuart Charters [ctb] (Data
contributor),\nShirley Gibbs [ctb] (Data contributor),\nAmnart Pohthong [ctb] (Data
contributor)","Depends":"R (>= 3.1.1)","Description":"The reproducer R package
includes data analysis functions and data\nsets (e.g., related to software defect
prediction) to streamline reproducible\nresearch in software
engineering.","Imports":"openxlsx (>= 2.4.0), ggplot2 (>= 2.0.0), gridExtra(>=
0.9.1),\ntm(>= 0.6), wordcloud(>= 2.5), RColorBrewer(>= 1.1-2),\nxtable(>= 1.7-4),
metafor(>= 1.9-2)","License":"CC BY
4.0","NeedsCompilation":"no","Package":"reproducer","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Reproduce Statistical Analyses and Meta-
Analyses","URL":"http:\/\/madeyski.e-informatyka.pl\/reproducible-
research\/","Version":"0.1.4"},"request":{"Author":"Scott Chamberlain [aut,
cre]","Depends":"httr (>= 1.0.0)","Description":"High level and easy 'HTTP' client
for 'R'. Provides functions for\nbuilding 'HTTP' queries, including query
parameters, body requests, headers,\nauthentication, and more.","Imports":"methods,
stats, utils, curl (>= 0.9.4), jsonlite (>= 0.9.19),\nmagrittr (>= 1.5), lazyeval
(>= 0.1.10), whisker (>= 0.3-2), R6\n(>= 2.1.1)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"request","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat","Title":"High Level 'HTTP'
Client","URL":"https:\/\/github.com\/sckott\/request","Version":"0.1.0"},"rerddap":
{"Author":"Scott
Chamberlain [aut, cre]","Description":"General purpose R client for 'ERDDAP'
servers. Includes\nfunctions to search for 'datasets', get summary information
on\n'datasets', and fetch 'datasets', in either 'csv' or 'netCDF' format.\n'ERDDAP'
information:
http:\/\/upwell.pfeg.noaa.gov\/erddap\/information.html.","Enhances":"taxize","Impo
rts":"methods, utils, stats, httr (>= 1.0.0), dplyr, data.table,\njsonlite (>=
0.9.17), xml2, digest, ncdf4","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rerddap","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"roxygen2, knitr, testthat","Title":"General
Purpose Client for 'ERDDAP'
Servers","URL":"https:\/\/github.com\/ropensci\/rerddap","Version":"0.3.4"},"resamp
le":{"Author":"Tim Hesterberg","Depends":"R (>= 3.1.0), graphics,
stats","Description":"Bootstrap, permutation tests, and other resampling
functions,\nfeaturing easy-to-use syntax.","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"resample","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"splus2R","Title":"Resampling
Functions","Version":"0.4"},"resemble":{"Author":"Leonardo Ramirez-Lopez [aut,
cre], Antoine Stevens [aut]","Depends":"R (>= 3.2.2)","Description":"Implementation
of functions for spectral similarity\/dissimilarity\nanalysis and memory-based
learning (MBL) for non-linear modeling\nin complex spectral datasets. In
chemometrics MBL is also known as local modeling.","Imports":"foreach, iterators,
Rcpp (>= 0.12.0)","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"resemble","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"prospectr, parallel, doParallel","Title":"Regression
and Similarity Evaluation for Memory-Based Learning\nin Spectral
Chemometrics","URL":"http:\/\/l-ramirez-
lopez.github.io\/resemble\/","Version":"1.2.2"},"reservoir":{"Author":"Sean Turner
[aut, cre],\nJia Yi Ng [aut],\nStefano Galelli [aut]","Description":"Measure
single-storage water supply system performance using resilience,\nreliability, and
vulnerability metrics; assess storage-yield-reliability\nrelationships; determine
no-fail storage with sequent peak analysis; optimize\nrelease decisions for water
supply, hydropower, and multi-objective reservoirs\nusing deterministic and
stochastic dynamic programming; evaluate inflow\npersistence using the Hurst
coefficient.","Imports":"gtools, stats, graphics","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"reservoir","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Tools for Analysis, Design, and Operation of Water
Supply\nStorages","URL":"https:\/\/cran.r-
project.org\/package=reservoir","Version":"1.1.4"},"reshape":{"Author":"Hadley
Wickham <h.wickham@gmail.com>","Depends":"R (>= 2.6.1)","Description":"Reshape lets
you flexibly restructure and aggregate data using just two functions: melt and
cast.","Imports":"plyr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"reshape","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Flexibly reshape
data","URL":"http:\/\/had.co.nz\/reshape","Version":"0.8.5"},"reshape2":
{"Author":"Hadley Wickham <h.wickham@gmail.com>","Description":"Flexibly
restructure and aggregate data using just two\nfunctions: melt and dcast (or
acast).","Imports":"plyr (>= 1.8.1), stringr, Rcpp","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"reshape2","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat (>= 0.8.0), lattice","Title":"Flexibly
Reshape Data: A Reboot of the Reshape
Package","URL":"https:\/\/github.com\/hadley\/reshape","Version":"1.4.1"},"reshapeG
UI":{"Author":"Jason Crowley <crowley.jason.s@gmail.com>","Depends":"reshape2,
plyr, gWidgets, gWidgetsRGtk2","Description":"A tool for learning how to use the
functions, melt,\nacast\/dcast, and ddply.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"reshapeGUI","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"A GUI for the reshape2 and plyr
packages","Version":"0.1.0"},"restimizeapi":{"Author":"Thomas P. Fuller
<thomas.fuller@coherentlogic.com>","Depends":"R (>= 3.1.3), RCurl,
RJSONIO","Description":"Provides the user with functions to develop their trading
strategy,\nuncover actionable trading ideas, and monitor consensus shifts
with\ncrowdsourced earnings and economic estimate data directly
from\n<www.estimize.com>. Further information regarding the web services
this\npackage invokes can be found at <www.estimize.com\/api>.","License":"LGPL-
3","NeedsCompilation":"no","Package":"restimizeapi","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat","Title":"Functions for Working with the
'www.estimize.com' Web Services","URL":"http:\/\/www.r-
project.org,\nhttp:\/\/coherentlogic.com\/middleware-development\/r-package-for-
the-estimize-com-api?source=cran,\nhttps:\/\/www.estimize.com?
source=cran","Version":"1.0.0"},"restlos":{"Author":"Steffen Liebscher and Thomas
Kirschstein","Depends":"R (>= 3.2.1)","Description":"The restlos package provides
algorithms for robust estimation of location (mean and mode) and scatter based on
minimum spanning trees (pMST), self-organizing maps (Flood Algorithm), Delaunay
triangulations (RDELA), and nested minimum volume convex sets (MVCH). The functions
are also suitable for outlier detection.","Imports":"som (>= 0.3-5), rgl (>=
0.95.1247), geometry (>= 0.3-5),\nigraph (>= 1.0.1), limSolve (>=
1.5.5.1)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"restlos","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Robust Estimation of Location and
Scatter","Version":"0.2-2"},"restorepoint":{"Author":"Sebastian
Kranz","Description":"Debugging with restore points instead of break points. A
restore\npoint stores all local variables when called inside a function. The
stored\nvalues can later be retrieved and evaluated in a modified R console
that\nreplicates the function's environment. To debug step by step, one can\nsimply
copy & paste the function body from the R script. Particularly\nconvenient in
combination with RStudio. See the github page for a tutorial.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"restorepoint","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Debugging with Restore
Points","URL":"https:\/\/github.com\/skranz\/restorepoint","Version":"0.1.7"},"resu
mer":{"Author":"Jared Lander [aut, cre]","Depends":"R (>=
3.2.1)","Description":"Using a database, LaTeX and R easily build attractive
resumes.","Imports":"useful, dplyr, rmarkdown","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"resumer","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat","Title":"Build Resumes with
R","URL":"https:\/\/github.com\/jaredlander\/resumer","Version":"0.0.1"},"rethinker
":{"Author":"Miron B. Kursa","Description":"Simple, native RethinkDB
client.","Imports":"rjson","License":"GPL-
3","NeedsCompilation":"no","Package":"rethinker","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat","Title":"RethinkDB
Client","URL":"https:\/\/github.com\/mbq\/rethinker","Version":"1.0.0"},"retimes":
{"Author":"Davide Massidda
<davide.massidda@humandata.it>","Depends":"methods","Description":"Reaction time
analysis by maximum likelihood","License":"GPL-
3","NeedsCompilation":"yes","Package":"retimes","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Reaction Time
Analysis","URL":"http:\/\/www.humandata.it\/","Version":"0.1-2"},"retistruct":
{"Author":"David C. Sterratt [aut, cre, cph],\nDaniel Lyngholm [aut,
cph]","Depends":"R (>= 3.1.0)","Description":"Reconstructs retinae by morphing a
flat surface with\ncuts (a dissected flat-mount retina) onto a curvilinear surface
(the a\nstandard retinal shape). It can estimate the position of a point on
the\nintact adult retina to within 8 degrees of arc (3.6% of nasotemporal
axis).\nThe coordinates in reconstructed retinae can be transformed to
visuotopic\ncoordinates.","Imports":"foreign, RImageJROI, png, ttutils, sp,
geometry (>= 0.2-1),\nRTriangle (>= 1.6-0.4), rgl, R.matlab","License":"CC BY-NC-SA
4.0","NeedsCompilation":"yes","Package":"retistruct","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat, gWidgetsRGtk2, gWidgets,
cairoDevice","Title":"Retinal Reconstruction Program","URL":"http:\/\/retistruct.r-
forge.r-project.org\/","Version":"0.5.10"},"retrosheet":{"Author":"Richard Scriven
[aut, cre]","Depends":"R (>= 2.10)","Description":"A collection of tools to import
and structure the (currently) single-season\nevent, game-log, roster, and schedule
data available from http:\/\/www.retrosheet.org.\nIn particular, the event (a.k.a.
play-by-play) files can be especially difficult to parse.\nThis package does the
parsing on those files, returning the requested data in the most\npractical R
structure to use for sabermetric or other analyses.","Imports":"RCurl (>= 1.95-
4.5), XML (>= 3.98-1.1), data.table (>= 1.9.4),\nstringi (>= 0.4-1)","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"retrosheet","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Import Professional Baseball Data from
'Retrosheet'","URL":"http:\/\/github.com\/rmscriven\/retrosheet","Version":"1.0.2"}
,"reutils":{"Author":"Gerhard SchÃ¶fl <gerhard.schofl@gmail.com>","Depends":"R (>=
3.2.0)","Description":"An interface to NCBI databases such as PubMed, GenBank, or
GEO\npowered by the Entrez Programming Utilities (EUtils). The nine EUtils\nprovide
programmatic access to the NCBI Entrez query and database\nsystem for searching and
retrieving biological data.","Imports":"assertthat, jsonlite, methods, RCurl,
stats, XML","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"reutils","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat (>= 0.8)","Title":"Talk to the NCBI
EUtils","URL":"https:\/\/github.com\/gschofl\/reutils","Version":"0.2.2"},"reval":
{"Author":"Michael
C Koohafkan [aut, cre]","Depends":"R (>= 3.1.3)","Description":"Simplified
scenario testing and sensitivity analysis with R via a\ngeneralized function for
one-factor-at-a-time (OFAT) sensitivity analysis,\nevaluation of parameter sets and
(sampled) parameter permutations. Options\nfor formatting output and parallel
processing are also provided.","Imports":"doParallel (>= 1.0.8), foreach (>=
1.4.2)","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"reval","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"knitr, ggplot2, dplyr, rivr","Title":"Repeated Function
Evaluation for Sensitivity
Analysis","URL":"https:\/\/github.com\/mkoohafkan\/reval","Version":"2.0.0"},"revea
ledPrefs":{"Author":"Julien Boelaert
<jubo.stats@gmail.com>","Description":"Computation of (direct and indirect)
revealed preferences, fast non-parametric tests of rationality axioms (WARP, SARP,
GARP), simulation of axiom-consistent data, and detection of axiom-consistent
subpopulations.","Imports":"Rcpp","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"revealedPrefs","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"pso","Title":"Revealed Preferences and
Microeconomic Rationality","Version":"0.2"},"revealjs":{"Author":"Hakim El Hattab
[aut, cph] (reveal.js-3.2.0,\nhttps:\/\/github.com\/hakimel\/reveal.js),\nJJ
Allaire [aut, cre],\nRStudio [cph]","Depends":"R (>= 3.0)","Description":"R
Markdown format for 'reveal.js' presentations, a framework\nfor easily creating
beautiful presentations using HTML.","Imports":"rmarkdown(>= 0.3.3)","License":"MIT
+ file
LICENSE","NeedsCompilation":"no","Package":"revealjs","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat","Title":"R Markdown Format for
'reveal.js'
Presentations","URL":"https:\/\/github.com\/rstudio\/revealjs","Version":"0.6"},"re
weight":{"Author":"Feiming Chen","Description":"Adjusts the weights of survey
respondents so that the\nmarginal distributions of certain variables fit more
closely to\nthose from a more precise source (e.g. Census Bureau's
data).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"reweight","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Adjustment of Survey Respondent
Weights","Version":"1.2.1"},"rex":{"Author":"Kevin Ushey [aut],\nJim Hester [aut,
cre],\nRobert Krzyzanowski [aut]","Description":"A friendly interface for the
construction of regular expressions.","Imports":"magrittr, lazyeval","License":"MIT
+ file
LICENSE","NeedsCompilation":"no","Package":"rex","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat, knitr, rmarkdown, dplyr, ggplot2, lintr,
Hmisc,\nstringr, rvest, roxygen2","Title":"Friendly Regular
Expressions","URL":"https:\/\/github.com\/kevinushey\/rex","Version":"1.1.1"},"rexp
okit":{"Author":"Nicholas J. Matzke [aut, cre, cph],\nRoger B. Sidje [aut,
cph]","Depends":"methods, SparseM, Rcpp (>= 0.9.10)","Description":"This package
wraps some of the matrix exponentiation utilities from EXPOKIT
(http:\/\/www.maths.uq.edu.au\/expokit\/), a FORTRAN library that is widely
recommended for matrix exponentiation (Sidje RB, 1998. \"Expokit: A Software
Package for Computing Matrix Exponentials.\" ACM Trans. Math. Softw. 24(1): 130-
156). EXPOKIT includes functions for exponentiating both small, dense matrices,
and large, sparse matrices (in sparse matrices, most of the cells have value 0).
Rapid matrix exponentiation is useful in phylogenetics when we have a large number
of states (as we do when we are inferring the history of transitions between the
possible geographic ranges of a species), but is probably useful in other ways as
2)","NeedsCompilation":"yes","Package":"rexpokit","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"R wrappers for EXPOKIT; other matrix
functions","URL":"http:\/\/phylo.wikidot.com\/rexpokit","Version":"0.24.1"},"rfPerm
ute":{"Author":"Eric Archer","Depends":"R (>= 3.2.0),
randomForest","Description":"Estimate significance of importance metrics\nfor a
Random Forest model by permuting the response\nvariable. Produces null distribution
of importance\nmetrics for each predictor variable and p-value
of\nobserved.","Imports":"abind, ggplot2, graphics, grDevices, gridExtra,
stats,\nswfscMisc","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rfPermute","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Estimate Permutation p-Values for Random Forest
Importance\nMetrics","Version":"2.0"},"rfUtilities":{"Author":"Jeffrey S. Evans
[cre, aut],\nMelanie A. Murphy [ctb]","Depends":"R (>= 3.1.2), randomForest (>=
4.6-10)","Description":"Utilities for Random Forest model selection, class
balance\ncorrection, significance test, cross validation and partial
dependency\nplots.","License":"GPL-
3","NeedsCompilation":"no","Package":"rfUtilities","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Random Forests Model Selection and Performance
Evaluation","URL":"http:\/\/cran.r-
project.org\/package=rfUtilities","Version":"1.0-2"},"rfigshare":{"Author":"Carl
Boettiger [aut, cre],\nScott Chamberlain [aut],\nKarthik Ram [aut],\nEdmund Hart
[aut]","Depends":"R (>= 3.0), methods","Description":"An interface to 'figshare'
(http:\/\/figshare.com), a scientific repository to archive and assign 'DOIs' to
data, software, figures, and more.","Imports":"RJSONIO, httr (>= 0.3), httpuv,
plyr, yaml, ggplot2,
XML","License":"CC0","NeedsCompilation":"no","Package":"rfigshare","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Suggests":"testthat, gdata, uuid","Title":"An
R Interface to
'figshare'","URL":"https:\/\/github.com\/ropensci\/rfigshare","Version":"0.3.7"},"r
fishbase":{"Author":"Carl Boettiger [cre, aut],\nScott Chamberlain [aut],\nDuncan
Temple Lang [aut],\nPeter Wainwright [aut]","Depends":"R (>= 3.0)","Description":"A
programmatic interface to http:\/\/www.fishbase.org, re-written\nbased on an
accompanying 'RESTful' API. Access tables describing over 30,000\nspecies of fish,
their biology, ecology, morphology, and more. This package also\nsupports
experimental access to http:\/\/www.sealifebase.org data, which contains\nnearly
200,000 species records for all types of aquatic life not covered
by\n'FishBase.'","Imports":"dplyr (>= 0.4.0), lazyeval, httr (>= 1.0.0), tidyr,
methods,\nutils","License":"CC0","NeedsCompilation":"no","Package":"rfishbase","Rep
ository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"devtools, testthat,
rmarkdown, knitr","Title":"R Interface to
'FishBase'","URL":"https:\/\/github.com\/ropensci\/rfishbase","Version":"2.1.0"},"r
fisheries":{"Author":"Karthik Ram [aut, cre],\nCarl Boettiger [aut],\nAndrew Dyck
[aut]","Depends":"R (>= 2.15)","Description":"A programmatic interface to
'openfisheries.org'. This package is\npart of the 'rOpenSci' suite
(http:\/\/ropensci.org).","Imports":"httr, data.table, assertthat, ggplot2,
rjson","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rfisheries","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"'Programmatic Interface to the
'openfisheries.org'
API'","URL":"http:\/\/www.github.com\/ropensci\/rfisheries","Version":"0.2"},"rfml"
:{"Author":"Mats Stellwall [aut, cre],\nAbdulla Abdurakhmanov [ctb] (Code in
xml2json.sjs is from
https:\/\/code.google.com\/p\/x2js\/)","Description":"Functionality required to
efficiently use R with MarkLogic NoSQL Database Server,
<http:\/\/www.marklogic.com\/what-is-marklogic\/>. Many basic and complex R
operations are pushed down into the database, which removes the main memory
boundary of R and allows to make full use of MarkLogic server. In order to use the
package you need a MarkLogic Server version 8 or higher.","Imports":"stats, utils,
methods, httr, PKI, jsonlite, XML","License":"GPL-
3","NeedsCompilation":"no","Package":"rfml","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"arules, testthat, knitr, rmarkdown","Title":"MarkLogic
NoSQL Database Server in-Database Analytics for
R","URL":"https:\/\/github.com\/mstellwa\/rfml","Version":"0.1.0"},"rfoaas":
{"Author":"Dirk Eddelbuettel","Description":"R access to the FOAAS (F... Off As A
Service) web service is provided.","Imports":"httr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rfoaas","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"R Interface to FOAAS","Version":"0.1.8"},"rfordummies":
{"Author":"Andrie de Vries [aut, cre],\nJoris Meys [aut]","Description":"Contains
all the code examples in the book \"R for Dummies\" (1st\nedition). You can view
the table of contents as well as the sample code for
each\nchapter.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"rfordummies","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"fortunes, stringr, sos, XLConnect, reshape2,
ggplot2,\nforeign, lattice","Title":"Code Examples to Accompany the Book \"R for
Dummies\"","URL":"http:\/\/rfordummies.com","Version":"0.1.2"},"rforensicbatwing":
{"Author":"Mikkel Meyer Andersen and Ian J. Wilson","Description":"A modified
version (with great help from Ian J. Wilson) of Ian J. Wilson's program BATWING for
calculating forensic trace-suspect match
probabilities.","Imports":"Rcpp","License":"GPL","NeedsCompilation":"yes","Package"
:"rforensicbatwing","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"BA
TWING for calculating forensic trace-suspect
match\nprobabilities","Version":"1.3"},"rgabriel":{"Author":"Yihui XIE, Miao
YU","Description":"This package was created to analyze multi-level one-
way\nexperimental designs. It is designed to handle vectorized\nobservation and
factor data where there are unequal sample\nsizes and population variance
homogeneity can not be assumed.\nTo conduct the Gabriel test, create two vectors:
one for your\nobservations and one for the factor level of each observation.\nThe
function, rgabriel, conduct the test and save the output as\na
vector to input into the gabriel.plot function, which produces\na confidence
interval plot for Multiple Comparison.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rgabriel","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Gabriel Multiple Comparison Test and Plot the
Confidence\nInterval on
Barplot","URL":"https:\/\/github.com\/yufree\/rgabriel","Version":"0.7"},"rgam":
{"Author":"Matias Salibian-Barrera, Davor Cubranic, and Azadeh\nAlimadad, with
'loess' code from Cleveland, Grosse, and Shyu","Depends":"R (>= 3.0.2),
stats","Description":"Robust Generalized Additive Model","Imports":"Rcpp (>=
0.8.0)","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"rgam","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Robust Generalized Additive
Model","URL":"http:\/\/www.stat.ubc.ca\/~matias\/rgam\/","Version":"0.6.3"},"rgbif"
:{"Author":"Scott Chamberlain [aut, cre],\nKarthik Ram [aut],\nVijay Barve
[aut],\nDan Mcglinn [aut]","Description":"A programmatic interface to the Web
Service methods\nprovided by the Global Biodiversity Information Facility
('GBIF').\n'GBIF' is a database of species occurrence records from sources
all\nover the globe. 'rgbif' includes functions for searching for\ntaxonomic names,
retrieving information on data providers,\ngetting species occurrence records, and
getting counts of\noccurrence records.","Imports":"methods, utils, stats, xml2,
ggplot2, httr (>= 1.0.0),\ndata.table, whisker, magrittr, jsonlite (>= 0.9.16), V8,
oai,\ngeoaxe","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rgbif","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat, knitr, reshape2, maps, sp,
rgeos","Title":"Interface to the Global 'Biodiversity' Information
Facility\n'API'","URL":"https:\/\/github.com\/ropensci\/rgbif","Version":"0.9.3"},"
rgcvpack":{"Author":"Xianhong Xie <xianhong04@gmail.com>","Depends":"R (>=
2.1.0)","Description":"Thin plate spline fitting and prediction","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"rgcvpack","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"R Interface for GCVPACK Fortran
Package","URL":"http:\/\/www.stat.wisc.edu\/~xie","Version":"0.1-4"},"rgdal":
{"Author":"Roger Bivand [cre, aut],\nTim Keitt [aut],\nBarry Rowlingson
[aut],\nEdzer Pebesma [ctb],\nMichael Sumner [ctb],\nRobert Hijmans [ctb],\nEven
Rouault [ctb]","Depends":"R (>= 2.14.0), methods, sp (>= 1.1-
0)","Description":"Provides bindings to Frank Warmerdam's Geospatial Data
Abstraction Library (GDAL) (>= 1.6.3) and access to projection\/transformation
operations from the PROJ.4 library. The GDAL and PROJ.4 libraries are external to
the package, and, when installing the package from source, must be correctly
installed first. Both GDAL raster and OGR vector map data can be imported into R,
and GDAL raster data and OGR vector data exported. Use is made of classes defined
in the sp package. Windows and Mac Intel OS X binaries (including GDAL, PROJ.4 and
Expat) are provided on CRAN.","Imports":"grDevices, graphics, stats,
2)","NeedsCompilation":"yes","Package":"rgdal","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Bindings for the Geospatial Data Abstraction
Library","URL":"http:\/\/www.gdal.org, https:\/\/r-forge.r-
project.org\/projects\/rgdal\/","Version":"1.1-8"},"rgenoud":{"Author":"Walter R.
Mebane, Jr. <wmebane@umich.edu>,\nJasjeet Singh Sekhon
<sekhon@berkeley.edu>","Depends":"R (>= 2.15), utils","Description":"A genetic
algorithm plus derivative optimizer.","License":"GPL-
3","NeedsCompilation":"yes","Package":"rgenoud","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"parallel","Title":"R Version of GENetic Optimization
Using Derivatives","URL":"http:\/\/sekhon.berkeley.edu\/rgenoud\/","Version":"5.7-
12.4"},"rgeolocate":{"Author":"Oliver Keyes [aut, cre], Drew Schmidt [aut], David
Robinson [ctb], Maxmind, Inc. [cph], Pascal Gloor [cph]","Description":"Connectors
to online and offline sources for taking IP addresses and geolocating them to
country, city, timezone and other geographic ranges. For individual connectors, see
the package index.","Imports":"Rcpp, httr","License":"Apache License (==
2.0)","NeedsCompilation":"yes","Package":"rgeolocate","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat, knitr","Title":"IP Address
Geolocation","Version":"0.5.0"},"rgeos":{"Author":"Roger Bivand [cre, aut],\nColin
Rundel [aut],\nEdzer Pebesma [ctb],\nKarl Ove Hufthammer [ctb]","Depends":"R (>=
2.14.0)","Description":"Interface to Geometry Engine - Open Source (GEOS) using the
C API for topology operations on geometries. The GEOS library is external to the
package, and, when installing the package from source, must be correctly installed
first. Windows and Mac Intel OS X binaries are provided on
CRAN.","Imports":"methods, sp (>= 1.1-0), utils, stats, graphics","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"rgeos","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"maptools (>= 0.8-5), testthat, XML, maps,
rgdal","Title":"Interface to Geometry Engine - Open Source
(GEOS)","URL":"https:\/\/r-forge.r-
project.org\/projects\/rgeos\/\nhttp:\/\/trac.osgeo.org\/geos\/","Version":"0.3-
19"},"rgexf":{"Author":"George Vega Yon <gvegayon@caltech.edu> [aut], Jorge
FÃ¡brega Lacoa <jorge.fabrega@uai.cl> [ctb], Joshua B. Kunst <jbkunst@gmail.com>
[ctb]","Depends":"XML, Rook, igraph","Description":"Create, read and write GEXF
(Graph Exchange XML Format) graph files (used in Gephi and others). Using the XML
package, it allows the user to easily build\/read graph files including attributes,
GEXF viz attributes (such as color, size, and position), network dynamics (for both
edges and nodes) and edge weighting. Users can build\/handle graphs element-by-
element or massively through data-frames, visualize the graph on a web browser
through \"sigmajs\" (a javascript library) and interact with the igraph
3)","NeedsCompilation":"yes","Package":"rgexf","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Build, Import and Export GEXF Graph
Files","URL":"http:\/\/bitbucket.org\/gvegayon\/rgexf,
http:\/\/www.ggvega.com","Version":"0.15.3"},"rggobi":{"Author":"Duncan Temple Lang
<duncan@research.bell-labs.com>,\nDebby Swayne <dfs@research.att.com>,\nHadley
Wickham <h.wickham@gmail.com>,\nMichael Lawrence <michafla@gene.com>","Depends":"R
(>= 2.5.1)","Description":"The rggobi package provides a command-line interface to
GGobi, an\ninteractive and dynamic graphics package. Rggobi complements
GGobi's\ngraphical user interface, providing a way to fluidly transition
between\nanalysis and exploration, as well as automating common
tasks.","Imports":"RGtk2, utils","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"yes","Package":"rggobi","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"reshape, nlme","Title":"Interface between R and
GGobi","URL":"http:\/\/www.ggobi.org\/rggobi","Version":"2.1.20"},"rgho":
{"Author":"Antoine Filipovic-Pierucci [aut,cre]","Depends":"R (>=
3.2.2)","Description":"Access WHO Global Health Observatory\ndata from R via the
Athena web service,\nan application program interface providing\na simple query
interface to the World\nHealth Organization's data and statistics
content.","Imports":"httr, curl, xml2, memoise, readr, magrittr, dplyr,
tidyr,\nlazyeval","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"rgho","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat, knitr, rmarkdown","Title":"Access WHO Global
Health Observatory Data from R","URL":"https:\/\/github.com\/pierucci\/rgho,
https:\/\/pierucci.github.io","Version":"0.0.1"},"rgl":{"Author":"Daniel Adler
<dadler@uni-goettingen.de>, Duncan Murdoch <murdoch@stats.uwo.ca>, and others (see
README)","Depends":"R (>= 2.15.0)","Description":"Provides medium to high level
functions for 3D interactive graphics, including\nfunctions modelled on base
graphics (plot3d(), etc.) as well as functions for\nconstructing representations of
geometric objects (cube3d(), etc.). Output\nmay be on screen using OpenGL, or to
various standard 3D file formats including\nWebGL, PLY, OBJ, STL as well as 2D
image formats, including PNG, Postscript, SVG, PGF.","Imports":"graphics,
grDevices, stats,
utils","License":"GPL","NeedsCompilation":"yes","Package":"rgl","Repository":"http:
\/\/cran.csiro.au\/src\/contrib","Suggests":"MASS, rglwidget (>= 0.1.1427), knitr,
rmarkdown","Title":"3D Visualization Using OpenGL","URL":"https:\/\/r-forge.r-
project.org\/projects\/rgl\/","Version":"0.95.1441"},"rglobi":{"Author":"Jorrit
Poelen [aut, cre],\nStephen Gosnell [aut],\nSergey Slyusarev [aut]","Depends":"R
(>= 3.0.1)","Description":"A programmatic interface to the web service
methods\nprovided by Global Biotic Interactions (GloBI). GloBI provides\naccess to
spatial-temporal species interaction records from\nsources all over the world.
rglobi provides methods to search\nspecies interactions by location, interaction
type, and\ntaxonomic name. In addition, it supports Cypher, a graph
query\nlanguage, to allow for executing custom queries on the GloBI\naggregate
species interaction data set.","Imports":"rjson (>= 0.2.13), RCurl","License":"MIT
+ file
LICENSE","NeedsCompilation":"no","Package":"rglobi","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat, knitr","Title":"R Interface to Global
Biotic
Interactions","URL":"https:\/\/github.com\/ropensci\/rglobi","Version":"0.2.9"},"rg
lwidget":{"Author":"Duncan Murdoch","Description":"Provides an 'htmlwidgets'
framework for the 'rgl' package.","Imports":"htmlwidgets, htmltools, knitr,
jsonlite, shiny, magrittr, rgl\n(>= 0.95.1367)","License":"GPL-
2","NeedsCompilation":"no","Package":"rglwidget","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"'rgl' in 'htmlwidgets'
Framework","Version":"0.1.1434"},"rgp":{"Author":"Oliver
Flasch, Olaf Mersmann, Thomas Bartz-Beielstein, Joerg Stork,\nMartin
Zaefferer","Depends":"R (>= 3.0.0), utils","Description":"RGP is a simple modular
Genetic Programming (GP) system build in\npure R. In addition to general GP tasks,
the system supports Symbolic\nRegression by GP through the familiar R model formula
interface. GP\nindividuals are represented as R expressions, an (optional) type
system\nenables domain-specific function sets containing functions of
diverse\ndomain- and range types. A basic set of genetic operators for
variation\n(mutation and crossover) and selection is provided.","Imports":"emoa (>=
0.5-0)","License":"GPL-
2","NeedsCompilation":"yes","Package":"rgp","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"igraph (>= 0.5.5), rrules (>= 0.1-0), rgpui (>= 0.1-
0),\nsnowfall (>= 1.84-4)","Title":"R genetic programming
framework","URL":"http:\/\/rsymbolic.org\/projects\/show\/rgp","Version":"0.4-
1"},"rgpui":{"Author":"Oliver Flasch","Depends":"R (>= 3.0.0),
utils","Description":"RGP UI provides as modern web-based user interface to the
modular\nGenetic Programming (GP) system RGP.","Imports":"rgp (>= 0.3-5), shiny (>=
0.10.2), emoa (>= 0.5-0), parallel","License":"GPL-
2","NeedsCompilation":"no","Package":"rgpui","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"UI for the RGP genetic programming
framework","URL":"http:\/\/rsymbolic.org\/projects\/show\/rgp-ui","Version":"0.1-
2"},"rgr":{"Author":"Robert G. Garrett","Depends":"MASS,
fastICA","Description":"Geological Survey of Canada (GSC) functions for exploratory
data analysis with applied geochemical data, with special application to the
estimation of background ranges and identification of outliers, 'anomalies', to
support mineral exploration and environmental studies. Additional functions are
provided to support analytical data QA\/QC, ANOVA for investigations of field
sampling and analytical variability, and utility tasks. NOTE: function caplot()
for concentration-area plots employs package 'akima', however, 'akima' is only
licensed for not-for-profit use. Therefore, not-for-profit users of 'rgr' will
have to independently make package 'akima' available through library(....); and use
of function caplot() by for-profit users will fail.","License":"GPL-
2","NeedsCompilation":"no","Package":"rgr","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"akima","Title":"Applied Geochemistry
EDA","Version":"1.1.13"},"rgrass7":{"Author":"Roger Bivand [cre, aut],\nRainer Krug
[ctb],\nMarkus Neteler [ctb],\nSebastian Jeworutzki [ctb]","Depends":"R (>= 3.1),
sp (>= 0.9), XML","Description":"Interpreted interface between GRASS 7
geographical\ninformation system and R, based on starting R from within the GRASS
GIS\nenvironment, or running free-standing R in a temporary GRASS location;\nthe
package provides facilities for using all GRASS commands from the\nR command line.
This package may not be used for GRASS 6, for which\nspgrass6 should be
used.","Imports":"stats, utils, methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rgrass7","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"rgdal (>= 1.0-6), RSQLite","Title":"Interface Between
GRASS 7 Geographical Information System and
R","URL":"http:\/\/grass.osgeo.org\/,\nhttps:\/\/r-forge.r-
project.org\/projects\/spgrass\/","Version":"0.1-6"},"rhandsontable":
{"Author":"Jonathan Owen [aut, cre, cph],\nJeff Allen [ctb],\nYihui Xie
[ctb],\nEnzo Martoglio [ctb],\nWarpechowski Marcin [ctb, cph] (Handsontable.js
library),\nHandsoncode sp. z o.o. [ctb, cph] (Handsontable.js library),\nAisch
Gregor [ctb, cph] (Chroma.js library),\nWood Tim [ctb, cph] (Moment.js
library),\nChernev Iskren [ctb, cph] (Moment.js library),\nMoment.js contributors
[ctb, cph] (Moment.js library),\nBushell David [ctb, cph] (Pikaday.js
library),\njQuery Foundation [ctb, cph] (jQuery.js library),\nSplunk Inc [ctb, cph]
(Sparkline.js library),\nRohan Jon [ctb, cph] (ZeroClipboard library),\nGreene
James [ctb, cph] (ZeroClipboard library)","Description":"An R interface to the
'Handsontable' JavaScript library, which is a\nminimalist Excel-like data grid
editor.","Enhances":"shiny (>= 0.12)","Imports":"jsonlite, htmlwidgets (>= 0.3.3),
magrittr, methods","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rhandsontable","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Suggests":"knitr, rmarkdown","Title":"Interface to the
'Handsontable.js'
Library","URL":"http:\/\/jrowen.github.io\/rhandsontable\/","Version":"0.3.1"},"rho
sp":{"Author":"Christophe Dutang and Julie Barthes","Description":"Evaluating risk
(that a patient arises a side effect) during hospitalization is the main purpose of
this package. Several methods (Parametric, non parametric and De Vielder
estimation) to estimate the risk constant (R) are implemented in this package.
There are also functions to simulate the different models of this issue in order to
quantify the previous estimators. It is necessary to read at least the first six
pages of the report to understand the topic.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rhosp","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Side Effect Risks in Hospital : Simulation and
Estimation","Version":"1.07"},"ri":{"Author":"Peter M. Aronow
<peter.aronow@yale.edu> and Cyrus Samii\n<cds2083@nyu.edu>","Description":"This
package provides a set of tools for conducting exact\nor approximate randomization-
based inference for experiments of\narbitrary design. The primary functionality of
the package is\nin the generation, manipulation and use of permutation
matrices\nimplied by given experimental designs. Among other features,\nthe package
facilitates estimation of average treatment\neffects, constant effects variance
estimation, randomization\ninference for significance testing against sharp
null\nhypotheses and visualization of data and results.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ri","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"ri: R package for performing randomization-based inference
for\nexperiments","Version":"0.9"},"riceware":{"Author":"Francois Michonneau [aut,
cre],\nArnold G. Reinhold [cph]","Depends":"R (>= 3.1.3)","Description":"The
Diceware method can be used to generate strong passphrases.\nIn short, you roll a
6-faced dice 5 times in a row, the number obtained is\nmatched against a dictionary
of easily remembered words. By combining together 7\nwords thus generated, you
obtain a password that is relatively easy to remember,\nbut would take several
millions years (on average) for a powerful computer to guess.","Imports":"random
LICENSE","NeedsCompilation":"no","Package":"riceware","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat","Title":"A Diceware Passphrase
Implementation","URL":"https:\/\/github.com\/fmichonneau\/riceware","Version":"0.4"
},"rich":{"Author":"Jean-Pierre Rossi","Depends":"boot, vegan,
permute","Description":"Computes rarefaction curves, cumulated and mean
species\nrichness. Compares these estimates by means of
randomization\ntests.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rich","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Computes and compares species
richnesses","Version":"0.3"},"ridigbio":{"Author":"Francois Michonneau [aut,
cph],\nMatthew Collins [aut, cre],\nScott Chamberlain [ctb]","Depends":"R (>=
3.0.1)","Description":"An interface to iDigBio's search API that allows
downloading\nspecimen records. Searches are returned as a data.frame. Other
functions\nsuch as the metadata end points return lists of information. iDigBio is
a US\nproject focused on digitizing and serving museum specimen collections on
the\nweb. See <https:\/\/www.idigbio.org> for information on
iDigBio.","Imports":"plyr, httr, jsonlite","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"ridigbio","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat","Title":"Interface to the iDigBio Data
API","URL":"https:\/\/github.com\/iDigBio\/ridigbio","Version":"0.3.3"},"rinat":
{"Author":"Vijay Barve<vijay.barve@gmail.com>,\nEdmund Hart
<edmund.m.hart@gmail.com>","Description":"A programmatic interface to the\nAPI
provided by the iNaturalist website.","Imports":"httr, plyr, jsonlite, ggplot2,
maps","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rinat","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Access iNaturalist data through
APIs","Version":"0.1.4"},"rindex":{"Author":"Jens Oehlschlägel
<Jens.Oehlschlaegel@truecluster.com>","Depends":"R (>= 2.6.0),
regtest","Description":"Index structures allow quickly accessing elements
from\nlarge collections. While btree are optimized for disk databases\nand ttree
for ram databases we use hybrid static indexing which\nis quite optimal for
R.","License":"file
LICENSE","NeedsCompilation":"yes","Package":"rindex","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Indexing for R","Version":"0.12"},"rio":
{"Author":"Chung-hong Chan [aut],\nGeoffrey CH Chan [aut],\nThomas J. Leeper [aut,
cre],\nChristopher Gandrud [aut],\nIsta Zahn [aut]","Depends":"R (>=
2.15.0)","Description":"Streamlined data import and export by making assumptions
that the user is probably willing to make: 'import()' and 'export()' determine the
data structure from the file extension, reasonable defaults are used for data
import and export (e.g., 'stringsAsFactors=FALSE'), web-based import is natively
supported (including from SSL\/HTTPS), compressed files can be read directly
without explicit decompression, and fast import packages are used where
appropriate.","Imports":"tools, stats, utils, urltools, foreign, haven,
openxlsx,\nreadODS, jsonlite, XML, curl (>= 0.6), data.table (>= 1.9.5),\nreadxl,
yaml","License":"GPL-
2","NeedsCompilation":"no","Package":"rio","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"dataset
s, bit64, testthat, knitr, magrittr","Title":"A Swiss-Army Knife for Data
I\/O","Version":"0.3.0"},"rioja":{"Author":"Steve Juggins","Description":"Functions
for the analysis of Quaternary science data, including\nconstrained clustering, WA,
WAPLS, IKFA, MLRC and MAT transfer\nfunctions, and stratigraphic
diagrams.","Imports":"vegan, mgcv, lattice, gdata, grDevices","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"rioja","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"RODBC, akima","Title":"Analysis of Quaternary Science
Data","URL":"http:\/\/www.staff.ncl.ac.uk\/stephen.juggins\/","Version":"0.9-
6"},"ripa":{"Author":"Talita Perciano [aut, cre],\nAlejandro C Frery
[ctb]","Depends":"R (>= 2.8.1), tcltk, parallel","Description":"A package including
various functions for image processing and analysis. With this package is possible
to process and analyse RGB, LAN (multispectral) and AVIRIS (hyperspectral) images.
This packages also provides functions for reading JPEG files, extracted from the
archived 'rimage' package.","Enhances":"doMC","Imports":"Rcpp (>=
0.11.0)","License":"GPL (>= 2) | file
LICENSE","NeedsCompilation":"yes","Package":"ripa","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"e1071, rggobi, reshape, methods, jpeg, png,
tkrplot, fftw,\nforeach, doSNOW","Title":"R Image Processing and
Analysis","URL":"http:\/\/www.r-project.org","Version":"2.0-2"},"riskR":
{"Author":"Marcelo Brutti Righi","Description":"Computes risk measures from data,
as well as performs risk management procedures.","License":"GPL-
2","NeedsCompilation":"no","Package":"riskR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Risk Management","Version":"1.1"},"riskRegression":
{"Author":"Thomas Alexander Gerds, Thomas Harder Scheike","Depends":"R (>= 2.9.0),
prodlim (>= 1.4.9)","Description":"Risk regression models for survival analysis
with and without\ncompeting risks.","Imports":"rms (>= 4.2-0), pec (>= 2.4.3),
cmprsk (>= 2.2-7), survival\n(>= 2.37-7), randomForestSRC (>=
1.5.5)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"riskRegression","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"lava","Title":"Risk Regression Models for
Survival Analysis with Competing\nRisks","Version":"1.1.7"},"riskSimul":
{"Author":"Wolfgang Hormann, Ismail
Basoglu","Depends":"Runuran","Description":"Implements efficient simulation
procedures to estimate tail loss probabilities and conditional excess for a stock
portfolio. The log-returns are assumed to follow a t-copula model with generalized
hyperbolic or t marginals.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"riskSimul","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Risk Quantification for Stock Portfolios under the T-
Copula\nModel","Version":"0.1"},"risksetROC":{"Author":"Patrick J. Heagerty
<heagerty@u.washington.edu>, packaging by\nParamita Saha-Chaudhuri
<paramita.sahachaudhuri.work@gmail.com>","Depends":"R (>= 1.6.1), survival,
MASS","Description":"Compute time-dependent Incident\/dynamic accuracy
measures\n(ROC curve, AUC, integrated AUC )from censored survival data\nunder
proportional or non-proportional hazard assumption of\nHeagerty & Zheng
(Biometrics, Vol 61 No 1, 2005, PP 92-105).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"risksetROC","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Riskset ROC curve estimation from censored survival
data","Version":"1.0.4"},"rite":{"Author":"Thomas J. Leeper","Description":"A
simple yet powerful script editor built natively in R with
tcltk.","Imports":"tcltk, tcltk2, RCurl, tools, knitr, markdown","License":"GPL-
2","NeedsCompilation":"no","Package":"rite","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"The Right Editor to Write
R","URL":"https:\/\/github.com\/leeper\/rite","Version":"0.3.4"},"riv":
{"Author":"Gabriela Cohen-Freue and Davor Cubranic,\nwith contributions from B.
Kaufmann and R.H. Zamar","Depends":"MASS, rrcov, quantreg","Description":"Finds a
robust instrumental variables estimator using a\nhigh breakdown point S-estimator
of multivariate location\nand scatter matrix.","License":"GPL-
2","NeedsCompilation":"no","Package":"riv","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Robust instrumental variables estimator","Version":"2.0-
4"},"rivernet":{"Author":"Peter Reichert","Description":"Functions for reading,
analysing and plotting river networks.\nFor this package, river networks consist of
sections and nodes with associated attributes,\ne.g. to characterise their
morphological, chemical and biological state.\nThe package provides functions to
read this data from text files, to analyse the network\nstructure and network paths
and regions consisting of sections and nodes that fulfill\nprescribed criteria, and
to plot the river network and associated properties.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rivernet","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Read, Analyze and Plot River
Networks","Version":"1.0"},"riverplot":{"Author":"January Weiner
<january.weiner@gmail.com>","Description":"Sankey plots are a type of diagram that
is convenient to\nillustrate how flow of information, resources etc. separates and
joins,\nmuch like observing how rivers split and merge. For example, they can
be\nused to compare different clusterings.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"riverplot","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Sankey or Ribbon
Plots","URL":"http:\/\/logfc.wordpress.com","Version":"0.5"},"rivervis":
{"Author":"Feng Mao <rivervis@outlook.com>, Yichuan Shi <yichuan@live.com>,\nand
Keith Richards <ksr10@cam.ac.uk>","Description":"This R package is a flexible and
efficient tool to\nvisualise both quantitative and qualitative data from river
surveys.\nIt can be used to produce diagrams with the topological structure of\nthe
river network.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rivervis","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"River Visualisation Tool","Version":"0.46.0"},"rivr":
{"Author":"Michael C Koohafkan [aut, cre]","Depends":"R (>= 3.1.2), utils,
graphics","Description":"A tool for undergraduate and graduate courses in open-
channel\nhydraulics. Provides functions for computing normal and critical
depths,\nsteady-state water surface profiles (e.g. backwater curves) and unsteady
flow\ncomputations (e.g. flood wave routing).","Imports":"Rcpp (>=
0.11.3)","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"rivr","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"dplyr, ggplot2, knitr, shiny","Title":"Steady and
Unsteady Open-Channel Flow
Computation","URL":"https:\/\/github.com\/mkoohafkan\/rivr","Version":"1.2"},"rjade
":{"Author":"Jeroen Ooms, Forbes Lindesay","Description":"Jade is a high
performance template engine heavily influenced by\nHaml and implemented with
JavaScript for node and browsers.","Imports":"V8 (>= 0.5)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rjade","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr","Title":"A Clean, Whitespace-Sensitive
Template Language for Writing
HTML","URL":"https:\/\/github.com\/jeroenooms\/rjade\nhttps:\/\/www.npmjs.com\/pack
age\/jade","Version":"0.1"},"rjags":{"Author":"Martyn Plummer [aut, cre],\nAlexey
Stukalov [ctb],\nMatt Denwood [ctb]","Depends":"R (>= 2.14.0), coda (>=
0.13)","Description":"Interface to the JAGS MCMC library.","License":"GPL (==
2)","NeedsCompilation":"yes","Package":"rjags","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"tcltk","Title":"Bayesian Graphical Models using
MCMC","URL":"http:\/\/mcmc-jags.sourceforge.net","Version":"4-6"},"rje":
{"Author":"Robin Evans <evans@stats.ox.ac.uk>","Depends":"R (>=
2.0.0)","Description":"A series of useful functions, some available in
different\nforms in other packages, but which have been extended, sped up,
or\notherwise modified in some way considered useful to the author.","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"rje","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Miscellaneous useful functions","Version":"1.9"},"rjson":
{"Author":"Alex Couture-Beil <rjson_pkg@mofo.ca>","Depends":"R (>=
3.1.0)","Description":"Converts R object into JSON objects and vice-
versa","License":"GPL-
2","NeedsCompilation":"yes","Package":"rjson","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"JSON for R","Version":"0.2.15"},"rjstat":{"Author":"Aaron
Schumacher <ajschumacher@gmail.com>, HÃ¥kon Malmedal","Description":"Read and write
the 'JSON-stat' format (http:\/\/json-stat.org) to and\nfrom (lists of) R data
frames. Not all features are supported, especially\nthe extensive metadata features
of 'JSON-stat'.","Imports":"jsonlite (>= 0.9.8), assertthat","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rjstat","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat (>= 0.8), reshape (>= 0.7)","Title":"Read
and Write 'JSON-stat' Data
Sets","URL":"https:\/\/github.com\/ajschumacher\/rjstat","Version":"0.2.1"},"rkafka
":{"Author":"Shruti
Gupta[aut,cre]","Depends":"rJava,RUnit,rkafkajars","Description":"Apache 'Kafka' is
an open-source message broker project developed by the Apache Software Foundation
which can be thought of as a distributed, partitioned, replicated commit log
service.At a high level, producers send messages over the network to the 'Kafka'
cluster which in turn serves them up to consumers.See <http:\/\/kafka.apache.org\/>
for more information.Functions included in this package enable:1.Creating 'Kafka'
producer 2.Writing messages to a topic 3.Closing 'Kafka' producer 4.Creating
'Kafka' consumer 5.Reading messages from a topic 6.Closing 'Kafka' consumer. The
jars required for this package are included in a separate package
'rkafkajars'.Thanks to Mu Sigma for their continued support throughout the
development of the package.","License":"Apache License 2.0 | file
LICENSE","NeedsCompilation":"no","Package":"rkafka","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Using Apache 'Kafka' Messaging Queue Through
'R'","Version":"1.0"},"rkafkajars":{"Author":"Shruti Gupta [aut,cre], Coda Hale and
Yammer Inc.[ctb,cph],Sun Microsystems Inc.[ctb,cph],Marc
Prud'hommeaux[ctb,cph],Paul Holser[ctb],Junit[ctb,cph],The Apache Software
Foundation [ctb,cph],Stefan Groschupf[ctb,cph],Taro L.Saito[ctb],EPFL Typesafe Inc.
[ctb,cph],QOS.ch[ctb,cph]","Depends":"rJava","Description":"The 'rkafkajars'
package collects all the external jars required for the 'rkafka'
package.","Imports":"RUnit","License":"Apache License 2.0 | file
LICENSE","NeedsCompilation":"no","Package":"rkafkajars","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"External Jars Required for Package
'rkafka'","Version":"1.0"},"rknn":{"Author":"Shengqiao Li
<lishengqiao@yahoo.com>","Depends":"R (>= 2.14), gmp (>= 0.5-
5)","Description":"Random knn classification and regression are implemented. Random
knn based feature selection methods are also included. The approaches are mainly
developed for high-dimensional data with small sample size.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"rknn","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"Hmisc, Biobase, genefilter, golubEsets,
chemometrics","Title":"Random KNN Classification and Regression","Version":"1.2-
1"},"rkt":{"Author":"Aldo Marchetto","Description":"Contains function rkt which
computes the Mann-Kendall test (MK) and the Seasonal and the Regional Kendall Tests
for trend (SKT and RKT) and Theil-Sen's slope estimator.","License":"GPL-
2","NeedsCompilation":"no","Package":"rkt","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Mann-Kendall Test, Seasonal and Regional Kendall
Tests","Version":"1.4"},"rkvo":{"Author":"Vehbi Sinan Tunalioglu [aut,
cre]","Depends":"R (>= 3.1.0)","Description":"This package provides functionality
to read files\ncontaining observations which consist of arbitrary
key\/value\npairs.","Imports":"Rcpp (>= 0.11)","License":"GPL-
3","NeedsCompilation":"yes","Package":"rkvo","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Read Key\/Value Pair
Observations","Version":"0.1"},"rleafmap":{"Author":"Francois Keck
<francois.keck@gmail.com>","Depends":"R (>= 3.0.0)","Description":"Display spatial
data with interactive maps powered by the\nopen-source JavaScript library 'Leaflet'
(see <http:\/\/leafletjs.com\/>). Maps can be rendered in a web browser
or\ndisplayed in the HTML viewer pane of 'RStudio'. This package is designed to be
easy to use and\ncan create complex maps with vector and raster data, web served
map tiles and interface elements.","Imports":"knitr (>= 1.5), sp, raster, methods,
grDevices, graphics,\nutils","License":"GPL-
3","NeedsCompilation":"no","Package":"rleafmap","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Interactive Maps with R and
Leaflet","URL":"http:\/\/www.francoiskeck.fr\/rleafmap\/,\nhttps:\/\/github.com\/fk
eck\/rleafmap","Version":"0.2"},"rlecuyer":{"Author":"Hana Sevcikova [aut,
cre],\nTony Rossini [aut],\nPierre L'Ecuyer [cph] (author of the underlying C
code)","Description":"Provides an interface to the C implementation of the\nrandom
number generator with multiple independent streams\ndeveloped by L'Ecuyer et al
(2002). The main purpose of this\npackage is to enable the use of this random
number generator in\nparallel R applications.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"rlecuyer","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"R Interface to RNG with Multiple
Streams","URL":"http:\/\/www.iro.umontreal.ca\/~lecuyer\/myftp\/papers\/streams00.p
df","Version":"0.3-4"},"rlist":{"Author":"Kun Ren <ken@renkun.me>","Depends":"R (>=
2.15)","Description":"Provides a set of functions for data manipulation with\nlist
objects, including mapping, filtering, grouping, sorting,\nupdating, searching, and
other useful functions. Most functions\nare designed to be pipeline friendly so
that data processing with\nlists can be chained.","Imports":"yaml, jsonlite, XML,
data.table","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rlist","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat, stringdist, pipeR","Title":"A Toolbox for
Non-Tabular Data Manipulation","URL":"https:\/\/renkun.me\/rlist,
https:\/\/github.com\/renkun-ken\/rlist,\nhttps:\/\/renkun.me\/rlist-
tutorial","Version":"0.4.6.1"},"rlm":{"Author":"Oleg Yegorov
<egorov@smedx.com>","Description":"Robust fitting of linear model which can take
response in matrix form.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"rlm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Robust Fitting of Linear Model","Version":"1.2"},"rmaf":
{"Author":"Debin Qiu","Description":"Uses refined moving average filter based on
the optimal and data-driven moving average lag q or smoothing spline to estimate
trend and seasonal components, as well as irregularity (residuals) for univariate
time series or data.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rmaf","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Refined Moving Average
Filter","Version":"3.0.1"},"rmarkdown":{"Author":"JJ Allaire [aut, cre],\nJoe Cheng
[aut],\nYihui Xie [aut],\nJonathan McPherson [aut],\nWinston Chang [aut],\nJeff
Allen [aut],\nHadley Wickham [aut],\nAron Atkins [aut],\nRob Hyndman
[aut],\nRStudio, Inc. [cph],\njQuery Foundation [cph] (jQuery library),\njQuery
contributors [ctb, cph] (jQuery library; authors listed in\ninst\/rmd\/h\/jquery-
AUTHORS.txt),\njQuery UI contributors [ctb, cph] (jQuery UI library; authors listed
in\ninst\/rmd\/h\/jqueryui-AUTHORS.txt),\nMark Otto [ctb] (Bootstrap
library),\nJacob Thornton [ctb] (Bootstrap library),\nBootstrap contributors [ctb]
(Bootstrap library),\nTwitter, Inc [cph] (Bootstrap library),\nAlexander Farkas
[ctb, cph] (html5shiv library),\nScott Jehl [ctb, cph] (Respond.js library),\nIvan
Sagalaev [ctb, cph] (highlight.js library),\nGreg Franko [ctb, cph] (tocify
library),\nJohn MacFarlane [ctb, cph] (Pandoc templates),\nGoogle, Inc. [ctb, cph]
(ioslides library),\nDave Raggett [ctb] (slidy library),\nW3C [cph] (slidy
library)","Depends":"R (>= 3.0)","Description":"Convert R Markdown documents into a
variety of formats.","Imports":"tools, utils, grDevices, knitr (>= 1.11), yaml (>=
2.1.5),\nhtmltools (>= 0.2.4), caTools","License":"GPL-
3","NeedsCompilation":"no","Package":"rmarkdown","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"shiny (>= 0.11), tufte, testthat,
digest","Title":"Dynamic Documents for
R","URL":"http:\/\/rmarkdown.rstudio.com","Version":"0.9.5"},"rmatio":
{"Author":"Stefan Widgren [aut, cre] (Author of the R interface to the C-
library\nmatio),\nChristopher Hulbert [aut] (Author of the C-library
matio,\nhttp:\/\/sourceforge.net\/projects\/matio\/)","Depends":"R(>= 3.0.2),
Matrix, methods, lattice","Description":"rmatio is a package for reading and
writing Matlab MAT\nfiles from R. The rmatio package supports reading MAT version
4,\nMAT version 5 and MAT compressed version 5. The rmatio package can\nwrite
version 5 MAT files and version 5 files with
variable\ncompression.","License":"GPL-
3","NeedsCompilation":"yes","Package":"rmatio","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Read and Write Matlab
Files","URL":"https:\/\/github.com\/stewid\/rmatio","Version":"0.11.0"},"rmcfs":
{"Author":"Michal Draminski [aut, cre],\nJacek Koronacki [aut],\nJulian Zubek
[ctb]","Depends":"rJava (>= 0.5-0), R (>= 2.70)","Description":"MCFS-ID (Monte
Carlo Feature Selection and Interdependency Discovery) is a\nMonte Carlo method-
based tool for feature selection. It also allows for the discovery of
interdependencies between the relevant features. MCFS-ID is particularly suitable
for the analysis of high-dimensional, 'small n large p' transactional and
biological data.","Imports":"yaml, ggplot2, reshape2, dplyr, igraph (>=
1.0.1)","License":"GPL-3 + file
LICENSE","NeedsCompilation":"no","Package":"rmcfs","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"The MCFS-ID Algorithm for Feature Selection and
Interdependency\nDiscovery","URL":"http:\/\/www.ipipan.eu\/staff\/m.draminski\/mcfs
.htm","Version":"1.1.1"},"rmdHelpers":{"Author":"Mark
Peterson","Depends":"knitr","Description":"A series of functions to aid in repeated
tasks for Rmd documents. All details are to my personal preference, though I am
happy to add flexibility if there are use cases I am missing. I will continue
updating with new functions as I add utility functions for
myself.","License":"GPL","NeedsCompilation":"no","Package":"rmdHelpers","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Helper Functions for Rmd
Documents","Version":"1.0"},"rmdformats":{"Author":"Julien Barnier [aut,
cre]","Description":"HTML formats and templates for 'rmarkdown' documents, with
some extra\nfeatures such as automatic table of contents, lightboxed figures,
dynamic\ncrosstab helper.","Imports":"knitr, rmarkdown, htmltools,
questionr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rmdformats","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"HTML Output Formats and Templates for 'rmarkdown'
Documents","URL":"https:\/\/github.com\/juba\/rmdformats","Version":"0.2"},"rmdshow
er":{"Author":"Vadim Makeev [aut, cph] (shower,
https:\/\/github.com\/shower\/shower),\nOleg Jahson [aut, cph] (shower,
https:\/\/github.com\/shower\/shower),\nSlava Oliyanchuk [aut, cph] (shower,
https:\/\/github.com\/shower\/shower),\nRoman Komarov [aut, cph] (shower,
https:\/\/github.com\/shower\/shower),\nArtem Polikarpov [aut, cph] (shower,
https:\/\/github.com\/shower\/shower),\nTony
Ganch [aut, cph] (shower, https:\/\/github.com\/shower\/shower),\nDenis Hananein
[aut, cph] (shower, https:\/\/github.com\/shower\/shower),\nGabor Csardi [aut,
cre],\nJJ Allaire [aut],\nRStudio [cph],\nMango Solutions [cph]","Depends":"R (>=
3.0)","Description":"'R' 'Markdown' format for 'shower' presentations,
see\n<https:\/\/github.com\/shower\/shower>.","Imports":"rmarkdown (>=
LICENSE","NeedsCompilation":"no","Package":"rmdshower","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"'R' 'Markdown' Format for 'shower'
Presentations","URL":"https:\/\/github.com\/mangothecat\/rmdshower","Version":"1.0.
0"},"rmeta":{"Author":"Thomas Lumley
<tlumley@u.washington.edu>","Depends":"grid","Description":"Functions for simple
fixed and random effects\nmeta-analysis for two-sample comparisons and
cumulative\nmeta-analyses. Draws standard summary plots, funnel plots,
and\ncomputes summaries and tests for association and
heterogeneity","License":"GPL-
2","NeedsCompilation":"no","Package":"rmeta","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Meta-analysis","Version":"2.16"},"rmetasim":{"Author":"Allan
Strand <stranda@cofc.edu>,\nJames Niehaus","Description":"An interface between R
and the metasim simulation engine.\nThe simulation environment is documented
in: \"Strand, A.(2002) <DOI:10.1046\/j.1471-8286.2002.00208.x> Metasim 1.0: an
individual-based environment for simulating population genetics of\ncomplex
population dynamics. Mol. Ecol. Notes.\nPlease see the vignettes CreatingLandscapes
and Simulating to get some ideas on how to use the packages.\nSee the rmetasim
vignette to get an overview and to see important changes to the\ncode in the most
recent version.","Imports":"pegas, ade4, gtools,
adegenet","License":"GPL","NeedsCompilation":"yes","Package":"rmetasim","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"magrittr, knitr, ggplot2,
reshape2","Title":"An Individual-Based Population Genetic Simulation
Environment","Version":"3.0.5"},"rmgarch":{"Author":"Alexios Ghalanos
<alexios@4dscape.com>","Depends":"R (>= 3.0.2), methods, rugarch,
parallel","Description":"Feasible multivariate GARCH models including DCC, GO-GARCH
and Copula-GARCH.","Imports":"Rsolnp, MASS, Matrix, zoo, xts, Bessel, ff, shape,
pcaPP, spd,\nRcpp, utils, graphics, stats, grDevices","License":"GPL-
3","NeedsCompilation":"yes","Package":"rmgarch","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Multivariate GARCH
Models","URL":"http:\/\/www.unstarched.net,
https:\/\/bitbucket.org\/alexiosg","Version":"1.3-0"},"rminer":{"Author":"Paulo
Cortez","Depends":"kknn","Description":"Facilitates the use of data mining
algorithms in classification and regression (including time series forecasting)
tasks by presenting a short and coherent set of functions. Versions: 1.4.1 new
tutorial and more robust version; 1.4 - new classification and regression
models\/algorithms, with a total of 14 classification and 15 regression methods,
including: Decision Trees, Neural Networks, Support Vector Machines, Random
Forests, Bagging and Boosting; 1.3 and 1.3.1 - new classification and regression
metrics (improved mmetric function); 1.2 - new input importance methods (improved
Importance function); 1.0 - first version.","Imports":"methods, plotrix, lattice,
nnet, pls, MASS, mda, rpart,\nrandomForest, adabag, party, Cubist, kernlab,
e1071","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rminer","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Data Mining Classification and Regression
Methods","URL":"http:\/\/cran.r-
project.org\/package=rminer\nhttp:\/\/www3.dsi.uminho.pt\/pcortez\/rminer.html","Ve
rsion":"1.4.1"},"rmngb":{"Author":"Antoine Filipovic Pierucci","Description":"A
collection of miscellaneous functions for medical data analysis. Visualization\nof
multidimensional data, diagnostic test calibration, pairwise tests for qualitative
variables and outcome simulation.","Imports":"Hmisc","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"rmngb","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Miscellaneous Collection of Functions for Medical Data
Analysis","Version":"0.6-1"},"rmongodb":{"Author":"MongoDB, Inc. (mongo-c-driver) &
Markus Schmidberger (mongosoup.de).\nFormerly Gerald Lindsly.","Depends":"R (>=
2.10)","Description":"This R package provides an interface to the NoSQL MongoDB
database\nusing the MongoDB C-driver version 0.8.","Imports":"jsonlite,
plyr","License":"Apache License
2.0","NeedsCompilation":"yes","Package":"rmongodb","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"RUnit, knitr","Title":"R-MongoDB
driver","URL":"https:\/\/github.com\/mongosoup\/rmongodb,\nhttp:\/\/stackoverflow.c
om\/questions\/tagged\/rmongodb","Version":"1.8.0"},"rmp":{"Author":"Antonio Canale
[aut,cre], Nicola Lunardon [ctb]","Description":"Performs probability mass function
estimation with nonparametric mixtures of rounded kernels.","License":"GPL-
2","NeedsCompilation":"yes","Package":"rmp","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Rounded Mixture Package. Performs Probability Mass
Function\nEstimation with Nonparametric Mixtures of Rounded
Kernels","Version":"2.0"},"rms":{"Author":"Frank E Harrell Jr
<f.harrell@vanderbilt.edu>","Depends":"Hmisc (>= 3.17-3), survival (>= 2.37-6),
lattice, ggplot2 (>=\n2.0), SparseM","Description":"Regression modeling, testing,
estimation, validation,\ngraphics, prediction, and typesetting by storing enhanced
model design\nattributes in the fit. 'rms' is a collection of functions
that\nassist with and streamline modeling. It also contains functions for\nbinary
and ordinal logistic regression models, ordinal models for\ncontinuous Y with a
variety of distribution families, and the Buckley-James\nmultiple regression model
for right-censored responses, and implements\npenalized maximum likelihood
estimation for logistic and ordinary\nlinear models. 'rms' works with almost any
regression model, but it\nwas especially written to work with binary or ordinal
regression\nmodels, Cox regression, accelerated failure time models,\nordinary
linear models,\tthe Buckley-James model, generalized least\nsquares for serially or
spatially correlated observations, generalized\nlinear models, and quantile
regression.","Imports":"methods, quantreg, nlme (>= 3.1-123), rpart,
polspline,\nmultcomp","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"rms","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"boot, tcltk","Title":"Regression Modeling
Strategies","URL":"http:\/\/biostat.mc.vanderbilt.edu\/rms","Version":"4.5-
0"},"rms.gof":{"Author":"Shubhodeep Mukherji
<deep.mukherji@utexas.edu>","Description":"This package can be used to test any
simple null\nhypothesis using the root-mean-square goodness of fit test.\nMonte
Carlo estimation is used to calculate the associated\nP-value.","License":"GPL-
3","NeedsCompilation":"no","Package":"rms.gof","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Root-mean-square goodness-of-fit test for simple null
hypothesis","Version":"1.0"},"rmumps":{"Author":"Serguei
Sokol","Description":"Exported class can be used for storing sparse matrix\nand
solving corresponding linear system with one or many right\nhand sides. There is a
possibility to do separately symbolic analysis,\nLU factorization and system
solving.","Imports":"methods, Rcpp (>= 0.12.0)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"rmumps","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"testthat, Matrix, slam","Title":"Wrapper for MUMPS
Library","Version":"5.0.1.8"},"rnaseqWrapper":{"Author":"Mark
Peterson","Depends":"ecodist, gplots, gtools","Description":"This package is
designed to streamline several of the common steps for RNA-seq\nanalysis, including
differential expression and variant discovery.\nFor the development build, or to
contribute changes to this package,\nplease see our repository at
https:\/\/bitbucket.org\/petersmp\/rnaseqwrapper\/","License":"GPL","NeedsCompilati
on":"no","Package":"rnaseqWrapper","Repository":"http:\/\/cran.csiro.au\/src\/contr
ib","Suggests":"topGO,seqinr,DESeq","Title":"Wrapper for several R packages and
scripts to automate RNA-seq\nanalysis","Version":"1.0-1"},"rnbn":{"Author":"Stuart
Ball & Tom August","Depends":"R (>= 3.0.0)","Description":"Access to data held by
the National Biodiversity Network (NBN, www.nbn.org.uk). The NBN acts as a data
warehouse for biological records data in the UK and is the UK node of GBIF (Global
Biodiversity Information Facility). In this package NBN data is accessed via its
web-services.","Imports":"httr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rnbn","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat (>= 0.8.0), roxygen2,
knitr","Title":"Access NBN
Data","URL":"https:\/\/github.com\/ropensci\/rnbn","Version":"1.0.3"},"rncl":
{"Author":"Francois Michonneau [aut, cre],\nBen Bolker [aut],\nMark Holder
[aut],\nPaul Lewis [aut],\nBrian O'Meara [aut]","Depends":"R (>=
3.1.1)","Description":"An interface to the Nexus Class Library which allows
parsing\nof NEXUS, Newick and other phylogenetic tree file formats. It
provides\nelements of the file that can be used to build phylogenetic objects\nsuch
as ape's 'phylo' or phylobase's 'phylo4(d)'.","Imports":"Rcpp (>=
LICENSE","NeedsCompilation":"yes","Package":"rncl","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat, ape","Title":"An Interface to the Nexus
Class
Library","URL":"https:\/\/github.com\/fmichonneau\/rncl","Version":"0.6.0"},"rneos"
:{"Author":"Bernhard Pfaff [aut, cre]","Depends":"R (>= 2.10.0), methods, RCurl,
XML, stats","Description":"Within this package the XML-RPC API to NEOS is
implemented. This enables the user to pass optimization problems
to NEOS and retrieve results within R.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rneos","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"XMLRPC","Title":"XML-RPC Interface to
NEOS","Version":"0.3-1"},"rnetcarto":{"Author":"Guilhem Doulcier [aut, cre] (R
bindings, current implementation of the\nsimulated annealing algorithm),\nRoger
Guimera [ctb] (Author of the original rgraph library),\nDaniel B. Stouffer [aut,
ths]","Description":"It provides functions to compute the modularity and
modularity-related roles in networks. It is a wrapper around the rgraph library
(Guimera & Amaral, 2005, doi:10.1038\/nature03288).","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"rnetcarto","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat, knitr, rmarkdown, igraph","Title":"Fast
Network Modularity and Roles Computation by Simulated\nAnnealing (Rgraph C Library
Wrapper for R)","Version":"0.2.4"},"rngSetSeed":{"Author":"Petr
Savicky","Description":"A function setVectorSeed() is provided. Its argument\nis a
numeric vector of an arbitrary nonzero length, whose\ncomponents have integer
values from [0, 2^32-1]. The input\nvector is transformed using AES (Advanced
Encryption Standard)\nalgorithm into an initial state of Mersenne-Twister
random\nnumber generator. The function provides a better alternative\nto the R base
function set.seed(), if the input vector is\na single integer. Initializing a
stream of random numbers\nwith a vector is a convenient way to obtain several
streams,\neach of which is identified by several integer indices.","License":"GPL-
3","NeedsCompilation":"yes","Package":"rngSetSeed","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Seeding the Default RNG with a Numeric
Vector","Version":"0.3-2"},"rngWELL":{"Author":"C code by F. Panneton, P. L'Ecuyer
and M. Matsumoto and R port by Christophe Dutang and Petr Savicky
<savicky@cs.cas.cz>.","Depends":"R (>= 2.6.0)","Description":"It is a dedicated
package to WELL pseudo random generators, which were introduced in Panneton et al.
(2006), `Ìmproved Long-Period Generators Based on Linear Recurrences Modulo 2'',
ACM Transactions on Mathematical Software. But this package is not intended to be
used directly, you are strongly __encouraged__ to use the 'randtoolbox' package,
which depends on this package.","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"yes","Package":"rngWELL","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Toolbox for WELL Random Number
Generators","Version":"0.10-4"},"rngtools":{"Author":"Renaud Gaujoux","Depends":"R
(>= 3.0.0), methods, pkgmaker (>= 0.20)","Description":"This package contains a set
of functions for working with\nRandom Number Generators (RNGs). In particular, it
defines a generic\nS4 framework for getting\/setting the current RNG, or RNG
data\nthat are embedded into objects for reproducibility.\nNotably, convenient
default methods greatly facilitate the way current\nRNG settings can be
changed.","Imports":"stringr, digest","License":"GPL-
3","NeedsCompilation":"no","Package":"rngtools","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"parallel, RUnit, knitr","Title":"Utility functions for
working with Random Number
Generators","URL":"https:\/\/renozao.github.io\/rngtools","Version":"1.2.4"},"rngwe
ll19937":{"Author":"Petr Savicky <savicky@cs.cas.cz>","Description":"Long period
linear random number generator WELL19937a by\nF. Panneton, P. L'Ecuyer and M.
Matsumoto. The initialization\nalgorithm allows to seed the generator with
a\nnumeric vector of an arbitrary length and uses MRG32k5a by\nP. L'Ecuyer to
achieve good quality of the initialization. The\noutput function may be set to
provide numbers from the interval\n(0,1) with 53 (the default) or 32 random bits.
WELL19937a is of\nsimilar type as Mersenne Twister and has the same
period.\nWELL19937a is slightly slower than Mersenne Twister, but has\nbetter
equidistribution and \"bit-mixing\" properties and faster\nrecovery from states
with prevailing zeros than Mersenne\nTwister. All WELL generators with orders 512,
1024, 19937 and\n44497 can be found in randtoolbox package.","License":"file
LICENSE","NeedsCompilation":"yes","Package":"rngwell19937","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Title":"Random number generator WELL19937a with 53 or
32 bit output","Version":"0.6-0"},"rnn":{"Author":"Bastiaan Quast [aut,
cre]","Depends":"R (>= 3.2.2)","Description":"Implementation of a Recurrent Neural
Network in R.","License":"GPL-
3","NeedsCompilation":"no","Package":"rnn","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"testthat, knitr, rmarkdown","Title":"Recurrent Neural
Network","Version":"0.3.0"},"rnoaa":{"Author":"Scott Chamberlain [aut,
cre],\nKarthik Ram [ctb],\nAdam Erickson [ctb],\nNicholas Potter [ctb],\nJoseph
Stachelek [ctb],\nHart Edmund [ctb]","Description":"Client for many 'NOAA' data
sources including the 'NCDC' climate\n'API' at http:\/\/www.ncdc.noaa.gov\/cdo-
web\/webservices\/v2, with functions for\neach of the 'API' 'endpoints': data, data
categories, data sets, data types,\nlocations, location categories, and stations.
In addition, we have an interface\nfor 'NOAA' sea ice data, the 'NOAA' severe
weather inventory, 'NOAA' Historical\nObserving 'Metadata' Repository ('HOMR')
data, 'NOAA' storm data via 'IBTrACS',\ntornado data via the 'NOAA' storm
prediction center, and more.","Imports":"methods, stats, utils, httr (>= 1.0.0),
lubridate, dplyr,\ntidyr, ggplot2, scales, XML, jsonlite","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rnoaa","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat, roxygen2, knitr, taxize, ncdf4, leaflet,
geojsonio,\nlawn, rgdal","Title":"'NOAA' Weather Data from
R","URL":"https:\/\/github.com\/ropensci\/rnoaa","Version":"0.5.2"},"rnrfa":
{"Author":"Claudia Vitolo [aut, cre], Matthew Fry [ctb]","Depends":"R (>= 3.0.2),
utils","Description":"Utility functions to retrieve data from the UK National River
Flow\nArchive. The package contains R wrappers to the UK NRFA data temporary-
API.\nThere are functions to retrieve stations falling in a bounding box,\nto
generate a map and extracting time series and general
information.","Imports":"XML2R, RCurl, plyr, zoo, rjson, rgdal, sp,
3","NeedsCompilation":"no","Package":"rnrfa","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"UK National River Flow Archive Data from
R","URL":"http:\/\/cvitolo.github.io\/r_rnrfa\/","Version":"0.5.1"},"robComposition
s":{"Author":"Matthias Templ, Karel Hron, Peter Filzmoser","Depends":"R (>= 2.10),
robustbase, ggplot2, data.table, pls","Description":"Methods for analysis of
compositional data including robust\nmethods, imputation, methods to replace
rounded zeros, (robust) outlier\ndetection for compositional data, (robust)
principal component analysis for\ncompositional data, (robust) factor analysis for
compositional data, (robust)\ndiscriminant analysis for compositional data (Fisher
rule), robust regression\nwith compositional predictors and (robust) Anderson-
Darling normality tests for\ncompositional data as well as popular log-ratio
transformations (addLR, cenLR,\nisomLR, and their inverse transformations). In
addition, visualisation and\ndiagnostic tools are implemented as well as high and
low-level plot functions\nfor the ternary diagram.","Imports":"e1071, cvTools,
rrcov, GGally, MASS, sROC, VIM","License":"GPL-
2","NeedsCompilation":"yes","Package":"robCompositions","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"knitr","Title":"Robust Estimation for
Compositional Data","Version":"2.0.0"},"robcor":{"Author":"Paul
Smirnov","Depends":"R (>= 2.10.0), stats","Description":"Robust pairwise
correlations based on estimates of scale,\nparticularly on \"FastQn\" one-step M-
estimate.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"robcor","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"MASS, robustbase, sfsmisc","Title":"Robust
Correlations","Version":"0.1-6"},"robeth":{"Author":"Alfio Marazzi
<Alfio.Marazzi@chuv.ch>","Depends":"R (>= 2.9.2)","Description":"Locations
problems, M-estimates of coefficients and scale\nin linear regression, Weights for
bounded influence regression,\nCovariance matrix of the coefficient estimates,
Asymptotic\nrelative efficiency of regression M-estimates, Robust testing\nin
linear models, High breakdown point regression, M-estimates\nof covariance
matrices, M-estimates for discrete generalized\nlinear models.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"robeth","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"R functions for robust
statistics","URL":"http:\/\/www.iumsp.ch\/","Version":"2.7"},"robfilter":
{"Author":"Roland Fried <fried@statistik.tu-dortmund.de>, Karen\nSchettlinger
<schettlinger@statistik.tu-dortmund.de> and\nMatthias Borowski
<borowski@statistik.tu-dortmund.de>","Depends":"R (>= 2.5.0), robustbase, MASS,
lattice","Description":"A set of functions to filter time series based on
concepts\nfrom robust statistics.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"robfilter","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Robust Time Series
Filters","URL":"http:\/\/www.statistik.tu-
dortmund.de\/fried.html","Version":"4.1"},"robotstxt":{"Author":"Peter Meissner
[aut, cre],\nOliver Keys [ctb]","Depends":"R (>= 3.0.0)","Description":"Provides a
'Robotstxt' ('R6') class and accompanying methods to\nparse and check 'robots.txt'
files. Data fields are provided as\ndata frames and vectors. Permissions can be
checked by providing\npath character vectors and optional bot names.","Imports":"R6
(>= 2.1.1), stringr (>= 1.0.0), httr (>= 1.0.0)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"robotstxt","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"knitr,
rmarkdown, dplyr, testthat","Title":"A 'robots.txt' Parser and
'Webbot'\/'Spider'\/'Crawler'\nPermissions
Checker","URL":"https:\/\/github.com\/petermeissner\/robotstxt","Version":"0.1.2"},
"robreg3S":{"Author":"Andy Leung, Hongyang Zhang, Ruben Zamar","Depends":"GSE,
MASS","Description":"Three-step regression and inference for cellwise and casewise
contamination.","Imports":"robustbase","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"robreg3S","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Three-Step Regression and Inference for Cellwise and
Casewise\nContamination","Version":"0.3"},"robumeta":{"Author":"Zachary Fisher and
Elizabeth Tipton.","Depends":"grid","Description":"Functions for conducting robust
variance estimation (RVE) meta-regression using both large and small sample RVE
estimators under various weighting schemes. These methods are distribution free and
provide valid point estimates, standard errors and hypothesis tests even when the
degree and structure of dependence between effect sizes is unknown. Also included
are functions for conducting sensitivity analyses under correlated effects
weighting and producing RVE-based forest plots.","License":"GPL-
2","NeedsCompilation":"no","Package":"robumeta","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Robust Variance Meta-
Regression","Version":"1.6"},"robust":{"Author":"Jiahui Wang,\nRuben Zamar
<ruben@stat.ubc.ca>,\nAlfio Marazzi <Alfio.Marazzi@inst.hospvd.ch>,\nVictor Yohai
<vyohai@dm.uba.ar>,\nMatias Salibian-Barrera <matias@stat.ubc.ca>,\nRicardo Maronna
<maron@mate.unlp.edu.ar>,\nEric Zivot <ezivot@u.washington.edu>,\nDavid Rocke
<dmrocke@ucdavis.edu>,\nDoug Martin,\nMartin Maechler
<maechler@stat.math.ethz.ch>,\nKjell Konis
<kjell.konis@me.com>.","Depends":"fit.models, MASS, lattice, robustbase, rrcov,
stats","Description":"A package of robust methods.","License":"GPL-
2","NeedsCompilation":"yes","Package":"robust","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Robust Library","Version":"0.4-16"},"robustDA":
{"Author":"Charles Bouveyron & Stephane Girard","Depends":"MASS, mclust,
Rsolnp","Description":"Robust mixture discriminant analysis (RMDA, Bouveyron &
Girard, 2009) allows to build a robust supervised classifier from learning data
with label noise. The idea of the proposed method is to confront an unsupervised
modeling of the data with the supervised information carried by the labels of the
learning data in order to detect inconsistencies. The method is able afterward to
build a robust classifier taking into account the detected inconsistencies into the
labels.","License":"GPL-
2","NeedsCompilation":"no","Package":"robustDA","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Robust Mixture Discriminant
Analysis","Version":"1.1"},"robustETM":{"Author":"Chuan Hong, Yong Chen, Yang Ning,
Hao Wu","Depends":"R (>= 2.5.0)","Description":"Testing homogeneity for generalized
exponential tilt model. This package includes a collection of functions for (1)
implementing methods for testing homogeneity for generalized exponential tilt
model; and (2) implementing existing methods under
comparison.","Imports":"stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"robustETM","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Robust Methods using Exponential Tilt
Model","Version":"1.0"},"robustHD":{"Author":"Andreas Alfons [aut,
cre]","Depends":"R (>= 3.2.0), ggplot2 (>= 0.9.2), perry (>= 0.2.0),
robustbase\n(>= 0.9-5)","Description":"Robust methods for high-dimensional data, in
particular linear\nmodel selection techniques based on least angle regression and
sparse\nregression.","Imports":"MASS, grDevices, parallel, stats,
2)","NeedsCompilation":"yes","Package":"robustHD","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"mvtnorm","Title":"Robust Methods for High-
Dimensional Data","Version":"0.5.1"},"robustX":{"Author":"Werner Stahel, Martin
Maechler and potentially
others","Depends":"robustbase","Description":"eXperimental, eXtraneous, or
eXtraordinary Functionality\nfor Robust Statistics. In other words, methods which
are not\nyet well established, often related to methods in
package\nrobustbase.","Enhances":"ICS","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"robustX","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"MASS, lattice","Title":"eXperimental Functionality for
Robust Statistics","Version":"1.1-4"},"robustbase":{"Author":"Original code by many
authors, notably\nPeter Rousseeuw and Christophe Croux, see file
'Copyrights';\nValentin Todorov <valentin.todorov@chello.at>,\nAndreas Ruckstuhl
<andreas.ruckstuhl@zhaw.ch>,\nMatias Salibian-Barrera <matias@stat.ubc.ca>,\nTobias
Verbeke <tobias.verbeke@openanalytics.eu>,\nManuel Koller
<mkoller@ispm.unibe.ch>,\nMartin Maechler","Depends":"R (>=
3.0.2)","Description":"\"Essential\" Robust Statistics.\nTools allowing to analyze
data with robust methods. This includes\nregression methodology including model
selections and multivariate\nstatistics where we strive to cover the book \"Robust
Statistics,\nTheory and Methods\" by 'Maronna, Martin and Yohai'; Wiley
2006.","Imports":"stats, graphics, utils, methods, DEoptimR","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"robustbase","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"grid, MASS, lattice, boot, cluster, Matrix,
robust,\nfit.models, MPV, xtable, ggplot2, GGally, RColorBrewer,\nreshape2,
sfsmisc, catdata","Title":"Basic Robust Statistics","URL":"http:\/\/robustbase.r-
forge.r-project.org\/","Version":"0.92-5"},"robustfa":{"Author":"Ying-Ying Zhang
(Robert)","Depends":"rrcov, R (>= 2.15.0)","Description":"An object oriented
solution for robust factor analysis. In the solution, new S4
classes \"Fa\", \"FaClassic\", \"FaRobust\", \"FaCov\", \"SummaryFa\" are
created.","Imports":"methods, stats4, stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"robustfa","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"grid, lattice, cluster, mclust, MASS,
ellipse","Title":"An Object Oriented Solution for Robust Factor
Analysis","Version":"1.0-5"},"robustgam":{"Author":"Raymond K. W. Wong, Fang Yao
and Thomas C. M. Lee","Depends":"Rcpp (>= 0.9.13), RcppArmadillo (>= 0.3.4.4) ,
mgcv (>=\n1.7-20), robustbase (>= 0.9-3)","Description":"This package provides
robust estimation for generalized\nadditive models. It implements a fast and stable
algorithm in\nWong, Yao and Lee (2013). The implementation also contains\nthree
automatic selection methods for smoothing parameter. They\nare designed to be
robust to outliers. For more details, see\nWong, Yao and Lee
(2013).","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"robustgam","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Robust Estimation for Generalized Additive
Models","Version":"0.1.7"},"robustlmm":{"Author":"Manuel Koller","Depends":"lme4
(>= 1.1-9), Matrix (>= 1.0-13),","Description":"A method to fit linear mixed
effects models robustly.\nRobustness is achieved by modification of the scoring
equations\ncombined with the Design Adaptive Scale approach.","Imports":"ggplot2,
lattice, nlme, methods, robustbase (>= 0.9.5), xtable","License":"GPL-
2","NeedsCompilation":"no","Package":"robustlmm","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"digest, reshape2","Title":"Robust Linear Mixed
Effects
Models","URL":"https:\/\/github.com\/kollerma\/robustlmm","Version":"1.8"},"robustl
oggamma":{"Author":"Claudio Agostinelli <claudio@unive.it>, Alfio Marazzi
<Alfio.Marazzi@chuv.ch>, Victor Yohai <vyohai@uolsinectis.com.ar> and Alex
Randriamiharisoa <Alex.Randriamiharisoa@chuv.ch>","Depends":"R (>=
2.15.1)","Description":"Robust estimation of the generalized log gamma model is
provided using Quantile Tau estimator and Weighted Likelihood
estimator.","Imports":"robustbase","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"robustloggamma","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Robust estimation of the generalized log gamma
model","Version":"0.4-31"},"robustrao":{"Author":"MarÃa del Carmen Calatrava Moreno
[aut, cre],\nThomas Auzinger [aut]","Depends":"R (>= 3.2.3)","Description":"A
collection of functions to compute the Rao-Stirling diversity index\n(Porter and
Rafols, 2009) <DOI:10.1007\/s11192-008-2197-2> and its extension to\nacknowledge
missing data (i.e.,\tuncategorized references) by calculating its\ninterval of
uncertainty using\tmathematical optimization as proposed in Calatrava\net al.
(2016) <DOI:10.1007\/s11192-016-1842-4>.\nThe Rao-Stirling diversity index is a
well-established bibliometric indicator\nto measure the interdisciplinarity of
scientific publications. Apart from the\nobligatory dataset of publications with
their respective references and\ta\ntaxonomy of disciplines that categorizes
references as well as a measure of\nsimilarity between the disciplines, the Rao-
Stirling diversity index requires\na complete categorization of all references of a
publication into disciplines.\nThus, it fails for a incomplete categorization; in
this case, the robust\nextension has to be used, which encodes the uncertainty
caused by missing\nbibliographic data as an uncertainty
interval.\nClassification \/ ACM - 2012: Information systems ~ Similarity
measures,\nTheory of computation ~ Quadratic\tprogramming, Applied computing ~
Digital\nlibraries and archives.","Imports":"doParallel (>= 1.0.10), gmp (>= 0.5-
12), iterpc (>= 0.2.8),\nquadprog (>= 1.5-5), igraph (>= 1.0.1), foreach (>=
3","NeedsCompilation":"no","Package":"robustrao","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"An Extended Rao-Stirling Diversity Index to Handle
Missing
Data","URL":"https:\/\/gitlab.com\/mc.calatrava.moreno\/robustrao.git","Version":"1
.0-0"},"robustreg":{"Author":"Ian
M. Johnson <ian@alpha-analysis.com>","Depends":"R (>=
3.0.0)","Description":"Linear regression functions using Huber and bisquare psi
functions. Optimal weights are calculated using IRLS algorithm.","Imports":"stats
(>= 3.0.0), Matrix (>= 1.1.0), Rcpp (>= 0.11.3)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"robustreg","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Robust Regression Functions","Version":"0.1-
9"},"robustvarComp":{"Author":"Claudio Agostinelli <claudio@unive.it> and Victor J.
Yohai <victoryohai@gmail.com>","Depends":"R (>= 2.15.1)","Description":"Robust
Estimation of Variance Component Models by classic and composite robust procedures.
The composite procedures are robust against outliers generated by the Independent
Contamination Model.","Imports":"robustbase, GSE, numDeriv, robust,
2","NeedsCompilation":"yes","Package":"robustvarComp","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"nlme, Matrix, mvtnorm, WWGbook","Title":"Robust
Estimation of Variance Component Models","Version":"0.1-2"},"rocc":
{"Author":"Martin Lauss","Depends":"ROCR","Description":"Functions for a
classification method based on receiver\noperating characteristics (ROC). Briefly,
features are selected\naccording to their ranked AUC value in the training set.
The\nselected features are merged by the mean value to form a\nmetagene. The
samples are ranked by their metagene value and\nthe metagene threshold that has the
highest accuracy in\nsplitting the training samples is determined. A new sample
is\nclassified by its metagene value relative to the threshold. In\nthe first
place, the package is aimed at two class problems in\ngene expression data, but
might also apply to other problems.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rocc","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"ROC based classification","Version":"1.2"},"rockchalk":
{"Author":"Paul E. Johnson <pauljohn@ku.edu>","Depends":"R (>=
2.10)","Description":"A collection of functions for interpretation and
presentation\nof regression analysis. These functions are used\nto produce the
statistics lectures in\nhttp:\/\/pj.freefaculty.org\/guides. Includes
regression\ndiagnostics, regression tables, and plots of interactions
and\n\"moderator\" variables. The emphasis is on \"mean-centered\" and\n\"residual-
centered\" predictors. The vignette 'rockchalk' offers a\nfairly comprehensive
overview. The vignette 'Rstyle' has advice\nabout coding in R. The package title
'rockchalk' refers to our\nschool motto, 'Rock Chalk Jayhawk, Go
K.U.'.","Imports":"grDevices, methods, lme4, car, MASS","License":"GPL (>=
3.0)","NeedsCompilation":"no","Package":"rockchalk","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"tables, Hmisc","Title":"Regression Estimation and
Presentation","Version":"1.8.101"},"rococo":{"Author":"Martin Krone, Ulrich
Bodenhofer","Depends":"R (>= 3.0.0)","Description":"The rococo package provides a
robust gamma rank correlation\ncoefficient along with a permutation-based rank
correlation test.\nThe rank correlation coefficient and the test are
explicitly\ndesigned for dealing with noisy numerical data.","Imports":"Rcpp (>=
0.11.1), methods","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"rococo","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"compiler, datasets","Title":"RObust rank COrrelation
COefficient and
test","URL":"http:\/\/www.bioinf.jku.at\/software\/rococo\/","Version":"1.1.2"},"ro
dd":{"Author":"Roman Guchenko [aut, cre]","Depends":"R (>= 3.0.0)","Description":"A
collection of functions for numerical construction of optimal discriminating
designs. At the current moment T-optimal designs (which maximize the lower bound
for the power of F-test for regression model discrimination), KL-optimal designs
(for lognormal errors) and their robust analogues can be calculated with the
package.","Imports":"numDeriv, quadprog, Matrix, rootSolve,
matrixcalc","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rodd","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"mvtnorm","Title":"Optimal Discriminating
Designs","Version":"0.2-1"},"roll":{"Author":"Jason Foster","Description":"Parallel
functions for computing rolling statistics of time-series\ndata.","Imports":"Rcpp,
RcppParallel","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"roll","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Rolling Statistics","Version":"1.0.2"},"rollply":
{"Author":"\"Alexandre Genin <alex@lecairn.org> [aut, cre]\"","Depends":"R (>=
3.1.1)","Description":"Apply a function in a moving window, then\ncombine the
results in a data frame.","Imports":"plyr, Rcpp, stringr","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"rollply","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat, knitr, proj4, ggplot2, rgdal, tidyr,
alphahull,\nrmarkdown","Title":"Moving-Window Add-on for
'plyr'","URL":"http:\/\/alex.lecairn.org\/rollply.html,\nhttps:\/\/github.com\/alex
genin\/rollply","Version":"0.5.0"},"rootSolve":{"Author":"Karline Soetaert [aut,
cre],\nyale sparse matrix package authors [cph]","Depends":"R (>=
2.01)","Description":"Routines to find the root of nonlinear functions, and to
perform steady-state and equilibrium analysis of ordinary differential equations
(ODE).\nIncludes routines that: (1) generate gradient and Jacobian matrices (full
and banded),\n(2) find roots of non-linear equations by the Newton-Raphson
method,\n(3) estimate steady-state conditions of a system of (differential)
equations in full, banded or sparse form, using the Newton-Raphson method, or by
dynamically running,\n(4) solve the steady-state conditions for uni-and
multicomponent 1-D, 2-D, and 3-D partial differential equations, that have been
converted to ODEs\nby numerical differencing (using the method-of-lines
approach).\nIncludes fortran code.","Imports":"stats, graphics,
2)","NeedsCompilation":"yes","Package":"rootSolve","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Nonlinear Root Finding, Equilibrium and Steady-State
Analysis of\nOrdinary Differential Equations","Version":"1.6.6"},"ropensecretsapi":
{"Author":"Thomas P. Fuller <thomas.fuller@coherentlogic.com>","Depends":"R (>=
3.0.3), RJSONIO, RCurl","Description":"An R package for the OpenSecrets.org web
services API.","License":"LGPL-
3","NeedsCompilation":"no","Package":"ropensecretsapi","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"R Package for the OpenSecrets.org
API","URL":"http:\/\/www.r-project.org,\nhttp:\/\/coherentlogic.com\/r-package-for-
the-opensecrets-org-api?source=cran","Version":"1.0.1"},"ror":{"Author":"Tommi
Tervonen","Depends":"R (>= 2.7.0), rJava (>= 0.8-0), ROI (>=
0.0.7),\nROI.plugin.glpk (>= 0.0-1), igraph (>= 0.6.4)","Description":"An R package
for computing both exact- and stochastic\nrobust ordinal regression, and maximal
vectors.","License":"GPL-
3","NeedsCompilation":"no","Package":"ror","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Robust Ordinal Regression MCDA
library","Version":"1.2"},"rorcid":{"Author":"Scott Chamberlain [aut,
cre]","Description":"Client for the 'Orcid.org' 'API'
(http:\/\/orcid.org\/).\nFunctions included for searching for people, searching by
'DOI',\nand searching by 'Orcid' 'ID'.","Imports":"methods, stats, utils, httr (>=
1.1.0), jsonlite","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rorcid","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat","Title":"Interface to the 'Orcid.org'
'API'","URL":"https:\/\/github.com\/ropensci\/rorcid","Version":"0.2.2"},"rorutadis
":{"Author":"Krzysztof Ciomek","Depends":"Rglpk (>= 0.5-1), ggplot2 (>= 0.9.3.1),
gridExtra (>= 0.9.1),\nhitandrun (>= 0.5-2)","Description":"Implementation of
Robust Ordinal Regression for value-based sorting with some extensions and
additional tools. It is a novel Multiple-Criteria Decision Aiding (MCDA)
framework.","License":"GPL-
3","NeedsCompilation":"no","Package":"rorutadis","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat (>= 0.7.1)","Title":"Robust Ordinal
Regression
UTADIS","URL":"https:\/\/github.com\/kciomek\/rorutadis\/","Version":"0.3.1"},"rosm
":{"Author":"Dewey Dunnington [aut, cre],\nTimothÃ©e Giraud
[ctb]","Description":"Download and plot Open Street Map
<http:\/\/www.openstreetmap.org\/>,\nMapquest <http:\/\/www.mapquest.com\/>, Bing
Maps <http:\/\/www.bing.com\/maps> and\nother tiled map sources in a way that works
seamlessly with plotting from the\n'sp' package. Use to create high-resolution
basemaps and add hillshade to vector\nbased maps.","Imports":"abind, jpeg, png, sp,
rgdal, digest, rjson, methods, foreach","License":"GPL-
2","NeedsCompilation":"no","Package":"rosm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"prettymapr, rcanvec, cartography, raster","Title":"Plot
Raster Map Tiles from Open Street Map and Other
Sources","URL":"https:\/\/github.com\/paleolimbot\/rosm","Version":"0.1.4"},"rotati
onForest":{"Author":"Michel Ballings and Dirk Van den Poel","Description":"Fit and
deploy rotation forest models (\"Rodriguez, J.J., Kuncheva, L.I., 2006. Rotation
forest: A new classifier ensemble method. IEEE Trans. Pattern Anal. Mach. Intell.
28, 1619-1630\") for binary classification. Rotation forest is an ensemble method
where each base classifier (tree) is fit on the principal components of the
variables of random partitions of the feature
set.","Imports":"rpart","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rotationForest","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Fit and Deploy Rotation Forest
Models","Version":"0.1"},"rotations":{"Author":"Bryan Stanfill
<bstanfill2003@gmail.com>, Heike Hofmann\n<hofmann@iastate.edu>, Ulrike Genschel
<ulrike@iastate.edu>","Depends":"R
(>= 3.2), ggplot2, Rcpp, rgl","Description":"Tools for working with rotational
data, including\nsimulation from the most commonly used distributions on
SO(3),\nmethods for different Bayes, mean and median type estimators for\nthe
central orientation of a sample, confidence\/credible\nregions for the central
orientation based on those estimators and\na novel visualization technique for
rotation data. Most recently,\nfunctions to identify potentially discordant
(outlying) values\nhave been added.","Imports":"stats, utils, methods,
sphereplot","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"rotations","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"gridExtra, knitr, onion, orientlib,
testthat","Title":"Tools for Working with Rotation
Data","URL":"https:\/\/github.com\/stanfill\/rotationsC\/tree\/master\/rotations","
Version":"1.5"},"rotl":{"Author":"Francois Michonneau [aut, cre],\nJoseph Brown
[aut],\nDavid Winter [aut]","Depends":"R (>= 3.1.1)","Description":"An interface to
the 'Open Tree of Life' API to retrieve\nphylogenetic trees, information about
studies used to assemble the synthetic\ntree, and utilities to match taxonomic
names to 'Open Tree identifiers'. The\n'Open Tree of Life' aims at assembling a
comprehensive phylogenetic tree for all\nnamed species.","Imports":"httr, jsonlite,
assertthat, rncl (>= 0.6.0), ape","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"rotl","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr (>= 1.12), rmarkdown (>= 0.7), testthat,
RNeXML,\nphylobase, gdata (>= 2.17.0), MCMCglmm, fulltext (>=
0.1.6)","Title":"Interface to the 'Open Tree of Life'
API","URL":"https:\/\/github.com\/ropensci\/rotl","Version":"0.5.0"},"roughrf":
{"Author":"Kuangnan Xiong","Depends":"R (>= 2.5.0), randomForest, mice,
nnet","Description":"A set of functions to support Xiong K, 'Roughened Random
Forests for Binary Classification' (2014). The functions include RRFA, RRFB, RRFC1-
RRFC7, RRFD and RRFE. RRFB and RRFC6 are usually recommended. RRFB is much faster
than RRFC6.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"roughrf","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"MASS, caTools","Title":"Roughened Random Forests for
Binary
Classification","URL":"http:\/\/pqdtopen.proquest.com\/pqdtopen\/doc\/1554346548.ht
ml?FMT=ABS","Version":"1.0"},"rowr":{"Author":"Craig Varrichio
<canthony427@gmail.com>","Depends":"R (>= 3.0.1)","Description":"Allows the
manipulation of R objects as if they were\norganized rows in a way that is familiar
to people used to working with\ndatabases. It allows more consistent and
predictable output to common\nfunctions, and generalizes a number of utility
functions to to be failsafe\nwith any number and type of input
objects.","License":"GPL-
3","NeedsCompilation":"no","Package":"rowr","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Row-Based Functions for R
Objects","Version":"1.1.2"},"roxygen2":{"Author":"Hadley Wickham [aut, cre,
cph],\nPeter Danenberg [aut, cph],\nManuel Eugster [aut, cph],\nRStudio
[cph]","Depends":"R (>= 3.0.2)","Description":"A 'Doxygen'-like in-source
documentation system\nfor Rd, collation, and 'NAMESPACE' files.","Imports":"stringr
(>= 0.5), stringi, brew, digest, methods, Rcpp (>=\n0.11.0)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"roxygen2","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat (>= 0.8.0), knitr, devtools,
rmarkdown","Title":"In-Source Documentation for
R","URL":"https:\/\/github.com\/klutometis\/roxygen","Version":"5.0.1"},"royston":
{"Author":"Selcuk Korkmaz","Depends":"R (>= 2.15.0)","Description":"Performs a
multivariate normality test based on Royston's H test","Imports":"nortest,
moments","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"royston","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Royston's H Test: Multivariate Normality
Test","URL":"\nhttp:\/\/journal.r-project.org\/archive\/2014-2\/korkmaz-goksuluk-
zararsiz.pdf","Version":"1.2"},"rpanel":{"Author":"Bowman, Bowman, Gibson and
Crawford","Depends":"R (>= 2.14), tcltk","Description":"rpanel provides a set of
functions to build simple\nGUI controls for R functions. These are built on the
tcltk package.\nUses could include changing a parameter on a graph by animating
it\nwith a slider or a \"doublebutton\", up to more sophisticated
control\npanels.\nSome functions for specific graphical tasks, referred to as
'cartoons',\nare provided.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rpanel","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"tkrplot, rgl, sp, geoR, RandomFields, akima, MASS,
denstrip,\nlattice, sm, maps, mgcv","Title":"Simple interactive controls for R
using the tcltk library","Version":"1.1-3"},"rpart":{"Author":"Terry Therneau
[aut],\nBeth Atkinson [aut],\nBrian Ripley [aut, trl, cre] (author of initial R
port)","Depends":"R (>= 2.15.0), graphics, stats,
grDevices","Description":"Recursive partitioning for classification,\nregression
and survival trees. An implementation of most of the\nfunctionality of the 1984
book by Breiman, Friedman, Olshen and Stone.","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"rpart","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"survival","Title":"Recursive Partitioning and Regression
Trees","Version":"4.1-10"},"rpart.plot":{"Author":"Stephen
Milborrow","Depends":"rpart (>= 4.1-0)","Description":"Plot 'rpart' models. Extends
plot.rpart() and text.rpart()\nin the 'rpart' package.","License":"GPL-
3","NeedsCompilation":"no","Package":"rpart.plot","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"earth","Title":"Plot 'rpart' Models: An Enhanced
Version of 'plot.rpart'","URL":"http:\/\/www.milbo.org\/rpart-
plot","Version":"1.5.3"},"rpart.utils":{"Author":"Craig Varrichio
<canthony427@gmail.com>","Depends":"R (>= 3.1.0), rpart","Description":"This
package contains additional tools for working with rpart\nobjects. Most
importantly, it includes methods for converting rpart rules\ninto a series of
structured tables sufficient for executing the decision\ntree completely in
SQL.","License":"GPL-
3","NeedsCompilation":"no","Package":"rpart.utils","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"RODBC","Title":"Tools for parsing and manipulating
rpart objects, including\ngenerating machine readable
rules","Version":"0.5"},"rpartScore":{"Author":"Giuliano Galimberti, Gabriele
Soffritti, Matteo Di Maso","Depends":"R (>= 2.14.2), rpart","Description":"This
package contains functions that allow to build\nclassification trees for ordinal
responses within the CART\nframework. The trees are grown using the Generalized
Gini\nimpurity function, where the misclassification costs are given\nby the
absolute or squared differences in scores assigned to\nthe categories of the
response. Pruning is based on the total\nmisclassification rate or on the total
misclassification cost.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rpartScore","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"MASS","Title":"Classification trees for ordinal
responses","Version":"1.0-1"},"rpartitions":{"Author":"Ken Locey, Daniel
McGlinn","Depends":"R (>= 2.15.1), hash","Description":"Provides algorithims for
randomly sampling a feasible set defined\nby a given total and number of elements
using integer
partitioning.","License":"MIT","NeedsCompilation":"yes","Package":"rpartitions","Re
pository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"testthat (>=
0.2)","Title":"Code for integer
partitioning","URL":"https:\/\/github.com\/klocey\/partitions","Version":"0.1"},"rp
ca":{"Author":"Maciek Sykulski [aut, cre]","Description":"Suppose we have a data
matrix, which is the superposition of a low-rank component and a sparse component.
Candes, E. J., Li, X., Ma, Y., & Wright, J. (2011). Robust principal component
analysis?. Journal of the ACM (JACM), 58(3), 11. prove that we can recover each
component individually under some suitable assumptions. It is possible to recover
both the low-rank and the sparse components exactly by solving a very convenient
convex program called Principal Component Pursuit; among all feasible
decompositions, simply minimize a weighted combination of the nuclear norm and of
the L1 norm. This package implements this decomposition algorithm resulting with
Robust PCA approach.","Imports":"compiler","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"rpca","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"RobustPCA: Decompose a Matrix into Low-Rank and
Sparse\nComponents","Version":"0.2.3"},"rpcdsearch":{"Author":"David Springate
[aut, cre],\nEvangelos Kontopantelis [ctb],\nIvan Olier [ctb]","Depends":"R (>=
3.1.0)","Description":"Allows users to identify relevant clinical codes
and\nautomate the construction of clinical code lists for primary care
database\nstudies. This package is analogous to the Stata command
pcdsearch.","Imports":"assertthat, stringr, dplyr, combinat, xlsx, methods,
2)","NeedsCompilation":"no","Package":"rpcdsearch","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat, roxygen2, knitr","Title":"Tools for the
Construction of Clinical Code Lists for Primary\nCare Database
Studies","Version":"1.0"},"rpdo":{"Author":"Joe Thorley [aut, cre],\nNathan Mantua
[aut, dtc],\nSteven R. Hare [aut, dtc]","Depends":"R (>=
3.1.0)","Description":"Monthly Pacific Decadal Oscillation (PDO) index\nvalues from
January 1900 to
present.","License":"CC0","NeedsCompilation":"no","Package":"rpdo","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Suggests":"assertr, curl, datacheckr (>=
0.1.0), devtools, dplyr,\nggplot2, lubridate, magrittr, readr, tidyr, testthat,
knitr,\nrmarkdown","Title":"Pacific Decadal Oscillation
Index","URL":"https:\/\/github.com\/poissonconsulting\/rpdo","Version":"0.1.2"},"rp
f":{"Author":"Joshua Pritikin [cre, aut],\nJonathan Weeks [ctb],\nLi Cai
[ctb],\nCarrie Houts [ctb],\nPhil Chalmers [ctb],\nMichael D. Hunter [ctb],\nCarl
F. Falk [ctb]","Depends":"methods, parallel, R (>= 2.14.0)","Description":"The
purpose of this package is to factor out logic and math common\nto Item Factor
Analysis fitting, diagnostics, and analysis. It is\nenvisioned as core support code
suitable for more specialized IRT packages\nto build upon. Complete access to
optimized C functions are made available\nwith
R_RegisterCCallable.","Imports":"mvtnorm","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"rpf","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat, roxygen2, ggplot2, reshape2, gridExtra,
numDeriv,\nknitr, mirt","Title":"Response Probability
Functions","URL":"https:\/\/gitlab.com\/rpf\/rpf","Version":"0.51"},"rpg":
{"Author":"Timothy H. Keitt","Depends":"R (>= 3.0.0)","Description":"Allows ad hoc
queries and reading and\nwriting data frames to and from a
database.","Imports":"Rcpp (>= 0.11.1), uuid (>= 0.1-1), RApiSerialize (>=
0.1.0),\ntcltk (>= 3.0.0)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"rpg","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"foreach (>= 1.4.2), doParallel (>= 1.0.0), hflights (>=
0.1)","Title":"Easy Interface to Advanced PostgreSQL
Features","URL":"http:\/\/www.postgresql.org\/,
http:\/\/github.com\/thk686\/rpg,\nhttp:\/\/r-forge.r-
project.org\/projects\/rpg\/,\nhttp:\/\/www.keittlab.org\/","Version":"1.4"},"rphas
t":{"Author":"Melissa Hubisz, Katherine Pollard, and Adam
Siepel","Depends":"stats","Description":"RPHAST is an R interface to the PHAST
software\n(Phylogenetic Analysis with Space\/Time Models). It can be used
for\nmany types of analysis in comparative and evolutionary genomics,\nsuch as
estimating models of evolution from sequence data, scoring\nalignments for
conservation or acceleration, and predicting\nelements based on conservation or
custom phylogenetic hidden Markov\nmodels. It can also perform many basic
operations on multiple\nsequence alignments and phylogenetic
trees.","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"yes","Package":"rphast","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"ape, seqLogo","Title":"Interface to PHAST
Software for Comparative
Genomics","URL":"http:\/\/compgen.cshl.edu\/rphast","Version":"1.6"},"rpivotTable":
{"Author":"Enzo Martoglio [aut, cre] (R interface),\nNicolas kruchten [ctb, cph]
(pivottable library)","Depends":"R (>= 3.1.0)","Description":"Build powerful pivot
tables (aka Pivot Grid, Pivot Chart, Cross-Tab) and dynamically slice & dice \/
drag 'n' drop your data.\n'rpivotTable' is a wrapper of 'pivottable', a powerful
open-source Pivot Table library\nimplemented in 'JavaScript' by Nicolas Kruchten.
Aligned to 'pivottable' v1.6.3.","Enhances":"shiny (>=
0.12)","Imports":"htmlwidgets (>= 0.4)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rpivotTable","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"testthat, knitr, rmarkdown, devtools, dplyr,
data.table","Title":"Build Powerful Pivot Tables and Dynamically Slice & Dice
your\nData","URL":"https:\/\/github.com\/smartinsightsfromdata\/,\nhttp:\/\/smartin
sightsfromdata.github.io","Version":"0.1.5.7"},"rplexos":{"Author":"Eduardo Ibanez
[aut, cre],\nMarcin Kalicinski [ctb] (for the included RapidXml source),\nNational
Renewable Energy Laboratory [cph]","Depends":"R (>=
3.1.0)","Description":"Efficiently read and analyze 'PLEXOS' solutions by
converting them\ninto 'SQLite' databases that can be easily queried. It supports
collation of\nsolutions that may have been divided into different time
partitions,\nas well as the comparison across different scenarios. 'PLEXOS' is a
power systems\nproduction cost model, created and distributed by Energy
Exemplar\n(see URL below for more information).","Imports":"Rcpp (>= 0.11.5), dplyr
(>= 0.3), RSQLite (>= 1.0), DBI,\ndata.table, tidyr, lubridate, stringi, parallel,
doParallel,\nforeach","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"rplexos","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"knitr, testthat, ggplot2","Title":"Read and
Analyze 'PLEXOS'
Solutions","URL":"https:\/\/github.com\/NREL\/rplexos,\nhttp:\/\/energyexemplar.com
\/software\/plexos-desktop-edition\/","Version":"1.1.4"},"rplos":{"Author":"Scott
Chamberlain [aut, cre],\nCarl Boettiger [aut],\nKarthik Ram [aut]","Description":"A
programmatic interface to the 'SOLR' based\nsearch 'API' (http:\/\/api.plos.org\/)
provided by the Public\nLibrary of Science journals to search their
articles.\nFunctions are included for searching for articles, retrieving\narticles,
making plots, doing 'faceted' searches,\n'highlight' searches, and viewing results
of 'highlighted'\nsearches in a browser.","Enhances":"tm","Imports":"methods,
utils, stats, ggplot2, httr (>= 1.0.0), jsonlite,\ndplyr, plyr, lubridate,
reshape2, whisker, solr (<= 0.1.6)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rplos","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"XML, testthat, knitr","Title":"Interface to the
Search 'API' for 'PLoS'
Journals","URL":"https:\/\/github.com\/ropensci\/rplos","Version":"0.5.6"},"rploten
gine":{"Author":"Pedro-Pablo Garrido Abenza [aut, cre]","Depends":"R (>= 2.6.2),
xtable","Description":"This package is intended for using R as a plotting engine
either by custom\napplications, or from a small script launched from the system
console, or even within\nthe R console. Two ASCII text files are necessary:\n(1)
The graph parameters file, which name is passed to the function
'rplotengine()'.\nThe user can specify the titles, choose the type of the graph,
graph output formats\n(e.g. png, eps), proportion of the X-axis and Y-axis,
position of the legend,\nwhether to show or not a grid at the background, etc.\n(2)
The data to be plotted, which name is specified as a parameter
('data_filename')\nin the previous file. This data file has a tabulated format,
with a single character\n(e.g. tab) between each column, and a headers line located
in the first row.\nOptionally, the file could include data columns for showing
confidence intervals.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rplotengine","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"R as a plotting
engine","URL":"http:\/\/atc.umh.es\/pgarrido\/,
http:\/\/atc.umh.es\/gatcom\/","Version":"1.0-5"},"rpnf":{"Author":"Sascha
Herrmann","Depends":"R (>= 3.0.0)","Description":"A set of functions to analyze and
print the development of a commodity using the Point and Figure (P&F) approach. A
P&F processor can be used to calculate daily statistics for the time series. These
statistics can be used for deeper investigations as well as to create plots. Plots
can be generated as well known X\/O Plots in plain TXT format, and additionally in
a more graphical format.","License":"GPL-
3","NeedsCompilation":"no","Package":"rpnf","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"testthat","Title":"Point and Figure
Package","Version":"1.0.4"},"rportfolios":{"Author":"Frederick Novomestky
<fnovomes@poly.edu>","Depends":"R (>= 2.0.1)","Description":"A collection of
utility functions to generate\nvarious types of random portfolios. The weights of
these\nportfolios are random variables derived from uniformly\ndistributed random
variables","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rportfolios","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Random portfolio
generation","Version":"1.0"},"rprime":{"Author":"Tristan Mahr
<tristan.mahr@wisc.edu>","Depends":"R (>= 3.0.1)","Description":"'Eprime' is a set
of programs for administering psychological\nexperiments by computer. This package
provides functions for loading,\nparsing, filtering and exporting data in the text
files produced by\n'Eprime' experiments.","Imports":"stringr (>= 1.0.0), stringi,
plyr, tools, assertthat","License":"GPL-2 | file
LICENSE","NeedsCompilation":"no","Package":"rprime","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"knitr, rmarkdown, testthat","Title":"Functions for
Working with 'Eprime' Text
Files","URL":"http:\/\/github.com\/tjmahr\/rprime","Version":"0.1.0"},"rprintf":
{"Author":"Kun Ren <ken@renkun.me>","Depends":"R (>= 2.15)","Description":"Provides
a set of functions to facilitate building formatted strings\nunder various
replacement rules: C-style formatting, variable-based formatting,\nand number-based
formatting. C-style formatting is basically identical to built-in\nfunction
'sprintf'. Variable-based formatting allows users to put variable names\nin a
formatted string which will be replaced by variable values. Number-
based\nformatting allows users to use index numbers to represent the
corresponding\nargument value to appear in the
string.","Imports":"stringi","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rprintf","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat, knitr","Title":"Adaptive Builder for
Formatted Strings","URL":"http:\/\/renkun.me\/rprintf,
https:\/\/github.com\/renkun-ken\/rprintf","Version":"0.2.1"},"rprojroot":
{"Author":"Kirill MÃ¼ller [aut, cre]","Depends":"R (>=
3.0.0)","Description":"Robust, reliable and flexible paths to files below
a\nproject root. The 'root' of a project is defined as a directory\nthat matches a
certain criterion, e.g., it contains a certain\nregular file.","License":"GPL-
3","NeedsCompilation":"no","Package":"rprojroot","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat, knitr, withr, rmarkdown","Title":"Finding
Files in Project
Subdirectories","URL":"https:\/\/krlmlr.github.io\/rprojroot","Version":"1.0-
2"},"rpsychi":{"Author":"Yasuyuki
Okumura <yokumura@blue.zero.jp>","Depends":"gtools","Description":"The rpsychi
offers a number of functions for psychiatry, psychiatric nursing, clinical
psychology. Functions are primarily for statistical significance testing using
published work. For example, you can conduct a factorial analysis of variance
(ANOVA), which requires only the mean, standard deviation, and sample size for each
cell, rather than the individual data. This package covers fundamental statistical
tests such as t-test, chi-square test, analysis of variance, and multiple
regression analysis. With some exceptions, you can obtain effect size and its
confidence interval. These functions help you to obtain effect size from published
work, and then to conduct a priori power analysis or meta-analysis, even if a
researcher do not report effect size in a published work.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rpsychi","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Statistics for psychiatric
research","URL":"http:\/\/blue.zero.jp\/yokumura\/","Version":"0.8"},"rpubchem":
{"Author":"Rajarshi Guha <rajarshi.guha@gmail.com>","Depends":"R (>=
2.0.0)","Description":"Access PubChem data (compounds, substance,
assays).\nStructural information is provided in the form of SMILES\nstrings. This
package only provides access to a subset of the\nprecalculated data stored by
PubChem. Bio-assay data can be\naccessed to obtain descriptions as well as the
actual data. It\nis also possible to search for assay ID's by keyword.
Currently\nthe main limitation is that only 1000 molecules can be\ndownloaded at a
time from the PubChem servers","Imports":"XML, car, RCurl, RJSONIO","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"rpubchem","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"rpubchem - Interface to the PubChem
Collection","Version":"1.5.0.2"},"rqPen":{"Author":"Ben Sherwood [aut, cre], Adam
Maidman [ctb]","Depends":"R (>= 3.0.0),quantreg, regpro","Description":"Performs
penalized quantile regression for LASSO, SCAD and MCP functions including group
penalties. Provides a function that automatically generates lambdas and evaluates
different models with cross validation or BIC, including a large p version of
BIC.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rqPen","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Penalized Quantile Regression","Version":"1.3"},"rr":
{"Author":"Graeme Blair <graeme.blair@columbia.edu>, Yang-Yang Zhou
<yz3@princeton.edu>, Kosuke Imai <kimai@princeton.edu>","Depends":"R (>= 3.0.0),
utils","Description":"Enables researchers to conduct multivariate statistical
analyses of survey data with randomized response technique items from several
designs, including mirrored question, forced question, and unrelated question. This
includes regression with the randomized response as the outcome and logistic
regression with the randomized response item as a predictor. In addition, tools for
conducting power analysis for designing randomized response items are included. The
package implements methods described in Blair, Imai, and Zhou (2015) ''Design and
Analysis of the Randomized Response Technique,'' Working paper available at
<http:\/\/graemeblair.com\/papers\/randresp.pdf>.","Imports":"MASS (>= 7.3), arm
(>= 1.7-07), coda (>= 0.16-1)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"rr","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"testthat","Title":"Statistical Methods for the Randomized
Response Technique","Version":"1.3"},"rrBLUP":{"Author":"Jeffrey
Endelman","Depends":"R (>= 2.14)","Description":"Software for genomic prediction
with the RR-BLUP mixed model. One application is to estimate marker effects by
ridge regression; alternatively, BLUPs can be calculated based on an additive
relationship matrix or a Gaussian kernel.","License":"GPL-
3","NeedsCompilation":"no","Package":"rrBLUP","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"parallel","Title":"Ridge Regression and Other Kernels
for Genomic
Selection","URL":"http:\/\/potatobreeding.cals.wisc.edu\/software","Version":"4.4"}
,"rrBlupMethod6":{"Author":"Torben Schulz-Streeck, Boubacar Estaghvirou, Frank
Technow","Depends":"R (>= 2.11.0)","Description":"rrBlupMethod6 -- Re-
parametrization of mixed model\nformulation to allow for a fixed residual variance
when using\nRR-BLUP for genomwide estimation of marker effects and
linear\ntransformation of the adjusted means proposed by Piepho et\nal.
(2011)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rrBlupMethod6","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Re-parametrization of RR-BLUP to allow for a fixed
residual\nvariance","Version":"1.3"},"rrcov":{"Author":"Valentin Todorov
<valentin.todorov@chello.at>","Depends":"R (>= 2.10), robustbase (>= 0.92-1),
methods","Description":"Robust Location and Scatter Estimation and
Robust\nMultivariate Analysis with High Breakdown Point.","Imports":"stats, stats4,
mvtnorm, lattice, cluster, pcaPP","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"rrcov","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"grid, mclust, MASS, ellipse","Title":"Scalable Robust
Estimators with High Breakdown Point","Version":"1.3-11"},"rrcovHD":
{"Author":"Valentin Todorov <valentin.todorov@chello.at>","Depends":"rrcov (>= 1.3-
7), robustbase (>= 0.92-1), methods","Description":"Robust multivariate methods for
high dimensional data including\noutlier detection, PCA, PLS and
classification.","Imports":"stats4, pls, spls, pcaPP","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rrcovHD","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Robust Multivariate Methods for High Dimensional
Data","Version":"0.2-4"},"rrcovNA":{"Author":"Valentin Todorov
<valentin.todorov@chello.at>","Depends":"rrcov (>= 1.3-7), robustbase (>= 0.92-1),
methods","Description":"Robust Location and Scatter Estimation and
Robust\nMultivariate Analysis with High Breakdown Point for
Incomplete\nData.","Imports":"stats4, lattice, cluster, norm","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"rrcovNA","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"grid","Title":"Scalable Robust Estimators with High
Breakdown Point for\nIncomplete Data","Version":"0.4-8"},"rrecsys":
{"Author":"Ludovik Ã‡oba [aut, cre, cph],\nMarkus Zanker [ctb]","Depends":"R (>=
3.1.2), registry, proxy, MASS, stats","Description":"Provides implementations of
several popular recommendation systems. They can process standard recommendation
datasets (user\/item matrix) as input and generate rating predictions and
recommendation lists. Standard algorithm implementations included in this package
are: Global\/Item\/User-Average baselines, Item-Based KNN, FunkSVD, BPR and
weighted ALS. They can be assessed according to the standard offline evaluation
methodology for recommender systems using measures such as MAE, RMSE, Precision,
Recall, AUC, NDCG, RankScore and coverage measures. The package is intended for
rapid prototyping of recommendation algorithms and education
purposes.","Imports":"methods","License":"GPL-
3","NeedsCompilation":"no","Package":"rrecsys","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Environment for Assessing Recommender
Systems","Version":"0.9.2"},"rredis":{"Author":"B. W. Lewis","Description":"R
client interface to the \"Redis\" key-value database.","License":"Apache License
(>=
2.0)","NeedsCompilation":"yes","Package":"rredis","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"RUnit","Title":"\"Redis\" Key\/Value Database
Client","Version":"1.7.0"},"rredlist":{"Author":"Scott Chamberlain [aut,
cre]","Description":"'IUCN' Red List
(<http:\/\/apiv3.iucnredlist.org\/api\/v3\/docs>) client.\nThe 'IUCN' Red List is a
global list of threatened and endangered species.\nFunctions cover all of the Red
List 'API' routes. An 'API' key is required.","Imports":"httr (>= 1.0.0), jsonlite
LICENSE","NeedsCompilation":"no","Package":"rredlist","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat","Title":"'IUCN' Red List
Client","URL":"https:\/\/github.com\/ropenscilabs\/rredlist","Version":"0.1.0"},"rr
efine":{"Author":"VP Nagraj [aut, cre]","Description":"'OpenRefine' (formerly
'Google Refine') is a popular, open source data cleaning software. This package
enables users to programmatically trigger data transfer between R and 'OpenRefine'.
Available functionality includes project import, export and
deletion.","Imports":"httr (>= 1.1.0), rlist, readr","License":"GPL-
3","NeedsCompilation":"no","Package":"rrefine","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr, rmarkdown","Title":"R Client for OpenRefine
API","URL":"http:\/\/openrefine.org\/","Version":"1.0"},"rrepast":
{"Author":"Antonio Prestes Garcia [aut, cre],\nAlfonso Rodriguez-Paton [aut,
ths]","Depends":"rJava","Description":"An R and Repast integration tool for running
individual-based\n(IbM) simulation models developed using 'Repast Simphony' Agent-
Based framework\ndirectly from R code. This package integrates 'Repast Simphony'
models within\nR environment, making easier the tasks of running and analyzing
model output\ndata for automated parameter calibration and for carrying out
uncertainty and\nsensitivity analysis using the power of R
environment.","Imports":"lhs, sensitivity, ggplot2, digest, xlsx","License":"MIT +
file
LICENSE","NeedsCompilation":"no","Package":"rrepast","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Invoke 'Repast Simphony' Simulation
Models","URL":"https:\/\/github.com\/antonio-
pgarcia\/rrepast","Version":"0.4.0"},"rriskDistributions":{"Author":"Natalia
Belgorodski [aut] (STAT-UP Statistical Consulting),\nMatthias Greiner [aut, cre]
(Federal Institute for Risk Assessment,\nGermany),\nKristin
Tolksdorf [aut] (Federal Institute for Risk Assessment,\nGermany),\nKatharina
Schueller [aut] (STAT-UP Statistical Consulting),\nMatthias Flor [ctb] (Federal
Institute for Risk Assessment, Germany),\nLutz GÃ¶hring [ctb] (Lutz GÃ¶hring
Consulting)","Depends":"R(>= 2.11.0)","Description":"\nCollection of functions for
fitting distributions to given data or\nby known quantiles. Two main functions
fit.perc() and fit.cont() provide\nusers a GUI that allows to choose a most
appropriate distribution without\nany knowledge of the R syntax. Note, this package
is a part of the 'rrisk'\nproject.","Imports":"mc2d, eha, msm, tcltk,
tkrplot","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"rriskDistributions","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Title":"Fitting Distributions to Given Data or Known
Quantiles","URL":"http:\/\/www.bfr.bund.de\/cd\/52158","Version":"2.1"},"rrlda":
{"Author":"Moritz Gschwandtner, Peter Filzmoser, Christophe Croux,\nGentiane
Haesbroeck","Depends":"pcaPP, mvoutlier, glasso, matrixcalc","Description":"This
package offers methods to perform robust regularized\nlinear discriminant
3)","NeedsCompilation":"no","Package":"rrlda","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Robust Regularized Linear Discriminant
Analysis","Version":"1.1"},"rsae":{"Author":"Tobias Schoch","Description":"Robust
Small Area Estimation. Robust Basic Unit- and Area-Level Models","License":"GPL (>=
2) |
FreeBSD","NeedsCompilation":"yes","Package":"rsae","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"robustbase, nlme","Title":"Robust Small Area
Estimation","Version":"0.1-5"},"rsatscan":{"Author":"Ken Kleinman [aut,
cre]","Depends":"R (>= 3.0.2)","Description":"SaTScan(TM)
(http:\/\/www.satscan.org) is software for finding regions in\nTime, Space, or
Time-Space that have excess risk, based on scan statistics, and\nuses Monte Carlo
hypothesis testing to generate P-values for these regions. The\nrsatscan package
provides functions for writing R data frames in\nSaTScan-readable formats, for
setting SaTScan parameters, for running SaTScan in\nthe OS, and for reading the
files that SaTScan creates.","Imports":"utils, foreign","License":"GPL-
3","NeedsCompilation":"no","Package":"rsatscan","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr, rgdal (>= 0.9.1), sp (>= 1.0-
9)","Title":"Tools, Classes, and Methods for Interfacing with SaTScan\nStand-Alone
Software","URL":"http:\/\/www.satscan.org","Version":"0.3.9200"},"rscala":
{"Author":"David B. Dahl [aut, cre],\nScala developers [ctb] (see http:\/\/scala-
lang.org\/)","Description":"The Scala interpreter is embedded in R and callbacks to
R from the embedded interpreter are supported. Conversely, the R interpreter is
embedded in Scala. Scala versions 2.10 and 2.11 are
supported.","Imports":"utils","License":"GPL (>= 2) | BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"rscala","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Bi-Directional Interface Between R and Scala with
Callbacks","URL":"http:\/\/dahl.byu.edu\/software\/rscala\/","Version":"1.0.9"},"rs
cimark":{"Author":"Bernd Bischl [aut],\nJakob Bossek [aut, cre]","Description":"The
SciMark 2.0 benchmark was originally developed in Java as a benchmark for numerical
and scientific computational performance. It measures the performance of several
computational kernels which are frequently occurring in scientific applications.
This package is a simple wrapper around the ANSI C implementation of the
benchmark.","Imports":"checkmate","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"yes","Package":"rscimark","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat","Title":"SciMark 2.0 Benchmark for
Scientific and Numerical
Computing","URL":"https:\/\/github.com\/berndbischl\/rscimark","Version":"1.0"},"rs
connect":{"Author":"JJ Allaire","Depends":"R (>=
3.0.0)","Description":"Programmatic deployment interface for 'RPubs',
'shinyapps.io', and\n'RStudio Connect'. Supported content types include R Markdown
documents,\nShiny applications, plots, and static web
content.","Enhances":"BiocInstaller","Imports":"digest, PKI, RCurl, RJSONIO,
packrat (>= 0.4.7), yaml (>=\n2.1.5), rstudioapi (>= 0.5)","License":"GPL-
2","NeedsCompilation":"no","Package":"rsconnect","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"scrypt, knitr, testthat, rmarkdown (>=
0.9.2)","Title":"Deployment Interface for R Markdown Documents and
Shiny\nApplications","Version":"0.4.2.1"},"rscopus":{"Author":"John
Muschelli","Description":"Uses Elsevier Scopus API to download information about
authors and their citations.","Imports":"httr, utils","License":"GPL-
2","NeedsCompilation":"no","Package":"rscopus","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"xml2, rvest","Title":"Scopus Database API
Interface","Version":"0.1.2"},"rscorecard":{"Author":"Benjamin Skinner [aut,
cre]","Depends":"R (>= 3.2.3)","Description":"A method to download Department of
Education College Scorecard data\nusing the public API. It is based on the dplyr
model of\npiped commands to select and filter data in a single chained function
call.\nAn API key from the U.S. Department of Education is
required.","Imports":"dplyr, jsonlite, lazyeval, magrittr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rscorecard","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"knitr, rmarkdown, testthat","Title":"A Method
to Download Department of Education College
Scorecard\nData","URL":"http:\/\/github.com\/btskinner\/rscorecard","Version":"0.2.
4"},"rscproxy":{"Author":"Thomas Baier","Description":"rscproxy library provides an
interface to R used by third\nparty applications, most notable, but not limited
to,\nstatconnDCOM, ROOo and other systems.","License":"GPL-
2","NeedsCompilation":"yes","Package":"rscproxy","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"statconn: provides portable C-style interface to
R\n(StatConnector)","Version":"2.0-5"},"rsdepth":{"Author":"Nabil Mustafa
<http:\/\/sma.epfl.ch\/~moustafa\/index.html>, Saurabh Ray <http:\/\/www.mpi-
inf.mpg.de\/~saurabh\/>, Mudassir Shabbir
<http:\/\/paul.rutgers.edu\/~mudassir\/>.","Depends":"R (>=
2.4.0)","Description":"Ray Shooting Depth functions are provided for bivariate
2","NeedsCompilation":"yes","Package":"rsdepth","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Ray Shooting Depth (i.e. RS Depth) functions for
bivariate\nanalysis","Version":"0.1-5"},"rsdmx":{"Author":"Emmanuel Blondel [aut,
cre],\nMatthieu Stigler [ctb]","Depends":"R (>= 2.15)","Description":"Set of
classes and methods to read data and metadata documents\nexchanged through the
Statistical Data and Metadata Exchange (SDMX) framework,\ncurrently focusing on the
SDMX XML standard format (SDMX-ML).","Imports":"methods, XML (>= 3.98.1.3), RCurl,
plyr, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rsdmx","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat, knitr","Title":"Tools for Reading SDMX Data
and Metadata","URL":"https:\/\/github.com\/opensdmx\/rsdmx,
http:\/\/www.sdmx.org","Version":"0.5-3"},"rseedcalc":{"Author":"Kevin Wright [aut,
cre],\nJean-Louis Laffont [aut]","Description":"Estimate the percentage of seeds in
a seedlot that contain stacks\nof genetically modified traits. Estimates are
calculated using a\nmultinomial group testing model with maximum likelihood
estimation of the\nparameters.","Imports":"stats","License":"GPL-
2","NeedsCompilation":"no","Package":"rseedcalc","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Estimating the Proportion of Genetically Modified Seeds
in\nSeedlots via Multinomial Group Testing","Version":"1.3"},"rsem":{"Author":"Ke-
Hai Yuan and Zhiyong Zhang","Depends":"R (>= 2.7), MASS, lavaan","Description":"A
robust procedure is implemented to estimate means and covariance matrix of multiple
variables with missing data using Huber weight and then to estimate a structural
equation model.","License":"GPL-
2","NeedsCompilation":"no","Package":"rsem","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Robust Structural Equation Modeling with Missing Data
and\nAuxiliary
Variables","URL":"http:\/\/rpackages.psychstat.org","Version":"0.4.6"},"rsgcc":
{"Author":"Chuang Ma, Xiangfeng Wang","Depends":"R (>= 2.15.1), biwt, cairoDevice,
fBasics, grDevices, gplots,\ngWidgets, gWidgetsRGtk2, minerva, parmigene, stringr,
snowfall","Description":"This package provides functions for
calculating\nassociations between two genes with five correlation\nmethods(e.g.,
the Gini correlation coefficient [GCC], the\nPearson's product moment correlation
coefficient [PCC], the\nKendall tau rank correlation coefficient [KCC], the
Spearman's\nrank correlation coefficient [SCC] and the Tukey's
biweight\ncorrelation coefficient [BiWt], and three non-correlation\nmethods (e.g.,
mutual information [MI] and the maximal\ninformation-based nonparametric
exploration [MINE], and the\neuclidean distance [ED]). It can also been implemented
to\nperform the correlation and clustering analysis of\ntranscriptomic data
profiled by microarray and RNA-Seq\ntechnologies. Additionally, this package can be
further applied\nto construct gene co-expression networks (GCNs).","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"rsgcc","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"bigmemory, ctc","Title":"Gini methodology-based
correlation and clustering analysis of\nmicroarray and RNA-Seq gene expression
data","URL":"http:\/\/www.cmbb.arizona.edu\/","Version":"1.0.6"},"rsggm":
{"Author":"Kei Hirose","Depends":"MASS, Matrix, glasso, QUIC","Description":"Robust
estimation of sparse inverse covariance matrix via the gamma-
divergence.","Imports":"methods","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"rsggm","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Robust Sparse Gaussian Graphical Modeling via the\nGamma-
Divergence","URL":"http:\/\/www.keihirose.com","Version":"0.3"},"rsig":
{"Author":"Sangkyun Lee <sangkyun.lee@tu-dortmund.de>, Michel
Lang\n<michellang@gmail.com>","Depends":"R (>= 2.15.0), survival,
parallel","Description":"Robust and efficient feature selection algorithm
to\nidentify important features for predicting survival risk.\nThe method is based
on subsampling and averaging linear models\nobtained from the (preconditioned)
Lasso algorithm, with an extra\nshrinking procedure to reduce the size of
signatures. An\nevaluation procedure using subsampling is also
provided.","Imports":"BBmisc, glmnet, superpc, survcomp, Matrix","License":"GPL-
2","NeedsCompilation":"no","Package":"rsig","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"testthat","Title":"Robust Signature Selection for Survival
Outcomes","Version":"1.0"},"rsm":{"Author":"Russell V.
Lenth","Description":"Provides functions to generate response-surface designs, fit
first- and second-order response-surface models, make surface plots, obtain the
path of steepest ascent, and do canonical analysis.","License":"GPL-
2","NeedsCompilation":"no","Package":"rsm","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"Vdgraph, conf.design, DoE.base, FrF2","Title":"Response-
Surface Analysis","Version":"2.7-4"},"rsml":{"Author":"Guillaume
Lobet","Description":"Read and analyse Root System Markup Language (RSML) files,
used to\nstore plant root system architecture data. More information can be
found\nat the address
<http:\/\/rootsystemml.github.io\/>.","Imports":"XML,rgl","License":"GPL-
2","NeedsCompilation":"no","Package":"rsml","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Plant Root System Markup Language (RSML) File
Processing","Version":"1.3"},"rsnps":{"Author":"Scott Chamberlain [aut,
cre],\nKevin Ushey [aut]","Description":"A programmatic interface to various SNP
datasets\non the web: openSNP, NBCI's dbSNP database, and Broad Institute
SNP\nAnnotation and Proxy Search. Functions are included for searching for\nSNPs
for the Broad Institute and NCBI. For OpenSNP, functions are\nincluded for getting
SNPs, and data for genotypes, phenotypes,\nannotations, and bulk downloads of data
by user.","Imports":"plyr, stringr, httr, RCurl, XML, jsonlite","License":"MIT +
file
LICENSE","NeedsCompilation":"no","Package":"rsnps","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"roxygen2, testthat, rjson, knitr","Title":"Get SNP
(Single-Nucleotide Polymorphism) Data on the
Web","URL":"https:\/\/github.com\/ropensci\/rsnps","Version":"0.1.6"},"rspa":
{"Author":"Mark van der Loo","Depends":"R (>= 2.13.0)","Description":"Based on
(optionally sparse) quadratic optimization with the main algorithms implemented in
C. Includes features for easy processing of many (smaller) records. The algorithm
has been tested on fairly large optimization problems with up to a few million
variables and several hundred thousand restrictions.","Imports":"editrules,
3","NeedsCompilation":"yes","Package":"rspa","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr, testthat","Title":"Adapt Numerical Records to Fit
(in)Equality
Restrictions","URL":"https:\/\/github.com\/markvanderloo\/rspa","Version":"0.1.8"},
"rstackdeque":{"Author":"Shawn T. O'Neil","Depends":"utils","Description":"Provides
fast, persistent (side-effect-free) stack, queue and\ndeque (double-ended-queue)
data structures. While deques include a superset\nof functionality provided by
queues, in these implementations queues are\nmore efficient in some specialized
situations. See the documentation for\nrstack, rdeque, and rpqueue for
details.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rstackdeque","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Persistent Fast Amortized
Stack and Queue Data
Structures","URL":"https:\/\/github.com\/oneilsh\/rstackdeque","Version":"1.1.1"},"
rstan":{"Author":"Jiqiang Guo [aut],\nDaniel Lee [ctb],\nKrzysztof Sakrejda
[ctb],\nJonah Gabry [aut],\nBen Goodrich [cre, aut],\nJoel de Guzman [cph]
(Boost),\nEric Niebler [cph] (Boost),\nThomas Heller [cph] (Boost),\nJohn Fletcher
[cph] (Boost)","Depends":"R (>= 3.0.2), ggplot2 (>= 2.0.0)","Description":"User-
facing R functions are provided by this package to parse, compile, test, estimate,
and analyze Stan models by accessing the header-only Stan library provided by the
'StanHeaders' package. The Stan project develops a probabilistic programming
language that implements full Bayesian statistical inference via Markov Chain Monte
Carlo, rough Bayesian inference via variational approximation, and (optionally
penalized) maximum likelihood estimation via optimization. In all three cases,
automatic differentiation is used to quickly and accurately evaluate gradients
without burdening the user with the need to derive the partial
derivatives.","Imports":"methods, stats4, inline, gridExtra (>= 2.0.0), Rcpp
(>=\n0.11.0)","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"rstan","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"RUnit, RcppEigen, BH (>= 1.58), StanHeaders (>=
2.9.0),\nparallel, KernSmooth, RCurl, loo, rstudioapi, Matrix","Title":"R Interface
to Stan","URL":"https:\/\/groups.google.com\/forum\/#!forum\/stan-
users,\nhttp:\/\/mc-stan.org","Version":"2.9.0-3"},"rstanarm":{"Author":"Jonah
Gabry [aut],\nTrustees of Columbia University [cph],\nR Core Deveopment Team [cph]
(R\/pp_data.R, R\/stan_aov.R),\nDouglas Bates [cph] (R\/pp_data.R),\nMartin
Maechler [cph] (R\/pp_data.R),\nBen Bolker [cph] (R\/pp_data.R),\nSteve Walker
[cph] (R\/pp_data.R),\nBrian Ripley [cph] (R\/stan_aov.R, R\/stan_polr.R),\nWilliam
Venables [cph] (R\/stan_polr.R),\nBen Goodrich [cre, aut]","Depends":"R (>= 3.2.0),
Rcpp (>= 0.11.0), methods","Description":"Estimates pre-compiled regression models
using the 'rstan' package, which provides\nthe R interface to the Stan C++ library
for Bayesian estimation. Users specify models via the\ncustomary R syntax with a
formula and data.frame plus some additional arguments for
priors.","Imports":"ggplot2 (>= 2.0.0), lme4 (>= 1.1-8), loo (>= 0.1.4),
Matrix,\nnlme (>= 3.1-124), rstan (>= 2.9.0-3), shinystan (>= 2.1.0),\nstats,
3)","NeedsCompilation":"yes","Package":"rstanarm","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"arm, gamm4, gridExtra, HSAUR3, KernSmooth, knitr,
MASS,\nrmarkdown, testthat","Title":"Bayesian Applied Regression Modeling via
Stan","URL":"https:\/\/groups.google.com\/forum\/#!forum\/stan-users,\nhttp:\/\/mc-
stan.org\/","Version":"2.9.0-3"},"rstatscn":{"Author":"Xuehui YANG","Depends":"R
(>= 3.2.2)","Description":"R interface for china national data
http:\/\/data.stats.gov.cn\/,\nsome convenient functions for accessing the national
data are provided.","Imports":"httr(>= 1.1.0), jsonlite(>=
0.9.19)","License":"Apache License
2.0","NeedsCompilation":"no","Package":"rstatscn","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"R Interface for China National
Data","URL":"http:\/\/www.bagualu.net\/","Version":"1.0.2"},"rstiefel":
{"Author":"Peter Hoff","Description":"This package simulates random orthonormal
matrices from linear and quadratic exponential family distributions on the Stiefel
manifold. The most general type of distribution covered is the matrix-variate
Bingham-von Mises-Fisher distribution. Most of the simulation methods are presented
in Hoff(2009) \"Simulation of the Matrix Bingham-von Mises-Fisher Distribution,
With Applications to Multivariate and Relational Data.\"","License":"GPL-
3","NeedsCompilation":"yes","Package":"rstiefel","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Random orthonormal matrix generation on the Stiefel
manifold","Version":"0.10"},"rstpm2":{"Author":"Mark Clements [aut, cre], Xing-Rong
Liu [aut], Paul Lambert [ctb]","Depends":"R (>= 2.10), methods, survival,
splines","Description":"R implementation of generalized survival models, where
g(S(t(x))) for a link function g, survival S at time t with covariates x is
modelled using a linear predictor. The main assumption is that the time effect(s)
are smooth. For fully parametric models, this re-implements Stata's 'stpm2'
function, which are flexible parametric survival models developed by Royston and
colleagues. We have extended the parametric models to include any smooth parametric
smoothers. We have also extended the model to include any smooth penalized
smoothers from the 'mgcv' package, using penalized likelihood. These models have
all been extended to include left truncation, right censoring, interval censoring,
frailties and normal random effects.","Imports":"graphics, Rcpp (>= 0.10.2),
numDeriv, stats, mgcv, bbmle (>=\n1.0.3), fastGHQuad","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"rstpm2","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"RUnit, gaussquad","Title":"Generalized Survival
Models","URL":"http:\/\/github.com\/mclements\/rstpm2","Version":"1.3.1"},"rstream"
:{"Author":"Josef Leydold <josef.leydold@wu.ac.at>","Depends":"R (>=
2.0.0)","Description":"Unified object oriented interface for multiple independent
streams of random numbers from different sources.","Imports":"methods,
2","NeedsCompilation":"yes","Package":"rstream","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Streams of Random
Numbers","URL":"http:\/\/statmath.wu.ac.at\/arvag\/","Version":"1.3.4"},"rstudioapi
":{"Author":"Hadley Wickham [aut],\nJJ Allaire [aut, cre],\nKevin Ushey
[ctb],\nRStudio [cph]","Description":"Access the RStudio API (if available) and
provide informative error\nmessages when it's not.","License":"MIT
+ file
LICENSE","NeedsCompilation":"no","Package":"rstudioapi","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Safely Access the RStudio
API","Version":"0.5"},"rsubgroup":{"Author":"Martin Atzmueller","Depends":"R (>=
2.10), methods, rJava (>= 0.6.3), foreign (>= 0.8.40)","Description":"A collection
of efficient and effective tools and\nalgorithms for subgroup discovery and
analytics. The package\nintegrates an R interface to the org.vikamine.kernel
library\nof the VIKAMINE system (http:\/\/www.vikamine.org) implementing\nsubgroup
discovery, pattern mining and analytics in Java.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"rsubgroup","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Subgroup Discovery and
Analytics","URL":"http:\/\/www.rsubgroup.org","Version":"0.6"},"rsunlight":
{"Author":"Scott Chamberlain [aut, cre],\nThomas J. Leeper
[ctb]","Description":"Interface to three 'Sunlight' Foundation 'APIs'
(http:\/\/\nsunlightfoundation.com\/api\/) for government data, including
the\nCongress 'API' 'v3', the Capitol Words 'API', and the Open States\n'API'.
'Sunlight' Foundation is a 'nonpartison' 'nonprofit' that collects and\nprovides
data on government activities, and those that influence government.\nFunctions are
provided to interact with each of the three
'APIs'.","Enhances":"ggplot2","Imports":"methods, utils, httr, plyr, jsonlite,
stringr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rsunlight","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"knitr, testthat","Title":"Interface to
'Sunlight' Foundation
'APIs'","URL":"https:\/\/github.com\/ropengov\/rsunlight","Version":"0.4.2"},"rsvd"
:{"Author":"N. Benjamin Erichson [aut, cre]","Depends":"R (>=
3.2.2)","Description":"Randomized singular value decomposition (rsvd) is a very
fast probabilistic\nalgorithm to compute an approximated low-rank singular value
decomposition of large\ndata sets with high accuracy. SVD plays a central role in
data analysis and scientific computing.\nSVD is also widely used for computing
principal component analysis (PCA), a linear dimensionality reduction
technique.\nRandomized PCA (rpca) is using the approximated singular value
decomposition to compute the most significant principal components. In addition
several plot functions are provided.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rsvd","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"ggplot2, plyr, scales, grid,
testthat","Title":"Randomized Singular Value
Decomposition","URL":"https:\/\/github.com\/Benli11\/rPCA","Version":"0.3"},"rsvg":
{"Author":"Jeroen Ooms","Description":"Renders vector-based 'svg' images into high-
quality custom-size bitmap\narrays using 'librsvg'. The resulting bitmap can be
written to e.g. 'png', 'jpeg'\nor 'webp' format. In addition, the package can
convert images directly to various\nformats such as pdf or
postscript.","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"rsvg","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"svglite, png, jpeg, webp, ggplot2","Title":"Render
SVG Images into PDF, PNG, PostScript, or Bitmap
Arrays","URL":"https:\/\/github.com\/jeroenooms\/rsvg\nhttps:\/\/www.opencpu.org\/p
osts\/svg-release","Version":"0.5"},"rtable":{"Author":"David Gohel [aut,
cre]","Depends":"xtable, ReporteRs (>= 0.7.8)","Description":"Provides tabular
reporting functionalities to work with 'ReporteRs'\npackage: 'as.FlexTable' methods
are available for 'ftable' and 'xtable' objects,\nfunction 'FlexPivot' is producing
a pivot table and 'freqtable' a percentage table,\na 'knitr' print method and a
'shiny' render function are provided for 'FlexTable' objects.","Imports":"knitr,
tidyr (>= 0.3.1), shiny, stats","License":"GPL-
3","NeedsCompilation":"no","Package":"rtable","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"dplyr","Title":"Tabular Reporting
Functions","URL":"http:\/\/davidgohel.github.io\/tabular\/index.html","Version":"0.
1.5"},"rtape":{"Author":"Miron B. Kursa","Description":"Storing huge data in RData
format causes problems because\nof the necessity to load the whole file to the
memory in order\nto access and manipulate objects inside such file; rtape is
a\nsimple solution to this problem. The package contains several\nwrappers of R
built-in serialize\/unserialize mechanism allowing\nuser to quickly append objects
to a tape-like file and later\niterate over them requiring only one copy of each
stored object\nto reside in memory a time.","License":"GPL-
2","NeedsCompilation":"no","Package":"rtape","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Manage and manipulate large collections of R objects stored
as\ntape-like files","URL":"http:\/\/mbq.me\/rtape","Version":"2.2"},"rtdists":
{"Author":"Henrik Singmann [aut, cre],\nScott Brown [aut],\nMatthew Gretton
[aut],\nAndrew Heathcote [aut],\nAndreas Voss [ctb],\nJochen Voss [ctb],\nAndrew
Terry [ctb]","Depends":"R (>= 3.0.0)","Description":"Provides response time
distributions (density\/PDF, distribution\nfunction\/CDF, quantile function, and
random generation): (a) Ratcliff diffusion\nmodel based on C code by Andreas and
Jochen Voss and (b) linear ballistic\naccumulator (LBA) with different distribution
underlying the drift rate.","Imports":"evd, msm, gsl, stats, utils","License":"GPL
(>=
3)","NeedsCompilation":"yes","Package":"rtdists","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat, glba","Title":"Response Time
Distributions","URL":"https:\/\/github.com\/rtdists\/rtdists\/","Version":"0.4-
9"},"rtematres":{"Author":"Claas-Thido Pfaff <claas-thido.pfaff@idiv-
biodiversity.de>","Description":"Exploit controlled vocabularies organized on
tematres servers.","Imports":"XML, RCurl, plyr, gdata","License":"GPL-
3","NeedsCompilation":"no","Package":"rtematres","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"ggplot2,","Title":"The rtematres API
package","URL":"https:\/\/github.com\/cpfaff\/rtematres","Version":"0.2"},"rtf":
{"Author":"Michael E. Schaffer [aut, cre, cph]","Depends":"R (>=
2.10.1)","Description":"A set of R functions to output Rich Text Format (RTF) files
with high resolution tables and graphics that may be edited with a standard word
processor such as Microsoft Word.","Imports":"R.oo, R.methodsS3","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rtf","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"ggplot2, lattice, grid, xtable, gsubfn","Title":"Rich Text
Format (RTF) Output","Version":"0.4-11"},"rtfbs":{"Author":"Nicholas Peterson,
Andre Martins, Melissa Hubisz, and
Adam\nSiepel","Depends":"stats","Description":"RTFBS identifies and scores possible
Transcription Factor\nBinding Sites and allows for FDR analysis and pruning. It
supports\nsplitting of sequences based on size or a specified GFF, grouping\nby G+C
content, and specification of Markov model order. The heavy\nlifting is done in C
while all results are made available via
R.","Imports":"rphast","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"yes","Package":"rtfbs","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Transcription Factor Binding Site Identification
Tool","URL":"http:\/\/compgen.cshl.edu\/rtfbs","Version":"0.3.4"},"rticles":
{"Author":"JJ Allaire [aut, cre],\nR Foundation [aut, cph],\nHadley Wickham
[aut],\nJournal of Statistical Software [aut, cph],\nYihui Xie [aut],\nRStudio
[cph],\nRamnath Vaidyanathan [aut, cph],\nAssocation for Computing Machinery [aut,
cph],\nCarl Boettiger [aut, cph],\nElsevier [aut, cph],\nKarl Broman [aut,
cph],\nKirill Mueller [aut, cph],\nBastiaan Quast [aut, cph],\nRandall Pruim [aut,
cph],\nBen Marwick [aut, cph],\nCharlotte Wickham [aut, cph],\nOliver Keyes [aut,
cph]","Description":"A suite of custom R Markdown formats and templates
for\nauthoring journal articles and conference submissions.","Imports":"utils,
rmarkdown, knitr, yaml","License":"GPL-
3","NeedsCompilation":"no","Package":"rticles","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat","Title":"Article Formats for R
Markdown","Version":"0.1"},"rtiff":{"Author":"Eric Kort
<eric.kort@vai.org>","Depends":"pixmap","Description":"Reads and writes TIFF format
images and\nreturns them as a pixmap object. Because the resulting object\ncan be
very large for even modestly sized TIFF images, images\ncan be reduced as they are
read for improved performance. This\npackage is a wrapper around libtiff
(www.libtiff.org), on which\nit depends (i.e. the libtiff shared library must be on
your\nPATH for the binary to work, and tiffio.h must be on your\nsystem to build
the package from source). By using libtiff's\nhighlevel TIFFReadRGBAImage function,
this package inherently\nsupports a wide range of image formats and compression
schemes.\nThis package also provides an implementation of the
Ridler\nAutothresholding algorithm for easy generation of binary
masks.","License":"GPL-
3","NeedsCompilation":"yes","Package":"rtiff","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Read and Write TIFF Files","Version":"1.4.5"},"rtimes":
{"Author":"Scott Chamberlain [aut, cre]","Description":"Interface to Congress,
Campaign Finance, Article Search, and\nGeographic 'APIs' from the New York Times.
Documentation for New York\nTimes 'APIs' (http:\/\/developer.nytimes.com\/docs\/).
This client covers\na subset of the New York Times 'APIs'.","Imports":"httr,
jsonlite, dplyr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rtimes","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"knitr, testthat, lubridate, ggplot2, scales,
grid","Title":"Client for New York Times
'APIs'","URL":"https:\/\/github.com\/ropengov\/rtimes","Version":"0.3.0"},"rtkore":
{"Author":"Serge Iovleff [aut, cre],\nParmeet Bhatia [ctb]","Depends":"R (>=
3.0.2), Rcpp (>=
0.11.0)","Description":"STK++ (http:\/\/www.stkpp.org) is a collection of\nC++
classes for statistics, clustering, linear algebra, arrays (with an\nEigen-like
API), regression, dimension reduction, etc. The integration of\nthe library to R is
using Rcpp.\n\nThe rtkore package includes the header files from the STK++ core
library.\nAll files contain only templated classes or inlined functions.\n\nSTK++
is licensed under the GNU LGPL version 2 or later. rtkore\n(the stkpp integration
into R) is licensed under the\nGNU GPL version 2 or later. See file LICENSE.note
for details.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"rtkore","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"STK++ Core Library Integration to R using
Rcpp","URL":"http:\/\/www.stkpp.org","Version":"1.0.1"},"rtkpp":{"Author":"Serge
Iovleff [aut, cre],\nVincent Kubicki [ctb],\nQuentin Grimonprez [ctb],\nParmeet
Bhatia [ctb]","Depends":"R (>= 3.0.2), Rcpp","Description":"STK++
(http:\/\/www.stkpp.org) is a collection of\nC++ classes for statistics,
clustering, linear algebra, arrays (with an\nEigen-like API), regression, dimension
reduction, etc. The integration of\nthe library to R is using Rcpp.\n\nThe rtkpp
package includes the header files from the STK++\nlibrary (currently version
0.8.99). Thus users do not need to\ninstall STK++ itself in order to use
it.\n\nSTK++ is licensed under the GNU LGPL version 2 or later. rtkpp\n(the stkpp
integration into R) is licensed under the\nGNU GPL version 2 or
later.","License":"GPL (>= 2) | LGPL (>= 2) | file
LICENSE","NeedsCompilation":"yes","Package":"rtkpp","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"STK++ Integration to R using
Rcpp","URL":"http:\/\/www.stkpp.org","Version":"0.9.2"},"rtop":{"Author":"Jon Olav
Skoien","Depends":"sp","Description":"Geostatistical interpolation of data with
irregular spatial support such as runoff related data or data from administrative
units.","Imports":"gstat, graphics, stats, methods, utils,
2)","NeedsCompilation":"yes","Package":"rtop","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"parallel, igraph, rgdal, intamap, rgeos,
spacetime,\ndata.table, reshape2","Title":"Interpolation of Data with Variable
Spatial Support","Version":"0.5-5"},"rts":{"Author":"Babak
Naimi","Depends":"methods, sp (>= 1.0-13), raster, xts, zoo","Description":"This
framework aims to provide classes and methods for manipulating and processing of
raster time series data (e.g. a time series of satellite images).","License":"GPL
(>=
3)","NeedsCompilation":"no","Package":"rts","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"rgdal, RCurl","Title":"Raster Time Series
Analysis","URL":"http:\/\/r-gis.net","Version":"1.0-10"},"rtson":
{"Author":"Alexandre Maurel","Description":"TSON, short for Typed JSON, is a
binary-encoded serialization of\nJSON like document that support JavaScript typed
data (https:\/\/github.com\/amaurel\/TSON).","Imports":"R6","License":"Apache
License Version
2.0","NeedsCompilation":"no","Package":"rtson","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat","Title":"Typed
JSON","URL":"https:\/\/github.com\/amaurel\/TSON","Version":"1.1"},"rtype":
{"Author":"Kun Ren <ken@renkun.me>","Depends":"R (>= 2.15)","Description":"A strong
type system for R which supports\nsymbol declaration and assignment with type
checking\nand condition checking.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rtype","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat, knitr","Title":"A strong type system for
R","URL":"http:\/\/renkun.me\/rtype, https:\/\/github.com\/renkun-
ken\/rtype","Version":"0.1-1"},"rtypeform":{"Author":"Colin Gillespie [aut,
cre]","Description":"An R interface to the 'typeform' (https:\/\/typeform.com)
application program interface.\nAlso provides functions for downloading your
results.","Imports":"jsonlite","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"rtypeform","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat, curl","Title":"Interface to 'typeform'
Results","URL":"https:\/\/github.com\/csgillespie\/rtypeform","Version":"0.1.1"},"r
ucm":{"Author":"Kaushik Roy Chowdhury","Depends":"KFAS","Description":"Unobserved
Components Models (introduced in Harvey, A. (1989),\nForecasting, structural time
series models and the Kalman filter, Cambridge\nNew York: Cambridge University
Press) decomposes a time series into\ncomponents such as trend, seasonal, cycle,
and the regression effects due\nto predictor series which captures the salient
features of the series to\npredict its behavior.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rucm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr","Title":"Implementation of Unobserved Components
Model (UCM)","Version":"0.6"},"rugarch":{"Author":"Alexios Ghalanos
<alexios@4dscape.com>","Depends":"R (>= 3.0.2), methods,
parallel","Description":"ARFIMA, in-mean, external regressors and various GARCH
flavors, with methods for fit, forecast, simulation, inference and
plotting.","Imports":"Rsolnp, nloptr, ks, numDeriv, spd, xts, zoo,
chron,\nSkewHyperbolic, expm, Rcpp,graphics, stats, grDevices,
3","NeedsCompilation":"yes","Package":"rugarch","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Univariate GARCH
Models","URL":"http:\/\/www.unstarched.net,
https:\/\/bitbucket.org\/alexiosg","Version":"1.3-6"},"runittotestthat":
{"Author":"Richard Cotton [aut, cre]","Depends":"R (>=
2.15.0)","Description":"Automatically convert a file or package worth of 'RUnit'
test\nfunctions into 'testthat' tests.","Enhances":"devtools","Imports":"assertive
(>= 0.2-1),
RUnit","License":"Unlimited","NeedsCompilation":"no","Package":"runittotestthat","R
epository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Co
nvert 'RUnit' Test Functions into 'testthat' Tests","Version":"0.0-2"},"runjags":
{"Author":"Matthew Denwood [aut, cre],\nMartyn Plummer [cph] (Copyright holder of
the code in\n\/src\/distributions\/jags, src\/distributions\/DPar1.*,
configure.ac,\nand original copyright holder of some modified code
where\nindicated)","Depends":"R (>= 2.14.0)","Description":"User-friendly interface
utilities for MCMC models via\nJust Another Gibbs Sampler (JAGS), facilitating the
use of parallel\n(or distributed) processors for multiple chains, automated
control\nof convergence and sample length diagnostics, and evaluation of
the\nperformance of a model using drop-k validation or against simulated\ndata.
Template model specifications can be generated using a standard\nlme4-style formula
interface to assist users less familiar with the\nBUGS syntax. A JAGS extension
module provides additional distributions\nincluding the Pareto family of
distributions, the DuMouchel prior and\nthe half-Cauchy
prior.","Imports":"parallel, lattice (>= 0.20-10), coda (>= 0.17-1), stats,
2","NeedsCompilation":"yes","Package":"runjags","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"rjags, modeest, knitr","Title":"Interface Utilities,
Model Templates, Parallel Computing Methods\nand Additional Distributions for MCMC
Models in JAGS","URL":"http:\/\/runjags.sourceforge.net","Version":"2.0.3-
2"},"rusda":{"Author":"Franz-Sebastian Krah","Description":"An interface to the web
service methods provided by the United States Department of Agriculture (USDA). The
Agricultural Research Service (ARS) provides a large set of databases. The current
version of the package holds interfaces to the Systematic Mycology and Microbiology
Laboratory (SMML), which consists of four databases: Fungus-Host Distributions,
Specimens, Literature and the Nomenclature database. It provides functions for
querying these databases. The main function is \\code{associations}, which allows
searching for fungus-host combinations.","Imports":"XML, httr (>= 0.6.1), plyr,
foreach, stringr, testthat,\ntaxize, RCurl","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rusda","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Interface to USDA
Databases","URL":"http:\/\/www.usda.gov\/wps\/portal\/usda\/usdahome,\nhttp:\/\/nt.
ars-grin.gov\/fungaldatabases\/index.cfm","Version":"1.0.8"},"ruv":
{"Author":"Johann Gagnon-Bartsch <johanngb@umich.edu>","Description":"Implements
the 'RUV' (Remove Unwanted Variation) algorithms. These algorithms attempt to
adjust for systematic errors of unknown origin in high-dimensional data. The
algorithms were originally developed for use with genomic data, especially
microarray data, but may be useful with other types of high-dimensional data as
well. These algorithms were proposed by Gagnon-Bartsch and Speed (2012), and by
Gagnon-Bartsch, Jacob and Speed (2013). The algorithms require the user to specify
a set of negative control variables, as described in the references. The
algorithms included in this package are 'RUV-2', 'RUV-4', 'RUV-inv', and 'RUV-
rinv', along with various supporting
algorithms.","Imports":"stats","License":"GPL","NeedsCompilation":"yes","Package":"
ruv","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Detect and Remove
Unwanted Variation using Negative
Controls","URL":"http:\/\/www.stat.berkeley.edu\/~johann\/ruv","Version":"0.9.6"},"
rv":{"Author":"Jouni Kerman <jouni@kerman.com>","Depends":"R(>= 2.15.1), stats,
utils, grDevices, graphics, parallel","Description":"Simulation-based random
variable objects","License":"GPL-
2","NeedsCompilation":"no","Package":"rv","Repository":"http:\/\/cran.csiro.au\/src
\/contrib","Title":"Simulation-based random variable
objects","Version":"2.3.1"},"rvHPDT":{"Author":"Wei Guo
<wei.guo3@nih.gov>","Depends":"gtools, R(>= 2.15.0)","Description":"To detecting
rare variants for binary traits using general pedigrees, the pedigree
disequilibrium tests are proposed by collapsing rare haplotypes\/variants
with\/without weights. To run the test, MERLIN is needed in Linux for
haplotyping.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rvHPDT","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Calling haplotype-based and variant-based
pedigree\ndisequilibrium test for rare variants in
pedigrees","Version":"3.0"},"rvTDT":{"Author":"Yu Jiang, Andrew S.
Allen","Depends":"CompQuadForm (>= 1.4.1)","Description":"Used to compute
population controls weighted rare variants transmission distortion
test","License":"GPL-
3","NeedsCompilation":"no","Package":"rvTDT","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"population control weighted rare-variants
TDT","Version":"1.0"},"rvalues":{"Author":"Nicholas Henderson [cre],\nMichael
Newton [aut]","Description":"A collection of functions for computing \"r-values\"
from various\nkinds of user input such as MCMC output or a list of effect size
estimates\nand associated standard errors. Given a large collection of measurement
units,\nthe r-value, r, of a particular unit is a reported percentile that may
be\ninterpreted as the smallest percentile at which the unit should be placed in
the\ntop r-fraction of units.","Imports":"graphics, stats, utils","License":"GPL-
2","NeedsCompilation":"yes","Package":"rvalues","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"R-Values for Ranking in High-Dimensional
Settings","Version":"0.6"},"rversions":{"Author":"Gabor Csardi [aut, cre],\nJeroen
Ooms [ctb]","Description":"Query the main 'R' 'SVN' repository to find
the\nversions 'r-release' and 'r-oldrel' refer to, and also all\nprevious 'R'
versions and their release dates.","Imports":"curl, xml2, utils","License":"MIT +
file
LICENSE","NeedsCompilation":"no","Package":"rversions","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Query 'R' Versions, Including 'r-release' and 'r-
oldrel'","URL":"https:\/\/github.com\/metacran\/rversions","Version":"1.0.2"},"rver
tnet":{"Author":"Scott Chamberlain [aut, cre], Chris Ray [aut], Vijay Barve
[aut]","Description":"Retrieve, map and summarize data from the 'VertNet.org'
archives.\nFunctions allow searching by many parameters, including 'taxonomic'
names,\nplaces, and dates. In addition, there is an interface for conducting
spatially\ndelimited searches, and another for requesting large 'datasets' via
email.","Imports":"methods, stats, utils, plyr, jsonlite, httr, dplyr,
ggplot2,\nmaps","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"rvertnet","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat, knitr, RSQLite","Title":"Search
'Vertnet', a 'Database' of Vertebrate Specimen
Records","URL":"https:\/\/github.com\/ropensci\/rvertnet","Version":"0.4.1"},"rvest
":{"Author":"Hadley Wickham [aut, cre],\nRStudion [cph]","Depends":"R (>= 3.0.1),
xml2","Description":"Wrappers around the 'xml2' and 'httr' packages to make it easy
to\ndownload, then manipulate, HTML and XML.","Imports":"httr (>= 0.5), selectr,
3","NeedsCompilation":"no","Package":"rvest","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat, knitr, png, stringi (>= 0.3.1),
rmarkdown","Title":"Easily Harvest (Scrape) Web Pages","Version":"0.3.1"},"rvg":
{"Author":"David Gohel [aut, cre],\nBob Rudis [ctb] (the javascript code used by
function set_attr),\nFrancois Brunetti [ctb] (clipping algorithms)","Depends":"R
(>= 3.0)","Description":"Vector Graphics devices for 'SVG', 'DrawingML'
for\nMicrosoft Word and 'DrawingML' for Microsoft
PowerPoint.","Imports":"grDevices, Rcpp, xml2, gdtools, utils,
R.utils","License":"GPL-
3","NeedsCompilation":"yes","Package":"rvg","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"htmltools, testthat, covr, grid","Title":"R Graphics
Devices for Vector Graphics
Output","URL":"https:\/\/github.com\/davidgohel\/rvg","Version":"0.0.8"},"rvgtest":
{"Author":"Josef Leydold and Sougata Chaudhuri
<sgtchaudhuri@gmail.com>","Depends":"R (>= 3.0.0)","Description":"Test suite for
non-uniform pseudo-random number generators.","License":"GPL-
2","NeedsCompilation":"yes","Package":"rvgtest","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"Runuran (>= 0.18), testthat","Title":"Tools for
Analyzing Non-Uniform Pseudo-Random Variate
Generators","URL":"http:\/\/statmath.wu.ac.at\/unuran\/","Version":"0.7.4"},"rwfec"
:{"Author":"Alberto Gutierrez [aut, cre]","Depends":"R (>=
3.1)","Description":"Communications simulation package supporting forward error
correction.","Imports":"Rcpp (>= 0.11.6)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"rwfec","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"R Wireless, Forward Error
Correction","Version":"0.2"},"rwirelesscom":{"Author":"Alberto Gutierrez [aut,
cre]","Depends":"R (>= 3.1)","Description":"A communications simulation package
supporting common wireless modulation\nformats including BPSK, QPSK, 8-PSK, 16-PSK,
16-QAM and 64-QAM. The package includes AWGN\nnoise generation, and raised cosine
and square root raised cosine pulse shaping. It also\nincludes convenience
functions for plotting constellation diagrams, density plots, stem\nplots and eye
diagrams. Together these functions enable the evaluation of bit error and\nsymbol
error rates, evaluation of pulse shaping and inter-symbol interference and
support\nvisualization of the respective signals and noise in a variety of
formats.","Imports":"ggplot2, stats, Rcpp (>= 0.12.1)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"rwirelesscom","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat","Title":"Basic Wireless Communications
Simulation","Version":"1.4.3"},"rworldmap":{"Author":"Andy South","Depends":"R (>=
2.10.0), sp","Description":"Enables mapping of country level and gridded user
datasets.","Imports":"maptools, fields, methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rworldmap","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"rgdal, rworldxtra, RColorBrewer,
classInt","Title":"Mapping Global
Data","URL":"https:\/\/github.com\/AndySouth\/rworldmap\/,\nhttps:\/\/groups.google
.com\/forum\/#!forum\/rworldmap,\nhttp:\/\/andysouth.co.uk\/","Version":"1.3-
6"},"rworldxtra":{"Author":"Andy South","Depends":"R (>= 2.10.0),
sp","Description":"High resolution vector country boundaries derived from\nNatural
Earth data, can be plotted in rworldmap.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rworldxtra","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"rworldmap","Title":"Country boundaries at high
resolution","Version":"1.01"},"rwt":{"Author":"P. Roebuck, Rice University's DSP
group","Depends":"R (>= 2.15)","Description":"Provides a set of functions for
performing digital signal\nprocessing.","Imports":"matlab","License":"BSD_3_clause
+ file
LICENSE","NeedsCompilation":"yes","Package":"rwt","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Rice Wavelet Toolbox wrapper","URL":"http:\/\/cran.r-
project.org\/package=rwt","Version":"1.0.0"},"rwunderground":{"Author":"Alex Shum
<alex@ALShum.com>","Description":"Tools for getting historical weather information
and forecasts from wunderground.com. Historical weather and forecast data
includes, but is not limited to, temperature, humidity, windchill, wind speed, dew
point, heat index. Additionally, the weather underground weather API also includes
information on sunrise\/sunset, tidal conditions, satellite\/webcam imagery,
weather alerts, hurricane alerts and historical record high\/low
temperatures.","Imports":"httr, dplyr, countrycode","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"rwunderground","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"R Interface to Weather Underground
API","URL":"https:\/\/github.com\/ALShum\/rwunderground,\nhttp:\/\/www.wunderground
.com\/weather\/api","Version":"0.1.0"},"ryouready":{"Author":"Mark Heckmann [aut,
cre]","Description":"Package contains some data and functions that\nare used in my
forthcoming \"R you ready?\" book.","Imports":"stats, graphics, ggplot2, stringr,
2)","NeedsCompilation":"no","Package":"ryouready","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Companion to the Forthcoming Book - R you
Ready?","Version":"0.4"},"rysgran":{"Author":"Eliandro Ronael Gilbert, Mauricio
Garcia de Camargo, Leonardo Sandrini-Neto","Depends":"R (>= 2.10.0) , soiltexture ,
lattice","Description":"This package is a port to R of the SysGran program, written
in Delphi by Camargo (2006). It contains functions for the analysis of grain size
samples (in logarithmic (phi) and geometric (micrometers) scale) based on various
methods, like Folk & Ward (1957) and Methods of Moments (Tanner, 1995), among
others; textural classifications and distribution of unconsolidated sediments are
shown in histograms, bivariated plots and ternary diagrams of Shepard (1954) and
Pejrup (1988). English and Portuguese languages are supported in
outputs","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"rysgran","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"plotrix","Title":"Grain size analysis, textural
classifications and distribution\nof unconsolidated
sediments","Version":"2.1.0"},"rzmq":{"Author":"Whit Armstrong
<armstrong.whit@gmail.com>","Description":"Interface to the ZeroMQ lightweight
messaging kernel (see <http:\/\/www.zeromq.org\/> for more
information).","License":"GPL-
3","NeedsCompilation":"yes","Package":"rzmq","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"R Bindings for
ZeroMQ","URL":"http:\/\/github.com\/armstrtw\/rzmq","Version":"0.7.7"},"s20x":
{"Author":"Andrew Balemi, Dineika Chandra, James Curran, Brant Deppa, Mike Forster,
Brendan McArdle, Chris Wild","Description":"A set of functions
used in teaching STATS 201\/208 Data Analysis at the University of Auckland. The
functions are designed to make parts of R more accessible to a large undergraduate
population who are mostly not statistics majors.","License":"GPL-2 | file
LICENSE","NeedsCompilation":"no","Package":"s20x","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Functions for University of Auckland Course STATS
201\/208 Data\nAnalysis","Version":"3.1-16"},"s2dverification":{"Author":"Virginie
Guemas [aut],\nNicolau Manubens [aut, cre],\nLouis-Philippe Caron [aut],\nVerÃ³nica
Torralba [aut],\nChloÃ© Prodhomme [aut],\nMartin MÃ©nÃ©goz [aut],\nJavier Garcia-
Serrano [aut],\nFabian Lienert [aut],\nLudovic Auger [aut],\nIsabel Andreu-Burillo
[aut]","Depends":"R (>= 2.14.1), methods, maps","Description":"Set of tools to
verify forecasts through the computation of typical prediction scores against one
or more observational datasets or reanalyses (a reanalysis being a physical
extrapolation of observations that relies on the equations from a model, not a pure
observational dataset). Intended for seasonal to decadal climate forecasts although
can be useful to verify other kinds of forecasts. The package can be helpful in
climate sciences for other purposes than forecasting.","Imports":"ncdf4, GEOmap,
geomapdata, mapproj, abind, parallel,\nbigmemory, SpecsVerification,
3","NeedsCompilation":"no","Package":"s2dverification","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"easyVerification","Title":"Set of Common Tools
for Forecast
Verification","URL":"https:\/\/earth.bsc.es\/gitlab\/es\/s2dverification\/wikis\/ho
me","Version":"2.5.0"},"s4vd":{"Author":"Martin Sill, Sebastian
Kaiser","Depends":"biclust,methods,irlba,foreach","Description":"The main function
s4vd() performs a biclustering via sparse\nsingular value decomposition with a
nested stability selection.\nThe results is an biclust object and thus all methods
of the\nbiclust package can be applied.","License":"GPL-
2","NeedsCompilation":"no","Package":"s4vd","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Biclustering via Sparse Singular Value
Decomposition\nIncorporating Stability Selection","Version":"1.1-1"},"sBF":
{"Author":"A. Arcagni, L. Bagnato","Description":"Smooth Backfitting for additive
models using\nNadaraya-Watson estimator","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"sBF","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Smooth Backfitting","Version":"1.1.1"},"sExtinct":
{"Author":"Christopher Clements","Depends":"graphics, grDevices, stats, utils,
lattice","Description":"This package combines several sighting based estimators of
historical extinction, allowing them to be run simultaneously or individually. Code
for this package was contributed by Ben Collen, Gene Hunt and Tracy Rout.
Additional code was taken from McPherson & Myers (2009).","License":"GPL-
2","NeedsCompilation":"no","Package":"sExtinct","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Calculates the historic date of extinction given a series
of\nsighting events","Version":"1.1"},"sGPCA":{"Author":"Frederick
Campbell","Depends":"Matrix,fields","Description":"Functions for computing sparse
generalized principal components, including functions for modeling structured
correlation","License":"BSD","NeedsCompilation":"yes","Package":"sGPCA","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Sparse Generalized Principal
Component Analysis","Version":"1.0"},"sROC":{"Author":"Xiao-Feng
Wang","Description":"This package contains a collection of functions to
perform\nnonparametric estimation of receiver operating characteristic\n(ROC)
curves for continuous data.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"sROC","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Nonparametric Smooth ROC Curves for Continuous
Data","Version":"0.1-2"},"sSDR":{"Author":"Yang Liu <zjubioly@gmail.com>, Francesca
Chiaromonte, Bing Li","Depends":"R (>= 3.0.0), MASS,
Matrix","Description":"Performs structured OLS (sOLS) and structured SIR
(sSIR).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"sSDR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Tools Developed for Structured Sufficient Dimension
Reduction\n(sSDR)","Version":"1.2.0"},"sValues":{"Author":"Carlos
Cinelli","Description":"The sValues package implements the s-values proposed by Ed.
Leamer.\nIt provides a context-minimal approach for sensitivity analysis using
extreme\nbounds to assess the sturdiness of regression
coefficients.","Imports":"caTools, ggplot2, reshape2","License":"GPL-
3","NeedsCompilation":"no","Package":"sValues","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr, testthat","Title":"Measures of the Sturdiness of
Regression Coefficients","Version":"0.1.4"},"sac":{"Author":"Zhong Guan
<zguan@iusb.edu>","Depends":"R (>= 1.4)","Description":"Semiparametric empirical
likelihood ratio\nbased test of changepoint with one-change or epidemic
alternatives\nwith data-based model diagnostic","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"sac","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Semiparametric Analysis of
Changepoint","Version":"1.0.1"},"saccades":{"Author":"Titus von der Malsburg [aut,
cph, cre]","Depends":"R (>= 2.10), zoom","Description":"Functions for detecting eye
fixations in raw eye-tracking\ndata. The detection is done using a velocity-based
algorithm for\nsaccade detection proposed by Ralf Engbert and Reinhold Kliegl
in\n2003. The algorithm labels segments as saccades when the velocity of\nthe eye
movement exceeds a certain threshold. Anything between two\nsaccades is considered
a fixation. Thus the algorithm is not\nappropriate for data containing episodes of
smooth pursuit eye\nmovements.","License":"GPL-
2","NeedsCompilation":"no","Package":"saccades","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Detection of Fixations in Eye-Tracking
Data","URL":"https:\/\/github.com\/tmalsburg\/saccades","Version":"0.1-
1"},"sadists":{"Author":"Steven E. Pav [aut, cre]","Depends":"R (>=
3.0.2)","Description":"Provides the density, distribution, quantile and
generation\nfunctions of some obscure probability distributions, including the
doubly non-\ncentral t, F, Beta, and Eta distributions; Lecoutre's lambda-prime and
K-prime;\nthe upsilon distribution; the (weighted) sum of non-central chi-squares
to a\npower; the (weighted) sum of log non-central chi-squares; the product of
non-\ncentral chi-squares to powers; the product of doubly non-central F
variates.","Imports":"PDQutils (>= 0.1.1), hypergeo, orthopolynom","License":"LGPL-
3","NeedsCompilation":"no","Package":"sadists","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"shiny, testthat, ggplot2, xtable, knitr","Title":"Some
Additional
Distributions","URL":"https:\/\/github.com\/shabbychef\/sadists","Version":"0.2.2"}
,"sads":{"Author":"Paulo I. Prado, Murilo Dantas Miranda and Andre
Chalom","Depends":"stats, bbmle","Description":"Maximum likelihood tools to fit and
compare models of species\nabundance distributions and of species rank-abundance
distributions.","Imports":"MASS, methods, graphics, grDevices, VGAM, poilog,
GUILDS","License":"GPL-
2","NeedsCompilation":"yes","Package":"sads","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"vegan","Title":"Maximum Likelihood Models for Species
Abundance
Distributions","URL":"http:\/\/piLaboratory.github.io\/sads,\nhttps:\/\/github.com\
/piklprado\/sads","Version":"0.2.4"},"sae":{"Author":"Isabel Molina, Yolanda
Marhuenda","Depends":"stats, nlme, MASS","Description":"Functions for small area
estimation.","License":"GPL-
2","NeedsCompilation":"no","Package":"sae","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Small Area Estimation","Version":"1.1"},"sae2":
{"Author":"Robert E. Fay, Mamadou Diallo","Depends":"R (>= 2.14.0),
MASS","Description":"Time series models for small area estimation based on area-
level models.","License":"GPL-
2","NeedsCompilation":"no","Package":"sae2","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"sae","Title":"Small Area Estimation: Time-series
Models","Version":"0.1-1"},"saeSim":{"Author":"Sebastian Warnholz [aut, cre],\nTimo
Schmid [aut]","Depends":"R(>= 3.1), methods","Description":"Tools for the
simulation of data in the context of small area\nestimation. Combine all steps of
your simulation - from data generation\nover drawing samples to model fitting - in
one object. This enables easy\nmodification and combination of different scenarios.
You can store your\nresults in a folder or start the simulation in
parallel.","Imports":"dplyr(>= 0.2), functional, ggplot2, MASS, spdep,
parallelMap","License":"GPL-3 | file
LICENSE","NeedsCompilation":"no","Package":"saeSim","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat, knitr","Title":"Simulation Tools for
Small Area
Estimation","URL":"https:\/\/wahani.github.io\/saeSim","Version":"0.7.0"},"saemix":
{"Author":"Emmanuelle Comets, Audrey Lavenu, Marc Lavielle.","Description":"The
SAEMIX package implements the Stochastic Approximation EM algorithm for parameter
estimation in (non)linear mixed effects models. The SAEM algorithm: - computes the
maximum likelihood estimator of the population parameters, without any
approximation of the model (linearisation, quadrature approximation,...), using the
Stochastic Approximation Expectation Maximization (SAEM) algorithm, - provides
standard errors for the maximum likelihood estimator - estimates the conditional
modes, the conditional means and the conditional standard deviations of the
individual parameters, using the Hastings-Metropolis algorithm. Several
applications of SAEM in agronomy, animal breeding and PKPD analysis have been
published by members of the Monolix group
(http:\/\/group.monolix.org\/).","Imports":"graphics,
stats, methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"saemix","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Stochastic Approximation Expectation Maximization
(SAEM)\nalgorithm","Version":"1.2"},"saery":{"Author":"Maria Dolores Esteban
Lefler, Domingo Morales Gonzalez, Agustin Perez Martin","Description":"A complete
set of functions to calculate several EBLUP (Empirical Best Linear Unbiased
Predictor) estimators and their mean squared errors. All estimators are based on an
area-level linear mixed model introduced by Rao and Yu in 1994 (see documentation).
The REML method is used for fitting this model.","License":"GPL-
2","NeedsCompilation":"no","Package":"saery","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Small Area Estimation for Rao and Yu
Model","Version":"1.0"},"safeBinaryRegression":{"Author":"Kjell Konis
<kjell.konis@me.com>","Depends":"R (>= 2.9.1), lpSolveAPI (>=
5.5.0.14)","Description":"Overloads the glm function in the stats package so
that\na test for the existence of the maximum likelihood estimate is included\nin
the fitting procedure for binary regression models.","License":"GPL-
2","NeedsCompilation":"no","Package":"safeBinaryRegression","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Title":"Safe Binary Regression","Version":"0.1-
3"},"safi":{"Author":"Jana Fruth, Malte Jastrow","Description":"Design and
sensitivity analysis for computer experiments with scalar-valued output and
functional input, e.g. over time or space. The aim is to explore the behavior of
the sensitivity over the functional domain.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"safi","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Sensitivity Analysis for Functional
Input","Version":"1.0"},"sampSurf":{"Author":"Jeffrey H. Gove","Depends":"R (>=
2.13.1), methods(>= 2.13.1), sp(>= 0.9-84), raster(>=\n1.9-5), rasterVis(>= 0.10-
3), boot (>= 1.3-3)","Description":"Sampling surface simulation is useful in the
comparison of different areal sampling methods\nin forestry, ecology and natural
resources. The sampSurf package allows the simulation\nof numerous sampling methods
for standing trees and downed woody debris in a spatial context.\nIt also provides
an S4 class and method structure that facilitates the addition of new
sampling\nmethods.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"sampSurf","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"rgl, rgeos (>= 0.2-9)","Title":"Sampling Surface
Simulation for Areal Sampling Methods","URL":"http:\/\/sampsurf.r-forge.r-
project.org\/","Version":"0.7-3"},"sampleSelection":{"Author":"Arne Henningsen
<arne.henningsen@gmail.com>,\nOtt Toomet <otoomet@ut.ee>","Depends":"R (>= 2.10),
maxLik (>= 0.7-3), stats","Description":"Two-step estimation\nand maximum
likelihood estimation\nof Heckman-type sample selection models:\nstandard sample
selection models (Tobit-2)\nand endogenous switching regression models (Tobit-
5).","Imports":"miscTools (>= 0.6-3), systemfit (>= 1.0-0), Formula (>=\n1.1-1),
VGAM (>= 0.9-4), mvtnorm (>= 0.9-9994)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"sampleSelection","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"lmtest, Ecdat","Title":"Sample Selection
Models","URL":"http:\/\/www.sampleSelection.org","Version":"1.0-4"},"samplesize":
{"Author":"Ralph Scherer","Description":"Computes sample size for Student's t-test
and for the Wilcoxon-Mann-Whitney test for categorical data. The t-test function
allows paired and unpaired (balanced \/ unbalanced) designs as well as homogeneous
and heterogeneous variances. The Wilcoxon function allows for ties.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"samplesize","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Sample Size Calculation for Various t-Tests and
Wilcoxon-Test","URL":"https:\/\/github.com\/shearer\/samplesize","Version":"0.2-
2"},"samplesize4surveys":{"Author":"Hugo Andres Gutierrez Rojas","Depends":"R (>=
2.11), TeachingSampling","Description":"Computes the required sample size for
estimation of totals, means\nand proportions under complex sampling
2)","NeedsCompilation":"no","Package":"samplesize4surveys","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Suggests":"knitr","Title":"Sample Size Calculations
for Complex Surveys","Version":"2.4.0.900"},"sampling":{"Author":"Yves Tillé
<yves.tille@unine.ch>, Alina Matei <alina.matei@unine.ch>","Description":"Functions
for drawing and calibrating samples.","Imports":"MASS, lpSolve","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"sampling","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Survey Sampling","Version":"2.7"},"samplingEstimates":
{"Author":"Emilio Lopez Escobar [aut, cre]","Depends":"R (>= 3.0.0),
samplingVarEst","Description":"Functions to estimate from survey data. This package
is a user-friendly wrapper of the samplingVarEst package. It considers that the
user is more familiar with practical survey data rather than with research on
survey sampling (variance estimation). More functionalities are on the
way.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"samplingEstimates","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Title":"Sampling
Estimates","URL":"http:\/\/www.numerika.mx","Version":"0.1-3"},"samplingVarEst":
{"Author":"Emilio Lopez Escobar [aut, cre, cph] <emilio@numerika.mx>,\nErnesto
Barrios Zamudio [ctb] <ebarrios@itam.mx>,\nJuan Francisco Munoz Rosas [ctb]
<jfmunoz@go.ugr.es>","Depends":"R (>= 3.0.0)","Description":"Functions to calculate
some point estimators and estimating their variance under unequal probability
sampling without replacement. Single and two stage sampling designs are considered.
Some approximations for the second order inclusion probabilities are also available
(sample and population based).","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"samplingVarEst","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Sampling Variance
Estimation","URL":"http:\/\/www.numerika.mx, http:\/\/www.itam.mx","Version":"1.0-
1"},"samplingbook":{"Author":"Juliane Manitz <manitzj@gmx.de>, contributions by
Mark\nHempelmann <mark.hempelmann@o2online.de>, Goeran
Kauermann\n<gkauermann@wiwi.uni-bielefeld.de>, Helmut
Kuechenhoff\n<kuechenhoff@stat.uni-muenchen.de>, Shuai
Shao\n<shuai.shao@campus.lmu.de>, Cornelia Oberhauser\n<conny.oberhauser@gmx.de>,
Nina Westerheide\n<nwesterheide@wiwi.uni-bielefeld.de>, Manuel
Wiesenfarth\n<m.wiesenfarth@uni-goettingen.de>","Depends":"pps, sampling,
survey","Description":"Sampling procedures from the book 'Stichproben.
Methoden\nund praktische Umsetzung mit R' by Goeran Kauermann and
Helmut\nKuechenhoff (2010)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"samplingbook","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Survey Sampling
Procedures","Version":"1.2.0"},"samr":{"Author":"R. Tibshirani, G. Chu,
Balasubramanian Narasimhan, Jun Li","Depends":"impute,
matrixStats","Description":"Significance Analysis of
Microarrays","License":"LGPL","NeedsCompilation":"yes","Package":"samr","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Title":"SAM: Significance Analysis of
Microarrays","URL":"http:\/\/www-
stat.stanford.edu\/~tibs\/SAM","Version":"2.0"},"sand":{"Author":"Eric D Kolaczyk,
Gabor Csardi","Depends":"igraph, igraphdata","Description":"Data sets for the book
'Statistical Analysis of\nNetwork Data with R'.","License":"GPL-
3","NeedsCompilation":"no","Package":"sand","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"GO.db, GOstats, ROCR, ape, car, eigenmodel, ergm,
fdrtool,\nggplot2, huge, kernlab, lattice, mixer, network,\nnetworkDynamic,
networkTomography, ngspatial, org.Sc.sgd.db,\nsna, vioplot","Title":"Statistical
Analysis of Network Data with
R","URL":"https:\/\/github.com\/kolaczyk\/sand","Version":"1.0.2"},"sandwich":
{"Author":"Thomas Lumley [aut],\nAchim Zeileis [aut, cre]","Depends":"R (>=
2.0.0)","Description":"Model-robust standard error estimators for cross-sectional,
time series, and longitudinal data.","Imports":"stats, zoo","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"sandwich","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"car, lmtest, strucchange, AER, survival, MASS,
scatterplot3d","Title":"Robust Covariance Matrix Estimators","Version":"2.3-
4"},"sanitizers":{"Author":"Dirk Eddelbuettel","Description":"Recent gcc and clang
compiler versions provide functionality to\nmemory violations and other undefined
behaviour; this is often referred to as\n\"Address Sanitizer\" (or SAN)
and \"Undefined Behaviour Sanitizer\" (UBSAN).\nThe Writing R Extension manual
describes this in some detail in Section 4.9.\n\nThis feature has to be enabled in
the corresponding binary, eg in R, which\nis somewhat involved as it also required
a current compiler toolchain which\nis not yet widely available, or in the case of
Windows, not available at all\n(via the common Rtools mechanism).\n\nAs an
alternative, the pre-built Docker containers available via the Docker Hub\nat
https:\/\/registry.hub.docker.com\/u\/eddelbuettel\/docker-debian-r\/ can be
used\non Linux, and via boot2docker on Windows and OS X.\n\nThis package then
provides a means of testing the compiler setup as the\nknown code failures provides
in the sample code here should be detected\ncorrectly, whereas a default build of R
will let the package pass.\n\nThe code samples are based on the examples from the
Address Sanitizer\nWiki at https:\/\/code.google.com\/p\/address-
sanitizer\/wiki\/AddressSanitizer.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"sanitizers","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"C\/C++ source code to trigger Address and Undefined
Behaviour\nSanitizers","Version":"0.1.0"},"sankey":{"Author":"Gabor
Csardi, January Weiner","Description":"Sankey plots illustrate the flow of
information or material.","Imports":"simplegraph, utils, graphics,
2)","NeedsCompilation":"no","Package":"sankey","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat","Title":"Sankey
Diagrams","URL":"https:\/\/github.com\/mangothecat\/sankey","Version":"1.0.0"},"san
on":{"Author":"Atsushi Kawaguchi","Description":"There are several functions to
implement the method for analysis in a randomized clinical trial with strata with
following key features. A stratified Mann-Whitney estimator addresses the
comparison between two randomized groups for a strictly ordinal response variable.
The multivariate vector of such stratified Mann-Whitney estimators for multivariate
response variables can be considered for one or more response variables such as in
repeated measurements and these can have missing completely at random (MCAR) data.
Non-parametric covariance adjustment is also considered with the minimal assumption
of randomization. The p-value for hypothesis test and confidence interval are
2)","NeedsCompilation":"no","Package":"sanon","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Stratified Analysis with Nonparametric Covariable
Adjustment","Version":"1.5"},"sapa":{"Author":"William Constantine and Donald
Percival (Applied Physics\nLaboratory, University of Washington)","Depends":"R (>=
3.0.2)","Description":"Software for the book Spectral Analysis for
Physical\nApplications, Donald B. Percival and Andrew T. Walden,\nCambridge
University Press, 1993.","Imports":"ifultools (>= 2.0-0), splus2R (>= 1.2-
0)","License":"GPL-
2","NeedsCompilation":"yes","Package":"sapa","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Spectral Analysis for Physical Applications","Version":"2.0-
1"},"sas7bdat":{"Author":"Matt Shotwell","Depends":"R (>=
2.10)","Description":"Read SAS files in the sas7bdat data format.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"sas7bdat","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"SAS Database Reader
(experimental)","Version":"0.5"},"satellite":{"Author":"Thomas Nauss, Hanna Meyer,
Florian Detsch, Tim Appelhans","Depends":"R (>= 2.10), raster, Rcpp (>= 0.10.3),
methods, utils, stats,\ngrDevices, graphics","Description":"This smorgasbord
provides a variety of functions which are useful\nfor handling, manipulating and
visualizing remote sensing data.","Imports":"plyr, tools, stats4","License":"GPL-
3","NeedsCompilation":"yes","Package":"satellite","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"devtools, knitr, rgdal, testthat","Title":"Various
Functions for Handling and Manipulating Remote
Sensing\nData","Version":"0.2.0"},"saturnin":{"Author":"LoÃ¯c
Schwaller","Description":"Bayesian inference of graphical model structures using
spanning trees.","Imports":"Rcpp","License":"GPL-
2","NeedsCompilation":"yes","Package":"saturnin","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"parallel","Title":"Spanning Trees Used for Network
Inference","Version":"1.1.1"},"saves":{"Author":"Gergely DarÃ³czi
<gergely@snowl.net>","Description":"The purpose of this package is to be able to
save and load only\nthe needed variables\/columns of a dataframe in special binary
files (tar\narchives) - which seems to be a lot faster method than loading the
whole\nbinary object (RData files) via load() function, or than loading
columns\nfrom SQLite\/MySQL databases via SQL commands (see vignettes).
Performance\ngain on SSD drives is a lot more sensible compared to basic
load()\nfunction. The performance improvement gained by loading only the
chosen\nvariables in binary format can be useful in some special cases (e.g.
where\nmerging data tables is not an option and very different datasets are
needed\nfor reporting), but be sure if using this package that you really
need\nthis, as non-standard file formats are used!","License":"AGPL-
3","NeedsCompilation":"no","Package":"saves","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Fast load
variables","URL":"http:\/\/r.snowl.net\/saves\/","Version":"0.5"},"saws":
{"Author":"Michael P. Fay","Depends":"R (>= 2.6.0), gee,
stats","Description":"Tests coefficients with sandwich estimator of variance and
with small samples. Regression types supported are gee, linear regression, and
conditional logistic regression.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"saws","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"MASS","Title":"Small-Sample Adjustments for Wald tests
Using Sandwich\nEstimators","Version":"0.9-6.1"},"sbgcop":{"Author":"Peter
Hoff","Description":"This package estimates parameters of a Gaussian
copula,\ntreating the univariate marginal distributions as nuisance\nparameters as
described in Hoff(2007). It also provides a\nsemiparametric imputation procedure
for missing multivariate\ndata.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"sbgcop","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Semiparametric Bayesian Gaussian copula estimation
and\nimputation","URL":"http:\/\/www.stat.washington.edu\/hoff","Version":"0.975"},
"sbioPN":{"Author":"Roberto Bertolusso and Marek Kimmel","Description":"\nsbioPN is
a package suited to perform simulation of deterministic and stochastic systems of
biochemical reaction\nnetworks with spatial effects.\nModels are defined using a
subset of Petri Nets, in a way that is close at how chemical reactions are
defined.\nFor deterministic solutions, sbioPN creates the associated system of
differential equations \"on the fly\", and\nsolves it with a Runge Kutta Dormand
Prince 45 explicit algorithm.\nFor stochastic solutions, sbioPN offers two variants
of Gillespie algorithm, or SSA.\nFor hybrid deterministic\/stochastic,\nit employs
the Haseltine and Rawlings algorithm, that partitions the system in fast and slow
reactions.\nsbioPN algorithms are developed in C to achieve adequate
performance.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"sbioPN","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"sbioPN: Simulation of deterministic and stochastic
spatial\nbiochemical reaction networks using Petri
Nets","Version":"1.1.0"},"sbmSDP":{"Author":"Arash A. Amini","Description":"An ADMM
implementation of SDP-1, a semidefinite programming relaxation of the maximum
likelihood estimator for fitting a block model. SDP-1 has a tendency to produce
equal-sized blocks and is ideal for producing a form of network histogram
approximating a nonparametric graphon model. Alternatively, it can be used for
community detection. (This is experimental code, proceed with
caution.)","Imports":"Rcpp (>= 0.11.6)","License":"GPL-
3","NeedsCompilation":"yes","Package":"sbmSDP","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Semidefinite Programming for Fitting Block Models of Equal
Block\nSizes","Version":"0.2"},"sca":{"Author":"Valentin Rousson
<rousson@ifspm.unizh.ch> and Martin Maechler","Description":"Simple Component
Analysis (SCA) often provides much more\ninterpretable components than Principal
Components (PCA) while still\nrepresenting much of the variability in the
data.","Imports":"grDevices, graphics, stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"sca","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"MASS","Title":"Simple Component Analysis","Version":"0.9-
0"},"scaRabee":{"Author":"Sebastien Bihorel","Depends":"neldermead (>= 1.0-8),
lattice, grid, deSolve, utils","Description":"scaRabee is a port of the Scarabee
toolkit originally\nwritten as a Matlab-based application. It provides a
framework\nfor simulation and optimization of pharmacokinetic-
pharmacodynamic\nmodels at the individual and population level. It is built on top
of the\nneldermead package, which provides the direct search algorithm proposed\nby
Nelder and Mead for model optimization.","License":"GPL-
3","NeedsCompilation":"no","Package":"scaRabee","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Optimization Toolkit for Pharmacokinetic-Pharmacodynamic
Models","Version":"1.1-3"},"scagnostics":{"Author":"Lee Wilkinson
<leland.wilkinson@gmail.com> and Anushka
Anand","Depends":"rJava","Description":"Calculates graph theoretic scagnostics.
Scagnostics\ndescribe various measures of interest for pairs of variables,\nbased
on their appearance on a scatterplot. They are useful\ntool for discovering
interesting or unusual scatterplots from a\nscatterplot matrix, without having to
look at every individual\nplot.","License":"file
LICENSE","NeedsCompilation":"no","Package":"scagnostics","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Compute scagnostics - scatterplot
diagnostics","URL":"http:\/\/www.rforge.net\/scagnostics\/,\nhttp:\/\/www.cs.uic.ed
u\/~wilkinson\/","Version":"0.2-4"},"scales":{"Author":"Hadley Wickham [aut,
cre],\nRStudio [cph]","Depends":"R (>= 2.13)","Description":"Graphical scales map
data to aesthetics, and provide\nmethods for automatically determining breaks and
labels\nfor axes and legends.","Imports":"RColorBrewer, dichromat, plyr, munsell
(>= 0.2), labeling,\nmethods, Rcpp","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"scales","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat (>= 0.8), covr","Title":"Scale Functions
for
Visualization","URL":"https:\/\/github.com\/hadley\/scales","Version":"0.4.0"},"sca
lreg":{"Author":"Tingni Sun","Depends":"R (>= 2.10), lars,
MASS","Description":"Algorithms for fitting scaled sparse linear regression and
estimating precision matrices","License":"GPL-
2","NeedsCompilation":"no","Package":"scalreg","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Scaled sparse linear regression","Version":"1.0"},"scam":
{"Author":"Natalya Pya <nat.pya@gmail.com>","Depends":"R
(>= 2.15.0), mgcv (>= 1.8-2)","Description":"Routines for generalized additive
modelling under shape\nconstraints on the component functions of the linear
predictor.\nModels can contain multiple shape constrained (univariate\nand\/or
bivariate) and unconstrained terms. The routines of gam()\nin package 'mgcv' are
used for setting up the model matrix,\nprinting and plotting the results.
Penalized likelihood\nmaximization based on Newton-Raphson method is used to fit
a\nmodel with multiple smoothing parameter selection by GCV
or\nUBRE\/AIC.","Imports":"methods, stats, graphics, Matrix,
splines","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"scam","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"nlme","Title":"Shape Constrained Additive
Models","Version":"1.1-9"},"scape":{"Author":"Arni Magnusson [aut,
cre]","Depends":"R (>= 2.10)","Description":"Import, plot, and diagnose results
from statistical\ncatch-at-age models, used in fisheries stock
assessment.","Imports":"coda, Hmisc, lattice","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"scape","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"gdata","Title":"Statistical Catch-at-Age Plotting
Environment","Version":"2.2-0"},"scar":{"Author":"Yining Chen and Richard
Samworth","Depends":"R (>= 2.10.0)","Description":"This package computes the
maximum likelihood estimator of the generalised additive and index regression with
shape constraints. Each additive component function is assumed to obey one of the
nine possible shape restrictions: linear, increasing, decreasing, convex, convex
increasing, convex decreasing, concave, concave increasing, or concave
decreasing.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"scar","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Shape-Constrained Additive Regression: a Maximum
Likelihood\nApproach","Version":"0.2-1"},"scatterD3":{"Author":"Julien Barnier
[aut, cre],\nKent Russell [aut, ctb],\nMike Bostock [aut, cph] (d3.js library,
http:\/\/d3js.org),\nSusie Lu [aut, cph] (d3-legend library, http:\/\/d3-
legend.susielu.com\/),\nSperos Kokenes [aut, cph] (d3-lasso-plugin
library,\nhttps:\/\/github.com\/skokenes\/D3-Lasso-Plugin)","Description":"Creates
'D3' 'JavaScript' scatterplots from 'R' with interactive\nfeatures : panning,
zooming, tooltips, etc.","Enhances":"shiny","Imports":"htmlwidgets, digest,
ellipse","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"scatterD3","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr, rmarkdown","Title":"D3 JavaScript Scatterplot
from
R","URL":"https:\/\/github.com\/juba\/scatterD3","Version":"0.6.2"},"scatterplot3d"
:{"Author":"Uwe Ligges <ligges@statistik.tu-dortmund.de>, Martin Maechler, Sarah
Schnackenberg","Depends":"R (>= 2.7.0)","Description":"Plots a three dimensional
(3D) point cloud.","Imports":"grDevices, graphics, stats","License":"GPL-
2","NeedsCompilation":"no","Package":"scatterplot3d","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"3D Scatter Plot","Version":"0.3-36"},"scenario":
{"Author":"Sean Turner [aut, cre],\nStefano Galelli [aut]","Description":"Uses the
neural gas algorithm to construct\na scenario tree for use in multi-stage
stochastic programming.\nThe primary input is a set of initial scenarios or
realizations\nof a disturbance. The scenario tree nodal structure must
be\npredefined using a scenario tree nodal partition
matrix.","Imports":"graphics","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"scenario","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr","Title":"Construct Reduced Trees with
Predefined Nodal Structures","URL":"https:\/\/github.com\/swd-
turner\/scenario","Version":"1.0"},"schoRsch":{"Author":"Roland Pfister, Markus
Janczyk","Description":"Offers a helping hand to psychologists and other behavioral
scientists who routinely deal with experimental data from factorial experiments. It
includes several functions to format output from other R functions according to the
style guidelines of the APA (American Psychological Association). This formatted
output can be copied directly into manuscripts to facilitate data reporting. These
features are backed up by a toolkit of several small helper functions, e.g.,
offering out-of-the-box outlier removal. The package lends its name to
Georg \"Schorsch\" Schuessler, ingenious technician at the Department of Psychology
III, University of
Wuerzburg.","Imports":"utils","License":"GPL","NeedsCompilation":"no","Package":"sc
hoRsch","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"ez","Title"
:"Tools for Analyzing Factorial Experiments","Version":"1.2"},"scholar":
{"Author":"James Keirstead <james.keirstead@gmail.com>","Depends":"R (>=
2.15.1)","Description":"Provides functions to extract citation data from
Google\nScholar. Convenience functions are also provided for comparing\nmultiple
scholars and predicting future h-index values.","Imports":"R.cache, dplyr, httr,
rvest, stringr, xml2","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"scholar","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"roxygen2","Title":"Analyse Citation Data from
Google Scholar","Version":"0.1.4"},"schoolmath":{"Author":"Joerg Schlarmann, Josef
Wienand","Depends":"R (>= 2.10)","Description":"This package contains functions and
datasets for math\ntaught in school. A main focus is set to prime-
calculation","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"schoolmath","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Functions and datasets for math used in
school","Version":"0.4"},"schumaker":{"Author":"Stuart Baumann [aut, cre],
Margaryta Klymak[ctb]","Description":"This is a shape preserving spline which is
guaranteed\nto be monotonic and concave or convex if the data is monotonic\nand
concave or convex. It does not use any optimisation and is\ntherefore quick and
smoothly converges to a fixed point in\neconomic dynamics problems including value
function iteration.\nIt also automatically gives the first two derivatives of
the\nspline and options for determining behaviour when evaluated\noutside the
interpolation domain.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"schumaker","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"knitr, numDeriv, cobs, scam,
microbenchmark","Title":"Schumaker Shape-Preserving
Spline","Version":"0.3"},"schwartz97":{"Author":"Philipp Erb, David Luethi, Juri
Hinz, Simon Otziger","Depends":"R(>= 2.10), FKF(>= 0.1.0), mvtnorm, methods,
RUnit","Description":"This package provides detailed functionality for working with
the Schwartz 1997 two-factor commodity model. Essentially, it contains pricing
formulas for futures and European options and the standard d\/p\/q\/r functions for
the distribution of the state variables and futures prices. In addition, a
parameter estimation procedure is contained together with many utilities as
filtering and plotting functionality. This package is accompanied by futures data
of ten commodities.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"schwartz97","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"A package on the Schwartz two-factor commodity
model","Version":"0.0.6"},"scidb":{"Author":"Paradigm4, B. W. Lewis","Depends":"R
(>= 3.0.0), methods","Description":"An R interface to the SciDB array database
(http:\/\/scidb.org).","Imports":"Matrix, utils, stats, iterators, RCurl, zoo,
graphics, digest","License":"AGPL-
3","NeedsCompilation":"yes","Package":"scidb","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"An R Interface to
SciDB","URL":"http:\/\/paradigm4.github.io\/SciDBR","Version":"1.2-0"},"scio":
{"Author":"Xi (Rossi) LUO and Weidong Liu","Description":"Sparse Column-wise
Inverse Operator for estimating the inverse covariance matrix. Note that this is a
preliminary version accompanying the arXiv paper (arXiv:1203.3896) in 2012. This
version contains only the minimal set of functions for estimation and cross
validation.","License":"GPL-
2","NeedsCompilation":"yes","Package":"scio","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"clime, lorec, QUIC","Title":"Sparse Column-wise Inverse
Operator","Version":"0.6.1"},"sciplot":{"Author":"Manuel Morales
<mmorales@williams.edu>, with code developed by\nthe R Development Core Team and
with general advice from the\nR-help listserv community, especially Duncan
Murdoch.","Depends":"stats","Description":"A collection of functions that creates
graphs with error\nbars for data collected from one-way or higher
factorial\ndesigns.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"sciplot","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Scientific Graphing Functions for Factorial
Designs","Version":"1.1-0"},"sclero":{"Author":"Mikko Vihtakari [aut,
cre]","Depends":"R (>= 3.0), RImageJROI, spatstat, plyr","Description":"Provides
functions to measure growth patterns and align\nsampling spots in chronologically
deposited materials. The package is\nintended for the fields of sclerochronology,
dendrochronology and geology.","License":"GPL-
3","NeedsCompilation":"no","Package":"sclero","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Measure Growth Patterns and Align Sampling Spots in
Photographs","URL":"https:\/\/github.com\/MikkoVihtakari\/sclero","Version":"0.2"},
"scmamp":{"Author":"Borja Calvo [aut, cre],\nGuzman Santafe [aut]","Depends":"R (>=
2.10)","Description":"Given a matrix with results of different algorithms for
different\nproblems, the package uses statistical tests and corrections to assess
the\ndifferences between algorithms.","Imports":"ggplot2, graph, reshape2,
Rgraphviz, methods","License":"GPL-
2","NeedsCompilation":"no","Package":"scmamp","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"knitr","Title":"Statistical
Comparison of Multiple Algorithms in
Multiple\nProblems","Version":"0.2.5"},"score":{"Author":"Jaejoon
Song","Depends":"R (>= 2.10), msm (>= 1.5)","Description":"Provides routines for
scoring behavioral questionnaires. Includes scoring procedures for the
'International Physical Activity Questionnaire (IPAQ)' <http:\/\/www.ipaq.ki.se>.
Compares physical functional performance to the age- and gender-specific normal
ranges.","License":"GNU General Public License (>=
3)","NeedsCompilation":"no","Package":"score","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"A Package to Score Behavioral
Questionnaires","Version":"1.0.2"},"scorer":{"Author":"Paul Hendricks [aut,
cre]","Depends":"R (>= 3.2.3)","Description":"A set of tools for quickly scoring
models in data science and\nmachine learning. This toolset is written in C++ for
blazing fast performance.","Imports":"Rcpp (>= 0.12.3)","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"scorer","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat (>= 0.11.0)","Title":"Quickly Score
Models in Data Science and Machine
Learning","URL":"https:\/\/github.com\/paulhendricks\/scorer","Version":"0.2.0"},"s
coring":{"Author":"Ed Merkle","Depends":"R (>= 2.10)","Description":"Evaluating
probabilistic forecasts via proper scoring rules. scoring implements the beta,
power, and pseudospherical families of proper scoring rules, along with ordered
versions of the latter two families. Included among these families are popular
rules like the Brier (quadratic) score, logarithmic score, and spherical score.
For two-alternative forecasts, also includes functionality for plotting scores that
one would obtain under specific scoring rules.","License":"GPL-
2","NeedsCompilation":"no","Package":"scoring","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat","Title":"Proper scoring
rules","Version":"0.5-1"},"scout":{"Author":"Daniela M. Witten and Robert
Tibshirani","Description":"Implements the Scout method for regression, described in
\"Covariance-regularized regression and classification for high-dimensional
problems\", by Witten and Tibshirani (2008), Journal of the Royal Statistical
Society, Series B 71(3): 615-636.","Imports":"glasso, stats, grDevices,
2)","NeedsCompilation":"yes","Package":"scout","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"lars","Title":"Implements the Scout Method for
Covariance-Regularized\nRegression","Version":"1.0.4"},"scrapeR":{"Author":"Ryan M.
Acton <rmacton@gmail.com>","Depends":"XML,RCurl","Description":"Tools for Scraping
Data from Web-Based Documents","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"scrapeR","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Tools for Scraping Data from HTML and XML
Documents","URL":"http:\/\/www.ryanacton.com","Version":"0.1.6"},"scrime":
{"Author":"Holger Schwender, with a contribution of Arno
Fritsch","Description":"Tools for the analysis of high-dimensional data
developed\/implemented\nat the group \"Statistical Complexity Reduction In
Molecular Epidemiology\" (SCRIME).\nMain focus is on SNP data. But most of the
functions can also be applied to other\ntypes of categorical data.","License":"GPL-
2","NeedsCompilation":"no","Package":"scrime","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"MASS, RSQLite (>= 0.4-15), oligoClasses (>=
1.1.9)","Title":"Analysis of High-Dimensional Categorical Data such as SNP
Data","Version":"1.3.3"},"scriptests":{"Author":"Tony Plate","Description":"Support
for using .Rt (transcript) tests\nin the tests directory of a package. Provides
more\nconvenience and features than the standard .R\/.Rout.save\ntests. Tests can
be run under R CMD check and also\ninteractively. Provides source.pkg() for
quickly loading\ncode, DLLs, and data from a package for use in
an\nedit\/compile\/test development
cycle.","License":"GPL","NeedsCompilation":"no","Package":"scriptests","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Title":"Transcript-Based Unit Tests that
are Easy to Create and Maintain","Version":"1.0-15"},"scrm":{"Author":"Paul Staab
[aut, cre, cph],\nZhu Sha [aut, cph],\nDirk Metzler [aut, cph, ths],\nGerton Lunter
[aut, cph, ths]","Depends":"R (>= 3.1.0)","Description":"A coalescent simulator
that allows the rapid simulation of\nbiological sequences under neutral models of
evolution. Different to\nother coalescent based simulations, it has an optional
approximation\nparameter that allows for high accuracy while maintaining a linear
run time\ncost for long sequences. It is optimized for simulating massive data sets
as\nproduced by Next-Generation Sequencing technologies for up to several
thousand\nsequences.","Imports":"Rcpp (>= 0.11.2)","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"scrm","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat (>= 0.9.0), knitr, ape","Title":"Simulating the
Evolution of Biological Sequences","URL":"https:\/\/github.com\/scrm\/scrm-
r","Version":"1.6.0-2"},"scrubr":{"Author":"Scott Chamberlain [aut,
cre]","Description":"Clean biological occurrence records. Includes
functionality\nfor cleaning based on various aspects of spatial
coordinates,\nunlikely values due to political 'centroids', coordinates based
on\nwhere collections of specimens are held, and more.","Imports":"methods, stats,
utils, Matrix, magrittr, qlcMatrix, lazyeval","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"scrubr","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat, knitr, rgbif, sp, rworldmap,
maps","Title":"Clean Biological Occurrence
Records","URL":"https:\/\/github.com\/ropenscilabs\/scrubr","Version":"0.1.1"},"scr
ypt":{"Author":"RStudio, Inc.; Colin Percival","Depends":"R (>=
2.15.1)","Description":"scrypt is an R package for working with scrypt. Scrypt is
a\npassword-based key derivation function created by Colin Percival. The\nalgorithm
was specifically designed to make it costly to perform\nlarge-scale custom hardware
attacks by requiring large amounts of memory.","Imports":"Rcpp (>=
0.10.6)","License":"FreeBSD | file
LICENSE","NeedsCompilation":"yes","Package":"scrypt","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"scrypt key derivation functions for
R","URL":"https:\/\/github.com\/rstudio\/rscrypt","Version":"0.1.0"},"scs":
{"Author":"Florian Schwendinger [ctb, cre],\nBrendan O'Donoghue [aut,
cph],\nTimothy A. Davis [cph],\nPatrick R. Amestory [cph],\nIain S. Duff
[cph]","Depends":"R (>= 2.15)","Description":"Solves convex cone programs via
operator splitting. Can solve:\nlinear programs (LPs), second-order cone programs
(SOCPs), semidefinite programs\n(SDPs), exponential cone programs (ECPs), and power
cone programs (PCPs), or\nproblems with any combination of those cones. SCS uses
AMD (a set of routines for permuting sparse matrices prior to factorization) and
LDL (a sparse LDL' factorization and solve package) from 'SuiteSparse'
(<http:\/\/www.suitesparse.com>).","Imports":"Matrix, methods","License":"GPL-
3","NeedsCompilation":"yes","Package":"scs","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Splitting Conic
Solver","URL":"https:\/\/github.com\/cvxgrp\/scs","Version":"1.1-1"},"scuba":
{"Author":"Adrian Baddeley [aut, cre],\nVittorio Broglio [ctb, dtc],\nPedro Antonio
Neves [ctb, dtc],\nAndrew Bassom [ctb],\nPeter Buzzacott [ctb]","Depends":"R (>=
3.0.0)","Description":"Code for describing and manipulating scuba diving
profiles\n(depth-time curves) and decompression models,\nfor calculating the
predictions of decompression models,\nfor calculating maximum no-decompression time
and decompression tables,\nand for performing mixed gas
calculations.","Imports":"utils, graphics, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"scuba","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Diving Calculations and Decompression
Models","Version":"1.8-0"},"sdPrior":{"Author":"Nadja Klein <nklein@uni-
goettingen.de>","Depends":"R (>= 3.1.0)","Description":"Utility functions for
scale-dependent and alternative hyperpriors.","Imports":"splines, caTools, GB2,
MASS, stats","License":"GPL-
2","NeedsCompilation":"no","Package":"sdPrior","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Scale-Dependent Hyperpriors in Structured
Additive\nDistributional Regression","Version":"0.3"},"sda":{"Author":"Miika
Ahdesmaki, Verena Zuber, Sebastian Gibb, and Korbinian Strimmer","Depends":"R (>=
3.0.2), entropy (>= 1.2.1), corpcor (>= 1.6.8), fdrtool\n(>=
1.2.15)","Description":"Provides an efficient framework for\nhigh-dimensional
linear and diagonal discriminant analysis with\nvariable selection. The classifier
is trained using James-Stein-type\nshrinkage estimators and predictor variables are
ranked using\ncorrelation-adjusted t-scores (CAT scores). Variable selection
error\nis controlled using false non-discovery rates or higher
criticism.","Imports":"graphics, stats, utils","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"sda","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"crossval (>= 1.0.3)","Title":"Shrinkage Discriminant
Analysis and CAT Score Variable
Selection","URL":"http:\/\/strimmerlab.org\/software\/sda\/","Version":"1.3.7"},"sd
cMicro":{"Author":"Matthias Templ, Alexander Kowarik, Bernhard Meindl","Depends":"R
(>= 2.10),rmarkdown,knitr,data.table,xtable","Description":"Data from statistical
agencies and other institutions are mostly\nconfidential. This package can be used
for the generation of anonymized\n(micro)data, i.e. for the creation of public- and
scientific-use files.\nIn addition, various risk estimation methods are
included.\nNote that the package 'sdcMicroGUI' includes a graphical user interface
for various methods\nin this package.","Imports":"utils, stats, graphics, car,
robustbase,
cluster, MASS, e1071,\ntools, Rcpp, methods, sets, ggplot2","License":"GPL-
2","NeedsCompilation":"yes","Package":"sdcMicro","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"laeken,testthat","Title":"Statistical Disclosure
Control Methods for Anonymization of\nMicrodata and Risk
Estimation","URL":"https:\/\/github.com\/alexkowa\/sdcMicro","Version":"4.6.0"},"sd
cMicroGUI":{"Author":"Alexander Kowarik, Matthias Templ, Bernhard Meindl, Francois
Fonteneau","Depends":"sdcMicro (>= 4.5.0), gWidgetsRGtk2,gWidgets,
tcltk,\ncairoDevice","Description":"A point and click graphical user interface
based on top of the\n'sdcMicro' package to create anonymized data set. The
graphical user\ninterface provides full reproducibility of any result via the
script menu\nin the GUI.","Imports":"vcd, foreign, Hmisc,tools","License":"GPL-
2","NeedsCompilation":"no","Package":"sdcMicroGUI","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Graphical User Interface for Package
'sdcMicro'","URL":"https:\/\/github.com\/alexkowa\/sdcMicroGUI","Version":"1.2.0"},
"sdcTable":{"Author":"Bernhard Meindl","Depends":"stringr, methods, Rcpp (>=
0.11.0), Rglpk, lpSolveAPI","Description":"Methods for statistical disclosure
control in\ntabular data such as primary and secondary cell suppression are covered
in\nthis package.","Imports":"data.table","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"sdcTable","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat (>= 0.3)","Title":"Methods for Statistical
Disclosure Control in Tabular
Data","URL":"http:\/\/www.statistik.at","Version":"0.20.3"},"sdcTarget":
{"Author":"Emmanuel Lazaridis [aut, cre]","Depends":"R (>= 2.10.0), methods, magic,
foreach, parallel, doParallel,\ntuple (>= 0.4-02)","Description":"Classes and
methods to calculate and evaluate target matrices for\nstatistical disclosure
control.","License":"CC BY-NC
4.0","NeedsCompilation":"no","Package":"sdcTarget","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Statistical Disclosure Control Substitution Matrix
Calculator","URL":"http:\/\/statistics.lazaridis.eu","Version":"0.9-11"},"sddpack":
{"Author":"Tamara G. Kolda, Dianne P. O'Leary","Description":"The semidiscrete
decomposition (SDD) approximates a matrix\nas a weighted sum of outer products
formed by vectors with\nentries constrained to be in the set {-1, 0,
1}.","License":"GPL-
2","NeedsCompilation":"no","Package":"sddpack","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Semidiscrete Decomposition","Version":"0.9"},"sde":
{"Author":"Stefano Maria Iacus","Depends":"MASS, stats4, fda,
zoo","Description":"Companion package to the book Simulation and Inference
for\nStochastic Differential Equations With R Examples, ISBN\n978-0-387-75838-1,
Springer, NY.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"sde","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Simulation and Inference for Stochastic Differential
Equations","Version":"2.0.14"},"sdef":{"Author":"Alberto Cassese, Marta
Blangiardo","Description":"Performs two tests to evaluate if the\nexperiments are
associated and returns a list of interesting\nfeatures common to all the
experiments.","Imports":"graphics,grDevices,stats,utils","License":"GPL-
2","NeedsCompilation":"no","Package":"sdef","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Synthesizing List of Differentially Expressed
Features","Version":"1.6"},"sdm":{"Author":"Babak Naimi, Miguel B.
Araujo","Depends":"methods, sp (>= 1.0-13)","Description":"An extensible R
framework for developing species distribution\nmodels using individual and
community-based approaches, generate ensembles of\nmodels, evaluate the models, and
predict species potential distributions in\nspace and time.","Imports":"dismo,
raster","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"sdm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"rgdal (>= 0.8-12), knitr","Title":"Species Distribution
Modelling","URL":"http:\/\/biogeoinformatics.org","Version":"1.0-
10"},"sdmvspecies":{"Author":"Xiaoquan Kong [aut, cre, cph],\nRenyan Duan
[ths],\nMinyi Huang [ths]","Description":"A software package help user to create
virtual species for species distribution modelling. It includes\nseveral methods to
help user to create virtual species distribution map.\nThose maps can be used for
Species Distribution Modelling (SDM) study. SDM use\nenvironmental data for sites
of occurrence of a species to predict all the sites\nwhere the environmental
conditions are suitable for the species to persist, and\nmay be expected to
occur.","Imports":"stats, raster, psych, parallel","License":"AGPL-
3","NeedsCompilation":"no","Package":"sdmvspecies","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"ggplot2, testthat, roxygen2","Title":"Create
Virtual Species for Species Distribution
Modelling","URL":"http:\/\/www.sdmserialsoftware.org\/sdmvspecies\/","Version":"0.3
.2"},"sdnet":{"Author":"Nikolay Balov","Depends":"R (>=
3.0.2)","Description":"Fitting discrete Bayesian networks using marginal mixture
distributions","Imports":"methods, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"sdnet","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Soft Discretization-based Bayesian Network
Inference","Version":"2.03.3"},"sdprisk":{"Author":"Benjamin Baumgartner [aut,
cre],\nRiccardo Gatto [ctb, ths],\nSebastian Szugat [ctb]","Description":"The main
purpose of this package is to provide saddlepoint\napproximations to some measures
of risk, based on the compound Poisson risk\nprocess that is perturbed by a
Brownian motion. Various approximation\nmethods for the probability of ruin are
also included. Furthermore, exact\nvalues of both the risk measures as well as the
probability of ruin are\navailable if the individual claims follow a hypo-
exponential distribution\n(i. e., if it can be represented as a sum of independent
exponentially\ndistributed random variables with different rate
parameters).","Imports":"numDeriv, PolynomF, rootSolve","License":"AGPL-
3","NeedsCompilation":"yes","Package":"sdprisk","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Measures of Risk for the Compound Poisson Risk Process
with\nDiffusion","Version":"1.1-3"},"sdtoolkit":{"Author":"Benjamin P.
Bryant","Description":"Implements algorithms to help with scenario discovery -
currently only modified version of the the Patient Rule Induction
Method.","License":"GPL-
3","NeedsCompilation":"no","Package":"sdtoolkit","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Scenario Discovery Tools to Support Robust Decision
Making","Version":"2.33-1"},"sdwd":{"Author":"Boxiang Wang and Hui
Zou","Depends":"Matrix","Description":"Formulates a sparse distance weighted
discrimination (SDWD) for high-dimensional classification and implements a very
fast algorithm for computing its solution path with the L1, the elastic-net, and
the adaptive elastic-net penalties.","Imports":"grDevices, graphics, stats,
2","NeedsCompilation":"yes","Package":"sdwd","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Sparse Distance Weighted
Discrimination","Version":"1.0.2"},"seacarb":{"Author":"Jean-Pierre Gattuso [aut,
cre, cph],\nJean-Marie Epitalon [aut],\nHeloise Lavigne [aut],\nJames Orr
[ctb],\nBernard Gentili [ctb],\nAndreas Hofmann [ctb],\nAurÃ©lien Proye
[ctb],\nKarline Soetaert [ctb],\nJames Rae [ctb]","Depends":"R (>= 2.10),
oce","Description":"Calculates parameters of the seawater carbonate system and
assists\nthe design of ocean acidification perturbation
experiments.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"seacarb","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Seawater Carbonate Chemistry","URL":"http:\/\/CRAN.R-
project.org\/package=seacarb","Version":"3.0.14"},"sealasso":{"Author":"Wei Qian
<weiqian@stat.umn.edu>","Depends":"R (>= 2.9.1), lars","Description":"Standard
error adjusted adaptive lasso (SEA-lasso) is a version of the adaptive lasso, which
incorporates OLS standard error to the L1 penalty weight. This method is intended
for variable selection under linear regression settings (n > p). This new weight
assignment strategy is especially useful when the collinearity of the design matrix
is a concern.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"sealasso","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Standard Error Adjusted Adaptive Lasso","Version":"0.1-
2"},"searchConsoleR":{"Author":"Mark Edmondson [aut, cre],\nJennifer Bryan
[ctb]","Depends":"R (>= 3.2.0)","Description":"Provides an interface with the
Google Search Console,\nformally called Google Webmaster
Tools.","Imports":"googleAuthR (>= 0.2.0), stringr (>= 1.0.0)","License":"MIT +
file
LICENSE","NeedsCompilation":"no","Package":"searchConsoleR","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Suggests":"shiny (>= 0.12.1), knitr,
rmarkdown","Title":"Google Search Console R
Client","URL":"https:\/\/github.com\/MarkEdmondson1234\/searchConsoleR","Version":"
0.2.0"},"searchable":{"Author":"\"DecisionPatterns [aut, cre]\"","Depends":"R (>=
3.1.0)","Description":"Provides functionality for searching \/ subsetting and
slicing named\nobjects using 'stringr\/i'-style modifiers by case
(in)sensitivity,\nregular expressions or fixed expressions; searches uses the
standard '['\noperator and allows specification of default search behavior to
either the\nsearch target (named object) and\/or the search
pattern.","Imports":"methods, magrittr(>= 1.5), stringi(>= 0.4.1)","License":"GPL-
2","NeedsCompilation":"no","Package":"searchable","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat","Title":"Tools for Custom Searches \/
Subsets \/ Slices of Named R
Objects","URL":"https:\/\/github.com\/decisionpatterns\/searchable","Version":"0.3.
3.1"},"seas":{"Author":"Mike
Toews","Depends":"R(>= 2.10.0)","Description":"Capable of deriving seasonal
statistics, such as \"normals\", and\nanalysis of seasonal data, such as
departures. This package also has\ngraphics capabilities for representing seasonal
data, including boxplots for\nseasonal parameters, and bars for summed normals.
There are many specific\nfunctions related to climatology, including precipitation
normals,\ntemperature normals, cumulative precipitation departures and
precipitation\ninterarrivals. However, this package is designed to represent
any\ntime-varying parameter with a discernible seasonal signal, such as found\nin
hydrology and ecology.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"seas","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"MASS","Title":"Seasonal analysis and graphics,
especially for
climatology","URL":"http:\/\/github.com\/mwtoews\/seas","Version":"0.4-
3"},"season":{"Author":"Adrian Barnett and Peter Baker","Depends":"R (>= 3.0.1),
ggplot2 (>= 0.9.3), MASS, mgcv, survival, coda","Description":"Routines for the
seasonal analysis of health data,\nincluding regression models, time-stratified
case-crossover,\nplotting functions and residual checks. Thanks to Yuming Guo\nfor
checking the case-crossover code.","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"season","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Seasonal analysis of health data","Version":"0.3-
5"},"seasonal":{"Author":"Christoph Sax","Depends":"R (>=
2.15)","Description":"Easy-to-use interface to X-13-ARIMA-SEATS, the\nseasonal
adjustment software by the US Census Bureau. It offers full\naccess to almost all
options and outputs of X-13, including X-11 and SEATS,\nautomatic ARIMA model
search, outlier detection and support for user\ndefined holiday variables, such as
Chinese New Year or Indian Diwali. It\nalso includes a Shiny-based graphical user
interface. Seasonal uses the\nX-13 binaries from the 'x13binary'
package.","Imports":"x13binary","License":"GPL-
3","NeedsCompilation":"no","Package":"seasonal","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"shiny (>= 0.11.1),","Title":"R Interface to X-13-
ARIMA-SEATS","URL":"http:\/\/www.seasonal.website","Version":"1.2.1"},"seawaveQ":
{"Author":"Karen R. Ryberg and Aldo V. Vecchia","Depends":"R (>= 2.15.3), survival,
NADA, lubridate","Description":"A model and utilities for analyzing trends in
chemical concentrations in streams with a seasonal wave (seawave) and adjustment
for streamflow (Q) and other ancillary
variables","License":"Unlimited","NeedsCompilation":"no","Package":"seawaveQ","Repo
sitory":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"waterData","Title":"U.S.
Geological Survey seawaveQ
model","URL":"http:\/\/dx.doi.org\/10.3133\/ofr20131255","Version":"1.0.0"},"secr":
{"Author":"Murray Efford","Depends":"R (>= 3.2.0),
methods","Description":"Functions to estimate the density and size of a spatially
distributed animal population sampled with an array of passive detectors, such as
traps, or by searching polygons or transects. Models incorporating distance-
dependent detection are fitted by maximizing the likelihood. Tools are included for
data manipulation and model selection.","Imports":"abind, graphics, grDevices,
MASS, utils, parallel, nlme, sp,\nmgcv, raster, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"secr","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"maptools, spsurvey, rgdal, knitr, gdistance,
rgeos","Title":"Spatially Explicit Capture-
Recapture","URL":"http:\/\/www.otago.ac.nz\/density","Version":"2.10.2"},"secrdesig
n":{"Author":"Murray Efford","Depends":"R (>= 3.0.0), secr(>=
2.9.4)","Description":"Tools are provided for designing spatially explicit capture-
recapture studies of animal populations. This is primarily a simulation manager for
package 'secr'.","Imports":"parallel, abind","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"secrdesign","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr","Title":"Sampling Design for Spatially
Explicit Capture-
Recapture","URL":"http:\/\/www.otago.ac.nz\/density","Version":"2.3.0"},"secrlinear
":{"Author":"Murray Efford","Depends":"R (>= 3.0.0), secr(>= 2.9.1), sp,
igraph","Description":"Tools for spatially explicit capture-recapture analysis of
animal populations in linear habitats, extending package
'secr'","Imports":"parallel, maptools, MASS","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"secrlinear","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr, rgeos, secrdesign","Title":"Spatially
Explicit Capture-Recapture for Linear
Habitats","URL":"http:\/\/www.otago.ac.nz\/density","Version":"1.0.5"},"seeclickfix
r":{"Author":"Justin de Benedictis-Kessner [aut, cre],\nChristian Lemp
[ctb]","Depends":"R (>= 3.1.2)","Description":"Provides a wrapper to access data
from the SeeClickFix\nweb API for R. SeeClickFix is a central platform employed by
many cities\nthat allows citizens to request their city's services. This
package\ncreates several functions to work with all the built-in calls to
the\nSeeClickFix API. Allows users to download service request data from\nnumerous
locations in easy-to-use dataframe format manipulable in\nstandard R
functions.","Imports":"jsonlite, RCurl","License":"GPL-
3","NeedsCompilation":"no","Package":"seeclickfixr","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Access Data from the SeeClickFix Web
API","Version":"1.0.0"},"seedy":{"Author":"Colin Worby","Description":"Suite of
functions for the simulation, visualisation and analysis of bacterial evolution
within- and between-host.","License":"GPL-
3","NeedsCompilation":"no","Package":"seedy","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Simulation of Evolutionary and Epidemiological
Dynamics","Version":"1.3"},"seeg":{"Author":"Miguel F.
Acevedo","Depends":"car,spatstat,sgeostat","Description":"Supports the text
book \"Data Analysis and Statistics for\nGeography, Environmental Science, and
Engineering\"","License":"GPL-
2","NeedsCompilation":"no","Package":"seeg","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Statistics for Environmental Sciences, Engineering,
and\nGeography","Version":"1.0"},"seem":{"Author":"Miguel F.
Acevedo","Description":"Supports Simulation of Ecological and Environmental
Models","License":"GPL-
2","NeedsCompilation":"yes","Package":"seem","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Simulation of Ecological and Environmental
Models","Version":"1.0"},"seewave":{"Author":"Jerome Sueur <sueur@mnhn.fr> [cre,
au], Thierry Aubin [au],\nCaroline Simonis [au], Laurent Lellouch [main
ctrb]\nEthan C. Brown [ctrb], Marion Depraetere [ctrb],\nCamille Desjonqueres
[ctrb], Francois Fabianek [ctrb]\nAmandine Gasc [ctrb], Stefanie LaZerte [ctrb],
Jonathan Lees [ctrb],\nJean Marchal [ctrb], Sandrine Pavoine [ctrb], Alicia Stotz
[ctrb],\nLuis J. Villanueva-Rivera [ctrb], Zev Ross [ctrb],\nCarl G. Witthoft
[ctrb], Hristo Zhivomirov [ctrb].","Description":"Functions for analysing,
manipulating, displaying, editing and synthesizing time waves (particularly sound).
This package processes time analysis (oscillograms and envelopes), spectral
content, resonance quality factor, entropy, cross correlation and autocorrelation,
zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D and 3D
spectrograms and many other analyses.","Imports":"graphics, grDevices, stats,
utils, tuneR","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"seewave","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"audio, fftw, ggplot2, rgl, rpanel","Title":"Sound
Analysis and
Synthesis","URL":"http:\/\/rug.mnhn.fr\/seewave","Version":"2.0.2"},"seg":
{"Author":"Seong-Yun Hong [aut, cre],\nDavid O'Sullivan [ctb]","Depends":"R (>=
3.0.0), methods, stats, sp","Description":"A package that provides functions for
measuring spatial\nsegregation. The methods implemented in this package
include\nWhite's P index (1983), Morrill's D(adj) (1991), Wong's D(w)\nand D(s)
(1993), and Reardon and O'Sullivan's set of spatial\nsegregation measures
(2004).","Imports":"splancs","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"seg","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"spdep, spgrass6, rgdal","Title":"A set of tools for
measuring spatial
segregation","URL":"https:\/\/sites.google.com\/site\/hongseongyun\/seg","Version":
"0.5-1"},"segmag":{"Author":"Frank Papenmeier [aut, cre],\nKonstantin Sering
[ctb]","Description":"This package contains functions that help to determine
event\nboundaries in event segmentation experiments by bootstrapping a
critical\nsegmentation magnitude under the null hypothesis that all key presses
were\nrandomly distributed across the experiment. Segmentation magnitude
is\ndefined as the sum of Gaussians centered at the times of the segmentation\nkey
presses performed by the participants. Within a participant, the maximum\nof the
overlaid Gaussians is used to prevent an excessive influence of a\nsingle
participant on the overall outcome (e.g. if a participant is pressing\nthe key
multiple times in succession). Further functions are included, such\nas plotting
the results.","Imports":"Rcpp (>= 0.11.0)","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"segmag","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"testthat","Title":"Determine Event Boundaries in Event
Segmentation Experiments","Version":"1.2.2"},"segmented":{"Author":"Vito M. R.
Muggeo [aut, cre]","Description":"Given a regression model, segmented ùpdates' the
model by adding one or more segmented (i.e., piecewise-linear) relationships.
Several variables with multiple breakpoints are
allowed.","License":"GPL","NeedsCompilation":"no","Package":"segmented","Repository
":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Regression
Models with Breakpoints\/Changepoints Estimation","Version":"0.5-1.4"},"seismic":
{"Author":"Hera He, Murat Erdogdu, Qingyuan Zhao","Description":"An implementation
of self-exciting point process model for information cascades, which occurs when
many people engage in the same acts after observing the actions of others (e.g.
post resharings on Facebook or Twitter). It provides functions to estimate the
infectiousness of an information cascade and predict its popularity given the
observed history. See http:\/\/snap.stanford.edu\/seismic\/ for more information
and datasets.","License":"GPL-
3","NeedsCompilation":"no","Package":"seismic","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Predict Information Cascade by Self-Exciting Point
Process","URL":"http:\/\/snap.stanford.edu\/seismic\/","Version":"1.0"},"seismicRol
l":{"Author":"Jonathan Callahan [aut, cre],\nRob Casey [aut],\nMary Templeton
[aut]","Depends":"R (>= 2.14.1), Rcpp (>= 0.10.4)","Description":"Fast versions of
seismic analysis functions that 'roll' over a\nvector of values. See the RcppRoll
package for alternative\nversions of basic statistical functions such as rolling
mean,\nmedian, etc.","License":"GPL-
2","NeedsCompilation":"yes","Package":"seismicRoll","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"microbenchmark","Title":"Fast Rolling Functions
for Seismology using Rcpp","Version":"1.0.1"},"sejmRP":{"Author":"Piotr Smuda [aut,
cre],\nPrzemyslaw Biecek [aut],\nTomasz Mikolajczyk [ctb]","Depends":"R (>=
3.1.0)","Description":"Set of functions that access information about deputies and
votings\nin Polish diet from webpage <http:\/\/www.sejm.gov.pl\/>. The package was
developed\nas a result of an internship in MI2 Group -
<http:\/\/mi2.mini.pw.edu.pl\/>,\nFaculty of Mathematics and Information Science,
Warsaw University of Technology.","Imports":"DBI, dplyr, RPostgreSQL, rvest,
stringi, XML, xml2","License":"GPL-
2","NeedsCompilation":"no","Package":"sejmRP","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"An Information About Deputies and Votings in Polish Diet
from\nSeventh to Eighth Term of Office","Version":"1.3"},"selectMeta":
{"Author":"Kaspar Rufibach <kaspar.rufibach@gmail.com>","Depends":"DEoptim (>= 2.0-
6)","Description":"Publication bias, the fact that studies identified for inclusion
in a meta analysis do not represent all studies on the topic of interest, is
commonly recognized as a threat to the validity of the results of a meta analysis.
One way to explicitly model publication bias is via selection models or weighted
probability distributions. In this package we provide implementations of several
parametric and nonparametric weight functions. The novelty in Rufibach (2011) is
the proposal of a non-increasing variant of the nonparametric weight function of
Dear & Begg (1992). The new approach potentially offers more insight in the
selection process than other methods, but is more flexible than parametric
approaches. To maximize the log-likelihood function proposed by Dear & Begg (1992)
under a monotonicity constraint we use a differential evolution algorithm proposed
by Ardia et al (2010a, b) and implemented in Mullen et al (2009). In addition, we
offer a method to compute a confidence interval for the overall effect size theta,
adjusted for selection bias as well as a function that computes the simulation-
based p-value to assess the null hypothesis of no selection as described in
Rufibach (2011, Section 6).","Imports":"graphics, stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"selectMeta","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Estimation of Weight Functions in Meta
Analysis","URL":"http:\/\/www.kasparrufibach.ch","Version":"1.0.8"},"selection":
{"Author":"Dustin Fife","Depends":"norm, fifer","Description":"A collection of
functions for correcting biased estimates under\nselection (range
restriction).","License":"GPL-
2","NeedsCompilation":"no","Package":"selection","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Correcting Biased Estimates Under
Selection","Version":"1.0"},"selectiongain":{"Author":"Xuefei Mi, Jose Marulanda,
H. Friedrich Utz, Albrecht E. Melchinger (Project contact person: Melchinger@uni-
hohenheim.de )","Depends":"R (>= 3.0.0), mvtnorm,parallel","Description":"Multi-
stage selection is practiced in numerous fields of life and social sciences and
particularly in breeding. A special characteristic of multi-stage selection is that
candidates are evaluated in successive stages with increasing intensity and effort,
and only a fraction of the superior candidates is selected and promoted to the next
stage. For the optimum design of such selection programs, the selection gain plays
a crucial role. It can be calculated by integration of a truncated multivariate
normal (MVN) distribution. While mathematical formulas for calculating the
selection gain and the variance among selected candidates were developed long time
ago, solutions for numerical calculation were not available. This package can also
be used for optimizing multi-stage selection programs for a given total budget and
different costs of evaluating the candidates in each stage.","License":"GPL-
2","NeedsCompilation":"no","Package":"selectiongain","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"A Tool for Calculation and Optimization of the
Expected Gain\nfrom Multi-Stage
Selection","Version":"2.0.50.1"},"selectiveInference":{"Author":"Ryan Tibshirani,
Rob Tibshirani, Jonathan Taylor,\nJoshua Loftus, Stephen Reid","Depends":"glmnet,
intervals","Description":"New tools for post-selection inference, for use\nwith
forward stepwise regression, least angle regression, the\nlasso, and the many means
problem.","License":"GPL-
2","NeedsCompilation":"yes","Package":"selectiveInference","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Suggests":"Rmpfr","Title":"Tools for Post-Selection
Inference","Version":"1.1.3"},"selectr":{"Author":"Simon Potter [aut, trl,
cre],\nSimon Sapin [aut],\nIan Bicking [aut]","Depends":"R (>=
2.15.2)","Description":"Translates a CSS3 selector into an equivalent
XPath\nexpression. This allows us to use CSS selectors when working with\nthe XML
package as it can only evaluate XPath expressions. Also\nprovided are convenience
functions useful for using CSS selectors on\nXML nodes. This package is a port of
the Python
package \"cssselect\"\n(http:\/\/packages.python.org\/cssselect\/).","Imports":"met
hods, XML, stringr","License":"BSD_3_clause + file
LICENCE","NeedsCompilation":"no","Package":"selectr","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat","Title":"Translate CSS Selectors to
XPath Expressions","URL":"https:\/\/sjp.co.nz\/projects\/selectr","Version":"0.2-
3"},"selectspm":{"Author":"Marcelino de la Cruz","Depends":"spatstat,
ecespa","Description":"Fit and selects point pattern models based on minimum
contrast, AIC and and goodness of fit.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"selectspm","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Select Point Pattern Models Based on Minimum Contrast,
AIC and\nGoodness of Fit","Version":"0.2"},"selfea":{"Author":"Lang Ho Lee, Arnold
Saxton, Nathan Verberkmoes","Depends":"R (>= 3.1.0), pwr, MASS, plyr,
ggplot2","Description":"Functions using Cohen's effect sizes (Cohen, Jacob.
Statistical power analysis for the behavioral sciences. Academic press, 2013) are
provided for reliable feature selection in biology data analysis. In addition to
Cohen's effect sizes, p-values are calculated and adjusted from quasi-Poisson GLM,
negative binomial GLM and Normal distribution ANOVA. Significant features (genes,
RNAs or proteins) are selected by adjusted p-value and minimum Cohen's effect
sizes, calculated to keep certain level of statistical power of biology data
analysis given p-value threshold and sample size.","License":"GPL-
2","NeedsCompilation":"no","Package":"selfea","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Select Features Reliably with Cohen's Effect
Sizes","Version":"1.0.1"},"selfingTree":{"Author":"Frank Technow [aut, cre]
(Pioneer Hi-Bred International, Inc., Johnston, Iowa)","Depends":"R (>=
2.15.1),foreach","Description":"A probability tree allows to compute probabilities
of\ncomplex events, such as genotype probabilities in intermediate generations of
inbreeding\nthrough recurrent self-fertilization (selfing). This package implements
functionality to compute\nprobability trees for two- and three-marker genotypes in
the F2 to F7 selfing\ngenerations. The conditional probabilities are derived
automatically\nand in symbolic form. The package also provides functionality
to\nextract and evaluate the relevant probabilities.","License":"BSD_3_clause +
file
LICENSE","NeedsCompilation":"no","Package":"selfingTree","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Genotype Probabilities in Intermediate
Generations of Inbreeding\nThrough Selfing","Version":"0.2"},"sem":{"Author":"John
Fox [aut, cre],\nZhenghua Nie [aut],\nJarrett Byrnes [aut],\nMichael Culbertson
[ctb],\nSaikat DebRoy [ctb],\nMichael Friendly [ctb],\nGoodrich Benjamin
[ctb],\nRichard H. Jones [ctb],\nAdam Kramer [ctb],\nGeorges Monette [ctb],\nR-Core
[ctb]","Depends":"R (>= 2.14.0), stats","Description":"Functions for fitting
general linear structural\nequation models (with observed and latent variables)
using the RAM approach,\nand for fitting structural equations in observed-variable
models by two-stage least squares.","Imports":"matrixcalc, MASS, boot, mi (>= 0.9-
99), utils","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"sem","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"polycor, MBESS, DiagrammeR","Title":"Structural Equation
Models","URL":"http:\/\/www.r-project.org,
http:\/\/socserv.socsci.mcmaster.ca\/jfox\/","Version":"3.1-7"},"semGOF":
{"Author":"Elena
Bertossi <bertossielena@gmail.com>","Depends":"R (>= 2.14.0), sem, stats, MASS,
matrixcalc","Description":"This is an add-on package which provides
fourteen\ngoodness-of-fit indexes for structural equation models using\n'sem'
2)","NeedsCompilation":"no","Package":"semGOF","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"boot, tcltk, polycor","Title":"Goodness-of-fit indexes
for structural equation models","URL":"http:\/\/www.r-
project.org,\nhttp:\/\/sites.google.com\/site\/bertossielena","Version":"0.2-
0"},"semPLS":{"Author":"Armin Monecke <armin.monecke@stat.uni-
muenchen.de>","Depends":"lattice (>= 0.20-5)","Description":"Fits structural
equation models using partial least\nsquares (PLS). The PLS approach is referred to
as\n'soft-modeling' technique requiring no distributional\nassumptions on the
observed data.","License":"GPL-
2","NeedsCompilation":"no","Package":"semPLS","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"XML, boot, sem, matrixcalc","Title":"Structural Equation
Modeling Using Partial Least Squares","Version":"1.0-10"},"semPlot":
{"Author":"Sacha Epskamp","Depends":"R (>= 2.15.0)","Description":"Path diagrams
and visual analysis of various SEM packages' output","Imports":"qgraph (>= 1.2.4),
lavaan (>= 0.5-11), sem (>= 3.1-0), plyr,\nXML, igraph (>= 0.6-3), lisrelToR,
rockchalk, colorspace,\ncorpcor, methods","License":"GPL-
2","NeedsCompilation":"no","Package":"semPlot","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"MplusAutomation (>= 0.5-3)","Title":"Path diagrams and
visual analysis of various SEM
packages'\noutput","URL":"https:\/\/github.com\/SachaEpskamp\/semPlot","Version":"1
.0.1"},"semTools":{"Author":"Sunthud Pornprasertmanit [aut, cre],\nPatrick Miller
[aut],\nAlexander Schoemann [aut],\nYves Rosseel [aut],\nCorbin Quick
[ctb],\nMauricio Garnier-Villarreal [ctb],\nJames Selig [ctb],\nAaron Boulton
[ctb],\nKristopher Preacher [ctb],\nDonna Coffman [ctb],\nMijke Rhemtulla
[ctb],\nAlexander Robitzsch [ctb],\nCraig Enders [ctb],\nRuber Arslan [ctb],\nBell
Clinton [ctb],\nPavel Panko [ctb],\nEdgar Merkle [ctb],\nTerry Jorgensen
[ctb],\nSteven Chesnut [ctb],\nJarrett Byrnes [ctb],\nJason Rights
[ctb]","Depends":"R(>= 3.0), methods, lavaan(>= 0.5-20), utils, stats,
graphics","Description":"Provides useful tools for structural equation modeling
packages.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"semTools","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"MASS, parallel, Amelia, mice, foreign, OpenMx(>=
2.0.0),\nGPArotation, mnormt, boot","Title":"Useful Tools for Structural Equation
Modeling","URL":"https:\/\/github.com\/simsem\/semTools\/wiki","Version":"0.4-
11"},"semdiag":{"Author":"Zhiyong Zhang and Ke-Hai Yuan","Depends":"R (>= 2.10),
sem","Description":"Outlier and leverage diagnostics for SEM.","License":"GPL-
2","NeedsCompilation":"no","Package":"semdiag","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Structural equation modeling
diagnostics","Version":"0.1.2"},"semiArtificial":{"Author":"Marko Robnik-
Sikonja","Description":"Package semiArtificial contains methods to generate and
evaluate semi-artificial data sets.\nBased on a given data set different methods
learn data properties using machine learning algorithms and\ngenerate new data with
the same properties.\nThe package currently includes the following data
generator:\n-a RBF network based generator using rbfDDA from RSNNS package,\n-a
Random Forest based generator for both classification and regression problems\n-a
density forest based generator for unsupervised data\nData evaluation support tools
include:\n-single attribute based statistical evaluation: mean, median, standard
deviation, skewness, kurtosis, medcouple, L\/RMC, KS test, Hellinger distance\n-
evaluation based on clustering using Adjusted Rand Index (ARI) and FM\n-evaluation
based on classification performance with various learning models, eg, random
forests.","Imports":"\nCORElearn,RSNNS,MASS,nnet,cluster,mclust,fpc,stats,timeDate,
robustbase,dendextend,ks,logspline,methods","License":"GPL-
3","NeedsCompilation":"no","Package":"semiArtificial","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Generator of Semi-Artificial
Data","URL":"http:\/\/lkm.fri.uni-
lj.si\/rmarko\/software\/","Version":"2.0.1"},"semisupKernelPCA":
{"Author":"Pierrick Bruneau","Depends":"R (>= 2.10.0), datautils,
irlba","Description":"Functions to compute Gaussian and p-Gaussian
kernels,\ninclude supervision in these kernels, and perform kernel
PCA\nprojections.","License":"LGPL-
3","NeedsCompilation":"no","Package":"semisupKernelPCA","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Kernel PCA projection, and semi-supervised
variant","Version":"0.1.5"},"semsfa":{"Author":"Giancarlo Ferrara and Francesco
Vidoli","Depends":"R (>= 3.1.2), mgcv, np,","Description":"Semiparametric
Estimation of Stochastic Frontier Models following a two step procedure: in the
first step semiparametric or nonparametric regression techniques are used to relax
parametric restrictions of the functional form representing technology and in the
second step variance parameters are obtained by pseudolikelihood estimators or by
method of moments.","Imports":"moments, doParallel, foreach,
iterators","License":"GPL","NeedsCompilation":"no","Package":"semsfa","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Title":"Semiparametric Estimation of
Stochastic Frontier Models","Version":"1.0"},"sendmailR":{"Author":"Olaf Mersmann
[aut, cre],\nQuinn Weber [ctb]","Depends":"R (>= 3.0.0)","Description":"Package
contains a simple SMTP client which provides a\nportable solution for sending
email, including attachment, from\nwithin R.","Imports":"base64enc","License":"GPL-
2","NeedsCompilation":"no","Package":"sendmailR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"send email using R","Version":"1.2-1"},"sendplot":
{"Author":"Daniel P Gaile <dpgaile@buffalo.edu>, Lori A.
Shepherd\n<las65@buffalo.edu>, Lara Sucheston <lsuchest@buffalo.edu>,\nAndrew Bruno
<aebruno2@ccr.buffalo.edu>, Kenneth F. Manly\n<manly@buffalo.edu>","Depends":"R (>=
2.10), rtiff","Description":"A tool for visualizing data","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"sendplot","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"stats","Title":"Tool for sending interactive plots
with tool-tip
content","URL":"\nhttp:\/\/sphhp.buffalo.edu\/biostat\/research\/software\/sendplot
\/index.php","Version":"4.0.0"},"sensR":{"Author":"Rune Haubo Bojesen Christensen
[aut],\nPer Bruun Brockhoff [aut, cre]","Description":"Provides methods for sensory
discrimination methods;\nduotrio, tetrad, triangle, 2-AFC, 3-AFC, A-not A, same-
different,\n2-AC and degree-of-difference.\nThis enables the calculation of d-
primes, standard errors of\nd-primes, sample size and power computations,
and\ncomparisons of different d-primes. Methods for profile likelihood\nconfidence
intervals and plotting are included.","Imports":"multcomp, MASS,
numDeriv","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"sensR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"ordinal, parallel, testthat (>=
0.8)","Title":"Thurstonian Models for Sensory Discrimination","Version":"1.4-
7"},"sensitivity":{"Author":"Gilles Pujol, Bertrand Iooss, Alexandre Janon with
contributions from Sebastien Da Veiga, Jana Fruth, Laurent Gilquin, Joseph
Guillaume, Loic Le Gratiet, Paul Lemaitre, Bernardo Ramos, Taieb
Touati","Depends":"R (>= 3.0.0)","Description":"A collection of functions for
factor screening, global sensitivity analysis and reliability sensitivity analysis
of model output.","Imports":"boot","License":"GPL-
2","NeedsCompilation":"yes","Package":"sensitivity","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"DiceDesign, randtoolbox, DiceKriging, fanovaGraph,
rgl, evd,\nnumbers, ks, igraph, ggplot2, reshape2","Title":"Sensitivity
Analysis","Version":"1.11.1"},"sensitivity2x2xk":{"Author":"Paul R. Rosenbaum and
Dylan S. Small","Description":"Performs exact or approximate adaptive or
nonadaptive Cochran-Mantel-Haenszel-Birch tests and sensitivity analyses for one or
two 2x2xk tables in observational studies.","Imports":"stats, BiasedUrn,
2","NeedsCompilation":"no","Package":"sensitivity2x2xk","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Sensitivity Analysis for 2x2xk Tables in
Observational Studies","Version":"1.01"},"sensitivityPStrat":{"Author":"Charles
Dupont, Bryan Shepherd","Description":"This package provides functions to perform
principal stratification sensitivity analyses on datasets.","Imports":"stats,
survival","License":"GPL","NeedsCompilation":"yes","Package":"sensitivityPStrat","R
epository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Principal Stratification
Sensitivity Analysis Functions","Version":"1.0-6"},"sensitivitymv":{"Author":"Paul
R. Rosenbaum","Description":"Sensitivity analysis in observational studies,
including evidence factors and amplification, using the permutation distribution of
Huber-Maritz M-statistics, including the permutational t-test.","License":"GPL-
2","NeedsCompilation":"no","Package":"sensitivitymv","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Sensitivity Analysis in Observational
Studies","Version":"1.3"},"sensitivitymw":{"Author":"Paul R.
Rosenbaum","Description":"Sensitivity analysis analysis in matched observational
studies with multiple controls using weighted M-statistics to increase design
sensitivity.","License":"GPL-
2","NeedsCompilation":"no","Package":"sensitivitymw","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Sensitivity analysis using weighted M-
statistics","Version":"1.1"},"sensory":{"Author":"Brian C. Franczak, Ryan P. Browne
and Paul D. McNicholas","Depends":"Matrix, gtools, MASS, R (>=
3.2.2)","Description":"Contains
the function CUUimpute() which performs model-based clustering and imputation
simultaneously.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"sensory","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Simultaneous Model-Based Clustering and Imputation via
a\nProgressive Expectation-Maximization
Algorithm","Version":"1.1"},"separationplot":{"Author":"Brian D. Greenhill, Michael
D. Ward and Audrey Sacks","Description":"Functions to generate separation plots for
evaluation of\nmodel fit.","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"separationplot","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"MASS, Hmisc, RColorBrewer,
foreign","Title":"Separation Plots","Version":"1.1"},"seqCBS":{"Author":"Jeremy J.
Shen, Nancy R. Zhang","Depends":"R (>= 2.10), clue","Description":"This is a method
for DNA Copy Number Profiling using\nNext-Generation Sequencing. It has new model
and test\nstatistics based on non-homogeneous Poisson Processes with\nchange point
models. It uses an adaptation of Circular Binary\nSegmentation. Also included are
methods for point-wise Bayesian\nConfidence Interval and model selection method for
the\nchange-point model. A case and a control sample reads (normal\nand tumor) are
required.","License":"GPL-
2","NeedsCompilation":"yes","Package":"seqCBS","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"CN Profiling using Sequencing and
CBS","Version":"1.2"},"seqDesign":{"Author":"Michal Juraska and Doug Grove, with
contributions from Xuesong Yu and Peter B. Gilbert","Depends":"R (>= 2.16),
survival, xtable","Description":"A modification of the preventive vaccine efficacy
trial design of Gilbert, Grove et al. (2011, Statistical Communications in
Infectious Diseases) is implemented, with application generally to individual-
randomized clinical trials with multiple active treatment groups and a shared
control group, and a study endpoint that is a time-to-event endpoint subject to
right-censoring. The design accounts for the issues that the efficacy of the
treatment\/vaccine groups may take time to accrue while the multiple treatment
administrations\/vaccinations are given; there is interest in assessing the
durability of treatment efficacy over time; and group sequential monitoring of each
treatment group for potential harm, non-efficacy\/efficacy futility, and high
efficacy is warranted. The design divides the trial into two stages of time
periods, where each treatment is first evaluated for efficacy in the first stage of
follow-up, and, if and only if it shows significant treatment efficacy in stage
one, it is evaluated for longer-term durability of efficacy in stage two. The
package produces plots and tables describing operating characteristics of a
specified design including an unconditional power for intention-to-treat and per-
protocol\/as-treated analyses; trial duration; probabilities of the different
possible trial monitoring outcomes (e.g., stopping early for non-efficacy);
unconditional power for comparing treatment efficacies; and distributions of
numbers of endpoint events occurring after the treatments\/vaccinations are given,
useful as input parameters for the design of studies of the association of
biomarkers with a clinical outcome (surrogate endpoint problem). The code can be
used for a single active treatment versus control design and for a single-stage
design.","License":"GPL-
2","NeedsCompilation":"no","Package":"seqDesign","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Simulation and Group Sequential Monitoring of
Randomized\nTwo-Stage Treatment Efficacy Trials with Time-to-
Event\nEndpoints","Version":"1.1"},"seqHMM":{"Author":"Jouni Helske, Satu
Helske","Depends":"R (>= 3.2.0)","Description":"Designed for fitting hidden
(latent)\nMarkov models and mixture hidden Markov models for social\nsequence data
and other categorical time series. Also some more restricted\nversions of these
type of models are available: Markov models, mixture\nMarkov models, and latent
class models. The package supports models for one or\nmultiple subjects with one or
multiple parallel sequences (channels). External\ncovariates can be added to
explain cluster membership in mixture models. The\npackage provides functions for
evaluating and comparing models, as well as\nfunctions for easy plotting of
multichannel sequence data and hidden Markov\nmodels. Models are estimated using
maximum likelihood via the EM algorithm and\/or\ndirect numerical maximization with
analytical gradients.\nAll main algorithms are written in C++ with support for
parallel computation.","Imports":"gridBase, igraph, Matrix, nloptr, numDeriv, Rcpp
(>= 0.11.3),\nTraMineR (>= 1.8-8), graphics, grDevices, grid, methods,
2)","NeedsCompilation":"yes","Package":"seqHMM","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"MASS, nnet, knitr","Title":"Hidden Markov Models for
Life Sequences and Other Multivariate,\nMultichannel Categorical Time
Series","Version":"1.0.5"},"seqMeta":{"Author":"Arie Voorman, Jennifer Brody, Han
Chen, Thomas Lumley, Brian Davis","Depends":"R (>= 3.1.0), methods,
survival","Description":"Computes necessary information to meta analyze region-
based\ntests for rare genetic variants (e.g. SKAT, T1) in individual studies,
and\nperforms meta analysis.","Imports":"Matrix, coxme (>= 2.2-4),
CompQuadForm","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"seqMeta","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"SKAT, kinship2, testthat","Title":"Meta-Analysis of
Region-Based Tests of Rare DNA
Variants","URL":"https:\/\/github.com\/DavisBrian\/seqMeta","Version":"1.6.5"},"seq
PERM":{"Author":"Eric Golinko","Description":"User inputs a range of values r1 and
r2, as well as a\nnumber of columns v, in the function sq.pe(r1,r2,v).
The\nreturned statement is a permutation matrix.","License":"GPL-
3","NeedsCompilation":"no","Package":"seqPERM","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Generates a permutation matrix based upon a
sequence","Version":"1.0"},"seqRFLP":{"Author":"Qiong Ding, Jinlong
Zhang","Description":"This package includes functions for handling DNA\nsequences,
especially simulated RFLP and TRFLP pattern based on\nselected restriction enzyme
and DNA sequences.","License":"GPL-
2","NeedsCompilation":"no","Package":"seqRFLP","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Simulation and visualization of restriction enzyme
cutting\npattern from DNA sequences","Version":"1.0.1"},"seqinr":
{"Author":"Delphine Charif and Jean R. Lobry and Anamaria Necsulea and Leonor
Palmeira and Simon Penel and Guy Perriere","Depends":"ade4, R (>=
2.10.0)","Description":"Exploratory data analysis and data visualization\nfor
biological sequence (DNA and protein) data. Includes also\nutilities for sequence
data management under the ACNUC system.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"seqinr","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"segmented","Title":"Biological Sequences Retrieval and
Analysis","URL":"http:\/\/seqinr.r-forge.r-project.org\/, Mailing
list:\nhttp:\/\/r-forge.r-project.org\/mail\/?group_id=220","Version":"3.1-
3"},"seqminer":{"Author":"Xiaowei Zhan <zhanxw@gmail.com> and Dajiang
Liu\n<dajiang.liu@gmail.com>, with contributions from Heng Li\n<lh3@live.co.uk>
(Heng Li wrote tabix and with MIT license\nwe include tabix source
codes).","Description":"Integrate sequencing data (VCF\/BCF) or meta-analysis
results in R.","License":"GPL | file
LICENSE","NeedsCompilation":"yes","Package":"seqminer","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat, SKAT","Title":"Efficiently Read
Sequence Data (VCF Format, BCF Format and METAL\nFormat) into
R","URL":"http:\/\/seqminer.genomic.codes","Version":"5.0"},"seqmon":
{"Author":"David A. Schoenfeld <dschoenfeld@partners.org>","Description":"A program
that computes the probability of crossing\nsequential boundaries in a clinical
trial. It implements the\nArmitage-McPherson and Rowe Algorithm using the
method\ndescribed in Schoenfeld D. (2001)\" A simple Algorithm for\nDesigning Group
Sequential Clinical Trials\" Biometrics 27: pp,\n972-
974","License":"GPL","NeedsCompilation":"no","Package":"seqmon","Repository":"http:
\/\/cran.csiro.au\/src\/contrib","Title":"Sequential Monitoring of Clinical
Trials","Version":"0.2"},"seqtest":{"Author":"Takuya Yanagida [cre,
aut]","Depends":"R (>= 3.2.0)","Description":"Sequential triangular test for the
arithmetic mean in one- and two-\nsamples, proportions in one- and two-samples, and
the Pearson's correlation\ncoefficient.","License":"GPL-
3","NeedsCompilation":"no","Package":"seqtest","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Sequential Triangular Test","Version":"0.1-
0"},"sequences":{"Author":"Laurent Gatto [aut, cre],\nRobert Stojnic
[aut]","Depends":"methods, Rcpp","Description":"Educational package used in R
courses to illustrate\nobject-oriented programming and package\ndevelopment. Using
biological sequences (DNA and RNA) as\na working example.","License":"GPL-
3","NeedsCompilation":"yes","Package":"sequences","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat, knitr","Title":"Generic and Biological
Sequences","URL":"https:\/\/github.com\/lgatto\/sequences\/","Version":"0.5.9"},"se
quenza":{"Author":"Francesco Favero, Andrea M. Marquard, Tejal Joshi, Aron C.
Eklund","Depends":"R (>= 3.0.0), copynumber, parallel, squash","Description":"Tools
to analyze genomic sequencing data from\npaired normal-tumor samples, including
cellularity and ploidy estimation; mutation\nand copy number (allele-specific and
total copy number) detection, quantification\nand visualization.","License":"GPL-
3","NeedsCompilation":"no","Package":"sequenza","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Copy
Number Estimation from Tumor Genome Sequencing
Data","URL":"http:\/\/cbs.dtu.dk\/biotools\/sequenza\/, Mailing
list:\nhttps:\/\/groups.google.com\/forum\/#!forum\/sequenza-user-
group","Version":"2.1.2"},"serial":{"Author":"Martin Seilmayer","Depends":"R (>=
2.15.0)","Description":"Provides functionality for the use of the internal hardware
for\nRS232\/RS422\/RS485 and any other virtual serial interfaces of
the\ncomputer.","License":"GPL-
2","NeedsCompilation":"no","Package":"serial","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"The Serial Interface Package","Version":"1.2"},"seriation":
{"Author":"Michael Hahsler [aut, cre, cph],\nChristian Buchta [aut, cph],\nKurt
Hornik [aut, cph],\nFionn Murtagh [ctb, cph],\nMichael Brusco [ctb,
cph],\nStephanie Stahl [ctb, cph],\nHans-Friedrich Koehn [ctb, cph]","Depends":"R
(>= 2.14.0)","Description":"Infrastructure for seriation with an implementation of
several\nseriation\/sequencing techniques to reorder matrices,
dissimilarity\nmatrices, and dendrograms. Also provides (optimally) reordered
heatmaps,\ncolor images and clustering visualizations like dissimilarity plots,
and\nvisual assessment of cluster tendency plots (VAT and iVAT).","Imports":"TSP,
qap, grid, cluster, gclus, dendextend, colorspace, MASS,\ngplots, registry,
methods, stats, grDevices","License":"GPL-
3","NeedsCompilation":"yes","Package":"seriation","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"biclust, testthat, DendSer,
GA","Title":"Infrastructure for Ordering Objects Using
Seriation","URL":"http:\/\/lyle.smu.edu\/IDA\/seriation","Version":"1.2-
0"},"seroincidence":{"Author":"Peter Teunis [aut] (Author of the method and
original code),\nDaniel Lewandowski [com, ctb] (Creator of the R package),\nChantal
Quinten [ctb, cre] (Project manager and the package
maintainer)","Description":"Translates antibody levels measured in a (cross-
sectional)\npopulation sample into an estimate of the frequency with
which\nseroconversions (infections) occur in the sampled
population.","Imports":"stats, utils","License":"GPL-
3","NeedsCompilation":"no","Package":"seroincidence","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat, knitr","Title":"Estimating Infection
Rates from Serological Data","URL":"\nhttp:\/\/ecdc.europa.eu\/en\/data-
tools\/seroincidence-calculator-
tool\/Pages\/default.aspx","Version":"1.0.5"},"servr":{"Author":"Carson Sievert
[ctb],\nJesse Anderson [ctb],\nRamnath Vaidyanathan [ctb],\nYihui Xie [aut,
cre]","Depends":"R (>= 3.0.0)","Description":"Start an HTTP server in R to serve
static files, or dynamic\ndocuments that can be converted to HTML files (e.g., R
Markdown) under a\ngiven directory.","Imports":"mime (>= 0.2), httpuv (>= 1.3.2),
jsonlite","License":"GPL","NeedsCompilation":"no","Package":"servr","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Suggests":"tools, knitr (>= 1.9),
rmarkdown","Title":"A Simple HTTP Server to Serve Static Files or Dynamic
Documents","URL":"https:\/\/github.com\/yihui\/servr","Version":"0.3"},"sesem":
{"Author":"Eric Lamb [aut, cre],\nKerrie Mengersen [aut],\nKatherine Stewart
[aut],\nUdayanga Attanayake [aut],\nSteven Siciliano [aut]","Depends":"R (>=
1.8.0)","Description":"Structural equation modeling (SEM) is a powerful
statistical\napproach for the testing of networks of direct and indirect
theoretical\ncausal relationships in complex datasets with intercorrelated
dependent and\nindependent variables. Here we implement a simple method for
spatially\nexplicit SEM (SE-SEM) based on the analysis of variance covariance
matrices\ncalculated across a range of lag distances. This method provides
readily\ninterpretable plots of the change in path coefficients across
scale.","Imports":"lavaan, mgcv, gplots","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"sesem","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Spatially explicit structural equation
modeling","URL":"http:\/\/www.r-
project.org,\nhttp:\/\/homepage.usask.ca\/~egl388\/index.html","Version":"1.0.1"},"
session":{"Author":"Gregory R. Warnes.","Description":"Utility functions for
interacting with R processes from\nexternal programs. This package includes
functions to save and\nrestore session information (including loaded packages,
and\nattached data objects), as well as functions to evaluate\nstrings containing R
commands and return the printed results or\nan execution
transcript.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"session","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Functions for interacting with, saving and restoring R
sessions","Version":"1.0.3"},"setRNG":{"Author":"Paul Gilbert
<pgilbert.ttv9z@ncf.ca>","Depends":"R (>= 2.5.0)","Description":"SetRNG provides
utilities to help set and record the setting of\nthe seed and the uniform and
normal generators used when a random\nexperiment is run. The utilities can be used
in other functions\nthat do random experiments to simplify recording and\/or
setting all the\nnecessary information for reproducibility.\nSee the vignette and
reference manual for examples.","License":"GPL-2 | file
LICENSE","NeedsCompilation":"no","Package":"setRNG","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Set (Normal) Random Number Generator and
Seed","URL":"http:\/\/distr.r-forge.r-project.org\/","Version":"2013.9-1"},"sets":
{"Author":"David Meyer [aut, cre],\nKurt Hornik [aut],\nChristian Buchta
[ctb]","Depends":"R (>= 2.7.0)","Description":"Data structures and basic operations
for ordinary sets,\ngeneralizations such as fuzzy sets, multisets, and\nfuzzy
multisets, customizable sets, and
intervals.","Imports":"graphics,grDevices,stats,utils","License":"GPL-
2","NeedsCompilation":"yes","Package":"sets","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"proxy","Title":"Sets, Generalized Sets, Customizable Sets
and Intervals","Version":"1.0-16"},"setter":{"Author":"Richard Cotton [aut,
cre]","Depends":"R (>= 3.0.0), assertive.base (>= 0.0-5)","Description":"Mutators
to set attributes of variables, that work well in a pipe\n(much like
stats::setNames()).","License":"Unlimited","NeedsCompilation":"no","Package":"sette
r","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"magrittr,
testthat","Title":"Mutators that Work with
Pipes","URL":"https:\/\/bitbucket.org\/richierocks\/setter","Version":"0.0-
1"},"settings":{"Author":"Mark van der Loo","Description":"Provides option settings
management that goes\nbeyond R's default 'options' function. With this package,
users can define\ntheir own option settings manager holding option names, default
values and\n(if so desired) ranges or sets of allowed option values that will
be\nautomatically checked. Settings can then be retrieved, altered and reset\nto
defaults with ease. For R programmers and package developers it offers\ncloning and
merging functionality which allows for conveniently defining\nglobal and local
options, possibly in a multilevel options hierarchy. See\nthe package vignette for
some examples concerning functions, S4 classes,\nand reference classes. There are
convenience functions to reset par()\nand options() to their 'factory
defaults'.","Imports":"grDevices, graphics","License":"GPL-
3","NeedsCompilation":"no","Package":"settings","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"testthat, knitr","Title":"Software Option Settings
Manager for
R","URL":"https:\/\/github.com\/markvanderloo\/settings","Version":"0.2.4"},"severi
ty":{"Author":"Nicole Mee-Hyaang Jinn","Depends":"graphics","Description":"This
package contains functions for calculating severity\nand generating severity
curves. Specifically, the simple case\nof the one-parameter Normal distribution
(i.e., with known\nvariance) is considered.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"severity","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Mayo's Post-data Severity
Evaluation","Version":"2.0"},"sfa":{"Author":"Ariane Straub, under the supervision
of Torsten Hothorn","Description":"Stochastic Frontier Analysis\nintroduced by
Aigner, Lovell and Schmidt (1976)\nand Battese and Coelli (1992,
2","NeedsCompilation":"no","Package":"sfa","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Stochastic Frontier Analysis","Version":"1.0-1"},"sfsmisc":
{"Author":"Martin Maechler et al.","Depends":"R (>= 3.0.1)","Description":"Useful
utilities ['goodies'] from Seminar fuer Statistik ETH\nZurich, quite a few related
to graphics; many ported from S-plus times.","Enhances":"mgcv, rpart, nor1mix,
polycor, sm, tikzDevice","Imports":"grDevices, methods, utils,
2)","NeedsCompilation":"no","Package":"sfsmisc","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"datasets, tcltk, cluster, lattice, MASS, Matrix, nlme,
lokern","Title":"Utilities from \"Seminar fuer Statistik\" ETH
Zurich","Version":"1.1-0"},"sft":{"Author":"Joe Houpt <joseph.houpt@wright.edu>,
Leslie Blaha <Leslie.Blaha@wpafb.af.mil>","Depends":"R (>= 1.8.0), methods,
fda","Description":"This package contains a series of tools for analyzing Systems
Factorial Technology data. This includes functions for plotting and statistically
testing capacity coefficient functions and survivor interaction contrast
2)","NeedsCompilation":"no","Package":"sft","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Functions for Systems Factorial Technology Analysis of
Data","Version":"2.0-7"},"sgPLS":{"Author":"Benoit Liquet and Pierre Lafaye de
Micheaux","Depends":"mixOmics","Description":"The Sparse Group Partial Least Square
package (sgPLS) provides sparse, group, and sparse group versions of partial least
square regression models.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"sgPLS","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Sparse
Group Partial Least Square Methods","Version":"1.4"},"sgRSEA":{"Author":"Jungsik
Noh, Beibei Chen","Depends":"R (>= 2.10)","Description":"Provides functions to
implement sgRSEA (single-guide RNA Set Enrichment Analysis), which is a robust test
for identification of essential genes from genetic screening data using CRISPR
(clustered regularly interspaced short palindromic repeats) and Cas9 (CRISPR-
associated nuclease 9) system.","License":"GPL-
2","NeedsCompilation":"no","Package":"sgRSEA","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Enrichment Analysis of CRISPR\/Cas9 Knockout Screen
Data","Version":"0.1"},"sgd":{"Author":"Dustin Tran [aut, cre],\nPanos Toulis
[aut],\nTian Lian [ctb],\nYe Kuang [ctb],\nEdoardo Airoldi [ctb]","Description":"A
fast and flexible set of tools for large scale estimation. It\nfeatures many
stochastic gradient methods, built-in models, visualization\ntools, automated
hyperparameter tuning, model checking, interval estimation,\nand convergence
diagnostics.","Imports":"ggplot2, MASS, methods, Rcpp (>= 0.11.3)","License":"GPL-
2","NeedsCompilation":"yes","Package":"sgd","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"bigmemory, gridExtra, R.rsp, testthat","Title":"Stochastic
Gradient Descent for Scalable
Estimation","URL":"https:\/\/github.com\/airoldilab\/sgd","Version":"1.1"},"sgeosta
t":{"Author":"S original by James J. Majure <majure@iastate.edu> Iowa State
University, R port + extensions by Albrecht Gebhardt
<albrecht.gebhardt@aau.at>","Depends":"stats, grDevices, graphics, R (>=
2.0.0)","Description":"An Object-oriented Framework for Geostatistical Modeling in
S+\ncontaining functions for variogram estimation, variogram fitting and
kriging\nas well as some plot functions. Written entirely in S, therefore works
only\nfor small data sets in acceptable computing time.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"sgeostat","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"An Object-Oriented Framework for Geostatistical
Modeling in S+","Version":"1.0-27"},"sglOptim":{"Author":"Martin
Vincent","Depends":"R (>= 3.0.0), Matrix","Description":"Fast generic solver for
sparse group lasso optimization problems. The loss (objective) function must be
defined in a C++ module. Use of multiple processors for cross validation and
subsampling is supported through OpenMP. The optimization problem is solved using a
coordinate gradient descent algorithm. The algorithm is applicable to a broad class
of convex loss functions.Convergence of the algorithm is established (see
reference). Development version is on github.","Imports":"methods, stats,
2)","NeedsCompilation":"yes","Package":"sglOptim","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Generic Sparse Group Lasso
Solver","URL":"http:\/\/dx.doi.org\/10.1016\/j.csda.2013.06.004\nhttps:\/\/github.c
om\/vincent-dk\/sglOptim","Version":"1.2.0"},"sglasso":{"Author":"Luigi
Augugliaro","Depends":"Matrix, igraph","Description":"RCON(V, E) models (Højsgaard,
et al., 2008) are a kind of restriction of the Gaussian Graphical Models defined by
a set of equality constraints on the entries of the concentration matrix. 'sglasso'
package implements the structured graphical lasso (sglasso) estimator proposed in
Abbruzzo et al. (2014) for the weighted l1-penalized RCON(V, E) model. Two cyclic
coordinate algorithms are implemented to compute the sglasso estimator, i.e. a
cyclic coordinate minimization (CCM) and a cyclic coordinate descent (CCD)
algorithm.","Imports":"methods, graphics, grDevices","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"sglasso","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Lasso Method for RCON(V,E)
Models","URL":"http:\/\/www.unipa.it\/persone\/docenti\/a\/luigi.augugliaro","Versi
on":"1.2.2"},"sglr":{"Author":"Balasubramanian Narasimhan [aut, cre],\nMei-Chiung
Shih [aut]","Depends":"R (>= 3.0), ggplot2, shiny","Description":"Functions for
computing power and boundaries for pre-licensure vaccine trials using the
Generalized Likelihood Ratio tests proposed by Shih, Lai, Heyse and
Chen","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"sglr","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"An R package for power and boundary calculations in\npre-
licensure vaccine trials using a sequential generalized\nlikelihood ratio
test","Version":"0.7"},"sgof":{"Author":"Irene Castro Conde and Jacobo de Una
Alvarez","Depends":"R (>= 3.1.1), stats, poibin","Description":"seven different
methods for multiple testing problems. The SGoF-type methods and the BH and BY
false discovery rate controlling procedures.","License":"GPL-
2","NeedsCompilation":"no","Package":"sgof","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"discreteMTP","Title":"Multiple Hypothesis
Testing","Version":"2.2"},"sgr":{"Author":"Massimiliano Pastore & Luigi
Lombardi","Depends":"MASS","Description":"The package for Sample Generation by
Replacement simulations (SGR; Lombardi & Pastore, 2014; Pastore & Lombardi, 2014).
The package can be used to perform fake data analysis according to the sample
generation by replacement approach. It includes functions for making simple
inferences about discrete\/ordinal fake data. The package allows to study the
implications of fake data for empirical results.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"sgr","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"polycor","Title":"Sample Generation by
Replacement","Version":"1.3"},"sgt":{"Author":"Carter Davis","Depends":"R (>=
3.0.0), optimx (>= 2013.8.7), numDeriv (>= 2014.2-1)","Description":"Density,
distribution function, quantile function and random generation for the skewed
generalized t distribution. This package also provides a function that can fit data
to the skewed generalized t distribution using maximum likelihood
3)","NeedsCompilation":"no","Package":"sgt","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Skewed Generalized T Distribution
Tree","Version":"2.0"},"shades":{"Author":"Jon Clayden","Description":"Functions
for easily manipulating colours and creating colour scales.","Imports":"grDevices,
methods, colorspace","License":"BSD_3_clause + file
LICENCE","NeedsCompilation":"no","Package":"shades","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat","Title":"Simple Colour
Manipulation","Version":"0.1.0"},"shape":{"Author":"Karline Soetaert
<karline.soetaert@nioz.nl>","Depends":"R (>= 2.01), stats","Description":"Functions
for plotting graphical shapes\nsuch as ellipses, circles, cylinders,
arrows, ...","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"shape","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Functions for plotting graphical shapes,
colors","Version":"1.4.2"},"shapeR":{"Author":"Lisa Anne Libungan [aut,
cre],\nSnaebjorn Palsson [aut, ths]","Depends":"R (>=
3.0.2)","Description":"Studies otolith shape variation among fish
populations.\nOtoliths are calcified structures found in the inner ear of teleost
fish and their shape has\nbeen known to vary among several fish populations and
stocks, making them very useful in taxonomy,\nspecies identification and to study
geographic variations. The package extends previously described\nsoftware used for
otolith shape analysis by allowing the user to automatically extract
closed\ncontour outlines from a large number of images, perform smoothing to
eliminate pixel noise,\nchoose from conducting either a Fourier or wavelet
transform to the outlines and visualize\nthe mean shape. The output of the package
are independent Fourier or wavelet coefficients\nwhich can be directly imported
into a wide range of statistical packages in R. The package\nmight prove useful in
studies of any two dimensional objects.","Imports":"gplots, jpeg, pixmap,
wavethresh, methods, vegan, MASS","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"shapeR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Collection and Analysis of Otolith Shape
Data","URL":"https:\/\/github.com\/lisalibungan\/shapeR,\nhttp:\/\/journals.plos.or
g\/plosone\/article?id=10.1371\/journal.pone.0121102","Version":"0.1-
5"},"shapefiles":{"Author":"Ben Stabler <benstabler@yahoo.com>","Depends":"R (>=
1.6.0), foreign","Description":"Functions to read and write ESRI
shapefiles","License":"GPL","NeedsCompilation":"no","Package":"shapefiles","Reposit
ory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Read and Write ESRI
Shapefiles","Version":"0.7"},"shapes":{"Author":"Ian L. Dryden","Depends":"R (>=
2.10)","Description":"Routines for the statistical analysis of landmark\nshapes,
including Procrustes analysis, graphical displays, principal\ncomponents analysis,
permutation and bootstrap tests, thin-plate\nspline transformation grids and
comparing covariance matrices.","Imports":"scatterplot3d, rgl,
2","NeedsCompilation":"no","Package":"shapes","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Statistical Shape
Analysis","URL":"http:\/\/www.maths.nottingham.ac.uk\/~ild\/shapes","Version":"1.1-
11"},"sharpshootR":{"Author":"USDA-NRCS Soil Survey Staff","Depends":"R (>=
3.0.0)","Description":"Miscellaneous soil data management, summary, visualization,
and conversion utilities to support soil survey.","Imports":"grDevices, graphics,
methods, stats, utils, aqp, ape, soilDB,\nigraph, cluster, lattice, latticeExtra,
vegan, sp, reshape2,\nHmisc, scales, circular, RColorBrewer, plyr,
digest","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"sharpshootR","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"MASS, rgdal, spdep, circlize","Title":"A Soil
Survey Toolkit","URL":"http:\/\/aqp.r-forge.r-
project.org\/","Version":"0.9.1"},"sharx":{"Author":"Peter
Solymos","Depends":"methods, stats4,
Formula, dcmle, dclone","Description":"Hierarchical models for the analysis of
species-area\nrelationships (SARs) by combining several data sets and
covariates;\nwith a global data set combining individual SAR studies;\nas described
in Solymos and Lele\n(2012, Global Ecology and Biogeography 21, 109-
2","NeedsCompilation":"no","Package":"sharx","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Models and Data Sets for the Study of Species-Area
Relationships","URL":"https:\/\/github.com\/psolymos\/sharx","Version":"1.0-
5"},"shazam":{"Author":"Mohamed Uduman [aut],\nGur Yaari [aut],\nNamita Gupta
[aut],\nJason Vander Heiden [aut, cre],\nAng Cui [ctb],\nSusanna Marquez
[ctb],\nSteven Kleinstein [aut, cph]","Depends":"R (>= 3.1.2), alakazam (>= 0.2.1),
ggplot2 (>= 2.0.0)","Description":"Provides a computational framework for Bayesian
estimation of\nantigen-driven selection in immunoglobulin (Ig) sequences, providing
an\nintuitive means of analyzing selection by quantifying the degree of\nselective
pressure. Also provides tools to profile mutations in Ig\nsequences, build models
of somatic hypermutation (SHM) in Ig sequences,\nand make model-dependent distance
comparisons of Ig repertoires.","Imports":"data.table (>= 1.9.4), doParallel,
dplyr, foreach, graphics,\ngrid, iterators, methods, lazyeval, parallel, SDMTools,
scales,\nseqinr, stats, stringi, tidyr, utils","License":"CC BY-NC-SA
4.0","NeedsCompilation":"no","Package":"shazam","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr, rmarkdown, testthat","Title":"Immunoglobulin
Somatic Hypermutation
Analysis","URL":"http:\/\/clip.med.yale.edu\/changeo","Version":"0.1.2"},"shiny":
{"Author":"Winston Chang [aut, cre],\nJoe Cheng [aut],\nJJ Allaire [aut],\nYihui
Xie [aut],\nJonathan McPherson [aut],\nRStudio [cph],\njQuery Foundation [cph]
(jQuery library and jQuery UI library),\njQuery contributors [ctb, cph] (jQuery
library; authors listed in\ninst\/www\/shared\/jquery-AUTHORS.txt),\njQuery UI
contributors [ctb, cph] (jQuery UI library; authors listed
in\ninst\/www\/shared\/jqueryui\/1.10.4\/AUTHORS.txt),\nMark Otto [ctb] (Bootstrap
library),\nJacob Thornton [ctb] (Bootstrap library),\nBootstrap contributors [ctb]
(Bootstrap library),\nTwitter, Inc [cph] (Bootstrap library),\nAlexander Farkas
[ctb, cph] (html5shiv library),\nScott Jehl [ctb, cph] (Respond.js
library),\nStefan Petre [ctb, cph] (Bootstrap-datepicker library),\nAndrew Rowls
[ctb, cph] (Bootstrap-datepicker library),\nDave Gandy [ctb, cph] (Font-Awesome
font),\nBrian Reavis [ctb, cph] (selectize.js library),\nKristopher Michael Kowal
[ctb, cph] (es5-shim library),\nes5-shim contributors [ctb, cph] (es5-shim
library),\nDenis Ineshin [ctb, cph] (ion.rangeSlider library),\nSami Samhuri [ctb,
cph] (Javascript strftime library),\nSpryMedia Limited [ctb, cph] (DataTables
library),\nJohn Fraser [ctb, cph] (showdown.js library),\nJohn Gruber [ctb, cph]
(showdown.js library),\nIvan Sagalaev [ctb, cph] (highlight.js library),\nR Core
Team [ctb, cph] (tar implementation from R)","Depends":"R (>= 3.0.0),
methods","Description":"Makes it incredibly easy to build interactive
web\napplications with R. Automatic \"reactive\" binding between inputs
and\noutputs and extensive pre-built widgets make it possible to build\nbeautiful,
responsive, and powerful applications with minimal effort.","Imports":"utils,
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LICENSE","NeedsCompilation":"no","Package":"shiny","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"datasets, Cairo (>= 1.5-5), testthat, knitr (>=
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R","URL":"http:\/\/shiny.rstudio.com","Version":"0.13.2"},"shinyAce":
{"Author":"Trestle Technology, LLC [aut],\nJeff Allen [cre],\nInstitut de
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rich text editing environment\nwithin Shiny.","Imports":"shiny (>=
LICENSE","NeedsCompilation":"no","Package":"shinyAce","Repository":"http:\/\/cran.c
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Bailey","Description":"Adds additional Twitter Bootstrap components to
Shiny.","Imports":"shiny (>= 0.11), htmltools","License":"GPL-
3","NeedsCompilation":"no","Package":"shinyBS","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Twitter Bootstrap Components for
Shiny","URL":"https:\/\/ebailey78.github.io\/shinyBS","Version":"0.61"},"shinyFiles
":{"Author":"Thomas Lin Pedersen","Description":"Provides functionality for client-
side navigation of\nthe server side file system in shiny apps. In case the app is
running\nlocally this gives the user direct access to the file system without
the\nneed to \"download\" files to a temporary location. Both file and
folder\nselection as well as file saving is available.","Imports":"tools, shiny (>=
0.11), htmltools, RJSONIO","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"shinyFiles","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"A Server-Side File System Viewer For
Shiny","Version":"0.6.0"},"shinyRGL":{"Author":"Trestle Technology,
LLC.","Depends":"R (>= 2.15.0)","Description":"Shiny wrappers for the RGL package.
This package exposes RGL's\nability to export WebGL visualization in a shiny-
friendly format.","Imports":"rgl (>= 0.93.949), shiny (>= 0.6.0)","License":"MIT +
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LICENSE","NeedsCompilation":"no","Package":"shinyRGL","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat","Title":"Shiny Wrappers for
RGL","Version":"0.1.0"},"shinyTree":{"Author":"Trestle Technology, LLC [aut],\nJeff
Allen [cre],\nInstitut de Radioprotection et de S<c3><bb>ret<c3><a9>
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[ctb, cph] (require.js),\njQuery Foundation, Inc. [ctb, cph]","Depends":"R (>=
2.15.1), methods","Description":"Exposes bindings to jsTree -- a JavaScript
library\nthat supports interactive trees -- to enable a rich, editable trees
in\nShiny.","Imports":"shiny (>= 0.9.0)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"shinyTree","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat","Title":"jsTree Bindings for
Shiny","Version":"0.2.2"},"shinybootstrap2":{"Author":"Winston Chang [aut,
cre],\nRStudio [cph],\nMark Otto [ctb] (Bootstrap library),\nJacob Thornton [ctb]
(Bootstrap library),\nBootstrap contributors [ctb] (Bootstrap library; authors
listed at\nhttps:\/\/github.com\/twbs\/bootstrap\/graphs\/contributors),\nTwitter,
Inc [cph] (Bootstrap library),\nBrian Reavis [ctb, cph] (selectize.js
library),\nEgor Khmelev [ctb, cph] (jslider library),\nSpryMedia Limited [ctb, cph]
(DataTables library)","Depends":"R (>= 3.0.0)","Description":"Provides Bootstrap 2
web components for use with the Shiny\npackage. With versions of Shiny prior to
0.11, these Bootstrap 2 components\nwere included as part of the package. Later
versions of Shiny include\nBootstrap 3, so the Bootstrap 2 components have been
moved into this\npackage for those uses who rely on features specific to Bootstrap
2.","Imports":"htmltools (>= 0.2.6), jsonlite (>= 0.9.12), shiny","License":"GPL-3
| file
LICENSE","NeedsCompilation":"no","Package":"shinybootstrap2","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Title":"Bootstrap 2 Web Components for Use with
Shiny","Version":"0.2.1"},"shinydashboard":{"Author":"Winston Chang [aut,
cre],\nRStudio [cph],\nAlmasaeed Studio [ctb, cph] (AdminLTE theme for
Bootstrap),\nAdobe Systems Incorporated [ctb, cph] (Source Sans Pro
font)","Depends":"R (>= 3.0)","Description":"Create dashboards with 'Shiny'. This
package provides\na theme on top of 'Shiny', making it easy to create attractive
dashboards.","Imports":"utils, shiny (>= 0.11.1), htmltools (>=
0.2.6)","License":"GPL-2 | file
LICENSE","NeedsCompilation":"no","Package":"shinydashboard","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Title":"Create Dashboards with
'Shiny'","URL":"http:\/\/rstudio.github.io\/shinydashboard\/","Version":"0.5.1"},"s
hinyjs":{"Author":"Dean Attali [aut, cre]","Depends":"R (>=
3.1.0)","Description":"Perform common JavaScript operations in Shiny applications
without\nhaving to know any JavaScript. Examples include: hiding an element,
disabling\nan input, resetting an input back to its original value, delaying code
execution\nby a few seconds, and many more useful functions. 'shinyjs' also
includes\na colour picker widget, a colour picker RStudio addin, and can also be
used to\neasily run your own custom JavaScript functions from R.","Imports":"digest
(>= 0.6.8), htmltools (>= 0.2.6), miniUI (>= 0.1.1),\nshiny (>= 0.11.1),
stats","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"shinyjs","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"knitr (>= 1.7), rmarkdown, rstudioapi (>= 0.5),
testthat (>=\n0.9.1), V8 (>= 0.6)","Title":"Perform Common JavaScript Operations in
Shiny Apps using Plain
R\nCode","URL":"https:\/\/github.com\/daattali\/shinyjs","Version":"0.5.2"},"shinys
tan":{"Author":"Jonah Gabry [aut, cre],\nStan Development Team [ctb],\nMichael
Andreae [ctb],\nMichael Betancourt [ctb],\nBob Carpenter [ctb],\nYuanjun Gao
[ctb],\nAndrew Gelman [ctb],\nBen Goodrich [ctb],\nDaniel Lee [ctb],\nDongying Song
[ctb],\nRob Trangucci [ctb]","Depends":"R (>= 3.1.0), shiny (>=
0.12.1)","Description":"We provide a graphical user interface for interactive
Markov chain\nMonte Carlo (MCMC) diagnostics and plots and tables helpful for
analyzing a\nposterior sample. The interface is powered by RStudio's Shiny web
application\nframework
and works with the output of MCMC programs written in any programming\nlanguage
(and has extended functionality for Stan models fit using the rstan\npackage and
the No-U-Turn sampler).","Imports":"DT (>= 0.1), dygraphs (>= 0.4.5), ggplot2 (>=
2.0.0),\ngridExtra, gtools, markdown (>= 0.7.4), methods, reshape2,\nstats, shinyjs
(>= 0.1.0), shinythemes (>= 1.0.1), threejs (>=\n0.2.1), utils, xtable, xts (>=
0.9-7)","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"shinystan","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"coda, knitr (>= 1.9), rstan (>= 2.7), rmarkdown (>=
0.8.1),\ntestthat","Title":"Interactive Visual and Numerical Diagnostics and
Posterior\nAnalysis for Bayesian Models","URL":"https:\/\/github.com\/stan-
dev\/shinystan\/, http:\/\/mc-stan.org\/","Version":"2.1.0"},"shinythemes":
{"Author":"Winston Chang [aut, cre],\nRStudio [cph],\nThomas Park [ctb, cph]
(Bootswatch themes),\nLukasz Dziedzic [ctb, cph] (Lato font),\nNathan Willis [ctb,
cph] (News Cycle font),\nGoogle Corporation [ctb, cph] (Open Sans font),\nMatt
McInerney [ctb, cph] (Raleway font),\nAdobe Systems Incorporated [ctb, cph] (Source
Sans Pro font),\nCanonical Ltd [ctb, cph] (Ubuntu font)","Depends":"R (>=
3.0.0)","Description":"Themes for use with Shiny. Includes several Bootstrap
themes\nfrom http:\/\/bootswatch.com\/, which are packaged for use with
Shiny\napplications.","Imports":"shiny (>= 0.11)","License":"GPL-3 | file
LICENSE","NeedsCompilation":"no","Package":"shinythemes","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Themes for Shiny","Version":"1.0.1"},"shock":
{"Author":"Emilie Devijver, Melina Gallopin","Description":"Block-diagonal
covariance selection for high dimensional Gaussian\ngraphical models. The selection
procedure is based on the slope heuristics.","Imports":"glasso, mvtnorm, capushe,
GGMselect, igraph, stats","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"shock","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Slope Heuristic for Block-Diagonal Covariance Selection in
High\nDimensional Gaussian Graphical Models","Version":"1.0"},"shopifyr":
{"Author":"Charlie Friedemann","Depends":"R (>= 3.0), RCurl","Description":"An
interface to the API of the E-commerce service
Shopify\n(http:\/\/docs.shopify.com\/api)","Imports":"R6 (>= 2.0),
RJSONIO","License":"GPL-
3","NeedsCompilation":"no","Package":"shopifyr","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"An R Interface to the Shopify
API","URL":"https:\/\/github.com\/charliebone\/shopifyr\/","Version":"0.28"},"shotG
roups":{"Author":"Daniel Wollschlaeger","Depends":"R (>=
3.1.1)","Description":"Analyzes shooting data with respect to group
shape,\nprecision, and accuracy. This includes graphical methods,\ndescriptive
statistics, and inference tests using standard,\nbut also non-parametric and robust
statistical methods.\nImplements distributions for radial error in bivariate
normal\nvariables. Works with files exported by OnTarget PC\/TDS or\nTaran, as well
as with custom data files in text format.\nSupports inference from range statistics
like extreme spread.\nIncludes a set of web-based graphical user
interfaces.","Imports":"boot, coin, CompQuadForm, graphics, grDevices,
KernSmooth,\nrobustbase, stats, tools, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"shotGroups","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr, energy, mvoutlier, shiny","Title":"Analyze
Shot Group Data","Version":"0.7"},"showtext":{"Author":"Yixuan Qiu and
authors\/contributors of the\nincluded software. See file AUTHORS for
details.","Depends":"sysfonts","Description":"Making it easy to use various types
of fonts ('TrueType',\n'OpenType', Type 1, web fonts, etc.) in R graphs, and
supporting most output\nformats of R graphics including PNG, PDF and SVG. Text
glyphs will be converted\ninto polygons or raster images, hence after the plot has
been created, it no\nlonger relies on the font files. No external software such as
Ghostscript is\nneeded to use this package.","Imports":"showtextdb,
grDevices","License":"Apache License (>=
2.0)","NeedsCompilation":"yes","Package":"showtext","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Using Fonts More Easily in R
Graphs","URL":"https:\/\/github.com\/yixuan\/showtext","Version":"0.4-
4"},"showtextdb":{"Author":"Yixuan Qiu and authors\/contributors of the included
fonts. See file\nAUTHORS for
details.","Depends":"sysfonts","Description":"Providing font files that are needed
by the 'showtext' package.","License":"Apache License (>=
2.0)","NeedsCompilation":"no","Package":"showtextdb","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Font Files for the 'showtext'
Package","Version":"1.0"},"shp2graph":{"Author":"Binbin Lu","Depends":"R (>=
3.0.0),maptools,igraph","Description":"Functions for converting network data from
a\nSpatialLinesDataFrame object to a \"igraph-class\" object.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"shp2graph","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Convert a SpatialLinesDataFrame object to a \"igraph-
class\"\nobject","Version":"0-2"},"shrink":{"Author":"Daniela Dunkler [aut,
cre],\nGeorg Heinze [aut]","Depends":"R (>= 3.2.2)","Description":"The predictive
value of a statistical model can often be improved\nby applying shrinkage methods.
This can be achieved, e.g., by regularized\nregression or empirical Bayes
approaches. Various types of shrinkage factors can\nalso be estimated after a
maximum likelihood. While global shrinkage modifies\nall regression coefficients by
the same factor, parameterwise shrinkage factors\ndiffer between regression
coefficients. With variables which are either highly\ncorrelated or associated with
regard to contents, such as several columns of a\ndesign matrix describing a
nonlinear effect, parameterwise shrinkage factors are\nnot interpretable and a
compromise between global and parameterwise shrinkage,\ntermed 'joint shrinkage',
is a useful extension. A computational shortcut to\nresampling-based shrinkage
factor estimation based on DFBETA residuals can be\napplied. Global, parameterwise
and joint shrinkage for models fitted by lm(),\nglm(), coxph(), or mfp() is
available.","Imports":"survival, MASS, rms, mfp","License":"GPL-
2","NeedsCompilation":"no","Package":"shrink","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"aod, knitr, rmarkdown","Title":"Global, Parameterwise
and Joint Shrinkage Factor Estimation","Version":"1.2.1"},"shuffle":
{"Author":"Yuval Benjamini","Description":"Implementation of the shuffle estimator,
a non-parametric estimator for signal and noise variance under mild noise
correlations.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"shuffle","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"The shuffle estimator for explainable
variance","Version":"1.0"},"siRSM":{"Author":"Huan Cheng, Mu
Zhu","Description":"This package fits single-index (quadratic) response surface
models.","Imports":"rsm, MASS, foreach, doSNOW, parallel","License":"GPL-
2","NeedsCompilation":"no","Package":"siRSM","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Single-Index Response Surface
Models","Version":"1.1"},"siar":{"Author":"Andrew Parnell and Andrew
Jackson","Depends":"hdrcde, coda, MASS, bayesm, mnormt,
spatstat","Description":"This package takes data on organism isotopes and fits
a\nBayesian model to their dietary habits based upon a Gaussian\nlikelihood with a
mixture dirichlet-distributed prior on the\nmean. It also includes SiBER metrics.
See siardemo() for an\nexample. Version 4.1.2 contains bug fixes to allow more
than\nisotope numbers other than 2. Version 4.2 fixes a bug that\nstopped siar
working on 64-bit systems","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"siar","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Stable Isotope Analysis in
R","Version":"4.2"},"sideChannelAttack":{"Author":"Liran Lerman
<llerman@ulb.ac.be>, Gianluca Bontempi\n<gbonte@ulb.ac.be>, Olivier
Markowitch\n<olivier.markowitch@ulb.ac.be>","Depends":"R (>= 2.10), MASS, corpcor,
mmap, ade4, infotheo","Description":"This package has many purposes: first, it
gives to the\ncommunity an R implementation of each known side channel attack\nand
countermeasures as well as data to test it, second it\nallows to implement a side
channel attack quickly and easily.","License":"GPL-
3","NeedsCompilation":"no","Package":"sideChannelAttack","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Title":"Side Channel
Attack","URL":"http:\/\/student.ulb.ac.be\/~llerman\/","Version":"1.0-6"},"sidier":
{"Author":"A. Jesus MuÃ±oz Pajares","Depends":"R (>=
3.1.2)","Description":"Evolutionary reconstruction based on substitutions and
insertion-deletion (indels) analyses in a distance-based
framework.","Imports":"ape, network, igraph, gridBase, grid, ggmap,
2","NeedsCompilation":"no","Package":"sidier","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Substitution and Indel Distances to Infer
Evolutionary\nRelationships","Version":"3.0.1"},"sievetest":{"Author":"Petr
Matousu","Depends":"R (>= 3.1.0)","Description":"Functions for making sieve test
reports. Sieve test is widely used to obtain particle-size distribution of powders
or granular materials.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"sievetest","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Sieve test reporting
functions","Version":"1.2.2"},"sig":{"Author":"Richard Cotton [aut,
cre]","Depends":"R (>= 2.15.0)","Description":"Print function signatures and find
overly complicated
code.","License":"Unlimited","NeedsCompilation":"no","Package":"sig","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Title":"Print Function
Signatures","Version":"0.0-5"},"sigclust":{"Author":"Hanwen Huang, Yufeng
Liu & J. S. Marron","Depends":"R (>= 2.4.0), methods","Description":"SigClust is a
statistical method for testing the\nsignificance of clustering results. SigClust
can be applied to\nassess the statistical significance of splitting a data
set\ninto two clusters. For more than two clusters, SigClust can be\nused
iteratively.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"sigclust","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Statistical Significance of
Clustering","Version":"1.1.0"},"sigloc":{"Author":"Sergey S. Berg","Depends":"R (>=
2.15.3), nleqslv, ellipse","Description":"A collection of tools for estimating the
location of a transmitter signal from radio telemetry studies using the maximum
likelihood estimation (MLE) approach described in Lenth (1981).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"sigloc","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Signal Location Estimation","URL":"http:\/\/www.r-
project.org","Version":"0.0.4"},"signal":{"Author":"Uwe Ligges [aut, cre] (new
maintainer),\nTom Short [aut] (port to R),\nPaul Kienzle [aut] (majority of the
original sources),\nSarah Schnackenberg [ctb] (various test cases and bug
fixes),\nDavid Billinghurst [ctb],\nHans-Werner Borchers [ctb],\nAndre Carezia
[ctb],\nPascal Dupuis [ctb],\nJohn W. Eaton [ctb],\nE. Farhi [ctb],\nKai Habel
[ctb],\nKurt Hornik [ctb],\nSebastian Krey [ctb],\nBill Lash [ctb],\nFriedrich
Leisch [ctb],\nOlaf Mersmann [ctb],\nPaulo Neis [ctb],\nJaakko Ruohio
[ctb],\nJulius O. Smith III [ctb],\nDoug Stewart [ctb],\nAndreas Weingessel
[ctb]","Depends":"R (>= 2.14.0)","Description":"A set of signal processing
functions originally written for 'Matlab' and 'Octave'.\nIncludes filter generation
utilities, filtering functions,\nresampling routines, and visualization of filter
models. It also\nincludes interpolation functions.","Imports":"MASS, graphics,
2","NeedsCompilation":"yes","Package":"signal","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"pracma","Title":"Signal Processing","Version":"0.7-
6"},"signalHsmm":{"Author":"Michal Burdukiewicz [cre, aut],\nPiotr Sobczyk
[aut]","Depends":"R (>= 3.0.0)","Description":"Predicts the presence of signal
peptides in eukaryotic protein\nusing hidden semi-Markov models. The implemented
algorithm can be accessed from\nboth the command line and
GUI.","Imports":"graphics, seqinr, shiny, stats, utils","License":"GPL-
3","NeedsCompilation":"yes","Package":"signalHsmm","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"DT, rmarkdown","Title":"Predict Presence of Signal
Peptides","URL":"https:\/\/github.com\/michbur\/signalhsmm","Version":"1.4"},"signm
edian.test":{"Author":"Yeyun Yu and Ting Yang","Description":"Perform sign test on
one-sample data, which is one of the oldest non-parametric statistical methods.
Assume that X comes from a continuous distribution with median = v ( unknown ).
Test the null hypothesis H0: median of X v = mu ( mu is the location parameter and
is given in the test ) v.s. the alternative hypothesis H1: v > mu ( or v < mu or
v != mu ) and calculate the p-value. When the sample size is large, perform the
asymptotic sign test. In both ways, calculate the R-estimate of location of X and
the distribution free confidence interval for mu.","License":"GPL-
2","NeedsCompilation":"no","Package":"signmedian.test","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Perform Exact Sign Test and Asymptotic Sign Test
in Large\nSamples","Version":"1.5.1"},"simFrame":{"Author":"Andreas Alfons [aut,
cre]","Depends":"R (>= 2.14.0), Rcpp (>= 0.8.6), lattice,
parallel","Description":"A general framework for statistical
simulation.","Imports":"methods, stats4","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"simFrame","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"laeken, mvtnorm, robCompositions,
sampling","Title":"Simulation framework","Version":"0.5.3"},"simMSM":
{"Author":"Holger Reulen","Depends":"survival, mvna","Description":"Simulation of
event histories with possibly non-linear baseline hazard rate functions, non-linear
(time-varying) covariate effect functions, and dependencies on the past of the
history. Random generation of event histories is performed using inversion sampling
on the cumulative all-cause hazard rate functions.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"simMSM","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Simulation of Event Histories for Multi-State
Models","Version":"1.1.41"},"simPH":{"Author":"Christopher Gandrud [aut,
cre]","Depends":"R (>= 3.0.2)","Description":"Simulates and plots quantities of
interest (relative\nhazards, first differences, and hazard ratios) for linear
coefficients,\nmultiplicative interactions, polynomials, penalised splines,
and\nnon-proportional hazards, as well as stratified survival curves from
Cox\nProportional Hazard models. It also simulates and plots marginal effects\nfor
multiplicative interactions.","Imports":"data.table (>= 1.9.6), dplyr (>= 0.4),
ggplot2, gridExtra,\nlazyeval, MASS, mgcv, stringr, survival,
3","NeedsCompilation":"no","Package":"simPH","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"knitr, rio, stats","Title":"Tools for Simulating and
Plotting Quantities of Interest\nEstimated from Cox Proportional Hazards
project.org\/package=simPH","Version":"1.3.7"},"simPop":{"Author":"Bernhard Meindl,
Matthias Templ, Andreas Alfons, Alexander Kowarik, and\nwith contributions from
Mathieu Ribatet","Depends":"R(>= 3.0.0), lattice, vcd,
data.table","Description":"Tools and methods to simulate populations for surveys
based\non auxiliary data. The tools include model-based methods, calibration
and\ncombinatorial optimization algorithms. The package was developed with support
of\nthe International Household Survey Network, DFID Trust Fund TF011722 and funds
from the World bank.","Imports":"laeken, plyr, MASS, Rcpp (>= 0.11.0), e1071,
parallel, nnet,\ndoParallel, foreach, colorspace, VIM,
methods,party","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"simPop","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"haven","Title":"Simulation of Synthetic Populations
for Survey Data Considering\nAuxiliary
Information","Version":"0.3.0"},"simSummary":{"Author":"Gregor
Gorjanc","Depends":"abind (>= 1.4-0), svUnit (>= 0.7-5)","Description":"simSummary
is a small utility package which eases the\nprocess of summarizing simulation
results. Simulations often\nproduce intermediate results - some focal statistics
that need\nto be summarized over several scenarios and many replications.\nThis
step is in principle easy, but tedious. The package\nsimSummary fills this niche by
providing a generic way of\nsummarizing the focal statistics of simulations. The
useR must\nprovide properly structured input, holding focal statistics,\nand then
the summary step can be performed with one line of\ncode, calling the simSummary
function.","Imports":"gdata (>= 2.8.0)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"simSummary","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Simulation summary","Version":"0.1.0"},"simTool":
{"Author":"Marsel Scheer <scheer@freescience.de>","Depends":"R (>=
2.14.0)","Description":"The simTool package is designed for statistical simulations
that\nhave two components. One component generates the data and the other
one\nanalyzes the data. The main aims of the simTool package are the reduction\nof
the administrative source code (mainly loops and management code for the\nresults)
and a simple applicability of the package that allows the user to\nquickly learn
how to work with the simTool package. Parallel computing is\nalso supported.
Finally, convenient functions are provided to summarize the\nsimulation
results.","Imports":"plyr (>= 1.8.1), reshape (>= 0.8.5), parallel","License":"GPL-
3","NeedsCompilation":"no","Package":"simTool","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"ggplot2, knitr, boot, RUnit","Title":"Conduct
Simulation Studies with a Minimal Amount of Source
Code","Version":"1.0.3"},"simba":{"Author":"Gerald Jurasinski
<gerald.jurasinski@uni-rostock.de>, with\ncontributions from Vroni Retzer
<vroni.retzer@gmx.de>","Depends":"R (>= 2.12.0), stats,
vegan","Description":"Besides functions for the calculation of similarity
and\nmultiple plot similarity measures with binary data (for\ninstance
presence\/absence species data) the package contains\nsome simple wrapper functions
for reshaping species lists into\nmatrices and vice versa and some other functions
for further\nprocessing of similarity data (Mantel-like permutation\nprocedures) as
well as some other useful stuff for vegetation\nanalysis.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"simba","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"gplots, geoR, plotrix","Title":"A Collection of
functions for similarity analysis of vegetation\ndata","URL":"http:\/\/www.r-
project.org","Version":"0.3-5"},"simboot":{"Author":"Ralph Scherer, Philip
Pallmann","Depends":"boot, mvtnorm","Description":"Package simboot provides
estimation of simultaneous bootstrap and asymptotic confidence intervals for
diversity indices, namely the Shannon and the Simpson index. Several pre--specified
multiple comparison types are available to choose. Further user--defined contrast
matrices are applicable. In addition, simboot estimates adjusted as well as
unadjusted p--values for two of the three proposed bootstrap methods. Further
simboot allows for comparing biological diversities of two or more groups while
simultaneously testing a user-defined selection of Hill numbers of orders q, which
are considered as appropriate and useful indices for measuring
diversity.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"simboot","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Simultaneous inference for diversity
indices","URL":"https:\/\/github.com\/shearer\/simboot,\nhttp:\/\/shearer.github.io
\/simboot\/","Version":"0.2-5"},"simcausal":{"Author":"Oleg Sofrygin [aut,
cre],\nMark J. van der Laan [aut],\nRomain Neugebauer [aut]","Depends":"R (>=
3.2.0)","Description":"A flexible tool for simulating complex longitudinal data
using\nstructural equations, with emphasis on problems in causal
inference.\nSpecify interventions and simulate from intervened data
generating\ndistributions. Define and evaluate treatment-specific means, the
average\ntreatment effects and coefficients from working marginal structural
models.\nUser interface designed to facilitate the conduct of transparent
and\nreproducible simulation studies, and allows concise expression of
complex\nfunctional dependencies for a large number of time-varying nodes. See
the\npackage vignette for more information, documentation and
examples.","Imports":"data.table, igraph, stringr, R6, assertthat, Matrix,
2","NeedsCompilation":"no","Package":"simcausal","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"ltmle, tmlenet, RUnit, knitr, ggplot2, Hmisc,
copula,\nmvtnorm, bindata","Title":"Simulating Longitudinal Data with Causal
Inference
Applications","URL":"https:\/\/github.com\/osofr\/simcausal","Version":"0.5.0"},"si
mctest":{"Author":"Axel Gandy <a.gandy@imperial.ac.uk> with contributions from
Patrick Rubin-Delanchy <patrick.rubin-delanchy@imperial.ac.uk> and Georg Hahn
<g.hahn11@imperial.ac.uk>","Depends":"R (>= 2.2.0), methods,
stats","Description":"Algorithms for the implementation and evaluation of Monte
Carlo tests, as well as for their use in multiple testing
procedures.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"simctest","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Safe Implementation of Monte Carlo
Tests","URL":"http:\/\/www2.imperial.ac.uk\/~agandy","Version":"2.4.1"},"simecol":
{"Author":"Thomas Petzoldt","Depends":"R (>= 2.14), deSolve,
methods","Description":"An object oriented framework to simulate\necological (and
other) dynamic systems. It can be used for\ndifferential equations, individual-
based (or agent-based) and other\nmodels as well. The package helps to organize
scenarios (to avoid copy\nand paste) and aims to improve readability and usability
of code.","Imports":"graphics, grDevices, stats, utils, minqa","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"simecol","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"tcltk, FME, lattice","Title":"Simulation of
Ecological (and Other) Dynamic
Systems","URL":"http:\/\/www.simecol.de\/","Version":"0.8-7"},"simest":
{"Author":"Arun Kumar Kuchibhotla <arunku@wharton.upenn.edu>,\nRohit Kumar Patra
<rkp2117@columbia.edu>","Description":"Estimation of function and index vector in
single index model with and without shape constraints including different
smoothness conditions.","Imports":"nnls","License":"GPL-
2","NeedsCompilation":"yes","Package":"simest","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Constrained Single Index Model
Estimation","Version":"0.2"},"simex":{"Author":"Wolfgang Lederer
<Wolfgang.Lederer@gmail.com>, Helmut\nKüchenhoff <Kuechenhoff@stat.uni-
muenchen.de>","Depends":"stats","Description":"Implementation of the SIMEX-
Algorithm by Cook & Stefanski\nand MCSIMEX by Küchenhoff, Mwalili &
Lesaffre","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"simex","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"mgcv, nlme","Title":"SIMEX- and MCSIMEX-Algorithm for
measurement error models","Version":"1.5"},"simexaft":{"Author":"Juan Xiong
<xiongjuan2000@gmail.com>, Wenqing He <whe@stats.uwo.ca>, Grace Y.
Yi<yyi@uwaterloo.ca>","Description":"Implement of the Simulation-Extrapolation
(SIMEX) algorithm for the accelerated failure time (AFT) with covariates subject to
measurement error.","Imports":"mvtnorm,
survival","License":"GPL","NeedsCompilation":"no","Package":"simexaft","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Title":"simexaft","Version":"1.0.7"},"simm
er":{"Author":"Bart Smeets [aut],\nIÃ±aki Ucar [aut, cre]","Depends":"R (>=
3.1.2)","Description":"Discrete-Event Simulation (DES) package for
R.","Imports":"Rcpp, R6, magrittr, methods, utils","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"simmer","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"parallel, dplyr, tidyr, ggplot2, scales,
testthat, knitr,\nrmarkdown, covr","Title":"Just Let it
Simmer","URL":"https:\/\/github.com\/Enchufa2\/simmer","Version":"3.2.0"},"simmr":
{"Author":"Andrew Parnell","Depends":"R (>= 3.2.2), rjags,
ggplot2","Description":"Fits a stable isotope mixing model via JAGS in R. The
package allows for any number of isotopes or sources, as well as concentration
dependencies.","Imports":"MASS, compositions, boot, reshape2, coda, graphics,
stats,\nviridis","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"simmr","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"knitr","Title":"A Stable Isotope Mixing
Model","Version":"0.3"},"simone":{"Author":"Julien Chiquet
<julien.chiquet@genopole.cnrs.fr>, Gilles\nGrasseau
<gilles.grasseau@genopole.cnrs.fr>, Camille\nCharbonnier
<camille.charbonnier@genopole.cnrs.fr>, Christophe\nAmbroise
<christophe.ambroise@genopole.cnrs.fr>.","Depends":"R (>= 2.7),
mixer","Description":"Implements the inference of\nco-expression networks based on
partial correlation\ncoefficients from either steady-state or time-
course\ntranscriptomic data. Note that with both type of data this\npackage can
deal with samples collected in different\nexperimental conditions and therefore not
identically\ndistributed. In this particular case, multiple but related\nnetworks
are inferred on one simone run.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"simone","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Statistical Inference for MOdular NEtworks
(SIMoNe)","URL":"http:\/\/julien.cremeriefamily.info\/simone.html","Version":"1.0-
3"},"simpleNeural":{"Author":"David Dernoncourt [aut, cre] (LUNAM Universite,
Universite Angers,\nLaboratoire d'ergonomie et d'epidemiologie en sante au
travail\n(LEEST), w\/ support from the French National Research Program
for\nEnvironmental and Occupational Health of Anses (2012\/18))","Depends":"R (>=
3.1)","Description":"Trains neural networks (multilayer perceptrons with one hidden
layer) for bi- or multi-class classification.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"simpleNeural","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"verification","Title":"An Easy to Use
Multilayer
Perceptron","URL":"https:\/\/bitbucket.org\/patheticcockroach\/simpleneural","Versi
on":"0.1.1"},"simpleRCache":{"Author":"Augustin Luna, Vinodh
Rajapakse","Depends":"R (>= 3.1.1)","Description":"Simple result caching in R based
on Henrik\nBengtsson's R.cache. The global environment is not considered when
caching\nresults simplifying moving files between multiple instances of R. Relies
on\nmore base functions than R.cache (e.g. cached results are saved using
saveRDS()\nand
readRDS()).","Imports":"digest","License":"LGPL","NeedsCompilation":"no","Package":
"simpleRCache","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Simple
R Cache","Version":"0.2.2"},"simpleboot":{"Author":"Roger D. Peng
<rpeng@jhsph.edu>","Depends":"R (>= 2.7.0), boot","Description":"Simple bootstrap
routines","Imports":"stats, graphics","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"simpleboot","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Simple Bootstrap Routines","Version":"1.1-
3"},"simplegraph":{"Author":"Gabor Csardi","Description":"Simple classic graph
algorithms for simple graph classes.\nGraphs may possess vertex and edge
attributes. 'simplegraph' has\nso dependencies and it is written entirely in R, so
it is easy to\ninstall.","Imports":"utils","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"simplegraph","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Simple Graph Data Types
and Basic
Algorithms","URL":"https:\/\/github.com\/mangothecat\/simplegraph","Version":"1.0.0
"},"simplexreg":{"Author":"Peng Zhang, Zhengguo Qiu and Chengchun
Shi","Depends":"Formula, plotrix","Description":"Simplex density, distribution,
quantile functions as well as random variable\ngeneration of the simplex
distribution are given. Regression analysis of proportional data\nusing various
kinds of simplex models is available. In addition, GEE method can be applied\nto
longitudinal data to model the correlation. Residual analysis is also involved.
Some\nsubroutines are written in C with GNU Scientific Library (GSL) so as to
facilitate the\ncomputation.","License":"GPL-
2","NeedsCompilation":"yes","Package":"simplexreg","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Regression Analysis of Proportional Data Using
Simplex\nDistribution","Version":"1.1"},"simplr":{"Author":"Oliver Flasch [aut,
cre], Felix Gorschlueter [aut], Leo Liberti [ctb]","Depends":"R (>= 3.0.0),
utils","Description":"Basic tools for symbolic expression simplification, e.g.
simplify(x*1) => x, or simplify(sin(x)^2+cos(x)^2) => 1. Based on the \"Expression
v3\" (Ev3) 1.0 system by Leo
Liberti.","License":"CPL","NeedsCompilation":"yes","Package":"simplr","Repository":
"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Basic
Symbolic Expression Simplification","Version":"0.1-1"},"simr":{"Author":"Peter
Green, Catriona MacLeod","Depends":"lme4","Description":"Calculate power for
generalised linear mixed models, using\nsimulation. Designed to work with models
fit using the 'lme4'
package.","Imports":"\nbinom,iterators,pbkrtest,plotrix,plyr,RLRsim,stringr,stats,m
ethods,utils,graphics,grDev
ices","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"simr","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"testthat,knitr,rmarkdown","Title":"Power Analysis for
Generalised Linear Mixed Models by
Simulation","URL":"https:\/\/github.com\/pitakakariki\/simr","Version":"1.0.1"},"si
mrel":{"Author":"Solve Sæbø","Depends":"FrF2, sfsmisc","Description":"Facilitates
data simulation from a random regression model where the data properties can be
controlled by a few input parameters. The data simulation is based on the concept
of relevant latent components and relevant predictors, and was developed for the
purpose of testing methods for variable selection for prediction. Included are also
functions for designing computer experiments in order to investigate the effects of
the data properties on the performance of the tested methods. The design is
constructed using the Multi-level Binary Replacement (MBR) design approach which
makes it possible to set up fractional designs for multi-factor problems with
potentially many levels for each factor.","License":"GPL-
2","NeedsCompilation":"no","Package":"simrel","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"pls","Title":"Linear Model Data Simulation and Design of
Computer Experiments","Version":"1.0-1"},"simsalapar":{"Author":"Marius Hofert and
Martin Maechler <maechler@stat.math.ethz.ch>","Depends":"R (>= 3.1.0),
graphics","Description":"Tools for setting up (\"design\"), conducting, and
evaluating\nlarge-scale simulation studies with graphics and tables,
including\nparallel computations.","Imports":"stats, parallel, utils, grDevices,
methods, grid, sfsmisc,\ngridBase (>= 0.4-6), colorspace","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"simsalapar","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"lattice, Rmpi, Hmisc, copula, foreach, doParallel,
fGarch,\nrobustbase","Title":"Tools for Simulation Studies in
Parallel","Version":"1.0-9"},"simsem":{"Author":"Sunthud Pornprasertmanit [aut,
cre],\nPatrick Miller [aut],\nAlexander Schoemann [aut],\nCorbin Quick
[ctb],\nTerry Jorgensen [ctb]","Depends":"R(>= 3.0), methods, lavaan(>= 0.5-20),
utils, stats, graphics","Description":"Provides an easy framework for Monte Carlo
simulation in structural equation modeling, which can be used for various purposes,
such as such as model fit evaluation, power analysis, or missing data handling and
planning.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"simsem","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"parallel, Amelia, quantreg, splines, foreign,
KernSmooth,\nsemTools, OpenMx(>= 2.0.0), copula","Title":"SIMulated Structural
Equation Modeling","URL":"http:\/\/www.simsem.org","Version":"0.5-12"},"sinaplot":
{"Author":"Nikos Sidiropoulos [aut, cre],\nSina Hadi Sohi [aut],\nNicolas Rapin
[aut],\nFrederik Otzen Bagger [aut]","Depends":"R(>= 3.1.0), ggplot2(>=
1.0.1)","Description":"The sinaplot is a data visualization chart suitable for
plotting\nany single variable in a multiclass dataset. It is an enhanced jitter
strip\nchart, where the width of the jitter is controlled by the
density\ndistribution of the data within each class.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"sinaplot","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr, RColorBrewer","Title":"An Enhanced Chart for
Simple and Truthful Representation of\nSingle Observations over Multiple
Classes","Version":"0.1.3"},"siplab":{"Author":"Oscar Garcia","Depends":"spatstat
(>= 1.36-0)","Description":"A platform for experimenting with spatially explicit
individual-based vegetation models.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"siplab","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Spatial Individual-Plant
Modelling","URL":"http:\/\/forestgrowth.unbc.ca\/siplab","Version":"1.2"},"sirad":
{"Author":"Jedrzej S. Bojanowski","Depends":"R (>=
3.0.0)","Description":"Calculating daily global solar radiation at horizontal
surface using several well-known models (i.e. Angstrom-Prescott, Supit-Van Kappel,
Hargreaves, Bristow and Campbell, and Mahmood-Hubbard), and model calibration based
on ground-truth data, and (3) model auto-calibration. The FAO Penmann-Monteith
equation to calculate evapotranspiration is also included.","Imports":"stats, zoo,
raster","License":"GPL-
2","NeedsCompilation":"no","Package":"sirad","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Functions for Calculating Daily Solar Radiation
and\nEvapotranspiration","URL":"http:\/\/sirad.r-forge.r-
project.org\/,\nhttp:\/\/mars.jrc.ec.europa.eu\/mars\/Projects\/Solar-Radiation-in-
MCYFS,\nhttp:\/\/jbojanowski.pl","Version":"2.3-1"},"sirt":{"Author":"Alexander
Robitzsch [aut,cre]","Depends":"R (>= 2.15.0), CDM,
TAM","Description":"\nSupplementary item response theory models to complement
existing\nfunctions in R, including multidimensional compensatory
and\nnoncompensatory IRT models, MCMC for hierarchical IRT models and\ntestlet
models, NOHARM, faceted and hierarchical rater models,\nordinal IRT model (ISOP),
DETECT statistic, local structural\nequation modeling (LSEM).","Imports":"coda,
combinat, graphics, gtools, ic.infer, igraph, lavaan,\nlavaan.survey, MASS, Matrix,
methods, mirt, mvtnorm, pbivnorm,\nplyr, psych, Rcpp, sfsmisc, sm, stats, survey,
2)","NeedsCompilation":"yes","Package":"sirt","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"miceadds","Title":"Supplementary Item Response Theory
Models","Version":"1.10-0"},"sisVIVE":{"Author":"Hyunseung Kang
<hskang@stanford.edu>","Depends":"lars","Description":"Selects invalid instruments
amongst a candidate of potentially bad instruments. The algorithm selects
potentially invalid instruments and provides an estimate of the causal effect
between exposure and outcome.","License":"GPL-
2","NeedsCompilation":"no","Package":"sisVIVE","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"MASS","Title":"Some Invalid Some Valid Instrumental
Variables Estimator","Version":"1.2"},"sisal":{"Author":"Mikko Korpela [aut,
cre]","Depends":"R (>= 3.1.2)","Description":"Implements the SISAL algorithm by
Tikka and HollmÃ©n. It is\na sequential backward selection algorithm which uses a
linear\nmodel in a cross-validation setting. Starting from the full\nmodel, one
variable at a time is removed based on the\nregression coefficients. From this set
of models, a\nparsimonious (sparse) model is found by choosing the model with\nthe
smallest number of variables among those models where the\nvalidation error is
smaller than a threshold. Also implements\nextensions which explore larger parts of
the search space\nand\/or use ridge regression instead of ordinary least
squares.","Imports":"graphics, grDevices, grid, methods, stats, utils,
boot,\nlattice, mgcv, digest, R.matlab, R.methodsS3","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"sisal","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"graph, Rgraphviz, testthat (>= 0.8)","Title":"Sequential
Input Selection Algorithm","Version":"0.46"},"sisus":{"Author":"Erik Barry Erhardt
[aut, cre]","Depends":"R (>= 3.0.0)","Description":"SISUS for source partitioning
using stable isotopes.\nSISUS reads in a specific Excel-like workbook and performs
an IsoSource-type analysis by\nreturning a sample of feasible solutions to p in the
non-over constrained linear systems, b=Ap.\nEdit \\file{sisus_*_template.xls} and
input data values and run parameters.\nRun \\code{\\link{sisus.run}(filename)}. See
output in current working directory.","Imports":"MASS, RColorBrewer, coda, gdata,
gtools, moments, polyapost,\nrcdd, stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"sisus","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"SISUS: Stable Isotope Sourcing using
Sampling","URL":"http:\/\/StatAcumen.com\/sisus","Version":"3.9-13"},"sitar":
{"Author":"Tim Cole","Depends":"R (>= 3.0.0), nlme,
splines","Description":"Functions for fitting and plotting SITAR (Super Imposition
by Translation And Rotation) growth curve models. SITAR is a shape-invariant model
with a regression B-spline mean curve and subject-specific random effects on both
the measurement and age scales.","Imports":"quantreg","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"sitar","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Super Imposition by Translation and Rotation Growth
Curve\nAnalysis","Version":"1.0.4"},"sitools":{"Author":"Jonas Stein, Ben
Tupper","Description":"Format a number (or a list of numbers) to a string (or
a\nlist of strings) with SI prefix. Use SI prefixes as constants\nlike (4 *
milli)^2","License":"GPL-
3","NeedsCompilation":"no","Package":"sitools","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Format a number to a string with SI
prefix","Version":"1.4"},"sivipm":{"Author":"A. Bouvier [aut], J.-P. Gauchi [aut,
cre], E. Volatier [ctb]","Depends":"methods","Description":"Sensitivity indices
with dependent correlated inputs, using a\nmethod based on PLS
regression.","Imports":"stats, graphics, utils, seqinr","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"sivipm","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Sensitivity Indices with Dependent
Inputs","Version":"1.1-3"},"sjPlot":{"Author":"Daniel LÃ¼decke
<d.luedecke@uke.de>","Depends":"R (>= 3.2), graphics, grDevices, methods, stats,
utils","Description":"Collection of plotting and table output functions for
data\nvisualization. Results of various statistical analyses (that are commonly
used\nin social sciences) can be visualized using this package, including simple
and\ncross tabulated frequencies, histograms, box plots, (generalized) linear
models,\nmixed effects models, PCA and correlation matrices, cluster analyses,
scatter\nplots, Likert scales, effects plots
of regression models (including interaction\nterms) and much
more.","Imports":"car, dplyr (>= 0.4.3), effects, ggplot2 (>= 2.0.0), lme4
(>=\n1.1-8), MASS, magrittr, nlme, psych, scales, sjmisc (>= 1.6),\ntidyr (>=
3","NeedsCompilation":"no","Package":"sjPlot","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"AICcmodavg, arm, cluster, ggrepel, lmerTest, lmtest,
lsmeans,\npbkrtest (>= 0.4-6), testthat","Title":"Data Visualization for Statistics
in Social
Science","URL":"https:\/\/github.com\/sjPlot\/devel","Version":"1.9.4"},"sjdbc":
{"Author":"TIBCO Software Inc.","Depends":"rJava","Description":"Provides a
database-independent JDBC interface.","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"no","Package":"sjdbc","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"JDBC Driver Interface","Version":"1.5.0-71"},"sjmisc":
{"Author":"Daniel LÃ¼decke <d.luedecke@uke.de>","Depends":"R (>= 3.2), stats,
utils","Description":"Collection of miscellaneous utility functions (especially
intended\nfor people coming from other statistical software packages like 'SPSS',
and\/\nor who are new to R), supporting following common tasks: 1) Reading and
writing\ndata between R and other statistical software packages like 'SPSS', 'SAS'
or\n'Stata' and working with labelled data; this includes easy ways to get and
set\nlabel attributes, to convert labelled vectors into factors (and vice
versa),\nor to deal with multiple declared missing values etc. 2) Data
transformation\ntasks like recoding, dichotomizing or grouping variables, setting
and replacing\nmissing values. 3) Convenient functions to perform frequently used
statistical\ntests, or to calculate various commonly used statistical
coefficients.","Imports":"coin, dplyr, haven, lme4, MASS, Matrix, nlme, stringdist
(>=\n0.9.2), tidyr","License":"GPL-
3","NeedsCompilation":"no","Package":"sjmisc","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"AER, arm, foreign, Hmisc","Title":"Data Transformation
and Labelled Data Utility
Functions","URL":"https:\/\/github.com\/sjPlot\/sjmisc","Version":"1.7"},"skatMeta"
:{"Author":"Arend Voorman, Jennifer Brody, Thomas Lumley","Depends":"R (>= 2.10),
Matrix, coxme, survival, CompQuadForm","Description":"Computes necessary
information to meta analyze SKAT\nstatistics in each individual cohort, and then
performs the\nmeta analysis.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"skatMeta","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"SKAT, kinship2","Title":"Efficient meta analysis for
the SKAT test","Version":"1.4.3"},"skda":{"Author":"Len Stefanski, Yichao Wu, and
Kyle White","Depends":"parallel, R (>= 2.0)","Description":"Sparse (Multicategory)
Kernel Discriminant Analysis does variable selection for nonparametric
classification","License":"GPL-
2","NeedsCompilation":"yes","Package":"skda","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Sparse (Multicategory) Kernel Discriminant
Analysis","Version":"0.1"},"skellam":{"Author":"Jerry W. Lewis, Patrick E. Brown
<patrick.brown@utoronto.ca>","Description":"Functions for the Skellam distribution,
including: density\n(pmf), cdf, quantiles and random
variates.","Imports":"stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"skellam","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr","Title":"Densities and Sampling for the Skellam
Distribution","URL":"http:\/\/r-forge.r-
project.org\/projects\/healthqueues\/","Version":"0.1.3"},"skewt":{"Author":"Robert
King, <Robert.King@newcastle.edu.au>, with contributions\nfrom Emily Anderson
<emily.anderson@newcastle.edu.au>.","Description":"Density, distribution function,
quantile function and\nrandom generation for the skewed t distribution of
Fernandez\nand
Steel.","License":"GPL","NeedsCompilation":"no","Package":"skewt","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Title":"The Skewed Student-t
Distribution","Version":"0.1"},"skmeans":{"Author":"Kurt Hornik [aut, cre],\nIngo
Feinerer [aut],\nMartin Kober [aut]","Description":"Algorithms to compute spherical
k-means partitions.\nFeatures several methods, including a genetic and a fixed-
point\nalgorithm and an interface to the CLUTO vcluster
program.","Enhances":"Matrix, kmndirs","Imports":"slam (>= 0.1-31), clue (>= 0.3-
39), cluster, stats, utils","License":"GPL-
2","NeedsCompilation":"no","Package":"skmeans","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Spherical k-Means Clustering","Version":"0.2-8"},"sla":
{"Author":"W. Gregory Alvord [aut, cre],\nNick Carchedi [aut]","Depends":"R (>=
3.0.2)","Description":"Provides directly interpretable estimated coefficients\nfor
four models in connection with the two-group straight line\nANCOVA problem: (A) the
full model, which requires the fitting of\ntwo intercepts and two slopes; (B) a
reduced model, which requires\nthe fitting of a single intercept and single slope;
(C) a reduced\nmodel, which requires the fitting of two separate intercepts and
a\nsingle, common slope; and (D) a reduced model, which requires the\nfitting of a
single, common intercept and two separate slopes. The\nsummary function provides
tests of fit for the (null) hypotheses of:\n(1) equivalent data sets, (2)
equivalent slopes, and\n(3) equivalent intercepts.","License":"GPL-
2","NeedsCompilation":"no","Package":"sla","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"MASS, car, ISwR, knitr","Title":"Two-Group Straight Line
ANCOVA","Version":"0.1"},"slackr":{"Author":"Bob Rudis (@hrbrmstr) & Jay Jacobs
(@jayjacobs)","Depends":"R (>= 3.0.0), httr (>= 0.4.0), jsonlite, data.table
(>=\n1.9.2), ggplot2","Description":"Slackr contains functions that make it
possible to\ninteract with Slack.com messaging platform. When you need to
share\ninformation\/data from R, rather than resort to copy\/paste in e-mails\nor
other services like Skype, you can use this package to send\nwell-formatted output
from multiple R objects and expressions\nto all teammates at the same time with
little effort. You can also\nsend images from the current graphics device, R
objects (as RData),\nand upload files.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"slackr","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat","Title":"Send messages, images, R
objects and files to
Slack.com\nchannels\/users","URL":"http:\/\/github.com\/hrbrmstr\/slackr","Version"
:"1.2"},"slam":{"Author":"Kurt Hornik [aut, cre],\nDavid Meyer [aut],\nChristian
Buchta [aut]","Depends":"R (>= 2.8.0)","Description":"Data structures and
algorithms for sparse arrays and matrices,\nbased on index arrays and simple
triplet representations, respectively.","Enhances":"Matrix, SparseM,
spam","Imports":"stats","License":"GPL-
2","NeedsCompilation":"yes","Package":"slam","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Sparse Lightweight Arrays and Matrices","Version":"0.1-
32"},"sld":{"Author":"Robert King <Robert.King@newcastle.edu.au>, Paul van Staden
<paul.vanstaden@up.ac.za>","Depends":"stats, lmom","Description":"The skew logistic
distribution is a quantile-defined generalisation\nof the logistic distribution
(van Staden and King 2015). Provides random\nnumbers, quantiles, probabilities,
densities and density quantiles for the distribution.\nIt provides Quantile-
Quantile plots and method of L-Moments estimation\n(including asymptotic standard
errors) for the distribution.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"sld","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"graphics","Title":"Estimation and Use of the Quantile-
Based Skew
Logistic\nDistribution","URL":"http:\/\/tolstoy.newcastle.edu.au\/~rking\/SLD\/","V
ersion":"0.3"},"sleekts":{"Author":"Muntashir-Al-Arefin, Prof. Md. Ayub
Al.","Depends":"R (>= 3.2.0), stats","Description":"Compute Time series Resistant
Smooth 4253H, twice smoothing method.","License":"GPL-
3","NeedsCompilation":"no","Package":"sleekts","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"4253H, Twice Smoothing","Version":"1.0.2"},"slfm":
{"Author":"Joao Duarte and Vinicius Mayrink","Depends":"R (>=
3.1.0)","Description":"Set of tools to find coherent patterns in microarray
data\nusing a Bayesian sparse latent factor model (Duarte and Mayrink 2015
-\nhttp:\/\/link.springer.com\/chapter\/10.1007%2F978-3-319-12454-
4_15).\nConsiderable effort has been put into making slfm fast and memory
efficient,\nturning it an interesting alternative to simpler methods in terms\nof
execution time. It implements versions of the SLFM using both type\nof mixtures:
using a degenerate distribution or a very concentrated\nnormal distribution for the
spike part of the mixture. It also implements\nadditional functions to help pre-
process the data and fit the model\nfor a large number of arrays.","Imports":"Rcpp
(>= 0.11.0), coda, lattice","License":"GPL-
2","NeedsCompilation":"yes","Package":"slfm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Tools for Fitting Sparse Latent Factor
Model","URL":"https:\/\/github.com\/jdanielnd\/slfm","Version":"0.2.2"},"slp":
{"Author":"Wesley Burr, with contributions from Karim Rahim","Depends":"R (>=
2.15.1)","Description":"Interface for creation of 'slp' class smoother objects
for\nuse in Generalized Additive Models (as implemented by packages\n'gam' and
'mgcv').","Imports":"mgcv (>= 1.7.18)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"slp","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"gam (>= 1.09)","Title":"Discrete Prolate Spheroidal
(Slepian) Sequence Regression\nSmoothers","Version":"1.0-3"},"sm":{"Author":"Adrian
Bowman and Adelchi Azzalini.\nPorted to R by B. D. Ripley <ripley@stats.ox.ac.uk>
up to version 2.0,\nversion 2.1 by Adrian Bowman and Adelchi Azzalini,\nversion 2.2
by Adrian Bowman.","Depends":"R (>= 2.14.0)","Description":"This
is software linked to the book\n'Applied Smoothing Techniques for Data Analysis
-\nThe Kernel Approach with S-Plus Illustrations' Oxford University
Press.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"sm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"rpanel, tkrplot, rgl, misc3d, akima,
gam","Title":"Smoothing methods for nonparametric regression and
density\nestimation","URL":"http:\/\/www.stats.gla.ac.uk\/~adrian\/sm","Version":"2
.2-5.4"},"smaa":{"Author":"Gert van Valkenhoef","Description":"Implementation of
the Stochastic Multi-Criteria Acceptability Analysis (SMAA) family of Multiple
Criteria Decision Analysis (MCDA) methods.","Imports":"graphics","License":"GPL-
3","NeedsCompilation":"yes","Package":"smaa","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"hitandrun","Title":"Stochastic Multi-Criteria
Acceptability Analysis","URL":"http:\/\/github.com\/gertvv\/rsmaa","Version":"0.2-
4"},"smac":{"Author":"Chong Zhang, Guo Xian Yau, Yufeng Liu","Description":"This
package provides a solution path for L1-penalized angle-based classification. Three
loss functions are implemented in smac, including the deviance loss in logistic
regression, the exponential loss in boosting, and the proximal support vector
machine loss.","License":"GPL-
2","NeedsCompilation":"yes","Package":"smac","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Sparse Multi-category Angle-Based Large-Margin
Classifiers","Version":"1.0"},"smacof":{"Author":"Patrick Mair [aut, cre], Jan De
Leeuw [aut], Ingwer Borg [ctb], Patrick J. F. Groenen [ctb]","Depends":"R (>=
3.0.2)","Description":"Provides the following approaches for multidimensional
scaling (MDS) based on stress minimization by means of majorization (smacof): basic
MDS on symmetric dissimilarity matrices,\nMDS with external constraints on the
configuration, individual difference scaling (idioscal, indscal, and friends), MDS
with spherical restrictions, and unfolding. The MDS type can be ratio, interval,
ordinal, and monotone splines.\nVarious tools and extensions like jackknife MDS,
permutation tests, gravity models, inverse MDS, unidimensional scaling, classical
scaling, and Procrustes.","Imports":"graphics, stats, polynom, Hmisc, colorspace,
nnls, grDevices,\nMASS","License":"GPL-
3","NeedsCompilation":"yes","Package":"smacof","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"knitr, RgoogleMaps, plotrix","Title":"Multidimensional
Scaling","Version":"1.8-10"},"smacpod":{"Author":"Joshua French","Depends":"R (>=
3.1.1)","Description":"Various statistical methods for analyzing case-control point
data.\nThe methods available closely follow those in chapter 6 of Applied
Spatial\nStatistics for Public Health Data by Waller and Gotway
(2004).","Imports":"spatstat, SpatialTools, plotrix, parallel","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"smacpod","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"testthat","Title":"Statistical Methods for the
Analysis of Case-Control Point Data","Version":"1.4.1"},"smallarea":
{"Author":"Abhishek Nandy","Depends":"MASS","Description":"Inference techniques for
Fay Herriot Model.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"smallarea","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Fits a Fay Herriot Model","Version":"0.1"},"smam":
{"Author":"Jun Yan <jun.yan@uconn.edu> and\nVladimir Pozdnyakov
<vladimir.pozdnyakov@uconn.edu>","Depends":"R (>= 3.0.0),
Matrix","Description":"Animal movement models including moving-resting
process\nwith embedded Brownian motion, Brownian motion with measurement
error.","License":"GPL (>=
3.0)","NeedsCompilation":"yes","Package":"smam","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Statistical Modeling of Animal Movements","Version":"0.2-
2"},"smart":{"Author":"Fang Han, Han Liu","Depends":"R (>=
2.10)","Description":"The package \"smart\" provides a general framework
for\nanalyzing (including estimation, feature selection and\nprediction) and
visualize big data. It integrates several\nnovel, efficient and robust data
analysis tools, including\nTranselliptical Component Analysis (TCA),
Transelliptical\nCorrelation Estimation (TCE) and Group Nearest Shrunken\nCentroids
(gnsc). We target on high dimensional data\nanalysis(usually d >> n), and exploit
computationally\nefficiently approaches. Results are organized to be
visualized\nproperly for users.","Imports":"Matrix, gplots, gtools,PMA, elasticnet,
pcaPP, igraph","License":"GPL-
2","NeedsCompilation":"no","Package":"smart","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"huge","Title":"Sparse Multivariate Analysis via Rank
Transformation","Version":"1.0.1"},"smatr":{"Author":"David Warton
<David.Warton@unsw.edu.au>, Remko Duursma, Daniel Falster and Sara
Taskinen.","Depends":"plyr","Description":"This package provides methods of fitting
bivariate lines in allometry using the major axis (MA) or standardised major axis
(SMA), and for making inferences about such lines. The available methods of
inference include confidence intervals and one-sample tests for slope and
elevation, testing for a common slope or elevation amongst several allometric
lines, constructing a confidence interval for a common slope or elevation, and
testing for no shift along a common axis, amongst several samples.","License":"GPL-
2","NeedsCompilation":"no","Package":"smatr","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"(Standardised) Major Axis Estimation and Testing
Routines","URL":"http:\/\/web.maths.unsw.edu.au\/~dwarton,\nhttp:\/\/www.bitbucket.
org\/remkoduursma\/smatr","Version":"3.4-3"},"smbinning":{"Author":"Herman
Jopia","Depends":"R (>= 3.1.2),sqldf,partykit,Formula","Description":"It
categorizes a numeric variable into bins mapped to a binary target variable for its
ulterior usage in scoring modeling. Its purpose is to automate the time consuming
process of selecting the right cut points, quickly calculate metrics such as Weight
of Evidence and Information Value; and also document SQL codes, tables, and plots
used throughout the development stage. The package also allows users to establish
their own cut points for numeric characteristics and run the analysis for
categorical variables.","Imports":"gsubfn","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"smbinning","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Optimal Binning for Scoring
Modeling","URL":"http:\/\/www.scoringmodeling.com\/rpackage\/smbinning","Version":"
0.2"},"smcUtils":{"Author":"Author: Jarad
Niemi","Depends":"stats","Description":"Provides resampling functions (stratified,
residual,\nmultinomial, systematic, and branching), measures of weight\nuniformity
(coefficient of variation, effective sample size,\nand entropy), and a weight
renormalizing function.","License":"GPL-
3","NeedsCompilation":"yes","Package":"smcUtils","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"testthat, Hmisc","Title":"Utility functions for
sequential Monte
Carlo","URL":"https:\/\/github.com\/jarad\/smcUtils","Version":"0.2.2"},"smcfcs":
{"Author":"Jonathan Bartlett [aut, cre]","Depends":"R (>=
3.1.2)","Description":"Implements multiple imputation of missing covariates
by\nSubstantive Model Compatible Fully Conditional Specification.\nThis is a
modification of the popular FCS\/chained equations\nmultiple imputation approach,
and allows imputation of missing\ncovariate values from models which are compatible
with the user\nspecified substantive model.","Imports":"MASS, survival, VGAM,
3","NeedsCompilation":"no","Package":"smcfcs","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"knitr, rmarkdown, mitools","Title":"Multiple Imputation
of Covariates by Substantive Model\nCompatible Fully Conditional
Specification","URL":"http:\/\/www.missingdata.org.uk,
http:\/\/thestatsgeek.com","Version":"1.2.1"},"smco":{"Author":"Prof. Juan David
Velasquez H. Universidad Nacional de Colombia","Description":"This package is for
optimizing non-linear complex\nfunctions based on Monte Carlo random
sampling.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"smco","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"A simple Monte Carlo optimizer using adaptive
coordinate\nsampling","Version":"0.1"},"smcure":{"Author":"Chao Cai, Yubo Zou,
Yingwei Peng, Jiajia Zhang","Depends":"survival","Description":"An R-package for
Estimating Semiparametric PH and AFT\nMixture Cure Models","License":"GPL-
2","NeedsCompilation":"no","Package":"smcure","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Fit Semiparametric Mixture Cure
Models","Version":"2.0"},"smdata":{"Author":"Ed Merkle and Michael
Smithson","Description":"Contains data files to accompany Smithson & Merkle (2013),
Generalized Linear Models for Categorical and Continuous Limited Dependent
Variables.","License":"GPL-
2","NeedsCompilation":"no","Package":"smdata","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Data to accompany Smithson & Merkle,
2013","Version":"1.1"},"smdc":{"Author":"Masaaki
TAKADA","Depends":"proxy,tm","Description":"This package provides similarity among
documents.","License":"BSD","NeedsCompilation":"no","Package":"smdc","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Title":"Document
Similarity","Version":"0.0.2"},"smds":{"Author":"Yoshikazu Terada, Patrick J. F.
Groenen","Depends":"R (>= 1.8.0), MASS","Description":"Symbolic multidimensional
scaling for interval-valued dissimilarities. The hypersphere model and the hyperbox
model are available.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"smds","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Symbolic Multidimensional Scaling","Version":"1.0"},"sme":
{"Author":"Maurice Berk [aut, cre]","Depends":"R (>= 2.15.2), splines, lattice,
stats","Description":"A package
for fitting smoothing-splines mixed-effects models to replicated functional\ndata
3)","NeedsCompilation":"yes","Package":"sme","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Smoothing-splines Mixed-effects
Models","URL":"http:\/\/www2.imperial.ac.uk\/~mab201","Version":"0.8"},"smerc":
{"Author":"Joshua French","Description":"Provides statistical methods for the
analysis of data areal data, with a focus on cluster
detection.","Imports":"SpatialTools, fields, parallel, maps, smacpod, igraph,
spdep,\nutils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"smerc","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"testthat, sp","Title":"Statistical Methods for Regional
Counts","Version":"0.2.2"},"smfsb":{"Author":"Darren Wilkinson","Depends":"R (>=
2.9.0)","Description":"This package contains code and data for modelling and
simulation of stochastic kinetic biochemical network models. It contains the code
and data associated with the second edition of the book Stochastic Modelling for
Systems Biology, published by Chapman & Hall\/CRC Press, November
2011.","License":"LGPL-
3","NeedsCompilation":"yes","Package":"smfsb","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"deSolve (>= 1.9)","Title":"SMfSB 2e: Stochastic
Modelling for Systems Biology, second\nedition","Version":"1.1"},"smint":
{"Author":"Yves Deville <deville.yves@alpestat.com> Yann
Richet\n<yann.richet@irsn.fr>. Fortran codes by William Thacker, Manjula
Iyer\nJingwei Zhang, Laynet Watson, Jeffrey Birch, Manjula Iyer, Michael Berry\nand
Robert Renka. Fortran codes by Alain
Hebert.","Depends":"lattice","Description":"Smooth multivariate interpolation for
gridded and scattered data\nwith possibly large datasets. The code for scattered
data is taken from the\n'SHEPPACK' Fortran package.","Imports":"Matrix,
3","NeedsCompilation":"yes","Package":"smint","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Smooth Multivariate Interpolation for Gridded and Scattered
Data","Version":"0.4.2"},"smirnov":{"Author":"Alexey Shipunov (with help of Eugenij
Altshuler)","Description":"This tiny package contains one function smirnov()
which\ncalculates two scaled taxonomic coefficients, Txy (coefficient\nof
similarity) and Txx (coefficient of originality). These two\ncharacteristics may be
used for the analysis of similarities\nbetween any number of taxonomic groups, and
also for assessing\nuniqueness of giving taxon. It is possible to use
smirnov()\noutput as a distance measure: convert it to distance by\n\"as.dist(1 -
smirnov(x))\".","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"smirnov","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Provides two taxonomic coefficients from E. S.
Smirnov\n\"Taxonomic analysis\" (1969) book","Version":"1.0-1"},"smnet":
{"Author":"Alastair Rushworth","Depends":"SSN, spam","Description":"Fits flexible
additive models to data on stream networks, taking account of flow-connectivity of
the network. Models are fitted using penalised least squares.","Imports":"splines,
RSQLite, igraph, DBI","License":"GPL-
2","NeedsCompilation":"no","Package":"smnet","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Smoothing for Stream Network Data","Version":"2.0"},"smoof":
{"Author":"Jakob Bossek [aut, cre],\nPascal Kerschke [ctb]","Depends":"ParamHelpers
(>= 1.3), BBmisc (>= 1.6), checkmate (>= 1.1)","Description":"Provides generators
for a high number of both single- and multi-\nobjective test functions which are
frequently used for the benchmarking of\n(numerical) optimization algorithms.
Moreover, it offers a set of convenient\nfunctions to generate, plot and work with
objective functions.","Imports":"ggplot2, RColorBrewer, plot3D, mco, Rcpp (>=
LICENSE","NeedsCompilation":"yes","Package":"smoof","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"testthat, rPython (>= 0.0-5)","Title":"Single and
Multi-Objective Optimization Test
Functions","URL":"https:\/\/github.com\/jakobbossek\/smoof","Version":"1.3"},"smoot
hHR":{"Author":"Artur Araujo and Luis Meira-
Machado\n<lmachado@math.uminho.pt>","Depends":"R (>=
2.12.0),survival,splines","Description":"Provides flexible hazard ratio curves
allowing non-linear\nrelationships between continuous predictors and survival.
To\nbetter understand the effects that each continuous covariate\nhas on the
outcome, results are ex pressed in terms of hazard\nratio curves, taking a specific
covariate value as reference.\nConfidence bands for these curves are also
derived.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"smoothHR","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Smooth Hazard Ratio Curves Taking a Reference
Value","Version":"1.0.2"},"smoothSurv":{"Author":"ArnoÅ¡t KomÃ¡rek
<arnost.komarek@mff.cuni.cz>","Depends":"R (>= 3.0.0),
survival","Description":"Contains, as a main contribution, a function to fit\na
regression model with possibly right, left or interval\ncensored observations and
with the error distribution\nexpressed as a mixture of G-splines. Core part\nof the
computation is done in compiled C++ written\nusing the Scythe Statistical Library
Version 0.3.","Imports":"graphics, stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"smoothSurv","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Survival Regression with Smoothed Error
Distribution","URL":"http:\/\/msekce.karlin.mff.cuni.cz\/~komarek","Version":"1.6"}
,"smoother":{"Author":"Nicholas Hamilton","Depends":"TTR(>= 0.22)","Description":"A
collection of methods for smoothing numerical data, commencing with a port of the
Matlab gaussian window smoothing function. In addition, several functions typically
used in smoothing of financial data are included.","License":"GPL-
2","NeedsCompilation":"no","Package":"smoother","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Functions Relating to the Smoothing of Numerical
Data","Version":"1.1"},"smoothie":{"Author":"Eric Gilleland
<EricG@ucar.edu>","Depends":"R (>= 3.0.0)","Description":"Functions to smooth two-
dimensional fields using FFT and the convolution theorem","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"smoothie","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"SpatialVx, fields","Title":"Two-dimensional Field
Smoothing","URL":"http:\/\/www.ral.ucar.edu\/staff\/ericg","Version":"1.0-
1"},"smoothmest":{"Author":"Christian Hennig <chrish@stats.ucl.ac.uk>","Depends":"R
(>= 2.0), MASS","Description":"Some M-estimators for 1-dimensional location
(Bisquare, ML\nfor the Cauchy distribution, and the estimators from\napplication of
the smoothing principle introduced in Hampel,\nHennig and Ronchetti (2011) to the
above, the Huber\nM-estimator, and the median, main function is smoothm),
and\nPitman
estimator.","License":"GPL","NeedsCompilation":"no","Package":"smoothmest","Reposit
ory":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Smoothed M-estimators for 1-
dimensional
location","URL":"http:\/\/www.homepages.ucl.ac.uk\/~ucakche","Version":"0.1-
2"},"smoothtail":{"Author":"Kaspar Ru{f}{i}bach <kaspar.rufibach@gmail.com> and
Samuel Mueller <samuel.mueller@sydney.edu.au>","Depends":"logcondens (>=
2.0.0)","Description":"Given independent and identically distributed observations
X(1), ..., X(n) from a Generalized Pareto distribution with shape parameter gamma
in [-1,0], offers several estimates to compute estimates of gamma. The estimates
are based on the principle of replacing the order statistics by quantiles of a
distribution function based on a log--concave density function. This procedure is
justified by the fact that the GPD density is log--concave for gamma in [-
1,0].","Imports":"stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"smoothtail","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Smooth Estimation of GPD Shape
Parameter","URL":"http:\/\/www.kasparrufibach.ch,\nwww.maths.usyd.edu.au\/ut\/peopl
e?who=S_Mueller","Version":"2.0.4"},"sms":{"Author":"Dimitris Kavroudakis
<dimitris123@gmail.com>","Depends":"doParallel, foreach, parallel, methods,
iterators, stats","Description":"Produce small area population estimates by fitting
census data to\nsurvey data.","License":"GPL-
3","NeedsCompilation":"no","Package":"sms","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Spatial Microsimulation","Version":"2.3.1"},"smss":
{"Author":"Jeffrey B. Arnold [aut, cre],\nAlan Agresti [cph],\nBarbara Finlay
[cph]","Description":"Datasets used in \"Statistical Methods for the Social
Sciences\"\n(SMSS) by Alan Agresti and Barbara Finlay.","License":"GPL-
3","NeedsCompilation":"no","Package":"smss","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"devtools","Title":"Datasets for Agresti and
Finlay's \"Statistical Methods for the\nSocial Sciences\"","Version":"1.0-2"},"sn":
{"Author":"Adelchi Azzalini <adelchi.azzalini@unipd.it>","Depends":"R (>= 2.15.3),
methods, stats4","Description":"Build and manipulate probability distributions of
the skew-normal\nfamily and some related ones, notably the skew-t family, and
provide related\nstatistical methods for data fitting and diagnostics, in the
univariate and\nthe multivariate case.","Imports":"mnormt, numDeriv, stats,
grDevices, graphics, utils","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"sn","Repository":"http:\/\/cran.csiro.au\/src
\/contrib","Title":"The Skew-Normal and Skew-t
Distributions","URL":"http:\/\/azzalini.stat.unipd.it\/SN","Version":"1.3-
0"},"sna":{"Author":"Carter T. Butts [aut, cre, cph]","Depends":"R (>= 2.0.0),
utils","Description":"A range of tools for social network analysis, including node
and graph-level indices, structural distance and covariance methods, structural
equivalence detection, network regression, random graph generation,
and 2D\/3D network visualization.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"sna","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"network, rgl, numDeriv, SparseM","Title":"Tools for
Social Network Analysis","URL":"http:\/\/www.statnet.org","Version":"2.3-
2"},"snapshot":{"Author":"Aaron Robotham","Depends":"R (>=
2.13)","Description":"Functions for reading and writing Gadget N-body snapshots.
The Gadget code is popular in astronomy for running N-body \/ hydrodynamical
cosmological and merger simulations. To find out more about Gadget see the main
distribution page at www.mpa-garching.mpg.de\/gadget\/","License":"GPL-
2","NeedsCompilation":"no","Package":"snapshot","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Gadget N-body cosmological simulation code snapshot
I\/O\nutilities","Version":"0.1.2"},"snht":{"Author":"Josh Browning [aut,
cre],\nCarina Schneider [aut]","Description":"Implementation of robust and non-
robust Standard Normal Homogeneity\nTest (SNHT) for changepoint detection. This
test statistic is equal sided,\nas proposed in \"Homogenization of Radiosonde
Temperature Time Series Using\nInnovation Statistics\" by Haimberger, L., 2007.
However, the statistic contains\nan estimate of sigma^2 in the denominator instead
of sigma, which seems to\nbe a more appropriate value (based on the
paper \"Homogenization of Swedish\ntemperature data. Part I: Homogeneity test for
linear trends.\" by Alexandersson,\nH., and A. Moberg, 1997).","Imports":"mgcv,
ggplot2, gridExtra, zoo, plyr, reshape2, methods","License":"GPL-
3","NeedsCompilation":"no","Package":"snht","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"mvtnorm, knitr","Title":"Standard Normal Homogeneity
Test","Version":"1.0.4"},"snipEM":{"Author":"Alessio Farcomeni, Andy
Leung","Depends":"R (>= 3.0.0), Rcpp (>= 0.10.0), mvtnorm, MASS,
GSE","Description":"Snipping methods","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"snipEM","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Snipping methods for robust estimation and
clustering","Version":"1.0"},"snn":{"Author":"Wei Sun, Xingye Qiao, and Guang
Cheng","Depends":"R (>= 3.0.0), stats","Description":"Implement K-nearest neighbor
classifier, weighted nearest neighbor classifier, bagged nearest neighbor
classifier, optimal weighted nearest neighbor classifier and stabilized nearest
neighbor classifier, and perform model selection via 5 fold cross-validation for
them. This package also provides functions for computing the classification error
and classification instability of a classification procedure.","License":"GPL-
3","NeedsCompilation":"no","Package":"snn","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Stabilized Nearest Neighbor
Classifier","Version":"1.1"},"snow":{"Author":"Luke Tierney, A. J. Rossini, Na Li,
H. Sevcikova","Depends":"R (>= 2.13.1), utils","Description":"Support for simple
parallel computing in
R.","License":"GPL","NeedsCompilation":"no","Package":"snow","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Suggests":"Rmpi,rlecuyer,nws","Title":"Simple
Network of Workstations","Version":"0.4-1"},"snowFT":{"Author":"Hana Sevcikova, A.
J. Rossini","Depends":"R (>= 2.11), snow (>= 0.3-3),
rlecuyer","Description":"Extension of the snow package supporting fault tolerant
and reproducible applications, as well as supporting easy-to-use parallel
programming - only one function is needed.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"snowFT","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"Rmpi","Title":"Fault Tolerant Simple Network of
Workstations","URL":"http:\/\/www.stat.washington.edu\/hana\/parallel\/snowFT-
doc.pdf","Version":"1.4-0"},"snowboot":{"Author":"Leticia Ramirez-Ramirez, Kusha
Nezafati, Vyacheslav Lyubchich, Yulia Gel","Depends":"R (>=
3.2.2)","Description":"Functions for analysis of network objects, which are
imported or\nsimulated by the package. The non-parametric methods of analysis
center\naround snowball and bootstrap sampling.","Imports":"VGAM, igraph, stats,
3","NeedsCompilation":"yes","Package":"snowboot","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Bootstrap Methods for Network
Inference","Version":"0.5.1"},"snowfall":{"Author":"Jochen Knaus","Depends":"R (>=
2.10), snow","Description":"Usability wrapper around snow for easier development
of\nparallel R programs. This package offers e.g. extended error\nchecks, and
additional functions. All functions work in\nsequential mode, too, if no cluster is
present or wished.\nPackage is also designed as connector to the cluster
management\ntool sfCluster, but can also used without
it.","License":"GPL","NeedsCompilation":"no","Package":"snowfall","Repository":"htt
p:\/\/cran.csiro.au\/src\/contrib","Suggests":"Rmpi","Title":"Easier cluster
computing (based on snow)","Version":"1.84-6.1"},"snp.plotter":{"Author":"Augustin
Luna <augustin@mail.nih.gov>, Kristin K.
Nicodemus\n<kristin.nicodemus@well.ox.ac.uk>,
<nicodemusk@mail.nih.gov>","Depends":"R (>= 2.0.0), grid","Description":"Creates
plots of p-values using single SNP and\/or haplotype data.\nMain features of the
package include options to display a linkage\ndisequilibrium (LD) plot and the
ability to plot multiple datasets\nsimultaneously. Plots can be created using
global and\/or individual\nhaplotype p-values along with single SNP p-values.
Images are created as\neither PDF\/EPS files.","Imports":"genetics","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"snp.plotter","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"knitr","Title":"snp.plotter","URL":"https:\/\/gith
ub.com\/cannin\/snp_plotter
or\nhttp:\/\/cbdb.nimh.nih.gov\/~kristin\/snp.plotter.html","Version":"0.5.1"},"snp
Enrichment":{"Author":"Mickael Canouil [aut, cre],\nLoic Yengo [ctb]","Depends":"R
(>= 3.0.0), methods","Description":"Implements classes and methods for large scale
SNP enrichment analysis (e.g. SNPs associated with genes expression in a GWAS
signal).","Imports":"parallel, snpStats, grid, ggplot2, grDevices, graphics,
2)","NeedsCompilation":"no","Package":"snpEnrichment","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"SNPs Enrichment
Analysis","URL":"https:\/\/github.com\/mcanouil\/snpEnrichment","Version":"1.7.0"},
"snpRF":{"Author":"Fortran original by Leo Breiman and Adele Cutler, R port by Andy
Liaw and Matthew\nWiener. Modifications of randomForest v 4.6-7 for SNPs by Greg
Jenkins based on a\nmethod developed by Stacey Winham, Greg Jenkins and Joanna
Biernacka.","Depends":"R (>= 2.5.0), stats","Description":"A modification of
Breiman and Cutler's classification random forests modified for SNP (Single
Nucleotide Polymorphism) data (based on randomForest v4.6-7) to prevent X-
chromosome SNP variable importance bias compared to autosomal SNPs by simulating
the process of X chromosome inactivation. Classification is based on a forest of
trees using random subsets of SNPs and other variables as inputs.","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"snpRF","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"RColorBrewer, MASS","Title":"Random Forest for SNPs to
Prevent X-chromosome SNP Importance\nBias","Version":"0.4"},"snpar":
{"Author":"Debin Qiu","Description":"contains several supplementary non-parametric
statistics methods including quantile test, Cox-Stuart trend test, runs test,
normal score test, kernel PDF and CDF estimation, kernel regression estimation and
kernel Kolmogorov-Smirnov test.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"snpar","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Supplementary Non-parametric Statistics
Methods","Version":"1.0"},"snplist":{"Author":"Chanhee Yi, Alexander Sibley, and
Kouros Owzar","Depends":"R (>= 3.0.0), RSQLite (>= 0.11.4)","Description":"A set of
functions to create SQL tables of gene and SNP information and compose them into a
SNP Set, for example for use with the RSNPset package, or to export to a PLINK
set.","Imports":"biomaRt (>= 2.16.0), Rcpp (>= 0.10.5), R.utils (>= 1.27.1),\nDBI
(>= 0.3.1)","License":"GPL-
3","NeedsCompilation":"yes","Package":"snplist","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"knitr","Title":"Tools to Create Gene
Sets","Version":"0.15"},"sns":{"Author":"Alireza S. Mahani, Asad Hasan, Marshall
Jiang, Mansour T.A. Sharabiani","Description":"Stochastic Newton Sampler (SNS) is a
Metropolis-Hastings-based, Markov Chain Monte Carlo sampler for twice
differentiable, log-concave probability density functions (PDFs) where the proposal
density function is a multivariate Gaussian resulting from a second-order Taylor-
series expansion of log-density around the current point. The mean of the Gaussian
proposal is the full Newton-Raphson step from the current point. A Boolean flag
allows for switching from SNS to Newton-Raphson optimization (by choosing the mean
of proposal function as next point). This can be used during burn-in to get close
to the mode of the PDF (which is unique due to concavity). For high-dimensional
densities, mixing can be improved via 'state space partitioning' strategy, in which
SNS is applied to disjoint subsets of state space, wrapped in a Gibbs cycle.
Numerical differentiation is available when analytical expressions for gradient and
Hessian are not available. Facilities for validation and numerical differentiation
of log-density are provided.","Imports":"mvtnorm, coda, numDeriv","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"sns","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"RegressionFactory, MfUSampler","Title":"Stochastic Newton
Sampler (SNS)","Version":"1.1.0"},"soc.ca":{"Author":"Anton Grau Larsen, with
contributions from Christoph Ellersgaard and\nStefan Andrade","Depends":"R (>=
2.15.0),
ggplot2","Description":"Specific and class specific multiple correspondence
analysis on\nsurvey-like data. Soc.ca is optimized to the needs of the social
scientist and\npresents easily interpretable results in near publication ready
quality.","Imports":"gridExtra, ellipse, stats, utils, shiny, reshape2,
ggrepel","License":"GPL-
3","NeedsCompilation":"no","Package":"soc.ca","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Specific Correspondence Analysis for the Social
Sciences","URL":"https:\/\/github.com\/Rsoc\/soc.ca","Version":"0.7.3"},"sodavis":
{"Author":"Yang Li, Jun S. Liu","Depends":"R (>= 3.0.0), nnet,
MASS","Description":"Variable and interaction selection are essential to
classification in high-dimensional setting. In this package, we provide the
implementation of SODA procedure, which is a forward-backward algorithm that
selects both main and interaction effects under quadratic discriminant analysis and
logistic regression model.","License":"GPL-
2","NeedsCompilation":"no","Package":"sodavis","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"SODA: Main and Interaction Effects Selection for
Discriminant\nAnalysis and Logistic Regression","Version":"0.1"},"sodium":
{"Author":"Jeroen Ooms","Description":"Bindings to libsodium: a modern, easy-to-use
software library for\nencryption, decryption, signatures, password hashing and
more. Sodium uses\ncurve25519, a state-of-the-art Diffie-Hellman function by Daniel
Bernstein,\nwhich has become very popular after it was discovered that the NSA
had\nbackdoored Dual EC DRBG.","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"sodium","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"knitr, rmarkdown","Title":"A Modern and Easy-to-
Use Crypto
Library","URL":"https:\/\/github.com\/jeroenooms\/sodium\nhttps:\/\/download.libsod
ium.org\/doc\/","Version":"0.2"},"softImpute":{"Author":"Trevor Hastie
<hastie@stanford.edu> and Rahul Mazumder
<rahul.mazumder@gmail.com>","Depends":"Matrix, methods","Description":"Iterative
methods for matrix completion that use nuclear-norm regularization. There are two
main approaches.The one approach uses iterative soft-thresholded svds to impute the
missing values. The second approach uses alternating least squares. Both have
an \"EM\" flavor, in that at each iteration the matrix is completed with the
current estimate. For large matrices there is a special sparse-matrix class
named \"Incomplete\" that efficiently handles all computations. The package
includes procedures for centering and scaling rows, columns or both, and for
computing low-rank SVDs on large sparse centered matrices (i.e. principal
components)","License":"GPL-
2","NeedsCompilation":"yes","Package":"softImpute","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"knitr","Title":"Matrix Completion via Iterative
Soft-Thresholded SVD","Version":"1.4"},"softclassval":{"Author":"C. Beleites
<chemometrie@beleites.de>","Depends":"arrayhelpers (>= 0.76)","Description":"An
extension of sensitivity, specificity, positive and negative\npredictive value to
continuous predicted and reference memberships in\n[0,
1].","Imports":"svUnit","License":"GPL","NeedsCompilation":"no","Package":"softclas
sval","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Soft
Classification Performance Measures","URL":"http:\/\/softclassval.r-forge.r-
project.org\/","Version":"1.0-20150416"},"soil.spec":{"Author":"Andrew Sila,
Tomislav Hengl and Thomas Terhoeven-Urselmans","Depends":"R (>=
3.0)","Description":"Methods and classes for processing and analyzing soil and
plant infrared (MIR, alpha-MIR and VISNIR) spectroscopy readings based on the
Africa Soil Information Services (AfSIS) project data.","Imports":"methods, stats,
pls, KernSmooth, wavelets, hexView, sp, GSIF","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"soil.spec","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"e1071, class, chemometrics, plyr, plotKML, mgcv,
nlme,\nspatstat, scales, date, lava, rgdal","Title":"Soil Spectroscopy Tools and
Reference Models","URL":"http:\/\/worldagroforestry.org\/research\/land-
health,\nhttp:\/\/www.africasoils.net\/","Version":"2.1.4"},"soilDB":
{"Author":"D.E. Beaudette and J.M. Skovlin","Depends":"R (>= 3.0.0),
aqp","Description":"A collection of functions for reading data from USDA-NCSS soil
databases.","Imports":"grDevices, graphics, stats, utils, plyr, Hmisc, XML,
sp,\nreshape","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"soilDB","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"lattice, dismo, raster, rgdal, jsonlite, RODBC, httr,
rgeos","Title":"Soil Database Interface","URL":"http:\/\/aqp.r-forge.r-
project.org\/","Version":"1.7"},"soilphysics":{"Author":"Anderson Rodrigo da Silva,
Renato Paiva de Lima","Depends":"R (>= 2.15), rpanel, MASS, tcltk,
tkrplot","Description":"Basic and model-based soil physical
analyses.","Imports":"utils, stats, graphics, boot, grDevices,
datasets","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"soilphysics","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"soiltexture","Title":"Soil Physical
Analysis","Version":"3.0"},"soilprofile":{"Author":"Gianluca Filippa","Depends":"R
(>= 2.14.1), aqp, lattice, munsell, splancs, methods","Description":"This package
provides functions to graphically represent\nsoil properties. Morphological data
gathered in the field\nsuch as horizon boundaries, root abundance and
dimensions,\nskeletal shape, abundance and dimension as well as\nmeaningful soil
color may be represented via the plot\nfunction. A lattice-based plot.element
function has been\ndesigned to represent depth function of a given
variable.","License":"GPL-
2","NeedsCompilation":"no","Package":"soilprofile","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"A package to consistently represent soil properties
along a soil\nprofile","Version":"1.0"},"soiltexture":{"Author":"Julien Moeys [aut,
cre], Wei Shangguan [ctb], Rainer Petzold [ctb], Budiman Minasny [ctb], Bogdan
Rosca [ctb], Nic Jelinski [ctb], Wiktor Zelazny [ctb], Rodolfo Marcondes Silva
Souza [ctb], Jose Lucas Safanelli [ctb], Alexandre ten Caten [ctb]","Depends":"R
(>= 3.1.1), utils","Description":"\"The Soil Texture Wizard\" is a set of R
functions designed to produce texture triangles (also called texture plots, texture
diagrams, texture ternary plots), classify and transform soil textures data. These
functions virtually allows to plot any soil texture triangle (classification) into
any triangle geometry (isosceles, right-angled triangles, etc.). This set of
function is expected to be useful to people using soil textures data from different
soil texture classification or different particle size systems. Many (> 15) texture
triangles from all around the world are predefined in the package. A simple text
based graphical user interface is provided: soiltexture_gui().","Imports":"sp,
MASS, tools, tcltk","License":"AGPL (>=
3)","NeedsCompilation":"no","Package":"soiltexture","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"xtable","Title":"Functions for Soil Texture Plot,
Classification and\nTransformation","URL":"http:\/\/soiltexture.r-forge.r-
project.org\/","Version":"1.3.3"},"soilwater":{"Author":"Emanuele Cordano, Daniele
Andreis, Fabio Zottele","Description":"It is a set of R implementations of
parametric formulas of soil water\nretention or conductivity curve. At the moment,
only Van Genuchten (for\nsoil water retention curve) and Mualem (for hydraulic
conductivity) were\nimplemented. See
reference\n\\url{http:\/\/en.wikipedia.org\/wiki\/Water_retention_curve}.","License
":"GPL (>=
2)","NeedsCompilation":"no","Package":"soilwater","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"raster","Title":"Implementation of Parametric
Formulas for Soil Water Retention\nor Conductivity
Curve","URL":"https:\/\/github.com\/ecor\/soilwater","Version":"1.0.2"},"solaR":
{"Author":"Oscar PerpiÃ±Ã¡n Lamigueiro","Depends":"R (>= 2.10), methods, zoo,
lattice, latticeExtra","Description":"Calculation methods of solar radiation and
performance of photovoltaic systems from daily and intradaily irradiation data
sources.","Imports":"RColorBrewer","License":"GPL-
3","NeedsCompilation":"no","Package":"solaR","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"sp, raster, rasterVis, tdr","Title":"Radiation and
Photovoltaic
Systems","URL":"http:\/\/oscarperpinan.github.io\/solar\/","Version":"0.41"},"solar
Pos":{"Author":"Jasper Van doninck","Description":"Calculation of solar zenith and
azimuth angles.","License":"GPL-
2","NeedsCompilation":"no","Package":"solarPos","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Solar Position Algorithm for Solar Radiation
Applications","Version":"1.0"},"solidearthtide":{"Author":"Jose Gama [aut,
cre],\nDennis Milbert [aut, cph]","Depends":"R (>= 2.7.0)","Description":"Predicted
solid earth tide displacements in the meridional,\nzonal and vertical directions.
Based on \"Solid\" from Dennis Milbert,\nmodified from \"dehanttideinelMJD\" by V.
Dehant, S. Mathews, J. Gipson,\nand C. Bruyninx.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"solidearthtide","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Solid Earth Tide
Computation","Version":"1.0.2"},"solr":{"Author":"Scott Chamberlain [aut,
cre]","Description":"Provides a set of functions for querying and parsing\ndata
from Solr endpoints (local and remote), including search, faceting,\nhighlighting,
stats, and 'more like this'.","Imports":"methods, utils, plyr, httr, XML,
assertthat, rjson","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"solr","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat, roxygen2, knitr","Title":"General Purpose
R Interface to
Solr","URL":"https:\/\/github.com\/ropensci\/solr","Version":"0.1.6"},"solrium":
{"Author":"Scott
Chamberlain [aut, cre]","Description":"Provides a set of functions for querying
and parsing data\nfrom 'Solr' (<http:\/\/lucene.apache.org\/solr>) 'endpoints'
(local and\nremote), including search, 'faceting', 'highlighting', 'stats',
and\n'more like this'. In addition, some functionality is included for\ncreating,
deleting, and updating documents in a 'Solr' 'database'.","Imports":"stats, utils,
methods, dplyr, plyr, httr (>= 1.0.0), XML,\njsonlite","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"solrium","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat, knitr","Title":"General Purpose R
Interface to
'Solr'","URL":"https:\/\/github.com\/ropensci\/solrium","Version":"0.3.0"},"som":
{"Author":"Jun Yan <jyan@stat.uconn.edu>","Depends":"R (>=
1.9.0)","Description":"Self-Organizing Map (with application in gene
clustering)","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"som","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Self-Organizing Map","Version":"0.3-5"},"soma":
{"Author":"Jon Clayden; based on the work of Ivan Zelinka","Depends":"R (>=
2.5.0)","Description":"This package provides an R implementation of the Self-
Organising Migrating Algorithm, a general-purpose, stochastic optimisation
algorithm. The approach is similar to that of genetic algorithms, although it is
based on the idea of a series of ``migrations'' by a fixed set of individuals,
rather than the development of successive generations. It can be applied to any
cost-minimisation problem with a bounded parameter space, and is robust to local
minima.","Imports":"reportr","License":"GPL-
2","NeedsCompilation":"no","Package":"soma","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"General-Purpose Optimisation With the Self-Organising
Migrating\nAlgorithm","URL":"https:\/\/github.com\/jonclayden\/soma\/,\nhttp:\/\/ww
w.ft.utb.cz\/people\/zelinka\/soma\/","Version":"1.1.1"},"someKfwer":{"Author":"L.
Finos and A. Farcomeni","Description":"This package collects some procedures
controlling the\nGeneralized Familywise Error Rate.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"someKfwer","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Controlling the Generalized Familywise Error
Rate","Version":"1.2"},"someMTP":{"Author":"livio
finos","Depends":"methods","Description":"It's a collection of functions for
Multiplicity Correction and Multiple Testing.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"someMTP","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Some Multiple Testing
Procedures","Version":"1.4.1"},"somebm":{"Author":"Junwen Huang
<hjwdhjwd@gmail.com>","Depends":"R (>= 3.0.2)","Description":"some Brownian motions
simulation functions","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"somebm","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"some Brownian motions simulation
functions","Version":"0.1"},"sommer":{"Author":"Giovanny Covarrubias-
Pazaran","Depends":"R (>= 2.10), Matrix (>= 1.1.1), methods, stats,
MASS,\nmatrixcalc","Description":"Mixed model equation solver allowing the
specification of variance covariance structures of random effects and residual
structures. ML\/REML estimates are obtained using the Average Information and\/or
Expectation-Maximization algorithms. Designed for genomic prediction and genome
wide association studies (GWAS) to include additive, dominant and epistatic
relationship structures or other covariance structures in R.","License":"GPL-
3","NeedsCompilation":"no","Package":"sommer","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Solving Mixed Model Equations in
R","URL":"http:\/\/www.wisc.edu","Version":"1.4"},"somplot":{"Author":"Benjamin
Schulz, Andreas Dominik","Depends":"hexbin","Description":"The package provides the
plot function som.plot() to\ncreate high quality visualisations of hexagonal
Kohonen maps\n(self-organising maps).","License":"GPL-
2","NeedsCompilation":"no","Package":"somplot","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Visualisation of hexagonal Kohonen
maps","Version":"1.6.4"},"sonicLength":{"Author":"Charles Berry
<ccberry@ucsd.edu>","Depends":"R (>= 2.14.0), splines","Description":"Estimate the
abundance of cell clones from the\ndistribution of lengths of DNA fragments (as
created by\nsonication, whence `sonicLength'). The algorithm in\n\"Estimating
abundances of retroviral insertion sites from\nDNA fragment length data\" by Berry
CC, Gillet NA, Melamed\nA, Gormley N, Bangham CR, Bushman FD. Bioinformatics;\n2012
Mar 15;28(6):755-62 is implemented. The\nexperimental setting and estimation
details are described\nin detail there. Briefly, integration of new DNA in a\nhost
genome (due to retroviral infection or gene therapy)\ncan be tracked using DNA
sequencing, potentially allowing\ncharacterization of the abundance of individual
cell\nclones bearing distinct integration sites. The locations\nof integration
sites can be determined by fragmenting the\nhost DNA (via sonication or
fragmentase), breaking the\nnewly integrated DNA at a known sequence, amplifying
the\nfragments containing both host and integrated DNA,\nsequencing those
amplicons, then mapping the host\nsequences to positions on the reference genome.
The\nrelative number of fragments containing a given position\nin the host genome
estimates the relative abundance of\ncells hosting the corresponding integration
site, but\nthat number is not available and the count of amplicons\nper fragment
varies widely. However, the expected number\nof distinct fragment lengths is a
function of the\nabundance of cells hosting an integration site at a
given\nposition and a certain nuisance parameter. The algorithm\nimplicitly
estimates that function to estimate the\nrelative abundance.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"sonicLength","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Estimating Abundance of Clones from DNA fragmentation
data","Version":"1.4.4"},"soobench":{"Author":"Olaf Mersmann <olafm@p-value.net>
Bernd Bischl\n<bischl@statistik.tu-dortmund.de>","Description":"Collection of
different single objective test functions\nuseful for benchmarks and algorithm
development.","License":"BSD","NeedsCompilation":"yes","Package":"soobench","Reposi
tory":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"rgl","Title":"Single
Objective Optimization Benchmark Functions","Version":"1.0-73"},"soql":
{"Author":"Zeb Burke-Conte","Description":"Used to construct the URLs and
parameters of 'Socrata Open Data API' <https:\/\/dev.socrata.com> calls, using the
API's 'SoQL' parameter format. Has method-chained and sensical syntax. Plays well
with pipes.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"soql","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"magrittr","Title":"Helps Make Socrata Open Data API
Calls","Version":"0.1.1"},"sortinghat":{"Author":"John A. Ramey","Depends":"R (>=
3.0.1)","Description":"sortinghat is a classification framework to streamline
the\nevaluation of classifiers (classification models and algorithms) and seeks\nto
determine the best classifiers on a variety of simulated and benchmark\ndata sets.
Several error-rate estimators are included to evaluate the\nperformance of a
classifier. This package is intended to complement the\nwell-known 'caret'
package.","Imports":"MASS, bdsmatrix, mvtnorm","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"sortinghat","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"testthat","Title":"sortinghat","URL":"http:\/\
/github.com\/ramhiser\/sortinghat","Version":"0.1"},"sorvi":{"Author":"Leo Lahti,
Juuso Parkkinen, Joona Lehtomaki, Juuso Haapanen, Jussi\nPaananen, Einari
Happonen","Depends":"R (>= 3.0.2)","Description":"Algorithms for Finnish open
government data.","Imports":"ggplot2, RColorBrewer, dplyr,
reshape2","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"sorvi","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"gdata, knitr, rmarkdown, RCurl, rjson,
testthat","Title":"Finnish Open Government Data
Toolkit","URL":"https:\/\/github.com\/ropengov\/sorvi,\nhttp:\/\/cran.r-
project.org\/package=sorvi","Version":"0.7.26"},"sos":{"Author":"Spencer Graves,
Sundar Dorai-Raj, and Romain Francois","Depends":"brew","Description":"Search
contributed R packages, sort by package","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"sos","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"RODBC, WriteXLS, fda","Title":"Search contributed R
packages, sort by package","Version":"1.3-8"},"sos4R":{"Author":"Daniel Nuest [cre,
aut]","Depends":"R (>= 2.15.0), XML, RCurl (>= 1.4-1), sp, methods,
graphics","Description":"sos4R is a client for Sensor Observation Services (SOS)
as\nspecified by the Open Geospatial Consortium (OGC). It allows\nusers to
retrieve metadata from SOS web services and to\ninteractively create requests for
near real-time observation\ndata based on the available sensors, phenomena,
observations et\ncetera using thematic, temporal and spatial
filtering.","License":"GPL-
2","NeedsCompilation":"no","Package":"sos4R","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"spacetime (>= 0.2-0), gstat, maps, maptools,
mapdata,\ncshapes, xts, xtable, rgdal","Title":"An R client for the OGC Sensor
Observation
Service","URL":"http:\/\/www.nordholmen.net\/sos4r,\nhttp:\/\/www.52north.org\/geos
tatistics","Version":"0.2-11"},"sotkanet":{"Author":"Leo Lahti, Einari Happonen,
Juuso Parkkinen, Joona Lehtomaki","Depends":"R (>= 3.0.2),
RCurl","Description":"Tools to download data from the Sotkanet open data
portal.","Imports":"rjson","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"sotkanet","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"ggplot2,
knitr","Title":"Tools for Sotkanet Open Data
Portal","URL":"https:\/\/github.com\/ropengov\/sotkanet,\nhttp:\/\/cran.r-
project.org\/package=sotkanet","Version":"0.9.21"},"soundecology":{"Author":"Luis
J. Villanueva-Rivera and Bryan C. Pijanowski","Depends":"R(>=
2.14.0)","Description":"Functions to calculate indices for soundscape ecology and
other ecology research that uses audio recordings.","Imports":"parallel, pracma,
oce, ineq, vegan, tuneR, seewave","License":"GPL-
3","NeedsCompilation":"no","Package":"soundecology","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"knitr","Title":"Soundscape
Ecology","URL":"http:\/\/ljvillanueva.github.io\/soundecology\/","Version":"1.3.1"}
,"source.gist":{"Author":"Mason Simon","Depends":"RCurl,
rjson","Description":"Analogous to source(), but works when given a Gist URL
or\nID.","License":"MIT","NeedsCompilation":"no","Package":"source.gist","Repositor
y":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Read R code from a GitHub
Gist","Version":"1.0.0"},"sourcetools":{"Author":"Kevin Ushey","Depends":"R (>=
3.0.2)","Description":"Tools for the reading and tokenization of R code.\nThe
'sourcetools' package provides both an R and C++ interface\nfor the tokenization of
R code, and helpers for interacting\nwith the tokenized representation of R
code.","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"sourcetools","Repository":"http:\/\/cr
an.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Tools for the Reading and
Tokenization of R Code","Version":"0.1.2"},"sp":{"Author":"Edzer Pebesma [aut,
cre],\nRoger Bivand [aut],\nBarry Rowlingson [ctb],\nVirgilio Gomez-Rubio
[ctb],\nRobert Hijmans [ctb],\nMichael Sumner [ctb],\nDon MacQueen [ctb],\nJim
Lemon [ctb],\nJosh O'Brien [ctb]","Depends":"R (>= 3.0.0)","Description":"Classes
and methods for spatial\ndata; the classes document where the spatial location
information\nresides, for 2D or 3D data. Utility functions are provided, e.g.
for\nplotting data as maps, spatial selection, as well as methods for\nretrieving
coordinates, for subsetting, print, summary, etc.","Imports":"utils, stats,
graphics, grDevices, methods, lattice, grid","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"sp","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"RColorBrewer, rgdal (>= 0.8-7), rgeos (>= 0.3-13),
gstat,\nmaptools, deldir","Title":"Classes and Methods for Spatial
Data","URL":"https:\/\/github.com\/edzer\/sp\/\nhttp:\/\/rspatial.r-forge.r-
project.org\/","Version":"1.2-2"},"sp23design":{"Author":"Balasubramanian
Narasimhan [aut, cre],\nMei-Chiung Shih [aut], Pei He [aut]","Depends":"R (>= 3.0),
mvtnorm, survival","Description":"Provides methods for generating, exploring and
executing seamless Phase II-III designs of Lai, Lavori and Shih using generalized
likelihood ratio statistics. Includes pdf and source files that describe the entire
R implementation with the relevant mathematical details.","License":"LGPL-
3","NeedsCompilation":"no","Package":"sp23design","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"RUnit","Title":"Design and Simulation of seamless
Phase II-III Clinical Trials","Version":"0.9"},"spBayes":{"Author":"Andrew O.
Finley <finleya@msu.edu>, Sudipto
Banerjee\n<sudiptob@biostat.umn.edu>","Depends":"R (>= 1.8.0), coda, magic, abind,
Formula","Description":"Fits univariate and multivariate spatio-temporal\nmodels
with Markov chain Monte Carlo (MCMC).","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"spBayes","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"MBA, geoR","Title":"Univariate and Multivariate
Spatial-temporal
Modeling","URL":"http:\/\/blue.for.msu.edu\/software","Version":"0.3-
9"},"spBayesSurv":{"Author":"Haiming Zhou <zhouh@niu.edu> and Tim Hanson
<hansont@stat.sc.edu>","Depends":"R (>= 3.0.2)","Description":"Provides several
Bayesian survival models for spatial\/non-spatial survival data: marginal Bayesian
Nonparametric models, marginal Bayesian proportional hazards models, generalized
accelerated failure time frailty models, and standard semiparametric frailty models
within the context of proportional hazards, proportional odds and accelerated
failure time.","Imports":"Rcpp (>= 0.11.1), survival, coda, methods","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"spBayesSurv","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Bayesian Modeling and Analysis of Spatially
Correlated Survival\nData","Version":"1.0.3"},"spMC":{"Author":"Luca
Sartore","Depends":"R (>= 3.0.0), base, methods, datasets, utils,
grDevices,\ngraphics, stats","Description":"A set of functions is provided for 1)
the stratum lengths analysis along a chosen direction, 2) fast estimation of
continuous lag spatial Markov chains model parameters and probability computing
(also for large data sets), 3) transition probability maps and transiograms
drawing, 4) simulation methods for categorical random fields.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"spMC","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Continuous-Lag Spatial Markov
Chains","Version":"0.3.6"},"spTDyn":{"Author":"K. Shuvo Bakar, Philip Kokic,
Huidong Jin","Depends":"R (>= 3.2.0), coda, sp","Description":"Fits, spatially
predicts, and temporally forecasts space-time data using Gaussian Process (GP): (1)
spatially varying coefficient process models and (2) spatio-temporal dynamic linear
2)","NeedsCompilation":"yes","Package":"spTDyn","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Spatially Varying and Spatio-Temporal Dynamic Linear
Models","Version":"1.0"},"spTest":{"Author":"Zachary Weller [aut,
cre]","Depends":"R (>= 3.0.0)","Description":"Implements nonparametric hypothesis
tests to check isotropy and\nsymmetry properties for two-dimensional spatial
data.","Imports":"stats,fields,methods","License":"CC0","NeedsCompilation":"no","Pa
ckage":"spTest","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Suggests":"mvt
norm,geoR","Title":"Nonparametric Hypothesis Tests of Isotropy and
Symmetry","Version":"0.2.3"},"spThin":{"Author":"Matthew E. Aiello-Lammens, Robert
A. Boria, Aleksandar Radosavljevic,\nBruno Vilela, and Robert P.
Anderson","Depends":"spam, grid, fields, knitr","Description":"spThin is a set of
functions that can be used to spatially thin\nspecies occurrence data. The
resulting thinned data can be used in ecological\nmodeling, such as ecological
niche modeling.","License":"GPL-
3","NeedsCompilation":"no","Package":"spThin","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Functions for Spatial Thinning of Species Occurrence
Records for\nUse in Ecological Models","Version":"0.1.0"},"spTimer":{"Author":"K.
Shuvo Bakar & Sujit K. Sahu","Depends":"R (>= 2.15.0)","Description":"Fits,
spatially predicts and temporally forecasts large amounts of space-time data using
[1] Bayesian Gaussian Process (GP) Models, [2] Bayesian Auto-Regressive (AR)
Models, and [3] Bayesian Gaussian Predictive Processes (GPP) based AR Models for
spatio-temporal big-n problems.","Imports":"coda, sp, grDevices, graphics, stats,
2)","NeedsCompilation":"yes","Package":"spTimer","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Spatio-Temporal Bayesian Modelling Using
R","Version":"2.0-1"},"spa":{"Author":"Mark Culp","Depends":"R (>= 2.10), cluster,
MASS","Description":"Implements the Sequential Predictions
Algorithm","License":"GPL","NeedsCompilation":"no","Package":"spa","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"Implements The Sequential Predictions
Algorithm","Version":"2.0"},"spaMM":{"Author":"FranÃ§ois Rousset [aut, cre,
cph],\nJean-Baptiste Ferdy [aut, cph],\nAlexandre Courtiol [ctb],\nGSL authors
[ctb] (src\/gsl_bessel.*)","Depends":"R (>= 3.1.0)","Description":"Inference in
mixed models, including GLMMs with spatial correlations and models with non-
Gaussian random effects (e.g., Beta Binomial, or negative-binomial mixed models).
Heteroscedasticity can further be fitted by a linear model. The algorithms are
currently various Laplace approximations methods for ML or REML, in particular h-
likelihood and penalized-likelihood methods.","Imports":"methods, stats, graphics,
Matrix, MASS, lpSolveAPI (>=\n5.5.0.14), proxy, geometry, Rcpp (>= 0.11.0), nlme,
mvtnorm,\nnloptr","License":"CeCILL-
2","NeedsCompilation":"yes","Package":"spaMM","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"maps, testthat, lme4, rsae, ff, rasterVis, rgdal,
rcdd","Title":"Mixed Models, Particularly Spatial GLMMs","URL":"http:\/\/www.r-
project.org,\nhttp:\/\/kimura.univ-
montp2.fr\/~rousset\/spaMM.htm","Version":"1.8.0"},"spaa":{"Author":"Jinlong
Zhang","Description":"Miscellaneous functions for analysing species
association\nand niche overlap.","License":"GPL-
2","NeedsCompilation":"no","Package":"spaa","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"vegan","Title":"SPecies Association
Analysis","Version":"0.2.1"},"space":{"Author":"Jie Peng <jie@wald.ucdavis.edu> ,
Pei Wang <pwang@fhcrc.org>,\nNengfeng Zhou <nfzhou@umich.edu>, Ji Zhu
<jizhu@umich.edu>.","Description":"Partial correlation estimation with joint
sparse\nregression model","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"space","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Sparse PArtial Correlation Estimation","Version":"0.1-
1"},"spaceExt":{"Author":"Shiyuan He <flyoverearth@163.com>.","Depends":"limSolve,
glasso","Description":"undirected graph inference with missing data","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"spaceExt","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Extension of SPACE","Version":"1.0"},"spacejam":
{"Author":"Arend Voorman","Depends":"igraph (>= 0.6), splines,
Matrix","Description":"This package provides an extension of
conditional\nindependence
(CIG) and directed acyclic graph (DAG) estimation\nto the case where conditional
relationships are (non-linear)\nadditive models.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"spacejam","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Sparse conditional graph estimation with joint additive
models","Version":"1.1"},"spacetime":{"Author":"Edzer Pebesma [cre, aut],\nBenedikt
Graeler [ctb],\nTom Gottfried [ctb],\nRobert J. Hijmans [ctb]","Depends":"R (>=
3.0.0)","Description":"Classes and methods for spatio-temporal data, including
space-time regular lattices, sparse lattices, irregular data, and trajectories;
utility functions for plotting data as map sequences (lattice or animation) or
multiple time series; methods for spatial and temporal selection and subsetting, as
well as for spatial\/temporal\/spatio-temporal matching or aggregation, retrieving
coordinates, print, summary, etc.","Imports":"graphics, utils, stats, methods,
lattice, sp (>= 1.1-0), zoo\n(>= 1.7-9), xts (>= 0.8-8), intervals","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"spacetime","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"adehabitatLT, cshapes, diveMove, foreign, gstat (>=
1.0-16),\nmaps, mapdata, maptools, plm, raster, RColorBrewer, rgdal,\nrgeos,
RPostgreSQL, knitr, googleVis, ISOcodes","Title":"Classes and Methods for Spatio-
Temporal
Data","URL":"http:\/\/www.jstatsoft.org\/v51\/i07\/,\nhttp:\/\/github.com\/edzer\/s
pacetime","Version":"1.1-5"},"spacodiR":{"Author":"Jonathan Eastman, Timothy Paine,
and Olivier Hardy","Depends":"picante, colorspace, Rcpp","Description":"SPACoDi is
primarily designed to characterise the\nstructure and phylogenetic diversity of
communities using\nabundance or presence-absence data of species among
community\nplots.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"spacodiR","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Spatial and Phylogenetic Analysis of Community
Diversity","Version":"0.13.0115"},"spacom":{"Author":"Till Junge [aut,
cre],\nSandra Penic [aut],\nMathieu Cossuta [aut],\nGuy Elcheroth [aut],\nStephanie
Glaeser [ctb],\nDavide Morselli [ctb]","Depends":"R (>=
2.3.2)","Description":"Provides tools to construct and exploit spatially weighted
context data. Spatial weights are derived by a Kernel function from a user-defined
matrix of distances between contextual units. Spatial weights can then be applied
either to precise contextual measures or to aggregate estimates based on micro-
level survey data, to compute spatially weighted context data. Available
aggregation functions include indicators of central tendency, dispersion, or inter-
group variability, and take into account survey design weights. The package further
allows combining the resulting spatially weighted context data with individual-
level predictor and outcome variables, for the purposes of multilevel modelling. An
ad hoc stratified bootstrap resampling procedure generates robust point estimates
for multilevel regression coefficients and model fit indicators, and computes
confidence intervals adjusted for measurement dependency and measurement error of
aggregate estimates. As an additional feature, residual and explained spatial
dependency can be estimated for the tested models.","Imports":"methods, spdep,
foreach, iterators, lme4, nlme, Matrix","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"spacom","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Spatially Weighted Context Data for Multilevel
Modelling","Version":"1.0-5"},"spaero":{"Author":"Eamon O'Dea [aut,
cre]","Depends":"R (>= 3.2.1)","Description":"Implements methods for anticipating
the emergence and eradication\nof infectious diseases from surveillance time
series. Also provides support\nfor computational experiments testing the
performance of such methods.","Imports":"stats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"spaero","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"earlywarnings (>= 1.0.59), lintr (>= 0.3.3), testthat
(>=\n0.11.0), np (>= 0.60.2), pomp (>= 1.2.2.1), knitr (>= 1.11),\nrmarkdown (>=
0.9.2)","Title":"Software for Project AERO","Version":"0.1.0"},"spam":
{"Author":"Reinhard Furrer [aut, cre], Florian Gerber [ctb]","Depends":"R (>= 3.0),
grid","Description":"Set of functions for sparse matrix algebra.\nDifferences with
SparseM\/Matrix are:\n(1) we only support (essentially) one sparse matrix
format,\n(2) based on transparent and simple structure(s),\n(3) tailored for MCMC
calculations within GMRF.\n(4) S3 and S4 like-\"compatible\" ... and it is
fast.","Imports":"methods","License":"LGPL-
2","NeedsCompilation":"yes","Package":"spam","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"fields, Matrix, R.rsp, truncdist","Title":"SPArse
Matrix","URL":"http:\/\/www.math.uzh.ch\/furrer\/software\/spam\/","Version":"1.3-
0"},"spanel":{"Author":"Taha Zaghdoudi","Depends":"R (>=
2.12.0)","Description":"Fit the spatial panel data models: the fixed effects,
random\neffects and between models.","License":"GPL-
3","NeedsCompilation":"no","Package":"spanel","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Spatial Panel Data Models","Version":"0.1"},"spanr":
{"Author":"Roger Marshall","Description":"Carries out a search for an optimal
partition in terms of a\nregular Boolean expression","Imports":"plyr, stringr,
survival","License":"GPL-
2","NeedsCompilation":"yes","Package":"spanr","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Search Partition Analysis","Version":"1.0"},"sparc":
{"Author":"Tuo Zhao and Han Liu","Depends":"R (>= 2.15.2)","Description":"We
provide an efficient solver for estimating semiparametric generalized linear
2","NeedsCompilation":"yes","Package":"sparc","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Semiparametric Generalized Linear
Models","Version":"0.9.0"},"sparcl":{"Author":"Daniela M. Witten and Robert
Tibshirani","Description":"Implements the sparse clustering methods of Witten
and\nTibshirani (2010): \"A framework for feature selection in\nclustering\";
published in Journal of the American Statistical\nAssociation 105(490): 713-
2","NeedsCompilation":"yes","Package":"sparcl","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Perform sparse hierarchical clustering and sparse k-
means\nclustering","Version":"1.0.3"},"spareserver":{"Author":"Gabor
Csardi","Depends":"methods","Description":"Decide which server to connect
to,\nbased on previous response times, and configuration.","Imports":"assertthat,
pingr, httr, utils","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"spareserver","Repository":"http:\/\/cra
n.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Client Side Load
Balancing","URL":"https:\/\/github.com\/metacran\/spareserver","Version":"1.0.1"},"
spark":{"Author":"Gabor Csardi","Description":"A sparkline is a line chart, without
axes and labels.\nIts goal is to show the general shape of changes over time,
or\nanother quantity. This package is an 'R' implementation\nof the original shell
project: <http:\/\/zachholman.com\/spark\/>.","Imports":"magrittr,
LICENSE","NeedsCompilation":"no","Package":"spark","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"crayon, testthat","Title":"Sparklines in the 'R'
Terminal","URL":"https:\/\/github.com\/gaborcsardi\/spark","Version":"1.0.1"},"spar
kTable":{"Author":"Alexander Kowarik, Bernhard Meindl, Matthias
Templ","Depends":"utils, methods, Cairo, gridExtra, ggplot2,shiny,
Rglpk","Description":"Create sparklines and graphical tables for documents and
websites.","Imports":"xtable,StatMatch,boot,pixmap,RGraphics,grid","License":"GPL",
"NeedsCompilation":"no","Package":"sparkTable","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Sparklines and Graphical Tables for TeX and
HTML","URL":"https:\/\/github.com\/alexkowa\/sparkTable","Version":"1.2.0"},"sparkt
ex":{"Author":"Thomas Leeper [aut, cre], Andy Barbour [ctb]","Depends":"R (>=
3.0.0)","Description":"Generate syntax for use with the sparklines package
for\nLaTeX.","License":"GPL-
2","NeedsCompilation":"no","Package":"sparktex","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Generate LaTeX sparklines in
R","URL":"http:\/\/thomasleeper.com\/software.html","Version":"0.1"},"sparr":
{"Author":"T.M. Davies, M.L. Hazelton and J.C. Marshall","Depends":"R (>= 2.10.1),
spatstat","Description":"Provides functions to estimate kernel-smoothed relative
risk functions and perform subsequent inference.","Imports":"rgl,
2)","NeedsCompilation":"no","Package":"sparr","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"SPAtial Relative Risk","Version":"0.3-8"},"sparseBC":
{"Author":"Kean Ming Tan","Depends":"glasso","Description":"Implements the sparse
biclustering proposal of Tan and Witten (2014), Sparse biclustering of transposable
data. Journal of Computational and Graphical Statistics 23(4):985-
1008.","Imports":"fields","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"sparseBC","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Sparse Biclustering of Transposable
Data","Version":"1.1"},"sparseHessianFD":{"Author":"Michael Braun [aut, cre,
cph]","Depends":"R (>= 3.2.3)","Description":"Estimates Hessian of a scalar-valued
function, and returns it\nin a sparse Matrix format. The sparsity pattern must be
known in advance. The\nalgorithm is especially efficient for hierarchical models
with a large number of\nheterogeneous units.","Imports":"Matrix (>= 1.2.4),
methods, Rcpp (>= 0.12.3)","License":"MPL (==
2.0)","NeedsCompilation":"yes","Package":"sparseHessianFD","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Suggests":"testthat, numDeriv, scales,
knitr","Title":"Numerical Estimation of Sparse
Hessians","URL":"http:\/\/www.smu.edu\/Cox\/Departments\/FacultyDirectory\/BraunMic
hael","Version":"0.3.0"},"sparseLDA":{"Author":"Line Clemmensen <lhc@imm.dtu.dk>,
contributions by Max Kuhn","Depends":"R (>= 2.10)","Description":"Performs sparse
linear discriminant analysis for gaussians and mixture of gaussians
models.","Imports":"elasticnet, MASS, mda","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"sparseLDA","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Sparse Discriminant
Analysis","URL":"http:\/\/www.imm.dtu.dk\/~lhc,
https:\/\/github.com\/topepo\/sparselda","Version":"0.1-7"},"sparseLTSEigen":
{"Author":"Andreas Alfons [aut, cre]","Depends":"robustHD (>=
0.4.0)","Description":"Use RcppEigen to fit least trimmed squares\nregression
models with an L1 penalty in order to obtain\nsparse models.","Imports":"Rcpp (>=
0.9.10), RcppEigen (>= 0.2.0)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"sparseLTSEigen","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"mvtnorm","Title":"RcppEigen back end for
sparse least trimmed squares regression","Version":"0.2.0"},"sparseMVN":
{"Author":"Michael Braun [aut, cre, cph]","Depends":"Matrix (>= 1.1.4), R (>=
3.1.2)","Description":"Computes multivariate normal (MVN) densities, and\nsamples
from MVN distributions, when the covariance or\nprecision matrix is
sparse.","License":"MPL (>=
2.0)","NeedsCompilation":"no","Package":"sparseMVN","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"mvtnorm, plyr, knitr,
testthat","Title":"Multivariate Normal Functions for Sparse Covariance
and\nPrecision Matrices","Version":"0.2.0"},"sparseSEM":{"Author":"Anhui
Huang","Description":"Sparse-aware maximum likelihood for structural equation
models in inferring gene regulatory
networks","License":"GPL","NeedsCompilation":"yes","Package":"sparseSEM","Repositor
y":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Sparse-aware Maximum Likelihood
for Structural Equation Models","Version":"2.5"},"sparseSVM":{"Author":"Congrui Yi
and Yaohui Zeng","Depends":"parallel","Description":"Fast algorithm for fitting
solution paths of sparse linear SVM with lasso or elastic-net regularization
generate sparse solutions.","License":"GPL-
3","NeedsCompilation":"yes","Package":"sparseSVM","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Solution Paths of Sparse Linear Support Vector Machine
with\nLasso or ELastic-Net Regularization","Version":"1.1-2"},"sparsediscrim":
{"Author":"John A. Ramey <johnramey@gmail.com>","Description":"A collection of
sparse and regularized discriminant analysis\nmethods intended for small-sample,
high-dimensional data sets. The package\nfeatures the High-Dimensional Regularized
Discriminant Analysis classifier.","Imports":"corpcor, bdsmatrix,
mvtnorm","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"sparsediscrim","Repository":"http:\/\/c
ran.csiro.au\/src\/contrib","Title":"Sparse and Regularized Discriminant
Analysis","URL":"https:\/\/github.com\/ramey\/sparsediscrim,
http:\/\/ramhiser.com","Version":"0.2"},"sparsenet":{"Author":"Rahul Mazumder,
Trevor Hastie, Jerome Friedman","Depends":"glmnet, shape","Description":"Sparsenet
uses the MC+ penalty of Zhang. It computes the regularization surface over both the
family parameter and the tuning parameter by coordinate descent.","License":"GPL-
2","NeedsCompilation":"yes","Package":"sparsenet","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Fit sparse linear regression models via nonconvex
optimization","URL":"\nhttp:\/\/www.stanford.edu\/~hastie\/Papers\/Sparsenet\/jasa_
MFH_final.pdf","Version":"1.2"},"sparsereg":{"Author":"Marc Ratkovic and Dustin
Tingley","Depends":"R (>= 3.0.2), MASS, ggplot2","Description":"Sparse modeling
provides a mean selecting a small number of non-zero effects from a large possible
number of candidate effects. This package includes a suite of methods for sparse
modeling: estimation via EM or MCMC, approximate confidence intervals with nominal
coverage, and diagnostic and summary plots. The method can implement sparse linear
regression and sparse probit regression. Beyond regression analyses, applications
include subgroup analysis, particularly for conjoint experiments, and panel data.
Future versions will include extensions to models with truncated outcomes,
propensity score, and instrumental variable analysis.","Imports":"Rcpp (>= 0.11.0),
msm, VGAM, MCMCpack, coda, glmnet,\ngridExtra, grid, GIGrvg","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"sparsereg","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Sparse Bayesian Models for Regression, Subgroup
Analysis, and\nPanel Data","Version":"1.2"},"sparsesvd":{"Author":"Doug Rohde
[aut],\nMichael Berry [aut],\nTheresa Do [aut],\nGavin O'Brien [aut],\nVijay
Krishna [aut],\nSowmini Varadhan [aut],\nStefan Evert [cre] (http:\/\/www.stefan-
evert.de\/)","Depends":"R (>= 3.0)","Description":"Wrapper around the 'SVDLIBC'
library for (truncated) singular value decomposition of a sparse
matrix.\nCurrently, only sparse real matrices in the Matrix package format are
supported.","Imports":"Matrix, methods","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"yes","Package":"sparsesvd","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Sparse Truncated Singular Value Decomposition
(from
'SVDLIBC')","URL":"http:\/\/tedlab.mit.edu\/~dr\/SVDLIBC\/,\nhttp:\/\/wordspace.r-
forge.r-project.org\/","Version":"0.1"},"spartan":{"Author":"Kieran Alden, Mark
Read, Paul Andrews, Jon Timmis, Henrique Veiga-Fernandes, Mark
Coles","Description":"Computer simulations are becoming a popular technique to use
in attempts to further our understanding of complex systems. SPARTAN, described in
our 2013 publication in PLoS Computational Biology, provides code for four
techniques described in available literature which aid the analysis of simulation
results, at both single and multiple timepoints in the simulation run. The first
technique addresses aleatory uncertainty in the system caused through inherent
stochasticity, and determines the number of replicate runs necessary to generate a
representative result. The second examines how robust a simulation is to parameter
perturbation, through the use of a one-at-a-time parameter analysis technique.
Thirdly, a latin hypercube based sensitivity analysis technique is included which
can elucidate non-linear effects between parameters and indicate implications of
epistemic uncertainty with reference to the system being modelled. Finally, a
further sensitivity analysis technique, the extended Fourier Amplitude Sampling
Test (eFAST) has been included to partition the variance in simulation results
between input parameters, to determine the parameters which have a significant
effect on simulation behaviour. Version 1.3 adds support for Netlogo simulations,
aiding simulation developers who use Netlogo to build their simulations perform the
same analyses. We have also added user support through the group spartan-
group[AT]york[DOT]ac[DOT]uk. Version 2.0 added the ability to read all simulations
in from a single CSV file in addition to the prescribed folder structure in
previous versions.","License":"GPL-
2","NeedsCompilation":"no","Package":"spartan","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"lhs, gplots, XML, plotrix","Title":"Simulation
Parameter Analysis R Toolkit ApplicatioN: Spartan","Version":"2.3"},"spatcounts":
{"Author":"Holger Schabenberger","Description":"Fit spatial CAR count regression
models using MCMC","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"spatcounts","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Spatial count regression","Version":"1.1"},"spate":
{"Author":"Fabio Sigrist, Hans R. Kuensch, Werner A. Stahel","Depends":"R (>=
2.10), mvtnorm, truncnorm","Description":"This package provides functionality for
spatio-temporal modeling of large data sets. A Gaussian process in space and time
is defined through a stochastic partial differential equation (SPDE). The SPDE is
solved in the spectral space, and after discretizing in time and space, a linear
Gaussian state space model is obtained. When doing inference, the main
computational difficulty consists in evaluating the likelihood and in sampling from
the full conditional of the spectral coefficients, or equivalently, the latent
space-time process. In comparison to the traditional approach of using a spatio-
temporal covariance function, the spectral SPDE approach is computationally
advantageous. This package aims at providing tools for two different modeling
approaches. First, the SPDE based spatio-temporal model can be used as a component
in a customized hierarchical Bayesian model (HBM). The functions of the package
then provide parameterizations of the process part of the model as well as
computationally efficient algorithms needed for doing inference with the HBM.
Alternatively, the adaptive MCMC algorithm implemented in the package can be used
as an algorithm for doing inference without any additional modeling. The MCMC
algorithm supports data that follow a Gaussian or a censored distribution with
point mass at zero. Covariates can be included in the model through a regression
term.","License":"GPL-
2","NeedsCompilation":"yes","Package":"spate","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Spatio-Temporal Modeling of Large Data Using a Spectral
SPDE\nApproach","Version":"1.4"},"spatgraphs":{"Author":"Tuomas
Rajala","Description":"Graphs (or networks) and graph component\ncalculations for
spatial locations in *D.","Imports":"Rcpp (>= 0.11.6), Matrix, rgl,
2)","NeedsCompilation":"yes","Package":"spatgraphs","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Graph Edge Computations for Spatial Point
Patterns","Version":"3.0"},"spatial":{"Author":"Brian
Ripley [aut, cre, cph],\nRoger Bivand [ctb],\nWilliam Venables [cph]","Depends":"R
(>= 3.0.0), graphics, stats, utils","Description":"Functions for kriging and point
pattern analysis.","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"spatial","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"MASS","Title":"Functions for Kriging and Point Pattern
Analysis","URL":"http:\/\/www.stats.ox.ac.uk\/pub\/MASS4\/","Version":"7.3-
11"},"spatial.gev.bma":{"Author":"Alex
Lenkoski","Depends":"SpatialExtremes,msm,coda","Description":"This package fits a
hierarchical spatial model for the generalized extreme value distribution with the
option of model averaging over the space of
covariates.","License":"GPL","NeedsCompilation":"no","Package":"spatial.gev.bma","R
epository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Hierarchical spatial
generalized extreme value (GEV) modeling\nwith Bayesian Model Averaging
(BMA)","Version":"1.0"},"spatial.tools":{"Author":"Jonathan Asher
Greenberg","Depends":"parallel, iterators, foreach, rgdal, raster, R (>=
3.0.0)","Description":"Spatial functions meant to enhance the core functionality of
the\npackage \"raster\", including a parallel processing engine for use
with\nrasters.","Imports":"mmap, abind, doParallel, compiler","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"spatial.tools","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"R functions for working with spatial
data","URL":"\nhttp:\/\/www.geog.illinois.edu\/~jgrn\/software-and-
datasets\/rasterengine-tutorial\/","Version":"1.4.8"},"spatialCovariance":
{"Author":"David Clifford <david.clifford+CRAN@gmail.com>","Description":"Functions
that compute the spatial covariance matrix for the matern and power classes of
spatial models, for data that arise on rectangular units. This code can also be
used for the change of support problem and for spatial data that arise on
irregularly shaped regions like counties or zipcodes by laying a fine grid of
rectangles and aggregating the integrals in a form of Riemann
integration.","License":"GPL","NeedsCompilation":"no","Package":"spatialCovariance"
,"Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Computation of
Spatial Covariance Matrices for Data on\nRectangles","Version":"0.6-
9"},"spatialEco":{"Author":"Jeffrey S. Evans [aut, cre],\nKarthik Ram
[ctb]","Depends":"R (>= 3.2.1)","Description":"Utilities to support spatial data
manipulation, query, sampling\nand modelling. Functions include models for species
population density, download\nutilities for climate and global deforestation
spatial products, spatial\nsmoothing, multivariate separability, point process
model for creating pseudo-\nabsences and sub-sampling, polygon and point-distance
landscape metrics,\nauto-logistic model, sampling models, cluster optimization and
statistical\nexploratory tools.","Imports":"sp (>= 1.1-1), raster (>= 2.4-15),
spatstat (>= 1.35-0),\ncluster (>= 2.0.2), spdep (>= 0.5-88), SDMTools (>= 1.1-
221),\nRCurl (>= 1.95-4.7), rgeos (>= 0.3-11), RANN (>= 2.5), rms (>=\n4.3-1),
yaImpute (>= 1.0-26), methods","License":"GPL-
3","NeedsCompilation":"no","Package":"spatialEco","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Spatial Analysis and Modelling","URL":"http:\/\/cran.r-
project.org\/package=spatialEco","Version":"0.1-4"},"spatialTailDep":
{"Author":"Anna Kiriliouk, Johan Segers","Depends":"R (>= 3.0.1), cubature,
mvtnorm, SpatialExtremes","Description":"Provides functions implementing the
pairwise M-estimator for\nparametric models for stable tail dependence functions
described in \"An\nM-estimator of spatial tail dependence\"\n(Einmahl, J.H.J.,
Kiriliouk, A., Krajina, A. and Segers, J., 2014).\nSee
http:\/\/arxiv.org\/abs\/1403.1975.","License":"GPL-
3","NeedsCompilation":"yes","Package":"spatialTailDep","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Estimation of spatial tail dependence
models","Version":"1.0.2"},"spatialfil":{"Author":"Nicola Dinapoli, Roberto
Gatta","Depends":"R (>= 3.1.0), abind, fields, grDevices","Description":"Filter
matrices or (three dimensional) array data using different convolution
kernels.","License":"GPL-
2","NeedsCompilation":"yes","Package":"spatialfil","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Application of 2D Convolution Kernel Filters to
Matrices or 3D\nArrays","Version":"0.15"},"spatialkernel":{"Author":"Pingping Zheng
and Peter Diggle","Depends":"R (>= 1.9.0)","Description":"Edge-corrected kernel
density estimation and binary kernel\nregression estimation for multivariate
spatial point process\ndata","License":"CC BY-NC-SA 3.0 + file
LICENSE","NeedsCompilation":"yes","Package":"spatialkernel","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Title":"Nonparameteric estimation of spatial
segregation in a\nmultivariate point process","Version":"0.4-19"},"spatialnbda":
{"Author":"Glenna Nightingale","Depends":"SocialNetworks(>= 1.1), mvtnorm(>=
0.9)","Description":"Network based diffusion analysis (NBDA) allows inference
on\nthe asocial and social transmission of information. This may involve\nthe
social transmission of a particular behaviour such as tool use, for example.\nFor
the NBDA, the key parameters estimated are the social effect and baseline
rate\nparameters. The baseline rate parameter gives the rate at which the
behaviour\nis first performed (or acquired) asocially amongst the individuals in a
given population.\nThe social effect parameter quantifies the effect of the social
associations amongst\nthe individuals on the rate at which each individual first
performs or displays\nthe behaviour. Spatial NBDA involves incorporating spatial
information in the analysis.\nThis is done by incorporating social networks derived
from\nspatial point patterns (of the home bases of the individuals under study).
In addition,\na spatial covariate such as vegetation cover, or slope may be
included in the
modelling\nprocess.","License":"GPL","NeedsCompilation":"no","Package":"spatialnbda
","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"Performs spatial
NBDA in a Bayesian context","Version":"1.0"},"spatialprobit":{"Author":"Stefan
Wilhelm <wilhelm@financial.com> and Miguel Godinho de Matos
<miguelgodinhomatos@cmu.edu>","Depends":"R (>= 1.9.0), Matrix, spdep, mvtnorm,
tmvtnorm","Description":"Bayesian Estimation of Spatial Probit and Tobit
Models.","Imports":"stats","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"spatialprobit","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"RUnit, testthat","Title":"Spatial Probit
Models","URL":"http:\/\/www.r-project.org","Version":"0.9-
11"},"spatialsegregation":{"Author":"Tuomas Rajala","Depends":"spatstat (>= 1.15-
2)","Description":"Summaries for measuring segregation\/mingling in multitype
spatial point patterns with graph based neighbourhood description.\nIncluded
indices: Mingling, Shannon, Simpson (also the non-spatial)\nIncluded functionals:
Mingling, Shannon, Simpson, ISAR, MCI.\nIncluded neighbourhoods: Geometric, k-
nearest neighbours, Gabriel, Delaunay.","License":"GPL (>=
2.0)","NeedsCompilation":"yes","Package":"spatialsegregation","Repository":"http:\/
\/cran.csiro.au\/src\/contrib","Title":"Segregation measures for multitype spatial
point patterns","Version":"2.40"},"spatstat":{"Author":"Adrian Baddeley
<Adrian.Baddeley@curtin.edu.au>,\nRolf Turner <r.turner@auckland.ac.nz>\nand Ege
Rubak <rubak@math.aau.dk>,\nwith substantial contributions of code by\nKasper
Klitgaard Berthelsen;\nUte Hahn;\nAbdollah Jalilian;\nMarie-Colette van
Lieshout;\nTuomas Rajala;\nDominic Schuhmacher;\nand\nRasmus
Waagepetersen.\nAdditional contributions\nby M. Adepeju;\nQ.W. Ang;\nS. Azaele;\nM.
Baddeley;\nC. Beale;\nM. Bell;\nR. Bernhardt;\nT. Bendtsen;\nA. Bevan;\nB.
Biggerstaff;\nA. Bilgrau;\nL. Bischof;\nC. Biscio;\nR. Bivand;\nJ.M. Blanco
Moreno;\nF. Bonneu;\nJ. Burgos;\nS. Byers;\nY.M. Chang;\nJ.B. Chen;\nI.
Chernayavsky;\nY.C. Chin;\nB. Christensen;\nJ.-F. Coeurjolly;\nR. Corria
Ainslie;\nM. de la Cruz;\nP. Dalgaard;\nM. D'Antuono;\nS. Das;\nP.J. Diggle;\nP.
Donnelly;\nI. Dryden;\nS. Eglen;\nA. El-Gabbas;\nB. Fandohan;\nO. Flores;\nE.D.
Ford;\nP. Forbes;\nS. Frank;\nJ. Franklin;\nN. Funwi-Gabga;\nO. Garcia;\nA.
Gault;\nJ. Geldmann;\nM. Genton;\nS. Ghalandarayeshi;\nJ. Gilbey;\nJ.
Goldstick;\nP. Grabarnik;\nC. Graf;\nU. Hahn;\nA. Hardegen;\nM.B. Hansen;\nM.
Hazelton;\nJ. Heikkinen;\nM. Hering;\nM. Herrmann;\nP. Hewson;\nK. Hingee;\nK.
Hornik;\nP. Hunziker;\nJ. Hywood;\nR. Ihaka;\nA. Jammalamadaka;\nR. John-
Chandran;\nD. Johnson;\nM. Khanmohammadi;\nR. Klaver;\nP. Kovesi;\nM. Kuhn;\nJ.
Laake;\nF. Lavancier;\nT. Lawrence;\nR.A. Lamb;\nJ. Lee;\nG.P. Leser;\nH.T. Li;\nG.
Limitsios;\nA. Lister;\nB. Madin;\nM. Maechler;\nJ. Marcus;\nK. Marchikanti;\nR.
Mark;\nJ. Mateu;\nP. McCullagh;\nU. Mehlig;\nS. Meyer;\nX.C. Mi;\nL. De
Middeleer;\nR.K. Milne;\nE. Miranda;\nJ. Moller;\nE. Mudrak;\nG.M. Nair;\nN.
Nava;\nL.S. Nielsen;\nF. Nunes;\nJ.R. Nyengaard;\nJ. Oehlschlaegel;\nT.
Onkelinx;\nS. O'Riordan;\nE. Parilov;\nJ. Picka;\nN. Picard;\nM. Porter;\nS.
Protsiv;\nA. Raftery;\nS. Rakshit;\nB. Ramage;\nP. Ramon;\nX. Raynaud,\nM.
Reiter;\nI. Renner;\nT.O. Richardson;\nB.D. Ripley;\nE. Rosenbaum;\nB.
Rowlingson;\nJ. Rudokas;\nJ. Rudge;\nC. Ryan;\nF. Safavimanesh;\nA. Sarkka;\nC.
Schank;\nK. Schladitz;\nS. Schutte;\nB.T. Scott;\nO. Semboli;\nF. Semecurbe;\nV.
Shcherbakov;\nG.C. Shen;\nP. Shi;\nH.-J. Ship;\nI.-M. Sintorn;\nY. Song;\nM.
Spiess;\nM. Stevenson;\nK. Stucki;\nM. Sumner;\nP. Surovy;\nB. Taylor;\nT.
Thorarinsdottir;\nB. Turlach;\nT. Tvedebrink;\nK. Ummer;\nM. Uppala;\nA. van
Burgel;\nT. Verbeke;\nM. Vihtakari;\nA. Villers;\nF. Vinatier;\nS. Voss;\nS.
Wagner;\nH. Wang;\nH. Wendrock;\nJ. Wild;\nC. Witthoft;\nS. Wong;\nM.
Woringer;\nM.E. Zamboni\nand\nA. Zeileis.","Depends":"R (>= 3.2.2), stats,
graphics, grDevices, utils, methods, nlme","Description":"Comprehensive
open-source toolbox for analysing spatial data, mainly Spatial Point Patterns,
including multi-type\/marked points and spatial covariates, in any two-dimensional
spatial region. Also supports three-dimensional point patterns, space-time point
patterns in any number of dimensions, and point patterns on a linear
network.\nContains over 2000 functions for plotting spatial data, exploratory data
analysis, model-fitting, simulation, spatial sampling, model diagnostics, and
formal inference.\nData types include point patterns, line segment patterns,
spatial windows, pixel images, tessellations, and linear networks.\nExploratory
methods include quadrat counts, K-functions and their simulation envelopes, nearest
neighbour distance and empty space statistics, Fry plots, pair correlation
function, kernel smoothed intensity, relative risk estimation with cross-validated
bandwidth selection, mark correlation functions, segregation indices, mark
dependence diagnostics, and kernel estimates of covariate effects. Formal
hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Diggle-
Cressie-Loosmore-Ford, Dao-Genton) and tests for covariate effects (Cox-Berman-
Waller-Lawson, Kolmogorov-Smirnov) are also supported.\nParametric models can be
fitted to point pattern data using the functions ppm(), kppm(), slrm(), dppm()
similar to glm(). Types of models include Poisson, Gibbs and Cox point processes,
Neyman-Scott cluster processes, and determinantal point processes. Models may
involve dependence on covariates, inter-point interaction, cluster formation and
dependence on marks. Models are fitted by maximum likelihood, logistic regression,
minimum contrast, and composite likelihood methods.\nA model can be fitted to a
list of point patterns (replicated point pattern data) using the function mppm().
The model can include random effects and fixed effects depending on the
experimental design, in addition to all the features listed above.\nFitted point
process models can be simulated, automatically. Formal hypothesis tests of a fitted
model are supported (likelihood ratio test, analysis of deviance, Monte Carlo
tests) along with basic tools for model selection (stepwise(), AIC()). Tools for
validating the fitted model include simulation envelopes, residuals, residual plots
and Q-Q plots, leverage and influence diagnostics, partial residuals, and added
variable plots.","Imports":"mgcv, Matrix, deldir (>= 0.0-21), abind, tensor,
polyclip (>=\n1.3-0), goftest","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"spatstat","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"sm, maptools, gsl, locfit, spatial, rpanel,
tkrplot,\nRandomFields (>= 3.0.0)","Title":"Spatial Point Pattern Analysis, Model-
Fitting, Simulation, Tests","URL":"http:\/\/www.spatstat.org","Version":"1.45-
0"},"spatsurv":{"Author":"Benjamin M. Taylor and Barry S. Rowlingson","Depends":"R
(>= 2.10)","Description":"Bayesian inference for parametric proportional hazards
spatial survival models; flexible spatial survival models.","Imports":"survival,
sp, spatstat, raster, iterators, RandomFields,\nfields, rgl, Matrix, stringr,
rgeos, RColorBrewer, geostatsp,\nOpenStreetMap, methods","License":"GPL-
3","NeedsCompilation":"no","Package":"spatsurv","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"rgdal, gpclib","Title":"Bayesian Spatial Survival
Analysis with Parametric Proportional\nHazards Models","Version":"0.9-11"},"spc":
{"Author":"Sven Knoth","Depends":"R (>= 1.8.0)","Description":"Evaluation of
control charts by means of\nthe zero-state, steady-state ARL (Average Run Length)
and RL quantiles.\nSetting up control charts for given in-control ARL. The control
charts\nunder consideration are one- and two-sided EWMA, CUSUM, and\nShiryaev-
Roberts schemes for monitoring the mean of normally\ndistributed independent data.
ARL calculation\nof the same set of schemes under drift are added.\nOther charts
and parameters are in preparation.\nFurther SPC areas will be covered as
well\n(sampling plans, capability indices ...).","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"spc","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Statistical Process Control -- Collection of Some
Useful\nFunctions","URL":"http:\/\/www.r-
project.org","Version":"0.5.3"},"spcadjust":{"Author":"Axel Gandy
<a.gandy@imperial.ac.uk> and Jan Terje Kvaloy\n<jan.t.kvaloy@uis.no>.","Depends":"R
(>= 2.5.0)","Description":"Calibration of thresholds of control charts such
as\nCUSUM charts based on past data, taking estimation error into
account.","Imports":"methods, stats, utils, graphics","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"spcadjust","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"knitr, parallel, testthat","Title":"Functions for
Calibrating Control Charts","Version":"1.0"},"spcosa":{"Author":"Dennis Walvoort
[aut, cre, cph],\nDick Brus [aut, cph],\nJaap de Gruijter [aut, cph]","Depends":"R
(>= 3.1.0), rJava (>= 0.9-3), methods, utils","Description":"Spatial coverage
sampling and random sampling from compact\ngeographical strata created by k-
means.","Imports":"sp (>= 1.1-0), ggplot2 (>= 1.0.0)","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"spcosa","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"grid, gstat, rgdal, rgl, rglwidget, RUnit,
knitr","Title":"Spatial Coverage Sampling and Random Sampling from
Compact\nGeographical Strata","Version":"0.3-6"},"spcov":{"Author":"Jacob Bien and
Rob Tibshirani","Description":"Provides a covariance estimator for multivariate
normal\ndata that is sparse and positive definite. Implements the\nmajorize-
minimize algorithm described in Bien, J., and\nTibshirani, R. (2011), \"Sparse
Estimation of a Covariance\nMatrix,\" Biometrika. 98(4). 807--820.","License":"GPL-
2","NeedsCompilation":"no","Package":"spcov","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Sparse Estimation of a Covariance
Matrix","Version":"1.01"},"spcr":{"Author":"Shuichi Kawano","Description":"This
package computes the sparse principal component regression. The regularization
parameters are optimized by cross-validation.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"spcr","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Sparse principal component
regression","URL":"https:\/\/sites.google.com\/site\/shuichikawanoen\/","Version":"
1.2.1"},"spd":{"Author":"Alexios Ghalanos
<alexios@4dscape.com>","Depends":"methods","Description":"The Semi Parametric
Piecewise Distribution blends the Generalized Pareto Distribution for the tails
with a kernel based interior.","Imports":"KernSmooth, stats, graphics,
utils","License":"GPL","NeedsCompilation":"no","Package":"spd","Repository":"http:\
/\/cran.csiro.au\/src\/contrib","Title":"Semi Parametric
Distribution","URL":"http:\/\/www.unstarched.net,
https:\/\/bitbucket.org\/alexiosg","Version":"2.0-1"},"spdep":{"Author":"Roger
Bivand [cre, aut],\nMicah Altman [ctb],\nLuc Anselin [ctb],\nRenato AssunÃ§Ã£o
[ctb],\nOlaf Berke [ctb],\nAndrew Bernat [ctb],\nGuillaume Blanchet [ctb],\nEric
Blankmeyer [ctb],\nMarilia Carvalho [ctb],\nBjarke Christensen [ctb],\nYongwan Chun
[ctb],\nCarsten Dormann [ctb],\nStÃ©phane Dray [ctb],\nVirgilio GÃ³mez-Rubio
[ctb],\nMartin Gubri [ctb],\nRein Halbersma [ctb],\nElias Krainski [ctb],\nPierre
Legendre [ctb],\nNicholas Lewin-Koh [ctb],\nHongfei Li [ctb],\nJielai Ma
[ctb],\nGiovanni Millo [ctb],\nWerner Mueller [ctb],\nHisaji Ono [ctb],\nPedro
Peres-Neto [ctb],\nGianfranco Piras [ctb],\nMarkus Reder [ctb],\nMichael
Tiefelsdorf [ctb],\nDanlin Yu [ctb]","Depends":"R (>= 3.0.0), methods, sp (>= 1.0),
Matrix (>= 1.0.12)","Description":"A collection of functions to create spatial
weights matrix\nobjects from polygon contiguities, from point patterns by distance
and\ntessellations, for summarizing these objects, and for permitting their\nuse in
spatial data analysis, including regional aggregation by minimum\nspanning tree; a
collection of tests for spatial autocorrelation,\nincluding global Moran's I, APLE,
Geary's C, Hubert\/Mantel general cross\nproduct statistic, Empirical Bayes
estimates and AssunÃ§Ã£o\/Reis Index,\nGetis\/Ord G and multicoloured join count
statistics, local Moran's I\nand Getis\/Ord G, saddlepoint approximations and
exact tests for global\nand local Moran's I; and functions for estimating spatial
simultaneous\nautoregressive (SAR) lag and error models, impact measures for
lag\nmodels, weighted and unweighted SAR and CAR spatial regression models,\nsemi-
parametric and Moran eigenvector spatial filtering, GM SAR error\nmodels, and
generalized spatial two stage least squares models.","Imports":"LearnBayes, deldir,
boot (>= 1.3-1), splines, coda, nlme,\nMASS, stats, graphics, grDevices,
2)","NeedsCompilation":"yes","Package":"spdep","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"parallel, spam(>= 0.13-1), RANN, RColorBrewer,
lattice,\nxtable, maptools (>= 0.5-4), foreign, igraph, knitr","Title":"Spatial
Dependence: Weighting Schemes, Statistics and Models","Version":"0.5-
92"},"spduration":{"Author":"Andreas Beger [aut, cre],\nDaina Chiba [aut],\nDaniel
Hill [aut],\nNils Metternich [aut],\nShahryar Minhas [aut],\nMichael Ward
[cph]","Depends":"R (>= 3.1.2)","Description":"Functions for estimating split-
duration regression models and\nvarious associated generic function
methods.","Imports":"corpcor, graphics, plyr, MASS, separationplot, stats, Rcpp
(>=\n0.11.0), xtable","License":"GPL-
3","NeedsCompilation":"yes","Package":"spduration","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat","Title":"Split-Population Duration (Cure)
Regression","Version":"0.15.0"},"spdynmod":{"Author":"Javier Martinez-Lopez
<javi.martinez.lopez@gmail.com>, Babak Naimi\n<naimi.b@gmail.com>, Julia Martinez-
Fernandez <juliamf@um.es>","Depends":"raster,
sp","Description":"A spatio-dynamic modelling package that focuses on
three\ncharacteristic wetland plant communities in a semiarid
Mediterranean\nwetland in response to hydrological pressures from the catchment.
The\npackage includes the data on watershed hydrological pressure and the\ninitial
raster maps of plant communities but also allows for random initial\ndistribution
of plant communities. Ongoing developments of the package\nfocus on offering easy
to use tools for creating other spatio-dynamic\nmodels.","Imports":"deSolve,
animation","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"spdynmod","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"knitr, roxygen2, igraph, testthat","Title":"Spatio-
Dynamic Wetland Plant Communities
Model","URL":"https:\/\/github.com\/javimarlop\/spdynmod","Version":"1.1.3"},"spe":
{"Author":"Rajarshi Guha <rajarshi.guha@gmail.com>","Description":"Implements
stochastic proximity embedding as described by\nAgrafiotis et al. in PNAS, 2002,
99, pg 15869 and J. Comput. Chem., 2003,24, pg
1215","License":"GPL","NeedsCompilation":"yes","Package":"spe","Repository":"http:\
/\/cran.csiro.au\/src\/contrib","Title":"Stochastic Proximity
Embedding","Version":"1.1.2"},"speaq":{"Author":"Trung Nghia Vu, Kris Laukens and
Dirk Valkenborg","Depends":"R (>= 3.1.0), MassSpecWavelet","Description":"We
introduce a novel suite of informatics tools for the quantitative analysis of NMR
metabolomic profile data. The core of the processing cascade is a novel peak
alignment algorithm, called hierarchical Cluster-based Peak Alignment (CluPA). The
algorithm aligns a target spectrum to the reference spectrum in a top-down fashion
by building a hierarchical cluster tree from peak lists of reference and target
spectra and then dividing the spectra into smaller segments based on the most
distant clusters of the tree. To reduce the computational time to estimate the
spectral misalignment, the method makes use of Fast Fourier Transformation (FFT)
cross-correlation. Since the method returns a high-quality alignment, we can
propose a simple methodology to study the variability of the NMR spectra. For each
aligned NMR data point the ratio of the between-group and within-group sum of
squares (BW-ratio) is calculated to quantify the difference in variability between
and within predefined groups of NMR spectra. This differential analysis is related
to the calculation of the F-statistic or a one-way ANOVA, but without
distributional assumptions. Statistical inference based on the BW-ratio is achieved
by bootstrapping the null distribution from the experimental data. Related
publication is available at http:\/\/www.biomedcentral.com\/1471-
2105\/12\/405\/.","Imports":"graphics,stats","License":"Apache License
2.0","NeedsCompilation":"no","Package":"speaq","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Tools for Nuclear Magnetic Resonance Spectrum Alignment
and\nQuantitative
Analysis","URL":"https:\/\/github.com\/nghiavtr\/speaq","Version":"1.2.1"},"speccal
t":{"Author":"Pierrick Bruneau","Depends":"R (>=
2.10.0)","Description":"Alternative to the kernlab::specc function. Includes a
spectral clustering implementation, a locally adapted kernel function akin to what
is already proposed in kernlab, and an optional procedure that automatically
estimates the optimal number of clusters. Several sample data sets are also
included.","License":"LGPL-
3","NeedsCompilation":"no","Package":"speccalt","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Alternative spectral clustering, with automatic
estimation of k","Version":"0.1.1"},"speciesgeocodeR":{"Author":"Alexander Zizka
[aut, cre]","Depends":"R (>= 3.0.0), maps","Description":"Preparation of species
occurrences and distribution data for the use in phylogenetic analyses.
SpeciesgeocodeR is built for data cleaning, data exploration and data analysis and
especially suited for biogeographical and ecological questions on large datasets.
The package includes the easy creation of summary-tables and -graphs and
geographical maps, the automatic cleaning of geographic occurrence data, the
calculating of coexistence matrices and species ranges (EOO) as well as mapping
diversity in geographic areas.","Imports":"stats, methods, utils, grDevices,
graphics, sp, raster","License":"GPL-
3","NeedsCompilation":"no","Package":"speciesgeocodeR","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"ape, geiger, geosphere, rgbif,
maptools","Title":"Prepare Species Distributions for the Use in
Phylogenetic\nAnalyses","Version":"1.0-4"},"specificity":{"Author":"Kenn Konstabel,
Rene Mottus","Depends":"car","Description":"The package helps to test the
specificity of personality trait-outcome (or trait-trait) associations by comparing
the observed associations to those obtained using randomly created personality
scales.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"specificity","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Specificity of personality trait-outcome (or trait-
trait)\nassociations","Version":"0.1.1"},"specmine":{"Author":"Christopher Costa
<chrisbcl@hotmail.com>,\nMarcelo Maraschin <mtocsy@gmail.com>,\nMiguel Rocha
<mrocha@di.uminho.pt>","Depends":"R (>= 3.1.0)","Description":"Provides a set of
methods for metabolomics\ndata analysis, including data loading in different
formats,\npre-processing, metabolite identification, univariate and
multivariate\ndata analysis, machine learning and feature selection. Case
studies\ncan be found on the website:
http:\/\/darwin.di.uminho.pt\/metabolomics .","Imports":"compare, hyperSpec,
ChemoSpec, baseline, rgl, Metrics, GGally,\nggplot2, ellipse, ggdendro, caret, pls,
pcaPP, RColorBrewer,\ngrid, methods, qdap, MASS, scatterplot3d, xcms,
MAIT,\ngenefilter, impute","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"specmine","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Metabolomics and Spectral Data Analysis and
Mining","Version":"1.0"},"spectral.methods":{"Author":"Jannis v.
Buttlar","Depends":"R (>= 3.0.0)","Description":"Contains some implementations of
Singular Spectrum Analysis (SSA) for the gapfilling and spectral decomposition of
time series. It contains the code used by Buttlar et. al. (2014), Nonlinear
Processes in Geophysics. In addition, the iterative SSA gapfilling method of
Kondrashov and Ghil (2006) is implemented. All SSA calculations are done via the
truncated and fast SSA algorithm of Korobeynikov (2010) (package
'Rssa').","Imports":"Rssa (>= 0.11), raster, nnet, abind, RNetCDF,
ncdf.tools,\nforeach, JBTools, DistributionUtils, RColorBrewer","License":"GPL-
2","NeedsCompilation":"no","Package":"spectral.methods","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Singular Spectrum Analysis (SSA) Tools for Time
Series Analysis","Version":"0.7.2.133"},"spectralGP":{"Author":"Chris Paciorek
<paciorek@alumni.cmu.edu>","Depends":"R (>= 1.9.0)","Description":"Routines for
creating, manipulating, and performing\nBayesian inference about Gaussian processes
in\none and two dimensions using the Fourier basis approximation:\nsimulation and
plotting of processes, calculation of\ncoefficient variances, calculation of
process density,\ncoefficient proposals (for use in MCMC). It uses R environments
to\nstore GP objects as references\/pointers.","Imports":"graphics, stats,
2)","NeedsCompilation":"no","Package":"spectralGP","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Approximate Gaussian Processes Using the Fourier
Basis","URL":"http:\/\/www.jstatsoft.org\/v19\/a2","Version":"1.3.3"},"spectrino":
{"Author":"Teodor Krastev <spectrino@sicyon.com>","Depends":"R (>=
3.0.0)","Description":"Spectra visualization, organizer and data preparation\nfrom
within R or stand-alone. Binary (application) part is\ninstalled separately by
running spnInstallApp()\nimmediately after installing the
package.","Imports":"utils, httpuv, jsonlite","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"spectrino","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Spectra Visualization, Organizer and Data
Preparation","URL":"http:\/\/www.spectrino.com","Version":"1.6.0"},"speedglm":
{"Author":"Marco Enea [aut, cre], Ronen Meiri [ctb] (on behalf of DMWay Analytics
LTD), Tomer Kalimi [ctb] (on behalf of DMWay Analytics LTD)","Depends":"Matrix,
MASS","Description":"Fitting linear models and generalized linear models to large
data sets by updating algorithms.","Imports":"methods,
stats","License":"GPL","NeedsCompilation":"no","Package":"speedglm","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Title":"Fitting Linear and Generalized Linear
Models to Large Data Sets","Version":"0.3-1"},"speff2trial":{"Author":"Michal
Juraska <mjuraska@u.washington.edu>, with contributions\nfrom Peter B. Gilbert
<pgilbert@scharp.org>, Xiaomin Lu\n<xlu2@phhp.ufl.edu>, Min Zhang
<mzhangst@umich.edu>, Marie\nDavidian <davidian@stat.ncsu.edu>, and Anastasios A.
Tsiatis\n<tsiatis@stat.ncsu.edu>","Depends":"R (>= 2.7.2), leaps,
survival","Description":"The package performs estimation and testing of
the\ntreatment effect in a 2-group randomized clinical trial with a\nquantitative,
dichotomous, or right-censored time-to-event\nendpoint. The method improves
efficiency by leveraging baseline\npredictors of the endpoint. The inverse
probability weighting\ntechnique of Robins, Rotnitzky, and Zhao (JASA, 1994) is
used\nto provide unbiased estimation when the endpoint is missing
at\nrandom.","License":"GPL-
2","NeedsCompilation":"no","Package":"speff2trial","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Semiparametric efficient estimation for a two-sample
treatment\neffect","Version":"1.0.4"},"sperich":{"Author":"Maximilian Lange, Sven
Lautenbach, Claudia Raedig","Depends":"R (>= 2.13)","Description":"Provides some
easy-to-use functions
to interpolate species range based on species occurrences and to estimate centers
of biodiversity.","Imports":"sp, rgdal, SDMTools, foreach, methods, grDevices,
graphics,\nstats, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"sperich","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"lattice, RColorBrewer","Title":"Auxiliary Functions to
Estimate Centers of Biodiversity","Version":"1.5-7"},"sperrorest":
{"Author":"Alexander Brenning","Depends":"ROCR, rpart","Description":"This package
implements spatial error estimation and\npermutation-based variable importance
measures for predictive\nmodels using spatial cross-validation and spatial
block\nbootstrap.","License":"GPL-
2","NeedsCompilation":"no","Package":"sperrorest","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"ipred, RSAGA, sp","Title":"Spatial Error Estimation
and Variable Importance","Version":"0.2-1"},"spfrontier":{"Author":"Dmitry Pavlyuk
<Dmitry.V.Pavlyuk@gmail.com>","Depends":"R (>=
3.0),moments,ezsim,tmvtnorm,mvtnorm,maxLik","Description":"A set of tools for
estimation of various spatial specifications of stochastic frontier
models","Imports":"methods, parallel,spdep","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"spfrontier","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Spatial Stochastic Frontier models
estimation","Version":"0.1.12"},"spgrass6":{"Author":"Roger Bivand [cre,
aut],\nRainer Krug [ctb],\nMarkus Neteler [ctb]","Depends":"R (>= 2.12), sp (>=
0.9), XML","Description":"Interpreted interface between GRASS 6+
geographical\ninformation system and R, based on starting R from within the
GRASS\nenvironment, or running free-standing R in a temporary GRASS location;\nthe
package provides facilities for using all GRASS commands from the\nR command line.
This package may not be used for GRASS 7, for which\nrgrass7 should be
used.","Imports":"stats, utils, methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"spgrass6","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"rgdal (>= 0.8-8)","Title":"Interface Between GRASS 6+
Geographical Information System and
R","URL":"http:\/\/grass.osgeo.org\/","Version":"0.8-9"},"spgs":{"Author":"Andrew
Hart [aut, cre], Servet Martínez [aut], Universidad de Chile [cph], INRIA-Chile
[cph]","Depends":"R (>= 3.0)","Description":"A collection of statistical hypothesis
tests and other\ntechniques for identifying certain spatial
relationships\/phenomena in\nDNA sequences. In particular, it provides tests and
graphical methods for determining\nwhether or not DNA sequences comply with
Chargaff's second parity rule\nor exhibit purine-pyrimidine parity. In addition,
there are functions for\nefficiently simulating discrete state space Markov chains
and testing\narbitrary symbolic sequences of symbols for the presence of first-
order\nMarkovianness.\nAlso, it has functions for counting words\/k-mers (and
cylinder patterns) in\narbitrary symbolic sequences. Functions which take a DNA
sequence as input\ncan handle sequences stored as SeqFastadna objects from the
'seqinr' package.","Enhances":"seqinr","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"spgs","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Statistical Patterns in Genomic
Sequences","Version":"1.0"},"spgwr":{"Author":"Roger Bivand [cre, aut],\nDanlin Yu
[aut],\nTomoki Nakaya [ctb],\nMiquel-Angel Garcia-Lopez [ctb]","Depends":"R (>=
2.14), sp (>= 0.8-3)","Description":"Functions for computing geographically
weighted\nregressions are provided, based on work by Chris\nBrunsdon, Martin
Charlton and Stewart Fotheringham.","Imports":"stats, methods","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"spgwr","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"spdep, parallel, maptools (>= 0.7-
32)","Title":"Geographically Weighted Regression","Version":"0.6-28"},"sphereplot":
{"Author":"Aaron Robotham","Depends":"rgl","Description":"Various functions for
creating spherical coordinate system plots via extensions to rgl.","License":"GPL-
2","NeedsCompilation":"no","Package":"sphereplot","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Spherical plotting","Version":"1.5"},"sphet":
{"Author":"Gianfranco Piras <gpiras@mac.com>","Depends":"R (>=
3.0.1)","Description":"Generalized Method of Moment estimation of Cliff-Ord-
type\nspatial autoregressive models with and without
heteroskedastic\ninnovations","Imports":"nlme, spdep (>= 0.5-67), Matrix,
sp","License":"GPL-
2","NeedsCompilation":"no","Package":"sphet","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Estimation of spatial autoregressive models with and
without\nheteroskedastic innovations","Version":"1.6"},"spi":{"Author":"Josemir
Neves","Description":"Compute the SPI index using R","License":"GPL-
2","NeedsCompilation":"no","Package":"spi","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Compute SPI index","Version":"1.1"},"spider":{"Author":"Samuel
Brown, Rupert Collins, Stephane Boyer, Marie-Caroline Lefort, Jagoba Malumbres-
Olarte, Cor Vink, Rob Cruickshank","Depends":"ape, pegas","Description":"A package
for the analysis of species limits and DNA barcoding
data","License":"GPL","NeedsCompilation":"no","Package":"spider","Repository":"http
:\/\/cran.csiro.au\/src\/contrib","Title":"Species Identity and Evolution in
R","Version":"1.3-0"},"spiders":{"Author":"Edward A. Roualdes [cre, aut],\nSimon J.
Bonner [aut]","Depends":"R (>= 3.0.2)","Description":"Fits and simulates data from
our predator preferences model, <DOI:10.1007\/s10651-016-0341-
3>.","Imports":"plyr","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"spiders","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"testthat, knitr, rmarkdown","Title":"Fits Predator
Preferences Model","Version":"1.2"},"spikeSlabGAM":{"Author":"Fabian
Scheipl\n<fabian.scheipl@stat.uni-muenchen.de>","Depends":"R (>=
2.15.1)","Description":"Bayesian variable selection, model choice, and
regularized\nestimation for (spatial) generalized additive mixed regression
models\nvia stochastic search variable selection with spike-and-slab
priors.","Imports":"akima, coda, cluster, ggplot2 (>= 2.0.0), gridExtra
(>=\n2.0.0), MASS, MCMCpack, mvtnorm, R2WinBUGS, reshape, scales,\nsplines,
parallel","License":"CC BY-NC-SA
4.0","NeedsCompilation":"yes","Package":"spikeSlabGAM","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"mboost, mlbench, gtable","Title":"Bayesian
Variable Selection and Model Choice for Generalized\nAdditive Mixed
Models","URL":"https:\/\/github.com\/fabian-s\/spikeSlabGAM","Version":"1.1-
11"},"spikeslab":{"Author":"Hemant Ishwaran
<hemant.ishwaran@gmail.com>","Depends":"R (>= 3.0.0), lars, randomForest,
parallel","Description":"Spike and slab for prediction and variable selection
in\nlinear regression models. Uses a generalized elastic net for\nvariable
3)","NeedsCompilation":"yes","Package":"spikeslab","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Prediction and variable selection using spike and
slab\nregression","URL":"http:\/\/web.ccs.miami.edu\/~hishwaran
http:\/\/www.kogalur.com","Version":"1.1.5"},"spinyReg":{"Author":"Charles
Bouveyron, Julien Chiquet, Pierre Latouche, Pierre-
Alexandre\nMattei","Description":"Implements a generative model that uses a\nspike-
and-slab like prior distribution obtained by multiplying a\ndeterministic binary
vector. Such a model allows an EM algorithm,\noptimizing a type-II log-
likelihood.","Imports":"methods","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"spinyReg","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Sparse Generative Model and Its EM
Algorithm","Version":"0.1-0"},"splancs":{"Author":"Roger Bivand [cre],\nBarry
Rowlingson [aut],\nPeter Diggle [aut],\nGiovanni Petris [ctb],\nStephen Eglen
[ctb]","Depends":"R (>= 2.10.0), sp (>= 0.9)","Description":"The Splancs package
was written as an enhancement to S-Plus for display and analysis of spatial point
pattern data; it has been ported to R and is in \"maintenance
mode\".","Imports":"stats, graphics, grDevices, methods","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"splancs","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Spatial and Space-Time Point Pattern
Analysis","URL":"http:\/\/www.maths.lancs.ac.uk\/~rowlings\/Splancs\/","Version":"2
.01-38"},"splitstackshape":{"Author":"Ananda Mahto","Depends":"R (>= 2.10),
data.table (>= 1.9.4)","Description":"Online data collection tools like Google
Forms often export\nmultiple-response questions with data concatenated in cells.
The\nconcat.split (cSplit) family of functions splits such data into\nseparate
cells. The package also includes functions to stack groups\nof columns and to
reshape wide data, even when the data are\n\"unbalanced\"---something which reshape
(from base R) does not handle,\nand which melt and dcast from reshape2 do not
easily handle.","License":"GPL-
3","NeedsCompilation":"no","Package":"splitstackshape","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Stack and Reshape Datasets After Splitting
Concatenated
Values","URL":"http:\/\/github.com\/mrdwab\/splitstackshape","Version":"1.4.2"},"sp
lm":{"Author":"Giovanni Millo [aut, cre],\nGianfranco Piras [aut]","Depends":"R (>=
2.12.0), spdep","Description":"ML and GM estimation and diagnostic testing of
econometric models for spatial panel data.","Imports":"plm, maxLik, MASS,
bdsmatrix, ibdreg, nlme, Matrix, spam","License":"GPL-
2","NeedsCompilation":"no","Package":"splm","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Econometric Models for Spatial Panel Data","Version":"1.3-
7"},"spls":{"Author":"Dongjun Chung <chungdon@stat.wisc.edu>, Hyonho
Chun\n<chun@stat.wisc.edu>, Sunduz Keles <keles@stat.wisc.edu>","Depends":"R (>=
2.14)","Description":"This package provides
functions for fitting a Sparse\nPartial Least Squares Regression and
Classification","Imports":"MASS, nnet, parallel, pls","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"spls","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Sparse Partial Least Squares (SPLS) Regression
and\nClassification","Version":"2.2-1"},"splus2R":{"Author":"William Constantine,
Tim Hesterberg, Knut Wittkowski, Tingting\nSong, Stephen Kaluzny","Depends":"R (>=
2.7.2), methods","Description":"Currently there are many functions in S-PLUS that
are\nmissing in R. To facilitate the conversion of S-PLUS packages\nto R packages,
this package provides some missing S-PLUS\nfunctionality in R.","License":"GPL-
2","NeedsCompilation":"yes","Package":"splus2R","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Supplemental S-PLUS functionality in R","Version":"1.2-
0"},"splusTimeDate":{"Author":"TIBCO Software Inc.","Depends":"R (>= 2.12.0),
methods, stats","Description":"Classes and methods for times and dates (ported from
S-PLUS)","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"yes","Package":"splusTimeDate","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Title":"Times and Dates from S-
PLUS","Version":"2.5.0-135"},"splusTimeSeries":{"Author":"TIBCO Software
Inc.","Depends":"splusTimeDate, methods, R (>= 2.10)","Description":"Classes and
methods for time series (ported from S-PLUS).","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"yes","Package":"splusTimeSeries","Repository":"http:\/
\/cran.csiro.au\/src\/contrib","Title":"Time Series from S-PLUS","Version":"1.5.0-
73"},"spm12r":{"Author":"John Muschelli","Description":"Installs SPM12 to the R
library directory and has associated functions for fMRI and general imaging
utilities, called through MATLAB.","Imports":"R.utils, utils, matlabr, stringr,
oro.nifti, fslr, git2r","License":"GPL-2 | file
LICENCE","NeedsCompilation":"no","Package":"spm12r","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Wrapper Functions for SPM (Statistical Parametric
Mapping)\nVersion 12 from the Wellcome Trust Centre for
Neuroimaging","Version":"1.1.1"},"spnet":{"Author":"Emmanuel Rousseaux, Marion
Deville, Gilbert Ritschard","Depends":"R (>= 2.10), methods, sp,
shape","Description":"Facilitates the rendering of networks for which nodes have a
specific position on a map (cities, participants in a political debate, etc.). Map
data and network data are stored together in a single object which handles the
match between network nodes and their respective position on the map. The plot
method renders both the map and the network data. Several networks can be plot
simultaneously. The graphic is highly customisable and the legend is automatically
printed. Map data have to be supplied as 'SpatialPolygons' objects (from the 'sp'
package) and network data as 'named matrix'.","License":"GPL-
3","NeedsCompilation":"no","Package":"spnet","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Plotting (Social) Networks on
Maps","URL":"http:\/\/emmanuel.rousseaux.me\/r-package-spnet","Version":"0.9.1-
0"},"spocc":{"Author":"Scott Chamberlain [aut, cre],\nKarthik Ram [aut],\nTed Hart
[aut]","Description":"A programmatic interface to many species occurrence data
sources,\nincluding 'GBIF', 'USGS's' 'BISON', 'iNaturalist', Berkeley
'Ecoinformatics'\nEngine 'eBird', 'AntWeb', and 'iDigBio'. Includes functionality
for\nretrieving species occurrence data, and combining that
data.","Imports":"utils, methods, stats, rgbif (>= 0.9.0), rbison (>=
0.4.8),\nrebird (>= 0.2), rvertnet (>= 0.4.1), ridigbio (>= 0.3.3),\nlubridate (>=
1.5.0), httr (>= 1.0.0), whisker (>= 0.3-2), V8\n(>= 0.9), jsonlite (>= 0.9.19),
data.table (>= 1.9.6)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"spocc","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat, knitr, taxize","Title":"Interface to
Species Occurrence Data
Sources","URL":"https:\/\/github.com\/ropensci\/spocc","Version":"0.4.5"},"spoccuti
ls":{"Author":"Scott Chamberlain [aut,
cre]","Depends":"ggplot2","Description":"Utilities for use with 'spocc'. Includes
functions to\nclean occurrence data, find and remove duplicates, combine data,\nand
make maps with base 'R' plots, 'ggplot2', and various
interactive\nmaps.","Imports":"methods, utils, stats, graphics, spocc (>= 0.3.0),
ggmap,\ngrid, sp, rworldmap, RColorBrewer, httr, leafletR (>= 0.2-
0),\ngistr","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"spoccutils","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"roxygen2, testthat, knitr, taxize,
maptools","Title":"Utilities for Use with
'spocc'","URL":"https:\/\/github.com\/ropensci\/spoccutils","Version":"0.1.0"},"spo
rm":{"Author":"Zhong Guan <zguan@iusb.edu>; Cheng Peng
<cpeng@usm.maine.edu>","Description":"R implementation of the methods described
in \"A rank-based\nempirical likelihood approach to two-sample proportional
odds\nmodel and its goodness-of-fit\" by Zhong Guan and Cheng Peng,\nJournal of
Nonparametric Statistics, to appear.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"sporm","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Semiparametric proportional odds rate
model","Version":"1.1"},"spray":{"Author":"Robin K. S.
Hankin","Depends":"methods","Description":"Sparse arrays interpreted as
multivariate polynomials.","Imports":"Rcpp (>=
0.12.3),partitions,magic","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"spray","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Sparse Arrays and Multivariate
Polynomials","Version":"1.0"},"sprex":{"Author":"Eric Archer [aut,
cre]","Description":"Calculate species richness functions for rarefaction
and\nextrapolation.","Imports":"graphics, stats, swfscMisc","License":"GNU General
Public
License","NeedsCompilation":"no","Package":"sprex","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Calculate Species Richness and Extrapolation
Metrics","Version":"1.4"},"sprinter":{"Author":"Isabell Hoffmann","Depends":"R (>=
3.0.0), CoxBoost, survival","Description":"The main function of this package builds
prognostic models that consider interactions by combining available statistical
components. Furthermore, it provides a function for evaluating the relevance of the
selected interactions by resampling techniques.","Imports":"GAMBoost,
randomForestSRC, LogicReg","License":"GPL-
2","NeedsCompilation":"no","Package":"sprinter","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"parallel, knitr","Title":"Framework for Screening
Prognostic Interactions","Version":"1.1.0"},"sprintfr":{"Author":"Brandon Taylor
[aut, cre]","Depends":"R (>= 3.2.2)","Description":"Makes string formatting easy
with an accessible interface.","Imports":"dplyr (>= 0.4.3), lazyeval (>= 0.1.10),
magrittr (>= 1.5),\nstringi (>= 0.5-5), tidyr (>= 0.3.1)","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"sprintfr","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"knitr, rmarkdown","Title":"An Easy Interface to
String
Formatting","URL":"https:\/\/github.com\/bramtayl\/sprintfr","Version":"0.1.0"},"sp
rm":{"Author":"Sven Serneels (BASF Corp) and Irene Hoffmann","Depends":"ggplot2 (>=
2.0.0)","Description":"Robust dimension reduction methods for regression and
discriminant analysis are implemented that yield estimates with a partial least
squares alike interpretability. Partial robust M regression (PRM) is robust to both
vertical outliers and leverage points. Sparse partial robust M regression (SPRM) is
a related robust method with sparse coefficient estimate, and therefore with
intrinsic variable selection. For binary classification related discriminant
methods are PRM-DA and SPRM-DA.","Imports":"cvTools, graphics, grDevices, grid,
pcaPP, reshape2,\nrobustbase, stats","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"sprm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Sparse and Non-Sparse Partial Robust M Regression
and\nClassification","Version":"1.2.2"},"sprsmdl":{"Author":"Hiroshi
Saito","Description":"R functions to mine sparse models from data.","License":"GPL-
2","NeedsCompilation":"no","Package":"sprsmdl","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Sparse modeling toolkit","Version":"0.1-0"},"spsann":
{"Author":"Alessandro Samuel-Rosa [aut, cre],\nLucia Helena Cunha dos Anjos
[ths],\nGustavo de Mattos Vasques [ths],\nGerard B M Heuvelink [ths],\nEdzer
Pebesma [ctb],\nJon Skoien [ctb],\nJoshua French [ctb],\nPierre Roudier
[ctb],\nDick Brus [ctb],\nMurray Lark [ctb]","Description":"Methods to optimize
spatial sample configurations using spatial simulated annealing.
Multiple\nobjective functions are implemented for various purposes, such as
variogram estimation, spatial trend\nestimation, and spatial interpolation. A
general purpose spatial simulated annealing function enables the\nuser to define
his\/her own objective function.","Imports":"methods, pedometrics, Rcpp (>=
0.11.3), sp, SpatialTools","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"spsann","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"gstat, tcltk, knitr","Title":"Optimization of Sample
Configurations using Spatial Simulated\nAnnealing","Version":"2.0-0"},"spsi":
{"Author":"Szymon Sacher & Andrew Clausen, The University of Edinburgh. Excerpts
adapted from Fortran code Copyright (C) Paolo Costantini","Depends":"plot3D, R(>=
2.10.0)","Description":"Program uses method of polynomial of variable degrees to
interpolate gridded data preserving monotonicity and\/or convexity or none. Method
is implemented for univariate and bivariate cases. If values of derivatives are
provided, spline will fix them,if not program will estimate them numerically.
Package written purely in R.","License":"GPL (>=
2.0)","NeedsCompilation":"no","Package":"spsi","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Shape-Preserving
Uni-Variate and Bi-Variate Spline Interpolation","Version":"0.1"},"spsmooth":
{"Author":"Wesley Burr, with contributions from Karim Rahim","Depends":"R (>=
2.15)","Description":"Produces Slepian smoother basis objects for use in
Generalized Additive Models, as estimated by package:mgcv.","Imports":"mgcv (>=
1.7.18)","License":"GPL (>= 2) | file
LICENSE","NeedsCompilation":"yes","Package":"spsmooth","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"spsmooth: An Extension Package for
'mgcv'","Version":"1.1-3"},"spsurvey":{"Author":"Tom Kincaid [aut, cre],\nTony
Olsen [aut],\nDon Stevens [ctb],\nChristian Platt [ctb],\nDenis White
[ctb],\nRichard Remington [ctb]","Depends":"R (>= 2.10), sp","Description":"This
group of functions implements algorithms for design and\nanalysis of probability
surveys. The functions are tailored for Generalized\nRandom Tessellation
Stratified survey designs.","Imports":"methods, deldir, foreign, graphics,
grDevices, MASS, rgeos,\nstats","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"spsurvey","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Spatial Survey Design and
Analysis","URL":"http:\/\/www.epa.gov\/nheerl\/arm\/","Version":"3.1"},"spt":
{"Author":"Bin Wang <bwang@southalabama.edu>.","Description":"This package collects
algorithms related to Sierpinski pedal triangle
(SPT).","License":"Unlimited","NeedsCompilation":"yes","Package":"spt","Repository"
:"http:\/\/cran.csiro.au\/src\/contrib","Title":"Sierpinski Pedal
Triangle","Version":"1.13-8-8"},"sptm":{"Author":"Youyi Fong <yfong@fhcrc.org>,
Krisztian Sebestyen <ksebestyen@gmail.com>","Depends":"R (>= 3.0.0), survival,
survey","Description":"Semiparametric transformation model, calibration
weights","Imports":"kyotil","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"sptm","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"RUnit, mvtnorm, Matrix, MASS","Title":"SemiParametric
Transformation Model Methods","Version":"14.10-11"},"spuRs":{"Author":"Owen Jones,
Robert Maillardet, Andrew Robinson, Olga Borovkova, and Steven Carnie","Depends":"R
(>= 2.10), MASS, lattice","Description":"This package provides functions and
datasets from the book \"Introduction to Scientific Programming and Simulation
Using R\".","License":"GPL-
3","NeedsCompilation":"no","Package":"spuRs","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Functions and Datasets for \"Introduction to
Scientific\nProgramming and Simulation Using R\"","Version":"2.0.0"},"sqldf":
{"Author":"G. Grothendieck <ggrothendieck@gmail.com>","Depends":"R (>= 3.1.0),
gsubfn (>= 0.6), proto, RSQLite (>= 1.0.0)","Description":"Description: Manipulate
R data frames using SQL.","Imports":"DBI (>= 0.2-5), chron","License":"GPL-
2","NeedsCompilation":"no","Package":"sqldf","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"RH2, RMySQL, RPostgreSQL, svUnit, tcltk,
MASS","Title":"Perform SQL Selects on R Data
Frames","URL":"http:\/\/sqldf.googlecode.com","Version":"0.4-10"},"sqliter":
{"Author":"Wilson Freitas <wilson.freitas@gmail.com>","Description":"sqliter helps
users, mainly data munging practioneers, to organize\ntheir sql calls in a clean
structure. It simplifies the process of\nextracting and transforming data into
useful formats.","Imports":"stringr, functional, DBI, RSQLite","License":"MIT +
file
LICENSE","NeedsCompilation":"no","Package":"sqliter","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Connection wrapper to SQLite
databases","URL":"https:\/\/github.com\/wilsonfreitas\/sqliter\/","Version":"0.1.0"
},"sqlutils":{"Author":"Jason Bryer","Depends":"roxygen2, stringr,
DBI","Description":"This package provides utilities for working with a library of
SQL\nfiles.","Enhances":"RPostgreSQL, RODBC, RMySQL, RSQLite,
RJDBC","License":"GPL","NeedsCompilation":"no","Package":"sqlutils","Repository":"h
ttp:\/\/cran.csiro.au\/src\/contrib","Suggests":"tcltk, sqldf,
xtable","Title":"Utilities for working with SQL
files","URL":"http:\/\/jason.bryer.org\/sqlutils,
http:\/\/github.com\/jbryer\/sqlutils","Version":"1.2"},"squash":{"Author":"Aron C.
Eklund","Depends":"graphics, grDevices, methods","Description":"Functions for
color-based visualization of multivariate data, i.e. colorgrams or heatmaps.
Lower-level functions map numeric values to colors, display a matrix as an array
of colors, and draw color keys. Higher-level plotting functions generate a
bivariate histogram, a dendrogram aligned with a color-coded matrix, a triangular
distance matrix, and more.","License":"Artistic-
2.0","NeedsCompilation":"no","Package":"squash","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Color-Based Plots for Multivariate
Visualization","URL":"http:\/\/www.cbs.dtu.dk\/~eklund\/squash\/","Version":"1.0.7"
},"sra":{"Author":"Arnaud Le Rouzic <lerouzic@legs.cnrs-
gif.fr>","Description":"This package (sra) provides a set of tools to analyse
artificial-selection response datasets. The data typically feature for several
generations the average value of a trait in a population, the variance of the
trait, the population size and the average value of the parents that were chosen to
breed. Sra implements two families of models aiming at describing the dynamics of
the genetic architecture of the trait during the selection response. The first
family relies on purely descriptive (phenomenological) models, based on an
autoregressive framework. The second family provides different mechanistic models,
accounting e.g. for inbreeding, mutations, genetic and environmental canalization,
or epistasis. The parameters underlying the dynamics of the time series are
estimated by maximum likelihood. The sra package thus provides (i) a wrapper for
the R functions mle() and optim() aiming at fitting in a convenient way a
predetermined set of models, and (ii) some functions to plot and analyze the output
of the models.","Imports":"stats4","License":"GPL-
2","NeedsCompilation":"no","Package":"sra","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Selection Response Analysis","Version":"0.1.1"},"srd":
{"Author":"Roger Marshall","Description":"Draws scaled rectangle diagrams to
represent a 2^k contingency\ntable, for
k<=6","Imports":"plyr,animation,colorspace,stringr,survival","License":"GPL-
2","NeedsCompilation":"yes","Package":"srd","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Draws Scaled Rectangle Diagrams","Version":"1.0"},"srvyr":
{"Author":"Greg Freedman [aut, cre]","Depends":"R (>= 3.2.2)","Description":"Use
piping, verbs like 'group_by' and 'summarize', and other\n'dplyr' inspired
syntactic style when calculating summary statistics on survey\ndata using functions
from the 'survey' package.","Imports":"dplyr, lazyeval, magrittr,
survey","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"srvyr","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"ggplot2, knitr, Matrix, rmarkdown, pander, survival,
testthat","Title":"'dplyr'-Like Syntax for Summary Statistics of Survey
Data","URL":"https:\/\/github.com\/gergness\/srvyr","Version":"0.1.1"},"ss3sim":
{"Author":"Sean Anderson [aut, cre],\nCole Monnahan [aut],\nKelli Johnson
[aut],\nKotaro Ono [aut],\nJuan Valero [aut],\nCurry Cunningham [aut],\nAllan Hicks
[aut],\nFelipe Hurtado-Ferro [aut],\nPeter Kuriyama [aut],\nRoberto Licandeo
[aut],\nCarey McGilliard [aut],\nMelissa Muradian [ctb],\nMerrill Rudd
[aut],\nChristine Stawitz [aut],\nCody Szuwalski [aut],\nIan Taylor [aut],\nKatyana
Vert-pre [aut],\nAthol Whitten [aut]","Depends":"R (>= 3.2.2)","Description":"The
ss3sim package develops a framework for fisheries stock\nassessment simulation
testing with Stock Synthesis 3 (SS3).","Imports":"foreach, plyr, r4ss, gtools,
lubridate, ggplot2, bbmle, dplyr,\nmagrittr, grDevices, graphics, stats,
LICENSE","NeedsCompilation":"no","Package":"ss3sim","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"knitr, doParallel, reshape2","Title":"Fisheries
Stock Assessment Simulation Testing with
Stock\nSynthesis","Version":"0.9.0"},"ssa":{"Author":"Dave Zhao [aut,
cre]","Depends":"R (>= 3.2.2)","Description":"Procedures for analyzing simultaneous
signals, e.g., features that are simultaneously significant in two different
studies. Includes methods for detecting simultaneous signals and for identifying
them under false discovery rate control.","Imports":"stats","License":"GPL-
3","NeedsCompilation":"yes","Package":"ssa","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Title":"Simultaneous Signal Analysis","Version":"1.1.0"},"ssanv":
{"Author":"Michael P. Fay <mfay@niaid.nih.gov>","Depends":"R (>= 2.1.1),
stats","Description":"A set of functions to calculate sample size for two-sample
difference in means tests. Does adjustments for either nonadherence or variability
that comes from using data to estimate parameters.","License":"GPL-
3","NeedsCompilation":"no","Package":"ssanv","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Sample Size Adjusted for Nonadherence or Variability of
Input\nParameters","Version":"1.1"},"sscor":{"Author":"Alexander Duerre [aut,
cre],\nDaniel Vogel [aut]","Depends":"pcaPP, robustbase,
mvtnorm","Description":"Provides the spatial sign correlation and the two-stage
spatial sign correlation as well as a one-sample test for the correlation
coefficient.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"sscor","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Robust Correlation Estimation and Testing Based on Spatial
Signs","Version":"0.2"},"ssd":{"Author":"Junheng Ma and Jiayang
Sun","Description":"ssd calculates the sample size needed to detect the differences
between two sets of unordered categorical data.","License":"GPL-
2","NeedsCompilation":"no","Package":"ssd","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Title":"Sample Size Determination (SSD) for Unordered
Categorical Data","Version":"0.3"},"ssfa":{"Author":"Elisa Fusco, Francesco
Vidoli","Depends":"Matrix, maxLik, spdep, sp","Description":"Spatial Stochastic
Frontier Analysis (SSFA) is an original method for controlling the spatial
heterogeneity in Stochastic Frontier Analysis (SFA) models, for cross-sectional
data, by splitting the inefficiency term into three terms: the first one related to
spatial peculiarities of the territory in which each single unit operates, the
second one related to the specific production features and the third one
representing the error term.","License":"GPL-
3","NeedsCompilation":"no","Package":"ssfa","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"R.rsp","Title":"Spatial Stochastic Frontier
Analysis","Version":"1.1"},"ssfit":{"Author":"Christiana
Kartsonaki","Depends":"survey","Description":"Fits complex parametric models using
the method proposed by Cox and Kartsonaki (2012) without
likelihoods.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ssfit","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Fitting of parametric models using summary
statistics","Version":"1.1"},"ssize.fdr":{"Author":"Megan Orr, Peng
Liu","Description":"This package contains a set of functions that
calculates\nappropriate sample sizes for one-sample t-tests, two-sample t-
tests,\nand F-tests for microarray experiments based on desired power
while\ncontrolling for false discovery rates. For all tests, the
standard\ndeviations (variances) among genes can be assumed fixed or random.\nThis
is also true for effect sizes among genes in one-sample and two\nsample
experiments. Functions also output a chart of power versus sample\nsize, a table of
power at different sample sizes, and a table of critical\ntest values at different
sample sizes.","License":"GPL-
3","NeedsCompilation":"no","Package":"ssize.fdr","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Sample Size Calculations for Microarray
Experiments","Version":"1.2"},"ssizeRNA":{"Author":"Ran Bi [aut, cre],\nPeng Liu
[aut],\nTim Triche [ctb]","Depends":"R (>= 3.2.0)","Description":"We propose a
procedure for sample size calculation while\ncontrolling false discovery rate for
RNA-seq experimental design. Our\nprocedure depends on the Voom method proposed for
RNA-seq data analysis\nby Law et al. (2014) <DOI: 10.1186\/gb-2014-15-2-r29> and
the sample size\ncalculation method proposed for microarray experiments by Liu and
Hwang\n(2007) <DOI: 10.1093\/bioinformatics\/btl664>. We develop a set of
functions\nthat calculates appropriate sample sizes for two-sample t-test for RNA-
seq\nexperiments with fixed or varied set of parameters. The outputs also contain
a\nplot of power versus sample size, a table of power at different sample
sizes,\nand a table of critical test values at different sample sizes.\nTo install
this package, please use\n'source(\"http:\/\/bioconductor.org\/biocLite.R\");
biocLite(\"ssizeRNA\")'.","Imports":"MASS, Biobase, edgeR, limma, qvalue,
ssize.fdr","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ssizeRNA","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"BiocStyle, knitr","Title":"Sample Size Calculation
for RNA-Seq Experimental Design","Version":"1.2.4"},"ssmn":{"Author":"Luis Benites
Sanchez and Clecio da Silva Ferreira","Description":"Performs the EM algorithm for
regression models using Skew Scale Mixtures of Normal
Distributions.","Imports":"mnormt, moments, truncdist, sn","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ssmn","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Skew Scale Mixtures of Normal
Distributions","Version":"1.0"},"ssmrob":{"Author":"Mikhail Zhelonkin, Marc G.
Genton, Elvezio Ronchetti","Depends":"sampleSelection, robustbase, mvtnorm,
MASS","Description":"Package provides a set of tools for robust estimation and
inference for models with sample selectivity.","License":"GPL-
2","NeedsCompilation":"no","Package":"ssmrob","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Robust estimation and inference in sample selection
models","Version":"0.4"},"sspline":{"Author":"Xianhong Xie
<xianhong04@gmail.com>","Depends":"R (>= 2.10)","Description":"R package for
computing the spherical smoothing splines","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"sspline","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Smoothing Splines on the
Sphere","URL":"http:\/\/www.stat.wisc.edu\/~xie","Version":"0.1-6"},"sspse":
{"Author":"Mark S. Handcock [aut, cre, cph],\nKrista J. Gile [aut,
cph]","Depends":"parallel","Description":"An integrated set of tools to estimate
the size of a networked population based on respondent-driven sampling data. The
package is part of the \"RDS Analyst\" suite of packages for the analysis of
respondent-driven sampling data.","Imports":"coda","License":"GPL-3 + file
LICENSE","NeedsCompilation":"yes","Package":"sspse","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"network, testthat","Title":"Estimating Hidden
Population Size using Respondent Driven\nSampling
Data","URL":"http:\/\/www.hpmrg.org","Version":"0.5-1"},"sss":{"Author":"Andrie de
Vries [aut, cre]","Depends":"R (>= 2.11.0)","Description":"Tools to import survey
files\nin the .sss (triple-s) format. The package provides the function\nread.sss()
that reads the .asc and .sss files of a\ntriple-s survey data file. The package is
experimental\n- feedback, issues and bug reports are welcome.","Imports":"utils,
methods, XML","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"sss","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"testthat","Title":"Tools for Importing Files in the Triple-
s (Standard Survey\nStructure)
Format","URL":"https:\/\/github.com\/andrie\/sss","Version":"0.0-14"},"ssvd":
{"Author":"Dan Yang","Description":"Fast iterative thresholding sparse SVD,
together with an initialization algorithm","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"ssvd","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Sparse SVD","Version":"1.0"},"ssym":{"Author":"Luis Hernando
Vanegas <hvanegasp@gmail.com> and Gilberto A. Paula","Depends":"GIGrvg, numDeriv,
normalp, Formula, survival","Description":"Set of tools to fit a semi-parametric
regression model suitable for analysis of data sets in which the response variable
is continuous, strictly positive, asymmetric and possibly, censored. Under this
setup, both the median and the skewness of the response variable distribution are
explicitly modeled by using semi-parametric functions, whose non-parametric
components may be approximated by natural cubic splines or P-splines. Supported
distributions for the model error include log-normal, log-Student-t, log-power-
exponential, log-hyperbolic, log-contaminated-normal, log-slash, Birnbaum-Saunders
and Birnbaum-Saunders-t distributions.","Imports":"stats, sandwich, grDevices,
graphics, methods, utils","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"ssym","Repository":"http:\/\/cran.csiro.au\/s
rc\/contrib","Suggests":"NISTnls, gam, sn, MASS","Title":"Fitting Semi-Parametric
log-Symmetric Regression Models","Version":"1.5.5"},"st":{"Author":"Rainer Opgen-
Rhein, Verena Zuber, and Korbinian Strimmer.","Depends":"R (>= 3.0.2), sda (>=
1.3.7), fdrtool (>= 1.2.15), corpcor (>=\n1.6.8)","Description":"Implements
the \"shrinkage t\" statistic\nintroduced in Opgen-Rhein and Strimmer (2007) and a
shrinkage estimate\nof the \"correlation-adjusted t-score\" (CAT score) described
in\nZuber and Strimmer (2009). It also offers a convenient interface\nto a number
of other regularized t-statistics commonly\nemployed in high-dimensional case-
control studies.","Imports":"graphics, stats","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"st","Repository":"http:\/\/cran.csiro.au\/sr
c\/contrib","Suggests":"limma, samr","Title":"Shrinkage t Statistic and
Correlation-Adjusted t-
Score","URL":"http:\/\/strimmerlab.org\/software\/st\/","Version":"1.2.5"},"staTool
s":{"Author":"Alessandro Bessi","Depends":"R (>= 3.1.1)","Description":"A
collection of statistical tools for social network analysis, with strong emphasis
on the analysis of discrete powerlaw distributions and statistical hypothesis
tests.","Imports":"Rcpp, VGAM, magicaxis","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"staTools","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Statistical Tools for Social Network
Analysis","Version":"0.1.0"},"stabledist":{"Author":"Diethelm Wuertz, Martin
Maechler and Rmetrics core team members.","Depends":"R (>= 3.1.0), stats,
utils","Description":"Density, Probability and Quantile functions, and random
number\ngeneration for (skew) stable distributions, using the parametrizations
of\nNolan.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"stabledist","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"Matrix, fBasics, FMStable, RUnit, Rmpfr,
sfsmisc","Title":"Stable Distribution
Functions","URL":"http:\/\/www.rmetrics.org","Version":"0.7-0"},"stablespec":
{"Author":"Ridho Rahmadi [aut, cre],\nPerry Groot [aut, ths],\nTom Heskes [aut,
ths]","Depends":"R (>= 3.1.0)","Description":"An exploratory and heuristic approach
for specification search\nin Structural Equation Modeling. The basic idea is to
subsample\nthe original data, and for each subset we search the\noptimal models.
Here the criteria of an optimal model is defined\nby two objectives: to fit the
data well and is simple (parsimonious) model.\nAs these objectives are conflicting,
we apply NSGA-II to optimize,\nsuch that to get optimal models for the whole range
of model complexities.\nFrom these optimal models, we observe the model
specifications (structures)\nthat are both stable and parsimonious, called
relevant. At the end we infer\ncausal model from these relevant
structures.","Imports":"ggm, matrixcalc,
sem, nsga2R, graph, Rgraphviz, methods","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"stablespec","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Stable Specification Search
in Structural Equation Models","Version":"0.1.3"},"stabs":{"Author":"Benjamin
Hofner [aut, cre],\nTorsten Hothorn [aut]","Depends":"R (>= 2.14.0), methods,
stats, parallel","Description":"Resampling procedures to assess the stability of
selected variables\nwith additional finite sample error control for high-
dimensional variable\nselection procedures such as Lasso or
boosting","Enhances":"glmnet, lars, mboost (> 2.3-0), gamboostLSS (>= 1.2-
0)","License":"GPL-
2","NeedsCompilation":"no","Package":"stabs","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"TH.data, hdi","Title":"Stability Selection with Error
Control","URL":"https:\/\/github.com\/hofnerb\/stabs","Version":"0.5-
1"},"stackoverflow":{"Author":"Neal Fultz <nfultz@gmail.com> and the
StackOverflow.com community","Description":"Consists of helper functions collected
from StackOverflow.com, a\nquestion and answer site for professional and enthusiast
programmers.","License":"CC BY-SA
4.0","NeedsCompilation":"no","Package":"stackoverflow","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Stack Overflow's Greatest
Hits","URL":"http:\/\/stackoverflow.com","Version":"0.1.2"},"stacomirtools":
{"Author":"Cedric Briand","Depends":"RODBC,xtable,methods","Description":"S4 class
wrappers for ODBC connection.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"stacomirtools","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"stacomi ODBC connection
class","Version":"0.3"},"stagePop":{"Author":"Helen Kettle","Description":"Provides
facilities to implement and run population models of\nstage-structured
species...","Imports":"deSolve,PBSddesolve","License":"GPL-3 | file
LICENSE","NeedsCompilation":"no","Package":"stagePop","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"R.rsp","Title":"Modelling the Population
Dynamics of a Stage-Structured Species\nin Continuous
Time","URL":"https:\/\/github.com\/HelenKettle\/StagePop","Version":"1.1-
1"},"stam":{"Author":"Zhijie Zhang <epistat@gmail.com>","Depends":"R (>=
2.10.0),np,sp","Description":"stam is an evolving package that target on the
various\nmethods to conduct Spatio-Temporal Analysis and\nModelling,including
Exploratory Spatio-Temporal Analysis and\nInferred Spatio-Temporal
Modelling.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"stam","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Spatio-Temporal Analysis and Modelling","Version":"0.0-
1"},"stargazer":{"Author":"Marek Hlavac
<hlavac@fas.harvard.edu>","Description":"Produces LaTeX code, HTML\/CSS code and
ASCII text for well-formatted tables that hold\nregression analysis results from
several models side-by-side, as well as summary\nstatistics.","Enhances":"AER,
betareg, brglm, censReg, dynlm, eha, erer, ergm, fGarch,\ngee, glmx, gmm, lfe,
lme4, lmtest, MASS, mclogit, mgcv, mlogit,\nmnlogit, nlme, nnet, ordinal, plm,
pscl, quantreg, rms,\nrelevent, robustbase, sampleSelection, spdep, survey,
survival,\nZelig","Imports":"stats, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"stargazer","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Well-Formatted Regression and Summary Statistics
Tables","Version":"5.2"},"starma":{"Author":"Felix
Cheysson","Description":"Statistical functions to identify, estimate and diagnose a
Space-Time AutoRegressive Moving Average (STARMA) model.","Imports":"Rcpp (>=
0.11.1), ggplot2, scales, graphics, stats","License":"GPL-
2","NeedsCompilation":"yes","Package":"starma","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"spdep","Title":"Modelling Space Time AutoRegressive
Moving Average (STARMA)\nProcesses","Version":"1.3"},"startupmsg":{"Author":"Peter
Ruckdeschel","Depends":"R(>= 1.8.0)","Description":"Utilities for start-up
messages","License":"LGPL-
3","NeedsCompilation":"no","Package":"startupmsg","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Utilities for start-up
messages","Version":"0.9"},"stashR":{"Author":"Sandy Eckel, Roger D.
Peng","Depends":"R (>= 2.14.0), methods, filehash","Description":"A Set of Tools
for Administering SHared Repositories","Imports":"tools, digest","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"stashR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"A Set of Tools for Administering SHared
Repositories","Version":"0.3-5"},"statar":{"Author":"Matthieu Gomez [aut,
cre]","Depends":"R (>= 3.2.0)","Description":"A set of tools inspired by Stata to
explore data.frames (summarize,\ntabulate, xtile, pctile, binscatter, elapsed
quarters\/month, lead\/lag).","Imports":"data.table, dplyr (>= 0.4.3), ggplot2 (>=
2.0.0), lazyeval,\nmatrixStats, methods, stargazer, stringr, tidyr","License":"GPL-
2","NeedsCompilation":"no","Package":"statar","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"knitr, lubridate, testthat","Title":"Tools Inspired by
Stata to Manipulate Tabular
Data","URL":"https:\/\/github.com\/matthieugomez\/statar","Version":"0.6.0"},"statc
heck":{"Author":"Sacha Epskamp <mail@sachaepskamp.com> & Michele B.
Nuijten\n<m.b.nuijten@uvt.nl>","Depends":"R (>= 2.14.2),
plyr","Description":"Extract statistics from articles and recompute p
2","NeedsCompilation":"no","Package":"statcheck","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Extract Statistics from Articles and Recompute P
Values","Version":"1.0.1"},"statebins":{"Author":"Bob Rudis
(@hrbrmstr)","Depends":"R (>= 3.0.0),","Description":"Cartogram heatmaps are an
alternative to choropleth maps for USA States\nand are based on work by the
Washington Post graphics department in their report\non \"The states most
threatened by trade\". \"State bins\" preserve as much of the\ngeographic placement
of the states as possible but has the look and feel of a\ntraditional heatmap.
Functions are provided that allow for use of a binned,\ndiscrete scale, a
continuous scale or manually specified colors depending on\nwhat is needed for the
underlying data.","Imports":"ggplot2, grid, gridExtra, scales,
RColorBrewer","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"statebins","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"testthat","Title":"U.S. State Cartogram
Heatmaps in R; an Alternative to Choropleth\nMaps for USA
States","URL":"http:\/\/github.com\/hrbrmstr\/statebins","Version":"1.2.2"},"statfi
":{"Author":"Leo Lahti, Juuso Parkkinen, Joona Lehtomaki","Depends":"R (>= 3.0.2),
pxR","Description":"Statistics Finland (Tilastokeskus) Open Data R
Tools","License":"BSD_2_clause + file
LICENSE","NeedsCompilation":"no","Package":"statfi","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"statfi R
tools","URL":"https:\/\/github.com\/rOpenGov\/statfi","Version":"0.9.8"},"stationaR
y":{"Author":"Richard Iannone [aut, cre]","Description":"Selectively acquire hourly
meteorological data from stations located all over the world.","Imports":"plyr (>=
1.8.2), dplyr (>= 0.4.3), readr (>= 0.2.0),\ndownloader (>= 0.4), lubridate (>=
1.3.3), progress (>= 1.0.2),\nstringr (>= 1.0.0), leaflet (>=
LICENSE","NeedsCompilation":"no","Package":"stationaRy","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Suggests":"testthat","Title":"Get Hourly Meteorological
Data from Global Stations","URL":"https:\/\/github.com\/rich-
iannone\/stationaRy","Version":"0.4.1"},"statmod":{"Author":"Gordon Smyth [cre,
aut], Yifang Hu [ctb], Peter Dunn [ctb], Belinda Phipson [ctb], Yunshun Chen
[ctb]","Depends":"R (>= 1.6.1)","Description":"A collection of algorithms and
functions to aid statistical modeling. Includes growth curve comparisons, limiting
dilution analysis (aka ELDA), mixed linear models, heteroscedastic regression,
inverse-Gaussian probability calculations, Gauss quadrature and a secure
convergence algorithm for nonlinear models. Includes advanced generalized linear
model functions that implement secure convergence, dispersion modeling and Tweedie
power-law families.","Imports":"stats, graphics","License":"GPL-2 | GPL-
3","NeedsCompilation":"yes","Package":"statmod","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"MASS, tweedie","Title":"Statistical
Modeling","Version":"1.4.24"},"statnet":{"Author":"Mark S. Handcock [aut],\nDavid
R. Hunter [aut],\nCarter T. Butts [aut],\nSteven M. Goodreau [aut],\nPavel N.
Krivitsky [aut],\nSkye Bender-deMoll [aut],\nMartina Morris [aut,
cre]","Depends":"R (>= 3.0), tergm (>= 3.4), ergm.count (>= 3.2), sna
(>=\n2.3.2)","Description":"An integrated set of tools for the representation,
visualization, analysis, and simulation of network data. For an introduction, type
help(package='statnet').","Imports":"statnet.common (>= 3.3), network (>= 1.13),
networkDynamic (>=\n0.9), ergm (>= 3.6)","License":"GPL-3 + file
LICENSE","NeedsCompilation":"no","Package":"statnet","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"networksis (>= 2.1.3), degreenet (>= 1.3),
relevent (>=\n1.0.4), ndtv (>= 0.9), EpiModel (>= 1.2.4), latentnet (>=\n2.7.1),
tsna (>= 0.2)","Title":"Software Tools for the Statistical Analysis of Network
Data","URL":"http:\/\/statnet.org","Version":"2016.4"},"statnet.common":
{"Author":"Pavel N. Krivitsky [aut, cre],\nSkye Bender-deMoll
[ctb]","Description":"Non-statistical utilities used by the software developed by
the Statnet Project. They may also be of use to
others.","Imports":"utils","License":"GPL-3 + file
LICENSE","NeedsCompilation":"no","Package":"statnet.common","Repository":"http:\/\/
cran.csiro.au\/src\/contrib","Title":"Common R Scripts and Utilities Used by the
Statnet
Project\nSoftware","URL":"http:\/\/www.statnet.org","Version":"3.3.0"},"statnetWeb"
:{"Author":"Emily
Beylerian [cre, aut],\nKirk Li [ctb],\nSamuel Jenness [ctb],\nMartina Morris
[ctb]","Depends":"R (>= 3.1.0), shiny (>= 0.12.1), ergm (>= 3.2.4),
network,\nlattice, latticeExtra","Description":"A graphical user interface for
network modeling with the 'statnet'\nsoftware.","Imports":"sna,
3","NeedsCompilation":"no","Package":"statnetWeb","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"A Graphical User Interface for Network Modeling with
'Statnet'","Version":"0.4.0"},"stdReg":{"Author":"Arvid
Sjolander","Description":"Contains functionality for regression standardization.
Two general classes of models are allowed; generalized linear models and Cox
proportional hazards models.","Imports":"graphics, stats, survival,
data.table","License":"LGPL (>=
3)","NeedsCompilation":"no","Package":"stdReg","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Regression Standardization","Version":"1.1"},"steadyICA":
{"Author":"Benjamin B. Risk and Nicholas A. James and David S.
Matteson","Depends":"Rcpp (>= 0.9.13), MASS, clue,
combinat","Description":"Functions related to multivariate measures of independence
and ICA:\n-estimate independent components by minimizing distance covariance;\n-
conduct a test of mutual independence based on distance covariance;\n-estimate
independent components via infomax (a popular method but generally performs poorer
than mdcovica, ProDenICA, and\/or fastICA, but is useful for comparisons);\n-order
indepedent components by skewness;\n-match independent components from multiple
estimates;\n-other functions useful in ICA.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"steadyICA","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"irlba, JADE, ProDenICA, fastICA,
energy","Title":"ICA and Tests of Independence via Multivariate
Distance\nCovariance","Version":"1.0"},"steepness":{"Author":"David Leiva
<dleivaur@ub.edu> & Han de Vries\n<J.deVries1@uu.nl>.","Depends":"R (>=
3.1.0)","Description":"steepness is a package that computes steepness as
a\nproperty of dominance hierarchies. Steepness is defined as the\nabsolute slope
of the straight line fitted to the normalized\nDavid's scores. The normalized
David's scores can be obtained\non the basis of dyadic dominance indices corrected
for chance\nor by means of proportions of wins. Given an observed\nsociomatrix, it
computes hierarchy's steepness and estimates\nstatistical significance by means of
a randomization test.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"steepness","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"Testing Steepness of Dominance
Hierarchies","Version":"0.2-2"},"stellaR":{"Author":"Matteo Dell'Omodarme [aut,
cre], Giada Valle [aut]","Description":"A package to manage and display stellar
tracks and\nisochrones from Pisa low-mass database. Includes tools for\nisochrones
construction and tracks interpolation.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"stellaR","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"lattice","Title":"stellar evolution tracks and
isochrones","URL":"The database is described
at:\nhttp:\/\/astro.df.unipi.it\/stellar-models\/","Version":"0.3-3"},"stepPlr":
{"Author":"Mee Young Park, Trevor Hastie","Depends":"R (>= 2.0)","Description":"L2
penalized logistic regression for both continuous and\ndiscrete predictors, with
forward stagewise\/forward stepwise\nvariable selection procedure.","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"stepPlr","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"L2 penalized logistic regression with a stepwise
variable\nselection","Version":"0.92"},"stepR":{"Author":"Timo Aspelmeier [cre,
aut],\nThomas Hotz [aut],\nHannes Sieling [aut],\nPein Florian [ctb]","Depends":"R
(>= 2.15.3), stats, graphics","Description":"Allows to fit step-functions to
univariate serial data where neither the number of jumps nor their positions is
known.","License":"GPL-
3","NeedsCompilation":"yes","Package":"stepR","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Fitting Step-Functions","Version":"1.0-4"},"stepp":
{"Author":"Wai-ki Yip, with contributions from\nAnn Lazar, David Zahrieh, Chip
Cole, Ann Lazar, Marco Bonetti,\nVictoria Wang, William Barcella and Richard
Gelber","Depends":"methods, car, survival, splines","Description":"A method to
explore the treatment-covariate interactions in survival or generalized\nlinear
model (GLM) for continuous, binomial and count data arising from two
treatment\narms of a clinical trial. A permutation distribution approach to
inference is implemented,\nbased on permuting the covariate values within each
treatment group.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"stepp","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Subpopulation Treatment Effect Pattern Plot
(STEPP)","URL":"http:\/\/www.r-project.org","Version":"3.0-11"},"stepwise":
{"Author":"Jinko Graham <jgraham@stat.sfu.ca>, Brad McNeney\n<mcneney@sfu.ca>,
Francoise Seillier-Moiseiwitsch\n<seillier@math.umbc.edu>, R interface by Sigal
Blay\n<sblay@sfu.ca>","Depends":"R (>= 2.5.0)","Description":"A stepwise approach
to identifying recombination\nbreakpoints in a sequence alignment.","License":"GPL
(>=
2)","NeedsCompilation":"yes","Package":"stepwise","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Stepwise detection of recombination
breakpoints","URL":"http:\/\/stat.sfu.ca\/statgen\/research\/stepwise.html","Versio
n":"0.3"},"stheoreme":{"Author":"Vitaly Efremov","Description":"Functions
implementing the procedure of entropy comparison between two data samples after the
renormalization of respective probability distributions with the algorithm designed
by Klimontovich (Zeitschrift fur Physik B Condensed Matter. 1987, Volume 66, Issue
1, pp 125-127) and extended by Anishchenko (Proc. SPIE 2098, Computer Simulation in
Nonlinear Optics. 1994, pp.130-136). The package also includes data preparation
tools which can also be used separately for various applications.","License":"GPL-
2","NeedsCompilation":"no","Package":"stheoreme","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Klimontovich's S-Theorem Algorithm Implementation and
Data\nPreparation Tools","Version":"1.2"},"stilt":{"Author":"Roman Olson, Won
Chang, Klaus Keller, and Murali Haran","Depends":"R (>= 2.15.1),
fields","Description":"Functions to build and use an interpolator (\"emulator\")
for time series or 1D regularly spaced data in multidimensional space. The standard
usage is for interpolating time-resolved computer model output between model
parameter settings. It can also be used for interpolating multivariate data (e.g.,
oceanographic time-series data, etc.) in space. There are functions to test the
emulator using cross-validation, and to produce contour plots over 2D slices in
model input parameter (or physical) space.","License":"GPL-
3","NeedsCompilation":"no","Package":"stilt","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Title":"Separable Gaussian Process Interpolation
(Emulation)","Version":"1.0.1"},"stima":{"Author":"Elise Dusseldorp [aut, cre,
cph],\nClaudio Conversano [aut, cph],\nCor Ninaber [ctb],\nKristof Meers
[ctb],\nPeter Neufeglise [trl]","Depends":"R (>= 3.0.2),rpart","Description":"This
package enables you to estimate a regression trunk model, which is an integration
of a regression tree and a multiple regression model.","License":"GPL-
2","NeedsCompilation":"yes","Package":"stima","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Simultaneous Threshold Interaction Modeling
Algorithm","Version":"1.1"},"stinepack":{"Author":"Tomas Johannesson & Halldor
Bjornsson, Icelandic Met. Office;\nGabor Grothendieck","Description":"A
consistently well behaved method of interpolation based\non piecewise rational
functions using Stineman's algorithm","License":"GPL-
2","NeedsCompilation":"no","Package":"stinepack","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Stineman, a consistently well behaved method of
interpolation","Version":"1.3"},"stlplus":{"Author":"Ryan Hafen [aut,
cre]","Description":"Decompose a time series into seasonal, trend, and
remainder\ncomponents using an implementation of Seasonal Decomposition of
Time\nSeries by Loess (STL) that provides several enhancements over the STL\nmethod
in the stats package. These enhancements include handling missing\nvalues,
providing higher order (quadratic) loess smoothing with automated\nparameter
choices, frequency component smoothing beyond the seasonal and\ntrend components,
and some basic plot methods for diagnostics.","Imports":"lattice, yaImpute, stats,
Rcpp","License":"BSD_3_clause + file
LICENSE","NeedsCompilation":"yes","Package":"stlplus","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat","Title":"Enhanced Seasonal
Decomposition of Time Series by
Loess","URL":"https:\/\/github.com\/hafen\/stlplus","Version":"0.5.1"},"stm":
{"Author":"Margaret E. Roberts, Brandon M. Stewart and Dustin Tingley","Depends":"R
(>= 2.10)","Description":"The Structural Topic Model (STM) allows researchers\nto
estimate topic models with document-level covariates.\nThe package also includes
tools for model selection, visualization,\nand estimation of topic-covariate
regressions.","Imports":"matrixStats, splines, slam, lda, stringr, Matrix, glmnet,
Rcpp\n(>= 0.11.3), grDevices, graphics, stats, utils","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"stm","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"igraph, SnowballC, tm (>= 0.6), huge, clue,
wordcloud,\nKernSmooth, NLP, LDAvis, geometry, Rtsne","Title":"Estimation of the
Structural Topic
Model","URL":"http:\/\/structuraltopicmodel.com","Version":"1.1.3"},"stmBrowser":
{"Author":"Michael K. Freeman, Jason Chuang, Margaret E. Roberts, Brandon M.
Stewart and Dustin Tingley","Description":"This
visualization allows users to interactively explore the relationships between
topics and the covariates estimated from the stm package in R.","Imports":"rjson,
stm, jsonlite, httr, utils","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"stmBrowser","Repository":"http:\/\/cran
.csiro.au\/src\/contrib","Title":"Structural Topic Model
Browser","URL":"http:\/\/structuraltopicmodel.com","Version":"1.0"},"stmCorrViz":
{"Author":"Antonio Coppola, Margaret Roberts, Brandon Stewart, Dustin
Tingley","Description":"Generates an interactive visualization of topic
correlations\/hierarchy in a Structural Topic Model (STM) of Roberts, Stewart, and
Tingley. The package performs a hierarchical clustering of topics which are then
exported to a JSON object and visualized using D3.","Imports":"jsonlite, stm,
stats, methods, utils","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"stmCorrViz","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"A Tool for Structural Topic Model
Visualizations","Version":"1.2"},"stocc":{"Author":"Devin S.
Johnson","Description":"Fit a spatial-temporal occupancy models using\na probit
formulation instead of a traditional logit\nmodel.","Imports":"truncnorm, coda,
Matrix, fields,
rARPACK","License":"CC0","NeedsCompilation":"no","Package":"stocc","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Title":"Fit a Spatial Occupancy Model via
Gibbs Sampling","Version":"1.30"},"stochprofML":{"Author":"Christiane
Fuchs","Depends":"R (>= 2.0)","Description":"This is an R package accompanying the
paper \"Parameterizing cell-to-cell regulatory heterogeneities via stochastic
transcriptional profiles\" by Sameer S Bajikar, Christiane Fuchs, Andreas Roller,
Fabian J Theis and Kevin A Janes (PNAS 2014, 111(5), E626-635). In this paper, we
measure expression profiles from small heterogeneous populations of cells, where
each cell is assumed to be from a mixture of lognormal distributions. We perform
maximum likelihood estimation in order to infer the mixture ratio and the
parameters of these lognormal distributions from the cumulated expression
measurements.","Imports":"MASS, numDeriv","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"stochprofML","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Stochastic Profiling using Maximum Likelihood
Estimation","Version":"1.2"},"stochvol":{"Author":"Gregor Kastner [aut,
cre]","Depends":"R (>= 3.0.2), coda","Description":"Efficient algorithms for fully
Bayesian estimation of stochastic volatility (SV) models via Markov chain Monte
Carlo (MCMC) methods.","Imports":"Rcpp (>= 0.11), methods, stats, graphics,
2)","NeedsCompilation":"yes","Package":"stochvol","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"mvtnorm","Title":"Efficient Bayesian Inference for
Stochastic Volatility (SV)\nModels","Version":"1.2.3"},"stockPortfolio":
{"Author":"David Diez and Nicolas Christou","Depends":"stats, graphics, grDevices,
utils","Description":"Download stock data, build single index,
constant\ncorrelation, and multigroup models, and estimate optimal
stock\nportfolios. Plotting functions for the portfolio possibilities\ncurve and
portfolio cloud are included. A function to test a\nportfolio on a data set is also
2)","NeedsCompilation":"no","Package":"stockPortfolio","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Build stock models and analyze stock
portfolios","Version":"1.2"},"stocks":{"Author":"Dane R. Van Domelen","Depends":"R
(>= 3.0.0), rbenchmark","Description":"Provides functions for analyzing historical
performance of stocks or other investments. Functions are written in C++ to quickly
calculate maximum draw-down, Sharpe ratio, Sterling ratio, and other commonly used
metrics of stock performance.","Imports":"Rcpp (>= 0.11.0)","License":"GPL-
2","NeedsCompilation":"yes","Package":"stocks","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Fast Functions for Stock Market
Analysis","Version":"1.1.1"},"stoichcalc":{"Author":"Peter
Reichert","Description":"Given a list of substance compositions, a list
of\nsubstances involved in a process, and a list of constraints in\naddition to
mass conservation of elementary constituents, the\npackage contains functions to
build the substance composition\nmatrix, to analyze the uniqueness of process
stoichiometry, and\nto calculate stoichiometric coefficients if
process\nstoichiometry is unique. (See Reichert, P. and Schuwirth, N.,\nA generic
framework for deriving process stoichiometry in\nenviromental models, Environmental
Modelling and Software 25,\n1241-1251, 2010 for more details.)","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"stoichcalc","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"R Functions for Solving Stoichiometric
Equations","Version":"1.1-3"},"storr":{"Author":"Rich FitzJohn","Depends":"R (>=
3.1.0)","Description":"Creates and manages simple key-value stores. These can\nuse
a variety of approaches for storing the data. This package\nimplements the base
methods and support for file system and\nin-memory stores. A vignette shows how
additional drivers can be\ncreated, and stubs exist for supporting 'Redis'
databases.","Imports":"R6 (>= 2.1.0), digest","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"storr","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"DBI, RSQLite, knitr, microbenchmark,
testthat","Title":"Simple Key Value Stores","Version":"1.0.0"},"stosim":
{"Author":"Jacob T. Ormerod","Depends":"tcltk2","Description":"A toolkit for
Reliability Availability and Maintainability (RAM) modeling of industrial process
systems.","Imports":"Rcpp (>= 0.11.1)","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"stosim","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Stochastic Simulator for Reliability Modeling of
Repairable\nSystems","Version":"0.0.12"},"stplanr":{"Author":"Robin Lovelace [aut,
cre],\nRichard Ellison [aut],\nBarry Rowlingson [aut] (Author of overline),\nNick
Bearman [aut] (Co-author of gclip)","Depends":"sp, R (>=
3.0)","Description":"Functionality and data access tools for transport
planning,\nincluding origin-destination analysis, route allocation and modelling
travel\npatterns.","Imports":"jsonlite, maptools, raster, rgdal, rgeos, dplyr,
magrittr,\nRgoogleMaps, openxlsx, leaflet, methods, httr, R.utils,\nstringi,
stringr, readr, lubridate, RCurl, geosphere, Rcpp (>=\n0.12.1),
igraph","License":"MIT + file
LICENSE","NeedsCompilation":"yes","Package":"stplanr","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat, knitr, tmap,
rmarkdown","Title":"Sustainable Transport
Planning","URL":"https:\/\/github.com\/ropensci\/stplanr","Version":"0.1.1"},"stpm"
:{"Author":"I. Y. Zhbannikov, I. V. Akushevich, K. G. Arbeev, A. I.
Yashin.","Depends":"mice,sas7bdat,stats,nloptr,survival,tools","Description":"Utili
ties to estimate parameters of stochastic process and modeling survival
trajectories\nand time-to-event outcomes observed from longitudinal
studies.\nMiscellaneous function for data preparation is also provided.\nFor more
information, see: \"Stochastic model for analysis of longitudinal data on
aging\nand mortality\" by Yashin A. et al, 2007, Mathematical Biosciences, 208(2),
538-551\n<DOI:10.1016\/j.mbs.2006.11.006>.","Imports":"Rcpp (>=
0.11.1)","License":"GPL","NeedsCompilation":"yes","Package":"stpm","Repository":"ht
tp:\/\/cran.csiro.au\/src\/contrib","Suggests":"knitr (>=
1.11)","Title":"Stochastic Model for Analysis of Longitudinal
Data","Version":"1.1.2"},"stpp":{"Author":"Edith Gabriel, Peter J Diggle, stan
function by Barry Rowlingson","Depends":"R (>= 2.10), splancs, KernSmooth,
spatstat","Description":"A package for analysing, simulating and displaying space-
time point patterns","License":"GPL-
3","NeedsCompilation":"yes","Package":"stpp","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"rpanel, rgl","Title":"Space-Time Point Pattern
simulation, visualisation and analysis","Version":"1.0-5"},"stppResid":
{"Author":"Robert Clements","Depends":"deldir, splancs,
cubature","Description":"Implement transformation-based and pixel-based
residual\nanalysis of spatial-temporal point process models.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"stppResid","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Perform residual analysis on space-time point process
models","Version":"1.1"},"strap":{"Author":"Mark A. Bell <mark.bell521@gmail.com>
Graeme T. Lloyd
<graemetlloyd@gmail.com>.","Depends":"ape,geoscale","Description":"Functions for
the stratigraphic analysis of phylogenetic trees.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"strap","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"Stratigraphic Tree Analysis for
Palaeontology","Version":"1.4"},"strataG":{"Author":"Eric Archer [aut, cre],\nPaula
Adams [aut],\nBrita Schneiders [aut]","Depends":"R (>= 3.2.0), apex,
adegenet","Description":"A toolkit for analyzing stratified population genetic
data.","Imports":"ape, copula, ggplot2, graphics, Hmisc, methods,
pegas,\nRColorBrewer, Rcpp, reshape2, stats, swfscMisc, utils","License":"GNU
General Public
License","NeedsCompilation":"yes","Package":"strataG","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"knitr","Title":"Summaries and Population
Structure Analyses of Genetic Data","Version":"1.0.3"},"stratification":
{"Author":"Sophie Baillargeon and Louis-Paul Rivest","Description":"Univariate
stratification of survey populations with a generalization of the\nLavallee-
Hidiroglou method of stratum construction. The generalized method takes into
account\na discrepancy between the stratification variable and the survey variable.
The determination\nof the optimal boundaries also incorporate, if desired, an
anticipated non-response,
a take-all\nstratum for large units, a take-none stratum for small units, and a
certainty stratum to ensure\nthat some specific units are in the sample. The well
known cumulative root frequency rule of\nDalenius and Hodges and the geometric rule
of Gunning and Horgan are also implemented.","License":"GPL-
2","NeedsCompilation":"yes","Package":"stratification","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Univariate Stratification of Survey
Populations","Version":"2.2-5"},"stratigraph":{"Author":"Walton A.
Green","Depends":"R (>= 2.13.1), grid","Description":"A collection of tools for
plotting and analyzing paleontological and geological data distributed through
through time in stratigraphic cores or sections. Includes some miscellaneous
functions for handling other kinds of palaeontological and paleoecological
3)","NeedsCompilation":"no","Package":"stratigraph","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Toolkit for the plotting and analysis of
stratigraphic and\npalaeontological data","Version":"0.66"},"straweib":
{"Author":"Xiangdong Gu and Raji Balasubramanian","Description":"The main function
is icweib, which fits a stratified Weibull proportional hazards model for left
censored, right censored, interval censored, and non-censored survival data. We
parameterize the Weibull regression model so that it allows a stratum-specific
baseline hazard function, but where the effects of other covariates are assumed to
be constant across strata.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"straweib","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Stratified Weibull Regression
Model","Version":"1.0"},"stream":{"Author":"Michael Hahsler [aut, cre,
cph],\nMatthew Bolanos [aut, cph],\nJohn Forrest [aut, cph]","Depends":"R (>=
2.13.0), methods, proxy (>= 0.4-7)","Description":"A framework for data stream
modeling and associated data mining tasks such as clustering and classification.
The development of this package was supported in part by NSF IIS-0948893 and NIH
R21HG005912.","Imports":"animation, clue, cluster, clusterGeneration, dbscan
(>=\n0.9-2), fpc, graphics, grDevices, MASS, mlbench, Rcpp (>=\n0.11.4), stats,
3","NeedsCompilation":"yes","Package":"stream","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"DBI, rJava, RSQLite, testthat","Title":"Infrastructure
for Data Stream
Mining","URL":"http:\/\/lyle.smu.edu\/IDA\/TRACDS\/","Version":"1.2-
2"},"streamMOA":{"Author":"Michael Hahsler [aut, cre, cph],\nMatthew Bolanos [aut,
cph],\nJohn Forrest [aut, cph]","Depends":"stream (>= 1.1-2), rJava (>= 0.6-
3)","Description":"Interface for data stream clustering algorithms implemented in
the MOA (Massive Online Analysis) framework.","Imports":"graphics, stats,
3","NeedsCompilation":"no","Package":"streamMOA","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Interface for MOA Stream Clustering
Algorithms","Version":"1.1-2"},"streamR":{"Author":"Pablo Barbera
<pablo.barbera@nyu.edu>","Depends":"R (>= 2.12.0), RCurl,
rjson","Description":"This package provides a series of functions that allow R
users\nto access Twitter's filter, sample, and user streams, and to\nparse the
output into data frames.","License":"GPL-
2","NeedsCompilation":"no","Package":"streamR","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"ROAuth (>= 0.9.0)","Title":"Access to Twitter Streaming
API via R","Version":"0.2.1"},"stremo":{"Author":"Gustavo Carvalho, Marco Batalha,
and Owen Petchey.","Depends":"lavaan (>= 0.4-9), numDeriv,
MASS","Description":"Functions to assist the process of learning
structural\nequation
modeling","License":"GPL","NeedsCompilation":"no","Package":"stremo","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Title":"Functions to help the process of
learning structural equation\nmodelling","Version":"0.2"},"stressr":{"Author":"Matt
Barry <mrb@softisms.com>","Description":"Forms queries to submit to the Cleveland
Federal Reserve Bank web\nsite's financial stress index data site. Provides query
functions for both\nthe composite stress index and the components data. By default
the download\nincludes daily time series data starting September 25, 1991. The
functions\nreturn a class of either type easing or cfsi which contain a list of
items\nrelated to the query and its graphical presentation. The list includes
the\ntime series data as an xts object. The package provides four lattice
time\nseries plots to render the time series data in a manner similar to
the\nbank's own presentation.","Imports":"xts, XML, lattice,
latticeExtra","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"stressr","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Suggests":"testthat","Title":"Fetch and plot financial
stress index and component
data","URL":"https:\/\/github.com\/mrbcuda\/stressr","Version":"1.0.0"},"stringdist
":{"Author":"Mark van der Loo [aut, cre],\nJan van der Laan [ctb],\nR Core Team
[ctb],\nNick Logan [ctb]","Depends":"R (>= 2.15.3)","Description":"Implements an
approximate string matching version of R's native\n'match' function. Can calculate
various string distances based on edits\n(damerau-levenshtein, hamming,
levenshtein, optimal sting alignment), qgrams (q-\ngram, cosine, jaccard distance)
or heuristic metrics (jaro, jaro-winkler). An\nimplementation of soundex is
provided as well. Distances can be computed between\ncharacter vectors while taking
proper care of encoding or between integer\nvectors representing generic
sequences.","Imports":"parallel","License":"GPL-
3","NeedsCompilation":"yes","Package":"stringdist","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"testthat","Title":"Approximate String Matching and
String Distance
Functions","URL":"https:\/\/github.com\/markvanderloo\/stringdist","Version":"0.9.4
.1"},"stringgaussnet":{"Author":"Emmanuel Chaplais, Henri-Jean
Garchon","Description":"A toolbox for a construction of protein-protein interaction
networks through the 'STRING' application programming interface, and an inference
of Gaussian networks through 'SIMoNe' and 'WGCNA' approach, from DE genes analysis
results and expression data. Additional functions are provided to import
automatically networks into an active 'Cytoscape'
session.","Imports":"\nAnnotationDbi,GO.db,VennDiagram,simone,biomaRt,limma,pspearm
an,igraph,httr,RJSONIO,RCurl,org.Hs.eg.db,graphics,grDevices,stats,utils","License"
:"GPL-
3","NeedsCompilation":"no","Package":"stringgaussnet","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"knitr","Title":"PPI and Gaussian Network
Construction from Transcriptomic\nAnalysis Results Integrating a Multilevel
Factor","Version":"1.1"},"stringi":{"Author":"Marek Gagolewski and Bartek Tartanus
(stringi source code);\nIBM and other contributors (ICU4C 55.1 source
code);\nUnicode, Inc. (Unicode Character Database)","Depends":"R (>=
2.13.1)","Description":"Allows for fast, correct, consistent, portable,\nas well as
convenient character string\/text processing in every locale\nand any native
encoding. Owing to the use of the ICU library,\nthe package provides R users with
platform-independent functions\nknown to Java, Perl, Python, PHP, and Ruby
programmers. Among available\nfeatures there are: pattern searching (e.g., with ICU
Java-like regular\nexpressions or the Unicode Collation Algorithm), random string
generation,\ncase mapping, string transliteration, concatenation,\nUnicode
normalization, date-time formatting and parsing, etc.","Imports":"tools, utils,
stats","License":"file
LICENSE","NeedsCompilation":"yes","Package":"stringi","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Character String Processing
Facilities","URL":"http:\/\/stringi.rexamine.com\/ http:\/\/site.icu-
project.org\/\nhttp:\/\/www.unicode.org\/","Version":"1.0-1"},"stringr":
{"Author":"Hadley Wickham [aut, cre, cph],\nRStudio [cph]","Depends":"R (>=
2.14)","Description":"A consistent, simple and easy to use set of wrappers around
the\nfantastic 'stringi' package. All function and argument names (and
positions)\nare consistent, all functions deal with \"NA\"'s and zero length
vectors\nin the same way, and the output from one function is easy to feed
into\nthe input of another.","Imports":"stringi (>= 0.4.1),
2","NeedsCompilation":"no","Package":"stringr","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Suggests":"testthat, knitr","Title":"Simple, Consistent Wrappers
for Common String Operations","Version":"1.0.0"},"stripless":{"Author":"Bert Gunter
[aut, cre]","Depends":"R (>= 3.2.0), utils,lattice","Description":"For making
Trellis-type conditioning plots without strip labels.\nThis is useful for
displaying the structure of results from factorial designs\nand other studies when
many conditioning variables would clutter the display\nwith layers of redundant
strip labels. Settings of the variables are encoded by\nlayout and spacing in the
trellis array and decoded by a separate legend. The\nfunctionality is implemented
by a single S3 generic strucplot() function that\nis a wrapper for the Lattice
package's xyplot() function. This allows access to\nall Lattice graphics
capabilities in the usual way.","Imports":"stats,graphics,grid","License":"GPL-2 |
GPL-
3","NeedsCompilation":"no","Package":"stripless","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"datasets,grDevices","Title":"Structured Trellis
Displays Without Strips for Lattice Graphics","Version":"1.0-1"},"strptimer":
{"Author":"Brandon Taylor [aut, cre]","Depends":"R (>= 3.2.2)","Description":"Makes
time formatting easy with an accessible interface.","Imports":"dplyr (>= 0.4.3),
lazyeval (>= 0.1.10), magrittr (>= 1.5),\nstringi (>= 0.5-5), tidyr (>=
LICENSE","NeedsCompilation":"no","Package":"strptimer","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Suggests":"knitr,
rmarkdown","Title":"An Easy Interface to Time
Formatting","Version":"0.1.0"},"strucchange":{"Author":"Achim Zeileis [aut,
cre],\nFriedrich Leisch [aut],\nKurt Hornik [aut],\nChristian Kleiber [aut],\nBruce
Hansen [ctb],\nEdgar C. Merkle [ctb]","Depends":"R (>= 2.10.0), zoo,
sandwich","Description":"Testing, monitoring and dating structural changes in
(linear)\nregression models. strucchange features tests\/methods from\nthe
generalized fluctuation test framework as well as from\nthe F test (Chow test)
framework. This includes methods to\nfit, plot and test fluctuation processes
(e.g., CUSUM, MOSUM,\nrecursive\/moving estimates) and F statistics,
respectively.\nIt is possible to monitor incoming data online using\nfluctuation
processes.\nFinally, the breakpoints in regression models with structural\nchanges
can be estimated together with confidence intervals.\nEmphasis is always given to
methods for visualizing the data.","Imports":"graphics, stats","License":"GPL-2 |
GPL-
3","NeedsCompilation":"no","Package":"strucchange","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"stats4, car, dynlm, e1071, foreach, lmtest,
mvtnorm, tseries","Title":"Testing, Monitoring, and Dating Structural
Changes","Version":"1.5-1"},"structSSI":{"Author":"Kris
Sankaran","Depends":"methods","Description":"Performs multiple testing corrections
that take specific structure of hypotheses into account.","Imports":"multtest,
igraph, rjson, ggplot2, reshape2","License":"GPL-
2","NeedsCompilation":"no","Package":"structSSI","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Suggests":"ape, phyloseq","Title":"Multiple Testing for
Hypotheses with Hierarchical or Group\nStructure","Version":"1.1.1"},"strum":
{"Author":"Nathan Morris [aut, cre],\nYeunjoo Song [aut],\nStephen Cahn
[ctb]","Depends":"R (>= 3.0.0), methods, pedigree, Rgraphviz(>=
2.6.0)","Description":"Implements a broad class of latent variable and structural
equation models for general pedigree data.","Imports":"Matrix, MASS, Rcpp,
graph","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"strum","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"STRUctural Modeling of Latent Variables for General
Pedigree","Version":"0.6.2"},"strvalidator":{"Author":"Oskar Hansson","Depends":"R
(>= 3.1.3)","Description":"An open source platform for validation and process
control.\nTools to analyse data from internal validation of forensic short
tandem\nrepeat (STR) kits are provided. The tools are developed to provide\nthe
necessary data to conform with guidelines for internal validation\nissued by the
European Network of Forensic Science Institutes (ENFSI)\nDNA Working Group, and the
Scientific Working Group on DNA Analysis Methods\n(SWGDAM). A front-end graphical
user interface is provided.\nMore information about each function can be found in
the\nrespective help documentation.","Imports":"ggplot2 (>= 2.0.0), gWidgets,
gridExtra, grid, gtable, plyr,\nscales, gWidgetsRGtk2, RGtk2, data.table,
grDevices, graphics,\nstats, utils","License":"GPL-
2","NeedsCompilation":"no","Package":"strvalidator","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"ResourceSelection, testthat","Title":"Process
Control and Internal Validation of Forensic STR
Kits","URL":"https:\/\/sites.google.com\/site\/forensicapps\/strvalidator","Version
":"1.6.0"},"stsm":{"Author":"Javier LÃ³pez-de-Lacalle
<javlacalle@yahoo.es>","Depends":"R (>= 3.0.0), methods","Description":"Fit the
basic structural time series model by maximum likelihood.","Imports":"KFKSDS,
parallel, stats","License":"GPL-
2","NeedsCompilation":"yes","Package":"stsm","Repository":"http:\/\/cran.csiro.au\/
src\/contrib","Suggests":"mvtnorm, numDeriv","Title":"Structural Time Series
Models","URL":"http:\/\/jalobe.com","Version":"1.7"},"stsm.class":{"Author":"Javier
LÃ³pez-de-Lacalle <javlacalle@yahoo.es>","Depends":"R (>= 3.0.0),
methods","Description":"This package defines an S4 class for structural time series
models\nand provides some basic methods to work with it.","License":"GPL-
2","NeedsCompilation":"no","Package":"stsm.class","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"numDeriv","Title":"Class and Methods for Structural
Time Series Models","Version":"1.3"},"stubthat":{"Author":"Sainath Adapa [aut,
cre],\nNitin Madasu [aut]","Depends":"R (>= 3.1.2)","Description":"Create stubs of
functions for use while testing.","License":"MIT + file
LICENSE","NeedsCompilation":"no","Package":"stubthat","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Suggests":"testthat, knitr, httr","Title":"Stubbing
Framework for
R","URL":"https:\/\/github.com\/sainathadapa\/stubthat","Version":"1.0.0"},"stylo":
{"Author":"Maciej Eder, Jan Rybicki, Mike Kestemont","Depends":"R (>=
2.14)","Description":"A number of functions, supplemented by GUI, to perform
various analyses in the field of computational stylistics, authorship attribution,
etc.","Imports":"tcltk, tcltk2, ape, pamr, e1071, class, lattice,
tsne","License":"GPL (>=
3)","NeedsCompilation":"no","Package":"stylo","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Suggests":"stringi","Title":"Functions for a Variety of Stylometric
Analyses","URL":"https:\/\/sites.google.com\/site\/computationalstylistics\/","Vers
ion":"0.6.3"},"suRtex":{"Author":"Dustin Landers","Description":"suRtex was
designed for easy descriptive statistic reporting of categorical survey data (e.g.,
Likert scales) in LaTeX. suRtex takes a matrix or data frame and produces the LaTeX
code necessary for a sideways table creation. Mean, median, standard deviation, and
sample size are optional.","License":"GPL-
3","NeedsCompilation":"no","Package":"suRtex","Repository":"http:\/\/cran.csiro.au\
/src\/contrib","Title":"LaTeX descriptive statistic reporting for survey
data","Version":"0.9"},"subgroup":{"Author":"I. Manjula Schou","Depends":"graphics,
grDevices, utils, stats, R (>= 3.1)","Description":"Produces various measures of
expected treatment effect heterogeneity under an assumption of homogeneity across
subgroups. Graphical presentations are created to compare these expected
differences with the observed differences.","License":"GPL-2 | GPL-
3","NeedsCompilation":"no","Package":"subgroup","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Methods for exploring treatment effect heterogeneity in
subgroup\nanalysis of clinical trials","Version":"1.1"},"subplex":{"Author":"Aaron
A. King","Depends":"R(>= 2.5.1)","Description":"The subplex algorithm for
unconstrained optimization, developed by Tom Rowan.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"subplex","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Unconstrained Optimization using the Subplex
Algorithm","Version":"1.1-6"},"subrank":{"Author":"Jerome
Collet","Description":"Estimation of copula using ranks and subsampling. The main
feature of this method is that simulation studies show a low sensitivity to
dimension, on realistic cases. Vignette provides some theoretical
documentation.","License":"GPL (>=
3)","NeedsCompilation":"yes","Package":"subrank","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Computes Copula using Ranks and
Subsampling","Version":"0.9.7"},"subscore":{"Author":"Shenghai Dai [aut,
cre],\nXiaolin Wang [aut],\nDubravka Svetina [aut]","Depends":"R (>= 3.1.0), CTT,
stats","Description":"Functions that compute sub-scores for a test using different
methods in classical test theory (CTT).","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"subscore","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"SubScore Computing Functions in Classical Test
Theory","Version":"1.2"},"subselect":{"Author":"Jorge Orestes Cerdeira [aut], Pedro
Duarte Silva [aut], Jorge Cadima [aut, cre], Manuel Minhoto [aut]","Description":"A
collection of functions which (i) assess the quality of variable subsets as
surrogates for a full data set, in either an exploratory data analysis or in the
context of a multivariate linear model, and (ii) search for subsets which are
optimal under various criteria.","License":"GPL (>=
2)","NeedsCompilation":"yes","Package":"subselect","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Suggests":"MASS, ISwR, corpcor","Title":"Selecting Variable
Subsets","Version":"0.12-5"},"subsemble":{"Author":"Erin LeDell, Stephanie Sapp,
Mark van der Laan","Depends":"R (>= 2.14.0), SuperLearner","Description":"Subsemble
is a general subset ensemble prediction method, which can be used for small,
moderate, or large datasets. Subsemble partitions the full dataset into subsets of
observations, fits a specified underlying algorithm on each subset, and uses a
unique form of V-fold cross-validation to output a prediction function that
combines the subset-specific fits. An oracle result provides a theoretical
performance guarantee for Subsemble.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"subsemble","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"arm, caret, class, e1071, earth, gam, gbm, glmnet,
Hmisc,\nipred, lattice, LogicReg, MASS, mda, mlbench, nnet, parallel,\nparty,
polspline, quadprog, randomForest, rpart, SIS, spls,\nstepPlr","Title":"An Ensemble
Method for Combining Subset-Specific Algorithm Fits","Version":"0.0.9"},"subspace":
{"Author":"Marwan Hassani [aut, cre],\nMatthias Hansen [aut],\nEmmanuel MÃ¼ller
[ctb],\nIra Assent [ctb],\nStephan GÃ¼nnemann [ctb],\nTimm Jansen [ctb],\nThomas
Seidl [ctb],\nUniversity of Waikato [ctb, cph]","Depends":"R(>=
3.1.0)","Description":"An interface to 'OpenSubspace', an open source framework
for\nevaluation and exploration of subspace clustering algorithms in WEKA\n(see
<http:\/\/dme.rwth-aachen.de\/de\/opensubspace> for more\ninformation). Also
performs visualization.","Imports":"ggvis (>= 0.4.2), colorspace (>= 1.0), stringr
(>= 1.0.0),\nrJava(>= 0.9)","License":"GPL-
2","NeedsCompilation":"no","Package":"subspace","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Interface
to OpenSubspace","Version":"1.0.4"},"subtype":{"Author":"Andrey Alexeyenko, Woojoo
Lee and Yudi Pawitan","Depends":"penalized,ROCR","Description":"subtype performs a
biclustering procedure on a input\ndataset and assess whether resulting clusters
are promising\nsubtypes. Note that the R-package rsmooth should be
installed\nbefore implementing subtype. rsmooth can be downloaded
from\nhttp:\/\/www.meb.ki.se\/~yudpaw.","License":"GPL-
2","NeedsCompilation":"no","Package":"subtype","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Cluster analysis to find molecular subtypes and their
assessment","Version":"1.0"},"sudoku":{"Author":"David Brahm <brahm@alum.mit.edu>
and Greg Snow\n<Greg.Snow@intermountainmail.org>, with contributions from
Curt\nSeeliger <Seeliger.Curt@epamail.epa.gov> and Henrik
Bengtsson\n<hb@maths.lth.se>.","Description":"Generates, plays, and solves Sudoku
puzzles. The GUI\nplaySudoku() needs package \"tkrplot\" if you are not on
Windows.","License":"GPL","NeedsCompilation":"no","Package":"sudoku","Repository":"
http:\/\/cran.csiro.au\/src\/contrib","Suggests":"tkrplot","Title":"Sudoku Puzzle
Generator and Solver","Version":"2.6"},"sudokuAlt":{"Author":"Bill Venables
<Bill.Venables@gmail.com>","Depends":"R (>= 3.1.0), stats","Description":"Tools for
making, retrieving, displaying and solving sudoku games.\nThis package is an
alternative to the earlier sudoku-solver package,\n'sudoku'. The present package
uses a slightly different algorithm, has a\nsimpler coding and presents a few more
sugar tools, such as plot and print\nmethods. Solved sudoku games are of some
interest in Experimental Design\nas examples of Latin Square designs with
additional balance constraints.","Imports":"graphics","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"sudokuAlt","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Suggests":"sudoku","Title":"Tools for Making and Spoiling
Sudoku Games","Version":"0.1-6"},"summarytools":{"Author":"Dominic
Comtois","Depends":"htmltools","Description":"Generates formatted summary tables
for vectors and dataframes.\nThree summarizing functions: 1) 'freq' generates
frequency tables\nreporting counts and proportions (including cumulative); 2)
'descr'\ngives common central tendency statistics and measures of dispersion\nfor
numerical data; 3) 'dfSummary' gives as much information\nas possible about a
dataframe and its components in a clear,\nlegible table. All three functions can
either display plain text tables\nin the console or write markdown, text or html
files to disk. An\nadditional misc function, 'what.is', extends base 'is'
function,\nchecking the object against all 'is' functions and gives a variety\nof
other information about the object.","Imports":"methods, pryr, pander, xtable,
rapportools, rstudioapi, utils","License":"GPL-
2","NeedsCompilation":"no","Package":"summarytools","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Title":"Dataframe Summaries, Frequency Tables and Numerical
Summaries\nwith Customizable
Output","URL":"https:\/\/github.com\/dcomtois\/summarytools","Version":"0.4"},"supc
lust":{"Author":"Marcel Dettling <marcel.dettling@zhaw.ch> and Martin
Maechler","Depends":"R (>= 2.5.0)","Description":"Methodology for supervised
grouping aka \"clustering\" of\npotentially many predictor variables, such as genes
etc.","Imports":"rpart, class","License":"GPL-
2","NeedsCompilation":"yes","Package":"supclust","Repository":"http:\/\/cran.csiro.
au\/src\/contrib","Title":"Supervised Clustering of Predictor Variables such as
Genes","URL":"http:\/\/www.stat.math.ethz.ch\/~dettling\/","Version":"1.0-
7"},"supcluster":{"Author":"David A. Schoenfeld,\nJesse
Hsu","Description":"Clusters features under the assumption that each cluster has
a\nrandom effect and there is an outcome variable that is related to the
random\neffects by a linear regression. In this way the cluster analysis
is\n``supervised'' by the outcome variable. An alternate specification is
that\nfeatures in each cluster have the same compound symmetric normal
distribution,\nand the conditional distribution of the outcome given the
features\nhas the same coefficient for each feature in a
cluster.","Imports":"mvtnorm, gtools","License":"GPL-
2","NeedsCompilation":"no","Package":"supcluster","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Supervised Cluster
Analysis","Version":"1.0"},"superMDS":{"Author":"Daniela M.
Witten","Description":"Witten and Tibshirani (2011) Supervised multidimensional
scaling for visualization, classification, and bipartite ranking. Computational
Statistics and Data Analysis 55(1): 789-801.","License":"GPL-
2","NeedsCompilation":"no","Package":"superMDS","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Implements the supervised multidimensional scaling
(superMDS)\nproposal of Witten and Tibshirani
(2011)","Version":"1.0.2"},"superbiclust":{"Author":"Tatsiana
Khamiakova","Depends":"biclust, fabia","Description":"Biclusters are submatrices in
the data matrix which\nsatisfy certain conditions of homogeneity. Package
contains\nfunctions for generating robust biclusters with respect to
the\ninitialization parameters for a given bicluster solution\ncontained in a
bicluster set in data, the procedure is also\nknown as ensemble biclustering. The
set of biclusters is\nevaluated based on the similarity of its elements
(the\noverlap), and afterwards the hierarchical tree is constructed\nto obtain cut-
off points for the classes of robust biclusters.\nThe result is a number of robust
(or super) biclusters with\nnone or low overlap.","Imports":"methods,
2)","NeedsCompilation":"no","Package":"superbiclust","Repository":"http:\/\/cran.cs
iro.au\/src\/contrib","Title":"Generating Robust Biclusters from a Bicluster Set
(Ensemble\nBiclustering)","Version":"1.1"},"superdiag":{"Author":"Tsung-han Tsai
<t.tsai@wustl.edu>, Jeff Gill <jgill@wustl.edu>\nand Jonathan Rapkin
<rapkin@wustl.edu>","Depends":"R (>= 2.10), coda, boa","Description":"A
Comprehensive Test Suite for Markov
Chain\nNonconvergence.","License":"GPL","NeedsCompilation":"no","Package":"superdia
g","Repository":"http:\/\/cran.csiro.au\/src\/contrib","Title":"R Code for Testing
Markov Chain Nonconvergence","Version":"1.1"},"superpc":{"Author":"Eric Bair, R.
Tibshirani","Depends":"survival","Description":"Supervised principal components for
regression and\nsurvival analsysis. Especially useful for high-dimnesional\ndata,
including microarray data.","License":"GPL-
2","NeedsCompilation":"no","Package":"superpc","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"Supervised principal components","URL":"http:\/\/www-
stat.stanford.edu\/~tibs\/superpc","Version":"1.09"},"support.BWS":{"Author":"Hideo
Aizaki","Description":"Provides three basic functions that support an
implementation of object case (Case 1) best-worst scaling: one for converting a
two-level orthogonal main-effect design\/balanced incomplete block design into
questions; one for creating a data set suitable for analysis; and one for
calculating count-based scores.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"support.BWS","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"DoE.base, crossdes, survival","Title":"Basic
Functions for Supporting an Implementation of Best-Worst\nScaling","Version":"0.1-
3"},"support.CEs":{"Author":"Hideo Aizaki","Depends":"DoE.base, MASS, simex, stats,
RCurl, XML","Description":"Provides seven basic functions that support an
implementation of choice experiments.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"support.CEs","Repository":"http:\/\/cran.csi
ro.au\/src\/contrib","Suggests":"survival","Title":"Basic Functions for Supporting
an Implementation of Choice\nExperiments","Version":"0.4-1"},"surface":
{"Author":"Travis Ingram","Depends":"R (>= 2.6), ape, ouch, MASS,
geiger","Description":"SURFACE is a data-driven phylogenetic comparative method for
fitting stabilizing selection models to continuous trait data, building on the ouch
package. The main functions fit a series of Hansen models using stepwise AIC, then
identify cases of convergent evolution where multiple lineages have shifted to the
same adaptive peak.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"surface","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"igraph","Title":"Fitting Hansen Models to Investigate
Convergent
Evolution","URL":"http:\/\/www.people.fas.harvard.edu\/~ingram\/web\/surface.html",
"Version":"0.4-1"},"surv2sampleComp":{"Author":"Lu Tian, Hajime
Uno","Depends":"survival, plotrix, flexsurv, survC1","Description":"Performs
inference of several model-free group contrast measures, which include
difference\/ratio of cumulative incidence rates at given time points, quantiles,
and restricted mean survival times (RMST). Two kinds of covariate adjustment
procedures (i.e., regression and augmentation) for inference of the metrics based
on RMST are also included.","License":"GPL-
2","NeedsCompilation":"no","Package":"surv2sampleComp","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Inference for model-free between-group parameters
for censored\nsurvival data","Version":"1.0-4"},"survAUC":{"Author":"Sergej
Potapov, Werner Adler and Matthias Schmid.","Depends":"R (>= 2.6.0),
survival","Description":"The package provides a variety of functions to
estimate\ntime-dependent true\/false positive rates and AUC curves from a\nset of
censored survival data.","License":"GPL-
2","NeedsCompilation":"yes","Package":"survAUC","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Suggests":"rms","Title":"Estimators of prediction accuracy for
time-to-event data","Version":"1.0-5"},"survAccuracyMeasures":{"Author":"Yingye
Zheng, Tianxi Cai, and Marshall Brown","Depends":"survival,
splines","Description":"This package provides a function to estimate the AUC,
TPR(c),\nFPR(c),
PPV(c), and NPV(c) for for a specific timepoint and marker cutoff\nvalue c using
non-parametric and semi-parametric estimators. Standard errors\nand confidence
intervals are also computed. Either analytic or bootstrap\nstandard errors can be
computed.","Imports":"Rcpp","License":"GPL-
2","NeedsCompilation":"yes","Package":"survAccuracyMeasures","Repository":"http:\/\
/cran.csiro.au\/src\/contrib","Title":"Estimate accuracy measures for risk
prediction markers from\nsurvival
data","URL":"https:\/\/github.com\/mdbrown\/survRpackages","Version":"1.2"},"survC1
":{"Author":"Hajime Uno","Depends":"survival","Description":"Performs inference for
C of risk prediction models with\ncensored survival data, using the method proposed
by Uno et al.\n(2011). Inference for the difference in C between two
competing\nprediction models is also implemented.","License":"GPL-
2","NeedsCompilation":"yes","Package":"survC1","Repository":"http:\/\/cran.csiro.au
\/src\/contrib","Title":"C-statistics for risk prediction models with censored
survival\ndata","Version":"1.0-2"},"survIDINRI":{"Author":"Hajime Uno, Tianxi
Cai","Depends":"survival, survC1","Description":"Performs inference for a class of
measures to compare\ncompeting risk prediction models with censored survival
data.\nThe class includes the integrated discrimination improvement\nindex (IDI)
and category-less net reclassification index (NRI).","License":"GPL-
2","NeedsCompilation":"yes","Package":"survIDINRI","Repository":"http:\/\/cran.csir
o.au\/src\/contrib","Title":"IDI and NRI for comparing competing risk prediction
models with\ncensored survival data","Version":"1.1-1"},"survJamda":
{"Author":"Haleh Yasrebi","Depends":"survival,
survivalROC,ecodist,survcomp,survJamda.data","Description":"Microarray gene
expression data can be analyzed individually or jointly using merging methods or
meta-analysis to predict patients' survival and risk assessment.","License":"GPL
(>=
2)","NeedsCompilation":"no","Package":"survJamda","Repository":"http:\/\/cran.csiro
.au\/src\/contrib","Title":"Survival Prediction by Joint Analysis of Microarray
Gene\nExpression Data","Version":"1.1.4"},"survJamda.data":{"Author":"Haleh
Yasrebi","Depends":"R (>= 2.10)","Description":"Three breast cancer gene expression
data sets that can be used for package 'survJamda'. This package contains the gene
expression and phenotype data of GSE1992, GSE3143 and GSE4335.","License":"GPL (>=
2)","NeedsCompilation":"no","Package":"survJamda.data","Repository":"http:\/\/cran.
csiro.au\/src\/contrib","Title":"Data for Package
'survJambda'","Version":"1.0.2"},"survMisc":{"Author":"Chris
Dardis","Depends":"survival","Description":"A collection of functions to help in
the analysis of\nright-censored survival data. These extend the methods available
in\npackage:survival.","Imports":"graphics, grDevices, stats, utils, knitr, KMsurv,
ggplot2,\ndata.table, zoo, grid, gridExtra, km.ci","License":"GPL-
2","NeedsCompilation":"no","Package":"survMisc","Repository":"http:\/\/cran.csiro.a
u\/src\/contrib","Title":"Miscellaneous Functions for Survival
Data","Version":"0.5.0"},"survPresmooth":{"Author":"Ignacio Lopez de Ullibarri and
Maria Amalia Jacome","Depends":"R(>= 3.0.1)","Description":"Presmoothed estimators
of survival, density, cumulative and non-cumulative hazard functions with right-
censored survival data.","License":"GPL-
2","NeedsCompilation":"yes","Package":"survPresmooth","Repository":"http:\/\/cran.c
siro.au\/src\/contrib","Title":"Presmoothed Estimation in Survival
Analysis","Version":"1.1-9"},"survRM2":{"Author":"Hajime Uno, Lu Tian, Angel
Cronin, Chakib Battioui","Depends":"survival","Description":"Performs two-sample
comparisons using the restricted mean survival time (RMST) as a summary measure of
the survival time distribution. Three kinds of between-group contrast metrics
(i.e., the difference in RMST, the ratio of RMST and the ratio of the restricted
mean time lost (RMTL)) are computed. It performs an ANCOVA-typ

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