Computational Statistics

Setia Pramana

2015

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 Course Outline
• Introduction
– Different Statistical Software
• Data Preparation, Management, Manipulation,
Summarization with:
– SPSS
– R (R Commander)
– Ms. Excel
• Data Tabulation and Visualization

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 Course Outline

• Generate Different Statistical Distribution (with

Rcmdr)
• Simple Linear Regression and Correlation
• Basic R Programming
• Developing Simple Graphical User Interface in R
• Resampling Methods
• Statistical Inference (Point and interval
estimation)

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 Course Outline
• Hypothesis testing: one, two sample t-test (test
for mean difference, proportion and variance)
• Analysis of Variance (Anova): one and two way
Anova.
• Introduction to Design of Experiment
• Final Project

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 Course Workload

• 20% Theory, 80% practice

• Group Project (5 students)
• Presentation every week
• R code would be provided
• Slides can be seen at :
http://www.slideshare.net/hafidztio/

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Reference Books

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 Reference Books
• John Maindonald dan W. John Braun. Data Analysis and
Graphics Using R – an Example-Based Approach. 3rd
Edition. Cambridge University Press: Cambridge.2010.
• John Fox. Journal of Statistical Software, The R
Commander : A Basic-Statistics Graphical User Interface
to R.Volume 14, Issue 9, September 2005.
• Chris Beeley. Web Application Development with R
Using Shiny. Packt Publishing: Birmingham.2013.
• SPSS Statistics Base User’s Guide 17.0. Polar
Engineering and Consulting : Chicago, 2007.

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 Reference Books
• Jurusan Komputasi Statistik. Modul Mata Kuliah
Komputasi Statistik. 2014
• Kerns, G. Jays. Introduction to Probability and Statistics
Using R. E book. GNU Free Documentation License.
2010.
• Geof H. Givens dan Jennifer A. Hoeting. Computational
Statistics, 2nd edition. John Wiley and Sons : New
Jersey. 2013
• Jochen Voss. Statistical Computing. E book. 2011.
• Brent B. Welch, Ken Jones dan Jeffrey Hobbs. Practical
Programming in Tcl and Tk. 4Th edition. Prentice Hall
PTR: New Jersey.2003.
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 Other Materials
• https://sites.google.com/site/biostatinfocor
e/home/rworkshop
• https://sites.google.com/site/biostatinfocor
e/biostatistics-workshop

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Introduction

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Statistics?

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What is Statistics?

• Statistics: is the science which deals with

collection, classification and tabulation of
numerical facts as the basis for explanation,
description and comparison of phenomenon”.

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Observations on the
Bills of
Mortality (1662)

Recorded Plague
related death for
100 years

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 What is Statistics?
• Exploring data: Using graphical and numerical
techniques to study patterns and departures from
patterns (in order to interpreting data)
• Sampling and experimentation: Clarifying the
question, deciding on methods of collection and analysis
to produce valid information.
• Anticipating patterns: Exploring random phenomena
using probability and simulation. Probability is our tool for
anticipating distributions...
• Statistical Inference: Estimating population parameters
and testing hypothesis

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“Statistical thinking will one day be as
necessary for efficient citizenship as the
ability to read and write” HG Well

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 Areas of Statistics

Two areas of statistics:

Descriptive Statistics: collection, presentation,
and description of sample data.
Inferential Statistics: making decisions and
drawing conclusions about populations.

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 Statistics Descriptive

What is your conclusion?

The fatality rate is:

– 40% in the group of drivers who did not wear seat belts
– 20%in drivers who did wear seat belts

• Seat belts appear to save lives

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 Inferential Statistics

• Are results applicable to the population of all drivers?

(generalization)
• Does wearing seat belts save lives? (assess strength of
evidence)
• Is the fatality rate of those not wearing seat belts higher than
the fatality rate of those wearing seat belts? (comparison)
• How many lives can be saved by wearing seat belts?
(prediction)
• Do other variables influence the conclusion? For example:
the age of driver, alcohol use, type of car, speed at impact
(ask more questions)
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 Statistics and the Technology

• The electronic technology has had a tremendous effect

on the field of statistics.
• Many statistical techniques are repetitive in nature:
computers and calculators are good at this.
• Lots of statistical software packages: R, MINITAB,
SYSTAT, STATA, SAS, Statgraphics, SPSS, MS Excel,
and calculators.

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Available Statistical Packages

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 Available Statistical Packages

Proprietary Free Software

 Excel  LibreOffice Calc

 SPSS  R

 MINITAB  CS Pro

 SAS  WinBugs

 Stata  EpiInfo

 Statistica  Many more……..

 Many more ……

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Microsoft Excel

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Which one do you use?

Why?

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Statistical Software Used

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Statistical Software Used

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R is HOT !

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 R is HOT !

• R is HOT !

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http://r4stats.com/articles/popularity/ 32
 R is HOT !

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http://r4stats.com/articles/popularity/ 33
R is HOT !

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http://r4stats.com/articles/popularity/ 34
 What is R?

• A language and environment for statistical computing and

graphics.
• An integrated suite of software facilities for data
manipulation, calculation and graphical display.
• First appeared in 1996 by Prof. Ross Ihaka and Robert
Gentleman of the University of Auckland, NZ.
• GNU software -> Free. Similar like S language.
• Open source, maintained and developed by a community
of developers.
• Works in Windows, Unix, MacOs
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 R includes

• Effective data handling and storage facility,

• A suite of operators for calculations on arrays, in particular
matrices
• A large, coherent, integrated collection of intermediate
tools for data analysis,
• Graphical facilities for data analysis and display either on-
screen or on hardcopy
• Well-developed, simple and effective programming
language which includes conditionals, loops, user-defined
recursive functions and input and output facilities.
http://www.r-project.org/
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 Why R?

• It is not only statistical software but

also a language
• 5000 add-on packages  lots of pre-
prepared packages (http://cran.r-
project.org/web/packages/)
• With many applications http://cran.r-
project.org/web/views/,
http://www.revolutionanalytics.com/r-
language-features-applications-and-
extensions#thirdparty .
• Access to powerful, cutting-edge
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analytics
 Why R?
• Flexible (complex or standard statistical practices, bayesian
modelling, GIS map building, building interactive web
applications, building interactive tests, etc. )
• We can make our own package and publish it
• Great Graphics and data visualization
• Can be used for High Performance Computer Clusters
• Well Supported by R Community (http://www.inside-r.org/r-
resources-web)
• And many more…..

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 Why R?

• Can be integrated with other languages (C/C++,

Java).
• R can interact with many data sources and other
statistical packages (SAS, Stata, SPSS, and Minitab).
• For the high performance computing task 
multiple cores, either on a single machine or across a
network.

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 But…..

• R has no warranty
• Command Line Interface : difficult for some users.
• Users must learn a new way of thinking about data
and data analysis sequence
• That’s all ….. I guess

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 Companies using R in 2013

• The New York Times routinely uses R for interactive and print data
visualization.
• Google has more than 500 R users.
• The FDA supports the use of R for clinical trials of new drugs.
• The National Weather Service uses R to predict the extent of flooding
events.
• Zillow uses R to model housing prices.
• The Consumer Financial Protection Bureau uses R and other open
source tools.
• Twitter uses R for data science applications on the Twitter database.
• FourSquare uses R to develop its recommendation engine.
• Facebook uses R to model all sorts of user behaviour.

Source: Revolutionanalytics
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 R Library/packages

IsoGene nlme
lme4
foreign

survival
zoo R Base Packages

reshape2
ggplot2
zoo

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 My R Packages
• IsoGene
• IsoGeneGUI
• nea
• neaGUI
• biclustGUI
• OCRME
• More detail: http://setiopramono.wordpress.com/r-
programming/

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R For Cutting Edge
Technologies

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 R Graphics and Visualization

• R provides wide range graphics and visualizations

• Basic Plots: bar plots, basic 3D plots, heatmap.,etc
• Geographic Maps
• Projection Maps
• Social Network Graphs
• Animated graphics and movies (animation)
• Motion Charts (GoogleViz)
• Interactive Graphics (rggobi)
• Image format: BMP, JPEG, PDF, PNG etc…
• and….many more………
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R Graphics

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 R Graphics

RCircos
Computationalhttps://gjabel.wordpress.com/
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 R Graphics

A map of worldwide email traffic

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 R Graphics

Facebook connections between city centers around the world

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 R Graphical User Interfaces
• R uses Command line interface and it is preferred for
advanced users  allows direct control, more accurate,
flexible and the analysis is reproducible.
• Requires good knowledge of the language  difficult for
beginners or less frequent users.
• R provides tools for building GUIs  RGUI

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 R GUI Projects

• Integrated development environment (IDE)/Script

Editors aimed to provide feature-rich environments to
edit R scripts and code: Rstudio (www.rstudio.com),
and architect (www.Openanalytics.eu)
• Web based application: the Rweb (Banfield, 1999),
R.Net (www.u.arizona.edu/~ryckman/Net.php),
or gWidgetsWWW (Verzani, 2012).

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 R GUI Projects
• Python: OpenMeta-Analyst (Wallace et al, 2012)
• Java: JGR (Java GUI for R), Deducer (Fellows, 2012),
and Glotaran (Snellenburg, 2012).
• Php: R-php (http://dssm.unipa.it/R-php/)
• Other extensions connect R to graphical toolboxes for
developing menus and dialog boxes: Tcltk, Gtk.

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 R Studio

• Download from
Rstudio.com
• Powerfull IDE
(Integrated
Development
Environment) for R.

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RGUI Developed using tcltk

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 RGUI: RCommander

• Rcommander.com
• Helpful for R beginner
• Install inside R

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 RGUI using C#: Wires

• Developed by STIS
students
• For Spatial Data
Analysis
• Still developing…

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RGUI using C#: Wires

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RGUI: Web Based App

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 WebBUGS

• Conducting Bayesian
Statistical Analysis
Online
• Combines
OpenBUGS and R

www.webbugs.psychstat.org

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 RGUI: Shiny

• A new package from Rstudio to build interactive web

applications with R.
• Really Easy!
• Build useful web applications with only a few lines of
code—no JavaScript required.
• Self learning: http://shiny.rstudio.com/
• http://www.showmeshiny.com/

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RGUI using Shiny: FAST

Figure 5. FAST main page

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 Dynamic Report Generation

• Sweave
• knitr
• markdown

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 Want to Learn R? Need Help?
Lots of Self learning Resources
http://www.rdatamining.com/resources/onlinedocs
Blogs:
Software # Blogs Blogs Source
R 550 R-Bloggers.com
Python 60 SciPy.org
SAS 40 PROC-X.com, sasCommunity.org Planet
Stata 11 Stata-Bloggers.com
User Group: Stockholm R User group, etc…
Indonesia/Jakarta?
https://sites.google.com/site/biostatinfocore/introduction-to-r
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 Need Help?

Number of R- or SAS-related posts to Stack Overflow by week.

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