CRAN Task View: Agricultural Science https://cran.r-project.org/web/views/Agriculture.

html

CRAN Task View: Agricultural Science

Maintainer: Julia Piaskowski, Adam Sparks, Janet Williams

Contact: julia.piask at gmail.com
Version: 2023-12-01
URL: https://CRAN.R-project.org/view=Agriculture
Source: https://github.com/cran-task-views/Agriculture/
Contributions: Suggestions and improvements for this task view are very welcome and
can be made through issues or pull requests on GitHub or via e-mail to
the maintainer address. For further details see the Contributing guide.
Citation: Julia Piaskowski, Adam Sparks, Janet Williams (2023). CRAN Task
View: Agricultural Science. Version 2023-12-01. URL https://CRAN.R-
project.org/view=Agriculture.
Installation: The packages from this task view can be installed automatically using the
ctv package. For example, ctv::install.views("Agriculture", coreOnly
= TRUE) installs all the core packages or
ctv::update.views("Agriculture") installs all packages that are not yet
installed and up-to-date. See the CRAN Task View Initiative for more
details.

Agriculture encompasses a broad breadth of disciplines. Many packages in base R and

contributed packages are useful to agricultural researchers. For that reason, this is not an
exhaustive list of all packages useful to agricultural research. This CRAN task view is
intended to cover major packages that in most cases, have been developed to support
agricultural research and analytical needs.

Note that some of these packages are on CRAN and others are on GitHub, Bioconductor,
or R-Forge.

If you think that a package is missing from this list, please let us know through issues or
pull requests in the GitHub repository.

Table of contents

• Packages with general applications

◦ Agricultural & land use databases
◦ Agricultural data sets
◦ General analytical packages supporting agricultural research
• Discipline-specific packages
◦ Agricultural economics
◦ Agrometeorology
◦ Agronomic trials
▪ Experimental design
▪ High throughput phenotyping (HTP)
▪ Trial analysis
◦ Animal science
◦ Breeding & quantitative genetics

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▪ Linkage mapping & QTL analysis

▪ GWAS (Genome Wide Association Studies)
▪ Genomic prediction
◦ Crop growth models & crop modelling
◦ Entomology
◦ Food science
◦ Genotype-by-environment interactions
◦ Plant pathology
◦ Rural sociology
◦ Soil science and precision agriculture
▪ Remote sensing
◦ Weed science

Packages with general applications

Agricultural & land use databases

• USDA databases: Data from the United States Department of Agriculture’s National
Agricultural Statistical Service ‘Quick Stats’ web API can be accessed with rnassqs
or with tidyUSDA, which also offers some mapping capabilities. The USDA’s
Cropland Data Layer API can be accessed with CropScapeR and cdlTools, the latter
providing utility functions for processing CDL data. rusda provides an interface to
access the USDA-ARS Systematic Mycology and Microbiology Laboratory
(SMML)’s four databases: Fungus-Host Distributions, Specimens, Literature and the
Nomenclature database. The USDA’s Agricultural Resource Management Survey
(ARMS) data API can be accessed with rarms. The USDA’s Livestock Mandatory
Reporting data API can be accessed with usdampr. The packages FAOSTAT and
faobulk can be used to access data from the FAOSTAT Database from the United
Nations Food and Agricultural Organization (FAO).

• Most USDA-NRCS soils related databases and APIs can be accessed with soilDB.

• FedData provides access to geospatial data from the United States Soil Survey
Geographic (SSURGO) database, the Global Historical Climatology Network
(GHCN), the Daymet gridded estimates of daily weather parameters for North
America, the International Tree Ring Data Bank, and the National Land Cover
Database. SSURGO data can also be accessed and processed with XPolaris.

• NASA soil moisture active-passive (SMAP) data can be accessed and processed with
smapr (archived).

• SISINTAR provides access to SiSINTA (Sistema de información de Suelos del

INTA), a soil profile database for Argentina, and functions for processing the data.

• SILO weather data from the Queensland DES Longpaddock website can be accessed
with cropgrowdays.

• PGRdup provides functions to aid the identification of probable/possible duplicates

in plant genetic resources collections.

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• rfieldclimate provides functionality and parsers to interact with the FieldClimate

API.

• pestr offers tools to extract pest data from EPPO Data Services and EPPO Global
Database using EPPO database API and put them into tables with human-readable
formats.

• PesticideLoadIndicator computes the Danish Pesticide Load Indicator as described in

Kudsk (2018) and Moehring (2019) for pesticide use data.

• QBMS provides functions to query BrAPI-compliant databases with additional

functionality for the GIGWA platform.

Agricultural data sets

Many of the agriculture-focused packages listed in this guide also include data sets to
illustrate their functionality (e.g. agricolae, AgroTech, BGLR).

• agridat consists of a very large collection of agricultural data sets and example
analyses; the package contains a vignette detailing additional data sets and extensive
resources to support agricultural analysis.

• agriTutorial provides a collection of agricultural data sets and analysis with

particular attention to crop experiments.

• The soybean nested associated mapping population data set can be accessed via
SoyNAM.

• The FAOSTAT data set collection for the Food and Agriculture Biomass Input–
Output model (FABIO) is available through fabio.

• simplePhenotypes can be used for simulating pleiotropic, linked and epistatic

phenotypes.

• USGS county data on fertilizer sales can be accessed with ggfertilizer.

• Annual agriculture production data from the Peruvian Integrated System of

Agricultural Statistics (SIEA) covering 2004 to 2014 can be accessed with
cropdatape.

• ZeBook provides data sets and examples accompanying the book Working with
Dynamic Crop Models.

General analytical packages supporting agricultural research

The MixedModels task view provides a comprehensive list of packages relevant to fitting
general and generalized linear mixed models.

• The packages nlraa and AgroReg provides linear and nonlinear regression functions
specifically for agricultural applications. biotools can conduct a wide array of
multivariate analysis for agronomists including genetic covariance, optimal plot size,
tests for spatial dependence, and tests for seed lot heterogeneity.

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• agriCensData is a flexible package for working with censored data (e.g. time to
flowering, instrumentation values below the detection limit, disease scoring).

• grapesAgri1 houses a collection of Shiny apps, GRAPES (General R-shiny based

Analysis Platform Empowered by Statistics), that works as a graphical user interface
for individuals to upload data files and analyse. Linear models, ANOVA for CRD
and 2-way RCBD designs, correlation analysis, exploratory data analysis and other
common hypothesis tests are supported.

• ALUES implements methodology developed by the FAO and the International Rice
Research Institute for evaluating land suitability for different crop production.

• AGPRIS (AGricultural PRoductivity in Space) provides functions for different

spatial analyses in implemented in INLA and other spatial approaches. The package
KenSyn has example data sets and analytical code supporting the book De L’analyse
des Réseaux Expérimentaux à la Méta-analyse (French) or From Experimental
Network to Meta-analysis (English).

• AgroTech provides functions for making chemical application calculations and

example data sets.

Discipline-specific packages

Agricultural economics

The task views for Econometrics, (Empirical) Finance, and TimeSeries provide
information on packages and tools relevant to agriculture economics.

• Agricultural price forecasting: vmdTDNN forecasts univariate time series data using
variational mode decomposition based time delay neural network models as
described by Dragomiretskiy 2014. stlELM also conducts univariate time series
forecasting univariate time series, using seasonal-trend decomposition procedures
based on loess (STL) combined with the extreme learning machine developed by
Xiong 2018. The package eemdTDNN also conduct univariate forecasting, utilizing
different decomposition based time delay neural network models based on Yu 2008.

Agrometeorology

The Hydrology has many resources for accessing and processing weather and climate data.

• Data sources: Data from the Copernicus data set of agrometeorological indicators
can be downloaded and extracted using ag5Tools. Climate crop zones in Brazil can
be accessed and calculated with cropZoning using data sets from TerraClimate that
are calibrated to weather stations run by the National Meteorological Institute of
Brazil. acdcR (AgroClimatic Data by County) provides functions to calculate United
States county-level variables in agricultural production or agroclimatic and weather
analyses.

• Data preparation: meteor provides a set of functions for weather and climate data
manipulation to support crop and crop disease modeling. cropgrowdays and
climatrends can be used for calculating growing degree days, cumulative rainfall,

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number of stress day, mean radiation, crop sensitive indices, evapotranspiration and
other variables. agroclim and weaana have many utility functions to compute
agroclimatic indices useful to zoning areas based on climatic variables and to
evaluate the importance of temperature and precipitation for individual crops or in
general for agricultural lands.

• FAO56 and MeTo provide functions for calculating agrometeorological indicators

following the FAO Monograph 56, Crop evapotranspiration: Guidelines for
computing crop water requirements (1998).

• agriwater provides spatial modeling of energy balance and actual evapotranspiration

using satellite images and meteorological data. AquaBEHER computes and
integrates daily reference evapotranspiration into a water balance model to estimate
the calendar of wet-season (onset, cessation and duration) based on agroclimatic
approach.

• The frost package contains a compilation of empirical methods used by farmers and
agronomic engineers to predict the minimum temperature to detect a frost event.

• LWFBrook90R provides an implementation of the soil vegetation atmosphere

transport (SVAT) model LWF-BROOK90 to calculate daily evaporation
(transpiration, interception, and soil evaporation) and soil water fluxes, along with
soil water contents and soil water tension of a soil profile covered with vegetation.

• kgc identifies the Koeppen-Geiger climatic zone for a given location based on
relative heat and humidity.

Agronomic trials

Experimental design

The task view for ExperimentalDesign provide additional information on experimental

design for a wide variety of research problems.

• agricolae provides extensive resources for the planning and analysis of planned field
experiments. Designs constructed by agricolae can be visualised with agricolaeplotr.
Agricultural field trials layout can be also be visualised with desplot.

• PBIBD can construct partially balanced incomplete block designs and the Youden-m
square (row-column) design and can calculate design efficiency.

• biometryassist can be used for experimental design and analysis; it also includes
several function to interface with asreml objects.

• The package DiGGer was developed for rectangular field trials; its purpose is to help
users determine the optimal experimental design based on the treatment structure and
number of replicates.

• inti provides functionality for experimental design and manipulation and it is focused
on FieldBook compatibility.

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• FielDHub is a Shiny app for generating traditional, un-replicated, augmented and

partially-replicated designs applied to agriculture, plant breeding, forestry, animal
and biological sciences.

High throughput phenotyping (HTP)

• statgenHTP is for analyzing data from HTP platform experiments, with some
functions specifically designed to work with the proprietary software R-asreml.

• FIELDimageR is general-purpose package for processing and analyzing image data

from drones.

• tasselnetv2plus provides a fast implementation for high-throughput plant counting

from high-resolution RGB imagery.FWRGB can process plant images for
downstream machine learning models to predict fresh biomass. pliman provides
tools for image manipulation to quantify plant leaf area, disease severity, number of
disease lesions, and obtain statistics of image objects such as grains, pods, pollen,
leaves, and more.

Trial analysis

• General analysis: The package agricolae contains functions for analyzing many
common designs in agriculture trials such as split plot, lattice, Latin square and some
additional functions such AMMI and AUDPC calculations. The proprietary software
asreml provides an R version of their mixed model software for field trial analysis
(note this is not open source and requires an annual license). CRAN also contains an
add-on package asremlPlus that provides several accessory functions to asreml.
[INLA](https://www.r-inla.org/) provides tools for Bayesian inference of latent
Gaussian models, and it contains functions for modelling spatial variation, such as
field experiments or farm locations. The gosset package provides the toolkit for a
workflow to analyse experimental agriculture data, from data synthesis to model
selection and visualisation. AgroR has general functions and a Shiny app for analysis
of common designs in agriculture: CRD, RCBD and Latin square.

• Spatial analysis: the statgenSTA has functions for single trial analysis with and
without spatial components. SpATS can be used to adjust for field spatial variation
using p-splines. A localised method of spatial adjustment for unreplicated trials,
moving grid adjustment, is implemented with mvngGrAd.

• Trials utilizing an incomplete block design can be analysed used ispd.

• ClimMobTools is the API Client for the ClimMob citizen science platform in R for
agronomic field trials.

Animal science

The Tracking task view has many resources for working with tracked animal data and
studying animal movement.

• The package usdampr provides access to the USDA’s Livestock Mandatory

Reporting API.

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• Many of the genetic packages described in the breeding section of this task view can
also be applied to animals. visPedigree can be used to visualise complex animal
pedigrees.

Breeding & quantitative genetics

See the R package repository Bioconductor for bioinformatic tools to support the
processing of high-throughput genomic data.

• General plant breeding: st4gi and variability provides several common utility
functions for genetic improvement of crops. Also, please see the subsection on
“genotype-by-environment interactions” in this task view for packages integrating
environmental and genomic data in an analytical framework. gpbStat provides
functions for common plant breeding analyses including line-by-tester analysis
(Arunachalam 1974 and diallel analysis (Griffing 1956).

• lmDiallel provides service functions for analysing data sets obtained from diallel
experiments, as described in Onofri 2020.

• heritability implements marker-based estimation of heritability when observations on

genetically identical replicates are available.

• selection.index calculates a selection index using the method described by Smith

(1936).

• Breeding simulations AlphaSimR provides functions for stochastic modelling of

processes common to breeding programs such as selection and crossing, in plant or
animals Gaynor et al. 2020. SIMplyBee is an extension of AlphaSimR for honeybees
Obsteter et al. 2023. MoBPS also provides functions for stochastic modelling of
breeding programs Pook et al. 2020.

Linkage mapping & QTL analysis

There are several packages focused on linkage disequilibrium on Bioconductor.

• There are two notable and long-standing packages for quantitative trait loci (QTL)
analysis: (1) onemap, providing MapMaker/EXP-like performance and additional
tools; and (2) qtl providing standard QTL mapping functionality and accessory
functions for simulating crosses. BatchMap is a fork of onemap for fast computation
of high density linkage maps. ASMap can conduct fast linkage mapping with the
algorithm ‘MSTmap’. pergola implements the PERGOLA algorithm for ordering
markers in a linkage group. MapRtools is multipurpose linkage mapping package for
teaching and research.

• For polyploids, the packages mappoly and polymapR can be used for linkage
mapping and the packages qtlpoly and polyqtlR can be used for QTL estimation.
diaQTL is for QTL and haplotype analysis of diallel populations (diploid and
autotetraploid).

• statgenMPP can conduct QTL mapping in multi-parent populations.

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• Linkage maps can be visualized with LinkageMapView.

GWAS (Genome Wide Association Studies)

There are many GWAS packages on Bioconductor and a large number of other GWAS
packages in CRAN not listed here. The packages listed here have specific applications in
breeding populations common in agriculture.

• GWAS can be conducted using a stepwise mixed linear model for multilocus data
with mlmm.gwas or MultLocMixMod (use library(mlmm) to load the package in R).
The package statgenGWAS can fit GWAS models using the EMMAX algorithm.
GAPIT3 is wrapper for several GWAS algorithms including the original GAPIT,
FarmCPU and BLINK.

• GWAS models for a very large number of SNPs and/or observations can be
estimated with rMVP. GridLMM provides functions to conduct GWAS in models
that require two or more random effects (e.g. additive and dominance kinship
matrices, or kinship and spatial covariance matrices). Functions for conducting
GWAS in autotetraploids are provided by GWASpoly, and these functions also work
in diploid species. Variable selection for ultra-large dimensional GWAS data sets can
be done with bravo, which implements the Bayesian algorithm SVEN, selection of
variables with embedded screening.

• StageWise provides functions to conduct a 2-stage GWAS when the phenotypic data
are from multiple field trials.

• For polyploids, polyBreedR provides convenience functions to facilitate the use of

genome-wide markers for breeding autotetraploid species, and its functionality also
extends to diploids.

Genomic prediction

• General genomic selection packages: breedR is a general purpose package for

performing quantitative genetic analyses. Genome feature mixed linear models using
frequentist and Bayesian approaches can be implemented with qgg. The package
STGS implements several genomic selection models for single traits. BWGS, “Breed
Wheat Genomic Selection”, provides a pipeline of functions for conducting genomic
selection in hexaploid wheat.

• GBLUP: Packages supporting genetic prediction using mixed models augmented

with pedigree or genetic marker data include sommer, rrBLUP, BGLR, lme4GS (this
package has special installation instructions), lme4qtl, pedigreemm, qgtools, cpgen,
QTLRel, and the licensed software asreml. Many of these packages have built-in
functionality for data preparation steps including data imputation and calculation of
the relationship matrices.

• GBLUP: Packages supporting genetic prediction using mixed models augmented

with pedigree or genetic marker data include are listed in the MixedModels task
view. Many of these packages have built-in functionality for data preparation steps
including data imputation and calculation of the relationship matrices.

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• GSelection implements genomic selection integrating additive and non-additive

models.

• pedmod provides linear modelling functions integrating kinship for categorical traits.

• coxme can fit Cox proportional hazards models containing both fixed and random
effects with a kinship matrix.

• GSMX, multivariate genomic selection, estimates trait heritability and handles

overfitting through cross validation.

• TSDFGS can estimate the optimal training population size and composition for
genomic selection.

• PopVar has function for estimating population genetic variance from a biparental
cross.

• Multiple environments and traits: BGGE conducts genomic prediction for

continuous variables, focused on genotype-by-environment genomic selection
models following the methods of Jarquín 2014. megaLMM implements multivariate
genomic prediction with very large numbers of traits (up to several thousand) using
Bayesian genomic prediction models.

• Kinship and relatedness: AGHmatrix provides extensive options for calculating

pedigree and genomic relationships (additive and dominance). The pedigree
packages provides functionality for ordering pedigrees, calculating and inverting the
pedigree relationship matrix and other related tasks. statgenIBD can calculate IBD
probabilities for biparental, three-way and four-way crosses. kinship2 provides
functions for manipulating and visualising pedigree-based kinship data.

Crop growth models & crop modelling

• The apsimx package has functions to read, inspect, edit and run files for APSIM
“Next Generation” (.json, .apsimx) and APSIM “Classic” (.xml, .apsim) files.
rapsimng works with next generation APSIM files.

• DSSAT provides a comprehensive R interface to the Decision Support System for

Agrotechnology Transfer Cropping Systems Model (DSSAT-CSM) documented by
Jones (2003). This package provides cross-platform functions to read and write input
files, run DSSAT-CSM, and read output files. Dasst also interfaces with DSSAT
files.

• The modelling framework Simplace (Scientific Impact assessment and Modelling

Platform for Advanced Crop and Ecosystem management) can be accessed using r
pkg(“simplace”). Additionally, r github(“gk-crop/simplaceUtil”) provides additional
utility functions that make the setup and handling of simulations more convenient.

• fruclimadapt calculates several phenological variables important to grape vines and

fruit trees in order to evaluate climate adaptation and to estimate the incidence of
weather-related disorders in these species.

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• Crop Water Usage: cropDemand can be used to estimate crop water demand in
Brazilian production regions using the TerraClimate data set. Evapotranspiration can
estimate potential and actual evapotranspiration using 21 different models.

• metrica has many convenience functions for comparing model predictions with
ground truth data.

• Crop Growth Models: phenorice is an R implementation of the PhenoRice model for

remote sensing of rice crop production. phenoriceR provides helper functions for
processing data from the phenorice model. Rwofost is an implementation of the
WOFOST (World Food Studies) crop growth model (de Wit 2019). Rquefts provides
an implementation of the QUEFTS (Quantitative Evaluation of the Native Fertility
of Tropical Soils) model (Janssen 1990).

• Recocrop estimates environmental suitability for plants using a limiting factor

approach for plant growth following Hackett (1991).

• Ecophysiology: photosynthesis has an extensive number of tools for plant

ecophysiology modelling and analysis. tealeaves implements models for
understanding leaf temperature using energy balance. plantecophys supports the
coupled leaf gas exchange model, A-Ci curve simulation and fitting, Ball-Berry
stomatal conductance models, leaf energy balance using Penman-Monteith, Cowan-
Farquhar optimization, and humidity unit conversions. plantecowrap extends
plantecophys by adding capabilities for temperature responses of mesophyll
conductance, apparent Michaelis-Menten constant for rubisco carboxylation in
air,and photorespiratory CO2 compensation point for fitting A-Ci or A-Cc curves for
C3 plants.

• bigleaf calculates (e.g. aerodynamic conductance, surface temperature) and

physiological (e.g. canopy conductance, water-use efficiency) ecosystem properties
from eddy covariance data and accompanying meteorological measurements.

Entomology

• The Survival task view lists resources for working with censored data. The package
agriCensData provides functions for dealing with censored data in common
agricultural contexts.
• hnp Generates half-normal plots with simulation envelopes using different
diagnostics from a range of different fitted models.

Food science

For packages supporting sensory studies, see the Psychometrics task view.

• NutrienTrackeR provides convenience functions for calculating nutrient content

(macronutrients and micronutrients) of foods using food composition data from
several reference databases, including: ‘USDA’ (United States), ‘CIQUAL’ (France),
‘BEDCA’ (Spain) and ‘CNF’ (Canada).

Genotype-by-environment interactions

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• statgenGxE implements several analytical approaches for addressing genotype-by-

environment interactions.

• The package gge can generate GGE biplots, while bayesammi can conduct Bayesian
estimation of additive main effects multiplicative interaction (AMMI) model. metan
and geneticae can performs stability analysis of multi-environment trial data using a
wide range of parametric and non-parametric methods.

• EnvRtype can be used for assembling climate data, data set preparation and
environmental classification or envirotyping.

• FW implements Finlay-Wilkinson regression using a Gibbs sampler; spFW also

conducts spatial Finlay-Wilkinson analysis for multi-environmental trials using a
Bayesian hierarchical model.

• A wide variety of stability analysis statistics can be calculated via agrostab including
coefficient of homeostaticity, specific adaptive ability, weighted homeostaticity
index, superiority measure, regression on environmental index, Tai’s stability
parameters, stability variance, ecovalence and other stability parameters.
toolStability and stability also calculate stability analyses.

• IBCF.MTME implements item-based collaborative filtering for continuous data in

multi-trait and multi-environment trials following the methods described by
Montesinos-López (2018).

Plant pathology

The Epidemiology task view lists relevant package for modelling plant diseases.

• Epidemiology Simulation: Stochastic disease modelling of plant pathogens

incorporating spatial and genetic information can be done with landsepi. The
package ascotraceR can simulate an Ascochyta blight infection in a chickpea field
following the model developed by Diggle (2022).

• epiphy is a toolbox for analyzing plant disease epidemics. It provides a common

framework for plant disease intensity data recorded over time and/or space.

• epifitter provides functions for analysis and visualization of plant disease progress
curve data.

• Plant Pathogen Genetics: hagis has functions for analysis of plant pathogen
pathotype survey data. Functions provided calculate distribution of susceptibilities,
distribution of complexities with statistics, pathotype frequency distribution, as well
as diversity indices for pathotypes. Evolution of resistance genes under pesticide
pressure can be simulated under different numbers of pests, modes of pest
reproduction, resistance loci, number of pesticides and other facets with resevol.
Populations with mixed clonal/sexual reproductive strategies can be analyzed with
poppr, which has population genetic analysis tools for hierarchical analysis of
partially clonal populations.

Rural sociology

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See the task view for Psychometrics for general sociology packages.

• Both the Survival task view and the agriCensData package provide tools for working
with interval and censored data.

Soil science and precision agriculture

• Spatial: The Spatial and SpatioTemporal CRAN task views provide extensive
resources in spatial statistics. mpspline2 implements a mass-preserving spline to soil
attributes to make continuous down-profile estimates of attributes measured over
discrete, often discontinuous depth intervals.

• The sharpshootR contains a compendium of utility functions supporting soils survey

work including data management, summary, visualisations and conversions.

• For soil pedology, aqp provides a general toolkit for soil scientists: specialized data
structures, soil profile summary, visualisation, color conversion, and more.
SoilTaxonomy provides functions for parsing soil taxonomic terms. pedometrics has
many utility functions for common analyses of soil data.

• Soil water: Soil water retention curves can be calculated by the soilwater packages
using the Van Genuchten (1980) method for soil water retention and Mualem (1976)
method for hydraulic conductivity. Estimation and prediction of parameters of soil
hydraulic property models can be accomplished with spsh.

• SoilR models soil organic matter decomposition in terrestrial ecosystems with linear
and nonlinear models. The sorcering can be used to model soil organic carbon and
soil organic nitrogen and to calculate N mineralisation rates.

• Soil texture triangles can be graphed using soiltexture; this package can also classify
and transform soil texture data.

• QI can be used to calculate potassium intensity and exchangeability.

• DMMF implements the daily based Morgan-Morgan-Finney (DMMF) soil erosion

model (Choi 2017) for estimating surface runoff and sediment budgets from a field
or a catchment on a daily basis.

• OBIC calculate the Open Bodem Index, a method to evaluate the quality of soils of
agricultural fields in The Netherlands and the sustainability of the current
agricultural practices.

• Soil Fertility Testing: soiltestcorr has functions for conducting correlation analysis
between soil test values and crop yield data. SoilTesting provides functions for
calculating soil mineral concentrations from analytical lab results. fertplan provides
fertilizer recommendations based on soil test results (note this package is optimized
for horticultural crop production in Italy).

• The suitability of specific soils for crop production can be analyzed using
soilassessment, including soil fertility classes, soil erosion models and soil salinity
classification. Suitability requirements are for crops grouped into cereal crops, nuts,

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legumes, fruits, vegetables, industrial crops, and root crops.

Remote sensing

• spectralR can be used to access and process Sentinel 2 Level 2A satellite mission
optical bands pixel data, obtained from the Google Earth Engine. rsat and satellite
can be used to process remote sensing data.

• Agriculture image features from spectral data can extracted with agrifeature. It has
functions to calculate gray level co-occurrence matrix (GLCM), RGB-based
vegetative index (RGB VI) and normalized difference vegetation index (NDVI).

• Experimental units (e.g. plots) can be obtained from spectral images using rPAex. lue
implements the light Use efficiency Model to estimate biomass and yield. Leaf area
index and soil moisture from microwave backscattering data based on the WCM
model can be calculated with the WCM package.

• The mapsRinteractive package provides functions for working with soil point data in
raster format.

Weed science

For ecological studies and analytical applications, the Environmetrics task view provides a
list of existing R resources in this topic.

• Dose Response: the package drc offers versatile model fitting and after-fitting
functions for dose-response curves. LW1949 implements the Litchefield and
Wilcoxon (1949) dose-response model.

• drcte provides a framework for non-parametric and parametric time-to-event models

in agriculture, especially analysis of germination and emergence data.

• PROSPER is a package for simulating weed population dynamics at the individual

and population level under a range of conditions including herbicide resistance and
herbicide pressure.

CRAN packages

Core: AGHmatrix, agricolae, agridat, apsimx, aqp, cdlTools, drc, DSSAT, FedData,
inti, meteor, nlraa, qtl, sommer, tidyUSDA.
Regular: acdcR, ag5Tools, AGPRIS, agricolaeplotr, agrifeature, agriTutorial, agriwater,
AgroR, AgroReg, agrostab, AgroTech, AlphaSimR, ALUES, AquaBEHER,
ascotraceR, ASMap, asremlPlus, bayesammi, BGGE, BGLR, bigleaf,
biometryassist, biotools, bravo, BWGS, climatrends, ClimMobTools, coxme,
cropdatape, cropDemand, cropgrowdays, CropScapeR, cropZoning, Dasst,
desplot, DMMF, drcte, eemdTDNN, epifitter, Evapotranspiration, FAO56,
FAOSTAT, FielDHub, fruclimadapt, FWRGB, geneticae, gge, gosset, gpbStat,
grapesAgri1, GSelection, GSMX, hagis, heritability, hnp, IBCF.MTME, ispd,
KenSyn, kgc, kinship2, landsepi, LinkageMapView, lmDiallel, lue, LW1949,
LWFBrook90R, mappoly, mapsRinteractive, metan, MeTo, metrica,
mlmm.gwas, MoBPS, mpspline2, mvngGrAd, NutrienTrackeR, OBIC, onemap,

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PBIBD, pedigree, pedigreemm, pedmod, pedometrics, pergola,

PesticideLoadIndicator, pestr, PGRdup, photosynthesis, plantecophys, pliman,
polymapR, polyqtlR, poppr, PopVar, PROSPER, QBMS, qgg, qgtools, QI,
qtlpoly, QTLRel, rapsimng, rarms, Recocrop, resevol, rfieldclimate, rMVP,
rnassqs, rPAex, Rquefts, rrBLUP, rusda, Rwofost, satellite, selection.index,
sharpshootR, SIMplyBee, soilassessment, soilDB, SoilR, SoilTaxonomy,
soiltestcorr, SoilTesting, soiltexture, soilwater, sorcering, SoyNAM, SpATS,
spectralR, spFW, spsh, stability, statgenGWAS, statgenGxE, statgenHTP,
statgenIBD, statgenMPP, statgenSTA, STGS, stlELM, tealeaves, toolStability,
TSDFGS, usdampr, variability, WCM, weaana, ZeBook.
Archived: smapr.

Related links

• General web-based tutorials: R for Agricultural Statistics, AgStats.io, Data Science

for Agriculture in R
• Instructional materials for classroom or self-instruction: (Plant Disease) Ecology and
Epidemiology in R
• Website: Mixed Models in Agriculture
• MrBeanApp is a Shiny app utilizing ASReml to analyze plant breeding experiments
with mixed linear models including integrating spatial covariates.
• Additional data sets: the Github repository agroBioData houses a collection of data
sets supporting agriculture and applied biology (note that this is a collection of CSV
files and a .rda file, not a package)
• Additional web resources for accessing and analyzing the National Cooperative Soil
Survey
• Book: Applied Statistics in Agricultural, Biological, and Environmental Sciences
(2017) edited by B Glaz and KM Yeater
• Book: Experimental methods in agriculture (2022) by Andrea Onofri and Dario
Sacco (In English and Italian)
• Books published by ASA/CSSA/SSSA
• Books published by the ASHS
• Books published by the WSSA
• Books published by the APS
• Publications by the ESA
• Teaching curriculum: Crop Climate Change Course: materials for the course
Analyzing the Impact of Climate Change on Crops and Varieties
• Web book: Plant Disease Epidemiology in R (R4PDE)

Other resources

• CRAN Task View: Econometrics

• CRAN Task View: Environmetrics
• CRAN Task View: Epidemiology
• CRAN Task View: ExperimentalDesign
• CRAN Task View: Finance
• CRAN Task View: Hydrology
• CRAN Task View: MixedModels

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• CRAN Task View: Psychometrics

• CRAN Task View: Spatial
• CRAN Task View: SpatioTemporal
• CRAN Task View: Survival
• CRAN Task View: TimeSeries
• CRAN Task View: Tracking
• GitHub Project: agriCensData
• GitHub Project: agroclim
• GitHub Project: BatchMap
• GitHub Project: breedR
• GitHub Project: cpgen
• GitHub Project: diaQTL
• GitHub Project: EnvRtype
• GitHub Project: epiphy
• GitHub Project: fabio
• GitHub Project: faobulk
• GitHub Project: fertplan
• GitHub Project: FIELDimageR
• GitHub Project: frost
• GitHub Project: FW
• GitHub Project: GAPIT3
• GitHub Project: ggfertilizer
• GitHub Project: GridLMM
• GitHub Project: GWASpoly
• GitHub Project: INLA
• GitHub Project: lme4GS
• GitHub Project: lme4qtl
• GitHub Project: MapRtools
• GitHub Project: megaLMM
• GitHub Project: MultLocMixMod
• GitHub Project: phenorice
• GitHub Project: phenoriceR
• GitHub Project: plantecowrap
• GitHub Project: polyBreedR
• GitHub Project: rsat
• GitHub Project: simplePhenotypes
• GitHub Project: SISINTAR
• GitHub Project: st4gi
• GitHub Project: StageWise
• GitHub Project: tasselnetv2plus
• GitHub Project: visPedigree
• GitHub Project: vmdTDNN
• GitHub Project: XPolaris

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