CRAN Task View: Agricultural Science

Maintainer:Julia Piaskowski, Adam Sparks, Janet Williams
Contact:julia.piask at gmail.com
Version:2022-11-05
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 (2022). CRAN Task View: Agricultural Science. Version 2022-11-05. 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

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

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.

Discipline-specific packages

Agricultural economics

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

Agrometeorology

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

Agronomic trials

Experimental design

The task view for ExperimentalDesign provide additional information on experimental design for a wide variety of research problems.

High throughput phenotyping (HTP)

Trial analysis

Animal science

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

Breeding & quantitative genetics

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

Linkage mapping & QTL analysis

There are several packages focused on linkage disequilibrium on Bioconductor.

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.

Genomic prediction

Crop growth models & crop modelling

Entomology

Food science

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

Genotype-by-environment interactions

Plant pathology

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

Rural sociology

See the task view for Psychometrics for general sociology packages.

Soil science and precision agriculture

Remote sensing

Weed science

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

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, agroclim, AgroR, AgroReg, agrostab, AgroTech, AlphaSimR, ALUES, ascotraceR, asremlPlus, bayesammi, BGGE, BGLR, bigleaf, biometryassist, biotools, BMTME, bravo, BWGS, climatrends, ClimMobTools, coxme, cropdatape, cropDemand, CropDetectR, cropgrowdays, cropZoning, Dasst, desplot, DMMF, eemdTDNN, epifitter, Evapotranspiration, FAO56, FAOSTAT, febr, FielDHub, fruclimadapt, FWRGB, geneticae, gge, gosset, gpbStat, grapesAgri1, GSelection, GSMX, hagis, heritability, hnp, IBCF.MTME, ispd, isqg, KenSyn, kgc, kinship2, landsepi, LinkageMapView, lmDiallel, lue, LW1949, LWFBrook90R, mappoly, mapsRinteractive, metan, MeTo, metrica, mlmm.gwas, mpspline2, mvngGrAd, NutrienTrackeR, OBIC, onemap, PBIBD, pedigree, pedigreemm, pedmod, pedometrics, pergola, PesticideLoadIndicator, pestr, PGRdup, photosynthesis, plantecophys, pliman, polymapR, polyqtlR, poppr, PopVar, PROSPER, qgg, qgtools, QI, qtlpoly, QTLRel, rapsimng, rarms, Recocrop, resevol, rfieldclimate, RGISTools, rMVP, rnassqs, rPAex, Rquefts, rrBLUP, rusda, Rwofost, satellite, selection.index, sharpshootR, smapr, 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:ASMap, CropScapeR.

Related links

Other resources