EnvRtype: Envirotyping for Quantitative Genetics and Plant Breeding

An enviromics toolkit for genotype-by-environment analysis and envirotype-informed genomic prediction. Collects worldwide daily and hourly weather from 'NASA POWER', soil profiles from 'SoilGrids', elevation and bioclimatic layers from 'WorldClim', agro-ecological zones from 'FAO GAEZ', and downscaled 'CMIP6' climate scenarios, with checkpointed retrieval that can resume after an interrupted run. Derives agro-meteorological parameters (solar radiation, evapotranspiration, thermal time, atmospheric demand), runs a FAO-56 single crop coefficient soil water balance, and maps daily weather onto crop developmental stages. Builds environmental covariable matrices, envirotype typologies and frequency matrices, mega-environment clusters, historical risk profiles and target population of environments weights. Reduces interval-resolved envirotypes by principal component analysis, delineates soil zones with Gaussian mixture models, and constructs linear, Gaussian and arc-cosine environmental relatedness kernels. Fits Bayesian reaction-norm kernel models and predicts trained genotypes at untested locations and planting dates, with coverage diagnostics, spatial mapping and planting-window optimisation. Simulation functions generate multi-environment trials and enviromes with known architecture for power analysis. Methods are described in Costa-Neto, Galli, Carvalho, Crossa and Fritsche-Neto (2021) <doi:10.1093/g3journal/jkab040>, and build on the Bayesian genotype-by-environment kernel sampler of Granato, Cuevas, Luna-Vazquez, Crossa, Montesinos-Lopez, Burgueno and Fritsche-Neto (2018) <doi:10.1534/g3.118.200435>.

Version:	0.1.3
Imports:	ggplot2, grDevices, graphics, reshape2, stats, tools, utils
Suggests:	cluster, curl, geobr, ggrepel, httr, jsonlite, knitr, mclust, nasapower, parallel, randomForest, rmarkdown, sf, terra, testthat (≥ 3.0.0)
Published:	2026-10-22
DOI:	10.32614/CRAN.package.EnvRtype (may not be active yet)
Author:	Germano Costa-Neto [aut, cre], Fernanda Pontes [aut]
Maintainer:	Germano Costa-Neto <germano.cneto at gmail.com>
BugReports:	https://github.com/gcostaneto/EnvRtype/issues
License:	GPL-3
URL:	https://github.com/gcostaneto/EnvRtype, https://gcostaneto.github.io/EnvRtype/
NeedsCompilation:	no
Citation:	EnvRtype citation info
Materials:	README
CRAN checks:	EnvRtype results

Documentation:

Reference manual:	EnvRtype.html , EnvRtype.pdf
Vignettes:	EnvRtype: Envirotyping for Quantitative Genetics and Plant Breeding (source, R code)

Downloads:

Package source:	EnvRtype_0.1.3.tar.gz
Windows binaries:	r-devel: not available, r-release: not available, r-oldrel: not available
macOS binaries:	r-release (arm64): EnvRtype_0.1.3.tgz, r-oldrel (arm64): EnvRtype_0.1.3.tgz, r-release (x86_64): EnvRtype_0.1.3.tgz, r-oldrel (x86_64): EnvRtype_0.1.3.tgz

Linking:

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