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:
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