Package: EnvRtype
Type: Package
Title: Envirotyping for Quantitative Genetics and Plant Breeding
Version: 0.1.3
Authors@R: c(
    person(
      "Germano", "Costa-Neto",
      email = "germano.cneto@gmail.com",
      role = c("aut", "cre")
    ),
    person(
      "Fernanda", "Pontes",
      email = "ferpoontes@gmail.com",
      role = "aut"
    )
  )
Description: 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>.
License: GPL-3
URL: https://github.com/gcostaneto/EnvRtype,
        https://gcostaneto.github.io/EnvRtype/
BugReports: https://github.com/gcostaneto/EnvRtype/issues
Encoding: UTF-8
LazyData: true
Config/roxygen2/version: 8.1.0
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)
VignetteBuilder: knitr
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2026-10-14 18:51:47 UTC; qvt192
Author: Germano Costa-Neto [aut, cre],
  Fernanda Pontes [aut]
Maintainer: Germano Costa-Neto <germano.cneto@gmail.com>
Repository: CRAN
Date/Publication: 2026-10-22 16:50:13 UTC
Built: R 4.5.2; ; 2026-10-22 17:28:28 UTC; unix
