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: 2026-10-22 19:27:15 UTC; root
Author: Germano Costa-Neto [aut, cre], Fernanda Pontes [aut]
Maintainer: Germano Costa-Neto <germano.cneto@gmail.com>
Repository: https://cran.r-universe.dev
Date/Publication: 2026-10-22 19:19:55 UTC
RemoteUrl: https://github.com/cran/EnvRtype
RemoteRef: HEAD
RemoteSha: 72678f76658ce761e8769786f4aa75b934d2a247