baystability: Bayesian Stability Analysis of Genotype by Environment Interaction (GEI)

Performs the general Bayesian estimation method of linear-bilinear models for genotype x environment interaction of Perez-Elizalde, Jarquin and Crossa (2012) <doi:10.1007/s13253-011-0063-9>: the additive main effects and multiplicative interaction (AMMI) model and the sites regression (SREG, GGE) model, with the data of an earlier trial as the prior (conjugate normal and von Mises-Fisher priors weighted by its replicates) or with vague priors; a compiled Gibbs sampler; posterior summaries with highest posterior density intervals; convergence diagnostics; biplots with highest posterior density regions; DIC and WAIC; a plain-language interpretation of every result; and a built-in 'shiny' application. For Bayesian stability analysis in general (regression and variance models, stability indices, probabilities of superior performance), see the package 'bayesstability'.

Version: 1.0.0
Depends: R (≥ 4.2)
Imports: coda, collapse, data.table, ggplot2, ggrepel, grDevices, MASS, Rcpp, scales, stats, utils
LinkingTo: Rcpp, RcppArmadillo
Suggests: bayesplot, bslib, DT, flextable, knitr, lme4, loo, magick, officer, pkgload, posterior, quarto, ragg, R.rsp, shiny, svglite, testthat (≥ 3.0.0), withr
Published: 2026-11-10
DOI: 10.32614/CRAN.package.baystability
Author: Muhammad Yaseen ORCID iD [aut, cre], Diego Jarquin [aut, ctb], Sergio Perez-Elizalde [aut, ctb], Juan Burgueno [aut, ctb], Jose Crossa [aut, ctb]
Maintainer: Muhammad Yaseen <myaseen208 at gmail.com>
BugReports: https://github.com/myaseen208/baystability/issues
License: GPL-2
URL: https://myaseen208.com/baystability/, https://github.com/myaseen208/baystability
NeedsCompilation: yes
Language: en-US
Citation: baystability citation info
Materials: README, NEWS
CRAN checks: baystability results

Documentation:

Reference manual: baystability.html , baystability.pdf
Vignettes: Getting started with baystability (source, R code)
Model, priors from an earlier trial and the Gibbs sampler (source, R code)
Reproducing Perez-Elizalde et al. (2012) (source, R code)
The SREG (GGE) model, the weight of the earlier trial and the number of terms (source, R code)
Validation and corrections (source, R code)
The built-in application (source, R code)
Getting started with baystability (PDF) (source)
Model, priors from an earlier trial and the Gibbs sampler (PDF) (source)
Reproducing Perez-Elizalde et al. (2012) (PDF) (source)
The SREG (GGE) model, the weight of the earlier trial and the number of terms (PDF) (source)
Validation and corrections (PDF) (source)
The built-in application (PDF) (source)

Downloads:

Package source: baystability_1.0.0.tar.gz
Windows binaries: r-devel: baystability_0.2.0.zip, r-release: baystability_0.2.0.zip, r-oldrel: baystability_0.2.0.zip
macOS binaries: r-release (arm64): baystability_1.0.0.tgz, r-oldrel (arm64): baystability_1.0.0.tgz, r-release (x86_64): baystability_0.2.0.tgz, r-oldrel (x86_64): baystability_0.2.0.tgz
Old sources: baystability archive

Linking:

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