bayesammi: Bayesian Estimation of the Additive Main Effects and Multiplicative Interaction Model

Bayesian estimation of the additive main effects and multiplicative interaction (AMMI) model of multi-environment trials by the Gibbs sampler of Crossa, Perez-Elizalde, Jarquin, Cotes, Viele, Liu and Cornelius (2011) <doi:10.2135/cropsci2010.06.0343>: posterior distributions of the overall mean, genotype and environment effects, singular values, genotype and environment scores (von Mises-Fisher conditionals on the constrained spheres) and error variance; several chains with burn-in and thinning; posterior summaries with highest posterior density intervals; the convergence diagnostics of Raftery-Lewis, Heidelberger-Welch and Gelman-Rubin; the AMMI biplot with highest posterior density regions for inference on genotypes and environments; least-squares AMMI; and a plain-language interpretation of every result, computed from its numbers. Beyond the article: unbalanced trials with missing plots and cells (data augmentation), environment-specific error variances, the Bayesian GGE (sites regression) model of Perez-Elizalde, Jarquin and Crossa (2012) <doi:10.1007/s13253-011-0063-9>, probabilities of superior performance and stability (Dias et al. 2022 <doi:10.1007/s00122-022-04041-y>), posterior ranks, Bayesian stability measures, predictions and the winner of every environment, model choice by DIC and WAIC with posterior predictive checks, draws for the 'posterior', 'bayesplot' and 'coda' packages, a compiled sampler, and a built-in 'shiny' application. Bayesian stability analysis: the Finlay-Wilkinson, Eberhart-Russell and Shukla models by Gibbs sampling, and the posterior distributions of classical stability indices (Wricke, Shukla, Lin-Binns, Annicchiarico, Eskridge's safety-first) and of AMMI-based indices (ASV, SIPC, EV, Za, WAAS, WAASY). Every result prints the references of its method.

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.bayesammi
Author:	Muhammad Yaseen [aut, cre], Jose Crossa [aut, ctb], Sergio Perez-Elizalde [aut, ctb], Diego Jarquin [aut, ctb], Jose Miguel Cotes [aut, ctb], Kert Viele [aut, ctb], Genzhou Liu [aut, ctb], Paul L. Cornelius [aut, ctb], Julian Garcia Abadillo Velasco [aut, ctb]
Maintainer:	Muhammad Yaseen <myaseen208 at gmail.com>
BugReports:	https://github.com/myaseen208/bayesammi/issues
License:	GPL-2
URL:	https://myaseen208.com/bayesammi/, https://github.com/myaseen208/bayesammi
NeedsCompilation:	yes
Language:	en-US
Citation:	bayesammi citation info
Materials:	README, NEWS
In views:	Agriculture, Bayesian
CRAN checks:	bayesammi results

Documentation:

Reference manual:

bayesammi.html , bayesammi.pdf

Vignettes:

Getting started with bayesammi (source, R code) Model, priors and the Gibbs sampler (source, R code) Reproducing Crossa et al. (2011) (source, R code) Inference on the biplot (source, R code) Convergence of the chains (source, R code) Priors and the number of bilinear terms (source, R code) Unbalanced trials and environment-specific variances (source, R code) The Bayesian GGE (SREG) model (source, R code) Decision tools for breeders (source, R code) Bayesian stability models: Eberhart-Russell, Finlay-Wilkinson and Shukla (source, R code) Posterior distributions of stability indices (source, R code) The built-in application (source, R code) Validation and corrections (source, R code) Interpreting the results (source, R code) References of the methods (source, R code) Getting started with bayesammi (PDF) (source) Model, priors and the Gibbs sampler (PDF) (source) Reproducing Crossa et al. (2011) (PDF) (source) Inference on the biplot (PDF) (source) Convergence of the chains (PDF) (source) Priors and the number of bilinear terms (PDF) (source) Unbalanced trials and environment-specific variances (PDF) (source) The Bayesian GGE (SREG) model (PDF) (source) Decision tools for breeders (PDF) (source) Bayesian stability models: Eberhart-Russell, Finlay-Wilkinson and Shukla (PDF) (source) Posterior distributions of stability indices (PDF) (source) The built-in application (PDF) (source) Validation and corrections (PDF) (source) Interpreting the results (PDF) (source) References of the methods (PDF) (source)

Downloads:

Package source:	bayesammi_1.0.0.tar.gz
Windows binaries:	r-devel: bayesammi_0.3.0.zip, r-release: bayesammi_1.0.0.zip, r-oldrel: bayesammi_1.0.0.zip
macOS binaries:	r-release (arm64): bayesammi_1.0.0.tgz, r-oldrel (arm64): bayesammi_1.0.0.tgz, r-release (x86_64): bayesammi_0.3.0.tgz, r-oldrel (x86_64): bayesammi_0.3.0.tgz
Old sources:	bayesammi archive

Linking:

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