Package: baystability 1.0.0

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'.

Authors:Muhammad Yaseen [aut, cre], Diego Jarquin [aut, ctb], Sergio Perez-Elizalde [aut, ctb], Juan Burgueno [aut, ctb], Jose Crossa [aut, ctb]

baystability_1.0.0.tar.gz
baystability_1.0.0.zip(r-4.7-x86_64)baystability_1.0.0.zip(r-4.7-arm64)baystability_1.0.0.zip(r-4.6-x86_64)baystability_1.0.0.zip(r-4.6-arm64)baystability_1.0.0.zip(r-4.5-x86_64)
baystability_1.0.0.tgz(r-4.6-x86_64)baystability_1.0.0.tgz(r-4.6-arm64)baystability_1.0.0.tgz(r-4.5-x86_64)baystability_1.0.0.tgz(r-4.5-arm64)
baystability_1.0.0.tar.gz(r-4.7-arm64)baystability_1.0.0.tar.gz(r-4.7-x86_64)baystability_1.0.0.tar.gz(r-4.6-arm64)baystability_1.0.0.tar.gz(r-4.6-x86_64)
baystability_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
baystability/json (API)

# Install 'baystability' in R:
install.packages('baystability', repos = c('https://myaseen208.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/myaseen208/baystability/issues

Pkgdown/docs site:https://myaseen208.com

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:

On CRAN:

Conda:

quartoopenblascppopenmp

4.92 score 14 scripts 448 downloads 32 exports 25 dependencies

Last updated from:822f13ce52. Checks:13 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64NOTE162
linux-devel-x86_64NOTE196
source / vignettesOK324
linux-release-arm64NOTE198
linux-release-x86_64NOTE166
macos-release-arm64NOTE238
macos-release-x86_64NOTE418
macos-oldrel-arm64NOTE162
macos-oldrel-x86_64NOTE442
windows-devel-arm64NOTE302
windows-devel-x86_64NOTE256
windows-release-arm64NOTE345
windows-release-x86_64NOTE175
windows-oldrel-x86_64NOTE219
wasm-releaseOK116

Exports:bayes_ammibayes_ammi_biplotbayes_ggebayes_gge_biplotbys_appbys_app_objectbys_citebys_comparebys_contrastsbys_interpretbys_ls_ammibys_ls_env_effectsbys_ls_ge_effectsbys_ls_gen_effectsbys_ls_meansbys_ls_modelbys_ls_varbys_notationbys_orthonormalbys_priorsbys_referencebys_savebys_themee_effg_effge_ammige_effge_meange_modelge_varmatrix_korthnorm

Dependencies:clicodacollapsecpp11data.tablefarverggplot2ggrepelgluegtableisobandlabelinglatticelifecycleMASSR6RColorBrewerRcppRcppArmadillorlangS7scalesvctrsviridisLitewithr

Getting started with baystability
Abstract | The data | The least-squares AMMI fit of the second year | The Bayesian fit with the first year as prior | The biplot with HPD regions | Interpretation | Where to go next | References
Rendered frombaystability_01_getting_started.qmdusingquarto::html

Last update: 2026-11-07
Started: 2026-11-07

Getting started with baystability (PDF)
Abstract | The data | The least-squares AMMI fit of the second year | The Bayesian fit with the first year as prior | The biplot with HPD regions | Interpretation | Where to go next | References
Rendered frombaystability_01_getting_started-pdf.pdf.asisusingR.rsp::asis

Last update: 2026-11-07
Started: 2026-11-07

Model, priors from an earlier trial and the Gibbs sampler
Abstract | Models | Priors from an earlier trial | Conditional distributions | Drawing the score matrices | Signs and starting values | The sampler | References
Rendered frombaystability_02_theory.qmdusingquarto::html

Last update: 2026-11-07
Started: 2026-11-07

Model, priors from an earlier trial and the Gibbs sampler (PDF)
Abstract | Models | Priors from an earlier trial | Conditional distributions | Drawing the score matrices | Signs and starting values | The sampler | References
Rendered frombaystability_02_theory-pdf.pdf.asisusingR.rsp::asis

Last update: 2026-11-07
Started: 2026-11-07

Reproducing Perez-Elizalde et al. (2012)
Abstract | The fit | Table B.1: the linear effects | Why the posterior means are averages of the two years | Table 2: the residual standard deviation and the singular values | Table 2: the significant scores | Figure 4: the biplot | References
Rendered frombaystability_03_perez2012.qmdusingquarto::html

Last update: 2026-11-07
Started: 2026-11-07

Reproducing Perez-Elizalde et al. (2012) (PDF)
Abstract | The fit | Table B.1: the linear effects | Table 2: the residual standard deviation and the singular values | Table 2: the significant scores | Figure 4: the biplot | References
Rendered frombaystability_03_perez2012-pdf.pdf.asisusingR.rsp::asis

Last update: 2026-11-07
Started: 2026-11-07

The built-in application
Abstract | Starting the application | The pages | Reproducibility | Deploying | References
Rendered frombaystability_06_app.qmdusingquarto::html

Last update: 2026-11-07
Started: 2026-11-07

The built-in application (PDF)
Abstract | Starting the application | The pages | Reproducibility | Deploying | References
Rendered frombaystability_06_app-pdf.pdf.asisusingR.rsp::asis

Last update: 2026-11-07
Started: 2026-11-07

The SREG (GGE) model, the weight of the earlier trial and the number of terms
Abstract | The SREG model with the first year as prior | The weight of the earlier trial | How many terms? | References
Rendered frombaystability_04_sreg_terms.qmdusingquarto::html

Last update: 2026-11-07
Started: 2026-11-07

The SREG (GGE) model, the weight of the earlier trial and the number of terms (PDF)
Abstract | The SREG model with the first year as prior | The weight of the earlier trial | How many terms? | References
Rendered frombaystability_04_sreg_terms-pdf.pdf.asisusingR.rsp::asis

Last update: 2026-11-07
Started: 2026-11-07

Validation and corrections
Abstract | Corrections to version 0.2.0 | The compiled sampler and the R reference | The pair moves | Simulated data | The published analysis | References
Rendered frombaystability_05_validation.qmdusingquarto::html

Last update: 2026-11-07
Started: 2026-11-07

Validation and corrections (PDF)
Abstract | Corrections to version 0.2.0 | The compiled sampler and the R reference | The pair moves | Simulated data | The published analysis | References
Rendered frombaystability_05_validation-pdf.pdf.asisusingR.rsp::asis

Last update: 2026-11-07
Started: 2026-11-07

Readme and manuals

Help Manual

Help pageTopics
Bayesian estimation of linear-bilinear models: AMMI and SREG (GGE)bayes_ammi bayes_ammi.default
AMMI and GGE biplots with highest posterior density regionsbayes_ammi_biplot bayes_ammi_biplot.default bayes_gge_biplot bayes_gge_biplot.default
Bayesian GGE (sites regression) modelbayes_gge bayes_gge.default
Bayesian AMMI and SREG analysis in a web browserbys_app bys_app_object
References of a result or of the packagebys_cite bys_cite.default
Compare Bayesian AMMI and GGE modelsbys_compare bys_compare.default
Orthonormal contrast matrixbys_contrasts bys_contrasts.default
Interpretation of a Bayesian AMMI analysisbys_interpret bys_interpret.default format.bys_interpretation print.bys_interpretation
Least-squares AMMI modelbys_ls_ammi bys_ls_ammi.default
Environment effectsbys_ls_env_effects bys_ls_env_effects.default
Genotype-by-environment interaction effectsbys_ls_ge_effects bys_ls_ge_effects.default
Genotype effectsbys_ls_gen_effects bys_ls_gen_effects.default
Genotype-by-environment meansbys_ls_means bys_ls_means.default
Linear mixed model of a multi-environment trialbys_ls_model bys_ls_model.default
Genotype-by-environment variancesbys_ls_var bys_ls_var.default
Notation of baystabilitybys_notation
Gram-Schmidt orthonormalisationbys_orthonormal bys_orthonormal.default
Prior distributions of the Bayesian AMMI modelbys_priors print.bys_priors
Published values used by the tests and vignettesbys_reference
Save a figure (vector PDF by default)bys_save bys_save.default
ggplot2 theme of baystabilitybys_theme
The draws of a fit for posterior, bayesplot and codaas.mcmc.list.bys_bayes_ammi as_draws.bys_bayes_ammi as_draws_df.bys_bayes_ammi bys-draws
Methods for baystability resultsas.data.frame.bys_result as.data.table.bys_result bys-methods format.bys_result plot.bys_result print.bys_result print.summary.bys_result summary.bys_result
Maize trials of 2008 and 2009cultivo2008 cultivo2009