Package index

Bayesian AMMI

Priors, the Gibbs sampler of Crossa et al. (2011) and the biplot with HPD regions.

bam_priors() print(<bam_priors>)

Prior distributions of the Bayesian AMMI model

bayes_ammi()

Bayesian estimation of the AMMI and GGE models

biplots()

Biplots with highest posterior density regions

Decisions for breeders

Predictions, winners, probabilities of superior performance and stability, ranks and stability measures.

bam_predict()

Predictions of every genotype-environment cell

bam_winners()

Which genotype wins where: posterior probabilities

bam_superiority()

Probabilities of superior performance and stability

bam_ranks()

Posterior distribution of the ranks of the genotypes

bam_stability()

Bayesian stability of the genotypes

Bayesian stability analysis

Finlay-Wilkinson, Eberhart-Russell and Shukla models; posterior distributions of stability indices.

bayes_stability()

Bayesian stability analysis: Finlay-Wilkinson, Eberhart-Russell and Shukla models

bam_stab_priors()

Priors of the Bayesian stability models

bam_indices()

Posterior distributions of classical stability indices

bam_ammi_indices()

Posterior distributions of AMMI-based stability indices

Model choice

DIC and WAIC, posterior predictive checks and draws for posterior, bayesplot and coda.

bam_compare()

Compare Bayesian AMMI and GGE models

bam_ppc()

Posterior predictive checks

as_draws_df(<bam_bayes_ammi>) as_draws(<bam_bayes_ammi>) as.mcmc.list(<bam_bayes_ammi>)

The draws of a fit for posterior, bayesplot and coda

Application

bam_app() bam_app_object()

Bayesian AMMI and GGE analysis in a web browser

Interpretation and references

bam_interpret() print(<bam_interpretation>) format(<bam_interpretation>)

Interpretation of a Bayesian AMMI analysis

bam_cite()

References of a result or of the package

Tables and least-squares AMMI

Cell means and variances, main and interaction effects, least-squares AMMI and the mixed model.

ge_mean()

Genotype-by-environment means

ge_var()

Genotype-by-environment variances

g_eff()

Genotype effects

e_eff()

Environment effects

ge_eff()

Genotype-by-environment interaction effects

ge_ammi()

Least-squares AMMI model

ge_model()

Linear mixed model of a multi-environment trial

Matrices

matrix_k()

Orthonormal contrast matrix

orthnorm()

Gram-Schmidt orthonormalisation

Data

Maiz

Maize multi-environment trial

Results and utilities

print(<bam_result>) summary(<bam_result>) print(<summary.bam_result>) format(<bam_result>) as.data.table(<bam_result>) as.data.frame(<bam_result>) plot(<bam_result>)

Methods for bayesammi results

bam_theme()

ggplot2 theme of bayesammi

bam_save()

Save a figure (vector PDF by default)

bam_notation()

Notation of bayesammi

bam_reference()

Published values used by the tests and vignettes

bayesammi bayesammi-package

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