baystability 1.0.0

Changes visible to users

• bayes_ammi() keeps its arguments (.data, .y, .gen, .env, .rep, .nIter) and the components of its result (mu1, tau1, tao1, delta1, lambdas1, alphas1, gammas1, Mean_Alphas, Mean_Gammas), and gains:
  • .prior_data: the earlier trial used as prior (Perez-Elizalde et al. 2012, Section 2.2), and .n0, its weight (default its replicates); without it the priors are vague (bys_priors());
  • .model = "SREG" (sites regression, GGE) besides "AMMI";
  • .k (number of terms; default all, as before), .burnin, .thin, .chains, .seed, .level, .align, .waic;
  • the components summary (posterior mean, SD, Monte Carlo error, HPD interval, effective sample size, potential scale reduction factor), scores, draws (coda::mcmc.list), diagnostics, ls, prior, fit (DIC, WAIC) and settings;
  • print(), summary() and plot() methods.
• New names that follow the package stability and its Bayesian version bayesstability: the prefix bayes_ for Bayesian analyses and bys_ for tools. The least-squares tables ge_mean(), ge_var(), g_eff(), e_eff(), ge_eff(), ge_model() and ge_ammi() are bys_ls_means(), bys_ls_var(), bys_ls_gen_effects(), bys_ls_env_effects(), bys_ls_ge_effects(), bys_ls_model() and bys_ls_ammi(); matrix_k() and orthnorm() are bys_contrasts() and bys_orthonormal(). The old names still work, with a deprecation warning, and will be removed in a later version (?"bys-deprecated"). Every analysis is an S3 generic with a .default method.
• New bayes_gge() (the SREG model, bayes_ammi(.model = "SREG")), bayes_ammi_biplot() and bayes_gge_biplot() (HPD regions), bys_priors(), bys_compare(), bys_interpret(), bys_cite(); every printed result ends with the sources of its method.
• New bys_app(), a built-in ‘shiny’ application: data and earlier trial, model, biplot, model choice and references, each page with an interpretation, tables, plots and the R code that repeats the fit.
• The sampler is compiled (Rcpp, RcppArmadillo); a plain R version gives the same draws from the same seed.
• Six vignettes in HTML and PDF, among them a reproduction of the published analysis.

Corrections

• bayes_ammi() read the earlier trial from objects in the user’s workspace (n0, mu0, tau0, tao0, delta0, lambdas0, alphas0, gammas0, ge_means0) and stopped with “object ‘n0’ not found” without them.
• The singular values were computed once before the loop and never sampled.
• tau1 held a precision drawn from a residual matrix computed once before the loop and never updated; it now holds the draws of the error variance sigma^2.
• The scores were drawn without their constraints and orthogonalised afterwards; they are now drawn from their von Mises-Fisher conditionals on the constrained spheres.
• With all terms fitted (11 terms for 12 genotypes) a column-wise sampler cannot move the genotype scores: each column is fixed by the others up to its sign. Exact moves of every pair of columns (von Mises draws of a rotation angle) now let them mix.
• The columns of delta1 were named after the genotypes.
• The help page of cultivo2009 described another data set.

Reproduction of Perez-Elizalde et al. (2012)

• The 38 linear effects of Table B.1 agree to within 0.03 posterior standard deviations, their standard deviations to within 2%, and sigma of Table 2 to within 0.2 standard deviations. The singular values of Table 2 are not reproduced, and neither scores that cannot move nor a zero prior mean explains them: the published values disagree with eq. 2.15 of the paper (see the vignette on the published analysis).

Internal

• The tidyverse, rlang, rstiefel and lme4 (now suggested, only for bys_ls_model()) are no longer needed.

baystability 0.2.0

• Updated the DESCRIPTION file to meet the requirements of CRAN.

baystability 0.1.0

• First version of baystability.