Documentation / vignettes:
searchOptimalConfiguration() documentation around acceptable tree inputs, recommended mvgls() methods ("H&L" vs "LL"), and the role of error = TRUE.Citation / metadata:
citation("bifrost") for the live bioRxiv preprint and the in-press application paper.mvMORPH citations to the package citation metadata.Maintenance:
Addressed CRAN reviewer feedback following review of 0.1.2:
@return / \value{}) for the exported
print.bifrost_search() method, clarifying that the function returns the input object
invisibly and is called for its printing side effects.Plotting:
plot_ic_acceptance_matrix() gains an optional baseline_ic argument to plot and compute
diff(IC) relative to the true no-shift baseline (useful when matrix_data begins at the
first evaluated shift model rather than the true baseline).Documentation / vignettes:
Addressed CRAN reviewer feedback following review of 0.1.1:
plot_ic_acceptance_matrix() now saves and restores the user’s graphical parameters via an immediate on.exit() (prevents leaking par() settings across calls).Plotting:
rate_limits argument to plot_ic_acceptance_matrix() (default c(-400, 150)) to control the secondary y-axis limits for the rate-of-improvement overlay (validated numeric length-2, finite).Search results output:
bifrost_search S3 class and print.bifrost_search() method for searchOptimalConfiguration() results (compact console summary; optional ASCII IC-history plot via txtplot when store_model_fit_history = TRUE; prints IC weights when present).citation("bifrost")); package citation metadata updated in inst/CITATION.IC weights / no-shift behavior:
ic_weights output across serial and parallel uncertainty-weight modes; always returns a data.frame with consistent columns, and returns an empty data.frame with the same schema when no shifts are detected.model_no_uncertainty now returns the baseline mvgls model (instead of NULL).Documentation / vignettes / tests:
ic_weights to avoid RStudio paged/Unicode rendering issues.Config/testthat/parallel: false).T/F with TRUE/FALSE.message()/warning() and controlled by a verbose flag.tempdir() to comply with CRAN file system policies and avoid writing to the user’s working directory.on.exit() calls.future with multicore on Unix outside RStudio and multisession otherwise.num_cores = 1.