Changelog

Source: NEWS.md

bifrost 0.1.3

CRAN release: 2026-01-21

• Addressed CRAN reviewer feedback following review of 0.1.2:
  • Added explicit return-value documentation (@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:
  • Updated the jaw-shape vignette with additional static figures (evolutionary correlation heatmap, IC-trajectory plot, and branch-rate visualization) and improved plotting annotations.

bifrost 0.1.2

• 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:
  • Added 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:
  • Added a 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).
  • Print output includes a citation hint (citation("bifrost")); package citation metadata updated in inst/CITATION.
• IC weights / no-shift behavior:
  • Standardized 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.
  • When no shifts are detected, model_no_uncertainty now returns the baseline mvgls model (instead of NULL).
• Documentation / vignettes / tests:
  • Updated jaw-shape vignette chunk printing of ic_weights to avoid RStudio paged/Unicode rendering issues.
  • Expanded and stabilized unit tests and CI configuration (including Config/testthat/parallel: false).

bifrost 0.1.1

• Addressed CRAN reviewer feedback following review of 0.1.0:
  • Replaced all uses of shorthand T/F with TRUE/FALSE.
  • Ensured all informational output is suppressible via message()/warning() and controlled by a verbose flag.
  • Redirected all on-disk output generated during model fitting to tempdir() to comply with CRAN file system policies and avoid writing to the user’s working directory.
  • Ensured graphical parameters and global options are restored using immediate on.exit() calls.
  • Refined parallelization behavior to be CRAN-safe and cross-platform:
    • Parallel candidate evaluation uses future with multicore on Unix outside RStudio and multisession otherwise.
    • BLAS/OpenMP threads are capped to one per worker during parallel execution to avoid CPU oversubscription.
    • Sequential execution remains the default when num_cores = 1.
  • Improved documentation clarity around parallel execution, verbosity, and model fit history storage.

bifrost 0.1.0

• Initial CRAN submission.