NEWS.md

In bifrost: Branch-Level Inference Framework for Recognizing Optimal Shifts in Traits

bifrost 0.1.4

• Documentation / vignettes:
• Added a new "Quick Start with bifrost" vignette with a minimal end-to-end simulated example.
• Clarified searchOptimalConfiguration() documentation around acceptable tree inputs, recommended mvgls() methods ("H&L" vs "LL"), and the role of error = TRUE.
• Reworked the README to foreground installation, documentation, and citation guidance.

• Added two pkgdown-only background articles on multivariate Brownian motion / shifts and on whole-tree PCA / model-selection issues.

• Citation / metadata:

• Updated package authorship metadata to reflect the current author list.
• Updated citation("bifrost") for the live bioRxiv preprint and the in-press application paper.
• Added the foundational mvMORPH citations to the package citation metadata.

• Added a formatted citation section and dynamic bioRxiv badge to the README.

• Maintenance:

• Disabled a deprecated vignette-preview step in GitHub Actions CI.

bifrost 0.1.3

• 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.

bifrost documentation built on April 17, 2026, 9:07 a.m.