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Changelog

Source: NEWS.md

bifrost (development version)

  • Search progress:
    • searchOptimalConfiguration() now displays persistent, Future-compatible CLI progress for candidate scoring, greedy shift evaluation, and IC-weight re-estimation by default.
    • Reached stage rows remain stacked at the bottom while verbose = TRUE output streams above them.
    • Stage spinners now redraw continuously during long model fits while completion counts, percentages, and ETA advance only after a fit finishes.
    • Added progress = FALSE as an explicit opt-out independent of detailed verbose messages.
    • Captured expression-valued search inputs now print safely in print.bifrost_search() output.
  • Search inputs and diagnostics:
    • Formula-based searches now accept formula objects as well as character strings, numeric response-only data frames for intercept-only searches, and named-column data-frame formulas for pGLS-style workflows.
    • Added icTrajectory() and its plot() method for inspecting stored search histories; plot_ic_acceptance_matrix() remains available as a compatibility wrapper.
    • Stored model-fit histories now retain richer accepted, rejected, and errored candidate records.
  • Branch-rate summaries:
    • Added the rateMap() workflow and supporting view, control, flagging, print, and plot methods for summarizing branch-rate patterns across completed searches.
    • Improved category legends for uneven rate breaks and strengthened validation of category colors.
  • Documentation / vignettes:
    • Added two rate-map jaw-shape workflows and refreshed the existing jaw-shape vignette.
    • Added tooling and CI workflows for generated vignette PDFs and executable Colab notebooks.
  • Maintenance:
    • Added an automated CRAN downloads tracker and generated chart for the README and development website.

bifrost 0.1.4

CRAN release: 2026-04-17

  • 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

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:
  • 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.