Changelog

Source: NEWS.md

bifrost 0.2.0

• 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.

  • When IC = "BIC" and method is omitted, searches now use method = "LL"; an explicitly supplied method still takes precedence. GIC searches continue to use the mvgls() fitting-method default when method is omitted.

  • Added icTrajectory() and its plot() method for inspecting stored search histories.

  • Removed the superseded plot_ic_acceptance_matrix() wrapper. For a bifrost_search or compatible search-result list, migrate to plot(icTrajectory(x)).

  • Legacy callers that passed a raw two-column matrix_data object must wrap it as a search-like list before plotting:

    legacy <- list(
      baseline_ic = baseline_ic,
      IC_used = "GIC",
      model_fit_history = list(ic_acceptance_matrix = matrix_data)
    )
    plot(icTrajectory(legacy))

    The former plotting arguments map as follows: plot_title to main, plot_rate_of_improvement to show_delta, rate_limits to delta_limits, and baseline_ic to the icTrajectory() call.

  • Search results now include candidate_nodes, and user_input records the resolved progress setting. Stored model-fit histories retain proposal step, node, regime, IC, status, and explicit accepted, rejected, and errored records.

  • Search input validation now requires a positive integer min_descendant_tips and rejects simultaneous uncertaintyweights = TRUE and uncertaintyweights_par = TRUE before fitting begins.

• Branch-rate summaries:
  • Added the rateMap() workflow and supporting view, control, flagging, print, and plot methods for summarizing branch-rate patterns across completed searches.
  • Category legends represent uneven rate breaks proportionally, with strengthened validation of category-color counts.
  • generateViridisColorScale() now explicitly requires numeric input, and its documentation clarifies that colors encode sorted rank rather than numeric magnitude or distance.
• Lineage-rate and shift-distribution analyses:
  • Added lineage_rates() for tip-level summaries of inherited rate histories and associated branch and shift diagnostics.
  • Added tools for extracting shift nodes, transitions, waiting times, and magnitude groups; fitting waiting-time and lineage-rate distributions; bootstrapping rate-distribution summaries; and comparing shift magnitudes.
• Regime covariance and integration analyses:
  • Added fit_regime_covariances(), fit_regime_covariance_runs(), and their summary helpers for post-hoc covariance estimation across fitted regimes and search runs.
  • Added module diagnostics, correlation-matrix PCA, integration-relationship summaries, and regime_integration_pgls() for examining regime-specific covariance structure and downstream relationships.
• Simulation studies and tuning:
  • Added reproducible simulation templates, null and shifted dataset generators, false-positive and shift-recovery studies, recovery evaluation, and fixed-IC tuning grids.
  • Added empirical null, proportional-shift, and integration-rate robustness workflows centered on fitted residual covariance, with simulation_generator = c("original", "empirical") for explicit generator selection.
  • The new simulation generators default to "original" for exact reproduction of the published operations; the full-covariance Wishart/spectral generator remains available explicitly as simulation_generator = "empirical".
  • selectTunedSearchParameters() filters settings using null false-positive and evaluability safeguards, then ranks feasible settings by fuzzy balanced accuracy by default.
  • Reduced multisession transfer size by using compact namespace-level workers and by avoiding a complete calibration template inside every replicate’s call record.
• Documentation / vignettes:
  • All vignettes are now website-only. The source package and installed package no longer include vignettes/ or built inst/doc articles; the complete worked documentation remains available on the package website.
  • Removed all former system.file("extdata", ...) empirical paths intentionally. Use bifrost_example_file() instead for the eight named artifacts: jaw-tree, jaw-landmarks, passerine-tree, passerine-traits, passerine-search, passerine-sensitivity, passerine-posthoc, and simulation-preview-tables.
  • Reduced installed package size by no longer distributing repository/site empirical payloads through CRAN. Normal package installation, attachment, examples, and checks remain network-free.
  • Documented that the first uncached bifrost_example_file() request uses the checksum-verified artifact currently tracked on GitHub main; later calls reuse the verified cache unless refresh = TRUE requests a new check.
  • Added small, deterministic, runnable help examples for regime-integration, simulation, rate-map, lineage-rate, and tuning workflows; longer model-fitting examples now use bounded \donttest{} blocks that are exercised in CI.
  • Added two rate-map jaw-shape workflows and refreshed the existing jaw-shape vignette.
  • Added a five-part avian skeleton case study covering search inspection, lineage rates, shift distributions, magnitude comparisons, and post-hoc covariance and integration analyses.
  • Added a two-part empirically calibrated simulation guide covering performance assessment, search tuning, and empirical application.
  • Added downloadable vignette PDFs and executable Colab notebooks to the website articles.
  • Updated Berv et al. (2026) citation metadata and avian skeleton references for the published Nature Ecology & Evolution article DOI.
• Maintenance:
  • Increased the minimum supported R version from 4.1 to 4.2.
  • Added minimum versions future (>= 1.49.0) and phytools (>= 2.0-3), corrected runtime and optional dependency declarations, moved website-only packages to Config/Needs/website, and removed VignetteBuilder because vignettes are not built into the package.
  • Added plotrix as a direct dependency for rate-map arc and fan geometry.
  • Refactored searchOptimalConfiguration() into dedicated internal helpers for candidate evaluation, greedy search orchestration, history bookkeeping, and parallel result handling; the public entry point remains searchOptimalConfiguration(), and existing positional arguments remain compatible.
  • Parallel search and simulation paths preserve the caller’s Future plan and reproducible RNG state while avoiding nested worker oversubscription.
  • Hardened lineage-rate, regime-integration, simulation, and tuning workflows around malformed inputs, failed fits, reproducible parallel execution, and infeasible selections.
  • Added a CRAN downloads chart to 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 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:
  • 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.