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Development Status

Source: vignettes/articles/development-status.Rmd
development-status.Rmd

bifrost is available as a stable CRAN package and as a GitHub development version. The development version is where completed features and documentation are assembled and tested before the next CRAN release.

At a glance

Distribution Version Installation Best for
CRAN 0.1.4 install.packages("bifrost") Reproducible analyses using the current public release
GitHub 0.1.4.9000 remotes::install_github("jakeberv/bifrost") Evaluating unreleased features and following the latest documentation

The GitHub development version requires R 4.2 or newer. Because it is unreleased, its interfaces and defaults may still change before the next CRAN release.

What the development version adds

The development version currently extends the CRAN release in several related areas:

  • Search inspection and diagnostics. icTrajectory() and its plot() method expose search histories, while richer stored candidate records retain accepted, rejected, and errored fits.
  • Branch-rate summaries. rateMap() and its supporting view, control, flagging, print, and plot methods summarize branch-rate patterns across completed searches.
  • Lineage rates and shift distributions. lineage_rates() and related tools summarize inherited lineage rates, shift timing and waiting times, rate distributions, and shift magnitudes.
  • Regime covariance and integration. Post-hoc tools estimate and summarize regime-specific covariance structure, diagnose modules and correlation-space variation, compare integration relationships, and support pGLS analyses.
  • Simulation and tuning. Reproducible null and shifted simulations support strict and fuzzy recovery assessment, fixed-IC tuning grids, null safeguards, and tuning selection by fuzzy balanced accuracy.
  • Formula-based searches. Searches accept formula objects or character strings, response-only numeric data frames for intercept-only analyses, and named-column formulas such as cbind(y1, y2) ~ size + grp.
  • Expanded worked documentation. The website includes rate-mapping, five-part avian skeleton, and two-part simulation and calibration workflows, together with downloadable PDFs and executable Colab notebooks.

The detailed, itemized record of these changes is maintained in NEWS.

Current caveats

Some repository workflows and their methodological guidance remain under active development, especially pGLS-style uses of bifrost with hidden branch-specific rate variation. The simulation framework continues to use the original manuscript generator by default; the empirically calibrated full-covariance generator is available only when explicitly selected.

Repository automation and generated site assets, including the CRAN downloads tracker, support package development and documentation but are not part of the core CRAN API.

Website articles and the package tarball

The source files for the website articles are maintained in this repository but excluded from the CRAN source-package tarball. This keeps manuscript-scale demonstrations, including the five-part avian skeleton workflow, out of routine package installation and CRAN checks while preserving the complete rendered documentation on the pkgdown website.

For stable release information, use the CRAN package page. For unreleased changes, consult NEWS and the GitHub repository.