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Release Status

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

This page describes bifrost 0.2.0, its release status, and the relationship between the CRAN package and the fuller documentation maintained on GitHub.

At a glance

Distribution Version Installation Best for
CRAN 0.1.4 install.packages("bifrost") Current published release
GitHub 0.2.0 release candidate remotes::install_github("jakeberv/bifrost") Candidate source and the latest website documentation

The 0.2.0 release candidate requires R 4.2 or newer. Until CRAN accepts it, GitHub contains the candidate source while install.packages() installs the published 0.1.4 release.

What 0.2.0 adds

Version 0.2.0 extends 0.1.4 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. The former plot_ic_acceptance_matrix() wrapper has been removed; use plot(icTrajectory(x)) for a search object. Callers with a raw legacy IC matrix should follow the wrapping and argument-mapping example in NEWS.
  • 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.
  • BIC fitting default. When IC = "BIC" and method is omitted, the search uses method = "LL"; explicitly supplied methods still take precedence.
  • 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.
  • On-demand example data. bifrost_example_file() retrieves supported empirical case-study artifacts only when explicitly requested, verifies them against published checksums, and reuses a local cache. On the first uncached request it downloads and validates the manifest currently tracked on GitHub main, then verifies the selected artifact against its recorded checksum and byte size; refresh = TRUE checks main again. The artifacts are not distributed in the CRAN package.

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, example data, and the package tarball

The source files for the website articles and their empirical artifacts 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. Readers can explicitly request checksum-verified artifacts with bifrost_example_file(); later calls reuse the verified local cache. Package installation, attachment, and routine checks remain network-free.

For public-release information, use the CRAN package page. For the full 0.2.0 change record, consult NEWS and the GitHub repository.