bifrost: Branch-Level Inference Framework for Recognizing Optimal Shifts in Traits
Methods for detecting, visualizing, and evaluating cladogenic shifts in multivariate trait data on phylogenies. Implements penalized-likelihood multivariate generalized least squares models and a greedy step-wise shift search for high-dimensional trait datasets and large trees via searchOptimalConfiguration(). Provides tools for inspecting search trajectories, summarizing branch and lineage rates, analyzing shift timing and magnitudes, estimating post-hoc regime covariance and integration, and running simulation-based calibration and tuning. The search follows approaches developed in Smith et al. (2023) <doi:10.1111/nph.19099> and Berv et al. (2024) <doi:10.1126/sciadv.adp0114>. Methods build on multivariate generalized least squares approaches described in Clavel et al. (2019) <doi:10.1093/sysbio/syy045> and implemented in the mvgls() function from the 'mvMORPH' package. Documentation and worked examples are available at <https://jakeberv.com/bifrost/>.
| Version: | 0.2.0 |
| Depends: | R (≥ 4.2) |
| Imports: | ape, cli (≥ 3.6.0), digest, future (≥ 1.49.0), future.apply, parallel, progressr, phytools (≥ 2.0-3), plotrix, RRphylo, grDevices, graphics, grid, jsonlite, stats, mvMORPH, viridis, txtplot |
| Suggests: | ComplexHeatmap, RColorBrewer, circlize, evd, phylolm, rmarkdown, testthat (≥ 3.0.0), univariateML, withr, spelling |
| Published: | 2026-09-28 |
| DOI: | 10.32614/CRAN.package.bifrost |
| Author: | Jacob S. Berv 
[aut, cre, cph, fnd],
Nathan Fox [aut],
Matt J. Thorstensen
[aut],
Henry Lloyd-Laney
[aut],
Emily M. Troyer
[aut],
Rafael A. Rivero-Vega
[aut],
Stephen A. Smith
[aut, fnd],
Matt Friedman
[aut, fnd],
David F. Fouhey
[aut, fnd],
Brian C. Weeks
[aut, fnd] |
| Maintainer: | Jacob S. Berv <jacob.berv at gmail.com> |
| BugReports: | https://github.com/jakeberv/bifrost/issues |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| URL: | https://jakeberv.com/bifrost/, https://github.com/jakeberv/bifrost |
| NeedsCompilation: | no |
| Language: | en-US |
| Citation: | bifrost citation info |
| Materials: | README, NEWS |
| CRAN checks: | bifrost results |
Documentation:
| Reference manual: | bifrost.html , bifrost.pdf |
Downloads:
| Package source: | bifrost_0.2.0.tar.gz |
| Windows binaries: | r-devel: bifrost_0.1.4.zip, r-release: bifrost_0.1.4.zip, r-oldrel: bifrost_0.1.4.zip |
| macOS binaries: | r-release (arm64): bifrost_0.2.0.tgz, r-oldrel (arm64): bifrost_0.2.0.tgz, r-release (x86_64): bifrost_0.2.0.tgz, r-oldrel (x86_64): bifrost_0.2.0.tgz |
| Old sources: | bifrost archive |
Linking:
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