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 |