R Observatory: Metrics for bifrost version 0.1.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

bifrost

0.1.4

Branch-Level Inference Framework for Recognizing Optimal Shifts in Traits

0packages depend

3.5Kdownloads / year

99.8%test coverage

13/13checks pass

Overview

About

Maintained by Jacob S. BervFirst published 2026-01-212 releasesCRAN page ↗GitHub ↗

Methods for detecting and visualizing cladogenic shifts in multivariate trait data on phylogenies. Implements penalized-likelihood multivariate generalized least squares models, enabling analyses of high-dimensional trait datasets and large trees via searchOptimalConfiguration(). Includes a greedy step-wise shift-search algorithm following 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 GLS approaches described in Clavel et al. (2019) doi:10.1093/sysbio/syy045 and implemented in the mvgls() function from the 'mvMORPH' package. Documentation and vignettes are available at https://jakeberv.com/bifrost/, including worked examples for the jaw-shape dataset.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("bifrost", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("jakeberv/bifrost")

Development version from jakeberv/bifrost. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-bifrost

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-bifrost

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-bifrost

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 3.6 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 1.57

99.8%

Coverage · measured lines

100%

Documentation · exports

9

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,005 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

3.5K

CRAN downloads in the past year

Rank #7,166 · ~9/day · ~289/mo

Releases R versions

Daily download trend is not available in this view yet.

26330 days

1.2K90 days

3.5K1 year

Compare downloads with other packages →

Also on85 r2u43 autocran

Repository

GitHub ↗ jakeberv/bifrost

4Stars

1Forks

0Open issues

1Open PRs

2Releases

703Commits

6Contributors

brownian-motionhigh-dimensionalmultivariatemultivariate-regressionphylogenetic-analysisphylogenetic-comparative-methodsphylogenetics

License GPL-2.0 · 703 commits · Last activity 2026-08-10 · +33.3% stars, 30d

Stars over time

2025-09-12 · 12026-08-05 · 4

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/jakeberv/bifrost on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

26 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1

Imports (9)

ape future future.apply phytoolsgrDevicesstatsmvMORPH viridis txtplot

LinkingTo (0)

none

Suggests (21)

HDInterval RColorBrewerbootclassInt evd fitdistrplus knitr palaeoverseparallelpatchwork pbmcapply phylolm plotly readxl rmarkdown scales scatterplot3d testthat (>= 3.0.0)univariateML spelling htmltools

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (10)

Maintainer (1)

Jacob S. Berv

Author, Maintainer, Copyright holder, Funder

Authors (10)

Jacob S. Berv

Author, Maintainer, Copyright holder, Funder

Author, Funder

Author

Author, Funder

Author

Rafael A. Rivero-Vega

Author

Author, Funder

Author

Author

Author, Funder

Copyright holders (1)

Jacob S. Berv

Author, Maintainer, Copyright holder, Funder

Funders (5)

Jacob S. Berv

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Author, Funder

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Listed in earlier versions (7)

Berv