R Observatory: Metrics for bayou version 2.3.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

bayou

2.3.2

Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies

0packages depend

2.1Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Josef C. UyedaFirst published 2014-07-187 releasesCRAN page ↗

Fits and simulates multi-optima Ornstein-Uhlenbeck models to phylogenetic comparative data using Bayesian reversible-jump methods. See Uyeda and Harmon (2014) DOI:10.1093/sysbio/syu057.

Install

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

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

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

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-bayou

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-bayou

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-bayou

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

Health

CRAN checks

13OK

Slowest check: 4.4 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

15

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
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 80%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.1K

CRAN downloads in the past year

Rank #11,141 · ~6/day · ~173/mo

Releases R versions

Daily download trend is not available in this view yet.

26430 days

87990 days

2.1K1 year

Compare downloads with other packages →

Also on417 r2u57 autocran81 c2d4u

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Depends (5)

R >= 2.15.0ape coda geiger phytools

Imports (11)

assertthat denstrip fitdistrplus foreachgraphicsgrDevicesMASSMatrixmnormt Rcppstats

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (2)

doParallel testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Josef C. Uyeda

Author, Maintainer

Authors (1)

Josef C. Uyeda

Author, Maintainer

Contributors (3)

Jon Eastman

Contributor

Abhishek Hari

Contributor · added in 2.3.1

Luke Harmon

Contributor

Package Timeline

7 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
2.3.2Latest
2026-02-13 · current release · diff ↗
unarchivedReturned to CRAN
2026-02-13
archivedRemoved from CRAN
2025-06-30
issues were not corrected in time
2.3.1
2025-06-10 · diff ↗
unarchivedReturned to CRAN
2025-06-10
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
archivedRemoved from CRAN
2020-02-24
check problems were not corrected in time Simple fix needed to issues reported by LTO
R
R 3.6.0 released · 2019-04-26
2.1.1
2018-10-09 · diff ↗
2.1
2018-06-07 · diff ↗

Show 8 earlier events

R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
1.1.0
2015-10-25 · diff ↗
R
R 3.2.0 released · 2015-04-16
1.0.1
2014-07-31 · diff ↗
1.0
2014-07-18
R
R 3.1.0 released · 2014-04-10

Package metadata

First published: 2014-07-18
Total releases: 7 / 12 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 2.15.0
Download size: 93 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("bayou")

Format

Uyeda, J. C., Eastman, J., Hari, A., & Harmon, L. (2026). bayou: Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies (Version 2.3.2) [Computer software]. https://doi.org/10.32614/CRAN.package.bayou

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for bayou version 2.3.2 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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