R Observatory: Metrics for bayou version 2.3.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

bayou

2.3.2Package record

Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies

0packages depend

3Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Josef C. UyedaCRAN 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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

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

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-04-22

Show 2 earlier changesHide 2 earlier changes

ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.3.2

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 51 (1 internal)includes a package overview page
Examples that run: 80%4 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 14%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

3K

CRAN downloads in the past year

Rank #7,662 · ~8/day · ~247/mo

Releases R versions

Daily download trend is not available in this view yet.

40630 days

1.2K90 days

3K1 year

Compare downloads with other packages →

Also on411 r2u48 autocran117 c2d4u

How downloads are counted

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing bayou adds 40 packages (22 with compiled code, 36 MB of source tarballs). Heaviest: ncbit 9.4 MB, igraph 4.8 MB, fitdistrplus 2.4 MB.

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.

How these are counted

Code & Tests

People & History

People (4)

Josef C. Uyeda

Author, Maintainer since 1.0 (2013)

Jon Eastman

Contributor

Abhishek Hari

Contributor · added in 2.3.1

Luke Harmon

Contributor

Releases (7)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2026-02-13
2.3.2Latest
record
2026-02-13 · current release · diff ↗
archivedRemoved from CRAN
2025-06-30
issues were not corrected in time
unarchivedReturned to CRAN
2025-06-10
2.3.1
record
2025-06-10 · diff ↗ ·
removed 4 exports
.discard.burnin, bayou.mcmc, simmap.W, steppingstone

added 1 export
simmapW
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
record
2018-10-09 · diff ↗ ·
removed 1 export
regime.plot
2.1
record
2018-06-07 · diff ↗ ·
added 7 exports
bayou.checkModel, bayou.makeMCMC, makeBayouModel, plotBranchHeatMap, plotOUtreesim, plotShiftSummaries, shiftSummaries

Show 8 earlier eventsHide 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
record
2015-10-25 · diff ↗ ·
added 2 exports
plotRegimes, regime.plot
R
R 3.2.0 released · 2015-04-16
1.0.1
record
2014-07-31 · diff ↗
1.0
record
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

Appears in task views

Phylogenetics

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 package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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