R Observatory: Metrics for corHMM version 2.8

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

corHMM

2.8

Hidden Markov Models of Character Evolution

3packages depend

18Kdownloads / year

19.7%test coverage

13/13checks pass

Overview

About

Maintained by Jeremy BeaulieuFirst published 2013-05-1323 releasesCRAN page ↗

Fits hidden Markov models of discrete character evolution which allow different transition rate classes on different portions of a phylogeny. Beaulieu et al (2013) doi:10.1093/sysbio/syt034.

Install

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

install.packages("corHMM", 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-corhmm

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-corHMM

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-corHMM

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

Health

CRAN checks

13OK

Slowest check: 4.6 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.04

19.7%

Coverage · measured lines

100%

Documentation · exports

14

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
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-03-30
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 100%
Return-value docs: 91%
References docs: 83%

Downloads

18K

CRAN downloads in the past year

Rank #3,879 · ~49/day · ~1.5K/mo

Releases R versions

Daily download trend is not available in this view yet.

73130 days

2.3K90 days

18K1 year

Compare downloads with other packages →

Also on137 r2u17 autocran71 c2d4u

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Depends (3)

ape nloptr GenSA

Imports (11)

expm numDeriv corpcorMASSnnetphangornparallelviridis Rmpfr igraph phytools

LinkingTo (0)

none

Suggests (3)

testthat knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

0indirect

OUwie hisse DAISIEprep

Code & Tests

People & History

People (4)

Maintainer (1)

Jeremy Beaulieu

Author, Maintainer · added in 2.1

Authors (4)

Jeremy Beaulieu

Author, Maintainer · added in 2.1

James Boyko

Author · added in 2.1

Brian O'Meara

Author

Jeffrey Oliver

Author · added in 2.1

Listed in earlier versions (2)

Jeremy M. Beaulieu

no longer listed · 3.0.1 to 1.22

Jeffrey C. Oliver

no longer listed · 3.0.1 to 1.22

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
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
2.8Latest
2022-06-14 · current release · diff ↗
unarchivedReturned to CRAN
2022-06-14
archivedRemoved from CRAN
2022-06-11
check issues were not corrected in time
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
2.7
2021-05-14 · diff ↗
2.6
2021-01-06 · diff ↗
2.5
2020-11-24 · diff ↗
2.4
2020-10-01 · diff ↗
2.3
2020-08-05 · diff ↗
2.2
2020-07-09 · diff ↗
2.1
2020-07-08 · diff ↗

Show 25 earlier events

unarchivedReturned to CRAN
2020-07-08
archivedRemoved from CRAN
2020-06-15
check problems were not corrected in time
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
1.22
2017-07-20 · diff ↗
R
R 3.4.0 released · 2017-04-21
1.20
2016-09-27 · diff ↗
1.19
2016-06-09 · diff ↗
R
R 3.3.0 released · 2016-05-03
1.18
2016-01-07 · diff ↗
1.17
2015-10-30 · diff ↗
R
R 3.2.0 released · 2015-04-16
1.16
2015-04-08 · diff ↗
1.15
2014-09-18 · diff ↗
1.14
2014-07-11 · diff ↗
R
R 3.1.0 released · 2014-04-10
1.13
2014-02-20 · diff ↗
3.0.3
2014-02-17 · diff ↗
1.12
2013-09-24 · diff ↗
1.11
2013-09-23 · diff ↗
3.0.2
2013-09-22 · diff ↗
1.10
2013-05-13 · diff ↗
3.0.1
2013-04-30
R
R 3.0.0 released · 2013-04-03

Package metadata

First published: 2013-05-13
Total releases: 23 / 13 yrs
License: GPL (>= 2) OSI
Bundled data: 5.5 KB / 3 files
Download size: 473 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Phylogenetics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("corHMM")

Format

Beaulieu, J., Boyko, J., O'Meara, B., & Oliver, J. (2022). corHMM: Hidden Markov Models of Character Evolution (Version 2.8) [Computer software]. https://doi.org/10.32614/CRAN.package.corHMM

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 corHMM version 2.8 [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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