R Observatory: Metrics for ratematrix version 1.2.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ratematrix

1.2.5

Bayesian Estimation of the Evolutionary Rate Matrix

1packages depend

3.4Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Daniel CaetanoFirst published 2018-06-108 releasesCRAN page ↗GitHub ↗

The Evolutionary Rate Matrix is a variance-covariance matrix which describes both the rates of trait evolution and the evolutionary correlation among multiple traits. This package has functions to estimate these parameters using Bayesian MCMC. It is possible to test if the pattern of evolutionary correlations among traits has changed between predictive regimes painted along the branches of the phylogenetic tree. Regimes can be created a priori or estimated as part of the MCMC under a joint estimation approach. The package has functions to run MCMC chains, plot results, evaluate convergence, and summarize posterior distributions.

Install

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

install.packages("ratematrix", 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("Caetanods/ratematrix")

Development version from Caetanods/ratematrix. 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-ratematrix

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-ratematrix

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-ratematrix

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

Health

CRAN checks

13OK

Slowest check: 7.0 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

10

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
OK2026-05-06
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 4 earlier snapshots

ERROR2026-05-05
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-30
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 100%
Return-value docs: 100%
References docs: 23%

Downloads

3.4K

CRAN downloads in the past year

Rank #11,750 · ~9/day · ~280/mo

Releases R versions

Daily download trend is not available in this view yet.

19330 days

84390 days

3.4K1 year

Compare downloads with other packages →

Also on450 r2u17 autocran55 c2d4u

Repository

GitHub ↗ caetanods/ratematrix

10Stars

4Forks

5Open issues

1Open PRs

0Releases

584Commits

2Contributors

584 commits · Last activity 2025-12-08

Stars over time

2025-02-06 · 92026-07-07 · 10

Repository practices

Upstream repositoryBeta

Checks run against github.com/caetanods/ratematrix on 2026-08-16.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (10)

ape geiger coda corpcorMASSphylolm readr mvMORPH Rcpp ellipse

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (4)

knitr rmarkdown phytools markdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

do3PCA

Code & Tests

People & History

People (2)

Maintainer (1)

Daniel Caetano

Author, Maintainer

Authors (2)

Daniel Caetano

Author, Maintainer

Luke Harmon

Author

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.2.5Latest
2025-12-06 · current release · diff ↗
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
1.2.4
2022-06-03 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.2.3
2021-02-24 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.2.2
2020-02-26 · diff ↗
unarchivedReturned to CRAN
2020-02-26
archivedRemoved from CRAN
2020-02-19
check problems were not corrected despite reminders
1.2.1
2019-05-15 · diff ↗
1.2
2019-05-06 · diff ↗
R
R 3.6.0 released · 2019-04-26

Show 3 earlier events

1.1
2018-10-30 · diff ↗
1.0
2018-06-10
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-06-10
Total releases: 8 / 8 yrs
License: GPL (>= 2.0)
Minimum R: ≥ 3.5.0
Bundled data: 18 KB / 2 files
Download size: 1.0 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ratematrix")

Format

Caetano, D., & Harmon, L. (2025). ratematrix: Bayesian Estimation of the Evolutionary Rate Matrix (Version 1.2.5) [Computer software]. https://doi.org/10.32614/CRAN.package.ratematrix

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 ratematrix version 1.2.5 [Data set]. HJJB, LLC. Data release v2026-08-16. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-16, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →