R Observatory: Metrics for PCMBase version 1.2.15

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PCMBase

1.2.15

Simulation and Likelihood Calculation of Phylogenetic Comparative Models

2packages depend

6.7Kdownloads / year

13.7%test coverage

13/13checks pass

Overview

About

Maintained by Venelin MitovFirst published 2018-12-018 releasesCRAN page ↗GitHub ↗

Phylogenetic comparative methods represent models of continuous trait data associated with the tips of a phylogenetic tree. Examples of such models are Gaussian continuous time branching stochastic processes such as Brownian motion (BM) and Ornstein-Uhlenbeck (OU) processes, which regard the data at the tips of the tree as an observed (final) state of a Markov process starting from an initial state at the root and evolving along the branches of the tree. The PCMBase R package provides a general framework for manipulating such models. This framework consists of an application programming interface for specifying data and model parameters, and efficient algorithms for simulating trait evolution under a model and calculating the likelihood of model parameters for an assumed model and trait data. The package implements a growing collection of models, which currently includes BM, OU, BM/OU with jumps, two-speed OU as well as mixed Gaussian models, in which different types of the above models can be associated with different branches of the tree. The PCMBase package is limited to trait-simulation and likelihood calculation of (mixed) Gaussian phylogenetic models. The PCMFit package provides functionality for inference of these models to tree and trait data. The package web-site https://venelin.github.io/PCMBase/ provides access to the documentation and other resources.

Install

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

install.packages("PCMBase", 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("venelin/PCMBase")

Development version from venelin/PCMBase. 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-pcmbase

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-PCMBase

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-PCMBase

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

Health

CRAN checks

13OK

Slowest check: 6.4 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.05

13.7%

Coverage · measured lines

100%

Documentation · exports

7

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 · 982 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 91%
Return-value docs: 98%
References docs: 1%

Downloads

6.7K

CRAN downloads in the past year

Rank #10,617 · ~18/day · ~556/mo

Releases R versions

Daily download trend is not available in this view yet.

26130 days

91790 days

6.7K1 year

Compare downloads with other packages →

Also on151 r2u17 autocran

Repository

GitHub ↗ venelin/pcmbase

6Stars

1Forks

2Open issues

0Open PRs

7Releases

332Commits

6Contributors

332 commits · Last activity 2025-09-01

Stars over time

2023-07-25 · 62026-07-07 · 6

Repository practices

Upstream repositoryBeta

7 development-tooling and community-health practices detected across 7 families in the upstream repository

Checks run against github.com/venelin/pcmbase on 2026-08-16.

Continuous integration (1)

Travis CI

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

Coverage (1)

Codecov

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.1.0

Imports (7)

ape abind expm mvtnorm data.table ggplot2 xtable

LinkingTo (0)

none

Suggests (8)

testthat knitr rmarkdown ggtree cowplot covr mvSLOUCH BiocManager

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

1indirect

PCMBaseCpp mvSLOUCH

Code & Tests

People & History

People (4)

Maintainer (1)

Venelin Mitov

Author, Maintainer, Copyright holder

Authors (1)

Venelin Mitov

Author, Maintainer, Copyright holder

Contributors (2)

Georgios Asimomitis

Contributor

Krzysztof Bartoszek

Contributor

Copyright holders (1)

Venelin Mitov

Author, Maintainer, Copyright holder

Other (1)

Tanja Stadler

Thesis advisor

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
1.2.15Latest
2025-09-01 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.2.14
2024-03-15 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.2.13
2022-11-18 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.2.12
2021-06-07 · diff ↗
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
1.2.11
2019-12-12 · diff ↗
1.2.10
2019-09-11 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.2.9
2019-03-15 · diff ↗
1.2.7
2018-12-01

Show 1 earlier events

R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-12-01
Total releases: 8 / 8 yrs
License: GPL (>= 3.0)
Minimum R: ≥ 3.1.0
Bundled data: 23 KB / 2 files
Download size: 379 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PCMBase")

Format

Mitov, V., Asimomitis, G., Bartoszek, K., & Stadler, T. (2025). PCMBase: Simulation and Likelihood Calculation of Phylogenetic Comparative Models (Version 1.2.15) [Computer software]. https://doi.org/10.32614/CRAN.package.PCMBase

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 PCMBase version 1.2.15 [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.

Report a problem with this page →