R Observatory: Metrics for PCMBase version 1.2.15

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PCMBase

1.2.15Package record

Simulation and Likelihood Calculation of Phylogenetic Comparative Models

2packages depend

5.6Kdownloads / year

13.7%test coverage

13/13flavors OK

Overview

About

Maintained by Venelin MitovCRAN page ↗GitHub ↗Website ↗Issues ↗

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. 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-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). 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: 6.3 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.15

READMEYes · 982 wordsVignettesYes · 4 · dynamicNEWSYes · 100% structured · does not mention 1.2.15Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 135
Examples that run: 100%39 run in a plain check
Exported functions with examples: 31%
Documented parameters: 91%
Return-value docs: 98%
Help pages citing references: 1%

Vignettes (4)

How these are measured

Downloads

5.6K

CRAN downloads in the past year

Rank #8,139 · ~15/day · ~468/mo

Releases R versions

Daily download trend is not available in this view yet.

40530 days

1.1K90 days

5.6K1 year

Compare downloads with other packages →

Also on101 r2u7 autocran

How downloads are counted

Repository

venelin/pcmbase ↗Account: venelin

6Stars

1Forks

2Open issues

0Open PRs

7Releases

332Commits

6Commit identities

332 commits · Last activity 2025-09-01

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 3
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2023-07-25 · 62026-07-07 · 6

How these are measured

PracticesBeta

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

Checks run against github.com/venelin/pcmbase on 2026-10-18.

Continuous integration (1)

Travis CI (config file)

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2025-09-01

Coverage (1)

Coverage reporting (Codecov)

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 3 practices

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing PCMBase adds 25 packages (13 with compiled code, 24 MB of source tarballs). Heaviest: ggplot2 6.0 MB, data.table 5.7 MB, Rcpp 1.8 MB.

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

Imports 2

Depends, Imports or LinkingTo, most downloaded first

mvSLOUCH PCMBaseCpp

How these are counted

Code & Tests

Datasets

People & History

People (4)

Venelin Mitov

<a href="https://venelin.github.io">venelin.github.io</a>

Georgios Asimomitis

Contributor

Krzysztof Bartoszek

Contributor

Tanja Stadler

Thesis advisor

Releases (8)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.2.15Latest
record
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
record
2024-03-15 · diff ↗ ·
added 2 exports
PCMParamBindRegimeParams, RequireSuggestedPackages
R
R 4.3.0 released · 2023-04-21
1.2.13
record
2022-11-18 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.2.12
record
2021-06-07 · diff ↗ ·
added 7 exports
MixedGaussianTemplate, PCMTreeGetNodeLabels, PCMTreeGetRootLabel, PCMTreeGetTipLabels, PCMTreeInsertTipsOrSingletons, as.MixedGaussian, is.GaussianPCM
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
1.2.11
record
2019-12-12 · diff ↗ ·
removed 1 export
UpperChol

added 7 exports
MatchListMembers, PCMAddToListAttribute, PCMCombineListAttribute, PCMGetAttribute, PCMListMembers, PCMSetAttribute, UpperTriFactor
1.2.10
record
2019-09-11 · diff ↗ ·
removed 1 export
is.CholeskiFactor

added 11 exports
FormatTableAsLatex, PCMExtractDimensions, PCMExtractRegimes, PCMFindMethod, PCMLikTrace, PCMParamLocateInShortVector, PCMTable, PCMTreeGetTipsInRegime, PCMTreeVCV, UpperChol, is.CholeskyFactor
R
R 3.6.0 released · 2019-04-26
1.2.9
record
2019-03-15 · diff ↗ ·
removed 10 exports
PCMTreeDtNodeRegimes, PCMTreeExtractBackboneRegimes, PCMTreeGetRegimeForNode, PCMTreeGetStartingNodesRegimes, PCMTreeGetTipsInRegime, PCMTreeMatrixTipsInSameRegime, PCMTreeNumUniqueRegimes, PCMTreeSetDefaultRegime, PCMTreeSetRegimes, PCMTreeUniqueRegimes

added 31 exports
Args_MixedGaussian_MGPMDefaultModelTypes, Args_MixedGaussian_MGPMScalarOUType, Args_MixedGaussian_MGPMSurfaceOUType, FalsePositiveRate, MGPMDefaultModelTypes, MGPMScalarOUType, MGPMSurfaceOUType, PCMDefaultModelTypes, PCMGenerateModelTypes, PCMLikDmvNorm, PCMListDefaultParameterizations, PCMModelTypes, PCMTrajectory, PCMTree, PCMTreeBackbonePartition, PCMTreeDtNodes, PCMTreeGetPartNames, PCMTreeGetPartRegimes, PCMTreeGetPartition, PCMTreeGetPartsForNodes, PCMTreeGetRegimesForEdges, PCMTreeGetRegimesForNodes, PCMTreeGetTipsInPart, PCMTreeListAllPartitions, PCMTreeMatrixNodesInSamePart, PCMTreeNumParts, PCMTreeSetPartRegimes, PCMTreeSetPartition, PCMTreeSetRegimesForEdges, TruePositiveRate and 1 more
1.2.7
record
2018-12-01

Show 1 earlier eventHide 1 earlier event

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

Cite

Cite this package

Run in R for the authors' entry:

citation("PCMBase")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1016/j.tpb.2019.11.005, 10.1073/pnas.1813823116, 10.1111/2041-210x.13136.

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 v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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