R Observatory: Metrics for PCMBaseCpp version 0.1.12

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PCMBaseCpp

0.1.12

Fast Likelihood Calculation for Phylogenetic Comparative Models

1packages depend

7.2Kdownloads / year

60.5%test coverage

13/13checks pass

Overview

About

Maintained by Venelin MitovFirst published 2019-10-068 releasesCRAN page ↗GitHub ↗

Provides a C++ backend for multivariate phylogenetic comparative models implemented in the R-package 'PCMBase'. Can be used in combination with 'PCMBase' to enable fast and parallel likelihood calculation. Implements the pruning likelihood calculation algorithm described in Mitov et al. (2020) doi:10.1016/j.tpb.2019.11.005. Uses the 'SPLITT' C++ library for parallel tree traversal described in Mitov and Stadler (2018) doi:10.1111/2041-210X.13136.

Install

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

install.packages("PCMBaseCpp", 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/PCMBaseCpp")

Development version from venelin/PCMBaseCpp. 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-pcmbasecpp

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-PCMBaseCpp

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-PCMBaseCpp

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

Health

CRAN checks

13OK

Slowest check: 12.2 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 0.40

60.5%

Coverage · measured lines

100%

Documentation · exports

5

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
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 528 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 76%
Return-value docs: 100%
References docs: 0%

Downloads

7.2K

CRAN downloads in the past year

Rank #12,952 · ~20/day · ~599/mo

Releases R versions

Daily download trend is not available in this view yet.

23030 days

78390 days

7.2K1 year

Compare downloads with other packages →

Also on410 r2u14 autocran

Repository

GitHub ↗ venelin/pcmbasecpp

0Stars

1Forks

0Open issues

0Open PRs

9Releases

102Commits

2Contributors

102 commits · Last activity 2026-02-28

Forks over time

2025-07-20 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

6 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/venelin/pcmbasecpp on 2026-08-09.

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

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

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Depends (3)

R >= 3.1.0Rcppmethods

Imports (3)

PCMBase data.table abind

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (4)

testthat knitr rmarkdown covr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

mvSLOUCH

Code & Tests

People & History

People (1)

Maintainer (1)

Venelin Mitov

Author, Maintainer, Copyright holder

Authors (1)

Venelin Mitov

Author, Maintainer, Copyright holder

Copyright holders (1)

Venelin Mitov

Author, Maintainer, Copyright holder

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
0.1.12Latest
2026-02-28 · current release · diff ↗
0.1.11
2025-05-04 · diff ↗
0.1.10
2025-04-27 · 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
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
0.1.9
2020-03-23 · diff ↗
0.1.8
2020-02-23 · diff ↗
unarchivedReturned to CRAN
2020-02-23
archivedRemoved from CRAN
2020-01-09
check errors were not corrected in time
0.1.7
2019-11-21 · diff ↗
0.1.6
2019-11-11 · diff ↗

Show 2 earlier events

0.1.5
2019-10-06
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-10-06
Total releases: 8 / 7 yrs
License: GPL (>= 3.0)
Minimum R: ≥ 3.1.0
Bundled data: 965 KB / 3 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("PCMBaseCpp")

Format

Mitov, V. (2026). PCMBaseCpp: Fast Likelihood Calculation for Phylogenetic Comparative Models (Version 0.1.12) [Computer software]. https://doi.org/10.32614/CRAN.package.PCMBaseCpp

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 PCMBaseCpp version 0.1.12 [Data set]. HJJB, LLC. Data release v2026-08-11. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-11, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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