R Observatory: Metrics for PCMBaseCpp version 0.1.12

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PCMBaseCpp

0.1.12Package record

Fast Likelihood Calculation for Phylogenetic Comparative Models

0packages dependsuggested by 1

6.4Kdownloads / year

60.5%test coverage

13/13flavors OK

Overview

About

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

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.

Changes in 0.1.12

Fixed gcc compiler warning.

From NEWS.md in the release

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. 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-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). 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: 12.2 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-05-02

Show 3 earlier changesHide 3 earlier changes

NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.12

READMEYes · 528 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.1.12Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 10
Examples that run: 100%4 run in a plain check
Exported functions with examples: 67%
Documented parameters: 76%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Getting started

How these are measured

Downloads

6.4K

CRAN downloads in the past year

Rank #8,189 · ~17/day · ~532/mo

Releases R versions

Daily download trend is not available in this view yet.

44230 days

1.1K90 days

6.4K1 year

Compare downloads with other packages →

Also on383 r2u4 autocran

How downloads are counted

Repository

venelin/pcmbasecpp ↗Account: venelin

0Stars

1Forks

0Open issues

0Open PRs

9Releases

102Commits

2Commit identities

102 commits · Last activity 2026-02-28

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 72
Median days to close, 50 most recently updated closed PRs: not measured

Forks over time

2025-07-20 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/venelin/pcmbasecpp on 2026-10-21.

Continuous integration (1)

Travis CI (config file)

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-02-28

Coverage (1)

Coverage reporting (Codecov)

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 2 practices

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Installing PCMBaseCpp adds 27 packages (14 with compiled code, 26 MB of source tarballs). Heaviest: ggplot2 6.0 MB, data.table 5.7 MB, Rcpp 1.8 MB.

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

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

mvSLOUCH

How these are counted

Code & Tests

Datasets

People & History

People (1)

Venelin Mitov

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

Releases (8)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.1.12Latest
record
2026-02-28 · current release · diff ↗
0.1.11
record
2025-05-04 · diff ↗
0.1.10
record
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
record
2020-03-23 · diff ↗
unarchivedReturned to CRAN
2020-02-23
0.1.8
record
2020-02-23 · diff ↗
archivedRemoved from CRAN
2020-01-09
check errors were not corrected in time
0.1.7
record
2019-11-21 · diff ↗
0.1.6
record
2019-11-11 · diff ↗

Show 2 earlier eventsHide 2 earlier events

0.1.5
record
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

Cite

Cite this package

Run in R for the authors' entry:

citation("PCMBaseCpp")

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

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

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 v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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