R Observatory: Metrics for prepR4pcm version 1.0.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

prepR4pcm

1.0.3Package record

Prepare Data and Trees for Phylogenetic Comparative Methods

0packages depend

1.3Kdownloads / year

79.1%test coverage

13/13flavors OK

Overview

About

Maintained by Shinichi NakagawaCRAN page ↗GitHub ↗Website ↗Issues ↗

Reconcile species names across datasets and phylogenetic trees for comparative biology workflows. Identifies mismatches due to formatting differences, taxonomic synonymy, and spelling errors. Produces detailed reports documenting how each name was resolved, which taxonomic authority was used, and what remains unresolved. Supports exact matching, name normalisation, synonym resolution via local taxonomic databases, and fuzzy matching for likely typos. Detects taxonomic splits and lumps. For methodological context, see Nakagawa et al. (2026) doi:10.32942/X2468Z.

Changes in 1.0.3

Documentation now reports the synonym-stage match score as 0.95, matching the existing implementation. No matching behaviour or API changed.

From NEWS.md in the release

Install

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

install.packages("prepR4pcm", 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("itchyshin/prepR4pcm")

Development version from itchyshin/prepR4pcm. 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-prepr4pcm

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-prepR4pcm

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-prepR4pcm

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: 6.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK7 OK2026-06-26

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.3

READMEYes · 1,600 wordsVignettesYes · 6 · evaluation depends on the environmentNEWSYes · 100% structured · mentions 1.0.3Citation fileYes · computed when R runs itWebsiteYes · pkgdown

Help pages: 74 (32 internal)includes a package overview page
Examples that run: 97%31 run in a plain check (2 of them under a condition) · 1 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 16%

Vignettes (6)

How these are measured

Downloads

1.3K

CRAN downloads in the past year

Rank #10,021 · ~4/day · ~112/mo

Releases R versions

Daily download trend is not available in this view yet.

41830 days

1K90 days

1.3K1 year

Compare downloads with other packages →

Also on45 r2u3 autocran

How downloads are counted

Repository

itchyshin/prepr4pcm ↗Account: itchyshin

2Stars

0Forks

7Open issues

0Open PRs

3Releases

253Commits

1Commit identities

License file reads as MIT · 253 commits · Last activity 2026-10-21 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 99%
Median days to close, 50 most recently updated closed issues: 5
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2026-06-24 · 12026-09-03 · 2

How these are measured

PracticesBeta

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

Checks run against github.com/itchyshin/prepr4pcm on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-10-17

pkgdown site last built 2026-09-25

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Show all practicesHide 2 practices

Research and citation (1)

Zenodo

Lint, format, editor (1)

RStudio project

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-04-06
Seen in the repository: .mcp.json, CLAUDE.md
Named in .Rbuildignore: .claude, .mcp.json, CLAUDE.md
Named in .gitignore: .claude
Pull request it wrote: opened by a project member
Commits: at least 124 crediting it in the message
Cursorfirst seen 2026-09-12
Seen in the repository: .cursor
Named in .Rbuildignore: .cursor

Shared conventions any agent may read, so they name no particular tool.

Seen in the repository: AGENTS.md

Models named in its commits

Claude Opus 4.765 commits · Apr to May 2026
Claude Opus 4.621 commits · Apr 2026
Claude Sonnet 4.614 commits · Apr 2026

Some of these counts are a minimum, because the search stopped before the oldest commits.

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

24 external dependencies (excludes base and recommended)

Installing prepR4pcm adds 13 packages (10 with compiled code, 7.4 MB of source tarballs). Heaviest: Rcpp 1.8 MB, ape 1.4 MB, vctrs 1.0 MB.

Depends (1)

R >= 4.1.0

Imports (4)

ape cli rlang tibble

LinkingTo (0)

none

Suggests (20)

caper clootl digest dplyr fishtree httr2 knitr MCMCglmm phytools piggyback pkgdown readr rgnparser rmarkdown rotl rtrees spelling stringr taxadb testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (8)

Author

Author

Author

Author

Author

Author

Author

Releases (3)

Pick two releases to compare their code metrics.

1.0.3Latest
record
2026-09-18 · current release · diff ↗
1.0.2
record
2026-08-25 · diff ↗ ·
added 1 export
reconcile_crosswalk_supplement
1.0.0
record
2026-06-25
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-06-25
Total releases: 3 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 487 KB / 10 files
Download size: 3.4 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("prepR4pcm")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 prepR4pcm version 1.0.3 [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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