prepR4pcm: Prepare Data and Trees for Phylogenetic Comparative Methods

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>.

Version:	1.0.0
Depends:	R (≥ 4.1.0)
Imports:	ape, cli, rlang, tibble
Suggests:	caper, clootl, digest, dplyr, fishtree, httr2, knitr, MCMCglmm, phytools, piggyback, pkgdown, readr, rgnparser, rmarkdown, rotl, rtrees, spelling, stringr, taxadb, testthat (≥ 3.0.0)
Published:	2026-06-25
DOI:	10.32614/CRAN.package.prepR4pcm (may not be active yet)
Author:	Shinichi Nakagawa [aut, cre, cph], Santiago Ortega [aut], Ayumi Mizuno [aut], Eduardo S.A. Santos [aut], Malgorzata Lagisz [aut], Bhavya Jain [aut], Jimuel Jr Celeste [aut], Sergio Poo Hernandez [aut]
Maintainer:	Shinichi Nakagawa <itchyshin at gmail.com>
BugReports:	https://github.com/itchyshin/prepR4pcm/issues
License:	MIT + file LICENSE
URL:	https://github.com/itchyshin/prepR4pcm, https://itchyshin.github.io/prepR4pcm/
NeedsCompilation:	no
Language:	en-GB
Citation:	prepR4pcm citation info
Materials:	README, NEWS
CRAN checks:	prepR4pcm results

Documentation:

Reference manual:

prepR4pcm.html , prepR4pcm.pdf

Vignettes:

From Raw Data to PCM: A Complete Bird Trait Workflow (source, R code) Comparing tree backends — when do they agree? (source, R code) Assembling mammal trait databases for phylogenetic comparative models (source, R code) Getting Started with prepR4pcm (source, R code) Phylogenetic meta-analysis with rotl + prepR4pcm (source, R code) From species names to a phylogenetic posterior — prepR4pcm + pigauto (source, R code)

Downloads:

Package source:	prepR4pcm_1.0.0.tar.gz
Windows binaries:	r-devel: prepR4pcm_1.0.0.zip, r-release: not available, r-oldrel: not available
macOS binaries:	r-release (arm64): prepR4pcm_1.0.0.tgz, r-oldrel (arm64): prepR4pcm_1.0.0.tgz, r-release (x86_64): prepR4pcm_1.0.0.tgz, r-oldrel (x86_64): prepR4pcm_1.0.0.tgz

Linking:

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