Package: prepR4pcm
Title: Prepare Data and Trees for Phylogenetic Comparative Methods
Version: 1.0.0
Authors@R: c(
    person("Shinichi", "Nakagawa",
           email = "itchyshin@gmail.com",
           role = c("aut", "cre", "cph"),
           comment = c(ORCID = "0000-0002-7765-5182")),
    person("Santiago", "Ortega",
           role = "aut"),
    person("Ayumi", "Mizuno",
           role = "aut"),
    person("Eduardo S.A.", "Santos",
           role = "aut"),
    person("Malgorzata", "Lagisz",
           role = "aut",
           comment = c(ORCID = "0000-0002-3993-6127")),
    person("Bhavya", "Jain",
           role = "aut"),
    person("Jimuel Jr", "Celeste",
           role = "aut"),
    person("Sergio", "Poo Hernandez",
           email = "pooherna@ualberta.ca",
           role = "aut")
  )
Description: 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>.
License: MIT + file LICENSE
URL: https://github.com/itchyshin/prepR4pcm,
        https://itchyshin.github.io/prepR4pcm/
BugReports: https://github.com/itchyshin/prepR4pcm/issues
Date: 2026-06-16
Language: en-GB
Encoding: UTF-8
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)
LazyData: true
Config/testthat/edition: 3
VignetteBuilder: knitr
Config/roxygen2/version: 8.0.0
NeedsCompilation: no
Packaged: 2026-06-25 13:08:33 UTC; root
Author: Shinichi Nakagawa [aut, cre, cph] (ORCID:
        <https://orcid.org/0000-0002-7765-5182>), Santiago Ortega
        [aut], Ayumi Mizuno [aut], Eduardo S.A. Santos [aut],
        Malgorzata Lagisz [aut] (ORCID:
        <https://orcid.org/0000-0002-3993-6127>), Bhavya Jain [aut],
        Jimuel Jr Celeste [aut], Sergio Poo Hernandez [aut]
Maintainer: Shinichi Nakagawa <itchyshin@gmail.com>
Repository: https://cran.r-universe.dev
Date/Publication: 2026-06-25 12:36:49 UTC
RemoteUrl: https://github.com/cran/prepR4pcm
RemoteRef: HEAD
RemoteSha: b78fe29addf5d4cf917c17b421e31a2348ed37d8