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: 2026-06-20 18:45:02 UTC; z3437171
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: CRAN
Date/Publication: 2026-06-25 11:00:13 UTC
Built: R 4.5.3; ; 2026-07-11 04:36:55 UTC; windows
