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taxify: Offline Taxonomic Name Matching Against Darwin Core Backbones

Matches taxonomic names against local copies of published backbones ('Catalogue of Life', 'GBIF Backbone Taxonomy', 'ITIS', 'World Flora Online', 'WoRMS', 'NCBI Taxonomy', 'Open Tree of Life', 'Euro+Med', 'Species Fungorum', 'AlgaeBase', 'FishBase', 'SeaLifeBase', 'Reptile Database', 'LCVP', 'WCVP', 'Mammal Diversity Database', 'AviList', 'LPSN') and two vegetation classifications, and resolves each name to its accepted name. It performs the name-resolution step of 'taxize' and 'WorldFlora', run offline against these files. Names are cleaned of authors and qualifiers, matched exactly and then by edit distance within their genus, and followed from synonym to accepted name, with the backbone version recorded on every row. Published trait, status and distribution datasets are joined on the accepted name, and so is a table the user supplies. Matching runs in the 'vectra' column-store engine.

Version: 0.7.0
Depends: R (≥ 4.1.0)
Imports: curl, jsonlite, rlang, vectra (≥ 0.14.0)
Suggests: ape, DBI, knitr, openxlsx2, rgbif, rmarkdown, RSQLite, sf, taxifydb (≥ 0.1.19), terra, testthat (≥ 3.0.0), TR8, withr
Published: 2026-10-27
DOI: 10.32614/CRAN.package.taxify
Author: Gilles Colling ORCID iD [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051 at gmail.com>
BugReports: https://github.com/gcol33/taxify/issues
License: MIT + file LICENSE
URL: https://gillescolling.com/taxify/, https://github.com/gcol33/taxify
NeedsCompilation: no
Additional_repositories: https://gcol33.r-universe.dev
Citation: taxify citation info
Materials: README, NEWS
CRAN checks: taxify results

Documentation:

Reference manual: taxify.html , taxify.pdf
Vignettes: Choosing and combining backbones (source)
Joining your own data (source)
Attaching published data (source)
Exploring the backbone (source)
How names are matched (source)
Requesting GBIF data for a species list (source)
Hybrids and aggregates (source)
Checking a name list (source)
Matching large lists (source)
Compatibility with taxize and WorldFlora (source)
Matching within a region (source)
Get started (source)
Matching vegetation units (source)

Downloads:

Package source: taxify_0.7.0.tar.gz
Windows binaries: r-devel: taxify_0.7.0.zip, r-release: taxify_0.7.0.zip, r-oldrel: taxify_0.7.0.zip
macOS binaries: r-release (arm64): taxify_0.7.0.tgz, r-oldrel (arm64): taxify_0.7.0.tgz, r-release (x86_64): taxify_0.7.0.tgz, r-oldrel (x86_64): taxify_0.7.0.tgz
Old sources: taxify archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=taxify to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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