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The taxify package matches taxonomic names against Darwin Core backbones stored on your own disk. Hand it a column of messy species names and taxify() cleans them, matches them against the backbone, resolves synonyms to accepted names, detects hybrids, and returns one standardized data.frame. Every step runs locally against a versioned snapshot, so a list of thousands resolves in seconds, there are no API calls or rate limits, and the same input gives the same output on any machine.

The package ships ten backbones as compressed local snapshots, downloaded once and matched against in C: WFO, COL, GBIF, ITIS, NCBI Taxonomy, Open Tree of Life, WoRMS, Species Fungorum, and AlgaeBase. Pass several and they form a fallback chain, where a name unmatched by the first backbone cascades to the next. Matching is fuzzy or exact, with a unified output schema across all sources.

Beyond name resolution, a family of join verbs enriches the matched table from local trait and status databases: add_conservation_status() for IUCN Red List, add_invasive_status() for invasion data, add_woodiness(), add_eive() for ecological indicator values, add_fishbase() and add_fish_traits() for fish morphology and ecology, and add_data() for custom user-provided datasets. All heavy computation runs in the vectra C11 columnar engine.

Install the development version from GitHub:

install.packages("pak")
pak::pak("gcol33/taxify")

Citation

Gilles Colling

PhD student at University of Vienna. Physicist turned ecologist. R packages, spatial statistics, and computational ecology.