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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 thirteen backbones as compressed local snapshots, downloaded once and matched against in C: WFO, COL, GBIF, ITIS, NCBI Taxonomy, Open Tree of Life, WoRMS, Euro+Med, Species Fungorum, AlgaeBase, FishBase, SeaLifeBase, and Reptile Database. 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, more than sixty enrichment layers join local trait and status databases onto the accepted name: add_iucn() for IUCN Red List status, add_griis() for GRIIS invasion records, add_zanne() for woodiness, add_eive() for ecological indicator values, add_fishbase() and add_fishmorph() for fish ecology and morphology, add_trait() to gather one trait across every source that carries it, and add_data() for custom user-provided datasets. All heavy computation runs in the vectra C11 columnar engine.

To check a list before trusting it, inspect() returns only the names that look wrong, each labelled with what stands out and the name to use instead, and a region or coords argument steers fuzzy correction toward species that actually occur where you work.

Install from CRAN:

install.packages("taxify")

Or the development version from GitHub (vectra is installed automatically):

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

Source and issues: github.com/gcol33/taxify.

Citation

Gilles Colling

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