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taxify: Offline Taxonomic Name Matching Against Darwin Core Backbones

Source: R/taxify-package.R
taxify-package.Rd

taxify matches taxonomic names to their accepted names against local copies of published backbones, such as the Catalogue of Life, World Flora Online and WoRMS. It performs the name-resolution step of 'taxize' and 'WorldFlora', run offline against local backbone files. Each backbone is downloaded once and recorded by version on every result row.

Functions by task

Matching

taxify() matches a character vector of names and returns one row per name with its accepted name, how it was matched and the backbone version; summary() counts how a batch resolved.

Checking

inspect() returns only the names that need a look; reconcile() reports how a checklist maps onto a backbone's current treatment.

Joining data

add_data() joins a table the user supplies on the accepted name; each published dataset has its own add_<source>() function, listed by list_enrichments(); add_trait() gathers one trait from every dataset that carries it.

Exploring the backbone

synonyms(), children(), downstream(), upstream(), add_classification(), class2tree(), id2name(), parse_name(), comm2sci() and sci2comm().

Backbones and versions

list_backbones(), install_backbones(), taxify_download(), taxify_lock(), taxify_restore() and cite().

Where to start

vignette("taxify") goes from a messy list of names to accepted names with traits attached. The articles at https://gillescolling.com/taxify/ cover each task in full.

Citation

citation("taxify") gives the reference of the package; cite() on a result lists the references of every backbone and dataset it used.

See also

Useful links:

Author

Maintainer: Gilles Colling gilles.colling051@gmail.com (ORCID) [copyright holder]

Authors: