View source: R/get_gbif_taxonomy.R
get_gbif_taxonomy | R Documentation |
The function maps user provided names to accepted species names.
get_gbif_taxonomy( x, subspecies = TRUE, higherrank = FALSE, verbose = FALSE, fuzzy = TRUE, conf_threshold = 90, resolve_synonyms = TRUE )
x |
a character string or vector of species names. |
subspecies |
logical. If TRUE (default), the given name is resolved to subspecies epithet, otherwise it will be mapped to species level. |
higherrank |
logical. If FALSE (default), it will not allow remapping of unknown species names to higher taxon ranks (e.g. genus). |
verbose |
logical. If FALSE (default), warnings and messages are suppressed. |
fuzzy |
logical. Defaults to TRUE to deal with misspelled names. May produce wrong assignments in case of very similar taxon names. If FALSE (default), names are only resolved to exactly matching taxa on GBIF taxonomy service. |
conf_threshold |
numerical, ranging from 0 to 100 (default value = 90). Defines the confidence level of the request to be accepted. To cover for misspellings and errors, could go as low as 50. |
resolve_synonyms |
logical. If TRUE (default), user provided synonyms are mapped to the accepted names on GBIF taxonomy service. |
The function relies on package 'taxize' by Scott Chamberlain. It
uses the spell-checking and fuzzy matching algorithms provided by Global
Names Resolver (taxize::gnr_resolve()
) and forwards synonyms to the
accepted names as provided by GBIF Backbone Taxonomy
(taxize::get_gbif_id_()
).
If 'synonym' is returned as TRUE, the user provided name has been identified as a synonym and was mapped to an accepted name.
The field confidence reports the confidence of the matching procedure
performed by the function get_gbifid_()
of the package 'taxize'. The
taxonID is a globally valid URI that links to the taxon description of the
GBIF backbone taxonomy.
a data.frame mapping the user supplied names to the accepted taxon names and higher taxonomic information (kingdom, phylum, class, order, family, genus).
get_gbif_taxonomy(c("Chorthippus albomarginatus", "Chorthippus apricarius", "Chorthippus biguttulus", "Chorthippus dorsatus", "Chorthippus montanus", "Chorthippus parallelus", "Chrysochraon dispar", "Conocephalus dorsalis", "Conocephalus fuscus", "Decticus verrucivorus", "Euthystira brachyptera", "Gomphocerippus rufus", "Gryllus campestris", "Metrioptera roeselii", "Omocestus viridulus", "Phaneroptera falcata", "Platycleis albopunctata", "Spec", "Stenobothrus lineatus", "Stenobothrus stigmaticus", "Stethophyma grossum", "Tetrix kraussi", "Tetrix subulata", "Tetrix tenuicornis", "Tetrix undulata", "Tettigonia cantans", "Tettigonia viridissima") ) get_gbif_taxonomy("Vicia")
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