traitdataform (version 0.6.8)

get_gbif_taxonomy: Get accepted canonical names and taxonomy for a given species name

Description

The function maps user provided names to accepted species names.

Usage

get_gbif_taxonomy(
  x,
  subspecies = TRUE,
  higherrank = FALSE,
  verbose = FALSE,
  fuzzy = TRUE,
  conf_threshold = 90,
  resolve_synonyms = TRUE
)

Arguments

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.

Value

a data.frame mapping the user supplied names to the accepted taxon names and higher taxonomic information (kingdom, phylum, class, order, family, genus).

Details

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.

Examples

# NOT RUN {
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")
# }