Match names to GBIF backbone and other checklists.

Usage

name_backbone(
  name = NULL,
  rank = NULL,
  kingdom = NULL,
  phylum = NULL,
  class = NULL,
  order = NULL,
  superfamily = NULL,
  family = NULL,
  subfamily = NULL,
  tribe = NULL,
  subtribe = NULL,
  genus = NULL,
  subgenus = NULL,
  species = NULL,
  usageKey = NULL,
  taxonID = NULL,
  taxonConceptID = NULL,
  scientificNameID = NULL,
  scientificNameAuthorship = NULL,
  genericName = NULL,
  specificEpithet = NULL,
  infraspecificEpithet = NULL,
  verbatimTaxonRank = NULL,
  exclude = NULL,
  strict = NULL,
  verbose = FALSE,
  checklistKey = NULL,
  start = NULL,
  limit = NULL,
  curlopts = list(http_version = 2)
)

name_backbone_verbose(
  name = NULL,
  rank = NULL,
  kingdom = NULL,
  phylum = NULL,
  class = NULL,
  order = NULL,
  superfamily = NULL,
  family = NULL,
  subfamily = NULL,
  tribe = NULL,
  subtribe = NULL,
  genus = NULL,
  subgenus = NULL,
  species = NULL,
  usageKey = NULL,
  taxonID = NULL,
  taxonConceptID = NULL,
  scientificNameID = NULL,
  scientificNameAuthorship = NULL,
  genericName = NULL,
  specificEpithet = NULL,
  infraspecificEpithet = NULL,
  verbatimTaxonRank = NULL,
  exclude = NULL,
  strict = NULL,
  checklistKey = NULL,
  start = NULL,
  limit = NULL,
  curlopts = list(http_version = 2)
)

Arguments

name: (character) Full scientific name potentially with authorship (required)
rank: (character) Filter by taxonomic rank. See API reference for available values.
kingdom: (character) Kingdom to match.
phylum: (character) Phylum to match.
class: (character) Class to match.
order: (character) Order to match.
superfamily: (character) Superfamily to match.
family: (character) Family to match.
subfamily: (character) Subfamily to match.
tribe: (character) Tribe to match.
subtribe: (character) Subtribe to match.
genus: (character) Genus to match.
subgenus: (character) Subgenus to match.
species: (character) Species to match.
usageKey: (character) The usage key to look up. When provided, all other fields are ignored.
taxonID: (character) The taxon ID to look up. Matches to a taxonID will take precedence over scientificName values supplied. A comparison of the matched scientific and taxonID is performed tocheck for inconsistencies.
taxonConceptID: (character) The taxonConceptID to match. Matches to a taxonConceptID will take precedence over scientificName values supplied. A comparison of the matched scientific and taxonConceptID is performed to check for inconsistencies.
scientificNameID: (character) Matches to a scientificNameID will take precedence over scientificName values supplied. A comparison of the matched scientific and scientificNameID is performed to check for inconsistencies.
scientificNameAuthorship: (character) The scientific name authorship to match against.
genericName: (character) Generic part of the name to match when given as atomised parts instead of the full name parameter.
specificEpithet: (character) Specific epithet to match.
infraspecificEpithet: (character) Infraspecific epithet to match.
verbatimTaxonRank: (character) Filters by free text taxon rank.
exclude: (character) An array of usage keys to exclude from the match.
strict: (logical) If set to true, fuzzy matches only the given name, but never a taxon in the upper classification.
verbose: (logical) If set to true, it shows alternative matches which were considered but then rejected.
checklistKey: (character) The key of a checklist to use. The default is the GBIF Backbone taxanomy.
start: (integer) Currently ignored.
limit: (integer) Currently ignored.
curlopts: A list of curl options passed on to httr::GET().

Value

A single row tibble of the best matched name. If verbose=TRUE, a longer tibble with all potential alternatives is returned.

Details

If you don't get a match, GBIF gives back a data.frame with columns synonym, confidence, and matchType='NONE'.

name_backbone_verbose() is a legacy wrapper function that returns returns alternatives in a separate tibble.

References

https://techdocs.gbif.org/en/openapi/v1/species#/Searching%20names/matchNames

Examples

if (FALSE) { # \dontrun{
name_backbone("Calopteryx splendens") 
name_backbone("Calopteryx splendens", kingdom = "Animalia")
name_backbone("Calopteryx splendens", kingdom = "Animalia", verbose = TRUE)
name_backbone_verbose("Calopteryx splendens", kingdom = "Animalia")
name_backbone("Calopteryx splendens", kingdom = "Plantae")

} # }