Lookup names in the GBIF backbone taxonomy.

Usage

name_backbone(
  name,
  rank = NULL,
  kingdom = NULL,
  phylum = NULL,
  class = NULL,
  order = NULL,
  family = NULL,
  genus = NULL,
  strict = FALSE,
  verbose = FALSE,
  start = NULL,
  limit = 100,
  curlopts = list()
)

name_backbone_verbose(
  name,
  rank = NULL,
  kingdom = NULL,
  phylum = NULL,
  class = NULL,
  order = NULL,
  family = NULL,
  genus = NULL,
  strict = FALSE,
  start = NULL,
  limit = 100,
  curlopts = list()
)

Arguments

name: (character) Full scientific name potentially with authorship (required)
rank: (character) The rank given as our rank enum. (optional)
kingdom: (character) If provided default matching will also try to match against this if no direct match is found for the name alone. (optional)
phylum: (character) If provided default matching will also try to match against this if no direct match is found for the name alone. (optional)
class: (character) If provided default matching will also try to match against this if no direct match is found for the name alone. (optional)
order: (character) If provided default matching will also try to match against this if no direct match is found for the name alone. (optional)
family: (character) If provided default matching will also try to match against this if no direct match is found for the name alone. (optional)
genus: (character) If provided default matching will also try to match against this if no direct match is found for the name alone. (optional)
strict: (logical) If TRUE it (fuzzy) matches only the given name, but never a taxon in the upper classification (optional)
verbose: (logical) should the function give back more (less reliable) results. See function name_backbone_verbose()
start: Record number to start at. Default: 0. Use in combination with limit to page through results.
limit: Number of records to return. Default: 100. Maximum: 1000.
curlopts: list of named curl options passed on to HttpClient. see curl::curl_options for curl options

Value

For name_backbone, a data.frame for a single taxon with many columns. For name_backbone_verbose, a larger number of results in a data.frame the results of resulting from fuzzy matching. You will also get back your input name, rank, kingdom, phylum ect. as columns input_name, input_rank, input_kingdom ect. so you can check the results.

Details

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

References

https://www.gbif.org/developer/species#searching

Examples

if (FALSE) { # \dontrun{
name_backbone(name='Helianthus annuus', kingdom='plants')
name_backbone(name='Helianthus', rank='genus', kingdom='plants')
name_backbone(name='Poa', rank='genus', family='Poaceae')

# Verbose - gives back alternatives
## Strictness
name_backbone_verbose(name='Poa', kingdom='plants',
  strict=FALSE)
name_backbone_verbose(name='Helianthus annuus', kingdom='plants',
  strict=TRUE)

# Non-existent name - returns list of lenght 3 stating no match
name_backbone(name='Aso')
name_backbone(name='Oenante')

# Pass on curl options
name_backbone(name='Oenante', curlopts = list(verbose=TRUE))
} # }