Correct and match taxonomic names to the World Flora Online database

Match taxonomic names using the World Flora Online database, via their GraphQL API

Usage

correctTaxo(
  genus,
  species = NULL,
  interactive = TRUE,
  preferAccepted = FALSE,
  preferFuzzy = FALSE,
  sub_pattern = subPattern(),
  useCache = FALSE,
  useAPI = TRUE,
  capacity = 60,
  fill_time_s = 60,
  timeout = 10
)

Arguments

genus: vector of genera. Alternatively, the whole taxonomic name (genus + species)
species: optional, vector of species epithets to be checked (same length as genus)
interactive: logical, if TRUE (default) user will be prompted to pick names from a list where multiple ambiguous matches are found, otherwise names with multiple ambiguous matches will be skipped
preferAccepted: logical, if TRUE, if multiple ambiguous matches are found, and if only one candidate is an "accepted" name, automatically choose that name
preferFuzzy: logical, if TRUE, if multiple ambiguous matches are found, the accepted matched name with the lowest Levenshtein distance to the submitted name will be returned
sub_pattern: character vector of regex patterns which will be removed from paste(genus, species) using gsub(). The order of this vector matters, substitutions are applied sequentially. Sensible defaults are provided by subPattern()
useCache: logical, if TRUE use cached values in the$wfo_cache preferentially, to reduce the number of API calls
useAPI: logical, if TRUE (default) allow API calls
capacity: maximum number of API calls which can accumulate over the duration of fill_time_s. See documentation for httr2::req_throttle()
fill_time_s: time in seconds to refill the capacity for repeated API calls. See documentation for httr2::req_throttle()
timeout: time in seconds to wait before disconnecting from an unresponsive request

Value

data.frame of taxonomic names with rows matching genus + species.

nameOriginal: Original name as in genus + species
nameSubmitted: Name after optional sanitisation according to sub_pattern
nameMatched: Matched taxonomic name
nameAccepted: Accepted taxonomic name
familyAccepted: Family of accepted name
genusAccepted: Genus of accepted name
speciesAccepted: Species epithet of accepted name
nameModified: Flag indicating if matchedName is different from nameOriginal, not including the removal of excess whitespace

References

Borsch, T. et al. (2020). World Flora Online: Placing taxonomists at the heart of a definitive and comprehensive global resource on the world's plants. TAXON, 69, 6. doi10.1002/tax.12373:

Author

John L. Godlee

Examples

if (FALSE) { # \dontrun{
correctTaxo(genus = "Astrocarium", species = "standleanum")
correctTaxo(genus = "Astrocarium", species = "standleanum", interactive = F, preferFuzzy = T)
correctTaxo(genus = "Astrocarium standleanum", interactive = F, preferFuzzy = T)
} # }