Match taxonomic names/lineages against the GBIF taxonomy

This function uses the GBIF web API (through rgbif) to retrieve the currently accepted taxon name and lineage according to the GBIF backbone taxonomy.

Usage

get_gbif_taxa(
  taxa,
  cache_file,
  known_kingdom = NA,
  likely_kingdom = NA,
  verbose = FALSE
)

Arguments

taxa

A character vector of taxonomic names or a matrix/data frame with lineages; columns must have rank names and the first column should be name, containing taxonomic names such as "Russula sp." or "Bacteria". The lineages don't need to be complete (NA or only few ranks allowed), but their presence may help with the matching.'

cache_file

Path where past searches are stored in a tab-separated text format. This avoids havoing to query the GBIF API repeatedly for thousands of taxa. Delete the file (or individual lines) to re-query the GBIF API for the taxa.

known_kingdom

provide a known kingdom as alternative to providing the kingdom in a matrix of lineages. Supplying the kingdom may help to resolve ambiguous matches.

likely_kingdom

If the kingdom is not known for sure (but very likely), it can be provided here. The GBIF API will be searched without and with kingdom, and the result yielding a more complete lineage is returned

Value

A matrix with lineages; rows are in the same order as in the taxa vector or matrix