Adds columns to a traitdata object containing accepted species names and relates to globally unique taxon identifiers via URI.
standardize.taxonomy(x, method = get_gbif_taxonomy, subspecies = TRUE, fuzzy = TRUE, verbose = FALSE, return = c("kingdom", "phylum", "class", "order", "family"), ...)
a traitdata object (as returned by
only option is
logical. If TRUE (default), the given name is resolved to subspecies epithet, otherwise it will be mapped to species level.
if set to
has currently no effect.
a character vector containing the informatoin that should be
extracted into the output. Valid entries are the column names returned by
Taxonomic standardisation is an enormous challenge for biodiversity data management and research. Constant changes in species and higher taxa, refinements of phylogenetic trees and changing attribution to original authors, moving species into other genera or difficulties to place species into the Linean nomenclature results in highly fluctuent taxonomic definitions.
As a consequence, there is not one reference for accepted species names and dependin on the field of resaerch and taxonomic focus other authorities will be employed.
For reasons of simplicity and because of its high coverage of taxa, the
standardize.taxonomy() uses the GBIF Backbone Taxonomy as its
reference system and resolves all provided species names to the accepted
name according to GBIF (resolving misspellings and synonyms in the
process). We invite pull requests to make this function more general and
enable a choice of a taxonomic reference.
pulldata("carabids")#> The dataset 'carabids' is now available for use!dataset1 <- as.traitdata(carabids, taxa = "name_correct", traits = c("body_length", "antenna_length", "metafemur_length"), units = "mm", keep = c(datasetID = "source_measurement", measurementRemark = "note"), metadata = list( bibliographicCitation = attributes(carabids)$citeAs, author = "Fons van der Plas", license = "http://creativecommons.org/publicdomain/zero/1.0/" ) )#>dataset1Std <- standardize.taxonomy(dataset1)