Skip to contents

Standardize scientific names of species

Source: R/standardize.R
standardize_taxa.Rd

Adds columns to a traitdata object containing accepted species names and relates to globally unique taxon identifiers via URI.

Usage

standardize_taxa(
  x,
  method = get_gbif_taxonomy,
  method_options = c(subspecies = TRUE, higherrank = FALSE, verbose = FALSE, fuzzy =
    TRUE, conf_threshold = 90, resolve_synonyms = TRUE),
  return = c("kingdom", "phylum", "class", "order", "family"),
  ...
)

Arguments

x

a traitdata object (as returned by as.traitdata()) or a data table containing at least the column `verbatimScientificName.

method

default option is get_gbif_taxonomy. In principle, takes any function that takes a vector of species names as input to produce a taxonomy lookup table (i.e. mapping user-provided verbatimScientificName to taxonID and other taxon-level information). Will allow to chose from different sources of taxonomic reference.

method_options

a name vector of arguments to be passed on to method. See get_gbif_taxonomy for options.

return

a character vector containing the informatoin that should be extracted into the output. Valid entries are the column names returned by function get_gbif_taxonomy(). See 'Details'.

...

parameters to be ignored, forwarded from wrapper function standardize().

Value

A traidata object with standardized scientific taxon names according to GBif Backbone taxonomy.

Details

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 depending 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 function standardize_taxa() 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.

See also

Other standardize: standardize_traits(), standardize()

Examples


if (FALSE) {

pulldata("carabids")

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_taxa(dataset1)
}