standardize_taxonomy: Standardize scientific names of species

In RS-eco/traitdata: Easy access to various ecological trait data

Standardize scientific names of species

Description

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

Usage

standardize_taxonomy(x, preferred_data_sources=c(11:15), fuzzy = TRUE, verbose = TRUE,
return=c("kingdom", "phylum", "class", "order", "family", "scientificNameStd"))

Arguments

x	a data.frame containing at least the column scientificName.
preferred_data_sources	Select the datasources that should be used for name matching, default is GBIF.
fuzzy	if set to 'FALSE' (default mode), this disables fuzzy matching if problems with ambiguous species names arise.
verbose	has currently no effect.
return	a character vector containing the informatoin that should be extracted into the output. Valid entries are the column names returned by function ‘get_taxonomy()'. See ’Details'.

Details

Taxonomic standardisation is an enormous challenge, as species names constantly change and phylogenetic trees are regularly refined.

As a consequence, there is not one reference for accepted species names, as it often depends on the field of research and taxonomic focus.

For reasons of simplicity and because of its high coverage of taxa, the function 'standardize_taxonomy()' by default 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).

Author(s)

RS-eco

Source

The initial code from this function was obtained from the 'traitdataform' package, which is available on GitHub: https://github.com/EcologicalTraitData/traitdataform.

Examples

## Not run: 
standardize_taxonomy(x=data.frame(scientificName="Equus burchellii"))

standardize_taxonomy(x=data.frame(scientificName=c("Equus quagga")),
return=c("kingdom", "phylum", "class", "order", "family", "scientificNameStd"))

## End(Not run)

RS-eco/traitdata documentation built on Oct. 29, 2022, 7:52 p.m.