standardize_taxonomy: Standardize scientific names of species
View source: R/standardize_taxonomy.R
| standardize_taxonomy | R Documentation |
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 |
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)
