get_taxonomy: Get accepted canonical names and taxonomy for a given species...

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

Get accepted canonical names and taxonomy for a given species name

Description

Get accepted canonical names and taxonomy for a given species name

Usage

get_taxonomy(x, preferred_data_sources=c(11:15), fuzzy = TRUE, verbose = TRUE)

Arguments

x	a character string or vector of species names.
preferred_data_sources	Select the datasources that should be used for name matching, default is GBIF.
fuzzy	logical. If TRUE, function tries fuzzy matching for species requests. May produce output, if normal matching fails. (not working!)
verbose	logical. If FALSE, warnings and messages are suppressed.

Details

If 'synonym' is returned as TRUE, the user provided name has been identified as a synonym and was mapped to an accepted name. The field confidence reports the confidence of the matching procedure performed by the function 'get_gbifid_()' of the package 'taxize'. The taxonID is a globally valid URI that links to the taxon description of the GBIF backbone taxonomy.

Value

a data.frame mapping the user supplied names to the accepted taxon names and higher taxonomic information (kingdom, phylum, class, order, family, genus).

Author(s)

RS-eco

References

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

Examples

## Not run: 
get_taxonomy(x="Chorthippus albomarginatus")

get_taxonomy(x=c("Equus burchellii", "Equus quagga"))

get_taxonomy(x="Aegotheles tatei")

## End(Not run)

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