taxize (version 0.1.5)

get_ids: Retrieve taxonomic identifiers for a given taxon name.

Description

This is a convenience function to get identifiers across all data sources. You can use other get_* functions to get identifiers from specific sources if you like.

Usage

get_ids(names, db = NULL, ...)

Arguments

names

character; Taxonomic name to query.

db

character; database to query. One or more of ncbi, itis, eol, col, and/or tropicos

...

Other arguments passed to get_tsn, get_uid, get_eolid,

Value

• A vector of taxonomic identifiers, each retaining their respective S3 classes so that each element can be passed on to another function (see e.g.'s).

See Also

get_tsn, get_uid, get_eolid, get_colid, get_tpsid

Examples

# Plug in taxon names directly
get_ids(names="Chironomus riparius", db = 'ncbi')
get_ids(names=c("Chironomus riparius", "Poa annua"), db = 'ncbi')
get_ids(names=c("Chironomus riparius", "Poa annua"), db = c('ncbi','itis'))
get_ids(names=c("Chironomus riparius", "Poa annua"), db = c('ncbi','itis','col'))
get_ids(names="Poa annua", db = c('ncbi','itis','col','eol','tropicos'))
get_ids(names="ava avvva", db = c('ncbi','itis','col','eol','tropicos'))
get_ids(names="ava avvva", db = c('ncbi','itis','col','eol','tropicos'), verbose=FALSE)

# Pass on to other functions
out <- get_ids(names="Poa annua", db = c('ncbi','itis','col','eol','tropicos'))
classification(out$itis)
synonyms(out$tropicos)