get_ids {taxize}R Documentation

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 = c("itis", "ncbi", "eol", "col", "tropicos", "gbif",
  "nbn"), ...)

get_ids_(names, db = c("itis", "ncbi", "eol", "col", "tropicos", "gbif",
  "nbn"), rows = NA, ...)

Arguments

names

character; Taxonomic name to query.

db

character; database to query. One or more of ncbi, itis, eol, col, tropicos, gbif, or nbn. By default db is set to search all data sources. Note that each taxonomic data source has their own identifiers, so that if you vide the wrong db value for the identifier you could get a result, it will likely be wrong (not what you were expecting).

...

Other arguments passed to get_tsn, get_uid, get_eolid, get_colid, get_tpsid, get_gbifid, get_nbnid.

rows

numeric; Any number from 1 to infinity. If the default NA, all rows are returned. When used in get_ids this function still only gives back a ids class object with one to many identifiers. See get_ids_ to get back all, or a subset, of the raw data that you are presented during the ask process.

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).

Authentication

See taxize-authentication for help on authentication

Note

There is a timeout of 1/3 seconds between queries to NCBI.

See Also

classification

Other taxonomic-ids: get_boldid, get_colid, get_eolid, get_gbifid, get_iucn, get_natservid, get_nbnid, get_tolid, get_tpsid, get_tsn, get_uid, get_wiki, get_wormsid

Examples

## Not run: 
# Plug in taxon names directly
## By default you get ids for all data sources
get_ids(names="Chironomus riparius")

# specify rows to limit choices available
get_ids(names="Poa annua", db=c("col","eol"), rows=1)
get_ids(names="Poa annua", db=c("col","eol"), rows=1:2)

## Or you can specify which source you want via the db parameter
get_ids(names="Chironomus riparius", db = 'ncbi')
get_ids(names="Salvelinus fontinalis", db = 'nbn')

get_ids(names=c("Chironomus riparius", "Pinus contorta"), db = 'ncbi')
get_ids(names=c("Chironomus riparius", "Pinus contorta"), db = c('ncbi','itis'))
get_ids(names=c("Chironomus riparius", "Pinus contorta"), db = c('ncbi','itis','col'))
get_ids(names="Pinus contorta", db = c('ncbi','itis','col','eol','tropicos'))
get_ids(names="ava avvva", db = c('ncbi','itis','col','eol','tropicos'))

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

# Get all data back
get_ids_(c("Chironomus riparius", "Pinus contorta"), db = 'nbn', rows=1:10)
get_ids_(c("Chironomus riparius", "Pinus contorta"), db = c('nbn','gbif'), rows=1:10)

# use curl options
get_ids("Agapostemon", db = "ncbi", verbose = TRUE)

## End(Not run)
[Package taxize version 0.9.3 Index]