get_ids: Retrieve taxonomic identifiers for a given taxon name.

In taxize: Taxonomic Information from Around the Web

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(
  sci_com,
  db = c("itis", "ncbi", "eol", "tropicos", "gbif", "nbn", "pow"),
  suppress = FALSE,
  names = NULL,
  ...
)

get_ids_(
  sci_com,
  db = get_ids_dbs,
  rows = NA,
  suppress = FALSE,
  names = NULL,
  ...
)

Arguments

sci_com	(character) Taxonomic name to query.
db	(character) database to query. One or more of ncbi, itis, eol, tropicos, gbif, nbn, or pow. By default db is set to search all data sources. Note that each taxonomic data source has their own identifiers, so that if you give the wrong db value for the identifier you could get a result, it will likely be wrong (not what you were expecting). If using ncbi and/or tropicos we recommend getting API keys; see taxize-authentication
suppress	(logical) suppress cli separators with the database name being queried. default: FALSE
names	Deprecated, see sci_com
...	Other arguments passed to get_tsn(), get_uid(), get_eolid(), 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_eolid(), get_gbifid(), get_iucn(), get_natservid(), get_nbnid(), get_pow(), get_tolid(), get_tpsid(), get_tsn(), get_uid(), get_wiki(), get_wormsid()

Examples

## Not run: 
# Plug in taxon names directly
# specify rows to limit choices available
get_ids("Poa annua", db="eol", rows=1)
get_ids("Poa annua", db="eol", rows=1:2)

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

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

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

# 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)

taxize documentation built on Sept. 11, 2024, 6:13 p.m.