taxize: get_ids – R documentation

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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(
  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.

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

Taxonomic Information from Around the Web

v0.9.100

MIT + file LICENSE

Authors

Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>), Eduard Szoecs [aut], Zachary Foster [aut, cre], Zebulun Arendsee [aut], Carl Boettiger [ctb], Karthik Ram [ctb], Ignasi Bartomeus [ctb], John Baumgartner [ctb], James O'Donnell [ctb], Jari Oksanen [ctb], Bastian Greshake Tzovaras [ctb], Philippe Marchand [ctb], Vinh Tran [ctb], Maëlle Salmon [ctb], Gaopeng Li [ctb], Matthias Grenié [ctb], rOpenSci [fnd] (https://ropensci.org/)

Initial release