get_names: get_names

In cboettig/taxadb: A High-Performance Local Taxonomic Database Interface

get_names

Description

Translate identifiers into scientific names

Usage

get_names(
  id,
  provider = getOption("taxadb_default_provider", "itis"),
  version = latest_version(),
  format = c("guess", "prefix", "bare", "uri"),
  taxadb_db = td_connect(),
  db = NULL
)

Arguments

id	a list of taxonomic identifiers.
provider	abbreviation code for the provider. See details.
version	Which version of the taxadb provider database should we use? defaults to latest. see ⁠[avialable_releases()]⁠ for details.
format	Format for the returned identifier, one of prefix (e.g. NCBI:9606, the default), or bare (e.g. 9606, used in taxize::get_ids()), uri (e.g. ⁠http://ncbi.nlm.nih.gov/taxonomy/9606⁠).
taxadb_db	Connection to from ⁠[td_connect()]⁠.
db	previous name for provider argument, now deprecated

Details

Like all taxadb functions, this function will run fastest if a local copy of the provider is installed in advance using ⁠[td_create()]⁠.

Value

a vector of names, of the same length as the input ids. Any unmatched IDs will return as NAs.

See Also

Other get: get_ids()

Examples

get_names(c("ITIS:1025094", "ITIS:1025103"), format = "prefix")

cboettig/taxadb documentation built on April 17, 2024, 6:34 p.m.