get_ids(
names,
db = getOption("taxadb_default_provider", "itis"),
format = c("prefix", "bare", "uri"),
version = latest_version(),
taxadb_db = td_connect(),
ignore_case = TRUE,
...
)
Arguments
names
a list of scientific names (which may
include higher-order ranks in most authorities).
db
abbreviation code for the provider. See 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).
version
Which version of the taxadb provider database should we use?
defaults to latest. see [avialable_releases()] for details.
taxadb_db
Connection to from [td_connect()].
ignore_case
should we ignore case (capitalization) in matching names?
default is TRUE.
...
additional arguments (currently ignored)
Value
a vector of IDs, of the same length as the input names Any
unmatched names or multiply-matched names will return as NAs.
To resolve multi-matched names, use [filter_name()] instead to return
a table with a separate row for each separate match of the input name.
Details
Note that some taxize authorities: nbn, tropicos, and eol,
are not recognized by taxadb and will throw an error here. Meanwhile,
taxadb recognizes several authorities not known to [taxize::get_ids()].
Both include itis, ncbi, col, and gbif.
Like all taxadb functions, this function will run
fastest if a local copy of the provider is installed in advance
using [td_create()].