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Get WoRMS AphiaIDs from species names

Source: R/utility.R
get_aphia.Rd

Retrieves WoRMS AphiaIDs for one or more scientific species names. By default, the function matches names against the internal species_info table. Optionally, it can query the worrms package to look up AphiaIDs directly from WoRMS.

Usage

get_aphia(x, use_worrms = FALSE)

Arguments

x

A character vector of scientific species names.

use_worrms

Logical; if TRUE, AphiaIDs are retrieved using worrms::wm_name2id(). If FALSE (default), names are matched against the internal species_info table.

Value

If use_worrms = FALSE, an integer vector of WoRMS AphiaIDs with the same length and order as x. Names not found in species_info return NA.

If use_worrms = TRUE, the value returned by worrms::wm_name2id(), which may differ in structure from the internal lookup result depending on the queried names and the response from WoRMS.

Details

Using the internal species_info table provides a fast offline lookup, but only for names included in that table. Using use_worrms = TRUE allows direct lookup from WoRMS, but requires the worrms package to be installed and may depend on internet access.

See also

worrms::wm_name2id()

Examples

get_aphia("Gadus morhua")
#> [1] 126436

get_aphia(c("Gadus morhua", "Melanogrammus aeglefinus"))
#> [1] 126436 126437

if (FALSE) { # \dontrun{
get_aphia("Gadus morhua", use_worrms = TRUE)
} # }