wm_external {worrms}

Get an external ID via an AphiaID

Description

Get an external ID via an AphiaID

Usage

wm_external(id, type = "tsn", ...)

wm_external_(id = NULL, name = NULL, type = "tsn", ...)

Arguments

id

(numeric/integer) an AphiaID. For wm_external it's required and must be length(id) == 1, for wm_external_ it's optional and can be length(id) >= 1

type

(character) the type of external id. one of: tsn, bold, dyntaxa, eol, fishbase, iucn, lsid, ncbi, gisd. default: tsn

...

named curl options. see curl::curl_options

name

(character) one or more taxonomic names. optional

Value

An integer that is the ID. When using underscore method, a list, named by the input IDs

Singular vs. plural

Of the two sister functions, the one without the underscore is the original function that wraps the relavant WoRMS API method - and only accepts one thing (i.e., name or AphiaID) per request.

The sister function with the underscore at the end is the plural version, accepting more than one input. Internally this function loops over the non-underscore method, and labels output (whether it's a list or data.frame rows) with the input names or IDs so that you can easily parse output by your inputs.

Examples

## Not run: 
# by default, get a TSN (an ITIS code)
wm_external(id = 1080)

## get many
wm_external_(id = c(1080, 126436))

# BOLD code
wm_external(id = 278468, type = "bold")

# NCBI code
wm_external(id = 278468, type = "ncbi")

# fishbase code
wm_external(id = 278468, type = "fishbase")

# curl options
library(crul)
wm_external(id = 105706, verbose = TRUE)

## End(Not run)