get_id_details: Details on get_*() functions

In ropensci/taxize: Taxonomic Information from Around the Web

Details on ⁠get_*()⁠ functions

Description

Including outputs from ⁠get_*()⁠ functions, as well as their attributes, and all exception behaviors.

Details

This document applies to the following functions:

• get_boldid()

• get_eolid()

• get_gbifid()

• get_ids()

• get_iucn()

• get_natservid()

• get_nbnid()

• get_tolid()

• get_tpsid()

• get_tsn()

• get_ubioid()

• get_uid()

• get_wiki()

• get_wormsid()

attributes

Each output from ⁠get_*()⁠ functions have the following attributes:

• match (character) - the reason for NA, either 'not found', 'found' or if ask = FALSE then 'NA due to ask=FALSE')

• multiple_matches (logical) - Whether multiple matches were returned by the data source. This can be TRUE, even if you get 1 name back because we try to pattern match the name to see if there's any direct matches. So sometimes this attribute is TRUE, as well as pattern_match, which then returns 1 resulting name without user prompt.

• pattern_match (logical) - Whether a pattern match was made. If TRUE thenmultiple_matches must be TRUE, and we found a perfect match to your name, ignoring case. If FALSE, there wasn't a direct match, and likely you need to pick from many choices or further parameters can be used to limit results

• uri (character) - The URI where more information can be read on the taxon

• includes the taxonomic identifier in the URL somewhere. This may be missing if the value returned is NA

exceptions

The following are the various ways in which ⁠get_*()⁠ functions behave:

• success - the value returned is a character string or numeric

• no matches found - you'll get an NA, refine your search or possible the taxon searched for does not exist in the database you're using

• more than on match and ask = FALSE - if there's more than one matching result, and you have set ask = FALSE, then we can't determine the single match to return, so we give back NA. However, in this case we do set the match attribute to say ⁠NA due to ask=FALSE & > 1 result⁠ so it's very clear what happened - and you can even programatically check this as well

• NA due to some other reason - some ⁠get_*()⁠ functions have additional parameters for filtering taxa. It's possible that even though there's results (that is, found will say TRUE), you can get back an NA. This is most likely if the parameter filters taxa after they are returned from the data provider and the value passed to the parameter leads to no matches.

ropensci/taxize documentation built on Jan. 25, 2024, 6:49 p.m.