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List every accepted ID of each matched name

Source: R/browse.R
taxify_ids.Rd

taxify() returns one accepted ID per name, and, when any name has several, records in accepted_ids every accepted taxon the backbone files the name under: a homonym published by two authors, or a name held twice, once accepted and once as a doubtful or duplicate record. This verb lays those out one row per (name, accepted ID), resolved against the backbone, with the ID taxify() picked marked. On the GBIF backbone each ID carries its occurrence count, so the IDs to request occurrence data with can be read off directly.

Usage

taxify_ids(x, verbose = TRUE)

Arguments

x

A taxify() result.

verbose

Logical. Default TRUE.

Value

A data.frame with one row per (matched input row, accepted ID), in input order and, within a name, in the order of accepted_ids (the pick first):

input_name

The queried name.

backbone

Backbone that matched the name.

accepted_id

An accepted ID the name resolves to.

gbif_key

The legacy GBIF taxon key(s) of that taxon, the keys GBIF serves occurrence records for: the ID itself on the gbif backbone, and on a backbone whose build carries a crosswalk (COL XR) the |-delimited set of GBIF keys for the same name, several when GBIF files it under more than one. NA on a backbone with no crosswalk.

accepted_name

The name of that accepted taxon.

authorship

Its authorship.

rank

Its rank.

taxonomic_status

Its status in the backbone ("ACCEPTED", GBIF's "DOUBTFUL", WFO's "UNCHECKED", ...).

family

Its family.

n_occurrences

GBIF occurrence records under this ID, including those of its synonyms and descendants (what a GBIF download by this key returns), as counted when the backbone was built. NA on a backbone without counts, and for an ID whose count was not taken.

is_pick

Logical. Is this the accepted_id taxify() reported?

role

What the ID is to the queried name: "pick" (the accepted_id taxify() reported), "same_name" (another record of the same taxon, or a record keeping the queried name as its own concept, as GBIF's doubtful homonym records of Pinus sylvestris do) or "other_taxon" (the accepted taxon of a synonym record under another author, a different species: GBIF files Absinthium vulgare Dulac under Artemisia vulgaris subsp. vulgaris while the pick, Lam., goes to A. absinthium).

pick_basis

What decided the pick over the name's other accepted IDs, the same on every row of a name: "status", "priority" (publication year), "occurrences", "validity", "fuzzy", or "id" when only the lowest taxon ID separated them, which settles nothing about the taxon the name denotes; "authorship", "basionym" or "kingdom" when the input's author, the record's basionym link or the kingdom argument of taxify() moved the pick. NA for a name with one ID.

Unmatched names contribute no rows.

See also

taxify(), synonyms().

Examples

# Runs offline against the bundled example database.
old <- options(taxify.data_dir = taxify_example_data())

taxify(c("Quercus robur", "Pinus sylvestris")) |>
  taxify_ids()

options(old)