Encode an authority-prefixed taxon_key — taxon_key

The single rule for minting the global taxon key, stated once:

Usage

taxon_key_of(worms_id, itis_id = NA_integer_, class = NA_character_)

Arguments

worms_id: integer WoRMS AphiaID(s) (NA where unknown)
itis_id: integer ITIS TSN(s) (NA where unknown)
class: character; the taxon's class from the lineage ("Aves" selects the itis: authority). NA means "not known to be Aves".

Value

character vector of taxon_keys (NA where no authority id resolves)

Details

A taxon keys itis:<tsn> exactly when its class is Aves and an acceptedTSN resolves; otherwise worms:<aphia>; otherwise NA, which callersturn into the dataset-local fallback <dataset_key>:<code> thatcheck_taxon_ids() refuses unless allow-listed.

The class is a fact from the authority's classification (staged by ensure_taxon_lineage()), not a flag a source declares: only one dataset ever carried an is_bird column, so Aves reaching the release through any other dataset would have keyed worms: and one species could have carried two keys. Birds key on ITIS because WoRMS bird taxonomy lags (it still says Oceanodroma, Puffinus, Phalacrocorax). A bird with no accepted TSN keys worms: and gets a note in taxon.notes — visible, not silent. All prefixes are lowercase. Vectorized over the ids; class recycles.

Examples

taxon_key_of(217452L, 161729L)                       # "worms:217452"  (Pacific sardine)
#> [1] "worms:217452"
taxon_key_of(137179L, 174715L, class = "Aves")       # "itis:174715"   (Great Cormorant)
#> [1] "itis:174715"
taxon_key_of(137179L, NA_integer_, class = "Aves")   # "worms:137179"  (a bird with no TSN)
#> [1] "worms:137179"