The taxa that no authority resolved, per dataset — reported, and gated

A taxon that reaches the release without an authority id is invisible to any consumer that filters or joins on one, and nothing used to say so. That is how all 128 Farallon taxa and 64,956 observations became unreachable through db-viz-hex::get_sp()'s worms_id join while every check in the pipeline passed.

Usage

check_taxon_ids(con, allow = character(), halt = TRUE, verbose = TRUE)

Arguments

con

a DBI connection holding taxon and dataset_taxon (and obs, if present, for the observation-level counts)

allow

character vector of dataset-local taxon_keys that are known to be unresolvable and are accepted as such

halt

logical; stop() on an unallowlisted local key (default TRUE)

verbose

logical; message the summary

Value

a data.frame, one row per dataset_key, with the taxon- and observation-level counts (invisibly when verbose = FALSE)

Details

Two conditions, deliberately graded differently:

• A dataset-local taxon_key (no worms: / itis: prefix) means no authority resolved this taxon at all. This fails unless the key is in allow — the allowlist is where a genuinely non-taxonomic class such as cce-lter_zooscan:16 (naupliar stage) is declared, in the open, one key at a time. A new unresolved taxon can then never hide among the known ones.

• An authority key with no worms_id is reported but does not fail: WoRMS legitimately lacks some taxa (trinomial subspecies, mostly), and an itis:-keyed bird is correctly keyed either way.