Build the taxon_group grouping table (many taxa per group) from the registry

Groups come from metadata/taxon_group.csv (taxon plan D4), not from code:

Usage

build_taxon_group(con, rules = NULL, tbl = "taxon_group", ...)

Arguments

con: a DuckDB connection holding taxon and dataset_taxon
rules: the registry as read by read_taxon_group_rules(), or a path to it. NULL looks for metadata/taxon_group.csv under here::here().
tbl: target table name (default "taxon_group")
...: the pre-3.29 measurement_taxon / overrides arguments, accepted with a deprecation warning and ignored (the groups are not derived from them any more)

Value

(invisibly) the row count written

Details

class — every vocabulary taxon whose released class equals rule_value: calcofi:seabirds = Aves, calcofi:marine_mammals = Mammalia. Cross-dataset by construction; no dataset column. Scoped to taxa some dataset actually observes (present in dataset_taxon), never to a bare lineage ancestor — a group selects observed taxa, and the ancestors are reachable through parent_taxon_key anyway.
dataset_taxon — by (dataset_key, match_column, match_value) against dataset_taxon, the same matcher taxon_override.csv uses: the phytoplankton functional groups on ds_common_name.

A rule naming a match_column the vocabulary lacks errors; a rule for a dataset absent from this connection is skipped (it is another ingest's), and check_taxon_registries() catches one nobody supplies at the release. Needs taxon and dataset_taxon in con, i.e. call it after build_taxon_reference() and resolve_dataset_taxon().