Build the unified taxon reference table — build_taxon

Assembles one authoritative row per distinct taxon_key across every dataset's local taxa plus the WoRMS lineage ancestors (from the pre-built taxon hierarchy table, so parent_taxon_key chains resolve for descendant expansion). Duplicate taxa across datasets collapse — e.g. Appendicularia (AphiaID 146421) in both zoodb_taxon and zooscan_taxon becomes one worms:146421 row. Names/rank/lineage are coalesced with source priority (WoRMS hierarchy > CalCOFI species / seabird-mammal > per-dataset lineage > composite crosswalk). rank_order folds in the old taxa_rank lookup.

Usage

build_taxon_reference(
  con,
  measurement_taxon = NULL,
  overrides = NULL,
  tbl = "taxon"
)

Arguments

con: a DuckDB connection with the per-dataset taxon tables loaded
measurement_taxon: optional data.frame of the composite-type crosswalk (metadata/measurement_taxon.csv) so cufes/phyllosoma/euphausiid taxa, which live in measurement_type names not a taxon table, are included
overrides: optional data.frame of manual id resolution (metadata/taxon_override.csv) for coarse taxa (phyto groups, mammals)
tbl: target table name (default "taxon")

Value

(invisibly) the row count written