Materialize the authority cross-reference .taxon_norm_sources() reads

Works out which identifiers this dataset's vocabulary reaches, resolves them (cached), and stages the result in con as _taxon_xref. Every taxon builder then picks it up automatically: worms_id is filled on ITIS-keyed taxa, itis_id on WoRMS-keyed ones, deprecated ids are replaced by their accepted form, and taxonomic_status / status_checked / notes are carried through.

Usage

ensure_taxon_xref(
  con,
  measurement_taxon = NULL,
  overrides = NULL,
  cache_csv = NULL,
  tbl = "_taxon_xref",
  refresh = FALSE,
  sleep = 0.3,
  verbose = TRUE
)

Arguments

con

a DuckDB connection holding this dataset's taxon vocabulary tables

measurement_taxon

the composite crosswalk (metadata/measurement_taxon.csv), already filtered to this dataset

overrides

the manual id registry (metadata/taxon_override.csv)

cache_csv

path to the shared cross-reference cache (metadata/taxon_xref.csv)

tbl

staging table to write (default "_taxon_xref")

refresh

logical; re-fetch queries already cached (and re-date them)

sleep

seconds between API calls (rate limit)

verbose

logical; report what was cached vs fetched

Value

(invisibly) a list with n_queries, n_resolved, n_rekeyed

Details

Call it before ensure_taxon_lineage() and the three builders — the lineage fetch should ask about the accepted id, not the deprecated one.