Build the dataset_taxon crosswalk (per-dataset vocabulary -> taxon)

One row per (dataset, local taxon): the dataset's own ds_taxon_key ("<dataset-or-known-list>:<local id>", all lowercase — e.g. calcofi:19 for the shared CalCOFI species list, cce-lter_zoodb:3 otherwise), its ds_scientific_name / ds_common_name / ds_taxa_code, and the global taxon_key it resolves to. Deduped on ds_taxon_key.

Usage

build_dataset_taxon(
  con,
  measurement_taxon = NULL,
  overrides = NULL,
  tbl = "dataset_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 "dataset_taxon")

Value

(invisibly) the row count written