Build the taxon_group grouping table (many taxa per group)

Seeds portable, cross-dataset groupings (taxon_group_key = "<dataset-or-known-list>:<group>", lowercase; a description; many taxon_key) from the groupings each dataset already carries — phytoplankton functional groups (phyto_taxon.taxa, e.g. diatom, centric) and the seabird/mammal is_bird/is_mammal flags. Curated calcofi:* groups (e.g. forage_fish) can be appended later.

Usage

build_taxon_group(
  con,
  measurement_taxon = NULL,
  overrides = NULL,
  tbl = "taxon_group"
)

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_group")

Value

(invisibly) the row count written