Build Taxon Hierarchy from Local spp.duckdb via Recursive CTEs

Builds the taxon and taxa_rank tables using recursive CTEs against the local MarineSensitivity species database (spp.duckdb). This is much faster than build_taxon_table() which queries WoRMS/ITIS APIs for each species.

Usage

build_taxon_hierarchy(
  con,
  spp_db_path,
  species_tbl = "species",
  overwrite = FALSE
)

Arguments

con

DBI connection to DuckDB with a species table containing worms_id and itis_id columns

spp_db_path

Path to the MarineSensitivity spp.duckdb file

species_tbl

Character; name of species table (default "species")

overwrite

Logical; if TRUE, rebuild even if taxon table exists (default FALSE)

Value

Tibble of taxon hierarchy rows written to con

Details

Creates both WoRMS and ITIS hierarchies by walking up the parentNameUsageID chain from each species' WoRMS/ITIS ID.

Examples

if (FALSE) { # \dontrun{
con <- get_duckdb_con("calcofi.duckdb")
taxon <- build_taxon_hierarchy(
  con         = con,
  spp_db_path = "/path/to/spp.duckdb")
} # }