Build Taxonomic Hierarchy Table from WoRMS

For each unique worms_id in the species table, retrieves the full classification from WoRMS (kingdom, phylum, class, order, family, genus, species) and stores it in a taxon table. Optionally also fetches ITIS classification.

Usage

build_taxon_table(
  con,
  species_tbl = "species",
  taxon_tbl = "taxon",
  include_itis = TRUE,
  batch_size = 50
)

Arguments

con

DBI connection to DuckDB

species_tbl

character; name of species table with worms_id column

taxon_tbl

character; name for output taxon table (default "taxon")

include_itis

logical; also fetch ITIS classification (default TRUE)

batch_size

integer; number of species per API batch (default 50)

Value

tibble of taxon hierarchy rows written to con

Details

Also creates a taxa_rank lookup table with rank ordering consistent with the WoRMS taxonomy hierarchy.

Examples

if (FALSE) { # \dontrun{
con <- get_duckdb_con("calcofi.duckdb")
taxon_rows <- build_taxon_table(con)
} # }