Standardize Species Using Local spp.duckdb Lookups — standardize_species

Updates the species table with WoRMS AphiaID, ITIS TSN, and GBIF backbone key using fast SQL joins against a local MarineSensitivity species database (spp.duckdb). Falls back to the WoRMS API only for species not found locally.

Usage

standardize_species_local(
  con,
  spp_db_path,
  species_tbl = "species",
  overwrite = FALSE,
  api_fallback = TRUE
)

Arguments

con: DBI connection to DuckDB with a species table
spp_db_path: Path to the MarineSensitivity spp.duckdb file
species_tbl: Character; name of species table (default "species")
overwrite: Logical; if TRUE, re-standardize even if columns already populated (default FALSE)
api_fallback: Logical; if TRUE, query WoRMS API for species not found locally (default TRUE)

Value

Tibble with species_id, scientific_name, worms_id, itis_id, gbif_id

Details

This is much faster than standardize_species() which queries external APIs for every species. Intended for use in ingest workflows where the local spp.duckdb is available.

Examples

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