Standardize Species Identifiers Using WoRMS/ITIS/GBIF APIs

For each species in the species table, queries WoRMS (via worrms package) to get the current accepted AphiaID, then queries ITIS (via taxize) for the ITIS TSN, and optionally GBIF for the GBIF backbone key. Updates the species table with canonical identifiers.

Usage

standardize_species(
  con,
  species_tbl = "species",
  id_col = "species_id",
  sci_name_col = "scientific_name",
  update_in_place = TRUE,
  include_gbif = TRUE,
  batch_size = 50
)

Arguments

con

DBI connection to DuckDB with species table

species_tbl

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

id_col

character; name of species ID column (default "species_id")

sci_name_col

character; column with scientific names (default "scientific_name")

update_in_place

logical; if TRUE, UPDATE the table directly (default TRUE)

include_gbif

logical; if TRUE, also query GBIF backbone (default TRUE)

batch_size

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

Value

tibble with species_id, scientific_name, worms_id (AphiaID), itis_id (TSN), gbif_id, taxonomic_status, accepted_name

Examples

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