Retrieve COL and other database IDs — div_db

This function is used to retrieve the Catelogue of Life id and any additional database ids for each species in a data frame. This function requires the package 'taxize'

div_db_ids(data, species, db = NULL)

Arguments

data: A data frame
species: A character equal to the column name of the data frame that holds the species names
db: Optional. A character or vector eaqual to the data base names for which you want the ids in addition to Catelogue of Life (COL). By default only COL ids are returned. The possible data bases are Integrated Taxonomic Information System ('itis'), Global Biodiversity Information Facility ('gbif'), and The National Center for Biotechnology Information ('ncbi')

Value

A data frame with the COL IDs and the IDs of any other biodiversity database give in the db

parameter

Details

NOTE: Catelogue of Life is not supported by 'taxize' anymore... check back later for its incorporation

Examples

if (FALSE) {

library(here)
library(taxize)

herp <- read.csv(file.path(here(), 'data_raw', 'IBT_Herp_Records_final.csv'), header=TRUE)

ids <- div_db_ids(data = herp,
                  species = 'binomial',
                  db = c('itis', 'gbif', 'ncbi'))

}