Check species names against the ITIS taxonomic database

The function checks species names (common or scientific names) provided by the user with the ITIS taxonomic database (http://www.itis.gov/) via functions from the package taxize. It returns both common and scientific names, the taxon authors, taxon rank name and status, the TSN (taxonomic serial numbers) and ITIS urls.

checkSpeciesNames(speciesNames, searchtype, accepted = TRUE, ask = TRUE)

Arguments

speciesNames

character. Vector of species names to check. Either common names or scientific names.

searchtype

character. Type of names specified in speciesNames. One of 'scientific' or 'common'.

accepted

logical. Return only accepted valid names? If TRUE, invalid names are returned as NA. Set to FALSE to return both accepted and unaccepted names.

ask

logical. Should the function be run in interactive mode? If TRUE and more than one TSN is found for a species, the user is asked to choose one. If FALSE, NA is returned for multiple matches.

Value

A data.frame with the names supplied by the user, matching common and scientific names, taxon author and year, taxonomic rank, status, TSNs (taxonomic serial numbers) and ITIS urls.

Details

Arguments searchtype, accepted and ask are passed on to get_tsn.

References

http://www.itis.gov/

Author

Juergen Niedballa

Examples

if (FALSE) {


species_common <- c("Leopard Cat", "moonrat")

# ask = TRUE. Multiple matches for leopard cat will cause menu to pop up asking user input.

species.names.check1 <- checkSpeciesNames(speciesNames = species_common,
                                          searchtype   = "common",
                                          accepted     = TRUE,
                                          ask          = TRUE)
2   # we choose entry 2
species.names.check1


# ask = FALSE. Multiple matches for leopard cat will cause NA.

species.names.check2 <- checkSpeciesNames(speciesNames = species_common,
                                          searchtype   = "common",
                                          accepted     = TRUE,
                                          ask          = FALSE)
species.names.check2



# search for scientific names

species_scientific <- c("Tragulus", "Prionailurus bengalensis")

species.names.check3 <- checkSpeciesNames(speciesNames = species_scientific,
                                          searchtype   = "scientific",
                                          accepted     = TRUE,
                                          ask          = TRUE)
species.names.check3
}