checkSpeciesNames: Check species names against the ITIS taxonomic database

In camtrapR: Camera Trap Data Management and Preparation of Occupancy and Spatial Capture-Recapture Analyses

Check species names against the ITIS taxonomic database

Description

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.

Usage

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.

Details

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

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.

Author(s)

Juergen Niedballa

References

http://www.itis.gov/

Examples

## Not run: 


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

## End(Not run)

camtrapR documentation built on May 29, 2024, 6:45 a.m.