taxize (version 0.3.0)

get_tsn: Get the TSN code for a search term.

Description

Retrieve the taxonomic serial numbers (TSN) of a taxon from ITIS.

Usage

get_tsn(searchterm, searchtype = "scientific", accepted = TRUE,
  ask = TRUE, verbose = TRUE)

Arguments

searchterm

character; A vector of common or scientific names.

searchtype

character; One of 'scientific' or 'common', or any unique abbreviation

accepted

logical; If TRUE (default), removes names that are not accepted valid names by ITIS. Set to FALSE to give back both accepted and unaccepted names.

ask

logical; should get_tsn be run in interactive mode? If TRUE and more than one TSN is found for teh species, the user is asked for input. If FALSE NA is returned for multiple matches.

verbose

logical; should progress be printed?

Value

• A vector of taxonomic serial numbers (TSN). If a taxon is not found NA. If more than one TSN is found the function asks for user input (if ask = TRUE), otherwise returns NA. Comes with an attribute match to investigate the reason for NA (either 'not found', 'found' or if ask = FALSE 'multi match')

See Also

get_uid, classification

Examples

get_tsn(searchterm = "Quercus douglasii")
get_tsn(searchterm = "Chironomus riparius")
get_tsn(c("Chironomus riparius","Quercus douglasii"))
splist <- c("annona cherimola", 'annona muricata', "quercus robur",
		"shorea robusta", "pandanus patina", "oryza sativa", "durio zibethinus")
get_tsn(splist, verbose=FALSE)

# When not found
get_tsn("howdy")
get_tsn(c("Chironomus riparius", "howdy"))

# Using common names
get_tsn(searchterm="black bear", searchtype="c")