taxize (version 0.4.0)

get_tpsid: Get the NameID codes from Tropicos for taxonomic names.

Description

Get the NameID codes from Tropicos for taxonomic names.

Usage

get_tpsid(sciname, ask = TRUE, verbose = TRUE, key = NULL, ...)

Arguments

sciname

(character) One or more scientific name's as a vector or list.

ask

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

verbose

logical; If TRUE the actual taxon queried is printed on the console.

key

Your API key; loads from .Rprofile.

...

Other arguments passed to tp_search.

Value

• A vector of unique identifiers. If a taxon is not found NA. If more than one ID is found the function asks for user input.

See Also

get_tsn, get_uid

Examples

get_tpsid(sciname='Poa annua')
get_tpsid(sciname='Pinus contorta')

get_tpsid(c("Poa annua", "Pinus contorta"))

# When not found, NA given (howdy is not a species name, and Chrinomus is a fly)
get_tpsid("howdy")
get_tpsid(c("Chironomus riparius", "howdy"))

# pass to classification function to get a taxonomic hierarchy
classification(get_tpsid(sciname='Poa annua'))

# factor class names are converted to character internally
spnames <- as.factor(c("Poa annua", "Pinus contorta"))
class(spnames)
get_tpsid(spnames)

# pass in a list, works fine
get_tpsid(list("Poa annua", "Pinus contorta"))