taxize (version 0.5.2)

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, rows = NA,
  ...)
as.tpsid(x, check = TRUE)
## S3 method for class 'tpsid':
as.tpsid(x, check = TRUE)
## S3 method for class 'character':
as.tpsid(x, check = TRUE)
## S3 method for class 'list':
as.tpsid(x, check = TRUE)
## S3 method for class 'numeric':
as.tpsid(x, check = TRUE)
## S3 method for class 'data.frame':
as.tpsid(x, check = TRUE)
## S3 method for class 'tpsid':
as.data.frame(x, ...)
get_tpsid_(sciname, verbose = TRUE, key = NULL, rows = NA, ...)

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.

rows

numeric; Any number from 1 to inifity. If the default NA, all rows are considered. Note that this function still only gives back a tpsid class object with one to many identifiers. See get_tpsid_ to

...

Other arguments passed to tp_search.

x

Input to as.tpsid

check

logical; Check if ID matches any existing on the DB, only used in as.tpsid

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_tpsid

Examples

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

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

# specify rows to limit choices available
get_tpsid('Poa annua')
get_tpsid('Poa annua', rows=1)
get_tpsid('Poa annua', rows=25)
get_tpsid('Poa annua', rows=1:2)

# 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"))

# Convert a tpsid without class information to a tpsid class
as.tpsid(get_tpsid("Pinus contorta")) # already a tpsid, returns the same
as.tpsid(get_tpsid(c("Chironomus riparius","Pinus contorta"))) # same
as.tpsid(24900183) # numeric
as.tpsid(c(24900183,50150089,50079838)) # numeric vector, length > 1
as.tpsid("24900183") # character
as.tpsid(c("24900183","50150089","50079838")) # character vector, length > 1
as.tpsid(list("24900183","50150089","50079838")) # list, either numeric or character
## dont check, much faster
as.tpsid("24900183", check=FALSE)
as.tpsid(24900183, check=FALSE)
as.tpsid(c("24900183","50150089","50079838"), check=FALSE)
as.tpsid(list("24900183","50150089","50079838"), check=FALSE)

(out <- as.tpsid(c(24900183,50150089,50079838)))
data.frame(out)
as.tpsid( data.frame(out) )

# Get all data back
get_tpsid_("Poa annua")
get_tpsid_("Poa annua", rows=2)
get_tpsid_("Poa annua", rows=1:2)
get_tpsid_(c("asdfadfasd","Pinus contorta"), rows=1:5)