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,
  family = NULL, rank = NULL, ...)
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

family

(character) A family name. Optional. See Filtering below.

rank

(character) A taxonomic rank name. See rank_ref for possible options. Though note that some data sources use atypical ranks, so inspect the data itself for options. Optional. See Filtering bel

...

Other arguments passed to tp_search.

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.

Filtering

The parameters family and rank are not used in the search to the data provider, but are used in filtering the data down to a subset that is closer to the target you want. For all these parameters, you can use regex strings since we use grep internally to match.

Examples

Run this code

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"))

# Narrow down results to a division or rank, or both
## Satyrium example
### Results w/o narrowing
get_tpsid("Satyrium")
### w/ rank
get_tpsid("Satyrium", rank = "var.")
get_tpsid("Satyrium", rank = "sp.")

## w/ family
get_tpsid("Poa")
get_tpsid("Poa", family = "Iridaceae")
get_tpsid("Poa", family = "Orchidaceae")
get_tpsid("Poa", family = "Orchidaceae", rank = "gen.")

# Fuzzy filter on any filtering fields
## uses grep on the inside
get_tpsid("Poa", family = "orchidaceae")
get_tpsid("Aga", fuzzy = TRUE, parent = "*idae")

# 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)

# use curl options
library("httr")
get_tpsid("Quercus douglasii", config=verbose())
bb <- get_tpsid("Quercus douglasii", config=progress())