taxize (version 0.7.9)

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)
"as.tpsid"(x, check = TRUE)
"as.tpsid"(x, check = TRUE)
"as.tpsid"(x, check = TRUE)
"as.tpsid"(x, check = TRUE)
"as.tpsid"(x, check = TRUE)
"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 infinity. 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 get back all, or a subset, of the raw data that you are presented during the ask process.

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 below.

...

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 taxonomic identifiers as an S3 class. If a taxon is not found an NA is given. If more than one identifier is found the function asks for user input if ask = TRUE, otherwise returns NA. If ask=FALSE and rows does not equal NA, then a data.frame is given back, but not of the uid class, which you can't pass on to other functions as you normally can.Comes with the following attributes:

• match (character) - the reason for NA, either 'not found', 'found' or if ask = FALSE then 'NA due to ask=FALSE')
• multiple_matches (logical) - Whether multiple matches were returned by the data source. This can be TRUE, even if you get 1 name back because we try to pattern match the name to see if there's any direct matches. So sometimes this attribute is TRUE, as well as pattern_match, which then returns 1 resulting name without user prompt.
• pattern_match (logical) - Whether a pattern match was made. If TRUE then multiple_matches must be TRUE, and we found a perfect match to your name, ignoring case. If FALSE

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. Filtering narrows down to the set that matches your query, and removes the rest.

See Also

get_tsn, get_uid, get_nbnid, get_eolid, get_colid, get_gbifid, get_ids, classification

Examples

## Not run: 
# 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())
# ## End(Not run)