R: Get the OTT id for a search term

get_tolid {taxize} | R Documentation

## Get the OTT id for a search term

### Description

Retrieve the Open Tree of Life Taxonomy (OTT) id of a taxon from OpenTreeOfLife

### Usage

    get_tolid(sciname, ask = TRUE, verbose = TRUE, rows = NA, ...)

    as.tolid(x, check = TRUE)

    ## S3 method for class 'tolid'
    as.tolid(x, check = TRUE)

    ## S3 method for class 'character'
    as.tolid(x, check = TRUE)

    ## S3 method for class 'list'
    as.tolid(x, check = TRUE)

    ## S3 method for class 'numeric'
    as.tolid(x, check = TRUE)

    ## S3 method for class 'data.frame'
    as.tolid(x, check = TRUE)

    ## S3 method for class 'tolid'
    as.data.frame(x, ...)

    get_tolid_(sciname, verbose = TRUE, rows = NA)

### Arguments

`sciname` | character; scientific name.
`ask` | logical; should `get_tolid` be run in interactive mode? If `TRUE` and more than one TOL is found for the species, the user is asked for input. If `FALSE` NA is returned for multiple matches.
`verbose` | logical; should progress be printed?
`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 tol class object with one to many identifiers. See `get_tolid_` to get back all, or a subset, of the raw data that you are presented during the ask process.
`...` | Ignored
`x` | Input to `as.tolid`
`check` | logical; Check if ID matches any existing on the DB, only used in `as.tolid`

### 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.

See `get_id_details` for further details including attributes and exceptions

### See Also

`classification`

Other taxonomic-ids: `get_boldid`, `get_colid`, `get_eolid`, `get_gbifid`, `get_ids`, `get_iucn`, `get_natservid`, `get_nbnid`, `get_tpsid`, `get_tsn`, `get_uid`, `get_wiki`, `get_wormsid`

### Examples

    ## Not run:
    get_tolid(sciname = "Quercus douglasii")
    get_tolid(sciname = "Chironomus riparius")
    get_tolid(c("Chironomus riparius","Quercus douglasii"))
    splist <- c("annona cherimola", 'annona muricata', "quercus robur",
    		"shorea robusta", "pandanus patina", "oryza sativa", "durio zibethinus")
    get_tolid(splist, verbose=FALSE)

    # specify rows to limit choices available
    get_tolid('Arni')
    get_tolid('Arni', rows=1)
    get_tolid('Arni', rows=1:2)

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

    # Convert a tol without class information to a tol class
    as.tolid(get_tolid("Quercus douglasii")) # already a tol, returns the same
    as.tolid(get_tolid(c("Chironomus riparius","Pinus contorta"))) # same
    as.tolid(3930798) # numeric
    as.tolid(c(3930798,515712,872577)) # numeric vector, length > 1
    as.tolid("3930798") # character
    as.tolid(c("3930798","515712","872577")) # character vector, length > 1
    as.tolid(list("3930798","515712","872577")) # list, either numeric or character
    ## dont check, much faster
    as.tolid("3930798", check=FALSE)
    as.tolid(3930798, check=FALSE)
    as.tolid(c("3930798","515712","872577"), check=FALSE)
    as.tolid(list("3930798","515712","872577"), check=FALSE)

    (out <- as.tolid(c(3930798,515712,872577)))
    data.frame(out)
    as.tolid( data.frame(out) )

    # Get all data back
    get_tolid_(sciname="Arni")
    get_tolid_("Arni", rows=1)
    get_tolid_("Arni", rows=1:2)
    get_tolid_(c("asdfadfasd","Pinus contorta"))

    ## End(Not run)

[Package taxize version 0.9.0 Index]