R: Get the TSN code for a search term.

get_tsn {taxize} | R Documentation

## Get the TSN code for a search term.

### Description

Retrieve the taxonomic serial numbers (TSN) of a taxon from ITIS.

### Usage

    get_tsn(searchterm, searchtype = "scientific", accepted = FALSE,
      ask = TRUE, verbose = TRUE, rows = NA, ...)

    as.tsn(x, check = TRUE)

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

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

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

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

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

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

    get_tsn_(searchterm, verbose = TRUE, searchtype = "scientific",
      accepted = TRUE, rows = NA, ...)

### Arguments

`searchterm` | character; A vector of common or scientific names.
`searchtype` | character; One of 'scientific' or 'common', or any unique abbreviation
`accepted` | logical; If TRUE, removes names that are not accepted valid names by ITIS. Set to `FALSE` (default) to give back both accepted and unaccepted names.
`ask` | logical; should get_tsn be run in interactive mode? If `TRUE` and more than one TSN 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 tsn class object with one to many identifiers. See `get_tsn_` to get back all, or a subset, of the raw data that you are presented during the ask process.
`...` | Ignored
`x` | Input to as.tsn
`check` | logical; Check if ID matches any existing on the DB, only used in `as.tsn`

### 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_tolid`, `get_tpsid`, `get_uid`, `get_wiki`, `get_wormsid`

### Examples

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

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

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

    # Using common names
    get_tsn(searchterm="black bear", searchtype="common")

    # Convert a tsn without class information to a tsn class
    as.tsn(get_tsn("Quercus douglasii")) # already a tsn, returns the same
    as.tsn(get_tsn(c("Chironomus riparius","Pinus contorta"))) # same
    as.tsn(19322) # numeric
    as.tsn(c(19322,129313,506198)) # numeric vector, length > 1
    as.tsn("19322") # character
    as.tsn(c("19322","129313","506198")) # character vector, length > 1
    as.tsn(list("19322","129313","506198")) # list, either numeric or character
    ## dont check, much faster
    as.tsn("19322", check=FALSE)
    as.tsn(19322, check=FALSE)
    as.tsn(c("19322","129313","506198"), check=FALSE)
    as.tsn(list("19322","129313","506198"), check=FALSE)

    (out <- as.tsn(c(19322,129313,506198)))
    data.frame(out)
    as.tsn( data.frame(out) )

    # Get all data back
    get_tsn_("Arni")
    get_tsn_("Arni", rows=1)
    get_tsn_("Arni", rows=1:2)
    get_tsn_(c("asdfadfasd","Pinus contorta"), rows=1:5)

    ## End(Not run)

[Package taxize version 0.9.0 Index]