R: Get Worms ID for a taxon name

get_wormsid {taxize} | R Documentation

## Get Worms ID for a taxon name

### Description

Retrieve Worms ID of a taxon from World Register of Marine Species (WORMS).

### Usage

    get_wormsid(query, searchtype = "scientific", accepted = FALSE,
      ask = TRUE, verbose = TRUE, rows = NA, ...)

    as.wormsid(x, check = TRUE)

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

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

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

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

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

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

    get_wormsid_(query, verbose = TRUE, searchtype = "scientific",
      accepted = TRUE, rows = NA, ...)

### Arguments

`query` | 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 WORMS. Set to `FALSE` (default) to give back both accepted and unaccepted names.
`ask` | logical; should get_wormsid be run in interactive mode? If `TRUE` and more than one wormsid 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 NaN, all rows are considered. Note that this function still only gives back a wormsid class object with one to many identifiers. See `get_wormsid_` to get back all, or a subset, of the raw data that you are presented during the ask process.
`...` | Ignored
`x` | Input to as.wormsid
`check` | logical; Check if ID matches any existing on the DB, only used in `as.wormsid`

### 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_tsn`, `get_uid`, `get_wiki`

### Examples

    ## Not run:
    (x <- get_wormsid('Platanista gangetica'))
    attributes(x)
    attr(x, "match")
    attr(x, "multiple_matches")
    attr(x, "pattern_match")
    attr(x, "uri")

    get_wormsid('Gadus morhua')
    get_wormsid('Pomatomus saltatrix')
    get_wormsid(c("Platanista gangetica", "Lichenopora neapolitana"))

    # by common name
    get_wormsid("dolphin", 'common')
    get_wormsid("clam", 'common')

    # specify rows to limit choices available
    get_wormsid('Plat')
    get_wormsid('Plat', rows=1)
    get_wormsid('Plat', rows=1:2)

    # When not found
    get_wormsid("howdy")
    get_wormsid(c('Gadus morhua', "howdy"))

    # Convert a wormsid without class information to a wormsid class
    # already a wormsid, returns the same
    as.wormsid(get_wormsid('Gadus morhua'))
    # same
    as.wormsid(get_wormsid(c('Gadus morhua', 'Pomatomus saltatrix')))
    # numeric
    as.wormsid(126436)
    # numeric vector, length > 1
    as.wormsid(c(126436,151482))
    # character
    as.wormsid("126436")
    # character vector, length > 1
    as.wormsid(c("126436","151482"))
    # list, either numeric or character
    as.wormsid(list("126436","151482"))
    ## dont check, much faster
    as.wormsid("126436", check=FALSE)
    as.wormsid(126436, check=FALSE)
    as.wormsid(c("126436","151482"), check=FALSE)
    as.wormsid(list("126436","151482"), check=FALSE)

    (out <- as.wormsid(c(126436,151482)))
    data.frame(out)
    as.wormsid( data.frame(out) )

    # Get all data back
    get_wormsid_("Plat")
    get_wormsid_("Plat", rows=1)
    get_wormsid_("Plat", rows=1:2)
    get_wormsid_("Plat", rows=1:75)
    # get_wormsid_(c("asdfadfasd","Plat"), rows=1:5)

    ## End(Not run)

[Package taxize version 0.9.0 Index]