R: Get the NameID codes from Tropicos for taxonomic names.

get_tpsid {taxize} | R Documentation

## 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 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.

See `get_id_details` for further details including attributes and exceptions

### 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.

### Author(s)

Scott Chamberlain, myrmecocystus@gmail.com

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

### 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)

[Package taxize version 0.9.0 Index]