R: Get the uBio id for a search term

get_ubioid {taxize} | R Documentation

## Get the uBio id for a search term

### Description

THIS FUNCTION IS DEFUNCT.

### Usage

    get_ubioid(searchterm, searchtype = "scientific", ask = TRUE,
      verbose = TRUE, rows = NA, family = NULL, rank = NULL, ...)

    as.ubioid(x, check = TRUE)

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

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

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

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

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

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

    get_ubioid_(searchterm, verbose = TRUE, searchtype = "scientific",
      rows = NA)

### Arguments

`searchterm` | character; A vector of common or scientific names.
`searchtype` | character; One of 'scientific' or 'common', or any unique abbreviation
`ask` | logical; should get_tsn be run in interactive mode? If TRUE and more than one TSN is found for teh 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 ubioid class object with one to many identifiers. See `get_ubioid_` 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.
`...` | Ignored
`x` | Input to `as.ubioid`
`check` | logical; Check if ID matches any existing on the DB, only used in `as.ubioid`

### Value

A vector of uBio ids. If a taxon is not found NA is given. If more than one uBio id is found the function asks for user input (if ask = TRUE), otherwise returns NA. Comes with an attribute match to investigate the reason for NA (either 'not found', 'found' or if ask = FALSE 'NA due to ask=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_uid`, `ubio_search`

[Package taxize version 0.9.0 Index]