R: Retrieve immediate children taxa for a given taxon name or...

children {taxize} | R Documentation

## Retrieve immediate children taxa for a given taxon name or ID.

### Description

This function is different from `downstream` in that it only collects immediate taxonomic children, while `downstream` collects taxonomic names down to a specified taxonomic rank, e.g., getting all species in a family.

### Usage

    children(...)

    ## Default S3 method:
    children(x, db = NULL, rows = NA, ...)

    ## S3 method for class 'tsn'
    children(x, db = NULL, ...)

    ## S3 method for class 'colid'
    children(x, db = NULL, ...)

    ## S3 method for class 'wormsid'
    children(x, db = NULL, ...)

    ## S3 method for class 'ids'
    children(x, db = NULL, ...)

    ## S3 method for class 'uid'
    children(x, db = NULL, ...)

### Arguments

`...` | Further args passed on to `col_children`, `hierarchy_down`, `ncbi_children`, or `wm_children` See those functions for what parameters can be passed on.
`x` | Vector of taxa names (character) or IDs (character or numeric) to query.
`db` | character; database to query. One or more of `itis`, `col`, `ncbi`, or `worms`. Note that each taxonomic data source has their own identifiers, so that if you provide the wrong `db` value for the identifier you could get a result, but it will likely be wrong (not what you were expecting).
`rows` | (numeric) Any number from 1 to infinity. If the default NA, all rows are considered. Note that this parameter is ignored if you pass in a taxonomic id of any of the acceptable classes: tsn, colid. NCBI has a method for this function but rows doesn't work.

### Value

A named list of data.frames with the children names of every supplied taxa. You get an NA if there was no match in the database.

### Examples

    ## Not run:
    # Plug in taxonomic IDs
    children(161994, db = "itis")
    children(8028, db = "ncbi")
    children("578cbfd2674a9b589f19af71a33b89b6", db = "col")
    ## works with numeric if as character as well
    children("161994", db = "itis")

    # Plug in taxon names
    children("Salmo", db = 'col')
    children("Salmo", db = 'itis')
    children("Salmo", db = 'ncbi')
    children("Salmo", db = 'worms')

    # Plug in IDs
    (id <- get_colid("Apis"))
    children(id)

    (id <- get_wormsid("Platanista"))
    children(id)

    ## Equivalently, plug in the call to get the id via e.g., get_colid
    ## into children
    (id <- get_colid("Apis"))
    children(id)
    children(get_colid("Apis"))

    # Many taxa
    sp <- c("Tragia", "Schistocarpha", "Encalypta")
    children(sp, db = 'col')
    children(sp, db = 'itis')

    # Two data sources
    (ids <- get_ids("Apis", db = c('col','itis')))
    children(ids)
    ## same result
    children(get_ids("Apis", db = c('col','itis')))

    # Use the rows parameter
    children("Poa", db = 'col')
    children("Poa", db = 'col', rows=1)

    # use curl options
    library("httr")
    res <- children("Poa", db = 'col', rows=1, config=verbose())

    ## End(Not run)

[Package taxize version 0.9.0 Index]