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

In taxize: Taxonomic Information from Around the Web

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(sci_id, db = NULL, rows = NA, x = NULL, ...)

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

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

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

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

## S3 method for class 'boldid'
children(sci_id, db = NULL, ...)

Arguments

...	Further args passed on to ritis::hierarchy_down(), ncbi_children(), worrms::wm_children(), bold_children() See those functions for what parameters can be passed on.
sci_id	Vector of taxa names (character) or IDs (character or numeric) to query.
db	character; database to query. One or more of itis, ncbi, worms, or bold. 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). If using ncbi, we recommend getting an API key; see taxize-authentication
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. NCBI has a method for this function but rows doesn't work.
x	Deprecated, see sci_id

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.

ncbi

note that with db = "ncbi", we set ambiguous = TRUE; that is, children taxa with words like "unclassified", "unknown", "uncultured", "sp." are NOT removed

bold

BEWARE: db="bold" scrapes the BOLD website, so may be unstable. That is, one day it may work, and the next it may fail. Open an issue if you encounter an error: https://github.com/ropensci/taxize/issues

Examples

## Not run: 
# Plug in taxonomic IDs
children(161994, db = "itis")
children(8028, db = "ncbi")
## works with numeric if as character as well
children(161994, db = "itis")
children(88899, db = "bold")
children(as.boldid(88899))

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

# Plug in IDs
(id <- get_wormsid("Gadus"))
children(id)

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

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

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

# use curl options
res <- children("Poa", db = 'itis', rows=1, verbose = TRUE)

## End(Not run)

taxize documentation built on Sept. 11, 2024, 6:13 p.m.