taxize: children – R documentation

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children

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

Taxonomic Information from Around the Web

v0.9.100

MIT + file LICENSE

Authors

Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>), Eduard Szoecs [aut], Zachary Foster [aut, cre], Zebulun Arendsee [aut], Carl Boettiger [ctb], Karthik Ram [ctb], Ignasi Bartomeus [ctb], John Baumgartner [ctb], James O'Donnell [ctb], Jari Oksanen [ctb], Bastian Greshake Tzovaras [ctb], Philippe Marchand [ctb], Vinh Tran [ctb], Maëlle Salmon [ctb], Gaopeng Li [ctb], Matthias Grenié [ctb], rOpenSci [fnd] (https://ropensci.org/)

Initial release