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Search NCBI for children of a taxon

Source: R/ncbi_children.R
ncbi_children.Rd

Search the NCBI Taxonomy database for uids of children of taxa. Taxa can be referenced by name or uid. Referencing by name is faster

In a few cases, different taxa have the same name (e.g. Satyrium; see examples). If one of these are searched for then the children of both taxa will be returned. This can be avoided by using a uid instead of the name or specifying an ancestor. If an ancestor is provided, only children of both the taxon and its ancestor are returned. This will only fail if there are two taxa with the same name and the same specified ancestor.

Usage

ncbi_children(
  name = NULL,
  id = NULL,
  start = 0,
  max_return = 1000,
  ancestor = NULL,
  out_type = c("summary", "uid"),
  ambiguous = FALSE,
  key = NULL,
  ...
)

Arguments

name

(character) The string to search for. Only exact matches found the name given will be returned. Not compatible with id.

id

(character/numeric) The uid to search for. Not compatible with name.

start

The first record to return. If omitted, the results are returned from the first record (start=0).

max_return

(numeric; length=1) The maximum number of children to return.

ancestor

(character) The ancestor of the taxon being searched for. This is useful if there could be more than one taxon with the same name. Has no effect if id is used.

out_type

(character) Currently either "summary" or "uid":

  • summary The output is a list of data.frame with children uid, name, and rank.

  • uid A list of character vectors of children uids

ambiguous

logical; length 1 If FALSE, children taxa with words like "unclassified", "unknown", "uncultured", or "sp." are removed from the output. NOTE: This option only applies when out_type= "summary".

key

(character) NCBI Entrez API key. optional. See Details.

...

Curl options passed on to crul::HttpClient

Value

The output type depends on the value of the out_type parameter. Taxa that cannot be found will result in NAs and a lack of children results in an empty data structure.

Authentication

See taxize-authentication() for help on authentication. We strongly recommend getting an API key

HTTP version

We hard code http_version = 2L to use HTTP/1.1 in HTTP requests to the Entrez API. See curl::curl_symbols('CURL_HTTP_VERSION')

Rate limits

In case you run into errors due to your rate limit being exceeded, see taxize_options(), where you can set ncbi_sleep.

See also

ncbi_get_taxon_summary(), children()

Author

Zachary Foster zacharyfoster1989@gmail.com

Examples

if (FALSE) { # \dontrun{
ncbi_children(name="Satyrium") #Satyrium is the name of two different genera
ncbi_children(name="Satyrium", ancestor="Eumaeini") # A genus of butterflies
ncbi_children(name="Satyrium", ancestor="Orchidaceae") # A genus of orchids
ncbi_children(id="266948") #"266948" is the uid for the butterfly genus
ncbi_children(id="62858") #"62858" is the uid for the orchid genus

# use curl options
ncbi_children(name="Satyrium", ancestor="Eumaeini", verbose = TRUE)
} # }