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taxize (version 0.5.2)

ncbi_children: Search NCBI for children of a taxon

Description

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

Usage

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

Arguments

name
(character) The string to search for. Only exact matches found the name given will be returned. Not compatible with id.
id
(character) 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": [object Object],[object Object]
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".

Value

  • The output type depends on the value of the out_type parameter.

Details

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.

See Also

ncbi_get_taxon_summary, children

Examples

Run this code
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

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