taxdumpChildren: Utilities for NCBI Taxdump

In heibl/megaptera: MEGAPhylogeny Techniques in R

Description

Get all children of certain rank for a given taxon.

Usage

taxdumpChildren(
  tax,
  taxon,
  immediate = FALSE,
  query.rank = "any",
  tip.rank = "species",
  status = "scientific name",
  indet,
  quiet = FALSE
)

Arguments

tax	Either an object of class megapteraProj or a data frame as returned by dbReadTaxonomy.
taxon	A character string giving the name of the taxon.
immediate	Logical, if TRUE, only the immediate children of taxon will be returned. The default (FALSE) return all children.
query.rank	A character string giving the name of a rank that "taxon" must belong to. The default ("any") does not imply any restriction on the rank of the taxon queried.
tip.rank	A character string giving the name a rank. This rank will be treated as tip rank, i.e. all taxa of lower rank will be dicarded.
status	A character string defining the status of the taxon names to be returned, e.g. "scientific name" will return only currently accepted names, while "all" will return synonyms in addition.
indet	A vector of character strings containing regular expressions (see Examples).
quiet	Logical, use quiet = TRUE to suppress warning messages.

Value

A data frame.

See Also

ncbiTaxonomy for downloading the NCBI taxonomy and dbReadTaxonomy for reading the project taxonomy; other taxdump-related tools: taxdumpAddNode, taxdumpDropTip, taxdumpHigherRank, taxdumpMRCA, taxdumpSubset, taxdump2phylo and taxdump_isTerminal.

Examples

# The set of default regular expressions used to identify nonvalid species binomials
indet.strings(collapse = TRUE)

heibl/megaptera documentation built on Jan. 17, 2021, 3:34 a.m.