taxdumpSynonym: Utilities for NCBI Taxdump

In heibl/megaptera: MEGAPhylogeny Techniques in R

Description

Manage Synonyms

Usage

taxdumpSynonym(
  tax,
  binomials,
  keep.acc = FALSE,
  keep.syn = TRUE,
  add.syn = TRUE,
  quiet = TRUE
)

Arguments

tax	A data frame in parent-child format.
binomials	A vector of mode "character" giving one or more taxon names. The first name is considered to be the accepted name.
keep.acc	Logical, only applies when the accepted names in tax and binomial are not identical: TRUE means the accepted name from tax is kept, whereas the accepted name of binomials is taken if keep.acc = FALSE.
keep.syn	Logical, should synonyms present in tax be kept?
add.syn	Logical, should synonyms not present in tax be added?
quiet	Logical, if FALSE, progress is printed on screen for debugging.

Note

add.syn is only partly implemented and not tested, because under the current use (adding synonyms to NCBI taxonomy) it does not make sense.

See Also

taxdumpAddNode, taxdumpChildren, taxdumpMRCA, taxdumpSubset, taxdump2phylo

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