GetAncNodes: Get MRCA nodes of taxonomic groups from 'AssessMonophyly'...

In MonoPhy: Explore Monophyly of Taxonomic Groups in a Phylogeny

Description

Print MRCA node numbers of taxonomic groups from the output of 'AssessMonophyly', either the whole list or for specific groups.

Usage

GetAncNodes(solution, taxa = NULL, taxlevels='ALL')

Arguments

solution	Object with saved output of the 'AssessMonophyly' function.
taxa	Vector containing taxon names (genera or whichever taxonomic unit was used). Default is 'NULL'
taxlevels	Either an integer corresponding to the desired taxonomic level (i.e. the number of its column in the taxonimy table, not counting the tip names), the column name in the header of the taxonomy file, or 'ALL' (which is the default).

Details

Can be used after 'AssessMonophyly' is run to extract MRCA nodes of taxa from it. The argument 'taxa' allows to limit the output to one or several taxa of interest. The argument 'taxlevels' allows to limit the output if several taxonomic levels were used; 'ALL' is default, a specific level can be selected by entering its number or name instead.

Value

List of data frames.

Author(s)

Orlando Schwery

See Also

AssessMonophyly, MonoPhy-package

Examples

data(Ericactree)
solution <- AssessMonophyly(Ericactree)
GetAncNodes(solution=solution, taxa=c("Phyllodoce", "Vaccinium", "Erica"))

MonoPhy documentation built on Feb. 18, 2021, 1:06 a.m.