MonoPhy (version 1.3.2)

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

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')

Value

List of data frames.

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).

Author

Orlando Schwery

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.

See Also

AssessMonophyly, MonoPhy-package

Examples

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