R: Explore Monophyly of Taxonomic Groups in a Phylogeny

# Explore Monophyly of Taxonomic Groups in a Phylogeny

## Documentation for package ‘MonoPhy’ version 1.3.2

- DESCRIPTION file
- User guides, package vignettes and other documentation

## Help Pages

MonoPhy-package | Explore Monophyly of Taxonomic Groups in a Phylogeny.
AssessMonophyly | Assesses monophyly (or lack of it) of taxonomic groups in a phylogeny.
CollapseMonophyletics | Get tree with collapsed monophyletic groups
Ericacsubfams | Example dataset for the package MonoPhy.
Ericactree | Example dataset for the package MonoPhy.
Ericactribes | Example dataset for the package MonoPhy.
GetAncNodes | Get MRCA nodes of taxonomic groups from 'AssessMonophyly' output
GetIntruderTaxa | Get taxa or tips which are intruders or outliers to a taxon from AssessMonophyly
GetIntruderTips | Get taxa or tips which are intruders or outliers to a taxon from AssessMonophyly
GetOutlierTaxa | Get taxa or tips which are intruders or outliers to a taxon from AssessMonophyly
GetOutlierTips | Get taxa or tips which are intruders or outliers to a taxon from AssessMonophyly
GetResultMonophyly | Get main result table from 'AssessMonophyly' output
GetSummaryMonophyly | Get main result table from 'AssessMonophyly' output
MonoPhy | Explore Monophyly of Taxonomic Groups in a Phylogeny.
MonophylyData | Example dataset for the package MonoPhy.
PlotMonophyly | Plot output of AssessMonophyly