Explore Monophyly of Taxonomic Groups in a Phylogeny

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Documentation for package ‘MonoPhy’ version 1.3

• 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