getGenus {RRphylo}R Documentation

Taxonomic inspection of the tree at the genus level

Description

The function returns the most recent common ancestor and the number of species belonging to each or some user-specified genera within the phylogenetic tree.

Usage

getGenus(tree,genera=NULL)

Arguments

tree

a phylogenetic tree. The tree needs not to be ultrametric and fully dichotomous. Generic name and specific epithet must be separated by '_'.

genera

a character vector including one or more genera to focus on. Please notice the function is case sensitive.

Value

The function returns a data-frame including the number of species, the most recent common ancestor of each genera (if a genus includes one species this is the species tip number), and whether the genera form monophyletic or paraphyletic clades.

Author(s)

Silvia Castiglione, Pasquale Raia, Carmela Serio

Examples

DataCetaceans$treecet->treecet

getGenus(treecet)->gg1
getGenus(treecet,c("Mesoplodon","Balaenoptera"))->gg2

[Package RRphylo version 3.0.0 Index]