getGenus: Taxonomic inspection of the tree at the genus level

In RRphylo: Phylogenetic Ridge Regression Methods for Comparative Studies

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

RRphylo documentation built on April 3, 2025, 9:43 p.m.