monophyly.prop: Calculate the proportion of monophyletic group on a tree

In NicheBarcoding: Niche-model-Based Species Identification

Description

Calculate the proportion of monophyletic group on a tree given species vector and a tree.

Usage

monophyly.prop(phy, sppVector, singletonsMono = TRUE)

Arguments

phy	A tree of class phylo.
sppVector	Species vector.
singletonsMono	Logical. Should singletons (i.e. only a single specimen representing that species) be treated as monophyletic? Default of TRUE. Possible values of FALSE and NA.

Value

A list containing proportion and number of monophyly group.

A set monophyly and of non-monophyly group names.

Author(s)

Cai-qing YANG (Email: yangcq_ivy(at)163.com) and Ai-bing ZHANG (Email:zhangab2008(at)cnu.edu.cn), Capital Normal University (CNU), Beijing, CHINA.

Examples

library(ape)
tree<-ape::rtree(20)
tree$tip.label<-sample(tree$tip.label[1:10],size=20,replace = TRUE)
plot(tree)
sppVector<-tree$tip.label

MP<-monophyly.prop(tree,sppVector,singletonsMono = TRUE)
MP

NicheBarcoding documentation built on Dec. 21, 2021, 9:07 a.m.