NicheBarcoding (version 1.0)

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

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.

Examples

# NOT RUN {
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
# }