richYuleInputs: Generates the inputs necessary to run richness.yule.test() in...

In windex: Analysing Convergent Evolution using the Wheatsheaf Index

Generates the inputs necessary to run richness.yule.test() in ape

Description

The function richness.yule.test() in the package ape requires two inputs - a dataframe with species richness of pairs of sister lineages which differ in the presence of a binary trait of interest, and a vector of divergence times of each of those sister group pairs. The richYuleInputs function generates these in a format which can be entered as the two required arguments.

Usage

richYuleInputs(tree, x, rich=NULL)

Arguments

tree	Phylogenetic tree of class 'phylo' with branch lengths in units of time.
x	Named vector representing the binary trait (labelled as 0 and 1 for absence and presence respectively).
rich	Optional named vector of species richness for each tip (for instance to account for incomplete sampling or when tips represent more than one species).

Value

sisRich	Dataframe containing two columns (species richness in sister lineages with and without the trait of interest) and rows representing different sister pairs
divTimes	Vector of divergence times of sister pairs (corresponding to rows of sisRich) differing in possession of a trait.

Author(s)

Kevin Arbuckle

See Also

richness.yule.test

Examples

data(sample.data)
data(sample.tree)
trait<-sample.data$focals
names(trait)<-sample.data$species

ryi<-richYuleInputs(sample.tree,trait)
richness.yule.test(ryi$sisRich,ryi$divTimes)

windex documentation built on Oct. 11, 2023, 5:16 p.m.