GetTipRates: Calculate the rate of evolution on the leaves of a phylogeny

In coleoguy/evobir: Evolutionary Biology in R

Calculate the rate of evolution on the leaves of a phylogeny

Description

This function calculates the rate of change from parent nodes to extant tips of a phylogeny.

Usage

GetTipRates(tree, Q, tip.states, hyper, p.mat)

Arguments

tree	an ultrametric tree of class phylo
Q	transition matrix containing estimated rates with column names
tip.states	An integer vector with a length equal to the number of species on the phylogeny. It should have values of 1 to N with N being the number of total states. Elements of the vector should match the tip names for the phylogeny.
hyper	logical vector of length one. TRUE indicates the model includes a binary hyperstate. Default is FALSE and indicates no binary hyperstate
p.mat	a probability matrix where each column represent a discrete state and each row is a species. Values in the matrix describe the probability of being in any of these states

Value

A named numeric vector with the rate for each tip in the phylogeny.

Author(s)

Michelle M. Jonika and Heath Blackmon

References

http://coleoguy.github.io/

coleoguy/evobir documentation built on May 8, 2024, 6:57 p.m.