mutation_exp {phybase}R Documentation

Generate mutation rates for populations in the species tree

Description

In the non-clock species tree model (Liu, et.al), the lineages (populations) in the species tree are allowed to have variable mutation rates. This function is used to simulate mutation rates for the non-clock species tree model. There are many other ways to simulate variable mutation rates across populations in the species tree.

Usage

mutation_exp(sptree, root, inode, nspecies,alpha)

Arguments

sptree the species tree matrix
root the root of the species tree
inode the root of the species tree
nspecies the number of species in the species tree
alpha the parameter in the gamma distribution used to generate mutation rates.

Details

mutation rates are generated from gamma (alpha, alpha/w) where w is the mutation rate of the parent population of the current node. Thus the mean of the mutation rate of the current node equals to the mutation rate of its parent population.

Value

The function returns a species tree matrix with mutation rates in the last column.

Author(s)

Liang Liu

Examples

sptree<-"((((H:0.00402#0.01,C:0.00402#0.01):0.00304#0.01,G:0.00707#0.01):0.00929#0.01,O:0.01635#0.01):0.1#0.01,W:0.12#0.01);"
nodematrix<-read.tree.nodes(sptree)$nodes
mutation_exp(nodematrix, root=9, inode=9, nspecies=5, alpha=5)

[Package phybase version 1.1 Index]