K80: K80 Substiution Model

In OJWatson/sims4: Epidemic generational simualator

Description

This function creates the rate matrix of the K80 model before calculating the related transition matrix, P, using the mutation (mu), branch length/time (t) and transition transversion ratio (kappah)

Usage

K80(mu, t, kappa, pi = c(0.25, 0.25, 0.25, 0.25))

Arguments

mu	- Mutation rate
t	- Branch length, i.e. specific generation time
kappa	- ransition/transversion rate ratio
pi	- Base Frequencies

Value

This function returns a dgeMatrix containing the transition matrix P

OJWatson/sims4 documentation built on May 7, 2019, 8:33 p.m.