HKY85: HKY85 Substiution Model

In OJWatson/evoflution: Forward in time epidemic and genetic simulator with a focus on flu

Description

HKY85 creates the rate matrix of the HKY85 model before calculating the related transition matrix, P, using the mutation (mu), branch length/time (t) and transition transversion ratio (kappah)

Usage

HKY85(t, mu, kappa, pi, length = NULL)

Arguments

t	Branch length, i.e. specific generation time
mu	Mutation rate
kappa	ransition/transversion rate ratio
pi	Base Frequencies
length	Length of sequence that was used in creating the base frequencies. If provided the output will instead be the probability of mutation occuring

Value

This function returns a dgeMatrix containing the transition matrix P, except if length is provided

OJWatson/evoflution documentation built on May 7, 2019, 8:32 p.m.