JC69: JC69 Substiution Model

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

Description

JC69 creates the rate matrix of the JC69 model before calculating the related transition matrix, P, using the mutation and branch length/time from parent variables.

Usage

JC69(t, mu, length = NULL)

Arguments

t	- branch length, i.e. specific generation time
mu	- mutation rate
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.