Sequencing: Forwards genetic sequence simulator

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

Description

Sequencing uses the output of Infection_Sim to simualate the evolutionary process of the seqeunce from the root forwards

Usage

Sequencing(sim.out, seq.length = 1701, mu = 1.57e-05, Tg = 2.6,
  model = "HKY85", kappa = 2, root.path = NULL,
  evolution.model = "generational", outgroup = TRUE)

Arguments

sim.out	Output of Infection_Sim
seq.length	Sequence length. Will be overwritten accordingly if root.path given. Default = 1701
mu	Daily mutation rate. Default = 1.57e-05 sub / site / day
Tg	mean generation time. Default = 2.6 days
model	Nucleic subsitution model. Can be one of "JC69", "K80", "HKY85" (Default)
kappa	Tv/Ts ration. Default = 2
root.path	File path of saveRDS(root). Default = NULL
evolution.model	String variable detailing evolutionary model. Can be any of "generational", "within.host" and "parallel"

Value

Returns a list of 4 lists

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