simulateOutbreak: Simulate an outbreak

In TransPhylo: Inference of Transmission Tree from a Dated Phylogeny

Description

Simulate an outbreak

Usage

simulateOutbreak(
  off.r = 1,
  off.p = 0.5,
  neg = 0.25,
  nSampled = NA,
  pi = 0.5,
  w.shape = 2,
  w.scale = 1,
  ws.shape = NA,
  ws.scale = NA,
  w.mean = NA,
  w.std = NA,
  ws.mean = NA,
  ws.std = NA,
  dateStartOutbreak = 2000,
  dateT = Inf
)

Arguments

off.r	First parameter of the negative binomial distribution for offspring number
off.p	Second parameter of the negative binomial distribution for offspring number
neg	the within-host effective population size (Ne) timesgeneration duration (g)
nSampled	number of sampled infected individuals, or NA for any
pi	probability of sampling an infected individual
w.shape	Shape parameter of the Gamma probability density function representing the generation time
w.scale	Scale parameter of the Gamma probability density function representing the generation time
ws.shape	Shape parameter of the Gamma probability density function representing the sampling time
ws.scale	Scale parameter of the Gamma probability density function representing the sampling time
w.mean	Mean of the Gamma distribution representing the generation time
w.std	Std of the Gamma distribution representing the generation time
ws.mean	Mean of the Gamma distribution representing the sampling time
ws.std	Std of the Gamma distribution representing the sampling time
dateStartOutbreak	Date when index case becomes infected
dateT	Date when process stops (this can be Inf for fully simulated outbreaks)

Value

Combined phylogenetic and transmission tree

Examples

simulateOutbreak()
simulateOutbreak(off.r=2,dateStartOutbreak=2010,dateT=2015)

TransPhylo documentation built on April 20, 2021, 5:09 p.m.