makeTTree: Simulate a transmission tree

In TransPhylo: Inference of Transmission Tree from a Dated Phylogeny

Description

Simulate a transmission tree

Usage

makeTTree(
  off.r,
  off.p,
  pi,
  w.shape,
  w.scale,
  ws.shape = w.shape,
  ws.scale = w.scale,
  maxTime = Inf,
  nSampled = NA
)

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
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
maxTime	Duration of simulation (can be Inf)
nSampled	Number of sampled individuals (can be NA for any)

Value

A N*3 matrix in the following format with one row per infected host, first column is time of infection, second column is time of sampling, third column is infector

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