probTTreeR: Calculates the log-probability of a transmission tree

In TransPhylo: Inference of Transmission Tree from a Dated Phylogeny

Description

Calculates the log-probability of a transmission tree

Usage

probTTreeR(
  ttree,
  off.r,
  off.p,
  pi,
  w.shape,
  w.scale,
  ws.shape,
  ws.scale,
  dateT
)

Arguments

ttree	Transmission tree
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
dateT	Date when process stops (this can be Inf for fully simulated outbreaks)

Value

Probability of the transmission tree

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