probTTreeR {TransPhylo}

Calculates the log-probability of a transmission tree

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