probTTree {TransPhylo}

Calculates the log-probability of a transmission tree

Description

Calculates the log-probability of a transmission tree

Usage

probTTree(
  ttree,
  rOff,
  pOff,
  pi,
  shGen,
  scGen,
  shSam,
  scSam,
  dateT,
  delta_t = 0.01
)

Arguments

ttree

Transmission tree

rOff

First parameter of the negative binomial distribution for offspring number

pOff

Second parameter of the negative binomial distribution for offspring number

pi

probability of sampling an infected individual

shGen

Shape parameter of the Gamma probability density function representing the generation time

scGen

Scale parameter of the Gamma probability density function representing the generation time

shSam

Shape parameter of the Gamma probability density function representing the sampling time

scSam

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)

delta_t

Grid precision

Value

Probability of the transmission tree