R/pGenSwitch1.R

In branchingprocess: Calculate Outbreak Probabilities for a Branching Process Model

#' Probability that one initial case leads to an outbreak lasting
#' less than g generations of transmission, with offspring distribution 
#' parameters switched after generation one.
#'
#' @param gMax Maximum number of generations
#' @param R0 Basic reproduction number: mean of negative binomial offspring distribution from generation one
#' @param k0 Dispersion of negative binomial offspring distribution from generation one
#' @param Rc Control reproduction number: mean of negative binomial offspring distribution from generation two plus
#' @param kc Dispersion of negative binomial offspring distribution from generation two plus
#' @returns A vector of probabilities for each number of generations from 1 to gmax
#' @author Damon Toth
#' @examples
#' # Probability of outbreak lasting less than 1,2,3,...,10 generations:
#' pGenSwitch1(gMax=10, R0=3, k0=0.1, Rc=0.5, kc=1)
#' @export
pGenSwitch1 <- function(gMax,R0,k0,Rc,kc){
  pgl <- rep(0,gMax)
  pgl[1] <- (1+R0/k0)^(-k0)
  if(gMax > 1) for(g in 2:gMax) pgl[g] <- (1+Rc/kc*(1-pgl[g-1]))^(-kc)
  pgl
}