nmode's Git Repositories - Rnaught/blob - R/computeLL.R

   1 #' WP method background function computeLL
   2 #'
   3 #' This is a background/internal function called by \code{WP}.  It computes the log-likelihood.
   4 #'
   5 #' @param NT vector of case counts
   6 #' @param p discretized version of the serial distribution
   7 #' @param R0 basic reproductive ratio
   8 #' @return The function returns the variable \code{LL} which is the log-likelihood at the input variables and parameters.
   9 #'
  10 #' @export
  11 computeLL <- function(p, NT, R0) {
  12     k <- length(p)
  13     TT <- length(NT) - 1
  14     mu_t <- rep(0, TT)
  15
  16     for (i in 1:TT) {
  17         Nt <- NT[i:max(1, i-k+1)]
  18         mu_t[i] <- sum(p[1:min(k, i)] * Nt)
  19     }
  20
  21     mu_t <- R0 * mu_t
  22     LL <- sum(NT[-1] * log(mu_t)) - sum(mu_t)
  23
  24         return(LL)
  25 }