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 #'
   9 #' @return This function returns the log-likelihood at the input variables and parameters.
  10 #'
  11 #' @keywords internal
  12 computeLL <- function(p, NT, R0) {
  13     k <- length(p)
  14     TT <- length(NT) - 1
  15     mu_t <- rep(0, TT)
  16
  17     for (i in 1:TT) {
  18         Nt <- NT[i:max(1, i-k+1)]
  19         mu_t[i] <- sum(p[1:min(k, i)] * Nt)
  20     }
  21
  22     mu_t <- R0 * mu_t
  23     LL <- sum(NT[-1] * log(mu_t)) - sum(mu_t)
  24
  25         return(LL)
  26 }