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 #
  12 computeLL       <-      function(p, NT, R0){
  13
  14         k               <-      length(p)
  15         TT              <-      length(NT)-1
  16         mu_t    <-      rep(0, TT)
  17         for(i in 1:TT){
  18                 Nt              <-      NT[i:max(1,i-k+1)]
  19 #               print(Nt)
  20 #               print(p[1:min(k,i)])
  21                 mu_t[i] <-      sum(p[1:min(k,i)]*Nt)
  22         }
  23         mu_t    <-      R0*mu_t
  24         LL              <-      -sum(mu_t)+sum(NT[-1]*log(mu_t))
  25
  26         return(LL)
  27
  28 }
  29
  30