Fix code formatting and remove unnecessary comments

[Rnaught] / R / computeLL.R

diff --git a/R/computeLL.R b/R/computeLL.R
index 0730399eafa19c24de5ce5fc82fe0ca5f83cc3ef..6acfc786e34401e6f4f43543000f6d76b07a1ec6 100644 (file)
--- a/R/computeLL.R
+++ b/R/computeLL.R
@@ -3,28 +3,23 @@
 #' This is a background/internal function called by \code{WP}.  It computes the log-likelihood.
 #'
 #' @param NT vector of case counts
-#' @param p discretized version of the serial distribution 
+#' @param p discretized version of the serial distribution
 #' @param R0 basic reproductive ratio
 #' @return The function returns the variable \code{LL} which is the log-likelihood at the input variables and parameters.
-
+#'
 #' @export
-# 
-computeLL      <-      function(p, NT, R0){
+computeLL <- function(p, NT, R0) {
+    k <- length(p)
+    TT <- length(NT) - 1
+    mu_t <- rep(0, TT)
+
+    for (i in 1:TT) {
+        Nt <- NT[i:max(1, i-k+1)]
+        mu_t[i]        <- sum(p[1:min(k, i)] * Nt)
+    }
 
-       k               <-      length(p)
-       TT              <-      length(NT)-1
-       mu_t    <-      rep(0, TT)
-       for(i in 1:TT){
-               Nt              <-      NT[i:max(1,i-k+1)]
-#              print(Nt)
-#              print(p[1:min(k,i)])
-               mu_t[i] <-      sum(p[1:min(k,i)]*Nt)   
-       }
-       mu_t    <-      R0*mu_t
-       LL              <-      -sum(mu_t)+sum(NT[-1]*log(mu_t))
+    mu_t <- R0 * mu_t
+    LL <- sum(NT[-1] * log(mu_t)) - sum(mu_t)
 
        return(LL)
-       
 }
-
-