X-Git-Url: https://git.nmode.ca/Rnaught/blobdiff_plain/14ec98c9bfc49f963e30159dc7db9f554088fb44..c85280a9cfe1f46eb4bc260d7f479a33d86dceff:/R/computeLL.R

diff --git a/R/computeLL.R b/R/computeLL.R
index 0730399..9047777 100644
--- a/R/computeLL.R
+++ b/R/computeLL.R
@@ -2,29 +2,25 @@
 #'
 #' 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 R0 basic reproductive ratio
-#' @return The function returns the variable \code{LL} which is the log-likelihood at the input variables and parameters.
-
+#' @param NT Vector of case counts.
+#' @param p Discretized version of the serial distribution.
+#' @param R0 Basic reproductive ratio.
+#'
+#' @return This function returns 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)
 
-	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))
+    for (i in 1:TT) {
+        Nt <- NT[i:max(1, i-k+1)]
+        mu_t[i]	<- sum(p[1:min(k, i)] * Nt)
+    }
+
+    mu_t <- R0 * mu_t
+    LL <- sum(NT[-1] * log(mu_t)) - sum(mu_t)
 
 	return(LL)
-	
 }
-
-