Fixed syntax

R/computeDiffInCounts.R

@@ -6,7 +6,7 @@ computeDiffInCounts <- function(rows, max_noalle, nloci, data) {
 	diffInCounts <- zeros(max_noalle, nloci)
 	for (i in rows) {
 		row <- data[i, ]
-		notEmpty <- find(row>=0)
+		notEmpty <- as.matrix(find(row>=0))
 
 		if (length(notEmpty) > 0) {
 			diffInCounts[row(notEmpty) + (notEmpty - 1) * max_noalle] <-

R/computePopulationLogml.R

@@ -1,18 +1,26 @@
-computePopulationLogml <- function(pops, adjprior, priorTerm) {
+computePopulationLogml <- function(pops, adjprior, priorTerm = 0) {
 	# Palauttaa length(pops)*1 taulukon, jossa on laskettu korikohtaiset
 
+	# ======================================================== #
+	# Limiting COUNTS size                                     #
+	# ======================================================== #
+	COUNTS <- COUNTS[seq_len(nrow(adjprior)), seq_len(ncol(adjprior)), pops, drop=FALSE]
+
 	x <- size(COUNTS, 1)
 	y <- size(COUNTS, 2)
 	z <- length(pops)
 
-	popLogml <- squeeze(
+	# ======================================================== #
+	# Computation                                              #
+	# ======================================================== #
+	term1 <- squeeze(
 		# FIXME: assumes COUNTS has 3 dims. Where does this come from?
 		sum(
 			sum(
 				reshape(
 					lgamma(
 						repmat(adjprior, c(1, 1, length(pops))) +
-							COUNTS[, , pops]
+							COUNTS[seq_len(nrow(adjprior)), seq_len(ncol(adjprior)), pops, drop=FALSE]
 					),
 					c(x, y, z)
 				),
@@ -20,6 +28,7 @@ computePopulationLogml <- function(pops, adjprior, priorTerm) {
 			),
 			2
 		)
-	) - sum(lgamma(1 + SUMCOUNTS[pops, ]), 2) - priorTerm
+	)
+	popLogml <- term1 - sum(lgamma(1 + SUMCOUNTS[pops, ]), 2) - priorTerm
 	return(popLogml)
 }

R/indMix.R

@@ -137,11 +137,11 @@ indMix <- function(c, npops, dispText) {
 				round <- roundTypes[n]
 				kivaluku <- 0
 
-				if (kokeiltu(round) == 1) { #Askelta kokeiltu viime muutoksen j<>lkeen
+				if (kokeiltu[round] == 1) { #Askelta kokeiltu viime muutoksen j<>lkeen
 
 				} else if (round == 0 | round == 1) { #Yksil<69>n siirt<72>minen toiseen populaatioon.
 					inds <- 1:ninds
-					aputaulu <- c(t(inds), rand(ninds, 1))
+					aputaulu <- cbind(inds, rand(ninds, 1))
 					aputaulu <- sortrows(aputaulu, 2)
 					inds <- t(aputaulu[, 1])
 					muutosNyt <- 0