Merge branch 'issue-13' into develop

R/computeDiffInCounts.R

@@ -4,7 +4,7 @@ computeDiffInCounts <- function(rows, max_noalle, nloci, data) {
 	# % riveill<6C> rows. rows pit<69><74> olla vaakavektori.
 
 	diffInCounts <- zeros(max_noalle, nloci)
-	for (i in seq_len(nrow(data)) ) {
+	for (i in seq_len(nrow(data))) {
 		row <- data[i, ]
 		notEmpty <- as.matrix(find(row>=0))
 
@@ -13,5 +13,11 @@ computeDiffInCounts <- function(rows, max_noalle, nloci, data) {
 				diffInCounts[row(notEmpty) + (notEmpty - 1) * max_noalle] + 1
 		}
 	}
+	diffInCounts <- matrix(
+		data = diffInCounts[!is.na(diffInCounts)],
+		nrow = max_noalle,
+		ncol = nloci,
+		byrow = TRUE
+	)
 	return(diffInCounts)
 }

R/computePopulationLogml.R

@@ -14,6 +14,7 @@ computePopulationLogml <- function(pops, adjprior, priorTerm) {
 	# Computation                                              #
 	# ======================================================== #
 	isarray <- length(dim(repmat(adjprior, c(1, 1, length(pops))))) > 2
+	# FIXME: 3rd dimension of COUNTS getting dropped
 	term1 <- squeeze(
 		sum(
 			sum(

man/inputdlg.Rd

@@ -4,14 +4,14 @@
 \alias{inputdlg}
 \title{Gather user input}
 \usage{
-inputdlg(prompt, definput = NULL, dims = 1)
+inputdlg(prompt, dims = 1, definput = NULL)
 }
 \arguments{
 \item{prompt}{Text field with user instructions}
 
-\item{definput}{default value of the input}
-
 \item{dims}{number of dimensions in the answwers}
+
+\item{definput}{default value of the input}
 }
 \description{
 Replicates the functionality of the homonymous function in Matlab (sans dialog box)