From 67170d1c7bddc8325b1b12bc5d35dfc2ff745b47 Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <w.l.netto@medisin.uio.no>
Date: Tue, 29 Jun 2021 10:37:42 +0200
Subject: [PATCH 1/2] Refactoring

---
 R/computeDiffInCounts.R    | 2 +-
 R/computePopulationLogml.R | 1 +
 man/inputdlg.Rd            | 6 +++---
 3 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/R/computeDiffInCounts.R b/R/computeDiffInCounts.R
index 0f906e5..a76d797 100644
--- a/R/computeDiffInCounts.R
+++ b/R/computeDiffInCounts.R
@@ -4,7 +4,7 @@ computeDiffInCounts <- function(rows, max_noalle, nloci, data) {
 	# % riveill� rows. rows pit�� 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))
 
diff --git a/R/computePopulationLogml.R b/R/computePopulationLogml.R
index e0f4765..e598e05 100644
--- a/R/computePopulationLogml.R
+++ b/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(
diff --git a/man/inputdlg.Rd b/man/inputdlg.Rd
index 26b8fa1..48c3e4c 100644
--- a/man/inputdlg.Rd
+++ b/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)

From 7c2e4c431f433839ff1bdbae862925d402d19b8b Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <w.l.netto@medisin.uio.no>
Date: Tue, 29 Jun 2021 10:37:52 +0200
Subject: [PATCH 2/2] Reformatting output

---
 R/computeDiffInCounts.R | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/R/computeDiffInCounts.R b/R/computeDiffInCounts.R
index a76d797..40055d8 100644
--- a/R/computeDiffInCounts.R
+++ b/R/computeDiffInCounts.R
@@ -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)
 }