From 1b0319a88c6f9efe19d77ad5979fb3a11d029c3b Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <waldir.leoncio@gmail.com>
Date: Tue, 14 Jul 2020 15:47:01 +0200
Subject: [PATCH] Translated initialCounts()

---
 R/greedyMix.R     | 32 --------------------------------
 R/initialCounts.R | 25 +++++++++++++++++++++++++
 2 files changed, 25 insertions(+), 32 deletions(-)
 create mode 100644 R/initialCounts.R

diff --git a/R/greedyMix.R b/R/greedyMix.R
index 4aa71fc..0841ca5 100644
--- a/R/greedyMix.R
+++ b/R/greedyMix.R
@@ -877,38 +877,6 @@ greedyMix <- function(
 
 # 	%----------------------------------------------------------------------------------------
 
-
-# 	function logml = ...
-# 		initialCounts(partition, data, npops, rows, noalle, adjprior)
-
-# 	nloci=size(data,2);
-# 	ninds = size(rows, 1);
-
-# 	koot = rows(:,1) - rows(:,2) + 1;
-# 	maxSize = max(koot);
-
-# 	counts = zeros(max(noalle),nloci,npops);
-# 	sumcounts = zeros(npops,nloci);
-# 	for i=1:npops
-# 		for j=1:nloci
-# 			havainnotLokuksessa = find(partition==i & data(:,j)>=0);
-# 			sumcounts(i,j) = length(havainnotLokuksessa);
-# 			for k=1:noalle(j)
-# 				alleleCode = k;
-# 				N_ijk = length(find(data(havainnotLokuksessa,j)==alleleCode));
-# 				counts(k,j,i) = N_ijk;
-# 			end
-# 		end
-# 	end
-
-# 	%initializeGammaln(ninds, maxSize, max(noalle));
-
-# 	logml = laskeLoggis(counts, sumcounts, adjprior);
-
-
-# 	%-----------------------------------------------------------------------
-
-
 # 	function logml=computeLogml(counts, sumcounts, noalle, data, rowsFromInd)
 # 	nloci = size(counts,2);
 # 	npops = size(counts,3);
diff --git a/R/initialCounts.R b/R/initialCounts.R
new file mode 100644
index 0000000..9638e78
--- /dev/null
+++ b/R/initialCounts.R
@@ -0,0 +1,25 @@
+initialCounts <- function(partition, data, npops, rows, noalle, adjprior) {
+	nloci <- size(data, 2)
+	ninds <- size(rows, 1)
+
+	koot <- rows[, 1] - rows[, 2] + 1
+	maxSize <- max(koot)
+
+	counts <- zeros(max(noalle), nloci, npops)
+	sumcounts <- zeros(npops, nloci)
+	for (i in 1:npops) {
+		for (j in 1:nloci) {
+			havainnotLokuksessa <- find(partition == i & data[, j] >= 0)
+			sumcounts[i, j] <- length(havainnotLokuksessa)
+			for (k in 1:noalle[j]) {
+				alleleCode <- k
+				N_ijk <- length(
+					find(data[havainnotLokuksessa, j] == alleleCode)
+				)
+				counts[k, j, i] <- N_ijk
+			}
+		}
+	}
+	logml <- laskeLoggis(counts, sumcounts, adjprior)
+	return(logml)
+}
\ No newline at end of file