X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=memchi2.cpp;fp=memchi2.cpp;h=07edd66475c9680cdacd5b9ff7920863323dd525;hb=7d38edc137a66a33f67f8cf55cce88331290aaf7;hp=0000000000000000000000000000000000000000;hpb=75c5a235ac3eb22e0f97d36874f4b2dcf9591f2e;p=mothur.git

diff --git a/memchi2.cpp b/memchi2.cpp
new file mode 100644
index 0000000..07edd66
--- /dev/null
+++ b/memchi2.cpp
@@ -0,0 +1,55 @@
+/*
+ *  memchi2.cpp
+ *  Mothur
+ *
+ *  Created by westcott on 12/17/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "memchi2.h"
+
+/***********************************************************************/
+EstOutput MemChi2::getValues(vector<SharedRAbundVector*> shared) {
+	try {
+		data.resize(1,0);
+		
+		int nonZeroA = 0;
+		int nonZeroB = 0;
+		int totalOtus = shared[0]->getNumBins();
+		int totalGroups = shared.size();
+		
+		//for each otu
+		for (int i = 0; i < shared[0]->getNumBins(); i++) {
+			if (shared[0]->getAbundance(i) != 0) { nonZeroA++; }
+			if (shared[1]->getAbundance(i) != 0) { nonZeroB++; }
+		}
+		
+		double totalTerm = 1 / (float) totalGroups;
+		double sum = 0.0;
+		for (int i = 0; i < shared[0]->getNumBins(); i++) {
+			int A = shared[0]->getAbundance(i);
+			int B = shared[1]->getAbundance(i);
+			
+			if (A > 0) { A = 1; }
+			if (B > 0) { B = 1; }
+			
+			double Aterm = A / (float) nonZeroA;
+			double Bterm = B / (float) nonZeroB;
+			
+			sum += (totalTerm * ((Aterm-Bterm)*(Aterm-Bterm)));
+		}
+		
+		data[0] = sqrt((totalOtus * sum));
+		
+		if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+		
+		return data;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "MemChi2", "getValues");
+		exit(1);
+	}
+}
+/***********************************************************************/
+