X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mempearson.cpp;fp=mempearson.cpp;h=b39afd86f3d147f54d2e8ad9542c670955da961f;hb=7d38edc137a66a33f67f8cf55cce88331290aaf7;hp=0000000000000000000000000000000000000000;hpb=75c5a235ac3eb22e0f97d36874f4b2dcf9591f2e;p=mothur.git

diff --git a/mempearson.cpp b/mempearson.cpp
new file mode 100644
index 0000000..b39afd8
--- /dev/null
+++ b/mempearson.cpp
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+/*
+ *  mempearson.cpp
+ *  Mothur
+ *
+ *  Created by westcott on 12/17/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "mempearson.h"
+
+/***********************************************************************/
+EstOutput MemPearson::getValues(vector<SharedRAbundVector*> shared) {
+	try {
+		data.resize(1,0);
+		
+		int nonZeroA = 0;
+		int nonZeroB = 0;
+		int numOTUS = shared[0]->getNumBins();
+		
+		//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 numTerm1 = 0.0;
+		double numTerm2 = 0.0;
+		double denomTerm1 = 0.0;
+		double denomTerm2 = 0.0;
+		
+		for (int i = 0; i < shared[0]->getNumBins(); i++) { 
+			int Aij =  shared[0]->getAbundance(i);
+			int Bij =  shared[1]->getAbundance(i);
+			
+			if (Aij > 0) { Aij = 1; }
+			if (Bij > 0) { Bij = 1; }
+			
+			numTerm1 += (Aij - (nonZeroA / (float) numOTUS));
+			numTerm2 += (Bij - (nonZeroB / (float) numOTUS));
+			
+			denomTerm1 += ((Aij - (nonZeroA / (float) numOTUS)) * (Aij - (nonZeroA / (float) numOTUS)));
+			denomTerm2 += ((Bij - (nonZeroB / (float) numOTUS)) * (Bij - (nonZeroB / (float) numOTUS)));
+		}
+		
+		denomTerm1 = sqrt(denomTerm1);
+		denomTerm2 = sqrt(denomTerm2);
+		
+		double denom = denomTerm1 * denomTerm2;
+		double numerator = numTerm1 * numTerm2;
+		
+		if (denom != 0) { 
+			data[0] = 1.0 - (numerator / denom);
+		}else {
+			data[0] = 1.0;
+		}
+		
+		if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+		
+		return data;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "MemPearson", "getValues");
+		exit(1);
+	}
+}
+/***********************************************************************/
+