+/*
+ * 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);
+ }
+}
+/***********************************************************************/
+