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[mothur.git] / memchi2.cpp

diff --git a/memchi2.cpp b/memchi2.cpp
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+/*
+ *  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 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;
+
+                       int incidence = 0;
+                       for(int j=0;j<shared.size();j++){
+                               if(shared[j]->getAbundance(i) != 0){    incidence++;    }
+                       }
+                       
+                       if(incidence != 0){
+                               sum += (((Aterm-Bterm)*(Aterm-Bterm))/incidence);
+                       }
+               }
+               
+               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);
+       }
+}
+/***********************************************************************/
+