added odum, canberra, structchi2, structchord, structeuclidean, gower, hellinger...

[mothur.git] / mempearson.cpp

diff --git a/mempearson.cpp b/mempearson.cpp
new file mode 100644 (file)
index 0000000..b39afd8
--- /dev/null
+++ b/mempearson.cpp
@@ -0,0 +1,68 @@
+/*
+ *  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);
+       }
+}
+/***********************************************************************/
+