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

[mothur.git] / memchi2.cpp

diff --git a/memchi2.cpp b/memchi2.cpp
new file mode 100644 (file)
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);
+       }
+}
+/***********************************************************************/
+