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

[mothur.git] / structchi2.cpp

diff --git a/structchi2.cpp b/structchi2.cpp
new file mode 100644 (file)
index 0000000..00ec097
--- /dev/null
+++ b/structchi2.cpp
@@ -0,0 +1,56 @@
+/*
+ *  structchi2.cpp
+ *  Mothur
+ *
+ *  Created by westcott on 12/17/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "structchi2.h"
+
+/***********************************************************************/
+EstOutput StructChi2::getValues(vector<SharedRAbundVector*> shared) {
+       try {
+               data.resize(1,0);
+               
+               double sumA = shared[0]->getNumSeqs();
+               double sumB = shared[1]->getNumSeqs();
+               double totalSum = 0.0;
+               
+               for (int i = 0; i < shared.size(); i++) { totalSum += shared[i]->getNumSeqs();  }
+               
+               vector<int> sumOtus; sumOtus.resize(shared[0]->getNumBins(), 0);
+               //for each otu
+               for (int i = 0; i < shared[0]->getNumBins(); i++) {
+                       //for each group
+                       for (int j = 0; j < shared.size(); j++) { 
+                               sumOtus[i] += shared[j]->getAbundance(i);
+                       }
+               }
+               
+               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);
+                       
+                       double totalTerm = 1 / (float) sumOtus[i];
+                       double Aterm = A / sumA;
+                       double Bterm = B / sumB;
+                       
+                       sum += (totalTerm * ((Aterm-Bterm)*(Aterm-Bterm)));
+               }
+                               
+               data[0] = sqrt((totalSum * sum));
+               
+               if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+               
+               return data;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "StructChi2", "getValues");
+               exit(1);
+       }
+}
+/***********************************************************************/
+