changed random forest output filename

[mothur.git] / memchi2.cpp

diff --git a/memchi2.cpp b/memchi2.cpp
index 07edd66475c9680cdacd5b9ff7920863323dd525..f08b4b8561d9177fbd6f0a5a8f3337b95312e362 100644 (file)
--- a/memchi2.cpp
+++ b/memchi2.cpp
@@ -17,7 +17,7 @@ EstOutput MemChi2::getValues(vector<SharedRAbundVector*> shared) {
                int nonZeroA = 0;
                int nonZeroB = 0;
                int totalOtus = shared[0]->getNumBins();
-               int totalGroups = shared.size();
+               //int totalGroups = shared.size();
                
                //for each otu
                for (int i = 0; i < shared[0]->getNumBins(); i++) {
@@ -25,7 +25,6 @@ EstOutput MemChi2::getValues(vector<SharedRAbundVector*> shared) {
                        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);
@@ -36,11 +35,18 @@ EstOutput MemChi2::getValues(vector<SharedRAbundVector*> shared) {
                        
                        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++;    }
+                       }
                        
-                       sum += (totalTerm * ((Aterm-Bterm)*(Aterm-Bterm)));
+                       if(incidence != 0){
+                               sum += (((Aterm-Bterm)*(Aterm-Bterm))/incidence);
+                       }
                }
                
-               data[0] = sqrt((totalOtus * sum));
+               data[0] = sqrt(totalOtus * sum);
                
                if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }