X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=trialSwap2.cpp;h=9959443c9ffbb0c411dfcd0fc6dd6920fbe6f5c8;hp=2d25e835cbd5608bc1c4f4c6cc67397155f2c834;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=f67ace597e7147f3ca35201e3623abe6440a9d24

diff --git a/trialSwap2.cpp b/trialSwap2.cpp
index 2d25e83..9959443 100644
--- a/trialSwap2.cpp
+++ b/trialSwap2.cpp
@@ -50,9 +50,10 @@ double TrialSwap2::calc_c_score (vector<vector<int> > &co_matrix, vector<int> ro
             }
         }
         
-        cscore = cscore/(double)(nrows*(nrows-1)/2);
+        //cscore = cscore/(double)(nrows*(nrows-1)/2);  //not normalized
         //cout << "normalized c score: " << normcscore/nonzeros << endl;
-        
+        cscore = normcscore/(double)nonzeros;
+
         return cscore;
     }
     catch(exception& e) {
@@ -148,7 +149,7 @@ int TrialSwap2::calc_combo (int nrows, int ncols, vector<vector<int> > &nullmatr
 {
     try {
         //need to transpose so we can compare rows (row-major order)
-        int tmpnrows = nrows;
+        //int tmpnrows = nrows;
         vector<vector<int> > tmpmatrix;
         
         vector<int> tmprow;
@@ -291,6 +292,34 @@ double TrialSwap2::t_test (double initialscore, int runs, double nullMean, vecto
     }
 }
 /**************************************************************************************************/
+double TrialSwap2::getSD (int runs, vector<double> scorevec, double nullMean)
+{
+    try{
+        double sum = 0;
+        for(int i=0;i<runs;i++)
+            {
+                if (m->control_pressed) { return 0; }
+                sum += pow((scorevec[i] - nullMean),2);
+            }
+        return sqrt( (1/double(runs)) * sum );
+    }
+    catch(exception& e) {
+        m->errorOut(e, "TrialSwap2", "getSD");
+        exit(1);
+    }
+}
+/**************************************************************************************************/
+double TrialSwap2::get_zscore (double sd, double nullMean, double initscore)
+{
+    try {
+        return (initscore - nullMean) / sd;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "TrialSwap2", "get_zscore");
+        exit(1);
+    }
+}
+/**************************************************************************************************/
 int TrialSwap2::print_matrix(vector<vector<int> > &matrix, int nrows, int ncols)
 {
     try {