working on nmds

diff --git a/linearalgebra.cpp b/linearalgebra.cpp
index 39e0848003245351d86e9ed1fe1b1c238ff77213..27d35ac2cd7c40d4502aa469ffa62f2d01ff31ec 100644 (file)
--- a/linearalgebra.cpp
+++ b/linearalgebra.cpp
@@ -326,59 +326,31 @@ vector< vector<double> > LinearAlgebra::calculateEuclidianDistance(vector< vecto
        }
 }
 /*********************************************************************************************************************************/
+//assumes both matrices are square and the same size
 double LinearAlgebra::calcPearson(vector< vector<double> >& euclidDists, vector< vector<double> >& userDists){
        try {
                
-       /*      euclidDists.clear();
-               userDists.clear();
-               
-               euclidDists.resize(1);
-               userDists.resize(1);
-               
-               userDists[0].push_back(0.3070833);
-               userDists[0].push_back(0.3244475);
-               userDists[0].push_back(0.6055993);
-               userDists[0].push_back(0.3372481);
-               userDists[0].push_back(0.9151715);
-               userDists[0].push_back(0.6182255);
-               userDists[0].push_back(0.7748142);
-               userDists[0].push_back(0.08554735);
-               userDists[0].push_back(0.6343481);
-               userDists[0].push_back(0.4049274);
-               
-               euclidDists[0].push_back(0.3342815);
-               euclidDists[0].push_back(0.3173829);
-               euclidDists[0].push_back(0.6852404);
-               euclidDists[0].push_back(0.7819186);
-               euclidDists[0].push_back(0.5705242);
-               euclidDists[0].push_back(0.8007263);
-               euclidDists[0].push_back(0.8561724);
-               euclidDists[0].push_back(0.4901089);
-               euclidDists[0].push_back(0.7027247);
-               euclidDists[0].push_back(0.7669696);*/
-               
-               
                //find average for - X
                int count = 0;
-               vector<float> averageEuclid; averageEuclid.resize(euclidDists.size(), 0.0);
+               float averageEuclid = 0.0; 
                for (int i = 0; i < euclidDists.size(); i++) {
-                       for (int j = 0; j < euclidDists[i].size(); j++) {
-                               averageEuclid[i] += euclidDists[i][j];  
+                       for (int j = 0; j < i; j++) {
+                               averageEuclid += euclidDists[i][j];  
                                count++;
                        }
                }
-               for (int i = 0; i < averageEuclid.size(); i++) {  averageEuclid[i] = averageEuclid[i] / (float) count;   }
+               averageEuclid = averageEuclid / (float) count;   
                        
                //find average for - Y
                count = 0;
-               vector<float> averageUser; averageUser.resize(userDists.size(), 0.0);
+               float averageUser = 0.0; 
                for (int i = 0; i < userDists.size(); i++) {
-                       for (int j = 0; j < userDists[i].size(); j++) {
-                               averageUser[i] += userDists[i][j]; 
+                       for (int j = 0; j < i; j++) {
+                               averageUser += userDists[i][j]; 
                                count++;
                        }
                }
-               for (int i = 0; i < averageUser.size(); i++) {  averageUser[i] = averageUser[i] / (float) count;  }
+               averageUser = averageUser / (float) count;  
 
                double numerator = 0.0;
                double denomTerm1 = 0.0;
@@ -386,20 +358,20 @@ double LinearAlgebra::calcPearson(vector< vector<double> >& euclidDists, vector<
                
                for (int i = 0; i < euclidDists.size(); i++) {
                        
-                       for (int k = 0; k < euclidDists[i].size(); k++) {
+                       for (int k = 0; k < i; k++) { //just lt dists
                                
                                float Yi = userDists[i][k];
                                float Xi = euclidDists[i][k];
                                
-                               numerator += ((Xi - averageEuclid[i]) * (Yi - averageUser[i]));
-                               denomTerm1 += ((Xi - averageEuclid[i]) * (Xi - averageEuclid[i]));
-                               denomTerm2 += ((Yi - averageUser[i]) * (Yi - averageUser[i]));
+                               numerator += ((Xi - averageEuclid) * (Yi - averageUser));
+                               denomTerm1 += ((Xi - averageEuclid) * (Xi - averageEuclid));
+                               denomTerm2 += ((Yi - averageUser) * (Yi - averageUser));
                        }
                }
                
                double denom = (sqrt(denomTerm1) * sqrt(denomTerm2));
                double r = numerator / denom;
-
+               
                return r;
                
        }