working on nmds

[mothur.git] / linearalgebra.cpp

diff --git a/linearalgebra.cpp b/linearalgebra.cpp
index 6b56597f10501b4720d77b28ca08961d2c35554e..39e0848003245351d86e9ed1fe1b1c238ff77213 100644 (file)
--- a/linearalgebra.cpp
+++ b/linearalgebra.cpp
@@ -329,45 +329,79 @@ vector< vector<double> > LinearAlgebra::calculateEuclidianDistance(vector< vecto
 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);
                for (int i = 0; i < euclidDists.size(); i++) {
                        for (int j = 0; j < euclidDists[i].size(); j++) {
                                averageEuclid[i] += euclidDists[i][j];  
+                               count++;
                        }
                }
-               for (int i = 0; i < averageEuclid.size(); i++) {  averageEuclid[i] = averageEuclid[i] / (float) euclidDists.size();   }
-               
+               for (int i = 0; i < averageEuclid.size(); i++) {  averageEuclid[i] = averageEuclid[i] / (float) count;   }
+                       
                //find average for - Y
+               count = 0;
                vector<float> averageUser; averageUser.resize(userDists.size(), 0.0);
                for (int i = 0; i < userDists.size(); i++) {
                        for (int j = 0; j < userDists[i].size(); j++) {
-                               averageUser[i] += userDists[i][j];  
+                               averageUser[i] += userDists[i][j]; 
+                               count++;
                        }
                }
-               for (int i = 0; i < averageUser.size(); i++) {  averageUser[i] = averageUser[i] / (float) userDists.size();  }
-               
+               for (int i = 0; i < averageUser.size(); i++) {  averageUser[i] = averageUser[i] / (float) count;  }
+
                double numerator = 0.0;
                double denomTerm1 = 0.0;
                double denomTerm2 = 0.0;
                
                for (int i = 0; i < euclidDists.size(); i++) {
                        
-                       for (int k = 0; k < i; k++) {
+                       for (int k = 0; k < euclidDists[i].size(); k++) {
                                
                                float Yi = userDists[i][k];
                                float Xi = euclidDists[i][k];
                                
-                               numerator += ((Xi - averageEuclid[k]) * (Yi - averageUser[k]));
-                               denomTerm1 += ((Xi - averageEuclid[k]) * (Xi - averageEuclid[k]));
-                               denomTerm2 += ((Yi - averageUser[k]) * (Yi - averageUser[k]));
+                               numerator += ((Xi - averageEuclid[i]) * (Yi - averageUser[i]));
+                               denomTerm1 += ((Xi - averageEuclid[i]) * (Xi - averageEuclid[i]));
+                               denomTerm2 += ((Yi - averageUser[i]) * (Yi - averageUser[i]));
                        }
                }
                
                double denom = (sqrt(denomTerm1) * sqrt(denomTerm2));
                double r = numerator / denom;
-               
+
                return r;
+               
        }
        catch(exception& e) {
                m->errorOut(e, "LinearAlgebra", "calculateEuclidianDistance");