X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=linearalgebra.cpp;h=39e0848003245351d86e9ed1fe1b1c238ff77213;hb=e6c4a7223199d800d496356604eb34dfe273673d;hp=6b56597f10501b4720d77b28ca08961d2c35554e;hpb=41f654a317afba7f4dba3fcd0a6557773528845a;p=mothur.git

diff --git a/linearalgebra.cpp b/linearalgebra.cpp
index 6b56597..39e0848 100644
--- 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");