X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedrjsd.cpp;fp=sharedrjsd.cpp;h=46990540629aedc914d370a1672fe8273834f368;hp=0000000000000000000000000000000000000000;hb=0c5f99d1282405e20458e2822aa1a54774d2fa83;hpb=a38cc7240f45bd39aa60d0df75825c17af0a082c

diff --git a/sharedrjsd.cpp b/sharedrjsd.cpp
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+//
+//  sharedrjsd.cpp
+//  Mothur
+//
+//  Created by Sarah Westcott on 1/21/14.
+//  Copyright (c) 2014 Schloss Lab. All rights reserved.
+//
+
+#include "sharedrjsd.h"
+
+/***********************************************************************/
+//KLD <- function(x,y) sum(x *log(x/y))
+//JSD<- function(x,y) sqrt(0.5 * KLD(x, (x+y)/2) + 0.5 * KLD(y, (x+y)/2))
+EstOutput RJSD::getValues(vector<SharedRAbundVector*> shared) {
+	try {
+        
+		data.resize(1,0);
+        
+        double KLD1 = 0.0;
+        double KLD2 = 0.0;
+        
+        vector<int> countA = shared[0]->getAbundances();
+        vector<int> countB = shared[1]->getAbundances();
+        double totalA = 0;
+        double totalB = 0;
+        
+		for (int i = 0; i < shared[0]->getNumBins(); i++) {
+            totalA += countA[i];
+            totalB += countB[i];
+        }
+        
+        for (int i = 0; i < shared[0]->getNumBins(); i++) {
+            double tempA = countA[i] / totalA;
+            double tempB = countB[i] / totalB;
+            
+            tempA = countA[i] / totalA;
+            tempB = countB[i] / totalB;
+            
+            if (tempA == 0) { tempA = 0.000001; }
+            if (tempB == 0) { tempB = 0.000001; }
+            
+            double denom = (tempA+tempB)/(double)2.0;
+            
+            if (tempA != 0) {  KLD1 += tempA * log(tempA/denom); } //KLD(x,m)
+            if (tempB != 0) {  KLD2 += tempB * log(tempB/denom); } //KLD(y,m)
+            
+        }
+        
+        data[0] = sqrt((0.5*KLD1) + (0.5*KLD2));
+		
+		if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+		
+		return data;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "RJSD", "getValues");
+		exit(1);
+	}
+}