X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedthetayc.cpp;h=864c6e63712cdc78d2cc0320ff2869c6deff196f;hp=ca066dd04bdb586a86cd5e6716daa949ac458734;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=dfae916a398508554d35c6b3c8002b69becb53be

diff --git a/sharedthetayc.cpp b/sharedthetayc.cpp
index ca066dd..864c6e6 100644
--- a/sharedthetayc.cpp
+++ b/sharedthetayc.cpp
@@ -14,29 +14,29 @@ EstOutput ThetaYC::getValues(vector<SharedRAbundVector*> shared) {
 	try {	
 		data.resize(3,0.0000);
 		
-		float Atotal = 0;
-		float Btotal = 0;
-		float thetaYC = 0;
-		float pi = 0;
-		float qi = 0;
-		float a = 0;
-		float b = 0;
-		float d = 0;
+		double Atotal = 0;
+		double Btotal = 0;
+		double thetaYC = 0;
+		double pi = 0;
+		double qi = 0;
+		double a = 0;
+		double b = 0;
+		double d = 0;
 		
-		float sumPcubed = 0;
-		float sumQcubed = 0;
-		float sumPQsq = 0;
-		float sumPsqQ = 0;
+		double sumPcubed = 0;
+		double sumQcubed = 0;
+		double sumPQsq = 0;
+		double sumPsqQ = 0;
 		
 		//get the total values we need to calculate the theta denominator sums
-		for (int i = 0; i < shared[0]->size(); i++) {
+		for (int i = 0; i < shared[0]->getNumBins(); i++) {
 			//store in temps to avoid multiple repetitive function calls
-			Atotal += (float)shared[0]->getAbundance(i);
-			Btotal += (float)shared[1]->getAbundance(i);
+			Atotal += (double)shared[0]->getAbundance(i);
+			Btotal += (double)shared[1]->getAbundance(i);
 		}
 		
 		//calculate the theta denominator sums
-		for (int j = 0; j < shared[0]->size(); j++) {
+		for (int j = 0; j < shared[0]->getNumBins(); j++) {
 			//store in temps to avoid multiple repetitive function calls
 			pi = shared[0]->getAbundance(j) / Atotal;
 			qi = shared[1]->getAbundance(j) / Btotal;
@@ -55,16 +55,16 @@ EstOutput ThetaYC::getValues(vector<SharedRAbundVector*> shared) {
 		
 		if (isnan(thetaYC) || isinf(thetaYC)) { thetaYC = 0; }
 		
-		float varA = 4 / Atotal * (sumPcubed - a * a);
-		float varB = 4 / Btotal * (sumQcubed - b * b);
-		float varD = sumPQsq / Atotal + sumPsqQ / Btotal - d * d * (1/Atotal + 1/Btotal);
-		float covAD = 2 / Atotal * (sumPsqQ - a * d);
-		float covBD = 2 / Btotal * (sumPQsq - b* d);
+		double varA = 4 / Atotal * (sumPcubed - a * a);
+		double varB = 4 / Btotal * (sumQcubed - b * b);
+		double varD = sumPQsq / Atotal + sumPsqQ / Btotal - d * d * (1/Atotal + 1/Btotal);
+		double covAD = 2 / Atotal * (sumPsqQ - a * d);
+		double covBD = 2 / Btotal * (sumPQsq - b* d);
 		
-		float varT = d * d * (varA + varB) / pow(a + b - d, (float)4.0) + pow(a+b, (float)2.0) * varD / pow(a+b-d, (float)4.0)
-						- 2.0 * (a + b) * d / pow(a + b - d, (float)4.0) * (covAD + covBD);
+		double varT = d * d * (varA + varB) / pow(a + b - d, (double)4.0) + pow(a+b, (double)2.0) * varD / pow(a+b-d, (double)4.0)
+						- 2.0 * (a + b) * d / pow(a + b - d, (double)4.0) * (covAD + covBD);
 		
-		float ci = 1.95 * sqrt(varT);
+		double ci = 1.95 * sqrt(varT);
 		
 		data[0] = thetaYC;
 		data[1] = thetaYC - ci;
@@ -74,6 +74,11 @@ EstOutput ThetaYC::getValues(vector<SharedRAbundVector*> shared) {
 		if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; }
 		if (isnan(data[2]) || isinf(data[2])) { data[2] = 0; }
 		
+		data[0] = 1.0 - data[0];
+        double hold = data[1];
+        data[1] = 1.0 - data[2];
+        data[2] = 1.0 - hold;
+        
 		return data;
 	}
 	catch(exception& e) {