X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedthetayc.cpp;h=6f3f25001a73208caa74dc438a0b9c7652f70531;hb=0fb6d165c8dc8dc7153a101513a05f457431d0bc;hp=59cea4df6a8835210a33c2d1c815eb50550c6dbc;hpb=50ed3b6104d5821d6184f882e1e1423d47dcbf10;p=mothur.git

diff --git a/sharedthetayc.cpp b/sharedthetayc.cpp
index 59cea4d..6f3f250 100644
--- a/sharedthetayc.cpp
+++ b/sharedthetayc.cpp
@@ -12,49 +12,70 @@
 /***********************************************************************/
 EstOutput ThetaYC::getValues(vector<SharedRAbundVector*> shared) {
 	try {	
-		data.resize(1,0);
+		data.resize(3,0.0000);
 		
-		int Atotal = 0;
-		int Btotal = 0;
+		float Atotal = 0;
+		float Btotal = 0;
 		float thetaYC = 0;
-		float relA = 0;
-		float relB = 0;
+		float pi = 0;
+		float qi = 0;
 		float a = 0;
 		float b = 0;
+		float d = 0;
+		
+		float sumPcubed = 0;
+		float sumQcubed = 0;
+		float sumPQsq = 0;
+		float sumPsqQ = 0;
 		
 		//get the total values we need to calculate the theta denominator sums
 		for (int i = 0; i < shared[0]->size(); i++) {
 			//store in temps to avoid multiple repetitive function calls
-			Atotal += shared[0]->getAbundance(i);
-			Btotal += shared[1]->getAbundance(i);
+			Atotal += (float)shared[0]->getAbundance(i);
+			Btotal += (float)shared[1]->getAbundance(i);
 		}
 		
 		//calculate the theta denominator sums
 		for (int j = 0; j < shared[0]->size(); j++) {
 			//store in temps to avoid multiple repetitive function calls
-			relA = shared[0]->getAbundance(j) / (float)Atotal;
-			relB = shared[1]->getAbundance(j) / (float)Btotal;
+			pi = shared[0]->getAbundance(j) / Atotal;
+			qi = shared[1]->getAbundance(j) / Btotal;
 					
-			a += relA * relB;
-			b += pow((relA-relB),2);
+			a += pi * pi;
+			b += qi * qi;
+			d += pi * qi;
+			
+			sumPcubed += pi * pi * pi;
+			sumQcubed += qi * qi * qi;
+			sumPQsq += pi * qi * qi;
+			sumPsqQ += pi * pi * qi;
 		}
 
-		thetaYC = a / (float) (b+a);
+		thetaYC = d / (a + b - d);
 		
 		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);
+		
+		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);
+		
+		float ci = 1.95 * sqrt(varT);
+		
 		data[0] = thetaYC;
+		data[1] = thetaYC - ci;
+		data[2] = thetaYC + ci;
 		
 		return data;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ThetaYC class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "ThetaYC", "getValues");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ThetaYC class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /***********************************************************************/