X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedthetayc.cpp;h=864c6e63712cdc78d2cc0320ff2869c6deff196f;hp=ad2e1c574302b678f9d503dc235ef3b5a6b38db2;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=25cde7ff05bbe741da1712f2c740e0bc8706e523

diff --git a/sharedthetayc.cpp b/sharedthetayc.cpp
index ad2e1c5..864c6e6 100644
--- a/sharedthetayc.cpp
+++ b/sharedthetayc.cpp
@@ -10,55 +10,81 @@
 #include "sharedthetayc.h"
 
 /***********************************************************************/
-EstOutput SharedThetaYC::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+EstOutput ThetaYC::getValues(vector<SharedRAbundVector*> shared) {
 	try {	
-		data.resize(1,0);
+		data.resize(3,0.0000);
 		
-		int Atotal, Btotal, tempA, tempB;
-		Atotal = 0; Btotal = 0; 
-		float thetaYC, sumSharedA, sumSharedB, a, b, d;
-		thetaYC = 0.0; sumSharedA = 0.0; sumSharedB = 0.0; a = 0.0; b = 0.0; d = 0.0;
+		double Atotal = 0;
+		double Btotal = 0;
+		double thetaYC = 0;
+		double pi = 0;
+		double qi = 0;
+		double a = 0;
+		double b = 0;
+		double d = 0;
+		
+		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 < shared1->size(); i++) {
+		for (int i = 0; i < shared[0]->getNumBins(); i++) {
 			//store in temps to avoid multiple repetitive function calls
-			Atotal += shared1->getAbundance(i);
-			Btotal += shared2->getAbundance(i);
+			Atotal += (double)shared[0]->getAbundance(i);
+			Btotal += (double)shared[1]->getAbundance(i);
 		}
 		
 		//calculate the theta denominator sums
-		for (int j = 0; j < shared1->size(); j++) {
+		for (int j = 0; j < shared[0]->getNumBins(); j++) {
 			//store in temps to avoid multiple repetitive function calls
-			tempA = shared1->getAbundance(j);
-			tempB = shared2->getAbundance(j);
-			
-			//they are shared
-			if ((tempA != 0) && (tempB != 0)) {
-				if (Atotal != 0)	{ sumSharedA = (tempA / (float)Atotal); }
-				if (Btotal != 0)	{ sumSharedB = (tempB / (float)Btotal); }
+			pi = shared[0]->getAbundance(j) / Atotal;
+			qi = shared[1]->getAbundance(j) / Btotal;
+					
+			a += pi * pi;
+			b += qi * qi;
+			d += pi * qi;
 			
-				a += sumSharedA * sumSharedA;
-				b += sumSharedB * sumSharedB;
-				d += sumSharedA * sumSharedB;
-			}
+			sumPcubed += pi * pi * pi;
+			sumQcubed += qi * qi * qi;
+			sumPQsq += pi * qi * qi;
+			sumPsqQ += pi * pi * qi;
 		}
 
-		thetaYC = d / (float) (a + b - d);
+		thetaYC = d / (a + b - d);
 		
 		if (isnan(thetaYC) || isinf(thetaYC)) { thetaYC = 0; }
 		
+		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);
+		
+		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);
+		
+		double ci = 1.95 * sqrt(varT);
+		
 		data[0] = thetaYC;
+		data[1] = thetaYC - ci;
+		data[2] = thetaYC + ci;
+		
+		if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+		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) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SharedThetaYC 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 SharedThetaYC class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /***********************************************************************/