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[mothur.git] / sharedthetayc.cpp

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+/*
+ *  sharedthetayc.cpp
+ *  Dotur
+ *
+ *  Created by Sarah Westcott on 1/8/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "sharedthetayc.h"
+
+/***********************************************************************/
+EstOutput ThetaYC::getValues(vector<SharedRAbundVector*> shared) {
+       try {   
+               data.resize(3,0.0000);
+               
+               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 < shared[0]->getNumBins(); i++) {
+                       //store in temps to avoid multiple repetitive function calls
+                       Atotal += (double)shared[0]->getAbundance(i);
+                       Btotal += (double)shared[1]->getAbundance(i);
+               }
+               
+               //calculate the theta denominator sums
+               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;
+                                       
+                       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 = 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];
+               return data;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ThetaYC", "getValues");
+               exit(1);
+       }
+}
+
+/***********************************************************************/