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[mothur.git] / uvest.cpp

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+/*
+ *  uvest.cpp
+ *  Dotur
+ *
+ *  Created by Sarah Westcott on 1/8/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "uvest.h"
+
+/***********************************************************************/
+//This is used by SharedJAbund and SharedSorAbund
+EstOutput UVEst::getUVest(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+       try {   
+               EstOutput results;
+               results.resize(2,0);
+               
+               int S12, Atotal, Btotal, f1A, f2A, f1B, f2B, sumSharedA, sumSharedB, sumSharedA1, sumSharedB1, tempA, tempB;
+               S12 = 0; Atotal = 0; Btotal = 0; f1A = 0; f2A = 0; f1B = 0; f2B = 0; sumSharedA = 0; sumSharedB = 0; sumSharedA1 = 0; sumSharedB1 = 0;
+               float Upart1, Upart2, Upart3, Vpart1, Vpart2, Vpart3, Uest, Vest;
+               Upart1 = 0.0; Upart2 = 0.0; Upart3 = 0.0; Vpart1 = 0.0; Vpart2 = 0.0; Vpart3 = 0.0;
+               
+               /*Xi, Yi = abundance of the ith shared OTU in A and B 
+               ntotal, mtotal = total number of sequences sampled in A and B 
+               I(•) = if the argument, •, is true then I(•) is 1; otherwise it is 0. 
+               sumSharedA = the sum of all shared otus in A
+               sumSharedB = the sum of all shared otus in B
+               sumSharedA1 = the sum of all shared otus in A where B = 1
+               sumSharedB1 = the sum of all shared otus in B where A = 1 */
+               
+               for (int i = 0; i < shared1->size(); i++) {
+                       //store in temps to avoid multiple repetitive function calls
+                       tempA = shared1->getAbundance(i);
+                       tempB = shared2->getAbundance(i);
+
+                       Atotal += tempA;
+                       Btotal += tempB;
+                       
+                       if ((tempA != 0) && (tempB != 0)) {//they are shared
+                               sumSharedA += tempA;
+                               sumSharedB += tempB;
+                               
+                               //does A have one or two
+                               if (tempA == 1)                 { f1A++; sumSharedB1 += tempB;}
+                               else if (tempA == 2)    { f2A++; }
+                               
+                               //does B have one or two
+                               if (tempB == 1)                 { f1B++; sumSharedA1 += tempA;}
+                               else if (tempB == 2)    { f2B++; }
+                       }
+               }
+               
+               Upart1 = sumSharedA / (float) Atotal;
+               Upart2 = ((Btotal - 1) * f1B) / (float) (Btotal * 2 * f2B);
+               Upart3 = sumSharedA1 / (float) Atotal;
+               
+               if (isnan(Upart1) || isinf(Upart1)) { Upart1 = 0; }
+               if (isnan(Upart2) || isinf(Upart2)) { Upart2 = 0; }
+               if (isnan(Upart3) || isinf(Upart3)) { Upart3 = 0; }
+               
+               Uest = Upart1 + (Upart2 * Upart3);
+               
+               Vpart1 = sumSharedB / (float) Btotal;
+               Vpart2 = ((Atotal - 1) * f1A) / (float) (Atotal * 2 * f2A);
+               Vpart3 = sumSharedB1 / (float) Btotal;
+               
+               if (isnan(Vpart1) || isinf(Vpart1)) { Vpart1 = 0; }
+               if (isnan(Vpart2) || isinf(Vpart2)) { Vpart2 = 0; }
+               if (isnan(Vpart3) || isinf(Vpart3)) { Vpart3 = 0; }
+               
+               Vest = Vpart1 + (Vpart2 * Vpart3);
+               
+               if (Uest > 1) { Uest = 1; }
+               if (Vest > 1) { Vest = 1; }
+               
+               results[0] = Uest;
+               results[1] = Vest;
+               
+               return results;
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the UVEst class Function getUVest. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the UVEst class Function getUVest. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }       
+
+
+}
+
+/***********************************************************************/