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[mothur.git] / chao1.cpp

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+/*
+ *  chao1.cpp
+ *  Dotur
+ *
+ *  Created by Sarah Westcott on 1/7/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "chao1.h"
+
+/***********************************************************************/
+EstOutput Chao1::getValues(SAbundVector* rank){
+       try {
+               data.resize(3,0);
+       
+               double sobs = (double)rank->getNumBins();
+       
+               double singles = (double)rank->get(1);
+               double doubles = (double)rank->get(2);
+               double chaovar = 0.0000;
+       
+               double chao = sobs + pow(singles,2)/(2*(doubles+1)) - (singles*doubles/(2*pow(doubles+1,2)));
+       
+               if(doubles==0){chaovar=0;}
+               else{
+                       double g=singles/doubles;
+                       chaovar = doubles*(0.25*pow(g,4)+pow(g,3)+0.5*pow(g,2));
+               }
+
+       
+               double chaohci, chaolci;
+       
+               if(chao==sobs){
+                       double ci = 1.96*pow(chaovar,0.5);
+                       chaolci = chao-ci;//chao lci
+                       chaohci = chao+ci;//chao hci
+               }
+               else{
+                       double denom = pow(chao-sobs,2);
+                       double c = exp(1.96*pow((log(1+chaovar/denom)),0.5));
+                       chaolci = sobs+(chao-sobs)/c;//chao lci
+                       chaohci = sobs+(chao-sobs)*c;//chao hci
+               }
+               
+               data[0] = chao;
+               data[1] = chaolci;
+               data[2] = chaohci;
+
+           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; }
+               
+               return data;
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the Chao1 class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the Chao1 class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }       
+};
+
+/***********************************************************************/