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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();
+               
+               //this is a modification do to a vector fill error that occurs when an empty sharedRabund creates a sabund
+               //in that case there is no 1 0r 2.
+               double singles;
+               if (rank->size() > 1) {
+                       singles = (double)rank->get(1);
+               }else{ singles = 0.0;  }
+
+               double doubles;
+               if (rank->size() > 2) {
+                        doubles = (double)rank->get(2);
+               }else{ doubles = 0.0;  }
+
+               double chaovar = 0.0000;
+//cout << "singles = " << singles << " doubles = " << doubles << " sobs = " << sobs << endl;   
+               double chao = sobs + singles*(singles-1)/(2*(doubles+1));
+       
+               if(singles > 0 && doubles > 0){
+                       chaovar = singles*(singles-1)/(2*(doubles+1))
+                                       + singles*pow(2*singles-1, 2)/(4*pow(doubles+1,2))
+                                       + pow(singles, 2)*doubles*pow(singles-1, 2)/(4*pow(doubles+1,4));
+               }
+               else if(singles > 0 && doubles == 0){
+                       chaovar = singles*(singles-1)/2 + singles*pow(2*singles-1, 2)/4 - pow(singles, 4)/(4*chao); 
+               }
+               else if(singles == 0){
+                       chaovar = sobs*exp(-1*rank->getNumSeqs()/sobs)*(1-exp(-1*rank->getNumSeqs()/sobs));
+               }
+                       
+               double chaohci, chaolci;
+       
+               if(singles>0){
+                       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
+               }
+               else{
+                       double p = exp(-1*rank->getNumSeqs()/sobs);
+                       chaolci = sobs/(1-p)-1.96*pow(sobs*p/(1-p), 0.5);
+                       chaohci = sobs/(1-p)+1.96*pow(sobs*p/(1-p), 0.5);
+                       if(chaolci < sobs){     chaolci = sobs; }
+               }
+               
+               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) {
+               m->errorOut(e, "Chao1", "getValues");
+               exit(1);
+       }
+}
+
+/***********************************************************************/