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[mothur.git] / shannon.cpp

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+/*
+ *  shannon.cpp
+ *  Dotur
+ *
+ *  Created by Sarah Westcott on 1/7/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "shannon.h"
+
+/***********************************************************************/
+
+EstOutput Shannon::getValues(SAbundVector* rank){
+       try {
+               //vector<double> shannonData(3,0);
+               data.resize(3,0);
+       
+               double shannon = 0.0000;  //hprime
+               double hvara=0.0000;
+    
+               double maxRank = rank->getMaxRank();
+               int sampled = rank->getNumSeqs();
+               int sobs = rank->getNumBins();
+       
+               for(int i=1;i<=maxRank;i++){
+                       double p = ((double) i)/((double)sampled);
+                       shannon += (double)rank->get(i)*p*log(p); //hprime
+                       hvara  += (double)rank->get(i)*p*pow(log(p),2);
+               }
+               shannon = -shannon;
+    
+               double hvar = (hvara-pow(shannon,2))/(double)sampled+(double)sobs/(double)(2*sampled*sampled);
+    
+               double ci = 0;
+       
+               if(hvar>0){
+                       ci = 1.96*pow(hvar,0.5);
+               }
+       
+               double shannonhci = shannon + ci;
+               double shannonlci = shannon - ci;
+               
+               data[0] = shannon;
+               data[1] = shannonlci;
+               data[2] = shannonhci;
+               
+               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 Shannon class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the Shannon class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }       
+}
+
+/***********************************************************************/