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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-1)/(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) {
m->errorOut(e, "Shannon", "getValues");
exit(1);
}
}
/***********************************************************************/
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