1 /* 2 * shannon.cpp 3 * Dotur 4 * 5 * Created by Sarah Westcott on 1/7/09. 6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved. 7 * 8 */ 9 10 #include "shannon.h" 11 12 /***********************************************************************/ 13 getValues(SAbundVector * rank)14EstOutput Shannon::getValues(SAbundVector* rank){ 15 try { 16 //vector<double> shannonData(3,0); 17 data.resize(3,0); 18 19 double shannon = 0.0000; //hprime 20 double hvara=0.0000; 21 22 double maxRank = rank->getMaxRank(); 23 int sampled = rank->getNumSeqs(); 24 int sobs = rank->getNumBins(); 25 26 for(int i=1;i<=maxRank;i++){ 27 double p = ((double) i)/((double)sampled); 28 shannon += (double)rank->get(i)*p*log(p); //hprime 29 hvara += (double)rank->get(i)*p*pow(log(p),2); 30 } 31 shannon = -shannon; 32 33 double hvar = (hvara-pow(shannon,2))/(double)sampled+(double)(sobs-1)/(double)(2*sampled*sampled); 34 35 double ci = 0; 36 37 if(hvar>0){ 38 ci = 1.96*pow(hvar,0.5); 39 } 40 41 double shannonhci = shannon + ci; 42 double shannonlci = shannon - ci; 43 44 data[0] = shannon; 45 data[1] = shannonlci; 46 data[2] = shannonhci; 47 48 if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; } 49 if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; } 50 if (isnan(data[2]) || isinf(data[2])) { data[2] = 0; } 51 52 return data; 53 } 54 catch(exception& e) { 55 m->errorOut(e, "Shannon", "getValues"); 56 exit(1); 57 } 58 } 59 60 /***********************************************************************/ 61