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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;
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 && util.isEqual(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);
}
}
/***********************************************************************/
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