double doubles = (double)rank->get(2);
double chaovar = 0.0000;
- double chao = sobs + pow(singles,2)/(2*(doubles+1)) - (singles*doubles/(2*pow(doubles+1,2)));
+ double chao = sobs + singles*(singles-1)/(2*(doubles+1));
- if(doubles==0){chaovar=0;}
- else{
- double g=singles/doubles;
- chaovar = doubles*(0.25*pow(g,4)+pow(g,3)+0.5*pow(g,2));
+ 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(chao==sobs){
- double ci = 1.96*pow(chaovar,0.5);
- chaolci = chao-ci;//chao lci
- chaohci = chao+ci;//chao hci
- }
- else{
+ 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;
return data;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the Chao1 class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "Chao1", "getValues");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the Chao1 class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-};
+}
/***********************************************************************/