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/*
* ace.cpp
* Dotur
*
* Created by Sarah Westcott on 1/7/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "ace.h"
/***********************************************************************/
EstOutput Ace::getValues(SAbundVector* rank) {
try {
data.resize(3,0);
double ace, acelci, acehci;
double nrare = 0;
double srare = 0;
double sabund = 0;
double Cace, term1, gamace;
double numsum = 0;
double maxRank = (double)rank->getMaxRank();
for(int i=1;i<=maxRank;i++){
if(i<=abund){
srare += rank->get(i);
nrare += i*rank->get(i);
numsum += (i-1)*i*rank->get(i);
}
else if(i>abund) {sabund += rank->get(i);}
}
double sobs = srare + sabund;
if (nrare == 0){ Cace = 0.0000; }
else { Cace = 1.0000 -(double)rank->get(1)/(double)nrare; }
double denom = Cace * (double)(nrare * (nrare-1));
if(denom <= 0.0){ term1=0.0000; } else { term1 = (double)(srare * numsum)/(double)denom - 1.0; }
if(term1 >= 0.0){ gamace = term1; } else { gamace = 0.0; }
if(gamace >= 0.64){
gamace = gamace * (1 + (nrare * (1 - Cace) * numsum) / denom);
if(gamace<0){ gamace = 0; }
}
if(Cace == 0.0){
ace = 0.00;}//ace
else{
ace = (double)sabund+((double)srare+(double)rank->get(1)*gamace)/Cace;//ace
}
/*
The following code was obtained from Anne Chao for calculating the SE for her ACE estimator
My modification was to reset the frequencies so that a singleton is found in rank[1] insted
of in rank[0], etc.
I have also added the forumlae to calculate the 95% confidence intervals.
*/
double j,D_s=0,nn=0,ww=0;
int Max_Index=rank->getMaxRank()+1;
double pp, temp1, temp2;
vector<double> Part_N_Part_F(Max_Index+1,0.0);
for (j=1; j<Max_Index; j++) if(j<=abund) D_s += rank->get(j);
for (j=1; j<Max_Index; j++){
if(j<=abund){
nn += rank->get(j) * j;
ww += rank->get(j) * j * ( j - 1);
}
}
double C_hat = 1.-rank->get(1)/double(nn);
double Gamma = ( D_s * ww) / ( C_hat * nn * ( nn - 1.)) - 1.;
temp1 = double(nn - rank->get(1));
temp2 = double(nn - 1.);
if ( Gamma > 0.){
Part_N_Part_F[1] = ( D_s + nn) * ( 1. + rank->get(1) * ww / temp1 / temp2) / temp1 + nn * D_s * ww * ( temp1 - 1.) /
( temp1 * temp1 * temp2 * temp2) - ( nn + rank->get(1)) / temp1;
for ( j=2; j<=Max_Index; j++){
if(j<=abund){
Part_N_Part_F[j] = ( nn * temp1 - j * rank->get(1) * D_s) / temp1 / temp1 * ( 1. + rank->get(1) * ww / temp1 / temp2)
+ j * rank->get(1) * D_s * nn * ( ( j - 1.) * temp1 * temp2 - ww * ( temp1 + temp2))
/ temp1 / temp1 / temp1 / temp2 / temp2 + j * rank->get(1) * rank->get(1) / temp1 / temp1;
}
}
}
else{
Part_N_Part_F[1] = ( nn + D_s ) / temp1;
for ( j=2; j<=Max_Index; j++){
if(j<=abund){
Part_N_Part_F[j-1] = ( nn * temp1 - j * rank->get(1) * D_s ) / temp1 / temp1;
}
}
}
if(Max_Index>abund){
for ( j=abund+1; j<=Max_Index; j++){
Part_N_Part_F[j-1] = 1.;
}
}
for ( temp1=0., temp2=0., j=0; j<Max_Index; j++) {
pp = Part_N_Part_F[j];
temp1 += pp * rank->get(j);
temp2 += pp * pp * rank->get(j);
}
double se = temp2 - temp1 * temp1 / ace;
if(toString(se) == "nan"){
acelci = ace;
acehci = ace;
}
else if(ace==0.000){
acelci = ace;
acehci = ace;
}
else if(ace==sobs){
double ci = 1.96*pow(se,0.5);
acelci = ace-ci; //ace lci
acehci = ace+ci; //ace hci
}else{
double denom = pow(ace-sobs,2);
double c = exp(1.96*pow((log(1+se/denom)),0.5));
acelci = sobs+(ace-sobs)/c; //ace lci
acehci = sobs+(ace-sobs)*c; //ace hci
}
data[0] = ace;
data[1] = acelci;
data[2] = acehci;
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, "Ace", "getValues");
exit(1);
}
}
/***********************************************************************/
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