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/*
* jacknife.cpp
* Dotur
*
* Created by Sarah Westcott on 1/7/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "jackknife.h"
/***********************************************************************/
void Jackknife::getAMatrix(void){
try {
vector<vector<double> > B = m->binomial(maxOrder);
aMat.resize(maxOrder+1);
for(int i=0;i<=maxOrder;i++){
aMat[i].resize(maxOrder+1);
for(int j=1;j<=maxOrder;j++){
aMat[i][j] = 1 + B[i][j] * (int)(pow(-1.0,j+1));
}
}
}
catch(exception& e) {
m->errorOut(e, "Jackknife", "getAMatrix");
exit(1);
}
}
/**************************************************************************************************/
double Jackknife::CN(double z){
try {
if(z>6.0) { return 0.0; }
if(z<-6.0) { return 0.0; }
const double b1= 0.31938153;
const double b2= -0.356563782;
const double b3= 1.781477937;
const double b4= -1.821255978;
const double b5= 1.330274429;
const double p= 0.2316419;
const double c2= 0.3989423;
double a=abs(z);
double t=1.0/(1.0+a*p);
double b=c2*exp((-z)*(z/2.0));
double n=((((b5*t+b4)*t+b3)*t+b2)*t+b1)*t;
n = 2*b*n;
return n;
}
catch(exception& e) {
m->errorOut(e, "Jackknife", "CN");
exit(1);
}
}
/***********************************************************************/
EstOutput Jackknife::getValues(SAbundVector* rank){
try {
//EstOutput jackData(3,0);
data.resize(3,0);
double jack, jacklci, jackhci;
int maxRank = (double)rank->getMaxRank();
int S = rank->getNumBins();
double N[maxOrder+1];
double variance[maxOrder+1];
double p[maxOrder+1];
int k = 0;
for(int i=0;i<=maxOrder;i++){
N[i]=0.0000;
variance[i]=0.0000;
for(int j=1;j<=maxRank;j++){
if(j<=i){
N[i] += aMat[i][j]*rank->get(j);
variance[i] += aMat[i][j]*aMat[i][j]*rank->get(j);
}
else{
N[i] += rank->get(j);
variance[i] += rank->get(j);
}
}
variance[i] = variance[i]-N[i];
double var = 0.0000;
if(i>0){
for(int j=1;j<=maxRank;j++){
if(j<=i){ var += rank->get(j)*pow((aMat[i][j]-aMat[i-1][j]),2.0); }
else { var += 0.0000; }
}
var -= ((N[i]-N[i-1])*(N[i]-N[i-1]))/S;
var = var * S / (S-1);
double T = (N[i]-N[i-1])/sqrt(var);
if(T<=0.00){ p[i-1] = 1.00000; }
else{ p[i-1] = CN(T); }
if(p[i-1]>=0.05){
k = i-1;
break;
}
}
if(i == maxOrder){ k=1; }
}
double ci = 0;
if(k>1){
double c = (0.05-p[k-1])/(p[k]-p[k-1]);
ci = 0.0000;
jack = c*N[k]+(1-c)*N[k-1];
for(int j=1;j<=maxRank;j++){
if(j<=k){ ci += rank->get(j)*pow((c*aMat[k][j]+(1-c)*aMat[k-1][j]),2.0); }
else { ci += rank->get(j); }
}
ci = 1.96 * sqrt(ci - jack);
}
else if(k==1){
jack = N[1];
ci = 1.96*sqrt(variance[1]);
}else{
jack = 0.0;
ci = 0.0;
}
jacklci = jack-ci;
jackhci = jack+ci;
data[0] = jack;
data[1] = jacklci;
data[2] = jackhci;
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, "Jackknife", "getValues");
exit(1);
}
}
/***********************************************************************/
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