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/*
* mothurfisher.cpp
* Mothur
*
* Created by westcott on 7/8/11.
* Copyright 2011 Schloss Lab. All rights reserved.
*
*/
//translated to c++ using source code http://www.langsrud.com/stat/fisher.htm as a reference
#include "mothurfisher.h"
/***********************************************************/
double MothurFisher::fexact(double n11_, double n12_, double n21_, double n22_, string o) {
try {
sleft = 0.0; sright = 0.0; sless = 0.0; slarg = 0.0;
otuLabel = o;
if(n11_<0) n11_ *= -1;
if(n12_<0) n12_ *= -1;
if(n21_<0) n21_ *= -1;
if(n22_<0) n22_ *= -1;
double n1_ = n11_+n12_;
double n_1 = n11_+n21_;
double n = n11_ +n12_ +n21_ +n22_;
if (m->getDebug()) { m->mothurOut("[DEBUG]: fisher:fexact n11_, n1_, n_1, n " + toString(n11_) + " " + toString(n1_) + " " + toString(n_1) + " " + toString(n) + " \n"); }
exact(n11_,n1_,n_1,n);
double twotail = sleft+sright;
if(twotail>1) twotail=1;
double result = twotail;
return result;
}catch(exception& e) {
m->errorOut(e, "MothurFisher", "fexact");
exit(1);
}
}
/***********************************************************/
double MothurFisher::lngamm(double z) {
// Reference: "Lanczos, C. 'A precision approximation
// of the gamma function', J. SIAM Numer. Anal., B, 1, 86-96, 1964."
// Translation of Alan Miller's FORTRAN-implementation
// See http://lib.stat.cmu.edu/apstat/245
try {
double x = 0;
x += 0.1659470187408462e-06/(z+7);
x += 0.9934937113930748e-05/(z+6);
x -= 0.1385710331296526 /(z+5);
x += 12.50734324009056 /(z+4);
x -= 176.6150291498386 /(z+3);
x += 771.3234287757674 /(z+2);
x -= 1259.139216722289 /(z+1);
x += 676.5203681218835 /(z);
x += 0.9999999999995183;
return(log(x)-5.58106146679532777-z+(z-0.5)*log(z+6.5));
}catch(exception& e) {
m->errorOut(e, "MothurFisher", "lngamm");
exit(1);
}
}
/***********************************************************/
double MothurFisher::lnfact(double n){
try {
if(n <= 1) return(0);
return(lngamm(n+1));
}catch(exception& e) {
m->errorOut(e, "MothurFisher", "lnfact");
exit(1);
}
}
/***********************************************************/
double MothurFisher::lnbico(double n, double k){
try {
return(lnfact(n)-lnfact(k)-lnfact(n-k));
}catch(exception& e) {
m->errorOut(e, "MothurFisher", "lnbico");
exit(1);
}
}
/***********************************************************/
double MothurFisher::hyper_323(double n11, double n1_, double n_1, double n){
try {
return(exp(lnbico(n1_,n11)+lnbico(n-n1_,n_1-n11)-lnbico(n,n_1)));
}catch(exception& e) {
m->errorOut(e, "MothurFisher", "hyper_323");
exit(1);
}
}
/***********************************************************/
double MothurFisher::myhyper(double n11){
try {
double hyper0Result = hyper0(n11,0,0,0);
return hyper0Result;
}catch(exception& e) {
m->errorOut(e, "MothurFisher", "myhyper");
exit(1);
}
}
/***********************************************************/
double MothurFisher::hyper0(double n11i, double n1_i, double n_1i, double ni) {
try {
if (!( !util.isEqual(n1_i, 0) && !util.isEqual(n_1i,0) && !util.isEqual(ni, 0) )) {
if(!(((int)n11i % 10) == 0)){
if(util.isEqual(n11i,sn11+1))
{
sprob *= ((sn1_-sn11)/(n11i))*((sn_1-sn11)/(n11i+sn-sn1_-sn_1));
sn11 = n11i;
return sprob;
}
if(util.isEqual(n11i,sn11-1))
{
sprob *= ((sn11)/(sn1_-n11i))*((sn11+sn-sn1_-sn_1)/(sn_1-n11i));
sn11 = n11i;
return sprob;
}
}
sn11 = n11i;
}else{
sn11 = n11i;
sn1_=n1_i;
sn_1=n_1i;
sn=ni;
}
sprob = hyper_323(sn11,sn1_,sn_1,sn);
return sprob;
}catch(exception& e) {
m->errorOut(e, "MothurFisher", "hyper0");
exit(1);
}
}
/***********************************************************/
double MothurFisher::exact(double n11, double n1_, double n_1, double n){
try {
double p,i,j,prob;
double max=n1_;
if(n_1<max) max=n_1;
double min = n1_+n_1-n;
if(min<0) min=0;
if(util.isEqual(min,max))
{
sless = 1;
sright= 1;
sleft = 1;
slarg = 1;
return 1;
}
prob=hyper0(n11,n1_,n_1,n);
sleft=0;
p=myhyper(min);
for(i=min+1; p<0.99999999*prob; i++)
{
sleft += p;
p=myhyper(i);
if (i > max) {
m->mothurOut("[WARNING]: i value too high. Take a closer look at the pvalue for " + otuLabel + ".\n");
break;
}
}
i--;
if(p<1.00000001*prob) sleft += p;
else i--;
sright=0;
p=myhyper(max);
for(j=max-1; p<0.99999999*prob; j--)
{
sright += p;
p=myhyper(j);
if (j < 0) {
m->mothurOut("[WARNING]: j value too low. Take a closer look at the pvalue for " + otuLabel + ".\n");
break;
}
}
j++;
if(p<1.00000001*prob) sright += p;
else j++;
if(abs(i-n11)<abs(j-n11))
{
sless = sleft;
slarg = 1 - sleft + prob;
}
else
{
sless = 1 - sright + prob;
slarg = sright;
}
return prob;
}catch(exception& e) {
m->errorOut(e, "MothurFisher", "exact");
exit(1);
}
}
/***********************************************************/
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