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[mothur.git] / mothurfisher.cpp

diff --git a/mothurfisher.cpp b/mothurfisher.cpp
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+++ b/mothurfisher.cpp
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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_) {
+       try {
+               sleft = 0.0; sright = 0.0; sless = 0.0; slarg = 0.0;
+               
+               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_;
+               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 (!((n1_i != 0)&&(n_1i != 0)&&(ni != 0))) {
+                       if(!(((int)n11i % 10) == 0)){
+                               if(n11i==sn11+1)  
+                               {
+                                       sprob *= ((sn1_-sn11)/(n11i))*((sn_1-sn11)/(n11i+sn-sn1_-sn_1));
+                                       sn11 = n11i;
+                                       return sprob;
+                               }
+                               if(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(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);
+               }
+               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);
+               }
+               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);
+       }
+}
+/***********************************************************/
+
+
+