X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=jackknife.cpp;fp=jackknife.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=8f0629832208e797efbdc815e619bab28ed49046;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/jackknife.cpp b/jackknife.cpp
deleted file mode 100644
index 8f06298..0000000
--- a/jackknife.cpp
+++ /dev/null
@@ -1,152 +0,0 @@
-/*
- *  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);
-	}
-}
-
-/***********************************************************************/