X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedjackknife.cpp;fp=sharedjackknife.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=0998db8fe3106bbb40c26dc8621d37030fb275c3;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/sharedjackknife.cpp b/sharedjackknife.cpp
deleted file mode 100644
index 0998db8..0000000
--- a/sharedjackknife.cpp
+++ /dev/null
@@ -1,144 +0,0 @@
-/*
- *  sharedjackknife.cpp
- *  Mothur
- *
- *  Created by Thomas Ryabin on 3/30/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "sharedjackknife.h"
-
-/***************************************************************************************
-
-***************************************************************************************/
-double SharedJackknife::simpson(vector<int> abunds, double numInd, int numBins){
-	double denom = numInd*(numInd-1);
-	double sum = 0;
-	for(int i = 0; i < numBins; i++)
-		sum += (double)abunds[i]*((double)abunds[i]-1)/denom;
-	
-	return sum;
-}
-
-/*****************************************************************************************/
-
-double* SharedJackknife::jackknife(){		
-	int numBins = groups.at(0)->getNumBins()-1;
-	vector<int> cArray(numBins);
-	for(int i = 0; i < numBins; i++)
-		cArray[i] = 0;
-
-	double numInd = 0;
-	for(int i = 0; i < numGroups; i++)
-		for(int j = 0; j < numBins; j++) {
-			int curAbund = groups.at(i)->get(j+1).abundance;
-			cArray[j] += curAbund;
-			numInd += (double)curAbund;
-		}
-
-	double baseD = 1/simpson(cArray, numInd, numBins);
-	
-	vector<double> pseudoVals(numBins);
-	double jackknifeEstimate = 0;
-	for(int i = 0; i < numGroups; i++) {
-		for(int j = 0; j < numBins-1; j++) {
-			int abundDiff = -groups.at(i)->get(j+1).abundance;
-			if(i > 0)
-				abundDiff += groups.at(i-1)->get(j+1).abundance;
-
-			cArray[j] += abundDiff;
-			numInd += abundDiff;	
-		}
-		
-		double curD = 1/simpson(cArray, numInd, numBins);
-		pseudoVals[i] = (double)numGroups*(baseD - curD) + curD;
-		jackknifeEstimate += pseudoVals[i];
-	}
-	jackknifeEstimate /= (double)numGroups;
-		
-	double variance = 0;
-	for(int i = 0; i < numGroups; i++)
-		variance += pow(pseudoVals[i]-jackknifeEstimate, 2);
-		
-	variance /= (double)numGroups*((double)numGroups-1);
-	double stErr = sqrt(variance);
-	TDTable table;
-	double confLimit = 0;
-	if(numGroups <= 30)
-		confLimit = table.getConfLimit(numGroups-1, 1);
-	else
-		confLimit = 1.645;
-	
-	confLimit *= stErr;
-	
-	double* rdata = new double[3];
-	rdata[0] = baseD;
-	rdata[1] = jackknifeEstimate - confLimit;
-	rdata[2] = jackknifeEstimate + confLimit;
-	
-	return rdata;
-}
-
-/************************************************************************************************
-************************************************************************************************/
-
-EstOutput SharedJackknife::getValues(vector<SharedRAbundVector*> vectorShared){ //Fix this for collect, mistake was that it was made with summary in mind.
-	try {
-		SharedRAbundVector* shared1 = vectorShared[0];
-		SharedRAbundVector* shared2 = vectorShared[1];
-		if(numGroups == -1) {
-			numGroups = m->getNumGroups();
-		}
-
-		if(callCount == numGroups*(numGroups-1)/2) {
-			currentCallDone = true;
-			callCount = 0;
-		}
-		callCount++;
-
-		if(currentCallDone) {
-			groups.clear();	
-			currentCallDone = false;
-		}
-		
-		if(groups.size() != numGroups) {	
-			if(groups.size() == 0)
-				groups.push_back(shared1);
-			groups.push_back(shared2);
-		}
-		
-		if(groups.size() == numGroups && callCount < numGroups) {
-			data.resize(3,0);
-
-			double* rdata = jackknife();
-			data[0] = rdata[0];
-			data[1] = rdata[1];
-			data[2] = rdata[2];
-		
-			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[0])) { data[2] = 0; }
-			
-			return data;
-		}
-		
-		data.resize(3,0);
-		data[0] = 0;
-		data[1] = 0;
-		data[2] = 0;
-		
-		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, "SharedJackknife", "getValues");
-		exit(1);
-	}
-}
-
-/***********************************************************************/
-