X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=geom.cpp;fp=geom.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=5bd150ef7f8201254a392a52a7583b07b83e0b00;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/geom.cpp b/geom.cpp
deleted file mode 100644
index 5bd150e..0000000
--- a/geom.cpp
+++ /dev/null
@@ -1,101 +0,0 @@
-/*
- *  geom.cpp
- *  Mothur
- *
- *  Created by Thomas Ryabin on 2/23/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "geom.h"
-
-/***********************************************************************/
-
-double Geom::kEq(double k, double spec){
-	return k/(1-k)*pow(1-k, spec)/(1-pow(1-k, spec));
-}
-
-RAbundVector Geom::getRAbundVector(SAbundVector* rank){
-		vector <int> rData;
-		int mr = 1;
-		int nb = 0;
-		int ns = 0;
-		
-		for(int i = rank->size()-1; i > 0; i--) {
-			int cur = rank->get(i);
-			if(mr == 1 && cur > 0)
-				mr = i;
-			nb += cur;
-			ns += i*cur;
-			for(int j = 0; j < cur; j++)
-				rData.push_back(i);
-		}
-		
-		RAbundVector rav = RAbundVector(rData, mr, nb, ns);
-		rav.setLabel(rank->getLabel());
-		return rav;
-}
-
-/***********************************************************************************/
-
-/***********************************************************************************/
-EstOutput Geom::getValues(SAbundVector* rank){
-	try {
-		data.resize(3,0);
-		
-		rdata = getRAbundVector(rank);
-		double numInd = rdata.getNumSeqs();
-		double numSpec = rdata.getNumBins();
-		double min = rdata.get(rdata.size()-1);
-		double k = .5;
-		double step = .49999;
-		
-		while(fabs(min - numInd*kEq(k, (double)numSpec)) > .0001) { //This uses a binary search to find the value of k.
-			if(numInd*kEq(k, numSpec) > min)
-				k += step;
-			else
-				k -= step;
-			step /= 2;
-		}
-		
-		double cK = 1/(1-pow(1-k, numSpec));
-		double sumExp = 0;
-		double sumObs = 0;
-		double maxDiff = 0;
-		
-		for(int i = 0; i < numSpec; i++)
-		{
-			sumObs += rdata.get(i);
-			sumExp += numInd*cK*k*pow(1-k, i);
-			
-			double diff = fabs(sumObs-sumExp);
-			if(diff > maxDiff)	{	maxDiff = diff;		}
-			
-		}
-
-
-		data[0] = maxDiff/numInd;
-		data[1] = 0.886/sqrt(numSpec);
-		data[2] = 1.031/sqrt(numSpec);
-
-		
-		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, "Geom", "getValues");
-		exit(1);
-	}
-}
-
-/***********************************************************************/
-
-
-
-
-
-
-