X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=geom.cpp;fp=geom.cpp;h=5bd150ef7f8201254a392a52a7583b07b83e0b00;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/geom.cpp b/geom.cpp
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--- /dev/null
+++ b/geom.cpp
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+/*
+ *  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);
+	}
+}
+
+/***********************************************************************/
+
+
+
+
+
+
+