X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bstick.cpp;fp=bstick.cpp;h=67507a9967ef82effe923662298960ecf00618b8;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/bstick.cpp b/bstick.cpp
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--- /dev/null
+++ b/bstick.cpp
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+/*
+ *  bstick.cpp
+ *  Mothur
+ *
+ *  Created by Thomas Ryabin on 3/6/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "bstick.h"
+
+
+/***********************************************************************/
+double BStick::invSum(int index, double numSpec)
+{
+	double sum = 0;
+	for(int i = index; i <= numSpec; i++)
+		sum += 1/(double)i;
+	return sum;
+}
+/***********************************************************************/
+RAbundVector BStick::getRAbundVector(SAbundVector* rank){
+		vector <int> rData;
+		int mr = 1;
+		int nb = 0;
+		int ns = 0;
+		
+		for(int i = rank->size()-1; i > 0; i--) {
+			double 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 BStick::getValues(SAbundVector* rank){
+	try {
+		data.resize(3,0);
+		rdata = getRAbundVector(rank);
+		double numInd = (double)rdata.getNumSeqs();
+		double numSpec = (double)rdata.getNumBins();
+		
+		double sumExp = 0;
+		double sumObs = 0;
+		double maxDiff = 0;
+
+		for(int i = 0; i < rdata.size(); i++) {
+			sumObs += rdata.get(i);
+			sumExp += numInd/numSpec*invSum(i+1,numSpec);
+			double diff = fabs(sumObs-sumExp);
+			if(diff > maxDiff)
+				maxDiff = diff;
+		}
+		
+
+		data[0] = maxDiff/numInd;
+		data[1] = 0.886/sqrt(rdata.size());
+		data[2] = 1.031/sqrt(rdata.size());
+
+		/*m->mothurOut(critVal); m->mothurOutEndLine();
+		m->mothurOut("If D-Statistic is less than the critical value then the data fits the Broken Stick model w/ 95% confidence.\n");*/
+		
+
+		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, "BStick", "getValues");
+		exit(1);
+	}
+}
+
+/***********************************************************************/
+
+