X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bstick.cpp;fp=bstick.cpp;h=3a0e0e91a873f6692b585463ec324e33d3b2cd82;hb=eb1c88346fb246e95a6b38935b103f95e38b82ca;hp=0000000000000000000000000000000000000000;hpb=d53f63d7e0d9c3feeb8ded5a74e6c150fae50fe9;p=mothur.git

diff --git a/bstick.cpp b/bstick.cpp
new file mode 100644
index 0000000..3a0e0e9
--- /dev/null
+++ b/bstick.cpp
@@ -0,0 +1,103 @@
+/*
+ *  bstick.cpp
+ *  Mothur
+ *
+ *  Created by Thomas Ryabin on 3/6/09.
+ *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *
+ */
+
+#include "bstick.h"
+#include "calculator.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--)
+		{
+			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 BStick::getValues(SAbundVector* rank){
+	try {
+		data.resize(2,0);
+		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;
+		}
+		
+		double DStatistic = maxDiff/numInd;
+		double critVal = 0;
+		/*cout << "BStick:\n";
+		cout << "D-Statistic = " << DStatistic << "\n";
+		cout << "Critical value for 95% confidence interval = ";*/
+		if(rdata.size() > 20)
+		{
+			critVal = .886/sqrt(rdata.size());
+		}
+		else
+		{
+			KOSTable table;
+			critVal = table.getConfLimit(numSpec);
+		}
+		/*cout << critVal << "\n";
+		cout << "If D-Statistic is less than the critical value then the data fits the Broken Stick model w/ 95% confidence.\n\n";*/
+		
+		data[0] = DStatistic;
+		data[1] = critVal;
+		if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+		if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; }
+		
+		return data;
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the NPShannon class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the NPShannon class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
+}
+
+/***********************************************************************/
+
+