X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=geom.cpp;fp=geom.cpp;h=8b484de49bcd27c772ead83f10cbf77aa14adf91;hb=eb1c88346fb246e95a6b38935b103f95e38b82ca;hp=0000000000000000000000000000000000000000;hpb=d53f63d7e0d9c3feeb8ded5a74e6c150fae50fe9;p=mothur.git

diff --git a/geom.cpp b/geom.cpp
new file mode 100644
index 0000000..8b484de
--- /dev/null
+++ b/geom.cpp
@@ -0,0 +1,120 @@
+/*
+ *  geom.cpp
+ *  Mothur
+ *
+ *  Created by Thomas Ryabin on 2/23/09.
+ *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *
+ */
+
+#include "geom.h"
+#include "calculator.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(2,0);
+		
+		rdata = getRAbundVector(rank);
+		int numInd = rdata.getNumSeqs();
+		int numSpec = rdata.getNumBins();
+		int 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 < rdata.size(); i++)
+		{
+			sumObs += rdata.get(i);
+			sumExp += numInd*cK*k*pow(1-k, i);
+			double diff = fabs(sumObs-sumExp);
+			if(diff > maxDiff)
+				maxDiff = diff;
+		}
+
+		double DStatistic = maxDiff/numInd;
+		double critVal = 0;
+		/*cout << "Geom:\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 Geometric Series 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);
+	}	
+}
+
+/***********************************************************************/
+
+
+
+
+
+
+