X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=qstat.cpp;fp=qstat.cpp;h=591c36af19637184d9f43c6e23eeb6f4b47863d8;hb=eb1c88346fb246e95a6b38935b103f95e38b82ca;hp=0000000000000000000000000000000000000000;hpb=d53f63d7e0d9c3feeb8ded5a74e6c150fae50fe9;p=mothur.git

diff --git a/qstat.cpp b/qstat.cpp
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+++ b/qstat.cpp
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+/*
+ *  qstat.cpp
+ *  Mothur
+ *
+ *  Created by Thomas Ryabin on 3/4/09.
+ *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *
+ */
+
+#include "qstat.h"
+#include "calculator.h"
+
+/***********************************************************************/
+
+EstOutput QStat::getValues(SAbundVector* rank){
+	try {
+		
+		/*test data VVV
+		int dstring[] = {0,0,1,4,2,0,2,1,1,1,1,1,0,1,1,2,0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,0,0,2,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1};
+		vector<int> dvec;
+		for(int i = 0; i < 171; i++)
+			dvec.push_back(dstring[i]);
+		int mr = 170;
+		int nb = 29;
+		int ns = 884;
+		SAbundVector rankw = SAbundVector(dvec, mr,nb,ns);
+		SAbundVector *rank = &rankw;*/
+		data.resize(1,0);
+		int numSpec = rank->getNumBins();
+		int r1 = -1;
+		int r3 = -1;
+		int r1Ind = 0;
+		int r3Ind = 0;
+		int sumSpec = 0;
+		int iqSum = 0;
+		for(int i = 1; i < rank->size(); i++)
+		{
+			if(r1 != -1 && r3 != -1)
+				i = rank->size();
+				
+			sumSpec += rank->get(i);
+			
+			if(r1 == -1 && sumSpec >= numSpec*.25)
+			{
+				r1 = rank->get(i);
+				r1Ind = i;
+			}
+			else if(r3 == -1 && sumSpec >= numSpec*.75)
+			{
+				r3 = rank->get(i);
+				r3Ind = i;
+			}
+			else if(sumSpec >= numSpec*.25 && sumSpec < numSpec*.75)
+				iqSum += rank->get(i);
+		}
+		
+		double qstat = (.5*r1 + iqSum + .5*r3)/log((double)r3Ind/r1Ind);
+		//cout << "QStat:\nQStatistic = " << qstat << "\n\n";
+		
+		data[0] = qstat;
+		if (isnan(data[0]) || isinf(data[0])) { data[0] = 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);
+	}	
+}
+
+/***********************************************************************/
+