added the Calculators Thomas made in the fall. Added parameter and command error...

[mothur.git] / geom.cpp

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