* Mothur
*
* Created by Thomas Ryabin on 3/6/09.
- * Copyright 2009 __MyCompanyName__. All rights reserved.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "sharedkstest.h"
-#include "calculator.h"
-#include <algorithm>
/***********************************************************************/
-EstOutput SharedKSTest::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2){
+EstOutput KSTest::getValues(vector<SharedRAbundVector*> shared){
try {
- data.resize(2,0);
-
+ data.resize(3,0);
+
//Must return shared1 and shared2 to original order at conclusion of kstest
- vector <individual> initData1 = shared1->getData();
- vector <individual> initData2 = shared2->getData();
- shared1->sortD();
- shared2->sortD();
+ vector <individual> initData1 = shared[0]->getData();
+ vector <individual> initData2 = shared[1]->getData();
+ shared[0]->sortD();
+ shared[1]->sortD();
- int numNZ1 = shared1->numNZ();
- int numNZ2 = shared2->numNZ();
- double numInd1 = (double)shared1->getNumSeqs();
- double numInd2 = (double)shared2->getNumSeqs();
+ int numNZ1 = shared[0]->numNZ();
+ int numNZ2 = shared[1]->numNZ();
+ double numInd1 = (double)shared[0]->getNumSeqs();
+ double numInd2 = (double)shared[1]->getNumSeqs();
double maxDiff = -1;
double sum1 = 0;
double sum2 = 0;
- for(int i = 1; i < shared1->getNumBins(); i++)
+ for(int i = 1; i < shared[0]->getNumBins(); i++)
{
- sum1 += shared1->get(i).abundance;
- sum2 += shared2->get(i).abundance;
+ sum1 += shared[0]->get(i).abundance;
+ sum2 += shared[1]->get(i).abundance;
double diff = fabs((double)sum1/numInd1 - (double)sum2/numInd2);
if(diff > maxDiff)
maxDiff = diff;
double DStatistic = maxDiff*numNZ1*numNZ2;
double a = pow((double)(numNZ1 + numNZ2)/(numNZ1*numNZ2),.5);
- double pVal = exp(-2*pow(maxDiff/a,2));
+ //double pVal = exp(-2*pow(maxDiff/a,2));
double critVal = 1.36*a*numNZ1*numNZ2;
- /*cout << "Kolmogorov-Smirnov 2-sample test:\n";
- if(numNZ1 > 25 && numNZ2 > 25) //If the sample sizes are both bigger than 25.
- cout << "P-Value = " << pVal << "\nP-Value is the probability that the data sets are significantly different.\n";
- else
- {
- //cout << "90% Confidence Critical Value = " << 1.22*a*numNZ1*numNZ2 << "\n";
- cout << "D-Statistic = " << DStatistic << "\n";
- cout << "95% Confidence Critical Value = " << critVal << "\n";
- cout << "If D-Statistic is greater than the critical value then the data sets are significantly different at the 95% confidence level.\n\n";
- }*/
-
- shared1->setData(initData1);
- shared2->setData(initData2);
+ shared[0]->setData(initData1);
+ shared[1]->setData(initData2);
data[0] = DStatistic;
data[1] = critVal;
+ data[2] = 0;
+
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";
+ m->errorOut(e, "KSTest", "getValues");
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);
- }
}
/***********************************************************************/