changed random forest output filename

[mothur.git] / bstick.cpp

diff --git a/bstick.cpp b/bstick.cpp
index 3a0e0e91a873f6692b585463ec324e33d3b2cd82..67507a9967ef82effe923662298960ecf00618b8 100644 (file)
--- a/bstick.cpp
+++ b/bstick.cpp
@@ -3,12 +3,12 @@
  *  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 "bstick.h"
-#include "calculator.h"
+
 
 /***********************************************************************/
 double BStick::invSum(int index, double numSpec)
@@ -18,16 +18,15 @@ double BStick::invSum(int index, double numSpec)
                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);
+               for(int i = rank->size()-1; i > 0; i--) {
+                       double cur = rank->get(i);
                        if(mr == 1 && cur > 0)
                                mr = i;
                        nb += cur;
@@ -46,7 +45,7 @@ RAbundVector BStick::getRAbundVector(SAbundVector* rank){
 /***************************************************************************/
 EstOutput BStick::getValues(SAbundVector* rank){
        try {
-               data.resize(2,0);
+               data.resize(3,0);
                rdata = getRAbundVector(rank);
                double numInd = (double)rdata.getNumSeqs();
                double numSpec = (double)rdata.getNumBins();
@@ -55,8 +54,7 @@ EstOutput BStick::getValues(SAbundVector* rank){
                double sumObs = 0;
                double maxDiff = 0;
 
-               for(int i = 0; i < rdata.size(); i++)
-               {
+               for(int i = 0; i < rdata.size(); i++) {
                        sumObs += rdata.get(i);
                        sumExp += numInd/numSpec*invSum(i+1,numSpec);
                        double diff = fabs(sumObs-sumExp);
@@ -64,38 +62,25 @@ EstOutput BStick::getValues(SAbundVector* rank){
                                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] = maxDiff/numInd;
+               data[1] = 0.886/sqrt(rdata.size());
+               data[2] = 1.031/sqrt(rdata.size());
+
+               /*m->mothurOut(critVal); m->mothurOutEndLine();
+               m->mothurOut("If D-Statistic is less than the critical value then the data fits the Broken Stick model w/ 95% confidence.\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; }
+               if (isnan(data[2]) || isinf(data[2])) { data[2] = 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, "BStick", "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);
-       }       
 }
 
 /***********************************************************************/