moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / sharedjackknife.cpp

diff --git a/sharedjackknife.cpp b/sharedjackknife.cpp
deleted file mode 100644 (file)
index 0998db8..0000000
--- a/sharedjackknife.cpp
+++ /dev/null
@@ -1,144 +0,0 @@
-/*
- *  sharedjackknife.cpp
- *  Mothur
- *
- *  Created by Thomas Ryabin on 3/30/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "sharedjackknife.h"
-
-/***************************************************************************************
-
-***************************************************************************************/
-double SharedJackknife::simpson(vector<int> abunds, double numInd, int numBins){
-       double denom = numInd*(numInd-1);
-       double sum = 0;
-       for(int i = 0; i < numBins; i++)
-               sum += (double)abunds[i]*((double)abunds[i]-1)/denom;
-       
-       return sum;
-}
-
-/*****************************************************************************************/
-
-double* SharedJackknife::jackknife(){          
-       int numBins = groups.at(0)->getNumBins()-1;
-       vector<int> cArray(numBins);
-       for(int i = 0; i < numBins; i++)
-               cArray[i] = 0;
-
-       double numInd = 0;
-       for(int i = 0; i < numGroups; i++)
-               for(int j = 0; j < numBins; j++) {
-                       int curAbund = groups.at(i)->get(j+1).abundance;
-                       cArray[j] += curAbund;
-                       numInd += (double)curAbund;
-               }
-
-       double baseD = 1/simpson(cArray, numInd, numBins);
-       
-       vector<double> pseudoVals(numBins);
-       double jackknifeEstimate = 0;
-       for(int i = 0; i < numGroups; i++) {
-               for(int j = 0; j < numBins-1; j++) {
-                       int abundDiff = -groups.at(i)->get(j+1).abundance;
-                       if(i > 0)
-                               abundDiff += groups.at(i-1)->get(j+1).abundance;
-
-                       cArray[j] += abundDiff;
-                       numInd += abundDiff;    
-               }
-               
-               double curD = 1/simpson(cArray, numInd, numBins);
-               pseudoVals[i] = (double)numGroups*(baseD - curD) + curD;
-               jackknifeEstimate += pseudoVals[i];
-       }
-       jackknifeEstimate /= (double)numGroups;
-               
-       double variance = 0;
-       for(int i = 0; i < numGroups; i++)
-               variance += pow(pseudoVals[i]-jackknifeEstimate, 2);
-               
-       variance /= (double)numGroups*((double)numGroups-1);
-       double stErr = sqrt(variance);
-       TDTable table;
-       double confLimit = 0;
-       if(numGroups <= 30)
-               confLimit = table.getConfLimit(numGroups-1, 1);
-       else
-               confLimit = 1.645;
-       
-       confLimit *= stErr;
-       
-       double* rdata = new double[3];
-       rdata[0] = baseD;
-       rdata[1] = jackknifeEstimate - confLimit;
-       rdata[2] = jackknifeEstimate + confLimit;
-       
-       return rdata;
-}
-
-/************************************************************************************************
-************************************************************************************************/
-
-EstOutput SharedJackknife::getValues(vector<SharedRAbundVector*> vectorShared){ //Fix this for collect, mistake was that it was made with summary in mind.
-       try {
-               SharedRAbundVector* shared1 = vectorShared[0];
-               SharedRAbundVector* shared2 = vectorShared[1];
-               if(numGroups == -1) {
-                       numGroups = m->getNumGroups();
-               }
-
-               if(callCount == numGroups*(numGroups-1)/2) {
-                       currentCallDone = true;
-                       callCount = 0;
-               }
-               callCount++;
-
-               if(currentCallDone) {
-                       groups.clear(); 
-                       currentCallDone = false;
-               }
-               
-               if(groups.size() != numGroups) {        
-                       if(groups.size() == 0)
-                               groups.push_back(shared1);
-                       groups.push_back(shared2);
-               }
-               
-               if(groups.size() == numGroups && callCount < numGroups) {
-                       data.resize(3,0);
-
-                       double* rdata = jackknife();
-                       data[0] = rdata[0];
-                       data[1] = rdata[1];
-                       data[2] = rdata[2];
-               
-                       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[0])) { data[2] = 0; }
-                       
-                       return data;
-               }
-               
-               data.resize(3,0);
-               data[0] = 0;
-               data[1] = 0;
-               data[2] = 0;
-               
-               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) {
-               m->errorOut(e, "SharedJackknife", "getValues");
-               exit(1);
-       }
-}
-
-/***********************************************************************/
-