Revert to previous commit

[mothur.git] / spearman.cpp

diff --git a/spearman.cpp b/spearman.cpp
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+++ b/spearman.cpp
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+/*
+ *  spearman.cpp
+ *  Mothur
+ *
+ *  Created by westcott on 12/15/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "spearman.h"
+
+/***********************************************************************/
+
+EstOutput Spearman::getValues(vector<SharedRAbundVector*> shared) {
+       try {
+               data.resize(1,0);
+               
+               SAbundVector savA = shared[0]->getSAbundVector();
+               SAbundVector savB = shared[1]->getSAbundVector();
+               
+               double sumRanks = 0.0;
+               int numOTUS = shared[0]->getNumBins();
+               
+               vector<double> rankVectorA(savA.getMaxRank()+1, 0);
+               int currentRankA = 0;
+               for(int i=savA.getMaxRank();i>0;i--){   
+                       int numWithAbundanceI = savA.get(i);
+
+                       if(numWithAbundanceI > 1){      rankVectorA[i] = (currentRankA + 1 + currentRankA + numWithAbundanceI) / 2.0;   }
+                       else                                    {       rankVectorA[i] = currentRankA+numWithAbundanceI;        }
+                       currentRankA += numWithAbundanceI;
+               }
+               rankVectorA[0] = (numOTUS + currentRankA + 1) / 2.0;
+               
+               
+               vector<double> rankVectorB(savB.getMaxRank()+1, 0);
+               int currentRankB = 0;
+               for(int i=savB.getMaxRank();i>0;i--){   
+                       int numWithAbundanceI = savB.get(i);
+                       
+                       if(numWithAbundanceI > 1){      rankVectorB[i] = (currentRankB + 1 + currentRankB + numWithAbundanceI) / 2.0;   }
+                       else                                    {       rankVectorB[i] = currentRankB+numWithAbundanceI;        }
+                       currentRankB += numWithAbundanceI;
+               }
+               rankVectorB[0] = (numOTUS + currentRankB + 1) / 2.0;
+               
+               
+
+               for (int i = 0; i < shared[0]->getNumBins(); i++) { 
+                       int Aij = shared[0]->getAbundance(i);
+                       int Bij = shared[1]->getAbundance(i);
+                       
+                       float rankA = rankVectorA[Aij];
+                       float rankB = rankVectorB[Bij];
+                       
+                       sumRanks += ((rankA - rankB) * (rankA - rankB));
+               }
+               data[0] = 1.0 - ((6 * sumRanks) / (float) (numOTUS * ((numOTUS*numOTUS)-1)));
+               
+               if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+               
+               return data;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "Spearman", "getValues");
+               exit(1);
+       }
+}
+
+/***********************************************************************/
+