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

[mothur.git] / sharedace.cpp

diff --git a/sharedace.cpp b/sharedace.cpp
deleted file mode 100644 (file)
index 2a06380..0000000
--- a/sharedace.cpp
+++ /dev/null
@@ -1,109 +0,0 @@
-
-/*
- *  sharedace.cpp
- *  Dotur
- *
- *  Created by Sarah Westcott on 1/8/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "sharedace.h"
-
-/***********************************************************************/
-
-EstOutput SharedAce::getValues(vector<SharedRAbundVector*> shared) {
-       try {
-               data.resize(1,0);
-               string label;
-               label = shared[0]->getLabel();
-
-               double fARare, fBRare, S12Rare, S12Abund, S12, f11, tempA, tempB, t10, t01, t11, t21, t12, t22, C12Numerator;
-               fARare = 0; fBRare = 0; S12Rare = 0; S12Abund = 0; S12 = 0; f11 = 0; t10 = 0; t01 = 0; t11= 0; t21= 0; t12= 0; t22= 0; C12Numerator = 0;
-       
-               double Sharedace, C12, part1, part2, part3, part4, part5, Gamma1, Gamma2, Gamma3;
-       
-               /*fARare = number of OTUs with one individual found in A and less than or equal to 10 in B. 
-               fBRare = number of OTUs with one individual found in B and less than or equal to 10 in A. 
-               arare = number of sequences from A that contain less than 10 sequences. 
-               brare = number of sequences from B that contain less than 10 sequences. 
-               S12Rare = number of shared OTUs where both of the communities are represented by less than or equal to 10 sequences 
-               S12Abund = number of shared OTUs where at least one of the communities is represented by more than 10 sequences 
-               S12 = number of shared OTUs in A and B
-               This estimator was changed to reflect Caldwell's changes, eliminating the nrare / nrare - 1 */
-
-               for (int i = 0; i < shared[0]->getNumBins(); i++) {
-                       //store in temps to avoid multiple repetitive function calls
-                       tempA = shared[0]->getAbundance(i);
-                       tempB = shared[1]->getAbundance(i);
-                       if ((tempA != 0) && (tempB != 0)) {//they are shared
-                               S12++;
-                               //do both A and B have one
-                               if ((tempA == 1) && (tempB == 1))               {       f11++;   }
-                               //is A one and B rare
-                               if ((tempA == 1) && (tempB <= abund))   {  fARare++; }
-                               //is B one and A rare
-                               if ((tempB == 1) && (tempA <= abund))   {  fBRare++; }
-                       
-                               if ((tempA <= abund) && (tempB <= abund)) { //shared and both rare
-                                       S12Rare++;
-                                       t10 += tempA;   //Sum Xi
-                                       t01 += tempB;   //Sum Yi
-                                       
-                                       //calculate top of C12
-                                       // YiI(Xi = 1)
-                                       if (tempA == 1) { C12Numerator += tempB; }
-                                       //XiI(Yi = 1)
-                                       if (tempB == 1) { C12Numerator += tempA; }
-                                       //-I(Xi=Yi=1)
-                                       if ((tempA == 1) && (tempB == 1)) { C12Numerator--; }
-                                       
-                                       //calculate t11 - Sum of XiYi
-                                       t11 += tempA * tempB;
-                                       //calculate t21  - Sum of Xi(Xi - 1)Yi
-                                       t21 += tempA * (tempA - 1) * tempB;
-                                       //calculate t12  - Sum of Xi(Yi - 1)Yi
-                                       t12 += tempA * (tempB - 1) * tempB;
-                                       //calculate t22  - Sum of Xi(Xi - 1)Yi(Yi - 1)
-                                       t22 += tempA * (tempA - 1) * tempB * (tempB - 1);
-
-                               }
-                               if ((tempA > 10) || (tempB > 10)) {
-                                       S12Abund++;
-                               }
-                       }
-               }
-       
-               C12 = 1 - (C12Numerator /(float) t11);
-               part1 = S12Rare / (float)C12;
-               part2 = 1 / (float)C12;
-
-               //calculate gammas
-               Gamma1 = ((S12Rare * t21) / (float)((C12 * t10 * t11)) - 1);
-               Gamma2 = ((S12Rare * t12) / (float)((C12 * t01 * t11)) - 1);
-               Gamma3 = ((S12Rare / C12) * (S12Rare / C12)) * ( t22 / (float)(t10 * t01 * t11));
-               Gamma3 = Gamma3 - ((S12Rare * t11) / (float)(C12 * t01 * t10)) - Gamma1 - Gamma2;       
-
-               if (isnan(Gamma1) || isinf(Gamma1)) { Gamma1 = 0; }
-               if (isnan(Gamma2) || isinf(Gamma2)) { Gamma2 = 0; }
-               if (isnan(Gamma3) || isinf(Gamma3)) { Gamma3 = 0; }
-               if (isnan(part1)  || isinf(part1))  { part1 = 0;  }
-               if (isnan(part2)  || isinf(part2))  { part2 = 0;  }
-               
-               part3 = fARare * Gamma1;
-               part4 = fBRare * Gamma2;
-               part5 = f11 * Gamma3;
-
-               Sharedace = S12Abund + part1 + (part2 * (part3 + part4 + part5));
-               data[0] = Sharedace;
-       
-               return data;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SharedAce", "getValues");
-               exit(1);
-       }
-}
-/***********************************************************************/
-
-