X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=trialSwap2.cpp;h=9959443c9ffbb0c411dfcd0fc6dd6920fbe6f5c8;hp=ea43de551d2a8df83abd5594754f17ebca2f6760;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=c669e63b8cb1193d683a1016562d35b455f76575

diff --git a/trialSwap2.cpp b/trialSwap2.cpp
index ea43de5..9959443 100644
--- a/trialSwap2.cpp
+++ b/trialSwap2.cpp
@@ -4,27 +4,7 @@
 //The sum_of_squares, havel_hakimi and calc_c_score algorithms have been adapted from I. Miklos and J. Podani. 2004. Randomization of presence-absence matrices: comments and new algorithms. Ecology 85:86-92.
 
 
-/**************************************************************************************************
-int TrialSwap2::intrand(int n){
-    try {
-        double z;
-        
-        z = (double)random() * (double)n / (double)RAND_MAX;
-        if(z>=n)
-            z=n-1;
-        if(z<0)
-            z=0;
-        return((int)floor(z));
-    }
-	catch(exception& e) {
-		m->errorOut(e, "TrialSwap2", "intrand");
-		exit(1);
-	}
-}
-/**************************************************************************************************/
-
-/**************************************************************************************************/
-double TrialSwap2::calc_c_score (vector<vector<int> > &co_matrix, vector<int>  rowtotal, int ncols, int nrows)
+double TrialSwap2::calc_c_score (vector<vector<int> > &co_matrix, vector<int> rowtotal, int ncols, int nrows)
 {
     try {
         double cscore = 0.0;
@@ -32,10 +12,10 @@ double TrialSwap2::calc_c_score (vector<vector<int> > &co_matrix, vector<int>  r
         double D;
         double normcscore = 0.0;
         int nonzeros = 0;
-        //int ncols = co_matrix[0].size(); int nrows = rowtotal.size(); 
+        //int ncols = co_matrix[0].size(); int nrows = rowtotal.size();
         vector<vector<double> > s; s.resize(nrows);
         for (int i = 0; i < nrows; i++) { s[i].resize(nrows,0.0); }//only fill half the matrix
-
+        
         
         for(int i=0;i<nrows-1;i++)
         {
@@ -65,28 +45,29 @@ double TrialSwap2::calc_c_score (vector<vector<int> > &co_matrix, vector<int>  r
                 if(maxD != 0)
                 {
                     normcscore += D/maxD;
-                    nonzeros++;    
-                }            
+                    nonzeros++;
+                }
             }
         }
         
-        cscore = cscore/(double)(nrows*(nrows-1)/2);
+        //cscore = cscore/(double)(nrows*(nrows-1)/2);  //not normalized
         //cout << "normalized c score: " << normcscore/nonzeros << endl;
-        
+        cscore = normcscore/(double)nonzeros;
+
         return cscore;
     }
-	catch(exception& e) {
-		m->errorOut(e, "TrialSwap2", "calc_c_score");
-		exit(1);
-	}
+    catch(exception& e) {
+        m->errorOut(e, "TrialSwap2", "calc_c_score");
+        exit(1);
+    }
 }
 /**************************************************************************************************/
-int TrialSwap2::calc_checker (vector<vector<int> > &co_matrix, vector<int>  rowtotal, int ncols, int nrows)
+int TrialSwap2::calc_checker (vector<vector<int> > &co_matrix, vector<int> rowtotal, int ncols, int nrows)
 {
     try {
         int cunits=0;
         //int s[nrows][ncols];
-        //int ncols = co_matrix[0].size(); int nrows = rowtotal.size(); 
+        //int ncols = co_matrix[0].size(); int nrows = rowtotal.size();
         vector<vector<int> > s; s.resize(nrows);
         for (int i = 0; i < nrows; i++) { s[i].resize(nrows,0); }//only fill half the matrix
         
@@ -115,12 +96,12 @@ int TrialSwap2::calc_checker (vector<vector<int> > &co_matrix, vector<int>  rowt
             }
         }
         
-        return cunits;   
+        return cunits;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "TrialSwap2", "calc_checker");
+        exit(1);
     }
-	catch(exception& e) {
-		m->errorOut(e, "TrialSwap2", "calc_checker");
-		exit(1);
-	}
 }
 /**************************************************************************************************/
 double TrialSwap2::calc_vratio (int nrows, int ncols, vector<int> rowtotal, vector<int> columntotal)
@@ -129,14 +110,14 @@ double TrialSwap2::calc_vratio (int nrows, int ncols, vector<int> rowtotal, vect
         //int nrows = rowtotal.size();
         //int ncols = columntotal.size();
         int sumCol = accumulate(columntotal.begin(), columntotal.end(), 0 );
-       // int sumRow = accumulate(rowtotal.begin(), rowtotal.end(), 0 );
+        // int sumRow = accumulate(rowtotal.begin(), rowtotal.end(), 0 );
         
         double colAvg = (double) sumCol / (double) ncols;
- //       double rowAvg = (double) sumRow / (double) nrows;
+        // double rowAvg = (double) sumRow / (double) nrows;
         
         double p = 0.0;
         
- //       double totalRowVar = 0.0;
+        // double totalRowVar = 0.0;
         double rowVar = 0.0;
         double colVar = 0.0;
         
@@ -145,7 +126,7 @@ double TrialSwap2::calc_vratio (int nrows, int ncols, vector<int> rowtotal, vect
             if (m->control_pressed) { return 0; }
             p = (double) rowtotal[i]/(double) ncols;
             rowVar += p * (1.0-p);
-        } 
+        }
         
         for(int i=0;i<ncols;i++)
         {
@@ -161,30 +142,30 @@ double TrialSwap2::calc_vratio (int nrows, int ncols, vector<int> rowtotal, vect
         m->errorOut(e, "TrialSwap2", "calc_vratio");
         exit(1);
     }
-         
+    
 }
 /**************************************************************************************************/
 int TrialSwap2::calc_combo (int nrows, int ncols, vector<vector<int> > &nullmatrix)
 {
     try {
         //need to transpose so we can compare rows (row-major order)
-        int tmpnrows = nrows;
+        //int tmpnrows = nrows;
         vector<vector<int> > tmpmatrix;
-
+        
         vector<int> tmprow;
         if(!tmpmatrix.empty())
             tmpmatrix.clear();
         for (int i=0;i<ncols;i++)
-        {       
+        {
             for (int j=0;j<nrows;j++)
             {
                 tmprow.push_back(nullmatrix[j][i]);
             }
-
+            
             tmpmatrix.push_back(tmprow);
             tmprow.clear();
         }
-
+        
         int unique = 0;
         int match = 0;
         for(int j=0;j<ncols;j++)
@@ -193,44 +174,46 @@ int TrialSwap2::calc_combo (int nrows, int ncols, vector<vector<int> > &nullmatr
             for(int i=j+1;i<=ncols;i++)
             {
                 //comparing matrix rows
-                if( (tmpmatrix[j] == tmpmatrix[i])) 
+                if( (tmpmatrix[j] == tmpmatrix[i]))
                 {
                     match++;
                     break;
                 }
-            }        
-
+            }
+            
             //on the last iteration of a previously matched row it will add itself because it doesn't match any following rows, so that combination is counted
             if (match == 0)
                 unique++;
-    }
-    return unique;
+        }
+        return unique;
     }
     catch(exception& e) {
         m->errorOut(e, "TrialSwap2", "calc_combo");
         exit(1);
     }
-} 
+}
 /**************************************************************************************************/
-int TrialSwap2::swap_checkerboards (vector<vector<int> > &co_matrix)
+int TrialSwap2::swap_checkerboards (vector<vector<int> > &co_matrix, int ncols, int nrows)
 {
     try {
-        int ncols = co_matrix[0].size(); int nrows = co_matrix.size(); 
-        int i, j, k, l;
-        i = m->getRandomIndex(nrows-1);
-        while((j = m->getRandomIndex(nrows-1) ) == i ) {;if (m->control_pressed) { return 0; }}
-        k = m->getRandomIndex(ncols-1);
-        while((l = m->getRandomIndex(ncols-1)) == k ) {;if (m->control_pressed) { return 0; }}
+        //do 100 runs to make sure enough swaps are happening. This does NOT mean that there will be 1000 swaps, but that is the theoretical max.
+        for(int a=0;a<1000;a++){
+            int i, j, k, l;
+            i = m->getRandomIndex(nrows-1);
+            while((j = m->getRandomIndex(nrows-1) ) == i ) {;if (m->control_pressed) { return 0; }}
+            k = m->getRandomIndex(ncols-1);
+            while((l = m->getRandomIndex(ncols-1)) == k ) {;if (m->control_pressed) { return 0; }}
 
-        if((co_matrix[i][k]*co_matrix[j][l]==1 && co_matrix[i][l]+co_matrix[j][k]==0)||(co_matrix[i][k]+co_matrix[j][l]==0 && co_matrix[i][l]*co_matrix[j][k]==1)) //checking for checkerboard value and swap
-        {
-            co_matrix[i][k]=1-co_matrix[i][k];
-            co_matrix[i][l]=1-co_matrix[i][l];
-            co_matrix[j][k]=1-co_matrix[j][k];
-            co_matrix[j][l]=1-co_matrix[j][l];
+            if((co_matrix[i][k]*co_matrix[j][l]==1 && co_matrix[i][l]+co_matrix[j][k]==0)||(co_matrix[i][k]+co_matrix[j][l]==0 && co_matrix[i][l]*co_matrix[j][k]==1)) //checking for checkerboard value and swap
+            {
+                co_matrix[i][k]=1-co_matrix[i][k];
+                co_matrix[i][l]=1-co_matrix[i][l];
+                co_matrix[j][k]=1-co_matrix[j][k];
+                co_matrix[j][l]=1-co_matrix[j][l];
 
+            }
         }
-
+        
         return 0;
     }
     catch(exception& e) {
@@ -293,11 +276,11 @@ double TrialSwap2::t_test (double initialscore, int runs, double nullMean, vecto
         
         m->mothurOut("nullMean: " + toString(nullMean)); m->mothurOutEndLine();
         
-        m->mothurOut("sum: " + toString(sum));  m->mothurOutEndLine();
+        m->mothurOut("sum: " + toString(sum)); m->mothurOutEndLine();
         
         sampleSD = sqrt( (1/runs) * sum );
         
-        m->mothurOut("samplSD: " + toString(sampleSD));  m->mothurOutEndLine();
+        m->mothurOut("samplSD: " + toString(sampleSD)); m->mothurOutEndLine();
         
         t = (nullMean - initialscore) / (sampleSD / sqrt(runs));
         
@@ -309,18 +292,46 @@ double TrialSwap2::t_test (double initialscore, int runs, double nullMean, vecto
     }
 }
 /**************************************************************************************************/
+double TrialSwap2::getSD (int runs, vector<double> scorevec, double nullMean)
+{
+    try{
+        double sum = 0;
+        for(int i=0;i<runs;i++)
+            {
+                if (m->control_pressed) { return 0; }
+                sum += pow((scorevec[i] - nullMean),2);
+            }
+        return sqrt( (1/double(runs)) * sum );
+    }
+    catch(exception& e) {
+        m->errorOut(e, "TrialSwap2", "getSD");
+        exit(1);
+    }
+}
+/**************************************************************************************************/
+double TrialSwap2::get_zscore (double sd, double nullMean, double initscore)
+{
+    try {
+        return (initscore - nullMean) / sd;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "TrialSwap2", "get_zscore");
+        exit(1);
+    }
+}
+/**************************************************************************************************/
 int TrialSwap2::print_matrix(vector<vector<int> > &matrix, int nrows, int ncols)
 {
     try {
-         m->mothurOut("matrix:");  m->mothurOutEndLine();
+        m->mothurOut("matrix:"); m->mothurOutEndLine();
         
         for (int i = 0; i < nrows; i++)
         {
             if (m->control_pressed) { return 0; }
             for (int j = 0; j < ncols; j++)
             {
-                m->mothurOut(toString(matrix[i][j]));            
-            }    
+                m->mothurOut(toString(matrix[i][j]));
+            }
             m->mothurOutEndLine();
         }
         return 0;
@@ -336,4 +347,3 @@ int TrialSwap2::print_matrix(vector<vector<int> > &matrix, int nrows, int ncols)
 
 
 
-