working on chimera.perseus. made removeConfidences function smarter. Fixed bug in...

[mothur.git] / mothurmetastats.cpp

diff --git a/mothurmetastats.cpp b/mothurmetastats.cpp
index 6a834e96be802fe416949dc8910d8790a24ddf15..9ba40502a2294d5ce42ba591c076da6fd3015979 100644 (file)
--- a/mothurmetastats.cpp
+++ b/mothurmetastats.cpp
@@ -55,10 +55,10 @@ int MothurMetastats::runMetastats(string outputFileName, vector< vector<double>
                }
                
                //total for first grouping
-               for (int i = 0; i < (secondGroupingStart-1); i++) { total1 += total[i]; }
+               for (int i = 0; i < secondGroupingStart; i++) { total1 += total[i]; }
                
                //total for second grouping
-               for (int i = (secondGroupingStart-1); i < column; i++) { total2 += total[i]; }
+               for (int i = secondGroupingStart; i < column; i++) { total2 += total[i]; }
                
                //Creates the ratios by first finding the minimum of totals
                double min = total[0];
@@ -105,15 +105,15 @@ int MothurMetastats::runMetastats(string outputFileName, vector< vector<double>
                if (m->control_pressed) { return 1; }
                
                // Start the calculations.
-               if ( (column == 2) || ((secondGroupingStart-1) < 8) || ((column-secondGroupingStart+1) < 8) ){ 
+               if ( (column == 2) || (secondGroupingStart < 8) || ((column-secondGroupingStart) < 8) ){ 
                        
                        vector<double> fish;    fish.resize(row, 0.0);
                        vector<double> fish2;   fish2.resize(row, 0.0);
                        
                        for(int i = 0; i < row; i++){
                                
-                               for(int j = 0; j < (secondGroupingStart-1); j++)                { fish[i] += data[i][j];        }
-                               for(int j = (secondGroupingStart-1); j < column; j++)   { fish2[i] += data[i][j];       }
+                               for(int j = 0; j < secondGroupingStart; j++)            { fish[i] += data[i][j];        }
+                               for(int j = secondGroupingStart; j < column; j++)       { fish2[i] += data[i][j];       }
                                
                                //vector<double> tempData; tempData.resize(4, 0.0);
                                double f11, f12, f21, f22;
@@ -148,12 +148,12 @@ int MothurMetastats::runMetastats(string outputFileName, vector< vector<double>
                        
                        for(int i = 0; i < row; i++){
                                
-                               for(int j = 0; j < (secondGroupingStart-1); j++){       sparse[i] += data[i][j]; }
-                               if(sparse[i] < (double)(secondGroupingStart-1)){        c++; }
+                               for(int j = 0; j < secondGroupingStart; j++)    {       sparse[i] += data[i][j];        }
+                               if(sparse[i] < (double)secondGroupingStart)             {       c++;                                            }
                                
                                // ?<= for col
-                               for(int j = (secondGroupingStart-1); j < column; j++){  sparse2[i] += data[i][j]; }
-                               if( (sparse2[i] < (double)(column-secondGroupingStart+1))) { c++; }
+                               for(int j = secondGroupingStart; j < column; j++)               {  sparse2[i] += data[i][j]; }
+                               if( (sparse2[i] < (double)(column-secondGroupingStart)))        { c++;                                           }
                                
                                if (c == 2) {
                                        c=0;
@@ -190,11 +190,11 @@ int MothurMetastats::runMetastats(string outputFileName, vector< vector<double>
                for (int j = 0; j < row; j++){
                        if (m->control_pressed) { return 1; }
                        
-                       for (int i = 1; i <= (secondGroupingStart-1); i++){ temp[j][0] += data[j][i-1]; }
-                       temp[j][0] /= (double)(secondGroupingStart-1);
+                       for (int i = 0; i < secondGroupingStart; i++){ temp[j][0] += data[j][i]; }
+                       temp[j][0] /= (double)secondGroupingStart;
                        
-                       for(int i = secondGroupingStart; i <= column; i++){ temp[j][1] += data[j][i-1]; }
-                       temp[j][1] /= (double)(column-secondGroupingStart+1);
+                       for(int i = secondGroupingStart; i < column; i++){ temp[j][1] += data[j][i]; }
+                       temp[j][1] /= (double)(column-secondGroupingStart);
                }
                
                for(int i = 0; i < row; i++){
@@ -280,14 +280,14 @@ int MothurMetastats::start(vector<double>& Imatrix, int secondGroupingStart, vec
                        storage[i][0]=C1[i][0];
                        C1[i][1]=tool[i+row+row]; // var group 1
                        storage[i][1]=C1[i][1];
-                       C1[i][2]=C1[i][1]/(secondGroupingStart-1);
+                       C1[i][2]=C1[i][1]/(secondGroupingStart);
                        storage[i][2]=sqrt(C1[i][2]);
                        
                        C2[i][0]=tool[i+row]; // mean group 2
                        storage[i][4]=C2[i][0];    
                        C2[i][1]=tool[i+row+row+row]; // var group 2 
                        storage[i][5]=C2[i][1];        
-                       C2[i][2]=C2[i][1]/(column-secondGroupingStart+1);
+                       C2[i][2]=C2[i][1]/(column-secondGroupingStart);
                        storage[i][6]=sqrt(C2[i][2]);   
                }
                
@@ -314,7 +314,7 @@ int MothurMetastats::meanvar(vector<double>& pmatrix, int secondGroupingStart, v
                vector<double> var;             var.resize(row, 0.0);
                vector<double> var2;    var2.resize(row, 0.0);
                
-               double a = secondGroupingStart-1;
+               double a = secondGroupingStart;
                double b = column - a;
                int m = a * row;
                int n = row * column;
@@ -459,11 +459,11 @@ int MothurMetastats::calc_twosample_ts(vector<double>& Pmatrix, int secondGroupi
                        if (m->control_pressed) { return 0; }
                        C1[i][0]=tool[i];
                        C1[i][1]=tool[i+row+row];
-                       C1[i][2]=C1[i][1]/(secondGroupingStart-1);
+                       C1[i][2]=C1[i][1]/(secondGroupingStart);
                        
                        C2[i][0]=tool[i+row];
                        C2[i][1]=tool[i+row+row+row]; // var group 2 
-                       C2[i][2]=C2[i][1]/(column-secondGroupingStart+1);
+                       C2[i][2]=C2[i][1]/(column-secondGroupingStart);
                }
                
                for (int i = 0; i < row; i++){