X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=metastats2.c;h=70edc3d63cda154b51bca2dcb8ee36b9413a97a9;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=f5acb17540f6f8381dbc430bbbb3d2e3c8f10fbe;hpb=e99751591aa21705e58edda87383457b9738dd9e;p=mothur.git

diff --git a/metastats2.c b/metastats2.c
index f5acb17..70edc3d 100644
--- a/metastats2.c
+++ b/metastats2.c
@@ -4,573 +4,554 @@
 //The following code has been modified using the original Metastats program from White, J.R., Nagarajan, N. & Pop, M. Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 5, e1000352 (2009).
 
 int metastat_main (char* outputFileName, int numRows, int numCols, double threshold, int numPermutations, double** data, int secondGroupingStart){
-  
-  int size,c=0,i=0,j=0,k,counter=0, bflag=0; 
-  int B=numPermutations;
-  int row = numRows;
-  int col = numCols;
-  int g = secondGroupingStart;
-  double thresh=threshold;
-  double placeholder=0,min=0; 
-  
-  char output[1024];
-  strcpy(output, outputFileName);
-  FILE *out;
-  
-  if (g>=col || g<=0){
-  	printf("Check your g value\n");	
-  }
- 
-  // Initialize the matrices
+	
+	int size,c=0,i=0,j=0,counter=0, bflag=0; 
+	int B=numPermutations;
+	int row = numRows;
+	int col = numCols;
+	int g = secondGroupingStart;
+	double thresh=threshold;
+	double min=0; 
+	
+	char output[1024];
+	strcpy(output, outputFileName);
+	FILE *out;
+	
+	if (g>=col || g<=0){
+		printf("Check your g value\n");	
+	}
+	
+	// Initialize the matrices
 	size = row*col;
+	double matrix[row][col];
+	double pmatrix[size],permuted[size];  
+	double storage[row][9];
 	
-	double ** matrix, * pmatrix, * permuted, ** storage;
-	matrix = malloc(row*sizeof(double *));
-	storage =  malloc(row*sizeof(double *));
-	for (i = 0; i<row; i++){
-		matrix[i] = malloc(col*sizeof(double));
+	for (i=0;i<row;i++){
+		for (j =0;j<9;j++){
+			storage[i][j]=0; 		
+		}	
 	}
-	for (i = 0; i<row;i++){
-		storage[i] = malloc(9*sizeof(double));
+	
+	for(i=0; i<row; i++){
+		for(j=0; j<col;j++){
+			matrix[i][j]=data[i][j];
+			pmatrix[c]=0; // initializing to zero
+			permuted[c]=0;
+			c++;
+		}
 	}
 	
-	pmatrix = (double *) malloc(size*sizeof(double));
-	permuted = (double *) malloc(size*sizeof(double));
+	// Produces the sum of each column
+	double total[col],total1=0,total2=0;
+	double ratio[col];
 	
-  for(i=0; i<row; i++){
-    for(j=0; j<col;j++){
-      matrix[i][j]=data[i][j];
-      pmatrix[c]=0; // initializing to zero
-      permuted[c]=0;
-      c++;
-    }
-  }
-
-  // Produces the sum of each column
-  double total[col],total1=0,total2=0;
-  double ratio[col];
-  
-  for(i=0;i<col;i++){
-    total[i]=0;
-    ratio[i]=0; }
-  
-  for(i=0; i<col; i++){
-    for(j=0;j<row;j++){
-      total[i]=total[i]+matrix[j][i];  		
-    }
-  }
-  
-  for(i=0;i<g-1;i++){
-  	total1=total1+total[i];}
-  	
-  for(i=g-1;i<col;i++){
-    total2=total2+total[i];}
-  
-
-  // Creates the ratios by first finding the minimum of totals
-  min = total[0];
-  if (col==2){
-  if (total[0]<total[1]){
-  	min = total[1];}	
-  }
-  if (col >2){
-  for(i=1;i<col;i++){
-    if (min > total[i]){
-      min = total[i];}
-  }
-  }
-  if (min<=0){
-    printf("Error, the sum of one of the columns <= 0.");
-    return 0;	
-  }
-
-  
-  // Ratio time...
-  for(i=0;i<col;i++){
-    ratio[i]=total[i]/min;
-  }
-  
-  // Change matrix into an array as received by R for compatibility.
-  
-  c=0;
-  for(i=0;i<col;i++){
-    for(j=0;j<row;j++){
-      pmatrix[c]=matrix[j][i];
-      c++;
-    }
-  }
-  
-  if(row == 1){
-  	for (i =0; i<col;i++){
-  		pmatrix[i]=pmatrix[i]/ratio[i];
+	for(i=0;i<col;i++){
+		total[i]=0;
+		ratio[i]=0; }
+	
+	for(i=0; i<col; i++){
+		for(j=0;j<row;j++){
+			total[i]=total[i]+matrix[j][i];  		
+		}
 	}
-  }
-  else {
-    counter = 0;
-    j=-1;
-    for (i=0; i<size; i++) {
-      if (counter % row == 0) {
-        j++;
-      }
-      pmatrix[i]=pmatrix[i]/ratio[j];
-      counter++; 
-    }   
-  }
-  // pass everything to the rest of the code using pointers. then 
-  // write to output file. below pointers for most of the values are 
-  // created to send everything by reference.
-  
-  int ptt_size, *permutes,*nc,*nr,*gvalue;
-  
-  nc = &col;
-  nr = &row;
-  gvalue = &g;
-  
-  permutes = &B;
-  ptt_size = B*row;
-
-  //changing ptt_size to row
-  double * permuted_ttests, * pvalues, * tinitial;
-  permuted_ttests = (double *) malloc(size*sizeof(double));
-  pvalues = (double *) malloc(size*sizeof(double));
-  tinitial = (double *) malloc(size*sizeof(double));
-  
-  for(i=0;i<row;i++){
-    permuted_ttests[i]=0;}
-  
-  for(i=0;i<row;i++){
-    pvalues[i]=0;
-    tinitial[i]=0; }
-  
-  // Find the initial values for the matrix.
- 
-  start(pmatrix,gvalue,nr,nc,tinitial,storage);
-  
-  // Start the calculations.
- 
-  if ( (col==2) || ((g-1)<8) || ((col-g+1) < 8) ){  
-
-  double * fish, *fish2;
-  fish = (double *) malloc(size*sizeof(double));
-  fish2 = (double *) malloc(size*sizeof(double));
-	  
-  for(i=0;i<row;i++){
-  	fish[i]=0;
-  	fish2[i]=0;}
- 
-  for(i=0;i<row;i++){
+	
+	for(i=0;i<g-1;i++){
+		total1=total1+total[i];}
   	
-  	for(j=0;j<g-1;j++){
-  		fish[i]=fish[i]+matrix[i][j];
+	for(i=g-1;i<col;i++){
+		total2=total2+total[i];}
+	
+	
+	// Creates the ratios by first finding the minimum of totals
+	min = total[0];
+	if (col==2){
+		if (total[0]<total[1]){
+			min = total[1];}	
 	}
-
-	for(j=g-1;j<col;j++){ 
-  		fish2[i]=fish2[i]+matrix[i][j];
+	if (col >2){
+		for(i=1;i<col;i++){
+			if (min > total[i]){
+				min = total[i];}
+		}
+	}
+	if (min<=0){
+		printf("Error, the sum of one of the columns <= 0.");
+		return 0;	
 	}
 	
-	double  f11,f12,f21,f22;
-
-	f11=fish[i];
-	f12=fish2[i];
-
-	f21=total1-f11;
-	f22=total2-f12;
-	
-	double data[] = {f11, f12, f21, f22};
-	
-	// CONTINGENGCY TABLE:
-	//   f11   f12
-	//   f21   f22
-	
-	int *nr, *nc, *ldtabl, *work;
-	int nrow=2, ncol=2, ldtable=2;
-	int workspace = 6*(row*col*sizeof(double *)); 
-	double *expect, *prc, *emin,*prt,*pre;
-	double e=0, prc1=0, emin1=0, prt1=0, pre1=0;
-	  
-	prt = (double *) malloc(size*sizeof(double));
-	prc = (double *) malloc(size*sizeof(double));
-
-	nr = &nrow;
-	nc = &ncol;
-	ldtabl=&ldtable;
-	work = &workspace;
-	
-	expect = &e;
-	prc = &prc1;
-	emin=&emin1;
-	prt=&prt1;
-	pre=&pre1;
-
-	fexact(nr,nc,data, ldtabl,expect,prc,emin,prt,pre,work);
 	
-	if (*pre>.999999999){
-		*pre=1;
+	// Ratio time...
+	for(i=0;i<col;i++){
+		ratio[i]=total[i]/min;
 	}
-	storage[i][8] = *pre;
-	pvalues[i]=*pre;
-    }
-  }
-  else{
-	  	 
-  testp(permuted_ttests, permutes, permuted,pmatrix, nc, nr, gvalue,tinitial,pvalues);
-  	 
-  	       // Checks to make sure the matrix isn't sparse.
-  double * sparse, * sparse2;
-  sparse = (double *) malloc(size*sizeof(double));
-  sparse2 = (double *) malloc(size*sizeof(double));
-	  
-  for(i=0;i<row;i++){
-  	sparse[i]=0;
-  	sparse2[i]=0;}
-  
-  c=0;	
-  for(i=0;i<row;i++){
-  	
-  	for(j=0;j<g-1;j++){
-  		sparse[i]=sparse[i]+matrix[i][j];
+	
+	//Change matrix into an array as received by R for compatibility.
+	
+	c=0;
+	for(i=0;i<col;i++){
+		for(j=0;j<row;j++){
+			pmatrix[c]=matrix[j][i];
+			c++;
+		}
 	}
 	
-	if(sparse[i] < (double)(g-1)){
-		c++;
+	if(row == 1){
+		for (i =0; i<col;i++){
+			pmatrix[i]=pmatrix[i]/ratio[i];
+		}
 	}
-	for(j=g-1;j<col;j++){ // ?<= for col
-  		sparse2[i]=sparse2[i]+matrix[i][j];
+	else {
+		counter = 0;
+		j=-1;
+		for (i=0; i<size; i++) {
+			if (counter % row == 0) {
+				j++;
+			}
+			pmatrix[i]=pmatrix[i]/ratio[j];
+			counter++; 
+		}   
 	}
+	// pass everything to the rest of the code using pointers. then 
+	// write to output file. below pointers for most of the values are 
+	// created to send everything by reference.
 	
-	if( (sparse2[i] <(double)(col-g+1))) {
-		c++;
-	}
-		
-	if (c==2){
-		c=0;
+	int ptt_size, *permutes,*nc,*nr,*gvalue;
 	
-	double  f11,f12,f21,f22;
-
-	f11=sparse[i];
-	sparse[i]=0;
+	nc = &col;
+	nr = &row;
+	gvalue = &g;
 	
-	f12=sparse2[i];
-	sparse2[i]=0;
+	permutes = &B;
+	ptt_size = B*row;
 	
-	f21=total1-f11;
-	f22=total2-f12;
+	//changing ptt_size to row
+	double permuted_ttests[row], pvalues[row], tinitial[row];
 	
-	double data[] = {f11, f12, f21, f22};
-
-	int *nr, *nc, *ldtabl, *work;
-	int nrow=2, ncol=2, ldtable=2, workspace=INT_MAX; // I added two zeros for larger data sets
-	double *expect, *prc, *emin,*prt,*pre;
-	double e=0, prc1=0, emin1=0, prt1=0, pre1=0;
-
-	nr = &nrow;
-	nc = &ncol;
-	ldtabl=&ldtable;
-	work = &workspace;
+	for(i=0;i<row;i++){
+		permuted_ttests[i]=0;}
+	
+	for(i=0;i<row;i++){
+		pvalues[i]=0;
+		tinitial[i]=0; }
 	
-	expect = &e;
-	prc = &prc1;
-	emin=&emin1;
-	prt=&prt1;
-	pre=&pre1;
+	// Find the initial values for the matrix.
+	start(pmatrix,gvalue,nr,nc,tinitial,storage);
 	
-	fexact(nr,nc,data, ldtabl,expect,prc,emin,prt,pre,work);
+	// Start the calculations.
 	
-	if (*pre>.999999999){
-		*pre=1;
+	if ( (col==2) || ((g-1)<8) || ((col-g+1) < 8) ){  
+		
+		double fish[row], fish2[row];
+		for(i=0;i<row;i++){
+			fish[i]=0;
+			fish2[i]=0;}
+		
+		for(i=0;i<row;i++){
+			
+			for(j=0;j<g-1;j++){
+				fish[i]=fish[i]+matrix[i][j];
+			}
+			
+			for(j=g-1;j<col;j++){ 
+				fish2[i]=fish2[i]+matrix[i][j];
+			}
+			
+			double  f11,f12,f21,f22;
+			
+			f11=fish[i];
+			f12=fish2[i];
+			
+			f21=total1-f11;
+			f22=total2-f12;
+			
+			double data[] = {f11, f12, f21, f22};
+			
+			// CONTINGENGCY TABLE:
+			//   f11   f12
+			//   f21   f22
+			
+			int *nr, *nc, *ldtabl, *work;
+			int nrow=2, ncol=2, ldtable=2, workspace=100000;
+			double *expect, *prc, *emin,*prt,*pre;
+			double e=0, prc1=0, emin1=0, prt1=0, pre1=0;
+			
+			nr = &nrow;
+			nc = &ncol;
+			ldtabl=&ldtable;
+			work = &workspace;
+			
+			expect = &e;
+			prc = &prc1;
+			emin=&emin1;
+			prt=&prt1;
+			pre=&pre1;
+			
+			//MothurFisher fishtere;
+			//double mothurFex = fishtere.fexact(f11, f12, f21, f22);
+			
+			fexact(nr,nc,data, ldtabl,expect,prc,emin,prt,pre,work);
+			
+			if (*pre>.999999999){
+				*pre=1;
+			}
+			
+			//printf("feaxt = %f\t%f\t%f\t%f\t%f\t%f\n", *expect, *pre, f11, f12, f21, f22);
+			storage[i][8] = *pre;
+			pvalues[i]=*pre;
+		}
 	}
-	storage[i][8] = *pre;
-	pvalues[i]=*pre;
-    }
-  }  
-  // End of else statement
-  bflag = 1;
-  }
-  
-  // Calculates the mean of counts (not normalized)
-  double ** temp;
-  temp = malloc(row*sizeof(double *));
-  for (i = 0; i<row; i++){
-	 temp[i] = malloc(col*sizeof(double));
-  }
-	  
-  for(j=0;j<row;j++){
-  	for(i=0;i<2;i++){
-  		temp[j][i]=0;
+	else{
+		
+		testp(permuted_ttests, permutes, permuted,pmatrix, nc, nr, gvalue,tinitial,pvalues);
+		
+		// Checks to make sure the matrix isn't sparse.
+		double sparse[row], sparse2[row];
+		for(i=0;i<row;i++){
+			sparse[i]=0;
+			sparse2[i]=0;}
+		
+		c=0;	
+		for(i=0;i<row;i++){
+			
+			for(j=0;j<g-1;j++){
+				sparse[i]=sparse[i]+matrix[i][j];
+			}
+			
+			if(sparse[i] < (double)(g-1)){
+				c++;
+			}
+			for(j=g-1;j<col;j++){ // ?<= for col
+				sparse2[i]=sparse2[i]+matrix[i][j];
+			}
+			
+			if( (sparse2[i] <(double)(col-g+1))) {
+				c++;
+			}
+			
+			if (c==2){
+				c=0;
+				
+				double  f11,f12,f21,f22;
+				
+				f11=sparse[i];
+				sparse[i]=0;
+				
+				f12=sparse2[i];
+				sparse2[i]=0;
+				
+				f21=total1-f11;
+				f22=total2-f12;
+				
+				double data[] = {f11, f12, f21, f22};
+				
+				int *nr, *nc, *ldtabl, *work;
+				int nrow=2, ncol=2, ldtable=2, workspace=10000000; // I added two zeros for larger data sets
+				double *expect, *prc, *emin,*prt,*pre;
+				double e=0, prc1=0, emin1=0, prt1=0, pre1=0;
+				
+				nr = &nrow;
+				nc = &ncol;
+				ldtabl=&ldtable;
+				work = &workspace;
+				
+				expect = &e;
+				prc = &prc1;
+				emin=&emin1;
+				prt=&prt1;
+				pre=&pre1;
+				
+				fexact(nr,nc,data, ldtabl,expect,prc,emin,prt,pre,work);
+				
+				if (*pre>.999999999){
+					*pre=1;
+				}
+				storage[i][8] = *pre;
+				pvalues[i]=*pre;
+			}
+		}  
+		// End of else statement
+		bflag = 1;
 	}
-  }
-  
-  for (j=0;j<row;j++){
-  	for (i=1; i<=(g-1); i++){
-  		temp[j][0]=temp[j][0]+matrix[j][i-1];
-  	}
-  	temp[j][0]= (double) temp[j][0]/(g-1);
-  	for(i=g;i<=col;i++){
-  		temp[j][1]=temp[j][1]+matrix[j][i-1];
+	
+	// Calculates the mean of counts (not normalized)
+	double temp[row][2];
+	
+	for(j=0;j<row;j++){
+		for(i=0;i<2;i++){
+			temp[j][i]=0;
+		}
 	}
-	temp[j][1]= (double) temp[j][1]/(col-g+1);
-  }
-
-  for(i=0;i<row;i++){
-  	storage[i][3]=temp[i][0];
-  	storage[i][7]=temp[i][1];
-  	storage[i][8]=pvalues[i];
-  }
-  
-// BACKUP checks
-  
-  for (i=0;i<row;i++){
-    if(pvalues[i]<thresh){
-    	printf("Feature %d is significant, p = %.10lf \n",i+1,pvalues[i]);
-	}	
-  }
-  	  
-  // And now we write the files to a text file.
-  struct tm *local;
-  time_t t;
-  t = time(NULL);
-  local = localtime(&t);
-  
-  out = fopen(output,"w");
-  
-  fprintf(out,"Local time and date of test: %s\n", asctime(local));
-  fprintf(out,"# rows = %d, # col = %d, g = %d\n\n",row,col,g);
-  if (bflag == 1){
-    fprintf(out,"%d permutations\n\n",B);	
-  }
-  
-  //output column headings - not really sure... documentation labels 9 columns, there are 10 in the output file
-  //storage 0 = meanGroup1 - line 529, 1 = varGroup1 - line 532, 2 = err rate1 - line 534, 3 = mean of counts group1?? - line 291, 4 = meanGroup2 - line 536, 5 = varGroup2 - line 539, 6 = err rate2 - line 541, 7 = mean of counts group2?? - line 292, 8 = pvalues - line 293
-  fprintf(out, "OTU\tmean(group1)\tvariance(group1)\tstderr(group1)\tmean_of_counts(group1)\tmean(group2)\tvariance(group2)\tstderr(group2)\tmean_of_counts(group1)\tp-value\n");
+	
+	for (j=0;j<row;j++){
+		for (i=1; i<=(g-1); i++){
+			temp[j][0]=temp[j][0]+matrix[j][i-1];
+		}
+		temp[j][0]= (double) temp[j][0]/(g-1);
+		for(i=g;i<=col;i++){
+			temp[j][1]=temp[j][1]+matrix[j][i-1];
+		}
+		temp[j][1]= (double) temp[j][1]/(col-g+1);
+	}
+	
+	for(i=0;i<row;i++){
+		storage[i][3]=temp[i][0];
+		storage[i][7]=temp[i][1];
+		storage[i][8]=pvalues[i];
+	}
+	
+	// BACKUP checks
+	
+	for (i=0;i<row;i++){
+		if(pvalues[i]<thresh){
+			printf("Feature %d is significant, p = %.10lf \n",i+1,pvalues[i]);
+		}	
+	}
+	
+	// And now we write the files to a text file.
+	struct tm *local;
+	time_t t;
+	t = time(NULL);
+	local = localtime(&t);
+	
+	out = fopen(output,"w");
+	
+	fprintf(out,"Local time and date of test: %s\n", asctime(local));
+	fprintf(out,"# rows = %d, # col = %d, g = %d\n\n",row,col,g);
+	if (bflag == 1){
+		fprintf(out,"%d permutations\n\n",B);	
+	}
+	
+	//output column headings - not really sure... documentation labels 9 columns, there are 10 in the output file
+	//storage 0 = meanGroup1 - line 529, 1 = varGroup1 - line 532, 2 = err rate1 - line 534, 3 = mean of counts group1?? - line 291, 4 = meanGroup2 - line 536, 5 = varGroup2 - line 539, 6 = err rate2 - line 541, 7 = mean of counts group2?? - line 292, 8 = pvalues - line 293
+	fprintf(out, "OTU\tmean(group1)\tvariance(group1)\tstderr(group1)\tmean_of_counts(group1)\tmean(group2)\tvariance(group2)\tstderr(group2)\tmean_of_counts(group1)\tp-value\n");
     
-  for(i=0; i<row; i++){
-	fprintf(out,"%d",(i+1));
+	for(i=0; i<row; i++){
+		fprintf(out,"%d",(i+1));
+		
+		for(j=0; j<9;j++){
+			fprintf(out,"\t%.12lf",storage[i][j]);
+		}
+		fprintf(out,"\n");
+	}  
 	
-    for(j=0; j<9;j++){
-      fprintf(out,"\t%.12lf",storage[i][j]);
-    }
-    fprintf(out,"\n");
-  }  
-  
-  fprintf(out,"\n \n");
-  
- // fclose(jobj);
-  fclose(out);
-  
-  return 0;
+	fprintf(out,"\n \n");
+	
+	// fclose(jobj);
+	fclose(out);
+	
+	return 0;
 }
 
 void testp(double *permuted_ttests,int *B,double *permuted,
-	   double *Imatrix,int *nc,int *nr,int *g,double *Tinitial,double 
-	   *ps) {
-  
-  double Tvalues[*nr];
-  int a, b, n, i, j,k=0;
-  
-  a = *B;
-  b = *nr;
-  n = a*b;
-  
-  double counter[b];
-  
-  for(j=0;j<b;j++){
-    counter[j]=0;
-  }    
-
-  for (j=1; j<=*B; j++){
-    permute_matrix(Imatrix,nc,nr,permuted,g,Tvalues,Tinitial,counter);
-   // for(i=0;i<*nr;i++){
-   //   permuted_ttests[k]=fabs(Tvalues[i]);
-	//    k++;
+		   double *Imatrix,int *nc,int *nr,int *g,double *Tinitial,double 
+		   *ps) {
+	
+	double Tvalues[*nr];
+	int a, b, n, j;
+	
+	a = *B;
+	b = *nr;
+	n = a*b;
+	
+	double counter[b];
+	
+	for(j=0;j<b;j++){
+		counter[j]=0;
+	}    
+	
+	for (j=1; j<=*B; j++){
+		permute_matrix(Imatrix,nc,nr,permuted,g,Tvalues,Tinitial,counter);
+		// for(i=0;i<*nr;i++){
+		//   permuted_ttests[k]=fabs(Tvalues[i]);
+		//    k++;
     }
-  
-  
-  for(j=0;j<*nr;j++){
-    ps[j]=((counter[j]+1)/(double)(a+1));
-  }
+	
+	
+	for(j=0;j<*nr;j++){
+		ps[j]=((counter[j]+1)/(double)(a+1));
+	}
 }	
 
 void permute_matrix(double *Imatrix,int *nc,int *nr,double *permuted,
-		    int *g,double *trial_ts,double *Tinitial,double *counter1){
-		    	
-  int i=0,j=0,n=0,a=0,b=0,f=0,c=0,k=0;
-  
-  a = *nr; // number of rows
-  b = *nc;
-  n = a*b;
-  
-  int y[b];
-  
-  for (i=1; i<=*nc; i++){
-    y[i-1] = i;
-  }
-  
-  permute_array(y, b); 
-  
-  for (i=0; i<*nc; i++){
-    f = y[i]; //column number
-    c=1;
-    c*=(f-1);
-    c*=a;
-    if (f == 1){
-      c = 0;
-    } // starting value position in the Imatrix
-    for(j=1; j<=*nr; j++){
-      permuted[k] = Imatrix[c];
-      c++;
-      k++;
-    }
-  }
-  
-  calc_twosample_ts(permuted,g,nc,nr,trial_ts,Tinitial,counter1);
+					int *g,double *trial_ts,double *Tinitial,double *counter1){
+	
+	int i=0,j=0,n=0,a=0,b=0,f=0,c=0,k=0;
+	
+	a = *nr; // number of rows
+	b = *nc;
+	n = a*b;
+	
+	int y[b];
+	
+	for (i=1; i<=*nc; i++){
+		y[i-1] = i;
+	}
+	
+	permute_array(y, b); 
+	
+	for (i=0; i<*nc; i++){
+		f = y[i]; //column number
+		c=1;
+		c*=(f-1);
+		c*=a;
+		if (f == 1){
+			c = 0;
+		} // starting value position in the Imatrix
+		for(j=1; j<=*nr; j++){
+			permuted[k] = Imatrix[c];
+			c++;
+			k++;
+		}
+	}
+	
+	calc_twosample_ts(permuted,g,nc,nr,trial_ts,Tinitial,counter1);
 }
 
 void permute_array(int *array, int n) {
-  static int seeded = 0;
-  int i;
-  
-  if (! seeded) {
-    seeded = 1;
-    srand(time(NULL));
-  }
-  
-  for (i = 0; i < n; i++) {
-    int selection = rand() % (n - i);
-    int tmp = array[i + selection];
-    array[i + selection] = array[i];
-    array[i] = tmp;
-  }
+	static int seeded = 0;
+	int i;
+	
+	if (! seeded) {
+		seeded = 1;
+		srand(time(NULL));
+	}
+	
+	for (i = 0; i < n; i++) {
+		int selection = rand() % (n - i);
+		int tmp = array[i + selection];
+		array[i + selection] = array[i];
+		array[i] = tmp;
+	}
 }
 
 void calc_twosample_ts(double *Pmatrix,int *g,int *nc,int *nr,
-		       double *Ts,double *Tinitial,double *counter) {
-  int i,a;
-  a = *nr;
-  a*=4;
-  
-  double C1[*nr][3], C2[*nr][3], storage[a],tool[a];
-  double nrows,ncols,gvalue, xbardiff=0, denom=0;
-  
-  nrows = (double) *nr;
-  ncols = (double) *nc;
-  gvalue= (double) *g;
-  
+					   double *Ts,double *Tinitial,double *counter) {
+	int i,a;
+	a = *nr;
+	a*=4;
+	
+	double C1[*nr][3], C2[*nr][3], storage[a],tool[a];
+	double nrows,ncols,gvalue, xbardiff=0, denom=0;
+	
+	nrows = (double) *nr;
+	ncols = (double) *nc;
+	gvalue= (double) *g;
+	
     meanvar(Pmatrix,g,nr,nc,storage);
     for(i=0;i<=a-1;i++){
-      tool[i]=storage[i];
+		tool[i]=storage[i];
     }
     for (i=0; i<*nr;i++){
-      C1[i][0]=tool[i];
-      C1[i][1]=tool[i+*nr+*nr];
-      C1[i][2]=C1[i][1]/(gvalue-1);
-      
-      C2[i][0]=tool[i+*nr];
-      C2[i][1]=tool[i+*nr+*nr+*nr]; // var group 2 
-      C2[i][2]=C2[i][1]/(ncols-gvalue+1);
+		C1[i][0]=tool[i];
+		C1[i][1]=tool[i+*nr+*nr];
+		C1[i][2]=C1[i][1]/(gvalue-1);
+		
+		C2[i][0]=tool[i+*nr];
+		C2[i][1]=tool[i+*nr+*nr+*nr]; // var group 2 
+		C2[i][2]=C2[i][1]/(ncols-gvalue+1);
     }
     
     for (i=0; i<*nr; i++){
-      xbardiff = C1[i][0]-C2[i][0];
-      denom = sqrt(C1[i][2]+C2[i][2]);
-      Ts[i]=fabs(xbardiff/denom);
-      if (fabs(Ts[i])>(fabs(Tinitial[i])+.0000000000001)){ //13th place
-	    counter[i]++;
-      }
+		xbardiff = C1[i][0]-C2[i][0];
+		denom = sqrt(C1[i][2]+C2[i][2]);
+		Ts[i]=fabs(xbardiff/denom);
+		if (fabs(Ts[i])>(fabs(Tinitial[i])+.0000000000001)){ //13th place
+			counter[i]++;
+		}
     }	
 }
 
 void meanvar(double *pmatrix,int *g,int *nr,int *nc,double *store){
-  double temp[*nr], temp2[*nr],var[*nr],var2[*nr],a,b;
-  
-  int i,m,k,l,n;
-  
-  a = (double) *g-1;          
-  b = (double) (*nc-a);
-  
-  for (i = 0; i<*nr; i++){
-    temp[i]=0;
-    temp2[i]=0;
-    var[i]=0;
-    var2[i]=0;
-  }
-  
-  k = *nr; // number of rows 
-  l = *nc;
-  n = k*l;	
-  
+	double temp[*nr], temp2[*nr],var[*nr],var2[*nr],a,b;
+	
+	int i,m,k,l,n;
+	
+	a = (double) *g-1;          
+	b = (double) (*nc-a);
+	
+	for (i = 0; i<*nr; i++){
+		temp[i]=0;
+		temp2[i]=0;
+		var[i]=0;
+		var2[i]=0;
+	}
+	
+	k = *nr; // number of rows 
+	l = *nc;
+	n = k*l;	
+	
     m=0;
     m=*g-1;
     k=*nr;
     m*=k; // m = g * nr now
     for (i=0;i<m;i++){
-      temp[i%k]=temp[i%k]+pmatrix[i];
+		temp[i%k]=temp[i%k]+pmatrix[i];
     }
     for (i=0;i<n;i++){
-      temp2[i%k]=temp2[i%k]+pmatrix[i];
+		temp2[i%k]=temp2[i%k]+pmatrix[i];
     }
     for (i=0;i<*nr;i++){
-      temp2[i]=temp2[i]-temp[i];
+		temp2[i]=temp2[i]-temp[i];
     }
     for (i=0;i<=*nr-1;i++){
-      store[i]=temp[i]/a;
-      store[i+*nr]=temp2[i]/b;
+		store[i]=temp[i]/a;
+		store[i+*nr]=temp2[i]/b;
     }
     
     // That completes the mean calculations.
     
     for (i=0;i<m;i++){
-      var[i%k]=var[i%k]+pow((pmatrix[i]-store[i%k]),2);
+		var[i%k]=var[i%k]+pow((pmatrix[i]-store[i%k]),2);
     }
     for (i=m;i<n;i++){
-      var2[i%k]=var2[i%k]+pow((pmatrix[i]-store[(i%k)+*nr]),2);
+		var2[i%k]=var2[i%k]+pow((pmatrix[i]-store[(i%k)+*nr]),2);
     }
     
     for (i=0;i<=*nr-1;i++){
-      store[i+2*k]=var[i]/(a-1);
-      store[i+3*k]=var2[i]/(b-1);
+		store[i+2*k]=var[i]/(a-1);
+		store[i+3*k]=var2[i]/(b-1);
     }
     // That completes var calculations.
 }
 
 void start(double *Imatrix,int *g,int *nr,int *nc,double *initial,
-		double** storage){
-  int i, a = *nr;
-  a*=4;
-	
-  double store[a], tool[a], C1[*nr][3], C2[*nr][3];
-  double nrows,ncols,gvalue, xbardiff=0, denom=0;
- 
-  nrows = (double) *nr;
-  ncols = (double) *nc;
-  gvalue= (double) *g;
-   
-  meanvar(Imatrix,g,nr,nc,store);
-   
-  for(i=0;i<=a-1;i++){
-    tool[i]=store[i];
-  }
-
-  for (i=0; i<*nr;i++){ 
-    C1[i][0]=tool[i]; //mean group 1
-    storage[i][0]=C1[i][0];
-    C1[i][1]=tool[i+*nr+*nr]; // var group 1
-    storage[i][1]=C1[i][1];
-    C1[i][2]=C1[i][1]/(gvalue-1);
-    storage[i][2]=sqrt(C1[i][2]); 
-    C2[i][0]=tool[i+*nr]; // mean group 2
-    storage[i][4]=C2[i][0]; 
-    C2[i][1]=tool[i+*nr+*nr+*nr]; // var group 2 
-    storage[i][5]=C2[i][1];  
-	C2[i][2]=C2[i][1]/(ncols-gvalue+1);
-    storage[i][6]=sqrt(C2[i][2]);   
-	 
-  }
- 
-  for (i=0; i<*nr; i++){
-    xbardiff = C1[i][0]-C2[i][0];
-    denom = sqrt(C1[i][2]+C2[i][2]);
-    initial[i]=fabs(xbardiff/denom);
-  }	 
+		   double storage[][9]){
+	int i, a = *nr;
+	a*=4;
+	
+	double store[a], tool[a], C1[*nr][3], C2[*nr][3];
+	double nrows,ncols,gvalue, xbardiff=0, denom=0;
+	
+	nrows = (double) *nr;
+	ncols = (double) *nc;
+	gvalue= (double) *g;
+	
+	meanvar(Imatrix,g,nr,nc,store);
+	
+	for(i=0;i<=a-1;i++){
+		tool[i]=store[i];
+	}
+	for (i=0; i<*nr;i++){
+		C1[i][0]=tool[i]; //mean group 1
+		storage[i][0]=C1[i][0];
+		C1[i][1]=tool[i+*nr+*nr]; // var group 1
+		storage[i][1]=C1[i][1];
+		C1[i][2]=C1[i][1]/(gvalue-1);
+		storage[i][2]=sqrt(C1[i][2]);
+		
+		C2[i][0]=tool[i+*nr]; // mean group 2
+		storage[i][4]=C2[i][0];    
+		C2[i][1]=tool[i+*nr+*nr+*nr]; // var group 2 
+		storage[i][5]=C2[i][1];        
+		C2[i][2]=C2[i][1]/(ncols-gvalue+1);
+		storage[i][6]=sqrt(C2[i][2]);   
+	}
+	for (i=0; i<*nr; i++){
+		xbardiff = C1[i][0]-C2[i][0];
+		denom = sqrt(C1[i][2]+C2[i][2]);
+		initial[i]=fabs(xbardiff/denom);
+	}											
 }