--- imach/src/imach.c	2003/06/27 13:00:02	1.94
+++ imach/src/imach.c	2003/07/08 07:54:34	1.95
@@ -1,6 +1,11 @@
-/* $Id: imach.c,v 1.94 2003/06/27 13:00:02 brouard Exp $
+/* $Id: imach.c,v 1.95 2003/07/08 07:54:34 brouard Exp $
   $State: Exp $
   $Log: imach.c,v $
+  Revision 1.95  2003/07/08 07:54:34  brouard
+  * imach.c (Repository):
+  (Repository): Using imachwizard code to output a more meaningful covariance
+  matrix (cov(a12,c31) instead of numbers.
+
   Revision 1.94  2003/06/27 13:00:02  brouard
   Just cleaning
 
@@ -165,6 +170,9 @@
 #include <time.h>
 #include "timeval.h"
 
+/* #include <libintl.h> */
+/* #define _(String) gettext (String) */
+
 #define MAXLINE 256
 #define GNUPLOTPROGRAM "gnuplot"
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
@@ -193,11 +201,11 @@
 #define ODIRSEPARATOR '/'
 #endif
 
-/* $Id: imach.c,v 1.94 2003/06/27 13:00:02 brouard Exp $ */
+/* $Id: imach.c,v 1.95 2003/07/08 07:54:34 brouard Exp $ */
 /* $State: Exp $ */
 
 char version[]="Imach version 0.96b, June 2003, INED-EUROREVES ";
-char fullversion[]="$Revision: 1.94 $ $Date: 2003/06/27 13:00:02 $"; 
+char fullversion[]="$Revision: 1.95 $ $Date: 2003/07/08 07:54:34 $"; 
 int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 int nvar;
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
@@ -2291,7 +2299,7 @@ void evsij(char fileres[], double ***eij
 
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
 
-    /* Computing Variances of health expectancies */
+    /* Computing  Variances of health expectancies */
 
      for(theta=1; theta <=npar; theta++){
       for(i=1; i<=npar; i++){ 
@@ -2845,8 +2853,8 @@ void varprob(char optionfilefiname[], do
   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   fprintf(fichtm,"\n");
 
-  fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Computing matrix of variance-covariance of step probabilities</a></h4></li>\n",optionfilehtmcov);
-  fprintf(fichtmcov,"\n<h4>Computing matrix of variance-covariance of step probabilities</h4>\n\
+  fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
+  fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
   file %s<br>\n",optionfilehtmcov);
   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
 and drawn. It helps understanding how is the covariance between two incidences.\
@@ -3184,8 +3192,8 @@ fprintf(fichtm," <ul><li><b>Graphs</b></
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      }
      for(cpt=1; cpt<=nlstate;cpt++) {
-       fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
-interval) in state (%d): %s%d%d.png <br>\
+       fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
+prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
 <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
      }
    } /* end i1 */
@@ -3842,7 +3850,7 @@ void prwizard(int ncovmodel, int nlstate
 	} /* end k*/
       } /*end j */
     } /* end i */
-  }
+  } /* end itimes */
 
 } /* end of prwizard */
 
@@ -3855,8 +3863,11 @@ int main(int argc, char *argv[])
 {
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
-  int jj, imk;
+  int jj, ll, li, lj, lk, imk;
   int numlinepar=0; /* Current linenumber of parameter file */
+  int itimes;
+
+  char ca[32], cb[32], cc[32];
   /*  FILE *fichtm; *//* Html File */
   /* FILE *ficgp;*/ /*Gnuplot File */
   double agedeb, agefin,hf;
@@ -3911,6 +3922,12 @@ int main(int argc, char *argv[])
 
   long total_usecs;
  
+/*   setlocale (LC_ALL, ""); */
+/*   bindtextdomain (PACKAGE, LOCALEDIR); */
+/*   textdomain (PACKAGE); */
+/*   setlocale (LC_CTYPE, ""); */
+/*   setlocale (LC_MESSAGES, ""); */
+
   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
   (void) gettimeofday(&start_time,&tzp);
   curr_time=start_time;
@@ -4602,27 +4619,25 @@ Interval (in months) between two waves:
   fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
   
 
-  jk=1;
   fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
   fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
   for(i=1,jk=1; i <=nlstate; i++){
     for(k=1; k <=(nlstate+ndeath); k++){
-      if (k != i) 
-	{
-	  printf("%d%d ",i,k);
-	  fprintf(ficlog,"%d%d ",i,k);
-	  fprintf(ficres,"%1d%1d ",i,k);
-	  for(j=1; j <=ncovmodel; j++){
-	    printf("%f ",p[jk]);
-	    fprintf(ficlog,"%f ",p[jk]);
-	    fprintf(ficres,"%f ",p[jk]);
-	    jk++; 
-	  }
-	  printf("\n");
-	  fprintf(ficlog,"\n");
-	  fprintf(ficres,"\n");
+      if (k != i) {
+	printf("%d%d ",i,k);
+	fprintf(ficlog,"%d%d ",i,k);
+	fprintf(ficres,"%1d%1d ",i,k);
+	for(j=1; j <=ncovmodel; j++){
+	  printf("%f ",p[jk]);
+	  fprintf(ficlog,"%f ",p[jk]);
+	  fprintf(ficres,"%f ",p[jk]);
+	  jk++; 
 	}
+	printf("\n");
+	fprintf(ficlog,"\n");
+	fprintf(ficres,"\n");
+      }
     }
   }
   if(mle!=0){
@@ -4653,32 +4668,91 @@ Interval (in months) between two waves:
   }
    
   fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
-  if(mle==1)
+  if(mle>=1)
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
   fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
-  for(i=1,k=1;i<=npar;i++){
-    /*  if (k>nlstate) k=1;
-	i1=(i-1)/(ncovmodel*nlstate)+1; 
-	fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
-	printf("%s%d%d",alph[k],i1,tab[i]);
-    */
-    fprintf(ficres,"%3d",i);
-    if(mle==1)
-      printf("%3d",i);
-    fprintf(ficlog,"%3d",i);
-    for(j=1; j<=i;j++){
-      fprintf(ficres," %.5e",matcov[i][j]);
-      if(mle==1)
-	printf(" %.5e",matcov[i][j]);
-      fprintf(ficlog," %.5e",matcov[i][j]);
-    }
-    fprintf(ficres,"\n");
-    if(mle==1)
-      printf("\n");
-    fprintf(ficlog,"\n");
-    k++;
-  }
-   
+/* # 121 Var(a12)\n\ */
+/* # 122 Cov(b12,a12) Var(b12)\n\ */
+/* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+/* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+/* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+/* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+/* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+/* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+
+
+/* Just to have a covariance matrix which will be more understandable
+   even is we still don't want to manage dictionary of variables
+*/
+  for(itimes=1;itimes<=2;itimes++){
+    jj=0;
+    for(i=1; i <=nlstate; i++){
+      for(j=1; j <=nlstate+ndeath; j++){
+	if(j==i) continue;
+	for(k=1; k<=ncovmodel;k++){
+	  jj++;
+	  ca[0]= k+'a'-1;ca[1]='\0';
+	  if(itimes==1){
+	    if(mle>=1)
+	      printf("#%1d%1d%d",i,j,k);
+	    fprintf(ficlog,"#%1d%1d%d",i,j,k);
+	    fprintf(ficres,"#%1d%1d%d",i,j,k);
+	  }else{
+	    if(mle>=1)
+	      printf("%1d%1d%d",i,j,k);
+	    fprintf(ficlog,"%1d%1d%d",i,j,k);
+	    fprintf(ficres,"%1d%1d%d",i,j,k);
+	  }
+	  ll=0;
+	  for(li=1;li <=nlstate; li++){
+	    for(lj=1;lj <=nlstate+ndeath; lj++){
+	      if(lj==li) continue;
+	      for(lk=1;lk<=ncovmodel;lk++){
+		ll++;
+		if(ll<=jj){
+		  cb[0]= lk +'a'-1;cb[1]='\0';
+		  if(ll<jj){
+		    if(itimes==1){
+		      if(mle>=1)
+			printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+		      fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+		      fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+		    }else{
+		      if(mle>=1)
+			printf(" %.5e",matcov[jj][ll]); 
+		      fprintf(ficlog," %.5e",matcov[jj][ll]); 
+		      fprintf(ficres," %.5e",matcov[jj][ll]); 
+		    }
+		  }else{
+		    if(itimes==1){
+		      if(mle>=1)
+			printf(" Var(%s%1d%1d)",ca,i,j);
+		      fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+		      fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+		    }else{
+		      if(mle>=1)
+			printf(" %.5e",matcov[jj][ll]); 
+		      fprintf(ficlog," %.5e",matcov[jj][ll]); 
+		      fprintf(ficres," %.5e",matcov[jj][ll]); 
+		    }
+		  }
+		}
+	      } /* end lk */
+	    } /* end lj */
+	  } /* end li */
+	  if(mle>=1)
+	    printf("\n");
+	  fprintf(ficlog,"\n");
+	  fprintf(ficres,"\n");
+	  numlinepar++;
+	} /* end k*/
+      } /*end j */
+    } /* end i */
+  } /* end itimes */
+
+  fflush(ficlog);
+  fflush(ficres);
+
   while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);
@@ -5089,7 +5163,7 @@ ageminpar, agemax, s[lastpass][imx], age
   
 
   if((nberr >0) || (nbwarn>0)){
-    printf("End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+    printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
   }else{
     printf("End of Imach\n");