--- imach096d/src/imach.c	2002/04/03 12:19:36	1.38
+++ imach096d/src/imach.c	2002/05/21 18:44:41	1.42
@@ -1,4 +1,4 @@
-/* $Id: imach.c,v 1.38 2002/04/03 12:19:36 lievre Exp $
+/* $Id: imach.c,v 1.42 2002/05/21 18:44:41 brouard Exp $
    Interpolated Markov Chain
 
   Short summary of the programme:
@@ -14,7 +14,7 @@
   model. More health states you consider, more time is necessary to reach the
   Maximum Likelihood of the parameters involved in the model.  The
   simplest model is the multinomial logistic model where pij is the
-  probabibility to be observed in state j at the second wave
+  probability to be observed in state j at the second wave
   conditional to be observed in state i at the first wave. Therefore
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   'age' is age and 'sex' is a covariate. If you want to have a more
@@ -56,7 +56,7 @@
 #include <unistd.h>
 
 #define MAXLINE 256
-#define GNUPLOTPROGRAM "wgnuplot"
+#define GNUPLOTPROGRAM "gnuplot"
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define FILENAMELENGTH 80
 /*#define DEBUG*/
@@ -1330,10 +1330,10 @@ void prevalence(int agemin, float agemax
   j=cptcoveff;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}
   
- for(k1=1; k1<=j;k1++){
+  for(k1=1; k1<=j;k1++){
     for(i1=1; i1<=ncodemax[k1];i1++){
       j1++;
- 
+      
       for (i=-1; i<=nlstate+ndeath; i++)  
 	for (jk=-1; jk<=nlstate+ndeath; jk++)  
 	  for(m=agemin; m <= agemax+3; m++)
@@ -1352,41 +1352,46 @@ void prevalence(int agemin, float agemax
 	    if ((k2>=dateprev1) && (k2<=dateprev2)) {
 	      if(agev[m][i]==0) agev[m][i]=agemax+1;
 	      if(agev[m][i]==1) agev[m][i]=agemax+2;
-	      if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
-	      /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */ 
+	      if (m<lastpass) {
+	      	if (calagedate>0) 
+		  freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
+		else
+		  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+		freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; 
+	      }
 	    }
 	  }
 	}
       }
-	for(i=(int)agemin; i <= (int)agemax+3; i++){ 
-	  for(jk=1; jk <=nlstate ; jk++){
-	    for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
-	      pp[jk] += freq[jk][m][i]; 
-	  }
-	  for(jk=1; jk <=nlstate ; jk++){
-	    for(m=-1, pos=0; m <=0 ; m++)
+      for(i=(int)agemin; i <= (int)agemax+3; i++){ 
+	for(jk=1; jk <=nlstate ; jk++){
+	  for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+	    pp[jk] += freq[jk][m][i]; 
+	}
+	for(jk=1; jk <=nlstate ; jk++){
+	  for(m=-1, pos=0; m <=0 ; m++)
 	    pos += freq[jk][m][i];
 	}
 	
-	 for(jk=1; jk <=nlstate ; jk++){
-	   for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
-	     pp[jk] += freq[jk][m][i];
-	 }
-	 
-	 for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
-
-	 for(jk=1; jk <=nlstate ; jk++){	   
-	   if( i <= (int) agemax){
-	     if(pos>=1.e-5){
-	       probs[i][jk][j1]= pp[jk]/pos;
-	     }
-	   }
-	 }
-	 
+	for(jk=1; jk <=nlstate ; jk++){
+	  for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
+	    pp[jk] += freq[jk][m][i];
 	}
+	
+	for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
+	
+	for(jk=1; jk <=nlstate ; jk++){	   
+	  if( i <= (int) agemax){
+	    if(pos>=1.e-5){
+	      probs[i][jk][j1]= pp[jk]/pos;
+	    }
+	  }
+	}
+	
+      }
     }
   }
-  
+
   
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
   free_vector(pp,1,nlstate);
@@ -1503,7 +1508,7 @@ void tricode(int *Tvar, int **nbcode, in
       for (k=0; k<=19; k++) {
 	if (Ndum[k] != 0) {
 	  nbcode[Tvar[j]][ij]=k; 
-	  /*	 printf("nbcodeaaaaaaaaaaa=%d Tvar[j]=%d ij=%d j=%d",nbcode[Tvar[j]][ij],Tvar[j],ij,j);*/
+	  
 	  ij++;
 	}
 	if (ij > ncodemax[j]) break; 
@@ -1531,18 +1536,29 @@ void tricode(int *Tvar, int **nbcode, in
 
 /*********** Health Expectancies ****************/
 
-void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm)
+void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
+
 {
   /* Health expectancies */
-  int i, j, nhstepm, hstepm, h, nstepm;
+  int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
   double age, agelim, hf;
-  double ***p3mat;
+  double ***p3mat,***varhe;
+  double **dnewm,**doldm;
+  double *xp;
+  double **gp, **gm;
+  double ***gradg, ***trgradg;
+  int theta;
+
+  varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
+  xp=vector(1,npar);
+  dnewm=matrix(1,nlstate*2,1,npar);
+  doldm=matrix(1,nlstate*2,1,nlstate*2);
   
   fprintf(ficreseij,"# Health expectancies\n");
   fprintf(ficreseij,"# Age");
   for(i=1; i<=nlstate;i++)
     for(j=1; j<=nlstate;j++)
-      fprintf(ficreseij," %1d-%1d",i,j);
+      fprintf(ficreseij," %1d-%1d (SE)",i,j);
   fprintf(ficreseij,"\n");
 
   if(estepm < stepm){
@@ -1582,24 +1598,114 @@ void evsij(char fileres[], double ***eij
     /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
+    gp=matrix(0,nhstepm,1,nlstate*2);
+    gm=matrix(0,nhstepm,1,nlstate*2);
+
     /* Computed by stepm unit matrices, product of hstepm matrices, stored
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
+ 
+
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+
+    /* Computing Variances of health expectancies */
+
+     for(theta=1; theta <=npar; theta++){
+      for(i=1; i<=npar; i++){ 
+	xp[i] = x[i] + (i==theta ?delti[theta]:0);
+      }
+      hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
+  
+      cptj=0;
+      for(j=1; j<= nlstate; j++){
+	for(i=1; i<=nlstate; i++){
+	  cptj=cptj+1;
+	  for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
+	    gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
+	  }
+	}
+      }
+     
+     
+      for(i=1; i<=npar; i++) 
+	xp[i] = x[i] - (i==theta ?delti[theta]:0);
+      hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
+      
+      cptj=0;
+      for(j=1; j<= nlstate; j++){
+	for(i=1;i<=nlstate;i++){
+	  cptj=cptj+1;
+	  for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
+	    gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
+	  }
+	}
+      }
+     
+   
+
+      for(j=1; j<= nlstate*2; j++)
+	for(h=0; h<=nhstepm-1; h++){
+	  gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+	}
+
+     } 
+   
+/* End theta */
+
+     trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
+
+     for(h=0; h<=nhstepm-1; h++)
+      for(j=1; j<=nlstate*2;j++)
+	for(theta=1; theta <=npar; theta++)
+	trgradg[h][j][theta]=gradg[h][theta][j];
+
+
+     for(i=1;i<=nlstate*2;i++)
+      for(j=1;j<=nlstate*2;j++)
+	varhe[i][j][(int)age] =0.;
+
+     printf("%d||",(int)age);fflush(stdout);
+    for(h=0;h<=nhstepm-1;h++){
+      for(k=0;k<=nhstepm-1;k++){
+	matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
+	matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
+	for(i=1;i<=nlstate*2;i++)
+	  for(j=1;j<=nlstate*2;j++)
+	    varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
+      }
+    }
+
+     
+    /* Computing expectancies */
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
 	for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
 	  eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
-	  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
+	  
+/* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
+
 	}
+
     fprintf(ficreseij,"%3.0f",age );
+    cptj=0;
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){
-	fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);
+	cptj++;
+	fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
       }
     fprintf(ficreseij,"\n");
+   
+    free_matrix(gm,0,nhstepm,1,nlstate*2);
+    free_matrix(gp,0,nhstepm,1,nlstate*2);
+    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
+    free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }
+  free_vector(xp,1,npar);
+  free_matrix(dnewm,1,nlstate*2,1,npar);
+  free_matrix(doldm,1,nlstate*2,1,nlstate*2);
+  free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
 }
 
 /************ Variance ******************/
@@ -1822,9 +1928,9 @@ void varprevlim(char fileres[], double *
 }
 
 /************ Variance of one-step probabilities  ******************/
-void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)
+void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
 {
-  int i, j;
+  int i, j, i1, k1, j1, z1;
   int k=0, cptcode;
   double **dnewm,**doldm;
   double *xp;
@@ -1839,91 +1945,118 @@ void varprob(char fileres[], double **ma
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", fileresprob);
   }
-  printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);
+  printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   
+fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");
+  fprintf(ficresprob,"# Age");
+  for(i=1; i<=nlstate;i++)
+    for(j=1; j<=(nlstate+ndeath);j++)
+      fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+
+
+  fprintf(ficresprob,"\n");
+
 
   xp=vector(1,npar);
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));
   
   cov[1]=1;
-  for (age=bage; age<=fage; age ++){ 
-    cov[2]=age;
-    gradg=matrix(1,npar,1,9);
-    trgradg=matrix(1,9,1,npar);
-    gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
-    gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
+  j=cptcoveff;
+  if (cptcovn<1) {j=1;ncodemax[1]=1;}
+  j1=0;
+  for(k1=1; k1<=1;k1++){
+    for(i1=1; i1<=ncodemax[k1];i1++){ 
+    j1++;
+
+    if  (cptcovn>0) {
+      fprintf(ficresprob, "\n#********** Variable "); 
+      for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+      fprintf(ficresprob, "**********\n#");
+    }
     
-    for(theta=1; theta <=npar; theta++){
-      for(i=1; i<=npar; i++)
-	xp[i] = x[i] + (i==theta ?delti[theta]:0);
-     
-      pmij(pmmij,cov,ncovmodel,xp,nlstate);
-   
-      k=0;
-      for(i=1; i<= (nlstate+ndeath); i++){
-	for(j=1; j<=(nlstate+ndeath);j++){
-	   k=k+1;
-	  gp[k]=pmmij[i][j];
+      for (age=bage; age<=fage; age ++){ 
+	cov[2]=age;
+	for (k=1; k<=cptcovn;k++) {
+	  cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
+	  
 	}
-      }
-
-      for(i=1; i<=npar; i++)
-	xp[i] = x[i] - (i==theta ?delti[theta]:0);
+	for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+	for (k=1; k<=cptcovprod;k++)
+	  cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+	
+	gradg=matrix(1,npar,1,9);
+	trgradg=matrix(1,9,1,npar);
+	gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
+	gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
     
-
-      pmij(pmmij,cov,ncovmodel,xp,nlstate);
-      k=0;
-      for(i=1; i<=(nlstate+ndeath); i++){
-	for(j=1; j<=(nlstate+ndeath);j++){
-	  k=k+1;
-	  gm[k]=pmmij[i][j];
-	}
-      }
+	for(theta=1; theta <=npar; theta++){
+	  for(i=1; i<=npar; i++)
+	    xp[i] = x[i] + (i==theta ?delti[theta]:0);
+	  
+	  pmij(pmmij,cov,ncovmodel,xp,nlstate);
+	  
+	  k=0;
+	  for(i=1; i<= (nlstate+ndeath); i++){
+	    for(j=1; j<=(nlstate+ndeath);j++){
+	      k=k+1;
+	      gp[k]=pmmij[i][j];
+	    }
+	  }
+	  
+	  for(i=1; i<=npar; i++)
+	    xp[i] = x[i] - (i==theta ?delti[theta]:0);
+    
+	  pmij(pmmij,cov,ncovmodel,xp,nlstate);
+	  k=0;
+	  for(i=1; i<=(nlstate+ndeath); i++){
+	    for(j=1; j<=(nlstate+ndeath);j++){
+	      k=k+1;
+	      gm[k]=pmmij[i][j];
+	    }
+	  }
      
-       for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++) 
-	   gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
-    }
-
-     for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)
-      for(theta=1; theta <=npar; theta++)
-      trgradg[j][theta]=gradg[theta][j];
- 
-     matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);
-     matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);
-
-     pmij(pmmij,cov,ncovmodel,x,nlstate);
+	  for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++) 
+	    gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
+	}
 
-     k=0;
-     for(i=1; i<=(nlstate+ndeath); i++){
-       for(j=1; j<=(nlstate+ndeath);j++){
-	 k=k+1;
-	 gm[k]=pmmij[i][j];
+	for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)
+	  for(theta=1; theta <=npar; theta++)
+	    trgradg[j][theta]=gradg[theta][j];
+	
+	matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);
+	matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);
+	
+	pmij(pmmij,cov,ncovmodel,x,nlstate);
+	
+	k=0;
+	for(i=1; i<=(nlstate+ndeath); i++){
+	  for(j=1; j<=(nlstate+ndeath);j++){
+	    k=k+1;
+	    gm[k]=pmmij[i][j];
+	  }
 	}
-     }
      
      /*printf("\n%d ",(int)age);
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
-       
-
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
      }*/
 
-  fprintf(ficresprob,"\n%d ",(int)age);
-
-  for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
-    if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);
-if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);
-  }
+	fprintf(ficresprob,"\n%d ",(int)age);
 
+	for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)
+	  fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));
+  
+      }
+    }
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-}
- free_vector(xp,1,npar);
-fclose(ficresprob);
-
+  }
+  free_vector(xp,1,npar);
+  fclose(ficresprob);
+  
 }
 
 /******************* Printing html file ***********/
@@ -1958,9 +2091,10 @@ Interval (in months) between two waves:
 
  fprintf(fichtm,"\n
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n
- - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
+  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
+ - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n
- - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
+ - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
 
  if(popforecast==1) fprintf(fichtm,"\n
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
@@ -1983,24 +2117,24 @@ fprintf(fichtm," <li>Graphs</li><p>");
 	   fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
 	 fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
-       fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>
-<img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
+       fprintf(fichtm,"<br>- Probabilities: pe%s%d.png<br>
+<img src=\"pe%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
        for(cpt=1; cpt<nlstate;cpt++){
-	 fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>
-<img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+	 fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.png<br>
+<img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
        }
     for(cpt=1; cpt<=nlstate;cpt++) {
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
-interval) in state (%d): v%s%d%d.gif <br>
-<img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
+interval) in state (%d): v%s%d%d.png <br>
+<img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
      }
      for(cpt=1; cpt<=nlstate;cpt++) {
-        fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>
-<img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+        fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
+<img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
      }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and
-health expectancies in states (1) and (2): e%s%d.gif<br>
-<img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
+health expectancies in states (1) and (2): e%s%d.png<br>
+<img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
 fprintf(fichtm,"\n</body>");
    }
    }
@@ -2028,9 +2162,11 @@ m=pow(2,cptcoveff);
    for (k1=1; k1<= m ; k1 ++) {
 
 #ifdef windows
-    fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
+     fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n\n",strtok(optionfile, "."),cpt,k1);
+     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
 #endif
 #ifdef unix
+fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n\n",strtok(optionfile, "."),cpt,k1);
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);
 #endif
 
@@ -2050,15 +2186,15 @@ for (i=1; i<= nlstate ; i ++) {
 }  
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
 #ifdef unix
-fprintf(ficgp,"\nset ter gif small size 400,300");
+fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");
 #endif
-fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
    }
   }
   /*2 eme*/
 
   for (k1=1; k1<= m ; k1 ++) { 
-    fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);
+    fprintf(ficgp,"\nset out \"e%s%d.png\" \n\n",strtok(optionfile, "."),k1);
+    fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
     
     for (i=1; i<= nlstate+1 ; i ++) {
       k=2*i;
@@ -2083,27 +2219,36 @@ fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
       else fprintf(ficgp,"\" t\"\" w l 0,");
     }
-    fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);
   }
  
   /*3eme*/
 
   for (k1=1; k1<= m ; k1 ++) { 
     for (cpt=1; cpt<= nlstate ; cpt ++) {
-      k=2+nlstate*(cpt-1);
-      fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
+      k=2+nlstate*(2*cpt-2);
+      fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n\n",strtok(optionfile, "."),cpt,k1);
+      fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
+      /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+ for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+ for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+
+*/
       for (i=1; i< nlstate ; i ++) {
-	fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);
+	fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
+
       } 
-      fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
-    }
     }
+  }
  
   /* CV preval stat */
     for (k1=1; k1<= m ; k1 ++) { 
     for (cpt=1; cpt<nlstate ; cpt ++) {
       k=3;
-      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
+      fprintf(ficgp,"set out \"p%s%d%d.png\" \n\n",strtok(optionfile, "."),cpt,k1);
+      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
 
       for (i=1; i< nlstate ; i ++)
 	fprintf(ficgp,"+$%d",k+i+1);
@@ -2116,7 +2261,6 @@ fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
 	fprintf(ficgp,"+$%d",l+i+1);
       }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
-      fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
     } 
   }  
   
@@ -2132,50 +2276,50 @@ fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
 	}
       }
     }
-    }
+   }
 
-    for(jk=1; jk <=m; jk++) {
-  fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
-   i=1;
-   for(k2=1; k2<=nlstate; k2++) {
-     k3=i;
-     for(k=1; k<=(nlstate+ndeath); k++) {
-       if (k != k2){
-    	fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
-ij=1;
-	for(j=3; j <=ncovmodel; j++) {
-	  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
-	    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
-	    ij++;
-	  }
-	  else
-	  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-	}
-	  fprintf(ficgp,")/(1");
-	
-	for(k1=1; k1 <=nlstate; k1++){   
-	  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
-ij=1;
-	  for(j=3; j <=ncovmodel; j++){
-	  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
-	    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
-	    ij++;
-	  }
-	  else
-	    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-	  }
-	  fprintf(ficgp,")");
-	}
-	fprintf(ficgp,") t \"p%d%d\" ", k2,k);
-	if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
-	i=i+ncovmodel;
+   for(jk=1; jk <=m; jk++) {
+     fprintf(ficgp,"\nset out \"pe%s%d.png\" \n\n",strtok(optionfile, "."),jk); 
+     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+     i=1;
+     for(k2=1; k2<=nlstate; k2++) {
+       k3=i;
+       for(k=1; k<=(nlstate+ndeath); k++) {
+	 if (k != k2){
+	   fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+	   ij=1;
+	   for(j=3; j <=ncovmodel; j++) {
+	     if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+	       fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+	       ij++;
+	     }
+	     else
+	       fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+	   }
+	   fprintf(ficgp,")/(1");
+	   
+	   for(k1=1; k1 <=nlstate; k1++){   
+	     fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+	     ij=1;
+	     for(j=3; j <=ncovmodel; j++){
+	       if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+		 fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+		 ij++;
+	       }
+	       else
+		 fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+	     }
+	     fprintf(ficgp,")");
+	   }
+	   fprintf(ficgp,") t \"p%d%d\" ", k2,k);
+	   if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+	   i=i+ncovmodel;
+	 }
        }
      }
    }
-   fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk); 
-   }
    
-  fclose(ficgp);
+   fclose(ficgp);
 }  /* end gnuplot */
 
 
@@ -2493,7 +2637,7 @@ int main(int argc, char *argv[])
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab; 
   int mobilav=0,popforecast=0;
   int hstepm, nhstepm;
-  double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;
+  double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
 
   double bage, fage, age, agelim, agebase;
   double ftolpl=FTOL;
@@ -2511,7 +2655,7 @@ int main(int argc, char *argv[])
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
   
 
-  char version[80]="Imach version 0.8b, March 2002, INED-EUROREVES ";
+  char version[80]="Imach version 0.8d, May 2002, INED-EUROREVES ";
   char *alph[]={"a","a","b","c","d","e"}, str[4];
 
 
@@ -2751,11 +2895,10 @@ while((c=getc(ficpar))=='#' && c!= EOF){
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
     }*/
- 
-  /* for (i=1; i<=imx; i++){
+   /*  for (i=1; i<=imx; i++){
      if (s[4][i]==9)  s[4][i]=-1; 
-     printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}
-  */
+     printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
+  
  
   /* Calculation of the number of parameter from char model*/
   Tvar=ivector(1,15); 
@@ -3207,20 +3350,20 @@ while((c=getc(ficpar))=='#' && c!= EOF){
 	    for(j=1; j<=nlstate+ndeath;j++)
 	      fprintf(ficrespij," %1d-%1d",i,j);
 	  fprintf(ficrespij,"\n");
-	  for (h=0; h<=nhstepm; h++){
+	   for (h=0; h<=nhstepm; h++){
 	    fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
 	    for(i=1; i<=nlstate;i++)
 	      for(j=1; j<=nlstate+ndeath;j++)
 		fprintf(ficrespij," %.5f", p3mat[i][j][h]);
 	    fprintf(ficrespij,"\n");
-	  }
+	     }
 	  free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 	  fprintf(ficrespij,"\n");
 	}
     }
   }
 
-  /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/
+  varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
 
   fclose(ficrespij);
 
@@ -3229,9 +3372,7 @@ while((c=getc(ficpar))=='#' && c!= EOF){
   if((stepm == 1) && (strcmp(model,".")==0)){
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
-    free_matrix(mint,1,maxwav,1,n);
-    free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
-    free_vector(weight,1,n);}
+  } 
   else{
     erreur=108;
     printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
@@ -3261,6 +3402,8 @@ while((c=getc(ficpar))=='#' && c!= EOF){
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
   }
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+  calagedate=-1;
+prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
 
   k=0;
   for(cptcov=1;cptcov<=i1;cptcov++){
@@ -3283,7 +3426,8 @@ while((c=getc(ficpar))=='#' && c!= EOF){
 
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
       oldm=oldms;savm=savms;
-      evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm);  
+      evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
+ 
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
       oldm=oldms;savm=savms;
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);
@@ -3306,9 +3450,11 @@ while((c=getc(ficpar))=='#' && c!= EOF){
 	for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
 	  for(i=1, epj[j]=0.;i <=nlstate;i++) {
 	    epj[j] += prlim[i][i]*eij[i][j][(int)age];
+	    /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
 	  }
 	  epj[nlstate+1] +=epj[j];
 	}
+
 	for(i=1, vepp=0.;i <=nlstate;i++)
 	  for(j=1;j <=nlstate;j++)
 	    vepp += vareij[i][j][(int)age];
@@ -3320,7 +3466,9 @@ while((c=getc(ficpar))=='#' && c!= EOF){
       }
     }
   }
-
+free_matrix(mint,1,maxwav,1,n);
+    free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
+    free_vector(weight,1,n);
   fclose(ficreseij);
   fclose(ficresvij);
   fclose(ficrest);