--- imach/src/imach.c	2002/06/20 14:03:39	1.49
+++ imach/src/imach.c	2002/06/26 23:25:02	1.50
@@ -1,4 +1,4 @@
-/* $Id: imach.c,v 1.49 2002/06/20 14:03:39 lievre Exp $
+/* $Id: imach.c,v 1.50 2002/06/26 23:25:02 brouard Exp $
    Interpolated Markov Chain
 
   Short summary of the programme:
@@ -77,11 +77,13 @@
 #define AGEBASE 40
 #ifdef windows
 #define DIRSEPARATOR '\\'
+#define ODIRSEPARATOR '/'
 #else
 #define DIRSEPARATOR '/'
+#define ODIRSEPARATOR '\\'
 #endif
 
-char version[80]="Imach version 0.8h, May 2002, INED-EUROREVES ";
+char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";
 int erreur; /* Error number */
 int nvar;
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
@@ -101,7 +103,9 @@ double jmean; /* Mean space between 2 wa
 double **oldm, **newm, **savm; /* Working pointers to matrices */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+FILE *ficlog;
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
+FILE *ficresprobmorprev;
 FILE *fichtm; /* Html File */
 FILE *ficreseij;
 char filerese[FILENAMELENGTH];
@@ -114,7 +118,7 @@ char optionfile[FILENAMELENGTH], datafil
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
-
+char filelog[FILENAMELENGTH]; /* Log file */
 char filerest[FILENAMELENGTH];
 char fileregp[FILENAMELENGTH];
 char popfile[FILENAMELENGTH];
@@ -178,8 +182,10 @@ static	int split( char *path, char *dirc
 
    l1 = strlen( path );			/* length of path */
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
-   s = strrchr( path,  DIRSEPARATOR );		/* find last / */
+   s= strrchr( path, DIRSEPARATOR );		/* find last / */
    if ( s == NULL ) {			/* no directory, so use current */
+     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
+       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 #if	defined(__bsd__)		/* get current working directory */
       extern char	*getwd( );
 
@@ -245,6 +251,9 @@ int nbocc(char *s, char occ)
 
 void cutv(char *u,char *v, char*t, char occ)
 {
+  /* cuts string t into u and v where u is ended by char occ excluding it
+     and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
+     gives u="abcedf" and v="ghi2j" */
   int i,lg,j,p=0;
   i=0;
   for(j=0; j<=strlen(t)-1; j++) {
@@ -441,8 +450,10 @@ double brent(double ax, double bx, doubl
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     /*		if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     printf(".");fflush(stdout);
+    fprintf(ficlog,".");fflush(ficlog);
 #ifdef DEBUG
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
+    fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     /*		if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
 #endif
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
@@ -567,6 +578,7 @@ void linmin(double p[], double xi[], int
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
 #ifdef DEBUG
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+  fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 #endif
   for (j=1;j<=n;j++) { 
     xi[j] *= xmin; 
@@ -597,16 +609,21 @@ void powell(double p[], double **xi, int
     ibig=0; 
     del=0.0; 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
+    fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
     for (i=1;i<=n;i++) 
       printf(" %d %.12f",i, p[i]);
+    fprintf(ficlog," %d %.12f",i, p[i]);
     printf("\n");
+    fprintf(ficlog,"\n");
     for (i=1;i<=n;i++) { 
       for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       fptt=(*fret); 
 #ifdef DEBUG
       printf("fret=%lf \n",*fret);
+      fprintf(ficlog,"fret=%lf \n",*fret);
 #endif
       printf("%d",i);fflush(stdout);
+      fprintf(ficlog,"%d",i);fflush(ficlog);
       linmin(p,xit,n,fret,func); 
       if (fabs(fptt-(*fret)) > del) { 
 	del=fabs(fptt-(*fret)); 
@@ -614,13 +631,18 @@ void powell(double p[], double **xi, int
       } 
 #ifdef DEBUG
       printf("%d %.12e",i,(*fret));
+      fprintf(ficlog,"%d %.12e",i,(*fret));
       for (j=1;j<=n;j++) {
 	xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
 	printf(" x(%d)=%.12e",j,xit[j]);
+	fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       }
-      for(j=1;j<=n;j++) 
+      for(j=1;j<=n;j++) {
 	printf(" p=%.12e",p[j]);
+	fprintf(ficlog," p=%.12e",p[j]);
+      }
       printf("\n");
+      fprintf(ficlog,"\n");
 #endif
     } 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
@@ -629,15 +651,21 @@ void powell(double p[], double **xi, int
       k[0]=1;
       k[1]=-1;
       printf("Max: %.12e",(*func)(p));
-      for (j=1;j<=n;j++) 
+      fprintf(ficlog,"Max: %.12e",(*func)(p));
+      for (j=1;j<=n;j++) {
 	printf(" %.12e",p[j]);
+	fprintf(ficlog," %.12e",p[j]);
+      }
       printf("\n");
+      fprintf(ficlog,"\n");
       for(l=0;l<=1;l++) {
 	for (j=1;j<=n;j++) {
 	  ptt[j]=p[j]+(p[j]-pt[j])*k[l];
 	  printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+	  fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 	}
 	printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+	fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       }
 #endif
 
@@ -665,9 +693,13 @@ void powell(double p[], double **xi, int
 	}
 #ifdef DEBUG
 	printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-	for(j=1;j<=n;j++)
+	fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+	for(j=1;j<=n;j++){
 	  printf(" %.12e",xit[j]);
+	  fprintf(ficlog," %.12e",xit[j]);
+	}
 	printf("\n");
+	fprintf(ficlog,"\n");
 #endif
       } 
     } 
@@ -938,10 +970,11 @@ void mlikeli(FILE *ficres,double p[], in
   for (i=1;i<=npar;i++)
     for (j=1;j<=npar;j++)
       xi[i][j]=(i==j ? 1.0 : 0.0);
-  printf("Powell\n");
+  printf("Powell\n");  fprintf(ficlog,"Powell\n");
   powell(p,xi,npar,ftol,&iter,&fret,func);
 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
+  fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
 
 }
@@ -962,8 +995,10 @@ void hesscov(double **matcov, double p[]
   hess=matrix(1,npar,1,npar);
 
   printf("\nCalculation of the hessian matrix. Wait...\n");
+  fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   for (i=1;i<=npar;i++){
     printf("%d",i);fflush(stdout);
+    fprintf(ficlog,"%d",i);fflush(ficlog);
     hess[i][i]=hessii(p,ftolhess,i,delti);
     /*printf(" %f ",p[i]);*/
     /*printf(" %lf ",hess[i][i]);*/
@@ -973,6 +1008,7 @@ void hesscov(double **matcov, double p[]
     for (j=1;j<=npar;j++)  {
       if (j>i) { 
 	printf(".%d%d",i,j);fflush(stdout);
+	fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
 	hess[i][j]=hessij(p,delti,i,j);
 	hess[j][i]=hess[i][j];    
 	/*printf(" %lf ",hess[i][j]);*/
@@ -980,8 +1016,10 @@ void hesscov(double **matcov, double p[]
     }
   }
   printf("\n");
+  fprintf(ficlog,"\n");
 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
+  fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   
   a=matrix(1,npar,1,npar);
   y=matrix(1,npar,1,npar);
@@ -1001,11 +1039,14 @@ void hesscov(double **matcov, double p[]
   }
 
   printf("\n#Hessian matrix#\n");
+  fprintf(ficlog,"\n#Hessian matrix#\n");
   for (i=1;i<=npar;i++) { 
     for (j=1;j<=npar;j++) { 
       printf("%.3e ",hess[i][j]);
+      fprintf(ficlog,"%.3e ",hess[i][j]);
     }
     printf("\n");
+    fprintf(ficlog,"\n");
   }
 
   /* Recompute Inverse */
@@ -1022,8 +1063,10 @@ void hesscov(double **matcov, double p[]
     for (i=1;i<=npar;i++){ 
       y[i][j]=x[i];
       printf("%.3e ",y[i][j]);
+      fprintf(ficlog,"%.3e ",y[i][j]);
     }
     printf("\n");
+    fprintf(ficlog,"\n");
   }
   */
 
@@ -1065,6 +1108,7 @@ double hessii( double x[], double delta,
       
 #ifdef DEBUG
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
+      fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
 #endif
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
@@ -1112,6 +1156,7 @@ double hessij( double x[], double delti[
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
 #ifdef DEBUG
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+    fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
 #endif
   }
   return res;
@@ -1196,6 +1241,7 @@ void  freqsummary(char fileres[], int ag
 {  /* Some frequencies */
   
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;
+  int first;
   double ***freq; /* Frequencies */
   double *pp;
   double pos, k2, dateintsum=0,k2cpt=0;
@@ -1208,6 +1254,7 @@ void  freqsummary(char fileres[], int ag
   strcat(fileresp,fileres);
   if((ficresp=fopen(fileresp,"w"))==NULL) {
     printf("Problem with prevalence resultfile: %s\n", fileresp);
+    fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     exit(0);
   }
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
@@ -1215,7 +1262,9 @@ void  freqsummary(char fileres[], int ag
   
   j=cptcoveff;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-  
+
+  first=1;
+
   for(k1=1; k1<=j;k1++){
     for(i1=1; i1<=ncodemax[k1];i1++){
       j1++;
@@ -1267,10 +1316,15 @@ void  freqsummary(char fileres[], int ag
       fprintf(ficresp, "\n");
       
       for(i=(int)agemin; i <= (int)agemax+3; i++){
-	if(i==(int)agemax+3)
-	  printf("Total");
-	else
-	  printf("Age %d", i);
+	if(i==(int)agemax+3){
+	  fprintf(ficlog,"Total");
+	}else{
+	  if(first==1){
+	    first=0;
+	    printf("See log file for details...\n");
+	  }
+	  fprintf(ficlog,"Age %d", i);
+	}
 	for(jk=1; jk <=nlstate ; jk++){
 	  for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
 	    pp[jk] += freq[jk][m][i]; 
@@ -1278,10 +1332,16 @@ void  freqsummary(char fileres[], int ag
 	for(jk=1; jk <=nlstate ; jk++){
 	  for(m=-1, pos=0; m <=0 ; m++)
 	    pos += freq[jk][m][i];
-	  if(pp[jk]>=1.e-10)
+	  if(pp[jk]>=1.e-10){
+	    if(first==1){
 	    printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-	  else
-	    printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+	    }
+	    fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+	  }else{
+	    if(first==1)
+	      printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+	    fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+	  }
 	}
 
 	for(jk=1; jk <=nlstate ; jk++){
@@ -1292,10 +1352,15 @@ void  freqsummary(char fileres[], int ag
 	for(jk=1,pos=0; jk <=nlstate ; jk++)
 	  pos += pp[jk];
 	for(jk=1; jk <=nlstate ; jk++){
-	  if(pos>=1.e-5)
-	    printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-	  else
-	    printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+	  if(pos>=1.e-5){
+	    if(first==1)
+	      printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+	    fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+	  }else{
+	    if(first==1)
+	      printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+	    fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+	  }
 	  if( i <= (int) agemax){
 	    if(pos>=1.e-5){
 	      fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
@@ -1309,10 +1374,16 @@ void  freqsummary(char fileres[], int ag
 	
 	for(jk=-1; jk <=nlstate+ndeath; jk++)
 	  for(m=-1; m <=nlstate+ndeath; m++)
-	    if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+	    if(freq[jk][m][i] !=0 ) {
+	    if(first==1)
+	      printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+	      fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+	    }
 	if(i <= (int) agemax)
 	  fprintf(ficresp,"\n");
-	printf("\n");
+	if(first==1)
+	  printf("Others in log...\n");
+	fprintf(ficlog,"\n");
       }
     }
   }
@@ -1399,11 +1470,10 @@ void prevalence(int agemin, float agemax
 	      probs[i][jk][j1]= pp[jk]/pos;
 	    }
 	  }
-	}
-	
-      }
-    }
-  }
+	}/* end jk */
+      }/* end i */
+    } /* end i1 */
+  } /* end k1 */
 
   
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
@@ -1425,9 +1495,10 @@ void  concatwav(int wav[], int **dh, int
   int i, mi, m;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
      double sum=0., jmean=0.;*/
-
+  int first;
   int j, k=0,jk, ju, jl;
   double sum=0.;
+  first=0;
   jmin=1e+5;
   jmax=-1;
   jmean=0.;
@@ -1450,8 +1521,15 @@ void  concatwav(int wav[], int **dh, int
     }
 
     wav[i]=mi;
-    if(mi==0)
-      printf("Warning, no any valid information for:%d line=%d\n",num[i],i);
+    if(mi==0){
+      if(first==0){
+	printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
+	first=1;
+      }
+      if(first==1){
+	fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
+      }
+    } /* end mi==0 */
   }
 
   for(i=1; i<=imx; i++){
@@ -1492,7 +1570,9 @@ void  concatwav(int wav[], int **dh, int
   }
   jmean=sum/k;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
+  fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
  }
+
 /*********** Tricode ****************************/
 void tricode(int *Tvar, int **nbcode, int imx)
 {
@@ -1532,9 +1612,9 @@ void tricode(int *Tvar, int **nbcode, in
  for (k=0; k<19; k++) Ndum[k]=0;
 
  for (i=1; i<=ncovmodel-2; i++) {
-      ij=Tvar[i];
-      Ndum[ij]++; 
-    }
+   ij=Tvar[i];
+   Ndum[ij]++; 
+ }
 
  ij=1;
  for (i=1; i<=10; i++) {
@@ -1544,7 +1624,7 @@ void tricode(int *Tvar, int **nbcode, in
    }
  }
  
-    cptcoveff=ij-1;
+ cptcoveff=ij-1;
 }
 
 /*********** Health Expectancies ****************/
@@ -1675,6 +1755,7 @@ void evsij(char fileres[], double ***eij
 	varhe[i][j][(int)age] =0.;
 
      printf("%d|",(int)age);fflush(stdout);
+     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
      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);
@@ -1710,6 +1791,7 @@ void evsij(char fileres[], double ***eij
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }
   printf("\n");
+  fprintf(ficlog,"\n");
 
   free_vector(xp,1,npar);
   free_matrix(dnewm,1,nlstate*2,1,npar);
@@ -1718,20 +1800,71 @@ void evsij(char fileres[], double ***eij
 }
 
 /************ Variance ******************/
-void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)
+void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased)
 {
   /* Variance of health expectancies */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
-  double **newm;
+  /* double **newm;*/
   double **dnewm,**doldm;
+  double **dnewmp,**doldmp;
   int i, j, nhstepm, hstepm, h, nstepm ;
   int k, cptcode;
   double *xp;
-  double **gp, **gm;
-  double ***gradg, ***trgradg;
+  double **gp, **gm;  /* for var eij */
+  double ***gradg, ***trgradg; /*for var eij */
+  double **gradgp, **trgradgp; /* for var p point j */
+  double *gpp, *gmp; /* for var p point j */
+  double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   double ***p3mat;
   double age,agelim, hf;
   int theta;
+  char digit[4];
+  char digitp[16];
+
+  char fileresprobmorprev[FILENAMELENGTH];
+
+  if(popbased==1)
+    strcpy(digitp,"-populbased-");
+  else
+    strcpy(digitp,"-stablbased-");
+
+  strcpy(fileresprobmorprev,"prmorprev"); 
+  sprintf(digit,"%-d",ij);
+  /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
+  strcat(fileresprobmorprev,digit); /* Tvar to be done */
+  strcat(fileresprobmorprev,digitp); /* Popbased or not */
+  strcat(fileresprobmorprev,fileres);
+  if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
+    printf("Problem with resultfile: %s\n", fileresprobmorprev);
+    fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
+  }
+  printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+  fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+  fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");
+  fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
+  for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+    fprintf(ficresprobmorprev," p.%-d SE",j);
+    for(i=1; i<=nlstate;i++)
+      fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
+  }  
+  fprintf(ficresprobmorprev,"\n");
+  if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
+    printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
+    fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
+    exit(0);
+  }
+  else{
+    fprintf(ficgp,"\n# Routine varevsij");
+  }
+  if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
+    printf("Problem with html file: %s\n", optionfilehtm);
+    fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
+    exit(0);
+  }
+  else{
+    fprintf(fichtm,"\n<li><h4> Computing step probabilities of dying and weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
+  }
+  varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
   fprintf(ficresvij,"# Age");
@@ -1743,6 +1876,13 @@ void varevsij(char fileres[], double ***
   xp=vector(1,npar);
   dnewm=matrix(1,nlstate,1,npar);
   doldm=matrix(1,nlstate,1,nlstate);
+  dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
+  doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+
+  gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
+  gpp=vector(nlstate+1,nlstate+ndeath);
+  gmp=vector(nlstate+1,nlstate+ndeath);
+  trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   
   if(estepm < stepm){
     printf ("Problem %d lower than %d\n",estepm, stepm);
@@ -1770,6 +1910,7 @@ void varevsij(char fileres[], double ***
     gp=matrix(0,nhstepm,1,nlstate);
     gm=matrix(0,nhstepm,1,nlstate);
 
+
     for(theta=1; theta <=npar; theta++){
       for(i=1; i<=npar; i++){ /* Computes gradient */
 	xp[i] = x[i] + (i==theta ?delti[theta]:0);
@@ -1788,7 +1929,13 @@ void varevsij(char fileres[], double ***
 	    gp[h][j] += prlim[i][i]*p3mat[i][j][h];
 	}
       }
-    
+      /* This for computing forces of mortality (h=1)as a weighted average */
+      for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
+	for(i=1; i<= nlstate; i++)
+	  gpp[j] += prlim[i][i]*p3mat[i][j][1];
+      }    
+      /* end force of mortality */
+
       for(i=1; i<=npar; i++) /* Computes gradient */
 	xp[i] = x[i] - (i==theta ?delti[theta]:0);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
@@ -1805,20 +1952,34 @@ void varevsij(char fileres[], double ***
 	    gm[h][j] += prlim[i][i]*p3mat[i][j][h];
 	}
       }
+      /* This for computing force of mortality (h=1)as a weighted average */
+      for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
+	for(i=1; i<= nlstate; i++)
+	  gmp[j] += prlim[i][i]*p3mat[i][j][1];
+      }    
+      /* end force of mortality */
 
-      for(j=1; j<= nlstate; j++)
+      for(j=1; j<= nlstate; j++) /* vareij */
 	for(h=0; h<=nhstepm; h++){
 	  gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
 	}
+      for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+	gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
+      }
+
     } /* End theta */
 
-    trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);
+    trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
 
-    for(h=0; h<=nhstepm; h++)
+    for(h=0; h<=nhstepm; h++) /* veij */
       for(j=1; j<=nlstate;j++)
 	for(theta=1; theta <=npar; theta++)
 	  trgradg[h][j][theta]=gradg[h][theta][j];
 
+    for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+      for(theta=1; theta <=npar; theta++)
+	trgradgp[j][theta]=gradgp[theta][j];
+
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     for(i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate;j++)
@@ -1834,6 +1995,37 @@ void varevsij(char fileres[], double ***
       }
     }
 
+    /* pptj */
+    matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
+    matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
+    for(j=nlstate+1;j<=nlstate+ndeath;j++)
+      for(i=nlstate+1;i<=nlstate+ndeath;i++)
+	varppt[j][i]=doldmp[j][i];
+    /* end ppptj */
+    hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
+    prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
+ 
+    if (popbased==1) {
+      for(i=1; i<=nlstate;i++)
+	prlim[i][i]=probs[(int)age][i][ij];
+    }
+    
+    /* This for computing force of mortality (h=1)as a weighted average */
+    for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
+      for(i=1; i<= nlstate; i++)
+	gmp[j] += prlim[i][i]*p3mat[i][j][1];
+    }    
+    /* end force of mortality */
+
+    fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
+    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+      fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
+      for(i=1; i<=nlstate;i++){
+	fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
+      }
+    } 
+    fprintf(ficresprobmorprev,"\n");
+
     fprintf(ficresvij,"%.0f ",age );
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){
@@ -1846,10 +2038,29 @@ void varevsij(char fileres[], double ***
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   } /* End age */
-  
+  free_vector(gpp,nlstate+1,nlstate+ndeath);
+  free_vector(gmp,nlstate+1,nlstate+ndeath);
+  free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
+  free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+  fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
+  /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
+  fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
+  fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);
+  fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);
+  fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);
+  fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
+  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
+  fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
+
   free_vector(xp,1,npar);
-  free_matrix(doldm,1,nlstate,1,npar);
-  free_matrix(dnewm,1,nlstate,1,nlstate);
+  free_matrix(doldm,1,nlstate,1,nlstate);
+  free_matrix(dnewm,1,nlstate,1,npar);
+  free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+  free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
+  free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+  fclose(ficresprobmorprev);
+  fclose(ficgp);
+  fclose(fichtm);
 
 }
 
@@ -1942,7 +2153,7 @@ void varprob(char optionfilefiname[], do
   int i, j=0,  i1, k1, l1, t, tj;
   int k2, l2, j1,  z1;
   int k=0,l, cptcode;
-  int first=1;
+  int first=1, first1;
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;
   double **dnewm,**doldm;
   double *xp;
@@ -1962,20 +2173,26 @@ void varprob(char optionfilefiname[], do
   strcat(fileresprob,fileres);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", fileresprob);
+    fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   }
   strcpy(fileresprobcov,"probcov"); 
   strcat(fileresprobcov,fileres);
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", fileresprobcov);
+    fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   }
   strcpy(fileresprobcor,"probcor"); 
   strcat(fileresprobcor,fileres);
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", fileresprobcor);
+    fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   }
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+  fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+  fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+  fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   fprintf(ficresprob,"# Age");
@@ -2002,6 +2219,7 @@ void varprob(char optionfilefiname[], do
   first=1;
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
+    fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
     exit(0);
   }
   else{
@@ -2009,9 +2227,13 @@ void varprob(char optionfilefiname[], do
   }
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
     printf("Problem with html file: %s\n", optionfilehtm);
+    fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
     exit(0);
   }
   else{
+    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> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
     fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
@@ -2116,6 +2338,7 @@ void varprob(char optionfilefiname[], do
 	/*printf("\n%d ",(int)age);
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+       fprintf(ficlog,"%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);
@@ -2141,7 +2364,20 @@ void varprob(char optionfilefiname[], do
 	  }
 	}/* end of loop for state */
       } /* end of loop for age */
-	/* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+
+      /* Confidence intervalle of pij  */
+      /*
+      fprintf(ficgp,"\nset noparametric;unset label");
+      fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
+      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+      fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
+      fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
+      fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
+      fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
+      */
+
+      /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+      first1=1;
       for (k1=1; k1<=(nlstate);k1++){
 	for (l1=1; l1<=(nlstate+ndeath);l1++){ 
 	  if(l1==k1) continue;
@@ -2161,7 +2397,11 @@ void varprob(char optionfilefiname[], do
 		  /* Computing eigen value of matrix of covariance */
 		  lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));
 		  lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));
-		  printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);
+		  if(first1==1){
+		    first1=0;
+		    printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\nOthers in log...\n",v1,v2,cv12,lc1,lc2);
+		  }
+		  fprintf(ficlog,"Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);
 		  /* Eigen vectors */
 		  v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
 		  v21=sqrt(1.-v11*v11);
@@ -2172,7 +2412,7 @@ void varprob(char optionfilefiname[], do
 		  /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */
 		  if(first==1){
 		    first=0;
-		    fprintf(ficgp,"\nset parametric;set nolabel");
+ 		    fprintf(ficgp,"\nset parametric;set nolabel");
 		    fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);
 		    fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
 		    fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1);
@@ -2180,16 +2420,25 @@ void varprob(char optionfilefiname[], do
 		    fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k2,l2,k1,l1);
 		    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);
 		    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);
-		    fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\
+		    /*		    fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\
 			    mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \
 			    mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);
+		    */
+		    fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
+			    mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \
+			    mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));
 		  }else{
 		    first=0;
 		    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);
 		    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);
+		    /*
 		    fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\
 			    mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \
 			    mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);
+		    */
+		    fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
+			    mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \
+			    mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));
 		  }/* if first */
 		} /* age mod 5 */
 	      } /* end loop age */
@@ -2227,6 +2476,7 @@ void printinghtml(char fileres[], char t
   /*char optionfilehtm[FILENAMELENGTH];*/
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
     printf("Problem with %s \n",optionfilehtm), exit(0);
+    fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
   }
 
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
@@ -2237,6 +2487,44 @@ void printinghtml(char fileres[], char t
    <a href=\"e%s\">e%s</a> <br>\n</li>", \
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
 
+fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
+
+ m=cptcoveff;
+ if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+
+ jj1=0;
+ for(k1=1; k1<=m;k1++){
+   for(i1=1; i1<=ncodemax[k1];i1++){
+     jj1++;
+     if (cptcovn > 0) {
+       fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+       for (cpt=1; cpt<=cptcoveff;cpt++) 
+	 fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+       fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+     }
+     /* Pij */
+     fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>
+<img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
+     /* Quasi-incidences */
+     fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
+<img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
+       /* Stable prevalence in each health state */
+       for(cpt=1; cpt<nlstate;cpt++){
+	 fprintf(fichtm,"<br>- Stable prevalence in each health state : 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,"\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.png<br>
+<img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
+   } /* end i1 */
+ }/* End k1 */
+ fprintf(fichtm,"</ul>");
+
+
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
@@ -2252,7 +2540,7 @@ void printinghtml(char fileres[], char t
 	<br>",fileres,fileres,fileres,fileres);
  else 
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
-fprintf(fichtm," <li><b>Graphs</b></li><p>");
+fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
 
  m=cptcoveff;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
@@ -2267,31 +2555,14 @@ fprintf(fichtm," <li><b>Graphs</b></li><
 	 fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      }
-     /* Pij */
-     fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>
-<img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
-     /* Quasi-incidences */
-     fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
-<img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
-       /* Stable prevalence in each health state */
-       for(cpt=1; cpt<nlstate;cpt++){
-	 fprintf(fichtm,"<br>- Stable prevalence in each health state : 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++) {
+     for(cpt=1; cpt<=nlstate;cpt++) {
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
 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.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.png<br>
-<img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
-   }
- }
+   } /* end i1 */
+ }/* End k1 */
+ fprintf(fichtm,"</ul>");
 fclose(fichtm);
 }
 
@@ -2302,6 +2573,7 @@ void printinggnuplot(char fileres[], dou
   int ng;
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
     printf("Problem with file %s",optionfilegnuplot);
+    fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
   }
 
 #ifdef windows
@@ -2421,7 +2693,6 @@ fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     for(k=1; k <=(nlstate+ndeath); k++){
       if (k != i) {
 	for(j=1; j <=ncovmodel; j++){
-	
 	  fprintf(ficgp,"p%d=%f ",jk,p[jk]);
 	  jk++; 
 	  fprintf(ficgp,"\n");
@@ -2475,10 +2746,10 @@ fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
 	     if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
 	     i=i+ncovmodel;
 	   }
-	 }
-       }
-     }
-   }
+	 } /* end k */
+       } /* end k2 */
+     } /* end jk */
+   } /* end ng */
    fclose(ficgp); 
 }  /* end gnuplot */
 
@@ -2526,8 +2797,10 @@ calagedate=(anproj1+mproj1/12.+jproj1/36
   strcat(fileresf,fileres);
   if((ficresf=fopen(fileresf,"w"))==NULL) {
     printf("Problem with forecast resultfile: %s\n", fileresf);
+    fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
   }
   printf("Computing forecasting: result on file '%s' \n", fileresf);
+  fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
 
   if (cptcoveff==0) ncodemax[cptcoveff]=1;
 
@@ -2630,8 +2903,10 @@ populforecast(char fileres[], double anp
   strcat(filerespop,fileres);
   if((ficrespop=fopen(filerespop,"w"))==NULL) {
     printf("Problem with forecast resultfile: %s\n", filerespop);
+    fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
   }
   printf("Computing forecasting: result on file '%s' \n", filerespop);
+  fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
 
   if (cptcoveff==0) ncodemax[cptcoveff]=1;
 
@@ -2651,6 +2926,7 @@ populforecast(char fileres[], double anp
   if (popforecast==1) {
     if((ficpop=fopen(popfile,"r"))==NULL) {
       printf("Problem with population file : %s\n",popfile);exit(0);
+      fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
     } 
     popage=ivector(0,AGESUP);
     popeffectif=vector(0,AGESUP);
@@ -2779,7 +3055,7 @@ int main(int argc, char *argv[])
   double ***p3mat;
   int *indx;
   char line[MAXLINE], linepar[MAXLINE];
-  char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
+  char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
   int firstobs=1, lastobs=10;
   int sdeb, sfin; /* Status at beginning and end */
   int c,  h , cpt,l;
@@ -2840,6 +3116,20 @@ int main(int argc, char *argv[])
 
 /*-------- arguments in the command line --------*/
 
+  /* Log file */
+  strcat(filelog, optionfilefiname);
+  strcat(filelog,".log");    /* */
+  if((ficlog=fopen(filelog,"w"))==NULL)    {
+    printf("Problem with logfile %s\n",filelog);
+    goto end;
+  }
+  fprintf(ficlog,"Log filename:%s\n",filelog);
+  fprintf(ficlog,"\n%s",version);
+  fprintf(ficlog,"\nEnter the parameter file name: ");
+  fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+  fflush(ficlog);
+
+  /* */
   strcpy(fileres,"r");
   strcat(fileres, optionfilefiname);
   strcat(fileres,".txt");    /* Other files have txt extension */
@@ -2848,13 +3138,16 @@ int main(int argc, char *argv[])
 
   if((ficpar=fopen(optionfile,"r"))==NULL)    {
     printf("Problem with optionfile %s\n",optionfile);
+    fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
     goto end;
   }
 
   strcpy(filereso,"o");
   strcat(filereso,fileres);
   if((ficparo=fopen(filereso,"w"))==NULL) {
-    printf("Problem with Output resultfile: %s\n", filereso);goto end;
+    printf("Problem with Output resultfile: %s\n", filereso);
+    fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+    goto end;
   }
 
   /* Reads comments: lines beginning with '#' */
@@ -2866,7 +3159,7 @@ int main(int argc, char *argv[])
   }
   ungetc(c,ficpar);
 
-  fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
+  fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
 while((c=getc(ficpar))=='#' && c!= EOF){
@@ -2900,14 +3193,23 @@ while((c=getc(ficpar))=='#' && c!= EOF){
     for(j=1; j <=nlstate+ndeath-1; j++){
       fscanf(ficpar,"%1d%1d",&i1,&j1);
       fprintf(ficparo,"%1d%1d",i1,j1);
-      printf("%1d%1d",i,j);
+      if(mle==1)
+	printf("%1d%1d",i,j);
+      fprintf(ficlog,"%1d%1d",i,j);
       for(k=1; k<=ncovmodel;k++){
 	fscanf(ficpar," %lf",&param[i][j][k]);
-	printf(" %lf",param[i][j][k]);
+	if(mle==1){
+	  printf(" %lf",param[i][j][k]);
+	  fprintf(ficlog," %lf",param[i][j][k]);
+	}
+	else
+	  fprintf(ficlog," %lf",param[i][j][k]);
 	fprintf(ficparo," %lf",param[i][j][k]);
       }
       fscanf(ficpar,"\n");
-      printf("\n");
+      if(mle==1)
+	printf("\n");
+      fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
   
@@ -2955,22 +3257,33 @@ while((c=getc(ficpar))=='#' && c!= EOF){
   matcov=matrix(1,npar,1,npar);
   for(i=1; i <=npar; i++){
     fscanf(ficpar,"%s",&str);
-    printf("%s",str);
+    if(mle==1)
+      printf("%s",str);
+    fprintf(ficlog,"%s",str);
     fprintf(ficparo,"%s",str);
     for(j=1; j <=i; j++){
       fscanf(ficpar," %le",&matcov[i][j]);
-      printf(" %.5le",matcov[i][j]);
+      if(mle==1){
+	printf(" %.5le",matcov[i][j]);
+	fprintf(ficlog," %.5le",matcov[i][j]);
+      }
+      else
+	fprintf(ficlog," %.5le",matcov[i][j]);
       fprintf(ficparo," %.5le",matcov[i][j]);
     }
     fscanf(ficpar,"\n");
-    printf("\n");
+    if(mle==1)
+      printf("\n");
+    fprintf(ficlog,"\n");
     fprintf(ficparo,"\n");
   }
   for(i=1; i <=npar; i++)
     for(j=i+1;j<=npar;j++)
       matcov[i][j]=matcov[j][i];
    
-  printf("\n");
+  if(mle==1)
+    printf("\n");
+  fprintf(ficlog,"\n");
 
 
     /*-------- Rewriting paramater file ----------*/
@@ -2980,12 +3293,14 @@ while((c=getc(ficpar))=='#' && c!= EOF){
      strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
+      fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
     
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
+      fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
 
     n= lastobs;
@@ -3051,7 +3366,7 @@ while((c=getc(ficpar))=='#' && c!= EOF){
   
  
   /* Calculation of the number of parameter from char model*/
-  Tvar=ivector(1,15); 
+  Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
   Tprod=ivector(1,15); 
   Tvaraff=ivector(1,15); 
   Tvard=imatrix(1,15,1,2);
@@ -3067,38 +3382,39 @@ while((c=getc(ficpar))=='#' && c!= EOF){
     strcpy(modelsav,model); 
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
       printf("Error. Non available option model=%s ",model);
+      fprintf(ficlog,"Error. Non available option model=%s ",model);
       goto end;
     }
     
     for(i=(j+1); i>=1;i--){
-      cutv(stra,strb,modelsav,'+');
-      if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); 
+      cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
+      if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
       /*scanf("%d",i);*/
-      if (strchr(strb,'*')) {
-	cutv(strd,strc,strb,'*');
-	if (strcmp(strc,"age")==0) {
+      if (strchr(strb,'*')) {  /* Model includes a product */
+	cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
+	if (strcmp(strc,"age")==0) { /* Vn*age */
 	  cptcovprod--;
 	  cutv(strb,stre,strd,'V');
-	  Tvar[i]=atoi(stre);
+	  Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
 	  cptcovage++;
 	    Tage[cptcovage]=i;
 	    /*printf("stre=%s ", stre);*/
 	}
-	else if (strcmp(strd,"age")==0) {
+	else if (strcmp(strd,"age")==0) { /* or age*Vn */
 	  cptcovprod--;
 	  cutv(strb,stre,strc,'V');
 	  Tvar[i]=atoi(stre);
 	  cptcovage++;
 	  Tage[cptcovage]=i;
 	}
-	else {
-	  cutv(strb,stre,strc,'V');
+	else {  /* Age is not in the model */
+	  cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
 	  Tvar[i]=ncovcol+k1;
-	  cutv(strb,strc,strd,'V'); 
+	  cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
 	  Tprod[k1]=i;
-	  Tvard[k1][1]=atoi(strc);
-	  Tvard[k1][2]=atoi(stre);
+	  Tvard[k1][1]=atoi(strc); /* m*/
+	  Tvard[k1][2]=atoi(stre); /* n */
 	  Tvar[cptcovn+k2]=Tvard[k1][1];
 	  Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
 	  for (k=1; k<=lastobs;k++) 
@@ -3107,7 +3423,7 @@ while((c=getc(ficpar))=='#' && c!= EOF){
 	  k2=k2+2;
 	}
       }
-      else {
+      else { /* no more sum */
 	/*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
        /*  scanf("%d",i);*/
       cutv(strd,strc,strb,'V');
@@ -3116,11 +3432,12 @@ while((c=getc(ficpar))=='#' && c!= EOF){
       strcpy(modelsav,stra);  
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
 	scanf("%d",i);*/
-    }
-}
+    } /* end of loop + */
+  } /* end model */
   
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
   printf("cptcovprod=%d ", cptcovprod);
+  fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   scanf("%d ",i);*/
     fclose(fic);
 
@@ -3153,6 +3470,7 @@ while((c=getc(ficpar))=='#' && c!= EOF){
 	   else {
 	      if (andc[i]!=9999){
 	      printf("Warning negative age at death: %d line:%d\n",num[i],i);
+	      fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
 	      agev[m][i]=-1;
 	      }
 	    }
@@ -3185,13 +3503,15 @@ while((c=getc(ficpar))=='#' && c!= EOF){
     for (i=1; i<=imx; i++)  {
       for(m=1; (m<= maxwav); m++){
 	if (s[m][i] > (nlstate+ndeath)) {
-	  printf("Error: Wrong value in nlstate or ndeath\n");	
+	  printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);	
+	  fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);	
 	  goto end;
 	}
       }
     }
 
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+ fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
 
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
@@ -3267,102 +3587,118 @@ printf("Total number of individuals= %d,
    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(mle==1){
-    /* Computing hessian and covariance matrix */
-    ftolhess=ftol; /* Usually correct */
-    hesscov(matcov, p, npar, delti, ftolhess, func);
- }
-    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
-    printf("# Scales (for hessian or gradient estimation)\n");
-     for(i=1,jk=1; i <=nlstate; i++){
-      for(j=1; j <=nlstate+ndeath; j++){
-	if (j!=i) {
-	  fprintf(ficres,"%1d%1d",i,j);
-	  printf("%1d%1d",i,j);
-	  for(k=1; k<=ncovmodel;k++){
-	    printf(" %.5e",delti[jk]);
-	    fprintf(ficres," %.5e",delti[jk]);
-	    jk++;
-	  }
-	  printf("\n");
-	  fprintf(ficres,"\n");
-	}
-      }
+   if(mle==1){
+     /* Computing hessian and covariance matrix */
+     ftolhess=ftol; /* Usually correct */
+     hesscov(matcov, p, npar, delti, ftolhess, func);
+   }
+   fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+   printf("# Scales (for hessian or gradient estimation)\n");
+   fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+   for(i=1,jk=1; i <=nlstate; i++){
+     for(j=1; j <=nlstate+ndeath; j++){
+       if (j!=i) {
+	 fprintf(ficres,"%1d%1d",i,j);
+	 printf("%1d%1d",i,j);
+	 fprintf(ficlog,"%1d%1d",i,j);
+	 for(k=1; k<=ncovmodel;k++){
+	   printf(" %.5e",delti[jk]);
+	   fprintf(ficlog," %.5e",delti[jk]);
+	   fprintf(ficres," %.5e",delti[jk]);
+	   jk++;
+	 }
+	 printf("\n");
+	 fprintf(ficlog,"\n");
+	 fprintf(ficres,"\n");
+       }
      }
-    
-    k=1;
-    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");
-    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");
-    for(i=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);
-      printf("%3d",i);
-      for(j=1; j<=i;j++){
-	fprintf(ficres," %.5e",matcov[i][j]);
-	printf(" %.5e",matcov[i][j]);
-      }
-      fprintf(ficres,"\n");
-      printf("\n");
-      k++;
-    }
-    
-    while((c=getc(ficpar))=='#' && c!= EOF){
-      ungetc(c,ficpar);
-      fgets(line, MAXLINE, ficpar);
-      puts(line);
-      fputs(line,ficparo);
-    }
-    ungetc(c,ficpar);
-    estepm=0;
-    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
-    if (estepm==0 || estepm < stepm) estepm=stepm;
-    if (fage <= 2) {
-      bage = ageminpar;
-      fage = agemaxpar;
-    }
-    
-    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
-    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
-    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
- 
-    while((c=getc(ficpar))=='#' && c!= EOF){
-    ungetc(c,ficpar);
-    fgets(line, MAXLINE, ficpar);
-    puts(line);
-    fputs(line,ficparo);
-  }
-  ungetc(c,ficpar);
+   }
+   
+   k=1;
+   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)
+     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;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++;
+   }
+   
+   while((c=getc(ficpar))=='#' && c!= EOF){
+     ungetc(c,ficpar);
+     fgets(line, MAXLINE, ficpar);
+     puts(line);
+     fputs(line,ficparo);
+   }
+   ungetc(c,ficpar);
+   estepm=0;
+   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+   if (estepm==0 || estepm < stepm) estepm=stepm;
+   if (fage <= 2) {
+     bage = ageminpar;
+     fage = agemaxpar;
+   }
+   
+   fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
+   fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+   
+   while((c=getc(ficpar))=='#' && c!= EOF){
+     ungetc(c,ficpar);
+     fgets(line, MAXLINE, ficpar);
+     puts(line);
+     fputs(line,ficparo);
+   }
+   ungetc(c,ficpar);
   
-  fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);
-  fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
- fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
-     
-  while((c=getc(ficpar))=='#' && c!= EOF){
-    ungetc(c,ficpar);
-    fgets(line, MAXLINE, ficpar);
-    puts(line);
-    fputs(line,ficparo);
-  }
-  ungetc(c,ficpar);
+   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);
+   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
+   fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
+   
+   while((c=getc(ficpar))=='#' && c!= EOF){
+     ungetc(c,ficpar);
+     fgets(line, MAXLINE, ficpar);
+     puts(line);
+     fputs(line,ficparo);
+   }
+   ungetc(c,ficpar);
  
 
    dateprev1=anprev1+mprev1/12.+jprev1/365.;
@@ -3423,7 +3759,8 @@ Interval (in months) between two waves:
 <hr  size=\"2\" color=\"#EC5E5E\">
  <ul><li><h4>Parameter files</h4>\n
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
- - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);
+ - Log file of the run: <a href=\"%s\">%s</a><br>\n
+ - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
   fclose(fichtm);
 
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
@@ -3447,8 +3784,10 @@ Interval (in months) between two waves:
   strcat(filerespl,fileres);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;
+    fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;
   }
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);
+  fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);
   fprintf(ficrespl,"#Prevalence limit\n");
   fprintf(ficrespl,"#Age ");
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
@@ -3472,9 +3811,16 @@ Interval (in months) between two waves:
 	k=k+1;
 	/*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
 	fprintf(ficrespl,"\n#******");
-	for(j=1;j<=cptcoveff;j++) 
+	printf("\n#******");
+	fprintf(ficlog,"\n#******");
+	for(j=1;j<=cptcoveff;j++) {
 	  fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+	  printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+	  fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+	}
 	fprintf(ficrespl,"******\n");
+	printf("******\n");
+	fprintf(ficlog,"******\n");
 	
 	for (age=agebase; age<=agelim; age++){
 	  prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
@@ -3492,8 +3838,10 @@ Interval (in months) between two waves:
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
+    fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
   }
   printf("Computing pij: result on file '%s' \n", filerespij);
+  fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;
   /*if (stepm<=24) stepsize=2;*/
@@ -3553,6 +3901,7 @@ Interval (in months) between two waves:
   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);
+    fprintf(ficlog,"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);
   }
   
 
@@ -3562,30 +3911,36 @@ Interval (in months) between two waves:
   strcat(filerest,fileres);
   if((ficrest=fopen(filerest,"w"))==NULL) {
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+    fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
   }
   printf("Computing Total LEs with variances: file '%s' \n", filerest); 
+  fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
 
 
   strcpy(filerese,"e");
   strcat(filerese,fileres);
   if((ficreseij=fopen(filerese,"w"))==NULL) {
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+    fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
   }
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+  fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
 
- strcpy(fileresv,"v");
+  strcpy(fileresv,"v");
   strcat(fileresv,fileres);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+    fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
   }
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+  fprintf(ficlog,"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);
+  prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
 
   k=0;
   for(cptcov=1;cptcov<=i1;cptcov++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-      k=k+1;
+      k=k+1; 
       fprintf(ficrest,"\n#****** ");
       for(j=1;j<=cptcoveff;j++) 
 	fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
@@ -3607,8 +3962,10 @@ prevalence(ageminpar, agemax, s, agev, n
  
       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);
-    
+      varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);
+      if(popbased==1){
+	varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);
+       }
 
  
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
@@ -3701,9 +4058,15 @@ free_matrix(mint,1,maxwav,1,n);
   fclose(ficgp);
   
 
-  if(erreur >0)
+  if(erreur >0){
     printf("End of Imach with error or warning %d\n",erreur);
-  else   printf("End of Imach\n");
+    fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
+  }else{
+   printf("End of Imach\n");
+   fprintf(ficlog,"End of Imach\n");
+  }
+  printf("See log file on %s\n",filelog);
+  fclose(ficlog);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
   
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/