--- imach/src/imach.c	2002/03/12 22:13:38	1.33
+++ imach/src/imach.c	2002/07/19 12:22:25	1.51
@@ -1,4 +1,4 @@
-/* $Id: imach.c,v 1.33 2002/03/12 22:13:38 brouard Exp $
+/* $Id: imach.c,v 1.51 2002/07/19 12:22:25 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 +56,8 @@
 #include <unistd.h>
 
 #define MAXLINE 256
-#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"
+#define GNUPLOTPROGRAM "gnuplot"
+/*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define FILENAMELENGTH 80
 /*#define DEBUG*/
 #define windows
@@ -74,15 +75,22 @@
 #define YEARM 12. /* Number of months per year */
 #define AGESUP 130
 #define AGEBASE 40
+#ifdef windows
+#define DIRSEPARATOR '\\'
+#define ODIRSEPARATOR '/'
+#else
+#define DIRSEPARATOR '/'
+#define ODIRSEPARATOR '\\'
+#endif
 
-
+char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";
 int erreur; /* Error number */
 int nvar;
-int cptcovn, cptcovage=0, cptcoveff=0,cptcov;
+int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 int npar=NPARMAX;
 int nlstate=2; /* Number of live states */
 int ndeath=1; /* Number of dead states */
-int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
+int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 int popbased=0;
 
 int *wav; /* Number of waves for this individuual 0 is possible */
@@ -95,13 +103,27 @@ 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 *ficgp,*ficresprob,*ficpop;
+FILE *ficlog;
+FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
+FILE *ficresprobmorprev;
+FILE *fichtm; /* Html File */
 FILE *ficreseij;
-  char filerese[FILENAMELENGTH];
- FILE  *ficresvij;
-  char fileresv[FILENAMELENGTH];
- FILE  *ficresvpl;
-  char fileresvpl[FILENAMELENGTH];
+char filerese[FILENAMELENGTH];
+FILE  *ficresvij;
+char fileresv[FILENAMELENGTH];
+FILE  *ficresvpl;
+char fileresvpl[FILENAMELENGTH];
+char title[MAXLINE];
+char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+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];
+
+char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
 
 #define NR_END 1
 #define FREE_ARG char*
@@ -135,6 +157,9 @@ int imx;
 int stepm;
 /* Stepm, step in month: minimum step interpolation*/
 
+int estepm;
+/* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
+
 int m,nb;
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
@@ -157,12 +182,10 @@ static	int split( char *path, char *dirc
 
    l1 = strlen( path );			/* length of path */
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
-#ifdef windows
-   s = strrchr( path, '\\' );		/* find last / */
-#else
-   s = strrchr( path, '/' );		/* find last / */
-#endif
+   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( );
 
@@ -228,6 +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++) {
@@ -424,8 +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))){ 
@@ -550,6 +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; 
@@ -580,16 +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)); 
@@ -597,13 +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))) {
@@ -612,15 +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
 
@@ -648,9 +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
       } 
     } 
@@ -686,16 +735,15 @@ double **prevalim(double **prlim, int nl
   
       for (k=1; k<=cptcovn;k++) {
 	cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-	/*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/
+	/*	printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
       }
-      for (k=1; k<=cptcovage;k++)
-	cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+      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]]];
 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
-
+      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
 
     savm=oldm;
@@ -922,10 +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));
 
 }
@@ -946,8 +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]);*/
@@ -957,6 +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]);*/
@@ -964,8 +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);
@@ -985,11 +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 */
@@ -1006,8 +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");
   }
   */
 
@@ -1049,6 +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.)){
@@ -1096,6 +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;
@@ -1178,131 +1239,160 @@ void lubksb(double **a, int n, int *indx
 /************ Frequencies ********************/
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
 {  /* 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;
   FILE *ficresp;
   char fileresp[FILENAMELENGTH];
- 
+  
   pp=vector(1,nlstate);
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   strcpy(fileresp,"p");
   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);
   j1=0;
-
+  
   j=cptcoveff;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}
 
-  for(k1=1; k1<=j;k1++){
-   for(i1=1; i1<=ncodemax[k1];i1++){
-       j1++;
-       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
-	 scanf("%d", i);*/
-        for (i=-1; i<=nlstate+ndeath; i++)  
-	 for (jk=-1; jk<=nlstate+ndeath; jk++)  
-	   for(m=agemin; m <= agemax+3; m++)
-	     freq[i][jk][m]=0;
-
-	dateintsum=0;
-	k2cpt=0;
-       for (i=1; i<=imx; i++) {
-	 bool=1;
-	 if  (cptcovn>0) {
-	   for (z1=1; z1<=cptcoveff; z1++) 
-	     if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
-	       bool=0;
-	 }
-	 if (bool==1) {
-	   for(m=firstpass; m<=lastpass; m++){
-	     k2=anint[m][i]+(mint[m][i]/12.);
-	     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;
-	       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];
-	       if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
-		 dateintsum=dateintsum+k2;
-		 k2cpt++;
-	       }
+  first=1;
 
-	     }
-	   }
-	 }
-       }
-       
-       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
-
-        if  (cptcovn>0) {
-	 fprintf(ficresp, "\n#********** Variable "); 
-	 for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-       fprintf(ficresp, "**********\n#");
-	}
-       for(i=1; i<=nlstate;i++) 
-	 fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
-       fprintf(ficresp, "\n");
+  for(k1=1; k1<=j;k1++){
+    for(i1=1; i1<=ncodemax[k1];i1++){
+      j1++;
+      /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+	scanf("%d", i);*/
+      for (i=-1; i<=nlstate+ndeath; i++)  
+	for (jk=-1; jk<=nlstate+ndeath; jk++)  
+	  for(m=agemin; m <= agemax+3; m++)
+	    freq[i][jk][m]=0;
+      
+      dateintsum=0;
+      k2cpt=0;
+      for (i=1; i<=imx; i++) {
+	bool=1;
+	if  (cptcovn>0) {
+	  for (z1=1; z1<=cptcoveff; z1++) 
+	    if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
+	      bool=0;
+	}
+	if (bool==1) {
+	  for(m=firstpass; m<=lastpass; m++){
+	    k2=anint[m][i]+(mint[m][i]/12.);
+	    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]] += weight[i];
+		freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
+	      }
+	      
+	      if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
+		dateintsum=dateintsum+k2;
+		k2cpt++;
+	      }
+	    }
+	  }
+	}
+      }
        
-  for(i=(int)agemin; i <= (int)agemax+3; i++){
-    if(i==(int)agemax+3)
-      printf("Total");
-    else
-      printf("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]; 
-    }
-    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)
-	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(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
 
-     for(jk=1; jk <=nlstate ; jk++){
-      for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
-	pp[jk] += freq[jk][m][i];
-     }
+      if  (cptcovn>0) {
+	fprintf(ficresp, "\n#********** Variable "); 
+	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+	fprintf(ficresp, "**********\n#");
+      }
+      for(i=1; i<=nlstate;i++) 
+	fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+      fprintf(ficresp, "\n");
+      
+      for(i=(int)agemin; i <= (int)agemax+3; 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]; 
+	}
+	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(first==1){
+	    printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[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,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( i <= (int) agemax){
-	if(pos>=1.e-5){
-	  fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
-	  probs[i][jk][j1]= pp[jk]/pos;
-	  /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
+	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(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);
+	      probs[i][jk][j1]= pp[jk]/pos;
+	      /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
+	    }
+	    else
+	      fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
+	  }
 	}
-      else
-	  fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
+	
+	for(jk=-1; jk <=nlstate+ndeath; jk++)
+	  for(m=-1; m <=nlstate+ndeath; m++)
+	    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");
+	if(first==1)
+	  printf("Others in log...\n");
+	fprintf(ficlog,"\n");
       }
     }
-    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(i <= (int) agemax)
-      fprintf(ficresp,"\n");
-    printf("\n");
-    }
-    }
- }
+  }
   dateintmean=dateintsum/k2cpt; 
  
   fclose(ficresp);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
   free_vector(pp,1,nlstate);
-
+  
   /* End of Freq */
 }
 
@@ -1324,10 +1414,10 @@ 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++)
@@ -1346,41 +1436,45 @@ 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;
-	      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;
+	    }
+	  }
+	}/* end jk */
+      }/* end i */
+    } /* end i1 */
+  } /* end k1 */
+
   
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
   free_vector(pp,1,nlstate);
@@ -1401,9 +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.;
@@ -1426,8 +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++){
@@ -1468,7 +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)
 {
@@ -1497,6 +1601,7 @@ void tricode(int *Tvar, int **nbcode, in
       for (k=0; k<=19; k++) {
 	if (Ndum[k] != 0) {
 	  nbcode[Tvar[j]][ij]=k; 
+	  
 	  ij++;
 	}
 	if (ij > ncodemax[j]) break; 
@@ -1507,52 +1612,76 @@ 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++) {
-   if((Ndum[i]!=0) && (i<=ncov)){
+   if((Ndum[i]!=0) && (i<=ncovcol)){
      Tvaraff[ij]=i; 
      ij++;
    }
  }
  
-    cptcoveff=ij-1;
+ cptcoveff=ij-1;
 }
 
 /*********** Health Expectancies ****************/
 
-void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)
+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, k;
-  double age, agelim,hf;
-  double ***p3mat;
+  int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
+  double age, agelim, hf;
+  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");
 
-  k=1;             /* For example stepm=6 months */
-  hstepm=k*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */
-  hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */
+  if(estepm < stepm){
+    printf ("Problem %d lower than %d\n",estepm, stepm);
+  }
+  else  hstepm=estepm;   
+  /* We compute the life expectancy from trapezoids spaced every estepm months
+   * This is mainly to measure the difference between two models: for example
+   * if stepm=24 months pijx are given only every 2 years and by summing them
+   * we are calculating an estimate of the Life Expectancy assuming a linear 
+   * progression inbetween and thus overestimating or underestimating according
+   * to the curvature of the survival function. If, for the same date, we 
+   * estimate the model with stepm=1 month, we can keep estepm to 24 months
+   * to compare the new estimate of Life expectancy with the same linear 
+   * hypothesis. A more precise result, taking into account a more precise
+   * curvature will be obtained if estepm is as small as stepm. */
+
+  /* For example we decided to compute the life expectancy with the smallest unit */
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
      nhstepm is the number of hstepm from age to agelim 
      nstepm is the number of stepm from age to agelin. 
      Look at hpijx to understand the reason of that which relies in memory size
-     and note for a fixed period like k years */
+     and note for a fixed period like estepm months */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
      survival function given by stepm (the optimization length). Unfortunately it
      means that if the survival funtion is printed only each two years of age and if
      you sum them up and add 1 year (area under the trapezoids) you won't get the same 
      results. So we changed our mind and took the option of the best precision.
   */
-  hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */ 
+  hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 
   agelim=AGESUP;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
@@ -1562,43 +1691,182 @@ 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);
+     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);
+	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);
   }
+  printf("\n");
+  fprintf(ficlog,"\n");
+
+  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 ******************/
-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)
+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;
-  int i, j, nhstepm, hstepm, h;
+  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;
+  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,"# Covariances of life expectancies\n");
+  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");
   for(i=1; i<=nlstate;i++)
     for(j=1; j<=nlstate;j++)
@@ -1608,19 +1876,41 @@ 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*/
   
-  hstepm=1*YEARM; /* Every year of age */
-  hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
+  if(estepm < stepm){
+    printf ("Problem %d lower than %d\n",estepm, stepm);
+  }
+  else  hstepm=estepm;   
+  /* For example we decided to compute the life expectancy with the smallest unit */
+  /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
+     nhstepm is the number of hstepm from age to agelim 
+     nstepm is the number of stepm from age to agelin. 
+     Look at hpijx to understand the reason of that which relies in memory size
+     and note for a fixed period like k years */
+  /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+     survival function given by stepm (the optimization length). Unfortunately it
+     means that if the survival funtion is printed only each two years of age and if
+     you sum them up and add 1 year (area under the trapezoids) you won't get the same 
+     results. So we changed our mind and took the option of the best precision.
+  */
+  hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   agelim = AGESUP;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-    nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
-    if (stepm >= YEARM) hstepm=1;
-    nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+    nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
+    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);
     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);
@@ -1639,7 +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);  
@@ -1656,38 +1952,84 @@ 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++)
 	vareij[i][j][(int)age] =0.;
+
     for(h=0;h<=nhstepm;h++){
       for(k=0;k<=nhstepm;k++){
 	matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
 	matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
 	for(i=1;i<=nlstate;i++)
 	  for(j=1;j<=nlstate;j++)
-	    vareij[i][j][(int)age] += doldm[i][j];
+	    vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       }
     }
-    h=1;
-    if (stepm >= YEARM) h=stepm/YEARM;
+
+    /* 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++){
-	fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);
+	fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       }
     fprintf(ficresvij,"\n");
     free_matrix(gp,0,nhstepm,1,nlstate);
@@ -1696,10 +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);
 
 }
 
@@ -1718,7 +2079,7 @@ void varprevlim(char fileres[], double *
   double age,agelim;
   int theta;
    
-  fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");
+  fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");
   fprintf(ficresvpl,"# Age");
   for(i=1; i<=nlstate;i++)
       fprintf(ficresvpl," %1d-%1d",i,i);
@@ -1787,143 +2148,340 @@ 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 optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
 {
-  int i, j;
-  int k=0, cptcode;
+  int i, j=0,  i1, k1, l1, t, tj;
+  int k2, l2, j1,  z1;
+  int k=0,l, cptcode;
+  int first=1, first1;
+  double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   double **dnewm,**doldm;
   double *xp;
   double *gp, *gm;
   double **gradg, **trgradg;
+  double **mu;
   double age,agelim, cov[NCOVMAX];
+  double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   int theta;
   char fileresprob[FILENAMELENGTH];
+  char fileresprobcov[FILENAMELENGTH];
+  char fileresprobcor[FILENAMELENGTH];
+
+  double ***varpij;
 
   strcpy(fileresprob,"prob"); 
   strcat(fileresprob,fileres);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", fileresprob);
+    fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   }
-  printf("Computing variance of one-step probabilities: result on file '%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");
+  fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
+  fprintf(ficresprobcov,"# Age");
+  fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+  fprintf(ficresprobcov,"# Age");
+
 
+  for(i=1; i<=nlstate;i++)
+    for(j=1; j<=(nlstate+ndeath);j++){
+      fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+      fprintf(ficresprobcov," p%1d-%1d ",i,j);
+      fprintf(ficresprobcor," p%1d-%1d ",i,j);
+    }  
+  fprintf(ficresprob,"\n");
+  fprintf(ficresprobcov,"\n");
+  fprintf(ficresprobcor,"\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));
-    
-    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];
-	}
-      }
+  dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+  doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+  mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
+  varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
+  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{
+    fprintf(ficgp,"\n# Routine varprob");
+  }
+  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");
 
-      for(i=1; i<=npar; i++)
-	xp[i] = x[i] - (i==theta ?delti[theta]:0);
-    
+    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");
 
-      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);
+  cov[1]=1;
+  tj=cptcoveff;
+  if (cptcovn<1) {tj=1;ncodemax[1]=1;}
+  j1=0;
+  for(t=1; t<=tj;t++){
+    for(i1=1; i1<=ncodemax[t];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#");
+	fprintf(ficresprobcov, "\n#********** Variable "); 
+	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+	fprintf(ficresprobcov, "**********\n#");
+	
+	fprintf(ficgp, "\n#********** Variable "); 
+	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+	fprintf(ficgp, "**********\n#");
+	
+	
+	fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
+	for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+	fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+	
+	fprintf(ficresprobcor, "\n#********** Variable ");    
+	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+	fprintf(ficgp, "**********\n#");    
+      }
+      
+      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 (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,(nlstate)*(nlstate+ndeath));
+	trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+	gp=vector(1,(nlstate)*(nlstate+ndeath));
+	gm=vector(1,(nlstate)*(nlstate+ndeath));
+    
+	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); 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); i++){
+	    for(j=1; j<=(nlstate+ndeath);j++){
+	      k=k+1;
+	      gm[k]=pmmij[i][j];
+	    }
+	  }
+     
+	  for(i=1; i<= (nlstate)*(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)*(nlstate+ndeath);j++)
+	  for(theta=1; theta <=npar; theta++)
+	    trgradg[j][theta]=gradg[theta][j];
+	
+	matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
+	matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
+	
+	pmij(pmmij,cov,ncovmodel,x,nlstate);
+	
+	k=0;
+	for(i=1; i<=(nlstate); i++){
+	  for(j=1; j<=(nlstate+ndeath);j++){
+	    k=k+1;
+	    mu[k][(int) age]=pmmij[i][j];
+	  }
 	}
-     }
-     
-     /*printf("\n%d ",(int)age);
-     for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
-       
+     	for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
+	  for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
+	    varpij[i][j][(int)age] = doldm[i][j];
 
+	/*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);
-
-  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);
+	fprintf(ficresprobcov,"\n%d ",(int)age);
+	fprintf(ficresprobcor,"\n%d ",(int)age);
+
+	for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
+	  fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
+	for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+	  fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
+	  fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
+	}
+	i=0;
+	for (k=1; k<=(nlstate);k++){
+ 	  for (l=1; l<=(nlstate+ndeath);l++){ 
+ 	    i=i++;
+	    fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
+	    fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
+	    for (j=1; j<=i;j++){
+	      fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
+	      fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
+	    }
+	  }
+	}/* end of loop for state */
+      } /* end of loop for age */
 
+      /* 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 (k2=1; k2<=(nlstate);k2++){
+	for (l2=1; l2<=(nlstate+ndeath);l2++){ 
+	  if(l2==k2) continue;
+	  j=(k2-1)*(nlstate+ndeath)+l2;
+	  for (k1=1; k1<=(nlstate);k1++){
+	    for (l1=1; l1<=(nlstate+ndeath);l1++){ 
+	      if(l1==k1) continue;
+	      i=(k1-1)*(nlstate+ndeath)+l1;
+	      if(i<=j) continue;
+	      for (age=bage; age<=fage; age ++){ 
+		if ((int)age %5==0){
+		  v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
+		  v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+		  cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+		  mu1=mu[i][(int) age]/stepm*YEARM ;
+		  mu2=mu[j][(int) age]/stepm*YEARM;
+		  c12=cv12/sqrt(v1*v2);
+		  /* Computing eigen value of matrix of covariance */
+		  lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+		  lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+		  /* Eigen vectors */
+		  v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+		  /*v21=sqrt(1.-v11*v11); *//* error */
+		  v21=(lc1-v1)/cv12*v11;
+		  v12=-v21;
+		  v22=v11;
+		  tnalp=v21/v11;
+		  if(first1==1){
+		    first1=0;
+		    printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+		  }
+		  fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+		  /*printf(fignu*/
+		  /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+		  /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+		  if(first==1){
+		    first=0;
+ 		    fprintf(ficgp,"\nset parametric;unset label");
+		    fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
+		    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>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
+		    fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
+		    fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
+		    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+		    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+		    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",\
+			    mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+			    mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+		  }else{
+		    first=0;
+		    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+		    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+		    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",\
+			    mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+			    mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+		  }/* if first */
+		} /* age mod 5 */
+	      } /* end loop age */
+	      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
+	      first=1;
+	    } /*l12 */
+	  } /* k12 */
+	} /*l1 */
+      }/* k1 */
+    } /* loop covariates */
+    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     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);
+  fclose(ficresprobcov);
+  fclose(ficresprobcor);
+  fclose(ficgp);
+  fclose(fichtm);
 }
- free_vector(xp,1,npar);
-fclose(ficresprob);
 
-}
 
 /******************* Printing html file ***********/
-void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[],char rfileres[] ){
+void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+		  int lastpass, int stepm, int weightopt, char model[],\
+		  int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
+		  int popforecast, int estepm ,\
+		  double jprev1, double mprev1,double anprev1, \
+		  double jprev2, double mprev2,double anprev2){
   int jj1, k1, i1, cpt;
-  FILE *fichtm;
   /*char optionfilehtm[FILENAMELENGTH];*/
-
-  strcpy(optionfilehtm,optionfile);
-  strcat(optionfilehtm,".htm");
-  if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+  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,"<body><ul> <font size=\"6\">Imach, Version 0.71e </font> <hr size=\"2\" color=\"#EC5E5E\"> 
-Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>
+   fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
+ - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
+ - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
+ - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
+ - Life expectancies by age and initial health status (estepm=%2d months): 
+   <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);
 
-Total number of observations=%d <br>
-Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>
-<hr  size=\"2\" color=\"#EC5E5E\"> 
-<li>Outputs files<br><br>\n
-        - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n
-- Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>
-        - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>
-        - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>
-        - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>
-        - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>
-        - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>
-        - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>
-        - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>
-        - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>
-        - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>
-	<br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);
- 
-fprintf(fichtm," <li>Graphs</li><p>");
+fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
 
  m=cptcoveff;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
@@ -1931,46 +2489,85 @@ fprintf(fichtm," <li>Graphs</li><p>");
  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\">");
-       }
-       fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>
-<img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
+     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>- 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>- 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,"<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);  
-     }
      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);
-fprintf(fichtm,"\n</body>");
-   }
-   }
+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
+ - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
+ - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
+ - Variances and covariances 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 (no covariance): <a href=\"t%s\">t%s</a> <br>\n
+ - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,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
+ - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
+	<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," <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\">");
+     }
+     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);  
+     }
+   } /* end i1 */
+ }/* End k1 */
+ fprintf(fichtm,"</ul>");
 fclose(fichtm);
 }
 
 /******************* Gnuplot file **************/
-void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){
+void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
 
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
-
-  strcpy(optionfilegnuplot,optionfilefiname);
-  strcat(optionfilegnuplot,".plt");
-  if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+  int ng;
+  if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
     printf("Problem with file %s",optionfilegnuplot);
+    fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
   }
 
 #ifdef windows
@@ -1983,10 +2580,12 @@ 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",agemin,fage,fileres,k1-1,k1-1);
+     fprintf(ficgp,"\nset out \"v%s%d%d.png\" \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,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);
+fprintf(ficgp,"\nset out \"v%s%d%d.png\" \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
 
 for (i=1; i<= nlstate ; i ++) {
@@ -2005,15 +2604,15 @@ 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] ",agemin,fage);
+    fprintf(ficgp,"\nset out \"e%s%d.png\" \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;
@@ -2038,27 +2637,36 @@ 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",agemin,fage,fileres,k1-1,k1-1,k,cpt);
+      k=2+nlstate*(2*cpt-2);
+      fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \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",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);
+      fprintf(ficgp,"\nset out \"p%s%d%d.png\" \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,"+$%d",k+i+1);
@@ -2071,7 +2679,6 @@ fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
 	fprintf(ficgp,"+$%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);
     } 
   }  
   
@@ -2080,70 +2687,77 @@ fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
     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");
 	}
       }
     }
-    }
-
-    for(jk=1; jk <=m; jk++) {
-  fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,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);
+
+   for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
+     for(jk=1; jk <=m; jk++) {
+       fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
+       if (ng==2)
+	 fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
+       else
+	 fprintf(ficgp,"\nset title \"Probability\"\n");
+       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){
+	     if(ng==2)
+	       fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+	     else
+	       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;
+	   }
+	 } /* end k */
+       } /* end k2 */
+     } /* end jk */
+   } /* end ng */
+   fclose(ficgp); 
 }  /* end gnuplot */
 
 
 /*************** Moving average **************/
-void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){
+void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){
 
   int i, cpt, cptcod;
-    for (agedeb=agemin; agedeb<=fage; agedeb++)
+    for (agedeb=ageminpar; agedeb<=fage; agedeb++)
       for (i=1; i<=nlstate;i++)
 	for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
 	  mobaverage[(int)agedeb][i][cptcod]=0.;
     
-    for (agedeb=agemin+4; agedeb<=fage; agedeb++){
+    for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){
       for (i=1; i<=nlstate;i++){
 	for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
 	  for (cpt=0;cpt<=4;cpt++){
@@ -2158,7 +2772,7 @@ void movingaverage(double agedeb, double
 
 
 /************** Forecasting ******************/
-prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){
+prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){
   
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
   int *popage;
@@ -2170,21 +2784,23 @@ prevforecast(char fileres[], double anpr
  agelim=AGESUP;
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
 
-  prevalence(agemin, 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);
  
  
   strcpy(fileresf,"f"); 
   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;
 
   if (mobilav==1) {
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-    movingaverage(agedeb, fage, agemin, mobaverage);
+    movingaverage(agedeb, fage, ageminpar, mobaverage);
   }
 
   stepsize=(int) (stepm+YEARM-1)/YEARM;
@@ -2221,7 +2837,7 @@ calagedate=(anproj1+mproj1/12.+jproj1/36
 	fprintf(ficresf,"\n");
 	fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);   
 
-     	for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){ 
+     	for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
 	  nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
 	  nhstepm = nhstepm/hstepm; 
 	  
@@ -2231,7 +2847,7 @@ calagedate=(anproj1+mproj1/12.+jproj1/36
 	
 	  for (h=0; h<=nhstepm; h++){
 	    if (h==(int) (calagedate+YEARM*cpt)) {
-	      fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);
+	      fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
 	    } 
 	    for(j=1; j<=nlstate+ndeath;j++) {
 	      kk1=0.;kk2=0;
@@ -2260,7 +2876,7 @@ calagedate=(anproj1+mproj1/12.+jproj1/36
   fclose(ficresf);
 }
 /************** Forecasting ******************/
-populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
+populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
   
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
   int *popage;
@@ -2274,21 +2890,23 @@ populforecast(char fileres[], double anp
   agelim=AGESUP;
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
   
-  prevalence(agemin, 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);
   
   
   strcpy(filerespop,"pop"); 
   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;
 
   if (mobilav==1) {
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-    movingaverage(agedeb, fage, agemin, mobaverage);
+    movingaverage(agedeb, fage, ageminpar, mobaverage);
   }
 
   stepsize=(int) (stepm+YEARM-1)/YEARM;
@@ -2302,6 +2920,7 @@ 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);
@@ -2329,7 +2948,7 @@ populforecast(char fileres[], double anp
       for (cpt=0; cpt<=0;cpt++) { 
 	fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
 	
-     	for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){ 
+     	for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
 	  nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
 	  nhstepm = nhstepm/hstepm; 
 	  
@@ -2375,7 +2994,7 @@ populforecast(char fileres[], double anp
 
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
 	fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
-	for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){ 
+	for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
 	  nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
 	  nhstepm = nhstepm/hstepm; 
 	  
@@ -2421,7 +3040,7 @@ int main(int argc, char *argv[])
 
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
   double agedeb, agefin,hf;
-  double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+  double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
 
   double fret;
   double **xi,tmp,delta;
@@ -2430,16 +3049,7 @@ int main(int argc, char *argv[])
   double ***p3mat;
   int *indx;
   char line[MAXLINE], linepar[MAXLINE];
-  char title[MAXLINE];
-  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
-  char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
-  
-  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
-
-  char filerest[FILENAMELENGTH];
-  char fileregp[FILENAMELENGTH];
-  char popfile[FILENAMELENGTH];
-  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;
@@ -2448,7 +3058,7 @@ 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;
@@ -2466,7 +3076,6 @@ int main(int argc, char *argv[])
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
   
 
-  char version[80]="Imach version 0.71e, March 2002, INED-EUROREVES ";
   char *alph[]={"a","a","b","c","d","e"}, str[4];
 
 
@@ -2479,7 +3088,7 @@ int main(int argc, char *argv[])
   struct timeval start_time, end_time;
   
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
-
+  getcwd(pathcd, size);
 
   printf("\n%s",version);
   if(argc <=1){
@@ -2501,6 +3110,20 @@ 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 */
@@ -2509,13 +3132,16 @@ 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 '#' */
@@ -2527,9 +3153,9 @@ 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 ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
-  printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);
-  fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,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){
     ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);
@@ -2561,14 +3187,23 @@ 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");
     }
   
@@ -2616,22 +3251,33 @@ 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 ----------*/
@@ -2641,12 +3287,14 @@ 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;
@@ -2686,7 +3334,7 @@ while((c=getc(ficpar))=='#' && c!= EOF){
 	cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
 
 	cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
-	for (j=ncov;j>=1;j--){
+	for (j=ncovcol;j>=1;j--){
 	  cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
 	} 
 	num[i]=atol(stra);
@@ -2705,13 +3353,14 @@ while((c=getc(ficpar))=='#' && c!= EOF){
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
     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++)
-    if (covar[1][i]==0) 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]));*/
-
+    }*/
+   /*  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]));}*/
+  
+ 
   /* 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);
@@ -2724,51 +3373,51 @@ while((c=getc(ficpar))=='#' && c!= EOF){
     cptcovn=j+1;
     cptcovprod=j1;
     
-    
     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');
-	  Tvar[i]=ncov+k1;
-	  cutv(strb,strc,strd,'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'); /* 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++) 
-	    covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
+	    covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
 	  k1++;
 	  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');
@@ -2777,11 +3426,12 @@ 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("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);
 
@@ -2792,24 +3442,29 @@ while((c=getc(ficpar))=='#' && c!= EOF){
     /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
 
-   for (i=1; i<=imx; i++) 
-     for(m=2; (m<= maxwav); m++)
+    for (i=1; i<=imx; i++) {
+      for(m=2; (m<= maxwav); m++) {
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
 	 anint[m][i]=9999;
 	 s[m][i]=-1;
        }
-    
+     if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
+      }
+    }
+
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=1; (m<= maxwav); m++){
 	if(s[m][i] >0){
-	  if (s[m][i] == nlstate+1) {
+	  if (s[m][i] >= nlstate+1) {
 	    if(agedc[i]>0)
 	      if(moisdc[i]!=99 && andc[i]!=9999)
-	      agev[m][i]=agedc[i];
-	    else {
+		agev[m][i]=agedc[i];
+	    /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+	   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;
 	      }
 	    }
@@ -2842,13 +3497,15 @@ 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);
@@ -2882,20 +3539,21 @@ printf("Total number of individuals= %d,
        for(j=1; j <= ncodemax[k]; j++){
 	 for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
 	   h++;
-	   if (h>m) h=1;codtab[h][k]=j;
+	   if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
+	   /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
 	 } 
        }
      }
    } 
-
-
-   /*for(i=1; i <=m ;i++){ 
-     for(k=1; k <=cptcovn; k++){
-       printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);
-     }
-     printf("\n");
-   }
-   scanf("%d",i);*/
+   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
+      codtab[1][2]=1;codtab[2][2]=2; */
+   /* for(i=1; i <=m ;i++){ 
+      for(k=1; k <=cptcovn; k++){
+      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
+      }
+      printf("\n");
+      }
+      scanf("%d",i);*/
     
    /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
@@ -2917,108 +3575,124 @@ printf("Total number of individuals= %d,
     }
     
     /*--------- results files --------------*/
-    fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, weightopt,model);
+    fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
   
 
    jk=1;
-   fprintf(ficres,"# Parameters\n");
-   printf("# Parameters\n");
+   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\n");
-    printf("# Scales\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\n");
-    printf("# Covariance\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);
-  
-    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);
-    
-    if (fage <= 2) {
-      bage = agemin;
-      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\n",agemin,agemaxpar,bage,fage);
-    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);
- 
-    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.;
@@ -3056,7 +3730,34 @@ while((c=getc(ficpar))=='#' && c!= EOF){
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
 
 /*------------ gnuplot -------------*/
- printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);
+  strcpy(optionfilegnuplot,optionfilefiname);
+  strcat(optionfilegnuplot,".gp");
+  if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+    printf("Problem with file %s",optionfilegnuplot);
+  }
+  fclose(ficgp);
+ printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
+/*--------- index.htm --------*/
+
+  strcpy(optionfilehtm,optionfile);
+  strcat(optionfilehtm,".htm");
+  if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+    printf("Problem with %s \n",optionfilehtm), exit(0);
+  }
+
+  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
+Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
+\n
+Total number of observations=%d <br>\n
+Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
+<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
+ - 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);
  
 /*------------ free_vector  -------------*/
  chdir(path);
@@ -3070,19 +3771,17 @@ while((c=getc(ficpar))=='#' && c!= EOF){
  fclose(ficparo);
  fclose(ficres);
 
-/*--------- index.htm --------*/
-
-  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres);
 
-  
   /*--------------- Prevalence limit --------------*/
   
   strcpy(filerespl,"pl");
   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);
@@ -3095,7 +3794,7 @@ while((c=getc(ficpar))=='#' && c!= EOF){
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
   k=0;
-  agebase=agemin;
+  agebase=ageminpar;
   agelim=agemaxpar;
   ftolpl=1.e-10;
   i1=cptcoveff;
@@ -3106,9 +3805,16 @@ while((c=getc(ficpar))=='#' && c!= EOF){
 	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);
@@ -3126,8 +3832,10 @@ while((c=getc(ficpar))=='#' && c!= EOF){
   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;*/
@@ -3135,7 +3843,9 @@ while((c=getc(ficpar))=='#' && c!= EOF){
   agelim=AGESUP;
   hstepm=stepsize*YEARM; /* Every year of age */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
-  
+
+  /* hstepm=1;   aff par mois*/
+
   k=0;
   for(cptcov=1;cptcov<=i1;cptcov++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
@@ -3148,6 +3858,9 @@ while((c=getc(ficpar))=='#' && c!= EOF){
 	for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
 	  nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
 	  nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+
+	  /*	  nhstepm=nhstepm*YEARM; aff par mois*/
+
 	  p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 	  oldm=oldms;savm=savms;
 	  hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
@@ -3156,20 +3869,20 @@ 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++){
-	    fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
+	   for (h=0; h<=nhstepm; h++){
+	    fprintf(ficrespij,"%d %f %f",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(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
 
   fclose(ficrespij);
 
@@ -3178,12 +3891,11 @@ 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);
+    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);
   }
   
 
@@ -3193,28 +3905,36 @@ while((c=getc(ficpar))=='#' && c!= EOF){
   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);
 
   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]]);
@@ -3222,21 +3942,24 @@ while((c=getc(ficpar))=='#' && c!= EOF){
 
       fprintf(ficreseij,"\n#****** ");
       for(j=1;j<=cptcoveff;j++) 
-	fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);
+	fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       fprintf(ficreseij,"******\n");
 
       fprintf(ficresvij,"\n#****** ");
       for(j=1;j<=cptcoveff;j++) 
-	fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);
+	fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       fprintf(ficresvij,"******\n");
 
       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);  
+      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);
-    
+      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) ");
@@ -3255,21 +3978,25 @@ 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];
-	fprintf(ficrest," %7.2f (%7.2f)", epj[nlstate+1],sqrt(vepp));
+	fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
 	for(j=1;j <=nlstate;j++){
-	  fprintf(ficrest," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age]));
+	  fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
 	}
 	fprintf(ficrest,"\n");
       }
     }
   }
-
+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);
@@ -3320,9 +4047,20 @@ while((c=getc(ficpar))=='#' && c!= EOF){
   free_matrix(agev,1,maxwav,1,imx);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
 
-  if(erreur >0)
-    printf("End of Imach with error %d\n",erreur);
-  else   printf("End of Imach\n");
+  fprintf(fichtm,"\n</body>");
+  fclose(fichtm);
+  fclose(ficgp);
+  
+
+  if(erreur >0){
+    printf("End of Imach with error or warning %d\n",erreur);
+    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);*/
@@ -3345,14 +4083,12 @@ while((c=getc(ficpar))=='#' && c!= EOF){
 
 #ifdef windows
   while (z[0] != 'q') {
-    chdir(path); 
-    printf("\nType e to edit output files, c to start again, and q for exiting: ");
+    /* chdir(path); */
+    printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
     scanf("%s",z);
     if (z[0] == 'c') system("./imach");
-    else if (z[0] == 'e') {
-      chdir(path);
-      system(optionfilehtm);
-    }
+    else if (z[0] == 'e') system(optionfilehtm);
+    else if (z[0] == 'g') system(plotcmd);
     else if (z[0] == 'q') exit(0);
   }
 #endif