--- imach/src/imach.c	2001/05/17 16:07:14	1.11
+++ imach/src/imach.c	2002/06/26 23:25:02	1.50
@@ -1,34 +1,42 @@
-    
-/*********************** Imach **************************************        
-  This program computes Healthy Life Expectancies from cross-longitudinal 
-  data. Cross-longitudinal consist in a first survey ("cross") where 
-  individuals from different ages are interviewed on their health status
-  or degree of  disability. At least a second wave of interviews 
-  ("longitudinal") should  measure each new individual health status. 
-  Health expectancies are computed from the transistions observed between 
-  waves and are computed for each degree of severity of disability (number
-  of life states). More degrees 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 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 complex model than "constant and
-  age", you should modify the program where the markup 
-    *Covariates have to be included here again* invites you to do it.
-  More covariates you add, less is the speed of the convergence.
-
-  The advantage that this computer programme claims, comes from that if the 
-  delay between waves is not identical for each individual, or if some 
-  individual missed an interview, the information is not rounded or lost, but
-  taken into account using an interpolation or extrapolation.
-  hPijx is the probability to be
-  observed in state i at age x+h conditional to the observed state i at age 
-  x. The delay 'h' can be split into an exact number (nh*stepm) of 
-  unobserved intermediate  states. This elementary transition (by month or 
-  quarter trimester, semester or year) is model as a multinomial logistic. 
-  The hPx matrix is simply the matrix product of nh*stepm elementary matrices
-  and the contribution of each individual to the likelihood is simply hPijx.
+/* $Id: imach.c,v 1.50 2002/06/26 23:25:02 brouard Exp $
+   Interpolated Markov Chain
+
+  Short summary of the programme:
+  
+  This program computes Healthy Life Expectancies from
+  cross-longitudinal data. Cross-longitudinal data consist in: -1- a
+  first survey ("cross") where individuals from different ages are
+  interviewed on their health status or degree of disability (in the
+  case of a health survey which is our main interest) -2- at least a
+  second wave of interviews ("longitudinal") which measure each change
+  (if any) in individual health status.  Health expectancies are
+  computed from the time spent in each health state according to a
+  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
+  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
+  complex model than "constant and age", you should modify the program
+  where the markup *Covariates have to be included here again* invites
+  you to do it.  More covariates you add, slower the
+  convergence.
+
+  The advantage of this computer programme, compared to a simple
+  multinomial logistic model, is clear when the delay between waves is not
+  identical for each individual. Also, if a individual missed an
+  intermediate interview, the information is lost, but taken into
+  account using an interpolation or extrapolation.  
+
+  hPijx is the probability to be observed in state i at age x+h
+  conditional to the observed state i at age x. The delay 'h' can be
+  split into an exact number (nh*stepm) of unobserved intermediate
+  states. This elementary transition (by month or quarter trimester,
+  semester or year) is model as a multinomial logistic.  The hPx
+  matrix is simply the matrix product of nh*stepm elementary matrices
+  and the contribution of each individual to the likelihood is simply
+  hPijx.
 
   Also this programme outputs the covariance matrix of the parameters but also
   of the life expectancies. It also computes the prevalence limits. 
@@ -48,6 +56,8 @@
 #include <unistd.h>
 
 #define MAXLINE 256
+#define GNUPLOTPROGRAM "gnuplot"
+/*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define FILENAMELENGTH 80
 /*#define DEBUG*/
 #define windows
@@ -65,14 +75,23 @@
 #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 */
 int maxwav; /* Maxim number of waves */
@@ -83,14 +102,28 @@ int **dh; /* dh[mi][i] is number of step
 double jmean; /* Mean space between 2 waves */
 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;
-FILE *ficgp, *fichtm;
+FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+FILE *ficlog;
+FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
+FILE *ficresprobmorprev;
+FILE *fichtm; /* Html File */
 FILE *ficreseij;
-  char filerese[FILENAMELENGTH];
- 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*
@@ -112,7 +145,7 @@ FILE *ficreseij;
 static double maxarg1,maxarg2;
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
- 
+  
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 #define rint(a) floor(a+0.5)
 
@@ -124,10 +157,14 @@ 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;
-double **pmmij;
+double **pmmij, ***probs, ***mobaverage;
+double dateintmean=0;
 
 double *weight;
 int **s; /* Status */
@@ -138,15 +175,17 @@ double ftol=FTOL; /* Tolerance for compu
 double ftolhess; /* Tolerance for computing hessian */
 
 /**************** split *************************/
-static	int split( char *path, char *dirc, char *name )
+static	int split( char *path, char *dirc, char *name, char *ext, char *finame )
 {
    char	*s;				/* pointer */
    int	l1, l2;				/* length counters */
 
    l1 = strlen( path );			/* length of path */
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
-   s = strrchr( path, '\\' );		/* find last / */
+   s= strrchr( path, DIRSEPARATOR );		/* find last / */
    if ( s == NULL ) {			/* no directory, so use current */
+     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
+       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 #if	defined(__bsd__)		/* get current working directory */
       extern char	*getwd( );
 
@@ -168,7 +207,18 @@ static	int split( char *path, char *dirc
       dirc[l1-l2] = 0;			/* add zero */
    }
    l1 = strlen( dirc );			/* length of directory */
+#ifdef windows
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
+#else
+   if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
+#endif
+   s = strrchr( name, '.' );		/* find last / */
+   s++;
+   strcpy(ext,s);			/* save extension */
+   l1= strlen( name);
+   l2= strlen( s)+1;
+   strncpy( finame, name, l1-l2);
+   finame[l1-l2]= 0;
    return( 0 );				/* we're done */
 }
 
@@ -201,6 +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++) {
@@ -397,8 +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))){ 
@@ -523,6 +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; 
@@ -553,16 +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)); 
@@ -570,13 +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))) {
@@ -585,15 +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
 
@@ -621,9 +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
       } 
     } 
@@ -659,16 +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;
@@ -693,7 +768,7 @@ double **prevalim(double **prlim, int nl
   }
 }
 
-/*************** transition probabilities **********/ 
+/*************** transition probabilities ***************/ 
 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 {
@@ -719,6 +794,8 @@ double **pmij(double **ps, double *cov,
       ps[i][j]=s2;
     }
   }
+    /*ps[3][2]=1;*/
+
   for(i=1; i<= nlstate; i++){
      s1=0;
     for(j=1; j<i; j++)
@@ -740,6 +817,7 @@ double **pmij(double **ps, double *cov,
     }
   }
 
+
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){
     for(jj=1; jj<= nlstate+ndeath; jj++){
      printf("%lf ",ps[ii][jj]);
@@ -757,7 +835,7 @@ double **pmij(double **ps, double *cov,
 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
 {
-  /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
+  /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   /* in, b, out are matrice of pointers which should have been initialized 
      before: only the contents of out is modified. The function returns
@@ -804,9 +882,9 @@ double ***hpxij(double ***po, int nhstep
       cov[1]=1.;
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-for (k=1; k<=cptcovage;k++)
+      for (k=1; k<=cptcovage;k++)
 	cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-   for (k=1; k<=cptcovprod;k++)
+      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]]];
 
 
@@ -892,11 +970,12 @@ 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(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",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));
 
 }
 
@@ -913,28 +992,34 @@ void hesscov(double **matcov, double p[]
   void lubksb(double **a, int npar, int *indx, double b[]) ;
   void ludcmp(double **a, int npar, int *indx, double *d) ;
 
-
   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]);*/
   }
-
+  
   for (i=1;i<=npar;i++) {
     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];
+	hess[j][i]=hess[i][j];    
+	/*printf(" %lf ",hess[i][j]);*/
       }
     }
   }
   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);
@@ -954,11 +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 */
@@ -975,8 +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");
   }
   */
 
@@ -1018,6 +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.)){
@@ -1032,7 +1123,7 @@ double hessii( double x[], double delta,
     }
   }
   delti[theta]=delts;
-  return res;
+  return res; 
   
 }
 
@@ -1065,6 +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;
@@ -1145,114 +1237,248 @@ 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)
+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 i, m, jk, k1,i1, j1, bool, z1,z2,j;
+  int first;
   double ***freq; /* Frequencies */
   double *pp;
-  double pos;
+  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;}
 
+  first=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;
-       
-       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-1; m++){
-	     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  (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(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);
-    }
-    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,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);
-      else
-	  fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
+      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(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; 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);
+	  }
+	}
+	
+	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 */
+}
+
+/************ Prevalence ********************/
+void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
+{  /* Some frequencies */
+ 
+  int i, m, jk, k1, i1, j1, bool, z1,z2,j;
+  double ***freq; /* Frequencies */
+  double *pp;
+  double pos, k2;
+
+  pp=vector(1,nlstate);
+  probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+  
+  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++;
+      
+      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;
+     
+      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) {
+	      	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++)
+	    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;
+	    }
+	  }
+	}/* 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);
+  
 }  /* End of Freq */
 
 /************* Waves Concatenation ***************/
@@ -1269,9 +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.;
@@ -1294,8 +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++){
@@ -1311,7 +1545,7 @@ void  concatwav(int wav[], int **dh, int
 	  if (j >= jmax) jmax=j;
 	  if (j <= jmin) jmin=j;
 	  sum=sum+j;
-	  if (j<0) printf("j=%d num=%d ",j,i); 
+	  /*if (j<0) printf("j=%d num=%d \n",j,i); */
 	  }
 	}
 	else{
@@ -1319,6 +1553,7 @@ void  concatwav(int wav[], int **dh, int
 	  k=k+1;
 	  if (j >= jmax) jmax=j;
 	  else if (j <= jmin)jmin=j;
+	  /*	    if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
 	  sum=sum+j;
 	}
 	jk= j/stepm;
@@ -1335,7 +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)
 {
@@ -1364,6 +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; 
@@ -1373,89 +1611,262 @@ void tricode(int *Tvar, int **nbcode, in
 
  for (k=0; k<19; k++) Ndum[k]=0;
 
- for (i=1; i<=ncovmodel; i++) {
-      ij=Tvar[i];
-      Ndum[ij]++; 
-    }
+ for (i=1; i<=ncovmodel-2; i++) {
+   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;
-  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");
 
-  hstepm=1*YEARM; /*  Every j years of age (in month) */
-  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;   
+  /* 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 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 stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 
   agelim=AGESUP;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     /* nhstepm age range expressed in number of stepm */
-    nhstepm=(int) rint((agelim-age)*YEARM/stepm); 
-    /* Typically if 20 years = 20*12/6=40 stepm */ 
-    if (stepm >= YEARM) hstepm=1;
-    nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */
+    nstepm=(int) rint((agelim-age)*YEARM/stepm); 
+    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
+    /* 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; h++){
-	  eij[i][j][(int)age] +=p3mat[i][j][h];
+	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]);*/
+
 	}
-    
-    hf=1;
-    if (stepm >= YEARM) hf=stepm/YEARM;
-    fprintf(ficreseij,"%.0f",age );
+
+    fprintf(ficreseij,"%3.0f",age );
+    cptj=0;
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){
-	fprintf(ficreseij," %.4f", hf*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 *xp;
+  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++)
@@ -1465,73 +1876,160 @@ 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);
       }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+
+      if (popbased==1) {
+	for(i=1; i<=nlstate;i++)
+	  prlim[i][i]=probs[(int)age][i][ij];
+      }
+  
       for(j=1; j<= nlstate; j++){
 	for(h=0; h<=nhstepm; h++){
 	  for(i=1, gp[h][j]=0.;i<=nlstate;i++)
 	    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);  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+ 
+      if (popbased==1) {
+	for(i=1; i<=nlstate;i++)
+	  prlim[i][i]=probs[(int)age][i][ij];
+      }
+
       for(j=1; j<= nlstate; j++){
 	for(h=0; h<=nhstepm; h++){
 	  for(i=1, gm[h][j]=0.;i<=nlstate;i++)
 	    gm[h][j] += prlim[i][i]*p3mat[i][j][h];
 	}
       }
-      for(j=1; j<= nlstate; j++)
+      /* 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++) /* 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);
@@ -1540,10 +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);
 
 }
 
@@ -1562,7 +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);
@@ -1630,41 +2147,925 @@ void varprevlim(char fileres[], double *
 
 }
 
-
-
-/***********************************************/
-/**************** Main Program *****************/
-/***********************************************/
-
-/*int main(int argc, char *argv[])*/
-int main()
+/************ Variance of one-step probabilities  ******************/
+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=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;
+  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);
+  }
+  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");
 
-  int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
-  double agedeb, agefin,hf;
-  double agemin=1.e20, agemax=-1.e20;
 
-  double fret;
-  double **xi,tmp,delta;
+  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)*(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");
+
+    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");
 
-  double dum; /* Dummy variable */
-  double ***p3mat;
-  int *indx;
-  char line[MAXLINE], linepar[MAXLINE];
-  char title[MAXLINE];
-  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
-  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];
-  char filerest[FILENAMELENGTH];
-  char fileregp[FILENAMELENGTH];
-  char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
-  int firstobs=1, lastobs=10;
-  int sdeb, sfin; /* Status at beginning and end */
-  int c,  h , cpt,l;
+  }
+
+ 
+  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];  
+	}
+
+	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];
+	  }
+	}
+     	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);
+	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 (k1=1; k1<=(nlstate);k1++){
+	for (l1=1; l1<=(nlstate+ndeath);l1++){ 
+	  if(l1==k1) continue;
+	  i=(k1-1)*(nlstate+ndeath)+l1;
+	  for (k2=1; k2<=(nlstate);k2++){
+	    for (l2=1; l2<=(nlstate+ndeath);l2++){ 
+	      if(l2==k2) continue;
+	      j=(k2-1)*(nlstate+ndeath)+l2;
+	      if(j<=i) 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;
+		  /* Computing eigen value of matrix of covariance */
+		  lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));
+		  lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));
+		  if(first1==1){
+		    first1=0;
+		    printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\nOthers in log...\n",v1,v2,cv12,lc1,lc2);
+		  }
+		  fprintf(ficlog,"Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);
+		  /* Eigen vectors */
+		  v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+		  v21=sqrt(1.-v11*v11);
+		  v12=-v21;
+		  v22=v11;
+		  /*printf(fignu*/
+		  /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+		  /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */
+		  if(first==1){
+		    first=0;
+ 		    fprintf(ficgp,"\nset parametric;set nolabel");
+		    fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);
+		    fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+		    fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1);
+		    fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k2,l2,k1,l1);
+		    fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k2,l2,k1,l1);
+		    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);
+		    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);
+		    /*		    fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\
+			    mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \
+			    mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);
+		    */
+		    fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
+			    mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \
+			    mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));
+		  }else{
+		    first=0;
+		    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);
+		    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);
+		    /*
+		    fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\
+			    mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \
+			    mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);
+		    */
+		    fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
+			    mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \
+			    mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));
+		  }/* if first */
+		} /* age mod 5 */
+	      } /* end loop age */
+	      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k2,l2,k1,l1);
+	      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);
+}
+
+
+/******************* 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 rfileres[],\
+		  int popforecast, int estepm ,\
+		  double jprev1, double mprev1,double anprev1, \
+		  double jprev2, double mprev2,double anprev2){
+  int jj1, k1, i1, cpt;
+  /*char optionfilehtm[FILENAMELENGTH];*/
+  if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
+    printf("Problem with %s \n",optionfilehtm), exit(0);
+    fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
+  }
+
+   fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
+ - 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);
+
+fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
+
+ m=cptcoveff;
+ if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+
+ jj1=0;
+ for(k1=1; k1<=m;k1++){
+   for(i1=1; i1<=ncodemax[k1];i1++){
+     jj1++;
+     if (cptcovn > 0) {
+       fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+       for (cpt=1; cpt<=cptcoveff;cpt++) 
+	 fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+       fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+     }
+     /* Pij */
+     fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>
+<img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
+     /* Quasi-incidences */
+     fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
+<img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
+       /* Stable prevalence in each health state */
+       for(cpt=1; cpt<nlstate;cpt++){
+	 fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
+<img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+       }
+     for(cpt=1; cpt<=nlstate;cpt++) {
+        fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
+<img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+     }
+     fprintf(fichtm,"\n<br>- Total life expectancy by age and
+health expectancies in states (1) and (2): e%s%d.png<br>
+<img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
+   } /* end i1 */
+ }/* End k1 */
+ fprintf(fichtm,"</ul>");
+
+
+ fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
+ - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
+ - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
+ - 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[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+
+  int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+  int ng;
+  if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
+    printf("Problem with file %s",optionfilegnuplot);
+    fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
+  }
+
+#ifdef windows
+    fprintf(ficgp,"cd \"%s\" \n",pathc);
+#endif
+m=pow(2,cptcoveff);
+  
+ /* 1eme*/
+  for (cpt=1; cpt<= nlstate ; cpt ++) {
+   for (k1=1; k1<= m ; k1 ++) {
+
+#ifdef windows
+     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,"\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 ++) {
+  if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+  else fprintf(ficgp," \%%*lf (\%%*lf)");
+}
+    fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
+    for (i=1; i<= nlstate ; i ++) {
+  if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+  else fprintf(ficgp," \%%*lf (\%%*lf)");
+} 
+  fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); 
+     for (i=1; i<= nlstate ; i ++) {
+  if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+  else fprintf(ficgp," \%%*lf (\%%*lf)");
+}  
+     fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
+#ifdef unix
+fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");
+#endif
+   }
+  }
+  /*2 eme*/
+
+  for (k1=1; k1<= m ; k1 ++) { 
+    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;
+      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
+      for (j=1; j<= nlstate+1 ; j ++) {
+  if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+  else fprintf(ficgp," \%%*lf (\%%*lf)");
+}   
+      if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
+      else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
+    fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
+      for (j=1; j<= nlstate+1 ; j ++) {
+	if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+	else fprintf(ficgp," \%%*lf (\%%*lf)");
+}   
+      fprintf(ficgp,"\" t\"\" w l 0,");
+     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
+      for (j=1; j<= nlstate+1 ; j ++) {
+  if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+  else fprintf(ficgp," \%%*lf (\%%*lf)");
+}   
+      if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+      else fprintf(ficgp,"\" t\"\" w l 0,");
+    }
+  }
+ 
+  /*3eme*/
+
+  for (k1=1; k1<= m ; k1 ++) { 
+    for (cpt=1; cpt<= nlstate ; cpt ++) {
+      k=2+nlstate*(2*cpt-2);
+      fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
+      fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
+      /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%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+2*i,cpt,i+1);
+
+      } 
+    }
+  }
+ 
+  /* CV preval stat */
+    for (k1=1; k1<= m ; k1 ++) { 
+    for (cpt=1; cpt<nlstate ; cpt ++) {
+      k=3;
+      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);
+      fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
+      
+      l=3+(nlstate+ndeath)*cpt;
+      fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
+      for (i=1; i< nlstate ; i ++) {
+	l=3+(nlstate+ndeath)*cpt;
+	fprintf(ficgp,"+$%d",l+i+1);
+      }
+      fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
+    } 
+  }  
+  
+  /* proba elementaires */
+   for(i=1,jk=1; i <=nlstate; i++){
+    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(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 ageminpar, double ***mobaverage){
+
+  int i, cpt, cptcod;
+    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=ageminpar+4; agedeb<=fage; agedeb++){
+      for (i=1; i<=nlstate;i++){
+	for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+	  for (cpt=0;cpt<=4;cpt++){
+	    mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];
+	  }
+	  mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;
+	}
+      }
+    }
+    
+}
+
+
+/************** Forecasting ******************/
+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;
+  double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+  double *popeffectif,*popcount;
+  double ***p3mat;
+  char fileresf[FILENAMELENGTH];
+
+ agelim=AGESUP;
+calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
+
+  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, ageminpar, mobaverage);
+  }
+
+  stepsize=(int) (stepm+YEARM-1)/YEARM;
+  if (stepm<=12) stepsize=1;
+  
+  agelim=AGESUP;
+  
+  hstepm=1;
+  hstepm=hstepm/stepm; 
+  yp1=modf(dateintmean,&yp);
+  anprojmean=yp;
+  yp2=modf((yp1*12),&yp);
+  mprojmean=yp;
+  yp1=modf((yp2*30.5),&yp);
+  jprojmean=yp;
+  if(jprojmean==0) jprojmean=1;
+  if(mprojmean==0) jprojmean=1;
+  
+  fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean); 
+  
+  for(cptcov=1;cptcov<=i2;cptcov++){
+    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+      k=k+1;
+      fprintf(ficresf,"\n#******");
+      for(j=1;j<=cptcoveff;j++) {
+	fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+      }
+      fprintf(ficresf,"******\n");
+      fprintf(ficresf,"# StartingAge FinalAge");
+      for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
+      
+      
+      for (cpt=0; cpt<=(anproj2-anproj1);cpt++) { 
+	fprintf(ficresf,"\n");
+	fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);   
+
+     	for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
+	  nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
+	  nhstepm = nhstepm/hstepm; 
+	  
+	  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);  
+	
+	  for (h=0; h<=nhstepm; h++){
+	    if (h==(int) (calagedate+YEARM*cpt)) {
+	      fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
+	    } 
+	    for(j=1; j<=nlstate+ndeath;j++) {
+	      kk1=0.;kk2=0;
+	      for(i=1; i<=nlstate;i++) {	      
+		if (mobilav==1) 
+		  kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+		else {
+		  kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+		}
+		
+	      }
+	      if (h==(int)(calagedate+12*cpt)){
+		fprintf(ficresf," %.3f", kk1);
+	     		
+	      }
+	    }
+	  }
+	  free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+	}
+      }
+    }
+  }
+       
+  if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+
+  fclose(ficresf);
+}
+/************** Forecasting ******************/
+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;
+  double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+  double *popeffectif,*popcount;
+  double ***p3mat,***tabpop,***tabpopprev;
+  char filerespop[FILENAMELENGTH];
+
+  tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+  tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+  agelim=AGESUP;
+  calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
+  
+  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, ageminpar, mobaverage);
+  }
+
+  stepsize=(int) (stepm+YEARM-1)/YEARM;
+  if (stepm<=12) stepsize=1;
+  
+  agelim=AGESUP;
+  
+  hstepm=1;
+  hstepm=hstepm/stepm; 
+  
+  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);
+    popcount=vector(0,AGESUP);
+    
+    i=1;   
+    while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+   
+    imx=i;
+    for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
+  }
+
+  for(cptcov=1;cptcov<=i2;cptcov++){
+   for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+      k=k+1;
+      fprintf(ficrespop,"\n#******");
+      for(j=1;j<=cptcoveff;j++) {
+	fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+      }
+      fprintf(ficrespop,"******\n");
+      fprintf(ficrespop,"# Age");
+      for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
+      if (popforecast==1)  fprintf(ficrespop," [Population]");
+      
+      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>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
+	  nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
+	  nhstepm = nhstepm/hstepm; 
+	  
+	  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);  
+	
+	  for (h=0; h<=nhstepm; h++){
+	    if (h==(int) (calagedate+YEARM*cpt)) {
+	      fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+	    } 
+	    for(j=1; j<=nlstate+ndeath;j++) {
+	      kk1=0.;kk2=0;
+	      for(i=1; i<=nlstate;i++) {	      
+		if (mobilav==1) 
+		  kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+		else {
+		  kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+		}
+	      }
+	      if (h==(int)(calagedate+12*cpt)){
+		tabpop[(int)(agedeb)][j][cptcod]=kk1;
+		  /*fprintf(ficrespop," %.3f", kk1);
+		    if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+	      }
+	    }
+	    for(i=1; i<=nlstate;i++){
+	      kk1=0.;
+		for(j=1; j<=nlstate;j++){
+		  kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
+		}
+		  tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
+	    }
+
+	    if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) 
+	      fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
+	  }
+	  free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+	}
+      }
+ 
+  /******/
+
+      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>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
+	  nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
+	  nhstepm = nhstepm/hstepm; 
+	  
+	  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);  
+	  for (h=0; h<=nhstepm; h++){
+	    if (h==(int) (calagedate+YEARM*cpt)) {
+	      fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+	    } 
+	    for(j=1; j<=nlstate+ndeath;j++) {
+	      kk1=0.;kk2=0;
+	      for(i=1; i<=nlstate;i++) {	      
+		kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];	
+	      }
+	      if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);	
+	    }
+	  }
+	  free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+	}
+      }
+   } 
+  }
+ 
+  if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+
+  if (popforecast==1) {
+    free_ivector(popage,0,AGESUP);
+    free_vector(popeffectif,0,AGESUP);
+    free_vector(popcount,0,AGESUP);
+  }
+  free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+  free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+  fclose(ficrespop);
+}
+
+/***********************************************/
+/**************** Main Program *****************/
+/***********************************************/
+
+int main(int argc, char *argv[])
+{
+
+  int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
+  double agedeb, agefin,hf;
+  double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+
+  double fret;
+  double **xi,tmp,delta;
+
+  double dum; /* Dummy variable */
+  double ***p3mat;
+  int *indx;
+  char line[MAXLINE], linepar[MAXLINE];
+  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;
   int ju,jl, mi;
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
-  int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
-  
+  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, calagedate;
+
   double bage, fage, age, agelim, agebase;
   double ftolpl=FTOL;
   double **prlim;
@@ -1677,53 +3078,76 @@ int main()
   double ***eij, ***vareij;
   double **varpl; /* Variances of prevalence limits by age */
   double *epj, vepp;
-  char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";
+  double kk1, kk2;
+  double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
+  
+
   char *alph[]={"a","a","b","c","d","e"}, str[4];
 
+
   char z[1]="c", occ;
 #include <sys/time.h>
 #include <time.h>
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
+ 
   /* long total_usecs;
   struct timeval start_time, end_time;
   
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
-
-
-  printf("\nIMACH, Version 0.64b");
-  printf("\nEnter the parameter file name: ");
-
-#ifdef windows
-  scanf("%s",pathtot);
   getcwd(pathcd, size);
+
+  printf("\n%s",version);
+  if(argc <=1){
+    printf("\nEnter the parameter file name: ");
+    scanf("%s",pathtot);
+  }
+  else{
+    strcpy(pathtot,argv[1]);
+  }
+  /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
   /*cygwin_split_path(pathtot,path,optionfile);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
   /* cutv(path,optionfile,pathtot,'\\');*/
 
-split(pathtot, path,optionfile);
+  split(pathtot,path,optionfile,optionfilext,optionfilefiname);
+   printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   chdir(path);
   replace(pathc,path);
-#endif
-#ifdef unix
-  scanf("%s",optionfile);
-#endif
 
 /*-------- 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, optionfile);
+  strcat(fileres, optionfilefiname);
+  strcat(fileres,".txt");    /* Other files have txt extension */
 
   /*---------arguments file --------*/
 
   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 '#' */
@@ -1735,10 +3159,18 @@ split(pathtot, path,optionfile);
   }
   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);
+    puts(line);
+    fputs(line,ficparo);
+  }
+  ungetc(c,ficpar);
+  
+   
   covar=matrix(0,NCOVMAX,1,n); 
   cptcovn=0; 
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
@@ -1761,18 +3193,28 @@ split(pathtot, path,optionfile);
     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");
     }
   
-  npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
+    npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
+
   p=param[1][1];
   
   /* Reads comments: lines beginning with '#' */
@@ -1815,32 +3257,50 @@ split(pathtot, path,optionfile);
   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");
 
 
-    /*-------- data file ----------*/
-    if((ficres =fopen(fileres,"w"))==NULL) {
-      printf("Problem with resultfile: %s\n", fileres);goto end;
+    /*-------- Rewriting paramater file ----------*/
+     strcpy(rfileres,"r");    /* "Rparameterfile */
+     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+     strcat(rfileres,".");    /* */
+     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;
@@ -1862,7 +3322,7 @@ split(pathtot, path,optionfile);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
 
-    i=1; 
+    i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
 	
@@ -1880,22 +3340,33 @@ split(pathtot, path,optionfile);
 	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);
-
-	/*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]));*/
+	
+	/*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+	  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])); ij=ij+1;}*/
 
 	i=i+1;
       }
     } 
-
-    /*scanf("%d",i);*/
+    /* printf("ii=%d", ij);
+       scanf("%d",i);*/
   imx=i-1; /* Number of individuals */
 
+  /* for (i=1; i<=imx; i++){
+    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 (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);
@@ -1908,51 +3379,51 @@ split(pathtot, path,optionfile);
     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');
@@ -1961,11 +3432,12 @@ split(pathtot, path,optionfile);
       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);
 
@@ -1975,18 +3447,30 @@ split(pathtot, path,optionfile);
     }
     /*-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++) {
+       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;
 	      }
 	    }
@@ -2019,20 +3503,22 @@ split(pathtot, path,optionfile);
     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);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
-    free_matrix(mint,1,maxwav,1,n);
-    free_matrix(anint,1,maxwav,1,n);
+    /* free_matrix(mint,1,maxwav,1,n);
+       free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
 
@@ -2059,31 +3545,33 @@ 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'. */
-  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);
 
+    
+   
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
-    
+     
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
@@ -2093,275 +3581,133 @@ printf("Total number of individuals= %d,
     }
     
     /*--------- results files --------------*/
-    fprintf(ficres,"\ntitle=%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(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");
-	}
-      }
-      }
-    
-    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,&agemax, &bage, &fage);
-    
-    if (fage <= 2) {
-      bage = agemin;
-      fage = agemax;
-    }
-
-    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,agemax,bage,fage);
-
-   
-/*------------ gnuplot -------------*/
-chdir(pathcd);
-  if((ficgp=fopen("graph.plt","w"))==NULL) {
-    printf("Problem with file graph.gp");goto end;
-  }
-#ifdef windows
-  fprintf(ficgp,"cd \"%s\" \n",pathc);
-#endif
-m=pow(2,cptcoveff);
-  
- /* 1eme*/
-  for (cpt=1; cpt<= nlstate ; cpt ++) {
-   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);
-#endif
-#ifdef unix
-fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);
-#endif
-
-for (i=1; i<= nlstate ; i ++) {
-  if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-  else fprintf(ficgp," \%%*lf (\%%*lf)");
-}
-    fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
-    for (i=1; i<= nlstate ; i ++) {
-  if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-  else fprintf(ficgp," \%%*lf (\%%*lf)");
-} 
-  fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); 
-     for (i=1; i<= nlstate ; i ++) {
-  if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-  else fprintf(ficgp," \%%*lf (\%%*lf)");
-}  
-     fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%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");
-#endif
-fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
+   if(mle==1){
+     /* Computing hessian and covariance matrix */
+     ftolhess=ftol; /* Usually correct */
+     hesscov(matcov, p, npar, delti, ftolhess, func);
    }
-  }
-  /*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);
-    
-    for (i=1; i<= nlstate+1 ; i ++) {
-      k=2*i;
-      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
-      for (j=1; j<= nlstate+1 ; j ++) {
-  if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-  else fprintf(ficgp," \%%*lf (\%%*lf)");
-}   
-      if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
-      else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
-    fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
-      for (j=1; j<= nlstate+1 ; j ++) {
-	if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-	else fprintf(ficgp," \%%*lf (\%%*lf)");
-}   
-      fprintf(ficgp,"\" t\"\" w l 0,");
-     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
-      for (j=1; j<= nlstate+1 ; j ++) {
-  if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-  else fprintf(ficgp," \%%*lf (\%%*lf)");
-}   
-      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);
-      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,"\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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);
-      for (i=1; i< nlstate ; i ++)
-	fprintf(ficgp,"+$%d",k+i+1);
-      fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
-      
-      l=3+(nlstate+ndeath)*cpt;
-      fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
-      for (i=1; i< nlstate ; i ++) {
-	l=3+(nlstate+ndeath)*cpt;
-	fprintf(ficgp,"+$%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);
-    } 
-  }
-
-  /* proba elementaires */
+   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(k=1; k <=(nlstate+ndeath); k++){
-      if (k != i) {
-	for(j=1; j <=ncovmodel; j++){
-	  /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/
-	  /*fprintf(ficgp,"%s",alph[1]);*/
-	  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,agemax);
-   i=1;
-   for(k2=1; k2<=nlstate; k2++) {
-     k3=i;
-     for(k=1; k<=(nlstate+ndeath); k++) {
-       if (k != k2){
-    	fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
-ij=1;
-	for(j=3; j <=ncovmodel; j++) {
-	  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
-	    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
-	    ij++;
-	  }
-	  else
-	  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-	}
-	  fprintf(ficgp,")/(1");
-	
-	for(k1=1; k1 <=nlstate; k1++){   
-	  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
-ij=1;
-	  for(j=3; j <=ncovmodel; j++){
-	  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
-	    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
-	    ij++;
-	  }
-	  else
-	    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-	  }
-	  fprintf(ficgp,")");
-	}
-	fprintf(ficgp,") t \"p%d%d\" ", k2,k);
-	if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
-	i=i+ncovmodel;
+     for(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");
        }
      }
    }
-   fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk); 
-  }
    
-  fclose(ficgp);
+   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++;
+   }
    
-chdir(path);
-    free_matrix(agev,1,maxwav,1,imx);
-    free_ivector(wav,1,imx);
-    free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
-    free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
-    
-    free_imatrix(s,1,maxwav+1,1,n);
-    
-    
-    free_ivector(num,1,n);
-    free_vector(agedc,1,n);
-    free_vector(weight,1,n);
-    /*free_matrix(covar,1,NCOVMAX,1,n);*/
-    fclose(ficparo);
-    fclose(ficres);
-    /*  }*/
+   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;
+   }
    
-   /*________fin mle=1_________*/
+   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);
+ 
+
+   dateprev1=anprev1+mprev1/12.+jprev1/365.;
+   dateprev2=anprev2+mprev2/12.+jprev2/365.;
 
+  fscanf(ficpar,"pop_based=%d\n",&popbased);
+  fprintf(ficparo,"pop_based=%d\n",popbased);   
+  fprintf(ficres,"pop_based=%d\n",popbased);   
   
-    /* No more information from the sample is required now */
-  /* Reads comments: lines beginning with '#' */
   while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);
@@ -2369,71 +3715,68 @@ chdir(path);
     fputs(line,ficparo);
   }
   ungetc(c,ficpar);
-  
-  fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);
-  printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);
-  fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
+
+  fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);
+fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
+fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
+
+
+while((c=getc(ficpar))=='#' && c!= EOF){
+    ungetc(c,ficpar);
+    fgets(line, MAXLINE, ficpar);
+    puts(line);
+    fputs(line,ficparo);
+  }
+  ungetc(c,ficpar);
+
+  fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
+  fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
+  fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
+
+ freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
+
+/*------------ gnuplot -------------*/
+  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);goto end;
+    printf("Problem with %s \n",optionfilehtm), exit(0);
   }
 
- fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.64b </font> <hr size=\"2\" color=\"#EC5E5E\"> 
-Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>
-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><br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,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,"<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);
 
- m=cptcoveff;
- if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+ 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);
+ 
+ free_ivector(wav,1,imx);
+ free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+ free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
+ free_ivector(num,1,n);
+ free_vector(agedc,1,n);
+ /*free_matrix(covar,1,NCOVMAX,1,n);*/
+ fclose(ficparo);
+ fclose(ficres);
 
- j1=0;
- for(k1=1; k1<=m;k1++){
-   for(i1=1; i1<=ncodemax[k1];i1++){
-       j1++;
-       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[j1][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, "."),j1,strtok(optionfile, "."),j1);     
-       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,j1,strtok(optionfile, "."),cpt,j1);
-       }
-    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,j1,strtok(optionfile, "."),cpt,j1);  
-     }
-     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,j1,strtok(optionfile, "."),cpt,j1);
-     }
-     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, "."),j1,strtok(optionfile, "."),j1);
-fprintf(fichtm,"\n</body>");
-   }
- }
-fclose(fichtm);
 
   /*--------------- Prevalence limit --------------*/
   
@@ -2441,8 +3784,10 @@ fclose(fichtm);
   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);
@@ -2455,8 +3800,8 @@ fclose(fichtm);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
   k=0;
-  agebase=agemin;
-  agelim=agemax;
+  agebase=ageminpar;
+  agelim=agemaxpar;
   ftolpl=1.e-10;
   i1=cptcoveff;
   if (cptcovn < 1){i1=1;}
@@ -2466,9 +3811,16 @@ fclose(fichtm);
 	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);
@@ -2480,21 +3832,26 @@ fclose(fichtm);
       }
     }
   fclose(ficrespl);
+
   /*------------- h Pij x at various ages ------------*/
   
   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;
+  /*if (stepm<=24) stepsize=2;*/
 
   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++){
@@ -2507,6 +3864,9 @@ fclose(fichtm);
 	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);  
@@ -2515,49 +3875,72 @@ fclose(fichtm);
 	    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(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
+
   fclose(ficrespij);
 
+
+  /*---------- Forecasting ------------------*/
+  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);
+  } 
+  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);
+  }
+  
+
   /*---------- Health expectancies and variances ------------*/
 
   strcpy(filerest,"t");
   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]]);
@@ -2565,59 +3948,70 @@ fclose(fichtm);
 
       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) ");
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
       fprintf(ficrest,"\n");
-	
-      hf=1;
-      if (stepm >= YEARM) hf=stepm/YEARM;
+
       epj=vector(1,nlstate+1);
       for(age=bage; age <=fage ;age++){
 	prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
-	fprintf(ficrest," %.0f",age);
+	if (popbased==1) {
+	  for(i=1; i<=nlstate;i++)
+	    prlim[i][i]=probs[(int)age][i][k];
+	}
+	
+	fprintf(ficrest," %4.0f",age);
 	for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
 	  for(i=1, epj[j]=0.;i <=nlstate;i++) {
-	    epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];
+	    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," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));
+	fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
 	for(j=1;j <=nlstate;j++){
-	  fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));
+	  fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
 	}
 	fprintf(ficrest,"\n");
       }
     }
   }
-	
- fclose(ficreseij);
- fclose(ficresvij);
+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);
   fclose(ficpar);
   free_vector(epj,1,nlstate+1);
-  /*  scanf("%d ",i); */
-
+  
   /*------- Variance limit prevalence------*/   
 
-strcpy(fileresvpl,"vpl");
+  strcpy(fileresvpl,"vpl");
   strcat(fileresvpl,fileres);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);
@@ -2625,19 +4019,19 @@ strcpy(fileresvpl,"vpl");
   }
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);
 
- k=0;
- for(cptcov=1;cptcov<=i1;cptcov++){
-   for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-     k=k+1;
-     fprintf(ficresvpl,"\n#****** ");
-     for(j=1;j<=cptcoveff;j++) 
-       fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-     fprintf(ficresvpl,"******\n");
-     
-     varpl=matrix(1,nlstate,(int) bage, (int) fage);
-     oldm=oldms;savm=savms;
+  k=0;
+  for(cptcov=1;cptcov<=i1;cptcov++){
+    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+      k=k+1;
+      fprintf(ficresvpl,"\n#****** ");
+      for(j=1;j<=cptcoveff;j++) 
+	fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+      fprintf(ficresvpl,"******\n");
+      
+      varpl=matrix(1,nlstate,(int) bage, (int) fage);
+      oldm=oldms;savm=savms;
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
-   }
+    }
  }
 
   fclose(ficresvpl);
@@ -2653,38 +4047,54 @@ strcpy(fileresvpl,"vpl");
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
-  
+ 
   free_matrix(matcov,1,npar,1,npar);
   free_vector(delti,1,npar);
-  
+  free_matrix(agev,1,maxwav,1,imx);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
 
-  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);*/
   /*printf("Total time was %d uSec.\n", total_usecs);*/
   /*------ End -----------*/
 
+
  end:
 #ifdef windows
- chdir(pathcd);
+  /* chdir(pathcd);*/
 #endif 
  /*system("wgnuplot graph.plt");*/
  /*system("../gp37mgw/wgnuplot graph.plt");*/
  /*system("cd ../gp37mgw");*/
- system("..\\gp37mgw\\wgnuplot graph.plt");
+ /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
+ strcpy(plotcmd,GNUPLOTPROGRAM);
+ strcat(plotcmd," ");
+ strcat(plotcmd,optionfilegnuplot);
+ system(plotcmd);
 
 #ifdef windows
   while (z[0] != 'q') {
-    chdir(pathcd); 
-    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