--- imach096d/src/imach.c	2001/05/02 17:50:24	1.7
+++ imach096d/src/imach.c	2002/03/29 15:31:59	1.37
@@ -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 1.37 2002/03/29 15:31:59 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
+  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, 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 "wgnuplot"
+/*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define FILENAMELENGTH 80
 /*#define DEBUG*/
 #define windows
@@ -67,23 +77,26 @@
 #define AGEBASE 40
 
 
+int erreur; /* Error number */
 int nvar;
-static int cptcov;
-int cptcovn, cptcovage=0, cptcoveff=0;
+int cptcovn, 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 */
+int jmin, jmax; /* min, max spacing between 2 waves */
 int mle, weightopt;
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
+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 *ficgp,*ficresprob,*ficpop;
 FILE *ficreseij;
   char filerese[FILENAMELENGTH];
  FILE  *ficresvij;
@@ -111,7 +124,7 @@ 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)
 
@@ -123,10 +136,14 @@ 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 */
@@ -137,14 +154,18 @@ 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 );
+#ifdef windows
    s = strrchr( path, '\\' );		/* find last / */
+#else
+   s = strrchr( path, '/' );		/* find last / */
+#endif
    if ( s == NULL ) {			/* no directory, so use current */
 #if	defined(__bsd__)		/* get current working directory */
       extern char	*getwd( );
@@ -167,7 +188,18 @@ 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 */
 }
 
@@ -658,17 +690,15 @@ 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 +723,7 @@ double **prevalim(double **prlim, int nl
   }
 }
 
-/*************** transition probabilities **********/ 
+/*************** transition probabilities ***************/ 
 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 {
@@ -719,6 +749,8 @@ 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 +772,7 @@ 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 +790,7 @@ 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 +837,9 @@ 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]]];
 
 
@@ -841,34 +874,31 @@ double func( double *x)
   /* We are differentiating ll according to initial status */
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   /*for(i=1;i<imx;i++) 
-printf(" %d\n",s[4][i]);
+    printf(" %d\n",s[4][i]);
   */
   cov[1]=1.;
 
   for(k=1; k<=nlstate; k++) ll[k]=0.;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-       for(mi=1; mi<= wav[i]-1; mi++){
+    for(mi=1; mi<= wav[i]-1; mi++){
       for (ii=1;ii<=nlstate+ndeath;ii++)
 	for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-            for(d=0; d<dh[mi][i]; d++){
-	      newm=savm;
-	      cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-	      for (kk=1; kk<=cptcovage;kk++) {
-		 cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-		 /*printf("%d %d",kk,Tage[kk]);*/
-	      }
-	      /*cov[4]=covar[1][i]*cov[2];scanf("%d", i);*/
-	      /*cov[3]=pow(cov[2],2)/1000.;*/
-
-	  out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-		       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-	  savm=oldm;
-	  oldm=newm;
-
-
+      for(d=0; d<dh[mi][i]; d++){
+	newm=savm;
+	cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+	for (kk=1; kk<=cptcovage;kk++) {
+	  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+	}
+	
+	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+		     1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+	savm=oldm;
+	oldm=newm;
+	
+	
       } /* end mult */
-   
+      
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
       ipmx +=1;
@@ -899,7 +929,7 @@ void mlikeli(FILE *ficres,double p[], in
   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(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
 
 }
 
@@ -916,7 +946,6 @@ 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");
@@ -924,14 +953,16 @@ void hesscov(double **matcov, double p[]
     printf("%d",i);fflush(stdout);
     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);
 	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]);*/
       }
     }
   }
@@ -1035,7 +1066,7 @@ double hessii( double x[], double delta,
     }
   }
   delti[theta]=delts;
-  return res;
+  return res; 
   
 }
 
@@ -1148,18 +1179,18 @@ 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;
   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) {
@@ -1168,92 +1199,198 @@ void  freqsummary(char fileres[], int ag
   }
   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-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)
+	  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=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)
+	    printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+	  else
+	    printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+	  if( i <= (int) agemax){
+	    if(pos>=1.e-5){
+	      fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
+	      probs[i][jk][j1]= pp[jk]/pos;
+	      /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
+	    }
+	    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 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+	if(i <= (int) agemax)
+	  fprintf(ficresp,"\n");
+	printf("\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) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
+	      /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */ 
+	    }
+	  }
+	}
+      }
+	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;
+	     }
+	   }
+	 }
+	 
+	}
+    }
+  }
+  
+  
+  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
+  free_vector(pp,1,nlstate);
+  
 }  /* End of Freq */
 
 /************* Waves Concatenation ***************/
@@ -1268,9 +1405,14 @@ void  concatwav(int wav[], int **dh, int
      */
 
   int i, mi, m;
-  int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
-float sum=0.;
+  /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
+     double sum=0., jmean=0.;*/
 
+  int j, k=0,jk, ju, jl;
+  double sum=0.;
+  jmin=1e+5;
+  jmax=-1;
+  jmean=0.;
   for(i=1; i<=imx; i++){
     mi=0;
     m=firstpass;
@@ -1300,14 +1442,22 @@ float sum=0.;
 	dh[mi][i]=1;
       else{
 	if (s[mw[mi+1][i]][i] > nlstate) {
+	  if (agedc[i] < 2*AGESUP) {
 	  j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
-	  if(j=0) j=1;  /* Survives at least one month after exam */
+	  if(j==0) j=1;  /* Survives at least one month after exam */
+	  k=k+1;
+	  if (j >= jmax) jmax=j;
+	  if (j <= jmin) jmin=j;
+	  sum=sum+j;
+	  /*if (j<0) printf("j=%d num=%d \n",j,i); */
+	  }
 	}
 	else{
 	  j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
 	  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;
@@ -1322,8 +1472,9 @@ float sum=0.;
       }
     }
   }
-  printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);
-}
+  jmean=sum/k;
+  printf("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)
 {
@@ -1338,54 +1489,53 @@ void tricode(int *Tvar, int **nbcode, in
     for (i=1; i<=imx; i++) {
       ij=(int)(covar[Tvar[j]][i]);
       Ndum[ij]++; 
+      /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       if (ij > cptcode) cptcode=ij; 
     }
 
-    /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/
     for (i=0; i<=cptcode; i++) {
       if(Ndum[i]!=0) ncodemax[j]++;
     }
     ij=1; 
 
+
     for (i=1; i<=ncodemax[j]; i++) {
       for (k=0; k<=19; k++) {
 	if (Ndum[k] != 0) {
 	  nbcode[Tvar[j]][ij]=k; 
-	  /*   printf("ij=%d ",nbcode[Tvar[2]][1]);*/
+	  /*	 printf("nbcodeaaaaaaaaaaa=%d Tvar[j]=%d ij=%d j=%d",nbcode[Tvar[j]][ij],Tvar[j],ij,j);*/
 	  ij++;
 	}
 	if (ij > ncodemax[j]) break; 
       }  
     } 
   }  
- for (i=1; i<=10; i++) {
+
+ for (k=0; k<19; k++) Ndum[k]=0;
+
+ for (i=1; i<=ncovmodel-2; i++) {
       ij=Tvar[i];
       Ndum[ij]++; 
     }
+
  ij=1;
- for (i=1; i<=cptcovn; i++) {
-   if((Ndum[i]!=0) && (i<=ncov)){
-     Tvaraff[i]=ij; 
-   ij++;
+ for (i=1; i<=10; i++) {
+   if((Ndum[i]!=0) && (i<=ncovcol)){
+     Tvaraff[ij]=i; 
+     ij++;
    }
  }
  
- for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
-   if ((Tvar[j]>= cptcoveff) && (Tvar[j] <=ncov)) cptcoveff=Tvar[j];
-   /*printf("j=%d %d\n",j,Tvar[j]);*/
- }
- 
- /* printf("cptcoveff=%d Tvaraff=%d %d\n",cptcoveff, Tvaraff[1],Tvaraff[2]);
-    scanf("%d",i);*/
+    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)
 {
   /* Health expectancies */
-  int i, j, nhstepm, hstepm, h;
-  double age, agelim,hf;
+  int i, j, nhstepm, hstepm, h, nstepm;
+  double age, agelim, hf;
   double ***p3mat;
   
   fprintf(ficreseij,"# Health expectancies\n");
@@ -1395,34 +1545,57 @@ void evsij(char fileres[], double ***eij
       fprintf(ficreseij," %1d-%1d",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);
     /* 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. */
     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 );
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){
-	fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);
+	fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);
       }
     fprintf(ficreseij,"\n");
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
@@ -1430,19 +1603,19 @@ void evsij(char fileres[], double ***eij
 }
 
 /************ Variance ******************/
-void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
+void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)
 {
   /* Variance of health expectancies */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   double **newm;
   double **dnewm,**doldm;
-  int i, j, nhstepm, hstepm, h;
+  int i, j, nhstepm, hstepm, h, nstepm ;
   int k, cptcode;
-   double *xp;
+  double *xp;
   double **gp, **gm;
   double ***gradg, ***trgradg;
   double ***p3mat;
-  double age,agelim;
+  double age,agelim, hf;
   int theta;
 
    fprintf(ficresvij,"# Covariances of life expectancies\n");
@@ -1456,13 +1629,27 @@ void varevsij(char fileres[], double ***
   dnewm=matrix(1,nlstate,1,npar);
   doldm=matrix(1,nlstate,1,nlstate);
   
-  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);
@@ -1474,6 +1661,12 @@ void varevsij(char fileres[], double ***
       }
       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++)
@@ -1485,12 +1678,19 @@ void varevsij(char fileres[], double ***
 	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++)
 	for(h=0; h<=nhstepm; h++){
 	  gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
@@ -1504,24 +1704,25 @@ void varevsij(char fileres[], double ***
 	for(theta=1; theta <=npar; theta++)
 	  trgradg[h][j][theta]=gradg[h][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;
+
     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);
@@ -1530,7 +1731,7 @@ 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(xp,1,npar);
   free_matrix(doldm,1,nlstate,1,npar);
   free_matrix(dnewm,1,nlstate,1,nlstate);
@@ -1620,101 +1821,747 @@ void varprevlim(char fileres[], double *
 
 }
 
-
-
-/***********************************************/
-/**************** Main Program *****************/
-/***********************************************/
-
-/*int main(int argc, char *argv[])*/
-int main()
+/************ Variance of one-step probabilities  ******************/
+void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)
 {
+  int i, j;
+  int k=0, cptcode;
+  double **dnewm,**doldm;
+  double *xp;
+  double *gp, *gm;
+  double **gradg, **trgradg;
+  double age,agelim, cov[NCOVMAX];
+  int theta;
+  char fileresprob[FILENAMELENGTH];
 
-  int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;
-  double agedeb, agefin,hf;
-  double agemin=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 title[MAXLINE];
-  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[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;
-  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;
+  strcpy(fileresprob,"prob"); 
+  strcat(fileresprob,fileres);
+  if((ficresprob=fopen(fileresprob,"w"))==NULL) {
+    printf("Problem with resultfile: %s\n", fileresprob);
+  }
+  printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);
   
-  int hstepm, nhstepm;
-  double bage, fage, age, agelim, agebase;
-  double ftolpl=FTOL;
-  double **prlim;
-  double *severity;
-  double ***param; /* Matrix of parameters */
-  double  *p;
-  double **matcov; /* Matrix of covariance */
-  double ***delti3; /* Scale */
-  double *delti; /* Scale */
-  double ***eij, ***vareij;
-  double **varpl; /* Variances of prevalence limits by age */
-  double *epj, vepp;
-  char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";
-  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;
+  xp=vector(1,npar);
+  dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+  doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));
   
-  gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+  cov[1]=1;
+  for (age=bage; age<=fage; age ++){ 
+    cov[2]=age;
+    gradg=matrix(1,npar,1,9);
+    trgradg=matrix(1,9,1,npar);
+    gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
+    gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
+    
+    for(theta=1; theta <=npar; theta++){
+      for(i=1; i<=npar; i++)
+	xp[i] = x[i] + (i==theta ?delti[theta]:0);
+     
+      pmij(pmmij,cov,ncovmodel,xp,nlstate);
+   
+      k=0;
+      for(i=1; i<= (nlstate+ndeath); i++){
+	for(j=1; j<=(nlstate+ndeath);j++){
+	   k=k+1;
+	  gp[k]=pmmij[i][j];
+	}
+      }
 
+      for(i=1; i<=npar; i++)
+	xp[i] = x[i] - (i==theta ?delti[theta]:0);
+    
 
-  printf("\nIMACH, Version 0.64a");
-  printf("\nEnter the parameter file name: ");
+      pmij(pmmij,cov,ncovmodel,xp,nlstate);
+      k=0;
+      for(i=1; i<=(nlstate+ndeath); i++){
+	for(j=1; j<=(nlstate+ndeath);j++){
+	  k=k+1;
+	  gm[k]=pmmij[i][j];
+	}
+      }
+     
+       for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++) 
+	   gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
+    }
 
-#ifdef windows
-  scanf("%s",pathtot);
-  getcwd(pathcd, size);
-  /*cygwin_split_path(pathtot,path,optionfile);
-    printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
-  /* cutv(path,optionfile,pathtot,'\\');*/
+     for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)
+      for(theta=1; theta <=npar; theta++)
+      trgradg[j][theta]=gradg[theta][j];
+ 
+     matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);
+     matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);
 
-split(pathtot, path,optionfile);
-  chdir(path);
-  replace(pathc,path);
-#endif
-#ifdef unix
-  scanf("%s",optionfile);
-#endif
+     pmij(pmmij,cov,ncovmodel,x,nlstate);
 
-/*-------- arguments in the command line --------*/
+     k=0;
+     for(i=1; i<=(nlstate+ndeath); i++){
+       for(j=1; j<=(nlstate+ndeath);j++){
+	 k=k+1;
+	 gm[k]=pmmij[i][j];
+	}
+     }
+     
+     /*printf("\n%d ",(int)age);
+     for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
+       
 
-  strcpy(fileres,"r");
-  strcat(fileres, optionfile);
+       printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+     }*/
 
-  /*---------arguments file --------*/
+  fprintf(ficresprob,"\n%d ",(int)age);
 
-  if((ficpar=fopen(optionfile,"r"))==NULL)    {
-    printf("Problem with optionfile %s\n",optionfile);
-    goto end;
-  }
+  for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
+    if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);
+if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);
+  }
+
+    free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+    free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+    free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+    free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+}
+ free_vector(xp,1,npar);
+fclose(ficresprob);
 
-  strcpy(filereso,"o");
-  strcat(filereso,fileres);
-  if((ficparo=fopen(filereso,"w"))==NULL) {
-    printf("Problem with Output resultfile: %s\n", filereso);goto end;
-  }
+}
+
+/******************* Printing html file ***********/
+void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+ int lastpass, int stepm, int weightopt, char model[],\
+ int imx,int jmin, int jmax, double jmeanint,char optionfile[], \
+ char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\
+ char version[], int popforecast, int estepm ){
+  int jj1, k1, i1, cpt;
+  FILE *fichtm;
+  /*char optionfilehtm[FILENAMELENGTH];*/
+
+  strcpy(optionfilehtm,optionfile);
+  strcat(optionfilehtm,".htm");
+  if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+    printf("Problem with %s \n",optionfilehtm), exit(0);
+  }
+
+ fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
+Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
+\n
+Total number of observations=%d <br>\n
+Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
+<hr  size=\"2\" color=\"#EC5E5E\"> 
+ <ul><li>Outputs files<br>\n
+ - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
+ - Gnuplot file name: <a href=\"%s\">%s</a><br>\n
+ - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n
+ - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n
+ - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n
+ - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,estepm);
+
+ fprintf(fichtm,"\n
+ - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n
+ - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
+ - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n
+ - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
+
+ 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," <li>Graphs</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\">");
+       }
+       fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>
+<img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
+       for(cpt=1; cpt<nlstate;cpt++){
+	 fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>
+<img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+       }
+    for(cpt=1; cpt<=nlstate;cpt++) {
+       fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
+interval) in state (%d): v%s%d%d.gif <br>
+<img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
+     }
+     for(cpt=1; cpt<=nlstate;cpt++) {
+        fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>
+<img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+     }
+     fprintf(fichtm,"\n<br>- Total life expectancy by age and
+health expectancies in states (1) and (2): e%s%d.gif<br>
+<img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
+fprintf(fichtm,"\n</body>");
+   }
+   }
+fclose(fichtm);
+}
+
+/******************* Gnuplot file **************/
+void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+
+  int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+
+  strcpy(optionfilegnuplot,optionfilefiname);
+  strcat(optionfilegnuplot,".gp.txt");
+  if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+    printf("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,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
+#endif
+#ifdef unix
+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 gif small size 400,300");
+#endif
+fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
+   }
+  }
+  /*2 eme*/
+
+  for (k1=1; k1<= m ; k1 ++) { 
+    fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);
+    
+    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",ageminpar,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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
+
+      for (i=1; i< nlstate ; i ++)
+	fprintf(ficgp,"+$%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);   
+      fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
+    } 
+  }  
+  
+  /* 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(jk=1; jk <=m; jk++) {
+  fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+   i=1;
+   for(k2=1; k2<=nlstate; k2++) {
+     k3=i;
+     for(k=1; k<=(nlstate+ndeath); k++) {
+       if (k != k2){
+    	fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+ij=1;
+	for(j=3; j <=ncovmodel; j++) {
+	  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+	    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+	    ij++;
+	  }
+	  else
+	  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+	}
+	  fprintf(ficgp,")/(1");
+	
+	for(k1=1; k1 <=nlstate; k1++){   
+	  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+ij=1;
+	  for(j=3; j <=ncovmodel; j++){
+	  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+	    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+	    ij++;
+	  }
+	  else
+	    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+	  }
+	  fprintf(ficgp,")");
+	}
+	fprintf(ficgp,") t \"p%d%d\" ", k2,k);
+	if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+	i=i+ncovmodel;
+       }
+     }
+   }
+   fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk); 
+   }
+   
+  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);
+  }
+  printf("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);
+  }
+  printf("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);
+    } 
+    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 title[MAXLINE];
+  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+  char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
+  
+  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+
+  char filerest[FILENAMELENGTH];
+  char fileregp[FILENAMELENGTH];
+  char popfile[FILENAMELENGTH];
+  char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
+  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 mobilav=0,popforecast=0;
+  int hstepm, nhstepm;
+  double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;
+
+  double bage, fage, age, agelim, agebase;
+  double ftolpl=FTOL;
+  double **prlim;
+  double *severity;
+  double ***param; /* Matrix of parameters */
+  double  *p;
+  double **matcov; /* Matrix of covariance */
+  double ***delti3; /* Scale */
+  double *delti; /* Scale */
+  double ***eij, ***vareij;
+  double **varpl; /* Variances of prevalence limits by age */
+  double *epj, vepp;
+  double kk1, kk2;
+  double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
+  
+
+  char version[80]="Imach version 0.8b, March 2002, INED-EUROREVES ";
+  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 */
+  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,optionfilext,optionfilefiname);
+   printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+  chdir(path);
+  replace(pathc,path);
+
+/*-------- arguments in the command line --------*/
+
+  strcpy(fileres,"r");
+  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);
+    goto end;
+  }
+
+  strcpy(filereso,"o");
+  strcat(filereso,fileres);
+  if((ficparo=fopen(filereso,"w"))==NULL) {
+    printf("Problem with Output resultfile: %s\n", filereso);goto end;
+  }
 
   /* Reads comments: lines beginning with '#' */
   while((c=getc(ficpar))=='#' && c!= EOF){
@@ -1725,17 +2572,21 @@ 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);
-
-  covar=matrix(0,NCOVMAX,1,n);    
-  if (strlen(model)<=1) cptcovn=0;
-  else {
-    j=0;
-    j=nbocc(model,'+');
-    cptcovn=j+1;
+  fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
+  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;
 
   ncovmodel=2+cptcovn;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
@@ -1766,7 +2617,8 @@ split(pathtot, path,optionfile);
       fprintf(ficparo,"\n");
     }
   
-  npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
+    npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
+
   p=param[1][1];
   
   /* Reads comments: lines beginning with '#' */
@@ -1827,12 +2679,17 @@ split(pathtot, path,optionfile);
   printf("\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(ficres,"#%s\n",version);
     
+    /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
     }
@@ -1856,7 +2713,7 @@ 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)) {
 	
@@ -1874,20 +2731,32 @@ 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); 
   Tprod=ivector(1,15); 
@@ -1903,89 +2772,63 @@ split(pathtot, path,optionfile);
     cptcovprod=j1;
     
     strcpy(modelsav,model); 
-   if (j==0) {
-      if (j1==0){
-	cutv(stra,strb,modelsav,'V');
-	Tvar[1]=atoi(strb);
-      }
-      else if (j1==1) {
-	cutv(stra,strb,modelsav,'*');
-	Tage[1]=1; cptcovage++;
-	if (strcmp(stra,"age")==0) {
+    if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
+      printf("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); 
+      /*      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) {
 	  cptcovprod--;
-	  cutv(strd,strc,strb,'V');
-	  Tvar[1]=atoi(strc);
+	  cutv(strb,stre,strd,'V');
+	  Tvar[i]=atoi(stre);
+	  cptcovage++;
+	    Tage[cptcovage]=i;
+	    /*printf("stre=%s ", stre);*/
 	}
-	else if (strcmp(strb,"age")==0) {
+	else if (strcmp(strd,"age")==0) {
 	  cptcovprod--;
-	  cutv(strd,strc,stra,'V');
-	  Tvar[1]=atoi(strc);
+	  cutv(strb,stre,strc,'V');
+	  Tvar[i]=atoi(stre);
+	  cptcovage++;
+	  Tage[cptcovage]=i;
 	}
 	else {
-	  cutv(strd,strc,strb,'V');
-	  cutv(stre,strd,stra,'V');
-	  Tvar[1]=ncov+1;
+	  cutv(strb,stre,strc,'V');
+	  Tvar[i]=ncovcol+k1;
+	  cutv(strb,strc,strd,'V'); 
+	  Tprod[k1]=i;
+	  Tvard[k1][1]=atoi(strc);
+	  Tvard[k1][2]=atoi(stre);
+	  Tvar[cptcovn+k2]=Tvard[k1][1];
+	  Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
 	  for (k=1; k<=lastobs;k++) 
-	      covar[ncov+1][k]=covar[atoi(strc)][k]*covar[atoi(strd)][k];
+	    covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
+	  k1++;
+	  k2=k2+2;
 	}
-	/*printf("%s %s %s\n", stra,strb,modelsav);
-printf("%d ",Tvar[1]);
-scanf("%d",i);*/
-      }
-    }
-   else {
-      for(i=j; i>=1;i--){
-	cutv(stra,strb,modelsav,'+');
-	/*printf("%s %s %s\n", stra,strb,modelsav);
-	  scanf("%d",i);*/
-	if (strchr(strb,'*')) {
-	  cutv(strd,strc,strb,'*');
-	  if (strcmp(strc,"age")==0) {
-	    cptcovprod--;
-	    cutv(strb,stre,strd,'V');
-	    Tvar[i+1]=atoi(stre);
-	    cptcovage++;
-	    Tage[cptcovage]=i+1;
-	    printf("stre=%s ", stre);
-	  }
-	  else if (strcmp(strd,"age")==0) {
-	    cptcovprod--;
-	    cutv(strb,stre,strc,'V');
-	    Tvar[i+1]=atoi(stre);
-	    cptcovage++;
-	    Tage[cptcovage]=i+1;
-	  }
-	  else {
-	    cutv(strb,stre,strc,'V');
-	    Tvar[i+1]=ncov+k1;
-	    cutv(strb,strc,strd,'V'); 
-	    Tprod[k1]=i+1;
-	    Tvard[k1][1]=atoi(strc);
-	    Tvard[k1][2]=atoi(stre);
-	    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];
-	    k1++;
-	    k2=k2+2;
-	  }
-	}
-	else {
-	  cutv(strd,strc,strb,'V');
-	  /* printf("%s %s %s", strd,strc,strb);*/
-	  Tvar[i+1]=atoi(strc);
-	}
-	strcpy(modelsav,stra);   
       }
-      cutv(strd,strc,stra,'V');
-      Tvar[1]=atoi(strc);
+      else {
+	/*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+       /*  scanf("%d",i);*/
+      cutv(strd,strc,strb,'V');
+      Tvar[i]=atoi(strc);
+      }
+      strcpy(modelsav,stra);  
+      /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+	scanf("%d",i);*/
     }
-  }
-  /* for (i=1; i<=5; i++)
-     printf("i=%d %d ",i,Tvar[i]);*/
-  /* printf("tvar=%d %d cptcovage=%d %d",Tvar[1],Tvar[2],cptcovage,Tage[1]);*/
- /*printf("cptcovprod=%d ", cptcovprod);*/
-  /*  scanf("%d ",i);*/
+}
+  
+  /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
+  printf("cptcovprod=%d ", cptcovprod);
+  scanf("%d ",i);*/
     fclose(fic);
 
     /*  if(mle==1){*/
@@ -1994,18 +2837,31 @@ scanf("%d",i);*/
     }
     /*-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);
 	      agev[m][i]=-1;
+	      }
 	    }
 	  }
 	  else if(s[m][i] !=9){ /* Should no more exist */
@@ -2048,8 +2904,8 @@ printf("Total number of individuals= %d,
     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);
 
@@ -2063,7 +2919,7 @@ printf("Total number of individuals= %d,
 
 
       Tcode=ivector(1,100);
-      nbcode=imatrix(1,nvar,1,8); 
+      nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
       ncodemax[1]=1;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);
       
@@ -2076,31 +2932,33 @@ 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) */
@@ -2110,11 +2968,12 @@ 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");
    for(i=1,jk=1; i <=nlstate; i++){
      for(k=1; k <=(nlstate+ndeath); k++){
        if (k != i) 
@@ -2136,8 +2995,8 @@ printf("Total number of individuals= %d,
     ftolhess=ftol; /* Usually correct */
     hesscov(matcov, p, npar, delti, ftolhess, func);
  }
-    fprintf(ficres,"# Scales\n");
-    printf("# Scales\n");
+    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+    printf("# Scales (for hessian or gradient estimation)\n");
      for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
 	if (j!=i) {
@@ -2152,11 +3011,11 @@ printf("Total number of individuals= %d,
 	  fprintf(ficres,"\n");
 	}
       }
-      }
+     }
     
     k=1;
-    fprintf(ficres,"# Covariance\n");
-    printf("# Covariance\n");
+    fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+    printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
       i1=(i-1)/(ncovmodel*nlstate)+1; 
@@ -2180,205 +3039,46 @@ printf("Total number of individuals= %d,
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
-  
-    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);
-    
+    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 = agemin;
-      fage = agemax;
+      bage = ageminpar;
+      fage = agemaxpar;
     }
-
+    
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
-    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
-
-   
-/*------------ gnuplot -------------*/
-chdir(pathcd);
-  if((ficgp=fopen("graph.plt","w"))==NULL) {
-    printf("Problem with file graph.gp");goto end;
+    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);
   }
-#ifdef windows
-  fprintf(ficgp,"cd \"%s\" \n",pathc);
-#endif
-m=pow(2,cptcoveff);
+  ungetc(c,ficpar);
   
- /* 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);
-   }
-  }
-  /*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);
-    }
+  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);
  
-  /* 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 */
-   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;
-       }
-     }
-   }
-   fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk); 
-  }
-   
-  fclose(ficgp);
-   
-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);
-    /*  }*/
-   
-   /*________fin mle=1_________*/
-   
+   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);
@@ -2386,65 +3086,46 @@ 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);
-/*--------- index.htm --------*/
 
-  if((fichtm=fopen("index.htm","w"))==NULL)    {
-    printf("Problem with index.htm \n");goto end;
+  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);
 
- fprintf(fichtm,"<body><ul> Imach, Version 0.64a<hr> <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>",fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);
+  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);
 
- fprintf(fichtm," <li>Graphs</li>\n<p>");
+ freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
 
- m=cptcoveff;
- if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+/*------------ gnuplot -------------*/
+ printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);
+ 
+/*------------ 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>************ 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>");
-       }
-       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);
+/*--------- index.htm --------*/
+
+  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);
 
+  
   /*--------------- Prevalence limit --------------*/
   
   strcpy(filerespl,"pl");
@@ -2465,8 +3146,8 @@ 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;}
@@ -2490,6 +3171,7 @@ fclose(fichtm);
       }
     }
   fclose(ficrespl);
+
   /*------------- h Pij x at various ages ------------*/
   
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);
@@ -2499,7 +3181,7 @@ fclose(fichtm);
   printf("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 */
@@ -2538,8 +3220,24 @@ fclose(fichtm);
     }
   }
 
+  /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/
+
   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);
+    free_matrix(mint,1,maxwav,1,n);
+    free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
+    free_vector(weight,1,n);}
+  else{
+    erreur=108;
+    printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
+  }
+  
+
   /*---------- Health expectancies and variances ------------*/
 
   strcpy(filerest,"t");
@@ -2575,59 +3273,63 @@ 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);  
       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(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);
+    
+
+ 
       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];
 	  }
 	  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," %7.2f (%7.2f)", 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," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age]));
 	}
 	fprintf(ficrest,"\n");
       }
     }
   }
-	
- fclose(ficreseij);
- fclose(ficresvij);
+
+  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);
@@ -2635,19 +3337,19 @@ 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);
@@ -2663,35 +3365,43 @@ 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");
+  if(erreur >0)
+    printf("End of Imach with error or warning %d\n",erreur);
+  else   printf("End of Imach\n");
   /*  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("wgnuplot graph.plt");*/
+ /*system("../gp37mgw/wgnuplot graph.plt");*/
+ /*system("cd ../gp37mgw");*/
+ /* 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("index.htm");
-    }
+    else if (z[0] == 'e') system(optionfilehtm);
+    else if (z[0] == 'g') system(plotcmd);
     else if (z[0] == 'q') exit(0);
   }
 #endif