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Diff for /imach/src/imach.c between versions 1.1.1.1 and 1.60

-version 1.1.1.1, 2000/12/28 18:49:56
+version 1.60, 2002/11/19 00:17:38
  Line 1
+ /* $Id$
- /*********************** Imach **************************************
+    Interpolated Markov Chain
-   This program computes Healthy Life Expectancies from cross-longitudinal
-   data. Cross-longitudinal consist in a first survey ("cross") where
+   Short summary of the programme:
-   individuals from different ages are interviewed on their health status
-   or degree of  disability. At least a second wave of interviews
+   This program computes Healthy Life Expectancies from
-   ("longitudinal") should  measure each new individual health status.
+   cross-longitudinal data. Cross-longitudinal data consist in: -1- a
-   Health expectancies are computed from the transistions observed between
+   first survey ("cross") where individuals from different ages are
-   waves and are computed for each degree of severity of disability (number
+   interviewed on their health status or degree of disability (in the
-   of life states). More degrees you consider, more time is necessary to
+   case of a health survey which is our main interest) -2- at least a
-   reach the Maximum Likekilhood of the parameters involved in the model.
+   second wave of interviews ("longitudinal") which measure each change
-   The simplest model is the multinomial logistic model where pij is
+   (if any) in individual health status.  Health expectancies are
-   the probabibility to be observed in state j at the second wave conditional
+   computed from the time spent in each health state according to a
-   to be observed in state i at the first wave. Therefore the model is:
+   model. More health states you consider, more time is necessary to reach the
-   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'
+   Maximum Likelihood of the parameters involved in the model.  The
-   is a covariate. If you want to have a more complex model than "constant and
+   simplest model is the multinomial logistic model where pij is the
-   age", you should modify the program where the markup
+   probability to be observed in state j at the second wave
-     *Covariates have to be included here again* invites you to do it.
+   conditional to be observed in state i at the first wave. Therefore
-   More covariates you add, less is the speed of the convergence.
+   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
-   The advantage that this computer programme claims, comes from that if the
+   complex model than "constant and age", you should modify the program
-   delay between waves is not identical for each individual, or if some
+   where the markup *Covariates have to be included here again* invites
-   individual missed an interview, the information is not rounded or lost, but
+   you to do it.  More covariates you add, slower the
-   taken into account using an interpolation or extrapolation.
+   convergence.
-   hPijx is the probability to be
-   observed in state i at age x+h conditional to the observed state i at age
+   The advantage of this computer programme, compared to a simple
-   x. The delay 'h' can be split into an exact number (nh*stepm) of
+   multinomial logistic model, is clear when the delay between waves is not
-   unobserved intermediate  states. This elementary transition (by month or
+   identical for each individual. Also, if a individual missed an
-   quarter trimester, semester or year) is model as a multinomial logistic.
+   intermediate interview, the information is lost, but taken into
-   The hPx matrix is simply the matrix product of nh*stepm elementary matrices
+   account using an interpolation or extrapolation.
-   and the contribution of each individual to the likelihood is simply hPijx.
+   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.
+   of the life expectancies. It also computes the stable prevalence.
    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
             Institut national d'études démographiques, Paris.
- Line 48
+ Line 56
  #include <unistd.h>
  #define MAXLINE 256
+ #define GNUPLOTPROGRAM "gnuplot"
+ /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
  #define FILENAMELENGTH 80
  /*#define DEBUG*/
- /*#define win*/
+ #define windows
+ #define GLOCK_ERROR_NOPATH              -1      /* empty path */
+ #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
- #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncov */
+ #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
  #define NINTERVMAX 8
  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
- Line 63
+ Line 75
  #define YEARM 12. /* Number of months per year */
  #define AGESUP 130
  #define AGEBASE 40
+ #ifdef windows
+ #define DIRSEPARATOR '\\'
+ #define ODIRSEPARATOR '/'
+ #else
+ #define DIRSEPARATOR '/'
+ #define ODIRSEPARATOR '\\'
+ #endif
+ char version[80]="Imach version 0.9, November 2002, INED-EUROREVES ";
+ int erreur; /* Error number */
  int nvar;
+ int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
  int npar=NPARMAX;
  int nlstate=2; /* Number of live states */
  int ndeath=1; /* Number of dead states */
- int ncov;     /* Total number of covariables including constant a12*1 +b12*x ncov=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 */
+ int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
+            * wave mi and wave mi+1 is not an exact multiple of stepm. */
+ 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 *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
- FILE *ficgp, *fichtm;
+ FILE *ficlog;
+ FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
+ FILE *ficresprobmorprev;
+ FILE *fichtm; /* Html File */
+ FILE *ficreseij;
+ char filerese[FILENAMELENGTH];
+ FILE  *ficresvij;
+ char fileresv[FILENAMELENGTH];
+ FILE  *ficresvpl;
+ char fileresvpl[FILENAMELENGTH];
+ char title[MAXLINE];
+ char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+ char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
+ char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+ char filelog[FILENAMELENGTH]; /* Log file */
+ char filerest[FILENAMELENGTH];
+ char fileregp[FILENAMELENGTH];
+ char popfile[FILENAMELENGTH];
+ char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
  #define NR_END 1
  #define FREE_ARG char*
- Line 102  FILE *ficgp, *fichtm;
+ Line 147  FILE *ficgp, *fichtm;
  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)
- Line 114  int imx;
+ Line 159  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=2,*cod;
+ int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
- double **pmmij;
+ double **pmmij, ***probs;
+ double dateintmean=0;
  double *weight;
  int **s; /* Status */
  double *agedc, **covar, idx;
+ int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
  double ftolhess; /* Tolerance for computing hessian */
+ /**************** split *************************/
+ static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
+ {
+   char  *ss;                            /* pointer */
+   int   l1, l2;                         /* length counters */
+   l1 = strlen(path );                   /* length of path */
+   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
+   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
+   if ( ss == NULL ) {                   /* no directory, so use current */
+     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
+       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
+ #if     defined(__bsd__)                /* get current working directory */
+     extern char *getwd( );
+     if ( getwd( dirc ) == NULL ) {
+ #else
+     extern char *getcwd( );
+     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
+ #endif
+       return( GLOCK_ERROR_GETCWD );
+     }
+     strcpy( name, path );               /* we've got it */
+   } else {                              /* strip direcotry from path */
+     ss++;                               /* after this, the filename */
+     l2 = strlen( ss );                  /* length of filename */
+     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
+     strcpy( name, ss );         /* save file name */
+     strncpy( dirc, path, l1 - l2 );     /* now the directory */
+     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
+   ss = strrchr( name, '.' );            /* find last / */
+   ss++;
+   strcpy(ext,ss);                       /* save extension */
+   l1= strlen( name);
+   l2= strlen(ss)+1;
+   strncpy( finame, name, l1-l2);
+   finame[l1-l2]= 0;
+   return( 0 );                          /* we're done */
+ }
  /******************************************/
- Line 141  void replace(char *s, char*t)
+ Line 238  void replace(char *s, char*t)
      if (t[i]== '\\') s[i]='/';
    }
  }
- void cut(char *u,char *v, char*t)
+ int nbocc(char *s, char occ)
+ {
+   int i,j=0;
+   int lg=20;
+   i=0;
+   lg=strlen(s);
+   for(i=0; i<= lg; i++) {
+   if  (s[i] == occ ) j++;
+   }
+   return j;
+ }
+ void cutv(char *u,char *v, char*t, char occ)
  {
-   int i,lg,j,p;
+   /* cuts string t into u and v where u is ended by char occ excluding it
+      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
+      gives u="abcedf" and v="ghi2j" */
+   int i,lg,j,p=0;
    i=0;
-   for(j=0; j<=strlen(t); j++) {
+   for(j=0; j<=strlen(t)-1; j++) {
-     if(t[j]=='\\') p=j;
+     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
    }
    lg=strlen(t);
    for(j=0; j<p; j++) {
      (u[j] = t[j]);
-     u[p]='\0';
    }
+      u[p]='\0';
-   for(j=0; j<= lg; j++) {
+    for(j=0; j<= lg; j++) {
      if (j>=(p+1))(v[j-p-1] = t[j]);
    }
  }
- Line 166  void nrerror(char error_text[])
+ Line 279  void nrerror(char error_text[])
  {
    fprintf(stderr,"ERREUR ...\n");
    fprintf(stderr,"%s\n",error_text);
-   exit(1);
+   exit(EXIT_FAILURE);
  }
  /*********************** vector *******************/
  double *vector(int nl, int nh)
- Line 339  double brent(double ax, double bx, doubl
+ Line 452  double brent(double ax, double bx, doubl
      tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
      printf(".");fflush(stdout);
+     fprintf(ficlog,".");fflush(ficlog);
  #ifdef DEBUG
      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
+     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
  #endif
      if (fabs(x-xm) <= (tol2-0.5*(b-a))){
- Line 465  void linmin(double p[], double xi[], int
+ Line 580  void linmin(double p[], double xi[], int
    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
  #ifdef DEBUG
    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
  #endif
    for (j=1;j<=n;j++) {
      xi[j] *= xmin;
- Line 477  void linmin(double p[], double xi[], int
+ Line 593  void linmin(double p[], double xi[], int
  /*************** powell ************************/
  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
              double (*func)(double []))
  {
    void linmin(double p[], double xi[], int n, double *fret,
                double (*func)(double []));
    int i,ibig,j;
- Line 498  void powell(double p[], double **xi, int
+ Line 611  void powell(double p[], double **xi, int
      ibig=0;
      del=0.0;
      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
+     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
      for (i=1;i<=n;i++)
        printf(" %d %.12f",i, p[i]);
+     fprintf(ficlog," %d %.12f",i, p[i]);
      printf("\n");
+     fprintf(ficlog,"\n");
      for (i=1;i<=n;i++) {
        for (j=1;j<=n;j++) xit[j]=xi[j][i];
        fptt=(*fret);
  #ifdef DEBUG
        printf("fret=%lf \n",*fret);
+       fprintf(ficlog,"fret=%lf \n",*fret);
  #endif
        printf("%d",i);fflush(stdout);
+       fprintf(ficlog,"%d",i);fflush(ficlog);
        linmin(p,xit,n,fret,func);
        if (fabs(fptt-(*fret)) > del) {
          del=fabs(fptt-(*fret));
- Line 515  void powell(double p[], double **xi, int
+ Line 633  void powell(double p[], double **xi, int
        }
  #ifdef DEBUG
        printf("%d %.12e",i,(*fret));
+       fprintf(ficlog,"%d %.12e",i,(*fret));
        for (j=1;j<=n;j++) {
          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
          printf(" x(%d)=%.12e",j,xit[j]);
+         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
        }
-       for(j=1;j<=n;j++)
+       for(j=1;j<=n;j++) {
          printf(" p=%.12e",p[j]);
+         fprintf(ficlog," p=%.12e",p[j]);
+       }
        printf("\n");
+       fprintf(ficlog,"\n");
  #endif
      }
      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
- Line 530  void powell(double p[], double **xi, int
+ Line 653  void powell(double p[], double **xi, int
        k[0]=1;
        k[1]=-1;
        printf("Max: %.12e",(*func)(p));
-       for (j=1;j<=n;j++)
+       fprintf(ficlog,"Max: %.12e",(*func)(p));
+       for (j=1;j<=n;j++) {
          printf(" %.12e",p[j]);
+         fprintf(ficlog," %.12e",p[j]);
+       }
        printf("\n");
+       fprintf(ficlog,"\n");
        for(l=0;l<=1;l++) {
          for (j=1;j<=n;j++) {
            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
          }
          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
        }
  #endif
- Line 566  void powell(double p[], double **xi, int
+ Line 695  void powell(double p[], double **xi, int
          }
  #ifdef DEBUG
          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-         for(j=1;j<=n;j++)
+         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+         for(j=1;j<=n;j++){
            printf(" %.12e",xit[j]);
+           fprintf(ficlog," %.12e",xit[j]);
+         }
          printf("\n");
+         fprintf(ficlog,"\n");
  #endif
        }
      }
    }
  }
- /**** Prevalence limit ****************/
+ /**** Prevalence limit (stable prevalence)  ****************/
- double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl)
+ double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
  {
    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       matrix by transitions matrix until convergence is reached */
- Line 593  double **prevalim(double **prlim, int nl
+ Line 726  double **prevalim(double **prlim, int nl
      for (j=1;j<=nlstate+ndeath;j++){
        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      }
-   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+    cov[1]=1.;
+  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
      newm=savm;
      /* Covariates have to be included here again */
-     cov[1]=1.;
+      cov[2]=agefin;
-     cov[2]=agefin;
-     out=matprod2(newm, pmij(pmmij,cov,ncov,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
+       for (k=1; k<=cptcovn;k++) {
- /*    printf("age=%f agefin=%f po=%f pn=%f\n",age,agefin,oldm[1][1],newm[1][1]);*/
+         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[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<=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;
      oldm=newm;
      maxmax=0.;
- Line 624  double **prevalim(double **prlim, int nl
+ Line 770  double **prevalim(double **prlim, int nl
    }
  }
- /*************** transition probabilities **********/
+ /*************** transition probabilities ***************/
- double **pmij(double **ps, double *cov, int ncov, double *x, int nlstate )
+ double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
  {
    double s1, s2;
    /*double t34;*/
- Line 634  double **pmij(double **ps, double *cov,
+ Line 780  double **pmij(double **ps, double *cov,
      for(i=1; i<= nlstate; i++){
      for(j=1; j<i;j++){
-       for (nc=1, s2=0.;nc <=ncov; nc++){
+       for (nc=1, s2=0.;nc <=ncovmodel; nc++){
          /*s2 += param[i][j][nc]*cov[nc];*/
-         s2 += x[(i-1)*nlstate*ncov+(j-1)*ncov+nc+(i-1)*(ndeath-1)*ncov]*cov[nc];
+         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
        }
        ps[i][j]=s2;
        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
      }
      for(j=i+1; j<=nlstate+ndeath;j++){
-       for (nc=1, s2=0.;nc <=ncov; nc++){
+       for (nc=1, s2=0.;nc <=ncovmodel; nc++){
-         s2 += x[(i-1)*nlstate*ncov+(j-2)*ncov+nc+(i-1)*(ndeath-1)*ncov]*cov[nc];
+         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
        }
        ps[i][j]=s2;
      }
    }
+     /*ps[3][2]=1;*/
    for(i=1; i<= nlstate; i++){
       s1=0;
      for(j=1; j<i; j++)
- Line 671  double **pmij(double **ps, double *cov,
+ Line 819  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]);
- Line 688  double **pmij(double **ps, double *cov,
+ Line 837  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
- Line 705  double **matprod2(double **out, double *
+ Line 854  double **matprod2(double **out, double *
  /************* Higher Matrix Product ***************/
- double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm )
+ double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
  {
    /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month
       duration (i.e. until
- Line 717  double ***hpxij(double ***po, int nhstep
+ Line 866  double ***hpxij(double ***po, int nhstep
       */
-   int i, j, d, h;
+   int i, j, d, h, k;
    double **out, cov[NCOVMAX];
    double **newm;
- Line 734  double ***hpxij(double ***po, int nhstep
+ Line 883  double ***hpxij(double ***po, int nhstep
        /* Covariates have to be included here again */
        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++)
+         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("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
-                    pmij(pmmij,cov,ncov,x,nlstate));
+                    pmij(pmmij,cov,ncovmodel,x,nlstate));
        savm=oldm;
        oldm=newm;
      }
- Line 754  double ***hpxij(double ***po, int nhstep
+ Line 911  double ***hpxij(double ***po, int nhstep
  /*************** log-likelihood *************/
  double func( double *x)
  {
-   int i, ii, j, k, mi, d;
+   int i, ii, j, k, mi, d, kk;
    double l, ll[NLSTATEMAX], cov[NCOVMAX];
    double **out;
    double sw; /* Sum of weights */
    double lli; /* Individual log likelihood */
+   int s1, s2;
+   double bbh;
    long ipmx;
    /*extern weight */
    /* 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(mi=1; mi<= wav[i]-1; mi++){
+     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+     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 (j=1;j<=nlstate+ndeath;j++){
-             for(d=0; d<dh[mi][i]; d++){
+           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+           savm[ii][j]=(ii==j ? 1.0 : 0.0);
+         }
+       for(d=0; d<dh[mi][i]; d++){
          newm=savm;
-           cov[1]=1.;
+         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         for (kk=1; kk<=cptcovage;kk++) {
-             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-,nlstate+ndeath,pmij(pmmij,cov,ncov,x,nlstate));
+         }
-           savm=oldm;
-           oldm=newm;
+         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+,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]]);
+       /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
+       /* But now since version 0.9 we anticipate for bias and large stepm.
+        * If stepm is larger than one month (smallest stepm) and if the exact delay
+        * (in months) between two waves is not a multiple of stepm, we rounded to
+        * the nearest (and in case of equal distance, to the lowest) interval but now
+        * we keep into memory the bias bh[mi][i] and also the previous matrix product
+        * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
+        * probability in order to take into account the bias as a fraction of the way
+        * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
+        * -stepm/2 to stepm/2 .
+        * For stepm=1 the results are the same as for previous versions of Imach.
+        * For stepm > 1 the results are less biased than in previous versions.
+        */
+       s1=s[mw[mi][i]][i];
+       s2=s[mw[mi+1][i]][i];
+       bbh=(double)bh[mi][i]/(double)stepm;
+       lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-bbh)*out[s1][s2]));
+       /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-bbh)*out[s1][s2]));*/
+       /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
+       /*if(lli ==000.0)*/
+       /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
        ipmx +=1;
        sw += weight[i];
        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
- Line 801  printf(" %d\n",s[4][i]);
+ Line 987  printf(" %d\n",s[4][i]);
  /*********** Maximum Likelihood Estimation ***************/
- void mlikeli(FILE *ficres,double p[], int npar, int ncov, int nlstate, double ftol, double (*func)(double []))
+ void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
  {
    int i,j, iter;
    double **xi,*delti;
- Line 810  void mlikeli(FILE *ficres,double p[], in
+ Line 996  void mlikeli(FILE *ficres,double p[], in
    for (i=1;i<=npar;i++)
      for (j=1;j<=npar;j++)
        xi[i][j]=(i==j ? 1.0 : 0.0);
-   printf("Powell\n");
+   printf("Powell\n");  fprintf(ficlog,"Powell\n");
    powell(p,xi,npar,ftol,&iter,&fret,func);
     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
-   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));
+   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
  }
- Line 831  void hesscov(double **matcov, double p[]
+ Line 1018  void hesscov(double **matcov, double p[]
    void lubksb(double **a, int npar, int *indx, double b[]) ;
    void ludcmp(double **a, int npar, int *indx, double *d) ;
    hess=matrix(1,npar,1,npar);
    printf("\nCalculation of the hessian matrix. Wait...\n");
+   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
    for (i=1;i<=npar;i++){
      printf("%d",i);fflush(stdout);
+     fprintf(ficlog,"%d",i);fflush(ficlog);
      hess[i][i]=hessii(p,ftolhess,i,delti);
      /*printf(" %f ",p[i]);*/
+     /*printf(" %lf ",hess[i][i]);*/
    }
    for (i=1;i<=npar;i++) {
      for (j=1;j<=npar;j++)  {
        if (j>i) {
          printf(".%d%d",i,j);fflush(stdout);
+         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
          hess[i][j]=hessij(p,delti,i,j);
          hess[j][i]=hess[i][j];
+         /*printf(" %lf ",hess[i][j]);*/
        }
      }
    }
    printf("\n");
+   fprintf(ficlog,"\n");
    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
+   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
    a=matrix(1,npar,1,npar);
    y=matrix(1,npar,1,npar);
- Line 872  void hesscov(double **matcov, double p[]
+ Line 1065  void hesscov(double **matcov, double p[]
    }
    printf("\n#Hessian matrix#\n");
+   fprintf(ficlog,"\n#Hessian matrix#\n");
    for (i=1;i<=npar;i++) {
      for (j=1;j<=npar;j++) {
        printf("%.3e ",hess[i][j]);
+       fprintf(ficlog,"%.3e ",hess[i][j]);
      }
      printf("\n");
+     fprintf(ficlog,"\n");
    }
    /* Recompute Inverse */
- Line 893  void hesscov(double **matcov, double p[]
+ Line 1089  void hesscov(double **matcov, double p[]
      for (i=1;i<=npar;i++){
        y[i][j]=x[i];
        printf("%.3e ",y[i][j]);
+       fprintf(ficlog,"%.3e ",y[i][j]);
      }
      printf("\n");
+     fprintf(ficlog,"\n");
    }
    */
- Line 936  double hessii( double x[], double delta,
+ Line 1134  double hessii( double x[], double delta,
  #ifdef DEBUG
        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
+       fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
  #endif
        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
- Line 950  double hessii( double x[], double delta,
+ Line 1149  double hessii( double x[], double delta,
      }
    }
    delti[theta]=delts;
    return res;
  }
- Line 983  double hessij( double x[], double delti[
+ Line 1182  double hessij( double x[], double delti[
      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
  #ifdef DEBUG
      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+     fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
  #endif
    }
    return res;
- Line 1063  void lubksb(double **a, int n, int *indx
+ Line 1263  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)
+ void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, 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;
+   int i, m, jk, k1,i1, j1, bool, z1,z2,j;
+   int first;
    double ***freq; /* Frequencies */
    double *pp;
-   double pos;
+   double pos, k2, dateintsum=0,k2cpt=0;
    FILE *ficresp;
    char fileresp[FILENAMELENGTH];
    pp=vector(1,nlstate);
+   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
    strcpy(fileresp,"p");
    strcat(fileresp,fileres);
    if((ficresp=fopen(fileresp,"w"))==NULL) {
      printf("Problem with prevalence resultfile: %s\n", fileresp);
+     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
      exit(0);
    }
    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
-   for (i=-1; i<=nlstate+ndeath; i++)
+   j1=0;
-     for (jk=-1; jk<=nlstate+ndeath; jk++)
-       for(m=agemin; m <= agemax+3; m++)
+   j=cptcoveff;
-         freq[i][jk][m]=0;
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-   for (i=1; i<=imx; i++)  {
+   first=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];
-     }
-   }
-   fprintf(ficresp, "#");
+   for(k1=1; k1<=j;k1++){
-   for(i=1; i<=nlstate;i++)
+     for(i1=1; i1<=ncodemax[k1];i1++){
-     fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+       j1++;
- fprintf(ficresp, "\n");
+       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+         scanf("%d", i);*/
-   for(i=(int)agemin; i <= (int)agemax+3; i++){
+       for (i=-1; i<=nlstate+ndeath; i++)
-     if(i==(int)agemax+3)
+         for (jk=-1; jk<=nlstate+ndeath; jk++)
-       printf("Total");
+           for(m=agemin; m <= agemax+3; m++)
-     else
+             freq[i][jk][m]=0;
-       printf("Age %d", i);
-     for(jk=1; jk <=nlstate ; jk++){
+       dateintsum=0;
-       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+       k2cpt=0;
-         pp[jk] += freq[jk][m][i];
+       for (i=1; i<=imx; i++) {
-     }
+         bool=1;
-     for(jk=1; jk <=nlstate ; jk++){
+         if  (cptcovn>0) {
-       for(m=-1, pos=0; m <=0 ; m++)
+           for (z1=1; z1<=cptcoveff; z1++)
-         pos += freq[jk][m][i];
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
-       if(pp[jk]>=1.e-10)
+               bool=0;
-         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+         }
-       else
+         if (bool==1){
-         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+           for(m=firstpass; m<=lastpass; m++){
-     }
+             k2=anint[m][i]+(mint[m][i]/12.);
-     for(jk=1; jk <=nlstate ; jk++){
+             if ((k2>=dateprev1) && (k2<=dateprev2)) {
-       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)
+               if(agev[m][i]==0) agev[m][i]=agemax+1;
-         pp[jk] += freq[jk][m][i];
+               if(agev[m][i]==1) agev[m][i]=agemax+2;
-     }
+               if (m<lastpass) {
-     for(jk=1,pos=0; jk <=nlstate ; jk++)
+                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
-       pos += pp[jk];
+                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
-     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);
+               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
-       else
+                 dateintsum=dateintsum+k2;
-         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+                 k2cpt++;
-       if( i <= (int) agemax){
+               }
-         if(pos>=1.e-5)
+             }
-           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
+           }
-       else
+         }
-           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
+       }
+       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
+       if  (cptcovn>0) {
+         fprintf(ficresp, "\n#********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         fprintf(ficresp, "**********\n#");
+       }
+       for(i=1; i<=nlstate;i++)
+         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+       fprintf(ficresp, "\n");
+       for(i=(int)agemin; i <= (int)agemax+3; i++){
+         if(i==(int)agemax+3){
+           fprintf(ficlog,"Total");
+         }else{
+           if(first==1){
+             first=0;
+             printf("See log file for details...\n");
+           }
+           fprintf(ficlog,"Age %d", i);
+         }
+         for(jk=1; jk <=nlstate ; jk++){
+           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+             pp[jk] += freq[jk][m][i];
+         }
+         for(jk=1; jk <=nlstate ; jk++){
+           for(m=-1, pos=0; m <=0 ; m++)
+             pos += freq[jk][m][i];
+           if(pp[jk]>=1.e-10){
+             if(first==1){
+             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+             }
+             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+           }else{
+             if(first==1)
+               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+           }
+         }
+         for(jk=1; jk <=nlstate ; jk++){
+           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
+             pp[jk] += freq[jk][m][i];
+         }
+         for(jk=1,pos=0; jk <=nlstate ; jk++)
+           pos += pp[jk];
+         for(jk=1; jk <=nlstate ; jk++){
+           if(pos>=1.e-5){
+             if(first==1)
+               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+           }else{
+             if(first==1)
+               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+           }
+           if( i <= (int) agemax){
+             if(pos>=1.e-5){
+               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
+               probs[i][jk][j1]= pp[jk]/pos;
+               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
+             }
+             else
+               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
+           }
+         }
+         for(jk=-1; jk <=nlstate+ndeath; jk++)
+           for(m=-1; m <=nlstate+ndeath; m++)
+             if(freq[jk][m][i] !=0 ) {
+             if(first==1)
+               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+             }
+         if(i <= (int) agemax)
+           fprintf(ficresp,"\n");
+         if(first==1)
+           printf("Others in log...\n");
+         fprintf(ficlog,"\n");
        }
      }
-     for(jk=-1; jk <=nlstate+ndeath; jk++)
-       for(m=-1; m <=nlstate+ndeath; m++)
-         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
-     if(i <= (int) agemax)
-       fprintf(ficresp,"\n");
-     printf("\n");
    }
+   dateintmean=dateintsum/k2cpt;
    fclose(ficresp);
    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
    free_vector(pp,1,nlstate);
+   /* End of Freq */
+ }
+ /************ Prevalence ********************/
+ void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
+ {  /* Some frequencies */
+   int i, m, jk, k1, i1, j1, bool, z1,z2,j;
+   double ***freq; /* Frequencies */
+   double *pp;
+   double pos, k2;
+   pp=vector(1,nlstate);
+   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
+   j1=0;
+   j=cptcoveff;
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+   for(k1=1; k1<=j;k1++){
+     for(i1=1; i1<=ncodemax[k1];i1++){
+       j1++;
+       for (i=-1; i<=nlstate+ndeath; i++)
+         for (jk=-1; jk<=nlstate+ndeath; jk++)
+           for(m=agemin; m <= agemax+3; m++)
+             freq[i][jk][m]=0;
+       for (i=1; i<=imx; i++) {
+         bool=1;
+         if  (cptcovn>0) {
+           for (z1=1; z1<=cptcoveff; z1++)
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+               bool=0;
+         }
+         if (bool==1) {
+           for(m=firstpass; m<=lastpass; m++){
+             k2=anint[m][i]+(mint[m][i]/12.);
+             if ((k2>=dateprev1) && (k2<=dateprev2)) {
+               if(agev[m][i]==0) agev[m][i]=agemax+1;
+               if(agev[m][i]==1) agev[m][i]=agemax+2;
+               if (m<lastpass) {
+                 if (calagedate>0)
+                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
+                 else
+                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];
+               }
+             }
+           }
+         }
+       }
+       for(i=(int)agemin; i <= (int)agemax+3; i++){
+         for(jk=1; jk <=nlstate ; jk++){
+           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+             pp[jk] += freq[jk][m][i];
+         }
+         for(jk=1; jk <=nlstate ; jk++){
+           for(m=-1, pos=0; m <=0 ; m++)
+             pos += freq[jk][m][i];
+         }
+         for(jk=1; jk <=nlstate ; jk++){
+           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
+             pp[jk] += freq[jk][m][i];
+         }
+         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
+         for(jk=1; jk <=nlstate ; jk++){
+           if( i <= (int) agemax){
+             if(pos>=1.e-5){
+               probs[i][jk][j1]= pp[jk]/pos;
+             }
+           }
+         }/* end jk */
+       }/* end i */
+     } /* end i1 */
+   } /* end k1 */
+   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
+   free_vector(pp,1,nlstate);
  }  /* End of Freq */
  /************* Waves Concatenation ***************/
- void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
+ void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
  {
    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
       Death is a valid wave (if date is known).
       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
-      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]
+      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
       and mw[mi+1][i]. dh depends on stepm.
       */
    int i, mi, m;
-   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
+   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
- float sum=0.;
+      double sum=0., jmean=0.;*/
+   int first;
+   int j, k=0,jk, ju, jl;
+   double sum=0.;
+   first=0;
+   jmin=1e+5;
+   jmax=-1;
+   jmean=0.;
    for(i=1; i<=imx; i++){
      mi=0;
      m=firstpass;
- Line 1185  float sum=0.;
+ Line 1546  float sum=0.;
      }
      wav[i]=mi;
-     if(mi==0)
+     if(mi==0){
-       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);
+       if(first==0){
+         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
+         first=1;
+       }
+       if(first==1){
+         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
+       }
+     } /* end mi==0 */
    }
    for(i=1; i<=imx; i++){
- Line 1195  float sum=0.;
+ Line 1563  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;
          jl= j -jk*stepm;
          ju= j -(jk+1)*stepm;
-         if(jl <= -ju)
+         if(jl <= -ju){
            dh[mi][i]=jk;
-         else
+           bh[mi][i]=jl;
+         }
+         else{
            dh[mi][i]=jk+1;
-         if(dh[mi][i]==0)
+           bh[mi][i]=ju;
+         }
+         if(dh[mi][i]==0){
            dh[mi][i]=1; /* At least one step */
+           bh[mi][i]=ju; /* At least one step */
+           printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);
+         }
+         if(i==298 || i==287 || i==763 ||i==1061)printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d",bh[mi][i],ju,jl,dh[mi][i],jk,stepm);
        }
      }
    }
-   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);
+   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
+  }
+ /*********** Tricode ****************************/
+ void tricode(int *Tvar, int **nbcode, int imx)
+ {
+   int Ndum[20],ij=1, k, j, i, maxncov=19;
+   int cptcode=0;
+   cptcoveff=0;
+   for (k=0; k<maxncov; k++) Ndum[k]=0;
+   for (k=1; k<=7; k++) ncodemax[k]=0;
+   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
+     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
+                                modality*/
+       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
+       Ndum[ij]++; /*store the modality */
+       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
+       if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
+                                        Tvar[j]. If V=sex and male is 0 and
+                                        female is 1, then  cptcode=1.*/
+     }
+     for (i=0; i<=cptcode; i++) {
+       if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
+     }
+     ij=1;
+     for (i=1; i<=ncodemax[j]; i++) {
+       for (k=0; k<= maxncov; k++) {
+         if (Ndum[k] != 0) {
+           nbcode[Tvar[j]][ij]=k;
+           /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
+           ij++;
+         }
+         if (ij > ncodemax[j]) break;
+       }
+     }
+   }
+  for (k=0; k< maxncov; k++) Ndum[k]=0;
+  for (i=1; i<=ncovmodel-2; i++) {
+    /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+    ij=Tvar[i];
+    Ndum[ij]++;
+  }
+  ij=1;
+  for (i=1; i<= maxncov; i++) {
+    if((Ndum[i]!=0) && (i<=ncovcol)){
+      Tvaraff[ij]=i; /*For printing */
+      ij++;
+    }
+  }
+  cptcoveff=ij-1; /*Number of simple covariates*/
  }
  /*********** Health Expectancies ****************/
- void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm)
+ void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
  {
    /* Health expectancies */
-   int i, j, nhstepm, hstepm, h;
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
-   double age, agelim,hf;
+   double age, agelim, hf;
-   double ***p3mat;
+   double ***p3mat,***varhe;
+   double **dnewm,**doldm;
-   FILE  *ficreseij;
+   double *xp;
-   char filerese[FILENAMELENGTH];
+   double **gp, **gm;
+   double ***gradg, ***trgradg;
-   strcpy(filerese,"e");
+   int theta;
-   strcat(filerese,fileres);
-   if((ficreseij=fopen(filerese,"w"))==NULL) {
-     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
-   }
-   printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
+   xp=vector(1,npar);
+   dnewm=matrix(1,nlstate*2,1,npar);
+   doldm=matrix(1,nlstate*2,1,nlstate*2);
    fprintf(ficreseij,"# Health expectancies\n");
    fprintf(ficreseij,"# Age");
    for(i=1; i<=nlstate;i++)
      for(j=1; j<=nlstate;j++)
-       fprintf(ficreseij," %1d-%1d",i,j);
+       fprintf(ficreseij," %1d-%1d (SE)",i,j);
    fprintf(ficreseij,"\n");
-   hstepm=1*YEARM; /*  Every j years of age (in month) */
+   if(estepm < stepm){
-   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
+     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);
+     nstepm=(int) rint((agelim-age)*YEARM/stepm);
-     /* Typically if 20 years = 20*12/6=40 stepm */
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-     if (stepm >= YEARM) hstepm=1;
+     /* if (stepm >= YEARM) hstepm=1;*/
-     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */
+     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
+     gp=matrix(0,nhstepm,1,nlstate*2);
+     gm=matrix(0,nhstepm,1,nlstate*2);
      /* Computed by stepm unit matrices, product of hstepm matrices, stored
         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm);
+     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+     /* Computing Variances of health expectancies */
+      for(theta=1; theta <=npar; theta++){
+       for(i=1; i<=npar; i++){
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+       }
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+       cptj=0;
+       for(j=1; j<= nlstate; j++){
+         for(i=1; i<=nlstate; i++){
+           cptj=cptj+1;
+           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
+             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
+           }
+         }
+       }
+       for(i=1; i<=npar; i++)
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+       cptj=0;
+       for(j=1; j<= nlstate; j++){
+         for(i=1;i<=nlstate;i++){
+           cptj=cptj+1;
+           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
+             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
+           }
+         }
+       }
+       for(j=1; j<= nlstate*2; j++)
+         for(h=0; h<=nhstepm-1; h++){
+           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+         }
+      }
+ /* End theta */
+      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
+      for(h=0; h<=nhstepm-1; h++)
+       for(j=1; j<=nlstate*2;j++)
+         for(theta=1; theta <=npar; theta++)
+           trgradg[h][j][theta]=gradg[h][theta][j];
+      for(i=1;i<=nlstate*2;i++)
+       for(j=1;j<=nlstate*2;j++)
+         varhe[i][j][(int)age] =0.;
+      printf("%d|",(int)age);fflush(stdout);
+      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+      for(h=0;h<=nhstepm-1;h++){
+       for(k=0;k<=nhstepm-1;k++){
+         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
+         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
+         for(i=1;i<=nlstate*2;i++)
+           for(j=1;j<=nlstate*2;j++)
+             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
+       }
+     }
+     /* Computing expectancies */
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++)
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-           eij[i][j][(int)age] +=p3mat[i][j][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;
+     fprintf(ficreseij,"%3.0f",age );
-     if (stepm >= YEARM) hf=stepm/YEARM;
+     cptj=0;
-     fprintf(ficreseij,"%.0f",age );
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++){
-         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);
+         cptj++;
+         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
        }
      fprintf(ficreseij,"\n");
+     free_matrix(gm,0,nhstepm,1,nlstate*2);
+     free_matrix(gp,0,nhstepm,1,nlstate*2);
+     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
+     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    }
-   fclose(ficreseij);
+   printf("\n");
+   fprintf(ficlog,"\n");
+   free_vector(xp,1,npar);
+   free_matrix(dnewm,1,nlstate*2,1,npar);
+   free_matrix(doldm,1,nlstate*2,1,nlstate*2);
+   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
  }
  /************ Variance ******************/
- void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl)
+ void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
  {
    /* Variance of health expectancies */
    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
-   double **newm;
+   /* double **newm;*/
    double **dnewm,**doldm;
-   int i, j, nhstepm, hstepm, h;
+   double **dnewmp,**doldmp;
-   int k;
+   int i, j, nhstepm, hstepm, h, nstepm ;
-   FILE  *ficresvij;
+   int k, cptcode;
-   char fileresv[FILENAMELENGTH];
    double *xp;
-   double **gp, **gm;
+   double **gp, **gm;  /* for var eij */
-   double ***gradg, ***trgradg;
+   double ***gradg, ***trgradg; /*for var eij */
+   double **gradgp, **trgradgp; /* for var p point j */
+   double *gpp, *gmp; /* for var p point j */
+   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
    double ***p3mat;
-   double age,agelim;
+   double age,agelim, hf;
+   double ***mobaverage;
    int theta;
+   char digit[4];
+   char digitp[25];
-   strcpy(fileresv,"v");
+   char fileresprobmorprev[FILENAMELENGTH];
-   strcat(fileresv,fileres);
-   if((ficresvij=fopen(fileresv,"w"))==NULL) {
+   if(popbased==1){
-     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+     if(mobilav!=0)
+       strcpy(digitp,"-populbased-mobilav-");
+     else strcpy(digitp,"-populbased-nomobil-");
+   }
+   else
+     strcpy(digitp,"-stablbased-");
+   if (mobilav!=0) {
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+     }
    }
-   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+   strcpy(fileresprobmorprev,"prmorprev");
+   sprintf(digit,"%-d",ij);
+   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
+   strcat(fileresprobmorprev,digit); /* Tvar to be done */
+   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
+   strcat(fileresprobmorprev,fileres);
+   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
+     printf("Problem with resultfile: %s\n", fileresprobmorprev);
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
+   }
+   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");
+   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
+   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+     fprintf(ficresprobmorprev," p.%-d SE",j);
+     for(i=1; i<=nlstate;i++)
+       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
+   }
+   fprintf(ficresprobmorprev,"\n");
+   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
+     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
+     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
+     exit(0);
+   }
+   else{
+     fprintf(ficgp,"\n# Routine varevsij");
+   }
+   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
+     printf("Problem with html file: %s\n", optionfilehtm);
+     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
+     exit(0);
+   }
+   else{
+     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
+     fprintf(fichtm,"\n<br>%s (à revoir) <br>\n",digitp);
+   }
+   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   fprintf(ficresvij,"# Covariances of life expectancies\n");
+   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
    fprintf(ficresvij,"# Age");
    for(i=1; i<=nlstate;i++)
      for(j=1; j<=nlstate;j++)
- Line 1317  void varevsij(char fileres[], double ***
+ Line 1927  void varevsij(char fileres[], double ***
    xp=vector(1,npar);
    dnewm=matrix(1,nlstate,1,npar);
    doldm=matrix(1,nlstate,1,nlstate);
+   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
-   hstepm=1*YEARM; /* Every year of age */
+   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
+   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
+   gpp=vector(nlstate+1,nlstate+ndeath);
+   gmp=vector(nlstate+1,nlstate+ndeath);
+   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+   if(estepm < stepm){
+     printf ("Problem %d lower than %d\n",estepm, stepm);
+   }
+   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 */
+     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-     if (stepm >= YEARM) hstepm=1;
+     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
      gp=matrix(0,nhstepm,1,nlstate);
      gm=matrix(0,nhstepm,1,nlstate);
      for(theta=1; theta <=npar; theta++){
        for(i=1; i<=npar; i++){ /* Computes gradient */
          xp[i] = x[i] + (i==theta ?delti[theta]:0);
        }
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm);
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl);
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+       if (popbased==1) {
+         if(mobilav ==0){
+           for(i=1; i<=nlstate;i++)
+             prlim[i][i]=probs[(int)age][i][ij];
+         }else{ /* mobilav */
+           for(i=1; i<=nlstate;i++)
+             prlim[i][i]=mobaverage[(int)age][i][ij];
+         }
+       }
        for(j=1; j<= nlstate; j++){
          for(h=0; h<=nhstepm; h++){
            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
          }
        }
+       /* This for computing forces of mortality (h=1)as a weighted average */
+       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
+         for(i=1; i<= nlstate; i++)
+           gpp[j] += prlim[i][i]*p3mat[i][j][1];
+       }
+       /* end force of mortality */
        for(i=1; i<=npar; i++) /* Computes gradient */
          xp[i] = x[i] - (i==theta ?delti[theta]:0);
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm);
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl);
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+       if (popbased==1) {
+         if(mobilav ==0){
+           for(i=1; i<=nlstate;i++)
+             prlim[i][i]=probs[(int)age][i][ij];
+         }else{ /* mobilav */
+           for(i=1; i<=nlstate;i++)
+             prlim[i][i]=mobaverage[(int)age][i][ij];
+         }
+       }
        for(j=1; j<= nlstate; j++){
          for(h=0; h<=nhstepm; h++){
            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
          }
        }
-       for(j=1; j<= nlstate; j++)
+       /* This for computing force of mortality (h=1)as a weighted average */
+       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
+         for(i=1; i<= nlstate; i++)
+           gmp[j] += prlim[i][i]*p3mat[i][j][1];
+       }
+       /* end force of mortality */
+       for(j=1; j<= nlstate; j++) /* vareij */
          for(h=0; h<=nhstepm; h++){
            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
          }
+       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
+       }
      } /* End theta */
-     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);
+     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
-     for(h=0; h<=nhstepm; h++)
+     for(h=0; h<=nhstepm; h++) /* veij */
        for(j=1; j<=nlstate;j++)
          for(theta=1; theta <=npar; theta++)
            trgradg[h][j][theta]=gradg[h][theta][j];
+     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+       for(theta=1; theta <=npar; theta++)
+         trgradgp[j][theta]=gradgp[theta][j];
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      for(i=1;i<=nlstate;i++)
        for(j=1;j<=nlstate;j++)
          vareij[i][j][(int)age] =0.;
      for(h=0;h<=nhstepm;h++){
        for(k=0;k<=nhstepm;k++){
          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
          for(i=1;i<=nlstate;i++)
            for(j=1;j<=nlstate;j++)
-             vareij[i][j][(int)age] += doldm[i][j];
+             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
        }
      }
-     h=1;
-     if (stepm >= YEARM) h=stepm/YEARM;
+     /* pptj */
-     fprintf(ficresvij,"%.0f ",age );
+     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
-     for(i=1; i<=nlstate;i++)
+     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
-       for(j=1; j<=nlstate;j++){
+     for(j=nlstate+1;j<=nlstate+ndeath;j++)
-         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);
+       for(i=nlstate+1;i<=nlstate+ndeath;i++)
+         varppt[j][i]=doldmp[j][i];
+     /* end ppptj */
+     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
+     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
+     if (popbased==1) {
+       if(mobilav ==0){
+         for(i=1; i<=nlstate;i++)
+           prlim[i][i]=probs[(int)age][i][ij];
+       }else{ /* mobilav */
+         for(i=1; i<=nlstate;i++)
+           prlim[i][i]=mobaverage[(int)age][i][ij];
+       }
+     }
+     /* This for computing force of mortality (h=1)as a weighted average */
+     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
+       for(i=1; i<= nlstate; i++)
+         gmp[j] += prlim[i][i]*p3mat[i][j][1];
+     }
+     /* end force of mortality */
+     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
+     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
+       for(i=1; i<=nlstate;i++){
+         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
+       }
+     }
+     fprintf(ficresprobmorprev,"\n");
+     fprintf(ficresvij,"%.0f ",age );
+     for(i=1; i<=nlstate;i++)
+       for(j=1; j<=nlstate;j++){
+         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
        }
      fprintf(ficresvij,"\n");
      free_matrix(gp,0,nhstepm,1,nlstate);
- Line 1392  void varevsij(char fileres[], double ***
+ Line 2104  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 */
-   fclose(ficresvij);
+   free_vector(gpp,nlstate+1,nlstate+ndeath);
-   free_vector(xp,1,npar);
+   free_vector(gmp,nlstate+1,nlstate+ndeath);
-   free_matrix(doldm,1,nlstate,1,npar);
+   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
-   free_matrix(dnewm,1,nlstate,1,nlstate);
+   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
+   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
+   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
+   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);
+   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
+   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);
+   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
+ */
+   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
+   free_vector(xp,1,npar);
+   free_matrix(doldm,1,nlstate,1,nlstate);
+   free_matrix(dnewm,1,nlstate,1,npar);
+   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
+   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   fclose(ficresprobmorprev);
+   fclose(ficgp);
+   fclose(fichtm);
  }
  /************ Variance of prevlim ******************/
- void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl)
+ void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
  {
-   /* Variance of health expectancies */
+   /* Variance of prevalence limit */
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+   /*  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;
-   int k;
+   int k, cptcode;
-   FILE  *ficresvpl;
-   char fileresvpl[FILENAMELENGTH];
    double *xp;
    double *gp, *gm;
    double **gradg, **trgradg;
    double age,agelim;
    int theta;
-   strcpy(fileresvpl,"vpl");
+   fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
-   strcat(fileresvpl,fileres);
-   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
-     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);
-     exit(0);
-   }
-   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);
-   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");
    fprintf(ficresvpl,"# Age");
    for(i=1; i<=nlstate;i++)
        fprintf(ficresvpl," %1d-%1d",i,i);
- Line 1450  void varprevlim(char fileres[], double *
+ Line 2172  void varprevlim(char fileres[], double *
        for(i=1; i<=npar; i++){ /* Computes gradient */
          xp[i] = x[i] + (i==theta ?delti[theta]:0);
        }
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl);
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
        for(i=1;i<=nlstate;i++)
          gp[i] = prlim[i][i];
        for(i=1; i<=npar; i++) /* Computes gradient */
          xp[i] = x[i] - (i==theta ?delti[theta]:0);
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl);
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
        for(i=1;i<=nlstate;i++)
          gm[i] = prlim[i][i];
- Line 1486  void varprevlim(char fileres[], double *
+ Line 2208  void varprevlim(char fileres[], double *
      free_matrix(gradg,1,npar,1,nlstate);
      free_matrix(trgradg,1,nlstate,1,npar);
    } /* End age */
-   fclose(ficresvpl);
    free_vector(xp,1,npar);
    free_matrix(doldm,1,nlstate,1,npar);
    free_matrix(dnewm,1,nlstate,1,nlstate);
  }
+ /************ Variance of one-step probabilities  ******************/
+ void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
+ {
+   int i, j=0,  i1, k1, l1, t, tj;
+   int k2, l2, j1,  z1;
+   int k=0,l, cptcode;
+   int first=1, first1;
+   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
+   double **dnewm,**doldm;
+   double *xp;
+   double *gp, *gm;
+   double **gradg, **trgradg;
+   double **mu;
+   double age,agelim, cov[NCOVMAX];
+   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
+   int theta;
+   char fileresprob[FILENAMELENGTH];
+   char fileresprobcov[FILENAMELENGTH];
+   char fileresprobcor[FILENAMELENGTH];
+   double ***varpij;
+   strcpy(fileresprob,"prob");
+   strcat(fileresprob,fileres);
+   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
+     printf("Problem with resultfile: %s\n", fileresprob);
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
+   }
+   strcpy(fileresprobcov,"probcov");
+   strcat(fileresprobcov,fileres);
+   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
+     printf("Problem with resultfile: %s\n", fileresprobcov);
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
+   }
+   strcpy(fileresprobcor,"probcor");
+   strcat(fileresprobcor,fileres);
+   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
+     printf("Problem with resultfile: %s\n", fileresprobcor);
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
+   }
+   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
+   fprintf(ficresprob,"# Age");
+   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
+   fprintf(ficresprobcov,"# Age");
+   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+   fprintf(ficresprobcov,"# Age");
+   for(i=1; i<=nlstate;i++)
+     for(j=1; j<=(nlstate+ndeath);j++){
+       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+       fprintf(ficresprobcov," p%1d-%1d ",i,j);
+       fprintf(ficresprobcor," p%1d-%1d ",i,j);
+     }
+   fprintf(ficresprob,"\n");
+   fprintf(ficresprobcov,"\n");
+   fprintf(ficresprobcor,"\n");
+   xp=vector(1,npar);
+   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
+   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
+   first=1;
+   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
+     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
+     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
+     exit(0);
+   }
+   else{
+     fprintf(ficgp,"\n# Routine varprob");
+   }
+   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
+     printf("Problem with html file: %s\n", optionfilehtm);
+     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
+     exit(0);
+   }
+   else{
+     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+     fprintf(fichtm,"\n");
+     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
+     fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
+     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
+   }
+   cov[1]=1;
+   tj=cptcoveff;
+   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
+   j1=0;
+   for(t=1; t<=tj;t++){
+     for(i1=1; i1<=ncodemax[t];i1++){
+       j1++;
+       if  (cptcovn>0) {
+         fprintf(ficresprob, "\n#********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         fprintf(ficresprob, "**********\n#");
+         fprintf(ficresprobcov, "\n#********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         fprintf(ficresprobcov, "**********\n#");
+         fprintf(ficgp, "\n#********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         fprintf(ficgp, "**********\n#");
+         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+         fprintf(ficresprobcor, "\n#********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         fprintf(ficgp, "**********\n#");
+       }
+       for (age=bage; age<=fage; age ++){
+         cov[2]=age;
+         for (k=1; k<=cptcovn;k++) {
+           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
+         }
+         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+         for (k=1; k<=cptcovprod;k++)
+           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+         gp=vector(1,(nlstate)*(nlstate+ndeath));
+         gm=vector(1,(nlstate)*(nlstate+ndeath));
+         for(theta=1; theta <=npar; theta++){
+           for(i=1; i<=npar; i++)
+             xp[i] = x[i] + (i==theta ?delti[theta]:0);
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+           k=0;
+           for(i=1; i<= (nlstate); i++){
+             for(j=1; j<=(nlstate+ndeath);j++){
+               k=k+1;
+               gp[k]=pmmij[i][j];
+             }
+           }
+           for(i=1; i<=npar; i++)
+             xp[i] = x[i] - (i==theta ?delti[theta]:0);
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+           k=0;
+           for(i=1; i<=(nlstate); i++){
+             for(j=1; j<=(nlstate+ndeath);j++){
+               k=k+1;
+               gm[k]=pmmij[i][j];
+             }
+           }
+           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];
+         }
+         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
+           for(theta=1; theta <=npar; theta++)
+             trgradg[j][theta]=gradg[theta][j];
+         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
+         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
+         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);
+         pmij(pmmij,cov,ncovmodel,x,nlstate);
+         k=0;
+         for(i=1; i<=(nlstate); i++){
+           for(j=1; j<=(nlstate+ndeath);j++){
+             k=k+1;
+             mu[k][(int) age]=pmmij[i][j];
+           }
+         }
+         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
+           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
+             varpij[i][j][(int)age] = doldm[i][j];
+         /*printf("\n%d ",(int)age);
+           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+           }*/
+         fprintf(ficresprob,"\n%d ",(int)age);
+         fprintf(ficresprobcov,"\n%d ",(int)age);
+         fprintf(ficresprobcor,"\n%d ",(int)age);
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
+           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
+           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
+         }
+         i=0;
+         for (k=1; k<=(nlstate);k++){
+           for (l=1; l<=(nlstate+ndeath);l++){
+             i=i++;
+             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
+             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
+             for (j=1; j<=i;j++){
+               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
+               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
+             }
+           }
+         }/* end of loop for state */
+       } /* end of loop for age */
+       /* Confidence intervalle of pij  */
+       /*
+         fprintf(ficgp,"\nset noparametric;unset label");
+         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
+         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+         fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
+         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
+         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
+         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
+       */
+       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+       first1=1;
+       for (k2=1; k2<=(nlstate);k2++){
+         for (l2=1; l2<=(nlstate+ndeath);l2++){
+           if(l2==k2) continue;
+           j=(k2-1)*(nlstate+ndeath)+l2;
+           for (k1=1; k1<=(nlstate);k1++){
+             for (l1=1; l1<=(nlstate+ndeath);l1++){
+               if(l1==k1) continue;
+               i=(k1-1)*(nlstate+ndeath)+l1;
+               if(i<=j) continue;
+               for (age=bage; age<=fage; age ++){
+                 if ((int)age %5==0){
+                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
+                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+                   mu1=mu[i][(int) age]/stepm*YEARM ;
+                   mu2=mu[j][(int) age]/stepm*YEARM;
+                   c12=cv12/sqrt(v1*v2);
+                   /* Computing eigen value of matrix of covariance */
+                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+                   /* Eigen vectors */
+                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+                   /*v21=sqrt(1.-v11*v11); *//* error */
+                   v21=(lc1-v1)/cv12*v11;
+                   v12=-v21;
+                   v22=v11;
+                   tnalp=v21/v11;
+                   if(first1==1){
+                     first1=0;
+                     printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+                   }
+                   fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+                   /*printf(fignu*/
+                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+                   if(first==1){
+                     first=0;
+                     fprintf(ficgp,"\nset parametric;unset label");
+                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
+                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
+                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
+                     fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
+                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+                   }else{
+                     first=0;
+                     fprintf(fichtm," %d (%.3f),",(int) age, c12);
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+                   }/* if first */
+                 } /* age mod 5 */
+               } /* end loop age */
+               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
+               first=1;
+             } /*l12 */
+           } /* k12 */
+         } /*l1 */
+       }/* k1 */
+     } /* loop covariates */
+   }
+   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
+   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+   free_vector(xp,1,npar);
+   fclose(ficresprob);
+   fclose(ficresprobcov);
+   fclose(ficresprobcor);
+   fclose(ficgp);
+   fclose(fichtm);
+ }
+ /******************* Printing html file ***********/
+ void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+                   int lastpass, int stepm, int weightopt, char model[],\
+                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
+                   int popforecast, int estepm ,\
+                   double jprev1, double mprev1,double anprev1, \
+                   double jprev2, double mprev2,double anprev2){
+   int jj1, k1, i1, cpt;
+   /*char optionfilehtm[FILENAMELENGTH];*/
+   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
+     printf("Problem with %s \n",optionfilehtm), exit(0);
+     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
+   }
+    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
+  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
+  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
+  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
+  - Life expectancies by age and initial health status (estepm=%2d months):
+    <a href=\"e%s\">e%s</a> <br>\n</li>", \
+   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
+ fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
+  m=cptcoveff;
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+  jj1=0;
+  for(k1=1; k1<=m;k1++){
+    for(i1=1; i1<=ncodemax[k1];i1++){
+      jj1++;
+      if (cptcovn > 0) {
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+        for (cpt=1; cpt<=cptcoveff;cpt++)
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+      }
+      /* Pij */
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>
+ <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
+      /* Quasi-incidences */
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
+ <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
+        /* Stable prevalence in each health state */
+        for(cpt=1; cpt<nlstate;cpt++){
+          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
+ <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+        }
+      for(cpt=1; cpt<=nlstate;cpt++) {
+         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
+ <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+      }
+      fprintf(fichtm,"\n<br>- Total life expectancy by age and
+ health expectancies in states (1) and (2): e%s%d.png<br>
+ <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
+    } /* end i1 */
+  }/* End k1 */
+  fprintf(fichtm,"</ul>");
+  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
+  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
+  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
+  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
+  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
+  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
+  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
+  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
+  if(popforecast==1) fprintf(fichtm,"\n
+  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
+  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
+         <br>",fileres,fileres,fileres,fileres);
+  else
+    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
+ fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+  m=cptcoveff;
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+  jj1=0;
+  for(k1=1; k1<=m;k1++){
+    for(i1=1; i1<=ncodemax[k1];i1++){
+      jj1++;
+      if (cptcovn > 0) {
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+        for (cpt=1; cpt<=cptcoveff;cpt++)
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+      }
+      for(cpt=1; cpt<=nlstate;cpt++) {
+        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
+ interval) in state (%d): v%s%d%d.png <br>
+ <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+      }
+    } /* end i1 */
+  }/* End k1 */
+  fprintf(fichtm,"</ul>");
+ fclose(fichtm);
+ }
+ /******************* Gnuplot file **************/
+ void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+   int ng;
+   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
+     printf("Problem with file %s",optionfilegnuplot);
+     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
+   }
+   /*#ifdef windows */
+     fprintf(ficgp,"cd \"%s\" \n",pathc);
+     /*#endif */
+ m=pow(2,cptcoveff);
+  /* 1eme*/
+   for (cpt=1; cpt<= nlstate ; cpt ++) {
+    for (k1=1; k1<= m ; k1 ++) {
+      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
+      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
+      for (i=1; i<= nlstate ; i ++) {
+        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+        else fprintf(ficgp," \%%*lf (\%%*lf)");
+      }
+      fprintf(ficgp,"\" t\"Stable 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));
+    }
+   }
+   /*2 eme*/
+   for (k1=1; k1<= m ; k1 ++) {
+     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
+     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
+     for (i=1; i<= nlstate+1 ; i ++) {
+       k=2*i;
+       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
+       for (j=1; j<= nlstate+1 ; j ++) {
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
+       }
+       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
+       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
+       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
+       for (j=1; j<= nlstate+1 ; j ++) {
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
+       }
+       fprintf(ficgp,"\" t\"\" w l 0,");
+       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
+       for (j=1; j<= nlstate+1 ; j ++) {
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
+       }
+       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+       else fprintf(ficgp,"\" t\"\" w l 0,");
+     }
+   }
+   /*3eme*/
+   for (k1=1; k1<= m ; k1 ++) {
+     for (cpt=1; cpt<= nlstate ; cpt ++) {
+       k=2+nlstate*(2*cpt-2);
+       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
+       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
+       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+       */
+       for (i=1; i< nlstate ; i ++) {
+         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
+       }
+     }
+   }
+   /* CV preval stat */
+   for (k1=1; k1<= m ; k1 ++) {
+     for (cpt=1; cpt<nlstate ; cpt ++) {
+       k=3;
+       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
+       for (i=1; i< nlstate ; i ++)
+         fprintf(ficgp,"+$%d",k+i+1);
+       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
+       l=3+(nlstate+ndeath)*cpt;
+       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
+       for (i=1; i< nlstate ; i ++) {
+         l=3+(nlstate+ndeath)*cpt;
+         fprintf(ficgp,"+$%d",l+i+1);
+       }
+       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
+     }
+   }
+   /* proba elementaires */
+   for(i=1,jk=1; i <=nlstate; i++){
+     for(k=1; k <=(nlstate+ndeath); k++){
+       if (k != i) {
+         for(j=1; j <=ncovmodel; j++){
+           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+           jk++;
+           fprintf(ficgp,"\n");
+         }
+       }
+     }
+    }
+    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
+      for(jk=1; jk <=m; jk++) {
+        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
+        if (ng==2)
+          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
+        else
+          fprintf(ficgp,"\nset title \"Probability\"\n");
+        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+        i=1;
+        for(k2=1; k2<=nlstate; k2++) {
+          k3=i;
+          for(k=1; k<=(nlstate+ndeath); k++) {
+            if (k != k2){
+              if(ng==2)
+                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+              else
+                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+              ij=1;
+              for(j=3; j <=ncovmodel; j++) {
+                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+                  ij++;
+                }
+                else
+                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+              }
+              fprintf(ficgp,")/(1");
+              for(k1=1; k1 <=nlstate; k1++){
+                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+                ij=1;
+                for(j=3; j <=ncovmodel; j++){
+                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+                    ij++;
+                  }
+                  else
+                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+                }
+                fprintf(ficgp,")");
+              }
+              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
+              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+              i=i+ncovmodel;
+            }
+          } /* end k */
+        } /* end k2 */
+      } /* end jk */
+    } /* end ng */
+    fclose(ficgp);
+ }  /* end gnuplot */
+ /*************** Moving average **************/
+ int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
+   int i, cpt, cptcod;
+   int modcovmax =1;
+   int mobilavrange, mob;
+   double age;
+   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
+                            a covariate has 2 modalities */
+   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
+   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
+     if(mobilav==1) mobilavrange=5; /* default */
+     else mobilavrange=mobilav;
+     for (age=bage; age<=fage; age++)
+       for (i=1; i<=nlstate;i++)
+         for (cptcod=1;cptcod<=modcovmax;cptcod++)
+           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+     /* We keep the original values on the extreme ages bage, fage and for
+        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
+        we use a 5 terms etc. until the borders are no more concerned.
+     */
+     for (mob=3;mob <=mobilavrange;mob=mob+2){
+       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
+         for (i=1; i<=nlstate;i++){
+           for (cptcod=1;cptcod<=modcovmax;cptcod++){
+             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
+               for (cpt=1;cpt<=(mob-1)/2;cpt++){
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
+               }
+             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
+           }
+         }
+       }/* end age */
+     }/* end mob */
+   }else return -1;
+   return 0;
+ }/* End movingaverage */
+ /************** 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;
+   double ***mobaverage;
+   char fileresf[FILENAMELENGTH];
+  agelim=AGESUP;
+  calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
+   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
+   strcpy(fileresf,"f");
+   strcat(fileresf,fileres);
+   if((ficresf=fopen(fileresf,"w"))==NULL) {
+     printf("Problem with forecast resultfile: %s\n", fileresf);
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
+   }
+   printf("Computing forecasting: result on file '%s' \n", fileresf);
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+   if (mobilav!=0) {
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+     }
+   }
+   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!=0) 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;
+   double *popeffectif,*popcount;
+   double ***p3mat,***tabpop,***tabpopprev;
+   double ***mobaverage;
+   char filerespop[FILENAMELENGTH];
+   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   agelim=AGESUP;
+   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
+   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
+   strcpy(filerespop,"pop");
+   strcat(filerespop,fileres);
+   if((ficrespop=fopen(filerespop,"w"))==NULL) {
+     printf("Problem with forecast resultfile: %s\n", filerespop);
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
+   }
+   printf("Computing forecasting: result on file '%s' \n", filerespop);
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+   if (mobilav!=0) {
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+     }
+   }
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
+   if (stepm<=12) stepsize=1;
+   agelim=AGESUP;
+   hstepm=1;
+   hstepm=hstepm/stepm;
+   if (popforecast==1) {
+     if((ficpop=fopen(popfile,"r"))==NULL) {
+       printf("Problem with population file : %s\n",popfile);exit(0);
+       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
+     }
+     popage=ivector(0,AGESUP);
+     popeffectif=vector(0,AGESUP);
+     popcount=vector(0,AGESUP);
+     i=1;
+     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+     imx=i;
+     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
+   }
+   for(cptcov=1;cptcov<=i2;cptcov++){
+    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+       k=k+1;
+       fprintf(ficrespop,"\n#******");
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       }
+       fprintf(ficrespop,"******\n");
+       fprintf(ficrespop,"# Age");
+       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
+       if (popforecast==1)  fprintf(ficrespop," [Population]");
+       for (cpt=0; cpt<=0;cpt++) {
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+           nhstepm = nhstepm/hstepm;
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           oldm=oldms;savm=savms;
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+           for (h=0; h<=nhstepm; h++){
+             if (h==(int) (calagedate+YEARM*cpt)) {
+               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+             }
+             for(j=1; j<=nlstate+ndeath;j++) {
+               kk1=0.;kk2=0;
+               for(i=1; i<=nlstate;i++) {
+                 if (mobilav==1)
+                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+                 else {
+                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+                 }
+               }
+               if (h==(int)(calagedate+12*cpt)){
+                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
+                   /*fprintf(ficrespop," %.3f", kk1);
+                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+               }
+             }
+             for(i=1; i<=nlstate;i++){
+               kk1=0.;
+                 for(j=1; j<=nlstate;j++){
+                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
+                 }
+                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
+             }
+             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)
+               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
+           }
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         }
+       }
+   /******/
+       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+           nhstepm = nhstepm/hstepm;
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           oldm=oldms;savm=savms;
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+           for (h=0; h<=nhstepm; h++){
+             if (h==(int) (calagedate+YEARM*cpt)) {
+               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+             }
+             for(j=1; j<=nlstate+ndeath;j++) {
+               kk1=0.;kk2=0;
+               for(i=1; i<=nlstate;i++) {
+                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+               }
+               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);
+             }
+           }
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         }
+       }
+    }
+   }
+   if (mobilav!=0) 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 main(int argc, char *argv[])
- int main()
  {
-   int i,j, k, n=MAXN,iter,m,size;
+   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
    double agedeb, agefin,hf;
-   double agemin=1.e20, agemax=-1.e20;
+   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;
+   double ***mobaverage;
    int *indx;
    char line[MAXLINE], linepar[MAXLINE];
-   char title[MAXLINE];
+   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
-   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];
    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,jk,aa,bb, stepsize;
+   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
-   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
+   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
+   int mobilav=0,popforecast=0;
    int hstepm, nhstepm;
+   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
    double bage, fage, age, agelim, agebase;
    double ftolpl=FTOL;
    double **prlim;
- Line 1540  int main()
+ Line 3158  int main()
    double ***eij, ***vareij;
    double **varpl; /* Variances of prevalence limits by age */
    double *epj, vepp;
-   char version[80]="Imach version 0.64, May 2000, INED-EUROREVES ";
+   double kk1, kk2;
+   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
+   /*int *movingaverage; */
    char *alph[]={"a","a","b","c","d","e"}, str[4];
-   char z[1]="c";
+   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;
+      struct timeval start_time, end_time;
-   gettimeofday(&start_time, (struct timezone*)0); */ /* at first 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,'\\');*/
-   printf("\nIMACH, Version 0.64");
+   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
-   printf("\nEnter the parameter file name: ");
+   printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
- #define windows 1
- #ifdef windows
-   scanf("%s",pathtot);
-   getcwd(pathcd, size);
-   cut(path,optionfile,pathtot);
    chdir(path);
    replace(pathc,path);
- #endif
- #ifdef unix
-   scanf("%s",optionfile);
- #endif
- /*-------- arguments in the command line --------*/
+   /*-------- arguments in the command line --------*/
+   /* Log file */
+   strcat(filelog, optionfilefiname);
+   strcat(filelog,".log");    /* */
+   if((ficlog=fopen(filelog,"w"))==NULL)    {
+     printf("Problem with logfile %s\n",filelog);
+     goto end;
+   }
+   fprintf(ficlog,"Log filename:%s\n",filelog);
+   fprintf(ficlog,"\n%s",version);
+   fprintf(ficlog,"\nEnter the parameter file name: ");
+   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+   fflush(ficlog);
+   /* */
    strcpy(fileres,"r");
-   strcat(fileres, optionfile);
+   strcat(fileres, optionfilefiname);
+   strcat(fileres,".txt");    /* Other files have txt extension */
    /*---------arguments file --------*/
    if((ficpar=fopen(optionfile,"r"))==NULL)    {
      printf("Problem with optionfile %s\n",optionfile);
+     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
      goto end;
    }
    strcpy(filereso,"o");
    strcat(filereso,fileres);
    if((ficparo=fopen(filereso,"w"))==NULL) {
-     printf("Problem with Output resultfile: %s\n", filereso);goto end;
+     printf("Problem with Output resultfile: %s\n", filereso);
-   }
+     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+     goto end;
- /*--------- index.htm --------*/
-   if((fichtm=fopen("index.htm","w"))==NULL)    {
-     printf("Problem with index.htm \n");goto end;
    }
-  fprintf(fichtm,"<body><ul><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);
-  fprintf(fichtm," <li>Graphs<br> <br>");
- for(cpt=1; cpt<nlstate;cpt++)
-    fprintf(fichtm,"- Prevalence of disability: p%s1.gif<br>
- <img src=\"p%s1.gif\"><br>",strtok(optionfile, "."),strtok(optionfile, "."),cpt);
-  for(cpt=1; cpt<=nlstate;cpt++)
-      fprintf(fichtm,"- Observed and stationary  prevalence (with confident
- interval) in state (%d): v%s%d.gif <br>
- <img src=\"v%s%d.gif\"><br>",cpt,strtok(optionfile, "."),cpt,strtok(optionfile, "."),cpt);
-  for(cpt=1; cpt<=nlstate;cpt++)
-      fprintf(fichtm,"- Health life expectancies by age and initial health state (%d): exp%s%d.gif <br>
- <img src=\"ex%s%d.gif\"><br>",cpt,strtok(optionfile, "."),cpt,strtok(optionfile, "."),cpt);
-  fprintf(fichtm,"- Total life expectancy by age and
-         health expectancies in states (1) and (2): e%s.gif<br>
-         <img src=\"e%s.gif\"></li> </ul></body>",strtok(optionfile, "."),strtok(optionfile, "."));
- fclose(fichtm);
    /* Reads comments: lines beginning with '#' */
    while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);
- Line 1631  fclose(fichtm);
+ Line 3239  fclose(fichtm);
    }
    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\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt);
+   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
-   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt);
+   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 ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt);
+   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);
-   nvar=ncov-1; /* Suppressing age as a basic covariate */
+   covar=matrix(0,NCOVMAX,1,n);
+   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
+   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
+   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
+   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
    /* Read guess parameters */
    /* Reads comments: lines beginning with '#' */
- Line 1647  fclose(fichtm);
+ Line 3268  fclose(fichtm);
    }
    ungetc(c,ficpar);
-   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncov);
+   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-     for(i=1; i <=nlstate; i++)
+   for(i=1; i <=nlstate; i++)
      for(j=1; j <=nlstate+ndeath-1; j++){
        fscanf(ficpar,"%1d%1d",&i1,&j1);
        fprintf(ficparo,"%1d%1d",i1,j1);
-       printf("%1d%1d",i,j);
+       if(mle==1)
-       for(k=1; k<=ncov;k++){
+         printf("%1d%1d",i,j);
+       fprintf(ficlog,"%1d%1d",i,j);
+       for(k=1; k<=ncovmodel;k++){
          fscanf(ficpar," %lf",&param[i][j][k]);
-         printf(" %lf",param[i][j][k]);
+         if(mle==1){
+           printf(" %lf",param[i][j][k]);
+           fprintf(ficlog," %lf",param[i][j][k]);
+         }
+         else
+           fprintf(ficlog," %lf",param[i][j][k]);
          fprintf(ficparo," %lf",param[i][j][k]);
        }
        fscanf(ficpar,"\n");
-       printf("\n");
+       if(mle==1)
+         printf("\n");
+       fprintf(ficlog,"\n");
        fprintf(ficparo,"\n");
      }
-   npar= (nlstate+ndeath-1)*nlstate*ncov;
+   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
    p=param[1][1];
    /* Reads comments: lines beginning with '#' */
- Line 1675  fclose(fichtm);
+ Line 3306  fclose(fichtm);
    }
    ungetc(c,ficpar);
-   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncov);
+   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
    delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
    for(i=1; i <=nlstate; i++){
      for(j=1; j <=nlstate+ndeath-1; j++){
        fscanf(ficpar,"%1d%1d",&i1,&j1);
        printf("%1d%1d",i,j);
        fprintf(ficparo,"%1d%1d",i1,j1);
-       for(k=1; k<=ncov;k++){
+       for(k=1; k<=ncovmodel;k++){
          fscanf(ficpar,"%le",&delti3[i][j][k]);
          printf(" %le",delti3[i][j][k]);
          fprintf(ficparo," %le",delti3[i][j][k]);
- Line 1706  fclose(fichtm);
+ Line 3337  fclose(fichtm);
    matcov=matrix(1,npar,1,npar);
    for(i=1; i <=npar; i++){
      fscanf(ficpar,"%s",&str);
-     printf("%s",str);
+     if(mle==1)
+       printf("%s",str);
+     fprintf(ficlog,"%s",str);
      fprintf(ficparo,"%s",str);
      for(j=1; j <=i; j++){
        fscanf(ficpar," %le",&matcov[i][j]);
-       printf(" %.5le",matcov[i][j]);
+       if(mle==1){
+         printf(" %.5le",matcov[i][j]);
+         fprintf(ficlog," %.5le",matcov[i][j]);
+       }
+       else
+         fprintf(ficlog," %.5le",matcov[i][j]);
        fprintf(ficparo," %.5le",matcov[i][j]);
      }
      fscanf(ficpar,"\n");
-     printf("\n");
+     if(mle==1)
+       printf("\n");
+     fprintf(ficlog,"\n");
      fprintf(ficparo,"\n");
    }
    for(i=1; i <=npar; i++)
      for(j=i+1;j<=npar;j++)
        matcov[i][j]=matcov[j][i];
-   printf("\n");
+   if(mle==1)
+     printf("\n");
+   fprintf(ficlog,"\n");
-   if(mle==1){
-     /*-------- data file ----------*/
-     if((ficres =fopen(fileres,"w"))==NULL) {
+   /*-------- Rewriting paramater file ----------*/
-       printf("Problem with resultfile: %s\n", fileres);goto end;
+   strcpy(rfileres,"r");    /* "Rparameterfile */
+   strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+   strcat(rfileres,".");    /* */
+   strcat(rfileres,optionfilext);    /* Other files have txt extension */
+   if((ficres =fopen(rfileres,"w"))==NULL) {
+     printf("Problem writing new parameter file: %s\n", fileres);goto end;
+     fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
+   }
+   fprintf(ficres,"#%s\n",version);
+   /*-------- data file ----------*/
+   if((fic=fopen(datafile,"r"))==NULL)    {
+     printf("Problem with datafile: %s\n", datafile);goto end;
+     fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
+   }
+   n= lastobs;
+   severity = vector(1,maxwav);
+   outcome=imatrix(1,maxwav+1,1,n);
+   num=ivector(1,n);
+   moisnais=vector(1,n);
+   annais=vector(1,n);
+   moisdc=vector(1,n);
+   andc=vector(1,n);
+   agedc=vector(1,n);
+   cod=ivector(1,n);
+   weight=vector(1,n);
+   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+   mint=matrix(1,maxwav,1,n);
+   anint=matrix(1,maxwav,1,n);
+   s=imatrix(1,maxwav+1,1,n);
+   tab=ivector(1,NCOVMAX);
+   ncodemax=ivector(1,8);
+   i=1;
+   while (fgets(line, MAXLINE, fic) != NULL)    {
+     if ((i >= firstobs) && (i <=lastobs)) {
+       for (j=maxwav;j>=1;j--){
+         cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
+         strcpy(line,stra);
+         cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
+         cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
+       }
+       cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
+       cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
+       cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
+       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=ncovcol;j>=1;j--){
+         cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
+       }
+       num[i]=atol(stra);
+       /*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;
      }
-     fprintf(ficres,"#%s\n",version);
+   }
+   /* 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); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
+   Tprod=ivector(1,15);
+   Tvaraff=ivector(1,15);
+   Tvard=imatrix(1,15,1,2);
+   Tage=ivector(1,15);
+   if (strlen(model) >1){ /* If there is at least 1 covariate */
+     j=0, j1=0, k1=1, k2=1;
+     j=nbocc(model,'+'); /* j=Number of '+' */
+     j1=nbocc(model,'*'); /* j1=Number of '*' */
+     cptcovn=j+1;
+     cptcovprod=j1; /*Number of products */
-     if((fic=fopen(datafile,"r"))==NULL)    {
+     strcpy(modelsav,model);
-       printf("Problem with datafile: %s\n", datafile);goto end;
+     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
+       printf("Error. Non available option model=%s ",model);
+       fprintf(ficlog,"Error. Non available option model=%s ",model);
+       goto end;
      }
-     n= lastobs;
+     /* This loop fills the array Tvar from the string 'model'.*/
-     severity = vector(1,maxwav);
-     outcome=imatrix(1,maxwav+1,1,n);
-     num=ivector(1,n);
-     moisnais=vector(1,n);
-     annais=vector(1,n);
-     moisdc=vector(1,n);
-     andc=vector(1,n);
-     agedc=vector(1,n);
-     cod=ivector(1,n);
-     weight=vector(1,n);
-     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
-     mint=matrix(1,maxwav,1,n);
-     anint=matrix(1,maxwav,1,n);
-     covar=matrix(1,NCOVMAX,1,n);
-     s=imatrix(1,maxwav+1,1,n);
-     adl=imatrix(1,maxwav+1,1,n);
-     tab=ivector(1,NCOVMAX);
-     i=1;
-     while (fgets(line, MAXLINE, fic) != NULL)    {
-       if ((i >= firstobs) && (i <lastobs)) {
- sscanf(line,"%d %lf %lf %lf %lf/%lf %lf/%lf %lf/%lf %d %lf/%lf %d %lf/%lf %d %lf/%lf %d", &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]);
-         i=i+1;
-       }
-     }
-   imx=i-1; /* Number of individuals */
-     fclose(fic);
+     for(i=(j+1); i>=1;i--){
+       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
+       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+       /*scanf("%d",i);*/
+       if (strchr(strb,'*')) {  /* Model includes a product */
+         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
+         if (strcmp(strc,"age")==0) { /* Vn*age */
+           cptcovprod--;
+           cutv(strb,stre,strd,'V');
+           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
+           cptcovage++;
+             Tage[cptcovage]=i;
+             /*printf("stre=%s ", stre);*/
+         }
+         else if (strcmp(strd,"age")==0) { /* or age*Vn */
+           cptcovprod--;
+           cutv(strb,stre,strc,'V');
+           Tvar[i]=atoi(stre);
+           cptcovage++;
+           Tage[cptcovage]=i;
+         }
+         else {  /* Age is not in the model */
+           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
+           Tvar[i]=ncovcol+k1;
+           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
+           Tprod[k1]=i;
+           Tvard[k1][1]=atoi(strc); /* m*/
+           Tvard[k1][2]=atoi(stre); /* n */
+           Tvar[cptcovn+k2]=Tvard[k1][1];
+           Tvar[cptcovn+k2+1]=Tvard[k1][2];
+           for (k=1; k<=lastobs;k++)
+             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
+           k1++;
+           k2=k2+2;
+         }
+       }
+       else { /* no more sum */
+         /*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);*/
+     } /* end of loop + */
+   } /* end model */
+   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
+     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
+   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
+   printf("cptcovprod=%d ", cptcovprod);
+   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+   scanf("%d ",i);
+   fclose(fic);*/
+     /*  if(mle==1){*/
+   if (weightopt != 1) { /* Maximisation without weights*/
+     for(i=1;i<=n;i++) weight[i]=1.0;
+   }
+     /*-calculation of age at interview from date of interview and age at death -*/
+   agev=matrix(1,maxwav,1,imx);
-     if (weightopt != 1) { /* Maximisation without weights*/
+   for (i=1; i<=imx; i++) {
-       for(i=1;i<=n;i++) weight[i]=1.0;
+     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;
      }
-     /*-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 (i=1; i<=imx; i++)  {
+     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
-       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
+     for(m=1; (m<= maxwav); m++){
-       for(m=1; (m<= maxwav); m++){
+       if(s[m][i] >0){
-         if(s[m][i] >0){
+         if (s[m][i] >= nlstate+1) {
-           if (s[m][i] == nlstate+1) {
+           if(agedc[i]>0)
-             if(agedc[i]>0)
+             if(moisdc[i]!=99 && andc[i]!=9999)
                agev[m][i]=agedc[i];
-             else{
+           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
-               printf("Warning negative age at death: %d line:%d\n",num[i],i);
+             else {
-               agev[m][i]=-1;
+               if (andc[i]!=9999){
-             }
+                 printf("Warning negative age at death: %d line:%d\n",num[i],i);
-           }
+                 fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
-           else if(s[m][i] !=9){ /* Should no more exist */
+                 agev[m][i]=-1;
-             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
+               }
-             if(mint[m][i]==99 || anint[m][i]==9999)
-               agev[m][i]=1;
-             else if(agev[m][i] <agemin){
-               agemin=agev[m][i];
-               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
              }
-             else if(agev[m][i] >agemax){
+         }
-               agemax=agev[m][i];
+         else if(s[m][i] !=9){ /* Should no more exist */
-              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
+           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
-             }
+           if(mint[m][i]==99 || anint[m][i]==9999)
-             /*agev[m][i]=anint[m][i]-annais[i];*/
-             /*   agev[m][i] = age[i]+2*m;*/
-           }
-           else { /* =9 */
              agev[m][i]=1;
-             s[m][i]=-1;
+           else if(agev[m][i] <agemin){
+             agemin=agev[m][i];
+             /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
+           }
+           else if(agev[m][i] >agemax){
+             agemax=agev[m][i];
+             /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
            }
+           /*agev[m][i]=anint[m][i]-annais[i];*/
+           /*     agev[m][i] = age[i]+2*m;*/
          }
-         else /*= 0 Unknown */
+         else { /* =9 */
            agev[m][i]=1;
+           s[m][i]=-1;
+         }
        }
+       else /*= 0 Unknown */
+         agev[m][i]=1;
      }
-     for (i=1; i<=imx; i++)  {
-       for(m=1; (m<= maxwav); m++){
+   }
-         if (s[m][i] > (nlstate+ndeath)) {
+   for (i=1; i<=imx; i++)  {
-           printf("Error: Wrong value in nlstate or ndeath\n");
+     for(m=1; (m<= maxwav); m++){
-           goto end;
+       if (s[m][i] > (nlstate+ndeath)) {
-         }
+         printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+         fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+         goto end;
        }
      }
+   }
- printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
-     free_vector(severity,1,maxwav);
+   free_vector(severity,1,maxwav);
-     free_imatrix(outcome,1,maxwav+1,1,n);
+   free_imatrix(outcome,1,maxwav+1,1,n);
-     free_vector(moisnais,1,n);
+   free_vector(moisnais,1,n);
-     free_vector(annais,1,n);
+   free_vector(annais,1,n);
-     free_matrix(mint,1,maxwav,1,n);
+   /* free_matrix(mint,1,maxwav,1,n);
-     free_matrix(anint,1,maxwav,1,n);
+      free_matrix(anint,1,maxwav,1,n);*/
-     free_vector(moisdc,1,n);
+   free_vector(moisdc,1,n);
-     free_vector(andc,1,n);
+   free_vector(andc,1,n);
-     wav=ivector(1,imx);
+   wav=ivector(1,imx);
-     dh=imatrix(1,lastpass-firstpass+1,1,imx);
+   dh=imatrix(1,lastpass-firstpass+1,1,imx);
-     mw=imatrix(1,lastpass-firstpass+1,1,imx);
+   bh=imatrix(1,lastpass-firstpass+1,1,imx);
+   mw=imatrix(1,lastpass-firstpass+1,1,imx);
-     /* Concatenates waves */
+   /* Concatenates waves */
-       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
+   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
+   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
+   Tcode=ivector(1,100);
+   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
+   ncodemax[1]=1;
+   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
+   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
+                                  the estimations*/
+   h=0;
+   m=pow(2,cptcoveff);
+   for(k=1;k<=cptcoveff; k++){
+     for(i=1; i <=(m/pow(2,k));i++){
+       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;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]);*/
+         }
+       }
+     }
+   }
+   /* 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
+   /* Calculates basic frequencies. Computes observed prevalence at single age
-        and prints on file fileres'p'. */
+      and prints on file fileres'p'. */
-       freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx);
      pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
      oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
- Line 1845  printf("Total number of individuals= %d,
+ Line 3658  printf("Total number of individuals= %d,
      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] */
+   /* For Powell, parameters are in a vector p[] starting at p[1]
-     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
+      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) */
-     mlikeli(ficres,p, npar, ncov, nlstate, ftol, func);
+   if(mle==1){
+     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+   }
-     /*--------- results files --------------*/
+   /*--------- 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\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt);
+   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");
-    for(i=1,jk=1; i <=nlstate; i++){
-      for(k=1; k <=(nlstate+ndeath); k++){
-        if (k != i)
-          {
-            printf("%d%d ",i,k);
-            fprintf(ficres,"%1d%1d ",i,k);
-            for(j=1; j <=ncov; j++){
-              printf("%f ",p[jk]);
-              fprintf(ficres,"%f ",p[jk]);
-              jk++;
-            }
-            printf("\n");
-            fprintf(ficres,"\n");
-          }
-      }
-    }
-     /* Computing hessian and covariance matrix */
+   jk=1;
-     ftolhess=ftol; /* Usually correct */
+   fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-     hesscov(matcov, p, npar, delti, ftolhess, func);
+   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-     fprintf(ficres,"# Scales\n");
+   fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-     printf("# Scales\n");
+   for(i=1,jk=1; i <=nlstate; i++){
-      for(i=1,jk=1; i <=nlstate; i++){
+     for(k=1; k <=(nlstate+ndeath); k++){
-       for(j=1; j <=nlstate+ndeath; j++){
+       if (k != i)
-         if (j!=i) {
+         {
-           fprintf(ficres,"%1d%1d",i,j);
+           printf("%d%d ",i,k);
-           printf("%1d%1d",i,j);
+           fprintf(ficlog,"%d%d ",i,k);
-           for(k=1; k<=ncov;k++){
+           fprintf(ficres,"%1d%1d ",i,k);
-             printf(" %.5e",delti[jk]);
+           for(j=1; j <=ncovmodel; j++){
-             fprintf(ficres," %.5e",delti[jk]);
+             printf("%f ",p[jk]);
-             jk++;
+             fprintf(ficlog,"%f ",p[jk]);
+             fprintf(ficres,"%f ",p[jk]);
+             jk++;
            }
            printf("\n");
+           fprintf(ficlog,"\n");
            fprintf(ficres,"\n");
          }
+     }
+   }
+   if(mle==1){
+     /* Computing hessian and covariance matrix */
+     ftolhess=ftol; /* Usually correct */
+     hesscov(matcov, p, npar, delti, ftolhess, func);
+   }
+   fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+   printf("# Scales (for hessian or gradient estimation)\n");
+   fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+   for(i=1,jk=1; i <=nlstate; i++){
+     for(j=1; j <=nlstate+ndeath; j++){
+       if (j!=i) {
+         fprintf(ficres,"%1d%1d",i,j);
+         printf("%1d%1d",i,j);
+         fprintf(ficlog,"%1d%1d",i,j);
+         for(k=1; k<=ncovmodel;k++){
+           printf(" %.5e",delti[jk]);
+           fprintf(ficlog," %.5e",delti[jk]);
+           fprintf(ficres," %.5e",delti[jk]);
+           jk++;
+         }
+         printf("\n");
+         fprintf(ficlog,"\n");
+         fprintf(ficres,"\n");
        }
-       }
+     }
+   }
-     k=1;
-     fprintf(ficres,"# Covariance\n");
+   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\n");
+   if(mle==1)
-     for(i=1;i<=npar;i++){
+     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");
-       /*  if (k>nlstate) k=1;
+   fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
-       i1=(i-1)/(ncov*nlstate)+1;
+   for(i=1,k=1;i<=npar;i++){
-       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
+     /*  if (k>nlstate) k=1;
-       printf("%s%d%d",alph[k],i1,tab[i]);*/
+         i1=(i-1)/(ncovmodel*nlstate)+1;
-       fprintf(ficres,"%3d",i);
+         fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
+         printf("%s%d%d",alph[k],i1,tab[i]);
+     */
+     fprintf(ficres,"%3d",i);
+     if(mle==1)
        printf("%3d",i);
-       for(j=1; j<=i;j++){
+     fprintf(ficlog,"%3d",i);
-         fprintf(ficres," %.5e",matcov[i][j]);
+     for(j=1; j<=i;j++){
+       fprintf(ficres," %.5e",matcov[i][j]);
+       if(mle==1)
          printf(" %.5e",matcov[i][j]);
-       }
+       fprintf(ficlog," %.5e",matcov[i][j]);
-       fprintf(ficres,"\n");
-       printf("\n");
-       k++;
-     }
-     while((c=getc(ficpar))=='#' && c!= EOF){
-       ungetc(c,ficpar);
-       fgets(line, MAXLINE, ficpar);
-       puts(line);
-       fputs(line,ficparo);
      }
+     fprintf(ficres,"\n");
+     if(mle==1)
+       printf("\n");
+     fprintf(ficlog,"\n");
+     k++;
+   }
+   while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);
+     fgets(line, MAXLINE, ficpar);
-     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);
+     puts(line);
+     fputs(line,ficparo);
-     if (fage <= 2) {
-       bage = agemin;
-       fage = agemax;
-     }
-     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
-     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
- /*------------ gnuplot -------------*/
- chdir(pathcd);
-   if((ficgp=fopen("graph.gp","w"))==NULL) {
-     printf("Problem with file graph.gp");goto end;
    }
- #ifdef windows
+   ungetc(c,ficpar);
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
- #endif
-    /* 1eme*/
-   for (cpt=1; cpt<= nlstate ; cpt ++) {
+   estepm=0;
- #ifdef windows
+   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
-     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" u 1:%d \"\%%lf",agemin,fage,fileres,cpt*2);
+   if (estepm==0 || estepm < stepm) estepm=stepm;
- #endif
+   if (fage <= 2) {
- #ifdef unix
+     bage = ageminpar;
- fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:%d \"\%%lf",agemin,fage,fileres,cpt*2);
+     fage = agemaxpar;
- #endif
-     for (i=1; i<= nlstate ; i ++) fprintf(ficgp," \%%lf (\%%lf)");
-     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" u 1:($%d+2*$%d) \"\%%lf",fileres,2*cpt,cpt*2+1);
-     for (i=1; i<= nlstate ; i ++) fprintf(ficgp," \%%lf (\%%lf)");
-   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" u 1:($%d-2*$%d) \"\%%lf",fileres,2*cpt,2*cpt+1);
-      for (i=1; i<= nlstate ; i ++) fprintf(ficgp," \%%lf (\%%lf)");
-      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" u 1:($%d) t\"Observed prevalence \" w l 2",fileres,2+4*(cpt-1));
- #ifdef unix
- fprintf(ficgp,"\nset ter gif small size 400,300");
- #endif
- fprintf(ficgp,"\nset out \"v%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt);
    }
-   /*2 eme*/
+   fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
-   fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);
+   fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
-   for (i=1; i<= nlstate+1 ; i ++) {
+   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
- k=2*i;
-     fprintf(ficgp,"\"t%s\" u 1:%d \"\%%lf \%%lf (\%%lf) \%%lf (\%%lf)",fileres,k);
+   while((c=getc(ficpar))=='#' && c!= EOF){
-     for (j=1; j< nlstate ; j ++) fprintf(ficgp," \%%lf (\%%lf)");
+     ungetc(c,ficpar);
-     if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
+     fgets(line, MAXLINE, ficpar);
-     else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
+     puts(line);
-     fprintf(ficgp,"\"t%s\" u 1:($%d-2*$%d) \"\%%lf \%%lf (\%%lf) \%%lf (\%%lf)",fileres,k,k+1);
+     fputs(line,ficparo);
-     for (j=1; j< nlstate ; j ++) fprintf(ficgp," \%%lf (\%%lf)");
+   }
-     fprintf(ficgp,"\" t\"\" w l 0,");
+   ungetc(c,ficpar);
- fprintf(ficgp,"\"t%s\" u 1:($%d+2*$%d) \"\%%lf \%%lf (\%%lf) \%%lf (\%%lf)",fileres,k,k+1);
-     for (j=1; j< nlstate ; j ++) fprintf(ficgp," \%%lf (\%%lf)");
-     if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
- else fprintf(ficgp,"\" t\"\" w l 0,");
-   }
-   fprintf(ficgp,"\nset out \"e%s.gif\" \nreplot\n\n",strtok(optionfile, "."));
-   /*3eme*/
- for (cpt=1; cpt<= nlstate ; cpt ++) {
-   k=2+nlstate*(cpt-1);
-     fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k,cpt);
- for (i=1; i< nlstate ; i ++) {
- fprintf(ficgp,",\"e%s\" u 1:%d t \"e%d%d\" w l",fileres,k+1,cpt,i+1);
- }
- fprintf(ficgp,"\nset out \"ex%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt);
- }
- /* CV preval stat */
- for (cpt=1; cpt<nlstate ; cpt ++) {
-     k=3;
-     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u 2:($%d/($%d",agemin,agemax,fileres,k+cpt,k);
-     for (i=1; i< nlstate ; i ++)
-       fprintf(ficgp,"+$%d",k+i);
-     fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
-  l=3+(nlstate+ndeath)*cpt;
-    fprintf(ficgp,",\"pij%s\" u 2:($%d/($%d",fileres,l+cpt,l);
-    for (i=1; i< nlstate ; i ++) {
-    l=3+(nlstate+ndeath)*cpt;
-     fprintf(ficgp,"+$%d",l+i);
-    }
-   fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
-   fprintf(ficgp,"set out \"p%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt);
+   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
-   }
+   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+   fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-   fclose(ficgp);
- chdir(path);
+   while((c=getc(ficpar))=='#' && c!= EOF){
-     free_matrix(agev,1,maxwav,1,imx);
+     ungetc(c,ficpar);
-     free_ivector(wav,1,imx);
+     fgets(line, MAXLINE, ficpar);
-     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+     puts(line);
-     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+     fputs(line,ficparo);
-     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);
    }
+   ungetc(c,ficpar);
-   /*________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);
+   while((c=getc(ficpar))=='#' && c!= EOF){
+     ungetc(c,ficpar);
+     fgets(line, MAXLINE, ficpar);
+     puts(line);
+     fputs(line,ficparo);
+   }
+   ungetc(c,ficpar);
+   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);
+   fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
+   fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
-   /* 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);
- Line 2044  chdir(path);
+ Line 3816  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);
-   /*--------------- Prevalence limit --------------*/
+   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
+   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
+   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
+   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
+   /*------------ gnuplot -------------*/
+   strcpy(optionfilegnuplot,optionfilefiname);
+   strcat(optionfilegnuplot,".gp");
+   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+     printf("Problem with file %s",optionfilegnuplot);
+   }
+   else{
+     fprintf(ficgp,"\n# %s\n", version);
+     fprintf(ficgp,"# %s\n", optionfilegnuplot);
+     fprintf(ficgp,"set missing 'NaNq'\n");
+   }
+   fclose(ficgp);
+   printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
+   /*--------- index.htm --------*/
+   strcpy(optionfilehtm,optionfile);
+   strcat(optionfilehtm,".htm");
+   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+     printf("Problem with %s \n",optionfilehtm), exit(0);
+   }
+   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
+ \n
+ Total number of observations=%d <br>\n
+ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
+ <hr  size=\"2\" color=\"#EC5E5E\">
+  <ul><li><h4>Parameter files</h4>\n
+  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
+  - Log file of the run: <a href=\"%s\">%s</a><br>\n
+  - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
+   fclose(fichtm);
+   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+   /*------------ free_vector  -------------*/
+   chdir(path);
+   free_ivector(wav,1,imx);
+   free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+   free_imatrix(bh,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,0,NCOVMAX,1,n);
+   /*free_matrix(covar,1,NCOVMAX,1,n);*/
+   fclose(ficparo);
+   fclose(ficres);
+   /*--------------- Prevalence limit  (stable prevalence) --------------*/
    strcpy(filerespl,"pl");
    strcat(filerespl,fileres);
    if((ficrespl=fopen(filerespl,"w"))==NULL) {
-     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;
+     printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
+     fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
    }
-   printf("Computing prevalence limit: result on file '%s' \n", filerespl);
+   printf("Computing stable prevalence: result on file '%s' \n", filerespl);
-   fprintf(ficrespl,"#Prevalence limit\n");
+   fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
+   fprintf(ficrespl,"#Stable prevalence \n");
    fprintf(ficrespl,"#Age ");
    for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
    fprintf(ficrespl,"\n");
    prlim=matrix(1,nlstate,1,nlstate);
-   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+   agebase=ageminpar;
-   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+   agelim=agemaxpar;
-   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
-   agebase=agemin;
-   agelim=agemax;
    ftolpl=1.e-10;
-   for (age=agebase; age<=agelim; age++){
+   i1=cptcoveff;
-     prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl);
+   if (cptcovn < 1){i1=1;}
-     fprintf(ficrespl,"%.0f",age );
-     for(i=1; i<=nlstate;i++)
+   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-       fprintf(ficrespl," %.5f", prlim[i][i]);
+     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-     fprintf(ficrespl,"\n");
+       k=k+1;
+       /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
+       fprintf(ficrespl,"\n#******");
+       printf("\n#******");
+       fprintf(ficlog,"\n#******");
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       }
+       fprintf(ficrespl,"******\n");
+       printf("******\n");
+       fprintf(ficlog,"******\n");
+       for (age=agebase; age<=agelim; age++){
+         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+         fprintf(ficrespl,"%.0f",age );
+         for(i=1; i<=nlstate;i++)
+           fprintf(ficrespl," %.5f", prlim[i][i]);
+         fprintf(ficrespl,"\n");
+       }
+     }
    }
    fclose(ficrespl);
    /*------------- h Pij x at various ages ------------*/
    strcpy(filerespij,"pij");  strcat(filerespij,fileres);
    if((ficrespij=fopen(filerespij,"w"))==NULL) {
      printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
+     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
    }
    printf("Computing pij: result on file '%s' \n", filerespij);
+   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
    stepsize=(int) (stepm+YEARM-1)/YEARM;
-   if (stepm<=24) stepsize=2;
+   /*if (stepm<=24) stepsize=2;*/
    agelim=AGESUP;
    hstepm=stepsize*YEARM; /* Every year of age */
    hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
-   for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
-     nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+   /* hstepm=1;   aff par mois*/
-     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-     oldm=oldms;savm=savms;
+     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-     hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm);
+       k=k+1;
-     fprintf(ficrespij,"# Age");
+       fprintf(ficrespij,"\n#****** ");
-     for(i=1; i<=nlstate;i++)
+       for(j=1;j<=cptcoveff;j++)
-       for(j=1; j<=nlstate+ndeath;j++)
+         fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         fprintf(ficrespij," %1d-%1d",i,j);
+       fprintf(ficrespij,"******\n");
-     fprintf(ficrespij,"\n");
-     for (h=0; h<=nhstepm; h++){
+       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
-       fprintf(ficrespij,"%.0f %.0f",agedeb, agedeb+ h*hstepm/YEARM*stepm );
+         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-       for(i=1; i<=nlstate;i++)
+         nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-         for(j=1; j<=nlstate+ndeath;j++)
-           fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+         /*        nhstepm=nhstepm*YEARM; aff par mois*/
-       fprintf(ficrespij,"\n");
+         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);
+         fprintf(ficrespij,"# Age");
+         for(i=1; i<=nlstate;i++)
+           for(j=1; j<=nlstate+ndeath;j++)
+             fprintf(ficrespij," %1d-%1d",i,j);
+         fprintf(ficrespij,"\n");
+         for (h=0; h<=nhstepm; h++){
+           fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
+           for(i=1; i<=nlstate;i++)
+             for(j=1; j<=nlstate+ndeath;j++)
+               fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+           fprintf(ficrespij,"\n");
+         }
+         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         fprintf(ficrespij,"\n");
+       }
      }
-     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     fprintf(ficrespij,"\n");
    }
+   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
    fclose(ficrespij);
-   /*---------- Health expectancies and variances ------------*/
+   /*---------- Forecasting ------------------*/
+   if((stepm == 1) && (strcmp(model,".")==0)){
+     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
+     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
+   }
+   else{
+     erreur=108;
+     printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
+     fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
+   }
-   eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-   oldm=oldms;savm=savms;
+   /*---------- Health expectancies and variances ------------*/
-   evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm);
-   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);
    strcpy(filerest,"t");
    strcat(filerest,fileres);
    if((ficrest=fopen(filerest,"w"))==NULL) {
      printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+   }
+   printf("Computing Total LEs with variances: file '%s' \n", filerest);
+   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
+   strcpy(filerese,"e");
+   strcat(filerese,fileres);
+   if((ficreseij=fopen(filerese,"w"))==NULL) {
+     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
    }
-   printf("Computing Total LEs with variances: file '%s' \n", filerest);
+   printf("Computing Health Expectancies: result on file '%s' \n", filerese);
-   fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
+   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
-   for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
-   fprintf(ficrest,"\n");
+   strcpy(fileresv,"v");
+   strcat(fileresv,fileres);
-   hf=1;
+   if((ficresvij=fopen(fileresv,"w"))==NULL) {
-   if (stepm >= YEARM) hf=stepm/YEARM;
+     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
-   epj=vector(1,nlstate+1);
+     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
-   for(age=bage; age <=fage ;age++){
+   }
-     prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl);
+   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
-     fprintf(ficrest," %.0f",age);
+   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
-     for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
-       for(i=1, epj[j]=0.;i <=nlstate;i++) {
+   calagedate=-1;
-         epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];
-       }
+   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
-       epj[nlstate+1] +=epj[j];
-     }
+   if (mobilav!=0) {
-     for(i=1, vepp=0.;i <=nlstate;i++)
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-       for(j=1;j <=nlstate;j++)
+     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-         vepp += vareij[i][j][(int)age];
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-     fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-     for(j=1;j <=nlstate;j++){
+     }
-       fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));
+   }
+   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+       k=k+1;
+       fprintf(ficrest,"\n#****** ");
+       for(j=1;j<=cptcoveff;j++)
+         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       fprintf(ficrest,"******\n");
+       fprintf(ficreseij,"\n#****** ");
+       for(j=1;j<=cptcoveff;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 ",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, estepm, delti, matcov);
+       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+       oldm=oldms;savm=savms;
+       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
+       if(popbased==1){
+         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
+       }
+       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
+       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+       fprintf(ficrest,"\n");
+       epj=vector(1,nlstate+1);
+       for(age=bage; age <=fage ;age++){
+         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+         if (popbased==1) {
+           if(mobilav ==0){
+             for(i=1; i<=nlstate;i++)
+               prlim[i][i]=probs[(int)age][i][k];
+           }else{ /* mobilav */
+             for(i=1; i<=nlstate;i++)
+               prlim[i][i]=mobaverage[(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]*eij[i][j][(int)age];
+             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+           }
+           epj[nlstate+1] +=epj[j];
+         }
+         for(i=1, vepp=0.;i <=nlstate;i++)
+           for(j=1;j <=nlstate;j++)
+             vepp += vareij[i][j][(int)age];
+         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+         for(j=1;j <=nlstate;j++){
+           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+         }
+         fprintf(ficrest,"\n");
+       }
+       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+       free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+       free_vector(epj,1,nlstate+1);
      }
-     fprintf(ficrest,"\n");
    }
+   free_vector(weight,1,n);
+   free_imatrix(Tvard,1,15,1,2);
+   free_imatrix(s,1,maxwav+1,1,n);
+   free_matrix(anint,1,maxwav,1,n);
+   free_matrix(mint,1,maxwav,1,n);
+   free_ivector(cod,1,n);
+   free_ivector(tab,1,NCOVMAX);
+   fclose(ficreseij);
+   fclose(ficresvij);
    fclose(ficrest);
    fclose(ficpar);
-   free_vector(epj,1,nlstate+1);
+   /*------- Variance of stable prevalence------*/
-   /*------- Variance limit prevalence------*/
+   strcpy(fileresvpl,"vpl");
+   strcat(fileresvpl,fileres);
+   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+     printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
+     exit(0);
+   }
+   printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
-   varpl=matrix(1,nlstate,(int) bage, (int) fage);
+   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-   oldm=oldms;savm=savms;
+     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-   varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl);
+       k=k+1;
+       fprintf(ficresvpl,"\n#****** ");
+       for(j=1;j<=cptcoveff;j++)
-   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       fprintf(ficresvpl,"******\n");
-   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+       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);
+       free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+     }
+   }
+   fclose(ficresvpl);
+   /*---------- End : free ----------------*/
    free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
    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);
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   free_ivector(ncodemax,1,8);
+   free_ivector(Tvar,1,15);
+   free_ivector(Tprod,1,15);
+   free_ivector(Tvaraff,1,15);
+   free_ivector(Tage,1,15);
+   free_ivector(Tcode,1,100);
+   fprintf(fichtm,"\n</body>");
+   fclose(fichtm);
+   fclose(ficgp);
-   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncov);
-   printf("End of Imach\n");
+   if(erreur >0){
+     printf("End of Imach with error or warning %d\n",erreur);
+     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
+   }else{
+    printf("End of Imach\n");
+    fprintf(ficlog,"End of Imach\n");
+   }
+   printf("See log file on %s\n",filelog);
+   fclose(ficlog);
    /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
    /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
    /*printf("Total time was %d uSec.\n", total_usecs);*/
    /*------ End -----------*/
-  end:
+   end:
  #ifdef windows
-  chdir(pathcd);
+   /* chdir(pathcd);*/
  #endif
-  system("gnuplot graph.gp");
+  /*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);
+   printf("Starting: %s\n",plotcmd);fflush(stdout);
+   system(plotcmd);
- #ifdef windows
+  /*#ifdef windows*/
    while (z[0] != 'q') {
-     chdir(pathcd);
+     /* chdir(path); */
-     printf("\nType e to edit output files, c to start again, and q for exiting: ");
+     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') {
+     else if (z[0] == 'e') system(optionfilehtm);
-       chdir(path);
+     else if (z[0] == 'g') system(plotcmd);
-       system("index.htm");
-     }
      else if (z[0] == 'q') exit(0);
    }
- #endif
+   /*#endif */
  }

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