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version 1.25, 2002/02/26 17:11:54 version 1.77, 2003/05/16 16:49:47
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 /* $Id$  /* $Id$
    Interpolated Markov Chain     Interpolated Markov Chain
   
   Short summary of the programme:    Short summary of the programme:
      
   This program computes Healthy Life Expectancies from    This program computes Healthy Life Expectancies from
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   first survey ("cross") where individuals from different ages are    first survey ("cross") where individuals from different ages are
   interviewed on their health status or degree of disability (in the    interviewed on their health status or degree of disability (in the
   case of a health survey which is our main interest) -2- at least a    case of a health survey which is our main interest) -2- at least a
   second wave of interviews ("longitudinal") which measure each change    second wave of interviews ("longitudinal") which measure each change
   (if any) in individual health status.  Health expectancies are    (if any) in individual health status.  Health expectancies are
   computed from the time spent in each health state according to a    computed from the time spent in each health state according to a
   model. More health states you consider, more time is necessary to reach the    model. More health states you consider, more time is necessary to reach the
   Maximum Likelihood of the parameters involved in the model.  The    Maximum Likelihood of the parameters involved in the model.  The
   simplest model is the multinomial logistic model where pij is the    simplest model is the multinomial logistic model where pij is the
   probabibility to be observed in state j at the second wave    probability to be observed in state j at the second wave
   conditional to be observed in state i at the first wave. Therefore    conditional to be observed in state i at the first wave. Therefore
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    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    'age' is age and 'sex' is a covariate. If you want to have a more
   complex model than "constant and age", you should modify the program    complex model than "constant and age", you should modify the program
   where the markup *Covariates have to be included here again* invites    where the markup *Covariates have to be included here again* invites
   you to do it.  More covariates you add, slower the    you to do it.  More covariates you add, slower the
   convergence.    convergence.
   
   The advantage of this computer programme, compared to a simple    The advantage of this computer programme, compared to a simple
   multinomial logistic model, is clear when the delay between waves is not    multinomial logistic model, is clear when the delay between waves is not
   identical for each individual. Also, if a individual missed an    identical for each individual. Also, if a individual missed an
   intermediate interview, the information is lost, but taken into    intermediate interview, the information is lost, but taken into
   account using an interpolation or extrapolation.      account using an interpolation or extrapolation.  
   
   hPijx is the probability to be observed in state i at age x+h    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    conditional to the observed state i at age x. The delay 'h' can be
   split into an exact number (nh*stepm) of unobserved intermediate    split into an exact number (nh*stepm) of unobserved intermediate
   states. This elementary transition (by month or quarter trimester,    states. This elementary transition (by month, quarter,
   semester or year) is model as a multinomial logistic.  The hPx    semester or year) is modelled as a multinomial logistic.  The hPx
   matrix is simply the matrix product of nh*stepm elementary matrices    matrix is simply the matrix product of nh*stepm elementary matrices
   and the contribution of each individual to the likelihood is simply    and the contribution of each individual to the likelihood is simply
   hPijx.    hPijx.
   
   Also this programme outputs the covariance matrix of the parameters but also    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).    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
            Institut national d'études démographiques, Paris.             Institut national d'études démographiques, Paris.
   This software have been partly granted by Euro-REVES, a concerted action    This software have been partly granted by Euro-REVES, a concerted action
   from the European Union.    from the European Union.
   It is copyrighted identically to a GNU software product, ie programme and    It is copyrighted identically to a GNU software product, ie programme and
   software can be distributed freely for non commercial use. Latest version    software can be distributed freely for non commercial use. Latest version
   can be accessed at http://euroreves.ined.fr/imach .    can be accessed at http://euroreves.ined.fr/imach .
   **********************************************************************/  
      Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #include <math.h>    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #include <stdio.h>    
 #include <stdlib.h>    **********************************************************************/
 #include <unistd.h>  /*
     main
 #define MAXLINE 256    read parameterfile
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    read datafile
 #define FILENAMELENGTH 80    concatwav
 /*#define DEBUG*/    if (mle >= 1)
 #define windows      mlikeli
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    print results files
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    if mle==1 
        computes hessian
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    read end of parameter file: agemin, agemax, bage, fage, estepm
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */        begin-prev-date,...
     open gnuplot file
 #define NINTERVMAX 8    open html file
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    stable prevalence
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */     for age prevalim()
 #define NCOVMAX 8 /* Maximum number of covariates */    h Pij x
 #define MAXN 20000    variance of p varprob
 #define YEARM 12. /* Number of months per year */    forecasting if prevfcast==1 prevforecast call prevalence()
 #define AGESUP 130    health expectancies
 #define AGEBASE 40    Variance-covariance of DFLE
     prevalence()
      movingaverage()
 int erreur; /* Error number */    varevsij() 
 int nvar;    if popbased==1 varevsij(,popbased)
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    total life expectancies
 int npar=NPARMAX;    Variance of stable prevalence
 int nlstate=2; /* Number of live states */   end
 int ndeath=1; /* Number of dead states */  */
 int ncovmodel, ncov;     /* 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 */  #include <math.h>
 int jmin, jmax; /* min, max spacing between 2 waves */  #include <stdio.h>
 int mle, weightopt;  #include <stdlib.h>
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  #include <unistd.h>
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double jmean; /* Mean space between 2 waves */  #define MAXLINE 256
 double **oldm, **newm, **savm; /* Working pointers to matrices */  #define GNUPLOTPROGRAM "gnuplot"
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;  #define FILENAMELENGTH 80
 FILE *ficgp,*ficresprob,*ficpop;  /*#define DEBUG*/
 FILE *ficreseij;  #define windows
   char filerese[FILENAMELENGTH];  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
  FILE  *ficresvij;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   char fileresvpl[FILENAMELENGTH];  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
 #define NR_END 1  #define NINTERVMAX 8
 #define FREE_ARG char*  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #define FTOL 1.0e-10  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   #define NCOVMAX 8 /* Maximum number of covariates */
 #define NRANSI  #define MAXN 20000
 #define ITMAX 200  #define YEARM 12. /* Number of months per year */
   #define AGESUP 130
 #define TOL 2.0e-4  #define AGEBASE 40
   #ifdef windows
 #define CGOLD 0.3819660  #define DIRSEPARATOR '\\'
 #define ZEPS 1.0e-10  #define ODIRSEPARATOR '/'
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  #else
   #define DIRSEPARATOR '/'
 #define GOLD 1.618034  #define ODIRSEPARATOR '\\'
 #define GLIMIT 100.0  #endif
 #define TINY 1.0e-20  
   char version[80]="Imach version 0.95a, May 2003, INED-EUROREVES ";
 static double maxarg1,maxarg2;  int erreur; /* Error number */
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  int nvar;
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
    int npar=NPARMAX;
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  int nlstate=2; /* Number of live states */
 #define rint(a) floor(a+0.5)  int ndeath=1; /* Number of dead states */
   int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 static double sqrarg;  int popbased=0;
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  int *wav; /* Number of waves for this individuual 0 is possible */
   int maxwav; /* Maxim number of waves */
 int imx;  int jmin, jmax; /* min, max spacing between 2 waves */
 int stepm;  int mle, weightopt;
 /* Stepm, step in month: minimum step interpolation*/  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 m,nb;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  double jmean; /* Mean space between 2 waves */
 double **pmmij, ***probs, ***mobaverage;  double **oldm, **newm, **savm; /* Working pointers to matrices */
 double dateintmean=0;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 double *weight;  FILE *ficlog, *ficrespow;
 int **s; /* Status */  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 double *agedc, **covar, idx;  FILE *ficresprobmorprev;
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  FILE *fichtm; /* Html File */
   FILE *ficreseij;
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  char filerese[FILENAMELENGTH];
 double ftolhess; /* Tolerance for computing hessian */  FILE  *ficresvij;
   char fileresv[FILENAMELENGTH];
 /**************** split *************************/  FILE  *ficresvpl;
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  char fileresvpl[FILENAMELENGTH];
 {  char title[MAXLINE];
    char *s;                             /* pointer */  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
    int  l1, l2;                         /* length counters */  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   
    l1 = strlen( path );                 /* length of path */  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  char filelog[FILENAMELENGTH]; /* Log file */
 #ifdef windows  char filerest[FILENAMELENGTH];
    s = strrchr( path, '\\' );           /* find last / */  char fileregp[FILENAMELENGTH];
 #else  char popfile[FILENAMELENGTH];
    s = strrchr( path, '/' );            /* find last / */  
 #endif  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */  #define NR_END 1
       extern char       *getwd( );  #define FREE_ARG char*
   #define FTOL 1.0e-10
       if ( getwd( dirc ) == NULL ) {  
 #else  #define NRANSI 
       extern char       *getcwd( );  #define ITMAX 200 
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #define TOL 2.0e-4 
 #endif  
          return( GLOCK_ERROR_GETCWD );  #define CGOLD 0.3819660 
       }  #define ZEPS 1.0e-10 
       strcpy( name, path );             /* we've got it */  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */  #define GOLD 1.618034 
       l2 = strlen( s );                 /* length of filename */  #define GLIMIT 100.0 
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  #define TINY 1.0e-20 
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  static double maxarg1,maxarg2;
       dirc[l1-l2] = 0;                  /* add zero */  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
    }  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
    l1 = strlen( dirc );                 /* length of directory */    
 #ifdef windows  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  #define rint(a) floor(a+0.5)
 #else  
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  static double sqrarg;
 #endif  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
    s = strrchr( name, '.' );            /* find last / */  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
    s++;  
    strcpy(ext,s);                       /* save extension */  int imx; 
    l1= strlen( name);  int stepm;
    l2= strlen( s)+1;  /* Stepm, step in month: minimum step interpolation*/
    strncpy( finame, name, l1-l2);  
    finame[l1-l2]= 0;  int estepm;
    return( 0 );                         /* we're done */  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 }  
   int m,nb;
   int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 /******************************************/  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double **pmmij, ***probs;
 void replace(char *s, char*t)  double dateintmean=0;
 {  
   int i;  double *weight;
   int lg=20;  int **s; /* Status */
   i=0;  double *agedc, **covar, idx;
   lg=strlen(t);  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
     if (t[i]== '\\') s[i]='/';  double ftolhess; /* Tolerance for computing hessian */
   }  
 }  /**************** split *************************/
   static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 int nbocc(char *s, char occ)  {
 {    char  *ss;                            /* pointer */
   int i,j=0;    int   l1, l2;                         /* length counters */
   int lg=20;  
   i=0;    l1 = strlen(path );                   /* length of path */
   lg=strlen(s);    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   for(i=0; i<= lg; i++) {    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   if  (s[i] == occ ) j++;    if ( ss == NULL ) {                   /* no directory, so use current */
   }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   return j;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 }      /* get current working directory */
       /*    extern  char* getcwd ( char *buf , int len);*/
 void cutv(char *u,char *v, char*t, char occ)      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 {        return( GLOCK_ERROR_GETCWD );
   int i,lg,j,p=0;      }
   i=0;      strcpy( name, path );               /* we've got it */
   for(j=0; j<=strlen(t)-1; j++) {    } else {                              /* strip direcotry from path */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;      ss++;                               /* after this, the filename */
   }      l2 = strlen( ss );                  /* length of filename */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   lg=strlen(t);      strcpy( name, ss );         /* save file name */
   for(j=0; j<p; j++) {      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     (u[j] = t[j]);      dirc[l1-l2] = 0;                    /* add zero */
   }    }
      u[p]='\0';    l1 = strlen( dirc );                  /* length of directory */
   #ifdef windows
    for(j=0; j<= lg; j++) {    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
     if (j>=(p+1))(v[j-p-1] = t[j]);  #else
   }    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
 }  #endif
     ss = strrchr( name, '.' );            /* find last / */
 /********************** nrerror ********************/    ss++;
     strcpy(ext,ss);                       /* save extension */
 void nrerror(char error_text[])    l1= strlen( name);
 {    l2= strlen(ss)+1;
   fprintf(stderr,"ERREUR ...\n");    strncpy( finame, name, l1-l2);
   fprintf(stderr,"%s\n",error_text);    finame[l1-l2]= 0;
   exit(1);    return( 0 );                          /* we're done */
 }  }
 /*********************** vector *******************/  
 double *vector(int nl, int nh)  
 {  /******************************************/
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  void replace(char *s, char*t)
   if (!v) nrerror("allocation failure in vector");  {
   return v-nl+NR_END;    int i;
 }    int lg=20;
     i=0;
 /************************ free vector ******************/    lg=strlen(t);
 void free_vector(double*v, int nl, int nh)    for(i=0; i<= lg; i++) {
 {      (s[i] = t[i]);
   free((FREE_ARG)(v+nl-NR_END));      if (t[i]== '\\') s[i]='/';
 }    }
   }
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)  int nbocc(char *s, char occ)
 {  {
   int *v;    int i,j=0;
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    int lg=20;
   if (!v) nrerror("allocation failure in ivector");    i=0;
   return v-nl+NR_END;    lg=strlen(s);
 }    for(i=0; i<= lg; i++) {
     if  (s[i] == occ ) j++;
 /******************free ivector **************************/    }
 void free_ivector(int *v, long nl, long nh)    return j;
 {  }
   free((FREE_ARG)(v+nl-NR_END));  
 }  void cutv(char *u,char *v, char*t, char occ)
   {
 /******************* imatrix *******************************/    /* cuts string t into u and v where u is ended by char occ excluding it
 int **imatrix(long nrl, long nrh, long ncl, long nch)       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */       gives u="abcedf" and v="ghi2j" */
 {    int i,lg,j,p=0;
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    i=0;
   int **m;    for(j=0; j<=strlen(t)-1; j++) {
        if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   /* allocate pointers to rows */    }
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    lg=strlen(t);
   m += NR_END;    for(j=0; j<p; j++) {
   m -= nrl;      (u[j] = t[j]);
      }
         u[p]='\0';
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));     for(j=0; j<= lg; j++) {
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");      if (j>=(p+1))(v[j-p-1] = t[j]);
   m[nrl] += NR_END;    }
   m[nrl] -= ncl;  }
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  /********************** nrerror ********************/
    
   /* return pointer to array of pointers to rows */  void nrerror(char error_text[])
   return m;  {
 }    fprintf(stderr,"ERREUR ...\n");
     fprintf(stderr,"%s\n",error_text);
 /****************** free_imatrix *************************/    exit(EXIT_FAILURE);
 void free_imatrix(m,nrl,nrh,ncl,nch)  }
       int **m;  /*********************** vector *******************/
       long nch,ncl,nrh,nrl;  double *vector(int nl, int nh)
      /* free an int matrix allocated by imatrix() */  {
 {    double *v;
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   free((FREE_ARG) (m+nrl-NR_END));    if (!v) nrerror("allocation failure in vector");
 }    return v-nl+NR_END;
   }
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)  /************************ free vector ******************/
 {  void free_vector(double*v, int nl, int nh)
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  {
   double **m;    free((FREE_ARG)(v+nl-NR_END));
   }
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  /************************ivector *******************************/
   m += NR_END;  char *cvector(long nl,long nh)
   m -= nrl;  {
     char *v;
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    if (!v) nrerror("allocation failure in cvector");
   m[nrl] += NR_END;    return v-nl+NR_END;
   m[nrl] -= ncl;  }
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  /******************free ivector **************************/
   return m;  void free_cvector(char *v, long nl, long nh)
 }  {
     free((FREE_ARG)(v+nl-NR_END));
 /*************************free matrix ************************/  }
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  
 {  /************************ivector *******************************/
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  int *ivector(long nl,long nh)
   free((FREE_ARG)(m+nrl-NR_END));  {
 }    int *v;
     v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
 /******************* ma3x *******************************/    if (!v) nrerror("allocation failure in ivector");
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    return v-nl+NR_END;
 {  }
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;  /******************free ivector **************************/
   void free_ivector(int *v, long nl, long nh)
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  {
   if (!m) nrerror("allocation failure 1 in matrix()");    free((FREE_ARG)(v+nl-NR_END));
   m += NR_END;  }
   m -= nrl;  
   /******************* imatrix *******************************/
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   m[nrl] += NR_END;  { 
   m[nrl] -= ncl;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     int **m; 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    
     /* allocate pointers to rows */ 
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    if (!m) nrerror("allocation failure 1 in matrix()"); 
   m[nrl][ncl] += NR_END;    m += NR_END; 
   m[nrl][ncl] -= nll;    m -= nrl; 
   for (j=ncl+1; j<=nch; j++)    
     m[nrl][j]=m[nrl][j-1]+nlay;    
      /* allocate rows and set pointers to them */ 
   for (i=nrl+1; i<=nrh; i++) {    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     for (j=ncl+1; j<=nch; j++)    m[nrl] += NR_END; 
       m[i][j]=m[i][j-1]+nlay;    m[nrl] -= ncl; 
   }    
   return m;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
 }    
     /* return pointer to array of pointers to rows */ 
 /*************************free ma3x ************************/    return m; 
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  } 
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  /****************** free_imatrix *************************/
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  void free_imatrix(m,nrl,nrh,ncl,nch)
   free((FREE_ARG)(m+nrl-NR_END));        int **m;
 }        long nch,ncl,nrh,nrl; 
        /* free an int matrix allocated by imatrix() */ 
 /***************** f1dim *************************/  { 
 extern int ncom;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 extern double *pcom,*xicom;    free((FREE_ARG) (m+nrl-NR_END)); 
 extern double (*nrfunc)(double []);  } 
    
 double f1dim(double x)  /******************* matrix *******************************/
 {  double **matrix(long nrl, long nrh, long ncl, long nch)
   int j;  {
   double f;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   double *xt;    double **m;
    
   xt=vector(1,ncom);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    if (!m) nrerror("allocation failure 1 in matrix()");
   f=(*nrfunc)(xt);    m += NR_END;
   free_vector(xt,1,ncom);    m -= nrl;
   return f;  
 }    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 /*****************brent *************************/    m[nrl] += NR_END;
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    m[nrl] -= ncl;
 {  
   int iter;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   double a,b,d,etemp;    return m;
   double fu,fv,fw,fx;    /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
   double ftemp;     */
   double p,q,r,tol1,tol2,u,v,w,x,xm;  }
   double e=0.0;  
    /*************************free matrix ************************/
   a=(ax < cx ? ax : cx);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   b=(ax > cx ? ax : cx);  {
   x=w=v=bx;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   fw=fv=fx=(*f)(x);    free((FREE_ARG)(m+nrl-NR_END));
   for (iter=1;iter<=ITMAX;iter++) {  }
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  /******************* ma3x *******************************/
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     printf(".");fflush(stdout);  {
 #ifdef DEBUG    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     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);    double ***m;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  
 #endif    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    if (!m) nrerror("allocation failure 1 in matrix()");
       *xmin=x;    m += NR_END;
       return fx;    m -= nrl;
     }  
     ftemp=fu;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (fabs(e) > tol1) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       r=(x-w)*(fx-fv);    m[nrl] += NR_END;
       q=(x-v)*(fx-fw);    m[nrl] -= ncl;
       p=(x-v)*q-(x-w)*r;  
       q=2.0*(q-r);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       if (q > 0.0) p = -p;  
       q=fabs(q);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       etemp=e;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       e=d;    m[nrl][ncl] += NR_END;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    m[nrl][ncl] -= nll;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    for (j=ncl+1; j<=nch; j++) 
       else {      m[nrl][j]=m[nrl][j-1]+nlay;
         d=p/q;    
         u=x+d;    for (i=nrl+1; i<=nrh; i++) {
         if (u-a < tol2 || b-u < tol2)      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
           d=SIGN(tol1,xm-x);      for (j=ncl+1; j<=nch; j++) 
       }        m[i][j]=m[i][j-1]+nlay;
     } else {    }
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    return m; 
     }    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     fu=(*f)(u);    */
     if (fu <= fx) {  }
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)  /*************************free ma3x ************************/
         SHFT(fv,fw,fx,fu)  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
         } else {  {
           if (u < x) a=u; else b=u;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
           if (fu <= fw || w == x) {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
             v=w;    free((FREE_ARG)(m+nrl-NR_END));
             w=u;  }
             fv=fw;  
             fw=fu;  /***************** f1dim *************************/
           } else if (fu <= fv || v == x || v == w) {  extern int ncom; 
             v=u;  extern double *pcom,*xicom;
             fv=fu;  extern double (*nrfunc)(double []); 
           }   
         }  double f1dim(double x) 
   }  { 
   nrerror("Too many iterations in brent");    int j; 
   *xmin=x;    double f;
   return fx;    double *xt; 
 }   
     xt=vector(1,ncom); 
 /****************** mnbrak ***********************/    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     f=(*nrfunc)(xt); 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    free_vector(xt,1,ncom); 
             double (*func)(double))    return f; 
 {  } 
   double ulim,u,r,q, dum;  
   double fu;  /*****************brent *************************/
    double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   *fa=(*func)(*ax);  { 
   *fb=(*func)(*bx);    int iter; 
   if (*fb > *fa) {    double a,b,d,etemp;
     SHFT(dum,*ax,*bx,dum)    double fu,fv,fw,fx;
       SHFT(dum,*fb,*fa,dum)    double ftemp;
       }    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   *cx=(*bx)+GOLD*(*bx-*ax);    double e=0.0; 
   *fc=(*func)(*cx);   
   while (*fb > *fc) {    a=(ax < cx ? ax : cx); 
     r=(*bx-*ax)*(*fb-*fc);    b=(ax > cx ? ax : cx); 
     q=(*bx-*cx)*(*fb-*fa);    x=w=v=bx; 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    fw=fv=fx=(*f)(x); 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    for (iter=1;iter<=ITMAX;iter++) { 
     ulim=(*bx)+GLIMIT*(*cx-*bx);      xm=0.5*(a+b); 
     if ((*bx-u)*(u-*cx) > 0.0) {      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       fu=(*func)(u);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     } else if ((*cx-u)*(u-ulim) > 0.0) {      printf(".");fflush(stdout);
       fu=(*func)(u);      fprintf(ficlog,".");fflush(ficlog);
       if (fu < *fc) {  #ifdef DEBUG
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))      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);
           SHFT(*fb,*fc,fu,(*func)(u))      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)))) { */
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  #endif
       u=ulim;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       fu=(*func)(u);        *xmin=x; 
     } else {        return fx; 
       u=(*cx)+GOLD*(*cx-*bx);      } 
       fu=(*func)(u);      ftemp=fu;
     }      if (fabs(e) > tol1) { 
     SHFT(*ax,*bx,*cx,u)        r=(x-w)*(fx-fv); 
       SHFT(*fa,*fb,*fc,fu)        q=(x-v)*(fx-fw); 
       }        p=(x-v)*q-(x-w)*r; 
 }        q=2.0*(q-r); 
         if (q > 0.0) p = -p; 
 /*************** linmin ************************/        q=fabs(q); 
         etemp=e; 
 int ncom;        e=d; 
 double *pcom,*xicom;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
 double (*nrfunc)(double []);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
          else { 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))          d=p/q; 
 {          u=x+d; 
   double brent(double ax, double bx, double cx,          if (u-a < tol2 || b-u < tol2) 
                double (*f)(double), double tol, double *xmin);            d=SIGN(tol1,xm-x); 
   double f1dim(double x);        } 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,      } else { 
               double *fc, double (*func)(double));        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   int j;      } 
   double xx,xmin,bx,ax;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   double fx,fb,fa;      fu=(*f)(u); 
        if (fu <= fx) { 
   ncom=n;        if (u >= x) a=x; else b=x; 
   pcom=vector(1,n);        SHFT(v,w,x,u) 
   xicom=vector(1,n);          SHFT(fv,fw,fx,fu) 
   nrfunc=func;          } else { 
   for (j=1;j<=n;j++) {            if (u < x) a=u; else b=u; 
     pcom[j]=p[j];            if (fu <= fw || w == x) { 
     xicom[j]=xi[j];              v=w; 
   }              w=u; 
   ax=0.0;              fv=fw; 
   xx=1.0;              fw=fu; 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);            } else if (fu <= fv || v == x || v == w) { 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);              v=u; 
 #ifdef DEBUG              fv=fu; 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);            } 
 #endif          } 
   for (j=1;j<=n;j++) {    } 
     xi[j] *= xmin;    nrerror("Too many iterations in brent"); 
     p[j] += xi[j];    *xmin=x; 
   }    return fx; 
   free_vector(xicom,1,n);  } 
   free_vector(pcom,1,n);  
 }  /****************** mnbrak ***********************/
   
 /*************** powell ************************/  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,              double (*func)(double)) 
             double (*func)(double []))  { 
 {    double ulim,u,r,q, dum;
   void linmin(double p[], double xi[], int n, double *fret,    double fu; 
               double (*func)(double []));   
   int i,ibig,j;    *fa=(*func)(*ax); 
   double del,t,*pt,*ptt,*xit;    *fb=(*func)(*bx); 
   double fp,fptt;    if (*fb > *fa) { 
   double *xits;      SHFT(dum,*ax,*bx,dum) 
   pt=vector(1,n);        SHFT(dum,*fb,*fa,dum) 
   ptt=vector(1,n);        } 
   xit=vector(1,n);    *cx=(*bx)+GOLD*(*bx-*ax); 
   xits=vector(1,n);    *fc=(*func)(*cx); 
   *fret=(*func)(p);    while (*fb > *fc) { 
   for (j=1;j<=n;j++) pt[j]=p[j];      r=(*bx-*ax)*(*fb-*fc); 
   for (*iter=1;;++(*iter)) {      q=(*bx-*cx)*(*fb-*fa); 
     fp=(*fret);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     ibig=0;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
     del=0.0;      ulim=(*bx)+GLIMIT*(*cx-*bx); 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      if ((*bx-u)*(u-*cx) > 0.0) { 
     for (i=1;i<=n;i++)        fu=(*func)(u); 
       printf(" %d %.12f",i, p[i]);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     printf("\n");        fu=(*func)(u); 
     for (i=1;i<=n;i++) {        if (fu < *fc) { 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       fptt=(*fret);            SHFT(*fb,*fc,fu,(*func)(u)) 
 #ifdef DEBUG            } 
       printf("fret=%lf \n",*fret);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
 #endif        u=ulim; 
       printf("%d",i);fflush(stdout);        fu=(*func)(u); 
       linmin(p,xit,n,fret,func);      } else { 
       if (fabs(fptt-(*fret)) > del) {        u=(*cx)+GOLD*(*cx-*bx); 
         del=fabs(fptt-(*fret));        fu=(*func)(u); 
         ibig=i;      } 
       }      SHFT(*ax,*bx,*cx,u) 
 #ifdef DEBUG        SHFT(*fa,*fb,*fc,fu) 
       printf("%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]);  /*************** linmin ************************/
       }  
       for(j=1;j<=n;j++)  int ncom; 
         printf(" p=%.12e",p[j]);  double *pcom,*xicom;
       printf("\n");  double (*nrfunc)(double []); 
 #endif   
     }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  { 
 #ifdef DEBUG    double brent(double ax, double bx, double cx, 
       int k[2],l;                 double (*f)(double), double tol, double *xmin); 
       k[0]=1;    double f1dim(double x); 
       k[1]=-1;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       printf("Max: %.12e",(*func)(p));                double *fc, double (*func)(double)); 
       for (j=1;j<=n;j++)    int j; 
         printf(" %.12e",p[j]);    double xx,xmin,bx,ax; 
       printf("\n");    double fx,fb,fa;
       for(l=0;l<=1;l++) {   
         for (j=1;j<=n;j++) {    ncom=n; 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    pcom=vector(1,n); 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    xicom=vector(1,n); 
         }    nrfunc=func; 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    for (j=1;j<=n;j++) { 
       }      pcom[j]=p[j]; 
 #endif      xicom[j]=xi[j]; 
     } 
     ax=0.0; 
       free_vector(xit,1,n);    xx=1.0; 
       free_vector(xits,1,n);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       free_vector(ptt,1,n);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       free_vector(pt,1,n);  #ifdef DEBUG
       return;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     }    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  #endif
     for (j=1;j<=n;j++) {    for (j=1;j<=n;j++) { 
       ptt[j]=2.0*p[j]-pt[j];      xi[j] *= xmin; 
       xit[j]=p[j]-pt[j];      p[j] += xi[j]; 
       pt[j]=p[j];    } 
     }    free_vector(xicom,1,n); 
     fptt=(*func)(ptt);    free_vector(pcom,1,n); 
     if (fptt < fp) {  } 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  
       if (t < 0.0) {  /*************** powell ************************/
         linmin(p,xit,n,fret,func);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
         for (j=1;j<=n;j++) {              double (*func)(double [])) 
           xi[j][ibig]=xi[j][n];  { 
           xi[j][n]=xit[j];    void linmin(double p[], double xi[], int n, double *fret, 
         }                double (*func)(double [])); 
 #ifdef DEBUG    int i,ibig,j; 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    double del,t,*pt,*ptt,*xit;
         for(j=1;j<=n;j++)    double fp,fptt;
           printf(" %.12e",xit[j]);    double *xits;
         printf("\n");    pt=vector(1,n); 
 #endif    ptt=vector(1,n); 
       }    xit=vector(1,n); 
     }    xits=vector(1,n); 
   }    *fret=(*func)(p); 
 }    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for (*iter=1;;++(*iter)) { 
 /**** Prevalence limit ****************/      fp=(*fret); 
       ibig=0; 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)      del=0.0; 
 {      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
      matrix by transitions matrix until convergence is reached */      fprintf(ficrespow,"%d %.12f",*iter,*fret);
       for (i=1;i<=n;i++) {
   int i, ii,j,k;        printf(" %d %.12f",i, p[i]);
   double min, max, maxmin, maxmax,sumnew=0.;        fprintf(ficlog," %d %.12lf",i, p[i]);
   double **matprod2();        fprintf(ficrespow," %.12lf", p[i]);
   double **out, cov[NCOVMAX], **pmij();      }
   double **newm;      printf("\n");
   double agefin, delaymax=50 ; /* Max number of years to converge */      fprintf(ficlog,"\n");
       fprintf(ficrespow,"\n");
   for (ii=1;ii<=nlstate+ndeath;ii++)      for (i=1;i<=n;i++) { 
     for (j=1;j<=nlstate+ndeath;j++){        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        fptt=(*fret); 
     }  #ifdef DEBUG
         printf("fret=%lf \n",*fret);
    cov[1]=1.;        fprintf(ficlog,"fret=%lf \n",*fret);
    #endif
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        printf("%d",i);fflush(stdout);
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        fprintf(ficlog,"%d",i);fflush(ficlog);
     newm=savm;        linmin(p,xit,n,fret,func); 
     /* Covariates have to be included here again */        if (fabs(fptt-(*fret)) > del) { 
      cov[2]=agefin;          del=fabs(fptt-(*fret)); 
            ibig=i; 
       for (k=1; k<=cptcovn;k++) {        } 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  #ifdef DEBUG
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/        printf("%d %.12e",i,(*fret));
       }        fprintf(ficlog,"%d %.12e",i,(*fret));
       for (k=1; k<=cptcovage;k++)        for (j=1;j<=n;j++) {
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       for (k=1; k<=cptcovprod;k++)          printf(" x(%d)=%.12e",j,xit[j]);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         }
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/        for(j=1;j<=n;j++) {
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/          printf(" p=%.12e",p[j]);
           fprintf(ficlog," p=%.12e",p[j]);
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);        }
         printf("\n");
     savm=oldm;        fprintf(ficlog,"\n");
     oldm=newm;  #endif
     maxmax=0.;      } 
     for(j=1;j<=nlstate;j++){      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       min=1.;  #ifdef DEBUG
       max=0.;        int k[2],l;
       for(i=1; i<=nlstate; i++) {        k[0]=1;
         sumnew=0;        k[1]=-1;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        printf("Max: %.12e",(*func)(p));
         prlim[i][j]= newm[i][j]/(1-sumnew);        fprintf(ficlog,"Max: %.12e",(*func)(p));
         max=FMAX(max,prlim[i][j]);        for (j=1;j<=n;j++) {
         min=FMIN(min,prlim[i][j]);          printf(" %.12e",p[j]);
       }          fprintf(ficlog," %.12e",p[j]);
       maxmin=max-min;        }
       maxmax=FMAX(maxmax,maxmin);        printf("\n");
     }        fprintf(ficlog,"\n");
     if(maxmax < ftolpl){        for(l=0;l<=1;l++) {
       return prlim;          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]);
           }
 /*************** transition probabilities ***************/          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)));
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )        }
 {  #endif
   double s1, s2;  
   /*double t34;*/  
   int i,j,j1, nc, ii, jj;        free_vector(xit,1,n); 
         free_vector(xits,1,n); 
     for(i=1; i<= nlstate; i++){        free_vector(ptt,1,n); 
     for(j=1; j<i;j++){        free_vector(pt,1,n); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        return; 
         /*s2 += param[i][j][nc]*cov[nc];*/      } 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/      for (j=1;j<=n;j++) { 
       }        ptt[j]=2.0*p[j]-pt[j]; 
       ps[i][j]=s2;        xit[j]=p[j]-pt[j]; 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        pt[j]=p[j]; 
     }      } 
     for(j=i+1; j<=nlstate+ndeath;j++){      fptt=(*func)(ptt); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      if (fptt < fp) { 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/        if (t < 0.0) { 
       }          linmin(p,xit,n,fret,func); 
       ps[i][j]=s2;          for (j=1;j<=n;j++) { 
     }            xi[j][ibig]=xi[j][n]; 
   }            xi[j][n]=xit[j]; 
     /*ps[3][2]=1;*/          }
   #ifdef DEBUG
   for(i=1; i<= nlstate; i++){          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
      s1=0;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     for(j=1; j<i; j++)          for(j=1;j<=n;j++){
       s1+=exp(ps[i][j]);            printf(" %.12e",xit[j]);
     for(j=i+1; j<=nlstate+ndeath; j++)            fprintf(ficlog," %.12e",xit[j]);
       s1+=exp(ps[i][j]);          }
     ps[i][i]=1./(s1+1.);          printf("\n");
     for(j=1; j<i; j++)          fprintf(ficlog,"\n");
       ps[i][j]= exp(ps[i][j])*ps[i][i];  #endif
     for(j=i+1; j<=nlstate+ndeath; j++)        }
       ps[i][j]= exp(ps[i][j])*ps[i][i];      } 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    } 
   } /* end i */  } 
   
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  /**** Prevalence limit (stable prevalence)  ****************/
     for(jj=1; jj<= nlstate+ndeath; jj++){  
       ps[ii][jj]=0;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       ps[ii][ii]=1;  {
     }    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   }       matrix by transitions matrix until convergence is reached */
   
     int i, ii,j,k;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    double min, max, maxmin, maxmax,sumnew=0.;
     for(jj=1; jj<= nlstate+ndeath; jj++){    double **matprod2();
      printf("%lf ",ps[ii][jj]);    double **out, cov[NCOVMAX], **pmij();
    }    double **newm;
     printf("\n ");    double agefin, delaymax=50 ; /* Max number of years to converge */
     }  
     printf("\n ");printf("%lf ",cov[2]);*/    for (ii=1;ii<=nlstate+ndeath;ii++)
 /*      for (j=1;j<=nlstate+ndeath;j++){
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   goto end;*/      }
     return ps;  
 }     cov[1]=1.;
    
 /**************** Product of 2 matrices ******************/   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      newm=savm;
 {      /* Covariates have to be included here again */
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times       cov[2]=agefin;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    
   /* in, b, out are matrice of pointers which should have been initialized        for (k=1; k<=cptcovn;k++) {
      before: only the contents of out is modified. The function returns          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
      a pointer to pointers identical to out */          /*      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]]);*/
   long i, j, k;        }
   for(i=nrl; i<= nrh; i++)        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for(k=ncolol; k<=ncoloh; k++)        for (k=1; k<=cptcovprod;k++)
       for(j=ncl,out[i][k]=0.; j<=nch; j++)          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         out[i][k] +=in[i][j]*b[j][k];  
         /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   return out;        /*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);
   
 /************* Higher Matrix Product ***************/      savm=oldm;
       oldm=newm;
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      maxmax=0.;
 {      for(j=1;j<=nlstate;j++){
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month        min=1.;
      duration (i.e. until        max=0.;
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        for(i=1; i<=nlstate; i++) {
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step          sumnew=0;
      (typically every 2 years instead of every month which is too big).          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
      Model is determined by parameters x and covariates have to be          prlim[i][j]= newm[i][j]/(1-sumnew);
      included manually here.          max=FMAX(max,prlim[i][j]);
           min=FMIN(min,prlim[i][j]);
      */        }
         maxmin=max-min;
   int i, j, d, h, k;        maxmax=FMAX(maxmax,maxmin);
   double **out, cov[NCOVMAX];      }
   double **newm;      if(maxmax < ftolpl){
         return prlim;
   /* Hstepm could be zero and should return the unit matrix */      }
   for (i=1;i<=nlstate+ndeath;i++)    }
     for (j=1;j<=nlstate+ndeath;j++){  }
       oldm[i][j]=(i==j ? 1.0 : 0.0);  
       po[i][j][0]=(i==j ? 1.0 : 0.0);  /*************** transition probabilities ***************/ 
     }  
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   for(h=1; h <=nhstepm; h++){  {
     for(d=1; d <=hstepm; d++){    double s1, s2;
       newm=savm;    /*double t34;*/
       /* Covariates have to be included here again */    int i,j,j1, nc, ii, jj;
       cov[1]=1.;  
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      for(i=1; i<= nlstate; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      for(j=1; j<i;j++){
       for (k=1; k<=cptcovage;k++)        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          /*s2 += param[i][j][nc]*cov[nc];*/
       for (k=1; k<=cptcovprod;k++)          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
         }
         ps[i][j]=s2;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
       /*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,      for(j=i+1; j<=nlstate+ndeath;j++){
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       savm=oldm;          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       oldm=newm;          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
     }        }
     for(i=1; i<=nlstate+ndeath; i++)        ps[i][j]=s2;
       for(j=1;j<=nlstate+ndeath;j++) {      }
         po[i][j][h]=newm[i][j];    }
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      /*ps[3][2]=1;*/
          */  
       }    for(i=1; i<= nlstate; i++){
   } /* end h */       s1=0;
   return po;      for(j=1; j<i; j++)
 }        s1+=exp(ps[i][j]);
       for(j=i+1; j<=nlstate+ndeath; j++)
         s1+=exp(ps[i][j]);
 /*************** log-likelihood *************/      ps[i][i]=1./(s1+1.);
 double func( double *x)      for(j=1; j<i; j++)
 {        ps[i][j]= exp(ps[i][j])*ps[i][i];
   int i, ii, j, k, mi, d, kk;      for(j=i+1; j<=nlstate+ndeath; j++)
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        ps[i][j]= exp(ps[i][j])*ps[i][i];
   double **out;      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   double sw; /* Sum of weights */    } /* end i */
   double lli; /* Individual log likelihood */  
   long ipmx;    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   /*extern weight */      for(jj=1; jj<= nlstate+ndeath; jj++){
   /* We are differentiating ll according to initial status */        ps[ii][jj]=0;
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        ps[ii][ii]=1;
   /*for(i=1;i<imx;i++)      }
     printf(" %d\n",s[4][i]);    }
   */  
   cov[1]=1.;  
     /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   for(k=1; k<=nlstate; k++) ll[k]=0.;      for(jj=1; jj<= nlstate+ndeath; jj++){
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){       printf("%lf ",ps[ii][jj]);
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];     }
     for(mi=1; mi<= wav[i]-1; mi++){      printf("\n ");
       for (ii=1;ii<=nlstate+ndeath;ii++)      }
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      printf("\n ");printf("%lf ",cov[2]);*/
       for(d=0; d<dh[mi][i]; d++){  /*
         newm=savm;    for(i=1; i<= npar; i++) printf("%f ",x[i]);
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    goto end;*/
         for (kk=1; kk<=cptcovage;kk++) {      return ps;
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  }
         }  
          /**************** Product of 2 matrices ******************/
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
         savm=oldm;  {
         oldm=newm;    /* 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 
       } /* end mult */       before: only the contents of out is modified. The function returns
             a pointer to pointers identical to out */
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    long i, j, k;
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    for(i=nrl; i<= nrh; i++)
       ipmx +=1;      for(k=ncolol; k<=ncoloh; k++)
       sw += weight[i];        for(j=ncl,out[i][k]=0.; j<=nch; j++)
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;          out[i][k] +=in[i][j]*b[j][k];
     } /* end of wave */  
   } /* end of individual */    return out;
   }
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  /************* Higher Matrix Product ***************/
   return -l;  
 }  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 
 /*********** Maximum Likelihood Estimation ***************/       'nhstepm*hstepm*stepm' months (i.e. until
        age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))       nhstepm*hstepm matrices. 
 {       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   int i,j, iter;       (typically every 2 years instead of every month which is too big 
   double **xi,*delti;       for the memory).
   double fret;       Model is determined by parameters x and covariates have to be 
   xi=matrix(1,npar,1,npar);       included manually here. 
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++)       */
       xi[i][j]=(i==j ? 1.0 : 0.0);  
   printf("Powell\n");    int i, j, d, h, k;
   powell(p,xi,npar,ftol,&iter,&fret,func);    double **out, cov[NCOVMAX];
     double **newm;
    printf("\n#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));    /* Hstepm could be zero and should return the unit matrix */
     for (i=1;i<=nlstate+ndeath;i++)
 }      for (j=1;j<=nlstate+ndeath;j++){
         oldm[i][j]=(i==j ? 1.0 : 0.0);
 /**** Computes Hessian and covariance matrix ***/        po[i][j][0]=(i==j ? 1.0 : 0.0);
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      }
 {    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   double  **a,**y,*x,pd;    for(h=1; h <=nhstepm; h++){
   double **hess;      for(d=1; d <=hstepm; d++){
   int i, j,jk;        newm=savm;
   int *indx;        /* Covariates have to be included here again */
         cov[1]=1.;
   double hessii(double p[], double delta, int theta, double delti[]);        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   double hessij(double p[], double delti[], int i, int j);        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   void lubksb(double **a, int npar, int *indx, double b[]) ;        for (k=1; k<=cptcovage;k++)
   void ludcmp(double **a, int npar, int *indx, double *d) ;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++)
   hess=matrix(1,npar,1,npar);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
   printf("\nCalculation of the hessian matrix. Wait...\n");  
   for (i=1;i<=npar;i++){        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
     printf("%d",i);fflush(stdout);        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     hess[i][i]=hessii(p,ftolhess,i,delti);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
     /*printf(" %f ",p[i]);*/                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     /*printf(" %lf ",hess[i][i]);*/        savm=oldm;
   }        oldm=newm;
        }
   for (i=1;i<=npar;i++) {      for(i=1; i<=nlstate+ndeath; i++)
     for (j=1;j<=npar;j++)  {        for(j=1;j<=nlstate+ndeath;j++) {
       if (j>i) {          po[i][j][h]=newm[i][j];
         printf(".%d%d",i,j);fflush(stdout);          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
         hess[i][j]=hessij(p,delti,i,j);           */
         hess[j][i]=hess[i][j];            }
         /*printf(" %lf ",hess[i][j]);*/    } /* end h */
       }    return po;
     }  }
   }  
   printf("\n");  
   /*************** log-likelihood *************/
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  double func( double *x)
    {
   a=matrix(1,npar,1,npar);    int i, ii, j, k, mi, d, kk;
   y=matrix(1,npar,1,npar);    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   x=vector(1,npar);    double **out;
   indx=ivector(1,npar);    double sw; /* Sum of weights */
   for (i=1;i<=npar;i++)    double lli; /* Individual log likelihood */
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    int s1, s2;
   ludcmp(a,npar,indx,&pd);    double bbh, survp;
     long ipmx;
   for (j=1;j<=npar;j++) {    /*extern weight */
     for (i=1;i<=npar;i++) x[i]=0;    /* We are differentiating ll according to initial status */
     x[j]=1;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     lubksb(a,npar,indx,x);    /*for(i=1;i<imx;i++) 
     for (i=1;i<=npar;i++){      printf(" %d\n",s[4][i]);
       matcov[i][j]=x[i];    */
     }    cov[1]=1.;
   }  
     for(k=1; k<=nlstate; k++) ll[k]=0.;
   printf("\n#Hessian matrix#\n");  
   for (i=1;i<=npar;i++) {    if(mle==1){
     for (j=1;j<=npar;j++) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       printf("%.3e ",hess[i][j]);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     }        for(mi=1; mi<= wav[i]-1; mi++){
     printf("\n");          for (ii=1;ii<=nlstate+ndeath;ii++)
   }            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   /* Recompute Inverse */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (i=1;i<=npar;i++)            }
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];          for(d=0; d<dh[mi][i]; d++){
   ludcmp(a,npar,indx,&pd);            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   /*  printf("\n#Hessian matrix recomputed#\n");            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   for (j=1;j<=npar;j++) {            }
     for (i=1;i<=npar;i++) x[i]=0;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     x[j]=1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     lubksb(a,npar,indx,x);            savm=oldm;
     for (i=1;i<=npar;i++){            oldm=newm;
       y[i][j]=x[i];          } /* end mult */
       printf("%.3e ",y[i][j]);        
     }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     printf("\n");          /* 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
   free_matrix(a,1,npar,1,npar);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   free_matrix(y,1,npar,1,npar);           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   free_vector(x,1,npar);           * probability in order to take into account the bias as a fraction of the way
   free_ivector(indx,1,npar);           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   free_matrix(hess,1,npar,1,npar);           * -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];
 /*************** hessian matrix ****************/          s2=s[mw[mi+1][i]][i];
 double hessii( double x[], double delta, int theta, double delti[])          bbh=(double)bh[mi][i]/(double)stepm; 
 {          /* bias is positive if real duration
   int i;           * is higher than the multiple of stepm and negative otherwise.
   int l=1, lmax=20;           */
   double k1,k2;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   double p2[NPARMAX+1];          if( s2 > nlstate){ 
   double res;            /* i.e. if s2 is a death state and if the date of death is known then the contribution
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;               to the likelihood is the probability to die between last step unit time and current 
   double fx;               step unit time, which is also the differences between probability to die before dh 
   int k=0,kmax=10;               and probability to die before dh-stepm . 
   double l1;               In version up to 0.92 likelihood was computed
           as if date of death was unknown. Death was treated as any other
   fx=func(x);          health state: the date of the interview describes the actual state
   for (i=1;i<=npar;i++) p2[i]=x[i];          and not the date of a change in health state. The former idea was
   for(l=0 ; l <=lmax; l++){          to consider that at each interview the state was recorded
     l1=pow(10,l);          (healthy, disable or death) and IMaCh was corrected; but when we
     delts=delt;          introduced the exact date of death then we should have modified
     for(k=1 ; k <kmax; k=k+1){          the contribution of an exact death to the likelihood. This new
       delt = delta*(l1*k);          contribution is smaller and very dependent of the step unit
       p2[theta]=x[theta] +delt;          stepm. It is no more the probability to die between last interview
       k1=func(p2)-fx;          and month of death but the probability to survive from last
       p2[theta]=x[theta]-delt;          interview up to one month before death multiplied by the
       k2=func(p2)-fx;          probability to die within a month. Thanks to Chris
       /*res= (k1-2.0*fx+k2)/delt/delt; */          Jackson for correcting this bug.  Former versions increased
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          mortality artificially. The bad side is that we add another loop
                which slows down the processing. The difference can be up to 10%
 #ifdef DEBUG          lower mortality.
       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);            */
 #endif            lli=log(out[s1][s2] - savm[s1][s2]);
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          }else{
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         k=kmax;            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
       }          } 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         k=kmax; l=lmax*10.;          /*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); */
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          ipmx +=1;
         delts=delt;          sw += weight[i];
       }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }        } /* end of wave */
   }      } /* end of individual */
   delti[theta]=delts;    }  else if(mle==2){
   return res;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 }        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
 double hessij( double x[], double delti[], int thetai,int thetaj)            for (j=1;j<=nlstate+ndeath;j++){
 {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int l=1, l1, lmax=20;            }
   double k1,k2,k3,k4,res,fx;          for(d=0; d<=dh[mi][i]; d++){
   double p2[NPARMAX+1];            newm=savm;
   int k;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
   fx=func(x);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   for (k=1; k<=2; k++) {            }
     for (i=1;i<=npar;i++) p2[i]=x[i];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     p2[thetai]=x[thetai]+delti[thetai]/k;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            savm=oldm;
     k1=func(p2)-fx;            oldm=newm;
            } /* end mult */
     p2[thetai]=x[thetai]+delti[thetai]/k;        
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     k2=func(p2)-fx;          /* 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 
     p2[thetai]=x[thetai]-delti[thetai]/k;           * (in months) between two waves is not a multiple of stepm, we rounded to 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;           * the nearest (and in case of equal distance, to the lowest) interval but now
     k3=func(p2)-fx;           * 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
     p2[thetai]=x[thetai]-delti[thetai]/k;           * probability in order to take into account the bias as a fraction of the way
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     k4=func(p2)-fx;           * -stepm/2 to stepm/2 .
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */           * For stepm=1 the results are the same as for previous versions of Imach.
 #ifdef DEBUG           * For stepm > 1 the results are less biased than in previous versions. 
     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);           */
 #endif          s1=s[mw[mi][i]][i];
   }          s2=s[mw[mi+1][i]][i];
   return res;          bbh=(double)bh[mi][i]/(double)stepm; 
 }          /* bias is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
 /************** Inverse of matrix **************/           */
 void ludcmp(double **a, int n, int *indx, double *d)          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
 {          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   int i,imax,j,k;          /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
   double big,dum,sum,temp;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   double *vv;          /*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); */
   vv=vector(1,n);          ipmx +=1;
   *d=1.0;          sw += weight[i];
   for (i=1;i<=n;i++) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     big=0.0;        } /* end of wave */
     for (j=1;j<=n;j++)      } /* end of individual */
       if ((temp=fabs(a[i][j])) > big) big=temp;    }  else if(mle==3){  /* exponential inter-extrapolation */
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     vv[i]=1.0/big;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   }        for(mi=1; mi<= wav[i]-1; mi++){
   for (j=1;j<=n;j++) {          for (ii=1;ii<=nlstate+ndeath;ii++)
     for (i=1;i<j;i++) {            for (j=1;j<=nlstate+ndeath;j++){
       sum=a[i][j];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       a[i][j]=sum;            }
     }          for(d=0; d<dh[mi][i]; d++){
     big=0.0;            newm=savm;
     for (i=j;i<=n;i++) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       sum=a[i][j];            for (kk=1; kk<=cptcovage;kk++) {
       for (k=1;k<j;k++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         sum -= a[i][k]*a[k][j];            }
       a[i][j]=sum;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       if ( (dum=vv[i]*fabs(sum)) >= big) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         big=dum;            savm=oldm;
         imax=i;            oldm=newm;
       }          } /* end mult */
     }        
     if (j != imax) {          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       for (k=1;k<=n;k++) {          /* But now since version 0.9 we anticipate for bias and large stepm.
         dum=a[imax][k];           * If stepm is larger than one month (smallest stepm) and if the exact delay 
         a[imax][k]=a[j][k];           * (in months) between two waves is not a multiple of stepm, we rounded to 
         a[j][k]=dum;           * 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
       *d = -(*d);           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
       vv[imax]=vv[j];           * 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
     indx[j]=imax;           * -stepm/2 to stepm/2 .
     if (a[j][j] == 0.0) a[j][j]=TINY;           * For stepm=1 the results are the same as for previous versions of Imach.
     if (j != n) {           * For stepm > 1 the results are less biased than in previous versions. 
       dum=1.0/(a[j][j]);           */
       for (i=j+1;i<=n;i++) a[i][j] *= dum;          s1=s[mw[mi][i]][i];
     }          s2=s[mw[mi+1][i]][i];
   }          bbh=(double)bh[mi][i]/(double)stepm; 
   free_vector(vv,1,n);  /* Doesn't work */          /* bias is positive if real duration
 ;           * is higher than the multiple of stepm and negative otherwise.
 }           */
           /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
 void lubksb(double **a, int n, int *indx, double b[])          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
 {          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   int i,ii=0,ip,j;          /*if(lli ==000.0)*/
   double sum;          /*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;
   for (i=1;i<=n;i++) {          sw += weight[i];
     ip=indx[i];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     sum=b[ip];        } /* end of wave */
     b[ip]=b[i];      } /* end of individual */
     if (ii)    }else{  /* ml=4 no inter-extrapolation */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     else if (sum) ii=i;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     b[i]=sum;        for(mi=1; mi<= wav[i]-1; mi++){
   }          for (ii=1;ii<=nlstate+ndeath;ii++)
   for (i=n;i>=1;i--) {            for (j=1;j<=nlstate+ndeath;j++){
     sum=b[i];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     b[i]=sum/a[i][i];            }
   }          for(d=0; d<dh[mi][i]; d++){
 }            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 /************ Frequencies ********************/            for (kk=1; kk<=cptcovage;kk++) {
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 {  /* Some frequencies */            }
            
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double ***freq; /* Frequencies */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double *pp;            savm=oldm;
   double pos, k2, dateintsum=0,k2cpt=0;            oldm=newm;
   FILE *ficresp;          } /* end mult */
   char fileresp[FILENAMELENGTH];        
           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   pp=vector(1,nlstate);          ipmx +=1;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          sw += weight[i];
   strcpy(fileresp,"p");          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   strcat(fileresp,fileres);        } /* end of wave */
   if((ficresp=fopen(fileresp,"w"))==NULL) {      } /* end of individual */
     printf("Problem with prevalence resultfile: %s\n", fileresp);    } /* End of if */
     exit(0);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   j1=0;    return -l;
   }
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
   /*********** Maximum Likelihood Estimation ***************/
   for(k1=1; k1<=j;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
        j1++;  {
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    int i,j, iter;
          scanf("%d", i);*/    double **xi;
         for (i=-1; i<=nlstate+ndeath; i++)      double fret;
          for (jk=-1; jk<=nlstate+ndeath; jk++)      char filerespow[FILENAMELENGTH];
            for(m=agemin; m <= agemax+3; m++)    xi=matrix(1,npar,1,npar);
              freq[i][jk][m]=0;    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++)
         dateintsum=0;        xi[i][j]=(i==j ? 1.0 : 0.0);
         k2cpt=0;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
        for (i=1; i<=imx; i++) {    strcpy(filerespow,"pow"); 
          bool=1;    strcat(filerespow,fileres);
          if  (cptcovn>0) {    if((ficrespow=fopen(filerespow,"w"))==NULL) {
            for (z1=1; z1<=cptcoveff; z1++)      printf("Problem with resultfile: %s\n", filerespow);
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
                bool=0;    }
          }    fprintf(ficrespow,"# Powell\n# iter -2*LL");
          if (bool==1) {    for (i=1;i<=nlstate;i++)
            for(m=firstpass; m<=lastpass; m++){      for(j=1;j<=nlstate+ndeath;j++)
              k2=anint[m][i]+(mint[m][i]/12.);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
              if ((k2>=dateprev1) && (k2<=dateprev2)) {    fprintf(ficrespow,"\n");
                if(agev[m][i]==0) agev[m][i]=agemax+1;    powell(p,xi,npar,ftol,&iter,&fret,func);
                if(agev[m][i]==1) agev[m][i]=agemax+2;  
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    fclose(ficrespow);
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
                  dateintsum=dateintsum+k2;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
                  k2cpt++;  
                }  }
   
              }  /**** Computes Hessian and covariance matrix ***/
            }  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
          }  {
        }    double  **a,**y,*x,pd;
         if  (cptcovn>0) {    double **hess;
          fprintf(ficresp, "\n#********** Variable ");    int i, j,jk;
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    int *indx;
        fprintf(ficresp, "**********\n#");  
         }    double hessii(double p[], double delta, int theta, double delti[]);
        for(i=1; i<=nlstate;i++)    double hessij(double p[], double delti[], int i, int j);
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    void lubksb(double **a, int npar, int *indx, double b[]) ;
        fprintf(ficresp, "\n");    void ludcmp(double **a, int npar, int *indx, double *d) ;
          
   for(i=(int)agemin; i <= (int)agemax+3; i++){    hess=matrix(1,npar,1,npar);
     if(i==(int)agemax+3)  
       printf("Total");    printf("\nCalculation of the hessian matrix. Wait...\n");
     else    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       printf("Age %d", i);    for (i=1;i<=npar;i++){
     for(jk=1; jk <=nlstate ; jk++){      printf("%d",i);fflush(stdout);
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      fprintf(ficlog,"%d",i);fflush(ficlog);
         pp[jk] += freq[jk][m][i];      hess[i][i]=hessii(p,ftolhess,i,delti);
     }      /*printf(" %f ",p[i]);*/
     for(jk=1; jk <=nlstate ; jk++){      /*printf(" %lf ",hess[i][i]);*/
       for(m=-1, pos=0; m <=0 ; m++)    }
         pos += freq[jk][m][i];    
       if(pp[jk]>=1.e-10)    for (i=1;i<=npar;i++) {
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      for (j=1;j<=npar;j++)  {
       else        if (j>i) { 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          printf(".%d%d",i,j);fflush(stdout);
     }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
           hess[i][j]=hessij(p,delti,i,j);
      for(jk=1; jk <=nlstate ; jk++){          hess[j][i]=hess[i][j];    
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          /*printf(" %lf ",hess[i][j]);*/
         pp[jk] += freq[jk][m][i];        }
      }      }
     }
     for(jk=1,pos=0; jk <=nlstate ; jk++)    printf("\n");
       pos += pp[jk];    fprintf(ficlog,"\n");
     for(jk=1; jk <=nlstate ; jk++){  
       if(pos>=1.e-5)    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       else    
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    a=matrix(1,npar,1,npar);
       if( i <= (int) agemax){    y=matrix(1,npar,1,npar);
         if(pos>=1.e-5){    x=vector(1,npar);
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    indx=ivector(1,npar);
           probs[i][jk][j1]= pp[jk]/pos;    for (i=1;i<=npar;i++)
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
         }    ludcmp(a,npar,indx,&pd);
       else  
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    for (j=1;j<=npar;j++) {
       }      for (i=1;i<=npar;i++) x[i]=0;
     }      x[j]=1;
     for(jk=-1; jk <=nlstate+ndeath; jk++)      lubksb(a,npar,indx,x);
       for(m=-1; m <=nlstate+ndeath; m++)      for (i=1;i<=npar;i++){ 
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        matcov[i][j]=x[i];
     if(i <= (int) agemax)      }
       fprintf(ficresp,"\n");    }
     printf("\n");  
     }    printf("\n#Hessian matrix#\n");
     }    fprintf(ficlog,"\n#Hessian matrix#\n");
  }    for (i=1;i<=npar;i++) { 
   dateintmean=dateintsum/k2cpt;      for (j=1;j<=npar;j++) { 
          printf("%.3e ",hess[i][j]);
   fclose(ficresp);        fprintf(ficlog,"%.3e ",hess[i][j]);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      }
   free_vector(pp,1,nlstate);      printf("\n");
       fprintf(ficlog,"\n");
   /* End of Freq */    }
 }  
     /* Recompute Inverse */
 /************ Prevalence ********************/    for (i=1;i<=npar;i++)
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
 {  /* Some frequencies */    ludcmp(a,npar,indx,&pd);
    
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    /*  printf("\n#Hessian matrix recomputed#\n");
   double ***freq; /* Frequencies */  
   double *pp;    for (j=1;j<=npar;j++) {
   double pos, k2;      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
   pp=vector(1,nlstate);      lubksb(a,npar,indx,x);
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      for (i=1;i<=npar;i++){ 
          y[i][j]=x[i];
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        printf("%.3e ",y[i][j]);
   j1=0;        fprintf(ficlog,"%.3e ",y[i][j]);
        }
   j=cptcoveff;      printf("\n");
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      fprintf(ficlog,"\n");
      }
  for(k1=1; k1<=j;k1++){    */
     for(i1=1; i1<=ncodemax[k1];i1++){  
       j1++;    free_matrix(a,1,npar,1,npar);
      free_matrix(y,1,npar,1,npar);
       for (i=-1; i<=nlstate+ndeath; i++)      free_vector(x,1,npar);
         for (jk=-1; jk<=nlstate+ndeath; jk++)      free_ivector(indx,1,npar);
           for(m=agemin; m <= agemax+3; m++)    free_matrix(hess,1,npar,1,npar);
             freq[i][jk][m]=0;  
        
       for (i=1; i<=imx; i++) {  }
         bool=1;  
         if  (cptcovn>0) {  /*************** hessian matrix ****************/
           for (z1=1; z1<=cptcoveff; z1++)  double hessii( double x[], double delta, int theta, double delti[])
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  {
               bool=0;    int i;
         }    int l=1, lmax=20;
         if (bool==1) {    double k1,k2;
           for(m=firstpass; m<=lastpass; m++){    double p2[NPARMAX+1];
             k2=anint[m][i]+(mint[m][i]/12.);    double res;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
               if(agev[m][i]==0) agev[m][i]=agemax+1;    double fx;
               if(agev[m][i]==1) agev[m][i]=agemax+2;    int k=0,kmax=10;
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    double l1;
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];    
             }    fx=func(x);
           }    for (i=1;i<=npar;i++) p2[i]=x[i];
         }    for(l=0 ; l <=lmax; l++){
       }      l1=pow(10,l);
            delts=delt;
         for(i=(int)agemin; i <= (int)agemax+3; i++){      for(k=1 ; k <kmax; k=k+1){
           for(jk=1; jk <=nlstate ; jk++){        delt = delta*(l1*k);
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        p2[theta]=x[theta] +delt;
               pp[jk] += freq[jk][m][i];        k1=func(p2)-fx;
           }        p2[theta]=x[theta]-delt;
           for(jk=1; jk <=nlstate ; jk++){        k2=func(p2)-fx;
             for(m=-1, pos=0; m <=0 ; m++)        /*res= (k1-2.0*fx+k2)/delt/delt; */
             pos += freq[jk][m][i];        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         }        
          #ifdef DEBUG
          for(jk=1; jk <=nlstate ; jk++){        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);
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        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);
              pp[jk] += freq[jk][m][i];  #endif
          }        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
                  if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          k=kmax;
         }
          for(jk=1; jk <=nlstate ; jk++){                  else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
            if( i <= (int) agemax){          k=kmax; l=lmax*10.;
              if(pos>=1.e-5){        }
                probs[i][jk][j1]= pp[jk]/pos;        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
              }          delts=delt;
            }        }
          }      }
              }
         }    delti[theta]=delts;
     }    return res; 
   }    
    }
    
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  double hessij( double x[], double delti[], int thetai,int thetaj)
   free_vector(pp,1,nlstate);  {
      int i;
 }  /* End of Freq */    int l=1, l1, lmax=20;
     double k1,k2,k3,k4,res,fx;
 /************* Waves Concatenation ***************/    double p2[NPARMAX+1];
     int k;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  
 {    fx=func(x);
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    for (k=1; k<=2; k++) {
      Death is a valid wave (if date is known).      for (i=1;i<=npar;i++) p2[i]=x[i];
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      p2[thetai]=x[thetai]+delti[thetai]/k;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
      and mw[mi+1][i]. dh depends on stepm.      k1=func(p2)-fx;
      */    
       p2[thetai]=x[thetai]+delti[thetai]/k;
   int i, mi, m;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      k2=func(p2)-fx;
      double sum=0., jmean=0.;*/    
       p2[thetai]=x[thetai]-delti[thetai]/k;
   int j, k=0,jk, ju, jl;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   double sum=0.;      k3=func(p2)-fx;
   jmin=1e+5;    
   jmax=-1;      p2[thetai]=x[thetai]-delti[thetai]/k;
   jmean=0.;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   for(i=1; i<=imx; i++){      k4=func(p2)-fx;
     mi=0;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     m=firstpass;  #ifdef DEBUG
     while(s[m][i] <= nlstate){      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);
       if(s[m][i]>=1)      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);
         mw[++mi][i]=m;  #endif
       if(m >=lastpass)    }
         break;    return res;
       else  }
         m++;  
     }/* end while */  /************** Inverse of matrix **************/
     if (s[m][i] > nlstate){  void ludcmp(double **a, int n, int *indx, double *d) 
       mi++;     /* Death is another wave */  { 
       /* if(mi==0)  never been interviewed correctly before death */    int i,imax,j,k; 
          /* Only death is a correct wave */    double big,dum,sum,temp; 
       mw[mi][i]=m;    double *vv; 
     }   
     vv=vector(1,n); 
     wav[i]=mi;    *d=1.0; 
     if(mi==0)    for (i=1;i<=n;i++) { 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);      big=0.0; 
   }      for (j=1;j<=n;j++) 
         if ((temp=fabs(a[i][j])) > big) big=temp; 
   for(i=1; i<=imx; i++){      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     for(mi=1; mi<wav[i];mi++){      vv[i]=1.0/big; 
       if (stepm <=0)    } 
         dh[mi][i]=1;    for (j=1;j<=n;j++) { 
       else{      for (i=1;i<j;i++) { 
         if (s[mw[mi+1][i]][i] > nlstate) {        sum=a[i][j]; 
           if (agedc[i] < 2*AGESUP) {        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        a[i][j]=sum; 
           if(j==0) j=1;  /* Survives at least one month after exam */      } 
           k=k+1;      big=0.0; 
           if (j >= jmax) jmax=j;      for (i=j;i<=n;i++) { 
           if (j <= jmin) jmin=j;        sum=a[i][j]; 
           sum=sum+j;        for (k=1;k<j;k++) 
           /* if (j<10) printf("j=%d num=%d ",j,i); */          sum -= a[i][k]*a[k][j]; 
           }        a[i][j]=sum; 
         }        if ( (dum=vv[i]*fabs(sum)) >= big) { 
         else{          big=dum; 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          imax=i; 
           k=k+1;        } 
           if (j >= jmax) jmax=j;      } 
           else if (j <= jmin)jmin=j;      if (j != imax) { 
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        for (k=1;k<=n;k++) { 
           sum=sum+j;          dum=a[imax][k]; 
         }          a[imax][k]=a[j][k]; 
         jk= j/stepm;          a[j][k]=dum; 
         jl= j -jk*stepm;        } 
         ju= j -(jk+1)*stepm;        *d = -(*d); 
         if(jl <= -ju)        vv[imax]=vv[j]; 
           dh[mi][i]=jk;      } 
         else      indx[j]=imax; 
           dh[mi][i]=jk+1;      if (a[j][j] == 0.0) a[j][j]=TINY; 
         if(dh[mi][i]==0)      if (j != n) { 
           dh[mi][i]=1; /* At least one step */        dum=1.0/(a[j][j]); 
       }        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     }      } 
   }    } 
   jmean=sum/k;    free_vector(vv,1,n);  /* Doesn't work */
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);  ;
  }  } 
 /*********** Tricode ****************************/  
 void tricode(int *Tvar, int **nbcode, int imx)  void lubksb(double **a, int n, int *indx, double b[]) 
 {  { 
   int Ndum[20],ij=1, k, j, i;    int i,ii=0,ip,j; 
   int cptcode=0;    double sum; 
   cptcoveff=0;   
      for (i=1;i<=n;i++) { 
   for (k=0; k<19; k++) Ndum[k]=0;      ip=indx[i]; 
   for (k=1; k<=7; k++) ncodemax[k]=0;      sum=b[ip]; 
       b[ip]=b[i]; 
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {      if (ii) 
     for (i=1; i<=imx; i++) {        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       ij=(int)(covar[Tvar[j]][i]);      else if (sum) ii=i; 
       Ndum[ij]++;      b[i]=sum; 
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    } 
       if (ij > cptcode) cptcode=ij;    for (i=n;i>=1;i--) { 
     }      sum=b[i]; 
       for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     for (i=0; i<=cptcode; i++) {      b[i]=sum/a[i][i]; 
       if(Ndum[i]!=0) ncodemax[j]++;    } 
     }  } 
     ij=1;  
   /************ Frequencies ********************/
   void  freqsummary(char fileres[], int iagemin, int iagemax, 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)
     for (i=1; i<=ncodemax[j]; i++) {  {  /* Some frequencies */
       for (k=0; k<=19; k++) {    
         if (Ndum[k] != 0) {    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
           nbcode[Tvar[j]][ij]=k;    int first;
           ij++;    double ***freq; /* Frequencies */
         }    double *pp, **prop;
         if (ij > ncodemax[j]) break;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
       }      FILE *ficresp;
     }    char fileresp[FILENAMELENGTH];
   }      
     pp=vector(1,nlstate);
  for (k=0; k<19; k++) Ndum[k]=0;    prop=matrix(1,nlstate,iagemin,iagemax+3);
     strcpy(fileresp,"p");
  for (i=1; i<=ncovmodel-2; i++) {    strcat(fileresp,fileres);
       ij=Tvar[i];    if((ficresp=fopen(fileresp,"w"))==NULL) {
       Ndum[ij]++;      printf("Problem with prevalence resultfile: %s\n", fileresp);
     }      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       exit(0);
  ij=1;    }
  for (i=1; i<=10; i++) {    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
    if((Ndum[i]!=0) && (i<=ncov)){    j1=0;
      Tvaraff[ij]=i;    
      ij++;    j=cptcoveff;
    }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
  }  
      first=1;
     cptcoveff=ij-1;  
 }    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
 /*********** Health Expectancies ****************/        j1++;
         /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)          scanf("%d", i);*/
 {        for (i=-1; i<=nlstate+ndeath; i++)  
   /* Health expectancies */          for (jk=-1; jk<=nlstate+ndeath; jk++)  
   int i, j, nhstepm, hstepm, h;            for(m=iagemin; m <= iagemax+3; m++)
   double age, agelim,hf;              freq[i][jk][m]=0;
   double ***p3mat;  
        for (i=1; i<=nlstate; i++)  
   fprintf(ficreseij,"# Health expectancies\n");        for(m=iagemin; m <= iagemax+3; m++)
   fprintf(ficreseij,"# Age");          prop[i][m]=0;
   for(i=1; i<=nlstate;i++)        
     for(j=1; j<=nlstate;j++)        dateintsum=0;
       fprintf(ficreseij," %1d-%1d",i,j);        k2cpt=0;
   fprintf(ficreseij,"\n");        for (i=1; i<=imx; i++) {
           bool=1;
   hstepm=1*YEARM; /*  Every j years of age (in month) */          if  (cptcovn>0) {
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   agelim=AGESUP;                bool=0;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          }
     /* nhstepm age range expressed in number of stepm */          if (bool==1){
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);            for(m=firstpass; m<=lastpass; m++){
     /* Typically if 20 years = 20*12/6=40 stepm */              k2=anint[m][i]+(mint[m][i]/12.);
     if (stepm >= YEARM) hstepm=1;              if ((k2>=dateprev1) && (k2<=dateprev2)) {
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */                if (m<lastpass) {
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);                    freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                   freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                 }
     for(i=1; i<=nlstate;i++)                
       for(j=1; j<=nlstate;j++)                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){                  dateintsum=dateintsum+k2;
           eij[i][j][(int)age] +=p3mat[i][j][h];                  k2cpt++;
         }                }
                  }
     hf=1;            }
     if (stepm >= YEARM) hf=stepm/YEARM;          }
     fprintf(ficreseij,"%.0f",age );        }
     for(i=1; i<=nlstate;i++)         
       for(j=1; j<=nlstate;j++){        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);  
       }        if  (cptcovn>0) {
     fprintf(ficreseij,"\n");          fprintf(ficresp, "\n#********** Variable "); 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          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++) 
 /************ Variance ******************/          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)        fprintf(ficresp, "\n");
 {        
   /* Variance of health expectancies */        for(i=iagemin; i <= iagemax+3; i++){
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          if(i==iagemax+3){
   double **newm;            fprintf(ficlog,"Total");
   double **dnewm,**doldm;          }else{
   int i, j, nhstepm, hstepm, h;            if(first==1){
   int k, cptcode;              first=0;
   double *xp;              printf("See log file for details...\n");
   double **gp, **gm;            }
   double ***gradg, ***trgradg;            fprintf(ficlog,"Age %d", i);
   double ***p3mat;          }
   double age,agelim;          for(jk=1; jk <=nlstate ; jk++){
   int theta;            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
               pp[jk] += freq[jk][m][i]; 
    fprintf(ficresvij,"# Covariances of life expectancies\n");          }
   fprintf(ficresvij,"# Age");          for(jk=1; jk <=nlstate ; jk++){
   for(i=1; i<=nlstate;i++)            for(m=-1, pos=0; m <=0 ; m++)
     for(j=1; j<=nlstate;j++)              pos += freq[jk][m][i];
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);            if(pp[jk]>=1.e-10){
   fprintf(ficresvij,"\n");              if(first==1){
               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   xp=vector(1,npar);              }
   dnewm=matrix(1,nlstate,1,npar);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   doldm=matrix(1,nlstate,1,nlstate);            }else{
                if(first==1)
   hstepm=1*YEARM; /* Every year of age */                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   agelim = AGESUP;            }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  
     if (stepm >= YEARM) hstepm=1;          for(jk=1; jk <=nlstate ; jk++){
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              pp[jk] += freq[jk][m][i];
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          }       
     gp=matrix(0,nhstepm,1,nlstate);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     gm=matrix(0,nhstepm,1,nlstate);            pos += pp[jk];
             posprop += prop[jk][i];
     for(theta=1; theta <=npar; theta++){          }
       for(i=1; i<=npar; i++){ /* Computes gradient */          for(jk=1; jk <=nlstate ; jk++){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            if(pos>=1.e-5){
       }              if(first==1)
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                  printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             }else{
       if (popbased==1) {              if(first==1)
         for(i=1; i<=nlstate;i++)                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
           prlim[i][i]=probs[(int)age][i][ij];              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       }            }
                  if( i <= iagemax){
       for(j=1; j<= nlstate; j++){              if(pos>=1.e-5){
         for(h=0; h<=nhstepm; h++){                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)                probs[i][jk][j1]= pp[jk]/pos;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];                /*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,prop[jk][i],posprop);
       for(i=1; i<=npar; i++) /* Computes gradient */            }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          for(jk=-1; jk <=nlstate+ndeath; jk++)
             for(m=-1; m <=nlstate+ndeath; m++)
       if (popbased==1) {              if(freq[jk][m][i] !=0 ) {
         for(i=1; i<=nlstate;i++)              if(first==1)
           prlim[i][i]=probs[(int)age][i][ij];                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
       }                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
               }
       for(j=1; j<= nlstate; j++){          if(i <= iagemax)
         for(h=0; h<=nhstepm; h++){            fprintf(ficresp,"\n");
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          if(first==1)
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];            printf("Others in log...\n");
         }          fprintf(ficlog,"\n");
       }        }
       }
       for(j=1; j<= nlstate; j++)    }
         for(h=0; h<=nhstepm; h++){    dateintmean=dateintsum/k2cpt; 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];   
         }    fclose(ficresp);
     } /* End theta */    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
     free_vector(pp,1,nlstate);
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     /* End of Freq */
     for(h=0; h<=nhstepm; h++)  }
       for(j=1; j<=nlstate;j++)  
         for(theta=1; theta <=npar; theta++)  /************ Prevalence ********************/
           trgradg[h][j][theta]=gradg[h][theta][j];  void prevalence(double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
   {  
     for(i=1;i<=nlstate;i++)    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
       for(j=1;j<=nlstate;j++)       in each health status at the date of interview (if between dateprev1 and dateprev2).
         vareij[i][j][(int)age] =0.;       We still use firstpass and lastpass as another selection.
     for(h=0;h<=nhstepm;h++){    */
       for(k=0;k<=nhstepm;k++){   
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    double ***freq; /* Frequencies */
         for(i=1;i<=nlstate;i++)    double *pp, **prop;
           for(j=1;j<=nlstate;j++)    double pos,posprop; 
             vareij[i][j][(int)age] += doldm[i][j];    double  y2; /* in fractional years */
       }    int iagemin, iagemax;
     }  
     h=1;    iagemin= (int) agemin;
     if (stepm >= YEARM) h=stepm/YEARM;    iagemax= (int) agemax;
     fprintf(ficresvij,"%.0f ",age );    /*pp=vector(1,nlstate);*/
     for(i=1; i<=nlstate;i++)    prop=matrix(1,nlstate,iagemin,iagemax+3); 
       for(j=1; j<=nlstate;j++){    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    j1=0;
       }    
     fprintf(ficresvij,"\n");    j=cptcoveff;
     free_matrix(gp,0,nhstepm,1,nlstate);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     free_matrix(gm,0,nhstepm,1,nlstate);    
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    for(k1=1; k1<=j;k1++){
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      for(i1=1; i1<=ncodemax[k1];i1++){
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        j1++;
   } /* End age */        
          for (i=1; i<=nlstate; i++)  
   free_vector(xp,1,npar);          for(m=iagemin; m <= iagemax+3; m++)
   free_matrix(doldm,1,nlstate,1,npar);            prop[i][m]=0.0;
   free_matrix(dnewm,1,nlstate,1,nlstate);       
         for (i=1; i<=imx; i++) { /* Each individual */
 }          bool=1;
           if  (cptcovn>0) {
 /************ Variance of prevlim ******************/            for (z1=1; z1<=cptcoveff; z1++) 
 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)              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
 {                bool=0;
   /* Variance of prevalence limit */          } 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          if (bool==1) { 
   double **newm;            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   double **dnewm,**doldm;              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   int i, j, nhstepm, hstepm;              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   int k, cptcode;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   double *xp;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   double *gp, *gm;                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
   double **gradg, **trgradg;                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   double age,agelim;                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
   int theta;                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                      prop[s[m][i]][iagemax+3] += weight[i]; 
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");                } 
   fprintf(ficresvpl,"# Age");              }
   for(i=1; i<=nlstate;i++)            } /* end selection of waves */
       fprintf(ficresvpl," %1d-%1d",i,i);          }
   fprintf(ficresvpl,"\n");        }
         for(i=iagemin; i <= iagemax+3; i++){  
   xp=vector(1,npar);          
   dnewm=matrix(1,nlstate,1,npar);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   doldm=matrix(1,nlstate,1,nlstate);            posprop += prop[jk][i]; 
            } 
   hstepm=1*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          for(jk=1; jk <=nlstate ; jk++){     
   agelim = AGESUP;            if( i <=  iagemax){ 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */              if(posprop>=1.e-5){ 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                probs[i][jk][j1]= prop[jk][i]/posprop;
     if (stepm >= YEARM) hstepm=1;              } 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            } 
     gradg=matrix(1,npar,1,nlstate);          }/* end jk */ 
     gp=vector(1,nlstate);        }/* end i */ 
     gm=vector(1,nlstate);      } /* end i1 */
     } /* end k1 */
     for(theta=1; theta <=npar; theta++){    
       for(i=1; i<=npar; i++){ /* Computes gradient */    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    /*free_vector(pp,1,nlstate);*/
       }    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  }  /* End of prevalence */
       for(i=1;i<=nlstate;i++)  
         gp[i] = prlim[i][i];  /************* Waves Concatenation ***************/
      
       for(i=1; i<=npar; i++) /* Computes gradient */  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)
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  {
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
       for(i=1;i<=nlstate;i++)       Death is a valid wave (if date is known).
         gm[i] = prlim[i][i];       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
        dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
       for(i=1;i<=nlstate;i++)       and mw[mi+1][i]. dh depends on stepm.
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];       */
     } /* End theta */  
     int i, mi, m;
     trgradg =matrix(1,nlstate,1,npar);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
        double sum=0., jmean=0.;*/
     for(j=1; j<=nlstate;j++)    int first;
       for(theta=1; theta <=npar; theta++)    int j, k=0,jk, ju, jl;
         trgradg[j][theta]=gradg[theta][j];    double sum=0.;
     first=0;
     for(i=1;i<=nlstate;i++)    jmin=1e+5;
       varpl[i][(int)age] =0.;    jmax=-1;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    jmean=0.;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    for(i=1; i<=imx; i++){
     for(i=1;i<=nlstate;i++)      mi=0;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      m=firstpass;
       while(s[m][i] <= nlstate){
     fprintf(ficresvpl,"%.0f ",age );        if(s[m][i]>=1)
     for(i=1; i<=nlstate;i++)          mw[++mi][i]=m;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        if(m >=lastpass)
     fprintf(ficresvpl,"\n");          break;
     free_vector(gp,1,nlstate);        else
     free_vector(gm,1,nlstate);          m++;
     free_matrix(gradg,1,npar,1,nlstate);      }/* end while */
     free_matrix(trgradg,1,nlstate,1,npar);      if (s[m][i] > nlstate){
   } /* End age */        mi++;     /* Death is another wave */
         /* if(mi==0)  never been interviewed correctly before death */
   free_vector(xp,1,npar);           /* Only death is a correct wave */
   free_matrix(doldm,1,nlstate,1,npar);        mw[mi][i]=m;
   free_matrix(dnewm,1,nlstate,1,nlstate);      }
   
 }      wav[i]=mi;
       if(mi==0){
 /************ Variance of one-step probabilities  ******************/        if(first==0){
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)          printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
 {          first=1;
   int i, j;        }
   int k=0, cptcode;        if(first==1){
   double **dnewm,**doldm;          fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
   double *xp;        }
   double *gp, *gm;      } /* end mi==0 */
   double **gradg, **trgradg;    } /* End individuals */
   double age,agelim, cov[NCOVMAX];  
   int theta;    for(i=1; i<=imx; i++){
   char fileresprob[FILENAMELENGTH];      for(mi=1; mi<wav[i];mi++){
         if (stepm <=0)
   strcpy(fileresprob,"prob");          dh[mi][i]=1;
   strcat(fileresprob,fileres);        else{
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     printf("Problem with resultfile: %s\n", fileresprob);            if (agedc[i] < 2*AGESUP) {
   }            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);            if(j==0) j=1;  /* Survives at least one month after exam */
              k=k+1;
             if (j >= jmax) jmax=j;
   xp=vector(1,npar);            if (j <= jmin) jmin=j;
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            sum=sum+j;
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));            /*if (j<0) printf("j=%d num=%d \n",j,i);*/
              /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   cov[1]=1;            if(j<0)printf("Warning! Negative delay (%d) between waves %d and %d of individual at line %d who is aged %.1f with statuses %d %d\n ",j,mw[mi][i],mw[mi+1][i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   for (age=bage; age<=fage; age ++){            }
     cov[2]=age;          }
     gradg=matrix(1,npar,1,9);          else{
     trgradg=matrix(1,9,1,npar);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));            k=k+1;
                if (j >= jmax) jmax=j;
     for(theta=1; theta <=npar; theta++){            else if (j <= jmin)jmin=j;
       for(i=1; i<=npar; i++)            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
                  if(j<0)printf("Warning! Negative delay (%d to death) between waves %d and %d of individual at line %d who is aged %.1f with statuses %d %d\n ",j,mw[mi][i],mw[mi+1][i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       pmij(pmmij,cov,ncovmodel,xp,nlstate);            sum=sum+j;
              }
       k=0;          jk= j/stepm;
       for(i=1; i<= (nlstate+ndeath); i++){          jl= j -jk*stepm;
         for(j=1; j<=(nlstate+ndeath);j++){          ju= j -(jk+1)*stepm;
            k=k+1;          if(mle <=1){ 
           gp[k]=pmmij[i][j];            if(jl==0){
         }              dh[mi][i]=jk;
       }              bh[mi][i]=0;
             }else{ /* We want a negative bias in order to only have interpolation ie
       for(i=1; i<=npar; i++)                    * at the price of an extra matrix product in likelihood */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);              dh[mi][i]=jk+1;
                  bh[mi][i]=ju;
             }
       pmij(pmmij,cov,ncovmodel,xp,nlstate);          }else{
       k=0;            if(jl <= -ju){
       for(i=1; i<=(nlstate+ndeath); i++){              dh[mi][i]=jk;
         for(j=1; j<=(nlstate+ndeath);j++){              bh[mi][i]=jl;       /* bias is positive if real duration
           k=k+1;                                   * is higher than the multiple of stepm and negative otherwise.
           gm[k]=pmmij[i][j];                                   */
         }            }
       }            else{
                    dh[mi][i]=jk+1;
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)              bh[mi][i]=ju;
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];              }
     }            if(dh[mi][i]==0){
               dh[mi][i]=1; /* At least one step */
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)              bh[mi][i]=ju; /* At least one step */
       for(theta=1; theta <=npar; theta++)              /*  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);*/
       trgradg[j][theta]=gradg[theta][j];            }
            }
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);        } /* end if mle */
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);      } /* end wave */
     }
      pmij(pmmij,cov,ncovmodel,x,nlstate);    jmean=sum/k;
     printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
      k=0;    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
      for(i=1; i<=(nlstate+ndeath); i++){   }
        for(j=1; j<=(nlstate+ndeath);j++){  
          k=k+1;  /*********** Tricode ****************************/
          gm[k]=pmmij[i][j];  void tricode(int *Tvar, int **nbcode, int imx)
         }  {
      }    
          int Ndum[20],ij=1, k, j, i, maxncov=19;
      /*printf("\n%d ",(int)age);    int cptcode=0;
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    cptcoveff=0; 
           
     for (k=0; k<maxncov; k++) Ndum[k]=0;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    for (k=1; k<=7; k++) ncodemax[k]=0;
      }*/  
     for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   fprintf(ficresprob,"\n%d ",(int)age);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                  modality*/ 
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);        Ndum[ij]++; /*store the modality */
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);        /*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 
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));                                         female is 1, then  cptcode=1.*/
     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);      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 */
  free_vector(xp,1,npar);      }
 fclose(ficresprob);  
  exit(0);      ij=1; 
 }      for (i=1; i<=ncodemax[j]; i++) {
         for (k=0; k<= maxncov; k++) {
 /******************* Printing html file ***********/          if (Ndum[k] != 0) {
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[] ){            nbcode[Tvar[j]][ij]=k; 
   int jj1, k1, i1, cpt;            /* 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; */
   FILE *fichtm;            
   /*char optionfilehtm[FILENAMELENGTH];*/            ij++;
           }
   strcpy(optionfilehtm,optionfile);          if (ij > ncodemax[j]) break; 
   strcat(optionfilehtm,".htm");        }  
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {      } 
     printf("Problem with %s \n",optionfilehtm), exit(0);    }  
   }  
    for (k=0; k< maxncov; k++) Ndum[k]=0;
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">  
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>   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.*/
 Total number of observations=%d <br>     ij=Tvar[i];
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>     Ndum[ij]++;
 <hr  size=\"2\" color=\"#EC5E5E\">   }
 <li>Outputs files<br><br>\n  
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n   ij=1;
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>   for (i=1; i<= maxncov; i++) {
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>     if((Ndum[i]!=0) && (i<=ncovcol)){
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>       Tvaraff[ij]=i; /*For printing */
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>       ij++;
         - 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>   cptcoveff=ij-1; /*Number of simple covariates*/
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>  }
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);  
    /*********** Health Expectancies ****************/
 fprintf(fichtm," <li>Graphs</li><p>");  
   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 )
  m=cptcoveff;  
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  {
     /* Health expectancies */
  jj1=0;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
  for(k1=1; k1<=m;k1++){    double age, agelim, hf;
    for(i1=1; i1<=ncodemax[k1];i1++){    double ***p3mat,***varhe;
        jj1++;    double **dnewm,**doldm;
        if (cptcovn > 0) {    double *xp;
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    double **gp, **gm;
          for (cpt=1; cpt<=cptcoveff;cpt++)    double ***gradg, ***trgradg;
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    int theta;
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");  
        }    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    xp=vector(1,npar);
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        dnewm=matrix(1,nlstate*nlstate,1,npar);
        for(cpt=1; cpt<nlstate;cpt++){    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    fprintf(ficreseij,"# Health expectancies\n");
        }    fprintf(ficreseij,"# Age");
     for(cpt=1; cpt<=nlstate;cpt++) {    for(i=1; i<=nlstate;i++)
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      for(j=1; j<=nlstate;j++)
 interval) in state (%d): v%s%d%d.gif <br>        fprintf(ficreseij," %1d-%1d (SE)",i,j);
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      fprintf(ficreseij,"\n");
      }  
      for(cpt=1; cpt<=nlstate;cpt++) {    if(estepm < stepm){
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>      printf ("Problem %d lower than %d\n",estepm, stepm);
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    }
      }    else  hstepm=estepm;   
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    /* We compute the life expectancy from trapezoids spaced every estepm months
 health expectancies in states (1) and (2): e%s%d.gif<br>     * This is mainly to measure the difference between two models: for example
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     * if stepm=24 months pijx are given only every 2 years and by summing them
 fprintf(fichtm,"\n</body>");     * we are calculating an estimate of the Life Expectancy assuming a linear 
    }     * progression in between and thus overestimating or underestimating according
    }     * to the curvature of the survival function. If, for the same date, we 
 fclose(fichtm);     * 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
 /******************* Gnuplot file **************/     * curvature will be obtained if estepm is as small as stepm. */
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemax, double fage , char pathc[], double p[]){  
     /* For example we decided to compute the life expectancy with the smallest unit */
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    /* 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 
   strcpy(optionfilegnuplot,optionfilefiname);       nstepm is the number of stepm from age to agelin. 
   strcat(optionfilegnuplot,".plt");       Look at hpijx to understand the reason of that which relies in memory size
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {       and note for a fixed period like estepm months */
     printf("Problem with file %s",optionfilegnuplot);    /* 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
 #ifdef windows       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     fprintf(ficgp,"cd \"%s\" \n",pathc);       results. So we changed our mind and took the option of the best precision.
 #endif    */
 m=pow(2,cptcoveff);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
    
  /* 1eme*/    agelim=AGESUP;
   for (cpt=1; cpt<= nlstate ; cpt ++) {    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
    for (k1=1; k1<= m ; k1 ++) {      /* nhstepm age range expressed in number of stepm */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); 
 #ifdef windows      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);      /* if (stepm >= YEARM) hstepm=1;*/
 #endif      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 #ifdef unix      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
 #endif      gp=matrix(0,nhstepm,1,nlstate*nlstate);
       gm=matrix(0,nhstepm,1,nlstate*nlstate);
 for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   else fprintf(ficgp," \%%*lf (\%%*lf)");         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
 }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);   
     for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      /* Computing Variances of health expectancies */
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  
      for (i=1; i<= nlstate ; i ++) {       for(theta=1; theta <=npar; theta++){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        for(i=1; i<=npar; i++){ 
   else fprintf(ficgp," \%%*lf (\%%*lf)");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 }          }
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 #ifdef unix    
 fprintf(ficgp,"\nset ter gif small size 400,300");        cptj=0;
 #endif        for(j=1; j<= nlstate; j++){
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          for(i=1; i<=nlstate; i++){
    }            cptj=cptj+1;
   }            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
   /*2 eme*/              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
             }
   for (k1=1; k1<= m ; k1 ++) {          }
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);        }
           
     for (i=1; i<= nlstate+1 ; i ++) {       
       k=2*i;        for(i=1; i<=npar; i++) 
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       for (j=1; j<= nlstate+1 ; j ++) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        
   else fprintf(ficgp," \%%*lf (\%%*lf)");        cptj=0;
 }          for(j=1; j<= nlstate; j++){
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          for(i=1;i<=nlstate;i++){
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);            cptj=cptj+1;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
       for (j=1; j<= nlstate+1 ; j ++) {  
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
         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*nlstate; j++)
       for (j=1; j<= nlstate+1 ; j ++) {          for(h=0; h<=nhstepm-1; h++){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   else fprintf(ficgp," \%%*lf (\%%*lf)");          }
 }         } 
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");     
       else fprintf(ficgp,"\" t\"\" w l 0,");  /* End theta */
     }  
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   }  
         for(h=0; h<=nhstepm-1; h++)
   /*3eme*/        for(j=1; j<=nlstate*nlstate;j++)
           for(theta=1; theta <=npar; theta++)
   for (k1=1; k1<= m ; k1 ++) {            trgradg[h][j][theta]=gradg[h][theta][j];
     for (cpt=1; cpt<= nlstate ; cpt ++) {       
       k=2+nlstate*(cpt-1);  
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);       for(i=1;i<=nlstate*nlstate;i++)
       for (i=1; i< nlstate ; i ++) {        for(j=1;j<=nlstate*nlstate;j++)
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);          varhe[i][j][(int)age] =0.;
       }  
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);       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++){
   /* CV preval stat */          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
     for (k1=1; k1<= m ; k1 ++) {          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
     for (cpt=1; cpt<nlstate ; cpt ++) {          for(i=1;i<=nlstate*nlstate;i++)
       k=3;            for(j=1;j<=nlstate*nlstate;j++)
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       for (i=1; i< nlstate ; i ++)      }
         fprintf(ficgp,"+$%d",k+i+1);      /* Computing expectancies */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);      for(i=1; i<=nlstate;i++)
              for(j=1; j<=nlstate;j++)
       l=3+(nlstate+ndeath)*cpt;          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
       for (i=1; i< nlstate ; i ++) {            
         l=3+(nlstate+ndeath)*cpt;  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
         fprintf(ficgp,"+$%d",l+i+1);  
       }          }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);    
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      fprintf(ficreseij,"%3.0f",age );
     }      cptj=0;
   }        for(i=1; i<=nlstate;i++)
          for(j=1; j<=nlstate;j++){
   /* proba elementaires */          cptj++;
    for(i=1,jk=1; i <=nlstate; i++){          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
     for(k=1; k <=(nlstate+ndeath); k++){        }
       if (k != i) {      fprintf(ficreseij,"\n");
         for(j=1; j <=ncovmodel; j++){     
              free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
           jk++;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
           fprintf(ficgp,"\n");      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
         }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       }    }
     }    printf("\n");
     }    fprintf(ficlog,"\n");
   
     for(jk=1; jk <=m; jk++) {    free_vector(xp,1,npar);
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
    i=1;    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
    for(k2=1; k2<=nlstate; k2++) {    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
      k3=i;  }
      for(k=1; k<=(nlstate+ndeath); k++) {  
        if (k != k2){  /************ Variance ******************/
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);  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)
 ij=1;  {
         for(j=3; j <=ncovmodel; j++) {    /* Variance of health expectancies */
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    /* double **newm;*/
             ij++;    double **dnewm,**doldm;
           }    double **dnewmp,**doldmp;
           else    int i, j, nhstepm, hstepm, h, nstepm ;
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    int k, cptcode;
         }    double *xp;
           fprintf(ficgp,")/(1");    double **gp, **gm;  /* for var eij */
            double ***gradg, ***trgradg; /*for var eij */
         for(k1=1; k1 <=nlstate; k1++){      double **gradgp, **trgradgp; /* for var p point j */
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    double *gpp, *gmp; /* for var p point j */
 ij=1;    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
           for(j=3; j <=ncovmodel; j++){    double ***p3mat;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    double age,agelim, hf;
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    double ***mobaverage;
             ij++;    int theta;
           }    char digit[4];
           else    char digitp[25];
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  
           }    char fileresprobmorprev[FILENAMELENGTH];
           fprintf(ficgp,")");  
         }    if(popbased==1){
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);      if(mobilav!=0)
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");        strcpy(digitp,"-populbased-mobilav-");
         i=i+ncovmodel;      else strcpy(digitp,"-populbased-nomobil-");
        }    }
      }    else 
    }      strcpy(digitp,"-stablbased-");
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);  
    }    if (mobilav!=0) {
          mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   fclose(ficgp);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
 }  /* end gnuplot */        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
 /*************** Moving average **************/    }
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){  
     strcpy(fileresprobmorprev,"prmorprev"); 
   int i, cpt, cptcod;    sprintf(digit,"%-d",ij);
     for (agedeb=agemin; agedeb<=fage; agedeb++)    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
       for (i=1; i<=nlstate;i++)    strcat(fileresprobmorprev,digit); /* Tvar to be done */
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
           mobaverage[(int)agedeb][i][cptcod]=0.;    strcat(fileresprobmorprev,fileres);
        if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       for (i=1; i<=nlstate;i++){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    }
           for (cpt=0;cpt<=4;cpt++){    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
           }    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    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) {
 /**************** Main Program *****************/      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
 /***********************************************/      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
       exit(0);
 int main(int argc, char *argv[])    }
 {    else{
       fprintf(ficgp,"\n# Routine varevsij");
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    }
   double agedeb, agefin,hf;    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   double agemin=1.e20, agemax=-1.e20;      printf("Problem with html file: %s\n", optionfilehtm);
       fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   double fret;      exit(0);
   double **xi,tmp,delta;    }
     else{
   double dum; /* Dummy variable */      fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
   double ***p3mat;      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   int *indx;    }
   char line[MAXLINE], linepar[MAXLINE];    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   char title[MAXLINE];  
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    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");
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    fprintf(ficresvij,"# Age");
      for(i=1; i<=nlstate;i++)
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];      for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   char filerest[FILENAMELENGTH];    fprintf(ficresvij,"\n");
   char fileregp[FILENAMELENGTH];  
   char popfile[FILENAMELENGTH];    xp=vector(1,npar);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    dnewm=matrix(1,nlstate,1,npar);
   int firstobs=1, lastobs=10;    doldm=matrix(1,nlstate,1,nlstate);
   int sdeb, sfin; /* Status at beginning and end */    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   int c,  h , cpt,l;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   int ju,jl, mi;  
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    gpp=vector(nlstate+1,nlstate+ndeath);
   int mobilav=0,popforecast=0;    gmp=vector(nlstate+1,nlstate+ndeath);
   int hstepm, nhstepm;    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   int *popage;/*boolprev=0 if date and zero if wave*/    
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
   double bage, fage, age, agelim, agebase;    }
   double ftolpl=FTOL;    else  hstepm=estepm;   
   double **prlim;    /* For example we decided to compute the life expectancy with the smallest unit */
   double *severity;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   double ***param; /* Matrix of parameters */       nhstepm is the number of hstepm from age to agelim 
   double  *p;       nstepm is the number of stepm from age to agelin. 
   double **matcov; /* Matrix of covariance */       Look at hpijx to understand the reason of that which relies in memory size
   double ***delti3; /* Scale */       and note for a fixed period like k years */
   double *delti; /* Scale */    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   double ***eij, ***vareij;       survival function given by stepm (the optimization length). Unfortunately it
   double **varpl; /* Variances of prevalence limits by age */       means that if the survival funtion is printed every two years of age and if
   double *epj, vepp;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   double kk1, kk2;       results. So we changed our mind and took the option of the best precision.
   double *popeffectif,*popcount;    */
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   double yp,yp1,yp2;    agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   char *alph[]={"a","a","b","c","d","e"}, str[4];      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);
   char z[1]="c", occ;      gp=matrix(0,nhstepm,1,nlstate);
 #include <sys/time.h>      gm=matrix(0,nhstepm,1,nlstate);
 #include <time.h>  
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  
        for(theta=1; theta <=npar; theta++){
   /* long total_usecs;        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   struct timeval start_time, end_time;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
          }
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
   printf("\n%s",version);        if (popbased==1) {
   if(argc <=1){          if(mobilav ==0){
     printf("\nEnter the parameter file name: ");            for(i=1; i<=nlstate;i++)
     scanf("%s",pathtot);              prlim[i][i]=probs[(int)age][i][ij];
   }          }else{ /* mobilav */ 
   else{            for(i=1; i<=nlstate;i++)
     strcpy(pathtot,argv[1]);              prlim[i][i]=mobaverage[(int)age][i][ij];
   }          }
   /*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);*/        for(j=1; j<= nlstate; j++){
   /* cutv(path,optionfile,pathtot,'\\');*/          for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);          }
   chdir(path);        }
   replace(pathc,path);        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
 /*-------- arguments in the command line --------*/           as a weighted average of prlim.
         */
   strcpy(fileres,"r");        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   strcat(fileres, optionfilefiname);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
   strcat(fileres,".txt");    /* Other files have txt extension */            gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
   /*---------arguments file --------*/        /* end probability of death */
   
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
     printf("Problem with optionfile %s\n",optionfile);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     goto end;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
   strcpy(filereso,"o");        if (popbased==1) {
   strcat(filereso,fileres);          if(mobilav ==0){
   if((ficparo=fopen(filereso,"w"))==NULL) {            for(i=1; i<=nlstate;i++)
     printf("Problem with Output resultfile: %s\n", filereso);goto end;              prlim[i][i]=probs[(int)age][i][ij];
   }          }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
   /* Reads comments: lines beginning with '#' */              prlim[i][i]=mobaverage[(int)age][i][ij];
   while((c=getc(ficpar))=='#' && c!= EOF){          }
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);  
     puts(line);        for(j=1; j<= nlstate; j++){
     fputs(line,ficparo);          for(h=0; h<=nhstepm; h++){
   }            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   ungetc(c,ficpar);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);        }
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);        /* This for computing probability of death (h=1 means
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);           computed over hstepm matrices product = hstepm*stepm months) 
 while((c=getc(ficpar))=='#' && c!= EOF){           as a weighted average of prlim.
     ungetc(c,ficpar);        */
     fgets(line, MAXLINE, ficpar);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     puts(line);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
     fputs(line,ficparo);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
   }        }    
   ungetc(c,ficpar);        /* end probability of death */
    
            for(j=1; j<= nlstate; j++) /* vareij */
   covar=matrix(0,NCOVMAX,1,n);          for(h=0; h<=nhstepm; h++){
   cptcovn=0;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;          }
   
   ncovmodel=2+cptcovn;        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
          }
   /* Read guess parameters */  
   /* Reads comments: lines beginning with '#' */      } /* End theta */
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
     fgets(line, MAXLINE, ficpar);  
     puts(line);      for(h=0; h<=nhstepm; h++) /* veij */
     fputs(line,ficparo);        for(j=1; j<=nlstate;j++)
   }          for(theta=1; theta <=npar; theta++)
   ungetc(c,ficpar);            trgradg[h][j][theta]=gradg[h][theta][j];
    
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     for(i=1; i <=nlstate; i++)        for(theta=1; theta <=npar; theta++)
     for(j=1; j <=nlstate+ndeath-1; j++){          trgradgp[j][theta]=gradgp[theta][j];
       fscanf(ficpar,"%1d%1d",&i1,&j1);    
       fprintf(ficparo,"%1d%1d",i1,j1);  
       printf("%1d%1d",i,j);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(k=1; k<=ncovmodel;k++){      for(i=1;i<=nlstate;i++)
         fscanf(ficpar," %lf",&param[i][j][k]);        for(j=1;j<=nlstate;j++)
         printf(" %lf",param[i][j][k]);          vareij[i][j][(int)age] =0.;
         fprintf(ficparo," %lf",param[i][j][k]);  
       }      for(h=0;h<=nhstepm;h++){
       fscanf(ficpar,"\n");        for(k=0;k<=nhstepm;k++){
       printf("\n");          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
       fprintf(ficparo,"\n");          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
     }          for(i=1;i<=nlstate;i++)
              for(j=1;j<=nlstate;j++)
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
   p=param[1][1];      }
      
   /* Reads comments: lines beginning with '#' */      /* pptj */
   while((c=getc(ficpar))=='#' && c!= EOF){      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
     ungetc(c,ficpar);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
     fgets(line, MAXLINE, ficpar);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
     puts(line);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
     fputs(line,ficparo);          varppt[j][i]=doldmp[j][i];
   }      /* end ppptj */
   ungetc(c,ficpar);      /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */   
   for(i=1; i <=nlstate; i++){      if (popbased==1) {
     for(j=1; j <=nlstate+ndeath-1; j++){        if(mobilav ==0){
       fscanf(ficpar,"%1d%1d",&i1,&j1);          for(i=1; i<=nlstate;i++)
       printf("%1d%1d",i,j);            prlim[i][i]=probs[(int)age][i][ij];
       fprintf(ficparo,"%1d%1d",i1,j1);        }else{ /* mobilav */ 
       for(k=1; k<=ncovmodel;k++){          for(i=1; i<=nlstate;i++)
         fscanf(ficpar,"%le",&delti3[i][j][k]);            prlim[i][i]=mobaverage[(int)age][i][ij];
         printf(" %le",delti3[i][j][k]);        }
         fprintf(ficparo," %le",delti3[i][j][k]);      }
       }               
       fscanf(ficpar,"\n");      /* This for computing probability of death (h=1 means
       printf("\n");         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
       fprintf(ficparo,"\n");         as a weighted average of prlim.
     }      */
   }      for(j=nlstate+1;j<=nlstate+ndeath;j++){
   delti=delti3[1][1];        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
            gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   /* Reads comments: lines beginning with '#' */      }    
   while((c=getc(ficpar))=='#' && c!= EOF){      /* end probability of death */
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     puts(line);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     fputs(line,ficparo);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
   }        for(i=1; i<=nlstate;i++){
   ungetc(c,ficpar);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
          }
   matcov=matrix(1,npar,1,npar);      } 
   for(i=1; i <=npar; i++){      fprintf(ficresprobmorprev,"\n");
     fscanf(ficpar,"%s",&str);  
     printf("%s",str);      fprintf(ficresvij,"%.0f ",age );
     fprintf(ficparo,"%s",str);      for(i=1; i<=nlstate;i++)
     for(j=1; j <=i; j++){        for(j=1; j<=nlstate;j++){
       fscanf(ficpar," %le",&matcov[i][j]);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       printf(" %.5le",matcov[i][j]);        }
       fprintf(ficparo," %.5le",matcov[i][j]);      fprintf(ficresvij,"\n");
     }      free_matrix(gp,0,nhstepm,1,nlstate);
     fscanf(ficpar,"\n");      free_matrix(gm,0,nhstepm,1,nlstate);
     printf("\n");      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
     fprintf(ficparo,"\n");      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
   }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   for(i=1; i <=npar; i++)    } /* End age */
     for(j=i+1;j<=npar;j++)    free_vector(gpp,nlstate+1,nlstate+ndeath);
       matcov[i][j]=matcov[j][i];    free_vector(gmp,nlstate+1,nlstate+ndeath);
        free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   printf("\n");    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 */
     /*-------- data file ----------*/    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
     if((ficres =fopen(fileres,"w"))==NULL) {  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
       printf("Problem with resultfile: %s\n", fileres);goto end;  /*   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(ficres,"#%s\n",version);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
        fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
     if((fic=fopen(datafile,"r"))==NULL)    {    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
       printf("Problem with datafile: %s\n", datafile);goto end;    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%s.png\"> <br>\n", estepm,digitp,optionfilefiname,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);
     n= lastobs;  */
     severity = vector(1,maxwav);    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
     outcome=imatrix(1,maxwav+1,1,n);  
     num=ivector(1,n);    free_vector(xp,1,npar);
     moisnais=vector(1,n);    free_matrix(doldm,1,nlstate,1,nlstate);
     annais=vector(1,n);    free_matrix(dnewm,1,nlstate,1,npar);
     moisdc=vector(1,n);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     andc=vector(1,n);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     agedc=vector(1,n);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     cod=ivector(1,n);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     weight=vector(1,n);    fclose(ficresprobmorprev);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    fclose(ficgp);
     mint=matrix(1,maxwav,1,n);    fclose(fichtm);
     anint=matrix(1,maxwav,1,n);  }  
     s=imatrix(1,maxwav+1,1,n);  
     adl=imatrix(1,maxwav+1,1,n);      /************ Variance of prevlim ******************/
     tab=ivector(1,NCOVMAX);  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)
     ncodemax=ivector(1,8);  {
     /* Variance of prevalence limit */
     i=1;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     while (fgets(line, MAXLINE, fic) != NULL)    {    double **newm;
       if ((i >= firstobs) && (i <=lastobs)) {    double **dnewm,**doldm;
            int i, j, nhstepm, hstepm;
         for (j=maxwav;j>=1;j--){    int k, cptcode;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    double *xp;
           strcpy(line,stra);    double *gp, *gm;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    double **gradg, **trgradg;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    double age,agelim;
         }    int theta;
             
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        fprintf(ficresvpl," %1d-%1d",i,i);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficresvpl,"\n");
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    xp=vector(1,npar);
         for (j=ncov;j>=1;j--){    dnewm=matrix(1,nlstate,1,npar);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    doldm=matrix(1,nlstate,1,nlstate);
         }    
         num[i]=atol(stra);    hstepm=1*YEARM; /* Every year of age */
            hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    agelim = AGESUP;
           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;}*/    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         i=i+1;      if (stepm >= YEARM) hstepm=1;
       }      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
     }      gradg=matrix(1,npar,1,nlstate);
     /* printf("ii=%d", ij);      gp=vector(1,nlstate);
        scanf("%d",i);*/      gm=vector(1,nlstate);
   imx=i-1; /* Number of individuals */  
       for(theta=1; theta <=npar; theta++){
   /* for (i=1; i<=imx; i++){        for(i=1; i<=npar; i++){ /* Computes gradient */
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     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;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     }        for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
     for (i=1; i<=imx; i++)      
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/        for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
   /* Calculation of the number of parameter from char model*/        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   Tvar=ivector(1,15);        for(i=1;i<=nlstate;i++)
   Tprod=ivector(1,15);          gm[i] = prlim[i][i];
   Tvaraff=ivector(1,15);  
   Tvard=imatrix(1,15,1,2);        for(i=1;i<=nlstate;i++)
   Tage=ivector(1,15);                gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
          } /* End theta */
   if (strlen(model) >1){  
     j=0, j1=0, k1=1, k2=1;      trgradg =matrix(1,nlstate,1,npar);
     j=nbocc(model,'+');  
     j1=nbocc(model,'*');      for(j=1; j<=nlstate;j++)
     cptcovn=j+1;        for(theta=1; theta <=npar; theta++)
     cptcovprod=j1;          trgradg[j][theta]=gradg[theta][j];
      
          for(i=1;i<=nlstate;i++)
     strcpy(modelsav,model);        varpl[i][(int)age] =0.;
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       printf("Error. Non available option model=%s ",model);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       goto end;      for(i=1;i<=nlstate;i++)
     }        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
      
     for(i=(j+1); i>=1;i--){      fprintf(ficresvpl,"%.0f ",age );
       cutv(stra,strb,modelsav,'+');      for(i=1; i<=nlstate;i++)
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      fprintf(ficresvpl,"\n");
       /*scanf("%d",i);*/      free_vector(gp,1,nlstate);
       if (strchr(strb,'*')) {      free_vector(gm,1,nlstate);
         cutv(strd,strc,strb,'*');      free_matrix(gradg,1,npar,1,nlstate);
         if (strcmp(strc,"age")==0) {      free_matrix(trgradg,1,nlstate,1,npar);
           cptcovprod--;    } /* End age */
           cutv(strb,stre,strd,'V');  
           Tvar[i]=atoi(stre);    free_vector(xp,1,npar);
           cptcovage++;    free_matrix(doldm,1,nlstate,1,npar);
             Tage[cptcovage]=i;    free_matrix(dnewm,1,nlstate,1,nlstate);
             /*printf("stre=%s ", stre);*/  
         }  }
         else if (strcmp(strd,"age")==0) {  
           cptcovprod--;  /************ Variance of one-step probabilities  ******************/
           cutv(strb,stre,strc,'V');  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
           Tvar[i]=atoi(stre);  {
           cptcovage++;    int i, j=0,  i1, k1, l1, t, tj;
           Tage[cptcovage]=i;    int k2, l2, j1,  z1;
         }    int k=0,l, cptcode;
         else {    int first=1, first1;
           cutv(strb,stre,strc,'V');    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
           Tvar[i]=ncov+k1;    double **dnewm,**doldm;
           cutv(strb,strc,strd,'V');    double *xp;
           Tprod[k1]=i;    double *gp, *gm;
           Tvard[k1][1]=atoi(strc);    double **gradg, **trgradg;
           Tvard[k1][2]=atoi(stre);    double **mu;
           Tvar[cptcovn+k2]=Tvard[k1][1];    double age,agelim, cov[NCOVMAX];
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
           for (k=1; k<=lastobs;k++)    int theta;
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    char fileresprob[FILENAMELENGTH];
           k1++;    char fileresprobcov[FILENAMELENGTH];
           k2=k2+2;    char fileresprobcor[FILENAMELENGTH];
         }  
       }    double ***varpij;
       else {  
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    strcpy(fileresprob,"prob"); 
        /*  scanf("%d",i);*/    strcat(fileresprob,fileres);
       cutv(strd,strc,strb,'V');    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       Tvar[i]=atoi(strc);      printf("Problem with resultfile: %s\n", fileresprob);
       }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
       strcpy(modelsav,stra);      }
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    strcpy(fileresprobcov,"probcov"); 
         scanf("%d",i);*/    strcat(fileresprobcov,fileres);
     }    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
 }      printf("Problem with resultfile: %s\n", fileresprobcov);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    }
   printf("cptcovprod=%d ", cptcovprod);    strcpy(fileresprobcor,"probcor"); 
   scanf("%d ",i);*/    strcat(fileresprobcor,fileres);
     fclose(fic);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
     /*  if(mle==1){*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     if (weightopt != 1) { /* Maximisation without weights*/    }
       for(i=1;i<=n;i++) weight[i]=1.0;    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);
     /*-calculation of age at interview from date of interview and age at death -*/    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     agev=matrix(1,maxwav,1,imx);    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);
    for (i=1; i<=imx; i++)    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
      for(m=2; (m<= maxwav); m++)    
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
          anint[m][i]=9999;    fprintf(ficresprob,"# Age");
          s[m][i]=-1;    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
        }    fprintf(ficresprobcov,"# Age");
        fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     for (i=1; i<=imx; i++)  {    fprintf(ficresprobcov,"# Age");
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  
       for(m=1; (m<= maxwav); m++){  
         if(s[m][i] >0){    for(i=1; i<=nlstate;i++)
           if (s[m][i] == nlstate+1) {      for(j=1; j<=(nlstate+ndeath);j++){
             if(agedc[i]>0)        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
               if(moisdc[i]!=99 && andc[i]!=9999)        fprintf(ficresprobcov," p%1d-%1d ",i,j);
               agev[m][i]=agedc[i];        fprintf(ficresprobcor," p%1d-%1d ",i,j);
             else {      }  
               if (andc[i]!=9999){   /* fprintf(ficresprob,"\n");
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    fprintf(ficresprobcov,"\n");
               agev[m][i]=-1;    fprintf(ficresprobcor,"\n");
               }   */
             }   xp=vector(1,npar);
           }    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           else if(s[m][i] !=9){ /* Should no more exist */    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
             if(mint[m][i]==99 || anint[m][i]==9999)    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
               agev[m][i]=1;    first=1;
             else if(agev[m][i] <agemin){    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
               agemin=agev[m][i];      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
             }      exit(0);
             else if(agev[m][i] >agemax){    }
               agemax=agev[m][i];    else{
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      fprintf(ficgp,"\n# Routine varprob");
             }    }
             /*agev[m][i]=anint[m][i]-annais[i];*/    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
             /*   agev[m][i] = age[i]+2*m;*/      printf("Problem with html file: %s\n", optionfilehtm);
           }      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
           else { /* =9 */      exit(0);
             agev[m][i]=1;    }
             s[m][i]=-1;    else{
           }      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
         }      fprintf(fichtm,"\n");
         else /*= 0 Unknown */  
           agev[m][i]=1;      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");
     }  
     for (i=1; i<=imx; i++)  {    }
       for(m=1; (m<= maxwav); m++){  
         if (s[m][i] > (nlstate+ndeath)) {    cov[1]=1;
           printf("Error: Wrong value in nlstate or ndeath\n");      tj=cptcoveff;
           goto end;    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
         }    j1=0;
       }    for(t=1; t<=tj;t++){
     }      for(i1=1; i1<=ncodemax[t];i1++){ 
         j1++;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);        if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
     free_vector(severity,1,maxwav);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     free_imatrix(outcome,1,maxwav+1,1,n);          fprintf(ficresprob, "**********\n#\n");
     free_vector(moisnais,1,n);          fprintf(ficresprobcov, "\n#********** Variable "); 
     free_vector(annais,1,n);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     /* free_matrix(mint,1,maxwav,1,n);          fprintf(ficresprobcov, "**********\n#\n");
        free_matrix(anint,1,maxwav,1,n);*/          
     free_vector(moisdc,1,n);          fprintf(ficgp, "\n#********** Variable "); 
     free_vector(andc,1,n);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
              
     wav=ivector(1,imx);          
     dh=imatrix(1,lastpass-firstpass+1,1,imx);          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          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\">");
     /* Concatenates waves */          
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);          fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
       Tcode=ivector(1,100);        }
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);        
       ncodemax[1]=1;        for (age=bage; age<=fage; age ++){ 
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);          cov[2]=age;
                for (k=1; k<=cptcovn;k++) {
    codtab=imatrix(1,100,1,10);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
    h=0;          }
    m=pow(2,cptcoveff);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
            for (k=1; k<=cptcovprod;k++)
    for(k=1;k<=cptcoveff; k++){            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
      for(i=1; i <=(m/pow(2,k));i++){          
        for(j=1; j <= ncodemax[k]; j++){          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
            h++;          gp=vector(1,(nlstate)*(nlstate+ndeath));
            if (h>m) h=1;codtab[h][k]=j;          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]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
    /*for(i=1; i <=m ;i++){            
      for(k=1; k <=cptcovn; k++){            k=0;
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);            for(i=1; i<= (nlstate); i++){
      }              for(j=1; j<=(nlstate+ndeath);j++){
      printf("\n");                k=k+1;
    }                gp[k]=pmmij[i][j];
    scanf("%d",i);*/              }
                }
    /* Calculates basic frequencies. Computes observed prevalence at single age            
        and prints on file fileres'p'. */            for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
          
                pmij(pmmij,cov,ncovmodel,xp,nlstate);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            k=0;
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            for(i=1; i<=(nlstate); i++){
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              for(j=1; j<=(nlstate+ndeath);j++){
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                k=k+1;
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */                gm[k]=pmmij[i][j];
                    }
     /* For Powell, parameters are in a vector p[] starting at p[1]            }
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */       
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     if(mle==1){          }
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  
     }          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
                for(theta=1; theta <=npar; theta++)
     /*--------- results files --------------*/              trgradg[j][theta]=gradg[theta][j];
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);          
            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);
    jk=1;          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
    fprintf(ficres,"# Parameters\n");          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
    printf("# Parameters\n");          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
    for(i=1,jk=1; i <=nlstate; i++){          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
      for(k=1; k <=(nlstate+ndeath); k++){  
        if (k != i)          pmij(pmmij,cov,ncovmodel,x,nlstate);
          {          
            printf("%d%d ",i,k);          k=0;
            fprintf(ficres,"%1d%1d ",i,k);          for(i=1; i<=(nlstate); i++){
            for(j=1; j <=ncovmodel; j++){            for(j=1; j<=(nlstate+ndeath);j++){
              printf("%f ",p[jk]);              k=k+1;
              fprintf(ficres,"%f ",p[jk]);              mu[k][(int) age]=pmmij[i][j];
              jk++;            }
            }          }
            printf("\n");          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
            fprintf(ficres,"\n");            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
          }              varpij[i][j][(int)age] = doldm[i][j];
      }  
    }          /*printf("\n%d ",(int)age);
  if(mle==1){            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     /* Computing hessian and covariance matrix */            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     ftolhess=ftol; /* Usually correct */            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     hesscov(matcov, p, npar, delti, ftolhess, func);            }*/
  }  
     fprintf(ficres,"# Scales\n");          fprintf(ficresprob,"\n%d ",(int)age);
     printf("# Scales\n");          fprintf(ficresprobcov,"\n%d ",(int)age);
      for(i=1,jk=1; i <=nlstate; i++){          fprintf(ficresprobcor,"\n%d ",(int)age);
       for(j=1; j <=nlstate+ndeath; j++){  
         if (j!=i) {          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
           fprintf(ficres,"%1d%1d",i,j);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           printf("%1d%1d",i,j);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
           for(k=1; k<=ncovmodel;k++){            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             printf(" %.5e",delti[jk]);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
             fprintf(ficres," %.5e",delti[jk]);          }
             jk++;          i=0;
           }          for (k=1; k<=(nlstate);k++){
           printf("\n");            for (l=1; l<=(nlstate+ndeath);l++){ 
           fprintf(ficres,"\n");              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]);
     k=1;                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
     fprintf(ficres,"# Covariance\n");              }
     printf("# Covariance\n");            }
     for(i=1;i<=npar;i++){          }/* end of loop for state */
       /*  if (k>nlstate) k=1;        } /* end of loop for age */
       i1=(i-1)/(ncovmodel*nlstate)+1;  
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);        /* Confidence intervalle of pij  */
       printf("%s%d%d",alph[k],i1,tab[i]);*/        /*
       fprintf(ficres,"%3d",i);          fprintf(ficgp,"\nset noparametric;unset label");
       printf("%3d",i);          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
       for(j=1; j<=i;j++){          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
         fprintf(ficres," %.5e",matcov[i][j]);          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);
         printf(" %.5e",matcov[i][j]);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
       }          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
       fprintf(ficres,"\n");          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
       printf("\n");        */
       k++;  
     }        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
            first1=1;
     while((c=getc(ficpar))=='#' && c!= EOF){        for (k2=1; k2<=(nlstate);k2++){
       ungetc(c,ficpar);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
       fgets(line, MAXLINE, ficpar);            if(l2==k2) continue;
       puts(line);            j=(k2-1)*(nlstate+ndeath)+l2;
       fputs(line,ficparo);            for (k1=1; k1<=(nlstate);k1++){
     }              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
     ungetc(c,ficpar);                if(l1==k1) continue;
                  i=(k1-1)*(nlstate+ndeath)+l1;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);                if(i<=j) continue;
                    for (age=bage; age<=fage; age ++){ 
     if (fage <= 2) {                  if ((int)age %5==0){
       bage = agemin;                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
       fage = agemax;                    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 ;
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                    mu2=mu[j][(int) age]/stepm*YEARM;
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);                    c12=cv12/sqrt(v1*v2);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);                    /* Computing eigen value of matrix of covariance */
                      lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     while((c=getc(ficpar))=='#' && c!= EOF){                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     ungetc(c,ficpar);                    /* Eigen vectors */
     fgets(line, MAXLINE, ficpar);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
     puts(line);                    /*v21=sqrt(1.-v11*v11); *//* error */
     fputs(line,ficparo);                    v21=(lc1-v1)/cv12*v11;
   }                    v12=-v21;
   ungetc(c,ficpar);                    v22=v11;
                      tnalp=v21/v11;
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);                    if(first1==1){
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                      first1=0;
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                      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);
                          }
   while((c=getc(ficpar))=='#' && c!= EOF){                    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);
     ungetc(c,ficpar);                    /*printf(fignu*/
     fgets(line, MAXLINE, ficpar);                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
     puts(line);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
     fputs(line,ficparo);                    if(first==1){
   }                      first=0;
   ungetc(c,ficpar);                      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");
    dateprev1=anprev1+mprev1/12.+jprev1/365.;                      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);
    dateprev2=anprev2+mprev2/12.+jprev2/365.;                      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);
   fscanf(ficpar,"pop_based=%d\n",&popbased);                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
    fprintf(ficparo,"pop_based=%d\n",popbased);                        fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
    fprintf(ficres,"pop_based=%d\n",popbased);                        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",\
   while((c=getc(ficpar))=='#' && c!= EOF){                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     ungetc(c,ficpar);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     fgets(line, MAXLINE, ficpar);                    }else{
     puts(line);                      first=0;
     fputs(line,ficparo);                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
   }                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   ungetc(c,ficpar);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mob_average=%d\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);                      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",\
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mob_average=%d\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mob_average=%d\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);                  } /* age mod 5 */
                 } /* end loop age */
 /*------------ gnuplot -------------*/                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemax,fage, pathc,p);                first=1;
                } /*l12 */
 /*------------ free_vector  -------------*/            } /* k12 */
  chdir(path);          } /*l1 */
          }/* k1 */
  free_ivector(wav,1,imx);      } /* loop covariates */
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    }
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
  free_ivector(num,1,n);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
  free_vector(agedc,1,n);    free_vector(xp,1,npar);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    fclose(ficresprob);
  fclose(ficparo);    fclose(ficresprobcov);
  fclose(ficres);    fclose(ficresprobcor);
      fclose(ficgp);
   /* Reads comments: lines beginning with '#' */    fclose(fichtm);
   while((c=getc(ficpar))=='#' && c!= EOF){  }
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  
     puts(line);  /******************* Printing html file ***********/
     fputs(line,ficparo);  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
   }                    int lastpass, int stepm, int weightopt, char model[],\
   ungetc(c,ficpar);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                      int popforecast, int estepm ,\
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);                    double jprev1, double mprev1,double anprev1, \
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);                    double jprev2, double mprev2,double anprev2){
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    int jj1, k1, i1, cpt;
 /*--------- index.htm --------*/    /*char optionfilehtm[FILENAMELENGTH];*/
     if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm);      printf("Problem with %s \n",optionfilehtm), exit(0);
       fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
      }
   /*--------------- Prevalence limit --------------*/  
       fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
   strcpy(filerespl,"pl");   - 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
   strcat(filerespl,fileres);   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
   if((ficrespl=fopen(filerespl,"w"))==NULL) {   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;   - Life expectancies by age and initial health status (estepm=%2d months): 
   }     <a href=\"e%s\">e%s</a> <br>\n</li>", \
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
   fprintf(ficrespl,"#Prevalence limit\n");  
   fprintf(ficrespl,"#Age ");  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  
   fprintf(ficrespl,"\n");   m=cptcoveff;
     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   prlim=matrix(1,nlstate,1,nlstate);  
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   jj1=0;
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   for(k1=1; k1<=m;k1++){
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */     for(i1=1; i1<=ncodemax[k1];i1++){
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       jj1++;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */       if (cptcovn > 0) {
   k=0;         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   agebase=agemin;         for (cpt=1; cpt<=cptcoveff;cpt++) 
   agelim=agemax;           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   ftolpl=1.e-10;         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   i1=cptcoveff;       }
   if (cptcovn < 1){i1=1;}       /* 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>
   for(cptcov=1;cptcov<=i1;cptcov++){  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       /* Quasi-incidences */
         k=k+1;       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>
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
         fprintf(ficrespl,"\n#******");         /* Stable prevalence in each health state */
         for(j=1;j<=cptcoveff;j++)         for(cpt=1; cpt<nlstate;cpt++){
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
         fprintf(ficrespl,"******\n");  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
                 }
         for (age=agebase; age<=agelim; age++){       for(cpt=1; cpt<=nlstate;cpt++) {
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
           fprintf(ficrespl,"%.0f",age );  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
           for(i=1; i<=nlstate;i++)       }
           fprintf(ficrespl," %.5f", prlim[i][i]);       fprintf(fichtm,"\n<br>- Total life expectancy by age and
           fprintf(ficrespl,"\n");  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 */
   fclose(ficrespl);   fprintf(fichtm,"</ul>");
   
   /*------------- h Pij x at various ages ------------*/  
     fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
   if((ficrespij=fopen(filerespij,"w"))==NULL) {   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;   - 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
   printf("Computing pij: result on file '%s' \n", filerespij);   - 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
   stepsize=(int) (stepm+YEARM-1)/YEARM;   - 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 (stepm<=24) stepsize=2;*/  
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   agelim=AGESUP;  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   hstepm=stepsize*YEARM; /* Every year of age */  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */  /*      <br>",fileres,fileres,fileres,fileres); */
    /*  else  */
   k=0;  /*    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); */
   for(cptcov=1;cptcov<=i1;cptcov++){  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;   m=cptcoveff;
         fprintf(ficrespij,"\n#****** ");   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
         for(j=1;j<=cptcoveff;j++)  
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   jj1=0;
         fprintf(ficrespij,"******\n");   for(k1=1; k1<=m;k1++){
             for(i1=1; i1<=ncodemax[k1];i1++){
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */       jj1++;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */       if (cptcovn > 0) {
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);         for (cpt=1; cpt<=cptcoveff;cpt++) 
           oldm=oldms;savm=savms;           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);           fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
           fprintf(ficrespij,"# Age");       }
           for(i=1; i<=nlstate;i++)       for(cpt=1; cpt<=nlstate;cpt++) {
             for(j=1; j<=nlstate+ndeath;j++)         fprintf(fichtm,"<br>- Observed and period prevalence (with confident
               fprintf(ficrespij," %1d-%1d",i,j);  interval) in state (%d): v%s%d%d.png <br>
           fprintf(ficrespij,"\n");  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
           for (h=0; h<=nhstepm; h++){       }
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );     } /* end i1 */
             for(i=1; i<=nlstate;i++)   }/* End k1 */
               for(j=1; j<=nlstate+ndeath;j++)   fprintf(fichtm,"</ul>");
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  fclose(fichtm);
             fprintf(ficrespij,"\n");  }
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /******************* Gnuplot file **************/
           fprintf(ficrespij,"\n");  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) {
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/      printf("Problem with file %s",optionfilegnuplot);
       fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
   fclose(ficrespij);    }
   
   if(stepm == 1) {    /*#ifdef windows */
   /*---------- Forecasting ------------------*/      fprintf(ficgp,"cd \"%s\" \n",pathc);
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;      /*#endif */
   m=pow(2,cptcoveff);
   /*printf("calage= %f", calagedate);*/    
     /* 1eme*/
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    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);
   strcpy(fileresf,"f");       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);
   strcat(fileresf,fileres);  
   if((ficresf=fopen(fileresf,"w"))==NULL) {       for (i=1; i<= nlstate ; i ++) {
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   }         else fprintf(ficgp," \%%*lf (\%%*lf)");
   printf("Computing forecasting: result on file '%s' \n", fileresf);       }
        fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
   free_matrix(mint,1,maxwav,1,n);       for (i=1; i<= nlstate ; i ++) {
   free_matrix(anint,1,maxwav,1,n);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   free_matrix(agev,1,maxwav,1,imx);         else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
   /* Mobile average */       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
   if (cptcoveff==0) ncodemax[cptcoveff]=1;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
   if (mobilav==1) {       }  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
     movingaverage(agedeb, fage, agemin, mobaverage);     }
   }    }
     /*2 eme*/
   stepsize=(int) (stepm+YEARM-1)/YEARM;    
   if (stepm<=12) stepsize=1;    for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
   agelim=AGESUP;      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
   /*hstepm=stepsize*YEARM; *//* Every year of age */      
   hstepm=1;      for (i=1; i<= nlstate+1 ; i ++) {
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */        k=2*i;
   yp1=modf(dateintmean,&yp);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
   anprojmean=yp;        for (j=1; j<= nlstate+1 ; j ++) {
   yp2=modf((yp1*12),&yp);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   mprojmean=yp;          else fprintf(ficgp," \%%*lf (\%%*lf)");
   yp1=modf((yp2*30.5),&yp);        }   
   jprojmean=yp;        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
   if(jprojmean==0) jprojmean=1;        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
   if(mprojmean==0) jprojmean=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 ++) {
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
   if (popforecast==1) {        }   
     if((ficpop=fopen(popfile,"r"))==NULL)    {        fprintf(ficgp,"\" t\"\" w l 0,");
       printf("Problem with population file : %s\n",popfile);goto end;        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
     }        for (j=1; j<= nlstate+1 ; j ++) {
     popage=ivector(0,AGESUP);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     popeffectif=vector(0,AGESUP);          else fprintf(ficgp," \%%*lf (\%%*lf)");
     popcount=vector(0,AGESUP);        }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
     i=1;          else fprintf(ficgp,"\" t\"\" w l 0,");
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)      }
       {    }
         i=i+1;    
       }    /*3eme*/
     imx=i;    
        for (k1=1; k1<= m ; k1 ++) { 
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      for (cpt=1; cpt<= nlstate ; cpt ++) {
   }        k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
   for(cptcov=1;cptcov<=i1;cptcov++){        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
       k=k+1;          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
       fprintf(ficresf,"\n#******");          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
       for(j=1;j<=cptcoveff;j++) {          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
       }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
       fprintf(ficresf,"******\n");          
       fprintf(ficresf,"# StartingAge FinalAge");        */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        for (i=1; i< nlstate ; i ++) {
       if (popforecast==1)  fprintf(ficresf," [Population]");          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);
                
      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>=(agemin-((int)calagedate %12)/12.); agedeb--){    /* CV preval stable (period) */
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    for (k1=1; k1<= m ; k1 ++) { 
         nhstepm = nhstepm/hstepm;      for (cpt=1; cpt<=nlstate ; cpt ++) {
                k=3;
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
         oldm=oldms;savm=savms;        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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          
                for (i=1; i<= nlstate ; i ++)
         for (h=0; h<=nhstepm; h++){          fprintf(ficgp,"+$%d",k+i+1);
           if (h==(int) (calagedate+YEARM*cpt)) {        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
             fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);        
           }        l=3+(nlstate+ndeath)*cpt;
           for(j=1; j<=nlstate+ndeath;j++) {        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
             kk1=0.;kk2=0;        for (i=1; i< nlstate ; i ++) {
             for(i=1; i<=nlstate;i++) {                  l=3+(nlstate+ndeath)*cpt;
               if (mobilav==1)          fprintf(ficgp,"+$%d",l+i+1);
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        }
               else {        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      } 
                    }  
               }    
     /* proba elementaires */
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];    for(i=1,jk=1; i <=nlstate; i++){
             }      for(k=1; k <=(nlstate+ndeath); k++){
                  if (k != i) {
             if (h==(int)(calagedate+12*cpt)){          for(j=1; j <=ncovmodel; j++){
               fprintf(ficresf," %.3f", kk1);            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
                          jk++; 
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);            fprintf(ficgp,"\n");
             }          }
           }        }
         }      }
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     }
         }  
      }     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 (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);         if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
   if (popforecast==1) {         else
     free_ivector(popage,0,AGESUP);           fprintf(ficgp,"\nset title \"Probability\"\n");
     free_vector(popeffectif,0,AGESUP);         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
     free_vector(popcount,0,AGESUP);         i=1;
   }         for(k2=1; k2<=nlstate; k2++) {
   free_imatrix(s,1,maxwav+1,1,n);           k3=i;
   free_vector(weight,1,n);           for(k=1; k<=(nlstate+ndeath); k++) {
   fclose(ficresf);             if (k != k2){
   }/* End forecasting */               if(ng==2)
   else{                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
     erreur=108;               else
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);                 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]]]);
   /*---------- Health expectancies and variances ------------*/                   ij++;
                  }
   strcpy(filerest,"t");                 else
   strcat(filerest,fileres);                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   if((ficrest=fopen(filerest,"w"))==NULL) {               }
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;               fprintf(ficgp,")/(1");
   }               
   printf("Computing Total LEs with variances: file '%s' \n", filerest);               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;
   strcpy(filerese,"e");                 for(j=3; j <=ncovmodel; j++){
   strcat(filerese,fileres);                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   if((ficreseij=fopen(filerese,"w"))==NULL) {                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);                     ij++;
   }                   }
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);                   else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
  strcpy(fileresv,"v");                 }
   strcat(fileresv,fileres);                 fprintf(ficgp,")");
   if((ficresvij=fopen(fileresv,"w"))==NULL) {               }
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
   }               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);               i=i+ncovmodel;
              }
   k=0;           } /* end k */
   for(cptcov=1;cptcov<=i1;cptcov++){         } /* end k2 */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       } /* end jk */
       k=k+1;     } /* end ng */
       fprintf(ficrest,"\n#****** ");     fclose(ficgp); 
       for(j=1;j<=cptcoveff;j++)  }  /* end gnuplot */
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficrest,"******\n");  
   /*************** Moving average **************/
       fprintf(ficreseij,"\n#****** ");  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    int i, cpt, cptcod;
       fprintf(ficreseij,"******\n");    int modcovmax =1;
     int mobilavrange, mob;
       fprintf(ficresvij,"\n#****** ");    double age;
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
       fprintf(ficresvij,"******\n");                             a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);        if(mobilav==1) mobilavrange=5; /* default */
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      else mobilavrange=mobilav;
       oldm=oldms;savm=savms;      for (age=bage; age<=fage; age++)
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        for (i=1; i<=nlstate;i++)
                for (cptcod=1;cptcod<=modcovmax;cptcod++)
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      /* We keep the original values on the extreme ages bage, fage and for 
       fprintf(ficrest,"\n");         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. 
       hf=1;      */ 
       if (stepm >= YEARM) hf=stepm/YEARM;      for (mob=3;mob <=mobilavrange;mob=mob+2){
       epj=vector(1,nlstate+1);        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
       for(age=bage; age <=fage ;age++){          for (i=1; i<=nlstate;i++){
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            for (cptcod=1;cptcod<=modcovmax;cptcod++){
         if (popbased==1) {              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
           for(i=1; i<=nlstate;i++)                for (cpt=1;cpt<=(mob-1)/2;cpt++){
             prlim[i][i]=probs[(int)age][i][k];                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
         }                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                        }
         fprintf(ficrest," %.0f",age);              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){            }
           for(i=1, epj[j]=0.;i <=nlstate;i++) {          }
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];        }/* end age */
           }      }/* end mob */
           epj[nlstate+1] +=epj[j];    }else return -1;
         }    return 0;
         for(i=1, vepp=0.;i <=nlstate;i++)  }/* End movingaverage */
           for(j=1;j <=nlstate;j++)  
             vepp += vareij[i][j][(int)age];  
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));  /************** Forecasting ******************/
         for(j=1;j <=nlstate;j++){  prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    /* proj1, year, month, day of starting projection 
         }       agemin, agemax range of age
         fprintf(ficrest,"\n");       dateprev1 dateprev2 range of dates during which prevalence is computed
       }       anproj2 year of en of projection (same day and month as proj1).
     }    */
   }    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
            int *popage;
            double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
  fclose(ficreseij);    double ***p3mat;
  fclose(ficresvij);    double ***mobaverage;
   fclose(ficrest);    char fileresf[FILENAMELENGTH];
   fclose(ficpar);  
   free_vector(epj,1,nlstate+1);    agelim=AGESUP;
   /*  scanf("%d ",i); */    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
   /*------- Variance limit prevalence------*/      strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
 strcpy(fileresvpl,"vpl");    if((ficresf=fopen(fileresf,"w"))==NULL) {
   strcat(fileresvpl,fileres);      printf("Problem with forecast resultfile: %s\n", fileresf);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    }
     exit(0);    printf("Computing forecasting: result on file '%s' \n", fileresf);
   }    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
  k=0;  
  for(cptcov=1;cptcov<=i1;cptcov++){    if (mobilav!=0) {
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      k=k+1;      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
      fprintf(ficresvpl,"\n#****** ");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
      for(j=1;j<=cptcoveff;j++)        printf(" Error in movingaverage mobilav=%d\n",mobilav);
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      }
      fprintf(ficresvpl,"******\n");    }
        
      varpl=matrix(1,nlstate,(int) bage, (int) fage);    stepsize=(int) (stepm+YEARM-1)/YEARM;
      oldm=oldms;savm=savms;    if (stepm<=12) stepsize=1;
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    if(estepm < stepm){
    }      printf ("Problem %d lower than %d\n",estepm, stepm);
  }    }
     else  hstepm=estepm;   
   fclose(ficresvpl);  
     hstepm=hstepm/stepm; 
   /*---------- End : free ----------------*/    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);                                 fractional in yp1 */
      anprojmean=yp;
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    yp2=modf((yp1*12),&yp);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    mprojmean=yp;
      yp1=modf((yp2*30.5),&yp);
      jprojmean=yp;
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    if(jprojmean==0) jprojmean=1;
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    if(mprojmean==0) jprojmean=1;
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    i1=cptcoveff;
      if (cptcovn < 1){i1=1;}
   free_matrix(matcov,1,npar,1,npar);    
   free_vector(delti,1,npar);    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
      
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   if(erreur >0)  /*            if (h==(int)(YEARM*yearp)){ */
     printf("End of Imach with error %d\n",erreur);    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
   else   printf("End of Imach\n");      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */        k=k+1;
          fprintf(ficresf,"\n#******");
   /* 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);*/        for(j=1;j<=cptcoveff;j++) {
   /*printf("Total time was %d uSec.\n", total_usecs);*/          fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   /*------ End -----------*/        }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
  end:        for(j=1; j<=nlstate+ndeath;j++){ 
 #ifdef windows          for(i=1; i<=nlstate;i++)              
   /* chdir(pathcd);*/            fprintf(ficresf," p%d%d",i,j);
 #endif          fprintf(ficresf," p.%d",j);
  /*system("wgnuplot graph.plt");*/        }
  /*system("../gp37mgw/wgnuplot graph.plt");*/        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
  /*system("cd ../gp37mgw");*/          fprintf(ficresf,"\n");
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
  strcpy(plotcmd,GNUPLOTPROGRAM);  
  strcat(plotcmd," ");          for (agec=fage; agec>=(ageminpar-1); agec--){ 
  strcat(plotcmd,optionfilegnuplot);            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
  system(plotcmd);            nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 #ifdef windows            oldm=oldms;savm=savms;
   while (z[0] != 'q') {            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
     chdir(path);          
     printf("\nType e to edit output files, c to start again, and q for exiting: ");            for (h=0; h<=nhstepm; h++){
     scanf("%s",z);              if (h*hstepm/YEARM*stepm ==yearp) {
     if (z[0] == 'c') system("./imach");                fprintf(ficresf,"\n");
     else if (z[0] == 'e') {                for(j=1;j<=cptcoveff;j++) 
       chdir(path);                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       system(optionfilehtm);                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
     }              } 
     else if (z[0] == 'q') exit(0);              for(j=1; j<=nlstate+ndeath;j++) {
   }                ppij=0.;
 #endif                for(i=1; i<=nlstate;i++) {
 }                  if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   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 calagedatem, 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;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     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,k=0;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)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %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) (calagedatem+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)(calagedatem+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+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+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)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %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) (calagedatem+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)(calagedatem+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 movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     char z[1]="c", occ;
   #include <sys/time.h>
   #include <time.h>
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
    
     /* long total_usecs;
        struct timeval start_time, end_time;
     
        gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     getcwd(pathcd, size);
   
     printf("\n%s",version);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     replace(pathc,path);
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s",version);
     fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     fflush(ficlog);
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------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);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*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 '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     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);
         if(mle==1)
           printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
           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");
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     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<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     delti=delti3[1][1];
   
   
     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%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]);
         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");
       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];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     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;
       }
     }
     /* 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]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* 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 */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       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);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           printf("Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           printf("Error! Month of death of individual %d on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %d on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1;
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   printf("Warning negative age at death: %d line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)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];
               /* 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 { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         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;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=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 */
     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
        and prints on file fileres'p'. */
   
       pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     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 nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) 
           {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
       }
     }
     if(mle==1){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     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");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle==1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf 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);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/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,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     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
   Youngest age at first (selected) pass %.2f, oldest age %.2f<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,agemin,agemax,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 stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     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);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         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(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           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;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           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 %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     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);
       }
     }
   
     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);
       }
     }
     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);
     
     /*------- Variance of stable 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);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         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(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     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_ma3x(probs,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);
   
     /*  fclose(fichtm);*/
     /*  fclose(ficgp);*/ /* ALready done */
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     
     /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
     /*printf("Total time was %d uSec.\n", total_usecs);*/
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
    /*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 graphs with: %s",plotcmd);fflush(stdout);
     system(plotcmd);
     printf(" Wait...");
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   
Removed from v.1.25  
changed lines
  Added in v.1.77

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