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version 1.32, 2002/03/11 14:17:15 version 1.74, 2003/05/02 18:51:41
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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,*ficrespop;  #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 0.95, February 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;
 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;  int *ivector(long nl,long nh)
   m -= nrl;  {
     int *v;
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    if (!v) nrerror("allocation failure in ivector");
   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_ivector(int *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)  
 {  /******************* imatrix *******************************/
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   free((FREE_ARG)(m+nrl-NR_END));       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 }  { 
     long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
 /******************* ma3x *******************************/    int **m; 
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    
 {    /* allocate pointers to rows */ 
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   double ***m;    if (!m) nrerror("allocation failure 1 in matrix()"); 
     m += NR_END; 
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    m -= nrl; 
   if (!m) nrerror("allocation failure 1 in matrix()");    
   m += NR_END;    
   m -= nrl;    /* allocate rows and set pointers to them */ 
     m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    m[nrl] += NR_END; 
   m[nrl] += NR_END;    m[nrl] -= ncl; 
   m[nrl] -= ncl;    
     for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    
     /* return pointer to array of pointers to rows */ 
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    return m; 
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  } 
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;  /****************** free_imatrix *************************/
   for (j=ncl+1; j<=nch; j++)  void free_imatrix(m,nrl,nrh,ncl,nch)
     m[nrl][j]=m[nrl][j-1]+nlay;        int **m;
          long nch,ncl,nrh,nrl; 
   for (i=nrl+1; i<=nrh; i++) {       /* free an int matrix allocated by imatrix() */ 
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  { 
     for (j=ncl+1; j<=nch; j++)    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       m[i][j]=m[i][j-1]+nlay;    free((FREE_ARG) (m+nrl-NR_END)); 
   }  } 
   return m;  
 }  /******************* matrix *******************************/
   double **matrix(long nrl, long nrh, long ncl, long nch)
 /*************************free ma3x ************************/  {
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 {    double **m;
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   free((FREE_ARG)(m+nrl-NR_END));    if (!m) nrerror("allocation failure 1 in matrix()");
 }    m += NR_END;
     m -= nrl;
 /***************** f1dim *************************/  
 extern int ncom;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 extern double *pcom,*xicom;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 extern double (*nrfunc)(double []);    m[nrl] += NR_END;
      m[nrl] -= ncl;
 double f1dim(double x)  
 {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   int j;    return m;
   double f;    /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
   double *xt;     */
    }
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  /*************************free matrix ************************/
   f=(*nrfunc)(xt);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   free_vector(xt,1,ncom);  {
   return f;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 }    free((FREE_ARG)(m+nrl-NR_END));
   }
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  /******************* ma3x *******************************/
 {  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   int iter;  {
   double a,b,d,etemp;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   double fu,fv,fw,fx;    double ***m;
   double ftemp;  
   double p,q,r,tol1,tol2,u,v,w,x,xm;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double e=0.0;    if (!m) nrerror("allocation failure 1 in matrix()");
      m += NR_END;
   a=(ax < cx ? ax : cx);    m -= nrl;
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   fw=fv=fx=(*f)(x);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   for (iter=1;iter<=ITMAX;iter++) {    m[nrl] += NR_END;
     xm=0.5*(a+b);    m[nrl] -= ncl;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     printf(".");fflush(stdout);  
 #ifdef DEBUG    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     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);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    m[nrl][ncl] += NR_END;
 #endif    m[nrl][ncl] -= nll;
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    for (j=ncl+1; j<=nch; j++) 
       *xmin=x;      m[nrl][j]=m[nrl][j-1]+nlay;
       return fx;    
     }    for (i=nrl+1; i<=nrh; i++) {
     ftemp=fu;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     if (fabs(e) > tol1) {      for (j=ncl+1; j<=nch; j++) 
       r=(x-w)*(fx-fv);        m[i][j]=m[i][j-1]+nlay;
       q=(x-v)*(fx-fw);    }
       p=(x-v)*q-(x-w)*r;    return m; 
       q=2.0*(q-r);    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       if (q > 0.0) p = -p;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       q=fabs(q);    */
       etemp=e;  }
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  /*************************free ma3x ************************/
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       else {  {
         d=p/q;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
         u=x+d;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         if (u-a < tol2 || b-u < tol2)    free((FREE_ARG)(m+nrl-NR_END));
           d=SIGN(tol1,xm-x);  }
       }  
     } else {  /***************** f1dim *************************/
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  extern int ncom; 
     }  extern double *pcom,*xicom;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  extern double (*nrfunc)(double []); 
     fu=(*f)(u);   
     if (fu <= fx) {  double f1dim(double x) 
       if (u >= x) a=x; else b=x;  { 
       SHFT(v,w,x,u)    int j; 
         SHFT(fv,fw,fx,fu)    double f;
         } else {    double *xt; 
           if (u < x) a=u; else b=u;   
           if (fu <= fw || w == x) {    xt=vector(1,ncom); 
             v=w;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
             w=u;    f=(*nrfunc)(xt); 
             fv=fw;    free_vector(xt,1,ncom); 
             fw=fu;    return f; 
           } else if (fu <= fv || v == x || v == w) {  } 
             v=u;  
             fv=fu;  /*****************brent *************************/
           }  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
         }  { 
   }    int iter; 
   nrerror("Too many iterations in brent");    double a,b,d,etemp;
   *xmin=x;    double fu,fv,fw,fx;
   return fx;    double ftemp;
 }    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     double e=0.0; 
 /****************** mnbrak ***********************/   
     a=(ax < cx ? ax : cx); 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    b=(ax > cx ? ax : cx); 
             double (*func)(double))    x=w=v=bx; 
 {    fw=fv=fx=(*f)(x); 
   double ulim,u,r,q, dum;    for (iter=1;iter<=ITMAX;iter++) { 
   double fu;      xm=0.5*(a+b); 
        tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   *fa=(*func)(*ax);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   *fb=(*func)(*bx);      printf(".");fflush(stdout);
   if (*fb > *fa) {      fprintf(ficlog,".");fflush(ficlog);
     SHFT(dum,*ax,*bx,dum)  #ifdef DEBUG
       SHFT(dum,*fb,*fa,dum)      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       }      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   *cx=(*bx)+GOLD*(*bx-*ax);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   *fc=(*func)(*cx);  #endif
   while (*fb > *fc) {      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     r=(*bx-*ax)*(*fb-*fc);        *xmin=x; 
     q=(*bx-*cx)*(*fb-*fa);        return fx; 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/      } 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));      ftemp=fu;
     ulim=(*bx)+GLIMIT*(*cx-*bx);      if (fabs(e) > tol1) { 
     if ((*bx-u)*(u-*cx) > 0.0) {        r=(x-w)*(fx-fv); 
       fu=(*func)(u);        q=(x-v)*(fx-fw); 
     } else if ((*cx-u)*(u-ulim) > 0.0) {        p=(x-v)*q-(x-w)*r; 
       fu=(*func)(u);        q=2.0*(q-r); 
       if (fu < *fc) {        if (q > 0.0) p = -p; 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))        q=fabs(q); 
           SHFT(*fb,*fc,fu,(*func)(u))        etemp=e; 
           }        e=d; 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       u=ulim;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       fu=(*func)(u);        else { 
     } else {          d=p/q; 
       u=(*cx)+GOLD*(*cx-*bx);          u=x+d; 
       fu=(*func)(u);          if (u-a < tol2 || b-u < tol2) 
     }            d=SIGN(tol1,xm-x); 
     SHFT(*ax,*bx,*cx,u)        } 
       SHFT(*fa,*fb,*fc,fu)      } else { 
       }        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 }      } 
       u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
 /*************** linmin ************************/      fu=(*f)(u); 
       if (fu <= fx) { 
 int ncom;        if (u >= x) a=x; else b=x; 
 double *pcom,*xicom;        SHFT(v,w,x,u) 
 double (*nrfunc)(double []);          SHFT(fv,fw,fx,fu) 
            } else { 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))            if (u < x) a=u; else b=u; 
 {            if (fu <= fw || w == x) { 
   double brent(double ax, double bx, double cx,              v=w; 
                double (*f)(double), double tol, double *xmin);              w=u; 
   double f1dim(double x);              fv=fw; 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,              fw=fu; 
               double *fc, double (*func)(double));            } else if (fu <= fv || v == x || v == w) { 
   int j;              v=u; 
   double xx,xmin,bx,ax;              fv=fu; 
   double fx,fb,fa;            } 
            } 
   ncom=n;    } 
   pcom=vector(1,n);    nrerror("Too many iterations in brent"); 
   xicom=vector(1,n);    *xmin=x; 
   nrfunc=func;    return fx; 
   for (j=1;j<=n;j++) {  } 
     pcom[j]=p[j];  
     xicom[j]=xi[j];  /****************** mnbrak ***********************/
   }  
   ax=0.0;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   xx=1.0;              double (*func)(double)) 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  { 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    double ulim,u,r,q, dum;
 #ifdef DEBUG    double fu; 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);   
 #endif    *fa=(*func)(*ax); 
   for (j=1;j<=n;j++) {    *fb=(*func)(*bx); 
     xi[j] *= xmin;    if (*fb > *fa) { 
     p[j] += xi[j];      SHFT(dum,*ax,*bx,dum) 
   }        SHFT(dum,*fb,*fa,dum) 
   free_vector(xicom,1,n);        } 
   free_vector(pcom,1,n);    *cx=(*bx)+GOLD*(*bx-*ax); 
 }    *fc=(*func)(*cx); 
     while (*fb > *fc) { 
 /*************** powell ************************/      r=(*bx-*ax)*(*fb-*fc); 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      q=(*bx-*cx)*(*fb-*fa); 
             double (*func)(double []))      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 {        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   void linmin(double p[], double xi[], int n, double *fret,      ulim=(*bx)+GLIMIT*(*cx-*bx); 
               double (*func)(double []));      if ((*bx-u)*(u-*cx) > 0.0) { 
   int i,ibig,j;        fu=(*func)(u); 
   double del,t,*pt,*ptt,*xit;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   double fp,fptt;        fu=(*func)(u); 
   double *xits;        if (fu < *fc) { 
   pt=vector(1,n);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   ptt=vector(1,n);            SHFT(*fb,*fc,fu,(*func)(u)) 
   xit=vector(1,n);            } 
   xits=vector(1,n);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   *fret=(*func)(p);        u=ulim; 
   for (j=1;j<=n;j++) pt[j]=p[j];        fu=(*func)(u); 
   for (*iter=1;;++(*iter)) {      } else { 
     fp=(*fret);        u=(*cx)+GOLD*(*cx-*bx); 
     ibig=0;        fu=(*func)(u); 
     del=0.0;      } 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      SHFT(*ax,*bx,*cx,u) 
     for (i=1;i<=n;i++)        SHFT(*fa,*fb,*fc,fu) 
       printf(" %d %.12f",i, p[i]);        } 
     printf("\n");  } 
     for (i=1;i<=n;i++) {  
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  /*************** linmin ************************/
       fptt=(*fret);  
 #ifdef DEBUG  int ncom; 
       printf("fret=%lf \n",*fret);  double *pcom,*xicom;
 #endif  double (*nrfunc)(double []); 
       printf("%d",i);fflush(stdout);   
       linmin(p,xit,n,fret,func);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       if (fabs(fptt-(*fret)) > del) {  { 
         del=fabs(fptt-(*fret));    double brent(double ax, double bx, double cx, 
         ibig=i;                 double (*f)(double), double tol, double *xmin); 
       }    double f1dim(double x); 
 #ifdef DEBUG    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       printf("%d %.12e",i,(*fret));                double *fc, double (*func)(double)); 
       for (j=1;j<=n;j++) {    int j; 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    double xx,xmin,bx,ax; 
         printf(" x(%d)=%.12e",j,xit[j]);    double fx,fb,fa;
       }   
       for(j=1;j<=n;j++)    ncom=n; 
         printf(" p=%.12e",p[j]);    pcom=vector(1,n); 
       printf("\n");    xicom=vector(1,n); 
 #endif    nrfunc=func; 
     }    for (j=1;j<=n;j++) { 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      pcom[j]=p[j]; 
 #ifdef DEBUG      xicom[j]=xi[j]; 
       int k[2],l;    } 
       k[0]=1;    ax=0.0; 
       k[1]=-1;    xx=1.0; 
       printf("Max: %.12e",(*func)(p));    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       for (j=1;j<=n;j++)    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
         printf(" %.12e",p[j]);  #ifdef DEBUG
       printf("\n");    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       for(l=0;l<=1;l++) {    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         for (j=1;j<=n;j++) {  #endif
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    for (j=1;j<=n;j++) { 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);      xi[j] *= xmin; 
         }      p[j] += xi[j]; 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    } 
       }    free_vector(xicom,1,n); 
 #endif    free_vector(pcom,1,n); 
   } 
   
       free_vector(xit,1,n);  /*************** powell ************************/
       free_vector(xits,1,n);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       free_vector(ptt,1,n);              double (*func)(double [])) 
       free_vector(pt,1,n);  { 
       return;    void linmin(double p[], double xi[], int n, double *fret, 
     }                double (*func)(double [])); 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    int i,ibig,j; 
     for (j=1;j<=n;j++) {    double del,t,*pt,*ptt,*xit;
       ptt[j]=2.0*p[j]-pt[j];    double fp,fptt;
       xit[j]=p[j]-pt[j];    double *xits;
       pt[j]=p[j];    pt=vector(1,n); 
     }    ptt=vector(1,n); 
     fptt=(*func)(ptt);    xit=vector(1,n); 
     if (fptt < fp) {    xits=vector(1,n); 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    *fret=(*func)(p); 
       if (t < 0.0) {    for (j=1;j<=n;j++) pt[j]=p[j]; 
         linmin(p,xit,n,fret,func);    for (*iter=1;;++(*iter)) { 
         for (j=1;j<=n;j++) {      fp=(*fret); 
           xi[j][ibig]=xi[j][n];      ibig=0; 
           xi[j][n]=xit[j];      del=0.0; 
         }      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
 #ifdef DEBUG      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      for (i=1;i<=n;i++) 
         for(j=1;j<=n;j++)        printf(" %d %.12f",i, p[i]);
           printf(" %.12e",xit[j]);      fprintf(ficlog," %d %.12f",i, p[i]);
         printf("\n");      printf("\n");
 #endif      fprintf(ficlog,"\n");
       }      for (i=1;i<=n;i++) { 
     }        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   }        fptt=(*fret); 
 }  #ifdef DEBUG
         printf("fret=%lf \n",*fret);
 /**** Prevalence limit ****************/        fprintf(ficlog,"fret=%lf \n",*fret);
   #endif
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)        printf("%d",i);fflush(stdout);
 {        fprintf(ficlog,"%d",i);fflush(ficlog);
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit        linmin(p,xit,n,fret,func); 
      matrix by transitions matrix until convergence is reached */        if (fabs(fptt-(*fret)) > del) { 
           del=fabs(fptt-(*fret)); 
   int i, ii,j,k;          ibig=i; 
   double min, max, maxmin, maxmax,sumnew=0.;        } 
   double **matprod2();  #ifdef DEBUG
   double **out, cov[NCOVMAX], **pmij();        printf("%d %.12e",i,(*fret));
   double **newm;        fprintf(ficlog,"%d %.12e",i,(*fret));
   double agefin, delaymax=50 ; /* Max number of years to converge */        for (j=1;j<=n;j++) {
           xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   for (ii=1;ii<=nlstate+ndeath;ii++)          printf(" x(%d)=%.12e",j,xit[j]);
     for (j=1;j<=nlstate+ndeath;j++){          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        }
     }        for(j=1;j<=n;j++) {
           printf(" p=%.12e",p[j]);
    cov[1]=1.;          fprintf(ficlog," p=%.12e",p[j]);
          }
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        printf("\n");
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        fprintf(ficlog,"\n");
     newm=savm;  #endif
     /* Covariates have to be included here again */      } 
      cov[2]=agefin;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
    #ifdef DEBUG
       for (k=1; k<=cptcovn;k++) {        int k[2],l;
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        k[0]=1;
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/        k[1]=-1;
       }        printf("Max: %.12e",(*func)(p));
       for (k=1; k<=cptcovage;k++)        fprintf(ficlog,"Max: %.12e",(*func)(p));
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        for (j=1;j<=n;j++) {
       for (k=1; k<=cptcovprod;k++)          printf(" %.12e",p[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," %.12e",p[j]);
         }
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/        printf("\n");
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/        fprintf(ficlog,"\n");
         for(l=0;l<=1;l++) {
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);          for (j=1;j<=n;j++) {
             ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     savm=oldm;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     oldm=newm;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     maxmax=0.;          }
     for(j=1;j<=nlstate;j++){          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       min=1.;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       max=0.;        }
       for(i=1; i<=nlstate; i++) {  #endif
         sumnew=0;  
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  
         prlim[i][j]= newm[i][j]/(1-sumnew);        free_vector(xit,1,n); 
         max=FMAX(max,prlim[i][j]);        free_vector(xits,1,n); 
         min=FMIN(min,prlim[i][j]);        free_vector(ptt,1,n); 
       }        free_vector(pt,1,n); 
       maxmin=max-min;        return; 
       maxmax=FMAX(maxmax,maxmin);      } 
     }      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     if(maxmax < ftolpl){      for (j=1;j<=n;j++) { 
       return prlim;        ptt[j]=2.0*p[j]-pt[j]; 
     }        xit[j]=p[j]-pt[j]; 
   }        pt[j]=p[j]; 
 }      } 
       fptt=(*func)(ptt); 
 /*************** transition probabilities ***************/      if (fptt < fp) { 
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )        if (t < 0.0) { 
 {          linmin(p,xit,n,fret,func); 
   double s1, s2;          for (j=1;j<=n;j++) { 
   /*double t34;*/            xi[j][ibig]=xi[j][n]; 
   int i,j,j1, nc, ii, jj;            xi[j][n]=xit[j]; 
           }
     for(i=1; i<= nlstate; i++){  #ifdef DEBUG
     for(j=1; j<i;j++){          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         /*s2 += param[i][j][nc]*cov[nc];*/          for(j=1;j<=n;j++){
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];            printf(" %.12e",xit[j]);
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/            fprintf(ficlog," %.12e",xit[j]);
       }          }
       ps[i][j]=s2;          printf("\n");
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/          fprintf(ficlog,"\n");
     }  #endif
     for(j=i+1; j<=nlstate+ndeath;j++){        }
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      } 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    } 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  } 
       }  
       ps[i][j]=s2;  /**** Prevalence limit (stable prevalence)  ****************/
     }  
   }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     /*ps[3][2]=1;*/  {
     /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   for(i=1; i<= nlstate; i++){       matrix by transitions matrix until convergence is reached */
      s1=0;  
     for(j=1; j<i; j++)    int i, ii,j,k;
       s1+=exp(ps[i][j]);    double min, max, maxmin, maxmax,sumnew=0.;
     for(j=i+1; j<=nlstate+ndeath; j++)    double **matprod2();
       s1+=exp(ps[i][j]);    double **out, cov[NCOVMAX], **pmij();
     ps[i][i]=1./(s1+1.);    double **newm;
     for(j=1; j<i; j++)    double agefin, delaymax=50 ; /* Max number of years to converge */
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     for(j=i+1; j<=nlstate+ndeath; j++)    for (ii=1;ii<=nlstate+ndeath;ii++)
       ps[i][j]= exp(ps[i][j])*ps[i][i];      for (j=1;j<=nlstate+ndeath;j++){
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   } /* end i */      }
   
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){     cov[1]=1.;
     for(jj=1; jj<= nlstate+ndeath; jj++){   
       ps[ii][jj]=0;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       ps[ii][ii]=1;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     }      newm=savm;
   }      /* Covariates have to be included here again */
        cov[2]=agefin;
     
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        for (k=1; k<=cptcovn;k++) {
     for(jj=1; jj<= nlstate+ndeath; jj++){          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
      printf("%lf ",ps[ii][jj]);          /*      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]]);*/
    }        }
     printf("\n ");        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     }        for (k=1; k<=cptcovprod;k++)
     printf("\n ");printf("%lf ",cov[2]);*/          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<= npar; i++) printf("%f ",x[i]);        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   goto end;*/        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     return ps;        /*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);
   
 /**************** Product of 2 matrices ******************/      savm=oldm;
       oldm=newm;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      maxmax=0.;
 {      for(j=1;j<=nlstate;j++){
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        min=1.;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */        max=0.;
   /* in, b, out are matrice of pointers which should have been initialized        for(i=1; i<=nlstate; i++) {
      before: only the contents of out is modified. The function returns          sumnew=0;
      a pointer to pointers identical to out */          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   long i, j, k;          prlim[i][j]= newm[i][j]/(1-sumnew);
   for(i=nrl; i<= nrh; i++)          max=FMAX(max,prlim[i][j]);
     for(k=ncolol; k<=ncoloh; k++)          min=FMIN(min,prlim[i][j]);
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        }
         out[i][k] +=in[i][j]*b[j][k];        maxmin=max-min;
         maxmax=FMAX(maxmax,maxmin);
   return out;      }
 }      if(maxmax < ftolpl){
         return prlim;
       }
 /************* Higher Matrix Product ***************/    }
   }
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  
 {  /*************** transition probabilities ***************/ 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  
      duration (i.e. until  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  {
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    double s1, s2;
      (typically every 2 years instead of every month which is too big).    /*double t34;*/
      Model is determined by parameters x and covariates have to be    int i,j,j1, nc, ii, jj;
      included manually here.  
       for(i=1; i<= nlstate; i++){
      */      for(j=1; j<i;j++){
         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   int i, j, d, h, k;          /*s2 += param[i][j][nc]*cov[nc];*/
   double **out, cov[NCOVMAX];          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   double **newm;          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
         }
   /* Hstepm could be zero and should return the unit matrix */        ps[i][j]=s2;
   for (i=1;i<=nlstate+ndeath;i++)        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
     for (j=1;j<=nlstate+ndeath;j++){      }
       oldm[i][j]=(i==j ? 1.0 : 0.0);      for(j=i+1; j<=nlstate+ndeath;j++){
       po[i][j][0]=(i==j ? 1.0 : 0.0);        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     }          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   for(h=1; h <=nhstepm; h++){        }
     for(d=1; d <=hstepm; d++){        ps[i][j]=s2;
       newm=savm;      }
       /* Covariates have to be included here again */    }
       cov[1]=1.;      /*ps[3][2]=1;*/
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    for(i=1; i<= nlstate; i++){
       for (k=1; k<=cptcovage;k++)       s1=0;
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      for(j=1; j<i; j++)
       for (k=1; k<=cptcovprod;k++)        s1+=exp(ps[i][j]);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      for(j=i+1; j<=nlstate+ndeath; j++)
         s1+=exp(ps[i][j]);
       ps[i][i]=1./(s1+1.);
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      for(j=1; j<i; j++)
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        ps[i][j]= exp(ps[i][j])*ps[i][i];
       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));        ps[i][j]= exp(ps[i][j])*ps[i][i];
       savm=oldm;      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       oldm=newm;    } /* end i */
     }  
     for(i=1; i<=nlstate+ndeath; i++)    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       for(j=1;j<=nlstate+ndeath;j++) {      for(jj=1; jj<= nlstate+ndeath; jj++){
         po[i][j][h]=newm[i][j];        ps[ii][jj]=0;
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);        ps[ii][ii]=1;
          */      }
       }    }
   } /* end h */  
   return po;  
 }    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
       for(jj=1; jj<= nlstate+ndeath; jj++){
        printf("%lf ",ps[ii][jj]);
 /*************** log-likelihood *************/     }
 double func( double *x)      printf("\n ");
 {      }
   int i, ii, j, k, mi, d, kk;      printf("\n ");printf("%lf ",cov[2]);*/
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  /*
   double **out;    for(i=1; i<= npar; i++) printf("%f ",x[i]);
   double sw; /* Sum of weights */    goto end;*/
   double lli; /* Individual log likelihood */      return ps;
   long ipmx;  }
   /*extern weight */  
   /* We are differentiating ll according to initial status */  /**************** Product of 2 matrices ******************/
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  
   /*for(i=1;i<imx;i++)  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     printf(" %d\n",s[4][i]);  {
   */    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   cov[1]=1.;       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<=nlstate; k++) ll[k]=0.;       before: only the contents of out is modified. The function returns
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){       a pointer to pointers identical to out */
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    long i, j, k;
     for(mi=1; mi<= wav[i]-1; mi++){    for(i=nrl; i<= nrh; i++)
       for (ii=1;ii<=nlstate+ndeath;ii++)      for(k=ncolol; k<=ncoloh; k++)
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        for(j=ncl,out[i][k]=0.; j<=nch; j++)
       for(d=0; d<dh[mi][i]; d++){          out[i][k] +=in[i][j]*b[j][k];
         newm=savm;  
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    return out;
         for (kk=1; kk<=cptcovage;kk++) {  }
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  
         }  
          /************* Higher Matrix Product ***************/
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
         savm=oldm;  {
         oldm=newm;    /* Computes the transition matrix starting at age 'age' over 
               'nhstepm*hstepm*stepm' months (i.e. until
               age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
       } /* end mult */       nhstepm*hstepm matrices. 
             Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);       (typically every 2 years instead of every month which is too big 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/       for the memory).
       ipmx +=1;       Model is determined by parameters x and covariates have to be 
       sw += weight[i];       included manually here. 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  
     } /* end of wave */       */
   } /* end of individual */  
     int i, j, d, h, k;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    double **out, cov[NCOVMAX];
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    double **newm;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  
   return -l;    /* 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);
 /*********** Maximum Likelihood Estimation ***************/        po[i][j][0]=(i==j ? 1.0 : 0.0);
       }
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 {    for(h=1; h <=nhstepm; h++){
   int i,j, iter;      for(d=1; d <=hstepm; d++){
   double **xi,*delti;        newm=savm;
   double fret;        /* Covariates have to be included here again */
   xi=matrix(1,npar,1,npar);        cov[1]=1.;
   for (i=1;i<=npar;i++)        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     for (j=1;j<=npar;j++)        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       xi[i][j]=(i==j ? 1.0 : 0.0);        for (k=1; k<=cptcovage;k++)
   printf("Powell\n");          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   powell(p,xi,npar,ftol,&iter,&fret,func);        for (k=1; k<=cptcovprod;k++)
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
    printf("\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));  
         /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
 }        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
 /**** Computes Hessian and covariance matrix ***/                     pmij(pmmij,cov,ncovmodel,x,nlstate));
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        savm=oldm;
 {        oldm=newm;
   double  **a,**y,*x,pd;      }
   double **hess;      for(i=1; i<=nlstate+ndeath; i++)
   int i, j,jk;        for(j=1;j<=nlstate+ndeath;j++) {
   int *indx;          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]);
   double hessii(double p[], double delta, int theta, double delti[]);           */
   double hessij(double p[], double delti[], int i, int j);        }
   void lubksb(double **a, int npar, int *indx, double b[]) ;    } /* end h */
   void ludcmp(double **a, int npar, int *indx, double *d) ;    return po;
   }
   hess=matrix(1,npar,1,npar);  
   
   printf("\nCalculation of the hessian matrix. Wait...\n");  /*************** log-likelihood *************/
   for (i=1;i<=npar;i++){  double func( double *x)
     printf("%d",i);fflush(stdout);  {
     hess[i][i]=hessii(p,ftolhess,i,delti);    int i, ii, j, k, mi, d, kk;
     /*printf(" %f ",p[i]);*/    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     /*printf(" %lf ",hess[i][i]);*/    double **out;
   }    double sw; /* Sum of weights */
      double lli; /* Individual log likelihood */
   for (i=1;i<=npar;i++) {    int s1, s2;
     for (j=1;j<=npar;j++)  {    double bbh, survp;
       if (j>i) {    long ipmx;
         printf(".%d%d",i,j);fflush(stdout);    /*extern weight */
         hess[i][j]=hessij(p,delti,i,j);    /* We are differentiating ll according to initial status */
         hess[j][i]=hess[i][j];        /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         /*printf(" %lf ",hess[i][j]);*/    /*for(i=1;i<imx;i++) 
       }      printf(" %d\n",s[4][i]);
     }    */
   }    cov[1]=1.;
   printf("\n");  
     for(k=1; k<=nlstate; k++) ll[k]=0.;
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  
      if(mle==1){
   a=matrix(1,npar,1,npar);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   y=matrix(1,npar,1,npar);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   x=vector(1,npar);        for(mi=1; mi<= wav[i]-1; mi++){
   indx=ivector(1,npar);          for (ii=1;ii<=nlstate+ndeath;ii++)
   for (i=1;i<=npar;i++)            for (j=1;j<=nlstate+ndeath;j++){
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   ludcmp(a,npar,indx,&pd);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
   for (j=1;j<=npar;j++) {          for(d=0; d<dh[mi][i]; d++){
     for (i=1;i<=npar;i++) x[i]=0;            newm=savm;
     x[j]=1;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     lubksb(a,npar,indx,x);            for (kk=1; kk<=cptcovage;kk++) {
     for (i=1;i<=npar;i++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       matcov[i][j]=x[i];            }
     }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   printf("\n#Hessian matrix#\n");            oldm=newm;
   for (i=1;i<=npar;i++) {          } /* end mult */
     for (j=1;j<=npar;j++) {        
       printf("%.3e ",hess[i][j]);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     }          /* But now since version 0.9 we anticipate for bias and large stepm.
     printf("\n");           * 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
   /* Recompute Inverse */           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   for (i=1;i<=npar;i++)           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];           * probability in order to take into account the bias as a fraction of the way
   ludcmp(a,npar,indx,&pd);           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
            * -stepm/2 to stepm/2 .
   /*  printf("\n#Hessian matrix recomputed#\n");           * 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. 
   for (j=1;j<=npar;j++) {           */
     for (i=1;i<=npar;i++) x[i]=0;          s1=s[mw[mi][i]][i];
     x[j]=1;          s2=s[mw[mi+1][i]][i];
     lubksb(a,npar,indx,x);          bbh=(double)bh[mi][i]/(double)stepm; 
     for (i=1;i<=npar;i++){          /* bias is positive if real duration
       y[i][j]=x[i];           * is higher than the multiple of stepm and negative otherwise.
       printf("%.3e ",y[i][j]);           */
     }          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     printf("\n");          if( s2 > nlstate){ 
   }            /* i.e. if s2 is a death state and if the date of death is known then the contribution
   */               to the likelihood is the probability to die between last step unit time and current 
                step unit time, which is also the differences between probability to die before dh 
   free_matrix(a,1,npar,1,npar);               and probability to die before dh-stepm . 
   free_matrix(y,1,npar,1,npar);               In version up to 0.92 likelihood was computed
   free_vector(x,1,npar);          as if date of death was unknown. Death was treated as any other
   free_ivector(indx,1,npar);          health state: the date of the interview describes the actual state
   free_matrix(hess,1,npar,1,npar);          and not the date of a change in health state. The former idea was
           to consider that at each interview the state was recorded
           (healthy, disable or death) and IMaCh was corrected; but when we
 }          introduced the exact date of death then we should have modified
           the contribution of an exact death to the likelihood. This new
 /*************** hessian matrix ****************/          contribution is smaller and very dependent of the step unit
 double hessii( double x[], double delta, int theta, double delti[])          stepm. It is no more the probability to die between last interview
 {          and month of death but the probability to survive from last
   int i;          interview up to one month before death multiplied by the
   int l=1, lmax=20;          probability to die within a month. Thanks to Chris
   double k1,k2;          Jackson for correcting this bug.  Former versions increased
   double p2[NPARMAX+1];          mortality artificially. The bad side is that we add another loop
   double res;          which slows down the processing. The difference can be up to 10%
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          lower mortality.
   double fx;            */
   int k=0,kmax=10;            lli=log(out[s1][s2] - savm[s1][s2]);
   double l1;          }else{
             lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   fx=func(x);            /*  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 */
   for (i=1;i<=npar;i++) p2[i]=x[i];          } 
   for(l=0 ; l <=lmax; l++){          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     l1=pow(10,l);          /*if(lli ==000.0)*/
     delts=delt;          /*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); */
     for(k=1 ; k <kmax; k=k+1){          ipmx +=1;
       delt = delta*(l1*k);          sw += weight[i];
       p2[theta]=x[theta] +delt;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       k1=func(p2)-fx;        } /* end of wave */
       p2[theta]=x[theta]-delt;      } /* end of individual */
       k2=func(p2)-fx;    }  else if(mle==2){
       /*res= (k1-2.0*fx+k2)/delt/delt; */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
              for(mi=1; mi<= wav[i]-1; mi++){
 #ifdef DEBUG          for (ii=1;ii<=nlstate+ndeath;ii++)
       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 (j=1;j<=nlstate+ndeath;j++){
 #endif              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){            }
         k=kmax;          for(d=0; d<=dh[mi][i]; d++){
       }            newm=savm;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         k=kmax; l=lmax*10.;            for (kk=1; kk<=cptcovage;kk++) {
       }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){            }
         delts=delt;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }            savm=oldm;
   }            oldm=newm;
   delti[theta]=delts;          } /* end mult */
   return res;        
            /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
 }          /* 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 
 double hessij( double x[], double delti[], int thetai,int thetaj)           * (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
   int i;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   int l=1, l1, lmax=20;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   double k1,k2,k3,k4,res,fx;           * probability in order to take into account the bias as a fraction of the way
   double p2[NPARMAX+1];           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   int k;           * -stepm/2 to stepm/2 .
            * For stepm=1 the results are the same as for previous versions of Imach.
   fx=func(x);           * For stepm > 1 the results are less biased than in previous versions. 
   for (k=1; k<=2; k++) {           */
     for (i=1;i<=npar;i++) p2[i]=x[i];          s1=s[mw[mi][i]][i];
     p2[thetai]=x[thetai]+delti[thetai]/k;          s2=s[mw[mi+1][i]][i];
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          bbh=(double)bh[mi][i]/(double)stepm; 
     k1=func(p2)-fx;          /* bias is positive if real duration
             * is higher than the multiple of stepm and negative otherwise.
     p2[thetai]=x[thetai]+delti[thetai]/k;           */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          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 */
     k2=func(p2)-fx;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
            /*lli= (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 */
     p2[thetai]=x[thetai]-delti[thetai]/k;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          /*if(lli ==000.0)*/
     k3=func(p2)-fx;          /*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;
     p2[thetai]=x[thetai]-delti[thetai]/k;          sw += weight[i];
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     k4=func(p2)-fx;        } /* end of wave */
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */      } /* end of individual */
 #ifdef DEBUG    }  else if(mle==3){  /* exponential inter-extrapolation */
     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);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 #endif        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   }        for(mi=1; mi<= wav[i]-1; mi++){
   return res;          for (ii=1;ii<=nlstate+ndeath;ii++)
 }            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 /************** Inverse of matrix **************/              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 void ludcmp(double **a, int n, int *indx, double *d)            }
 {          for(d=0; d<dh[mi][i]; d++){
   int i,imax,j,k;            newm=savm;
   double big,dum,sum,temp;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double *vv;            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   vv=vector(1,n);            }
   *d=1.0;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   for (i=1;i<=n;i++) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     big=0.0;            savm=oldm;
     for (j=1;j<=n;j++)            oldm=newm;
       if ((temp=fabs(a[i][j])) > big) big=temp;          } /* end mult */
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        
     vv[i]=1.0/big;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   }          /* But now since version 0.9 we anticipate for bias and large stepm.
   for (j=1;j<=n;j++) {           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     for (i=1;i<j;i++) {           * (in months) between two waves is not a multiple of stepm, we rounded to 
       sum=a[i][j];           * the nearest (and in case of equal distance, to the lowest) interval but now
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       a[i][j]=sum;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     }           * probability in order to take into account the bias as a fraction of the way
     big=0.0;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     for (i=j;i<=n;i++) {           * -stepm/2 to stepm/2 .
       sum=a[i][j];           * For stepm=1 the results are the same as for previous versions of Imach.
       for (k=1;k<j;k++)           * For stepm > 1 the results are less biased than in previous versions. 
         sum -= a[i][k]*a[k][j];           */
       a[i][j]=sum;          s1=s[mw[mi][i]][i];
       if ( (dum=vv[i]*fabs(sum)) >= big) {          s2=s[mw[mi+1][i]][i];
         big=dum;          bbh=(double)bh[mi][i]/(double)stepm; 
         imax=i;          /* bias is positive if real duration
       }           * is higher than the multiple of stepm and negative otherwise.
     }           */
     if (j != imax) {          /* 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 */
       for (k=1;k<=n;k++) {          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 */
         dum=a[imax][k];          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         a[imax][k]=a[j][k];          /*if(lli ==000.0)*/
         a[j][k]=dum;          /*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;
       *d = -(*d);          sw += weight[i];
       vv[imax]=vv[j];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }        } /* end of wave */
     indx[j]=imax;      } /* end of individual */
     if (a[j][j] == 0.0) a[j][j]=TINY;    }else{  /* ml=4 no inter-extrapolation */
     if (j != n) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       dum=1.0/(a[j][j]);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        for(mi=1; mi<= wav[i]-1; mi++){
     }          for (ii=1;ii<=nlstate+ndeath;ii++)
   }            for (j=1;j<=nlstate+ndeath;j++){
   free_vector(vv,1,n);  /* Doesn't work */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 ;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 }            }
           for(d=0; d<dh[mi][i]; d++){
 void lubksb(double **a, int n, int *indx, double b[])            newm=savm;
 {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int i,ii=0,ip,j;            for (kk=1; kk<=cptcovage;kk++) {
   double sum;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
              }
   for (i=1;i<=n;i++) {          
     ip=indx[i];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     sum=b[ip];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     b[ip]=b[i];            savm=oldm;
     if (ii)            oldm=newm;
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          } /* end mult */
     else if (sum) ii=i;        
     b[i]=sum;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   }          ipmx +=1;
   for (i=n;i>=1;i--) {          sw += weight[i];
     sum=b[i];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        } /* end of wave */
     b[i]=sum/a[i][i];      } /* end of individual */
   }    } /* End of if */
 }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
 /************ Frequencies ********************/    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)    return -l;
 {  /* Some frequencies */  }
    
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  
   double ***freq; /* Frequencies */  /*********** Maximum Likelihood Estimation ***************/
   double *pp;  
   double pos, k2, dateintsum=0,k2cpt=0;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   FILE *ficresp;  {
   char fileresp[FILENAMELENGTH];    int i,j, iter;
      double **xi;
   pp=vector(1,nlstate);    double fret;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    xi=matrix(1,npar,1,npar);
   strcpy(fileresp,"p");    for (i=1;i<=npar;i++)
   strcat(fileresp,fileres);      for (j=1;j<=npar;j++)
   if((ficresp=fopen(fileresp,"w"))==NULL) {        xi[i][j]=(i==j ? 1.0 : 0.0);
     printf("Problem with prevalence resultfile: %s\n", fileresp);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     exit(0);    powell(p,xi,npar,ftol,&iter,&fret,func);
   }  
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   j1=0;    fprintf(ficlog,"\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));
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  }
   
   for(k1=1; k1<=j;k1++){  /**** Computes Hessian and covariance matrix ***/
    for(i1=1; i1<=ncodemax[k1];i1++){  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
        j1++;  {
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    double  **a,**y,*x,pd;
          scanf("%d", i);*/    double **hess;
         for (i=-1; i<=nlstate+ndeath; i++)      int i, j,jk;
          for (jk=-1; jk<=nlstate+ndeath; jk++)      int *indx;
            for(m=agemin; m <= agemax+3; m++)  
              freq[i][jk][m]=0;    double hessii(double p[], double delta, int theta, double delti[]);
     double hessij(double p[], double delti[], int i, int j);
         dateintsum=0;    void lubksb(double **a, int npar, int *indx, double b[]) ;
         k2cpt=0;    void ludcmp(double **a, int npar, int *indx, double *d) ;
        for (i=1; i<=imx; i++) {  
          bool=1;    hess=matrix(1,npar,1,npar);
          if  (cptcovn>0) {  
            for (z1=1; z1<=cptcoveff; z1++)    printf("\nCalculation of the hessian matrix. Wait...\n");
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
                bool=0;    for (i=1;i<=npar;i++){
          }      printf("%d",i);fflush(stdout);
          if (bool==1) {      fprintf(ficlog,"%d",i);fflush(ficlog);
            for(m=firstpass; m<=lastpass; m++){      hess[i][i]=hessii(p,ftolhess,i,delti);
              k2=anint[m][i]+(mint[m][i]/12.);      /*printf(" %f ",p[i]);*/
              if ((k2>=dateprev1) && (k2<=dateprev2)) {      /*printf(" %lf ",hess[i][i]);*/
                if(agev[m][i]==0) agev[m][i]=agemax+1;    }
                if(agev[m][i]==1) agev[m][i]=agemax+2;    
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    for (i=1;i<=npar;i++) {
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      for (j=1;j<=npar;j++)  {
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        if (j>i) { 
                  dateintsum=dateintsum+k2;          printf(".%d%d",i,j);fflush(stdout);
                  k2cpt++;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
                }          hess[i][j]=hessij(p,delti,i,j);
           hess[j][i]=hess[i][j];    
              }          /*printf(" %lf ",hess[i][j]);*/
            }        }
          }      }
        }    }
            printf("\n");
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    fprintf(ficlog,"\n");
   
         if  (cptcovn>0) {    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
          fprintf(ficresp, "\n#********** Variable ");    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    
        fprintf(ficresp, "**********\n#");    a=matrix(1,npar,1,npar);
         }    y=matrix(1,npar,1,npar);
        for(i=1; i<=nlstate;i++)    x=vector(1,npar);
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    indx=ivector(1,npar);
        fprintf(ficresp, "\n");    for (i=1;i<=npar;i++)
              for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   for(i=(int)agemin; i <= (int)agemax+3; i++){    ludcmp(a,npar,indx,&pd);
     if(i==(int)agemax+3)  
       printf("Total");    for (j=1;j<=npar;j++) {
     else      for (i=1;i<=npar;i++) x[i]=0;
       printf("Age %d", i);      x[j]=1;
     for(jk=1; jk <=nlstate ; jk++){      lubksb(a,npar,indx,x);
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      for (i=1;i<=npar;i++){ 
         pp[jk] += freq[jk][m][i];        matcov[i][j]=x[i];
     }      }
     for(jk=1; jk <=nlstate ; jk++){    }
       for(m=-1, pos=0; m <=0 ; m++)  
         pos += freq[jk][m][i];    printf("\n#Hessian matrix#\n");
       if(pp[jk]>=1.e-10)    fprintf(ficlog,"\n#Hessian matrix#\n");
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    for (i=1;i<=npar;i++) { 
       else      for (j=1;j<=npar;j++) { 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        printf("%.3e ",hess[i][j]);
     }        fprintf(ficlog,"%.3e ",hess[i][j]);
       }
      for(jk=1; jk <=nlstate ; jk++){      printf("\n");
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      fprintf(ficlog,"\n");
         pp[jk] += freq[jk][m][i];    }
      }  
     /* Recompute Inverse */
     for(jk=1,pos=0; jk <=nlstate ; jk++)    for (i=1;i<=npar;i++)
       pos += pp[jk];      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     for(jk=1; jk <=nlstate ; jk++){    ludcmp(a,npar,indx,&pd);
       if(pos>=1.e-5)  
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    /*  printf("\n#Hessian matrix recomputed#\n");
       else  
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    for (j=1;j<=npar;j++) {
       if( i <= (int) agemax){      for (i=1;i<=npar;i++) x[i]=0;
         if(pos>=1.e-5){      x[j]=1;
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);      lubksb(a,npar,indx,x);
           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]);*/        y[i][j]=x[i];
         }        printf("%.3e ",y[i][j]);
       else        fprintf(ficlog,"%.3e ",y[i][j]);
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);      }
       }      printf("\n");
     }      fprintf(ficlog,"\n");
     for(jk=-1; jk <=nlstate+ndeath; jk++)    }
       for(m=-1; m <=nlstate+ndeath; m++)    */
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  
     if(i <= (int) agemax)    free_matrix(a,1,npar,1,npar);
       fprintf(ficresp,"\n");    free_matrix(y,1,npar,1,npar);
     printf("\n");    free_vector(x,1,npar);
     }    free_ivector(indx,1,npar);
     }    free_matrix(hess,1,npar,1,npar);
  }  
   dateintmean=dateintsum/k2cpt;  
    }
   fclose(ficresp);  
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  /*************** hessian matrix ****************/
   free_vector(pp,1,nlstate);  double hessii( double x[], double delta, int theta, double delti[])
   {
   /* End of Freq */    int i;
 }    int l=1, lmax=20;
     double k1,k2;
 /************ Prevalence ********************/    double p2[NPARMAX+1];
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)    double res;
 {  /* Some frequencies */    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
      double fx;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    int k=0,kmax=10;
   double ***freq; /* Frequencies */    double l1;
   double *pp;  
   double pos, k2;    fx=func(x);
     for (i=1;i<=npar;i++) p2[i]=x[i];
   pp=vector(1,nlstate);    for(l=0 ; l <=lmax; l++){
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      l1=pow(10,l);
        delts=delt;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      for(k=1 ; k <kmax; k=k+1){
   j1=0;        delt = delta*(l1*k);
          p2[theta]=x[theta] +delt;
   j=cptcoveff;        k1=func(p2)-fx;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        p2[theta]=x[theta]-delt;
          k2=func(p2)-fx;
  for(k1=1; k1<=j;k1++){        /*res= (k1-2.0*fx+k2)/delt/delt; */
     for(i1=1; i1<=ncodemax[k1];i1++){        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
       j1++;        
    #ifdef DEBUG
       for (i=-1; i<=nlstate+ndeath; i++)          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 (jk=-1; jk<=nlstate+ndeath; jk++)          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);
           for(m=agemin; m <= agemax+3; m++)  #endif
             freq[i][jk][m]=0;        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
              if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
       for (i=1; i<=imx; i++) {          k=kmax;
         bool=1;        }
         if  (cptcovn>0) {        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           for (z1=1; z1<=cptcoveff; z1++)          k=kmax; l=lmax*10.;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        }
               bool=0;        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
         }          delts=delt;
         if (bool==1) {        }
           for(m=firstpass; m<=lastpass; m++){      }
             k2=anint[m][i]+(mint[m][i]/12.);    }
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    delti[theta]=delts;
               if(agev[m][i]==0) agev[m][i]=agemax+1;    return res; 
               if(agev[m][i]==1) agev[m][i]=agemax+2;    
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];  }
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */  
             }  double hessij( double x[], double delti[], int thetai,int thetaj)
           }  {
         }    int i;
       }    int l=1, l1, lmax=20;
         for(i=(int)agemin; i <= (int)agemax+3; i++){    double k1,k2,k3,k4,res,fx;
           for(jk=1; jk <=nlstate ; jk++){    double p2[NPARMAX+1];
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    int k;
               pp[jk] += freq[jk][m][i];  
           }    fx=func(x);
           for(jk=1; jk <=nlstate ; jk++){    for (k=1; k<=2; k++) {
             for(m=-1, pos=0; m <=0 ; m++)      for (i=1;i<=npar;i++) p2[i]=x[i];
             pos += freq[jk][m][i];      p2[thetai]=x[thetai]+delti[thetai]/k;
         }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
              k1=func(p2)-fx;
          for(jk=1; jk <=nlstate ; jk++){    
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      p2[thetai]=x[thetai]+delti[thetai]/k;
              pp[jk] += freq[jk][m][i];      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
          }      k2=func(p2)-fx;
              
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
          for(jk=1; jk <=nlstate ; jk++){                k3=func(p2)-fx;
            if( i <= (int) agemax){    
              if(pos>=1.e-5){      p2[thetai]=x[thetai]-delti[thetai]/k;
                probs[i][jk][j1]= pp[jk]/pos;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
              }      k4=func(p2)-fx;
            }      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
          }  #ifdef DEBUG
                printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
         }      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     }  #endif
   }    }
      return res;
    }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  
   free_vector(pp,1,nlstate);  /************** Inverse of matrix **************/
    void ludcmp(double **a, int n, int *indx, double *d) 
 }  /* End of Freq */  { 
     int i,imax,j,k; 
 /************* Waves Concatenation ***************/    double big,dum,sum,temp; 
     double *vv; 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)   
 {    vv=vector(1,n); 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    *d=1.0; 
      Death is a valid wave (if date is known).    for (i=1;i<=n;i++) { 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      big=0.0; 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      for (j=1;j<=n;j++) 
      and mw[mi+1][i]. dh depends on stepm.        if ((temp=fabs(a[i][j])) > big) big=temp; 
      */      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       vv[i]=1.0/big; 
   int i, mi, m;    } 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    for (j=1;j<=n;j++) { 
      double sum=0., jmean=0.;*/      for (i=1;i<j;i++) { 
         sum=a[i][j]; 
   int j, k=0,jk, ju, jl;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   double sum=0.;        a[i][j]=sum; 
   jmin=1e+5;      } 
   jmax=-1;      big=0.0; 
   jmean=0.;      for (i=j;i<=n;i++) { 
   for(i=1; i<=imx; i++){        sum=a[i][j]; 
     mi=0;        for (k=1;k<j;k++) 
     m=firstpass;          sum -= a[i][k]*a[k][j]; 
     while(s[m][i] <= nlstate){        a[i][j]=sum; 
       if(s[m][i]>=1)        if ( (dum=vv[i]*fabs(sum)) >= big) { 
         mw[++mi][i]=m;          big=dum; 
       if(m >=lastpass)          imax=i; 
         break;        } 
       else      } 
         m++;      if (j != imax) { 
     }/* end while */        for (k=1;k<=n;k++) { 
     if (s[m][i] > nlstate){          dum=a[imax][k]; 
       mi++;     /* Death is another wave */          a[imax][k]=a[j][k]; 
       /* if(mi==0)  never been interviewed correctly before death */          a[j][k]=dum; 
          /* Only death is a correct wave */        } 
       mw[mi][i]=m;        *d = -(*d); 
     }        vv[imax]=vv[j]; 
       } 
     wav[i]=mi;      indx[j]=imax; 
     if(mi==0)      if (a[j][j] == 0.0) a[j][j]=TINY; 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);      if (j != n) { 
   }        dum=1.0/(a[j][j]); 
         for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   for(i=1; i<=imx; i++){      } 
     for(mi=1; mi<wav[i];mi++){    } 
       if (stepm <=0)    free_vector(vv,1,n);  /* Doesn't work */
         dh[mi][i]=1;  ;
       else{  } 
         if (s[mw[mi+1][i]][i] > nlstate) {  
           if (agedc[i] < 2*AGESUP) {  void lubksb(double **a, int n, int *indx, double b[]) 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  { 
           if(j==0) j=1;  /* Survives at least one month after exam */    int i,ii=0,ip,j; 
           k=k+1;    double sum; 
           if (j >= jmax) jmax=j;   
           if (j <= jmin) jmin=j;    for (i=1;i<=n;i++) { 
           sum=sum+j;      ip=indx[i]; 
           /*if (j<0) printf("j=%d num=%d \n",j,i); */      sum=b[ip]; 
           }      b[ip]=b[i]; 
         }      if (ii) 
         else{        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));      else if (sum) ii=i; 
           k=k+1;      b[i]=sum; 
           if (j >= jmax) jmax=j;    } 
           else if (j <= jmin)jmin=j;    for (i=n;i>=1;i--) { 
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */      sum=b[i]; 
           sum=sum+j;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
         }      b[i]=sum/a[i][i]; 
         jk= j/stepm;    } 
         jl= j -jk*stepm;  } 
         ju= j -(jk+1)*stepm;  
         if(jl <= -ju)  /************ Frequencies ********************/
           dh[mi][i]=jk;  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)
         else  {  /* Some frequencies */
           dh[mi][i]=jk+1;    
         if(dh[mi][i]==0)    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
           dh[mi][i]=1; /* At least one step */    int first;
       }    double ***freq; /* Frequencies */
     }    double *pp, **prop;
   }    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   jmean=sum/k;    FILE *ficresp;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    char fileresp[FILENAMELENGTH];
  }    
 /*********** Tricode ****************************/    pp=vector(1,nlstate);
 void tricode(int *Tvar, int **nbcode, int imx)    prop=matrix(1,nlstate,iagemin,iagemax+3);
 {    strcpy(fileresp,"p");
   int Ndum[20],ij=1, k, j, i;    strcat(fileresp,fileres);
   int cptcode=0;    if((ficresp=fopen(fileresp,"w"))==NULL) {
   cptcoveff=0;      printf("Problem with prevalence resultfile: %s\n", fileresp);
        fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   for (k=0; k<19; k++) Ndum[k]=0;      exit(0);
   for (k=1; k<=7; k++) ncodemax[k]=0;    }
     freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    j1=0;
     for (i=1; i<=imx; i++) {    
       ij=(int)(covar[Tvar[j]][i]);    j=cptcoveff;
       Ndum[ij]++;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  
       if (ij > cptcode) cptcode=ij;    first=1;
     }  
     for(k1=1; k1<=j;k1++){
     for (i=0; i<=cptcode; i++) {      for(i1=1; i1<=ncodemax[k1];i1++){
       if(Ndum[i]!=0) ncodemax[j]++;        j1++;
     }        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     ij=1;          scanf("%d", i);*/
         for (i=-1; i<=nlstate+ndeath; i++)  
           for (jk=-1; jk<=nlstate+ndeath; jk++)  
     for (i=1; i<=ncodemax[j]; i++) {            for(m=iagemin; m <= iagemax+3; m++)
       for (k=0; k<=19; k++) {              freq[i][jk][m]=0;
         if (Ndum[k] != 0) {  
           nbcode[Tvar[j]][ij]=k;      for (i=1; i<=nlstate; i++)  
           ij++;        for(m=iagemin; m <= iagemax+3; m++)
         }          prop[i][m]=0;
         if (ij > ncodemax[j]) break;        
       }          dateintsum=0;
     }        k2cpt=0;
   }          for (i=1; i<=imx; i++) {
           bool=1;
  for (k=0; k<19; k++) Ndum[k]=0;          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
  for (i=1; i<=ncovmodel-2; i++) {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       ij=Tvar[i];                bool=0;
       Ndum[ij]++;          }
     }          if (bool==1){
             for(m=firstpass; m<=lastpass; m++){
  ij=1;              k2=anint[m][i]+(mint[m][i]/12.);
  for (i=1; i<=10; i++) {              if ((k2>=dateprev1) && (k2<=dateprev2)) {
    if((Ndum[i]!=0) && (i<=ncov)){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
      Tvaraff[ij]=i;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
      ij++;                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
    }                if (m<lastpass) {
  }                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                    freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     cptcoveff=ij-1;                }
 }                
                 if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
 /*********** Health Expectancies ****************/                  dateintsum=dateintsum+k2;
                   k2cpt++;
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)                }
 {              }
   /* Health expectancies */            }
   int i, j, nhstepm, hstepm, h, nstepm, k;          }
   double age, agelim,hf;        }
   double ***p3mat;         
          fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   fprintf(ficreseij,"# Health expectancies\n");  
   fprintf(ficreseij,"# Age");        if  (cptcovn>0) {
   for(i=1; i<=nlstate;i++)          fprintf(ficresp, "\n#********** Variable "); 
     for(j=1; j<=nlstate;j++)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       fprintf(ficreseij," %1d-%1d",i,j);          fprintf(ficresp, "**********\n#");
   fprintf(ficreseij,"\n");        }
         for(i=1; i<=nlstate;i++) 
   k=1;             /* For example stepm=6 months */          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   hstepm=k*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */        fprintf(ficresp, "\n");
   hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */        
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        for(i=iagemin; i <= iagemax+3; i++){
      nhstepm is the number of hstepm from age to agelim          if(i==iagemax+3){
      nstepm is the number of stepm from age to agelin.            fprintf(ficlog,"Total");
      Look at hpijx to understand the reason of that which relies in memory size          }else{
      and note for a fixed period like k years */            if(first==1){
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the              first=0;
      survival function given by stepm (the optimization length). Unfortunately it              printf("See log file for details...\n");
      means that if the survival funtion is printed only each two years of age and if            }
      you sum them up and add 1 year (area under the trapezoids) you won't get the same            fprintf(ficlog,"Age %d", i);
      results. So we changed our mind and took the option of the best precision.          }
   */          for(jk=1; jk <=nlstate ; jk++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
               pp[jk] += freq[jk][m][i]; 
   agelim=AGESUP;          }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          for(jk=1; jk <=nlstate ; jk++){
     /* nhstepm age range expressed in number of stepm */            for(m=-1, pos=0; m <=0 ; m++)
     nstepm=(int) rint((agelim-age)*YEARM/stepm);              pos += freq[jk][m][i];
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */            if(pp[jk]>=1.e-10){
     if (stepm >= YEARM) hstepm=1;              if(first==1){
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              }
     /* Computed by stepm unit matrices, product of hstepm matrices, stored              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */            }else{
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);                if(first==1)
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     for(i=1; i<=nlstate;i++)              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       for(j=1; j<=nlstate;j++)            }
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          }
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;  
           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/          for(jk=1; jk <=nlstate ; jk++){
         }            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     fprintf(ficreseij,"%3.0f",age );              pp[jk] += freq[jk][m][i];
     for(i=1; i<=nlstate;i++)          }       
       for(j=1; j<=nlstate;j++){          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);            pos += pp[jk];
       }            posprop += prop[jk][i];
     fprintf(ficreseij,"\n");          }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(jk=1; jk <=nlstate ; jk++){
   }            if(pos>=1.e-5){
 }              if(first==1)
                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 /************ Variance ******************/              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 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)            }else{
 {              if(first==1)
   /* Variance of health expectancies */                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   double **newm;            }
   double **dnewm,**doldm;            if( i <= iagemax){
   int i, j, nhstepm, hstepm, h;              if(pos>=1.e-5){
   int k, cptcode;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   double *xp;                probs[i][jk][j1]= pp[jk]/pos;
   double **gp, **gm;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   double ***gradg, ***trgradg;              }
   double ***p3mat;              else
   double age,agelim;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   int theta;            }
           }
    fprintf(ficresvij,"# Covariances of life expectancies\n");          
   fprintf(ficresvij,"# Age");          for(jk=-1; jk <=nlstate+ndeath; jk++)
   for(i=1; i<=nlstate;i++)            for(m=-1; m <=nlstate+ndeath; m++)
     for(j=1; j<=nlstate;j++)              if(freq[jk][m][i] !=0 ) {
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);              if(first==1)
   fprintf(ficresvij,"\n");                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                 fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   xp=vector(1,npar);              }
   dnewm=matrix(1,nlstate,1,npar);          if(i <= iagemax)
   doldm=matrix(1,nlstate,1,nlstate);            fprintf(ficresp,"\n");
            if(first==1)
   hstepm=1*YEARM; /* Every year of age */            printf("Others in log...\n");
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          fprintf(ficlog,"\n");
   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;    dateintmean=dateintsum/k2cpt; 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */   
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fclose(ficresp);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
     gp=matrix(0,nhstepm,1,nlstate);    free_vector(pp,1,nlstate);
     gm=matrix(0,nhstepm,1,nlstate);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     /* End of Freq */
     for(theta=1; theta <=npar; theta++){  }
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  /************ Prevalence ********************/
       }  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)
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    {  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        in each health status at the date of interview (if between dateprev1 and dateprev2).
       if (popbased==1) {       We still use firstpass and lastpass as another selection.
         for(i=1; i<=nlstate;i++)    */
           prlim[i][i]=probs[(int)age][i][ij];   
       }    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
      double ***freq; /* Frequencies */
       for(j=1; j<= nlstate; j++){    double *pp, **prop;
         for(h=0; h<=nhstepm; h++){    double pos,posprop; 
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    double  y2; /* in fractional years */
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    int iagemin, iagemax;
         }  
       }    iagemin= (int) agemin;
        iagemax= (int) agemax;
       for(i=1; i<=npar; i++) /* Computes gradient */    /*pp=vector(1,nlstate);*/
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    j1=0;
      
       if (popbased==1) {    j=cptcoveff;
         for(i=1; i<=nlstate;i++)    if (cptcovn<1) {j=1;ncodemax[1]=1;}
           prlim[i][i]=probs[(int)age][i][ij];    
       }    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
       for(j=1; j<= nlstate; j++){        j1++;
         for(h=0; h<=nhstepm; h++){        
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        for (i=1; i<=nlstate; i++)  
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          for(m=iagemin; m <= iagemax+3; m++)
         }            prop[i][m]=0.0;
       }       
         for (i=1; i<=imx; i++) { /* Each individual */
       for(j=1; j<= nlstate; j++)          bool=1;
         for(h=0; h<=nhstepm; h++){          if  (cptcovn>0) {
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            for (z1=1; z1<=cptcoveff; z1++) 
         }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     } /* End theta */                bool=0;
           } 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          if (bool==1) { 
             for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     for(h=0; h<=nhstepm; h++)              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
       for(j=1; j<=nlstate;j++)              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
         for(theta=1; theta <=npar; theta++)                if(agev[m][i]==0) agev[m][i]=iagemax+1;
           trgradg[h][j][theta]=gradg[h][theta][j];                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 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); 
     for(i=1;i<=nlstate;i++)                if (s[m][i]>0 && s[m][i]<=nlstate) { 
       for(j=1;j<=nlstate;j++)                  /*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]]);*/
         vareij[i][j][(int)age] =0.;                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
     for(h=0;h<=nhstepm;h++){                  prop[s[m][i]][iagemax+3] += weight[i]; 
       for(k=0;k<=nhstepm;k++){                } 
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);              }
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);            } /* end selection of waves */
         for(i=1;i<=nlstate;i++)          }
           for(j=1;j<=nlstate;j++)        }
             vareij[i][j][(int)age] += doldm[i][j];        for(i=iagemin; i <= iagemax+3; i++){  
       }          
     }          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     h=1;            posprop += prop[jk][i]; 
     if (stepm >= YEARM) h=stepm/YEARM;          } 
     fprintf(ficresvij,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)          for(jk=1; jk <=nlstate ; jk++){     
       for(j=1; j<=nlstate;j++){            if( i <=  iagemax){ 
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);              if(posprop>=1.e-5){ 
       }                probs[i][jk][j1]= prop[jk][i]/posprop;
     fprintf(ficresvij,"\n");              } 
     free_matrix(gp,0,nhstepm,1,nlstate);            } 
     free_matrix(gm,0,nhstepm,1,nlstate);          }/* end jk */ 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        }/* end i */ 
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      } /* end i1 */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    } /* end k1 */
   } /* End age */    
      /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   free_vector(xp,1,npar);    /*free_vector(pp,1,nlstate);*/
   free_matrix(doldm,1,nlstate,1,npar);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   free_matrix(dnewm,1,nlstate,1,nlstate);  }  /* End of prevalence */
   
 }  /************* Waves Concatenation ***************/
   
 /************ Variance of prevlim ******************/  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)
 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)  {
 {    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   /* Variance of prevalence limit */       Death is a valid wave (if date is known).
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   double **newm;       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   double **dnewm,**doldm;       and mw[mi+1][i]. dh depends on stepm.
   int i, j, nhstepm, hstepm;       */
   int k, cptcode;  
   double *xp;    int i, mi, m;
   double *gp, *gm;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   double **gradg, **trgradg;       double sum=0., jmean=0.;*/
   double age,agelim;    int first;
   int theta;    int j, k=0,jk, ju, jl;
        double sum=0.;
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    first=0;
   fprintf(ficresvpl,"# Age");    jmin=1e+5;
   for(i=1; i<=nlstate;i++)    jmax=-1;
       fprintf(ficresvpl," %1d-%1d",i,i);    jmean=0.;
   fprintf(ficresvpl,"\n");    for(i=1; i<=imx; i++){
       mi=0;
   xp=vector(1,npar);      m=firstpass;
   dnewm=matrix(1,nlstate,1,npar);      while(s[m][i] <= nlstate){
   doldm=matrix(1,nlstate,1,nlstate);        if(s[m][i]>=1)
            mw[++mi][i]=m;
   hstepm=1*YEARM; /* Every year of age */        if(m >=lastpass)
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          break;
   agelim = AGESUP;        else
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          m++;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      }/* end while */
     if (stepm >= YEARM) hstepm=1;      if (s[m][i] > nlstate){
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        mi++;     /* Death is another wave */
     gradg=matrix(1,npar,1,nlstate);        /* if(mi==0)  never been interviewed correctly before death */
     gp=vector(1,nlstate);           /* Only death is a correct wave */
     gm=vector(1,nlstate);        mw[mi][i]=m;
       }
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */      wav[i]=mi;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      if(mi==0){
       }        if(first==0){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
       for(i=1;i<=nlstate;i++)          first=1;
         gp[i] = prlim[i][i];        }
            if(first==1){
       for(i=1; i<=npar; i++) /* Computes gradient */          fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      } /* end mi==0 */
       for(i=1;i<=nlstate;i++)    }
         gm[i] = prlim[i][i];  
     for(i=1; i<=imx; i++){
       for(i=1;i<=nlstate;i++)      for(mi=1; mi<wav[i];mi++){
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        if (stepm <=0)
     } /* End theta */          dh[mi][i]=1;
         else{
     trgradg =matrix(1,nlstate,1,npar);          if (s[mw[mi+1][i]][i] > nlstate) {
             if (agedc[i] < 2*AGESUP) {
     for(j=1; j<=nlstate;j++)            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
       for(theta=1; theta <=npar; theta++)            if(j==0) j=1;  /* Survives at least one month after exam */
         trgradg[j][theta]=gradg[theta][j];            k=k+1;
             if (j >= jmax) jmax=j;
     for(i=1;i<=nlstate;i++)            if (j <= jmin) jmin=j;
       varpl[i][(int)age] =0.;            sum=sum+j;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);            /*if (j<0) printf("j=%d num=%d \n",j,i); */
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     for(i=1;i<=nlstate;i++)            /*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]);*/
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */            }
           }
     fprintf(ficresvpl,"%.0f ",age );          else{
     for(i=1; i<=nlstate;i++)            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     fprintf(ficresvpl,"\n");            k=k+1;
     free_vector(gp,1,nlstate);            if (j >= jmax) jmax=j;
     free_vector(gm,1,nlstate);            else if (j <= jmin)jmin=j;
     free_matrix(gradg,1,npar,1,nlstate);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     free_matrix(trgradg,1,nlstate,1,npar);            /*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]);*/
   } /* End age */            sum=sum+j;
           }
   free_vector(xp,1,npar);          jk= j/stepm;
   free_matrix(doldm,1,nlstate,1,npar);          jl= j -jk*stepm;
   free_matrix(dnewm,1,nlstate,1,nlstate);          ju= j -(jk+1)*stepm;
           if(mle <=1){ 
 }            if(jl==0){
               dh[mi][i]=jk;
 /************ Variance of one-step probabilities  ******************/              bh[mi][i]=0;
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)            }else{ /* We want a negative bias in order to only have interpolation ie
 {                    * at the price of an extra matrix product in likelihood */
   int i, j;              dh[mi][i]=jk+1;
   int k=0, cptcode;              bh[mi][i]=ju;
   double **dnewm,**doldm;            }
   double *xp;          }else{
   double *gp, *gm;            if(jl <= -ju){
   double **gradg, **trgradg;              dh[mi][i]=jk;
   double age,agelim, cov[NCOVMAX];              bh[mi][i]=jl;       /* bias is positive if real duration
   int theta;                                   * is higher than the multiple of stepm and negative otherwise.
   char fileresprob[FILENAMELENGTH];                                   */
             }
   strcpy(fileresprob,"prob");            else{
   strcat(fileresprob,fileres);              dh[mi][i]=jk+1;
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {              bh[mi][i]=ju;
     printf("Problem with resultfile: %s\n", fileresprob);            }
   }            if(dh[mi][i]==0){
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);              dh[mi][i]=1; /* At least one step */
                bh[mi][i]=ju; /* At least one step */
               /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
   xp=vector(1,npar);            }
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          }
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));        } /* end if mle */
        } /* end wave */
   cov[1]=1;    }
   for (age=bage; age<=fage; age ++){    jmean=sum/k;
     cov[2]=age;    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     gradg=matrix(1,npar,1,9);    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     trgradg=matrix(1,9,1,npar);   }
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  /*********** Tricode ****************************/
      void tricode(int *Tvar, int **nbcode, int imx)
     for(theta=1; theta <=npar; theta++){  {
       for(i=1; i<=npar; i++)    
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    int Ndum[20],ij=1, k, j, i, maxncov=19;
          int cptcode=0;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    cptcoveff=0; 
       
       k=0;    for (k=0; k<maxncov; k++) Ndum[k]=0;
       for(i=1; i<= (nlstate+ndeath); i++){    for (k=1; k<=7; k++) ncodemax[k]=0;
         for(j=1; j<=(nlstate+ndeath);j++){  
            k=k+1;    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
           gp[k]=pmmij[i][j];      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
         }                                 modality*/ 
       }        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
         Ndum[ij]++; /*store the modality */
       for(i=1; i<=npar; i++)        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
                                             Tvar[j]. If V=sex and male is 0 and 
                                          female is 1, then  cptcode=1.*/
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      }
       k=0;  
       for(i=1; i<=(nlstate+ndeath); i++){      for (i=0; i<=cptcode; i++) {
         for(j=1; j<=(nlstate+ndeath);j++){        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 */
           k=k+1;      }
           gm[k]=pmmij[i][j];  
         }      ij=1; 
       }      for (i=1; i<=ncodemax[j]; i++) {
              for (k=0; k<= maxncov; k++) {
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)          if (Ndum[k] != 0) {
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];              nbcode[Tvar[j]][ij]=k; 
     }            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
             
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)            ij++;
       for(theta=1; theta <=npar; theta++)          }
       trgradg[j][theta]=gradg[theta][j];          if (ij > ncodemax[j]) break; 
          }  
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);      } 
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    }  
   
      pmij(pmmij,cov,ncovmodel,x,nlstate);   for (k=0; k< maxncov; k++) Ndum[k]=0;
   
      k=0;   for (i=1; i<=ncovmodel-2; i++) { 
      for(i=1; i<=(nlstate+ndeath); i++){     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
        for(j=1; j<=(nlstate+ndeath);j++){     ij=Tvar[i];
          k=k+1;     Ndum[ij]++;
          gm[k]=pmmij[i][j];   }
         }  
      }   ij=1;
         for (i=1; i<= maxncov; i++) {
      /*printf("\n%d ",(int)age);     if((Ndum[i]!=0) && (i<=ncovcol)){
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){       Tvaraff[ij]=i; /*For printing */
               ij++;
      }
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));   }
      }*/   
    cptcoveff=ij-1; /*Number of simple covariates*/
   fprintf(ficresprob,"\n%d ",(int)age);  }
   
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){  /*********** Health Expectancies ****************/
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  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 )
   }  
   {
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    /* Health expectancies */
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    double age, agelim, hf;
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    double ***p3mat,***varhe;
 }    double **dnewm,**doldm;
  free_vector(xp,1,npar);    double *xp;
 fclose(ficresprob);    double **gp, **gm;
     double ***gradg, ***trgradg;
 }    int theta;
   
 /******************* Printing html file ***********/    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[],char rfileres[] ){    xp=vector(1,npar);
   int jj1, k1, i1, cpt;    dnewm=matrix(1,nlstate*nlstate,1,npar);
   FILE *fichtm;    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   /*char optionfilehtm[FILENAMELENGTH];*/    
     fprintf(ficreseij,"# Health expectancies\n");
   strcpy(optionfilehtm,optionfile);    fprintf(ficreseij,"# Age");
   strcat(optionfilehtm,".htm");    for(i=1; i<=nlstate;i++)
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {      for(j=1; j<=nlstate;j++)
     printf("Problem with %s \n",optionfilehtm), exit(0);        fprintf(ficreseij," %1d-%1d (SE)",i,j);
   }    fprintf(ficreseij,"\n");
   
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.71c </font> <hr size=\"2\" color=\"#EC5E5E\">    if(estepm < stepm){
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
 Total number of observations=%d <br>    else  hstepm=estepm;   
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>    /* We compute the life expectancy from trapezoids spaced every estepm months
 <hr  size=\"2\" color=\"#EC5E5E\">     * This is mainly to measure the difference between two models: for example
 <li>Outputs files<br><br>\n     * if stepm=24 months pijx are given only every 2 years and by summing them
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n     * we are calculating an estimate of the Life Expectancy assuming a linear 
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>     * progression in between and thus overestimating or underestimating according
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>     * to the curvature of the survival function. If, for the same date, we 
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>     * estimate the model with stepm=1 month, we can keep estepm to 24 months
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>     * to compare the new estimate of Life expectancy with the same linear 
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>     * hypothesis. A more precise result, taking into account a more precise
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>     * curvature will be obtained if estepm is as small as stepm. */
         - 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>    /* For example we decided to compute the life expectancy with the smallest unit */
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>       nhstepm is the number of hstepm from age to agelim 
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);       nstepm is the number of stepm from age to agelin. 
         Look at hpijx to understand the reason of that which relies in memory size
 fprintf(fichtm," <li>Graphs</li><p>");       and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
  m=cptcoveff;       survival function given by stepm (the optimization length). Unfortunately it
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}       means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
  jj1=0;       results. So we changed our mind and took the option of the best precision.
  for(k1=1; k1<=m;k1++){    */
    for(i1=1; i1<=ncodemax[k1];i1++){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
        jj1++;  
        if (cptcovn > 0) {    agelim=AGESUP;
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
          for (cpt=1; cpt<=cptcoveff;cpt++)      /* nhstepm age range expressed in number of stepm */
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
        }      /* if (stepm >= YEARM) hstepm=1;*/
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        for(cpt=1; cpt<nlstate;cpt++){      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>      gp=matrix(0,nhstepm,1,nlstate*nlstate);
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      gm=matrix(0,nhstepm,1,nlstate*nlstate);
        }  
     for(cpt=1; cpt<=nlstate;cpt++) {      /* Computed by stepm unit matrices, product of hstepm matrices, stored
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
 interval) in state (%d): v%s%d%d.gif <br>      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);     
      }  
      for(cpt=1; cpt<=nlstate;cpt++) {      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>  
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      /* Computing Variances of health expectancies */
      }  
      fprintf(fichtm,"\n<br>- Total life expectancy by age and       for(theta=1; theta <=npar; theta++){
 health expectancies in states (1) and (2): e%s%d.gif<br>        for(i=1; i<=npar; i++){ 
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 fprintf(fichtm,"\n</body>");        }
    }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
    }    
 fclose(fichtm);        cptj=0;
 }        for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
 /******************* Gnuplot file **************/            cptj=cptj+1;
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
               gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;            }
           }
   strcpy(optionfilegnuplot,optionfilefiname);        }
   strcat(optionfilegnuplot,".plt");       
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {       
     printf("Problem with file %s",optionfilegnuplot);        for(i=1; i<=npar; i++) 
   }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 #ifdef windows        
     fprintf(ficgp,"cd \"%s\" \n",pathc);        cptj=0;
 #endif        for(j=1; j<= nlstate; j++){
 m=pow(2,cptcoveff);          for(i=1;i<=nlstate;i++){
              cptj=cptj+1;
  /* 1eme*/            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   for (cpt=1; cpt<= nlstate ; cpt ++) {              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
    for (k1=1; k1<= m ; k1 ++) {            }
           }
 #ifdef windows        }
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);        for(j=1; j<= nlstate*nlstate; j++)
 #endif          for(h=0; h<=nhstepm-1; h++){
 #ifdef unix            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);          }
 #endif       } 
      
 for (i=1; i<= nlstate ; i ++) {  /* End theta */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
 }  
     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(h=0; h<=nhstepm-1; h++)
     for (i=1; i<= nlstate ; i ++) {        for(j=1; j<=nlstate*nlstate;j++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          for(theta=1; theta <=npar; theta++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");            trgradg[h][j][theta]=gradg[h][theta][j];
 }       
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  
      for (i=1; i<= nlstate ; i ++) {       for(i=1;i<=nlstate*nlstate;i++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        for(j=1;j<=nlstate*nlstate;j++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");          varhe[i][j][(int)age] =0.;
 }    
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));       printf("%d|",(int)age);fflush(stdout);
 #ifdef unix       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
 fprintf(ficgp,"\nset ter gif small size 400,300");       for(h=0;h<=nhstepm-1;h++){
 #endif        for(k=0;k<=nhstepm-1;k++){
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
    }          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   }          for(i=1;i<=nlstate*nlstate;i++)
   /*2 eme*/            for(j=1;j<=nlstate*nlstate;j++)
               varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
   for (k1=1; k1<= m ; k1 ++) {        }
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);      }
          /* Computing expectancies */
     for (i=1; i<= nlstate+1 ; i ++) {      for(i=1; i<=nlstate;i++)
       k=2*i;        for(j=1; j<=nlstate;j++)
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       for (j=1; j<= nlstate+1 ; j ++) {            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            
   else fprintf(ficgp," \%%*lf (\%%*lf)");  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
 }    
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          }
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);  
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);      fprintf(ficreseij,"%3.0f",age );
       for (j=1; j<= nlstate+1 ; j ++) {      cptj=0;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      for(i=1; i<=nlstate;i++)
         else fprintf(ficgp," \%%*lf (\%%*lf)");        for(j=1; j<=nlstate;j++){
 }            cptj++;
       fprintf(ficgp,"\" t\"\" w l 0,");          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
      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(ficreseij,"\n");
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");     
   else fprintf(ficgp," \%%*lf (\%%*lf)");      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
 }        free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
       else fprintf(ficgp,"\" t\"\" w l 0,");      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    }
   }    printf("\n");
      fprintf(ficlog,"\n");
   /*3eme*/  
     free_vector(xp,1,npar);
   for (k1=1; k1<= m ; k1 ++) {    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     for (cpt=1; cpt<= nlstate ; cpt ++) {    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
       k=2+nlstate*(cpt-1);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);  }
       for (i=1; i< nlstate ; i ++) {  
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);  /************ Variance ******************/
       }  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)
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  {
     }    /* Variance of health expectancies */
     }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
      /* double **newm;*/
   /* CV preval stat */    double **dnewm,**doldm;
     for (k1=1; k1<= m ; k1 ++) {    double **dnewmp,**doldmp;
     for (cpt=1; cpt<nlstate ; cpt ++) {    int i, j, nhstepm, hstepm, h, nstepm ;
       k=3;    int k, cptcode;
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);    double *xp;
     double **gp, **gm;  /* for var eij */
       for (i=1; i< nlstate ; i ++)    double ***gradg, ***trgradg; /*for var eij */
         fprintf(ficgp,"+$%d",k+i+1);    double **gradgp, **trgradgp; /* for var p point j */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    double *gpp, *gmp; /* for var p point j */
          double **varppt; /* for var p point j nlstate to nlstate+ndeath */
       l=3+(nlstate+ndeath)*cpt;    double ***p3mat;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    double age,agelim, hf;
       for (i=1; i< nlstate ; i ++) {    double ***mobaverage;
         l=3+(nlstate+ndeath)*cpt;    int theta;
         fprintf(ficgp,"+$%d",l+i+1);    char digit[4];
       }    char digitp[25];
       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);    char fileresprobmorprev[FILENAMELENGTH];
     }  
   }      if(popbased==1){
        if(mobilav!=0)
   /* proba elementaires */        strcpy(digitp,"-populbased-mobilav-");
    for(i=1,jk=1; i <=nlstate; i++){      else strcpy(digitp,"-populbased-nomobil-");
     for(k=1; k <=(nlstate+ndeath); k++){    }
       if (k != i) {    else 
         for(j=1; j <=ncovmodel; j++){      strcpy(digitp,"-stablbased-");
          
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    if (mobilav!=0) {
           jk++;      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           fprintf(ficgp,"\n");      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(jk=1; jk <=m; jk++) {    strcpy(fileresprobmorprev,"prmorprev"); 
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);    sprintf(digit,"%-d",ij);
    i=1;    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
    for(k2=1; k2<=nlstate; k2++) {    strcat(fileresprobmorprev,digit); /* Tvar to be done */
      k3=i;    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
      for(k=1; k<=(nlstate+ndeath); k++) {    strcat(fileresprobmorprev,fileres);
        if (k != k2){    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
 ij=1;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
         for(j=3; j <=ncovmodel; j++) {    }
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
             ij++;    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);
           }    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
           else    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      fprintf(ficresprobmorprev," p.%-d SE",j);
         }      for(i=1; i<=nlstate;i++)
           fprintf(ficgp,")/(1");        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
            }  
         for(k1=1; k1 <=nlstate; k1++){      fprintf(ficresprobmorprev,"\n");
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
 ij=1;      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
           for(j=3; j <=ncovmodel; j++){      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      exit(0);
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    }
             ij++;    else{
           }      fprintf(ficgp,"\n# Routine varevsij");
           else    }
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
           }      printf("Problem with html file: %s\n", optionfilehtm);
           fprintf(ficgp,")");      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
         }      exit(0);
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    }
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    else{
         i=i+ncovmodel;      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");
        }      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
      }    }
    }    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);  
    }    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
        fprintf(ficresvij,"# Age");
   fclose(ficgp);    for(i=1; i<=nlstate;i++)
 }  /* end gnuplot */      for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     fprintf(ficresvij,"\n");
 /*************** Moving average **************/  
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){    xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
   int i, cpt, cptcod;    doldm=matrix(1,nlstate,1,nlstate);
     for (agedeb=agemin; agedeb<=fage; agedeb++)    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
       for (i=1; i<=nlstate;i++)    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)  
           mobaverage[(int)agedeb][i][cptcod]=0.;    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
        gpp=vector(nlstate+1,nlstate+ndeath);
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){    gmp=vector(nlstate+1,nlstate+ndeath);
       for (i=1; i<=nlstate;i++){    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    
           for (cpt=0;cpt<=4;cpt++){    if(estepm < stepm){
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];      printf ("Problem %d lower than %d\n",estepm, stepm);
           }    }
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    else  hstepm=estepm;   
         }    /* For example we decided to compute the life expectancy with the smallest unit */
       }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     }       nhstepm is the number of hstepm from age to agelim 
           nstepm is the number of stepm from age to agelin. 
 }       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like k years */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 /************** Forecasting ******************/       survival function given by stepm (the optimization length). Unfortunately it
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){       means that if the survival funtion is printed every two years of age and if
         you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;       results. So we changed our mind and took the option of the best precision.
   int *popage;    */
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   double *popeffectif,*popcount;    agelim = AGESUP;
   double ***p3mat;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   char fileresf[FILENAMELENGTH];      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
  agelim=AGESUP;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      gm=matrix(0,nhstepm,1,nlstate);
    
    
   strcpy(fileresf,"f");      for(theta=1; theta <=npar; theta++){
   strcat(fileresf,fileres);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   if((ficresf=fopen(fileresf,"w"))==NULL) {          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     printf("Problem with forecast resultfile: %s\n", fileresf);        }
   }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   printf("Computing forecasting: result on file '%s' \n", fileresf);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        if (popbased==1) {
           if(mobilav ==0){
   if (mobilav==1) {            for(i=1; i<=nlstate;i++)
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              prlim[i][i]=probs[(int)age][i][ij];
     movingaverage(agedeb, fage, agemin, mobaverage);          }else{ /* mobilav */ 
   }            for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
   stepsize=(int) (stepm+YEARM-1)/YEARM;          }
   if (stepm<=12) stepsize=1;        }
      
   agelim=AGESUP;        for(j=1; j<= nlstate; j++){
            for(h=0; h<=nhstepm; h++){
   hstepm=1;            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   hstepm=hstepm/stepm;              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   yp1=modf(dateintmean,&yp);          }
   anprojmean=yp;        }
   yp2=modf((yp1*12),&yp);        /* This for computing probability of death (h=1 means
   mprojmean=yp;           computed over hstepm matrices product = hstepm*stepm months) 
   yp1=modf((yp2*30.5),&yp);           as a weighted average of prlim.
   jprojmean=yp;        */
   if(jprojmean==0) jprojmean=1;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   if(mprojmean==0) jprojmean=1;          for(i=1,gpp[j]=0.; i<= nlstate; i++)
              gpp[j] += prlim[i][i]*p3mat[i][j][1];
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);        }    
          /* end probability of death */
   for(cptcov=1;cptcov<=i2;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
       k=k+1;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       fprintf(ficresf,"\n#******");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       for(j=1;j<=cptcoveff;j++) {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   
       }        if (popbased==1) {
       fprintf(ficresf,"******\n");          if(mobilav ==0){
       fprintf(ficresf,"# StartingAge FinalAge");            for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);              prlim[i][i]=probs[(int)age][i][ij];
                }else{ /* mobilav */ 
                  for(i=1; i<=nlstate;i++)
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {              prlim[i][i]=mobaverage[(int)age][i][ij];
         fprintf(ficresf,"\n");          }
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);          }
   
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){        for(j=1; j<= nlstate; j++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          for(h=0; h<=nhstepm; h++){
           nhstepm = nhstepm/hstepm;            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
                        gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           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);          /* This for computing probability of death (h=1 means
                   computed over hstepm matrices product = hstepm*stepm months) 
           for (h=0; h<=nhstepm; h++){           as a weighted average of prlim.
             if (h==(int) (calagedate+YEARM*cpt)) {        */
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
             }          for(i=1,gmp[j]=0.; i<= nlstate; i++)
             for(j=1; j<=nlstate+ndeath;j++) {           gmp[j] += prlim[i][i]*p3mat[i][j][1];
               kk1=0.;kk2=0;        }    
               for(i=1; i<=nlstate;i++) {                      /* end probability of death */
                 if (mobilav==1)  
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        for(j=1; j<= nlstate; j++) /* vareij */
                 else {          for(h=0; h<=nhstepm; h++){
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
                 }          }
                  
               }        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
               if (h==(int)(calagedate+12*cpt)){          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
                 fprintf(ficresf," %.3f", kk1);        }
                          
               }      } /* End theta */
             }  
           }      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }      for(h=0; h<=nhstepm; h++) /* veij */
       }        for(j=1; j<=nlstate;j++)
     }          for(theta=1; theta <=npar; theta++)
   }            trgradg[h][j][theta]=gradg[h][theta][j];
          
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
   fclose(ficresf);          trgradgp[j][theta]=gradgp[theta][j];
 }    
 /************** Forecasting ******************/  
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
        for(i=1;i<=nlstate;i++)
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        for(j=1;j<=nlstate;j++)
   int *popage;          vareij[i][j][(int)age] =0.;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  
   double *popeffectif,*popcount;      for(h=0;h<=nhstepm;h++){
   double ***p3mat,***tabpop,***tabpopprev;        for(k=0;k<=nhstepm;k++){
   char filerespop[FILENAMELENGTH];          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for(i=1;i<=nlstate;i++)
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            for(j=1;j<=nlstate;j++)
   agelim=AGESUP;              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;        }
        }
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    
        /* pptj */
        matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   strcpy(filerespop,"pop");      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   strcat(filerespop,fileres);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   if((ficrespop=fopen(filerespop,"w"))==NULL) {        for(i=nlstate+1;i<=nlstate+ndeath;i++)
     printf("Problem with forecast resultfile: %s\n", filerespop);          varppt[j][i]=doldmp[j][i];
   }      /* end ppptj */
   printf("Computing forecasting: result on file '%s' \n", filerespop);      /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
   if (mobilav==1) {      if (popbased==1) {
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        if(mobilav ==0){
     movingaverage(agedeb, fage, agemin, mobaverage);          for(i=1; i<=nlstate;i++)
   }            prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
   stepsize=(int) (stepm+YEARM-1)/YEARM;          for(i=1; i<=nlstate;i++)
   if (stepm<=12) stepsize=1;            prlim[i][i]=mobaverage[(int)age][i][ij];
          }
   agelim=AGESUP;      }
                 
   hstepm=1;      /* This for computing probability of death (h=1 means
   hstepm=hstepm/stepm;         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
           as a weighted average of prlim.
   if (popforecast==1) {      */
     if((ficpop=fopen(popfile,"r"))==NULL) {      for(j=nlstate+1;j<=nlstate+ndeath;j++){
       printf("Problem with population file : %s\n",popfile);exit(0);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
     }          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     popage=ivector(0,AGESUP);      }    
     popeffectif=vector(0,AGESUP);      /* end probability of death */
     popcount=vector(0,AGESUP);  
          fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     i=1;        for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
            for(i=1; i<=nlstate;i++){
     imx=i;          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];        }
   }      } 
       fprintf(ficresprobmorprev,"\n");
   for(cptcov=1;cptcov<=i2;cptcov++){  
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      fprintf(ficresvij,"%.0f ",age );
       k=k+1;      for(i=1; i<=nlstate;i++)
       fprintf(ficrespop,"\n#******");        for(j=1; j<=nlstate;j++){
       for(j=1;j<=cptcoveff;j++) {          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        }
       }      fprintf(ficresvij,"\n");
       fprintf(ficrespop,"******\n");      free_matrix(gp,0,nhstepm,1,nlstate);
       fprintf(ficrespop,"# Age");      free_matrix(gm,0,nhstepm,1,nlstate);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       if (popforecast==1)  fprintf(ficrespop," [Population]");      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       for (cpt=0; cpt<=0;cpt++) {    } /* End age */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      free_vector(gpp,nlstate+1,nlstate+ndeath);
            free_vector(gmp,nlstate+1,nlstate+ndeath);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
           nhstepm = nhstepm/hstepm;    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 */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
           oldm=oldms;savm=savms;  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    /*   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); */
           for (h=0; h<=nhstepm; h++){    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
             if (h==(int) (calagedate+YEARM*cpt)) {    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
             }    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
             for(j=1; j<=nlstate+ndeath;j++) {    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);
               kk1=0.;kk2=0;    /*  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);
               for(i=1; i<=nlstate;i++) {                */
                 if (mobilav==1)    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  
                 else {    free_vector(xp,1,npar);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    free_matrix(doldm,1,nlstate,1,nlstate);
                 }    free_matrix(dnewm,1,nlstate,1,npar);
               }    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
               if (h==(int)(calagedate+12*cpt)){    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   /*fprintf(ficrespop," %.3f", kk1);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/    fclose(ficresprobmorprev);
               }    fclose(ficgp);
             }    fclose(fichtm);
             for(i=1; i<=nlstate;i++){  }  
               kk1=0.;  
                 for(j=1; j<=nlstate;j++){  /************ Variance of prevlim ******************/
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];  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)
                 }  {
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    /* Variance of prevalence limit */
             }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **newm;
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    double **dnewm,**doldm;
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    int i, j, nhstepm, hstepm;
           }    int k, cptcode;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double *xp;
         }    double *gp, *gm;
       }    double **gradg, **trgradg;
      double age,agelim;
   /******/    int theta;
      
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      fprintf(ficresvpl,"# Age");
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){    for(i=1; i<=nlstate;i++)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        fprintf(ficresvpl," %1d-%1d",i,i);
           nhstepm = nhstepm/hstepm;    fprintf(ficresvpl,"\n");
            
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    xp=vector(1,npar);
           oldm=oldms;savm=savms;    dnewm=matrix(1,nlstate,1,npar);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      doldm=matrix(1,nlstate,1,nlstate);
           for (h=0; h<=nhstepm; h++){    
             if (h==(int) (calagedate+YEARM*cpt)) {    hstepm=1*YEARM; /* Every year of age */
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
             }    agelim = AGESUP;
             for(j=1; j<=nlstate+ndeath;j++) {    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
               kk1=0.;kk2=0;      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
               for(i=1; i<=nlstate;i++) {                    if (stepm >= YEARM) hstepm=1;
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];          nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
               }      gradg=matrix(1,npar,1,nlstate);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);      gp=vector(1,nlstate);
             }      gm=vector(1,nlstate);
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for(theta=1; theta <=npar; theta++){
         }        for(i=1; i<=npar; i++){ /* Computes gradient */
       }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
    }        }
   }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
          for(i=1;i<=nlstate;i++)
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          gp[i] = prlim[i][i];
       
   if (popforecast==1) {        for(i=1; i<=npar; i++) /* Computes gradient */
     free_ivector(popage,0,AGESUP);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     free_vector(popeffectif,0,AGESUP);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     free_vector(popcount,0,AGESUP);        for(i=1;i<=nlstate;i++)
   }          gm[i] = prlim[i][i];
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(i=1;i<=nlstate;i++)
   fclose(ficrespop);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
 }      } /* End theta */
   
 /***********************************************/      trgradg =matrix(1,nlstate,1,npar);
 /**************** Main Program *****************/  
 /***********************************************/      for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
 int main(int argc, char *argv[])          trgradg[j][theta]=gradg[theta][j];
 {  
       for(i=1;i<=nlstate;i++)
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;        varpl[i][(int)age] =0.;
   double agedeb, agefin,hf;      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
   double fret;        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   double **xi,tmp,delta;  
       fprintf(ficresvpl,"%.0f ",age );
   double dum; /* Dummy variable */      for(i=1; i<=nlstate;i++)
   double ***p3mat;        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   int *indx;      fprintf(ficresvpl,"\n");
   char line[MAXLINE], linepar[MAXLINE];      free_vector(gp,1,nlstate);
   char title[MAXLINE];      free_vector(gm,1,nlstate);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];      free_matrix(gradg,1,npar,1,nlstate);
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];      free_matrix(trgradg,1,nlstate,1,npar);
      } /* End age */
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  
     free_vector(xp,1,npar);
   char filerest[FILENAMELENGTH];    free_matrix(doldm,1,nlstate,1,npar);
   char fileregp[FILENAMELENGTH];    free_matrix(dnewm,1,nlstate,1,nlstate);
   char popfile[FILENAMELENGTH];  
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];  }
   int firstobs=1, lastobs=10;  
   int sdeb, sfin; /* Status at beginning and end */  /************ Variance of one-step probabilities  ******************/
   int c,  h , cpt,l;  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
   int ju,jl, mi;  {
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    int i, j=0,  i1, k1, l1, t, tj;
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    int k2, l2, j1,  z1;
   int mobilav=0,popforecast=0;    int k=0,l, cptcode;
   int hstepm, nhstepm;    int first=1, first1;
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
   double bage, fage, age, agelim, agebase;    double *xp;
   double ftolpl=FTOL;    double *gp, *gm;
   double **prlim;    double **gradg, **trgradg;
   double *severity;    double **mu;
   double ***param; /* Matrix of parameters */    double age,agelim, cov[NCOVMAX];
   double  *p;    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   double **matcov; /* Matrix of covariance */    int theta;
   double ***delti3; /* Scale */    char fileresprob[FILENAMELENGTH];
   double *delti; /* Scale */    char fileresprobcov[FILENAMELENGTH];
   double ***eij, ***vareij;    char fileresprobcor[FILENAMELENGTH];
   double **varpl; /* Variances of prevalence limits by age */  
   double *epj, vepp;    double ***varpij;
   double kk1, kk2;  
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    strcpy(fileresprob,"prob"); 
      strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   char version[80]="Imach version 0.71c, March 2002, INED-EUROREVES ";      printf("Problem with resultfile: %s\n", fileresprob);
   char *alph[]={"a","a","b","c","d","e"}, str[4];      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
   char z[1]="c", occ;    strcat(fileresprobcov,fileres);
 #include <sys/time.h>    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
 #include <time.h>      printf("Problem with resultfile: %s\n", fileresprobcov);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
      }
   /* long total_usecs;    strcpy(fileresprobcor,"probcor"); 
   struct timeval start_time, end_time;    strcat(fileresprobcor,fileres);
      if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
   printf("\n%s",version);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   if(argc <=1){    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("\nEnter the parameter file name: ");    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     scanf("%s",pathtot);    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);
   else{    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     strcpy(pathtot,argv[1]);    
   }    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    fprintf(ficresprob,"# Age");
   /*cygwin_split_path(pathtot,path,optionfile);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    fprintf(ficresprobcov,"# Age");
   /* cutv(path,optionfile,pathtot,'\\');*/    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcov,"# Age");
   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);    for(i=1; i<=nlstate;i++)
   replace(pathc,path);      for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
 /*-------- arguments in the command line --------*/        fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
   strcpy(fileres,"r");      }  
   strcat(fileres, optionfilefiname);   /* fprintf(ficresprob,"\n");
   strcat(fileres,".txt");    /* Other files have txt extension */    fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
   /*---------arguments file --------*/   */
    xp=vector(1,npar);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     printf("Problem with optionfile %s\n",optionfile);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     goto end;    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   }    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
   strcpy(filereso,"o");    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   strcat(filereso,fileres);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   if((ficparo=fopen(filereso,"w"))==NULL) {      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      exit(0);
   }    }
     else{
   /* Reads comments: lines beginning with '#' */      fprintf(ficgp,"\n# Routine varprob");
   while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
     fgets(line, MAXLINE, ficpar);      printf("Problem with html file: %s\n", optionfilehtm);
     puts(line);      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
     fputs(line,ficparo);      exit(0);
   }    }
   ungetc(c,ficpar);    else{
       fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   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);      fprintf(fichtm,"\n");
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);  
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
 while((c=getc(ficpar))=='#' && c!= EOF){      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");
     ungetc(c,ficpar);      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");
     fgets(line, MAXLINE, ficpar);  
     puts(line);    }
     fputs(line,ficparo);  
   }    cov[1]=1;
   ungetc(c,ficpar);    tj=cptcoveff;
      if (cptcovn<1) {tj=1;ncodemax[1]=1;}
        j1=0;
   covar=matrix(0,NCOVMAX,1,n);    for(t=1; t<=tj;t++){
   cptcovn=0;      for(i1=1; i1<=ncodemax[t];i1++){ 
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;        j1++;
         if  (cptcovn>0) {
   ncovmodel=2+cptcovn;          fprintf(ficresprob, "\n#********** Variable "); 
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficresprob, "**********\n#\n");
   /* Read guess parameters */          fprintf(ficresprobcov, "\n#********** Variable "); 
   /* Reads comments: lines beginning with '#' */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficresprobcov, "**********\n#\n");
     ungetc(c,ficpar);          
     fgets(line, MAXLINE, ficpar);          fprintf(ficgp, "\n#********** Variable "); 
     puts(line);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fputs(line,ficparo);          fprintf(ficgp, "**********\n#\n");
   }          
   ungetc(c,ficpar);          
            fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     for(i=1; i <=nlstate; i++)          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     for(j=1; j <=nlstate+ndeath-1; j++){          
       fscanf(ficpar,"%1d%1d",&i1,&j1);          fprintf(ficresprobcor, "\n#********** Variable ");    
       fprintf(ficparo,"%1d%1d",i1,j1);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       printf("%1d%1d",i,j);          fprintf(ficresprobcor, "**********\n#");    
       for(k=1; k<=ncovmodel;k++){        }
         fscanf(ficpar," %lf",&param[i][j][k]);        
         printf(" %lf",param[i][j][k]);        for (age=bage; age<=fage; age ++){ 
         fprintf(ficparo," %lf",param[i][j][k]);          cov[2]=age;
       }          for (k=1; k<=cptcovn;k++) {
       fscanf(ficpar,"\n");            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
       printf("\n");          }
       fprintf(ficparo,"\n");          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     }          for (k=1; k<=cptcovprod;k++)
              cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;          
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   p=param[1][1];          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
            gp=vector(1,(nlstate)*(nlstate+ndeath));
   /* Reads comments: lines beginning with '#' */          gm=vector(1,(nlstate)*(nlstate+ndeath));
   while((c=getc(ficpar))=='#' && c!= EOF){      
     ungetc(c,ficpar);          for(theta=1; theta <=npar; theta++){
     fgets(line, MAXLINE, ficpar);            for(i=1; i<=npar; i++)
     puts(line);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
     fputs(line,ficparo);            
   }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   ungetc(c,ficpar);            
             k=0;
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            for(i=1; i<= (nlstate); i++){
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */              for(j=1; j<=(nlstate+ndeath);j++){
   for(i=1; i <=nlstate; i++){                k=k+1;
     for(j=1; j <=nlstate+ndeath-1; j++){                gp[k]=pmmij[i][j];
       fscanf(ficpar,"%1d%1d",&i1,&j1);              }
       printf("%1d%1d",i,j);            }
       fprintf(ficparo,"%1d%1d",i1,j1);            
       for(k=1; k<=ncovmodel;k++){            for(i=1; i<=npar; i++)
         fscanf(ficpar,"%le",&delti3[i][j][k]);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
         printf(" %le",delti3[i][j][k]);      
         fprintf(ficparo," %le",delti3[i][j][k]);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       }            k=0;
       fscanf(ficpar,"\n");            for(i=1; i<=(nlstate); i++){
       printf("\n");              for(j=1; j<=(nlstate+ndeath);j++){
       fprintf(ficparo,"\n");                k=k+1;
     }                gm[k]=pmmij[i][j];
   }              }
   delti=delti3[1][1];            }
         
   /* Reads comments: lines beginning with '#' */            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
   while((c=getc(ficpar))=='#' && c!= EOF){              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);  
     puts(line);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
     fputs(line,ficparo);            for(theta=1; theta <=npar; theta++)
   }              trgradg[j][theta]=gradg[theta][j];
   ungetc(c,ficpar);          
            matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   matcov=matrix(1,npar,1,npar);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   for(i=1; i <=npar; i++){          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     fscanf(ficpar,"%s",&str);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
     printf("%s",str);          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     fprintf(ficparo,"%s",str);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     for(j=1; j <=i; j++){  
       fscanf(ficpar," %le",&matcov[i][j]);          pmij(pmmij,cov,ncovmodel,x,nlstate);
       printf(" %.5le",matcov[i][j]);          
       fprintf(ficparo," %.5le",matcov[i][j]);          k=0;
     }          for(i=1; i<=(nlstate); i++){
     fscanf(ficpar,"\n");            for(j=1; j<=(nlstate+ndeath);j++){
     printf("\n");              k=k+1;
     fprintf(ficparo,"\n");              mu[k][(int) age]=pmmij[i][j];
   }            }
   for(i=1; i <=npar; i++)          }
     for(j=i+1;j<=npar;j++)          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
       matcov[i][j]=matcov[j][i];            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
                  varpij[i][j][(int)age] = doldm[i][j];
   printf("\n");  
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     /*-------- Rewriting paramater file ----------*/            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
      strcpy(rfileres,"r");    /* "Rparameterfile */            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/            }*/
      strcat(rfileres,".");    /* */  
      strcat(rfileres,optionfilext);    /* Other files have txt extension */          fprintf(ficresprob,"\n%d ",(int)age);
     if((ficres =fopen(rfileres,"w"))==NULL) {          fprintf(ficresprobcov,"\n%d ",(int)age);
       printf("Problem writing new parameter file: %s\n", fileres);goto end;          fprintf(ficresprobcor,"\n%d ",(int)age);
     }  
     fprintf(ficres,"#%s\n",version);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
                fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
     /*-------- data file ----------*/          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     if((fic=fopen(datafile,"r"))==NULL)    {            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
       printf("Problem with datafile: %s\n", datafile);goto end;            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     }          }
           i=0;
     n= lastobs;          for (k=1; k<=(nlstate);k++){
     severity = vector(1,maxwav);            for (l=1; l<=(nlstate+ndeath);l++){ 
     outcome=imatrix(1,maxwav+1,1,n);              i=i++;
     num=ivector(1,n);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
     moisnais=vector(1,n);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
     annais=vector(1,n);              for (j=1; j<=i;j++){
     moisdc=vector(1,n);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
     andc=vector(1,n);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
     agedc=vector(1,n);              }
     cod=ivector(1,n);            }
     weight=vector(1,n);          }/* end of loop for state */
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        } /* end of loop for age */
     mint=matrix(1,maxwav,1,n);  
     anint=matrix(1,maxwav,1,n);        /* Confidence intervalle of pij  */
     s=imatrix(1,maxwav+1,1,n);        /*
     adl=imatrix(1,maxwav+1,1,n);              fprintf(ficgp,"\nset noparametric;unset label");
     tab=ivector(1,NCOVMAX);          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
     ncodemax=ivector(1,8);          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
     i=1;          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
     while (fgets(line, MAXLINE, fic) != NULL)    {          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
       if ((i >= firstobs) && (i <=lastobs)) {          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
                */
         for (j=maxwav;j>=1;j--){  
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
           strcpy(line,stra);        first1=1;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        for (k2=1; k2<=(nlstate);k2++){
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
         }            if(l2==k2) continue;
                    j=(k2-1)*(nlstate+ndeath)+l2;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);            for (k1=1; k1<=(nlstate);k1++){
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);                i=(k1-1)*(nlstate+ndeath)+l1;
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);                if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);                  if ((int)age %5==0){
         for (j=ncov;j>=1;j--){                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
         }                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
         num[i]=atol(stra);                    mu1=mu[i][(int) age]/stepm*YEARM ;
                            mu2=mu[j][(int) age]/stepm*YEARM;
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){                    c12=cv12/sqrt(v1*v2);
           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;}*/                    /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
         i=i+1;                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       }                    /* Eigen vectors */
     }                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
     /* printf("ii=%d", ij);                    /*v21=sqrt(1.-v11*v11); *//* error */
        scanf("%d",i);*/                    v21=(lc1-v1)/cv12*v11;
   imx=i-1; /* Number of individuals */                    v12=-v21;
                     v22=v11;
   /* for (i=1; i<=imx; i++){                    tnalp=v21/v11;
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;                    if(first1==1){
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;                      first1=0;
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
     }                    }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
     for (i=1; i<=imx; i++)                    /*printf(fignu*/
     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]));*/                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   /* Calculation of the number of parameter from char model*/                    if(first==1){
   Tvar=ivector(1,15);                      first=0;
   Tprod=ivector(1,15);                      fprintf(ficgp,"\nset parametric;unset label");
   Tvaraff=ivector(1,15);                      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);
   Tvard=imatrix(1,15,1,2);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   Tage=ivector(1,15);                            fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
                          fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
   if (strlen(model) >1){                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
     j=0, j1=0, k1=1, k2=1;                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
     j=nbocc(model,'+');                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     j1=nbocc(model,'*');                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     cptcovn=j+1;                      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",\
     cptcovprod=j1;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                                  mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                        }else{
     strcpy(modelsav,model);                      first=0;
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
       printf("Error. Non available option model=%s ",model);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
       goto end;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     }                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                                  mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     for(i=(j+1); i>=1;i--){                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
       cutv(stra,strb,modelsav,'+');                    }/* if first */
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);                  } /* age mod 5 */
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/                } /* end loop age */
       /*scanf("%d",i);*/                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
       if (strchr(strb,'*')) {                first=1;
         cutv(strd,strc,strb,'*');              } /*l12 */
         if (strcmp(strc,"age")==0) {            } /* k12 */
           cptcovprod--;          } /*l1 */
           cutv(strb,stre,strd,'V');        }/* k1 */
           Tvar[i]=atoi(stre);      } /* loop covariates */
           cptcovage++;    }
             Tage[cptcovage]=i;    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
             /*printf("stre=%s ", stre);*/    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
         }    free_vector(xp,1,npar);
         else if (strcmp(strd,"age")==0) {    fclose(ficresprob);
           cptcovprod--;    fclose(ficresprobcov);
           cutv(strb,stre,strc,'V');    fclose(ficresprobcor);
           Tvar[i]=atoi(stre);    fclose(ficgp);
           cptcovage++;    fclose(fichtm);
           Tage[cptcovage]=i;  }
         }  
         else {  
           cutv(strb,stre,strc,'V');  /******************* Printing html file ***********/
           Tvar[i]=ncov+k1;  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
           cutv(strb,strc,strd,'V');                    int lastpass, int stepm, int weightopt, char model[],\
           Tprod[k1]=i;                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
           Tvard[k1][1]=atoi(strc);                    int popforecast, int estepm ,\
           Tvard[k1][2]=atoi(stre);                    double jprev1, double mprev1,double anprev1, \
           Tvar[cptcovn+k2]=Tvard[k1][1];                    double jprev2, double mprev2,double anprev2){
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    int jj1, k1, i1, cpt;
           for (k=1; k<=lastobs;k++)    /*char optionfilehtm[FILENAMELENGTH];*/
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
           k1++;      printf("Problem with %s \n",optionfilehtm), exit(0);
           k2=k2+2;      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
         }    }
       }  
       else {     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/   - 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
        /*  scanf("%d",i);*/   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
       cutv(strd,strc,strb,'V');   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
       Tvar[i]=atoi(strc);   - Life expectancies by age and initial health status (estepm=%2d months): 
       }     <a href=\"e%s\">e%s</a> <br>\n</li>", \
       strcpy(modelsav,stra);      jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);  
         scanf("%d",i);*/  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
     }  
 }   m=cptcoveff;
     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);  
   printf("cptcovprod=%d ", cptcovprod);   jj1=0;
   scanf("%d ",i);*/   for(k1=1; k1<=m;k1++){
     fclose(fic);     for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
     /*  if(mle==1){*/       if (cptcovn > 0) {
     if (weightopt != 1) { /* Maximisation without weights*/         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
       for(i=1;i<=n;i++) weight[i]=1.0;         for (cpt=1; cpt<=cptcoveff;cpt++) 
     }           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     /*-calculation of age at interview from date of interview and age at death -*/         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     agev=matrix(1,maxwav,1,imx);       }
        /* Pij */
    for (i=1; i<=imx; i++)       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(m=2; (m<= maxwav); m++)  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){       /* Quasi-incidences */
          anint[m][i]=9999;       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>
          s[m][i]=-1;  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
        }         /* Stable prevalence in each health state */
             for(cpt=1; cpt<nlstate;cpt++){
     for (i=1; i<=imx; i++)  {           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
       for(m=1; (m<= maxwav); m++){         }
         if(s[m][i] >0){       for(cpt=1; cpt<=nlstate;cpt++) {
           if (s[m][i] == nlstate+1) {          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
             if(agedc[i]>0)  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
               if(moisdc[i]!=99 && andc[i]!=9999)       }
               agev[m][i]=agedc[i];       fprintf(fichtm,"\n<br>- Total life expectancy by age and
             else {  health expectancies in states (1) and (2): e%s%d.png<br>
               if (andc[i]!=9999){  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);     } /* end i1 */
               agev[m][i]=-1;   }/* End k1 */
               }   fprintf(fichtm,"</ul>");
             }  
           }  
           else if(s[m][i] !=9){ /* Should no more exist */   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
             if(mint[m][i]==99 || anint[m][i]==9999)   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
               agev[m][i]=1;   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
             else if(agev[m][i] <agemin){   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
               agemin=agev[m][i];   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
             }   - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
             else if(agev[m][i] >agemax){  
               agemax=agev[m][i];   if(popforecast==1) fprintf(fichtm,"\n
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/   - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
             }   - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
             /*agev[m][i]=anint[m][i]-annais[i];*/          <br>",fileres,fileres,fileres,fileres);
             /*   agev[m][i] = age[i]+2*m;*/   else 
           }     fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
           else { /* =9 */  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
             agev[m][i]=1;  
             s[m][i]=-1;   m=cptcoveff;
           }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
         }  
         else /*= 0 Unknown */   jj1=0;
           agev[m][i]=1;   for(k1=1; k1<=m;k1++){
       }     for(i1=1; i1<=ncodemax[k1];i1++){
           jj1++;
     }       if (cptcovn > 0) {
     for (i=1; i<=imx; i++)  {         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
       for(m=1; (m<= maxwav); m++){         for (cpt=1; cpt<=cptcoveff;cpt++) 
         if (s[m][i] > (nlstate+ndeath)) {           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
           printf("Error: Wrong value in nlstate or ndeath\n");           fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
           goto end;       }
         }       for(cpt=1; cpt<=nlstate;cpt++) {
       }         fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
     }  interval) in state (%d): v%s%d%d.png <br>
   <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);       }
      } /* end i1 */
     free_vector(severity,1,maxwav);   }/* End k1 */
     free_imatrix(outcome,1,maxwav+1,1,n);   fprintf(fichtm,"</ul>");
     free_vector(moisnais,1,n);  fclose(fichtm);
     free_vector(annais,1,n);  }
     /* free_matrix(mint,1,maxwav,1,n);  
        free_matrix(anint,1,maxwav,1,n);*/  /******************* Gnuplot file **************/
     free_vector(moisdc,1,n);  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
     free_vector(andc,1,n);  
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
        int ng;
     wav=ivector(1,imx);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      printf("Problem with file %s",optionfilegnuplot);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
        }
     /* Concatenates waves */  
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    /*#ifdef windows */
       fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
       Tcode=ivector(1,100);  m=pow(2,cptcoveff);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    
       ncodemax[1]=1;   /* 1eme*/
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    for (cpt=1; cpt<= nlstate ; cpt ++) {
           for (k1=1; k1<= m ; k1 ++) {
    codtab=imatrix(1,100,1,10);       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
    h=0;       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);
    m=pow(2,cptcoveff);  
         for (i=1; i<= nlstate ; i ++) {
    for(k=1;k<=cptcoveff; k++){         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
      for(i=1; i <=(m/pow(2,k));i++){         else fprintf(ficgp," \%%*lf (\%%*lf)");
        for(j=1; j <= ncodemax[k]; j++){       }
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){       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);
            h++;       for (i=1; i<= nlstate ; i ++) {
            if (h>m) h=1;codtab[h][k]=j;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          }         else fprintf(ficgp," \%%*lf (\%%*lf)");
        }       } 
      }       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
    }       for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
    /*for(i=1; i <=m ;i++){       }  
      for(k=1; k <=cptcovn; k++){       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);     }
      }    }
      printf("\n");    /*2 eme*/
    }    
    scanf("%d",i);*/    for (k1=1; k1<= m ; k1 ++) { 
          fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
    /* Calculates basic frequencies. Computes observed prevalence at single age      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
        and prints on file fileres'p'. */      
       for (i=1; i<= nlstate+1 ; i ++) {
            k=2*i;
            fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for (j=1; j<= nlstate+1 ; j ++) {
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          else fprintf(ficgp," \%%*lf (\%%*lf)");
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        }   
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
              else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
     /* For Powell, parameters are in a vector p[] starting at p[1]        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */        for (j=1; j<= nlstate+1 ; j ++) {
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
     if(mle==1){        }   
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        fprintf(ficgp,"\" t\"\" w l 0,");
     }        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
            for (j=1; j<= nlstate+1 ; j ++) {
     /*--------- results files --------------*/          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, weightopt,model);          else fprintf(ficgp," \%%*lf (\%%*lf)");
          }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
    jk=1;        else fprintf(ficgp,"\" t\"\" w l 0,");
    fprintf(ficres,"# Parameters\n");      }
    printf("# Parameters\n");    }
    for(i=1,jk=1; i <=nlstate; i++){    
      for(k=1; k <=(nlstate+ndeath); k++){    /*3eme*/
        if (k != i)    
          {    for (k1=1; k1<= m ; k1 ++) { 
            printf("%d%d ",i,k);      for (cpt=1; cpt<= nlstate ; cpt ++) {
            fprintf(ficres,"%1d%1d ",i,k);        k=2+nlstate*(2*cpt-2);
            for(j=1; j <=ncovmodel; j++){        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
              printf("%f ",p[jk]);        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
              fprintf(ficres,"%f ",p[jk]);        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
              jk++;          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
            }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
            printf("\n");          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
            fprintf(ficres,"\n");          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
          }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
      }          
    }        */
  if(mle==1){        for (i=1; i< nlstate ; i ++) {
     /* Computing hessian and covariance matrix */          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);
     ftolhess=ftol; /* Usually correct */          
     hesscov(matcov, p, npar, delti, ftolhess, func);        } 
  }      }
     fprintf(ficres,"# Scales\n");    }
     printf("# Scales\n");    
      for(i=1,jk=1; i <=nlstate; i++){    /* CV preval stat */
       for(j=1; j <=nlstate+ndeath; j++){    for (k1=1; k1<= m ; k1 ++) { 
         if (j!=i) {      for (cpt=1; cpt<nlstate ; cpt ++) {
           fprintf(ficres,"%1d%1d",i,j);        k=3;
           printf("%1d%1d",i,j);        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
           for(k=1; k<=ncovmodel;k++){        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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
             printf(" %.5e",delti[jk]);        
             fprintf(ficres," %.5e",delti[jk]);        for (i=1; i< nlstate ; i ++)
             jk++;          fprintf(ficgp,"+$%d",k+i+1);
           }        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
           printf("\n");        
           fprintf(ficres,"\n");        l=3+(nlstate+ndeath)*cpt;
         }        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
       }        for (i=1; i< nlstate ; i ++) {
      }          l=3+(nlstate+ndeath)*cpt;
              fprintf(ficgp,"+$%d",l+i+1);
     k=1;        }
     fprintf(ficres,"# Covariance\n");        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
     printf("# Covariance\n");      } 
     for(i=1;i<=npar;i++){    }  
       /*  if (k>nlstate) k=1;    
       i1=(i-1)/(ncovmodel*nlstate)+1;    /* proba elementaires */
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    for(i=1,jk=1; i <=nlstate; i++){
       printf("%s%d%d",alph[k],i1,tab[i]);*/      for(k=1; k <=(nlstate+ndeath); k++){
       fprintf(ficres,"%3d",i);        if (k != i) {
       printf("%3d",i);          for(j=1; j <=ncovmodel; j++){
       for(j=1; j<=i;j++){            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
         fprintf(ficres," %.5e",matcov[i][j]);            jk++; 
         printf(" %.5e",matcov[i][j]);            fprintf(ficgp,"\n");
       }          }
       fprintf(ficres,"\n");        }
       printf("\n");      }
       k++;     }
     }  
         for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
     while((c=getc(ficpar))=='#' && c!= EOF){       for(jk=1; jk <=m; jk++) {
       ungetc(c,ficpar);         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
       fgets(line, MAXLINE, ficpar);         if (ng==2)
       puts(line);           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
       fputs(line,ficparo);         else
     }           fprintf(ficgp,"\nset title \"Probability\"\n");
     ungetc(c,ficpar);         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
           i=1;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);         for(k2=1; k2<=nlstate; k2++) {
               k3=i;
     if (fage <= 2) {           for(k=1; k<=(nlstate+ndeath); k++) {
       bage = agemin;             if (k != k2){
       fage = agemaxpar;               if(ng==2)
     }                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                   else
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);               ij=1;
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);               for(j=3; j <=ncovmodel; j++) {
                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
     while((c=getc(ficpar))=='#' && c!= EOF){                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
     ungetc(c,ficpar);                   ij++;
     fgets(line, MAXLINE, ficpar);                 }
     puts(line);                 else
     fputs(line,ficparo);                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   }               }
   ungetc(c,ficpar);               fprintf(ficgp,")/(1");
                 
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);               for(k1=1; k1 <=nlstate; k1++){   
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                 ij=1;
                       for(j=3; j <=ncovmodel; j++){
   while((c=getc(ficpar))=='#' && c!= EOF){                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
     ungetc(c,ficpar);                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
     fgets(line, MAXLINE, ficpar);                     ij++;
     puts(line);                   }
     fputs(line,ficparo);                   else
   }                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   ungetc(c,ficpar);                 }
                   fprintf(ficgp,")");
                }
    dateprev1=anprev1+mprev1/12.+jprev1/365.;               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
    dateprev2=anprev2+mprev2/12.+jprev2/365.;               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
   fscanf(ficpar,"pop_based=%d\n",&popbased);             }
   fprintf(ficparo,"pop_based=%d\n",popbased);             } /* end k */
   fprintf(ficres,"pop_based=%d\n",popbased);           } /* end k2 */
         } /* end jk */
   while((c=getc(ficpar))=='#' && c!= EOF){     } /* end ng */
     ungetc(c,ficpar);     fclose(ficgp); 
     fgets(line, MAXLINE, ficpar);  }  /* end gnuplot */
     puts(line);  
     fputs(line,ficparo);  
   }  /*************** Moving average **************/
   ungetc(c,ficpar);  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);    int i, cpt, cptcod;
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);    int modcovmax =1;
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);    int mobilavrange, mob;
     double age;
   
 while((c=getc(ficpar))=='#' && c!= EOF){    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
     ungetc(c,ficpar);                             a covariate has 2 modalities */
     fgets(line, MAXLINE, ficpar);    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
     puts(line);  
     fputs(line,ficparo);    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
   }      if(mobilav==1) mobilavrange=5; /* default */
   ungetc(c,ficpar);      else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);        for (i=1; i<=nlstate;i++)
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          for (cptcod=1;cptcod<=modcovmax;cptcod++)
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);         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. 
 /*------------ gnuplot -------------*/      */ 
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);      for (mob=3;mob <=mobilavrange;mob=mob+2){
          for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
 /*------------ free_vector  -------------*/          for (i=1; i<=nlstate;i++){
  chdir(path);            for (cptcod=1;cptcod<=modcovmax;cptcod++){
                mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
  free_ivector(wav,1,imx);                for (cpt=1;cpt<=(mob-1)/2;cpt++){
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                    mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
  free_ivector(num,1,n);                }
  free_vector(agedc,1,n);              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
  /*free_matrix(covar,1,NCOVMAX,1,n);*/            }
  fclose(ficparo);          }
  fclose(ficres);        }/* end age */
       }/* end mob */
 /*--------- index.htm --------*/    }else return -1;
     return 0;
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres);  }/* End movingaverage */
   
    
   /*--------------- Prevalence limit --------------*/  /************** Forecasting ******************/
    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){
   strcpy(filerespl,"pl");    /* proj1, year, month, day of starting projection 
   strcat(filerespl,fileres);       agemin, agemax range of age
   if((ficrespl=fopen(filerespl,"w"))==NULL) {       dateprev1 dateprev2 range of dates during which prevalence is computed
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;       anproj2 year of en of projection (same day and month as proj1).
   }    */
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
   fprintf(ficrespl,"#Prevalence limit\n");    int *popage;
   fprintf(ficrespl,"#Age ");    double agec; /* generic age */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
   fprintf(ficrespl,"\n");    double *popeffectif,*popcount;
      double ***p3mat;
   prlim=matrix(1,nlstate,1,nlstate);    double ***mobaverage;
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    char fileresf[FILENAMELENGTH];
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    agelim=AGESUP;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */   
   k=0;    strcpy(fileresf,"f"); 
   agebase=agemin;    strcat(fileresf,fileres);
   agelim=agemaxpar;    if((ficresf=fopen(fileresf,"w"))==NULL) {
   ftolpl=1.e-10;      printf("Problem with forecast resultfile: %s\n", fileresf);
   i1=cptcoveff;      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
   if (cptcovn < 1){i1=1;}    }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
   for(cptcov=1;cptcov<=i1;cptcov++){    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
         k=k+1;    if (cptcoveff==0) ncodemax[cptcoveff]=1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  
         fprintf(ficrespl,"\n#******");    if (mobilav!=0) {
         for(j=1;j<=cptcoveff;j++)      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficrespl,"******\n");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
                printf(" Error in movingaverage mobilav=%d\n",mobilav);
         for (age=agebase; age<=agelim; age++){      }
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    }
           fprintf(ficrespl,"%.0f",age );  
           for(i=1; i<=nlstate;i++)    stepsize=(int) (stepm+YEARM-1)/YEARM;
           fprintf(ficrespl," %.5f", prlim[i][i]);    if (stepm<=12) stepsize=1;
           fprintf(ficrespl,"\n");    if(estepm < stepm){
         }      printf ("Problem %d lower than %d\n",estepm, stepm);
       }    }
     }    else  hstepm=estepm;   
   fclose(ficrespl);  
     hstepm=hstepm/stepm; 
   /*------------- h Pij x at various ages ------------*/    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                   fractional in yp1 */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    anprojmean=yp;
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    yp2=modf((yp1*12),&yp);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    mprojmean=yp;
   }    yp1=modf((yp2*30.5),&yp);
   printf("Computing pij: result on file '%s' \n", filerespij);    jprojmean=yp;
      if(jprojmean==0) jprojmean=1;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    if(mprojmean==0) jprojmean=1;
   /*if (stepm<=24) stepsize=2;*/  
     i1=cptcoveff;
   agelim=AGESUP;    if (cptcovn < 1){i1=1;}
   hstepm=stepsize*YEARM; /* Every year of age */    
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
      
   k=0;    fprintf(ficresf,"#****** Routine prevforecast **\n");
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       k=k+1;      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         fprintf(ficrespij,"\n#****** ");        k=k+1;
         for(j=1;j<=cptcoveff;j++)        fprintf(ficresf,"\n#******");
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for(j=1;j<=cptcoveff;j++) {
         fprintf(ficrespij,"******\n");          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]]);
                }
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */        fprintf(ficresf,"******\n");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        for(j=1; j<=nlstate+ndeath;j++){ 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(i=1; i<=nlstate;i++)              
           oldm=oldms;savm=savms;            fprintf(ficresf," p%d%d",i,j);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            fprintf(ficresf," p.%d",j);
           fprintf(ficrespij,"# Age");        }
           for(i=1; i<=nlstate;i++)        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
             for(j=1; j<=nlstate+ndeath;j++)          fprintf(ficresf,"\n");
               fprintf(ficrespij," %1d-%1d",i,j);          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
           fprintf(ficrespij,"\n");  
           for (h=0; h<=nhstepm; h++){          for (agec=fage; agec>=(ageminpar-1); agec--){ 
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             for(i=1; i<=nlstate;i++)            nhstepm = nhstepm/hstepm; 
               for(j=1; j<=nlstate+ndeath;j++)            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);            oldm=oldms;savm=savms;
             fprintf(ficrespij,"\n");            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           }          
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for (h=0; h<=nhstepm; h++){
           fprintf(ficrespij,"\n");              if (h==(int) (YEARM*yearp)) {
         }                fprintf(ficresf,"\n");
     }                for(j=1;j<=cptcoveff;j++) 
   }                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/              } 
               for(j=1; j<=nlstate+ndeath;j++) {
   fclose(ficrespij);                ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
   /*---------- Forecasting ------------------*/                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
   if((stepm == 1) && (strcmp(model,".")==0)){                  else {
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);                  }
     free_matrix(mint,1,maxwav,1,n);                  if (h==(int)(YEARM*yearp))
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
     free_vector(weight,1,n);}                }
   else{                if (h==(int)(YEARM*yearp)){
     erreur=108;                  fprintf(ficresf," %.3f", ppij);
     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);                }
   }              }
              }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /*---------- 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;    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   }  
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    fclose(ficresf);
   }
   
   strcpy(filerese,"e");  /************** Forecasting *****not tested NB*************/
   strcat(filerese,fileres);  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){
   if((ficreseij=fopen(filerese,"w"))==NULL) {    
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
   }    int *popage;
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
  strcpy(fileresv,"v");    double ***p3mat,***tabpop,***tabpopprev;
   strcat(fileresv,fileres);    double ***mobaverage;
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    char filerespop[FILENAMELENGTH];
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  
   }    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
   k=0;    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
   for(cptcov=1;cptcov<=i1;cptcov++){    
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       k=k+1;    
       fprintf(ficrest,"\n#****** ");    
       for(j=1;j<=cptcoveff;j++)    strcpy(filerespop,"pop"); 
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    strcat(filerespop,fileres);
       fprintf(ficrest,"******\n");    if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficreseij,"\n#****** ");      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
       for(j=1;j<=cptcoveff;j++)    }
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    printf("Computing forecasting: result on file '%s' \n", filerespop);
       fprintf(ficreseij,"******\n");    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
       fprintf(ficresvij,"\n#****** ");    if (cptcoveff==0) ncodemax[cptcoveff]=1;
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    if (mobilav!=0) {
       fprintf(ficresvij,"******\n");      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       oldm=oldms;savm=savms;        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);        }
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    }
       oldm=oldms;savm=savms;  
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    stepsize=(int) (stepm+YEARM-1)/YEARM;
        if (stepm<=12) stepsize=1;
     
      agelim=AGESUP;
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    hstepm=1;
       fprintf(ficrest,"\n");    hstepm=hstepm/stepm; 
     
       hf=1;    if (popforecast==1) {
       if (stepm >= YEARM) hf=stepm/YEARM;      if((ficpop=fopen(popfile,"r"))==NULL) {
       epj=vector(1,nlstate+1);        printf("Problem with population file : %s\n",popfile);exit(0);
       for(age=bage; age <=fage ;age++){        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      } 
         if (popbased==1) {      popage=ivector(0,AGESUP);
           for(i=1; i<=nlstate;i++)      popeffectif=vector(0,AGESUP);
             prlim[i][i]=probs[(int)age][i][k];      popcount=vector(0,AGESUP);
         }      
              i=1;   
         fprintf(ficrest," %.0f",age);      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){     
           for(i=1, epj[j]=0.;i <=nlstate;i++) {      imx=i;
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
           }    }
           epj[nlstate+1] +=epj[j];  
         }    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
         for(i=1, vepp=0.;i <=nlstate;i++)     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
           for(j=1;j <=nlstate;j++)        k=k+1;
             vepp += vareij[i][j][(int)age];        fprintf(ficrespop,"\n#******");
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));        for(j=1;j<=cptcoveff;j++) {
         for(j=1;j <=nlstate;j++){          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));        }
         }        fprintf(ficrespop,"******\n");
         fprintf(ficrest,"\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++) { 
   fclose(ficreseij);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
   fclose(ficresvij);          
   fclose(ficrest);          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
   fclose(ficpar);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   free_vector(epj,1,nlstate+1);            nhstepm = nhstepm/hstepm; 
              
   /*------- Variance limit prevalence------*/              p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
   strcpy(fileresvpl,"vpl");            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
   strcat(fileresvpl,fileres);          
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {            for (h=0; h<=nhstepm; h++){
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);              if (h==(int) (calagedatem+YEARM*cpt)) {
     exit(0);                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
   }              } 
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);              for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
   k=0;                for(i=1; i<=nlstate;i++) {              
   for(cptcov=1;cptcov<=i1;cptcov++){                  if (mobilav==1) 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
       k=k+1;                  else {
       fprintf(ficresvpl,"\n#****** ");                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
       for(j=1;j<=cptcoveff;j++)                  }
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                }
       fprintf(ficresvpl,"******\n");                if (h==(int)(calagedatem+12*cpt)){
                        tabpop[(int)(agedeb)][j][cptcod]=kk1;
       varpl=matrix(1,nlstate,(int) bage, (int) fage);                    /*fprintf(ficrespop," %.3f", kk1);
       oldm=oldms;savm=savms;                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);                }
     }              }
  }              for(i=1; i<=nlstate;i++){
                 kk1=0.;
   fclose(ficresvpl);                  for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
   /*---------- End : free ----------------*/                  }
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
                }
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                  fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
              }
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);          }
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);        }
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);   
      /******/
   free_matrix(matcov,1,npar,1,npar);  
   free_vector(delti,1,npar);        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
   free_matrix(agev,1,maxwav,1,imx);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   if(erreur >0)            nhstepm = nhstepm/hstepm; 
     printf("End of Imach with error %d\n",erreur);            
   else   printf("End of Imach\n");            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */            oldm=oldms;savm=savms;
              hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
   /* 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 (h=0; h<=nhstepm; h++){
   /*printf("Total time was %d uSec.\n", total_usecs);*/              if (h==(int) (calagedatem+YEARM*cpt)) {
   /*------ End -----------*/                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
  end:                kk1=0.;kk2=0;
 #ifdef windows                for(i=1; i<=nlstate;i++) {              
   /* chdir(pathcd);*/                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
 #endif                }
  /*system("wgnuplot graph.plt");*/                if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
  /*system("../gp37mgw/wgnuplot graph.plt");*/              }
  /*system("cd ../gp37mgw");*/            }
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  strcpy(plotcmd,GNUPLOTPROGRAM);          }
  strcat(plotcmd," ");        }
  strcat(plotcmd,optionfilegnuplot);     } 
  system(plotcmd);    }
    
 #ifdef windows    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   while (z[0] != 'q') {  
     chdir(path);    if (popforecast==1) {
     printf("\nType e to edit output files, c to start again, and q for exiting: ");      free_ivector(popage,0,AGESUP);
     scanf("%s",z);      free_vector(popeffectif,0,AGESUP);
     if (z[0] == 'c') system("./imach");      free_vector(popcount,0,AGESUP);
     else if (z[0] == 'e') {    }
       chdir(path);    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       system(optionfilehtm);    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }    fclose(ficrespop);
     else if (z[0] == 'q') exit(0);  }
   }  
 #endif  /***********************************************/
 }  /**************** 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 ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if(moisdc[i]!=99 && andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if (andc[i]!=9999){
                   printf("Warning negative age at death: %d line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           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(mint[m][i]==99 || anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* 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
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
   <hr  size=\"2\" color=\"#EC5E5E\">
    <ul><li><h4>Parameter files</h4>\n
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
    - Log file of the run: <a href=\"%s\">%s</a><br>\n
    - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
      fclose(fichtm);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     chdir(path);
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_ivector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with 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: %s\n",plotcmd);fflush(stdout);
     system(plotcmd);
   
    /*#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.1.32  
changed lines
  Added in v.1.74

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