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version 1.28, 2002/03/01 17:56:23 version 1.81, 2003/06/05 15:41:51
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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  
   /* $Id$ */
 static double maxarg1,maxarg2;  /* $Log$
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))   * Revision 1.81  2003/06/05 15:41:51  brouard
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))   * *** empty log message ***
     *
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  /* Revision 1.80  2003/06/05 15:34:14  brouard
 #define rint(a) floor(a+0.5)  /* Trying to add the true revision in the program and log
   /*
 static double sqrarg;  /* Revision 1.79  2003/06/05 15:17:23  brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  /* *** empty log message ***
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  /* */
   /* $Revision$ */
 int imx;  /* $Date$ */
 int stepm;  /* $State$ */
 /* Stepm, step in month: minimum step interpolation*/  
   char version[80]="Imach version 0.95a1, June 2003, INED-EUROREVES ";
 int m,nb;  char fullversion[]="$Revision$ $Date$"; 
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  int erreur; /* Error number */
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  int nvar;
 double **pmmij, ***probs, ***mobaverage;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 double dateintmean=0;  int npar=NPARMAX;
   int nlstate=2; /* Number of live states */
 double *weight;  int ndeath=1; /* Number of dead states */
 int **s; /* Status */  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 double *agedc, **covar, idx;  int popbased=0;
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
   int *wav; /* Number of waves for this individuual 0 is possible */
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  int maxwav; /* Maxim number of waves */
 double ftolhess; /* Tolerance for computing hessian */  int jmin, jmax; /* min, max spacing between 2 waves */
   int mle, weightopt;
 /**************** split *************************/  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 {  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
    char *s;                             /* pointer */             * wave mi and wave mi+1 is not an exact multiple of stepm. */
    int  l1, l2;                         /* length counters */  double jmean; /* Mean space between 2 waves */
   double **oldm, **newm, **savm; /* Working pointers to matrices */
    l1 = strlen( path );                 /* length of path */  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 #ifdef windows  FILE *ficlog, *ficrespow;
    s = strrchr( path, '\\' );           /* find last / */  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 #else  FILE *ficresprobmorprev;
    s = strrchr( path, '/' );            /* find last / */  FILE *fichtm; /* Html File */
 #endif  FILE *ficreseij;
    if ( s == NULL ) {                   /* no directory, so use current */  char filerese[FILENAMELENGTH];
 #if     defined(__bsd__)                /* get current working directory */  FILE  *ficresvij;
       extern char       *getwd( );  char fileresv[FILENAMELENGTH];
   FILE  *ficresvpl;
       if ( getwd( dirc ) == NULL ) {  char fileresvpl[FILENAMELENGTH];
 #else  char title[MAXLINE];
       extern char       *getcwd( );  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
          return( GLOCK_ERROR_GETCWD );  char filelog[FILENAMELENGTH]; /* Log file */
       }  char filerest[FILENAMELENGTH];
       strcpy( name, path );             /* we've got it */  char fileregp[FILENAMELENGTH];
    } else {                             /* strip direcotry from path */  char popfile[FILENAMELENGTH];
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */  #define NR_END 1
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  #define FREE_ARG char*
       dirc[l1-l2] = 0;                  /* add zero */  #define FTOL 1.0e-10
    }  
    l1 = strlen( dirc );                 /* length of directory */  #define NRANSI 
 #ifdef windows  #define ITMAX 200 
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else  #define TOL 2.0e-4 
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif  #define CGOLD 0.3819660 
    s = strrchr( name, '.' );            /* find last / */  #define ZEPS 1.0e-10 
    s++;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
    strcpy(ext,s);                       /* save extension */  
    l1= strlen( name);  #define GOLD 1.618034 
    l2= strlen( s)+1;  #define GLIMIT 100.0 
    strncpy( finame, name, l1-l2);  #define TINY 1.0e-20 
    finame[l1-l2]= 0;  
    return( 0 );                         /* we're done */  static double maxarg1,maxarg2;
 }  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     
 /******************************************/  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   #define rint(a) floor(a+0.5)
 void replace(char *s, char*t)  
 {  static double sqrarg;
   int i;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   int lg=20;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   i=0;  
   lg=strlen(t);  int imx; 
   for(i=0; i<= lg; i++) {  int stepm;
     (s[i] = t[i]);  /* Stepm, step in month: minimum step interpolation*/
     if (t[i]== '\\') s[i]='/';  
   }  int estepm;
 }  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   
 int nbocc(char *s, char occ)  int m,nb;
 {  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
   int i,j=0;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   int lg=20;  double **pmmij, ***probs;
   i=0;  double dateintmean=0;
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {  double *weight;
   if  (s[i] == occ ) j++;  int **s; /* Status */
   }  double *agedc, **covar, idx;
   return j;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 }  
   double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 void cutv(char *u,char *v, char*t, char occ)  double ftolhess; /* Tolerance for computing hessian */
 {  
   int i,lg,j,p=0;  /**************** split *************************/
   i=0;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   for(j=0; j<=strlen(t)-1; j++) {  {
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    char  *ss;                            /* pointer */
   }    int   l1, l2;                         /* length counters */
   
   lg=strlen(t);    l1 = strlen(path );                   /* length of path */
   for(j=0; j<p; j++) {    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     (u[j] = t[j]);    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   }    if ( ss == NULL ) {                   /* no directory, so use current */
      u[p]='\0';      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
         printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
    for(j=0; j<= lg; j++) {      /* get current working directory */
     if (j>=(p+1))(v[j-p-1] = t[j]);      /*    extern  char* getcwd ( char *buf , int len);*/
   }      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 }        return( GLOCK_ERROR_GETCWD );
       }
 /********************** nrerror ********************/      strcpy( name, path );               /* we've got it */
     } else {                              /* strip direcotry from path */
 void nrerror(char error_text[])      ss++;                               /* after this, the filename */
 {      l2 = strlen( ss );                  /* length of filename */
   fprintf(stderr,"ERREUR ...\n");      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   fprintf(stderr,"%s\n",error_text);      strcpy( name, ss );         /* save file name */
   exit(1);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
 }      dirc[l1-l2] = 0;                    /* add zero */
 /*********************** vector *******************/    }
 double *vector(int nl, int nh)    l1 = strlen( dirc );                  /* length of directory */
 {  #ifdef windows
   double *v;    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  #else
   if (!v) nrerror("allocation failure in vector");    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   return v-nl+NR_END;  #endif
 }    ss = strrchr( name, '.' );            /* find last / */
     ss++;
 /************************ free vector ******************/    strcpy(ext,ss);                       /* save extension */
 void free_vector(double*v, int nl, int nh)    l1= strlen( name);
 {    l2= strlen(ss)+1;
   free((FREE_ARG)(v+nl-NR_END));    strncpy( finame, name, l1-l2);
 }    finame[l1-l2]= 0;
     return( 0 );                          /* we're done */
 /************************ivector *******************************/  }
 int *ivector(long nl,long nh)  
 {  
   int *v;  /******************************************/
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");  void replace(char *s, char*t)
   return v-nl+NR_END;  {
 }    int i;
     int lg=20;
 /******************free ivector **************************/    i=0;
 void free_ivector(int *v, long nl, long nh)    lg=strlen(t);
 {    for(i=0; i<= lg; i++) {
   free((FREE_ARG)(v+nl-NR_END));      (s[i] = t[i]);
 }      if (t[i]== '\\') s[i]='/';
     }
 /******************* imatrix *******************************/  }
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  int nbocc(char *s, char occ)
 {  {
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    int i,j=0;
   int **m;    int lg=20;
      i=0;
   /* allocate pointers to rows */    lg=strlen(s);
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    for(i=0; i<= lg; i++) {
   if (!m) nrerror("allocation failure 1 in matrix()");    if  (s[i] == occ ) j++;
   m += NR_END;    }
   m -= nrl;    return j;
    }
    
   /* allocate rows and set pointers to them */  void cutv(char *u,char *v, char*t, char occ)
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  {
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    /* cuts string t into u and v where u is ended by char occ excluding it
   m[nrl] += NR_END;       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   m[nrl] -= ncl;       gives u="abcedf" and v="ghi2j" */
      int i,lg,j,p=0;
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    i=0;
      for(j=0; j<=strlen(t)-1; j++) {
   /* return pointer to array of pointers to rows */      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   return m;    }
 }  
     lg=strlen(t);
 /****************** free_imatrix *************************/    for(j=0; j<p; j++) {
 void free_imatrix(m,nrl,nrh,ncl,nch)      (u[j] = t[j]);
       int **m;    }
       long nch,ncl,nrh,nrl;       u[p]='\0';
      /* free an int matrix allocated by imatrix() */  
 {     for(j=0; j<= lg; j++) {
   free((FREE_ARG) (m[nrl]+ncl-NR_END));      if (j>=(p+1))(v[j-p-1] = t[j]);
   free((FREE_ARG) (m+nrl-NR_END));    }
 }  }
   
 /******************* matrix *******************************/  /********************** nrerror ********************/
 double **matrix(long nrl, long nrh, long ncl, long nch)  
 {  void nrerror(char error_text[])
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  {
   double **m;    fprintf(stderr,"ERREUR ...\n");
     fprintf(stderr,"%s\n",error_text);
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    exit(EXIT_FAILURE);
   if (!m) nrerror("allocation failure 1 in matrix()");  }
   m += NR_END;  /*********************** vector *******************/
   m -= nrl;  double *vector(int nl, int nh)
   {
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    double *v;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   m[nrl] += NR_END;    if (!v) nrerror("allocation failure in vector");
   m[nrl] -= ncl;    return v-nl+NR_END;
   }
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;  /************************ free vector ******************/
 }  void free_vector(double*v, int nl, int nh)
   {
 /*************************free matrix ************************/    free((FREE_ARG)(v+nl-NR_END));
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  }
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  /************************ivector *******************************/
   free((FREE_ARG)(m+nrl-NR_END));  char *cvector(long nl,long nh)
 }  {
     char *v;
 /******************* ma3x *******************************/    v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    if (!v) nrerror("allocation failure in cvector");
 {    return v-nl+NR_END;
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  }
   double ***m;  
   /******************free ivector **************************/
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  void free_cvector(char *v, long nl, long nh)
   if (!m) nrerror("allocation failure 1 in matrix()");  {
   m += NR_END;    free((FREE_ARG)(v+nl-NR_END));
   m -= nrl;  }
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  /************************ivector *******************************/
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int *ivector(long nl,long nh)
   m[nrl] += NR_END;  {
   m[nrl] -= ncl;    int *v;
     v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    if (!v) nrerror("allocation failure in ivector");
     return v-nl+NR_END;
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  }
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;  /******************free ivector **************************/
   m[nrl][ncl] -= nll;  void free_ivector(int *v, long nl, long nh)
   for (j=ncl+1; j<=nch; j++)  {
     m[nrl][j]=m[nrl][j-1]+nlay;    free((FREE_ARG)(v+nl-NR_END));
    }
   for (i=nrl+1; i<=nrh; i++) {  
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  /******************* imatrix *******************************/
     for (j=ncl+1; j<=nch; j++)  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       m[i][j]=m[i][j-1]+nlay;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   }  { 
   return m;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
 }    int **m; 
     
 /*************************free ma3x ************************/    /* allocate pointers to rows */ 
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 {    if (!m) nrerror("allocation failure 1 in matrix()"); 
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    m += NR_END; 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    m -= nrl; 
   free((FREE_ARG)(m+nrl-NR_END));    
 }    
     /* allocate rows and set pointers to them */ 
 /***************** f1dim *************************/    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
 extern int ncom;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
 extern double *pcom,*xicom;    m[nrl] += NR_END; 
 extern double (*nrfunc)(double []);    m[nrl] -= ncl; 
      
 double f1dim(double x)    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
 {    
   int j;    /* return pointer to array of pointers to rows */ 
   double f;    return m; 
   double *xt;  } 
    
   xt=vector(1,ncom);  /****************** free_imatrix *************************/
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  void free_imatrix(m,nrl,nrh,ncl,nch)
   f=(*nrfunc)(xt);        int **m;
   free_vector(xt,1,ncom);        long nch,ncl,nrh,nrl; 
   return f;       /* free an int matrix allocated by imatrix() */ 
 }  { 
     free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 /*****************brent *************************/    free((FREE_ARG) (m+nrl-NR_END)); 
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  } 
 {  
   int iter;  /******************* matrix *******************************/
   double a,b,d,etemp;  double **matrix(long nrl, long nrh, long ncl, long nch)
   double fu,fv,fw,fx;  {
   double ftemp;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   double p,q,r,tol1,tol2,u,v,w,x,xm;    double **m;
   double e=0.0;  
      m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   a=(ax < cx ? ax : cx);    if (!m) nrerror("allocation failure 1 in matrix()");
   b=(ax > cx ? ax : cx);    m += NR_END;
   x=w=v=bx;    m -= nrl;
   fw=fv=fx=(*f)(x);  
   for (iter=1;iter<=ITMAX;iter++) {    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     xm=0.5*(a+b);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    m[nrl] += NR_END;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    m[nrl] -= ncl;
     printf(".");fflush(stdout);  
 #ifdef DEBUG    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     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);    return m;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
 #endif     */
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  }
       *xmin=x;  
       return fx;  /*************************free matrix ************************/
     }  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     ftemp=fu;  {
     if (fabs(e) > tol1) {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       r=(x-w)*(fx-fv);    free((FREE_ARG)(m+nrl-NR_END));
       q=(x-v)*(fx-fw);  }
       p=(x-v)*q-(x-w)*r;  
       q=2.0*(q-r);  /******************* ma3x *******************************/
       if (q > 0.0) p = -p;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       q=fabs(q);  {
       etemp=e;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       e=d;    double ***m;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       else {    if (!m) nrerror("allocation failure 1 in matrix()");
         d=p/q;    m += NR_END;
         u=x+d;    m -= nrl;
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     } else {    m[nrl] += NR_END;
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    m[nrl] -= ncl;
     }  
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     fu=(*f)(u);  
     if (fu <= fx) {    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       if (u >= x) a=x; else b=x;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       SHFT(v,w,x,u)    m[nrl][ncl] += NR_END;
         SHFT(fv,fw,fx,fu)    m[nrl][ncl] -= nll;
         } else {    for (j=ncl+1; j<=nch; j++) 
           if (u < x) a=u; else b=u;      m[nrl][j]=m[nrl][j-1]+nlay;
           if (fu <= fw || w == x) {    
             v=w;    for (i=nrl+1; i<=nrh; i++) {
             w=u;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
             fv=fw;      for (j=ncl+1; j<=nch; j++) 
             fw=fu;        m[i][j]=m[i][j-1]+nlay;
           } else if (fu <= fv || v == x || v == w) {    }
             v=u;    return m; 
             fv=fu;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
           }             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
         }    */
   }  }
   nrerror("Too many iterations in brent");  
   *xmin=x;  /*************************free ma3x ************************/
   return fx;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 }  {
     free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
 /****************** mnbrak ***********************/    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  }
             double (*func)(double))  
 {  /***************** f1dim *************************/
   double ulim,u,r,q, dum;  extern int ncom; 
   double fu;  extern double *pcom,*xicom;
    extern double (*nrfunc)(double []); 
   *fa=(*func)(*ax);   
   *fb=(*func)(*bx);  double f1dim(double x) 
   if (*fb > *fa) {  { 
     SHFT(dum,*ax,*bx,dum)    int j; 
       SHFT(dum,*fb,*fa,dum)    double f;
       }    double *xt; 
   *cx=(*bx)+GOLD*(*bx-*ax);   
   *fc=(*func)(*cx);    xt=vector(1,ncom); 
   while (*fb > *fc) {    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     r=(*bx-*ax)*(*fb-*fc);    f=(*nrfunc)(xt); 
     q=(*bx-*cx)*(*fb-*fa);    free_vector(xt,1,ncom); 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    return f; 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  } 
     ulim=(*bx)+GLIMIT*(*cx-*bx);  
     if ((*bx-u)*(u-*cx) > 0.0) {  /*****************brent *************************/
       fu=(*func)(u);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     } else if ((*cx-u)*(u-ulim) > 0.0) {  { 
       fu=(*func)(u);    int iter; 
       if (fu < *fc) {    double a,b,d,etemp;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    double fu,fv,fw,fx;
           SHFT(*fb,*fc,fu,(*func)(u))    double ftemp;
           }    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    double e=0.0; 
       u=ulim;   
       fu=(*func)(u);    a=(ax < cx ? ax : cx); 
     } else {    b=(ax > cx ? ax : cx); 
       u=(*cx)+GOLD*(*cx-*bx);    x=w=v=bx; 
       fu=(*func)(u);    fw=fv=fx=(*f)(x); 
     }    for (iter=1;iter<=ITMAX;iter++) { 
     SHFT(*ax,*bx,*cx,u)      xm=0.5*(a+b); 
       SHFT(*fa,*fb,*fc,fu)      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       }      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
 }      printf(".");fflush(stdout);
       fprintf(ficlog,".");fflush(ficlog);
 /*************** linmin ************************/  #ifdef DEBUG
       printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
 int ncom;      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);
 double *pcom,*xicom;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
 double (*nrfunc)(double []);  #endif
        if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))        *xmin=x; 
 {        return fx; 
   double brent(double ax, double bx, double cx,      } 
                double (*f)(double), double tol, double *xmin);      ftemp=fu;
   double f1dim(double x);      if (fabs(e) > tol1) { 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,        r=(x-w)*(fx-fv); 
               double *fc, double (*func)(double));        q=(x-v)*(fx-fw); 
   int j;        p=(x-v)*q-(x-w)*r; 
   double xx,xmin,bx,ax;        q=2.0*(q-r); 
   double fx,fb,fa;        if (q > 0.0) p = -p; 
          q=fabs(q); 
   ncom=n;        etemp=e; 
   pcom=vector(1,n);        e=d; 
   xicom=vector(1,n);        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   nrfunc=func;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   for (j=1;j<=n;j++) {        else { 
     pcom[j]=p[j];          d=p/q; 
     xicom[j]=xi[j];          u=x+d; 
   }          if (u-a < tol2 || b-u < tol2) 
   ax=0.0;            d=SIGN(tol1,xm-x); 
   xx=1.0;        } 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);      } else { 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 #ifdef DEBUG      } 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
 #endif      fu=(*f)(u); 
   for (j=1;j<=n;j++) {      if (fu <= fx) { 
     xi[j] *= xmin;        if (u >= x) a=x; else b=x; 
     p[j] += xi[j];        SHFT(v,w,x,u) 
   }          SHFT(fv,fw,fx,fu) 
   free_vector(xicom,1,n);          } else { 
   free_vector(pcom,1,n);            if (u < x) a=u; else b=u; 
 }            if (fu <= fw || w == x) { 
               v=w; 
 /*************** powell ************************/              w=u; 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,              fv=fw; 
             double (*func)(double []))              fw=fu; 
 {            } else if (fu <= fv || v == x || v == w) { 
   void linmin(double p[], double xi[], int n, double *fret,              v=u; 
               double (*func)(double []));              fv=fu; 
   int i,ibig,j;            } 
   double del,t,*pt,*ptt,*xit;          } 
   double fp,fptt;    } 
   double *xits;    nrerror("Too many iterations in brent"); 
   pt=vector(1,n);    *xmin=x; 
   ptt=vector(1,n);    return fx; 
   xit=vector(1,n);  } 
   xits=vector(1,n);  
   *fret=(*func)(p);  /****************** mnbrak ***********************/
   for (j=1;j<=n;j++) pt[j]=p[j];  
   for (*iter=1;;++(*iter)) {  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     fp=(*fret);              double (*func)(double)) 
     ibig=0;  { 
     del=0.0;    double ulim,u,r,q, dum;
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    double fu; 
     for (i=1;i<=n;i++)   
       printf(" %d %.12f",i, p[i]);    *fa=(*func)(*ax); 
     printf("\n");    *fb=(*func)(*bx); 
     for (i=1;i<=n;i++) {    if (*fb > *fa) { 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];      SHFT(dum,*ax,*bx,dum) 
       fptt=(*fret);        SHFT(dum,*fb,*fa,dum) 
 #ifdef DEBUG        } 
       printf("fret=%lf \n",*fret);    *cx=(*bx)+GOLD*(*bx-*ax); 
 #endif    *fc=(*func)(*cx); 
       printf("%d",i);fflush(stdout);    while (*fb > *fc) { 
       linmin(p,xit,n,fret,func);      r=(*bx-*ax)*(*fb-*fc); 
       if (fabs(fptt-(*fret)) > del) {      q=(*bx-*cx)*(*fb-*fa); 
         del=fabs(fptt-(*fret));      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         ibig=i;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       }      ulim=(*bx)+GLIMIT*(*cx-*bx); 
 #ifdef DEBUG      if ((*bx-u)*(u-*cx) > 0.0) { 
       printf("%d %.12e",i,(*fret));        fu=(*func)(u); 
       for (j=1;j<=n;j++) {      } else if ((*cx-u)*(u-ulim) > 0.0) { 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);        fu=(*func)(u); 
         printf(" x(%d)=%.12e",j,xit[j]);        if (fu < *fc) { 
       }          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       for(j=1;j<=n;j++)            SHFT(*fb,*fc,fu,(*func)(u)) 
         printf(" p=%.12e",p[j]);            } 
       printf("\n");      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
 #endif        u=ulim; 
     }        fu=(*func)(u); 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      } else { 
 #ifdef DEBUG        u=(*cx)+GOLD*(*cx-*bx); 
       int k[2],l;        fu=(*func)(u); 
       k[0]=1;      } 
       k[1]=-1;      SHFT(*ax,*bx,*cx,u) 
       printf("Max: %.12e",(*func)(p));        SHFT(*fa,*fb,*fc,fu) 
       for (j=1;j<=n;j++)        } 
         printf(" %.12e",p[j]);  } 
       printf("\n");  
       for(l=0;l<=1;l++) {  /*************** linmin ************************/
         for (j=1;j<=n;j++) {  
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  int ncom; 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  double *pcom,*xicom;
         }  double (*nrfunc)(double []); 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));   
       }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
 #endif  { 
     double brent(double ax, double bx, double cx, 
                  double (*f)(double), double tol, double *xmin); 
       free_vector(xit,1,n);    double f1dim(double x); 
       free_vector(xits,1,n);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       free_vector(ptt,1,n);                double *fc, double (*func)(double)); 
       free_vector(pt,1,n);    int j; 
       return;    double xx,xmin,bx,ax; 
     }    double fx,fb,fa;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");   
     for (j=1;j<=n;j++) {    ncom=n; 
       ptt[j]=2.0*p[j]-pt[j];    pcom=vector(1,n); 
       xit[j]=p[j]-pt[j];    xicom=vector(1,n); 
       pt[j]=p[j];    nrfunc=func; 
     }    for (j=1;j<=n;j++) { 
     fptt=(*func)(ptt);      pcom[j]=p[j]; 
     if (fptt < fp) {      xicom[j]=xi[j]; 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    } 
       if (t < 0.0) {    ax=0.0; 
         linmin(p,xit,n,fret,func);    xx=1.0; 
         for (j=1;j<=n;j++) {    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
           xi[j][ibig]=xi[j][n];    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
           xi[j][n]=xit[j];  #ifdef DEBUG
         }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 #ifdef DEBUG    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  #endif
         for(j=1;j<=n;j++)    for (j=1;j<=n;j++) { 
           printf(" %.12e",xit[j]);      xi[j] *= xmin; 
         printf("\n");      p[j] += xi[j]; 
 #endif    } 
       }    free_vector(xicom,1,n); 
     }    free_vector(pcom,1,n); 
   }  } 
 }  
   /*************** powell ************************/
 /**** Prevalence limit ****************/  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
               double (*func)(double [])) 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  { 
 {    void linmin(double p[], double xi[], int n, double *fret, 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit                double (*func)(double [])); 
      matrix by transitions matrix until convergence is reached */    int i,ibig,j; 
     double del,t,*pt,*ptt,*xit;
   int i, ii,j,k;    double fp,fptt;
   double min, max, maxmin, maxmax,sumnew=0.;    double *xits;
   double **matprod2();    pt=vector(1,n); 
   double **out, cov[NCOVMAX], **pmij();    ptt=vector(1,n); 
   double **newm;    xit=vector(1,n); 
   double agefin, delaymax=50 ; /* Max number of years to converge */    xits=vector(1,n); 
     *fret=(*func)(p); 
   for (ii=1;ii<=nlstate+ndeath;ii++)    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for (j=1;j<=nlstate+ndeath;j++){    for (*iter=1;;++(*iter)) { 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      fp=(*fret); 
     }      ibig=0; 
       del=0.0; 
    cov[1]=1.;      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
        fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      fprintf(ficrespow,"%d %.12f",*iter,*fret);
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){      for (i=1;i<=n;i++) {
     newm=savm;        printf(" %d %.12f",i, p[i]);
     /* Covariates have to be included here again */        fprintf(ficlog," %d %.12lf",i, p[i]);
      cov[2]=agefin;        fprintf(ficrespow," %.12lf", p[i]);
        }
       for (k=1; k<=cptcovn;k++) {      printf("\n");
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      fprintf(ficlog,"\n");
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/      fprintf(ficrespow,"\n");
       }      for (i=1;i<=n;i++) { 
       for (k=1; k<=cptcovage;k++)        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        fptt=(*fret); 
       for (k=1; k<=cptcovprod;k++)  #ifdef DEBUG
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        printf("fret=%lf \n",*fret);
         fprintf(ficlog,"fret=%lf \n",*fret);
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  #endif
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/        printf("%d",i);fflush(stdout);
         fprintf(ficlog,"%d",i);fflush(ficlog);
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
     savm=oldm;          del=fabs(fptt-(*fret)); 
     oldm=newm;          ibig=i; 
     maxmax=0.;        } 
     for(j=1;j<=nlstate;j++){  #ifdef DEBUG
       min=1.;        printf("%d %.12e",i,(*fret));
       max=0.;        fprintf(ficlog,"%d %.12e",i,(*fret));
       for(i=1; i<=nlstate; i++) {        for (j=1;j<=n;j++) {
         sumnew=0;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];          printf(" x(%d)=%.12e",j,xit[j]);
         prlim[i][j]= newm[i][j]/(1-sumnew);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         max=FMAX(max,prlim[i][j]);        }
         min=FMIN(min,prlim[i][j]);        for(j=1;j<=n;j++) {
       }          printf(" p=%.12e",p[j]);
       maxmin=max-min;          fprintf(ficlog," p=%.12e",p[j]);
       maxmax=FMAX(maxmax,maxmin);        }
     }        printf("\n");
     if(maxmax < ftolpl){        fprintf(ficlog,"\n");
       return prlim;  #endif
     }      } 
   }      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
 }  #ifdef DEBUG
         int k[2],l;
 /*************** transition probabilities ***************/        k[0]=1;
         k[1]=-1;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )        printf("Max: %.12e",(*func)(p));
 {        fprintf(ficlog,"Max: %.12e",(*func)(p));
   double s1, s2;        for (j=1;j<=n;j++) {
   /*double t34;*/          printf(" %.12e",p[j]);
   int i,j,j1, nc, ii, jj;          fprintf(ficlog," %.12e",p[j]);
         }
     for(i=1; i<= nlstate; i++){        printf("\n");
     for(j=1; j<i;j++){        fprintf(ficlog,"\n");
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        for(l=0;l<=1;l++) {
         /*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];            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       }            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       ps[i][j]=s2;          }
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     }          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     for(j=i+1; j<=nlstate+ndeath;j++){        }
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  #endif
         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);*/  
       }        free_vector(xit,1,n); 
       ps[i][j]=s2;        free_vector(xits,1,n); 
     }        free_vector(ptt,1,n); 
   }        free_vector(pt,1,n); 
     /*ps[3][2]=1;*/        return; 
       } 
   for(i=1; i<= nlstate; i++){      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
      s1=0;      for (j=1;j<=n;j++) { 
     for(j=1; j<i; j++)        ptt[j]=2.0*p[j]-pt[j]; 
       s1+=exp(ps[i][j]);        xit[j]=p[j]-pt[j]; 
     for(j=i+1; j<=nlstate+ndeath; j++)        pt[j]=p[j]; 
       s1+=exp(ps[i][j]);      } 
     ps[i][i]=1./(s1+1.);      fptt=(*func)(ptt); 
     for(j=1; j<i; j++)      if (fptt < fp) { 
       ps[i][j]= exp(ps[i][j])*ps[i][i];        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     for(j=i+1; j<=nlstate+ndeath; j++)        if (t < 0.0) { 
       ps[i][j]= exp(ps[i][j])*ps[i][i];          linmin(p,xit,n,fret,func); 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */          for (j=1;j<=n;j++) { 
   } /* end i */            xi[j][ibig]=xi[j][n]; 
             xi[j][n]=xit[j]; 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){          }
     for(jj=1; jj<= nlstate+ndeath; jj++){  #ifdef DEBUG
       ps[ii][jj]=0;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       ps[ii][ii]=1;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     }          for(j=1;j<=n;j++){
   }            printf(" %.12e",xit[j]);
             fprintf(ficlog," %.12e",xit[j]);
           }
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){          printf("\n");
     for(jj=1; jj<= nlstate+ndeath; jj++){          fprintf(ficlog,"\n");
      printf("%lf ",ps[ii][jj]);  #endif
    }        }
     printf("\n ");      } 
     }    } 
     printf("\n ");printf("%lf ",cov[2]);*/  } 
 /*  
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  /**** Prevalence limit (stable prevalence)  ****************/
   goto end;*/  
     return ps;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
 }  {
     /* Computes the prevalence limit in each live state at age x by left multiplying the unit
 /**************** Product of 2 matrices ******************/       matrix by transitions matrix until convergence is reached */
   
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    int i, ii,j,k;
 {    double min, max, maxmin, maxmax,sumnew=0.;
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    double **matprod2();
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    double **out, cov[NCOVMAX], **pmij();
   /* in, b, out are matrice of pointers which should have been initialized    double **newm;
      before: only the contents of out is modified. The function returns    double agefin, delaymax=50 ; /* Max number of years to converge */
      a pointer to pointers identical to out */  
   long i, j, k;    for (ii=1;ii<=nlstate+ndeath;ii++)
   for(i=nrl; i<= nrh; i++)      for (j=1;j<=nlstate+ndeath;j++){
     for(k=ncolol; k<=ncoloh; k++)        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      }
         out[i][k] +=in[i][j]*b[j][k];  
      cov[1]=1.;
   return out;   
 }   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       newm=savm;
 /************* Higher Matrix Product ***************/      /* Covariates have to be included here again */
        cov[2]=agefin;
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    
 {        for (k=1; k<=cptcovn;k++) {
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
      duration (i.e. until          /*      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]]);*/
      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        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
      (typically every 2 years instead of every month which is too big).        for (k=1; k<=cptcovprod;k++)
      Model is determined by parameters x and covariates have to be          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
      included manually here.  
         /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
      */        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
         /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   int i, j, d, h, k;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   double **out, cov[NCOVMAX];  
   double **newm;      savm=oldm;
       oldm=newm;
   /* Hstepm could be zero and should return the unit matrix */      maxmax=0.;
   for (i=1;i<=nlstate+ndeath;i++)      for(j=1;j<=nlstate;j++){
     for (j=1;j<=nlstate+ndeath;j++){        min=1.;
       oldm[i][j]=(i==j ? 1.0 : 0.0);        max=0.;
       po[i][j][0]=(i==j ? 1.0 : 0.0);        for(i=1; i<=nlstate; i++) {
     }          sumnew=0;
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   for(h=1; h <=nhstepm; h++){          prlim[i][j]= newm[i][j]/(1-sumnew);
     for(d=1; d <=hstepm; d++){          max=FMAX(max,prlim[i][j]);
       newm=savm;          min=FMIN(min,prlim[i][j]);
       /* Covariates have to be included here again */        }
       cov[1]=1.;        maxmin=max-min;
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        maxmax=FMAX(maxmax,maxmin);
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      }
       for (k=1; k<=cptcovage;k++)      if(maxmax < ftolpl){
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        return prlim;
       for (k=1; k<=cptcovprod;k++)      }
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    }
   }
   
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  /*************** transition probabilities ***************/ 
       /*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,  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  {
       savm=oldm;    double s1, s2;
       oldm=newm;    /*double t34;*/
     }    int i,j,j1, nc, ii, jj;
     for(i=1; i<=nlstate+ndeath; i++)  
       for(j=1;j<=nlstate+ndeath;j++) {      for(i=1; i<= nlstate; i++){
         po[i][j][h]=newm[i][j];      for(j=1; j<i;j++){
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
          */          /*s2 += param[i][j][nc]*cov[nc];*/
       }          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   } /* end h */          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
   return po;        }
 }        ps[i][j]=s2;
         /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
       }
 /*************** log-likelihood *************/      for(j=i+1; j<=nlstate+ndeath;j++){
 double func( double *x)        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];
   int i, ii, j, k, mi, d, kk;          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        }
   double **out;        ps[i][j]=s2;
   double sw; /* Sum of weights */      }
   double lli; /* Individual log likelihood */    }
   long ipmx;      /*ps[3][2]=1;*/
   /*extern weight */  
   /* We are differentiating ll according to initial status */    for(i=1; i<= nlstate; i++){
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/       s1=0;
   /*for(i=1;i<imx;i++)      for(j=1; j<i; j++)
     printf(" %d\n",s[4][i]);        s1+=exp(ps[i][j]);
   */      for(j=i+1; j<=nlstate+ndeath; j++)
   cov[1]=1.;        s1+=exp(ps[i][j]);
       ps[i][i]=1./(s1+1.);
   for(k=1; k<=nlstate; k++) ll[k]=0.;      for(j=1; j<i; j++)
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        ps[i][j]= exp(ps[i][j])*ps[i][i];
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      for(j=i+1; j<=nlstate+ndeath; j++)
     for(mi=1; mi<= wav[i]-1; mi++){        ps[i][j]= exp(ps[i][j])*ps[i][i];
       for (ii=1;ii<=nlstate+ndeath;ii++)      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    } /* end i */
       for(d=0; d<dh[mi][i]; d++){  
         newm=savm;    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      for(jj=1; jj<= nlstate+ndeath; jj++){
         for (kk=1; kk<=cptcovage;kk++) {        ps[ii][jj]=0;
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        ps[ii][ii]=1;
         }      }
            }
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  
         savm=oldm;    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
         oldm=newm;      for(jj=1; jj<= nlstate+ndeath; jj++){
               printf("%lf ",ps[ii][jj]);
             }
       } /* end mult */      printf("\n ");
            }
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);      printf("\n ");printf("%lf ",cov[2]);*/
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  /*
       ipmx +=1;    for(i=1; i<= npar; i++) printf("%f ",x[i]);
       sw += weight[i];    goto end;*/
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;      return ps;
     } /* end of wave */  }
   } /* end of individual */  
   /**************** Product of 2 matrices ******************/
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  {
   return -l;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
 }       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     /* in, b, out are matrice of pointers which should have been initialized 
        before: only the contents of out is modified. The function returns
 /*********** Maximum Likelihood Estimation ***************/       a pointer to pointers identical to out */
     long i, j, k;
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    for(i=nrl; i<= nrh; i++)
 {      for(k=ncolol; k<=ncoloh; k++)
   int i,j, iter;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   double **xi,*delti;          out[i][k] +=in[i][j]*b[j][k];
   double fret;  
   xi=matrix(1,npar,1,npar);    return out;
   for (i=1;i<=npar;i++)  }
     for (j=1;j<=npar;j++)  
       xi[i][j]=(i==j ? 1.0 : 0.0);  
   printf("Powell\n");  /************* Higher Matrix Product ***************/
   powell(p,xi,npar,ftol,&iter,&fret,func);  
   double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
    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));    /* 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 
        nhstepm*hstepm matrices. 
 /**** Computes Hessian and covariance matrix ***/       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))       (typically every 2 years instead of every month which is too big 
 {       for the memory).
   double  **a,**y,*x,pd;       Model is determined by parameters x and covariates have to be 
   double **hess;       included manually here. 
   int i, j,jk;  
   int *indx;       */
   
   double hessii(double p[], double delta, int theta, double delti[]);    int i, j, d, h, k;
   double hessij(double p[], double delti[], int i, int j);    double **out, cov[NCOVMAX];
   void lubksb(double **a, int npar, int *indx, double b[]) ;    double **newm;
   void ludcmp(double **a, int npar, int *indx, double *d) ;  
     /* Hstepm could be zero and should return the unit matrix */
   hess=matrix(1,npar,1,npar);    for (i=1;i<=nlstate+ndeath;i++)
       for (j=1;j<=nlstate+ndeath;j++){
   printf("\nCalculation of the hessian matrix. Wait...\n");        oldm[i][j]=(i==j ? 1.0 : 0.0);
   for (i=1;i<=npar;i++){        po[i][j][0]=(i==j ? 1.0 : 0.0);
     printf("%d",i);fflush(stdout);      }
     hess[i][i]=hessii(p,ftolhess,i,delti);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     /*printf(" %f ",p[i]);*/    for(h=1; h <=nhstepm; h++){
     /*printf(" %lf ",hess[i][i]);*/      for(d=1; d <=hstepm; d++){
   }        newm=savm;
          /* Covariates have to be included here again */
   for (i=1;i<=npar;i++) {        cov[1]=1.;
     for (j=1;j<=npar;j++)  {        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       if (j>i) {        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         printf(".%d%d",i,j);fflush(stdout);        for (k=1; k<=cptcovage;k++)
         hess[i][j]=hessij(p,delti,i,j);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         hess[j][i]=hess[i][j];            for (k=1; k<=cptcovprod;k++)
         /*printf(" %lf ",hess[i][j]);*/          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       }  
     }  
   }        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   printf("\n");        /*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, 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");                     pmij(pmmij,cov,ncovmodel,x,nlstate));
          savm=oldm;
   a=matrix(1,npar,1,npar);        oldm=newm;
   y=matrix(1,npar,1,npar);      }
   x=vector(1,npar);      for(i=1; i<=nlstate+ndeath; i++)
   indx=ivector(1,npar);        for(j=1;j<=nlstate+ndeath;j++) {
   for (i=1;i<=npar;i++)          po[i][j][h]=newm[i][j];
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
   ludcmp(a,npar,indx,&pd);           */
         }
   for (j=1;j<=npar;j++) {    } /* end h */
     for (i=1;i<=npar;i++) x[i]=0;    return po;
     x[j]=1;  }
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){  
       matcov[i][j]=x[i];  /*************** log-likelihood *************/
     }  double func( double *x)
   }  {
     int i, ii, j, k, mi, d, kk;
   printf("\n#Hessian matrix#\n");    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   for (i=1;i<=npar;i++) {    double **out;
     for (j=1;j<=npar;j++) {    double sw; /* Sum of weights */
       printf("%.3e ",hess[i][j]);    double lli; /* Individual log likelihood */
     }    int s1, s2;
     printf("\n");    double bbh, survp;
   }    long ipmx;
     /*extern weight */
   /* Recompute Inverse */    /* We are differentiating ll according to initial status */
   for (i=1;i<=npar;i++)    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    /*for(i=1;i<imx;i++) 
   ludcmp(a,npar,indx,&pd);      printf(" %d\n",s[4][i]);
     */
   /*  printf("\n#Hessian matrix recomputed#\n");    cov[1]=1.;
   
   for (j=1;j<=npar;j++) {    for(k=1; k<=nlstate; k++) ll[k]=0.;
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;    if(mle==1){
     lubksb(a,npar,indx,x);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for (i=1;i<=npar;i++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       y[i][j]=x[i];        for(mi=1; mi<= wav[i]-1; mi++){
       printf("%.3e ",y[i][j]);          for (ii=1;ii<=nlstate+ndeath;ii++)
     }            for (j=1;j<=nlstate+ndeath;j++){
     printf("\n");              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++){
   free_matrix(a,1,npar,1,npar);            newm=savm;
   free_matrix(y,1,npar,1,npar);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   free_vector(x,1,npar);            for (kk=1; kk<=cptcovage;kk++) {
   free_ivector(indx,1,npar);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   free_matrix(hess,1,npar,1,npar);            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 }            savm=oldm;
             oldm=newm;
 /*************** hessian matrix ****************/          } /* end mult */
 double hessii( double x[], double delta, int theta, double delti[])        
 {          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   int i;          /* But now since version 0.9 we anticipate for bias and large stepm.
   int l=1, lmax=20;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   double k1,k2;           * (in months) between two waves is not a multiple of stepm, we rounded to 
   double p2[NPARMAX+1];           * the nearest (and in case of equal distance, to the lowest) interval but now
   double res;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   double fx;           * probability in order to take into account the bias as a fraction of the way
   int k=0,kmax=10;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   double l1;           * -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 (i=1;i<=npar;i++) p2[i]=x[i];           */
   for(l=0 ; l <=lmax; l++){          s1=s[mw[mi][i]][i];
     l1=pow(10,l);          s2=s[mw[mi+1][i]][i];
     delts=delt;          bbh=(double)bh[mi][i]/(double)stepm; 
     for(k=1 ; k <kmax; k=k+1){          /* bias is positive if real duration
       delt = delta*(l1*k);           * is higher than the multiple of stepm and negative otherwise.
       p2[theta]=x[theta] +delt;           */
       k1=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]));*/
       p2[theta]=x[theta]-delt;          if( s2 > nlstate){ 
       k2=func(p2)-fx;            /* i.e. if s2 is a death state and if the date of death is known then the contribution
       /*res= (k1-2.0*fx+k2)/delt/delt; */               to the likelihood is the probability to die between last step unit time and current 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */               step unit time, which is also the differences between probability to die before dh 
                     and probability to die before dh-stepm . 
 #ifdef DEBUG               In version up to 0.92 likelihood was computed
       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);          as if date of death was unknown. Death was treated as any other
 #endif          health state: the date of the interview describes the actual state
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          and not the date of a change in health state. The former idea was
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          to consider that at each interview the state was recorded
         k=kmax;          (healthy, disable or death) and IMaCh was corrected; but when we
       }          introduced the exact date of death then we should have modified
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          the contribution of an exact death to the likelihood. This new
         k=kmax; l=lmax*10.;          contribution is smaller and very dependent of the step unit
       }          stepm. It is no more the probability to die between last interview
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          and month of death but the probability to survive from last
         delts=delt;          interview up to one month before death multiplied by the
       }          probability to die within a month. Thanks to Chris
     }          Jackson for correcting this bug.  Former versions increased
   }          mortality artificially. The bad side is that we add another loop
   delti[theta]=delts;          which slows down the processing. The difference can be up to 10%
   return res;          lower mortality.
              */
 }            lli=log(out[s1][s2] - savm[s1][s2]);
           }else{
 double hessij( double x[], double delti[], int thetai,int thetaj)            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 {            /*  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 */
   int i;          } 
   int l=1, l1, lmax=20;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   double k1,k2,k3,k4,res,fx;          /*if(lli ==000.0)*/
   double p2[NPARMAX+1];          /*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); */
   int k;          ipmx +=1;
           sw += weight[i];
   fx=func(x);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   for (k=1; k<=2; k++) {        } /* end of wave */
     for (i=1;i<=npar;i++) p2[i]=x[i];      } /* end of individual */
     p2[thetai]=x[thetai]+delti[thetai]/k;    }  else if(mle==2){
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     k1=func(p2)-fx;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          for(mi=1; mi<= wav[i]-1; mi++){
     p2[thetai]=x[thetai]+delti[thetai]/k;          for (ii=1;ii<=nlstate+ndeath;ii++)
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;            for (j=1;j<=nlstate+ndeath;j++){
     k2=func(p2)-fx;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                savm[ii][j]=(ii==j ? 1.0 : 0.0);
     p2[thetai]=x[thetai]-delti[thetai]/k;            }
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          for(d=0; d<=dh[mi][i]; d++){
     k3=func(p2)-fx;            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     p2[thetai]=x[thetai]-delti[thetai]/k;            for (kk=1; kk<=cptcovage;kk++) {
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     k4=func(p2)-fx;            }
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 #ifdef DEBUG                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);            savm=oldm;
 #endif            oldm=newm;
   }          } /* 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.
 /************** Inverse of matrix **************/           * If stepm is larger than one month (smallest stepm) and if the exact delay 
 void ludcmp(double **a, int n, int *indx, double *d)           * (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,imax,j,k;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   double big,dum,sum,temp;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   double *vv;           * probability in order to take into account the bias as a fraction of the way
             * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   vv=vector(1,n);           * -stepm/2 to stepm/2 .
   *d=1.0;           * For stepm=1 the results are the same as for previous versions of Imach.
   for (i=1;i<=n;i++) {           * For stepm > 1 the results are less biased than in previous versions. 
     big=0.0;           */
     for (j=1;j<=n;j++)          s1=s[mw[mi][i]][i];
       if ((temp=fabs(a[i][j])) > big) big=temp;          s2=s[mw[mi+1][i]][i];
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          bbh=(double)bh[mi][i]/(double)stepm; 
     vv[i]=1.0/big;          /* bias is positive if real duration
   }           * is higher than the multiple of stepm and negative otherwise.
   for (j=1;j<=n;j++) {           */
     for (i=1;i<j;i++) {          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 */
       sum=a[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]));*/
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];          /*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 */
       a[i][j]=sum;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     }          /*if(lli ==000.0)*/
     big=0.0;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
     for (i=j;i<=n;i++) {          ipmx +=1;
       sum=a[i][j];          sw += weight[i];
       for (k=1;k<j;k++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         sum -= a[i][k]*a[k][j];        } /* end of wave */
       a[i][j]=sum;      } /* end of individual */
       if ( (dum=vv[i]*fabs(sum)) >= big) {    }  else if(mle==3){  /* exponential inter-extrapolation */
         big=dum;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         imax=i;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       }        for(mi=1; mi<= wav[i]-1; mi++){
     }          for (ii=1;ii<=nlstate+ndeath;ii++)
     if (j != imax) {            for (j=1;j<=nlstate+ndeath;j++){
       for (k=1;k<=n;k++) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         dum=a[imax][k];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         a[imax][k]=a[j][k];            }
         a[j][k]=dum;          for(d=0; d<dh[mi][i]; d++){
       }            newm=savm;
       *d = -(*d);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       vv[imax]=vv[j];            for (kk=1; kk<=cptcovage;kk++) {
     }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     indx[j]=imax;            }
     if (a[j][j] == 0.0) a[j][j]=TINY;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     if (j != n) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       dum=1.0/(a[j][j]);            savm=oldm;
       for (i=j+1;i<=n;i++) a[i][j] *= dum;            oldm=newm;
     }          } /* end mult */
   }        
   free_vector(vv,1,n);  /* Doesn't work */          /*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 
            * (in months) between two waves is not a multiple of stepm, we rounded to 
 void lubksb(double **a, int n, int *indx, double b[])           * the nearest (and in case of equal distance, to the lowest) interval but now
 {           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   int i,ii=0,ip,j;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   double sum;           * probability in order to take into account the bias as a fraction of the way
             * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   for (i=1;i<=n;i++) {           * -stepm/2 to stepm/2 .
     ip=indx[i];           * For stepm=1 the results are the same as for previous versions of Imach.
     sum=b[ip];           * For stepm > 1 the results are less biased than in previous versions. 
     b[ip]=b[i];           */
     if (ii)          s1=s[mw[mi][i]][i];
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          s2=s[mw[mi+1][i]][i];
     else if (sum) ii=i;          bbh=(double)bh[mi][i]/(double)stepm; 
     b[i]=sum;          /* bias is positive if real duration
   }           * is higher than the multiple of stepm and negative otherwise.
   for (i=n;i>=1;i--) {           */
     sum=b[i];          /* 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 (j=i+1;j<=n;j++) sum -= a[i][j]*b[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])); /* exponential inter-extrapolation */
     b[i]=sum/a[i][i];          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   }          /*if(lli ==000.0)*/
 }          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
           ipmx +=1;
 /************ Frequencies ********************/          sw += weight[i];
 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)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 {  /* Some frequencies */        } /* end of wave */
        } /* end of individual */
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    }else{  /* ml=4 no inter-extrapolation */
   double ***freq; /* Frequencies */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double *pp;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double pos, k2, dateintsum=0,k2cpt=0;        for(mi=1; mi<= wav[i]-1; mi++){
   FILE *ficresp;          for (ii=1;ii<=nlstate+ndeath;ii++)
   char fileresp[FILENAMELENGTH];            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   pp=vector(1,nlstate);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            }
   strcpy(fileresp,"p");          for(d=0; d<dh[mi][i]; d++){
   strcat(fileresp,fileres);            newm=savm;
   if((ficresp=fopen(fileresp,"w"))==NULL) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     printf("Problem with prevalence resultfile: %s\n", fileresp);            for (kk=1; kk<=cptcovage;kk++) {
     exit(0);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   }            }
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          
   j1=0;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   j=cptcoveff;            savm=oldm;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            oldm=newm;
           } /* end mult */
   for(k1=1; k1<=j;k1++){        
    for(i1=1; i1<=ncodemax[k1];i1++){          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
        j1++;          ipmx +=1;
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);          sw += weight[i];
          scanf("%d", i);*/          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         for (i=-1; i<=nlstate+ndeath; i++)          } /* end of wave */
          for (jk=-1; jk<=nlstate+ndeath; jk++)        } /* end of individual */
            for(m=agemin; m <= agemax+3; m++)    } /* End of if */
              freq[i][jk][m]=0;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         dateintsum=0;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         k2cpt=0;    return -l;
        for (i=1; i<=imx; i++) {  }
          bool=1;  
          if  (cptcovn>0) {  
            for (z1=1; z1<=cptcoveff; z1++)  /*********** Maximum Likelihood Estimation ***************/
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  
                bool=0;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
          }  {
          if (bool==1) {    int i,j, iter;
            for(m=firstpass; m<=lastpass; m++){    double **xi;
              k2=anint[m][i]+(mint[m][i]/12.);    double fret;
              if ((k2>=dateprev1) && (k2<=dateprev2)) {    char filerespow[FILENAMELENGTH];
                if(agev[m][i]==0) agev[m][i]=agemax+1;    xi=matrix(1,npar,1,npar);
                if(agev[m][i]==1) agev[m][i]=agemax+2;    for (i=1;i<=npar;i++)
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      for (j=1;j<=npar;j++)
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        xi[i][j]=(i==j ? 1.0 : 0.0);
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    printf("Powell\n");  fprintf(ficlog,"Powell\n");
                  dateintsum=dateintsum+k2;    strcpy(filerespow,"pow"); 
                  k2cpt++;    strcat(filerespow,fileres);
                }    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
              }      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
            }    }
          }    fprintf(ficrespow,"# Powell\n# iter -2*LL");
        }    for (i=1;i<=nlstate;i++)
              for(j=1;j<=nlstate+ndeath;j++)
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     fprintf(ficrespow,"\n");
         if  (cptcovn>0) {    powell(p,xi,npar,ftol,&iter,&fret,func);
          fprintf(ficresp, "\n#********** Variable ");  
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    fclose(ficrespow);
        fprintf(ficresp, "**********\n#");    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
         }    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
        for(i=1; i<=nlstate;i++)    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  
        fprintf(ficresp, "\n");  }
          
   for(i=(int)agemin; i <= (int)agemax+3; i++){  /**** Computes Hessian and covariance matrix ***/
     if(i==(int)agemax+3)  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
       printf("Total");  {
     else    double  **a,**y,*x,pd;
       printf("Age %d", i);    double **hess;
     for(jk=1; jk <=nlstate ; jk++){    int i, j,jk;
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    int *indx;
         pp[jk] += freq[jk][m][i];  
     }    double hessii(double p[], double delta, int theta, double delti[]);
     for(jk=1; jk <=nlstate ; jk++){    double hessij(double p[], double delti[], int i, int j);
       for(m=-1, pos=0; m <=0 ; m++)    void lubksb(double **a, int npar, int *indx, double b[]) ;
         pos += freq[jk][m][i];    void ludcmp(double **a, int npar, int *indx, double *d) ;
       if(pp[jk]>=1.e-10)  
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    hess=matrix(1,npar,1,npar);
       else  
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    printf("\nCalculation of the hessian matrix. Wait...\n");
     }    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     for (i=1;i<=npar;i++){
      for(jk=1; jk <=nlstate ; jk++){      printf("%d",i);fflush(stdout);
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      fprintf(ficlog,"%d",i);fflush(ficlog);
         pp[jk] += freq[jk][m][i];      hess[i][i]=hessii(p,ftolhess,i,delti);
      }      /*printf(" %f ",p[i]);*/
       /*printf(" %lf ",hess[i][i]);*/
     for(jk=1,pos=0; jk <=nlstate ; jk++)    }
       pos += pp[jk];    
     for(jk=1; jk <=nlstate ; jk++){    for (i=1;i<=npar;i++) {
       if(pos>=1.e-5)      for (j=1;j<=npar;j++)  {
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        if (j>i) { 
       else          printf(".%d%d",i,j);fflush(stdout);
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
       if( i <= (int) agemax){          hess[i][j]=hessij(p,delti,i,j);
         if(pos>=1.e-5){          hess[j][i]=hess[i][j];    
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          /*printf(" %lf ",hess[i][j]);*/
           probs[i][jk][j1]= pp[jk]/pos;        }
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/      }
         }    }
       else    printf("\n");
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    fprintf(ficlog,"\n");
       }  
     }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     for(jk=-1; jk <=nlstate+ndeath; jk++)    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       for(m=-1; m <=nlstate+ndeath; m++)    
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    a=matrix(1,npar,1,npar);
     if(i <= (int) agemax)    y=matrix(1,npar,1,npar);
       fprintf(ficresp,"\n");    x=vector(1,npar);
     printf("\n");    indx=ivector(1,npar);
     }    for (i=1;i<=npar;i++)
     }      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
  }    ludcmp(a,npar,indx,&pd);
   dateintmean=dateintsum/k2cpt;  
      for (j=1;j<=npar;j++) {
   fclose(ficresp);      for (i=1;i<=npar;i++) x[i]=0;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      x[j]=1;
   free_vector(pp,1,nlstate);      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
   /* End of Freq */        matcov[i][j]=x[i];
 }      }
     }
 /************ Prevalence ********************/  
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)    printf("\n#Hessian matrix#\n");
 {  /* Some frequencies */    fprintf(ficlog,"\n#Hessian matrix#\n");
      for (i=1;i<=npar;i++) { 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      for (j=1;j<=npar;j++) { 
   double ***freq; /* Frequencies */        printf("%.3e ",hess[i][j]);
   double *pp;        fprintf(ficlog,"%.3e ",hess[i][j]);
   double pos, k2;      }
       printf("\n");
   pp=vector(1,nlstate);      fprintf(ficlog,"\n");
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    }
    
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    /* Recompute Inverse */
   j1=0;    for (i=1;i<=npar;i++)
        for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   j=cptcoveff;    ludcmp(a,npar,indx,&pd);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
      /*  printf("\n#Hessian matrix recomputed#\n");
  for(k1=1; k1<=j;k1++){  
     for(i1=1; i1<=ncodemax[k1];i1++){    for (j=1;j<=npar;j++) {
       j1++;      for (i=1;i<=npar;i++) x[i]=0;
        x[j]=1;
       for (i=-1; i<=nlstate+ndeath; i++)        lubksb(a,npar,indx,x);
         for (jk=-1; jk<=nlstate+ndeath; jk++)        for (i=1;i<=npar;i++){ 
           for(m=agemin; m <= agemax+3; m++)        y[i][j]=x[i];
             freq[i][jk][m]=0;        printf("%.3e ",y[i][j]);
              fprintf(ficlog,"%.3e ",y[i][j]);
       for (i=1; i<=imx; i++) {      }
         bool=1;      printf("\n");
         if  (cptcovn>0) {      fprintf(ficlog,"\n");
           for (z1=1; z1<=cptcoveff; z1++)    }
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    */
               bool=0;  
         }    free_matrix(a,1,npar,1,npar);
         if (bool==1) {    free_matrix(y,1,npar,1,npar);
           for(m=firstpass; m<=lastpass; m++){    free_vector(x,1,npar);
             k2=anint[m][i]+(mint[m][i]/12.);    free_ivector(indx,1,npar);
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    free_matrix(hess,1,npar,1,npar);
               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]+1-((int)calagedate %12)/12.)] += weight[i];  }
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */  
             }  /*************** hessian matrix ****************/
           }  double hessii( double x[], double delta, int theta, double delti[])
         }  {
       }    int i;
         for(i=(int)agemin; i <= (int)agemax+3; i++){    int l=1, lmax=20;
           for(jk=1; jk <=nlstate ; jk++){    double k1,k2;
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    double p2[NPARMAX+1];
               pp[jk] += freq[jk][m][i];    double res;
           }    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
           for(jk=1; jk <=nlstate ; jk++){    double fx;
             for(m=-1, pos=0; m <=0 ; m++)    int k=0,kmax=10;
             pos += freq[jk][m][i];    double l1;
         }  
            fx=func(x);
          for(jk=1; jk <=nlstate ; jk++){    for (i=1;i<=npar;i++) p2[i]=x[i];
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    for(l=0 ; l <=lmax; l++){
              pp[jk] += freq[jk][m][i];      l1=pow(10,l);
          }      delts=delt;
                for(k=1 ; k <kmax; k=k+1){
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        delt = delta*(l1*k);
         p2[theta]=x[theta] +delt;
          for(jk=1; jk <=nlstate ; jk++){                  k1=func(p2)-fx;
            if( i <= (int) agemax){        p2[theta]=x[theta]-delt;
              if(pos>=1.e-5){        k2=func(p2)-fx;
                probs[i][jk][j1]= pp[jk]/pos;        /*res= (k1-2.0*fx+k2)/delt/delt; */
              }        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
            }        
          }  #ifdef DEBUG
                  printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         }        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     }  #endif
   }        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
          if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
            k=kmax;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        }
   free_vector(pp,1,nlstate);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
            k=kmax; l=lmax*10.;
 }  /* End of Freq */        }
         else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
 /************* Waves Concatenation ***************/          delts=delt;
         }
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      }
 {    }
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    delti[theta]=delts;
      Death is a valid wave (if date is known).    return res; 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  }
      and mw[mi+1][i]. dh depends on stepm.  
      */  double hessij( double x[], double delti[], int thetai,int thetaj)
   {
   int i, mi, m;    int i;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    int l=1, l1, lmax=20;
      double sum=0., jmean=0.;*/    double k1,k2,k3,k4,res,fx;
     double p2[NPARMAX+1];
   int j, k=0,jk, ju, jl;    int k;
   double sum=0.;  
   jmin=1e+5;    fx=func(x);
   jmax=-1;    for (k=1; k<=2; k++) {
   jmean=0.;      for (i=1;i<=npar;i++) p2[i]=x[i];
   for(i=1; i<=imx; i++){      p2[thetai]=x[thetai]+delti[thetai]/k;
     mi=0;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     m=firstpass;      k1=func(p2)-fx;
     while(s[m][i] <= nlstate){    
       if(s[m][i]>=1)      p2[thetai]=x[thetai]+delti[thetai]/k;
         mw[++mi][i]=m;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       if(m >=lastpass)      k2=func(p2)-fx;
         break;    
       else      p2[thetai]=x[thetai]-delti[thetai]/k;
         m++;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     }/* end while */      k3=func(p2)-fx;
     if (s[m][i] > nlstate){    
       mi++;     /* Death is another wave */      p2[thetai]=x[thetai]-delti[thetai]/k;
       /* if(mi==0)  never been interviewed correctly before death */      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
          /* Only death is a correct wave */      k4=func(p2)-fx;
       mw[mi][i]=m;      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);
     wav[i]=mi;      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);
     if(mi==0)  #endif
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    }
   }    return res;
   }
   for(i=1; i<=imx; i++){  
     for(mi=1; mi<wav[i];mi++){  /************** Inverse of matrix **************/
       if (stepm <=0)  void ludcmp(double **a, int n, int *indx, double *d) 
         dh[mi][i]=1;  { 
       else{    int i,imax,j,k; 
         if (s[mw[mi+1][i]][i] > nlstate) {    double big,dum,sum,temp; 
           if (agedc[i] < 2*AGESUP) {    double *vv; 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);   
           if(j==0) j=1;  /* Survives at least one month after exam */    vv=vector(1,n); 
           k=k+1;    *d=1.0; 
           if (j >= jmax) jmax=j;    for (i=1;i<=n;i++) { 
           if (j <= jmin) jmin=j;      big=0.0; 
           sum=sum+j;      for (j=1;j<=n;j++) 
           /* if (j<10) printf("j=%d num=%d ",j,i); */        if ((temp=fabs(a[i][j])) > big) big=temp; 
           }      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
         }      vv[i]=1.0/big; 
         else{    } 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    for (j=1;j<=n;j++) { 
           k=k+1;      for (i=1;i<j;i++) { 
           if (j >= jmax) jmax=j;        sum=a[i][j]; 
           else if (j <= jmin)jmin=j;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        a[i][j]=sum; 
           sum=sum+j;      } 
         }      big=0.0; 
         jk= j/stepm;      for (i=j;i<=n;i++) { 
         jl= j -jk*stepm;        sum=a[i][j]; 
         ju= j -(jk+1)*stepm;        for (k=1;k<j;k++) 
         if(jl <= -ju)          sum -= a[i][k]*a[k][j]; 
           dh[mi][i]=jk;        a[i][j]=sum; 
         else        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           dh[mi][i]=jk+1;          big=dum; 
         if(dh[mi][i]==0)          imax=i; 
           dh[mi][i]=1; /* At least one step */        } 
       }      } 
     }      if (j != imax) { 
   }        for (k=1;k<=n;k++) { 
   jmean=sum/k;          dum=a[imax][k]; 
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          a[imax][k]=a[j][k]; 
  }          a[j][k]=dum; 
 /*********** Tricode ****************************/        } 
 void tricode(int *Tvar, int **nbcode, int imx)        *d = -(*d); 
 {        vv[imax]=vv[j]; 
   int Ndum[20],ij=1, k, j, i;      } 
   int cptcode=0;      indx[j]=imax; 
   cptcoveff=0;      if (a[j][j] == 0.0) a[j][j]=TINY; 
        if (j != n) { 
   for (k=0; k<19; k++) Ndum[k]=0;        dum=1.0/(a[j][j]); 
   for (k=1; k<=7; k++) ncodemax[k]=0;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       } 
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    } 
     for (i=1; i<=imx; i++) {    free_vector(vv,1,n);  /* Doesn't work */
       ij=(int)(covar[Tvar[j]][i]);  ;
       Ndum[ij]++;  } 
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  
       if (ij > cptcode) cptcode=ij;  void lubksb(double **a, int n, int *indx, double b[]) 
     }  { 
     int i,ii=0,ip,j; 
     for (i=0; i<=cptcode; i++) {    double sum; 
       if(Ndum[i]!=0) ncodemax[j]++;   
     }    for (i=1;i<=n;i++) { 
     ij=1;      ip=indx[i]; 
       sum=b[ip]; 
       b[ip]=b[i]; 
     for (i=1; i<=ncodemax[j]; i++) {      if (ii) 
       for (k=0; k<=19; k++) {        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
         if (Ndum[k] != 0) {      else if (sum) ii=i; 
           nbcode[Tvar[j]][ij]=k;      b[i]=sum; 
           ij++;    } 
         }    for (i=n;i>=1;i--) { 
         if (ij > ncodemax[j]) break;      sum=b[i]; 
       }        for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     }      b[i]=sum/a[i][i]; 
   }      } 
   } 
  for (k=0; k<19; k++) Ndum[k]=0;  
   /************ Frequencies ********************/
  for (i=1; i<=ncovmodel-2; i++) {  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)
       ij=Tvar[i];  {  /* Some frequencies */
       Ndum[ij]++;    
     }    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     int first;
  ij=1;    double ***freq; /* Frequencies */
  for (i=1; i<=10; i++) {    double *pp, **prop;
    if((Ndum[i]!=0) && (i<=ncov)){    double pos,posprop, k2, dateintsum=0,k2cpt=0;
      Tvaraff[ij]=i;    FILE *ficresp;
      ij++;    char fileresp[FILENAMELENGTH];
    }    
  }    pp=vector(1,nlstate);
      prop=matrix(1,nlstate,iagemin,iagemax+3);
     cptcoveff=ij-1;    strcpy(fileresp,"p");
 }    strcat(fileresp,fileres);
     if((ficresp=fopen(fileresp,"w"))==NULL) {
 /*********** Health Expectancies ****************/      printf("Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)      exit(0);
 {    }
   /* Health expectancies */    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
   int i, j, nhstepm, hstepm, h;    j1=0;
   double age, agelim,hf;    
   double ***p3mat;    j=cptcoveff;
      if (cptcovn<1) {j=1;ncodemax[1]=1;}
   fprintf(ficreseij,"# Health expectancies\n");  
   fprintf(ficreseij,"# Age");    first=1;
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=nlstate;j++)    for(k1=1; k1<=j;k1++){
       fprintf(ficreseij," %1d-%1d",i,j);      for(i1=1; i1<=ncodemax[k1];i1++){
   fprintf(ficreseij,"\n");        j1++;
         /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   hstepm=1*YEARM; /*  Every j years of age (in month) */          scanf("%d", i);*/
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        for (i=-1; i<=nlstate+ndeath; i++)  
           for (jk=-1; jk<=nlstate+ndeath; jk++)  
   agelim=AGESUP;            for(m=iagemin; m <= iagemax+3; m++)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */              freq[i][jk][m]=0;
     /* nhstepm age range expressed in number of stepm */  
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);      for (i=1; i<=nlstate; i++)  
     /* Typically if 20 years = 20*12/6=40 stepm */        for(m=iagemin; m <= iagemax+3; m++)
     if (stepm >= YEARM) hstepm=1;          prop[i][m]=0;
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */        
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        dateintsum=0;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        k2cpt=0;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        for (i=1; i<=imx; i++) {
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            bool=1;
           if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
     for(i=1; i<=nlstate;i++)              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       for(j=1; j<=nlstate;j++)                bool=0;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){          }
           eij[i][j][(int)age] +=p3mat[i][j][h];          if (bool==1){
         }            for(m=firstpass; m<=lastpass; m++){
                  k2=anint[m][i]+(mint[m][i]/12.);
     hf=1;              if ((k2>=dateprev1) && (k2<=dateprev2)) {
     if (stepm >= YEARM) hf=stepm/YEARM;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     fprintf(ficreseij,"%.0f",age );                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     for(i=1; i<=nlstate;i++)                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
       for(j=1; j<=nlstate;j++){                if (m<lastpass) {
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);                  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];
     fprintf(ficreseij,"\n");                }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                
   }                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
 }                  dateintsum=dateintsum+k2;
                   k2cpt++;
 /************ Variance ******************/                }
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)              }
 {            }
   /* Variance of health expectancies */          }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        }
   double **newm;         
   double **dnewm,**doldm;        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   int i, j, nhstepm, hstepm, h;  
   int k, cptcode;        if  (cptcovn>0) {
   double *xp;          fprintf(ficresp, "\n#********** Variable "); 
   double **gp, **gm;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   double ***gradg, ***trgradg;          fprintf(ficresp, "**********\n#");
   double ***p3mat;        }
   double age,agelim;        for(i=1; i<=nlstate;i++) 
   int theta;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         fprintf(ficresp, "\n");
    fprintf(ficresvij,"# Covariances of life expectancies\n");        
   fprintf(ficresvij,"# Age");        for(i=iagemin; i <= iagemax+3; i++){
   for(i=1; i<=nlstate;i++)          if(i==iagemax+3){
     for(j=1; j<=nlstate;j++)            fprintf(ficlog,"Total");
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          }else{
   fprintf(ficresvij,"\n");            if(first==1){
               first=0;
   xp=vector(1,npar);              printf("See log file for details...\n");
   dnewm=matrix(1,nlstate,1,npar);            }
   doldm=matrix(1,nlstate,1,nlstate);            fprintf(ficlog,"Age %d", i);
            }
   hstepm=1*YEARM; /* Every year of age */          for(jk=1; jk <=nlstate ; jk++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   agelim = AGESUP;              pp[jk] += freq[jk][m][i]; 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          for(jk=1; jk <=nlstate ; jk++){
     if (stepm >= YEARM) hstepm=1;            for(m=-1, pos=0; m <=0 ; m++)
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */              pos += freq[jk][m][i];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            if(pp[jk]>=1.e-10){
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);              if(first==1){
     gp=matrix(0,nhstepm,1,nlstate);              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     gm=matrix(0,nhstepm,1,nlstate);              }
               fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     for(theta=1; theta <=npar; theta++){            }else{
       for(i=1; i<=npar; i++){ /* Computes gradient */              if(first==1)
         xp[i] = x[i] + (i==theta ?delti[theta]:0);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       }              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          }
   
       if (popbased==1) {          for(jk=1; jk <=nlstate ; jk++){
         for(i=1; i<=nlstate;i++)            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
           prlim[i][i]=probs[(int)age][i][ij];              pp[jk] += freq[jk][m][i];
       }          }       
            for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
       for(j=1; j<= nlstate; j++){            pos += pp[jk];
         for(h=0; h<=nhstepm; h++){            posprop += prop[jk][i];
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          }
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];          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);
       for(i=1; i<=npar; i++) /* Computes gradient */              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            }else{
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                if(first==1)
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       if (popbased==1) {            }
         for(i=1; i<=nlstate;i++)            if( i <= iagemax){
           prlim[i][i]=probs[(int)age][i][ij];              if(pos>=1.e-5){
       }                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                 probs[i][jk][j1]= pp[jk]/pos;
       for(j=1; j<= nlstate; j++){                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
         for(h=0; h<=nhstepm; h++){              }
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)              else
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
         }            }
       }          }
           
       for(j=1; j<= nlstate; j++)          for(jk=-1; jk <=nlstate+ndeath; jk++)
         for(h=0; h<=nhstepm; h++){            for(m=-1; m <=nlstate+ndeath; m++)
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];              if(freq[jk][m][i] !=0 ) {
         }              if(first==1)
     } /* End theta */                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                 fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);              }
           if(i <= iagemax)
     for(h=0; h<=nhstepm; h++)            fprintf(ficresp,"\n");
       for(j=1; j<=nlstate;j++)          if(first==1)
         for(theta=1; theta <=npar; theta++)            printf("Others in log...\n");
           trgradg[h][j][theta]=gradg[h][theta][j];          fprintf(ficlog,"\n");
         }
     for(i=1;i<=nlstate;i++)      }
       for(j=1;j<=nlstate;j++)    }
         vareij[i][j][(int)age] =0.;    dateintmean=dateintsum/k2cpt; 
     for(h=0;h<=nhstepm;h++){   
       for(k=0;k<=nhstepm;k++){    fclose(ficresp);
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    free_vector(pp,1,nlstate);
         for(i=1;i<=nlstate;i++)    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
           for(j=1;j<=nlstate;j++)    /* End of Freq */
             vareij[i][j][(int)age] += doldm[i][j];  }
       }  
     }  /************ Prevalence ********************/
     h=1;  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)
     if (stepm >= YEARM) h=stepm/YEARM;  {  
     fprintf(ficresvij,"%.0f ",age );    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     for(i=1; i<=nlstate;i++)       in each health status at the date of interview (if between dateprev1 and dateprev2).
       for(j=1; j<=nlstate;j++){       We still use firstpass and lastpass as another selection.
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    */
       }   
     fprintf(ficresvij,"\n");    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     free_matrix(gp,0,nhstepm,1,nlstate);    double ***freq; /* Frequencies */
     free_matrix(gm,0,nhstepm,1,nlstate);    double *pp, **prop;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    double pos,posprop; 
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    double  y2; /* in fractional years */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int iagemin, iagemax;
   } /* End age */  
      iagemin= (int) agemin;
   free_vector(xp,1,npar);    iagemax= (int) agemax;
   free_matrix(doldm,1,nlstate,1,npar);    /*pp=vector(1,nlstate);*/
   free_matrix(dnewm,1,nlstate,1,nlstate);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
 }    j1=0;
     
 /************ Variance of prevlim ******************/    j=cptcoveff;
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)    if (cptcovn<1) {j=1;ncodemax[1]=1;}
 {    
   /* Variance of prevalence limit */    for(k1=1; k1<=j;k1++){
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      for(i1=1; i1<=ncodemax[k1];i1++){
   double **newm;        j1++;
   double **dnewm,**doldm;        
   int i, j, nhstepm, hstepm;        for (i=1; i<=nlstate; i++)  
   int k, cptcode;          for(m=iagemin; m <= iagemax+3; m++)
   double *xp;            prop[i][m]=0.0;
   double *gp, *gm;       
   double **gradg, **trgradg;        for (i=1; i<=imx; i++) { /* Each individual */
   double age,agelim;          bool=1;
   int theta;          if  (cptcovn>0) {
                for (z1=1; z1<=cptcoveff; z1++) 
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   fprintf(ficresvpl,"# Age");                bool=0;
   for(i=1; i<=nlstate;i++)          } 
       fprintf(ficresvpl," %1d-%1d",i,i);          if (bool==1) { 
   fprintf(ficresvpl,"\n");            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
               y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   xp=vector(1,npar);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   dnewm=matrix(1,nlstate,1,npar);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   doldm=matrix(1,nlstate,1,nlstate);                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); 
   hstepm=1*YEARM; /* Every year of age */                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */                  /*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]]);*/
   agelim = AGESUP;                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */                  prop[s[m][i]][iagemax+3] += weight[i]; 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                } 
     if (stepm >= YEARM) hstepm=1;              }
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            } /* end selection of waves */
     gradg=matrix(1,npar,1,nlstate);          }
     gp=vector(1,nlstate);        }
     gm=vector(1,nlstate);        for(i=iagemin; i <= iagemax+3; i++){  
           
     for(theta=1; theta <=npar; theta++){          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
       for(i=1; i<=npar; i++){ /* Computes gradient */            posprop += prop[jk][i]; 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          } 
       }  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          for(jk=1; jk <=nlstate ; jk++){     
       for(i=1;i<=nlstate;i++)            if( i <=  iagemax){ 
         gp[i] = prlim[i][i];              if(posprop>=1.e-5){ 
                    probs[i][jk][j1]= prop[jk][i]/posprop;
       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);          }/* end jk */ 
       for(i=1;i<=nlstate;i++)        }/* end i */ 
         gm[i] = prlim[i][i];      } /* end i1 */
     } /* end k1 */
       for(i=1;i<=nlstate;i++)    
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     } /* End theta */    /*free_vector(pp,1,nlstate);*/
     free_matrix(prop,1,nlstate, iagemin,iagemax+3);
     trgradg =matrix(1,nlstate,1,npar);  }  /* End of prevalence */
   
     for(j=1; j<=nlstate;j++)  /************* Waves Concatenation ***************/
       for(theta=1; theta <=npar; theta++)  
         trgradg[j][theta]=gradg[theta][j];  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)
   {
     for(i=1;i<=nlstate;i++)    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
       varpl[i][(int)age] =0.;       Death is a valid wave (if date is known).
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     for(i=1;i<=nlstate;i++)       and mw[mi+1][i]. dh depends on stepm.
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */       */
   
     fprintf(ficresvpl,"%.0f ",age );    int i, mi, m;
     for(i=1; i<=nlstate;i++)    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));       double sum=0., jmean=0.;*/
     fprintf(ficresvpl,"\n");    int first;
     free_vector(gp,1,nlstate);    int j, k=0,jk, ju, jl;
     free_vector(gm,1,nlstate);    double sum=0.;
     free_matrix(gradg,1,npar,1,nlstate);    first=0;
     free_matrix(trgradg,1,nlstate,1,npar);    jmin=1e+5;
   } /* End age */    jmax=-1;
     jmean=0.;
   free_vector(xp,1,npar);    for(i=1; i<=imx; i++){
   free_matrix(doldm,1,nlstate,1,npar);      mi=0;
   free_matrix(dnewm,1,nlstate,1,nlstate);      m=firstpass;
       while(s[m][i] <= nlstate){
 }        if(s[m][i]>=1)
           mw[++mi][i]=m;
 /************ Variance of one-step probabilities  ******************/        if(m >=lastpass)
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)          break;
 {        else
   int i, j;          m++;
   int k=0, cptcode;      }/* end while */
   double **dnewm,**doldm;      if (s[m][i] > nlstate){
   double *xp;        mi++;     /* Death is another wave */
   double *gp, *gm;        /* if(mi==0)  never been interviewed correctly before death */
   double **gradg, **trgradg;           /* Only death is a correct wave */
   double age,agelim, cov[NCOVMAX];        mw[mi][i]=m;
   int theta;      }
   char fileresprob[FILENAMELENGTH];  
       wav[i]=mi;
   strcpy(fileresprob,"prob");      if(mi==0){
   strcat(fileresprob,fileres);        if(first==0){
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {          printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
     printf("Problem with resultfile: %s\n", fileresprob);          first=1;
   }        }
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);        if(first==1){
            fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
         }
   xp=vector(1,npar);      } /* end mi==0 */
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    } /* End individuals */
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));  
      for(i=1; i<=imx; i++){
   cov[1]=1;      for(mi=1; mi<wav[i];mi++){
   for (age=bage; age<=fage; age ++){        if (stepm <=0)
     cov[2]=age;          dh[mi][i]=1;
     gradg=matrix(1,npar,1,9);        else{
     trgradg=matrix(1,9,1,npar);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));            if (agedc[i] < 2*AGESUP) {
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
                if(j==0) j=1;  /* Survives at least one month after exam */
     for(theta=1; theta <=npar; theta++){            k=k+1;
       for(i=1; i<=npar; i++)            if (j >= jmax) jmax=j;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            if (j <= jmin) jmin=j;
                  sum=sum+j;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);            /*if (j<0) printf("j=%d num=%d \n",j,i);*/
                /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       k=0;            if(j<0)printf("Error! Negative delay (%d to death) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       for(i=1; i<= (nlstate+ndeath); i++){            }
         for(j=1; j<=(nlstate+ndeath);j++){          }
            k=k+1;          else{
           gp[k]=pmmij[i][j];            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
         }            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       }            k=k+1;
             if (j >= jmax) jmax=j;
       for(i=1; i<=npar; i++)            else if (j <= jmin)jmin=j;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,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]);*/
             if(j<0)printf("Error! Negative delay (%d) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       pmij(pmmij,cov,ncovmodel,xp,nlstate);            sum=sum+j;
       k=0;          }
       for(i=1; i<=(nlstate+ndeath); i++){          jk= j/stepm;
         for(j=1; j<=(nlstate+ndeath);j++){          jl= j -jk*stepm;
           k=k+1;          ju= j -(jk+1)*stepm;
           gm[k]=pmmij[i][j];          if(mle <=1){ 
         }            if(jl==0){
       }              dh[mi][i]=jk;
                    bh[mi][i]=0;
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)            }else{ /* We want a negative bias in order to only have interpolation ie
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];                      * at the price of an extra matrix product in likelihood */
     }              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)            }
       for(theta=1; theta <=npar; theta++)          }else{
       trgradg[j][theta]=gradg[theta][j];            if(jl <= -ju){
                dh[mi][i]=jk;
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);              bh[mi][i]=jl;       /* bias is positive if real duration
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);                                   * is higher than the multiple of stepm and negative otherwise.
                                    */
      pmij(pmmij,cov,ncovmodel,x,nlstate);            }
             else{
      k=0;              dh[mi][i]=jk+1;
      for(i=1; i<=(nlstate+ndeath); i++){              bh[mi][i]=ju;
        for(j=1; j<=(nlstate+ndeath);j++){            }
          k=k+1;            if(dh[mi][i]==0){
          gm[k]=pmmij[i][j];              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);*/
                  }
      /*printf("\n%d ",(int)age);          }
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        } /* end if mle */
              } /* end wave */
     }
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    jmean=sum/k;
      }*/    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   fprintf(ficresprob,"\n%d ",(int)age);   }
   
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){  /*********** Tricode ****************************/
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  void tricode(int *Tvar, int **nbcode, int imx)
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  {
   }    
     int Ndum[20],ij=1, k, j, i, maxncov=19;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    int cptcode=0;
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    cptcoveff=0; 
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);   
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    for (k=0; k<maxncov; k++) Ndum[k]=0;
 }    for (k=1; k<=7; k++) ncodemax[k]=0;
  free_vector(xp,1,npar);  
 fclose(ficresprob);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
       for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
 }                                 modality*/ 
         ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
 /******************* Printing html file ***********/        Ndum[ij]++; /*store the modality */
 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[] ){        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   int jj1, k1, i1, cpt;        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
   FILE *fichtm;                                         Tvar[j]. If V=sex and male is 0 and 
   /*char optionfilehtm[FILENAMELENGTH];*/                                         female is 1, then  cptcode=1.*/
       }
   strcpy(optionfilehtm,optionfile);  
   strcat(optionfilehtm,".htm");      for (i=0; i<=cptcode; i++) {
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {        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 */
     printf("Problem with %s \n",optionfilehtm), exit(0);      }
   }  
       ij=1; 
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">      for (i=1; i<=ncodemax[j]; i++) {
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>        for (k=0; k<= maxncov; k++) {
           if (Ndum[k] != 0) {
 Total number of observations=%d <br>            nbcode[Tvar[j]][ij]=k; 
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>            /* 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; */
 <hr  size=\"2\" color=\"#EC5E5E\">            
 <li>Outputs files<br><br>\n            ij++;
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n          }
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>          if (ij > ncodemax[j]) break; 
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>        }  
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>      } 
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    }  
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>  
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>   for (k=0; k< maxncov; k++) Ndum[k]=0;
         - 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 (i=1; i<=ncovmodel-2; i++) { 
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>     ij=Tvar[i];
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);     Ndum[ij]++;
     }
 fprintf(fichtm," <li>Graphs</li><p>");  
    ij=1;
  m=cptcoveff;   for (i=1; i<= maxncov; i++) {
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}     if((Ndum[i]!=0) && (i<=ncovcol)){
        Tvaraff[ij]=i; /*For printing */
  jj1=0;       ij++;
  for(k1=1; k1<=m;k1++){     }
    for(i1=1; i1<=ncodemax[k1];i1++){   }
        jj1++;   
        if (cptcovn > 0) {   cptcoveff=ij-1; /*Number of simple covariates*/
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");  }
          for (cpt=1; cpt<=cptcoveff;cpt++)  
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);  /*********** Health Expectancies ****************/
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");  
        }  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 )
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>  
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      {
        for(cpt=1; cpt<nlstate;cpt++){    /* Health expectancies */
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    double age, agelim, hf;
        }    double ***p3mat,***varhe;
     for(cpt=1; cpt<=nlstate;cpt++) {    double **dnewm,**doldm;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    double *xp;
 interval) in state (%d): v%s%d%d.gif <br>    double **gp, **gm;
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      double ***gradg, ***trgradg;
      }    int theta;
      for(cpt=1; cpt<=nlstate;cpt++) {  
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    xp=vector(1,npar);
      }    dnewm=matrix(1,nlstate*nlstate,1,npar);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
 health expectancies in states (1) and (2): e%s%d.gif<br>    
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    fprintf(ficreseij,"# Health expectancies\n");
 fprintf(fichtm,"\n</body>");    fprintf(ficreseij,"# Age");
    }    for(i=1; i<=nlstate;i++)
    }      for(j=1; j<=nlstate;j++)
 fclose(fichtm);        fprintf(ficreseij," %1d-%1d (SE)",i,j);
 }    fprintf(ficreseij,"\n");
   
 /******************* Gnuplot file **************/    if(estepm < stepm){
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
   strcpy(optionfilegnuplot,optionfilefiname);     * This is mainly to measure the difference between two models: for example
   strcat(optionfilegnuplot,".plt");     * if stepm=24 months pijx are given only every 2 years and by summing them
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {     * we are calculating an estimate of the Life Expectancy assuming a linear 
     printf("Problem with file %s",optionfilegnuplot);     * progression in between and thus overestimating or underestimating according
   }     * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
 #ifdef windows     * to compare the new estimate of Life expectancy with the same linear 
     fprintf(ficgp,"cd \"%s\" \n",pathc);     * hypothesis. A more precise result, taking into account a more precise
 #endif     * curvature will be obtained if estepm is as small as stepm. */
 m=pow(2,cptcoveff);  
      /* For example we decided to compute the life expectancy with the smallest unit */
  /* 1eme*/    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   for (cpt=1; cpt<= nlstate ; cpt ++) {       nhstepm is the number of hstepm from age to agelim 
    for (k1=1; k1<= m ; k1 ++) {       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
 #ifdef windows       and note for a fixed period like estepm months */
     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);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 #endif       survival function given by stepm (the optimization length). Unfortunately it
 #ifdef unix       means that if the survival funtion is printed only each two years of age and if
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
 #endif       results. So we changed our mind and took the option of the best precision.
     */
 for (i=1; i<= nlstate ; i ++) {    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    agelim=AGESUP;
 }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);      /* nhstepm age range expressed in number of stepm */
     for (i=1; i<= nlstate ; i ++) {      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   else fprintf(ficgp," \%%*lf (\%%*lf)");      /* if (stepm >= YEARM) hstepm=1;*/
 }      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      for (i=1; i<= nlstate ; i ++) {      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      gp=matrix(0,nhstepm,1,nlstate*nlstate);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      gm=matrix(0,nhstepm,1,nlstate*nlstate);
 }    
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      /* Computed by stepm unit matrices, product of hstepm matrices, stored
 #ifdef unix         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
 fprintf(ficgp,"\nset ter gif small size 400,300");      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
 #endif   
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
    }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   }  
   /*2 eme*/      /* Computing Variances of health expectancies */
   
   for (k1=1; k1<= m ; k1 ++) {       for(theta=1; theta <=npar; theta++){
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);        for(i=1; i<=npar; i++){ 
              xp[i] = x[i] + (i==theta ?delti[theta]:0);
     for (i=1; i<= nlstate+1 ; i ++) {        }
       k=2*i;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    
       for (j=1; j<= nlstate+1 ; j ++) {        cptj=0;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        for(j=1; j<= nlstate; j++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for(i=1; i<=nlstate; i++){
 }              cptj=cptj+1;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);            }
       for (j=1; j<= nlstate+1 ; j ++) {          }
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        }
         else fprintf(ficgp," \%%*lf (\%%*lf)");       
 }         
       fprintf(ficgp,"\" t\"\" w l 0,");        for(i=1; i<=npar; i++) 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       for (j=1; j<= nlstate+1 ; j ++) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        
   else fprintf(ficgp," \%%*lf (\%%*lf)");        cptj=0;
 }          for(j=1; j<= nlstate; j++){
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          for(i=1;i<=nlstate;i++){
       else fprintf(ficgp,"\" t\"\" w l 0,");            cptj=cptj+1;
     }            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);  
   }              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
              }
   /*3eme*/          }
         }
   for (k1=1; k1<= m ; k1 ++) {        for(j=1; j<= nlstate*nlstate; j++)
     for (cpt=1; cpt<= nlstate ; cpt ++) {          for(h=0; h<=nhstepm-1; h++){
       k=2+nlstate*(cpt-1);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
       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);     
       }  /* End theta */
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
     }       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     }  
         for(h=0; h<=nhstepm-1; h++)
   /* CV preval stat */        for(j=1; j<=nlstate*nlstate;j++)
     for (k1=1; k1<= m ; k1 ++) {          for(theta=1; theta <=npar; theta++)
     for (cpt=1; cpt<nlstate ; cpt ++) {            trgradg[h][j][theta]=gradg[h][theta][j];
       k=3;       
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);  
        for(i=1;i<=nlstate*nlstate;i++)
       for (i=1; i< nlstate ; i ++)        for(j=1;j<=nlstate*nlstate;j++)
         fprintf(ficgp,"+$%d",k+i+1);          varhe[i][j][(int)age] =0.;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);  
             printf("%d|",(int)age);fflush(stdout);
       l=3+(nlstate+ndeath)*cpt;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);       for(h=0;h<=nhstepm-1;h++){
       for (i=1; i< nlstate ; i ++) {        for(k=0;k<=nhstepm-1;k++){
         l=3+(nlstate+ndeath)*cpt;          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
         fprintf(ficgp,"+$%d",l+i+1);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
       }          for(i=1;i<=nlstate*nlstate;i++)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);              for(j=1;j<=nlstate*nlstate;j++)
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
     }        }
   }        }
        /* Computing expectancies */
   /* proba elementaires */      for(i=1; i<=nlstate;i++)
    for(i=1,jk=1; i <=nlstate; i++){        for(j=1; j<=nlstate;j++)
     for(k=1; k <=(nlstate+ndeath); k++){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       if (k != i) {            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
         for(j=1; j <=ncovmodel; j++){            
          /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);  
           jk++;          }
           fprintf(ficgp,"\n");  
         }      fprintf(ficreseij,"%3.0f",age );
       }      cptj=0;
     }      for(i=1; i<=nlstate;i++)
     }        for(j=1; j<=nlstate;j++){
           cptj++;
     for(jk=1; jk <=m; jk++) {          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);        }
    i=1;      fprintf(ficreseij,"\n");
    for(k2=1; k2<=nlstate; k2++) {     
      k3=i;      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
      for(k=1; k<=(nlstate+ndeath); k++) {      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
        if (k != k2){      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
 ij=1;      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         for(j=3; j <=ncovmodel; j++) {    }
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    printf("\n");
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    fprintf(ficlog,"\n");
             ij++;  
           }    free_vector(xp,1,npar);
           else    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
         }    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
           fprintf(ficgp,")/(1");  }
          
         for(k1=1; k1 <=nlstate; k1++){    /************ Variance ******************/
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
 ij=1;  {
           for(j=3; j <=ncovmodel; j++){    /* Variance of health expectancies */
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    /* double **newm;*/
             ij++;    double **dnewm,**doldm;
           }    double **dnewmp,**doldmp;
           else    int i, j, nhstepm, hstepm, h, nstepm ;
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    int k, cptcode;
           }    double *xp;
           fprintf(ficgp,")");    double **gp, **gm;  /* for var eij */
         }    double ***gradg, ***trgradg; /*for var eij */
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    double **gradgp, **trgradgp; /* for var p point j */
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    double *gpp, *gmp; /* for var p point j */
         i=i+ncovmodel;    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
        }    double ***p3mat;
      }    double age,agelim, hf;
    }    double ***mobaverage;
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    int theta;
    }    char digit[4];
        char digitp[25];
   fclose(ficgp);  
 }  /* end gnuplot */    char fileresprobmorprev[FILENAMELENGTH];
   
     if(popbased==1){
 /*************** Moving average **************/      if(mobilav!=0)
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){        strcpy(digitp,"-populbased-mobilav-");
       else strcpy(digitp,"-populbased-nomobil-");
   int i, cpt, cptcod;    }
     for (agedeb=agemin; agedeb<=fage; agedeb++)    else 
       for (i=1; i<=nlstate;i++)      strcpy(digitp,"-stablbased-");
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)  
           mobaverage[(int)agedeb][i][cptcod]=0.;    if (mobilav!=0) {
          mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
       for (i=1; i<=nlstate;i++){        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        printf(" Error in movingaverage mobilav=%d\n",mobilav);
           for (cpt=0;cpt<=4;cpt++){      }
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    }
           }  
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    strcpy(fileresprobmorprev,"prmorprev"); 
         }    sprintf(digit,"%-d",ij);
       }    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     }    strcat(fileresprobmorprev,digit); /* Tvar to be done */
        strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
 }    strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
 /************** Forecasting ******************/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
 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){    }
      printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   int *popage;    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);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   double *popeffectif,*popcount;    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   double ***p3mat;      fprintf(ficresprobmorprev," p.%-d SE",j);
   char fileresf[FILENAMELENGTH];      for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
  agelim=AGESUP;    }  
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    fprintf(ficresprobmorprev,"\n");
     if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
        fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
        exit(0);
   strcpy(fileresf,"f");    }
   strcat(fileresf,fileres);    else{
   if((ficresf=fopen(fileresf,"w"))==NULL) {      fprintf(ficgp,"\n# Routine varevsij");
     printf("Problem with forecast resultfile: %s\n", fileresf);    }
   }    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   printf("Computing forecasting: result on file '%s' \n", fileresf);      printf("Problem with html file: %s\n", optionfilehtm);
       fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      exit(0);
     }
   if (mobilav==1) {    else{
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      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");
     movingaverage(agedeb, fage, agemin, mobaverage);      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   }    }
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   if (stepm<=12) stepsize=1;    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");
   agelim=AGESUP;    for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++)
   hstepm=1;        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   hstepm=hstepm/stepm;    fprintf(ficresvij,"\n");
   yp1=modf(dateintmean,&yp);  
   anprojmean=yp;    xp=vector(1,npar);
   yp2=modf((yp1*12),&yp);    dnewm=matrix(1,nlstate,1,npar);
   mprojmean=yp;    doldm=matrix(1,nlstate,1,nlstate);
   yp1=modf((yp2*30.5),&yp);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   jprojmean=yp;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   if(jprojmean==0) jprojmean=1;  
   if(mprojmean==0) jprojmean=1;    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
      gpp=vector(nlstate+1,nlstate+ndeath);
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    gmp=vector(nlstate+1,nlstate+ndeath);
      trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   for(cptcov=1;cptcov<=i2;cptcov++){    
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    if(estepm < stepm){
       k=k+1;      printf ("Problem %d lower than %d\n",estepm, stepm);
       fprintf(ficresf,"\n#******");    }
       for(j=1;j<=cptcoveff;j++) {    else  hstepm=estepm;   
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /* 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. 
       fprintf(ficresf,"******\n");       nhstepm is the number of hstepm from age to agelim 
       fprintf(ficresf,"# StartingAge FinalAge");       nstepm is the number of stepm from age to agelin. 
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);       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
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {       survival function given by stepm (the optimization length). Unfortunately it
         fprintf(ficresf,"\n");       means that if the survival funtion is printed every two years of age and if
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);         you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){    */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           nhstepm = nhstepm/hstepm;    agelim = AGESUP;
              for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           oldm=oldms;savm=savms;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
              gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
           for (h=0; h<=nhstepm; h++){      gp=matrix(0,nhstepm,1,nlstate);
             if (h==(int) (calagedate+YEARM*cpt)) {      gm=matrix(0,nhstepm,1,nlstate);
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);  
             }  
             for(j=1; j<=nlstate+ndeath;j++) {      for(theta=1; theta <=npar; theta++){
               kk1=0.;kk2=0;        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
               for(i=1; i<=nlstate;i++) {                        xp[i] = x[i] + (i==theta ?delti[theta]:0);
                 if (mobilav==1)        }
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                 else {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  
                 }        if (popbased==1) {
                          if(mobilav ==0){
               }            for(i=1; i<=nlstate;i++)
               if (h==(int)(calagedate+12*cpt)){              prlim[i][i]=probs[(int)age][i][ij];
                 fprintf(ficresf," %.3f", kk1);          }else{ /* mobilav */ 
                                    for(i=1; i<=nlstate;i++)
               }              prlim[i][i]=mobaverage[(int)age][i][ij];
             }          }
           }        }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
         }        for(j=1; j<= nlstate; j++){
       }          for(h=0; h<=nhstepm; h++){
     }            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   }              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
                  }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        }
         /* This for computing probability of death (h=1 means
   fclose(ficresf);           computed over hstepm matrices product = hstepm*stepm months) 
 }           as a weighted average of prlim.
 /************** 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){        for(j=nlstate+1;j<=nlstate+ndeath;j++){
            for(i=1,gpp[j]=0.; i<= nlstate; i++)
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;            gpp[j] += prlim[i][i]*p3mat[i][j][1];
   int *popage;        }    
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        /* end probability of death */
   double *popeffectif,*popcount;  
   double ***p3mat,***tabpop,***tabpopprev;        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   char filerespop[FILENAMELENGTH];          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   
   agelim=AGESUP;        if (popbased==1) {
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;          if(mobilav ==0){
              for(i=1; i<=nlstate;i++)
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);              prlim[i][i]=probs[(int)age][i][ij];
            }else{ /* mobilav */ 
              for(i=1; i<=nlstate;i++)
   strcpy(filerespop,"pop");              prlim[i][i]=mobaverage[(int)age][i][ij];
   strcat(filerespop,fileres);          }
   if((ficrespop=fopen(filerespop,"w"))==NULL) {        }
     printf("Problem with forecast resultfile: %s\n", filerespop);  
   }        for(j=1; j<= nlstate; j++){
   printf("Computing forecasting: result on file '%s' \n", filerespop);          for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   if (cptcoveff==0) ncodemax[cptcoveff]=1;              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
   if (mobilav==1) {        }
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        /* This for computing probability of death (h=1 means
     movingaverage(agedeb, fage, agemin, mobaverage);           computed over hstepm matrices product = hstepm*stepm months) 
   }           as a weighted average of prlim.
         */
   stepsize=(int) (stepm+YEARM-1)/YEARM;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   if (stepm<=12) stepsize=1;          for(i=1,gmp[j]=0.; i<= nlstate; i++)
             gmp[j] += prlim[i][i]*p3mat[i][j][1];
   agelim=AGESUP;        }    
          /* end probability of death */
   hstepm=1;  
   hstepm=hstepm/stepm;        for(j=1; j<= nlstate; j++) /* vareij */
            for(h=0; h<=nhstepm; h++){
   if (popforecast==1) {            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     if((ficpop=fopen(popfile,"r"))==NULL) {          }
       printf("Problem with population file : %s\n",popfile);exit(0);  
     }        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
     popage=ivector(0,AGESUP);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
     popeffectif=vector(0,AGESUP);        }
     popcount=vector(0,AGESUP);  
          } /* End theta */
     i=1;    
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
      
     imx=i;      for(h=0; h<=nhstepm; h++) /* veij */
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];        for(j=1; j<=nlstate;j++)
   }          for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   for(cptcov=1;cptcov<=i2;cptcov++){  
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
       k=k+1;        for(theta=1; theta <=npar; theta++)
       fprintf(ficrespop,"\n#******");          trgradgp[j][theta]=gradgp[theta][j];
       for(j=1;j<=cptcoveff;j++) {    
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       fprintf(ficrespop,"******\n");      for(i=1;i<=nlstate;i++)
       fprintf(ficrespop,"# Age");        for(j=1;j<=nlstate;j++)
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);          vareij[i][j][(int)age] =0.;
       if (popforecast==1)  fprintf(ficrespop," [Population]");  
            for(h=0;h<=nhstepm;h++){
       for (cpt=0; cpt<=0;cpt++) {        for(k=0;k<=nhstepm;k++){
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
                  matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
         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);            for(j=1;j<=nlstate;j++)
           nhstepm = nhstepm/hstepm;              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
                  }
           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);        /* pptj */
              matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
           for (h=0; h<=nhstepm; h++){      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
             if (h==(int) (calagedate+YEARM*cpt)) {      for(j=nlstate+1;j<=nlstate+ndeath;j++)
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
             }          varppt[j][i]=doldmp[j][i];
             for(j=1; j<=nlstate+ndeath;j++) {      /* end ppptj */
               kk1=0.;kk2=0;      /*  x centered again */
               for(i=1; i<=nlstate;i++) {                    hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
                 if (mobilav==1)      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];   
                 else {      if (popbased==1) {
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        if(mobilav ==0){
                 }          for(i=1; i<=nlstate;i++)
               }            prlim[i][i]=probs[(int)age][i][ij];
               if (h==(int)(calagedate+12*cpt)){        }else{ /* mobilav */ 
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;          for(i=1; i<=nlstate;i++)
                   /*fprintf(ficrespop," %.3f", kk1);            prlim[i][i]=mobaverage[(int)age][i][ij];
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/        }
               }      }
             }               
             for(i=1; i<=nlstate;i++){      /* This for computing probability of death (h=1 means
               kk1=0.;         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
                 for(j=1; j<=nlstate;j++){         as a weighted average of prlim.
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];      */
                 }      for(j=nlstate+1;j<=nlstate+ndeath;j++){
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
             }          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)      /* end probability of death */
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);  
           }      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         }        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
       }        for(i=1; i<=nlstate;i++){
            fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   /******/        }
       } 
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {      fprintf(ficresprobmorprev,"\n");
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){      fprintf(ficresvij,"%.0f ",age );
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      for(i=1; i<=nlstate;i++)
           nhstepm = nhstepm/hstepm;        for(j=1; j<=nlstate;j++){
                    fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
           oldm=oldms;savm=savms;      fprintf(ficresvij,"\n");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        free_matrix(gp,0,nhstepm,1,nlstate);
           for (h=0; h<=nhstepm; h++){      free_matrix(gm,0,nhstepm,1,nlstate);
             if (h==(int) (calagedate+YEARM*cpt)) {      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
             }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             for(j=1; j<=nlstate+ndeath;j++) {    } /* End age */
               kk1=0.;kk2=0;    free_vector(gpp,nlstate+1,nlstate+ndeath);
               for(i=1; i<=nlstate;i++) {                  free_vector(gmp,nlstate+1,nlstate+ndeath);
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
               }    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
             }    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
           }    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
         }  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
       }  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
    }    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
   }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
      fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
   if (popforecast==1) {    /*  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);
     free_ivector(popage,0,AGESUP);  */
     free_vector(popeffectif,0,AGESUP);    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
     free_vector(popcount,0,AGESUP);  
   }    free_vector(xp,1,npar);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    free_matrix(doldm,1,nlstate,1,nlstate);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    free_matrix(dnewm,1,nlstate,1,npar);
   fclose(ficrespop);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 }    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 /***********************************************/    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 /**************** Main Program *****************/    fclose(ficresprobmorprev);
 /***********************************************/    fclose(ficgp);
     fclose(fichtm);
 int main(int argc, char *argv[])  }  
 {  
   /************ Variance of prevlim ******************/
   int i,j, k, n=MAXN,iter,m,size,cptcode, 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)
   double agedeb, agefin,hf;  {
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   double fret;    double **newm;
   double **xi,tmp,delta;    double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
   double dum; /* Dummy variable */    int k, cptcode;
   double ***p3mat;    double *xp;
   int *indx;    double *gp, *gm;
   char line[MAXLINE], linepar[MAXLINE];    double **gradg, **trgradg;
   char title[MAXLINE];    double age,agelim;
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    int theta;
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];     
      fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];    fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
   char filerest[FILENAMELENGTH];        fprintf(ficresvpl," %1d-%1d",i,i);
   char fileregp[FILENAMELENGTH];    fprintf(ficresvpl,"\n");
   char popfile[FILENAMELENGTH];  
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    xp=vector(1,npar);
   int firstobs=1, lastobs=10;    dnewm=matrix(1,nlstate,1,npar);
   int sdeb, sfin; /* Status at beginning and end */    doldm=matrix(1,nlstate,1,nlstate);
   int c,  h , cpt,l;    
   int ju,jl, mi;    hstepm=1*YEARM; /* Every year of age */
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    agelim = AGESUP;
   int mobilav=0,popforecast=0;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   int hstepm, nhstepm;      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;      if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   double bage, fage, age, agelim, agebase;      gradg=matrix(1,npar,1,nlstate);
   double ftolpl=FTOL;      gp=vector(1,nlstate);
   double **prlim;      gm=vector(1,nlstate);
   double *severity;  
   double ***param; /* Matrix of parameters */      for(theta=1; theta <=npar; theta++){
   double  *p;        for(i=1; i<=npar; i++){ /* Computes gradient */
   double **matcov; /* Matrix of covariance */          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   double ***delti3; /* Scale */        }
   double *delti; /* Scale */        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   double ***eij, ***vareij;        for(i=1;i<=nlstate;i++)
   double **varpl; /* Variances of prevalence limits by age */          gp[i] = prlim[i][i];
   double *epj, vepp;      
   double kk1, kk2;        for(i=1; i<=npar; i++) /* Computes gradient */
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";          gm[i] = prlim[i][i];
   char *alph[]={"a","a","b","c","d","e"}, str[4];  
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   char z[1]="c", occ;      } /* End theta */
 #include <sys/time.h>  
 #include <time.h>      trgradg =matrix(1,nlstate,1,npar);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  
        for(j=1; j<=nlstate;j++)
   /* long total_usecs;        for(theta=1; theta <=npar; theta++)
   struct timeval start_time, end_time;          trgradg[j][theta]=gradg[theta][j];
    
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   printf("\n%s",version);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   if(argc <=1){      for(i=1;i<=nlstate;i++)
     printf("\nEnter the parameter file name: ");        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
     scanf("%s",pathtot);  
   }      fprintf(ficresvpl,"%.0f ",age );
   else{      for(i=1; i<=nlstate;i++)
     strcpy(pathtot,argv[1]);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   }      fprintf(ficresvpl,"\n");
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/      free_vector(gp,1,nlstate);
   /*cygwin_split_path(pathtot,path,optionfile);      free_vector(gm,1,nlstate);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      free_matrix(gradg,1,npar,1,nlstate);
   /* cutv(path,optionfile,pathtot,'\\');*/      free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);  
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    free_vector(xp,1,npar);
   chdir(path);    free_matrix(doldm,1,nlstate,1,npar);
   replace(pathc,path);    free_matrix(dnewm,1,nlstate,1,nlstate);
   
 /*-------- arguments in the command line --------*/  }
   
   strcpy(fileres,"r");  /************ Variance of one-step probabilities  ******************/
   strcat(fileres, optionfilefiname);  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
   strcat(fileres,".txt");    /* Other files have txt extension */  {
     int i, j=0,  i1, k1, l1, t, tj;
   /*---------arguments file --------*/    int k2, l2, j1,  z1;
     int k=0,l, cptcode;
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    int first=1, first1;
     printf("Problem with optionfile %s\n",optionfile);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     goto end;    double **dnewm,**doldm;
   }    double *xp;
     double *gp, *gm;
   strcpy(filereso,"o");    double **gradg, **trgradg;
   strcat(filereso,fileres);    double **mu;
   if((ficparo=fopen(filereso,"w"))==NULL) {    double age,agelim, cov[NCOVMAX];
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   }    int theta;
     char fileresprob[FILENAMELENGTH];
   /* Reads comments: lines beginning with '#' */    char fileresprobcov[FILENAMELENGTH];
   while((c=getc(ficpar))=='#' && c!= EOF){    char fileresprobcor[FILENAMELENGTH];
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    double ***varpij;
     puts(line);  
     fputs(line,ficparo);    strcpy(fileresprob,"prob"); 
   }    strcat(fileresprob,fileres);
   ungetc(c,ficpar);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
   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(ficlog,"Problem with resultfile: %s\n", fileresprob);
   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);    strcpy(fileresprobcov,"probcov"); 
 while((c=getc(ficpar))=='#' && c!= EOF){    strcat(fileresprobcov,fileres);
     ungetc(c,ficpar);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     fgets(line, MAXLINE, ficpar);      printf("Problem with resultfile: %s\n", fileresprobcov);
     puts(line);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     fputs(line,ficparo);    }
   }    strcpy(fileresprobcor,"probcor"); 
   ungetc(c,ficpar);    strcat(fileresprobcor,fileres);
      if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
          printf("Problem with resultfile: %s\n", fileresprobcor);
   covar=matrix(0,NCOVMAX,1,n);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   cptcovn=0;    }
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   ncovmodel=2+cptcovn;    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    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);
   /* Read guess parameters */    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   /* Reads comments: lines beginning with '#' */    
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     ungetc(c,ficpar);    fprintf(ficresprob,"# Age");
     fgets(line, MAXLINE, ficpar);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     puts(line);    fprintf(ficresprobcov,"# Age");
     fputs(line,ficparo);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   }    fprintf(ficresprobcov,"# Age");
   ungetc(c,ficpar);  
    
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    for(i=1; i<=nlstate;i++)
     for(i=1; i <=nlstate; i++)      for(j=1; j<=(nlstate+ndeath);j++){
     for(j=1; j <=nlstate+ndeath-1; j++){        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
       fscanf(ficpar,"%1d%1d",&i1,&j1);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
       fprintf(ficparo,"%1d%1d",i1,j1);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
       printf("%1d%1d",i,j);      }  
       for(k=1; k<=ncovmodel;k++){   /* fprintf(ficresprob,"\n");
         fscanf(ficpar," %lf",&param[i][j][k]);    fprintf(ficresprobcov,"\n");
         printf(" %lf",param[i][j][k]);    fprintf(ficresprobcor,"\n");
         fprintf(ficparo," %lf",param[i][j][k]);   */
       }   xp=vector(1,npar);
       fscanf(ficpar,"\n");    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       printf("\n");    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
       fprintf(ficparo,"\n");    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;
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   p=param[1][1];      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
        exit(0);
   /* Reads comments: lines beginning with '#' */    }
   while((c=getc(ficpar))=='#' && c!= EOF){    else{
     ungetc(c,ficpar);      fprintf(ficgp,"\n# Routine varprob");
     fgets(line, MAXLINE, ficpar);    }
     puts(line);    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
     fputs(line,ficparo);      printf("Problem with html file: %s\n", optionfilehtm);
   }      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   ungetc(c,ficpar);      exit(0);
     }
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    else{
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   for(i=1; i <=nlstate; i++){      fprintf(fichtm,"\n");
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
       printf("%1d%1d",i,j);      fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
       fprintf(ficparo,"%1d%1d",i1,j1);      fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
       for(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]);    cov[1]=1;
       }    tj=cptcoveff;
       fscanf(ficpar,"\n");    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
       printf("\n");    j1=0;
       fprintf(ficparo,"\n");    for(t=1; t<=tj;t++){
     }      for(i1=1; i1<=ncodemax[t];i1++){ 
   }        j1++;
   delti=delti3[1][1];        if  (cptcovn>0) {
            fprintf(ficresprob, "\n#********** Variable "); 
   /* Reads comments: lines beginning with '#' */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficresprob, "**********\n#\n");
     ungetc(c,ficpar);          fprintf(ficresprobcov, "\n#********** Variable "); 
     fgets(line, MAXLINE, ficpar);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     puts(line);          fprintf(ficresprobcov, "**********\n#\n");
     fputs(line,ficparo);          
   }          fprintf(ficgp, "\n#********** Variable "); 
   ungetc(c,ficpar);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficgp, "**********\n#\n");
   matcov=matrix(1,npar,1,npar);          
   for(i=1; i <=npar; i++){          
     fscanf(ficpar,"%s",&str);          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
     printf("%s",str);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fprintf(ficparo,"%s",str);          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     for(j=1; j <=i; j++){          
       fscanf(ficpar," %le",&matcov[i][j]);          fprintf(ficresprobcor, "\n#********** Variable ");    
       printf(" %.5le",matcov[i][j]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       fprintf(ficparo," %.5le",matcov[i][j]);          fprintf(ficresprobcor, "**********\n#");    
     }        }
     fscanf(ficpar,"\n");        
     printf("\n");        for (age=bage; age<=fage; age ++){ 
     fprintf(ficparo,"\n");          cov[2]=age;
   }          for (k=1; k<=cptcovn;k++) {
   for(i=1; i <=npar; i++)            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     for(j=i+1;j<=npar;j++)          }
       matcov[i][j]=matcov[j][i];          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
              for (k=1; k<=cptcovprod;k++)
   printf("\n");            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
     /*-------- data file ----------*/          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     if((ficres =fopen(fileres,"w"))==NULL) {          gp=vector(1,(nlstate)*(nlstate+ndeath));
       printf("Problem with resultfile: %s\n", fileres);goto end;          gm=vector(1,(nlstate)*(nlstate+ndeath));
     }      
     fprintf(ficres,"#%s\n",version);          for(theta=1; theta <=npar; theta++){
                for(i=1; i<=npar; i++)
     if((fic=fopen(datafile,"r"))==NULL)    {              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
       printf("Problem with datafile: %s\n", datafile);goto end;            
     }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
     n= lastobs;            k=0;
     severity = vector(1,maxwav);            for(i=1; i<= (nlstate); i++){
     outcome=imatrix(1,maxwav+1,1,n);              for(j=1; j<=(nlstate+ndeath);j++){
     num=ivector(1,n);                k=k+1;
     moisnais=vector(1,n);                gp[k]=pmmij[i][j];
     annais=vector(1,n);              }
     moisdc=vector(1,n);            }
     andc=vector(1,n);            
     agedc=vector(1,n);            for(i=1; i<=npar; i++)
     cod=ivector(1,n);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
     weight=vector(1,n);      
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     mint=matrix(1,maxwav,1,n);            k=0;
     anint=matrix(1,maxwav,1,n);            for(i=1; i<=(nlstate); i++){
     s=imatrix(1,maxwav+1,1,n);              for(j=1; j<=(nlstate+ndeath);j++){
     adl=imatrix(1,maxwav+1,1,n);                    k=k+1;
     tab=ivector(1,NCOVMAX);                gm[k]=pmmij[i][j];
     ncodemax=ivector(1,8);              }
             }
     i=1;       
     while (fgets(line, MAXLINE, fic) != NULL)    {            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
       if ((i >= firstobs) && (i <=lastobs)) {              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
                  }
         for (j=maxwav;j>=1;j--){  
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
           strcpy(line,stra);            for(theta=1; theta <=npar; theta++)
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);              trgradg[j][theta]=gradg[theta][j];
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          
         }          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
                  matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);  
           pmij(pmmij,cov,ncovmodel,x,nlstate);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);          
         for (j=ncov;j>=1;j--){          k=0;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);          for(i=1; i<=(nlstate); i++){
         }            for(j=1; j<=(nlstate+ndeath);j++){
         num[i]=atol(stra);              k=k+1;
                      mu[k][(int) age]=pmmij[i][j];
         /*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;}*/          }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
         i=i+1;            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
       }              varpij[i][j][(int)age] = doldm[i][j];
     }  
     /* printf("ii=%d", ij);          /*printf("\n%d ",(int)age);
        scanf("%d",i);*/            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   imx=i-1; /* Number of individuals */            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   /* 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;          fprintf(ficresprob,"\n%d ",(int)age);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;          fprintf(ficresprobcov,"\n%d ",(int)age);
     }          fprintf(ficresprobcor,"\n%d ",(int)age);
   
     for (i=1; i<=imx; i++)          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   /* Calculation of the number of parameter from char model*/            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   Tvar=ivector(1,15);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
   Tprod=ivector(1,15);          }
   Tvaraff=ivector(1,15);          i=0;
   Tvard=imatrix(1,15,1,2);          for (k=1; k<=(nlstate);k++){
   Tage=ivector(1,15);                  for (l=1; l<=(nlstate+ndeath);l++){ 
                  i=i++;
   if (strlen(model) >1){              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
     j=0, j1=0, k1=1, k2=1;              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
     j=nbocc(model,'+');              for (j=1; j<=i;j++){
     j1=nbocc(model,'*');                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
     cptcovn=j+1;                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
     cptcovprod=j1;              }
                }
              }/* end of loop for state */
     strcpy(modelsav,model);        } /* end of loop for age */
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){  
       printf("Error. Non available option model=%s ",model);        /* Confidence intervalle of pij  */
       goto end;        /*
     }          fprintf(ficgp,"\nset noparametric;unset label");
              fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
     for(i=(j+1); i>=1;i--){          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
       cutv(stra,strb,modelsav,'+');          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);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
       /*scanf("%d",i);*/          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
       if (strchr(strb,'*')) {        */
         cutv(strd,strc,strb,'*');  
         if (strcmp(strc,"age")==0) {        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
           cptcovprod--;        first1=1;
           cutv(strb,stre,strd,'V');        for (k2=1; k2<=(nlstate);k2++){
           Tvar[i]=atoi(stre);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
           cptcovage++;            if(l2==k2) continue;
             Tage[cptcovage]=i;            j=(k2-1)*(nlstate+ndeath)+l2;
             /*printf("stre=%s ", stre);*/            for (k1=1; k1<=(nlstate);k1++){
         }              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
         else if (strcmp(strd,"age")==0) {                if(l1==k1) continue;
           cptcovprod--;                i=(k1-1)*(nlstate+ndeath)+l1;
           cutv(strb,stre,strc,'V');                if(i<=j) continue;
           Tvar[i]=atoi(stre);                for (age=bage; age<=fage; age ++){ 
           cptcovage++;                  if ((int)age %5==0){
           Tage[cptcovage]=i;                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
         }                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
         else {                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
           cutv(strb,stre,strc,'V');                    mu1=mu[i][(int) age]/stepm*YEARM ;
           Tvar[i]=ncov+k1;                    mu2=mu[j][(int) age]/stepm*YEARM;
           cutv(strb,strc,strd,'V');                    c12=cv12/sqrt(v1*v2);
           Tprod[k1]=i;                    /* Computing eigen value of matrix of covariance */
           Tvard[k1][1]=atoi(strc);                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
           Tvard[k1][2]=atoi(stre);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
           Tvar[cptcovn+k2]=Tvard[k1][1];                    /* Eigen vectors */
           Tvar[cptcovn+k2+1]=Tvard[k1][2];                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
           for (k=1; k<=lastobs;k++)                    /*v21=sqrt(1.-v11*v11); *//* error */
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];                    v21=(lc1-v1)/cv12*v11;
           k1++;                    v12=-v21;
           k2=k2+2;                    v22=v11;
         }                    tnalp=v21/v11;
       }                    if(first1==1){
       else {                      first1=0;
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/                      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);
        /*  scanf("%d",i);*/                    }
       cutv(strd,strc,strb,'V');                    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);
       Tvar[i]=atoi(strc);                    /*printf(fignu*/
       }                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
       strcpy(modelsav,stra);                      /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);                    if(first==1){
         scanf("%d",i);*/                      first=0;
     }                      fprintf(ficgp,"\nset parametric;unset label");
 }                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);                      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);
   printf("cptcovprod=%d ", cptcovprod);                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
   scanf("%d ",i);*/                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
     fclose(fic);                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     /*  if(mle==1){*/                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     if (weightopt != 1) { /* Maximisation without weights*/                      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",\
       for(i=1;i<=n;i++) weight[i]=1.0;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     }                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     /*-calculation of age at interview from date of interview and age at death -*/                    }else{
     agev=matrix(1,maxwav,1,imx);                      first=0;
                       fprintf(fichtm," %d (%.3f),",(int) age, c12);
    for (i=1; i<=imx; i++)                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
      for(m=2; (m<= maxwav); m++)                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){                      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",\
          anint[m][i]=9999;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
          s[m][i]=-1;                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
        }                    }/* if first */
                      } /* age mod 5 */
     for (i=1; i<=imx; i++)  {                } /* end loop age */
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
       for(m=1; (m<= maxwav); m++){                first=1;
         if(s[m][i] >0){              } /*l12 */
           if (s[m][i] == nlstate+1) {            } /* k12 */
             if(agedc[i]>0)          } /*l1 */
               if(moisdc[i]!=99 && andc[i]!=9999)        }/* k1 */
               agev[m][i]=agedc[i];      } /* loop covariates */
             else {    }
               if (andc[i]!=9999){    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
               agev[m][i]=-1;    free_vector(xp,1,npar);
               }    fclose(ficresprob);
             }    fclose(ficresprobcov);
           }    fclose(ficresprobcor);
           else if(s[m][i] !=9){ /* Should no more exist */    fclose(ficgp);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    fclose(fichtm);
             if(mint[m][i]==99 || anint[m][i]==9999)  }
               agev[m][i]=1;  
             else if(agev[m][i] <agemin){  
               agemin=agev[m][i];  /******************* Printing html file ***********/
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
             }                    int lastpass, int stepm, int weightopt, char model[],\
             else if(agev[m][i] >agemax){                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
               agemax=agev[m][i];                    int popforecast, int estepm ,\
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/                    double jprev1, double mprev1,double anprev1, \
             }                    double jprev2, double mprev2,double anprev2){
             /*agev[m][i]=anint[m][i]-annais[i];*/    int jj1, k1, i1, cpt;
             /*   agev[m][i] = age[i]+2*m;*/    /*char optionfilehtm[FILENAMELENGTH];*/
           }    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
           else { /* =9 */      printf("Problem with %s \n",optionfilehtm), exit(0);
             agev[m][i]=1;      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
             s[m][i]=-1;    }
           }  
         }     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
         else /*= 0 Unknown */   - 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
           agev[m][i]=1;   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
       }   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
       - Life expectancies by age and initial health status (estepm=%2d months): 
     }     <a href=\"e%s\">e%s</a> <br>\n</li>", \
     for (i=1; i<=imx; i++)  {    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
       for(m=1; (m<= maxwav); m++){  
         if (s[m][i] > (nlstate+ndeath)) {  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
           printf("Error: Wrong value in nlstate or ndeath\n");    
           goto end;   m=cptcoveff;
         }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       }  
     }   jj1=0;
    for(k1=1; k1<=m;k1++){
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);     for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
     free_vector(severity,1,maxwav);       if (cptcovn > 0) {
     free_imatrix(outcome,1,maxwav+1,1,n);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     free_vector(moisnais,1,n);         for (cpt=1; cpt<=cptcoveff;cpt++) 
     free_vector(annais,1,n);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     /* free_matrix(mint,1,maxwav,1,n);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        free_matrix(anint,1,maxwav,1,n);*/       }
     free_vector(moisdc,1,n);       /* Pij */
     free_vector(andc,1,n);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: pe%s%d1.png<br>
   <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
           /* Quasi-incidences */
     wav=ivector(1,imx);       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>
     dh=imatrix(1,lastpass-firstpass+1,1,imx);  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
     mw=imatrix(1,lastpass-firstpass+1,1,imx);         /* Stable prevalence in each health state */
             for(cpt=1; cpt<nlstate;cpt++){
     /* Concatenates waves */           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
       Tcode=ivector(1,100);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
       ncodemax[1]=1;       }
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);       fprintf(fichtm,"\n<br>- Total life expectancy by age and
        health expectancies in states (1) and (2): e%s%d.png<br>
    codtab=imatrix(1,100,1,10);  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
    h=0;     } /* end i1 */
    m=pow(2,cptcoveff);   }/* End k1 */
     fprintf(fichtm,"</ul>");
    for(k=1;k<=cptcoveff; k++){  
      for(i=1; i <=(m/pow(2,k));i++){  
        for(j=1; j <= ncodemax[k]; j++){   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
            h++;   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
            if (h>m) h=1;codtab[h][k]=j;   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
          }   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
        }   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
      }   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
    }   - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
    /*for(i=1; i <=m ;i++){  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
      for(k=1; k <=cptcovn; k++){  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);  /*      <br>",fileres,fileres,fileres,fileres); */
      }  /*  else  */
      printf("\n");  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    }  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
    scanf("%d",i);*/  
       m=cptcoveff;
    /* Calculates basic frequencies. Computes observed prevalence at single age   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
        and prints on file fileres'p'. */  
    jj1=0;
       for(k1=1; k1<=m;k1++){
         for(i1=1; i1<=ncodemax[k1];i1++){
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       jj1++;
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       if (cptcovn > 0) {
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */         for (cpt=1; cpt<=cptcoveff;cpt++) 
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
               fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     /* For Powell, parameters are in a vector p[] starting at p[1]       }
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */       for(cpt=1; cpt<=nlstate;cpt++) {
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */         fprintf(fichtm,"<br>- Observed and period prevalence (with confident
   interval) in state (%d): v%s%d%d.png <br>
     if(mle==1){  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);       }
     }     } /* end i1 */
       }/* End k1 */
     /*--------- results files --------------*/   fprintf(fichtm,"</ul>");
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);  fclose(fichtm);
    }
   
    jk=1;  /******************* Gnuplot file **************/
    fprintf(ficres,"# Parameters\n");  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
    printf("# Parameters\n");  
    for(i=1,jk=1; i <=nlstate; i++){    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
      for(k=1; k <=(nlstate+ndeath); k++){    int ng;
        if (k != i)    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
          {      printf("Problem with file %s",optionfilegnuplot);
            printf("%d%d ",i,k);      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
            fprintf(ficres,"%1d%1d ",i,k);    }
            for(j=1; j <=ncovmodel; j++){  
              printf("%f ",p[jk]);    /*#ifdef windows */
              fprintf(ficres,"%f ",p[jk]);      fprintf(ficgp,"cd \"%s\" \n",pathc);
              jk++;      /*#endif */
            }  m=pow(2,cptcoveff);
            printf("\n");    
            fprintf(ficres,"\n");   /* 1eme*/
          }    for (cpt=1; cpt<= nlstate ; cpt ++) {
      }     for (k1=1; k1<= m ; k1 ++) {
    }       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
  if(mle==1){       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);
     /* Computing hessian and covariance matrix */  
     ftolhess=ftol; /* Usually correct */       for (i=1; i<= nlstate ; i ++) {
     hesscov(matcov, p, npar, delti, ftolhess, func);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
  }         else fprintf(ficgp," \%%*lf (\%%*lf)");
     fprintf(ficres,"# Scales\n");       }
     printf("# Scales\n");       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);
      for(i=1,jk=1; i <=nlstate; i++){       for (i=1; i<= nlstate ; i ++) {
       for(j=1; j <=nlstate+ndeath; j++){         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         if (j!=i) {         else fprintf(ficgp," \%%*lf (\%%*lf)");
           fprintf(ficres,"%1d%1d",i,j);       } 
           printf("%1d%1d",i,j);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
           for(k=1; k<=ncovmodel;k++){       for (i=1; i<= nlstate ; i ++) {
             printf(" %.5e",delti[jk]);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
             fprintf(ficres," %.5e",delti[jk]);         else fprintf(ficgp," \%%*lf (\%%*lf)");
             jk++;       }  
           }       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
           printf("\n");     }
           fprintf(ficres,"\n");    }
         }    /*2 eme*/
       }    
      }    for (k1=1; k1<= m ; k1 ++) { 
          fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
     k=1;      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
     fprintf(ficres,"# Covariance\n");      
     printf("# Covariance\n");      for (i=1; i<= nlstate+1 ; i ++) {
     for(i=1;i<=npar;i++){        k=2*i;
       /*  if (k>nlstate) k=1;        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
       i1=(i-1)/(ncovmodel*nlstate)+1;        for (j=1; j<= nlstate+1 ; j ++) {
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       printf("%s%d%d",alph[k],i1,tab[i]);*/          else fprintf(ficgp," \%%*lf (\%%*lf)");
       fprintf(ficres,"%3d",i);        }   
       printf("%3d",i);        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
       for(j=1; j<=i;j++){        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficres," %.5e",matcov[i][j]);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
         printf(" %.5e",matcov[i][j]);        for (j=1; j<= nlstate+1 ; j ++) {
       }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       fprintf(ficres,"\n");          else fprintf(ficgp," \%%*lf (\%%*lf)");
       printf("\n");        }   
       k++;        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 ++) {
     while((c=getc(ficpar))=='#' && c!= EOF){          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       ungetc(c,ficpar);          else fprintf(ficgp," \%%*lf (\%%*lf)");
       fgets(line, MAXLINE, ficpar);        }   
       puts(line);        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
       fputs(line,ficparo);        else fprintf(ficgp,"\" t\"\" w l 0,");
     }      }
     ungetc(c,ficpar);    }
      
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);    /*3eme*/
        
     if (fage <= 2) {    for (k1=1; k1<= m ; k1 ++) { 
       bage = agemin;      for (cpt=1; cpt<= nlstate ; cpt ++) {
       fage = agemaxpar;        k=2+nlstate*(2*cpt-2);
     }        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
            fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
            fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     while((c=getc(ficpar))=='#' && c!= EOF){          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     ungetc(c,ficpar);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     fgets(line, MAXLINE, ficpar);          
     puts(line);        */
     fputs(line,ficparo);        for (i=1; i< nlstate ; i ++) {
   }          fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
   ungetc(c,ficpar);          
          } 
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);      }
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    }
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    
          /* CV preval stable (period) */
   while((c=getc(ficpar))=='#' && c!= EOF){    for (k1=1; k1<= m ; k1 ++) { 
     ungetc(c,ficpar);      for (cpt=1; cpt<=nlstate ; cpt ++) {
     fgets(line, MAXLINE, ficpar);        k=3;
     puts(line);        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     fputs(line,ficparo);        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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
   }        
   ungetc(c,ficpar);        for (i=1; i<= nlstate ; i ++)
            fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
    dateprev1=anprev1+mprev1/12.+jprev1/365.;        
    dateprev2=anprev2+mprev2/12.+jprev2/365.;        l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
   fscanf(ficpar,"pop_based=%d\n",&popbased);        for (i=1; i< nlstate ; i ++) {
   fprintf(ficparo,"pop_based=%d\n",popbased);            l=3+(nlstate+ndeath)*cpt;
   fprintf(ficres,"pop_based=%d\n",popbased);            fprintf(ficgp,"+$%d",l+i+1);
          }
   while((c=getc(ficpar))=='#' && c!= EOF){        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
     ungetc(c,ficpar);      } 
     fgets(line, MAXLINE, ficpar);    }  
     puts(line);    
     fputs(line,ficparo);    /* proba elementaires */
   }    for(i=1,jk=1; i <=nlstate; i++){
   ungetc(c,ficpar);      for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
   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);          for(j=1; j <=ncovmodel; j++){
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
 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);            jk++; 
             fprintf(ficgp,"\n");
           }
 while((c=getc(ficpar))=='#' && c!= EOF){        }
     ungetc(c,ficpar);      }
     fgets(line, MAXLINE, ficpar);     }
     puts(line);  
     fputs(line,ficparo);     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
   }       for(jk=1; jk <=m; jk++) {
   ungetc(c,ficpar);         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
          if (ng==2)
   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(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);         else
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);           fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);         i=1;
          for(k2=1; k2<=nlstate; k2++) {
 /*------------ gnuplot -------------*/           k3=i;
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);           for(k=1; k<=(nlstate+ndeath); k++) {
               if (k != k2){
 /*------------ free_vector  -------------*/               if(ng==2)
  chdir(path);                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                 else
  free_ivector(wav,1,imx);                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);               ij=1;
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                 for(j=3; j <=ncovmodel; j++) {
  free_ivector(num,1,n);                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
  free_vector(agedc,1,n);                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/                   ij++;
  fclose(ficparo);                 }
  fclose(ficres);                 else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
 /*--------- index.htm --------*/               }
                fprintf(ficgp,")/(1");
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm);               
                for(k1=1; k1 <=nlstate; k1++){   
                   fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
   /*--------------- Prevalence limit --------------*/                 ij=1;
                   for(j=3; j <=ncovmodel; j++){
   strcpy(filerespl,"pl");                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   strcat(filerespl,fileres);                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {                     ij++;
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;                   }
   }                   else
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   fprintf(ficrespl,"#Prevalence limit\n");                 }
   fprintf(ficrespl,"#Age ");                 fprintf(ficgp,")");
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);               }
   fprintf(ficrespl,"\n");               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                 if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
   prlim=matrix(1,nlstate,1,nlstate);               i=i+ncovmodel;
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */             }
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */           } /* end k */
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */         } /* end k2 */
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       } /* end jk */
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */     } /* end ng */
   k=0;     fclose(ficgp); 
   agebase=agemin;  }  /* end gnuplot */
   agelim=agemaxpar;  
   ftolpl=1.e-10;  
   i1=cptcoveff;  /*************** Moving average **************/
   if (cptcovn < 1){i1=1;}  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
   for(cptcov=1;cptcov<=i1;cptcov++){    int i, cpt, cptcod;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    int modcovmax =1;
         k=k+1;    int mobilavrange, mob;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    double age;
         fprintf(ficrespl,"\n#******");  
         for(j=1;j<=cptcoveff;j++)    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                             a covariate has 2 modalities */
         fprintf(ficrespl,"******\n");    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
          
         for (age=agebase; age<=agelim; age++){    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      if(mobilav==1) mobilavrange=5; /* default */
           fprintf(ficrespl,"%.0f",age );      else mobilavrange=mobilav;
           for(i=1; i<=nlstate;i++)      for (age=bage; age<=fage; age++)
           fprintf(ficrespl," %.5f", prlim[i][i]);        for (i=1; i<=nlstate;i++)
           fprintf(ficrespl,"\n");          for (cptcod=1;cptcod<=modcovmax;cptcod++)
         }            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       }      /* We keep the original values on the extreme ages bage, fage and for 
     }         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
   fclose(ficrespl);         we use a 5 terms etc. until the borders are no more concerned. 
       */ 
   /*------------- h Pij x at various ages ------------*/      for (mob=3;mob <=mobilavrange;mob=mob+2){
          for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);          for (i=1; i<=nlstate;i++){
   if((ficrespij=fopen(filerespij,"w"))==NULL) {            for (cptcod=1;cptcod<=modcovmax;cptcod++){
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
   }                for (cpt=1;cpt<=(mob-1)/2;cpt++){
   printf("Computing pij: result on file '%s' \n", filerespij);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                    mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
   stepsize=(int) (stepm+YEARM-1)/YEARM;                }
   /*if (stepm<=24) stepsize=2;*/              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
   agelim=AGESUP;          }
   hstepm=stepsize*YEARM; /* Every year of age */        }/* end age */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */      }/* end mob */
      }else return -1;
   k=0;    return 0;
   for(cptcov=1;cptcov<=i1;cptcov++){  }/* End movingaverage */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;  
         fprintf(ficrespij,"\n#****** ");  /************** Forecasting ******************/
         for(j=1;j<=cptcoveff;j++)  prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /* proj1, year, month, day of starting projection 
         fprintf(ficrespij,"******\n");       agemin, agemax range of age
               dateprev1 dateprev2 range of dates during which prevalence is computed
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */       anproj2 year of en of projection (same day and month as proj1).
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int *popage;
           oldm=oldms;savm=savms;    double agec; /* generic age */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
           fprintf(ficrespij,"# Age");    double *popeffectif,*popcount;
           for(i=1; i<=nlstate;i++)    double ***p3mat;
             for(j=1; j<=nlstate+ndeath;j++)    double ***mobaverage;
               fprintf(ficrespij," %1d-%1d",i,j);    char fileresf[FILENAMELENGTH];
           fprintf(ficrespij,"\n");  
           for (h=0; h<=nhstepm; h++){    agelim=AGESUP;
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
             for(i=1; i<=nlstate;i++)   
               for(j=1; j<=nlstate+ndeath;j++)    strcpy(fileresf,"f"); 
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    strcat(fileresf,fileres);
             fprintf(ficrespij,"\n");    if((ficresf=fopen(fileresf,"w"))==NULL) {
           }      printf("Problem with forecast resultfile: %s\n", fileresf);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
           fprintf(ficrespij,"\n");    }
         }    printf("Computing forecasting: result on file '%s' \n", fileresf);
     }    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   }  
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/  
     if (mobilav!=0) {
   fclose(ficrespij);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   /*---------- Forecasting ------------------*/        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   if(stepm == 1) {      }
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    }
 if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);  
     free_matrix(mint,1,maxwav,1,n);    stepsize=(int) (stepm+YEARM-1)/YEARM;
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    if (stepm<=12) stepsize=1;
     free_vector(weight,1,n);}    if(estepm < stepm){
   else{      printf ("Problem %d lower than %d\n",estepm, stepm);
     erreur=108;    }
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);    else  hstepm=estepm;   
   }  
      hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
   /*---------- Health expectancies and variances ------------*/                                 fractional in yp1 */
     anprojmean=yp;
   strcpy(filerest,"t");    yp2=modf((yp1*12),&yp);
   strcat(filerest,fileres);    mprojmean=yp;
   if((ficrest=fopen(filerest,"w"))==NULL) {    yp1=modf((yp2*30.5),&yp);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    jprojmean=yp;
   }    if(jprojmean==0) jprojmean=1;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
   strcpy(filerese,"e");    if (cptcovn < 1){i1=1;}
   strcat(filerese,fileres);    
   if((ficreseij=fopen(filerese,"w"))==NULL) {    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    
   }    fprintf(ficresf,"#****** Routine prevforecast **\n");
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  
   /*            if (h==(int)(YEARM*yearp)){ */
  strcpy(fileresv,"v");    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
   strcat(fileresv,fileres);      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   if((ficresvij=fopen(fileresv,"w"))==NULL) {        k=k+1;
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        fprintf(ficresf,"\n#******");
   }        for(j=1;j<=cptcoveff;j++) {
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          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]]);
         }
   k=0;        fprintf(ficresf,"******\n");
   for(cptcov=1;cptcov<=i1;cptcov++){        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for(j=1; j<=nlstate+ndeath;j++){ 
       k=k+1;          for(i=1; i<=nlstate;i++)              
       fprintf(ficrest,"\n#****** ");            fprintf(ficresf," p%d%d",i,j);
       for(j=1;j<=cptcoveff;j++)          fprintf(ficresf," p.%d",j);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        }
       fprintf(ficrest,"******\n");        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
       fprintf(ficreseij,"\n#****** ");          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);          for (agec=fage; agec>=(ageminpar-1); agec--){ 
       fprintf(ficreseij,"******\n");            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
       fprintf(ficresvij,"\n#****** ");            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       for(j=1;j<=cptcoveff;j++)            oldm=oldms;savm=savms;
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
       fprintf(ficresvij,"******\n");          
             for (h=0; h<=nhstepm; h++){
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);              if (h*hstepm/YEARM*stepm ==yearp) {
       oldm=oldms;savm=savms;                fprintf(ficresf,"\n");
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);                  for(j=1;j<=cptcoveff;j++) 
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       oldm=oldms;savm=savms;                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);              } 
                  for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                  for(i=1; i<=nlstate;i++) {
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");                  if (mobilav==1) 
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
       fprintf(ficrest,"\n");                  else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
       hf=1;                  }
       if (stepm >= YEARM) hf=stepm/YEARM;                  if (h*hstepm/YEARM*stepm== yearp) {
       epj=vector(1,nlstate+1);                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
       for(age=bage; age <=fage ;age++){                  }
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                } /* end i */
         if (popbased==1) {                if (h*hstepm/YEARM*stepm==yearp) {
           for(i=1; i<=nlstate;i++)                  fprintf(ficresf," %.3f", ppij);
             prlim[i][i]=probs[(int)age][i][k];                }
         }              }/* end j */
                    } /* end h */
         fprintf(ficrest," %.0f",age);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){          } /* end agec */
           for(i=1, epj[j]=0.;i <=nlstate;i++) {        } /* end yearp */
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];      } /* end cptcod */
           }    } /* end  cptcov */
           epj[nlstate+1] +=epj[j];         
         }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         for(i=1, vepp=0.;i <=nlstate;i++)  
           for(j=1;j <=nlstate;j++)    fclose(ficresf);
             vepp += vareij[i][j][(int)age];  }
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));  
         for(j=1;j <=nlstate;j++){  /************** Forecasting *****not tested NB*************/
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));  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){
         }    
         fprintf(ficrest,"\n");    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
       }    int *popage;
     }    double calagedatem, agelim, kk1, kk2;
   }    double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
   fclose(ficreseij);    double ***mobaverage;
   fclose(ficresvij);    char filerespop[FILENAMELENGTH];
   fclose(ficrest);  
   fclose(ficpar);    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   free_vector(epj,1,nlstate+1);    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      agelim=AGESUP;
   /*------- Variance limit prevalence------*/      calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
   strcpy(fileresvpl,"vpl");    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   strcat(fileresvpl,fileres);    
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    strcpy(filerespop,"pop"); 
     exit(0);    strcat(filerespop,fileres);
   }    if((ficrespop=fopen(filerespop,"w"))==NULL) {
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);      printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
   k=0;    }
   for(cptcov=1;cptcov<=i1;cptcov++){    printf("Computing forecasting: result on file '%s' \n", filerespop);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
       k=k+1;  
       fprintf(ficresvpl,"\n#****** ");    if (cptcoveff==0) ncodemax[cptcoveff]=1;
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    if (mobilav!=0) {
       fprintf(ficresvpl,"******\n");      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
            if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
       varpl=matrix(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);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      }
     }    }
  }  
     stepsize=(int) (stepm+YEARM-1)/YEARM;
   fclose(ficresvpl);    if (stepm<=12) stepsize=1;
     
   /*---------- End : free ----------------*/    agelim=AGESUP;
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    
      hstepm=1;
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    hstepm=hstepm/stepm; 
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    
      if (popforecast==1) {
        if((ficpop=fopen(popfile,"r"))==NULL) {
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);        printf("Problem with population file : %s\n",popfile);exit(0);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      } 
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);      popage=ivector(0,AGESUP);
        popeffectif=vector(0,AGESUP);
   free_matrix(matcov,1,npar,1,npar);      popcount=vector(0,AGESUP);
   free_vector(delti,1,npar);      
   free_matrix(agev,1,maxwav,1,imx);      i=1;   
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
   if(erreur >0)      imx=i;
     printf("End of Imach with error %d\n",erreur);      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
   else   printf("End of Imach\n");    }
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */  
      for(cptcov=1,k=0;cptcov<=i2;cptcov++){
   /* 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(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   /*printf("Total time was %d uSec.\n", total_usecs);*/        k=k+1;
   /*------ End -----------*/        fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
  end:        }
 #ifdef windows        fprintf(ficrespop,"******\n");
   /* chdir(pathcd);*/        fprintf(ficrespop,"# Age");
 #endif        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
  /*system("wgnuplot graph.plt");*/        if (popforecast==1)  fprintf(ficrespop," [Population]");
  /*system("../gp37mgw/wgnuplot graph.plt");*/        
  /*system("cd ../gp37mgw");*/        for (cpt=0; cpt<=0;cpt++) { 
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
  strcpy(plotcmd,GNUPLOTPROGRAM);          
  strcat(plotcmd," ");          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
  strcat(plotcmd,optionfilegnuplot);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
  system(plotcmd);            nhstepm = nhstepm/hstepm; 
             
 #ifdef windows            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   while (z[0] != 'q') {            oldm=oldms;savm=savms;
     chdir(path);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
     printf("\nType e to edit output files, c to start again, and q for exiting: ");          
     scanf("%s",z);            for (h=0; h<=nhstepm; h++){
     if (z[0] == 'c') system("./imach");              if (h==(int) (calagedatem+YEARM*cpt)) {
     else if (z[0] == 'e') {                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
       chdir(path);              } 
       system(optionfilehtm);              for(j=1; j<=nlstate+ndeath;j++) {
     }                kk1=0.;kk2=0;
     else if (z[0] == 'q') exit(0);                for(i=1; i<=nlstate;i++) {              
   }                  if (mobilav==1) 
 #endif                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
 }                  else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   }
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     char z[1]="c", occ;
   #include <sys/time.h>
   #include <time.h>
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
    
     /* long total_usecs;
        struct timeval start_time, end_time;
     
        gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     replace(pathc,path);
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s",version);
     fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     fflush(ficlog);
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       goto end;
     }
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) {
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     
     /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++)
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)
           printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){
             printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
           }
           else
             fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);
         }
         fscanf(ficpar,"\n");
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     delti=delti3[1][1];
   
   
     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
           fprintf(ficlog," %.5le",matcov[i][j]);
         }
         else
           fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=ivector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           printf("Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           printf("Error! Month of death of individual %d on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %d on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1;
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   printf("Warning negative age at death: %d line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
   
       pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     jk=1;
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) 
           {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
       }
     }
     if(mle==1){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle==1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     fclose(ficgp);
     printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfile);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
   \n
   Total number of observations=%d <br>\n
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
   <hr  size=\"2\" color=\"#EC5E5E\">
    <ul><li><h4>Parameter files</h4>\n
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
    - Log file of the run: <a href=\"%s\">%s</a><br>\n
    - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,agemin,agemax,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
      fclose(fichtm);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     chdir(path);
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_ivector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     /*  fclose(fichtm);*/
     /*  fclose(ficgp);*/ /* ALready done */
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     
     /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
     /*printf("Total time was %d uSec.\n", total_usecs);*/
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     system(plotcmd);
     printf(" Wait...");
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   
Removed from v.1.28  
changed lines
  Added in v.1.81

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