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version 1.40, 2002/04/19 13:46:19 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
   probability 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 "wgnuplot"    read datafile
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    concatwav
 #define FILENAMELENGTH 80    if (mle >= 1)
 /*#define DEBUG*/      mlikeli
 #define windows    print results files
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    if mle==1 
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */       computes hessian
     read end of parameter file: agemin, agemax, bage, fage, estepm
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */        begin-prev-date,...
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    open gnuplot file
     open html file
 #define NINTERVMAX 8    stable prevalence
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */     for age prevalim()
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    h Pij x
 #define NCOVMAX 8 /* Maximum number of covariates */    variance of p varprob
 #define MAXN 20000    forecasting if prevfcast==1 prevforecast call prevalence()
 #define YEARM 12. /* Number of months per year */    health expectancies
 #define AGESUP 130    Variance-covariance of DFLE
 #define AGEBASE 40    prevalence()
      movingaverage()
     varevsij() 
 int erreur; /* Error number */    if popbased==1 varevsij(,popbased)
 int nvar;    total life expectancies
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Variance of stable prevalence
 int npar=NPARMAX;   end
 int nlstate=2; /* Number of live states */  */
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;  
    
 int *wav; /* Number of waves for this individuual 0 is possible */  #include <math.h>
 int maxwav; /* Maxim number of waves */  #include <stdio.h>
 int jmin, jmax; /* min, max spacing between 2 waves */  #include <stdlib.h>
 int mle, weightopt;  #include <unistd.h>
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  #define MAXLINE 256
 double jmean; /* Mean space between 2 waves */  #define GNUPLOTPROGRAM "gnuplot"
 double **oldm, **newm, **savm; /* Working pointers to matrices */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  #define FILENAMELENGTH 80
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  /*#define DEBUG*/
 FILE *ficgp,*ficresprob,*ficpop;  #define windows
 FILE *ficreseij;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   char filerese[FILENAMELENGTH];  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
  FILE  *ficresvij;  
   char fileresv[FILENAMELENGTH];  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
  FILE  *ficresvpl;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   char fileresvpl[FILENAMELENGTH];  
   #define NINTERVMAX 8
 #define NR_END 1  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #define FREE_ARG char*  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #define FTOL 1.0e-10  #define NCOVMAX 8 /* Maximum number of covariates */
   #define MAXN 20000
 #define NRANSI  #define YEARM 12. /* Number of months per year */
 #define ITMAX 200  #define AGESUP 130
   #define AGEBASE 40
 #define TOL 2.0e-4  #ifdef windows
   #define DIRSEPARATOR '\\'
 #define CGOLD 0.3819660  #define ODIRSEPARATOR '/'
 #define ZEPS 1.0e-10  #else
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  #define DIRSEPARATOR '/'
   #define ODIRSEPARATOR '\\'
 #define GOLD 1.618034  #endif
 #define GLIMIT 100.0  
 #define TINY 1.0e-20  /* $Id$ */
   /* $Log$
 static double maxarg1,maxarg2;   * Revision 1.81  2003/06/05 15:41:51  brouard
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))   * *** empty log message ***
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))   *
    /* Revision 1.80  2003/06/05 15:34:14  brouard
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  /* Trying to add the true revision in the program and log
 #define rint(a) floor(a+0.5)  /*
   /* Revision 1.79  2003/06/05 15:17:23  brouard
 static double sqrarg;  /* *** empty log message ***
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  /* */
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  /* $Revision$ */
   /* $Date$ */
 int imx;  /* $State$ */
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/  char version[80]="Imach version 0.95a1, June 2003, INED-EUROREVES ";
   char fullversion[]="$Revision$ $Date$"; 
 int estepm;  int erreur; /* Error number */
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  int nvar;
   int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 int m,nb;  int npar=NPARMAX;
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  int nlstate=2; /* Number of live states */
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  int ndeath=1; /* Number of dead states */
 double **pmmij, ***probs, ***mobaverage;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 double dateintmean=0;  int popbased=0;
   
 double *weight;  int *wav; /* Number of waves for this individuual 0 is possible */
 int **s; /* Status */  int maxwav; /* Maxim number of waves */
 double *agedc, **covar, idx;  int jmin, jmax; /* min, max spacing between 2 waves */
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  int mle, weightopt;
   int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 double ftolhess; /* Tolerance for computing hessian */  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
              * wave mi and wave mi+1 is not an exact multiple of stepm. */
 /**************** split *************************/  double jmean; /* Mean space between 2 waves */
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  double **oldm, **newm, **savm; /* Working pointers to matrices */
 {  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
    char *s;                             /* pointer */  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
    int  l1, l2;                         /* length counters */  FILE *ficlog, *ficrespow;
   FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
    l1 = strlen( path );                 /* length of path */  FILE *ficresprobmorprev;
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  FILE *fichtm; /* Html File */
 #ifdef windows  FILE *ficreseij;
    s = strrchr( path, '\\' );           /* find last / */  char filerese[FILENAMELENGTH];
 #else  FILE  *ficresvij;
    s = strrchr( path, '/' );            /* find last / */  char fileresv[FILENAMELENGTH];
 #endif  FILE  *ficresvpl;
    if ( s == NULL ) {                   /* no directory, so use current */  char fileresvpl[FILENAMELENGTH];
 #if     defined(__bsd__)                /* get current working directory */  char title[MAXLINE];
       extern char       *getwd( );  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
       if ( getwd( dirc ) == NULL ) {  
 #else  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       extern char       *getcwd( );  char filelog[FILENAMELENGTH]; /* Log file */
   char filerest[FILENAMELENGTH];
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  char fileregp[FILENAMELENGTH];
 #endif  char popfile[FILENAMELENGTH];
          return( GLOCK_ERROR_GETCWD );  
       }  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */  #define NR_END 1
       s++;                              /* after this, the filename */  #define FREE_ARG char*
       l2 = strlen( s );                 /* length of filename */  #define FTOL 1.0e-10
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */  #define NRANSI 
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  #define ITMAX 200 
       dirc[l1-l2] = 0;                  /* add zero */  
    }  #define TOL 2.0e-4 
    l1 = strlen( dirc );                 /* length of directory */  
 #ifdef windows  #define CGOLD 0.3819660 
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  #define ZEPS 1.0e-10 
 #else  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif  #define GOLD 1.618034 
    s = strrchr( name, '.' );            /* find last / */  #define GLIMIT 100.0 
    s++;  #define TINY 1.0e-20 
    strcpy(ext,s);                       /* save extension */  
    l1= strlen( name);  static double maxarg1,maxarg2;
    l2= strlen( s)+1;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
    strncpy( finame, name, l1-l2);  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
    finame[l1-l2]= 0;    
    return( 0 );                         /* we're done */  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 }  #define rint(a) floor(a+0.5)
   
   static double sqrarg;
 /******************************************/  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 void replace(char *s, char*t)  
 {  int imx; 
   int i;  int stepm;
   int lg=20;  /* Stepm, step in month: minimum step interpolation*/
   i=0;  
   lg=strlen(t);  int estepm;
   for(i=0; i<= lg; i++) {  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';  int m,nb;
   }  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 }  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double **pmmij, ***probs;
 int nbocc(char *s, char occ)  double dateintmean=0;
 {  
   int i,j=0;  double *weight;
   int lg=20;  int **s; /* Status */
   i=0;  double *agedc, **covar, idx;
   lg=strlen(s);  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   }  double ftolhess; /* Tolerance for computing hessian */
   return j;  
 }  /**************** split *************************/
   static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 void cutv(char *u,char *v, char*t, char occ)  {
 {    char  *ss;                            /* pointer */
   int i,lg,j,p=0;    int   l1, l2;                         /* length counters */
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {    l1 = strlen(path );                   /* length of path */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   }    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     if ( ss == NULL ) {                   /* no directory, so use current */
   lg=strlen(t);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   for(j=0; j<p; j++) {        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     (u[j] = t[j]);      /* get current working directory */
   }      /*    extern  char* getcwd ( char *buf , int len);*/
      u[p]='\0';      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
         return( GLOCK_ERROR_GETCWD );
    for(j=0; j<= lg; j++) {      }
     if (j>=(p+1))(v[j-p-1] = t[j]);      strcpy( name, path );               /* we've got it */
   }    } else {                              /* strip direcotry from path */
 }      ss++;                               /* after this, the filename */
       l2 = strlen( ss );                  /* length of filename */
 /********************** nrerror ********************/      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       strcpy( name, ss );         /* save file name */
 void nrerror(char error_text[])      strncpy( dirc, path, l1 - l2 );     /* now the directory */
 {      dirc[l1-l2] = 0;                    /* add zero */
   fprintf(stderr,"ERREUR ...\n");    }
   fprintf(stderr,"%s\n",error_text);    l1 = strlen( dirc );                  /* length of directory */
   exit(1);  #ifdef windows
 }    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
 /*********************** vector *******************/  #else
 double *vector(int nl, int nh)    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
 {  #endif
   double *v;    ss = strrchr( name, '.' );            /* find last / */
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    ss++;
   if (!v) nrerror("allocation failure in vector");    strcpy(ext,ss);                       /* save extension */
   return v-nl+NR_END;    l1= strlen( name);
 }    l2= strlen(ss)+1;
     strncpy( finame, name, l1-l2);
 /************************ free vector ******************/    finame[l1-l2]= 0;
 void free_vector(double*v, int nl, int nh)    return( 0 );                          /* we're done */
 {  }
   free((FREE_ARG)(v+nl-NR_END));  
 }  
   /******************************************/
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)  void replace(char *s, char*t)
 {  {
   int *v;    int i;
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    int lg=20;
   if (!v) nrerror("allocation failure in ivector");    i=0;
   return v-nl+NR_END;    lg=strlen(t);
 }    for(i=0; i<= lg; i++) {
       (s[i] = t[i]);
 /******************free ivector **************************/      if (t[i]== '\\') s[i]='/';
 void free_ivector(int *v, long nl, long nh)    }
 {  }
   free((FREE_ARG)(v+nl-NR_END));  
 }  int nbocc(char *s, char occ)
   {
 /******************* imatrix *******************************/    int i,j=0;
 int **imatrix(long nrl, long nrh, long ncl, long nch)    int lg=20;
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    i=0;
 {    lg=strlen(s);
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    for(i=0; i<= lg; i++) {
   int **m;    if  (s[i] == occ ) j++;
      }
   /* allocate pointers to rows */    return j;
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  }
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  void cutv(char *u,char *v, char*t, char occ)
   m -= nrl;  {
      /* cuts string t into u and v where u is ended by char occ excluding it
         and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   /* allocate rows and set pointers to them */       gives u="abcedf" and v="ghi2j" */
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    int i,lg,j,p=0;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    i=0;
   m[nrl] += NR_END;    for(j=0; j<=strlen(t)-1; j++) {
   m[nrl] -= ncl;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
      }
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
      lg=strlen(t);
   /* return pointer to array of pointers to rows */    for(j=0; j<p; j++) {
   return m;      (u[j] = t[j]);
 }    }
        u[p]='\0';
 /****************** free_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)     for(j=0; j<= lg; j++) {
       int **m;      if (j>=(p+1))(v[j-p-1] = t[j]);
       long nch,ncl,nrh,nrl;    }
      /* free an int matrix allocated by imatrix() */  }
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  /********************** nrerror ********************/
   free((FREE_ARG) (m+nrl-NR_END));  
 }  void nrerror(char error_text[])
   {
 /******************* matrix *******************************/    fprintf(stderr,"ERREUR ...\n");
 double **matrix(long nrl, long nrh, long ncl, long nch)    fprintf(stderr,"%s\n",error_text);
 {    exit(EXIT_FAILURE);
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  }
   double **m;  /*********************** vector *******************/
   double *vector(int nl, int nh)
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  {
   if (!m) nrerror("allocation failure 1 in matrix()");    double *v;
   m += NR_END;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   m -= nrl;    if (!v) nrerror("allocation failure in vector");
     return v-nl+NR_END;
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  }
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  /************************ free vector ******************/
   m[nrl] -= ncl;  void free_vector(double*v, int nl, int nh)
   {
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    free((FREE_ARG)(v+nl-NR_END));
   return m;  }
 }  
   /************************ivector *******************************/
 /*************************free matrix ************************/  char *cvector(long nl,long nh)
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  {
 {    char *v;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
   free((FREE_ARG)(m+nrl-NR_END));    if (!v) nrerror("allocation failure in cvector");
 }    return v-nl+NR_END;
   }
 /******************* ma3x *******************************/  
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  /******************free ivector **************************/
 {  void free_cvector(char *v, long nl, long nh)
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  {
   double ***m;    free((FREE_ARG)(v+nl-NR_END));
   }
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  /************************ivector *******************************/
   m += NR_END;  int *ivector(long nl,long nh)
   m -= nrl;  {
     int *v;
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    if (!v) nrerror("allocation failure in ivector");
   m[nrl] += NR_END;    return v-nl+NR_END;
   m[nrl] -= ncl;  }
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  /******************free ivector **************************/
   void free_ivector(int *v, long nl, long nh)
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  {
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    free((FREE_ARG)(v+nl-NR_END));
   m[nrl][ncl] += NR_END;  }
   m[nrl][ncl] -= nll;  
   for (j=ncl+1; j<=nch; j++)  /******************* imatrix *******************************/
     m[nrl][j]=m[nrl][j-1]+nlay;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
         /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   for (i=nrl+1; i<=nrh; i++) {  { 
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     for (j=ncl+1; j<=nch; j++)    int **m; 
       m[i][j]=m[i][j-1]+nlay;    
   }    /* allocate pointers to rows */ 
   return m;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 }    if (!m) nrerror("allocation failure 1 in matrix()"); 
     m += NR_END; 
 /*************************free ma3x ************************/    m -= nrl; 
 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));    /* allocate rows and set pointers to them */ 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   free((FREE_ARG)(m+nrl-NR_END));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
 }    m[nrl] += NR_END; 
     m[nrl] -= ncl; 
 /***************** f1dim *************************/    
 extern int ncom;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
 extern double *pcom,*xicom;    
 extern double (*nrfunc)(double []);    /* return pointer to array of pointers to rows */ 
      return m; 
 double f1dim(double x)  } 
 {  
   int j;  /****************** free_imatrix *************************/
   double f;  void free_imatrix(m,nrl,nrh,ncl,nch)
   double *xt;        int **m;
          long nch,ncl,nrh,nrl; 
   xt=vector(1,ncom);       /* free an int matrix allocated by imatrix() */ 
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  { 
   f=(*nrfunc)(xt);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   free_vector(xt,1,ncom);    free((FREE_ARG) (m+nrl-NR_END)); 
   return f;  } 
 }  
   /******************* matrix *******************************/
 /*****************brent *************************/  double **matrix(long nrl, long nrh, long ncl, long nch)
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  {
 {    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   int iter;    double **m;
   double a,b,d,etemp;  
   double fu,fv,fw,fx;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double ftemp;    if (!m) nrerror("allocation failure 1 in matrix()");
   double p,q,r,tol1,tol2,u,v,w,x,xm;    m += NR_END;
   double e=0.0;    m -= nrl;
    
   a=(ax < cx ? ax : cx);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   b=(ax > cx ? ax : cx);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   x=w=v=bx;    m[nrl] += NR_END;
   fw=fv=fx=(*f)(x);    m[nrl] -= ncl;
   for (iter=1;iter<=ITMAX;iter++) {  
     xm=0.5*(a+b);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    return m;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
     printf(".");fflush(stdout);     */
 #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);  
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  /*************************free matrix ************************/
 #endif  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  {
       *xmin=x;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       return fx;    free((FREE_ARG)(m+nrl-NR_END));
     }  }
     ftemp=fu;  
     if (fabs(e) > tol1) {  /******************* ma3x *******************************/
       r=(x-w)*(fx-fv);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       q=(x-v)*(fx-fw);  {
       p=(x-v)*q-(x-w)*r;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       q=2.0*(q-r);    double ***m;
       if (q > 0.0) p = -p;  
       q=fabs(q);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       etemp=e;    if (!m) nrerror("allocation failure 1 in matrix()");
       e=d;    m += NR_END;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    m -= nrl;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  
       else {    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         d=p/q;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         u=x+d;    m[nrl] += NR_END;
         if (u-a < tol2 || b-u < tol2)    m[nrl] -= ncl;
           d=SIGN(tol1,xm-x);  
       }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     }    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    m[nrl][ncl] += NR_END;
     fu=(*f)(u);    m[nrl][ncl] -= nll;
     if (fu <= fx) {    for (j=ncl+1; j<=nch; j++) 
       if (u >= x) a=x; else b=x;      m[nrl][j]=m[nrl][j-1]+nlay;
       SHFT(v,w,x,u)    
         SHFT(fv,fw,fx,fu)    for (i=nrl+1; i<=nrh; i++) {
         } else {      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
           if (u < x) a=u; else b=u;      for (j=ncl+1; j<=nch; j++) 
           if (fu <= fw || w == x) {        m[i][j]=m[i][j-1]+nlay;
             v=w;    }
             w=u;    return m; 
             fv=fw;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
             fw=fu;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
           } else if (fu <= fv || v == x || v == w) {    */
             v=u;  }
             fv=fu;  
           }  /*************************free ma3x ************************/
         }  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   }  {
   nrerror("Too many iterations in brent");    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   *xmin=x;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   return fx;    free((FREE_ARG)(m+nrl-NR_END));
 }  }
   
 /****************** mnbrak ***********************/  /***************** f1dim *************************/
   extern int ncom; 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  extern double *pcom,*xicom;
             double (*func)(double))  extern double (*nrfunc)(double []); 
 {   
   double ulim,u,r,q, dum;  double f1dim(double x) 
   double fu;  { 
      int j; 
   *fa=(*func)(*ax);    double f;
   *fb=(*func)(*bx);    double *xt; 
   if (*fb > *fa) {   
     SHFT(dum,*ax,*bx,dum)    xt=vector(1,ncom); 
       SHFT(dum,*fb,*fa,dum)    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       }    f=(*nrfunc)(xt); 
   *cx=(*bx)+GOLD*(*bx-*ax);    free_vector(xt,1,ncom); 
   *fc=(*func)(*cx);    return f; 
   while (*fb > *fc) {  } 
     r=(*bx-*ax)*(*fb-*fc);  
     q=(*bx-*cx)*(*fb-*fa);  /*****************brent *************************/
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  { 
     ulim=(*bx)+GLIMIT*(*cx-*bx);    int iter; 
     if ((*bx-u)*(u-*cx) > 0.0) {    double a,b,d,etemp;
       fu=(*func)(u);    double fu,fv,fw,fx;
     } else if ((*cx-u)*(u-ulim) > 0.0) {    double ftemp;
       fu=(*func)(u);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       if (fu < *fc) {    double e=0.0; 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))   
           SHFT(*fb,*fc,fu,(*func)(u))    a=(ax < cx ? ax : cx); 
           }    b=(ax > cx ? ax : cx); 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    x=w=v=bx; 
       u=ulim;    fw=fv=fx=(*f)(x); 
       fu=(*func)(u);    for (iter=1;iter<=ITMAX;iter++) { 
     } else {      xm=0.5*(a+b); 
       u=(*cx)+GOLD*(*cx-*bx);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       fu=(*func)(u);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     }      printf(".");fflush(stdout);
     SHFT(*ax,*bx,*cx,u)      fprintf(ficlog,".");fflush(ficlog);
       SHFT(*fa,*fb,*fc,fu)  #ifdef DEBUG
       }      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
 }      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
 /*************** linmin ************************/  #endif
       if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
 int ncom;        *xmin=x; 
 double *pcom,*xicom;        return fx; 
 double (*nrfunc)(double []);      } 
        ftemp=fu;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))      if (fabs(e) > tol1) { 
 {        r=(x-w)*(fx-fv); 
   double brent(double ax, double bx, double cx,        q=(x-v)*(fx-fw); 
                double (*f)(double), double tol, double *xmin);        p=(x-v)*q-(x-w)*r; 
   double f1dim(double x);        q=2.0*(q-r); 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,        if (q > 0.0) p = -p; 
               double *fc, double (*func)(double));        q=fabs(q); 
   int j;        etemp=e; 
   double xx,xmin,bx,ax;        e=d; 
   double fx,fb,fa;        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)); 
   ncom=n;        else { 
   pcom=vector(1,n);          d=p/q; 
   xicom=vector(1,n);          u=x+d; 
   nrfunc=func;          if (u-a < tol2 || b-u < tol2) 
   for (j=1;j<=n;j++) {            d=SIGN(tol1,xm-x); 
     pcom[j]=p[j];        } 
     xicom[j]=xi[j];      } else { 
   }        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   ax=0.0;      } 
   xx=1.0;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);      fu=(*f)(u); 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);      if (fu <= fx) { 
 #ifdef DEBUG        if (u >= x) a=x; else b=x; 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);        SHFT(v,w,x,u) 
 #endif          SHFT(fv,fw,fx,fu) 
   for (j=1;j<=n;j++) {          } else { 
     xi[j] *= xmin;            if (u < x) a=u; else b=u; 
     p[j] += xi[j];            if (fu <= fw || w == x) { 
   }              v=w; 
   free_vector(xicom,1,n);              w=u; 
   free_vector(pcom,1,n);              fv=fw; 
 }              fw=fu; 
             } else if (fu <= fv || v == x || v == w) { 
 /*************** powell ************************/              v=u; 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,              fv=fu; 
             double (*func)(double []))            } 
 {          } 
   void linmin(double p[], double xi[], int n, double *fret,    } 
               double (*func)(double []));    nrerror("Too many iterations in brent"); 
   int i,ibig,j;    *xmin=x; 
   double del,t,*pt,*ptt,*xit;    return fx; 
   double fp,fptt;  } 
   double *xits;  
   pt=vector(1,n);  /****************** mnbrak ***********************/
   ptt=vector(1,n);  
   xit=vector(1,n);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   xits=vector(1,n);              double (*func)(double)) 
   *fret=(*func)(p);  { 
   for (j=1;j<=n;j++) pt[j]=p[j];    double ulim,u,r,q, dum;
   for (*iter=1;;++(*iter)) {    double fu; 
     fp=(*fret);   
     ibig=0;    *fa=(*func)(*ax); 
     del=0.0;    *fb=(*func)(*bx); 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    if (*fb > *fa) { 
     for (i=1;i<=n;i++)      SHFT(dum,*ax,*bx,dum) 
       printf(" %d %.12f",i, p[i]);        SHFT(dum,*fb,*fa,dum) 
     printf("\n");        } 
     for (i=1;i<=n;i++) {    *cx=(*bx)+GOLD*(*bx-*ax); 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    *fc=(*func)(*cx); 
       fptt=(*fret);    while (*fb > *fc) { 
 #ifdef DEBUG      r=(*bx-*ax)*(*fb-*fc); 
       printf("fret=%lf \n",*fret);      q=(*bx-*cx)*(*fb-*fa); 
 #endif      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       printf("%d",i);fflush(stdout);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       linmin(p,xit,n,fret,func);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       if (fabs(fptt-(*fret)) > del) {      if ((*bx-u)*(u-*cx) > 0.0) { 
         del=fabs(fptt-(*fret));        fu=(*func)(u); 
         ibig=i;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       }        fu=(*func)(u); 
 #ifdef DEBUG        if (fu < *fc) { 
       printf("%d %.12e",i,(*fret));          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       for (j=1;j<=n;j++) {            SHFT(*fb,*fc,fu,(*func)(u)) 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);            } 
         printf(" x(%d)=%.12e",j,xit[j]);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       }        u=ulim; 
       for(j=1;j<=n;j++)        fu=(*func)(u); 
         printf(" p=%.12e",p[j]);      } else { 
       printf("\n");        u=(*cx)+GOLD*(*cx-*bx); 
 #endif        fu=(*func)(u); 
     }      } 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      SHFT(*ax,*bx,*cx,u) 
 #ifdef DEBUG        SHFT(*fa,*fb,*fc,fu) 
       int k[2],l;        } 
       k[0]=1;  } 
       k[1]=-1;  
       printf("Max: %.12e",(*func)(p));  /*************** linmin ************************/
       for (j=1;j<=n;j++)  
         printf(" %.12e",p[j]);  int ncom; 
       printf("\n");  double *pcom,*xicom;
       for(l=0;l<=1;l++) {  double (*nrfunc)(double []); 
         for (j=1;j<=n;j++) {   
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  { 
         }    double brent(double ax, double bx, double cx, 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));                 double (*f)(double), double tol, double *xmin); 
       }    double f1dim(double x); 
 #endif    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                 double *fc, double (*func)(double)); 
     int j; 
       free_vector(xit,1,n);    double xx,xmin,bx,ax; 
       free_vector(xits,1,n);    double fx,fb,fa;
       free_vector(ptt,1,n);   
       free_vector(pt,1,n);    ncom=n; 
       return;    pcom=vector(1,n); 
     }    xicom=vector(1,n); 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    nrfunc=func; 
     for (j=1;j<=n;j++) {    for (j=1;j<=n;j++) { 
       ptt[j]=2.0*p[j]-pt[j];      pcom[j]=p[j]; 
       xit[j]=p[j]-pt[j];      xicom[j]=xi[j]; 
       pt[j]=p[j];    } 
     }    ax=0.0; 
     fptt=(*func)(ptt);    xx=1.0; 
     if (fptt < fp) {    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       if (t < 0.0) {  #ifdef DEBUG
         linmin(p,xit,n,fret,func);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         for (j=1;j<=n;j++) {    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
           xi[j][ibig]=xi[j][n];  #endif
           xi[j][n]=xit[j];    for (j=1;j<=n;j++) { 
         }      xi[j] *= xmin; 
 #ifdef DEBUG      p[j] += xi[j]; 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    } 
         for(j=1;j<=n;j++)    free_vector(xicom,1,n); 
           printf(" %.12e",xit[j]);    free_vector(pcom,1,n); 
         printf("\n");  } 
 #endif  
       }  /*************** powell ************************/
     }  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   }              double (*func)(double [])) 
 }  { 
     void linmin(double p[], double xi[], int n, double *fret, 
 /**** Prevalence limit ****************/                double (*func)(double [])); 
     int i,ibig,j; 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    double del,t,*pt,*ptt,*xit;
 {    double fp,fptt;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    double *xits;
      matrix by transitions matrix until convergence is reached */    pt=vector(1,n); 
     ptt=vector(1,n); 
   int i, ii,j,k;    xit=vector(1,n); 
   double min, max, maxmin, maxmax,sumnew=0.;    xits=vector(1,n); 
   double **matprod2();    *fret=(*func)(p); 
   double **out, cov[NCOVMAX], **pmij();    for (j=1;j<=n;j++) pt[j]=p[j]; 
   double **newm;    for (*iter=1;;++(*iter)) { 
   double agefin, delaymax=50 ; /* Max number of years to converge */      fp=(*fret); 
       ibig=0; 
   for (ii=1;ii<=nlstate+ndeath;ii++)      del=0.0; 
     for (j=1;j<=nlstate+ndeath;j++){      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
     }      fprintf(ficrespow,"%d %.12f",*iter,*fret);
       for (i=1;i<=n;i++) {
    cov[1]=1.;        printf(" %d %.12f",i, p[i]);
          fprintf(ficlog," %d %.12lf",i, p[i]);
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        fprintf(ficrespow," %.12lf", p[i]);
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){      }
     newm=savm;      printf("\n");
     /* Covariates have to be included here again */      fprintf(ficlog,"\n");
      cov[2]=agefin;      fprintf(ficrespow,"\n");
        for (i=1;i<=n;i++) { 
       for (k=1; k<=cptcovn;k++) {        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        fptt=(*fret); 
         /*      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]]);*/  #ifdef DEBUG
       }        printf("fret=%lf \n",*fret);
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        fprintf(ficlog,"fret=%lf \n",*fret);
       for (k=1; k<=cptcovprod;k++)  #endif
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        printf("%d",i);fflush(stdout);
         fprintf(ficlog,"%d",i);fflush(ficlog);
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/        linmin(p,xit,n,fret,func); 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/        if (fabs(fptt-(*fret)) > del) { 
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/          del=fabs(fptt-(*fret)); 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);          ibig=i; 
         } 
     savm=oldm;  #ifdef DEBUG
     oldm=newm;        printf("%d %.12e",i,(*fret));
     maxmax=0.;        fprintf(ficlog,"%d %.12e",i,(*fret));
     for(j=1;j<=nlstate;j++){        for (j=1;j<=n;j++) {
       min=1.;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       max=0.;          printf(" x(%d)=%.12e",j,xit[j]);
       for(i=1; i<=nlstate; i++) {          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         sumnew=0;        }
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        for(j=1;j<=n;j++) {
         prlim[i][j]= newm[i][j]/(1-sumnew);          printf(" p=%.12e",p[j]);
         max=FMAX(max,prlim[i][j]);          fprintf(ficlog," p=%.12e",p[j]);
         min=FMIN(min,prlim[i][j]);        }
       }        printf("\n");
       maxmin=max-min;        fprintf(ficlog,"\n");
       maxmax=FMAX(maxmax,maxmin);  #endif
     }      } 
     if(maxmax < ftolpl){      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       return prlim;  #ifdef DEBUG
     }        int k[2],l;
   }        k[0]=1;
 }        k[1]=-1;
         printf("Max: %.12e",(*func)(p));
 /*************** transition probabilities ***************/        fprintf(ficlog,"Max: %.12e",(*func)(p));
         for (j=1;j<=n;j++) {
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )          printf(" %.12e",p[j]);
 {          fprintf(ficlog," %.12e",p[j]);
   double s1, s2;        }
   /*double t34;*/        printf("\n");
   int i,j,j1, nc, ii, jj;        fprintf(ficlog,"\n");
         for(l=0;l<=1;l++) {
     for(i=1; i<= nlstate; i++){          for (j=1;j<=n;j++) {
     for(j=1; j<i;j++){            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         /*s2 += param[i][j][nc]*cov[nc];*/            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];          }
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/          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)));
       ps[i][j]=s2;        }
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  #endif
     }  
     for(j=i+1; j<=nlstate+ndeath;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        free_vector(xit,1,n); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        free_vector(xits,1,n); 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/        free_vector(ptt,1,n); 
       }        free_vector(pt,1,n); 
       ps[i][j]=s2;        return; 
     }      } 
   }      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     /*ps[3][2]=1;*/      for (j=1;j<=n;j++) { 
         ptt[j]=2.0*p[j]-pt[j]; 
   for(i=1; i<= nlstate; i++){        xit[j]=p[j]-pt[j]; 
      s1=0;        pt[j]=p[j]; 
     for(j=1; j<i; j++)      } 
       s1+=exp(ps[i][j]);      fptt=(*func)(ptt); 
     for(j=i+1; j<=nlstate+ndeath; j++)      if (fptt < fp) { 
       s1+=exp(ps[i][j]);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     ps[i][i]=1./(s1+1.);        if (t < 0.0) { 
     for(j=1; j<i; j++)          linmin(p,xit,n,fret,func); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];          for (j=1;j<=n;j++) { 
     for(j=i+1; j<=nlstate+ndeath; j++)            xi[j][ibig]=xi[j][n]; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];            xi[j][n]=xit[j]; 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */          }
   } /* end i */  #ifdef DEBUG
           printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     for(jj=1; jj<= nlstate+ndeath; jj++){          for(j=1;j<=n;j++){
       ps[ii][jj]=0;            printf(" %.12e",xit[j]);
       ps[ii][ii]=1;            fprintf(ficlog," %.12e",xit[j]);
     }          }
   }          printf("\n");
           fprintf(ficlog,"\n");
   #endif
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        }
     for(jj=1; jj<= nlstate+ndeath; jj++){      } 
      printf("%lf ",ps[ii][jj]);    } 
    }  } 
     printf("\n ");  
     }  /**** Prevalence limit (stable prevalence)  ****************/
     printf("\n ");printf("%lf ",cov[2]);*/  
 /*  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  {
   goto end;*/    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     return ps;       matrix by transitions matrix until convergence is reached */
 }  
     int i, ii,j,k;
 /**************** Product of 2 matrices ******************/    double min, max, maxmin, maxmax,sumnew=0.;
     double **matprod2();
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    double **out, cov[NCOVMAX], **pmij();
 {    double **newm;
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    double agefin, delaymax=50 ; /* Max number of years to converge */
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  
   /* in, b, out are matrice of pointers which should have been initialized    for (ii=1;ii<=nlstate+ndeath;ii++)
      before: only the contents of out is modified. The function returns      for (j=1;j<=nlstate+ndeath;j++){
      a pointer to pointers identical to out */        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   long i, j, k;      }
   for(i=nrl; i<= nrh; i++)  
     for(k=ncolol; k<=ncoloh; k++)     cov[1]=1.;
       for(j=ncl,out[i][k]=0.; j<=nch; j++)   
         out[i][k] +=in[i][j]*b[j][k];   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   return out;      newm=savm;
 }      /* Covariates have to be included here again */
        cov[2]=agefin;
     
 /************* Higher Matrix Product ***************/        for (k=1; k<=cptcovn;k++) {
           cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )          /*      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]]);*/
 {        }
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
      duration (i.e. until        for (k=1; k<=cptcovprod;k++)
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  
      (typically every 2 years instead of every month which is too big).        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
      Model is determined by parameters x and covariates have to be        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
      included manually here.        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
      */  
       savm=oldm;
   int i, j, d, h, k;      oldm=newm;
   double **out, cov[NCOVMAX];      maxmax=0.;
   double **newm;      for(j=1;j<=nlstate;j++){
         min=1.;
   /* Hstepm could be zero and should return the unit matrix */        max=0.;
   for (i=1;i<=nlstate+ndeath;i++)        for(i=1; i<=nlstate; i++) {
     for (j=1;j<=nlstate+ndeath;j++){          sumnew=0;
       oldm[i][j]=(i==j ? 1.0 : 0.0);          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       po[i][j][0]=(i==j ? 1.0 : 0.0);          prlim[i][j]= newm[i][j]/(1-sumnew);
     }          max=FMAX(max,prlim[i][j]);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */          min=FMIN(min,prlim[i][j]);
   for(h=1; h <=nhstepm; h++){        }
     for(d=1; d <=hstepm; d++){        maxmin=max-min;
       newm=savm;        maxmax=FMAX(maxmax,maxmin);
       /* Covariates have to be included here again */      }
       cov[1]=1.;      if(maxmax < ftolpl){
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        return prlim;
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      }
       for (k=1; k<=cptcovage;k++)    }
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  }
       for (k=1; k<=cptcovprod;k++)  
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  /*************** transition probabilities ***************/ 
   
   double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  {
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    double s1, s2;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    /*double t34;*/
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    int i,j,j1, nc, ii, jj;
       savm=oldm;  
       oldm=newm;      for(i=1; i<= nlstate; i++){
     }      for(j=1; j<i;j++){
     for(i=1; i<=nlstate+ndeath; i++)        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       for(j=1;j<=nlstate+ndeath;j++) {          /*s2 += param[i][j][nc]*cov[nc];*/
         po[i][j][h]=newm[i][j];          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
          */        }
       }        ps[i][j]=s2;
   } /* end h */        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
   return po;      }
 }      for(j=i+1; j<=nlstate+ndeath;j++){
         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
 /*************** log-likelihood *************/          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
 double func( double *x)        }
 {        ps[i][j]=s2;
   int i, ii, j, k, mi, d, kk;      }
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    }
   double **out;      /*ps[3][2]=1;*/
   double sw; /* Sum of weights */  
   double lli; /* Individual log likelihood */    for(i=1; i<= nlstate; i++){
   long ipmx;       s1=0;
   /*extern weight */      for(j=1; j<i; j++)
   /* We are differentiating ll according to initial status */        s1+=exp(ps[i][j]);
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      for(j=i+1; j<=nlstate+ndeath; j++)
   /*for(i=1;i<imx;i++)        s1+=exp(ps[i][j]);
     printf(" %d\n",s[4][i]);      ps[i][i]=1./(s1+1.);
   */      for(j=1; j<i; j++)
   cov[1]=1.;        ps[i][j]= exp(ps[i][j])*ps[i][i];
       for(j=i+1; j<=nlstate+ndeath; j++)
   for(k=1; k<=nlstate; k++) ll[k]=0.;        ps[i][j]= exp(ps[i][j])*ps[i][i];
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    } /* end i */
     for(mi=1; mi<= wav[i]-1; mi++){  
       for (ii=1;ii<=nlstate+ndeath;ii++)    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      for(jj=1; jj<= nlstate+ndeath; jj++){
       for(d=0; d<dh[mi][i]; d++){        ps[ii][jj]=0;
         newm=savm;        ps[ii][ii]=1;
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      }
         for (kk=1; kk<=cptcovage;kk++) {    }
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  
         }  
            /*   for(ii=1; ii<= nlstate+ndeath; ii++){
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      for(jj=1; jj<= nlstate+ndeath; jj++){
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));       printf("%lf ",ps[ii][jj]);
         savm=oldm;     }
         oldm=newm;      printf("\n ");
              }
              printf("\n ");printf("%lf ",cov[2]);*/
       } /* end mult */  /*
          for(i=1; i<= npar; i++) printf("%f ",x[i]);
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    goto end;*/
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/      return ps;
       ipmx +=1;  }
       sw += weight[i];  
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  /**************** Product of 2 matrices ******************/
     } /* end of wave */  
   } /* end of individual */  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   {
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    /* in, b, out are matrice of pointers which should have been initialized 
   return -l;       before: only the contents of out is modified. The function returns
 }       a pointer to pointers identical to out */
     long i, j, k;
     for(i=nrl; i<= nrh; i++)
 /*********** Maximum Likelihood Estimation ***************/      for(k=ncolol; k<=ncoloh; k++)
         for(j=ncl,out[i][k]=0.; j<=nch; j++)
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))          out[i][k] +=in[i][j]*b[j][k];
 {  
   int i,j, iter;    return out;
   double **xi,*delti;  }
   double fret;  
   xi=matrix(1,npar,1,npar);  
   for (i=1;i<=npar;i++)  /************* Higher Matrix Product ***************/
     for (j=1;j<=npar;j++)  
       xi[i][j]=(i==j ? 1.0 : 0.0);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   printf("Powell\n");  {
   powell(p,xi,npar,ftol,&iter,&fret,func);    /* Computes the transition matrix starting at age 'age' over 
        'nhstepm*hstepm*stepm' months (i.e. until
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));       nhstepm*hstepm matrices. 
        Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
 }       (typically every 2 years instead of every month which is too big 
        for the memory).
 /**** Computes Hessian and covariance matrix ***/       Model is determined by parameters x and covariates have to be 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))       included manually here. 
 {  
   double  **a,**y,*x,pd;       */
   double **hess;  
   int i, j,jk;    int i, j, d, h, k;
   int *indx;    double **out, cov[NCOVMAX];
     double **newm;
   double hessii(double p[], double delta, int theta, double delti[]);  
   double hessij(double p[], double delti[], int i, int j);    /* Hstepm could be zero and should return the unit matrix */
   void lubksb(double **a, int npar, int *indx, double b[]) ;    for (i=1;i<=nlstate+ndeath;i++)
   void ludcmp(double **a, int npar, int *indx, double *d) ;      for (j=1;j<=nlstate+ndeath;j++){
         oldm[i][j]=(i==j ? 1.0 : 0.0);
   hess=matrix(1,npar,1,npar);        po[i][j][0]=(i==j ? 1.0 : 0.0);
       }
   printf("\nCalculation of the hessian matrix. Wait...\n");    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   for (i=1;i<=npar;i++){    for(h=1; h <=nhstepm; h++){
     printf("%d",i);fflush(stdout);      for(d=1; d <=hstepm; d++){
     hess[i][i]=hessii(p,ftolhess,i,delti);        newm=savm;
     /*printf(" %f ",p[i]);*/        /* Covariates have to be included here again */
     /*printf(" %lf ",hess[i][i]);*/        cov[1]=1.;
   }        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
          for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   for (i=1;i<=npar;i++) {        for (k=1; k<=cptcovage;k++)
     for (j=1;j<=npar;j++)  {          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       if (j>i) {        for (k=1; k<=cptcovprod;k++)
         printf(".%d%d",i,j);fflush(stdout);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         hess[i][j]=hessij(p,delti,i,j);  
         hess[j][i]=hess[i][j];      
         /*printf(" %lf ",hess[i][j]);*/        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       }        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     }        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   }                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   printf("\n");        savm=oldm;
         oldm=newm;
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");      }
        for(i=1; i<=nlstate+ndeath; i++)
   a=matrix(1,npar,1,npar);        for(j=1;j<=nlstate+ndeath;j++) {
   y=matrix(1,npar,1,npar);          po[i][j][h]=newm[i][j];
   x=vector(1,npar);          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
   indx=ivector(1,npar);           */
   for (i=1;i<=npar;i++)        }
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    } /* end h */
   ludcmp(a,npar,indx,&pd);    return po;
   }
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;  /*************** log-likelihood *************/
     lubksb(a,npar,indx,x);  double func( double *x)
     for (i=1;i<=npar;i++){  {
       matcov[i][j]=x[i];    int i, ii, j, k, mi, d, kk;
     }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   }    double **out;
     double sw; /* Sum of weights */
   printf("\n#Hessian matrix#\n");    double lli; /* Individual log likelihood */
   for (i=1;i<=npar;i++) {    int s1, s2;
     for (j=1;j<=npar;j++) {    double bbh, survp;
       printf("%.3e ",hess[i][j]);    long ipmx;
     }    /*extern weight */
     printf("\n");    /* We are differentiating ll according to initial status */
   }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
   /* Recompute Inverse */      printf(" %d\n",s[4][i]);
   for (i=1;i<=npar;i++)    */
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    cov[1]=1.;
   ludcmp(a,npar,indx,&pd);  
     for(k=1; k<=nlstate; k++) ll[k]=0.;
   /*  printf("\n#Hessian matrix recomputed#\n");  
     if(mle==1){
   for (j=1;j<=npar;j++) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for (i=1;i<=npar;i++) x[i]=0;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     x[j]=1;        for(mi=1; mi<= wav[i]-1; mi++){
     lubksb(a,npar,indx,x);          for (ii=1;ii<=nlstate+ndeath;ii++)
     for (i=1;i<=npar;i++){            for (j=1;j<=nlstate+ndeath;j++){
       y[i][j]=x[i];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       printf("%.3e ",y[i][j]);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     }            }
     printf("\n");          for(d=0; d<dh[mi][i]; d++){
   }            newm=savm;
   */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
   free_matrix(a,1,npar,1,npar);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   free_matrix(y,1,npar,1,npar);            }
   free_vector(x,1,npar);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   free_ivector(indx,1,npar);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   free_matrix(hess,1,npar,1,npar);            savm=oldm;
             oldm=newm;
           } /* end mult */
 }        
           /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
 /*************** hessian matrix ****************/          /* But now since version 0.9 we anticipate for bias and large stepm.
 double hessii( double x[], double delta, int theta, double delti[])           * 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 
   int i;           * the nearest (and in case of equal distance, to the lowest) interval but now
   int l=1, lmax=20;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   double k1,k2;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   double p2[NPARMAX+1];           * probability in order to take into account the bias as a fraction of the way
   double res;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;           * -stepm/2 to stepm/2 .
   double fx;           * For stepm=1 the results are the same as for previous versions of Imach.
   int k=0,kmax=10;           * For stepm > 1 the results are less biased than in previous versions. 
   double l1;           */
           s1=s[mw[mi][i]][i];
   fx=func(x);          s2=s[mw[mi+1][i]][i];
   for (i=1;i<=npar;i++) p2[i]=x[i];          bbh=(double)bh[mi][i]/(double)stepm; 
   for(l=0 ; l <=lmax; l++){          /* bias is positive if real duration
     l1=pow(10,l);           * is higher than the multiple of stepm and negative otherwise.
     delts=delt;           */
     for(k=1 ; k <kmax; k=k+1){          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       delt = delta*(l1*k);          if( s2 > nlstate){ 
       p2[theta]=x[theta] +delt;            /* i.e. if s2 is a death state and if the date of death is known then the contribution
       k1=func(p2)-fx;               to the likelihood is the probability to die between last step unit time and current 
       p2[theta]=x[theta]-delt;               step unit time, which is also the differences between probability to die before dh 
       k2=func(p2)-fx;               and probability to die before dh-stepm . 
       /*res= (k1-2.0*fx+k2)/delt/delt; */               In version up to 0.92 likelihood was computed
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          as if date of death was unknown. Death was treated as any other
                health state: the date of the interview describes the actual state
 #ifdef DEBUG          and not the date of a change in health state. The former idea was
       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);          to consider that at each interview the state was recorded
 #endif          (healthy, disable or death) and IMaCh was corrected; but when we
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          introduced the exact date of death then we should have modified
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          the contribution of an exact death to the likelihood. This new
         k=kmax;          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/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          and month of death but the probability to survive from last
         k=kmax; l=lmax*10.;          interview up to one month before death multiplied by the
       }          probability to die within a month. Thanks to Chris
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          Jackson for correcting this bug.  Former versions increased
         delts=delt;          mortality artificially. The bad side is that we add another loop
       }          which slows down the processing. The difference can be up to 10%
     }          lower mortality.
   }            */
   delti[theta]=delts;            lli=log(out[s1][s2] - savm[s1][s2]);
   return res;          }else{
              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 */
           } 
 double hessij( double x[], double delti[], int thetai,int thetaj)          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 {          /*if(lli ==000.0)*/
   int i;          /*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 l=1, l1, lmax=20;          ipmx +=1;
   double k1,k2,k3,k4,res,fx;          sw += weight[i];
   double p2[NPARMAX+1];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int k;        } /* end of wave */
       } /* end of individual */
   fx=func(x);    }  else if(mle==2){
   for (k=1; k<=2; k++) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for (i=1;i<=npar;i++) p2[i]=x[i];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     p2[thetai]=x[thetai]+delti[thetai]/k;        for(mi=1; mi<= wav[i]-1; mi++){
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          for (ii=1;ii<=nlstate+ndeath;ii++)
     k1=func(p2)-fx;            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     p2[thetai]=x[thetai]+delti[thetai]/k;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;            }
     k2=func(p2)-fx;          for(d=0; d<=dh[mi][i]; d++){
              newm=savm;
     p2[thetai]=x[thetai]-delti[thetai]/k;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            for (kk=1; kk<=cptcovage;kk++) {
     k3=func(p2)-fx;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
              }
     p2[thetai]=x[thetai]-delti[thetai]/k;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     k4=func(p2)-fx;            savm=oldm;
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */            oldm=newm;
 #ifdef DEBUG          } /* end mult */
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);        
 #endif          /*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.
   return res;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
 }           * (in months) between two waves is not a multiple of stepm, we rounded to 
            * the nearest (and in case of equal distance, to the lowest) interval but now
 /************** Inverse of matrix **************/           * we keep into memory the bias bh[mi][i] and also the previous matrix product
 void ludcmp(double **a, int n, int *indx, double *d)           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
 {           * probability in order to take into account the bias as a fraction of the way
   int i,imax,j,k;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   double big,dum,sum,temp;           * -stepm/2 to stepm/2 .
   double *vv;           * For stepm=1 the results are the same as for previous versions of Imach.
             * For stepm > 1 the results are less biased than in previous versions. 
   vv=vector(1,n);           */
   *d=1.0;          s1=s[mw[mi][i]][i];
   for (i=1;i<=n;i++) {          s2=s[mw[mi+1][i]][i];
     big=0.0;          bbh=(double)bh[mi][i]/(double)stepm; 
     for (j=1;j<=n;j++)          /* bias is positive if real duration
       if ((temp=fabs(a[i][j])) > big) big=temp;           * is higher than the multiple of stepm and negative otherwise.
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");           */
     vv[i]=1.0/big;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   }          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   for (j=1;j<=n;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 */
     for (i=1;i<j;i++) {          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       sum=a[i][j];          /*if(lli ==000.0)*/
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];          /*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); */
       a[i][j]=sum;          ipmx +=1;
     }          sw += weight[i];
     big=0.0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for (i=j;i<=n;i++) {        } /* end of wave */
       sum=a[i][j];      } /* end of individual */
       for (k=1;k<j;k++)    }  else if(mle==3){  /* exponential inter-extrapolation */
         sum -= a[i][k]*a[k][j];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       a[i][j]=sum;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       if ( (dum=vv[i]*fabs(sum)) >= big) {        for(mi=1; mi<= wav[i]-1; mi++){
         big=dum;          for (ii=1;ii<=nlstate+ndeath;ii++)
         imax=i;            for (j=1;j<=nlstate+ndeath;j++){
       }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     if (j != imax) {            }
       for (k=1;k<=n;k++) {          for(d=0; d<dh[mi][i]; d++){
         dum=a[imax][k];            newm=savm;
         a[imax][k]=a[j][k];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         a[j][k]=dum;            for (kk=1; kk<=cptcovage;kk++) {
       }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       *d = -(*d);            }
       vv[imax]=vv[j];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     indx[j]=imax;            savm=oldm;
     if (a[j][j] == 0.0) a[j][j]=TINY;            oldm=newm;
     if (j != n) {          } /* end mult */
       dum=1.0/(a[j][j]);        
       for (i=j+1;i<=n;i++) a[i][j] *= dum;          /*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 
   free_vector(vv,1,n);  /* Doesn't work */           * (in months) between two waves is not a multiple of stepm, we rounded to 
 ;           * the nearest (and in case of equal distance, to the lowest) interval but now
 }           * we keep into memory the bias bh[mi][i] and also the previous matrix product
            * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
 void lubksb(double **a, int n, int *indx, double b[])           * 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
   int i,ii=0,ip,j;           * -stepm/2 to stepm/2 .
   double sum;           * For stepm=1 the results are the same as for previous versions of Imach.
             * For stepm > 1 the results are less biased than in previous versions. 
   for (i=1;i<=n;i++) {           */
     ip=indx[i];          s1=s[mw[mi][i]][i];
     sum=b[ip];          s2=s[mw[mi+1][i]][i];
     b[ip]=b[i];          bbh=(double)bh[mi][i]/(double)stepm; 
     if (ii)          /* bias is positive if real duration
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];           * is higher than the multiple of stepm and negative otherwise.
     else if (sum) ii=i;           */
     b[i]=sum;          /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
   }          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   for (i=n;i>=1;i--) {          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     sum=b[i];          /*if(lli ==000.0)*/
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          /*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); */
     b[i]=sum/a[i][i];          ipmx +=1;
   }          sw += weight[i];
 }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
 /************ Frequencies ********************/      } /* end of individual */
 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)    }else{  /* ml=4 no inter-extrapolation */
 {  /* Some frequencies */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;        for(mi=1; mi<= wav[i]-1; mi++){
   double ***freq; /* Frequencies */          for (ii=1;ii<=nlstate+ndeath;ii++)
   double *pp;            for (j=1;j<=nlstate+ndeath;j++){
   double pos, k2, dateintsum=0,k2cpt=0;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   FILE *ficresp;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   char fileresp[FILENAMELENGTH];            }
            for(d=0; d<dh[mi][i]; d++){
   pp=vector(1,nlstate);            newm=savm;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   strcpy(fileresp,"p");            for (kk=1; kk<=cptcovage;kk++) {
   strcat(fileresp,fileres);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   if((ficresp=fopen(fileresp,"w"))==NULL) {            }
     printf("Problem with prevalence resultfile: %s\n", fileresp);          
     exit(0);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            savm=oldm;
   j1=0;            oldm=newm;
            } /* end mult */
   j=cptcoveff;        
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
            ipmx +=1;
   for(k1=1; k1<=j;k1++){          sw += weight[i];
     for(i1=1; i1<=ncodemax[k1];i1++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       j1++;        } /* end of wave */
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);      } /* end of individual */
         scanf("%d", i);*/    } /* End of if */
       for (i=-1; i<=nlstate+ndeath; i++)      for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         for (jk=-1; jk<=nlstate+ndeath; jk++)      /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
           for(m=agemin; m <= agemax+3; m++)    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
             freq[i][jk][m]=0;    return -l;
        }
       dateintsum=0;  
       k2cpt=0;  
       for (i=1; i<=imx; i++) {  /*********** Maximum Likelihood Estimation ***************/
         bool=1;  
         if  (cptcovn>0) {  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
           for (z1=1; z1<=cptcoveff; z1++)  {
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    int i,j, iter;
               bool=0;    double **xi;
         }    double fret;
         if (bool==1) {    char filerespow[FILENAMELENGTH];
           for(m=firstpass; m<=lastpass; m++){    xi=matrix(1,npar,1,npar);
             k2=anint[m][i]+(mint[m][i]/12.);    for (i=1;i<=npar;i++)
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      for (j=1;j<=npar;j++)
               if(agev[m][i]==0) agev[m][i]=agemax+1;        xi[i][j]=(i==j ? 1.0 : 0.0);
               if(agev[m][i]==1) agev[m][i]=agemax+2;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
               if (m<lastpass) {    strcpy(filerespow,"pow"); 
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    strcat(filerespow,fileres);
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    if((ficrespow=fopen(filerespow,"w"))==NULL) {
               }      printf("Problem with resultfile: %s\n", filerespow);
                    fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    }
                 dateintsum=dateintsum+k2;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
                 k2cpt++;    for (i=1;i<=nlstate;i++)
               }      for(j=1;j<=nlstate+ndeath;j++)
             }        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
           }    fprintf(ficrespow,"\n");
         }    powell(p,xi,npar,ftol,&iter,&fret,func);
       }  
            fclose(ficrespow);
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    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));
       if  (cptcovn>0) {    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         fprintf(ficresp, "\n#********** Variable ");  
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  }
         fprintf(ficresp, "**********\n#");  
       }  /**** Computes Hessian and covariance matrix ***/
       for(i=1; i<=nlstate;i++)  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  {
       fprintf(ficresp, "\n");    double  **a,**y,*x,pd;
          double **hess;
       for(i=(int)agemin; i <= (int)agemax+3; i++){    int i, j,jk;
         if(i==(int)agemax+3)    int *indx;
           printf("Total");  
         else    double hessii(double p[], double delta, int theta, double delti[]);
           printf("Age %d", i);    double hessij(double p[], double delti[], int i, int j);
         for(jk=1; jk <=nlstate ; jk++){    void lubksb(double **a, int npar, int *indx, double b[]) ;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    void ludcmp(double **a, int npar, int *indx, double *d) ;
             pp[jk] += freq[jk][m][i];  
         }    hess=matrix(1,npar,1,npar);
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=-1, pos=0; m <=0 ; m++)    printf("\nCalculation of the hessian matrix. Wait...\n");
             pos += freq[jk][m][i];    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
           if(pp[jk]>=1.e-10)    for (i=1;i<=npar;i++){
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      printf("%d",i);fflush(stdout);
           else      fprintf(ficlog,"%d",i);fflush(ficlog);
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      hess[i][i]=hessii(p,ftolhess,i,delti);
         }      /*printf(" %f ",p[i]);*/
       /*printf(" %lf ",hess[i][i]);*/
         for(jk=1; jk <=nlstate ; jk++){    }
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    
             pp[jk] += freq[jk][m][i];    for (i=1;i<=npar;i++) {
         }      for (j=1;j<=npar;j++)  {
         if (j>i) { 
         for(jk=1,pos=0; jk <=nlstate ; jk++)          printf(".%d%d",i,j);fflush(stdout);
           pos += pp[jk];          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
         for(jk=1; jk <=nlstate ; jk++){          hess[i][j]=hessij(p,delti,i,j);
           if(pos>=1.e-5)          hess[j][i]=hess[i][j];    
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          /*printf(" %lf ",hess[i][j]);*/
           else        }
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      }
           if( i <= (int) agemax){    }
             if(pos>=1.e-5){    printf("\n");
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    fprintf(ficlog,"\n");
               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]);*/    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
             }    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
             else    
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    a=matrix(1,npar,1,npar);
           }    y=matrix(1,npar,1,npar);
         }    x=vector(1,npar);
            indx=ivector(1,npar);
         for(jk=-1; jk <=nlstate+ndeath; jk++)    for (i=1;i<=npar;i++)
           for(m=-1; m <=nlstate+ndeath; m++)      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    ludcmp(a,npar,indx,&pd);
         if(i <= (int) agemax)  
           fprintf(ficresp,"\n");    for (j=1;j<=npar;j++) {
         printf("\n");      for (i=1;i<=npar;i++) x[i]=0;
       }      x[j]=1;
     }      lubksb(a,npar,indx,x);
   }      for (i=1;i<=npar;i++){ 
   dateintmean=dateintsum/k2cpt;        matcov[i][j]=x[i];
        }
   fclose(ficresp);    }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  
   free_vector(pp,1,nlstate);    printf("\n#Hessian matrix#\n");
      fprintf(ficlog,"\n#Hessian matrix#\n");
   /* End of Freq */    for (i=1;i<=npar;i++) { 
 }      for (j=1;j<=npar;j++) { 
         printf("%.3e ",hess[i][j]);
 /************ Prevalence ********************/        fprintf(ficlog,"%.3e ",hess[i][j]);
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)      }
 {  /* Some frequencies */      printf("\n");
        fprintf(ficlog,"\n");
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    }
   double ***freq; /* Frequencies */  
   double *pp;    /* Recompute Inverse */
   double pos, k2;    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   pp=vector(1,nlstate);    ludcmp(a,npar,indx,&pd);
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  
      /*  printf("\n#Hessian matrix recomputed#\n");
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  
   j1=0;    for (j=1;j<=npar;j++) {
        for (i=1;i<=npar;i++) x[i]=0;
   j=cptcoveff;      x[j]=1;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      lubksb(a,npar,indx,x);
        for (i=1;i<=npar;i++){ 
  for(k1=1; k1<=j;k1++){        y[i][j]=x[i];
     for(i1=1; i1<=ncodemax[k1];i1++){        printf("%.3e ",y[i][j]);
       j1++;        fprintf(ficlog,"%.3e ",y[i][j]);
        }
       for (i=-1; i<=nlstate+ndeath; i++)        printf("\n");
         for (jk=-1; jk<=nlstate+ndeath; jk++)        fprintf(ficlog,"\n");
           for(m=agemin; m <= agemax+3; m++)    }
             freq[i][jk][m]=0;    */
        
       for (i=1; i<=imx; i++) {    free_matrix(a,1,npar,1,npar);
         bool=1;    free_matrix(y,1,npar,1,npar);
         if  (cptcovn>0) {    free_vector(x,1,npar);
           for (z1=1; z1<=cptcoveff; z1++)    free_ivector(indx,1,npar);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    free_matrix(hess,1,npar,1,npar);
               bool=0;  
         }  
         if (bool==1) {  }
           for(m=firstpass; m<=lastpass; m++){  
             k2=anint[m][i]+(mint[m][i]/12.);  /*************** hessian matrix ****************/
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  double hessii( double x[], double delta, int theta, double delti[])
               if(agev[m][i]==0) agev[m][i]=agemax+1;  {
               if(agev[m][i]==1) agev[m][i]=agemax+2;    int i;
               if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    int l=1, lmax=20;
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */    double k1,k2;
             }    double p2[NPARMAX+1];
           }    double res;
         }    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       }    double fx;
         for(i=(int)agemin; i <= (int)agemax+3; i++){    int k=0,kmax=10;
           for(jk=1; jk <=nlstate ; jk++){    double l1;
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  
               pp[jk] += freq[jk][m][i];    fx=func(x);
           }    for (i=1;i<=npar;i++) p2[i]=x[i];
           for(jk=1; jk <=nlstate ; jk++){    for(l=0 ; l <=lmax; l++){
             for(m=-1, pos=0; m <=0 ; m++)      l1=pow(10,l);
             pos += freq[jk][m][i];      delts=delt;
         }      for(k=1 ; k <kmax; k=k+1){
                delt = delta*(l1*k);
          for(jk=1; jk <=nlstate ; jk++){        p2[theta]=x[theta] +delt;
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        k1=func(p2)-fx;
              pp[jk] += freq[jk][m][i];        p2[theta]=x[theta]-delt;
          }        k2=func(p2)-fx;
                  /*res= (k1-2.0*fx+k2)/delt/delt; */
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         
          for(jk=1; jk <=nlstate ; jk++){            #ifdef DEBUG
            if( i <= (int) agemax){        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);
              if(pos>=1.e-5){        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);
                probs[i][jk][j1]= pp[jk]/pos;  #endif
              }        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
            }        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
          }          k=kmax;
                  }
         }        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     }          k=kmax; l=lmax*10.;
   }        }
          else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
            delts=delt;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        }
   free_vector(pp,1,nlstate);      }
      }
 }  /* End of Freq */    delti[theta]=delts;
     return res; 
 /************* Waves Concatenation ***************/    
   }
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  
 {  double hessij( double x[], double delti[], int thetai,int thetaj)
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  {
      Death is a valid wave (if date is known).    int i;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    int l=1, l1, lmax=20;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    double k1,k2,k3,k4,res,fx;
      and mw[mi+1][i]. dh depends on stepm.    double p2[NPARMAX+1];
      */    int k;
   
   int i, mi, m;    fx=func(x);
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    for (k=1; k<=2; k++) {
      double sum=0., jmean=0.;*/      for (i=1;i<=npar;i++) p2[i]=x[i];
       p2[thetai]=x[thetai]+delti[thetai]/k;
   int j, k=0,jk, ju, jl;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   double sum=0.;      k1=func(p2)-fx;
   jmin=1e+5;    
   jmax=-1;      p2[thetai]=x[thetai]+delti[thetai]/k;
   jmean=0.;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   for(i=1; i<=imx; i++){      k2=func(p2)-fx;
     mi=0;    
     m=firstpass;      p2[thetai]=x[thetai]-delti[thetai]/k;
     while(s[m][i] <= nlstate){      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       if(s[m][i]>=1)      k3=func(p2)-fx;
         mw[++mi][i]=m;    
       if(m >=lastpass)      p2[thetai]=x[thetai]-delti[thetai]/k;
         break;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       else      k4=func(p2)-fx;
         m++;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     }/* end while */  #ifdef DEBUG
     if (s[m][i] > nlstate){      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       mi++;     /* Death is another wave */      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)  never been interviewed correctly before death */  #endif
          /* Only death is a correct wave */    }
       mw[mi][i]=m;    return res;
     }  }
   
     wav[i]=mi;  /************** Inverse of matrix **************/
     if(mi==0)  void ludcmp(double **a, int n, int *indx, double *d) 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  { 
   }    int i,imax,j,k; 
     double big,dum,sum,temp; 
   for(i=1; i<=imx; i++){    double *vv; 
     for(mi=1; mi<wav[i];mi++){   
       if (stepm <=0)    vv=vector(1,n); 
         dh[mi][i]=1;    *d=1.0; 
       else{    for (i=1;i<=n;i++) { 
         if (s[mw[mi+1][i]][i] > nlstate) {      big=0.0; 
           if (agedc[i] < 2*AGESUP) {      for (j=1;j<=n;j++) 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        if ((temp=fabs(a[i][j])) > big) big=temp; 
           if(j==0) j=1;  /* Survives at least one month after exam */      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
           k=k+1;      vv[i]=1.0/big; 
           if (j >= jmax) jmax=j;    } 
           if (j <= jmin) jmin=j;    for (j=1;j<=n;j++) { 
           sum=sum+j;      for (i=1;i<j;i++) { 
           /*if (j<0) printf("j=%d num=%d \n",j,i); */        sum=a[i][j]; 
           }        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         }        a[i][j]=sum; 
         else{      } 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));      big=0.0; 
           k=k+1;      for (i=j;i<=n;i++) { 
           if (j >= jmax) jmax=j;        sum=a[i][j]; 
           else if (j <= jmin)jmin=j;        for (k=1;k<j;k++) 
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          sum -= a[i][k]*a[k][j]; 
           sum=sum+j;        a[i][j]=sum; 
         }        if ( (dum=vv[i]*fabs(sum)) >= big) { 
         jk= j/stepm;          big=dum; 
         jl= j -jk*stepm;          imax=i; 
         ju= j -(jk+1)*stepm;        } 
         if(jl <= -ju)      } 
           dh[mi][i]=jk;      if (j != imax) { 
         else        for (k=1;k<=n;k++) { 
           dh[mi][i]=jk+1;          dum=a[imax][k]; 
         if(dh[mi][i]==0)          a[imax][k]=a[j][k]; 
           dh[mi][i]=1; /* At least one step */          a[j][k]=dum; 
       }        } 
     }        *d = -(*d); 
   }        vv[imax]=vv[j]; 
   jmean=sum/k;      } 
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);      indx[j]=imax; 
  }      if (a[j][j] == 0.0) a[j][j]=TINY; 
 /*********** Tricode ****************************/      if (j != n) { 
 void tricode(int *Tvar, int **nbcode, int imx)        dum=1.0/(a[j][j]); 
 {        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   int Ndum[20],ij=1, k, j, i;      } 
   int cptcode=0;    } 
   cptcoveff=0;    free_vector(vv,1,n);  /* Doesn't work */
    ;
   for (k=0; k<19; k++) Ndum[k]=0;  } 
   for (k=1; k<=7; k++) ncodemax[k]=0;  
   void lubksb(double **a, int n, int *indx, double b[]) 
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  { 
     for (i=1; i<=imx; i++) {    int i,ii=0,ip,j; 
       ij=(int)(covar[Tvar[j]][i]);    double sum; 
       Ndum[ij]++;   
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    for (i=1;i<=n;i++) { 
       if (ij > cptcode) cptcode=ij;      ip=indx[i]; 
     }      sum=b[ip]; 
       b[ip]=b[i]; 
     for (i=0; i<=cptcode; i++) {      if (ii) 
       if(Ndum[i]!=0) ncodemax[j]++;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     }      else if (sum) ii=i; 
     ij=1;      b[i]=sum; 
     } 
     for (i=n;i>=1;i--) { 
     for (i=1; i<=ncodemax[j]; i++) {      sum=b[i]; 
       for (k=0; k<=19; k++) {      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
         if (Ndum[k] != 0) {      b[i]=sum/a[i][i]; 
           nbcode[Tvar[j]][ij]=k;    } 
            } 
           ij++;  
         }  /************ Frequencies ********************/
         if (ij > ncodemax[j]) break;  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)
       }    {  /* Some frequencies */
     }    
   }      int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     int first;
  for (k=0; k<19; k++) Ndum[k]=0;    double ***freq; /* Frequencies */
     double *pp, **prop;
  for (i=1; i<=ncovmodel-2; i++) {    double pos,posprop, k2, dateintsum=0,k2cpt=0;
       ij=Tvar[i];    FILE *ficresp;
       Ndum[ij]++;    char fileresp[FILENAMELENGTH];
     }    
     pp=vector(1,nlstate);
  ij=1;    prop=matrix(1,nlstate,iagemin,iagemax+3);
  for (i=1; i<=10; i++) {    strcpy(fileresp,"p");
    if((Ndum[i]!=0) && (i<=ncovcol)){    strcat(fileresp,fileres);
      Tvaraff[ij]=i;    if((ficresp=fopen(fileresp,"w"))==NULL) {
      ij++;      printf("Problem with prevalence resultfile: %s\n", fileresp);
    }      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
  }      exit(0);
      }
     cptcoveff=ij-1;    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
 }    j1=0;
     
 /*********** Health Expectancies ****************/    j=cptcoveff;
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm)  
 {    first=1;
   /* Health expectancies */  
   int i, j, nhstepm, hstepm, h, nstepm;    for(k1=1; k1<=j;k1++){
   double age, agelim, hf;      for(i1=1; i1<=ncodemax[k1];i1++){
   double ***p3mat;        j1++;
          /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   fprintf(ficreseij,"# Health expectancies\n");          scanf("%d", i);*/
   fprintf(ficreseij,"# Age");        for (i=-1; i<=nlstate+ndeath; i++)  
   for(i=1; i<=nlstate;i++)          for (jk=-1; jk<=nlstate+ndeath; jk++)  
     for(j=1; j<=nlstate;j++)            for(m=iagemin; m <= iagemax+3; m++)
       fprintf(ficreseij," %1d-%1d",i,j);              freq[i][jk][m]=0;
   fprintf(ficreseij,"\n");  
       for (i=1; i<=nlstate; i++)  
   if(estepm < stepm){        for(m=iagemin; m <= iagemax+3; m++)
     printf ("Problem %d lower than %d\n",estepm, stepm);          prop[i][m]=0;
   }        
   else  hstepm=estepm;          dateintsum=0;
   /* We compute the life expectancy from trapezoids spaced every estepm months        k2cpt=0;
    * This is mainly to measure the difference between two models: for example        for (i=1; i<=imx; i++) {
    * if stepm=24 months pijx are given only every 2 years and by summing them          bool=1;
    * we are calculating an estimate of the Life Expectancy assuming a linear          if  (cptcovn>0) {
    * progression inbetween and thus overestimating or underestimating according            for (z1=1; z1<=cptcoveff; z1++) 
    * to the curvature of the survival function. If, for the same date, we              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
    * estimate the model with stepm=1 month, we can keep estepm to 24 months                bool=0;
    * to compare the new estimate of Life expectancy with the same linear          }
    * hypothesis. A more precise result, taking into account a more precise          if (bool==1){
    * curvature will be obtained if estepm is as small as stepm. */            for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
   /* For example we decided to compute the life expectancy with the smallest unit */              if ((k2>=dateprev1) && (k2<=dateprev2)) {
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.                if(agev[m][i]==0) agev[m][i]=iagemax+1;
      nhstepm is the number of hstepm from age to agelim                if(agev[m][i]==1) agev[m][i]=iagemax+2;
      nstepm is the number of stepm from age to agelin.                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
      Look at hpijx to understand the reason of that which relies in memory size                if (m<lastpass) {
      and note for a fixed period like estepm months */                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
      survival function given by stepm (the optimization length). Unfortunately it                }
      means that if the survival funtion is printed only each two years of age and if                
      you sum them up and add 1 year (area under the trapezoids) you won't get the same                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
      results. So we changed our mind and took the option of the best precision.                  dateintsum=dateintsum+k2;
   */                  k2cpt++;
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */                }
               }
   agelim=AGESUP;            }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          }
     /* nhstepm age range expressed in number of stepm */        }
     nstepm=(int) rint((agelim-age)*YEARM/stepm);         
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
     /* if (stepm >= YEARM) hstepm=1;*/  
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */        if  (cptcovn>0) {
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficresp, "\n#********** Variable "); 
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          fprintf(ficresp, "**********\n#");
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          }
          for(i=1; i<=nlstate;i++) 
     /*for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++) printf("%f %.5f\n", age*12+h, p3mat[1][1][h]);*/          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         fprintf(ficresp, "\n");
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        
     for(i=1; i<=nlstate;i++)        for(i=iagemin; i <= iagemax+3; i++){
       for(j=1; j<=nlstate;j++)          if(i==iagemax+3){
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){            fprintf(ficlog,"Total");
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;          }else{
           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/            if(first==1){
         }              first=0;
     fprintf(ficreseij,"%3.0f",age );              printf("See log file for details...\n");
     for(i=1; i<=nlstate;i++)            }
       for(j=1; j<=nlstate;j++){            fprintf(ficlog,"Age %d", i);
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);          }
       }          for(jk=1; jk <=nlstate ; jk++){
     fprintf(ficreseij,"\n");            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              pp[jk] += freq[jk][m][i]; 
   }          }
 }          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pos=0; m <=0 ; m++)
 /************ Variance ******************/              pos += freq[jk][m][i];
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)            if(pp[jk]>=1.e-10){
 {              if(first==1){
   /* Variance of health expectancies */              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/              }
   double **newm;              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   double **dnewm,**doldm;            }else{
   int i, j, nhstepm, hstepm, h, nstepm ;              if(first==1)
   int k, cptcode;                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   double *xp;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   double **gp, **gm;            }
   double ***gradg, ***trgradg;          }
   double ***p3mat;  
   double age,agelim, hf;          for(jk=1; jk <=nlstate ; jk++){
   int theta;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
               pp[jk] += freq[jk][m][i];
    fprintf(ficresvij,"# Covariances of life expectancies\n");          }       
   fprintf(ficresvij,"# Age");          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   for(i=1; i<=nlstate;i++)            pos += pp[jk];
     for(j=1; j<=nlstate;j++)            posprop += prop[jk][i];
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          }
   fprintf(ficresvij,"\n");          for(jk=1; jk <=nlstate ; jk++){
             if(pos>=1.e-5){
   xp=vector(1,npar);              if(first==1)
   dnewm=matrix(1,nlstate,1,npar);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   doldm=matrix(1,nlstate,1,nlstate);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
              }else{
   if(estepm < stepm){              if(first==1)
     printf ("Problem %d lower than %d\n",estepm, stepm);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   }              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   else  hstepm=estepm;              }
   /* For example we decided to compute the life expectancy with the smallest unit */            if( i <= iagemax){
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.              if(pos>=1.e-5){
      nhstepm is the number of hstepm from age to agelim                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
      nstepm is the number of stepm from age to agelin.                probs[i][jk][j1]= pp[jk]/pos;
      Look at hpijx to understand the reason of that which relies in memory size                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
      and note for a fixed period like k years */              }
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the              else
      survival function given by stepm (the optimization length). Unfortunately it                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
      means that if the survival funtion is printed only each two years of age and if            }
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          }
      results. So we changed our mind and took the option of the best precision.          
   */          for(jk=-1; jk <=nlstate+ndeath; jk++)
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */            for(m=-1; m <=nlstate+ndeath; m++)
   agelim = AGESUP;              if(freq[jk][m][i] !=0 ) {
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */              if(first==1)
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          if(i <= iagemax)
     gp=matrix(0,nhstepm,1,nlstate);            fprintf(ficresp,"\n");
     gm=matrix(0,nhstepm,1,nlstate);          if(first==1)
             printf("Others in log...\n");
     for(theta=1; theta <=npar; theta++){          fprintf(ficlog,"\n");
       for(i=1; i<=npar; i++){ /* Computes gradient */        }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      }
       }    }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      dateintmean=dateintsum/k2cpt; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);   
     fclose(ficresp);
       if (popbased==1) {    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
         for(i=1; i<=nlstate;i++)    free_vector(pp,1,nlstate);
           prlim[i][i]=probs[(int)age][i][ij];    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
       }    /* End of Freq */
    }
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){  /************ Prevalence ********************/
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  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)
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  {  
         }    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
       }       in each health status at the date of interview (if between dateprev1 and dateprev2).
           We still use firstpass and lastpass as another selection.
       for(i=1; i<=npar; i++) /* Computes gradient */    */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);   
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      int i, m, jk, k1, i1, j1, bool, z1,z2,j;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double ***freq; /* Frequencies */
      double *pp, **prop;
       if (popbased==1) {    double pos,posprop; 
         for(i=1; i<=nlstate;i++)    double  y2; /* in fractional years */
           prlim[i][i]=probs[(int)age][i][ij];    int iagemin, iagemax;
       }  
     iagemin= (int) agemin;
       for(j=1; j<= nlstate; j++){    iagemax= (int) agemax;
         for(h=0; h<=nhstepm; h++){    /*pp=vector(1,nlstate);*/
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    prop=matrix(1,nlstate,iagemin,iagemax+3); 
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
         }    j1=0;
       }    
     j=cptcoveff;
       for(j=1; j<= nlstate; j++)    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         for(h=0; h<=nhstepm; h++){    
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    for(k1=1; k1<=j;k1++){
         }      for(i1=1; i1<=ncodemax[k1];i1++){
     } /* End theta */        j1++;
         
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);        for (i=1; i<=nlstate; i++)  
           for(m=iagemin; m <= iagemax+3; m++)
     for(h=0; h<=nhstepm; h++)            prop[i][m]=0.0;
       for(j=1; j<=nlstate;j++)       
         for(theta=1; theta <=npar; theta++)        for (i=1; i<=imx; i++) { /* Each individual */
           trgradg[h][j][theta]=gradg[h][theta][j];          bool=1;
           if  (cptcovn>0) {
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */            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;
         vareij[i][j][(int)age] =0.;          } 
           if (bool==1) { 
     for(h=0;h<=nhstepm;h++){            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
       for(k=0;k<=nhstepm;k++){              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         for(i=1;i<=nlstate;i++)                if(agev[m][i]==1) agev[m][i]=iagemax+2;
           for(j=1;j<=nlstate;j++)                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); 
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;                if (s[m][i]>0 && s[m][i]<=nlstate) { 
       }                  /*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]]);*/
     }                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                   prop[s[m][i]][iagemax+3] += weight[i]; 
     fprintf(ficresvij,"%.0f ",age );                } 
     for(i=1; i<=nlstate;i++)              }
       for(j=1; j<=nlstate;j++){            } /* end selection of waves */
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);          }
       }        }
     fprintf(ficresvij,"\n");        for(i=iagemin; i <= iagemax+3; i++){  
     free_matrix(gp,0,nhstepm,1,nlstate);          
     free_matrix(gm,0,nhstepm,1,nlstate);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);            posprop += prop[jk][i]; 
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          } 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   } /* End age */          for(jk=1; jk <=nlstate ; jk++){     
              if( i <=  iagemax){ 
   free_vector(xp,1,npar);              if(posprop>=1.e-5){ 
   free_matrix(doldm,1,nlstate,1,npar);                probs[i][jk][j1]= prop[jk][i]/posprop;
   free_matrix(dnewm,1,nlstate,1,nlstate);              } 
             } 
 }          }/* end jk */ 
         }/* end i */ 
 /************ Variance of prevlim ******************/      } /* end i1 */
 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)    } /* end k1 */
 {    
   /* Variance of prevalence limit */    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    /*free_vector(pp,1,nlstate);*/
   double **newm;    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   double **dnewm,**doldm;  }  /* End of prevalence */
   int i, j, nhstepm, hstepm;  
   int k, cptcode;  /************* Waves Concatenation ***************/
   double *xp;  
   double *gp, *gm;  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)
   double **gradg, **trgradg;  {
   double age,agelim;    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   int theta;       Death is a valid wave (if date is known).
           mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   fprintf(ficresvpl,"# Age");       and mw[mi+1][i]. dh depends on stepm.
   for(i=1; i<=nlstate;i++)       */
       fprintf(ficresvpl," %1d-%1d",i,i);  
   fprintf(ficresvpl,"\n");    int i, mi, m;
     /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   xp=vector(1,npar);       double sum=0., jmean=0.;*/
   dnewm=matrix(1,nlstate,1,npar);    int first;
   doldm=matrix(1,nlstate,1,nlstate);    int j, k=0,jk, ju, jl;
      double sum=0.;
   hstepm=1*YEARM; /* Every year of age */    first=0;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    jmin=1e+5;
   agelim = AGESUP;    jmax=-1;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    jmean=0.;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    for(i=1; i<=imx; i++){
     if (stepm >= YEARM) hstepm=1;      mi=0;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      m=firstpass;
     gradg=matrix(1,npar,1,nlstate);      while(s[m][i] <= nlstate){
     gp=vector(1,nlstate);        if(s[m][i]>=1)
     gm=vector(1,nlstate);          mw[++mi][i]=m;
         if(m >=lastpass)
     for(theta=1; theta <=npar; theta++){          break;
       for(i=1; i<=npar; i++){ /* Computes gradient */        else
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          m++;
       }      }/* end while */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      if (s[m][i] > nlstate){
       for(i=1;i<=nlstate;i++)        mi++;     /* Death is another wave */
         gp[i] = prlim[i][i];        /* if(mi==0)  never been interviewed correctly before death */
               /* Only death is a correct wave */
       for(i=1; i<=npar; i++) /* Computes gradient */        mw[mi][i]=m;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)      wav[i]=mi;
         gm[i] = prlim[i][i];      if(mi==0){
         if(first==0){
       for(i=1;i<=nlstate;i++)          printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          first=1;
     } /* End theta */        }
         if(first==1){
     trgradg =matrix(1,nlstate,1,npar);          fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
         }
     for(j=1; j<=nlstate;j++)      } /* end mi==0 */
       for(theta=1; theta <=npar; theta++)    } /* End individuals */
         trgradg[j][theta]=gradg[theta][j];  
     for(i=1; i<=imx; i++){
     for(i=1;i<=nlstate;i++)      for(mi=1; mi<wav[i];mi++){
       varpl[i][(int)age] =0.;        if (stepm <=0)
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          dh[mi][i]=1;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        else{
     for(i=1;i<=nlstate;i++)          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */            if (agedc[i] < 2*AGESUP) {
             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     fprintf(ficresvpl,"%.0f ",age );            if(j==0) j=1;  /* Survives at least one month after exam */
     for(i=1; i<=nlstate;i++)            k=k+1;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));            if (j >= jmax) jmax=j;
     fprintf(ficresvpl,"\n");            if (j <= jmin) jmin=j;
     free_vector(gp,1,nlstate);            sum=sum+j;
     free_vector(gm,1,nlstate);            /*if (j<0) printf("j=%d num=%d \n",j,i);*/
     free_matrix(gradg,1,npar,1,nlstate);            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     free_matrix(trgradg,1,nlstate,1,npar);            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]);
   } /* End age */            }
           }
   free_vector(xp,1,npar);          else{
   free_matrix(doldm,1,nlstate,1,npar);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   free_matrix(dnewm,1,nlstate,1,nlstate);            /*      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;
             else if (j <= jmin)jmin=j;
 /************ Variance of one-step probabilities  ******************/            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)            /*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]);
   int i, j, i1, k1, j1, z1;            sum=sum+j;
   int k=0, cptcode;          }
   double **dnewm,**doldm;          jk= j/stepm;
   double *xp;          jl= j -jk*stepm;
   double *gp, *gm;          ju= j -(jk+1)*stepm;
   double **gradg, **trgradg;          if(mle <=1){ 
   double age,agelim, cov[NCOVMAX];            if(jl==0){
   int theta;              dh[mi][i]=jk;
   char fileresprob[FILENAMELENGTH];              bh[mi][i]=0;
             }else{ /* We want a negative bias in order to only have interpolation ie
   strcpy(fileresprob,"prob");                    * at the price of an extra matrix product in likelihood */
   strcat(fileresprob,fileres);              dh[mi][i]=jk+1;
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {              bh[mi][i]=ju;
     printf("Problem with resultfile: %s\n", fileresprob);            }
   }          }else{
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);            if(jl <= -ju){
                dh[mi][i]=jk;
               bh[mi][i]=jl;       /* bias is positive if real duration
   xp=vector(1,npar);                                   * is higher than the multiple of stepm and negative otherwise.
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);                                   */
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));            }
              else{
   cov[1]=1;              dh[mi][i]=jk+1;
   j=cptcoveff;              bh[mi][i]=ju;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            }
   j1=0;            if(dh[mi][i]==0){
   for(k1=1; k1<=1;k1++){              dh[mi][i]=1; /* At least one step */
     for(i1=1; i1<=ncodemax[k1];i1++){              bh[mi][i]=ju; /* At least one step */
     j1++;              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
             }
     if  (cptcovn>0) {          }
       fprintf(ficresprob, "\n#********** Variable ");        } /* end if mle */
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      } /* end wave */
       fprintf(ficresprob, "**********\n#");    }
     }    jmean=sum/k;
        printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
       for (age=bage; age<=fage; age ++){    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
         cov[2]=age;   }
         for (k=1; k<=cptcovn;k++) {  
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];  /*********** Tricode ****************************/
            void tricode(int *Tvar, int **nbcode, int imx)
         }  {
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    
         for (k=1; k<=cptcovprod;k++)    int Ndum[20],ij=1, k, j, i, maxncov=19;
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    int cptcode=0;
            cptcoveff=0; 
         gradg=matrix(1,npar,1,9);   
         trgradg=matrix(1,9,1,npar);    for (k=0; k<maxncov; k++) Ndum[k]=0;
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    for (k=1; k<=7; k++) ncodemax[k]=0;
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  
        for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
         for(theta=1; theta <=npar; theta++){      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
           for(i=1; i<=npar; i++)                                 modality*/ 
             xp[i] = x[i] + (i==theta ?delti[theta]:0);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
                  Ndum[ij]++; /*store the modality */
           pmij(pmmij,cov,ncovmodel,xp,nlstate);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
                  if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
           k=0;                                         Tvar[j]. If V=sex and male is 0 and 
           for(i=1; i<= (nlstate+ndeath); i++){                                         female is 1, then  cptcode=1.*/
             for(j=1; j<=(nlstate+ndeath);j++){      }
               k=k+1;  
               gp[k]=pmmij[i][j];      for (i=0; i<=cptcode; i++) {
             }        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
           }      }
            
           for(i=1; i<=npar; i++)      ij=1; 
             xp[i] = x[i] - (i==theta ?delti[theta]:0);      for (i=1; i<=ncodemax[j]; i++) {
            for (k=0; k<= maxncov; k++) {
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          if (Ndum[k] != 0) {
           k=0;            nbcode[Tvar[j]][ij]=k; 
           for(i=1; i<=(nlstate+ndeath); i++){            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
             for(j=1; j<=(nlstate+ndeath);j++){            
               k=k+1;            ij++;
               gm[k]=pmmij[i][j];          }
             }          if (ij > ncodemax[j]) break; 
           }        }  
            } 
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    }  
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];    
         }   for (k=0; k< maxncov; k++) Ndum[k]=0;
   
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)   for (i=1; i<=ncovmodel-2; i++) { 
           for(theta=1; theta <=npar; theta++)     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
             trgradg[j][theta]=gradg[theta][j];     ij=Tvar[i];
             Ndum[ij]++;
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);   }
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);  
           ij=1;
         pmij(pmmij,cov,ncovmodel,x,nlstate);   for (i=1; i<= maxncov; i++) {
             if((Ndum[i]!=0) && (i<=ncovcol)){
         k=0;       Tvaraff[ij]=i; /*For printing */
         for(i=1; i<=(nlstate+ndeath); i++){       ij++;
           for(j=1; j<=(nlstate+ndeath);j++){     }
             k=k+1;   }
             gm[k]=pmmij[i][j];   
           }   cptcoveff=ij-1; /*Number of simple covariates*/
         }  }
        
      /*printf("\n%d ",(int)age);  /*********** Health Expectancies ****************/
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){  
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
      }*/  
   {
         fprintf(ficresprob,"\n%d ",(int)age);    /* Health expectancies */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)    double age, agelim, hf;
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],doldm[i][i]);    double ***p3mat,***varhe;
      double **dnewm,**doldm;
       }    double *xp;
     }    double **gp, **gm;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    double ***gradg, ***trgradg;
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    int theta;
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   }    xp=vector(1,npar);
   free_vector(xp,1,npar);    dnewm=matrix(1,nlstate*nlstate,1,npar);
   fclose(ficresprob);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
      
 }    fprintf(ficreseij,"# Health expectancies\n");
     fprintf(ficreseij,"# Age");
 /******************* Printing html file ***********/    for(i=1; i<=nlstate;i++)
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \      for(j=1; j<=nlstate;j++)
  int lastpass, int stepm, int weightopt, char model[],\        fprintf(ficreseij," %1d-%1d (SE)",i,j);
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \    fprintf(ficreseij,"\n");
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\  
  char version[], int popforecast, int estepm ){    if(estepm < stepm){
   int jj1, k1, i1, cpt;      printf ("Problem %d lower than %d\n",estepm, stepm);
   FILE *fichtm;    }
   /*char optionfilehtm[FILENAMELENGTH];*/    else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
   strcpy(optionfilehtm,optionfile);     * This is mainly to measure the difference between two models: for example
   strcat(optionfilehtm,".htm");     * if stepm=24 months pijx are given only every 2 years and by summing them
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {     * we are calculating an estimate of the Life Expectancy assuming a linear 
     printf("Problem with %s \n",optionfilehtm), exit(0);     * 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
  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n     * to compare the new estimate of Life expectancy with the same linear 
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n     * hypothesis. A more precise result, taking into account a more precise
 \n     * curvature will be obtained if estepm is as small as stepm. */
 Total number of observations=%d <br>\n  
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n    /* For example we decided to compute the life expectancy with the smallest unit */
 <hr  size=\"2\" color=\"#EC5E5E\">    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
  <ul><li>Outputs files<br>\n       nhstepm is the number of hstepm from age to agelim 
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n       nstepm is the number of stepm from age to agelin. 
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n       Look at hpijx to understand the reason of that which relies in memory size
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n       and note for a fixed period like estepm months */
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n       survival function given by stepm (the optimization length). Unfortunately it
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,estepm,fileres,fileres);       means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
  fprintf(fichtm,"\n       results. So we changed our mind and took the option of the best precision.
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n    */
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n  
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);    agelim=AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
  if(popforecast==1) fprintf(fichtm,"\n      /* nhstepm age range expressed in number of stepm */
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
         <br>",fileres,fileres,fileres,fileres);      /* if (stepm >= YEARM) hstepm=1;*/
  else      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
    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);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 fprintf(fichtm," <li>Graphs</li><p>");      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
       gp=matrix(0,nhstepm,1,nlstate*nlstate);
  m=cptcoveff;      gm=matrix(0,nhstepm,1,nlstate*nlstate);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  
       /* Computed by stepm unit matrices, product of hstepm matrices, stored
  jj1=0;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
  for(k1=1; k1<=m;k1++){      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
    for(i1=1; i1<=ncodemax[k1];i1++){   
        jj1++;  
        if (cptcovn > 0) {      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");  
          for (cpt=1; cpt<=cptcoveff;cpt++)      /* Computing Variances of health expectancies */
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);  
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");       for(theta=1; theta <=npar; theta++){
        }        for(i=1; i<=npar; i++){ 
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            }
        for(cpt=1; cpt<nlstate;cpt++){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        cptj=0;
        }        for(j=1; j<= nlstate; j++){
     for(cpt=1; cpt<=nlstate;cpt++) {          for(i=1; i<=nlstate; i++){
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident            cptj=cptj+1;
 interval) in state (%d): v%s%d%d.gif <br>            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);                gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
      }            }
      for(cpt=1; cpt<=nlstate;cpt++) {          }
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>        }
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);       
      }       
      fprintf(fichtm,"\n<br>- Total life expectancy by age and        for(i=1; i<=npar; i++) 
 health expectancies in states (1) and (2): e%s%d.gif<br>          xp[i] = x[i] - (i==theta ?delti[theta]:0);
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 fprintf(fichtm,"\n</body>");        
    }        cptj=0;
    }        for(j=1; j<= nlstate; j++){
 fclose(fichtm);          for(i=1;i<=nlstate;i++){
 }            cptj=cptj+1;
             for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
 /******************* Gnuplot file **************/  
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
             }
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;          }
         }
   strcpy(optionfilegnuplot,optionfilefiname);        for(j=1; j<= nlstate*nlstate; j++)
   strcat(optionfilegnuplot,".gp.txt");          for(h=0; h<=nhstepm-1; h++){
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     printf("Problem with file %s",optionfilegnuplot);          }
   }       } 
      
 #ifdef windows  /* End theta */
     fprintf(ficgp,"cd \"%s\" \n",pathc);  
 #endif       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
 m=pow(2,cptcoveff);  
         for(h=0; h<=nhstepm-1; h++)
  /* 1eme*/        for(j=1; j<=nlstate*nlstate;j++)
   for (cpt=1; cpt<= nlstate ; cpt ++) {          for(theta=1; theta <=npar; theta++)
    for (k1=1; k1<= m ; k1 ++) {            trgradg[h][j][theta]=gradg[h][theta][j];
        
 #ifdef windows  
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);       for(i=1;i<=nlstate*nlstate;i++)
 #endif        for(j=1;j<=nlstate*nlstate;j++)
 #ifdef unix          varhe[i][j][(int)age] =0.;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);  
 #endif       printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
 for (i=1; i<= nlstate ; i ++) {       for(h=0;h<=nhstepm-1;h++){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        for(k=0;k<=nhstepm-1;k++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
 }          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);          for(i=1;i<=nlstate*nlstate;i++)
     for (i=1; i<= nlstate ; i ++) {            for(j=1;j<=nlstate*nlstate;j++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
   else fprintf(ficgp," \%%*lf (\%%*lf)");        }
 }      }
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      /* Computing expectancies */
      for (i=1; i<= nlstate ; i ++) {      for(i=1; i<=nlstate;i++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        for(j=1; j<=nlstate;j++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
 }              eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));            
 #ifdef unix  /* 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,"\nset ter gif small size 400,300");  
 #endif          }
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
    }      fprintf(ficreseij,"%3.0f",age );
   }      cptj=0;
   /*2 eme*/      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
   for (k1=1; k1<= m ; k1 ++) {          cptj++;
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
            }
     for (i=1; i<= nlstate+1 ; i ++) {      fprintf(ficreseij,"\n");
       k=2*i;     
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
       for (j=1; j<= nlstate+1 ; j ++) {      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
 }        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    }
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    printf("\n");
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    fprintf(ficlog,"\n");
       for (j=1; j<= nlstate+1 ; j ++) {  
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    free_vector(xp,1,npar);
         else fprintf(ficgp," \%%*lf (\%%*lf)");    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
 }      free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
       fprintf(ficgp,"\" t\"\" w l 0,");    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
      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)");  /************ Variance ******************/
   else fprintf(ficgp," \%%*lf (\%%*lf)");  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)
 }    {
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    /* Variance of health expectancies */
       else fprintf(ficgp,"\" t\"\" w l 0,");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     }    /* double **newm;*/
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    double **dnewm,**doldm;
   }    double **dnewmp,**doldmp;
      int i, j, nhstepm, hstepm, h, nstepm ;
   /*3eme*/    int k, cptcode;
     double *xp;
   for (k1=1; k1<= m ; k1 ++) {    double **gp, **gm;  /* for var eij */
     for (cpt=1; cpt<= nlstate ; cpt ++) {    double ***gradg, ***trgradg; /*for var eij */
       k=2+nlstate*(cpt-1);    double **gradgp, **trgradgp; /* for var p point j */
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    double *gpp, *gmp; /* for var p point j */
       for (i=1; i< nlstate ; i ++) {    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
         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);    double ***p3mat;
       }    double age,agelim, hf;
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    double ***mobaverage;
     }    int theta;
     }    char digit[4];
      char digitp[25];
   /* CV preval stat */  
     for (k1=1; k1<= m ; k1 ++) {    char fileresprobmorprev[FILENAMELENGTH];
     for (cpt=1; cpt<nlstate ; cpt ++) {  
       k=3;    if(popbased==1){
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);      if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
       for (i=1; i< nlstate ; i ++)      else strcpy(digitp,"-populbased-nomobil-");
         fprintf(ficgp,"+$%d",k+i+1);    }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    else 
            strcpy(digitp,"-stablbased-");
       l=3+(nlstate+ndeath)*cpt;  
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    if (mobilav!=0) {
       for (i=1; i< nlstate ; i ++) {      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         l=3+(nlstate+ndeath)*cpt;      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficgp,"+$%d",l+i+1);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       }        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);        }
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    }
     }  
   }      strcpy(fileresprobmorprev,"prmorprev"); 
      sprintf(digit,"%-d",ij);
   /* proba elementaires */    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
    for(i=1,jk=1; i <=nlstate; i++){    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     for(k=1; k <=(nlstate+ndeath); k++){    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
       if (k != i) {    strcat(fileresprobmorprev,fileres);
         for(j=1; j <=ncovmodel; j++){    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
              printf("Problem with resultfile: %s\n", fileresprobmorprev);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
           jk++;    }
           fprintf(ficgp,"\n");    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         }    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       }    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     }    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     }    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
     for(jk=1; jk <=m; jk++) {      for(i=1; i<=nlstate;i++)
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
    i=1;    }  
    for(k2=1; k2<=nlstate; k2++) {    fprintf(ficresprobmorprev,"\n");
      k3=i;    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
      for(k=1; k<=(nlstate+ndeath); k++) {      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
        if (k != k2){      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);      exit(0);
 ij=1;    }
         for(j=3; j <=ncovmodel; j++) {    else{
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      fprintf(ficgp,"\n# Routine varevsij");
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    }
             ij++;    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
           }      printf("Problem with html file: %s\n", optionfilehtm);
           else      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      exit(0);
         }    }
           fprintf(ficgp,")/(1");    else{
              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");
         for(k1=1; k1 <=nlstate; k1++){        fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    }
 ij=1;    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           for(j=3; j <=ncovmodel; j++){  
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    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(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    fprintf(ficresvij,"# Age");
             ij++;    for(i=1; i<=nlstate;i++)
           }      for(j=1; j<=nlstate;j++)
           else        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    fprintf(ficresvij,"\n");
           }  
           fprintf(ficgp,")");    xp=vector(1,npar);
         }    dnewm=matrix(1,nlstate,1,npar);
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    doldm=matrix(1,nlstate,1,nlstate);
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
         i=i+ncovmodel;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
        }  
      }    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
    }    gpp=vector(nlstate+1,nlstate+ndeath);
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    gmp=vector(nlstate+1,nlstate+ndeath);
    }    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
        
   fclose(ficgp);    if(estepm < stepm){
 }  /* end gnuplot */      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
 /*************** Moving average **************/    /* For example we decided to compute the life expectancy with the smallest unit */
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
   int i, cpt, cptcod;       nstepm is the number of stepm from age to agelin. 
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)       Look at hpijx to understand the reason of that which relies in memory size
       for (i=1; i<=nlstate;i++)       and note for a fixed period like k years */
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           mobaverage[(int)agedeb][i][cptcod]=0.;       survival function given by stepm (the optimization length). Unfortunately it
           means that if the survival funtion is printed every two years of age and if
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       for (i=1; i<=nlstate;i++){       results. So we changed our mind and took the option of the best precision.
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    */
           for (cpt=0;cpt<=4;cpt++){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    agelim = AGESUP;
           }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         }      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       }      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
          gp=matrix(0,nhstepm,1,nlstate);
 }      gm=matrix(0,nhstepm,1,nlstate);
   
   
 /************** Forecasting ******************/      for(theta=1; theta <=npar; theta++){
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
            xp[i] = x[i] + (i==theta ?delti[theta]:0);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        }
   int *popage;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   double *popeffectif,*popcount;  
   double ***p3mat;        if (popbased==1) {
   char fileresf[FILENAMELENGTH];          if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
  agelim=AGESUP;              prlim[i][i]=probs[(int)age][i][ij];
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;          }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);              prlim[i][i]=mobaverage[(int)age][i][ij];
            }
          }
   strcpy(fileresf,"f");    
   strcat(fileresf,fileres);        for(j=1; j<= nlstate; j++){
   if((ficresf=fopen(fileresf,"w"))==NULL) {          for(h=0; h<=nhstepm; h++){
     printf("Problem with forecast resultfile: %s\n", fileresf);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   }              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   printf("Computing forecasting: result on file '%s' \n", fileresf);          }
         }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
   if (mobilav==1) {           as a weighted average of prlim.
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        */
     movingaverage(agedeb, fage, ageminpar, mobaverage);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   }          for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
   stepsize=(int) (stepm+YEARM-1)/YEARM;        }    
   if (stepm<=12) stepsize=1;        /* end probability of death */
    
   agelim=AGESUP;        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
            xp[i] = x[i] - (i==theta ?delti[theta]:0);
   hstepm=1;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   hstepm=hstepm/stepm;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   yp1=modf(dateintmean,&yp);   
   anprojmean=yp;        if (popbased==1) {
   yp2=modf((yp1*12),&yp);          if(mobilav ==0){
   mprojmean=yp;            for(i=1; i<=nlstate;i++)
   yp1=modf((yp2*30.5),&yp);              prlim[i][i]=probs[(int)age][i][ij];
   jprojmean=yp;          }else{ /* mobilav */ 
   if(jprojmean==0) jprojmean=1;            for(i=1; i<=nlstate;i++)
   if(mprojmean==0) jprojmean=1;              prlim[i][i]=mobaverage[(int)age][i][ij];
            }
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);        }
    
   for(cptcov=1;cptcov<=i2;cptcov++){        for(j=1; j<= nlstate; j++){
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          for(h=0; h<=nhstepm; h++){
       k=k+1;            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
       fprintf(ficresf,"\n#******");              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
       for(j=1;j<=cptcoveff;j++) {          }
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        }
       }        /* This for computing probability of death (h=1 means
       fprintf(ficresf,"******\n");           computed over hstepm matrices product = hstepm*stepm months) 
       fprintf(ficresf,"# StartingAge FinalAge");           as a weighted average of prlim.
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        */
              for(j=nlstate+1;j<=nlstate+ndeath;j++){
                for(i=1,gmp[j]=0.; i<= nlstate; i++)
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {           gmp[j] += prlim[i][i]*p3mat[i][j][1];
         fprintf(ficresf,"\n");        }    
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);          /* end probability of death */
   
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        for(j=1; j<= nlstate; j++) /* vareij */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          for(h=0; h<=nhstepm; h++){
           nhstepm = nhstepm/hstepm;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
                    }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
                }
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {      } /* End theta */
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);  
             }      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;      for(h=0; h<=nhstepm; h++) /* veij */
               for(i=1; i<=nlstate;i++) {                      for(j=1; j<=nlstate;j++)
                 if (mobilav==1)          for(theta=1; theta <=npar; theta++)
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];            trgradg[h][j][theta]=gradg[h][theta][j];
                 else {  
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
                 }        for(theta=1; theta <=npar; theta++)
                          trgradgp[j][theta]=gradgp[theta][j];
               }    
               if (h==(int)(calagedate+12*cpt)){  
                 fprintf(ficresf," %.3f", kk1);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
                              for(i=1;i<=nlstate;i++)
               }        for(j=1;j<=nlstate;j++)
             }          vareij[i][j][(int)age] =0.;
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for(h=0;h<=nhstepm;h++){
         }        for(k=0;k<=nhstepm;k++){
       }          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
     }          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   }          for(i=1;i<=nlstate;i++)
                    for(j=1;j<=nlstate;j++)
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
   fclose(ficresf);      }
 }    
 /************** Forecasting ******************/      /* pptj */
 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){      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
        matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   int *popage;        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          varppt[j][i]=doldmp[j][i];
   double *popeffectif,*popcount;      /* end ppptj */
   double ***p3mat,***tabpop,***tabpopprev;      /*  x centered again */
   char filerespop[FILENAMELENGTH];      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      if (popbased==1) {
   agelim=AGESUP;        if(mobilav ==0){
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;          for(i=1; i<=nlstate;i++)
              prlim[i][i]=probs[(int)age][i][ij];
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        }else{ /* mobilav */ 
            for(i=1; i<=nlstate;i++)
              prlim[i][i]=mobaverage[(int)age][i][ij];
   strcpy(filerespop,"pop");        }
   strcat(filerespop,fileres);      }
   if((ficrespop=fopen(filerespop,"w"))==NULL) {               
     printf("Problem with forecast resultfile: %s\n", filerespop);      /* This for computing probability of death (h=1 means
   }         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   printf("Computing forecasting: result on file '%s' \n", filerespop);         as a weighted average of prlim.
       */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   if (mobilav==1) {          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      }    
     movingaverage(agedeb, fage, ageminpar, mobaverage);      /* end probability of death */
   }  
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   stepsize=(int) (stepm+YEARM-1)/YEARM;      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   if (stepm<=12) stepsize=1;        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
          for(i=1; i<=nlstate;i++){
   agelim=AGESUP;          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
          }
   hstepm=1;      } 
   hstepm=hstepm/stepm;      fprintf(ficresprobmorprev,"\n");
    
   if (popforecast==1) {      fprintf(ficresvij,"%.0f ",age );
     if((ficpop=fopen(popfile,"r"))==NULL) {      for(i=1; i<=nlstate;i++)
       printf("Problem with population file : %s\n",popfile);exit(0);        for(j=1; j<=nlstate;j++){
     }          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     popage=ivector(0,AGESUP);        }
     popeffectif=vector(0,AGESUP);      fprintf(ficresvij,"\n");
     popcount=vector(0,AGESUP);      free_matrix(gp,0,nhstepm,1,nlstate);
          free_matrix(gm,0,nhstepm,1,nlstate);
     i=1;        free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     imx=i;    } /* End age */
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    free_vector(gpp,nlstate+1,nlstate+ndeath);
   }    free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   for(cptcov=1;cptcov<=i2;cptcov++){    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
       k=k+1;    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
       fprintf(ficrespop,"\n#******");    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
       for(j=1;j<=cptcoveff;j++) {  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  /*   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(ficrespop,"******\n");    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
       fprintf(ficrespop,"# Age");    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
       if (popforecast==1)  fprintf(ficrespop," [Population]");    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);
       for (cpt=0; cpt<=0;cpt++) {    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    */
            fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    free_vector(xp,1,npar);
           nhstepm = nhstepm/hstepm;    free_matrix(doldm,1,nlstate,1,nlstate);
              free_matrix(dnewm,1,nlstate,1,npar);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           oldm=oldms;savm=savms;    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
            if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           for (h=0; h<=nhstepm; h++){    fclose(ficresprobmorprev);
             if (h==(int) (calagedate+YEARM*cpt)) {    fclose(ficgp);
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    fclose(fichtm);
             }  }  
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;  /************ Variance of prevlim ******************/
               for(i=1; i<=nlstate;i++) {                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 (mobilav==1)  {
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    /* Variance of prevalence limit */
                 else {    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    double **newm;
                 }    double **dnewm,**doldm;
               }    int i, j, nhstepm, hstepm;
               if (h==(int)(calagedate+12*cpt)){    int k, cptcode;
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    double *xp;
                   /*fprintf(ficrespop," %.3f", kk1);    double *gp, *gm;
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/    double **gradg, **trgradg;
               }    double age,agelim;
             }    int theta;
             for(i=1; i<=nlstate;i++){     
               kk1=0.;    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
                 for(j=1; j<=nlstate;j++){    fprintf(ficresvpl,"# Age");
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    for(i=1; i<=nlstate;i++)
                 }        fprintf(ficresvpl," %1d-%1d",i,i);
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    fprintf(ficresvpl,"\n");
             }  
     xp=vector(1,npar);
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    dnewm=matrix(1,nlstate,1,npar);
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    doldm=matrix(1,nlstate,1,nlstate);
           }    
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    hstepm=1*YEARM; /* Every year of age */
         }    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
       }    agelim = AGESUP;
      for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   /******/      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);        gradg=matrix(1,npar,1,nlstate);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      gp=vector(1,nlstate);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      gm=vector(1,nlstate);
           nhstepm = nhstepm/hstepm;  
                for(theta=1; theta <=npar; theta++){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(i=1; i<=npar; i++){ /* Computes gradient */
           oldm=oldms;savm=savms;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          }
           for (h=0; h<=nhstepm; h++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
             if (h==(int) (calagedate+YEARM*cpt)) {        for(i=1;i<=nlstate;i++)
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          gp[i] = prlim[i][i];
             }      
             for(j=1; j<=nlstate+ndeath;j++) {        for(i=1; i<=npar; i++) /* Computes gradient */
               kk1=0.;kk2=0;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
               for(i=1; i<=nlstate;i++) {                      prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];            for(i=1;i<=nlstate;i++)
               }          gm[i] = prlim[i][i];
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);  
             }        for(i=1;i<=nlstate;i++)
           }          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      } /* End theta */
         }  
       }      trgradg =matrix(1,nlstate,1,npar);
    }  
   }      for(j=1; j<=nlstate;j++)
          for(theta=1; theta <=npar; theta++)
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          trgradg[j][theta]=gradg[theta][j];
   
   if (popforecast==1) {      for(i=1;i<=nlstate;i++)
     free_ivector(popage,0,AGESUP);        varpl[i][(int)age] =0.;
     free_vector(popeffectif,0,AGESUP);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
     free_vector(popcount,0,AGESUP);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   }      for(i=1;i<=nlstate;i++)
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   fclose(ficrespop);      fprintf(ficresvpl,"%.0f ",age );
 }      for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
 /***********************************************/      fprintf(ficresvpl,"\n");
 /**************** Main Program *****************/      free_vector(gp,1,nlstate);
 /***********************************************/      free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
 int main(int argc, char *argv[])      free_matrix(trgradg,1,nlstate,1,npar);
 {    } /* End age */
   
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    free_vector(xp,1,npar);
   double agedeb, agefin,hf;    free_matrix(doldm,1,nlstate,1,npar);
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    free_matrix(dnewm,1,nlstate,1,nlstate);
   
   double fret;  }
   double **xi,tmp,delta;  
   /************ Variance of one-step probabilities  ******************/
   double dum; /* Dummy variable */  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
   double ***p3mat;  {
   int *indx;    int i, j=0,  i1, k1, l1, t, tj;
   char line[MAXLINE], linepar[MAXLINE];    int k2, l2, j1,  z1;
   char title[MAXLINE];    int k=0,l, cptcode;
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    int first=1, first1;
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
      double **dnewm,**doldm;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    double *xp;
     double *gp, *gm;
   char filerest[FILENAMELENGTH];    double **gradg, **trgradg;
   char fileregp[FILENAMELENGTH];    double **mu;
   char popfile[FILENAMELENGTH];    double age,agelim, cov[NCOVMAX];
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   int firstobs=1, lastobs=10;    int theta;
   int sdeb, sfin; /* Status at beginning and end */    char fileresprob[FILENAMELENGTH];
   int c,  h , cpt,l;    char fileresprobcov[FILENAMELENGTH];
   int ju,jl, mi;    char fileresprobcor[FILENAMELENGTH];
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;  
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    double ***varpij;
   int mobilav=0,popforecast=0;  
   int hstepm, nhstepm;    strcpy(fileresprob,"prob"); 
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;    strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   double bage, fage, age, agelim, agebase;      printf("Problem with resultfile: %s\n", fileresprob);
   double ftolpl=FTOL;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   double **prlim;    }
   double *severity;    strcpy(fileresprobcov,"probcov"); 
   double ***param; /* Matrix of parameters */    strcat(fileresprobcov,fileres);
   double  *p;    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   double **matcov; /* Matrix of covariance */      printf("Problem with resultfile: %s\n", fileresprobcov);
   double ***delti3; /* Scale */      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   double *delti; /* Scale */    }
   double ***eij, ***vareij;    strcpy(fileresprobcor,"probcor"); 
   double **varpl; /* Variances of prevalence limits by age */    strcat(fileresprobcor,fileres);
   double *epj, vepp;    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   double kk1, kk2;      printf("Problem with resultfile: %s\n", fileresprobcor);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
      }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   char version[80]="Imach version 0.8b, March 2002, INED-EUROREVES ";    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   char *alph[]={"a","a","b","c","d","e"}, str[4];    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   char z[1]="c", occ;    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
 #include <sys/time.h>    
 #include <time.h>    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    fprintf(ficresprob,"# Age");
      fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   /* long total_usecs;    fprintf(ficresprobcov,"# Age");
   struct timeval start_time, end_time;    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
      fprintf(ficresprobcov,"# Age");
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */  
   getcwd(pathcd, size);  
     for(i=1; i<=nlstate;i++)
   printf("\n%s",version);      for(j=1; j<=(nlstate+ndeath);j++){
   if(argc <=1){        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
     printf("\nEnter the parameter file name: ");        fprintf(ficresprobcov," p%1d-%1d ",i,j);
     scanf("%s",pathtot);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
   }      }  
   else{   /* fprintf(ficresprob,"\n");
     strcpy(pathtot,argv[1]);    fprintf(ficresprobcov,"\n");
   }    fprintf(ficresprobcor,"\n");
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/   */
   /*cygwin_split_path(pathtot,path,optionfile);   xp=vector(1,npar);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   /* cutv(path,optionfile,pathtot,'\\');*/    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    first=1;
   chdir(path);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   replace(pathc,path);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
       fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
 /*-------- arguments in the command line --------*/      exit(0);
     }
   strcpy(fileres,"r");    else{
   strcat(fileres, optionfilefiname);      fprintf(ficgp,"\n# Routine varprob");
   strcat(fileres,".txt");    /* Other files have txt extension */    }
     if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   /*---------arguments file --------*/      printf("Problem with html file: %s\n", optionfilehtm);
       fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {      exit(0);
     printf("Problem with optionfile %s\n",optionfile);    }
     goto end;    else{
   }      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
       fprintf(fichtm,"\n");
   strcpy(filereso,"o");  
   strcat(filereso,fileres);      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
   if((ficparo=fopen(filereso,"w"))==NULL) {      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");
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      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");
   }  
     }
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){    cov[1]=1;
     ungetc(c,ficpar);    tj=cptcoveff;
     fgets(line, MAXLINE, ficpar);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     puts(line);    j1=0;
     fputs(line,ficparo);    for(t=1; t<=tj;t++){
   }      for(i1=1; i1<=ncodemax[t];i1++){ 
   ungetc(c,ficpar);        j1++;
         if  (cptcovn>0) {
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);          fprintf(ficresprob, "\n#********** Variable "); 
   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);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   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);          fprintf(ficresprob, "**********\n#\n");
 while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficresprobcov, "\n#********** Variable "); 
     ungetc(c,ficpar);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fgets(line, MAXLINE, ficpar);          fprintf(ficresprobcov, "**********\n#\n");
     puts(line);          
     fputs(line,ficparo);          fprintf(ficgp, "\n#********** Variable "); 
   }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   ungetc(c,ficpar);          fprintf(ficgp, "**********\n#\n");
            
              
   covar=matrix(0,NCOVMAX,1,n);          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   cptcovn=0;          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
   ncovmodel=2+cptcovn;          fprintf(ficresprobcor, "\n#********** Variable ");    
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficresprobcor, "**********\n#");    
   /* Read guess parameters */        }
   /* Reads comments: lines beginning with '#' */        
   while((c=getc(ficpar))=='#' && c!= EOF){        for (age=bage; age<=fage; age ++){ 
     ungetc(c,ficpar);          cov[2]=age;
     fgets(line, MAXLINE, ficpar);          for (k=1; k<=cptcovn;k++) {
     puts(line);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     fputs(line,ficparo);          }
   }          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   ungetc(c,ficpar);          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]]];
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          
     for(i=1; i <=nlstate; i++)          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
     for(j=1; j <=nlstate+ndeath-1; j++){          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       fscanf(ficpar,"%1d%1d",&i1,&j1);          gp=vector(1,(nlstate)*(nlstate+ndeath));
       fprintf(ficparo,"%1d%1d",i1,j1);          gm=vector(1,(nlstate)*(nlstate+ndeath));
       printf("%1d%1d",i,j);      
       for(k=1; k<=ncovmodel;k++){          for(theta=1; theta <=npar; theta++){
         fscanf(ficpar," %lf",&param[i][j][k]);            for(i=1; i<=npar; i++)
         printf(" %lf",param[i][j][k]);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
         fprintf(ficparo," %lf",param[i][j][k]);            
       }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       fscanf(ficpar,"\n");            
       printf("\n");            k=0;
       fprintf(ficparo,"\n");            for(i=1; i<= (nlstate); i++){
     }              for(j=1; j<=(nlstate+ndeath);j++){
                  k=k+1;
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;                gp[k]=pmmij[i][j];
               }
   p=param[1][1];            }
              
   /* Reads comments: lines beginning with '#' */            for(i=1; i<=npar; i++)
   while((c=getc(ficpar))=='#' && c!= EOF){              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
     ungetc(c,ficpar);      
     fgets(line, MAXLINE, ficpar);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     puts(line);            k=0;
     fputs(line,ficparo);            for(i=1; i<=(nlstate); i++){
   }              for(j=1; j<=(nlstate+ndeath);j++){
   ungetc(c,ficpar);                k=k+1;
                 gm[k]=pmmij[i][j];
   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++){            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
       fscanf(ficpar,"%1d%1d",&i1,&j1);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
       printf("%1d%1d",i,j);          }
       fprintf(ficparo,"%1d%1d",i1,j1);  
       for(k=1; k<=ncovmodel;k++){          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
         fscanf(ficpar,"%le",&delti3[i][j][k]);            for(theta=1; theta <=npar; theta++)
         printf(" %le",delti3[i][j][k]);              trgradg[j][theta]=gradg[theta][j];
         fprintf(ficparo," %le",delti3[i][j][k]);          
       }          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
       fscanf(ficpar,"\n");          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
       printf("\n");          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
       fprintf(ficparo,"\n");          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
     }          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   }          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   delti=delti3[1][1];  
            pmij(pmmij,cov,ncovmodel,x,nlstate);
   /* Reads comments: lines beginning with '#' */          
   while((c=getc(ficpar))=='#' && c!= EOF){          k=0;
     ungetc(c,ficpar);          for(i=1; i<=(nlstate); i++){
     fgets(line, MAXLINE, ficpar);            for(j=1; j<=(nlstate+ndeath);j++){
     puts(line);              k=k+1;
     fputs(line,ficparo);              mu[k][(int) age]=pmmij[i][j];
   }            }
   ungetc(c,ficpar);          }
            for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   matcov=matrix(1,npar,1,npar);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   for(i=1; i <=npar; i++){              varpij[i][j][(int)age] = doldm[i][j];
     fscanf(ficpar,"%s",&str);  
     printf("%s",str);          /*printf("\n%d ",(int)age);
     fprintf(ficparo,"%s",str);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     for(j=1; j <=i; j++){            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
       fscanf(ficpar," %le",&matcov[i][j]);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
       printf(" %.5le",matcov[i][j]);            }*/
       fprintf(ficparo," %.5le",matcov[i][j]);  
     }          fprintf(ficresprob,"\n%d ",(int)age);
     fscanf(ficpar,"\n");          fprintf(ficresprobcov,"\n%d ",(int)age);
     printf("\n");          fprintf(ficresprobcor,"\n%d ",(int)age);
     fprintf(ficparo,"\n");  
   }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
   for(i=1; i <=npar; i++)            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
     for(j=i+1;j<=npar;j++)          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
       matcov[i][j]=matcov[j][i];            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
                fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
   printf("\n");          }
           i=0;
           for (k=1; k<=(nlstate);k++){
     /*-------- Rewriting paramater file ----------*/            for (l=1; l<=(nlstate+ndeath);l++){ 
      strcpy(rfileres,"r");    /* "Rparameterfile */              i=i++;
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
      strcat(rfileres,".");    /* */              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
      strcat(rfileres,optionfilext);    /* Other files have txt extension */              for (j=1; j<=i;j++){
     if((ficres =fopen(rfileres,"w"))==NULL) {                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
       printf("Problem writing new parameter file: %s\n", fileres);goto end;                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
     }              }
     fprintf(ficres,"#%s\n",version);            }
              }/* end of loop for state */
     /*-------- data file ----------*/        } /* end of loop for age */
     if((fic=fopen(datafile,"r"))==NULL)    {  
       printf("Problem with datafile: %s\n", datafile);goto end;        /* Confidence intervalle of pij  */
     }        /*
           fprintf(ficgp,"\nset noparametric;unset label");
     n= lastobs;          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
     severity = vector(1,maxwav);          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     outcome=imatrix(1,maxwav+1,1,n);          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);
     num=ivector(1,n);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
     moisnais=vector(1,n);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
     annais=vector(1,n);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
     moisdc=vector(1,n);        */
     andc=vector(1,n);  
     agedc=vector(1,n);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
     cod=ivector(1,n);        first1=1;
     weight=vector(1,n);        for (k2=1; k2<=(nlstate);k2++){
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
     mint=matrix(1,maxwav,1,n);            if(l2==k2) continue;
     anint=matrix(1,maxwav,1,n);            j=(k2-1)*(nlstate+ndeath)+l2;
     s=imatrix(1,maxwav+1,1,n);            for (k1=1; k1<=(nlstate);k1++){
     adl=imatrix(1,maxwav+1,1,n);                  for (l1=1; l1<=(nlstate+ndeath);l1++){ 
     tab=ivector(1,NCOVMAX);                if(l1==k1) continue;
     ncodemax=ivector(1,8);                i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
     i=1;                for (age=bage; age<=fage; age ++){ 
     while (fgets(line, MAXLINE, fic) != NULL)    {                  if ((int)age %5==0){
       if ((i >= firstobs) && (i <=lastobs)) {                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                            v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
         for (j=maxwav;j>=1;j--){                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);                    mu1=mu[i][(int) age]/stepm*YEARM ;
           strcpy(line,stra);                    mu2=mu[j][(int) age]/stepm*YEARM;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                    c12=cv12/sqrt(v1*v2);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                    /* Computing eigen value of matrix of covariance */
         }                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                            lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);                    /* Eigen vectors */
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);                    v21=(lc1-v1)/cv12*v11;
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);                    v12=-v21;
                     v22=v11;
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);                    tnalp=v21/v11;
         for (j=ncovcol;j>=1;j--){                    if(first1==1){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);                      first1=0;
         }                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
         num[i]=atol(stra);                    }
                            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);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){                    /*printf(fignu*/
           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;}*/                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
         i=i+1;                    if(first==1){
       }                      first=0;
     }                      fprintf(ficgp,"\nset parametric;unset label");
     /* printf("ii=%d", ij);                      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);
        scanf("%d",i);*/                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   imx=i-1; /* Number of individuals */                      fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
                       fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
   /* for (i=1; i<=imx; i++){                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     }*/                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
    /*  for (i=1; i<=imx; i++){                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
      if (s[4][i]==9)  s[4][i]=-1;                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
      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]));}*/                    }else{
                        first=0;
                        fprintf(fichtm," %d (%.3f),",(int) age, c12);
   /* Calculation of the number of parameter from char model*/                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   Tvar=ivector(1,15);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   Tprod=ivector(1,15);                      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",\
   Tvaraff=ivector(1,15);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   Tvard=imatrix(1,15,1,2);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   Tage=ivector(1,15);                          }/* if first */
                      } /* age mod 5 */
   if (strlen(model) >1){                } /* end loop age */
     j=0, j1=0, k1=1, k2=1;                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
     j=nbocc(model,'+');                first=1;
     j1=nbocc(model,'*');              } /*l12 */
     cptcovn=j+1;            } /* k12 */
     cptcovprod=j1;          } /*l1 */
            }/* k1 */
     strcpy(modelsav,model);      } /* loop covariates */
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    }
       printf("Error. Non available option model=%s ",model);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
       goto end;    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     }    free_vector(xp,1,npar);
        fclose(ficresprob);
     for(i=(j+1); i>=1;i--){    fclose(ficresprobcov);
       cutv(stra,strb,modelsav,'+');    fclose(ficresprobcor);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    fclose(ficgp);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    fclose(fichtm);
       /*scanf("%d",i);*/  }
       if (strchr(strb,'*')) {  
         cutv(strd,strc,strb,'*');  
         if (strcmp(strc,"age")==0) {  /******************* Printing html file ***********/
           cptcovprod--;  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
           cutv(strb,stre,strd,'V');                    int lastpass, int stepm, int weightopt, char model[],\
           Tvar[i]=atoi(stre);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
           cptcovage++;                    int popforecast, int estepm ,\
             Tage[cptcovage]=i;                    double jprev1, double mprev1,double anprev1, \
             /*printf("stre=%s ", stre);*/                    double jprev2, double mprev2,double anprev2){
         }    int jj1, k1, i1, cpt;
         else if (strcmp(strd,"age")==0) {    /*char optionfilehtm[FILENAMELENGTH];*/
           cptcovprod--;    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
           cutv(strb,stre,strc,'V');      printf("Problem with %s \n",optionfilehtm), exit(0);
           Tvar[i]=atoi(stre);      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
           cptcovage++;    }
           Tage[cptcovage]=i;  
         }     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
         else {   - 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
           cutv(strb,stre,strc,'V');   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
           Tvar[i]=ncovcol+k1;   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
           cutv(strb,strc,strd,'V');   - Life expectancies by age and initial health status (estepm=%2d months): 
           Tprod[k1]=i;     <a href=\"e%s\">e%s</a> <br>\n</li>", \
           Tvard[k1][1]=atoi(strc);    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
           Tvard[k1][2]=atoi(stre);  
           Tvar[cptcovn+k2]=Tvard[k1][1];  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
           Tvar[cptcovn+k2+1]=Tvard[k1][2];  
           for (k=1; k<=lastobs;k++)   m=cptcoveff;
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
           k1++;  
           k2=k2+2;   jj1=0;
         }   for(k1=1; k1<=m;k1++){
       }     for(i1=1; i1<=ncodemax[k1];i1++){
       else {       jj1++;
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/       if (cptcovn > 0) {
        /*  scanf("%d",i);*/         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
       cutv(strd,strc,strb,'V');         for (cpt=1; cpt<=cptcoveff;cpt++) 
       Tvar[i]=atoi(strc);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
       }         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
       strcpy(modelsav,stra);         }
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);       /* Pij */
         scanf("%d",i);*/       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: pe%s%d1.png<br>
     }  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
 }       /* Quasi-incidences */
         fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
   printf("cptcovprod=%d ", cptcovprod);         /* Stable prevalence in each health state */
   scanf("%d ",i);*/         for(cpt=1; cpt<nlstate;cpt++){
     fclose(fic);           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
   <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
     /*  if(mle==1){*/         }
     if (weightopt != 1) { /* Maximisation without weights*/       for(cpt=1; cpt<=nlstate;cpt++) {
       for(i=1;i<=n;i++) weight[i]=1.0;          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
     }  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
     /*-calculation of age at interview from date of interview and age at death -*/       }
     agev=matrix(1,maxwav,1,imx);       fprintf(fichtm,"\n<br>- Total life expectancy by age and
   health expectancies in states (1) and (2): e%s%d.png<br>
     for (i=1; i<=imx; i++) {  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
       for(m=2; (m<= maxwav); m++) {     } /* end i1 */
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){   }/* End k1 */
          anint[m][i]=9999;   fprintf(fichtm,"</ul>");
          s[m][i]=-1;  
        }  
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
       }   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
     }   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
    - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
     for (i=1; i<=imx; i++)  {   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
       for(m=1; (m<= maxwav); m++){   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
         if(s[m][i] >0){   - 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 (s[m][i] >= nlstate+1) {  
             if(agedc[i]>0)  /*  if(popforecast==1) fprintf(fichtm,"\n */
               if(moisdc[i]!=99 && andc[i]!=9999)  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
                 agev[m][i]=agedc[i];  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/  /*      <br>",fileres,fileres,fileres,fileres); */
            else {  /*  else  */
               if (andc[i]!=9999){  /*    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); */
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
               agev[m][i]=-1;  
               }   m=cptcoveff;
             }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
           }  
           else if(s[m][i] !=9){ /* Should no more exist */   jj1=0;
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);   for(k1=1; k1<=m;k1++){
             if(mint[m][i]==99 || anint[m][i]==9999)     for(i1=1; i1<=ncodemax[k1];i1++){
               agev[m][i]=1;       jj1++;
             else if(agev[m][i] <agemin){       if (cptcovn > 0) {
               agemin=agev[m][i];         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/         for (cpt=1; cpt<=cptcoveff;cpt++) 
             }           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
             else if(agev[m][i] >agemax){         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
               agemax=agev[m][i];       }
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/       for(cpt=1; cpt<=nlstate;cpt++) {
             }         fprintf(fichtm,"<br>- Observed and period prevalence (with confident
             /*agev[m][i]=anint[m][i]-annais[i];*/  interval) in state (%d): v%s%d%d.png <br>
             /*   agev[m][i] = age[i]+2*m;*/  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
           }       }
           else { /* =9 */     } /* end i1 */
             agev[m][i]=1;   }/* End k1 */
             s[m][i]=-1;   fprintf(fichtm,"</ul>");
           }  fclose(fichtm);
         }  }
         else /*= 0 Unknown */  
           agev[m][i]=1;  /******************* Gnuplot file **************/
       }  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
      
     }    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     for (i=1; i<=imx; i++)  {    int ng;
       for(m=1; (m<= maxwav); m++){    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
         if (s[m][i] > (nlstate+ndeath)) {      printf("Problem with file %s",optionfilegnuplot);
           printf("Error: Wrong value in nlstate or ndeath\n");        fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
           goto end;    }
         }  
       }    /*#ifdef windows */
     }      fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);  m=pow(2,cptcoveff);
     
     free_vector(severity,1,maxwav);   /* 1eme*/
     free_imatrix(outcome,1,maxwav+1,1,n);    for (cpt=1; cpt<= nlstate ; cpt ++) {
     free_vector(moisnais,1,n);     for (k1=1; k1<= m ; k1 ++) {
     free_vector(annais,1,n);       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     /* free_matrix(mint,1,maxwav,1,n);       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);
        free_matrix(anint,1,maxwav,1,n);*/  
     free_vector(moisdc,1,n);       for (i=1; i<= nlstate ; i ++) {
     free_vector(andc,1,n);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
           }
     wav=ivector(1,imx);       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);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);       for (i=1; i<= nlstate ; i ++) {
     mw=imatrix(1,lastpass-firstpass+1,1,imx);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
             else fprintf(ficgp," \%%*lf (\%%*lf)");
     /* Concatenates waves */       } 
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       Tcode=ivector(1,100);         else fprintf(ficgp," \%%*lf (\%%*lf)");
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);       }  
       ncodemax[1]=1;       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);     }
          }
    codtab=imatrix(1,100,1,10);    /*2 eme*/
    h=0;    
    m=pow(2,cptcoveff);    for (k1=1; k1<= m ; k1 ++) { 
        fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
    for(k=1;k<=cptcoveff; k++){      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
      for(i=1; i <=(m/pow(2,k));i++){      
        for(j=1; j <= ncodemax[k]; j++){      for (i=1; i<= nlstate+1 ; i ++) {
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){        k=2*i;
            h++;        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;        for (j=1; j<= nlstate+1 ; j ++) {
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
          }          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }        }   
      }        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
    }        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
       codtab[1][2]=1;codtab[2][2]=2; */        for (j=1; j<= nlstate+1 ; j ++) {
    /* for(i=1; i <=m ;i++){          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       for(k=1; k <=cptcovn; k++){          else fprintf(ficgp," \%%*lf (\%%*lf)");
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);        }   
       }        fprintf(ficgp,"\" t\"\" w l 0,");
       printf("\n");        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
       }        for (j=1; j<= nlstate+1 ; j ++) {
       scanf("%d",i);*/          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
              else fprintf(ficgp," \%%*lf (\%%*lf)");
    /* Calculates basic frequencies. Computes observed prevalence at single age        }   
        and prints on file fileres'p'. */        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
          }
        }
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    /*3eme*/
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    for (k1=1; k1<= m ; k1 ++) { 
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      for (cpt=1; cpt<= nlstate ; cpt ++) {
              k=2+nlstate*(2*cpt-2);
     /* For Powell, parameters are in a vector p[] starting at p[1]        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     if(mle==1){          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     }          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
              fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     /*--------- 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);        */
          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);
    jk=1;          
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");        } 
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      }
    for(i=1,jk=1; i <=nlstate; i++){    }
      for(k=1; k <=(nlstate+ndeath); k++){    
        if (k != i)    /* CV preval stable (period) */
          {    for (k1=1; k1<= m ; k1 ++) { 
            printf("%d%d ",i,k);      for (cpt=1; cpt<=nlstate ; cpt ++) {
            fprintf(ficres,"%1d%1d ",i,k);        k=3;
            for(j=1; j <=ncovmodel; j++){        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
              printf("%f ",p[jk]);        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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
              fprintf(ficres,"%f ",p[jk]);        
              jk++;        for (i=1; i<= nlstate ; i ++)
            }          fprintf(ficgp,"+$%d",k+i+1);
            printf("\n");        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
            fprintf(ficres,"\n");        
          }        l=3+(nlstate+ndeath)*cpt;
      }        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
    }        for (i=1; i< nlstate ; i ++) {
  if(mle==1){          l=3+(nlstate+ndeath)*cpt;
     /* Computing hessian and covariance matrix */          fprintf(ficgp,"+$%d",l+i+1);
     ftolhess=ftol; /* Usually correct */        }
     hesscov(matcov, p, npar, delti, ftolhess, func);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
  }      } 
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    }  
     printf("# Scales (for hessian or gradient estimation)\n");    
      for(i=1,jk=1; i <=nlstate; i++){    /* proba elementaires */
       for(j=1; j <=nlstate+ndeath; j++){    for(i=1,jk=1; i <=nlstate; i++){
         if (j!=i) {      for(k=1; k <=(nlstate+ndeath); k++){
           fprintf(ficres,"%1d%1d",i,j);        if (k != i) {
           printf("%1d%1d",i,j);          for(j=1; j <=ncovmodel; j++){
           for(k=1; k<=ncovmodel;k++){            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             printf(" %.5e",delti[jk]);            jk++; 
             fprintf(ficres," %.5e",delti[jk]);            fprintf(ficgp,"\n");
             jk++;          }
           }        }
           printf("\n");      }
           fprintf(ficres,"\n");     }
         }  
       }     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
      }       for(jk=1; jk <=m; jk++) {
             fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
     k=1;         if (ng==2)
     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");           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");         else
     for(i=1;i<=npar;i++){           fprintf(ficgp,"\nset title \"Probability\"\n");
       /*  if (k>nlstate) k=1;         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
       i1=(i-1)/(ncovmodel*nlstate)+1;         i=1;
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);         for(k2=1; k2<=nlstate; k2++) {
       printf("%s%d%d",alph[k],i1,tab[i]);*/           k3=i;
       fprintf(ficres,"%3d",i);           for(k=1; k<=(nlstate+ndeath); k++) {
       printf("%3d",i);             if (k != k2){
       for(j=1; j<=i;j++){               if(ng==2)
         fprintf(ficres," %.5e",matcov[i][j]);                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
         printf(" %.5e",matcov[i][j]);               else
       }                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
       fprintf(ficres,"\n");               ij=1;
       printf("\n");               for(j=3; j <=ncovmodel; j++) {
       k++;                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
     }                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                       ij++;
     while((c=getc(ficpar))=='#' && c!= EOF){                 }
       ungetc(c,ficpar);                 else
       fgets(line, MAXLINE, ficpar);                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
       puts(line);               }
       fputs(line,ficparo);               fprintf(ficgp,")/(1");
     }               
     ungetc(c,ficpar);               for(k1=1; k1 <=nlstate; k1++){   
     estepm=0;                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);                 ij=1;
     if (estepm==0 || estepm < stepm) estepm=stepm;                 for(j=3; j <=ncovmodel; j++){
     if (fage <= 2) {                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
       bage = ageminpar;                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
       fage = agemaxpar;                     ij++;
     }                   }
                       else
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
     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);                 fprintf(ficgp,")");
                 }
     while((c=getc(ficpar))=='#' && c!= EOF){               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
     ungetc(c,ficpar);               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
     fgets(line, MAXLINE, ficpar);               i=i+ncovmodel;
     puts(line);             }
     fputs(line,ficparo);           } /* end k */
   }         } /* end k2 */
   ungetc(c,ficpar);       } /* end jk */
       } /* end ng */
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);     fclose(ficgp); 
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  }  /* end gnuplot */
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  
        
   while((c=getc(ficpar))=='#' && c!= EOF){  /*************** Moving average **************/
     ungetc(c,ficpar);  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
     fgets(line, MAXLINE, ficpar);  
     puts(line);    int i, cpt, cptcod;
     fputs(line,ficparo);    int modcovmax =1;
   }    int mobilavrange, mob;
   ungetc(c,ficpar);    double age;
    
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
    dateprev1=anprev1+mprev1/12.+jprev1/365.;                             a covariate has 2 modalities */
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
   fscanf(ficpar,"pop_based=%d\n",&popbased);    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
   fprintf(ficparo,"pop_based=%d\n",popbased);        if(mobilav==1) mobilavrange=5; /* default */
   fprintf(ficres,"pop_based=%d\n",popbased);        else mobilavrange=mobilav;
        for (age=bage; age<=fage; age++)
   while((c=getc(ficpar))=='#' && c!= EOF){        for (i=1; i<=nlstate;i++)
     ungetc(c,ficpar);          for (cptcod=1;cptcod<=modcovmax;cptcod++)
     fgets(line, MAXLINE, ficpar);            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
     puts(line);      /* We keep the original values on the extreme ages bage, fage and for 
     fputs(line,ficparo);         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
   }         we use a 5 terms etc. until the borders are no more concerned. 
   ungetc(c,ficpar);      */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
   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 (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
 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);          for (i=1; i<=nlstate;i++){
 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);            for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
 while((c=getc(ficpar))=='#' && c!= EOF){                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
     ungetc(c,ficpar);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
     fgets(line, MAXLINE, ficpar);                }
     puts(line);              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
     fputs(line,ficparo);            }
   }          }
   ungetc(c,ficpar);        }/* end age */
       }/* end mob */
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);    }else return -1;
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    return 0;
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);  }/* End movingaverage */
   
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  
   /************** Forecasting ******************/
 /*------------ gnuplot -------------*/  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){
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);    /* proj1, year, month, day of starting projection 
         agemin, agemax range of age
 /*------------ free_vector  -------------*/       dateprev1 dateprev2 range of dates during which prevalence is computed
  chdir(path);       anproj2 year of en of projection (same day and month as proj1).
      */
  free_ivector(wav,1,imx);    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    int *popage;
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      double agec; /* generic age */
  free_ivector(num,1,n);    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
  free_vector(agedc,1,n);    double *popeffectif,*popcount;
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    double ***p3mat;
  fclose(ficparo);    double ***mobaverage;
  fclose(ficres);    char fileresf[FILENAMELENGTH];
   
 /*--------- index.htm --------*/    agelim=AGESUP;
     prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);   
     strcpy(fileresf,"f"); 
      strcat(fileresf,fileres);
   /*--------------- Prevalence limit --------------*/    if((ficresf=fopen(fileresf,"w"))==NULL) {
        printf("Problem with forecast resultfile: %s\n", fileresf);
   strcpy(filerespl,"pl");      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
   strcat(filerespl,fileres);    }
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    printf("Computing forecasting: result on file '%s' \n", fileresf);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   }  
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    if (cptcoveff==0) ncodemax[cptcoveff]=1;
   fprintf(ficrespl,"#Prevalence limit\n");  
   fprintf(ficrespl,"#Age ");    if (mobilav!=0) {
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   fprintf(ficrespl,"\n");      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
          fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   prlim=matrix(1,nlstate,1,nlstate);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   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 */    stepsize=(int) (stepm+YEARM-1)/YEARM;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    if (stepm<=12) stepsize=1;
   k=0;    if(estepm < stepm){
   agebase=ageminpar;      printf ("Problem %d lower than %d\n",estepm, stepm);
   agelim=agemaxpar;    }
   ftolpl=1.e-10;    else  hstepm=estepm;   
   i1=cptcoveff;  
   if (cptcovn < 1){i1=1;}    hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
   for(cptcov=1;cptcov<=i1;cptcov++){                                 fractional in yp1 */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    anprojmean=yp;
         k=k+1;    yp2=modf((yp1*12),&yp);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    mprojmean=yp;
         fprintf(ficrespl,"\n#******");    yp1=modf((yp2*30.5),&yp);
         for(j=1;j<=cptcoveff;j++)    jprojmean=yp;
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    if(jprojmean==0) jprojmean=1;
         fprintf(ficrespl,"******\n");    if(mprojmean==0) jprojmean=1;
          
         for (age=agebase; age<=agelim; age++){    i1=cptcoveff;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    if (cptcovn < 1){i1=1;}
           fprintf(ficrespl,"%.0f",age );    
           for(i=1; i<=nlstate;i++)    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
           fprintf(ficrespl," %.5f", prlim[i][i]);    
           fprintf(ficrespl,"\n");    fprintf(ficresf,"#****** Routine prevforecast **\n");
         }  
       }  /*            if (h==(int)(YEARM*yearp)){ */
     }    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
   fclose(ficrespl);      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
   /*------------- h Pij x at various ages ------------*/        fprintf(ficresf,"\n#******");
          for(j=1;j<=cptcoveff;j++) {
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);          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]]);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {        }
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;        fprintf(ficresf,"******\n");
   }        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
   printf("Computing pij: result on file '%s' \n", filerespij);        for(j=1; j<=nlstate+ndeath;j++){ 
            for(i=1; i<=nlstate;i++)              
   stepsize=(int) (stepm+YEARM-1)/YEARM;            fprintf(ficresf," p%d%d",i,j);
   /*if (stepm<=24) stepsize=2;*/          fprintf(ficresf," p.%d",j);
         }
   agelim=AGESUP;        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
   hstepm=stepsize*YEARM; /* Every year of age */          fprintf(ficresf,"\n");
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
    
   k=0;          for (agec=fage; agec>=(ageminpar-1); agec--){ 
   for(cptcov=1;cptcov<=i1;cptcov++){            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            nhstepm = nhstepm/hstepm; 
       k=k+1;            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(ficrespij,"\n#****** ");            oldm=oldms;savm=savms;
         for(j=1;j<=cptcoveff;j++)            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          
         fprintf(ficrespij,"******\n");            for (h=0; h<=nhstepm; h++){
                      if (h*hstepm/YEARM*stepm ==yearp) {
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */                fprintf(ficresf,"\n");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                for(j=1;j<=cptcoveff;j++) 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
           oldm=oldms;savm=savms;              } 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                for(j=1; j<=nlstate+ndeath;j++) {
           fprintf(ficrespij,"# Age");                ppij=0.;
           for(i=1; i<=nlstate;i++)                for(i=1; i<=nlstate;i++) {
             for(j=1; j<=nlstate+ndeath;j++)                  if (mobilav==1) 
               fprintf(ficrespij," %1d-%1d",i,j);                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
           fprintf(ficrespij,"\n");                  else {
            for (h=0; h<=nhstepm; h++){                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );                  }
             for(i=1; i<=nlstate;i++)                  if (h*hstepm/YEARM*stepm== yearp) {
               for(j=1; j<=nlstate+ndeath;j++)                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);                  }
             fprintf(ficrespij,"\n");                } /* end i */
              }                if (h*hstepm/YEARM*stepm==yearp) {
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                  fprintf(ficresf," %.3f", ppij);
           fprintf(ficrespij,"\n");                }
         }              }/* end j */
     }            } /* end h */
   }            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);        } /* end yearp */
       } /* end cptcod */
   fclose(ficrespij);    } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   /*---------- Forecasting ------------------*/  
   if((stepm == 1) && (strcmp(model,".")==0)){    fclose(ficresf);
     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);  /************** Forecasting *****not tested NB*************/
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);  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){
     free_vector(weight,1,n);}    
   else{    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     erreur=108;    int *popage;
     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);    double calagedatem, agelim, kk1, kk2;
   }    double *popeffectif,*popcount;
      double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
   /*---------- Health expectancies and variances ------------*/    char filerespop[FILENAMELENGTH];
   
   strcpy(filerest,"t");    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   strcat(filerest,fileres);    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   if((ficrest=fopen(filerest,"w"))==NULL) {    agelim=AGESUP;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
   }    
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
   strcpy(filerese,"e");    strcpy(filerespop,"pop"); 
   strcat(filerese,fileres);    strcat(filerespop,fileres);
   if((ficreseij=fopen(filerese,"w"))==NULL) {    if((ficrespop=fopen(filerespop,"w"))==NULL) {
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      printf("Problem with forecast resultfile: %s\n", filerespop);
   }      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
  strcpy(fileresv,"v");    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   strcat(fileresv,fileres);  
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    if (cptcoveff==0) ncodemax[cptcoveff]=1;
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  
   }    if (mobilav!=0) {
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
   k=0;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   for(cptcov=1;cptcov<=i1;cptcov++){        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      }
       k=k+1;    }
       fprintf(ficrest,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)    stepsize=(int) (stepm+YEARM-1)/YEARM;
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    if (stepm<=12) stepsize=1;
       fprintf(ficrest,"******\n");    
     agelim=AGESUP;
       fprintf(ficreseij,"\n#****** ");    
       for(j=1;j<=cptcoveff;j++)    hstepm=1;
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    hstepm=hstepm/stepm; 
       fprintf(ficreseij,"******\n");    
     if (popforecast==1) {
       fprintf(ficresvij,"\n#****** ");      if((ficpop=fopen(popfile,"r"))==NULL) {
       for(j=1;j<=cptcoveff;j++)        printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       fprintf(ficresvij,"******\n");      } 
       popage=ivector(0,AGESUP);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      popeffectif=vector(0,AGESUP);
       oldm=oldms;savm=savms;      popcount=vector(0,AGESUP);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm);        
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      i=1;   
       oldm=oldms;savm=savms;      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);     
          imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
      }
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");  
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
       fprintf(ficrest,"\n");     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
       epj=vector(1,nlstate+1);        fprintf(ficrespop,"\n#******");
       for(age=bage; age <=fage ;age++){        for(j=1;j<=cptcoveff;j++) {
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         if (popbased==1) {        }
           for(i=1; i<=nlstate;i++)        fprintf(ficrespop,"******\n");
             prlim[i][i]=probs[(int)age][i][k];        fprintf(ficrespop,"# Age");
         }        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
                if (popforecast==1)  fprintf(ficrespop," [Population]");
         fprintf(ficrest," %4.0f",age);        
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){        for (cpt=0; cpt<=0;cpt++) { 
           for(i=1, epj[j]=0.;i <=nlstate;i++) {          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
             epj[j] += prlim[i][i]*eij[i][j][(int)age];          
           }          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
           epj[nlstate+1] +=epj[j];            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
         }            nhstepm = nhstepm/hstepm; 
         for(i=1, vepp=0.;i <=nlstate;i++)            
           for(j=1;j <=nlstate;j++)            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             vepp += vareij[i][j][(int)age];            oldm=oldms;savm=savms;
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
         for(j=1;j <=nlstate;j++){          
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));            for (h=0; h<=nhstepm; h++){
         }              if (h==(int) (calagedatem+YEARM*cpt)) {
         fprintf(ficrest,"\n");                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
       }              } 
     }              for(j=1; j<=nlstate+ndeath;j++) {
   }                kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
   fclose(ficreseij);                  if (mobilav==1) 
   fclose(ficresvij);                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
   fclose(ficrest);                  else {
   fclose(ficpar);                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
   free_vector(epj,1,nlstate+1);                  }
                  }
   /*------- Variance limit prevalence------*/                  if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
   strcpy(fileresvpl,"vpl");                    /*fprintf(ficrespop," %.3f", kk1);
   strcat(fileresvpl,fileres);                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {                }
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);              }
     exit(0);              for(i=1; i<=nlstate;i++){
   }                kk1=0.;
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);                  for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
   k=0;                  }
   for(cptcov=1;cptcov<=i1;cptcov++){                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              }
       k=k+1;  
       fprintf(ficresvpl,"\n#****** ");              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
       for(j=1;j<=cptcoveff;j++)                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            }
       fprintf(ficresvpl,"******\n");            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                }
       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);    /******/
     }  
  }        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
   fclose(ficresvpl);          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   /*---------- End : free ----------------*/            nhstepm = nhstepm/hstepm; 
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);            
              p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);            oldm=oldms;savm=savms;
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
              for (h=0; h<=nhstepm; h++){
                if (h==(int) (calagedatem+YEARM*cpt)) {
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);              } 
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);              for(j=1; j<=nlstate+ndeath;j++) {
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);                kk1=0.;kk2=0;
                  for(i=1; i<=nlstate;i++) {              
   free_matrix(matcov,1,npar,1,npar);                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
   free_vector(delti,1,npar);                }
   free_matrix(agev,1,maxwav,1,imx);                if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);              }
             }
   if(erreur >0)            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("End of Imach with error or warning %d\n",erreur);          }
   else   printf("End of Imach\n");        }
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */     } 
      }
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/   
   /*printf("Total time was %d uSec.\n", total_usecs);*/    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   /*------ End -----------*/  
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
  end:      free_vector(popeffectif,0,AGESUP);
 #ifdef windows      free_vector(popcount,0,AGESUP);
   /* chdir(pathcd);*/    }
 #endif    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  /*system("wgnuplot graph.plt");*/    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  /*system("../gp37mgw/wgnuplot graph.plt");*/    fclose(ficrespop);
  /*system("cd ../gp37mgw");*/  }
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/  
  strcpy(plotcmd,GNUPLOTPROGRAM);  /***********************************************/
  strcat(plotcmd," ");  /**************** Main Program *****************/
  strcat(plotcmd,optionfilegnuplot);  /***********************************************/
  system(plotcmd);  
   int main(int argc, char *argv[])
 #ifdef windows  {
   while (z[0] != 'q') {    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     /* chdir(path); */    int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    double agedeb, agefin,hf;
     scanf("%s",z);    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
     if (z[0] == 'c') system("./imach");  
     else if (z[0] == 'e') system(optionfilehtm);    double fret;
     else if (z[0] == 'g') system(plotcmd);    double **xi,tmp,delta;
     else if (z[0] == 'q') exit(0);  
   }    double dum; /* Dummy variable */
 #endif    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.1.40  
changed lines
  Added in v.1.81

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