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version 1.45, 2002/05/24 16:34:18 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 "gnuplot"    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) {    int l=1, lmax=20;
                 if (calagedate>0)    double k1,k2;
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    double p2[NPARMAX+1];
                 else    double res;
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];    double fx;
               }    int k=0,kmax=10;
             }    double l1;
           }  
         }    fx=func(x);
       }    for (i=1;i<=npar;i++) p2[i]=x[i];
       for(i=(int)agemin; i <= (int)agemax+3; i++){    for(l=0 ; l <=lmax; l++){
         for(jk=1; jk <=nlstate ; jk++){      l1=pow(10,l);
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      delts=delt;
             pp[jk] += freq[jk][m][i];      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=-1, pos=0; m <=0 ; m++)        k1=func(p2)-fx;
             pos += freq[jk][m][i];        p2[theta]=x[theta]-delt;
         }        k2=func(p2)-fx;
                /*res= (k1-2.0*fx+k2)/delt/delt; */
         for(jk=1; jk <=nlstate ; jk++){        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        
             pp[jk] += freq[jk][m][i];  #ifdef DEBUG
         }        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
                fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];  #endif
                /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         for(jk=1; jk <=nlstate ; jk++){            if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           if( i <= (int) agemax){          k=kmax;
             if(pos>=1.e-5){        }
               probs[i][jk][j1]= pp[jk]/pos;        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;
       }        }
     }      }
   }    }
     delti[theta]=delts;
      return res; 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    
   free_vector(pp,1,nlstate);  }
    
 }  /* End of Freq */  double hessij( double x[], double delti[], int thetai,int thetaj)
   {
 /************* Waves Concatenation ***************/    int i;
     int l=1, l1, lmax=20;
 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 k1,k2,k3,k4,res,fx;
 {    double p2[NPARMAX+1];
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    int k;
      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    fx=func(x);
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    for (k=1; k<=2; k++) {
      and mw[mi+1][i]. dh depends on stepm.      for (i=1;i<=npar;i++) p2[i]=x[i];
      */      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   int i, mi, m;      k1=func(p2)-fx;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    
      double sum=0., jmean=0.;*/      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   int j, k=0,jk, ju, jl;      k2=func(p2)-fx;
   double sum=0.;    
   jmin=1e+5;      p2[thetai]=x[thetai]-delti[thetai]/k;
   jmax=-1;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   jmean=0.;      k3=func(p2)-fx;
   for(i=1; i<=imx; i++){    
     mi=0;      p2[thetai]=x[thetai]-delti[thetai]/k;
     m=firstpass;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     while(s[m][i] <= nlstate){      k4=func(p2)-fx;
       if(s[m][i]>=1)      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
         mw[++mi][i]=m;  #ifdef DEBUG
       if(m >=lastpass)      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);
         break;      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);
       else  #endif
         m++;    }
     }/* end while */    return res;
     if (s[m][i] > nlstate){  }
       mi++;     /* Death is another wave */  
       /* if(mi==0)  never been interviewed correctly before death */  /************** Inverse of matrix **************/
          /* Only death is a correct wave */  void ludcmp(double **a, int n, int *indx, double *d) 
       mw[mi][i]=m;  { 
     }    int i,imax,j,k; 
     double big,dum,sum,temp; 
     wav[i]=mi;    double *vv; 
     if(mi==0)   
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    vv=vector(1,n); 
   }    *d=1.0; 
     for (i=1;i<=n;i++) { 
   for(i=1; i<=imx; i++){      big=0.0; 
     for(mi=1; mi<wav[i];mi++){      for (j=1;j<=n;j++) 
       if (stepm <=0)        if ((temp=fabs(a[i][j])) > big) big=temp; 
         dh[mi][i]=1;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       else{      vv[i]=1.0/big; 
         if (s[mw[mi+1][i]][i] > nlstate) {    } 
           if (agedc[i] < 2*AGESUP) {    for (j=1;j<=n;j++) { 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);      for (i=1;i<j;i++) { 
           if(j==0) j=1;  /* Survives at least one month after exam */        sum=a[i][j]; 
           k=k+1;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
           if (j >= jmax) jmax=j;        a[i][j]=sum; 
           if (j <= jmin) jmin=j;      } 
           sum=sum+j;      big=0.0; 
           /*if (j<0) printf("j=%d num=%d \n",j,i); */      for (i=j;i<=n;i++) { 
           }        sum=a[i][j]; 
         }        for (k=1;k<j;k++) 
         else{          sum -= a[i][k]*a[k][j]; 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        a[i][j]=sum; 
           k=k+1;        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           if (j >= jmax) jmax=j;          big=dum; 
           else if (j <= jmin)jmin=j;          imax=i; 
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        } 
           sum=sum+j;      } 
         }      if (j != imax) { 
         jk= j/stepm;        for (k=1;k<=n;k++) { 
         jl= j -jk*stepm;          dum=a[imax][k]; 
         ju= j -(jk+1)*stepm;          a[imax][k]=a[j][k]; 
         if(jl <= -ju)          a[j][k]=dum; 
           dh[mi][i]=jk;        } 
         else        *d = -(*d); 
           dh[mi][i]=jk+1;        vv[imax]=vv[j]; 
         if(dh[mi][i]==0)      } 
           dh[mi][i]=1; /* At least one step */      indx[j]=imax; 
       }      if (a[j][j] == 0.0) a[j][j]=TINY; 
     }      if (j != n) { 
   }        dum=1.0/(a[j][j]); 
   jmean=sum/k;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);      } 
  }    } 
 /*********** Tricode ****************************/    free_vector(vv,1,n);  /* Doesn't work */
 void tricode(int *Tvar, int **nbcode, int imx)  ;
 {  } 
   int Ndum[20],ij=1, k, j, i;  
   int cptcode=0;  void lubksb(double **a, int n, int *indx, double b[]) 
   cptcoveff=0;  { 
      int i,ii=0,ip,j; 
   for (k=0; k<19; k++) Ndum[k]=0;    double sum; 
   for (k=1; k<=7; k++) ncodemax[k]=0;   
     for (i=1;i<=n;i++) { 
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {      ip=indx[i]; 
     for (i=1; i<=imx; i++) {      sum=b[ip]; 
       ij=(int)(covar[Tvar[j]][i]);      b[ip]=b[i]; 
       Ndum[ij]++;      if (ii) 
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       if (ij > cptcode) cptcode=ij;      else if (sum) ii=i; 
     }      b[i]=sum; 
     } 
     for (i=0; i<=cptcode; i++) {    for (i=n;i>=1;i--) { 
       if(Ndum[i]!=0) ncodemax[j]++;      sum=b[i]; 
     }      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     ij=1;      b[i]=sum/a[i][i]; 
     } 
   } 
     for (i=1; i<=ncodemax[j]; i++) {  
       for (k=0; k<=19; k++) {  /************ Frequencies ********************/
         if (Ndum[k] != 0) {  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)
           nbcode[Tvar[j]][ij]=k;  {  /* Some frequencies */
              
           ij++;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
         }    int first;
         if (ij > ncodemax[j]) break;    double ***freq; /* Frequencies */
       }      double *pp, **prop;
     }    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   }      FILE *ficresp;
     char fileresp[FILENAMELENGTH];
  for (k=0; k<19; k++) Ndum[k]=0;    
     pp=vector(1,nlstate);
  for (i=1; i<=ncovmodel-2; i++) {    prop=matrix(1,nlstate,iagemin,iagemax+3);
       ij=Tvar[i];    strcpy(fileresp,"p");
       Ndum[ij]++;    strcat(fileresp,fileres);
     }    if((ficresp=fopen(fileresp,"w"))==NULL) {
       printf("Problem with prevalence resultfile: %s\n", fileresp);
  ij=1;      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
  for (i=1; i<=10; i++) {      exit(0);
    if((Ndum[i]!=0) && (i<=ncovcol)){    }
      Tvaraff[ij]=i;    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
      ij++;    j1=0;
    }    
  }    j=cptcoveff;
      if (cptcovn<1) {j=1;ncodemax[1]=1;}
     cptcoveff=ij-1;  
 }    first=1;
   
 /*********** Health Expectancies ****************/    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
 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 )        j1++;
         /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
 {          scanf("%d", i);*/
   /* Health expectancies */        for (i=-1; i<=nlstate+ndeath; i++)  
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;          for (jk=-1; jk<=nlstate+ndeath; jk++)  
   double age, agelim, hf;            for(m=iagemin; m <= iagemax+3; m++)
   double ***p3mat,***varhe;              freq[i][jk][m]=0;
   double **dnewm,**doldm;  
   double *xp;      for (i=1; i<=nlstate; i++)  
   double **gp, **gm;        for(m=iagemin; m <= iagemax+3; m++)
   double ***gradg, ***trgradg;          prop[i][m]=0;
   int theta;        
         dateintsum=0;
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);        k2cpt=0;
   xp=vector(1,npar);        for (i=1; i<=imx; i++) {
   dnewm=matrix(1,nlstate*2,1,npar);          bool=1;
   doldm=matrix(1,nlstate*2,1,nlstate*2);          if  (cptcovn>0) {
              for (z1=1; z1<=cptcoveff; z1++) 
   fprintf(ficreseij,"# Health expectancies\n");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   fprintf(ficreseij,"# Age");                bool=0;
   for(i=1; i<=nlstate;i++)          }
     for(j=1; j<=nlstate;j++)          if (bool==1){
       fprintf(ficreseij," %1d-%1d (SE)",i,j);            for(m=firstpass; m<=lastpass; m++){
   fprintf(ficreseij,"\n");              k2=anint[m][i]+(mint[m][i]/12.);
               if ((k2>=dateprev1) && (k2<=dateprev2)) {
   if(estepm < stepm){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     printf ("Problem %d lower than %d\n",estepm, stepm);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   }                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   else  hstepm=estepm;                  if (m<lastpass) {
   /* We compute the life expectancy from trapezoids spaced every estepm months                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
    * This is mainly to measure the difference between two models: for example                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
    * if stepm=24 months pijx are given only every 2 years and by summing them                }
    * we are calculating an estimate of the Life Expectancy assuming a linear                
    * progression inbetween and thus overestimating or underestimating according                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
    * to the curvature of the survival function. If, for the same date, we                  dateintsum=dateintsum+k2;
    * estimate the model with stepm=1 month, we can keep estepm to 24 months                  k2cpt++;
    * to compare the new estimate of Life expectancy with the same linear                }
    * hypothesis. A more precise result, taking into account a more precise              }
    * curvature will be obtained if estepm is as small as stepm. */            }
           }
   /* For example we decided to compute the life expectancy with the smallest unit */        }
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.         
      nhstepm is the number of hstepm from age to agelim        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
      nstepm is the number of stepm from age to agelin.  
      Look at hpijx to understand the reason of that which relies in memory size        if  (cptcovn>0) {
      and note for a fixed period like estepm months */          fprintf(ficresp, "\n#********** Variable "); 
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
      survival function given by stepm (the optimization length). Unfortunately it          fprintf(ficresp, "**********\n#");
      means that if the survival funtion is printed only each two years of age and if        }
      you sum them up and add 1 year (area under the trapezoids) you won't get the same        for(i=1; i<=nlstate;i++) 
      results. So we changed our mind and took the option of the best precision.          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   */        fprintf(ficresp, "\n");
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        
         for(i=iagemin; i <= iagemax+3; i++){
   agelim=AGESUP;          if(i==iagemax+3){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            fprintf(ficlog,"Total");
     /* nhstepm age range expressed in number of stepm */          }else{
     nstepm=(int) rint((agelim-age)*YEARM/stepm);            if(first==1){
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */              first=0;
     /* if (stepm >= YEARM) hstepm=1;*/              printf("See log file for details...\n");
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */            }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            fprintf(ficlog,"Age %d", i);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);          }
     gp=matrix(0,nhstepm,1,nlstate*2);          for(jk=1; jk <=nlstate ; jk++){
     gm=matrix(0,nhstepm,1,nlstate*2);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
               pp[jk] += freq[jk][m][i]; 
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          }
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          for(jk=1; jk <=nlstate ; jk++){
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);              for(m=-1, pos=0; m <=0 ; m++)
                pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */              if(first==1){
               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     /* Computing Variances of health expectancies */              }
               fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
      for(theta=1; theta <=npar; theta++){            }else{
       for(i=1; i<=npar; i++){              if(first==1)
         xp[i] = x[i] + (i==theta ?delti[theta]:0);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       }              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              }
            }
       cptj=0;  
       for(j=1; j<= nlstate; j++){          for(jk=1; jk <=nlstate ; jk++){
         for(i=1; i<=nlstate; i++){            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
           cptj=cptj+1;              pp[jk] += freq[jk][m][i];
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){          }       
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
           }            pos += pp[jk];
         }            posprop += prop[jk][i];
       }          }
                for(jk=1; jk <=nlstate ; jk++){
                  if(pos>=1.e-5){
       for(i=1; i<=npar; i++)              if(first==1)
         xp[i] = x[i] - (i==theta ?delti[theta]:0);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                  }else{
       cptj=0;              if(first==1)
       for(j=1; j<= nlstate; j++){                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         for(i=1;i<=nlstate;i++){              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
           cptj=cptj+1;            }
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){            if( i <= iagemax){
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;              if(pos>=1.e-5){
           }                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
         }                probs[i][jk][j1]= pp[jk]/pos;
       }                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
                    }
                  else
                 fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
       for(j=1; j<= nlstate*2; j++)            }
         for(h=0; h<=nhstepm-1; h++){          }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          
         }          for(jk=-1; jk <=nlstate+ndeath; jk++)
             for(m=-1; m <=nlstate+ndeath; m++)
      }              if(freq[jk][m][i] !=0 ) {
                  if(first==1)
 /* End theta */                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                 fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);              }
           if(i <= iagemax)
      for(h=0; h<=nhstepm-1; h++)            fprintf(ficresp,"\n");
       for(j=1; j<=nlstate*2;j++)          if(first==1)
         for(theta=1; theta <=npar; theta++)            printf("Others in log...\n");
         trgradg[h][j][theta]=gradg[h][theta][j];          fprintf(ficlog,"\n");
         }
       }
      for(i=1;i<=nlstate*2;i++)    }
       for(j=1;j<=nlstate*2;j++)    dateintmean=dateintsum/k2cpt; 
         varhe[i][j][(int)age] =0.;   
     fclose(ficresp);
      printf("%d|",(int)age);fflush(stdout);    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
     for(h=0;h<=nhstepm-1;h++){    free_vector(pp,1,nlstate);
       for(k=0;k<=nhstepm-1;k++){    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);    /* End of Freq */
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);  }
         for(i=1;i<=nlstate*2;i++)  
           for(j=1;j<=nlstate*2;j++)  /************ Prevalence ********************/
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;  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)
       }  {  
     }    /* 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.
     /* Computing expectancies */    */
     for(i=1; i<=nlstate;i++)   
       for(j=1; j<=nlstate;j++)    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    double ***freq; /* Frequencies */
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;    double *pp, **prop;
              double pos,posprop; 
 /* 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]);*/    double  y2; /* in fractional years */
     int iagemin, iagemax;
         }  
     iagemin= (int) agemin;
     fprintf(ficreseij,"%3.0f",age );    iagemax= (int) agemax;
     cptj=0;    /*pp=vector(1,nlstate);*/
     for(i=1; i<=nlstate;i++)    prop=matrix(1,nlstate,iagemin,iagemax+3); 
       for(j=1; j<=nlstate;j++){    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
         cptj++;    j1=0;
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );    
       }    j=cptcoveff;
     fprintf(ficreseij,"\n");    if (cptcovn<1) {j=1;ncodemax[1]=1;}
        
     free_matrix(gm,0,nhstepm,1,nlstate*2);    for(k1=1; k1<=j;k1++){
     free_matrix(gp,0,nhstepm,1,nlstate*2);      for(i1=1; i1<=ncodemax[k1];i1++){
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);        j1++;
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);        
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for (i=1; i<=nlstate; i++)  
   }          for(m=iagemin; m <= iagemax+3; m++)
   free_vector(xp,1,npar);            prop[i][m]=0.0;
   free_matrix(dnewm,1,nlstate*2,1,npar);       
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);        for (i=1; i<=imx; i++) { /* Each individual */
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);          bool=1;
 }          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
 /************ Variance ******************/              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
 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)                bool=0;
 {          } 
   /* Variance of health expectancies */          if (bool==1) { 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   double **newm;              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   double **dnewm,**doldm;              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   int i, j, nhstepm, hstepm, h, nstepm ;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   int k, cptcode;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   double *xp;                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
   double **gp, **gm;                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   double ***gradg, ***trgradg;                  /*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]]);*/
   double ***p3mat;                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   double age,agelim, hf;                  prop[s[m][i]][iagemax+3] += weight[i]; 
   int theta;                } 
               }
   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");            } /* end selection of waves */
   fprintf(ficresvij,"# Age");          }
   for(i=1; i<=nlstate;i++)        }
     for(j=1; j<=nlstate;j++)        for(i=iagemin; i <= iagemax+3; i++){  
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          
   fprintf(ficresvij,"\n");          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
             posprop += prop[jk][i]; 
   xp=vector(1,npar);          } 
   dnewm=matrix(1,nlstate,1,npar);  
   doldm=matrix(1,nlstate,1,nlstate);          for(jk=1; jk <=nlstate ; jk++){     
              if( i <=  iagemax){ 
   if(estepm < stepm){              if(posprop>=1.e-5){ 
     printf ("Problem %d lower than %d\n",estepm, stepm);                probs[i][jk][j1]= prop[jk][i]/posprop;
   }              } 
   else  hstepm=estepm;              } 
   /* For example we decided to compute the life expectancy with the smallest unit */          }/* end jk */ 
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        }/* end i */ 
      nhstepm is the number of hstepm from age to agelim      } /* end i1 */
      nstepm is the number of stepm from age to agelin.    } /* end k1 */
      Look at hpijx to understand the reason of that which relies in memory size    
      and note for a fixed period like k years */    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    /*free_vector(pp,1,nlstate);*/
      survival function given by stepm (the optimization length). Unfortunately it    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
      means that if the survival funtion is printed only each two years of age and if  }  /* End of prevalence */
      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.  /************* Waves Concatenation ***************/
   */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */  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)
   agelim = AGESUP;  {
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */       Death is a valid wave (if date is known).
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);       and mw[mi+1][i]. dh depends on stepm.
     gp=matrix(0,nhstepm,1,nlstate);       */
     gm=matrix(0,nhstepm,1,nlstate);  
     int i, mi, m;
     for(theta=1; theta <=npar; theta++){    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
       for(i=1; i<=npar; i++){ /* Computes gradient */       double sum=0., jmean=0.;*/
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    int first;
       }    int j, k=0,jk, ju, jl;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      double sum=0.;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    first=0;
     jmin=1e+5;
       if (popbased==1) {    jmax=-1;
         for(i=1; i<=nlstate;i++)    jmean=0.;
           prlim[i][i]=probs[(int)age][i][ij];    for(i=1; i<=imx; i++){
       }      mi=0;
        m=firstpass;
       for(j=1; j<= nlstate; j++){      while(s[m][i] <= nlstate){
         for(h=0; h<=nhstepm; h++){        if(s[m][i]>=1)
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          mw[++mi][i]=m;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        if(m >=lastpass)
         }          break;
       }        else
              m++;
       for(i=1; i<=npar; i++) /* Computes gradient */      }/* end while */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      if (s[m][i] > nlstate){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          mi++;     /* Death is another wave */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        /* if(mi==0)  never been interviewed correctly before death */
             /* Only death is a correct wave */
       if (popbased==1) {        mw[mi][i]=m;
         for(i=1; i<=nlstate;i++)      }
           prlim[i][i]=probs[(int)age][i][ij];  
       }      wav[i]=mi;
       if(mi==0){
       for(j=1; j<= nlstate; j++){        if(first==0){
         for(h=0; h<=nhstepm; h++){          printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          first=1;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        }
         }        if(first==1){
       }          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(h=0; h<=nhstepm; h++){    } /* End individuals */
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  
         }    for(i=1; i<=imx; i++){
     } /* End theta */      for(mi=1; mi<wav[i];mi++){
         if (stepm <=0)
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          dh[mi][i]=1;
         else{
     for(h=0; h<=nhstepm; h++)          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
       for(j=1; j<=nlstate;j++)            if (agedc[i] < 2*AGESUP) {
         for(theta=1; theta <=npar; theta++)            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
           trgradg[h][j][theta]=gradg[h][theta][j];            if(j==0) j=1;  /* Survives at least one month after exam */
             k=k+1;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */            if (j >= jmax) jmax=j;
     for(i=1;i<=nlstate;i++)            if (j <= jmin) jmin=j;
       for(j=1;j<=nlstate;j++)            sum=sum+j;
         vareij[i][j][(int)age] =0.;            /*if (j<0) printf("j=%d num=%d \n",j,i);*/
             /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     for(h=0;h<=nhstepm;h++){            if(j<0)printf("Error! Negative delay (%d to death) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       for(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]);          else{
         for(i=1;i<=nlstate;i++)            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
           for(j=1;j<=nlstate;j++)            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;            k=k+1;
       }            if (j >= jmax) jmax=j;
     }            else if (j <= jmin)jmin=j;
             /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     fprintf(ficresvij,"%.0f ",age );            /*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]);*/
     for(i=1; i<=nlstate;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]);
       for(j=1; j<=nlstate;j++){            sum=sum+j;
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);          }
       }          jk= j/stepm;
     fprintf(ficresvij,"\n");          jl= j -jk*stepm;
     free_matrix(gp,0,nhstepm,1,nlstate);          ju= j -(jk+1)*stepm;
     free_matrix(gm,0,nhstepm,1,nlstate);          if(mle <=1){ 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);            if(jl==0){
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);              dh[mi][i]=jk;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              bh[mi][i]=0;
   } /* End age */            }else{ /* We want a negative bias in order to only have interpolation ie
                      * at the price of an extra matrix product in likelihood */
   free_vector(xp,1,npar);              dh[mi][i]=jk+1;
   free_matrix(doldm,1,nlstate,1,npar);              bh[mi][i]=ju;
   free_matrix(dnewm,1,nlstate,1,nlstate);            }
           }else{
 }            if(jl <= -ju){
               dh[mi][i]=jk;
 /************ Variance of prevlim ******************/              bh[mi][i]=jl;       /* bias is positive if real duration
 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)                                   * is higher than the multiple of stepm and negative otherwise.
 {                                   */
   /* Variance of prevalence limit */            }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            else{
   double **newm;              dh[mi][i]=jk+1;
   double **dnewm,**doldm;              bh[mi][i]=ju;
   int i, j, nhstepm, hstepm;            }
   int k, cptcode;            if(dh[mi][i]==0){
   double *xp;              dh[mi][i]=1; /* At least one step */
   double *gp, *gm;              bh[mi][i]=ju; /* At least one step */
   double **gradg, **trgradg;              /*  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);*/
   double age,agelim;            }
   int theta;          }
            } /* end if mle */
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");      } /* end wave */
   fprintf(ficresvpl,"# Age");    }
   for(i=1; i<=nlstate;i++)    jmean=sum/k;
       fprintf(ficresvpl," %1d-%1d",i,i);    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   fprintf(ficresvpl,"\n");    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
    }
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);  /*********** Tricode ****************************/
   doldm=matrix(1,nlstate,1,nlstate);  void tricode(int *Tvar, int **nbcode, int imx)
    {
   hstepm=1*YEARM; /* Every year of age */    
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    int Ndum[20],ij=1, k, j, i, maxncov=19;
   agelim = AGESUP;    int cptcode=0;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    cptcoveff=0; 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */   
     if (stepm >= YEARM) hstepm=1;    for (k=0; k<maxncov; k++) Ndum[k]=0;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    for (k=1; k<=7; k++) ncodemax[k]=0;
     gradg=matrix(1,npar,1,nlstate);  
     gp=vector(1,nlstate);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     gm=vector(1,nlstate);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                  modality*/ 
     for(theta=1; theta <=npar; theta++){        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
       for(i=1; i<=npar; i++){ /* Computes gradient */        Ndum[ij]++; /*store the modality */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        /*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 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);                                         Tvar[j]. If V=sex and male is 0 and 
       for(i=1;i<=nlstate;i++)                                         female is 1, then  cptcode=1.*/
         gp[i] = prlim[i][i];      }
      
       for(i=1; i<=npar; i++) /* Computes gradient */      for (i=0; i<=cptcode; i++) {
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        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 */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      }
       for(i=1;i<=nlstate;i++)  
         gm[i] = prlim[i][i];      ij=1; 
       for (i=1; i<=ncodemax[j]; i++) {
       for(i=1;i<=nlstate;i++)        for (k=0; k<= maxncov; k++) {
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          if (Ndum[k] != 0) {
     } /* End theta */            nbcode[Tvar[j]][ij]=k; 
             /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
     trgradg =matrix(1,nlstate,1,npar);            
             ij++;
     for(j=1; j<=nlstate;j++)          }
       for(theta=1; theta <=npar; theta++)          if (ij > ncodemax[j]) break; 
         trgradg[j][theta]=gradg[theta][j];        }  
       } 
     for(i=1;i<=nlstate;i++)    }  
       varpl[i][(int)age] =0.;  
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);   for (k=0; k< maxncov; k++) Ndum[k]=0;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);  
     for(i=1;i<=nlstate;i++)   for (i=1; i<=ncovmodel-2; i++) { 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
      ij=Tvar[i];
     fprintf(ficresvpl,"%.0f ",age );     Ndum[ij]++;
     for(i=1; i<=nlstate;i++)   }
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  
     fprintf(ficresvpl,"\n");   ij=1;
     free_vector(gp,1,nlstate);   for (i=1; i<= maxncov; i++) {
     free_vector(gm,1,nlstate);     if((Ndum[i]!=0) && (i<=ncovcol)){
     free_matrix(gradg,1,npar,1,nlstate);       Tvaraff[ij]=i; /*For printing */
     free_matrix(trgradg,1,nlstate,1,npar);       ij++;
   } /* End age */     }
    }
   free_vector(xp,1,npar);   
   free_matrix(doldm,1,nlstate,1,npar);   cptcoveff=ij-1; /*Number of simple covariates*/
   free_matrix(dnewm,1,nlstate,1,nlstate);  }
   
 }  /*********** Health Expectancies ****************/
   
 /************ Variance of one-step probabilities  ******************/  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 )
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)  
 {  {
   int i, j, i1, k1, j1, z1;    /* Health expectancies */
   int k=0, cptcode;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
   double **dnewm,**doldm;    double age, agelim, hf;
   double *xp;    double ***p3mat,***varhe;
   double *gp, *gm;    double **dnewm,**doldm;
   double **gradg, **trgradg;    double *xp;
   double age,agelim, cov[NCOVMAX];    double **gp, **gm;
   int theta;    double ***gradg, ***trgradg;
   char fileresprob[FILENAMELENGTH];    int theta;
   
   strcpy(fileresprob,"prob");    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   strcat(fileresprob,fileres);    xp=vector(1,npar);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    dnewm=matrix(1,nlstate*nlstate,1,npar);
     printf("Problem with resultfile: %s\n", fileresprob);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   }    
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    fprintf(ficreseij,"# Health expectancies\n");
      fprintf(ficreseij,"# Age");
 fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");    for(i=1; i<=nlstate;i++)
   fprintf(ficresprob,"# Age");      for(j=1; j<=nlstate;j++)
   for(i=1; i<=nlstate;i++)        fprintf(ficreseij," %1d-%1d (SE)",i,j);
     for(j=1; j<=(nlstate+ndeath);j++)    fprintf(ficreseij,"\n");
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);  
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
   fprintf(ficresprob,"\n");    }
     else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
   xp=vector(1,npar);     * This is mainly to measure the difference between two models: for example
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);     * if stepm=24 months pijx are given only every 2 years and by summing them
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));     * we are calculating an estimate of the Life Expectancy assuming a linear 
       * progression in between and thus overestimating or underestimating according
   cov[1]=1;     * to the curvature of the survival function. If, for the same date, we 
   j=cptcoveff;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   if (cptcovn<1) {j=1;ncodemax[1]=1;}     * to compare the new estimate of Life expectancy with the same linear 
   j1=0;     * hypothesis. A more precise result, taking into account a more precise
   for(k1=1; k1<=1;k1++){     * curvature will be obtained if estepm is as small as stepm. */
     for(i1=1; i1<=ncodemax[k1];i1++){  
     j1++;    /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     if  (cptcovn>0) {       nhstepm is the number of hstepm from age to agelim 
       fprintf(ficresprob, "\n#********** Variable ");       nstepm is the number of stepm from age to agelin. 
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);       Look at hpijx to understand the reason of that which relies in memory size
       fprintf(ficresprob, "**********\n#");       and note for a fixed period like estepm months */
     }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           survival function given by stepm (the optimization length). Unfortunately it
       for (age=bage; age<=fage; age ++){       means that if the survival funtion is printed only each two years of age and if
         cov[2]=age;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         for (k=1; k<=cptcovn;k++) {       results. So we changed our mind and took the option of the best precision.
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];    */
              hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         }  
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    agelim=AGESUP;
         for (k=1; k<=cptcovprod;k++)    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      /* nhstepm age range expressed in number of stepm */
              nstepm=(int) rint((agelim-age)*YEARM/stepm); 
         gradg=matrix(1,npar,1,9);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
         trgradg=matrix(1,9,1,npar);      /* if (stepm >= YEARM) hstepm=1;*/
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
         for(theta=1; theta <=npar; theta++){      gp=matrix(0,nhstepm,1,nlstate*nlstate);
           for(i=1; i<=npar; i++)      gm=matrix(0,nhstepm,1,nlstate*nlstate);
             xp[i] = x[i] + (i==theta ?delti[theta]:0);  
                /* Computed by stepm unit matrices, product of hstepm matrices, stored
           pmij(pmmij,cov,ncovmodel,xp,nlstate);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
                hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
           k=0;   
           for(i=1; i<= (nlstate+ndeath); i++){  
             for(j=1; j<=(nlstate+ndeath);j++){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
               k=k+1;  
               gp[k]=pmmij[i][j];      /* Computing Variances of health expectancies */
             }  
           }       for(theta=1; theta <=npar; theta++){
                  for(i=1; i<=npar; i++){ 
           for(i=1; i<=npar; i++)          xp[i] = x[i] + (i==theta ?delti[theta]:0);
             xp[i] = x[i] - (i==theta ?delti[theta]:0);        }
            hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    
           k=0;        cptj=0;
           for(i=1; i<=(nlstate+ndeath); i++){        for(j=1; j<= nlstate; j++){
             for(j=1; j<=(nlstate+ndeath);j++){          for(i=1; i<=nlstate; i++){
               k=k+1;            cptj=cptj+1;
               gm[k]=pmmij[i][j];            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
             }              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
           }            }
                }
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)        }
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];         
         }       
         for(i=1; i<=npar; i++) 
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           for(theta=1; theta <=npar; theta++)        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
             trgradg[j][theta]=gradg[theta][j];        
                cptj=0;
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);        for(j=1; j<= nlstate; j++){
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          for(i=1;i<=nlstate;i++){
                    cptj=cptj+1;
         pmij(pmmij,cov,ncovmodel,x,nlstate);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
          
         k=0;              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
         for(i=1; i<=(nlstate+ndeath); i++){            }
           for(j=1; j<=(nlstate+ndeath);j++){          }
             k=k+1;        }
             gm[k]=pmmij[i][j];        for(j=1; j<= nlstate*nlstate; j++)
           }          for(h=0; h<=nhstepm-1; h++){
         }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
                }
      /*printf("\n%d ",(int)age);       } 
      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]));  /* End theta */
      }*/  
        trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
         fprintf(ficresprob,"\n%d ",(int)age);  
        for(h=0; h<=nhstepm-1; h++)
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)        for(j=1; j<=nlstate*nlstate;j++)
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));          for(theta=1; theta <=npar; theta++)
              trgradg[h][j][theta]=gradg[h][theta][j];
       }       
     }  
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));       for(i=1;i<=nlstate*nlstate;i++)
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));        for(j=1;j<=nlstate*nlstate;j++)
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          varhe[i][j][(int)age] =0.;
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
   }       printf("%d|",(int)age);fflush(stdout);
   free_vector(xp,1,npar);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   fclose(ficresprob);       for(h=0;h<=nhstepm-1;h++){
          for(k=0;k<=nhstepm-1;k++){
 }          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           for(i=1;i<=nlstate*nlstate;i++)
 /******************* Printing html file ***********/            for(j=1;j<=nlstate*nlstate;j++)
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
                   int lastpass, int stepm, int weightopt, char model[],\        }
                   int imx,int jmin, int jmax, double jmeanint,char optionfile[], \      }
                   char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\      /* Computing expectancies */
                   char version[], int popforecast, int estepm ,\      for(i=1; i<=nlstate;i++)
                   double jprev1, double mprev1,double anprev1, \        for(j=1; j<=nlstate;j++)
                   double jprev2, double mprev2,double anprev2){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   int jj1, k1, i1, cpt;            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   FILE *fichtm;            
   /*char optionfilehtm[FILENAMELENGTH];*/  /* 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]);*/
   
   strcpy(optionfilehtm,optionfile);          }
   strcat(optionfilehtm,".htm");  
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {      fprintf(ficreseij,"%3.0f",age );
     printf("Problem with %s \n",optionfilehtm), exit(0);      cptj=0;
   }      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n          cptj++;
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
 \n        }
 Total number of observations=%d <br>\n      fprintf(ficreseij,"\n");
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n     
 <hr  size=\"2\" color=\"#EC5E5E\">      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
  <ul><li>Parameter files<br>\n      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
  - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n    }
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n    printf("\n");
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n    fprintf(ficlog,"\n");
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n  
  - Life expectancies by age and initial health status (estepm=%2d months):    free_vector(xp,1,npar);
    <a href=\"e%s\">e%s</a> <br>\n</li>", \    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\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 ******************/
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n  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)
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n  {
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);    /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
  if(popforecast==1) fprintf(fichtm,"\n    /* double **newm;*/
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    double **dnewm,**doldm;
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n    double **dnewmp,**doldmp;
         <br>",fileres,fileres,fileres,fileres);    int i, j, nhstepm, hstepm, h, nstepm ;
  else    int k, cptcode;
    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);    double *xp;
 fprintf(fichtm," <li>Graphs</li><p>");    double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
  m=cptcoveff;    double **gradgp, **trgradgp; /* for var p point j */
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
  jj1=0;    double ***p3mat;
  for(k1=1; k1<=m;k1++){    double age,agelim, hf;
    for(i1=1; i1<=ncodemax[k1];i1++){    double ***mobaverage;
      jj1++;    int theta;
      if (cptcovn > 0) {    char digit[4];
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    char digitp[25];
        for (cpt=1; cpt<=cptcoveff;cpt++)  
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    char fileresprobmorprev[FILENAMELENGTH];
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");  
      }    if(popbased==1){
      /* Pij */      if(mobilav!=0)
      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>        strcpy(digitp,"-populbased-mobilav-");
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          else strcpy(digitp,"-populbased-nomobil-");
      /* 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>    else 
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      strcpy(digitp,"-stablbased-");
        /* Stable prevalence in each health state */  
        for(cpt=1; cpt<nlstate;cpt++){    if (mobilav!=0) {
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
        }        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     for(cpt=1; cpt<=nlstate;cpt++) {        printf(" Error in movingaverage mobilav=%d\n",mobilav);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      }
 interval) in state (%d): v%s%d%d.png <br>    }
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    
      }    strcpy(fileresprobmorprev,"prmorprev"); 
      for(cpt=1; cpt<=nlstate;cpt++) {    sprintf(digit,"%-d",ij);
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
      }    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    strcat(fileresprobmorprev,fileres);
 health expectancies in states (1) and (2): e%s%d.png<br>    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
 fprintf(fichtm,"\n</body>");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
    }    }
  }    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
 fclose(fichtm);    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);
 /******************* Gnuplot file **************/    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){      fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   int ng;    }  
   strcpy(optionfilegnuplot,optionfilefiname);    fprintf(ficresprobmorprev,"\n");
   strcat(optionfilegnuplot,".gp.txt");    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
     printf("Problem with file %s",optionfilegnuplot);      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
   }      exit(0);
     }
 #ifdef windows    else{
     fprintf(ficgp,"cd \"%s\" \n",pathc);      fprintf(ficgp,"\n# Routine varevsij");
 #endif    }
 m=pow(2,cptcoveff);    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
        printf("Problem with html file: %s\n", optionfilehtm);
  /* 1eme*/      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   for (cpt=1; cpt<= nlstate ; cpt ++) {      exit(0);
    for (k1=1; k1<= m ; k1 ++) {    }
     else{
 #ifdef windows      fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
      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);    }
 #endif    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 #ifdef unix  
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    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,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);    fprintf(ficresvij,"# Age");
 #endif    for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
 for (i=1; i<= nlstate ; i ++) {        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    fprintf(ficresvij,"\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }    xp=vector(1,npar);
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    dnewm=matrix(1,nlstate,1,npar);
     for (i=1; i<= nlstate ; i ++) {    doldm=matrix(1,nlstate,1,nlstate);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 }  
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
      for (i=1; i<= nlstate ; i ++) {    gpp=vector(nlstate+1,nlstate+ndeath);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    gmp=vector(nlstate+1,nlstate+ndeath);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
 }      
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    if(estepm < stepm){
 #ifdef unix      printf ("Problem %d lower than %d\n",estepm, stepm);
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");    }
 #endif    else  hstepm=estepm;   
    }    /* For example we decided to compute the life expectancy with the smallest unit */
   }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   /*2 eme*/       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
   for (k1=1; k1<= m ; k1 ++) {       Look at hpijx to understand the reason of that which relies in memory size
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);       and note for a fixed period like k years */
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           survival function given by stepm (the optimization length). Unfortunately it
     for (i=1; i<= nlstate+1 ; i ++) {       means that if the survival funtion is printed every two years of age and if
       k=2*i;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);       results. So we changed our mind and took the option of the best precision.
       for (j=1; j<= nlstate+1 ; j ++) {    */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   else fprintf(ficgp," \%%*lf (\%%*lf)");    agelim = AGESUP;
 }      for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       for (j=1; j<= nlstate+1 ; j ++) {      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      gp=matrix(0,nhstepm,1,nlstate);
         else fprintf(ficgp," \%%*lf (\%%*lf)");      gm=matrix(0,nhstepm,1,nlstate);
 }    
       fprintf(ficgp,"\" t\"\" w l 0,");  
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      for(theta=1; theta <=npar; theta++){
       for (j=1; j<= nlstate+1 ; j ++) {        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   else fprintf(ficgp," \%%*lf (\%%*lf)");        }
 }          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       else fprintf(ficgp,"\" t\"\" w l 0,");  
     }        if (popbased==1) {
   }          if(mobilav ==0){
              for(i=1; i<=nlstate;i++)
   /*3eme*/              prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
   for (k1=1; k1<= m ; k1 ++) {            for(i=1; i<=nlstate;i++)
     for (cpt=1; cpt<= nlstate ; cpt ++) {              prlim[i][i]=mobaverage[(int)age][i][ij];
       k=2+nlstate*(2*cpt-2);          }
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        }
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);        for(j=1; j<= nlstate; j++){
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          for(h=0; h<=nhstepm; h++){
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          }
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);        }
         /* This for computing probability of death (h=1 means
 */           computed over hstepm matrices product = hstepm*stepm months) 
       for (i=1; i< nlstate ; i ++) {           as a weighted average of prlim.
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);        */
         for(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];
   }        }    
          /* end probability of death */
   /* CV preval stat */  
     for (k1=1; k1<= m ; k1 ++) {        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
     for (cpt=1; cpt<nlstate ; cpt ++) {          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       k=3;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);   
         if (popbased==1) {
       for (i=1; i< nlstate ; i ++)          if(mobilav ==0){
         fprintf(ficgp,"+$%d",k+i+1);            for(i=1; i<=nlstate;i++)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);              prlim[i][i]=probs[(int)age][i][ij];
                }else{ /* mobilav */ 
       l=3+(nlstate+ndeath)*cpt;            for(i=1; i<=nlstate;i++)
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);              prlim[i][i]=mobaverage[(int)age][i][ij];
       for (i=1; i< nlstate ; i ++) {          }
         l=3+(nlstate+ndeath)*cpt;        }
         fprintf(ficgp,"+$%d",l+i+1);  
       }        for(j=1; j<= nlstate; j++){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            for(h=0; h<=nhstepm; h++){
     }            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   }                gm[h][j] += prlim[i][i]*p3mat[i][j][h];
            }
   /* proba elementaires */        }
    for(i=1,jk=1; i <=nlstate; i++){        /* This for computing probability of death (h=1 means
     for(k=1; k <=(nlstate+ndeath); k++){           computed over hstepm matrices product = hstepm*stepm months) 
       if (k != i) {           as a weighted average of prlim.
         for(j=1; j <=ncovmodel; j++){        */
                for(j=nlstate+1;j<=nlstate+ndeath;j++){
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
           jk++;           gmp[j] += prlim[i][i]*p3mat[i][j][1];
           fprintf(ficgp,"\n");        }    
         }        /* end probability of death */
       }  
     }        for(j=1; j<= nlstate; j++) /* vareij */
    }          for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
    for(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);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
        if (ng==2)          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");        }
        else  
          fprintf(ficgp,"\nset title \"Probability\"\n");      } /* End theta */
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);  
        i=1;      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
        for(k2=1; k2<=nlstate; k2++) {  
          k3=i;      for(h=0; h<=nhstepm; h++) /* veij */
          for(k=1; k<=(nlstate+ndeath); k++) {        for(j=1; j<=nlstate;j++)
            if (k != k2){          for(theta=1; theta <=npar; theta++)
              if(ng==2)            trgradg[h][j][theta]=gradg[h][theta][j];
                fprintf(ficgp," %f*exp(p%d+p%d*x",stepm/YEARM,i,i+1);  
              else      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);        for(theta=1; theta <=npar; theta++)
              ij=1;          trgradgp[j][theta]=gradgp[theta][j];
              for(j=3; j <=ncovmodel; j++) {    
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {  
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
                  ij++;      for(i=1;i<=nlstate;i++)
                }        for(j=1;j<=nlstate;j++)
                else          vareij[i][j][(int)age] =0.;
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  
              }      for(h=0;h<=nhstepm;h++){
              fprintf(ficgp,")/(1");        for(k=0;k<=nhstepm;k++){
                        matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
              for(k1=1; k1 <=nlstate; k1++){            matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);          for(i=1;i<=nlstate;i++)
                ij=1;            for(j=1;j<=nlstate;j++)
                for(j=3; j <=ncovmodel; j++){              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        }
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      }
                    ij++;    
                  }      /* pptj */
                  else      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
                }      for(j=nlstate+1;j<=nlstate+ndeath;j++)
                fprintf(ficgp,")");        for(i=nlstate+1;i<=nlstate+ndeath;i++)
              }          varppt[j][i]=doldmp[j][i];
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);      /* end ppptj */
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      /*  x centered again */
              i=i+ncovmodel;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
            }      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
          }   
        }      if (popbased==1) {
      }        if(mobilav ==0){
    }          for(i=1; i<=nlstate;i++)
    fclose(ficgp);            prlim[i][i]=probs[(int)age][i][ij];
 }  /* end gnuplot */        }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
 /*************** Moving average **************/        }
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){      }
                
   int i, cpt, cptcod;      /* This for computing probability of death (h=1 means
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
       for (i=1; i<=nlstate;i++)         as a weighted average of prlim.
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)      */
           mobaverage[(int)agedeb][i][cptcod]=0.;      for(j=nlstate+1;j<=nlstate+ndeath;j++){
            for(i=1,gmp[j]=0.;i<= nlstate; i++) 
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       for (i=1; i<=nlstate;i++){      }    
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      /* end probability of death */
           for (cpt=0;cpt<=4;cpt++){  
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
           }      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         }        for(i=1; i<=nlstate;i++){
       }          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     }        }
          } 
 }      fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
 /************** Forecasting ******************/      for(i=1; i<=nlstate;i++)
 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(j=1; j<=nlstate;j++){
            fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        }
   int *popage;      fprintf(ficresvij,"\n");
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      free_matrix(gp,0,nhstepm,1,nlstate);
   double *popeffectif,*popcount;      free_matrix(gm,0,nhstepm,1,nlstate);
   double ***p3mat;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   char fileresf[FILENAMELENGTH];      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  agelim=AGESUP;    } /* End age */
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
      free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
      fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
   strcpy(fileresf,"f");    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
   strcat(fileresf,fileres);    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   if((ficresf=fopen(fileresf,"w"))==NULL) {  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
     printf("Problem with forecast resultfile: %s\n", fileresf);  /*   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); */
   printf("Computing forecasting: result on file '%s' \n", fileresf);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
   if (mobilav==1) {    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);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /*  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);
     movingaverage(agedeb, fage, ageminpar, mobaverage);  */
   }    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;    free_vector(xp,1,npar);
   if (stepm<=12) stepsize=1;    free_matrix(doldm,1,nlstate,1,nlstate);
      free_matrix(dnewm,1,nlstate,1,npar);
   agelim=AGESUP;    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   hstepm=1;    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   hstepm=hstepm/stepm;    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   yp1=modf(dateintmean,&yp);    fclose(ficresprobmorprev);
   anprojmean=yp;    fclose(ficgp);
   yp2=modf((yp1*12),&yp);    fclose(fichtm);
   mprojmean=yp;  }  
   yp1=modf((yp2*30.5),&yp);  
   jprojmean=yp;  /************ Variance of prevlim ******************/
   if(jprojmean==0) jprojmean=1;  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(mprojmean==0) jprojmean=1;  {
      /* Variance of prevalence limit */
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
      double **newm;
   for(cptcov=1;cptcov<=i2;cptcov++){    double **dnewm,**doldm;
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    int i, j, nhstepm, hstepm;
       k=k+1;    int k, cptcode;
       fprintf(ficresf,"\n#******");    double *xp;
       for(j=1;j<=cptcoveff;j++) {    double *gp, *gm;
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double **gradg, **trgradg;
       }    double age,agelim;
       fprintf(ficresf,"******\n");    int theta;
       fprintf(ficresf,"# StartingAge FinalAge");     
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
          fprintf(ficresvpl,"# Age");
          for(i=1; i<=nlstate;i++)
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {        fprintf(ficresvpl," %1d-%1d",i,i);
         fprintf(ficresf,"\n");    fprintf(ficresvpl,"\n");
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);    
     xp=vector(1,npar);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    dnewm=matrix(1,nlstate,1,npar);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    doldm=matrix(1,nlstate,1,nlstate);
           nhstepm = nhstepm/hstepm;    
              hstepm=1*YEARM; /* Every year of age */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
           oldm=oldms;savm=savms;    agelim = AGESUP;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
              nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           for (h=0; h<=nhstepm; h++){      if (stepm >= YEARM) hstepm=1;
             if (h==(int) (calagedate+YEARM*cpt)) {      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);      gradg=matrix(1,npar,1,nlstate);
             }      gp=vector(1,nlstate);
             for(j=1; j<=nlstate+ndeath;j++) {      gm=vector(1,nlstate);
               kk1=0.;kk2=0;  
               for(i=1; i<=nlstate;i++) {                    for(theta=1; theta <=npar; theta++){
                 if (mobilav==1)        for(i=1; i<=npar; i++){ /* Computes gradient */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          xp[i] = x[i] + (i==theta ?delti[theta]:0);
                 else {        }
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                 }        for(i=1;i<=nlstate;i++)
                          gp[i] = prlim[i][i];
               }      
               if (h==(int)(calagedate+12*cpt)){        for(i=1; i<=npar; i++) /* Computes gradient */
                 fprintf(ficresf," %.3f", kk1);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
                                prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
               }        for(i=1;i<=nlstate;i++)
             }          gm[i] = prlim[i][i];
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(i=1;i<=nlstate;i++)
         }          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       }      } /* End theta */
     }  
   }      trgradg =matrix(1,nlstate,1,npar);
          
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
   fclose(ficresf);          trgradg[j][theta]=gradg[theta][j];
 }  
 /************** Forecasting ******************/      for(i=1;i<=nlstate;i++)
 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){        varpl[i][(int)age] =0.;
        matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   int *popage;      for(i=1;i<=nlstate;i++)
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   double *popeffectif,*popcount;  
   double ***p3mat,***tabpop,***tabpopprev;      fprintf(ficresvpl,"%.0f ",age );
   char filerespop[FILENAMELENGTH];      for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      fprintf(ficresvpl,"\n");
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      free_vector(gp,1,nlstate);
   agelim=AGESUP;      free_vector(gm,1,nlstate);
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;      free_matrix(gradg,1,npar,1,nlstate);
        free_matrix(trgradg,1,nlstate,1,npar);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    } /* End age */
    
      free_vector(xp,1,npar);
   strcpy(filerespop,"pop");    free_matrix(doldm,1,nlstate,1,npar);
   strcat(filerespop,fileres);    free_matrix(dnewm,1,nlstate,1,nlstate);
   if((ficrespop=fopen(filerespop,"w"))==NULL) {  
     printf("Problem with forecast resultfile: %s\n", filerespop);  }
   }  
   printf("Computing forecasting: result on file '%s' \n", filerespop);  /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  {
     int i, j=0,  i1, k1, l1, t, tj;
   if (mobilav==1) {    int k2, l2, j1,  z1;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    int k=0,l, cptcode;
     movingaverage(agedeb, fage, ageminpar, mobaverage);    int first=1, first1;
   }    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    double *xp;
   if (stepm<=12) stepsize=1;    double *gp, *gm;
      double **gradg, **trgradg;
   agelim=AGESUP;    double **mu;
      double age,agelim, cov[NCOVMAX];
   hstepm=1;    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   hstepm=hstepm/stepm;    int theta;
      char fileresprob[FILENAMELENGTH];
   if (popforecast==1) {    char fileresprobcov[FILENAMELENGTH];
     if((ficpop=fopen(popfile,"r"))==NULL) {    char fileresprobcor[FILENAMELENGTH];
       printf("Problem with population file : %s\n",popfile);exit(0);  
     }    double ***varpij;
     popage=ivector(0,AGESUP);  
     popeffectif=vector(0,AGESUP);    strcpy(fileresprob,"prob"); 
     popcount=vector(0,AGESUP);    strcat(fileresprob,fileres);
        if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     i=1;        printf("Problem with resultfile: %s\n", fileresprob);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
        }
     imx=i;    strcpy(fileresprobcov,"probcov"); 
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    strcat(fileresprobcov,fileres);
   }    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
   for(cptcov=1;cptcov<=i2;cptcov++){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    }
       k=k+1;    strcpy(fileresprobcor,"probcor"); 
       fprintf(ficrespop,"\n#******");    strcat(fileresprobcor,fileres);
       for(j=1;j<=cptcoveff;j++) {    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      printf("Problem with resultfile: %s\n", fileresprobcor);
       }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficrespop,"******\n");    }
       fprintf(ficrespop,"# Age");    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       if (popforecast==1)  fprintf(ficrespop," [Population]");    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);
       for (cpt=0; cpt<=0;cpt++) {    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
            
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    fprintf(ficresprob,"# Age");
           nhstepm = nhstepm/hstepm;    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
              fprintf(ficresprobcov,"# Age");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
           oldm=oldms;savm=savms;    fprintf(ficresprobcov,"# Age");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
          
           for (h=0; h<=nhstepm; h++){    for(i=1; i<=nlstate;i++)
             if (h==(int) (calagedate+YEARM*cpt)) {      for(j=1; j<=(nlstate+ndeath);j++){
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
             }        fprintf(ficresprobcov," p%1d-%1d ",i,j);
             for(j=1; j<=nlstate+ndeath;j++) {        fprintf(ficresprobcor," p%1d-%1d ",i,j);
               kk1=0.;kk2=0;      }  
               for(i=1; i<=nlstate;i++) {                 /* fprintf(ficresprob,"\n");
                 if (mobilav==1)    fprintf(ficresprobcov,"\n");
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    fprintf(ficresprobcor,"\n");
                 else {   */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];   xp=vector(1,npar);
                 }    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
               }    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
               if (h==(int)(calagedate+12*cpt)){    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
                   /*fprintf(ficrespop," %.3f", kk1);    first=1;
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
               }      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
             }      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
             for(i=1; i<=nlstate;i++){      exit(0);
               kk1=0.;    }
                 for(j=1; j<=nlstate;j++){    else{
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];      fprintf(ficgp,"\n# Routine varprob");
                 }    }
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
             }      printf("Problem with html file: %s\n", optionfilehtm);
       fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)      exit(0);
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    }
           }    else{
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
         }      fprintf(fichtm,"\n");
       }  
        fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
   /******/      fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
       fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {  
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      }
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    cov[1]=1;
           nhstepm = nhstepm/hstepm;    tj=cptcoveff;
              if (cptcovn<1) {tj=1;ncodemax[1]=1;}
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    j1=0;
           oldm=oldms;savm=savms;    for(t=1; t<=tj;t++){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        for(i1=1; i1<=ncodemax[t];i1++){ 
           for (h=0; h<=nhstepm; h++){        j1++;
             if (h==(int) (calagedate+YEARM*cpt)) {        if  (cptcovn>0) {
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          fprintf(ficresprob, "\n#********** Variable "); 
             }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
             for(j=1; j<=nlstate+ndeath;j++) {          fprintf(ficresprob, "**********\n#\n");
               kk1=0.;kk2=0;          fprintf(ficresprobcov, "\n#********** Variable "); 
               for(i=1; i<=nlstate;i++) {                        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];              fprintf(ficresprobcov, "**********\n#\n");
               }          
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);          fprintf(ficgp, "\n#********** Variable "); 
             }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           }          fprintf(ficgp, "**********\n#\n");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          
         }          
       }          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
    }          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   }          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
            
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   if (popforecast==1) {          fprintf(ficresprobcor, "**********\n#");    
     free_ivector(popage,0,AGESUP);        }
     free_vector(popeffectif,0,AGESUP);        
     free_vector(popcount,0,AGESUP);        for (age=bage; age<=fage; age ++){ 
   }          cov[2]=age;
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for (k=1; k<=cptcovn;k++) {
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
   fclose(ficrespop);          }
 }          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]]];
 /**************** Main Program *****************/          
 /***********************************************/          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
 int main(int argc, char *argv[])          gp=vector(1,(nlstate)*(nlstate+ndeath));
 {          gm=vector(1,(nlstate)*(nlstate+ndeath));
       
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;          for(theta=1; theta <=npar; theta++){
   double agedeb, agefin,hf;            for(i=1; i<=npar; i++)
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
   double fret;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   double **xi,tmp,delta;            
             k=0;
   double dum; /* Dummy variable */            for(i=1; i<= (nlstate); i++){
   double ***p3mat;              for(j=1; j<=(nlstate+ndeath);j++){
   int *indx;                k=k+1;
   char line[MAXLINE], linepar[MAXLINE];                gp[k]=pmmij[i][j];
   char title[MAXLINE];              }
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];            }
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];            
              for(i=1; i<=npar; i++)
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
   char filerest[FILENAMELENGTH];            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   char fileregp[FILENAMELENGTH];            k=0;
   char popfile[FILENAMELENGTH];            for(i=1; i<=(nlstate); i++){
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];              for(j=1; j<=(nlstate+ndeath);j++){
   int firstobs=1, lastobs=10;                k=k+1;
   int sdeb, sfin; /* Status at beginning and end */                gm[k]=pmmij[i][j];
   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,**adl,*tab;            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
   int mobilav=0,popforecast=0;              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
   int hstepm, nhstepm;          }
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;  
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   double bage, fage, age, agelim, agebase;            for(theta=1; theta <=npar; theta++)
   double ftolpl=FTOL;              trgradg[j][theta]=gradg[theta][j];
   double **prlim;          
   double *severity;          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   double ***param; /* Matrix of parameters */          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   double  *p;          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   double **matcov; /* Matrix of covariance */          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
   double ***delti3; /* Scale */          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   double *delti; /* Scale */          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   double ***eij, ***vareij;  
   double **varpl; /* Variances of prevalence limits by age */          pmij(pmmij,cov,ncovmodel,x,nlstate);
   double *epj, vepp;          
   double kk1, kk2;          k=0;
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;          for(i=1; i<=(nlstate); i++){
              for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
   char version[80]="Imach version 0.8f, May 2002, INED-EUROREVES ";              mu[k][(int) age]=pmmij[i][j];
   char *alph[]={"a","a","b","c","d","e"}, str[4];            }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   char z[1]="c", occ;            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
 #include <sys/time.h>              varpij[i][j][(int)age] = doldm[i][j];
 #include <time.h>  
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];          /*printf("\n%d ",(int)age);
              for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   /* long total_usecs;            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   struct timeval start_time, end_time;            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
              }*/
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */  
   getcwd(pathcd, size);          fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
   printf("\n%s",version);          fprintf(ficresprobcor,"\n%d ",(int)age);
   if(argc <=1){  
     printf("\nEnter the parameter file name: ");          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
     scanf("%s",pathtot);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
   }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   else{            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
     strcpy(pathtot,argv[1]);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
   }          }
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/          i=0;
   /*cygwin_split_path(pathtot,path,optionfile);          for (k=1; k<=(nlstate);k++){
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/            for (l=1; l<=(nlstate+ndeath);l++){ 
   /* cutv(path,optionfile,pathtot,'\\');*/              i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);              for (j=1; j<=i;j++){
   chdir(path);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   replace(pathc,path);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
 /*-------- arguments in the command line --------*/            }
           }/* end of loop for state */
   strcpy(fileres,"r");        } /* end of loop for age */
   strcat(fileres, optionfilefiname);  
   strcat(fileres,".txt");    /* Other files have txt extension */        /* Confidence intervalle of pij  */
         /*
   /*---------arguments file --------*/          fprintf(ficgp,"\nset noparametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   if((ficpar=fopen(optionfile,"r"))==NULL)    {          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     printf("Problem with optionfile %s\n",optionfile);          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);
     goto end;          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   }          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
   strcpy(filereso,"o");        */
   strcat(filereso,fileres);  
   if((ficparo=fopen(filereso,"w"))==NULL) {        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
     printf("Problem with Output resultfile: %s\n", filereso);goto end;        first1=1;
   }        for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
   /* Reads comments: lines beginning with '#' */            if(l2==k2) continue;
   while((c=getc(ficpar))=='#' && c!= EOF){            j=(k2-1)*(nlstate+ndeath)+l2;
     ungetc(c,ficpar);            for (k1=1; k1<=(nlstate);k1++){
     fgets(line, MAXLINE, ficpar);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
     puts(line);                if(l1==k1) continue;
     fputs(line,ficparo);                i=(k1-1)*(nlstate+ndeath)+l1;
   }                if(i<=j) continue;
   ungetc(c,ficpar);                for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==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);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   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);                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   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);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
 while((c=getc(ficpar))=='#' && c!= EOF){                    mu1=mu[i][(int) age]/stepm*YEARM ;
     ungetc(c,ficpar);                    mu2=mu[j][(int) age]/stepm*YEARM;
     fgets(line, MAXLINE, ficpar);                    c12=cv12/sqrt(v1*v2);
     puts(line);                    /* Computing eigen value of matrix of covariance */
     fputs(line,ficparo);                    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.;
   ungetc(c,ficpar);                    /* Eigen vectors */
                      v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                        /*v21=sqrt(1.-v11*v11); *//* error */
   covar=matrix(0,NCOVMAX,1,n);                    v21=(lc1-v1)/cv12*v11;
   cptcovn=0;                    v12=-v21;
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;                    v22=v11;
                     tnalp=v21/v11;
   ncovmodel=2+cptcovn;                    if(first1==1){
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */                      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);
   /* Read guess parameters */                    }
   /* Reads comments: lines beginning with '#' */                    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);
   while((c=getc(ficpar))=='#' && c!= EOF){                    /*printf(fignu*/
     ungetc(c,ficpar);                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
     fgets(line, MAXLINE, ficpar);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
     puts(line);                    if(first==1){
     fputs(line,ficparo);                      first=0;
   }                      fprintf(ficgp,"\nset parametric;unset label");
   ungetc(c,ficpar);                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);                      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);
     for(i=1; i <=nlstate; i++)                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
     for(j=1; j <=nlstate+ndeath-1; j++){                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
       fscanf(ficpar,"%1d%1d",&i1,&j1);                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
       fprintf(ficparo,"%1d%1d",i1,j1);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
       printf("%1d%1d",i,j);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
       for(k=1; k<=ncovmodel;k++){                      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",\
         fscanf(ficpar," %lf",&param[i][j][k]);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
         printf(" %lf",param[i][j][k]);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
         fprintf(ficparo," %lf",param[i][j][k]);                    }else{
       }                      first=0;
       fscanf(ficpar,"\n");                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
       printf("\n");                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
       fprintf(ficparo,"\n");                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     }                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                                mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
   p=param[1][1];                  } /* age mod 5 */
                  } /* end loop age */
   /* Reads comments: lines beginning with '#' */                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
   while((c=getc(ficpar))=='#' && c!= EOF){                first=1;
     ungetc(c,ficpar);              } /*l12 */
     fgets(line, MAXLINE, ficpar);            } /* k12 */
     puts(line);          } /*l1 */
     fputs(line,ficparo);        }/* k1 */
   }      } /* loop covariates */
   ungetc(c,ficpar);    }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    free_vector(xp,1,npar);
   for(i=1; i <=nlstate; i++){    fclose(ficresprob);
     for(j=1; j <=nlstate+ndeath-1; j++){    fclose(ficresprobcov);
       fscanf(ficpar,"%1d%1d",&i1,&j1);    fclose(ficresprobcor);
       printf("%1d%1d",i,j);    fclose(ficgp);
       fprintf(ficparo,"%1d%1d",i1,j1);    fclose(fichtm);
       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]);  /******************* Printing html file ***********/
       }  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
       fscanf(ficpar,"\n");                    int lastpass, int stepm, int weightopt, char model[],\
       printf("\n");                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
       fprintf(ficparo,"\n");                    int popforecast, int estepm ,\
     }                    double jprev1, double mprev1,double anprev1, \
   }                    double jprev2, double mprev2,double anprev2){
   delti=delti3[1][1];    int jj1, k1, i1, cpt;
      /*char optionfilehtm[FILENAMELENGTH];*/
   /* Reads comments: lines beginning with '#' */    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
   while((c=getc(ficpar))=='#' && c!= EOF){      printf("Problem with %s \n",optionfilehtm), exit(0);
     ungetc(c,ficpar);      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
     fgets(line, MAXLINE, ficpar);    }
     puts(line);  
     fputs(line,ficparo);     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
   }   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
   ungetc(c,ficpar);   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
     - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
   matcov=matrix(1,npar,1,npar);   - Life expectancies by age and initial health status (estepm=%2d months): 
   for(i=1; i <=npar; i++){     <a href=\"e%s\">e%s</a> <br>\n</li>", \
     fscanf(ficpar,"%s",&str);    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
     printf("%s",str);  
     fprintf(ficparo,"%s",str);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
     for(j=1; j <=i; j++){  
       fscanf(ficpar," %le",&matcov[i][j]);   m=cptcoveff;
       printf(" %.5le",matcov[i][j]);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       fprintf(ficparo," %.5le",matcov[i][j]);  
     }   jj1=0;
     fscanf(ficpar,"\n");   for(k1=1; k1<=m;k1++){
     printf("\n");     for(i1=1; i1<=ncodemax[k1];i1++){
     fprintf(ficparo,"\n");       jj1++;
   }       if (cptcovn > 0) {
   for(i=1; i <=npar; i++)         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     for(j=i+1;j<=npar;j++)         for (cpt=1; cpt<=cptcoveff;cpt++) 
       matcov[i][j]=matcov[j][i];           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
             fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   printf("\n");       }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: pe%s%d1.png<br>
     /*-------- Rewriting paramater file ----------*/  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
      strcpy(rfileres,"r");    /* "Rparameterfile */       /* Quasi-incidences */
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/       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>
      strcat(rfileres,".");    /* */  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
      strcat(rfileres,optionfilext);    /* Other files have txt extension */         /* Stable prevalence in each health state */
     if((ficres =fopen(rfileres,"w"))==NULL) {         for(cpt=1; cpt<nlstate;cpt++){
       printf("Problem writing new parameter file: %s\n", fileres);goto end;           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);
     fprintf(ficres,"#%s\n",version);         }
           for(cpt=1; cpt<=nlstate;cpt++) {
     /*-------- data file ----------*/          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
     if((fic=fopen(datafile,"r"))==NULL)    {  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
       printf("Problem with datafile: %s\n", datafile);goto end;       }
     }       fprintf(fichtm,"\n<br>- Total life expectancy by age and
   health expectancies in states (1) and (2): e%s%d.png<br>
     n= lastobs;  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
     severity = vector(1,maxwav);     } /* end i1 */
     outcome=imatrix(1,maxwav+1,1,n);   }/* End k1 */
     num=ivector(1,n);   fprintf(fichtm,"</ul>");
     moisnais=vector(1,n);  
     annais=vector(1,n);  
     moisdc=vector(1,n);   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
     andc=vector(1,n);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
     agedc=vector(1,n);   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
     cod=ivector(1,n);   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
     weight=vector(1,n);   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
     mint=matrix(1,maxwav,1,n);   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
     anint=matrix(1,maxwav,1,n);   - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
     s=imatrix(1,maxwav+1,1,n);  
     adl=imatrix(1,maxwav+1,1,n);      /*  if(popforecast==1) fprintf(fichtm,"\n */
     tab=ivector(1,NCOVMAX);  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
     ncodemax=ivector(1,8);  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
     i=1;  /*  else  */
     while (fgets(line, MAXLINE, fic) != NULL)    {  /*    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); */
       if ((i >= firstobs) && (i <=lastobs)) {  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
          
         for (j=maxwav;j>=1;j--){   m=cptcoveff;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
           strcpy(line,stra);  
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);   jj1=0;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);   for(k1=1; k1<=m;k1++){
         }     for(i1=1; i1<=ncodemax[k1];i1++){
               jj1++;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);       if (cptcovn > 0) {
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);       for(cpt=1; cpt<=nlstate;cpt++) {
         for (j=ncovcol;j>=1;j--){         fprintf(fichtm,"<br>- Observed and period prevalence (with confident
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);  interval) in state (%d): v%s%d%d.png <br>
         }  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
         num[i]=atol(stra);       }
             } /* end i1 */
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){   }/* End k1 */
           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;}*/   fprintf(fichtm,"</ul>");
   fclose(fichtm);
         i=i+1;  }
       }  
     }  /******************* Gnuplot file **************/
     /* printf("ii=%d", ij);  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
        scanf("%d",i);*/  
   imx=i-1; /* Number of individuals */    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   /* for (i=1; i<=imx; i++){    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;      printf("Problem with file %s",optionfilegnuplot);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    }
     }*/  
    /*  for (i=1; i<=imx; i++){    /*#ifdef windows */
      if (s[4][i]==9)  s[4][i]=-1;      fprintf(ficgp,"cd \"%s\" \n",pathc);
      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]));}*/      /*#endif */
    m=pow(2,cptcoveff);
      
   /* Calculation of the number of parameter from char model*/   /* 1eme*/
   Tvar=ivector(1,15);    for (cpt=1; cpt<= nlstate ; cpt ++) {
   Tprod=ivector(1,15);     for (k1=1; k1<= m ; k1 ++) {
   Tvaraff=ivector(1,15);       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
   Tvard=imatrix(1,15,1,2);       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);
   Tage=ivector(1,15);        
           for (i=1; i<= nlstate ; i ++) {
   if (strlen(model) >1){         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     j=0, j1=0, k1=1, k2=1;         else fprintf(ficgp," \%%*lf (\%%*lf)");
     j=nbocc(model,'+');       }
     j1=nbocc(model,'*');       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);
     cptcovn=j+1;       for (i=1; i<= nlstate ; i ++) {
     cptcovprod=j1;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
             else fprintf(ficgp," \%%*lf (\%%*lf)");
     strcpy(modelsav,model);       } 
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
       printf("Error. Non available option model=%s ",model);       for (i=1; i<= nlstate ; i ++) {
       goto end;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     }         else fprintf(ficgp," \%%*lf (\%%*lf)");
           }  
     for(i=(j+1); i>=1;i--){       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
       cutv(stra,strb,modelsav,'+');     }
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    }
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    /*2 eme*/
       /*scanf("%d",i);*/    
       if (strchr(strb,'*')) {    for (k1=1; k1<= m ; k1 ++) { 
         cutv(strd,strc,strb,'*');      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
         if (strcmp(strc,"age")==0) {      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
           cptcovprod--;      
           cutv(strb,stre,strd,'V');      for (i=1; i<= nlstate+1 ; i ++) {
           Tvar[i]=atoi(stre);        k=2*i;
           cptcovage++;        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
             Tage[cptcovage]=i;        for (j=1; j<= nlstate+1 ; j ++) {
             /*printf("stre=%s ", stre);*/          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
         }          else fprintf(ficgp," \%%*lf (\%%*lf)");
         else if (strcmp(strd,"age")==0) {        }   
           cptcovprod--;        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
           cutv(strb,stre,strc,'V');        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
           Tvar[i]=atoi(stre);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
           cptcovage++;        for (j=1; j<= nlstate+1 ; j ++) {
           Tage[cptcovage]=i;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
         }          else fprintf(ficgp," \%%*lf (\%%*lf)");
         else {        }   
           cutv(strb,stre,strc,'V');        fprintf(ficgp,"\" t\"\" w l 0,");
           Tvar[i]=ncovcol+k1;        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
           cutv(strb,strc,strd,'V');        for (j=1; j<= nlstate+1 ; j ++) {
           Tprod[k1]=i;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           Tvard[k1][1]=atoi(strc);          else fprintf(ficgp," \%%*lf (\%%*lf)");
           Tvard[k1][2]=atoi(stre);        }   
           Tvar[cptcovn+k2]=Tvard[k1][1];        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
           Tvar[cptcovn+k2+1]=Tvard[k1][2];        else fprintf(ficgp,"\" t\"\" w l 0,");
           for (k=1; k<=lastobs;k++)      }
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    }
           k1++;    
           k2=k2+2;    /*3eme*/
         }    
       }    for (k1=1; k1<= m ; k1 ++) { 
       else {      for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/        k=2+nlstate*(2*cpt-2);
        /*  scanf("%d",i);*/        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
       cutv(strd,strc,strb,'V');        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
       Tvar[i]=atoi(strc);        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
       }          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
       strcpy(modelsav,stra);            fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
         scanf("%d",i);*/          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
 }          
          */
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);        for (i=1; i< nlstate ; i ++) {
   printf("cptcovprod=%d ", cptcovprod);          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);
   scanf("%d ",i);*/          
     fclose(fic);        } 
       }
     /*  if(mle==1){*/    }
     if (weightopt != 1) { /* Maximisation without weights*/    
       for(i=1;i<=n;i++) weight[i]=1.0;    /* CV preval stable (period) */
     }    for (k1=1; k1<= m ; k1 ++) { 
     /*-calculation of age at interview from date of interview and age at death -*/      for (cpt=1; cpt<=nlstate ; cpt ++) {
     agev=matrix(1,maxwav,1,imx);        k=3;
         fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     for (i=1; i<=imx; i++) {        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
       for(m=2; (m<= maxwav); m++) {        
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){        for (i=1; i<= nlstate ; i ++)
          anint[m][i]=9999;          fprintf(ficgp,"+$%d",k+i+1);
          s[m][i]=-1;        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
        }        
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;        l=3+(nlstate+ndeath)*cpt;
       }        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
     }        for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
     for (i=1; i<=imx; i++)  {          fprintf(ficgp,"+$%d",l+i+1);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        }
       for(m=1; (m<= maxwav); m++){        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
         if(s[m][i] >0){      } 
           if (s[m][i] >= nlstate+1) {    }  
             if(agedc[i]>0)    
               if(moisdc[i]!=99 && andc[i]!=9999)    /* proba elementaires */
                 agev[m][i]=agedc[i];    for(i=1,jk=1; i <=nlstate; i++){
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/      for(k=1; k <=(nlstate+ndeath); k++){
            else {        if (k != i) {
               if (andc[i]!=9999){          for(j=1; j <=ncovmodel; j++){
               printf("Warning negative age at death: %d line:%d\n",num[i],i);            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
               agev[m][i]=-1;            jk++; 
               }            fprintf(ficgp,"\n");
             }          }
           }        }
           else if(s[m][i] !=9){ /* Should no more exist */      }
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);     }
             if(mint[m][i]==99 || anint[m][i]==9999)  
               agev[m][i]=1;     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
             else if(agev[m][i] <agemin){       for(jk=1; jk <=m; jk++) {
               agemin=agev[m][i];         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/         if (ng==2)
             }           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
             else if(agev[m][i] >agemax){         else
               agemax=agev[m][i];           fprintf(ficgp,"\nset title \"Probability\"\n");
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
             }         i=1;
             /*agev[m][i]=anint[m][i]-annais[i];*/         for(k2=1; k2<=nlstate; k2++) {
             /*   agev[m][i] = age[i]+2*m;*/           k3=i;
           }           for(k=1; k<=(nlstate+ndeath); k++) {
           else { /* =9 */             if (k != k2){
             agev[m][i]=1;               if(ng==2)
             s[m][i]=-1;                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
           }               else
         }                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
         else /*= 0 Unknown */               ij=1;
           agev[m][i]=1;               for(j=3; j <=ncovmodel; j++) {
       }                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                       fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
     }                   ij++;
     for (i=1; i<=imx; i++)  {                 }
       for(m=1; (m<= maxwav); m++){                 else
         if (s[m][i] > (nlstate+ndeath)) {                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
           printf("Error: Wrong value in nlstate or ndeath\n");                 }
           goto end;               fprintf(ficgp,")/(1");
         }               
       }               for(k1=1; k1 <=nlstate; k1++){   
     }                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);                 for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
     free_vector(severity,1,maxwav);                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
     free_imatrix(outcome,1,maxwav+1,1,n);                     ij++;
     free_vector(moisnais,1,n);                   }
     free_vector(annais,1,n);                   else
     /* free_matrix(mint,1,maxwav,1,n);                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
        free_matrix(anint,1,maxwav,1,n);*/                 }
     free_vector(moisdc,1,n);                 fprintf(ficgp,")");
     free_vector(andc,1,n);               }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                   if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
     wav=ivector(1,imx);               i=i+ncovmodel;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);             }
     mw=imatrix(1,lastpass-firstpass+1,1,imx);           } /* end k */
             } /* end k2 */
     /* Concatenates waves */       } /* end jk */
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);     } /* end ng */
      fclose(ficgp); 
   }  /* end gnuplot */
       Tcode=ivector(1,100);  
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);  
       ncodemax[1]=1;  /*************** Moving average **************/
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
        
    codtab=imatrix(1,100,1,10);    int i, cpt, cptcod;
    h=0;    int modcovmax =1;
    m=pow(2,cptcoveff);    int mobilavrange, mob;
      double age;
    for(k=1;k<=cptcoveff; k++){  
      for(i=1; i <=(m/pow(2,k));i++){    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
        for(j=1; j <= ncodemax[k]; j++){                             a covariate has 2 modalities */
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
            h++;  
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/      if(mobilav==1) mobilavrange=5; /* default */
          }      else mobilavrange=mobilav;
        }      for (age=bage; age<=fage; age++)
      }        for (i=1; i<=nlstate;i++)
    }          for (cptcod=1;cptcod<=modcovmax;cptcod++)
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       codtab[1][2]=1;codtab[2][2]=2; */      /* We keep the original values on the extreme ages bage, fage and for 
    /* for(i=1; i <=m ;i++){         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
       for(k=1; k <=cptcovn; k++){         we use a 5 terms etc. until the borders are no more concerned. 
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);      */ 
       }      for (mob=3;mob <=mobilavrange;mob=mob+2){
       printf("\n");        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
       }          for (i=1; i<=nlstate;i++){
       scanf("%d",i);*/            for (cptcod=1;cptcod<=modcovmax;cptcod++){
                  mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
    /* Calculates basic frequencies. Computes observed prevalence at single age                for (cpt=1;cpt<=(mob-1)/2;cpt++){
        and prints on file fileres'p'. */                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                    }
                  mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
     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 */        }/* end age */
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      }/* end mob */
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    }else return -1;
          return 0;
     /* For Powell, parameters are in a vector p[] starting at p[1]  }/* End movingaverage */
        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) */  
   /************** Forecasting ******************/
     if(mle==1){  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){
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    /* proj1, year, month, day of starting projection 
     }       agemin, agemax range of age
           dateprev1 dateprev2 range of dates during which prevalence is computed
     /*--------- results files --------------*/       anproj2 year of en of projection (same day and month as proj1).
     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);    */
      int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
    jk=1;    double agec; /* generic age */
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    double *popeffectif,*popcount;
    for(i=1,jk=1; i <=nlstate; i++){    double ***p3mat;
      for(k=1; k <=(nlstate+ndeath); k++){    double ***mobaverage;
        if (k != i)    char fileresf[FILENAMELENGTH];
          {  
            printf("%d%d ",i,k);    agelim=AGESUP;
            fprintf(ficres,"%1d%1d ",i,k);    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
            for(j=1; j <=ncovmodel; j++){   
              printf("%f ",p[jk]);    strcpy(fileresf,"f"); 
              fprintf(ficres,"%f ",p[jk]);    strcat(fileresf,fileres);
              jk++;    if((ficresf=fopen(fileresf,"w"))==NULL) {
            }      printf("Problem with forecast resultfile: %s\n", fileresf);
            printf("\n");      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
            fprintf(ficres,"\n");    }
          }    printf("Computing forecasting: result on file '%s' \n", fileresf);
      }    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
    }  
  if(mle==1){    if (cptcoveff==0) ncodemax[cptcoveff]=1;
     /* Computing hessian and covariance matrix */  
     ftolhess=ftol; /* Usually correct */    if (mobilav!=0) {
     hesscov(matcov, p, npar, delti, ftolhess, func);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  }      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     printf("# Scales (for hessian or gradient estimation)\n");        printf(" Error in movingaverage mobilav=%d\n",mobilav);
      for(i=1,jk=1; i <=nlstate; i++){      }
       for(j=1; j <=nlstate+ndeath; j++){    }
         if (j!=i) {  
           fprintf(ficres,"%1d%1d",i,j);    stepsize=(int) (stepm+YEARM-1)/YEARM;
           printf("%1d%1d",i,j);    if (stepm<=12) stepsize=1;
           for(k=1; k<=ncovmodel;k++){    if(estepm < stepm){
             printf(" %.5e",delti[jk]);      printf ("Problem %d lower than %d\n",estepm, stepm);
             fprintf(ficres," %.5e",delti[jk]);    }
             jk++;    else  hstepm=estepm;   
           }  
           printf("\n");    hstepm=hstepm/stepm; 
           fprintf(ficres,"\n");    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
         }                                 fractional in yp1 */
       }    anprojmean=yp;
      }    yp2=modf((yp1*12),&yp);
        mprojmean=yp;
     k=1;    yp1=modf((yp2*30.5),&yp);
     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");    jprojmean=yp;
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");    if(jprojmean==0) jprojmean=1;
     for(i=1;i<=npar;i++){    if(mprojmean==0) jprojmean=1;
       /*  if (k>nlstate) k=1;  
       i1=(i-1)/(ncovmodel*nlstate)+1;    i1=cptcoveff;
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    if (cptcovn < 1){i1=1;}
       printf("%s%d%d",alph[k],i1,tab[i]);*/    
       fprintf(ficres,"%3d",i);    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
       printf("%3d",i);    
       for(j=1; j<=i;j++){    fprintf(ficresf,"#****** Routine prevforecast **\n");
         fprintf(ficres," %.5e",matcov[i][j]);  
         printf(" %.5e",matcov[i][j]);  /*            if (h==(int)(YEARM*yearp)){ */
       }    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       fprintf(ficres,"\n");      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
       printf("\n");        k=k+1;
       k++;        fprintf(ficresf,"\n#******");
     }        for(j=1;j<=cptcoveff;j++) {
              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]]);
     while((c=getc(ficpar))=='#' && c!= EOF){        }
       ungetc(c,ficpar);        fprintf(ficresf,"******\n");
       fgets(line, MAXLINE, ficpar);        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
       puts(line);        for(j=1; j<=nlstate+ndeath;j++){ 
       fputs(line,ficparo);          for(i=1; i<=nlstate;i++)              
     }            fprintf(ficresf," p%d%d",i,j);
     ungetc(c,ficpar);          fprintf(ficresf," p.%d",j);
     estepm=0;        }
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
     if (estepm==0 || estepm < stepm) estepm=stepm;          fprintf(ficresf,"\n");
     if (fage <= 2) {          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
       bage = ageminpar;  
       fage = agemaxpar;          for (agec=fage; agec>=(ageminpar-1); agec--){ 
     }            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
                nhstepm = nhstepm/hstepm; 
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);            oldm=oldms;savm=savms;
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
            
     while((c=getc(ficpar))=='#' && c!= EOF){            for (h=0; h<=nhstepm; h++){
     ungetc(c,ficpar);              if (h*hstepm/YEARM*stepm ==yearp) {
     fgets(line, MAXLINE, ficpar);                fprintf(ficresf,"\n");
     puts(line);                for(j=1;j<=cptcoveff;j++) 
     fputs(line,ficparo);                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   }                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
   ungetc(c,ficpar);              } 
                for(j=1; j<=nlstate+ndeath;j++) {
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);                ppij=0.;
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                for(i=1; i<=nlstate;i++) {
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                  if (mobilav==1) 
                          ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
   while((c=getc(ficpar))=='#' && c!= EOF){                  else {
     ungetc(c,ficpar);                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
     fgets(line, MAXLINE, ficpar);                  }
     puts(line);                  if (h*hstepm/YEARM*stepm== yearp) {
     fputs(line,ficparo);                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
   }                  }
   ungetc(c,ficpar);                } /* end i */
                  if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
    dateprev1=anprev1+mprev1/12.+jprev1/365.;                }
    dateprev2=anprev2+mprev2/12.+jprev2/365.;              }/* end j */
             } /* end h */
   fscanf(ficpar,"pop_based=%d\n",&popbased);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fprintf(ficparo,"pop_based=%d\n",popbased);            } /* end agec */
   fprintf(ficres,"pop_based=%d\n",popbased);          } /* end yearp */
        } /* end cptcod */
   while((c=getc(ficpar))=='#' && c!= EOF){    } /* end  cptcov */
     ungetc(c,ficpar);         
     fgets(line, MAXLINE, ficpar);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     puts(line);  
     fputs(line,ficparo);    fclose(ficresf);
   }  }
   ungetc(c,ficpar);  
   /************** Forecasting *****not tested NB*************/
   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);  populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);    
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
 while((c=getc(ficpar))=='#' && c!= EOF){    double *popeffectif,*popcount;
     ungetc(c,ficpar);    double ***p3mat,***tabpop,***tabpopprev;
     fgets(line, MAXLINE, ficpar);    double ***mobaverage;
     puts(line);    char filerespop[FILENAMELENGTH];
     fputs(line,ficparo);  
   }    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   ungetc(c,ficpar);    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
   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);    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    
     strcpy(filerespop,"pop"); 
 /*------------ gnuplot -------------*/    strcat(filerespop,fileres);
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);    if((ficrespop=fopen(filerespop,"w"))==NULL) {
        printf("Problem with forecast resultfile: %s\n", filerespop);
 /*------------ free_vector  -------------*/      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
  chdir(path);    }
      printf("Computing forecasting: result on file '%s' \n", filerespop);
  free_ivector(wav,1,imx);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      if (cptcoveff==0) ncodemax[cptcoveff]=1;
  free_ivector(num,1,n);  
  free_vector(agedc,1,n);    if (mobilav!=0) {
  /*free_matrix(covar,1,NCOVMAX,1,n);*/      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  fclose(ficparo);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
  fclose(ficres);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
 /*--------- index.htm --------*/      }
     }
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);  
     stepsize=(int) (stepm+YEARM-1)/YEARM;
      if (stepm<=12) stepsize=1;
   /*--------------- Prevalence limit --------------*/    
      agelim=AGESUP;
   strcpy(filerespl,"pl");    
   strcat(filerespl,fileres);    hstepm=1;
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    hstepm=hstepm/stepm; 
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    
   }    if (popforecast==1) {
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      if((ficpop=fopen(popfile,"r"))==NULL) {
   fprintf(ficrespl,"#Prevalence limit\n");        printf("Problem with population file : %s\n",popfile);exit(0);
   fprintf(ficrespl,"#Age ");        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      } 
   fprintf(ficrespl,"\n");      popage=ivector(0,AGESUP);
        popeffectif=vector(0,AGESUP);
   prlim=matrix(1,nlstate,1,nlstate);      popcount=vector(0,AGESUP);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      i=1;   
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */     
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      imx=i;
   k=0;      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
   agebase=ageminpar;    }
   agelim=agemaxpar;  
   ftolpl=1.e-10;    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
   i1=cptcoveff;     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   if (cptcovn < 1){i1=1;}        k=k+1;
         fprintf(ficrespop,"\n#******");
   for(cptcov=1;cptcov<=i1;cptcov++){        for(j=1;j<=cptcoveff;j++) {
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         k=k+1;        }
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/        fprintf(ficrespop,"******\n");
         fprintf(ficrespl,"\n#******");        fprintf(ficrespop,"# Age");
         for(j=1;j<=cptcoveff;j++)        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        if (popforecast==1)  fprintf(ficrespop," [Population]");
         fprintf(ficrespl,"******\n");        
                for (cpt=0; cpt<=0;cpt++) { 
         for (age=agebase; age<=agelim; age++){          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          
           fprintf(ficrespl,"%.0f",age );          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
           for(i=1; i<=nlstate;i++)            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
           fprintf(ficrespl," %.5f", prlim[i][i]);            nhstepm = nhstepm/hstepm; 
           fprintf(ficrespl,"\n");            
         }            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       }            oldm=oldms;savm=savms;
     }            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
   fclose(ficrespl);          
             for (h=0; h<=nhstepm; h++){
   /*------------- h Pij x at various ages ------------*/              if (h==(int) (calagedatem+YEARM*cpt)) {
                  fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);              } 
   if((ficrespij=fopen(filerespij,"w"))==NULL) {              for(j=1; j<=nlstate+ndeath;j++) {
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;                kk1=0.;kk2=0;
   }                for(i=1; i<=nlstate;i++) {              
   printf("Computing pij: result on file '%s' \n", filerespij);                  if (mobilav==1) 
                      kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
   stepsize=(int) (stepm+YEARM-1)/YEARM;                  else {
   /*if (stepm<=24) stepsize=2;*/                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
   agelim=AGESUP;                }
   hstepm=stepsize*YEARM; /* Every year of age */                if (h==(int)(calagedatem+12*cpt)){
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
                      /*fprintf(ficrespop," %.3f", kk1);
   k=0;                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
   for(cptcov=1;cptcov<=i1;cptcov++){                }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              }
       k=k+1;              for(i=1; i<=nlstate;i++){
         fprintf(ficrespij,"\n#****** ");                kk1=0.;
         for(j=1;j<=cptcoveff;j++)                  for(j=1; j<=nlstate;j++){
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
         fprintf(ficrespij,"******\n");                  }
                            tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
         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 */              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
           oldm=oldms;savm=savms;            }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"# Age");          }
           for(i=1; i<=nlstate;i++)        }
             for(j=1; j<=nlstate+ndeath;j++)   
               fprintf(ficrespij," %1d-%1d",i,j);    /******/
           fprintf(ficrespij,"\n");  
            for (h=0; h<=nhstepm; h++){        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
             for(i=1; i<=nlstate;i++)          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
               for(j=1; j<=nlstate+ndeath;j++)            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);            nhstepm = nhstepm/hstepm; 
             fprintf(ficrespij,"\n");            
              }            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            oldm=oldms;savm=savms;
           fprintf(ficrespij,"\n");            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
         }            for (h=0; h<=nhstepm; h++){
     }              if (h==(int) (calagedatem+YEARM*cpt)) {
   }                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);              for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
   fclose(ficrespij);                for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
   /*---------- Forecasting ------------------*/                if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
   if((stepm == 1) && (strcmp(model,".")==0)){              }
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);            }
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }          }
   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);    }
   }   
      if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
   /*---------- Health expectancies and variances ------------*/    if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
   strcpy(filerest,"t");      free_vector(popeffectif,0,AGESUP);
   strcat(filerest,fileres);      free_vector(popcount,0,AGESUP);
   if((ficrest=fopen(filerest,"w"))==NULL) {    }
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   }    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    fclose(ficrespop);
   }
   
   strcpy(filerese,"e");  /***********************************************/
   strcat(filerese,fileres);  /**************** Main Program *****************/
   if((ficreseij=fopen(filerese,"w"))==NULL) {  /***********************************************/
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  
   }  int main(int argc, char *argv[])
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
  strcpy(fileresv,"v");    int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
   strcat(fileresv,fileres);    double agedeb, agefin,hf;
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  
   }    double fret;
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    double **xi,tmp,delta;
   calagedate=-1;  
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    double dum; /* Dummy variable */
     double ***p3mat;
   k=0;    double ***mobaverage;
   for(cptcov=1;cptcov<=i1;cptcov++){    int *indx;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    char line[MAXLINE], linepar[MAXLINE];
       k=k+1;    char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
       fprintf(ficrest,"\n#****** ");    int firstobs=1, lastobs=10;
       for(j=1;j<=cptcoveff;j++)    int sdeb, sfin; /* Status at beginning and end */
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    int c,  h , cpt,l;
       fprintf(ficrest,"******\n");    int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
       fprintf(ficreseij,"\n#****** ");    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
       for(j=1;j<=cptcoveff;j++)    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    int mobilav=0,popforecast=0;
       fprintf(ficreseij,"******\n");    int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
       fprintf(ficresvij,"\n#****** ");    double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double bage, fage, age, agelim, agebase;
       fprintf(ficresvij,"******\n");    double ftolpl=FTOL;
     double **prlim;
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    double *severity;
       oldm=oldms;savm=savms;    double ***param; /* Matrix of parameters */
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);      double  *p;
      double **matcov; /* Matrix of covariance */
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    double ***delti3; /* Scale */
       oldm=oldms;savm=savms;    double *delti; /* Scale */
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);    double ***eij, ***vareij;
        double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
      double kk1, kk2;
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);  
       fprintf(ficrest,"\n");    char *alph[]={"a","a","b","c","d","e"}, str[4];
   
       epj=vector(1,nlstate+1);  
       for(age=bage; age <=fage ;age++){    char z[1]="c", occ;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  #include <sys/time.h>
         if (popbased==1) {  #include <time.h>
           for(i=1; i<=nlstate;i++)    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
             prlim[i][i]=probs[(int)age][i][k];   
         }    /* long total_usecs;
               struct timeval start_time, end_time;
         fprintf(ficrest," %4.0f",age);    
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){       gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    getcwd(pathcd, size);
             epj[j] += prlim[i][i]*eij[i][j][(int)age];  
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    printf("\n%s\n%s",version,fullversion);
           }    if(argc <=1){
           epj[nlstate+1] +=epj[j];      printf("\nEnter the parameter file name: ");
         }      scanf("%s",pathtot);
     }
         for(i=1, vepp=0.;i <=nlstate;i++)    else{
           for(j=1;j <=nlstate;j++)      strcpy(pathtot,argv[1]);
             vepp += vareij[i][j][(int)age];    }
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
         for(j=1;j <=nlstate;j++){    /*cygwin_split_path(pathtot,path,optionfile);
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
         }    /* cutv(path,optionfile,pathtot,'\\');*/
         fprintf(ficrest,"\n");  
       }    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);
 free_matrix(mint,1,maxwav,1,n);    replace(pathc,path);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);  
     free_vector(weight,1,n);    /*-------- arguments in the command line --------*/
   fclose(ficreseij);  
   fclose(ficresvij);    /* Log file */
   fclose(ficrest);    strcat(filelog, optionfilefiname);
   fclose(ficpar);    strcat(filelog,".log");    /* */
   free_vector(epj,1,nlstate+1);    if((ficlog=fopen(filelog,"w"))==NULL)    {
        printf("Problem with logfile %s\n",filelog);
   /*------- Variance limit prevalence------*/        goto end;
     }
   strcpy(fileresvpl,"vpl");    fprintf(ficlog,"Log filename:%s\n",filelog);
   strcat(fileresvpl,fileres);    fprintf(ficlog,"\n%s",version);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    fprintf(ficlog,"\nEnter the parameter file name: ");
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     exit(0);    fflush(ficlog);
   }  
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    /* */
     strcpy(fileres,"r");
   k=0;    strcat(fileres, optionfilefiname);
   for(cptcov=1;cptcov<=i1;cptcov++){    strcat(fileres,".txt");    /* Other files have txt extension */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;    /*---------arguments file --------*/
       fprintf(ficresvpl,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)    if((ficpar=fopen(optionfile,"r"))==NULL)    {
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficresvpl,"******\n");      fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
            goto end;
       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);    strcpy(filereso,"o");
     }    strcat(filereso,fileres);
  }    if((ficparo=fopen(filereso,"w"))==NULL) {
       printf("Problem with Output resultfile: %s\n", filereso);
   fclose(ficresvpl);      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       goto end;
   /*---------- End : free ----------------*/    }
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  
      /* Reads comments: lines beginning with '#' */
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    while((c=getc(ficpar))=='#' && c!= EOF){
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);      ungetc(c,ficpar);
        fgets(line, MAXLINE, ficpar);
        puts(line);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      fputs(line,ficparo);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    }
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    ungetc(c,ficpar);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);  
      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);
   free_matrix(matcov,1,npar,1,npar);    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);
   free_vector(delti,1,npar);    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);
   free_matrix(agev,1,maxwav,1,imx);    while((c=getc(ficpar))=='#' && c!= EOF){
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
   if(erreur >0)      puts(line);
     printf("End of Imach with error or warning %d\n",erreur);      fputs(line,ficparo);
   else   printf("End of Imach\n");    }
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    ungetc(c,ficpar);
      
   /* 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);*/    covar=matrix(0,NCOVMAX,1,n); 
   /*------ End -----------*/    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
  end:    ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
 #ifdef windows    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
   /* chdir(pathcd);*/    
 #endif    /* Read guess parameters */
  /*system("wgnuplot graph.plt");*/    /* Reads comments: lines beginning with '#' */
  /*system("../gp37mgw/wgnuplot graph.plt");*/    while((c=getc(ficpar))=='#' && c!= EOF){
  /*system("cd ../gp37mgw");*/      ungetc(c,ficpar);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/      fgets(line, MAXLINE, ficpar);
  strcpy(plotcmd,GNUPLOTPROGRAM);      puts(line);
  strcat(plotcmd," ");      fputs(line,ficparo);
  strcat(plotcmd,optionfilegnuplot);    }
  system(plotcmd);    ungetc(c,ficpar);
     
 #ifdef windows    param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
   while (z[0] != 'q') {    for(i=1; i <=nlstate; i++)
     /* chdir(path); */      for(j=1; j <=nlstate+ndeath-1; j++){
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");        fscanf(ficpar,"%1d%1d",&i1,&j1);
     scanf("%s",z);        fprintf(ficparo,"%1d%1d",i1,j1);
     if (z[0] == 'c') system("./imach");        if(mle==1)
     else if (z[0] == 'e') system(optionfilehtm);          printf("%1d%1d",i,j);
     else if (z[0] == 'g') system(plotcmd);        fprintf(ficlog,"%1d%1d",i,j);
     else if (z[0] == 'q') exit(0);        for(k=1; k<=ncovmodel;k++){
   }          fscanf(ficpar," %lf",&param[i][j][k]);
 #endif          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.1.45  
changed lines
  Added in v.1.81

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