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version 1.41.2.2, 2003/06/13 07:45:28 version 1.81, 2003/06/05 15:41:51
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 /* $Id$  /* $Id$
    Interpolated Markov Chain     Interpolated Markov Chain
   
   Short summary of the programme:    Short summary of the programme:
      
   This program computes Healthy Life Expectancies from    This program computes Healthy Life Expectancies from
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   first survey ("cross") where individuals from different ages are    first survey ("cross") where individuals from different ages are
   interviewed on their health status or degree of disability (in the    interviewed on their health status or degree of disability (in the
   case of a health survey which is our main interest) -2- at least a    case of a health survey which is our main interest) -2- at least a
   second wave of interviews ("longitudinal") which measure each change    second wave of interviews ("longitudinal") which measure each change
   (if any) in individual health status.  Health expectancies are    (if any) in individual health status.  Health expectancies are
   computed from the time spent in each health state according to a    computed from the time spent in each health state according to a
   model. More health states you consider, more time is necessary to reach the    model. More health states you consider, more time is necessary to reach the
   Maximum Likelihood of the parameters involved in the model.  The    Maximum Likelihood of the parameters involved in the model.  The
   simplest model is the multinomial logistic model where pij is the    simplest model is the multinomial logistic model where pij is the
   probability to be observed in state j at the second wave    probability to be observed in state j at the second wave
   conditional to be observed in state i at the first wave. Therefore    conditional to be observed in state i at the first wave. Therefore
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   'age' is age and 'sex' is a covariate. If you want to have a more    'age' is age and 'sex' is a covariate. If you want to have a more
   complex model than "constant and age", you should modify the program    complex model than "constant and age", you should modify the program
   where the markup *Covariates have to be included here again* invites    where the markup *Covariates have to be included here again* invites
   you to do it.  More covariates you add, slower the    you to do it.  More covariates you add, slower the
   convergence.    convergence.
   
   The advantage of this computer programme, compared to a simple    The advantage of this computer programme, compared to a simple
   multinomial logistic model, is clear when the delay between waves is not    multinomial logistic model, is clear when the delay between waves is not
   identical for each individual. Also, if a individual missed an    identical for each individual. Also, if a individual missed an
   intermediate interview, the information is lost, but taken into    intermediate interview, the information is lost, but taken into
   account using an interpolation or extrapolation.      account using an interpolation or extrapolation.  
   
   hPijx is the probability to be observed in state i at age x+h    hPijx is the probability to be observed in state i at age x+h
   conditional to the observed state i at age x. The delay 'h' can be    conditional to the observed state i at age x. The delay 'h' can be
   split into an exact number (nh*stepm) of unobserved intermediate    split into an exact number (nh*stepm) of unobserved intermediate
   states. This elementary transition (by month or quarter trimester,    states. This elementary transition (by month, quarter,
   semester or year) is model as a multinomial logistic.  The hPx    semester or year) is modelled as a multinomial logistic.  The hPx
   matrix is simply the matrix product of nh*stepm elementary matrices    matrix is simply the matrix product of nh*stepm elementary matrices
   and the contribution of each individual to the likelihood is simply    and the contribution of each individual to the likelihood is simply
   hPijx.    hPijx.
   
   Also this programme outputs the covariance matrix of the parameters but also    Also this programme outputs the covariance matrix of the parameters but also
   of the life expectancies. It also computes the prevalence limits.    of the life expectancies. It also computes the stable prevalence. 
      
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
            Institut national d'études démographiques, Paris.             Institut national d'études démographiques, Paris.
   This software have been partly granted by Euro-REVES, a concerted action    This software have been partly granted by Euro-REVES, a concerted action
   from the European Union.    from the European Union.
   It is copyrighted identically to a GNU software product, ie programme and    It is copyrighted identically to a GNU software product, ie programme and
   software can be distributed freely for non commercial use. Latest version    software can be distributed freely for non commercial use. Latest version
   can be accessed at http://euroreves.ined.fr/imach .    can be accessed at http://euroreves.ined.fr/imach .
   **********************************************************************/  
      Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #include <math.h>    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #include <stdio.h>    
 #include <stdlib.h>    **********************************************************************/
 #include <unistd.h>  /*
     main
 #define MAXLINE 256    read parameterfile
 #define GNUPLOTPROGRAM "wgnuplot"    read datafile
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    concatwav
 #define FILENAMELENGTH 80    if (mle >= 1)
 /*#define DEBUG*/      mlikeli
     print results files
 /*#define windows*/    if mle==1 
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */       computes hessian
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    read end of parameter file: agemin, agemax, bage, fage, estepm
         begin-prev-date,...
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    open gnuplot file
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    open html file
     stable prevalence
 #define NINTERVMAX 8     for age prevalim()
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    h Pij x
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    variance of p varprob
 #define NCOVMAX 8 /* Maximum number of covariates */    forecasting if prevfcast==1 prevforecast call prevalence()
 #define MAXN 20000    health expectancies
 #define YEARM 12. /* Number of months per year */    Variance-covariance of DFLE
 #define AGESUP 130    prevalence()
 #define AGEBASE 40     movingaverage()
     varevsij() 
     if popbased==1 varevsij(,popbased)
 int erreur; /* Error number */    total life expectancies
 int nvar;    Variance of stable prevalence
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;   end
 int npar=NPARMAX;  */
 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;   
   #include <math.h>
 int *wav; /* Number of waves for this individuual 0 is possible */  #include <stdio.h>
 int maxwav; /* Maxim number of waves */  #include <stdlib.h>
 int jmin, jmax; /* min, max spacing between 2 waves */  #include <unistd.h>
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  #define MAXLINE 256
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  #define GNUPLOTPROGRAM "gnuplot"
 double jmean; /* Mean space between 2 waves */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 double **oldm, **newm, **savm; /* Working pointers to matrices */  #define FILENAMELENGTH 80
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  /*#define DEBUG*/
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  #define windows
 FILE *ficgp,*ficresprob,*ficpop;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 FILE *ficreseij;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   char fileresv[FILENAMELENGTH];  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];  #define NINTERVMAX 8
   #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #define NR_END 1  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #define FREE_ARG char*  #define NCOVMAX 8 /* Maximum number of covariates */
 #define FTOL 1.0e-10  #define MAXN 20000
   #define YEARM 12. /* Number of months per year */
 #define NRANSI  #define AGESUP 130
 #define ITMAX 200  #define AGEBASE 40
   #ifdef windows
 #define TOL 2.0e-4  #define DIRSEPARATOR '\\'
   #define ODIRSEPARATOR '/'
 #define CGOLD 0.3819660  #else
 #define ZEPS 1.0e-10  #define DIRSEPARATOR '/'
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  #define ODIRSEPARATOR '\\'
   #endif
 #define GOLD 1.618034  
 #define GLIMIT 100.0  /* $Id$ */
 #define TINY 1.0e-20  /* $Log$
    * Revision 1.81  2003/06/05 15:41:51  brouard
 static double maxarg1,maxarg2;   * *** empty log message ***
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))   *
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  /* Revision 1.80  2003/06/05 15:34:14  brouard
    /* Trying to add the true revision in the program and log
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  /*
 #define rint(a) floor(a+0.5)  /* Revision 1.79  2003/06/05 15:17:23  brouard
   /* *** empty log message ***
 static double sqrarg;  /* */
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  /* $Revision$ */
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  /* $Date$ */
   /* $State$ */
 int imx;  
 int stepm;  char version[80]="Imach version 0.95a1, June 2003, INED-EUROREVES ";
 /* Stepm, step in month: minimum step interpolation*/  char fullversion[]="$Revision$ $Date$"; 
   int erreur; /* Error number */
 int estepm;  int nvar;
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   int npar=NPARMAX;
 int m,nb;  int nlstate=2; /* Number of live states */
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  int ndeath=1; /* Number of dead states */
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 double **pmmij, ***probs, ***mobaverage;  int popbased=0;
 double dateintmean=0;  
   int *wav; /* Number of waves for this individuual 0 is possible */
 double *weight;  int maxwav; /* Maxim number of waves */
 int **s; /* Status */  int jmin, jmax; /* min, max spacing between 2 waves */
 double *agedc, **covar, idx;  int mle, weightopt;
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  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 */
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 double ftolhess; /* Tolerance for computing hessian */             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double jmean; /* Mean space between 2 waves */
 /**************** split *************************/  double **oldm, **newm, **savm; /* Working pointers to matrices */
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 {  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
    char *s;                             /* pointer */  FILE *ficlog, *ficrespow;
    int  l1, l2;                         /* length counters */  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
    l1 = strlen( path );                 /* length of path */  FILE *fichtm; /* Html File */
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  FILE *ficreseij;
 #ifdef windows  char filerese[FILENAMELENGTH];
    s = strrchr( path, '\\' );           /* find last / */  FILE  *ficresvij;
 #else  char fileresv[FILENAMELENGTH];
    s = strrchr( path, '/' );            /* find last / */  FILE  *ficresvpl;
 #endif  char fileresvpl[FILENAMELENGTH];
    if ( s == NULL ) {                   /* no directory, so use current */  char title[MAXLINE];
 #if     defined(__bsd__)                /* get current working directory */  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       extern char       *getwd( );  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   
       if ( getwd( dirc ) == NULL ) {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 #else  char filelog[FILENAMELENGTH]; /* Log file */
       extern char       *getcwd( );  char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  char popfile[FILENAMELENGTH];
 #endif  
          return( GLOCK_ERROR_GETCWD );  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
       }  
       strcpy( name, path );             /* we've got it */  #define NR_END 1
    } else {                             /* strip direcotry from path */  #define FREE_ARG char*
       s++;                              /* after this, the filename */  #define FTOL 1.0e-10
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  #define NRANSI 
       strcpy( name, s );                /* save file name */  #define ITMAX 200 
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */  #define TOL 2.0e-4 
    }  
    l1 = strlen( dirc );                 /* length of directory */  #define CGOLD 0.3819660 
 #ifdef windows  #define ZEPS 1.0e-10 
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 #else  
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  #define GOLD 1.618034 
 #endif  #define GLIMIT 100.0 
    s = strrchr( name, '.' );            /* find last / */  #define TINY 1.0e-20 
    s++;  
    strcpy(ext,s);                       /* save extension */  static double maxarg1,maxarg2;
    l1= strlen( name);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
    l2= strlen( s)+1;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
    strncpy( finame, name, l1-l2);    
    finame[l1-l2]= 0;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
    return( 0 );                         /* we're done */  #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 stepm;
   int i;  /* Stepm, step in month: minimum step interpolation*/
   int lg=20;  
   i=0;  int estepm;
   lg=strlen(t);  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);  int m,nb;
     if (t[i]== '\\') s[i]='/';  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
   }  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 }  double **pmmij, ***probs;
   double dateintmean=0;
 int nbocc(char *s, char occ)  
 {  double *weight;
   int i,j=0;  int **s; /* Status */
   int lg=20;  double *agedc, **covar, idx;
   i=0;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   if  (s[i] == occ ) j++;  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   l1, l2;                         /* length counters */
   int i,lg,j,p=0;  
   i=0;    l1 = strlen(path );                   /* length of path */
   for(j=0; j<=strlen(t)-1; j++) {    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   }    if ( ss == NULL ) {                   /* no directory, so use current */
       /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   lg=strlen(t);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   for(j=0; j<p; j++) {      /* get current working directory */
     (u[j] = t[j]);      /*    extern  char* getcwd ( char *buf , int len);*/
   }      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
      u[p]='\0';        return( GLOCK_ERROR_GETCWD );
       }
    for(j=0; j<= lg; j++) {      strcpy( name, path );               /* we've got it */
     if (j>=(p+1))(v[j-p-1] = t[j]);    } else {                              /* strip direcotry from path */
   }      ss++;                               /* after this, the filename */
 }      l2 = strlen( ss );                  /* length of filename */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 /********************** nrerror ********************/      strcpy( name, ss );         /* save file name */
       strncpy( dirc, path, l1 - l2 );     /* now the directory */
 void nrerror(char error_text[])      dirc[l1-l2] = 0;                    /* add zero */
 {    }
   fprintf(stderr,"ERREUR ...\n");    l1 = strlen( dirc );                  /* length of directory */
   fprintf(stderr,"%s\n",error_text);  #ifdef windows
   exit(1);    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
 }  #else
 /*********************** vector *******************/    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
 double *vector(int nl, int nh)  #endif
 {    ss = strrchr( name, '.' );            /* find last / */
   double *v;    ss++;
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    strcpy(ext,ss);                       /* save extension */
   if (!v) nrerror("allocation failure in vector");    l1= strlen( name);
   return v-nl+NR_END;    l2= strlen(ss)+1;
 }    strncpy( finame, name, l1-l2);
     finame[l1-l2]= 0;
 /************************ free vector ******************/    return( 0 );                          /* we're done */
 void free_vector(double*v, int nl, int nh)  }
 {  
   free((FREE_ARG)(v+nl-NR_END));  
 }  /******************************************/
   
 /************************ivector *******************************/  void replace(char *s, char*t)
 int *ivector(long nl,long nh)  {
 {    int i;
   int *v;    int lg=20;
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    i=0;
   if (!v) nrerror("allocation failure in ivector");    lg=strlen(t);
   return v-nl+NR_END;    for(i=0; i<= lg; i++) {
 }      (s[i] = t[i]);
       if (t[i]== '\\') s[i]='/';
 /******************free ivector **************************/    }
 void free_ivector(int *v, long nl, long nh)  }
 {  
   free((FREE_ARG)(v+nl-NR_END));  int nbocc(char *s, char occ)
 }  {
     int i,j=0;
 /******************* imatrix *******************************/    int lg=20;
 int **imatrix(long nrl, long nrh, long ncl, long nch)    i=0;
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    lg=strlen(s);
 {    for(i=0; i<= lg; i++) {
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    if  (s[i] == occ ) j++;
   int **m;    }
      return j;
   /* allocate pointers to rows */  }
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  void cutv(char *u,char *v, char*t, char occ)
   m += NR_END;  {
   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)
         gives u="abcedf" and v="ghi2j" */
   /* allocate rows and set pointers to them */    int i,lg,j,p=0;
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    i=0;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    for(j=0; j<=strlen(t)-1; j++) {
   m[nrl] += NR_END;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   m[nrl] -= ncl;    }
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    lg=strlen(t);
      for(j=0; j<p; j++) {
   /* return pointer to array of pointers to rows */      (u[j] = t[j]);
   return m;    }
 }       u[p]='\0';
   
 /****************** free_imatrix *************************/     for(j=0; j<= lg; j++) {
 void free_imatrix(m,nrl,nrh,ncl,nch)      if (j>=(p+1))(v[j-p-1] = t[j]);
       int **m;    }
       long nch,ncl,nrh,nrl;  }
      /* free an int matrix allocated by imatrix() */  
 {  /********************** nrerror ********************/
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));  void nrerror(char error_text[])
 }  {
     fprintf(stderr,"ERREUR ...\n");
 /******************* matrix *******************************/    fprintf(stderr,"%s\n",error_text);
 double **matrix(long nrl, long nrh, long ncl, long nch)    exit(EXIT_FAILURE);
 {  }
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  /*********************** vector *******************/
   double **m;  double *vector(int nl, int nh)
   {
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    double *v;
   if (!m) nrerror("allocation failure 1 in matrix()");    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   m += NR_END;    if (!v) nrerror("allocation failure in vector");
   m -= nrl;    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()");  /************************ free vector ******************/
   m[nrl] += NR_END;  void free_vector(double*v, int nl, int nh)
   m[nrl] -= ncl;  {
     free((FREE_ARG)(v+nl-NR_END));
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  }
   return m;  
 }  /************************ivector *******************************/
   char *cvector(long nl,long nh)
 /*************************free matrix ************************/  {
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    char *v;
 {    v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    if (!v) nrerror("allocation failure in cvector");
   free((FREE_ARG)(m+nrl-NR_END));    return v-nl+NR_END;
 }  }
   
 /******************* ma3x *******************************/  /******************free ivector **************************/
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  void free_cvector(char *v, long nl, long nh)
 {  {
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    free((FREE_ARG)(v+nl-NR_END));
   double ***m;  }
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  /************************ivector *******************************/
   if (!m) nrerror("allocation failure 1 in matrix()");  int *ivector(long nl,long nh)
   m += NR_END;  {
   m -= nrl;    int *v;
     v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    if (!v) nrerror("allocation failure in ivector");
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    return v-nl+NR_END;
   m[nrl] += NR_END;  }
   m[nrl] -= ncl;  
   /******************free ivector **************************/
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  void free_ivector(int *v, long nl, long nh)
   {
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    free((FREE_ARG)(v+nl-NR_END));
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  }
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;  /******************* imatrix *******************************/
   for (j=ncl+1; j<=nch; j++)  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     m[nrl][j]=m[nrl][j-1]+nlay;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
    { 
   for (i=nrl+1; i<=nrh; i++) {    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    int **m; 
     for (j=ncl+1; j<=nch; j++)    
       m[i][j]=m[i][j-1]+nlay;    /* allocate pointers to rows */ 
   }    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   return m;    if (!m) nrerror("allocation failure 1 in matrix()"); 
 }    m += NR_END; 
     m -= nrl; 
 /*************************free ma3x ************************/    
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    
 {    /* allocate rows and set pointers to them */ 
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   free((FREE_ARG)(m+nrl-NR_END));    m[nrl] += NR_END; 
 }    m[nrl] -= ncl; 
     
 /***************** f1dim *************************/    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
 extern int ncom;    
 extern double *pcom,*xicom;    /* return pointer to array of pointers to rows */ 
 extern double (*nrfunc)(double []);    return m; 
    } 
 double f1dim(double x)  
 {  /****************** free_imatrix *************************/
   int j;  void free_imatrix(m,nrl,nrh,ncl,nch)
   double f;        int **m;
   double *xt;        long nch,ncl,nrh,nrl; 
         /* free an int matrix allocated by imatrix() */ 
   xt=vector(1,ncom);  { 
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   f=(*nrfunc)(xt);    free((FREE_ARG) (m+nrl-NR_END)); 
   free_vector(xt,1,ncom);  } 
   return f;  
 }  /******************* matrix *******************************/
   double **matrix(long nrl, long nrh, long ncl, long nch)
 /*****************brent *************************/  {
 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;
 {    double **m;
   int iter;  
   double a,b,d,etemp;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double fu,fv,fw,fx;    if (!m) nrerror("allocation failure 1 in matrix()");
   double ftemp;    m += NR_END;
   double p,q,r,tol1,tol2,u,v,w,x,xm;    m -= nrl;
   double e=0.0;  
      m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   a=(ax < cx ? ax : cx);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   b=(ax > cx ? ax : cx);    m[nrl] += NR_END;
   x=w=v=bx;    m[nrl] -= ncl;
   fw=fv=fx=(*f)(x);  
   for (iter=1;iter<=ITMAX;iter++) {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     xm=0.5*(a+b);    return m;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/     */
     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);  /*************************free matrix ************************/
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
 #endif  {
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       *xmin=x;    free((FREE_ARG)(m+nrl-NR_END));
       return fx;  }
     }  
     ftemp=fu;  /******************* ma3x *******************************/
     if (fabs(e) > tol1) {  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       r=(x-w)*(fx-fv);  {
       q=(x-v)*(fx-fw);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       p=(x-v)*q-(x-w)*r;    double ***m;
       q=2.0*(q-r);  
       if (q > 0.0) p = -p;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       q=fabs(q);    if (!m) nrerror("allocation failure 1 in matrix()");
       etemp=e;    m += NR_END;
       e=d;    m -= nrl;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       else {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         d=p/q;    m[nrl] += NR_END;
         u=x+d;    m[nrl] -= ncl;
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       }  
     } else {    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     }    m[nrl][ncl] += NR_END;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    m[nrl][ncl] -= nll;
     fu=(*f)(u);    for (j=ncl+1; j<=nch; j++) 
     if (fu <= fx) {      m[nrl][j]=m[nrl][j-1]+nlay;
       if (u >= x) a=x; else b=x;    
       SHFT(v,w,x,u)    for (i=nrl+1; i<=nrh; i++) {
         SHFT(fv,fw,fx,fu)      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
         } else {      for (j=ncl+1; j<=nch; j++) 
           if (u < x) a=u; else b=u;        m[i][j]=m[i][j-1]+nlay;
           if (fu <= fw || w == x) {    }
             v=w;    return m; 
             w=u;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
             fv=fw;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
             fw=fu;    */
           } 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)
         }  {
   }    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   nrerror("Too many iterations in brent");    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   *xmin=x;    free((FREE_ARG)(m+nrl-NR_END));
   return fx;  }
 }  
   /***************** f1dim *************************/
 /****************** mnbrak ***********************/  extern int ncom; 
   extern double *pcom,*xicom;
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  extern double (*nrfunc)(double []); 
             double (*func)(double))   
 {  double f1dim(double x) 
   double ulim,u,r,q, dum;  { 
   double fu;    int j; 
      double f;
   *fa=(*func)(*ax);    double *xt; 
   *fb=(*func)(*bx);   
   if (*fb > *fa) {    xt=vector(1,ncom); 
     SHFT(dum,*ax,*bx,dum)    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       SHFT(dum,*fb,*fa,dum)    f=(*nrfunc)(xt); 
       }    free_vector(xt,1,ncom); 
   *cx=(*bx)+GOLD*(*bx-*ax);    return f; 
   *fc=(*func)(*cx);  } 
   while (*fb > *fc) {  
     r=(*bx-*ax)*(*fb-*fc);  /*****************brent *************************/
     q=(*bx-*cx)*(*fb-*fa);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  { 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    int iter; 
     ulim=(*bx)+GLIMIT*(*cx-*bx);    double a,b,d,etemp;
     if ((*bx-u)*(u-*cx) > 0.0) {    double fu,fv,fw,fx;
       fu=(*func)(u);    double ftemp;
     } else if ((*cx-u)*(u-ulim) > 0.0) {    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       fu=(*func)(u);    double e=0.0; 
       if (fu < *fc) {   
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    a=(ax < cx ? ax : cx); 
           SHFT(*fb,*fc,fu,(*func)(u))    b=(ax > cx ? ax : cx); 
           }    x=w=v=bx; 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    fw=fv=fx=(*f)(x); 
       u=ulim;    for (iter=1;iter<=ITMAX;iter++) { 
       fu=(*func)(u);      xm=0.5*(a+b); 
     } else {      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       u=(*cx)+GOLD*(*cx-*bx);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       fu=(*func)(u);      printf(".");fflush(stdout);
     }      fprintf(ficlog,".");fflush(ficlog);
     SHFT(*ax,*bx,*cx,u)  #ifdef DEBUG
       SHFT(*fa,*fb,*fc,fu)      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)))) { */
   #endif
 /*************** linmin ************************/      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         *xmin=x; 
 int ncom;        return fx; 
 double *pcom,*xicom;      } 
 double (*nrfunc)(double []);      ftemp=fu;
        if (fabs(e) > tol1) { 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))        r=(x-w)*(fx-fv); 
 {        q=(x-v)*(fx-fw); 
   double brent(double ax, double bx, double cx,        p=(x-v)*q-(x-w)*r; 
                double (*f)(double), double tol, double *xmin);        q=2.0*(q-r); 
   double f1dim(double x);        if (q > 0.0) p = -p; 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,        q=fabs(q); 
               double *fc, double (*func)(double));        etemp=e; 
   int j;        e=d; 
   double xx,xmin,bx,ax;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   double fx,fb,fa;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
          else { 
   ncom=n;          d=p/q; 
   pcom=vector(1,n);          u=x+d; 
   xicom=vector(1,n);          if (u-a < tol2 || b-u < tol2) 
   nrfunc=func;            d=SIGN(tol1,xm-x); 
   for (j=1;j<=n;j++) {        } 
     pcom[j]=p[j];      } else { 
     xicom[j]=xi[j];        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   }      } 
   ax=0.0;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   xx=1.0;      fu=(*f)(u); 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);      if (fu <= fx) { 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);        if (u >= x) a=x; else b=x; 
 #ifdef DEBUG        SHFT(v,w,x,u) 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);          SHFT(fv,fw,fx,fu) 
 #endif          } else { 
   for (j=1;j<=n;j++) {            if (u < x) a=u; else b=u; 
     xi[j] *= xmin;            if (fu <= fw || w == x) { 
     p[j] += xi[j];              v=w; 
   }              w=u; 
   free_vector(xicom,1,n);              fv=fw; 
   free_vector(pcom,1,n);              fw=fu; 
 }            } else if (fu <= fv || v == x || v == w) { 
               v=u; 
 /*************** powell ************************/              fv=fu; 
 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,    nrerror("Too many iterations in brent"); 
               double (*func)(double []));    *xmin=x; 
   int i,ibig,j;    return fx; 
   double del,t,*pt,*ptt,*xit;  } 
   double fp,fptt;  
   double *xits;  /****************** mnbrak ***********************/
   pt=vector(1,n);  
   ptt=vector(1,n);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   xit=vector(1,n);              double (*func)(double)) 
   xits=vector(1,n);  { 
   *fret=(*func)(p);    double ulim,u,r,q, dum;
   for (j=1;j<=n;j++) pt[j]=p[j];    double fu; 
   for (*iter=1;;++(*iter)) {   
     fp=(*fret);    *fa=(*func)(*ax); 
     ibig=0;    *fb=(*func)(*bx); 
     del=0.0;    if (*fb > *fa) { 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      SHFT(dum,*ax,*bx,dum) 
     for (i=1;i<=n;i++)        SHFT(dum,*fb,*fa,dum) 
       printf(" %d %.12f",i, p[i]);        } 
     printf("\n");    *cx=(*bx)+GOLD*(*bx-*ax); 
     for (i=1;i<=n;i++) {    *fc=(*func)(*cx); 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    while (*fb > *fc) { 
       fptt=(*fret);      r=(*bx-*ax)*(*fb-*fc); 
 #ifdef DEBUG      q=(*bx-*cx)*(*fb-*fa); 
       printf("fret=%lf \n",*fret);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 #endif        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       printf("%d",i);fflush(stdout);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       linmin(p,xit,n,fret,func);      if ((*bx-u)*(u-*cx) > 0.0) { 
       if (fabs(fptt-(*fret)) > del) {        fu=(*func)(u); 
         del=fabs(fptt-(*fret));      } else if ((*cx-u)*(u-ulim) > 0.0) { 
         ibig=i;        fu=(*func)(u); 
       }        if (fu < *fc) { 
 #ifdef DEBUG          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       printf("%d %.12e",i,(*fret));            SHFT(*fb,*fc,fu,(*func)(u)) 
       for (j=1;j<=n;j++) {            } 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
         printf(" x(%d)=%.12e",j,xit[j]);        u=ulim; 
       }        fu=(*func)(u); 
       for(j=1;j<=n;j++)      } else { 
         printf(" p=%.12e",p[j]);        u=(*cx)+GOLD*(*cx-*bx); 
       printf("\n");        fu=(*func)(u); 
 #endif      } 
     }      SHFT(*ax,*bx,*cx,u) 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {        SHFT(*fa,*fb,*fc,fu) 
 #ifdef DEBUG        } 
       int k[2],l;  } 
       k[0]=1;  
       k[1]=-1;  /*************** linmin ************************/
       printf("Max: %.12e",(*func)(p));  
       for (j=1;j<=n;j++)  int ncom; 
         printf(" %.12e",p[j]);  double *pcom,*xicom;
       printf("\n");  double (*nrfunc)(double []); 
       for(l=0;l<=1;l++) {   
         for (j=1;j<=n;j++) {  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  { 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    double brent(double ax, double bx, double cx, 
         }                 double (*f)(double), double tol, double *xmin); 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    double f1dim(double x); 
       }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
 #endif                double *fc, double (*func)(double)); 
     int j; 
     double xx,xmin,bx,ax; 
       free_vector(xit,1,n);    double fx,fb,fa;
       free_vector(xits,1,n);   
       free_vector(ptt,1,n);    ncom=n; 
       free_vector(pt,1,n);    pcom=vector(1,n); 
       return;    xicom=vector(1,n); 
     }    nrfunc=func; 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    for (j=1;j<=n;j++) { 
     for (j=1;j<=n;j++) {      pcom[j]=p[j]; 
       ptt[j]=2.0*p[j]-pt[j];      xicom[j]=xi[j]; 
       xit[j]=p[j]-pt[j];    } 
       pt[j]=p[j];    ax=0.0; 
     }    xx=1.0; 
     fptt=(*func)(ptt);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     if (fptt < fp) {    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  #ifdef DEBUG
       if (t < 0.0) {    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         linmin(p,xit,n,fret,func);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         for (j=1;j<=n;j++) {  #endif
           xi[j][ibig]=xi[j][n];    for (j=1;j<=n;j++) { 
           xi[j][n]=xit[j];      xi[j] *= xmin; 
         }      p[j] += xi[j]; 
 #ifdef DEBUG    } 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    free_vector(xicom,1,n); 
         for(j=1;j<=n;j++)    free_vector(pcom,1,n); 
           printf(" %.12e",xit[j]);  } 
         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, 
                 double (*func)(double [])); 
 /**** Prevalence limit ****************/    int i,ibig,j; 
     double del,t,*pt,*ptt,*xit;
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    double fp,fptt;
 {    double *xits;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    pt=vector(1,n); 
      matrix by transitions matrix until convergence is reached */    ptt=vector(1,n); 
     xit=vector(1,n); 
   int i, ii,j,k;    xits=vector(1,n); 
   double min, max, maxmin, maxmax,sumnew=0.;    *fret=(*func)(p); 
   double **matprod2();    for (j=1;j<=n;j++) pt[j]=p[j]; 
   double **out, cov[NCOVMAX], **pmij();    for (*iter=1;;++(*iter)) { 
   double **newm;      fp=(*fret); 
   double agefin, delaymax=50 ; /* Max number of years to converge */      ibig=0; 
       del=0.0; 
   for (ii=1;ii<=nlstate+ndeath;ii++)      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
     for (j=1;j<=nlstate+ndeath;j++){      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      fprintf(ficrespow,"%d %.12f",*iter,*fret);
     }      for (i=1;i<=n;i++) {
         printf(" %d %.12f",i, p[i]);
    cov[1]=1.;        fprintf(ficlog," %d %.12lf",i, p[i]);
          fprintf(ficrespow," %.12lf", p[i]);
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      }
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){      printf("\n");
     newm=savm;      fprintf(ficlog,"\n");
     /* Covariates have to be included here again */      fprintf(ficrespow,"\n");
      cov[2]=agefin;      for (i=1;i<=n;i++) { 
          for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       for (k=1; k<=cptcovn;k++) {        fptt=(*fret); 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  #ifdef DEBUG
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/        printf("fret=%lf \n",*fret);
       }        fprintf(ficlog,"fret=%lf \n",*fret);
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  #endif
       for (k=1; k<=cptcovprod;k++)        printf("%d",i);fflush(stdout);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        fprintf(ficlog,"%d",i);fflush(ficlog);
         linmin(p,xit,n,fret,func); 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/        if (fabs(fptt-(*fret)) > del) { 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/          del=fabs(fptt-(*fret)); 
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/          ibig=i; 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);        } 
   #ifdef DEBUG
     savm=oldm;        printf("%d %.12e",i,(*fret));
     oldm=newm;        fprintf(ficlog,"%d %.12e",i,(*fret));
     maxmax=0.;        for (j=1;j<=n;j++) {
     for(j=1;j<=nlstate;j++){          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       min=1.;          printf(" x(%d)=%.12e",j,xit[j]);
       max=0.;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       for(i=1; i<=nlstate; i++) {        }
         sumnew=0;        for(j=1;j<=n;j++) {
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];          printf(" p=%.12e",p[j]);
         prlim[i][j]= newm[i][j]/(1-sumnew);          fprintf(ficlog," p=%.12e",p[j]);
         max=FMAX(max,prlim[i][j]);        }
         min=FMIN(min,prlim[i][j]);        printf("\n");
       }        fprintf(ficlog,"\n");
       maxmin=max-min;  #endif
       maxmax=FMAX(maxmax,maxmin);      } 
     }      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     if(maxmax < ftolpl){  #ifdef DEBUG
       return prlim;        int k[2],l;
     }        k[0]=1;
   }        k[1]=-1;
 }        printf("Max: %.12e",(*func)(p));
         fprintf(ficlog,"Max: %.12e",(*func)(p));
 /*************** transition probabilities ***************/        for (j=1;j<=n;j++) {
           printf(" %.12e",p[j]);
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )          fprintf(ficlog," %.12e",p[j]);
 {        }
   double s1, s2;        printf("\n");
   /*double t34;*/        fprintf(ficlog,"\n");
   int i,j,j1, nc, ii, jj;        for(l=0;l<=1;l++) {
           for (j=1;j<=n;j++) {
     for(i=1; i<= nlstate; i++){            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     for(j=1; j<i;j++){            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       for (nc=1, s2=0.;nc <=ncovmodel; 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 += param[i][j][nc]*cov[nc];*/          }
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       }        }
       ps[i][j]=s2;  #endif
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  
     }  
     for(j=i+1; j<=nlstate+ndeath;j++){        free_vector(xit,1,n); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        free_vector(xits,1,n); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        free_vector(ptt,1,n); 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/        free_vector(pt,1,n); 
       }        return; 
       ps[i][j]=s2;      } 
     }      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   }      for (j=1;j<=n;j++) { 
     /*ps[3][2]=1;*/        ptt[j]=2.0*p[j]-pt[j]; 
         xit[j]=p[j]-pt[j]; 
   for(i=1; i<= nlstate; i++){        pt[j]=p[j]; 
      s1=0;      } 
     for(j=1; j<i; j++)      fptt=(*func)(ptt); 
       s1+=exp(ps[i][j]);      if (fptt < fp) { 
     for(j=i+1; j<=nlstate+ndeath; j++)        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       s1+=exp(ps[i][j]);        if (t < 0.0) { 
     ps[i][i]=1./(s1+1.);          linmin(p,xit,n,fret,func); 
     for(j=1; j<i; j++)          for (j=1;j<=n;j++) { 
       ps[i][j]= exp(ps[i][j])*ps[i][i];            xi[j][ibig]=xi[j][n]; 
     for(j=i+1; j<=nlstate+ndeath; j++)            xi[j][n]=xit[j]; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];          }
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  #ifdef DEBUG
   } /* end i */          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           fprintf(ficlog,"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++){          for(j=1;j<=n;j++){
     for(jj=1; jj<= nlstate+ndeath; jj++){            printf(" %.12e",xit[j]);
       ps[ii][jj]=0;            fprintf(ficlog," %.12e",xit[j]);
       ps[ii][ii]=1;          }
     }          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]);    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   goto end;*/       matrix by transitions matrix until convergence is reached */
     return ps;  
 }    int i, ii,j,k;
     double min, max, maxmin, maxmax,sumnew=0.;
 /**************** Product of 2 matrices ******************/    double **matprod2();
     double **out, cov[NCOVMAX], **pmij();
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    double **newm;
 {    double agefin, delaymax=50 ; /* Max number of years to converge */
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    for (ii=1;ii<=nlstate+ndeath;ii++)
   /* in, b, out are matrice of pointers which should have been initialized      for (j=1;j<=nlstate+ndeath;j++){
      before: only the contents of out is modified. The function returns        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      a pointer to pointers identical to out */      }
   long i, j, k;  
   for(i=nrl; i<= nrh; i++)     cov[1]=1.;
     for(k=ncolol; k<=ncoloh; k++)   
       for(j=ncl,out[i][k]=0.; j<=nch; j++)   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         out[i][k] +=in[i][j]*b[j][k];    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       newm=savm;
   return out;      /* Covariates have to be included here again */
 }       cov[2]=agefin;
     
         for (k=1; k<=cptcovn;k++) {
 /************* Higher Matrix Product ***************/          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
           /*      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]]);*/
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )        }
 {        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month        for (k=1; k<=cptcovprod;k++)
      duration (i.e. until          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
      (typically every 2 years instead of every month which is too big).        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
      Model is determined by parameters x and covariates have to be        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
      included manually here.      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   
      */      savm=oldm;
       oldm=newm;
   int i, j, d, h, k;      maxmax=0.;
   double **out, cov[NCOVMAX];      for(j=1;j<=nlstate;j++){
   double **newm;        min=1.;
         max=0.;
   /* Hstepm could be zero and should return the unit matrix */        for(i=1; i<=nlstate; i++) {
   for (i=1;i<=nlstate+ndeath;i++)          sumnew=0;
     for (j=1;j<=nlstate+ndeath;j++){          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       oldm[i][j]=(i==j ? 1.0 : 0.0);          prlim[i][j]= newm[i][j]/(1-sumnew);
       po[i][j][0]=(i==j ? 1.0 : 0.0);          max=FMAX(max,prlim[i][j]);
     }          min=FMIN(min,prlim[i][j]);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */        }
   for(h=1; h <=nhstepm; h++){        maxmin=max-min;
     for(d=1; d <=hstepm; d++){        maxmax=FMAX(maxmax,maxmin);
       newm=savm;      }
       /* Covariates have to be included here again */      if(maxmax < ftolpl){
       cov[1]=1.;        return prlim;
       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 (k=1; k<=cptcovage;k++)  }
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  
       for (k=1; k<=cptcovprod;k++)  /*************** transition probabilities ***************/ 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  
   double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   {
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    double s1, s2;
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    /*double t34;*/
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    int i,j,j1, nc, ii, jj;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  
       savm=oldm;      for(i=1; i<= nlstate; i++){
       oldm=newm;      for(j=1; j<i;j++){
     }        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     for(i=1; i<=nlstate+ndeath; i++)          /*s2 += param[i][j][nc]*cov[nc];*/
       for(j=1;j<=nlstate+ndeath;j++) {          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
         po[i][j][h]=newm[i][j];          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);        }
          */        ps[i][j]=s2;
       }        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
   } /* end h */      }
   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];
           /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
 /*************** log-likelihood *************/        }
 double func( double *x)        ps[i][j]=s2;
 {      }
   int i, ii, j, k, mi, d, kk;    }
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      /*ps[3][2]=1;*/
   double **out;  
   double sw; /* Sum of weights */    for(i=1; i<= nlstate; i++){
   double lli; /* Individual log likelihood */       s1=0;
   int s1, s2;      for(j=1; j<i; j++)
   long ipmx;        s1+=exp(ps[i][j]);
   /*extern weight */      for(j=i+1; j<=nlstate+ndeath; j++)
   /* We are differentiating ll according to initial status */        s1+=exp(ps[i][j]);
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      ps[i][i]=1./(s1+1.);
   /*for(i=1;i<imx;i++)      for(j=1; j<i; j++)
     printf(" %d\n",s[4][i]);        ps[i][j]= exp(ps[i][j])*ps[i][i];
   */      for(j=i+1; j<=nlstate+ndeath; j++)
   cov[1]=1.;        ps[i][j]= exp(ps[i][j])*ps[i][i];
       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   for(k=1; k<=nlstate; k++) ll[k]=0.;    } /* end i */
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     for(mi=1; mi<= wav[i]-1; mi++){      for(jj=1; jj<= nlstate+ndeath; jj++){
       for (ii=1;ii<=nlstate+ndeath;ii++)        ps[ii][jj]=0;
         for (j=1;j<=nlstate+ndeath;j++){        ps[ii][ii]=1;
           oldm[ii][j]=(ii==j ? 1.0 : 0.0);      }
           savm[ii][j]=(ii==j ? 1.0 : 0.0);    }
         }  
       for(d=0; d<dh[mi][i]; d++){  
         newm=savm;    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      for(jj=1; jj<= nlstate+ndeath; jj++){
         for (kk=1; kk<=cptcovage;kk++) {       printf("%lf ",ps[ii][jj]);
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];     }
         }      printf("\n ");
              }
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      printf("\n ");printf("%lf ",cov[2]);*/
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  /*
         savm=oldm;    for(i=1; i<= npar; i++) printf("%f ",x[i]);
         oldm=newm;    goto end;*/
              return ps;
          }
       } /* end mult */  
        /**************** Product of 2 matrices ******************/
       s1=s[mw[mi][i]][i];  
       s2=s[mw[mi+1][i]][i];  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
       if( s2 > nlstate){  {
         /* i.e. if s2 is a death state and if the date of death is known then the contribution    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
            to the likelihood is the probability to die between last step unit time and current       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
            step unit time, which is also the differences between probability to die before dh    /* in, b, out are matrice of pointers which should have been initialized 
            and probability to die before dh-stepm .       before: only the contents of out is modified. The function returns
            In version up to 0.92 likelihood was computed       a pointer to pointers identical to out */
            as if date of death was unknown. Death was treated as any other    long i, j, k;
            health state: the date of the interview describes the actual state    for(i=nrl; i<= nrh; i++)
            and not the date of a change in health state. The former idea was      for(k=ncolol; k<=ncoloh; k++)
            to consider that at each interview the state was recorded        for(j=ncl,out[i][k]=0.; j<=nch; j++)
            (healthy, disable or death) and IMaCh was corrected; but when we          out[i][k] +=in[i][j]*b[j][k];
            introduced the exact date of death then we should have modified  
            the contribution of an exact death to the likelihood. This new    return out;
            contribution is smaller and very dependent of the step unit  }
            stepm. It is no more the probability to die between last interview  
            and month of death but the probability to survive from last  
            interview up to one month before death multiplied by the  /************* Higher Matrix Product ***************/
            probability to die within a month. Thanks to Chris  
            Jackson for correcting this bug.  Former versions increased  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
            mortality artificially. The bad side is that we add another loop  {
            which slows down the processing. The difference can be up to 10%    /* Computes the transition matrix starting at age 'age' over 
            lower mortality.       'nhstepm*hstepm*stepm' months (i.e. until
         */       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         lli=log(out[s1][s2] - savm[s1][s2]);       nhstepm*hstepm matrices. 
       }else{       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
         lli=log(out[s1][s2]); /* or     lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); */       (typically every 2 years instead of every month which is too big 
         /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/       for the memory).
       }       Model is determined by parameters x and covariates have to be 
       ipmx +=1;       included manually here. 
       sw += weight[i];  
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;       */
       /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d lli=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],lli,weight[i],out[s1][s2],savm[s1][s2]);*/  
     } /* end of wave */    int i, j, d, h, k;
   } /* end of individual */    double **out, cov[NCOVMAX];
     double **newm;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    /* Hstepm could be zero and should return the unit matrix */
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    for (i=1;i<=nlstate+ndeath;i++)
   /*exit(0);*/      for (j=1;j<=nlstate+ndeath;j++){
   return -l;        oldm[i][j]=(i==j ? 1.0 : 0.0);
 }        po[i][j][0]=(i==j ? 1.0 : 0.0);
       }
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 /*********** Maximum Likelihood Estimation ***************/    for(h=1; h <=nhstepm; h++){
       for(d=1; d <=hstepm; d++){
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        newm=savm;
 {        /* Covariates have to be included here again */
   int i,j, iter;        cov[1]=1.;
   double **xi,*delti;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   double fret;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   xi=matrix(1,npar,1,npar);        for (k=1; k<=cptcovage;k++)
   for (i=1;i<=npar;i++)          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for (j=1;j<=npar;j++)        for (k=1; k<=cptcovprod;k++)
       xi[i][j]=(i==j ? 1.0 : 0.0);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   printf("Powell\n");  
   powell(p,xi,npar,ftol,&iter,&fret,func);  
         /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                      pmij(pmmij,cov,ncovmodel,x,nlstate));
 }        savm=oldm;
         oldm=newm;
 /**** Computes Hessian and covariance matrix ***/      }
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      for(i=1; i<=nlstate+ndeath; i++)
 {        for(j=1;j<=nlstate+ndeath;j++) {
   double  **a,**y,*x,pd;          po[i][j][h]=newm[i][j];
   double **hess;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
   int i, j,jk;           */
   int *indx;        }
     } /* end h */
   double hessii(double p[], double delta, int theta, double delti[]);    return po;
   double hessij(double p[], double delti[], int i, int j);  }
   void lubksb(double **a, int npar, int *indx, double b[]) ;  
   void ludcmp(double **a, int npar, int *indx, double *d) ;  
   /*************** log-likelihood *************/
   hess=matrix(1,npar,1,npar);  double func( double *x)
   {
   printf("\nCalculation of the hessian matrix. Wait...\n");    int i, ii, j, k, mi, d, kk;
   for (i=1;i<=npar;i++){    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     printf("%d",i);fflush(stdout);    double **out;
     hess[i][i]=hessii(p,ftolhess,i,delti);    double sw; /* Sum of weights */
     /*printf(" %f ",p[i]);*/    double lli; /* Individual log likelihood */
     /*printf(" %lf ",hess[i][i]);*/    int s1, s2;
   }    double bbh, survp;
      long ipmx;
   for (i=1;i<=npar;i++) {    /*extern weight */
     for (j=1;j<=npar;j++)  {    /* We are differentiating ll according to initial status */
       if (j>i) {    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         printf(".%d%d",i,j);fflush(stdout);    /*for(i=1;i<imx;i++) 
         hess[i][j]=hessij(p,delti,i,j);      printf(" %d\n",s[4][i]);
         hess[j][i]=hess[i][j];        */
         /*printf(" %lf ",hess[i][j]);*/    cov[1]=1.;
       }  
     }    for(k=1; k<=nlstate; k++) ll[k]=0.;
   }  
   printf("\n");    if(mle==1){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          for(mi=1; mi<= wav[i]-1; mi++){
   a=matrix(1,npar,1,npar);          for (ii=1;ii<=nlstate+ndeath;ii++)
   y=matrix(1,npar,1,npar);            for (j=1;j<=nlstate+ndeath;j++){
   x=vector(1,npar);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   indx=ivector(1,npar);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (i=1;i<=npar;i++)            }
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];          for(d=0; d<dh[mi][i]; d++){
   ludcmp(a,npar,indx,&pd);            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for (j=1;j<=npar;j++) {            for (kk=1; kk<=cptcovage;kk++) {
     for (i=1;i<=npar;i++) x[i]=0;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     x[j]=1;            }
     lubksb(a,npar,indx,x);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for (i=1;i<=npar;i++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       matcov[i][j]=x[i];            savm=oldm;
     }            oldm=newm;
   }          } /* end mult */
         
   printf("\n#Hessian matrix#\n");          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   for (i=1;i<=npar;i++) {          /* But now since version 0.9 we anticipate for bias and large stepm.
     for (j=1;j<=npar;j++) {           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       printf("%.3e ",hess[i][j]);           * (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
     printf("\n");           * 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
            * probability in order to take into account the bias as a fraction of the way
   /* Recompute Inverse */           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   for (i=1;i<=npar;i++)           * -stepm/2 to stepm/2 .
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];           * For stepm=1 the results are the same as for previous versions of Imach.
   ludcmp(a,npar,indx,&pd);           * For stepm > 1 the results are less biased than in previous versions. 
            */
   /*  printf("\n#Hessian matrix recomputed#\n");          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
   for (j=1;j<=npar;j++) {          bbh=(double)bh[mi][i]/(double)stepm; 
     for (i=1;i<=npar;i++) x[i]=0;          /* bias is positive if real duration
     x[j]=1;           * is higher than the multiple of stepm and negative otherwise.
     lubksb(a,npar,indx,x);           */
     for (i=1;i<=npar;i++){          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       y[i][j]=x[i];          if( s2 > nlstate){ 
       printf("%.3e ",y[i][j]);            /* i.e. if s2 is a death state and if the date of death is known then the contribution
     }               to the likelihood is the probability to die between last step unit time and current 
     printf("\n");               step unit time, which is also the differences between probability to die before dh 
   }               and probability to die before dh-stepm . 
   */               In version up to 0.92 likelihood was computed
           as if date of death was unknown. Death was treated as any other
   free_matrix(a,1,npar,1,npar);          health state: the date of the interview describes the actual state
   free_matrix(y,1,npar,1,npar);          and not the date of a change in health state. The former idea was
   free_vector(x,1,npar);          to consider that at each interview the state was recorded
   free_ivector(indx,1,npar);          (healthy, disable or death) and IMaCh was corrected; but when we
   free_matrix(hess,1,npar,1,npar);          introduced the exact date of death then we should have modified
           the contribution of an exact death to the likelihood. This new
           contribution is smaller and very dependent of the step unit
 }          stepm. It is no more the probability to die between last interview
           and month of death but the probability to survive from last
 /*************** hessian matrix ****************/          interview up to one month before death multiplied by the
 double hessii( double x[], double delta, int theta, double delti[])          probability to die within a month. Thanks to Chris
 {          Jackson for correcting this bug.  Former versions increased
   int i;          mortality artificially. The bad side is that we add another loop
   int l=1, lmax=20;          which slows down the processing. The difference can be up to 10%
   double k1,k2;          lower mortality.
   double p2[NPARMAX+1];            */
   double res;            lli=log(out[s1][s2] - savm[s1][s2]);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          }else{
   double fx;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   int k=0,kmax=10;            /*  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 l1;          } 
           /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   fx=func(x);          /*if(lli ==000.0)*/
   for (i=1;i<=npar;i++) p2[i]=x[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); */
   for(l=0 ; l <=lmax; l++){          ipmx +=1;
     l1=pow(10,l);          sw += weight[i];
     delts=delt;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(k=1 ; k <kmax; k=k+1){        } /* end of wave */
       delt = delta*(l1*k);      } /* end of individual */
       p2[theta]=x[theta] +delt;    }  else if(mle==2){
       k1=func(p2)-fx;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       p2[theta]=x[theta]-delt;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       k2=func(p2)-fx;        for(mi=1; mi<= wav[i]-1; mi++){
       /*res= (k1-2.0*fx+k2)/delt/delt; */          for (ii=1;ii<=nlstate+ndeath;ii++)
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */            for (j=1;j<=nlstate+ndeath;j++){
                    oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 #ifdef DEBUG              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);            }
 #endif          for(d=0; d<=dh[mi][i]; d++){
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */            newm=savm;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         k=kmax;            for (kk=1; kk<=cptcovage;kk++) {
       }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */            }
         k=kmax; l=lmax*10.;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){            savm=oldm;
         delts=delt;            oldm=newm;
       }          } /* end mult */
     }        
   }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   delti[theta]=delts;          /* 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
            * we keep into memory the bias bh[mi][i] and also the previous matrix product
 double hessij( double x[], double delti[], int thetai,int thetaj)           * (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;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   int l=1, l1, lmax=20;           * -stepm/2 to stepm/2 .
   double k1,k2,k3,k4,res,fx;           * For stepm=1 the results are the same as for previous versions of Imach.
   double p2[NPARMAX+1];           * For stepm > 1 the results are less biased than in previous versions. 
   int k;           */
           s1=s[mw[mi][i]][i];
   fx=func(x);          s2=s[mw[mi+1][i]][i];
   for (k=1; k<=2; k++) {          bbh=(double)bh[mi][i]/(double)stepm; 
     for (i=1;i<=npar;i++) p2[i]=x[i];          /* bias is positive if real duration
     p2[thetai]=x[thetai]+delti[thetai]/k;           * is higher than the multiple of stepm and negative otherwise.
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;           */
     k1=func(p2)-fx;          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]));*/
     p2[thetai]=x[thetai]+delti[thetai]/k;          /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     k2=func(p2)-fx;          /*if(lli ==000.0)*/
            /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
     p2[thetai]=x[thetai]-delti[thetai]/k;          ipmx +=1;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          sw += weight[i];
     k3=func(p2)-fx;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          } /* end of wave */
     p2[thetai]=x[thetai]-delti[thetai]/k;      } /* end of individual */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    }  else if(mle==3){  /* exponential inter-extrapolation */
     k4=func(p2)-fx;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 #ifdef DEBUG        for(mi=1; mi<= wav[i]-1; mi++){
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);          for (ii=1;ii<=nlstate+ndeath;ii++)
 #endif            for (j=1;j<=nlstate+ndeath;j++){
   }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   return res;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 }            }
           for(d=0; d<dh[mi][i]; d++){
 /************** Inverse of matrix **************/            newm=savm;
 void ludcmp(double **a, int n, int *indx, double *d)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 {            for (kk=1; kk<=cptcovage;kk++) {
   int i,imax,j,k;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double big,dum,sum,temp;            }
   double *vv;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   vv=vector(1,n);            savm=oldm;
   *d=1.0;            oldm=newm;
   for (i=1;i<=n;i++) {          } /* end mult */
     big=0.0;        
     for (j=1;j<=n;j++)          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       if ((temp=fabs(a[i][j])) > big) big=temp;          /* But now since version 0.9 we anticipate for bias and large stepm.
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     vv[i]=1.0/big;           * (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
   for (j=1;j<=n;j++) {           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     for (i=1;i<j;i++) {           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
       sum=a[i][j];           * probability in order to take into account the bias as a fraction of the way
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
       a[i][j]=sum;           * -stepm/2 to stepm/2 .
     }           * For stepm=1 the results are the same as for previous versions of Imach.
     big=0.0;           * For stepm > 1 the results are less biased than in previous versions. 
     for (i=j;i<=n;i++) {           */
       sum=a[i][j];          s1=s[mw[mi][i]][i];
       for (k=1;k<j;k++)          s2=s[mw[mi+1][i]][i];
         sum -= a[i][k]*a[k][j];          bbh=(double)bh[mi][i]/(double)stepm; 
       a[i][j]=sum;          /* bias is positive if real duration
       if ( (dum=vv[i]*fabs(sum)) >= big) {           * is higher than the multiple of stepm and negative otherwise.
         big=dum;           */
         imax=i;          /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
       }          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
     }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     if (j != imax) {          /*if(lli ==000.0)*/
       for (k=1;k<=n;k++) {          /*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); */
         dum=a[imax][k];          ipmx +=1;
         a[imax][k]=a[j][k];          sw += weight[i];
         a[j][k]=dum;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       }        } /* end of wave */
       *d = -(*d);      } /* end of individual */
       vv[imax]=vv[j];    }else{  /* ml=4 no inter-extrapolation */
     }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     indx[j]=imax;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     if (a[j][j] == 0.0) a[j][j]=TINY;        for(mi=1; mi<= wav[i]-1; mi++){
     if (j != n) {          for (ii=1;ii<=nlstate+ndeath;ii++)
       dum=1.0/(a[j][j]);            for (j=1;j<=nlstate+ndeath;j++){
       for (i=j+1;i<=n;i++) a[i][j] *= dum;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   }            }
   free_vector(vv,1,n);  /* Doesn't work */          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++) {
 void lubksb(double **a, int n, int *indx, double b[])              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 {            }
   int i,ii=0,ip,j;          
   double sum;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   for (i=1;i<=n;i++) {            savm=oldm;
     ip=indx[i];            oldm=newm;
     sum=b[ip];          } /* end mult */
     b[ip]=b[i];        
     if (ii)          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          ipmx +=1;
     else if (sum) ii=i;          sw += weight[i];
     b[i]=sum;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   }        } /* end of wave */
   for (i=n;i>=1;i--) {      } /* end of individual */
     sum=b[i];    } /* End of if */
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     b[i]=sum/a[i][i];    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   }    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
 }    return -l;
   }
 /************ Frequencies ********************/  
 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)  
 {  /* Some frequencies */  /*********** Maximum Likelihood Estimation ***************/
    
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   double ***freq; /* Frequencies */  {
   double *pp;    int i,j, iter;
   double pos, k2, dateintsum=0,k2cpt=0;    double **xi;
   FILE *ficresp;    double fret;
   char fileresp[FILENAMELENGTH];    char filerespow[FILENAMELENGTH];
      xi=matrix(1,npar,1,npar);
   pp=vector(1,nlstate);    for (i=1;i<=npar;i++)
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      for (j=1;j<=npar;j++)
   strcpy(fileresp,"p");        xi[i][j]=(i==j ? 1.0 : 0.0);
   strcat(fileresp,fileres);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   if((ficresp=fopen(fileresp,"w"))==NULL) {    strcpy(filerespow,"pow"); 
     printf("Problem with prevalence resultfile: %s\n", fileresp);    strcat(filerespow,fileres);
     exit(0);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", filerespow);
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   j1=0;    }
      fprintf(ficrespow,"# Powell\n# iter -2*LL");
   j=cptcoveff;    for (i=1;i<=nlstate;i++)
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      for(j=1;j<=nlstate+ndeath;j++)
          if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   for(k1=1; k1<=j;k1++){    fprintf(ficrespow,"\n");
     for(i1=1; i1<=ncodemax[k1];i1++){    powell(p,xi,npar,ftol,&iter,&fret,func);
       j1++;  
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    fclose(ficrespow);
         scanf("%d", i);*/    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
       for (i=-1; i<=nlstate+ndeath; i++)      fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         for (jk=-1; jk<=nlstate+ndeath; jk++)      fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
           for(m=agemin; m <= agemax+3; m++)  
             freq[i][jk][m]=0;  }
        
       dateintsum=0;  /**** Computes Hessian and covariance matrix ***/
       k2cpt=0;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
       for (i=1; i<=imx; i++) {  {
         bool=1;    double  **a,**y,*x,pd;
         if  (cptcovn>0) {    double **hess;
           for (z1=1; z1<=cptcoveff; z1++)    int i, j,jk;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    int *indx;
               bool=0;  
         }    double hessii(double p[], double delta, int theta, double delti[]);
         if (bool==1) {    double hessij(double p[], double delti[], int i, int j);
           for(m=firstpass; m<=lastpass; m++){    void lubksb(double **a, int npar, int *indx, double b[]) ;
             k2=anint[m][i]+(mint[m][i]/12.);    void ludcmp(double **a, int npar, int *indx, double *d) ;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  
               if(agev[m][i]==0) agev[m][i]=agemax+1;    hess=matrix(1,npar,1,npar);
               if(agev[m][i]==1) agev[m][i]=agemax+2;  
               if (m<lastpass) {    printf("\nCalculation of the hessian matrix. Wait...\n");
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    for (i=1;i<=npar;i++){
               }      printf("%d",i);fflush(stdout);
                    fprintf(ficlog,"%d",i);fflush(ficlog);
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {      hess[i][i]=hessii(p,ftolhess,i,delti);
                 dateintsum=dateintsum+k2;      /*printf(" %f ",p[i]);*/
                 k2cpt++;      /*printf(" %lf ",hess[i][i]);*/
               }    }
             }    
           }    for (i=1;i<=npar;i++) {
         }      for (j=1;j<=npar;j++)  {
       }        if (j>i) { 
                  printf(".%d%d",i,j);fflush(stdout);
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
           hess[i][j]=hessij(p,delti,i,j);
       if  (cptcovn>0) {          hess[j][i]=hess[i][j];    
         fprintf(ficresp, "\n#********** Variable ");          /*printf(" %lf ",hess[i][j]);*/
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        }
         fprintf(ficresp, "**********\n#");      }
       }    }
       for(i=1; i<=nlstate;i++)    printf("\n");
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    fprintf(ficlog,"\n");
       fprintf(ficresp, "\n");  
          printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       for(i=(int)agemin; i <= (int)agemax+3; i++){    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
         if(i==(int)agemax+3)    
           printf("Total");    a=matrix(1,npar,1,npar);
         else    y=matrix(1,npar,1,npar);
           printf("Age %d", i);    x=vector(1,npar);
         for(jk=1; jk <=nlstate ; jk++){    indx=ivector(1,npar);
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    for (i=1;i<=npar;i++)
             pp[jk] += freq[jk][m][i];      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
         }    ludcmp(a,npar,indx,&pd);
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=-1, pos=0; m <=0 ; m++)    for (j=1;j<=npar;j++) {
             pos += freq[jk][m][i];      for (i=1;i<=npar;i++) x[i]=0;
           if(pp[jk]>=1.e-10)      x[j]=1;
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      lubksb(a,npar,indx,x);
           else      for (i=1;i<=npar;i++){ 
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        matcov[i][j]=x[i];
         }      }
     }
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    printf("\n#Hessian matrix#\n");
             pp[jk] += freq[jk][m][i];    fprintf(ficlog,"\n#Hessian matrix#\n");
         }    for (i=1;i<=npar;i++) { 
       for (j=1;j<=npar;j++) { 
         for(jk=1,pos=0; jk <=nlstate ; jk++)        printf("%.3e ",hess[i][j]);
           pos += pp[jk];        fprintf(ficlog,"%.3e ",hess[i][j]);
         for(jk=1; jk <=nlstate ; jk++){      }
           if(pos>=1.e-5)      printf("\n");
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      fprintf(ficlog,"\n");
           else    }
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  
           if( i <= (int) agemax){    /* Recompute Inverse */
             if(pos>=1.e-5){    for (i=1;i<=npar;i++)
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
               probs[i][jk][j1]= pp[jk]/pos;    ludcmp(a,npar,indx,&pd);
               /*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("\n#Hessian matrix recomputed#\n");
             else  
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    for (j=1;j<=npar;j++) {
           }      for (i=1;i<=npar;i++) x[i]=0;
         }      x[j]=1;
              lubksb(a,npar,indx,x);
         for(jk=-1; jk <=nlstate+ndeath; jk++)      for (i=1;i<=npar;i++){ 
           for(m=-1; m <=nlstate+ndeath; m++)        y[i][j]=x[i];
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        printf("%.3e ",y[i][j]);
         if(i <= (int) agemax)        fprintf(ficlog,"%.3e ",y[i][j]);
           fprintf(ficresp,"\n");      }
         printf("\n");      printf("\n");
       }      fprintf(ficlog,"\n");
     }    }
   }    */
   dateintmean=dateintsum/k2cpt;  
      free_matrix(a,1,npar,1,npar);
   fclose(ficresp);    free_matrix(y,1,npar,1,npar);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    free_vector(x,1,npar);
   free_vector(pp,1,nlstate);    free_ivector(indx,1,npar);
      free_matrix(hess,1,npar,1,npar);
   /* End of Freq */  
 }  
   }
 /************ Prevalence ********************/  
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)  /*************** hessian matrix ****************/
 {  /* Some frequencies */  double hessii( double x[], double delta, int theta, double delti[])
    {
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    int i;
   double ***freq; /* Frequencies */    int l=1, lmax=20;
   double *pp;    double k1,k2;
   double pos, k2;    double p2[NPARMAX+1];
     double res;
   pp=vector(1,nlstate);    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    double fx;
      int k=0,kmax=10;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    double l1;
   j1=0;  
      fx=func(x);
   j=cptcoveff;    for (i=1;i<=npar;i++) p2[i]=x[i];
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    for(l=0 ; l <=lmax; l++){
        l1=pow(10,l);
  for(k1=1; k1<=j;k1++){      delts=delt;
     for(i1=1; i1<=ncodemax[k1];i1++){      for(k=1 ; k <kmax; k=k+1){
       j1++;        delt = delta*(l1*k);
          p2[theta]=x[theta] +delt;
       for (i=-1; i<=nlstate+ndeath; i++)          k1=func(p2)-fx;
         for (jk=-1; jk<=nlstate+ndeath; jk++)          p2[theta]=x[theta]-delt;
           for(m=agemin; m <= agemax+3; m++)        k2=func(p2)-fx;
             freq[i][jk][m]=0;        /*res= (k1-2.0*fx+k2)/delt/delt; */
              res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
       for (i=1; i<=imx; i++) {        
         bool=1;  #ifdef DEBUG
         if  (cptcovn>0) {        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
           for (z1=1; z1<=cptcoveff; z1++)        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);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  #endif
               bool=0;        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         }        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         if (bool==1) {          k=kmax;
           for(m=firstpass; m<=lastpass; m++){        }
             k2=anint[m][i]+(mint[m][i]/12.);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          k=kmax; l=lmax*10.;
               if(agev[m][i]==0) agev[m][i]=agemax+1;        }
               if(agev[m][i]==1) agev[m][i]=agemax+2;        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
               if (m<lastpass)          delts=delt;
                 if (calagedate>0) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];        }
               else      }
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    }
                freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];    delti[theta]=delts;
             }    return res; 
           }    
         }  }
       }  
         for(i=(int)agemin; i <= (int)agemax+3; i++){  double hessij( double x[], double delti[], int thetai,int thetaj)
           for(jk=1; jk <=nlstate ; jk++){  {
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    int i;
               pp[jk] += freq[jk][m][i];    int l=1, l1, lmax=20;
           }    double k1,k2,k3,k4,res,fx;
           for(jk=1; jk <=nlstate ; jk++){    double p2[NPARMAX+1];
             for(m=-1, pos=0; m <=0 ; m++)    int k;
             pos += freq[jk][m][i];  
         }    fx=func(x);
            for (k=1; k<=2; k++) {
          for(jk=1; jk <=nlstate ; jk++){      for (i=1;i<=npar;i++) p2[i]=x[i];
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      p2[thetai]=x[thetai]+delti[thetai]/k;
              pp[jk] += freq[jk][m][i];      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
          }      k1=func(p2)-fx;
              
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
          for(jk=1; jk <=nlstate ; jk++){                k2=func(p2)-fx;
            if( i <= (int) agemax){    
              if(pos>=1.e-5){      p2[thetai]=x[thetai]-delti[thetai]/k;
                probs[i][jk][j1]= pp[jk]/pos;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
              }      k3=func(p2)-fx;
            }    
          }      p2[thetai]=x[thetai]-delti[thetai]/k;
                p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         }      k4=func(p2)-fx;
     }      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   }  #ifdef DEBUG
       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
        fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  #endif
   free_vector(pp,1,nlstate);    }
      return res;
 }  /* End of Freq */  }
   
 /************* Waves Concatenation ***************/  /************** Inverse of matrix **************/
   void ludcmp(double **a, int n, int *indx, double *d) 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  { 
 {    int i,imax,j,k; 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    double big,dum,sum,temp; 
      Death is a valid wave (if date is known).    double *vv; 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i   
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    vv=vector(1,n); 
      and mw[mi+1][i]. dh depends on stepm.    *d=1.0; 
      */    for (i=1;i<=n;i++) { 
       big=0.0; 
   int i, mi, m;      for (j=1;j<=n;j++) 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        if ((temp=fabs(a[i][j])) > big) big=temp; 
      double sum=0., jmean=0.;*/      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       vv[i]=1.0/big; 
   int j, k=0,jk, ju, jl;    } 
   double sum=0.;    for (j=1;j<=n;j++) { 
   jmin=1e+5;      for (i=1;i<j;i++) { 
   jmax=-1;        sum=a[i][j]; 
   jmean=0.;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   for(i=1; i<=imx; i++){        a[i][j]=sum; 
     mi=0;      } 
     m=firstpass;      big=0.0; 
     while(s[m][i] <= nlstate){      for (i=j;i<=n;i++) { 
       if(s[m][i]>=1)        sum=a[i][j]; 
         mw[++mi][i]=m;        for (k=1;k<j;k++) 
       if(m >=lastpass)          sum -= a[i][k]*a[k][j]; 
         break;        a[i][j]=sum; 
       else        if ( (dum=vv[i]*fabs(sum)) >= big) { 
         m++;          big=dum; 
     }/* end while */          imax=i; 
     if (s[m][i] > nlstate){        } 
       mi++;     /* Death is another wave */      } 
       /* if(mi==0)  never been interviewed correctly before death */      if (j != imax) { 
          /* Only death is a correct wave */        for (k=1;k<=n;k++) { 
       mw[mi][i]=m;          dum=a[imax][k]; 
     }          a[imax][k]=a[j][k]; 
           a[j][k]=dum; 
     wav[i]=mi;        } 
     if(mi==0)        *d = -(*d); 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        vv[imax]=vv[j]; 
   }      } 
       indx[j]=imax; 
   for(i=1; i<=imx; i++){      if (a[j][j] == 0.0) a[j][j]=TINY; 
     for(mi=1; mi<wav[i];mi++){      if (j != n) { 
       if (stepm <=0)        dum=1.0/(a[j][j]); 
         dh[mi][i]=1;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       else{      } 
         if (s[mw[mi+1][i]][i] > nlstate) {    } 
           if (agedc[i] < 2*AGESUP) {    free_vector(vv,1,n);  /* Doesn't work */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  ;
           if(j==0) j=1;  /* Survives at least one month after exam */  } 
           k=k+1;  
           if (j >= jmax) jmax=j;  void lubksb(double **a, int n, int *indx, double b[]) 
           if (j <= jmin) jmin=j;  { 
           sum=sum+j;    int i,ii=0,ip,j; 
           /*if (j<0) printf("j=%d num=%d \n",j,i); */    double sum; 
           }   
         }    for (i=1;i<=n;i++) { 
         else{      ip=indx[i]; 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));      sum=b[ip]; 
           k=k+1;      b[ip]=b[i]; 
           if (j >= jmax) jmax=j;      if (ii) 
           else if (j <= jmin)jmin=j;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */      else if (sum) ii=i; 
           sum=sum+j;      b[i]=sum; 
         }    } 
         jk= j/stepm;    for (i=n;i>=1;i--) { 
         jl= j -jk*stepm;      sum=b[i]; 
         ju= j -(jk+1)*stepm;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
         if(jl <= -ju)      b[i]=sum/a[i][i]; 
           dh[mi][i]=jk;    } 
         else  } 
           dh[mi][i]=jk+1;  
         if(dh[mi][i]==0)  /************ Frequencies ********************/
           dh[mi][i]=1; /* At least one step */  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
       }  {  /* Some frequencies */
     }    
   }    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   jmean=sum/k;    int first;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    double ***freq; /* Frequencies */
  }    double *pp, **prop;
 /*********** Tricode ****************************/    double pos,posprop, k2, dateintsum=0,k2cpt=0;
 void tricode(int *Tvar, int **nbcode, int imx)    FILE *ficresp;
 {    char fileresp[FILENAMELENGTH];
   int Ndum[20],ij=1, k, j, i;    
   int cptcode=0;    pp=vector(1,nlstate);
   cptcoveff=0;    prop=matrix(1,nlstate,iagemin,iagemax+3);
      strcpy(fileresp,"p");
   for (k=0; k<19; k++) Ndum[k]=0;    strcat(fileresp,fileres);
   for (k=1; k<=7; k++) ncodemax[k]=0;    if((ficresp=fopen(fileresp,"w"))==NULL) {
       printf("Problem with prevalence resultfile: %s\n", fileresp);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     for (i=1; i<=imx; i++) {      exit(0);
       ij=(int)(covar[Tvar[j]][i]);    }
       Ndum[ij]++;    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    j1=0;
       if (ij > cptcode) cptcode=ij;    
     }    j=cptcoveff;
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
     for (i=0; i<=cptcode; i++) {  
       if(Ndum[i]!=0) ncodemax[j]++;    first=1;
     }  
     ij=1;    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
     for (i=1; i<=ncodemax[j]; i++) {        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       for (k=0; k<=19; k++) {          scanf("%d", i);*/
         if (Ndum[k] != 0) {        for (i=-1; i<=nlstate+ndeath; i++)  
           nbcode[Tvar[j]][ij]=k;          for (jk=-1; jk<=nlstate+ndeath; jk++)  
                      for(m=iagemin; m <= iagemax+3; m++)
           ij++;              freq[i][jk][m]=0;
         }  
         if (ij > ncodemax[j]) break;      for (i=1; i<=nlstate; i++)  
       }          for(m=iagemin; m <= iagemax+3; m++)
     }          prop[i][m]=0;
   }          
         dateintsum=0;
  for (k=0; k<19; k++) Ndum[k]=0;        k2cpt=0;
         for (i=1; i<=imx; i++) {
  for (i=1; i<=ncovmodel-2; i++) {          bool=1;
       ij=Tvar[i];          if  (cptcovn>0) {
       Ndum[ij]++;            for (z1=1; z1<=cptcoveff; z1++) 
     }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                 bool=0;
  ij=1;          }
  for (i=1; i<=10; i++) {          if (bool==1){
    if((Ndum[i]!=0) && (i<=ncovcol)){            for(m=firstpass; m<=lastpass; m++){
      Tvaraff[ij]=i;              k2=anint[m][i]+(mint[m][i]/12.);
      ij++;              if ((k2>=dateprev1) && (k2<=dateprev2)) {
    }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
  }                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];
     cptcoveff=ij-1;                if (m<lastpass) {
 }                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                   freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
 /*********** Health Expectancies ****************/                }
                 
 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 )                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   dateintsum=dateintsum+k2;
 {                  k2cpt++;
   /* Health expectancies */                }
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;              }
   double age, agelim, hf;            }
   double ***p3mat,***varhe;          }
   double **dnewm,**doldm;        }
   double *xp;         
   double **gp, **gm;        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   double ***gradg, ***trgradg;  
   int theta;        if  (cptcovn>0) {
           fprintf(ficresp, "\n#********** Variable "); 
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   xp=vector(1,npar);          fprintf(ficresp, "**********\n#");
   dnewm=matrix(1,nlstate*2,1,npar);        }
   doldm=matrix(1,nlstate*2,1,nlstate*2);        for(i=1; i<=nlstate;i++) 
            fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   fprintf(ficreseij,"# Health expectancies\n");        fprintf(ficresp, "\n");
   fprintf(ficreseij,"# Age");        
   for(i=1; i<=nlstate;i++)        for(i=iagemin; i <= iagemax+3; i++){
     for(j=1; j<=nlstate;j++)          if(i==iagemax+3){
       fprintf(ficreseij," %1d-%1d (SE)",i,j);            fprintf(ficlog,"Total");
   fprintf(ficreseij,"\n");          }else{
             if(first==1){
   if(estepm < stepm){              first=0;
     printf ("Problem %d lower than %d\n",estepm, stepm);              printf("See log file for details...\n");
   }            }
   else  hstepm=estepm;              fprintf(ficlog,"Age %d", i);
   /* We compute the life expectancy from trapezoids spaced every estepm months          }
    * This is mainly to measure the difference between two models: for example          for(jk=1; jk <=nlstate ; jk++){
    * if stepm=24 months pijx are given only every 2 years and by summing them            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
    * we are calculating an estimate of the Life Expectancy assuming a linear              pp[jk] += freq[jk][m][i]; 
    * progression inbetween and thus overestimating or underestimating according          }
    * to the curvature of the survival function. If, for the same date, we          for(jk=1; jk <=nlstate ; jk++){
    * estimate the model with stepm=1 month, we can keep estepm to 24 months            for(m=-1, pos=0; m <=0 ; m++)
    * to compare the new estimate of Life expectancy with the same linear              pos += freq[jk][m][i];
    * hypothesis. A more precise result, taking into account a more precise            if(pp[jk]>=1.e-10){
    * curvature will be obtained if estepm is as small as stepm. */              if(first==1){
               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   /* For example we decided to compute the life expectancy with the smallest unit */              }
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
      nhstepm is the number of hstepm from age to agelim            }else{
      nstepm is the number of stepm from age to agelin.              if(first==1)
      Look at hpijx to understand the reason of that which relies in memory size                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
      and note for a fixed period like estepm months */              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the            }
      survival function given by stepm (the optimization length). Unfortunately it          }
      means that if the survival funtion is printed only each two years of age and if  
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          for(jk=1; jk <=nlstate ; jk++){
      results. So we changed our mind and took the option of the best precision.            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   */              pp[jk] += freq[jk][m][i];
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */          }       
           for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   agelim=AGESUP;            pos += pp[jk];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            posprop += prop[jk][i];
     /* nhstepm age range expressed in number of stepm */          }
     nstepm=(int) rint((agelim-age)*YEARM/stepm);          for(jk=1; jk <=nlstate ; jk++){
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */            if(pos>=1.e-5){
     /* if (stepm >= YEARM) hstepm=1;*/              if(first==1)
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);            }else{
     gp=matrix(0,nhstepm,1,nlstate*2);              if(first==1)
     gm=matrix(0,nhstepm,1,nlstate*2);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            }
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */            if( i <= iagemax){
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);                if(pos>=1.e-5){
                  fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                 probs[i][jk][j1]= pp[jk]/pos;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
               }
     /* Computing Variances of health expectancies */              else
                 fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
      for(theta=1; theta <=npar; theta++){            }
       for(i=1; i<=npar; i++){          }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          
       }          for(jk=-1; jk <=nlstate+ndeath; jk++)
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              for(m=-1; m <=nlstate+ndeath; m++)
                if(freq[jk][m][i] !=0 ) {
       cptj=0;              if(first==1)
       for(j=1; j<= nlstate; j++){                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
         for(i=1; i<=nlstate; i++){                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
           cptj=cptj+1;              }
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){          if(i <= iagemax)
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;            fprintf(ficresp,"\n");
           }          if(first==1)
         }            printf("Others in log...\n");
       }          fprintf(ficlog,"\n");
              }
            }
       for(i=1; i<=npar; i++)    }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    dateintmean=dateintsum/k2cpt; 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);     
          fclose(ficresp);
       cptj=0;    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
       for(j=1; j<= nlstate; j++){    free_vector(pp,1,nlstate);
         for(i=1;i<=nlstate;i++){    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
           cptj=cptj+1;    /* End of Freq */
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){  }
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;  
           }  /************ Prevalence ********************/
         }  void prevalence(double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
       }  {  
          /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
           in each health status at the date of interview (if between dateprev1 and dateprev2).
        We still use firstpass and lastpass as another selection.
       for(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];    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
         }    double ***freq; /* Frequencies */
     double *pp, **prop;
      }    double pos,posprop; 
        double  y2; /* in fractional years */
 /* End theta */    int iagemin, iagemax;
   
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);    iagemin= (int) agemin;
     iagemax= (int) agemax;
      for(h=0; h<=nhstepm-1; h++)    /*pp=vector(1,nlstate);*/
       for(j=1; j<=nlstate*2;j++)    prop=matrix(1,nlstate,iagemin,iagemax+3); 
         for(theta=1; theta <=npar; theta++)    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
         trgradg[h][j][theta]=gradg[h][theta][j];    j1=0;
     
     j=cptcoveff;
      for(i=1;i<=nlstate*2;i++)    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       for(j=1;j<=nlstate*2;j++)    
         varhe[i][j][(int)age] =0.;    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
     for(h=0;h<=nhstepm-1;h++){        j1++;
       for(k=0;k<=nhstepm-1;k++){        
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);        for (i=1; i<=nlstate; i++)  
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);          for(m=iagemin; m <= iagemax+3; m++)
         for(i=1;i<=nlstate*2;i++)            prop[i][m]=0.0;
           for(j=1;j<=nlstate*2;j++)       
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;        for (i=1; i<=imx; i++) { /* Each individual */
       }          bool=1;
     }          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
                    if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     /* Computing expectancies */                bool=0;
     for(i=1; i<=nlstate;i++)          } 
       for(j=1; j<=nlstate;j++)          if (bool==1) { 
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
                        if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
         }                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
                 if (s[m][i]>0 && s[m][i]<=nlstate) { 
     fprintf(ficreseij,"%3.0f",age );                  /*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]]);*/
     cptj=0;                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
     for(i=1; i<=nlstate;i++)                  prop[s[m][i]][iagemax+3] += weight[i]; 
       for(j=1; j<=nlstate;j++){                } 
         cptj++;              }
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );            } /* end selection of waves */
       }          }
     fprintf(ficreseij,"\n");        }
            for(i=iagemin; i <= iagemax+3; i++){  
     free_matrix(gm,0,nhstepm,1,nlstate*2);          
     free_matrix(gp,0,nhstepm,1,nlstate*2);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);            posprop += prop[jk][i]; 
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);          } 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   }          for(jk=1; jk <=nlstate ; jk++){     
   free_vector(xp,1,npar);            if( i <=  iagemax){ 
   free_matrix(dnewm,1,nlstate*2,1,npar);              if(posprop>=1.e-5){ 
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);                probs[i][jk][j1]= prop[jk][i]/posprop;
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);              } 
 }            } 
           }/* end jk */ 
 /************ Variance ******************/        }/* end i */ 
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)      } /* end i1 */
 {    } /* end k1 */
   /* Variance of health expectancies */    
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   double **newm;    /*free_vector(pp,1,nlstate);*/
   double **dnewm,**doldm;    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   int i, j, nhstepm, hstepm, h, nstepm ;  }  /* End of prevalence */
   int k, cptcode;  
   double *xp;  /************* Waves Concatenation ***************/
   double **gp, **gm;  
   double ***gradg, ***trgradg;  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
   double ***p3mat;  {
   double age,agelim, hf;    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   int theta;       Death is a valid wave (if date is known).
        mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
    fprintf(ficresvij,"# Covariances of life expectancies\n");       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   fprintf(ficresvij,"# Age");       and mw[mi+1][i]. dh depends on stepm.
   for(i=1; i<=nlstate;i++)       */
     for(j=1; j<=nlstate;j++)  
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    int i, mi, m;
   fprintf(ficresvij,"\n");    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
        double sum=0., jmean=0.;*/
   xp=vector(1,npar);    int first;
   dnewm=matrix(1,nlstate,1,npar);    int j, k=0,jk, ju, jl;
   doldm=matrix(1,nlstate,1,nlstate);    double sum=0.;
      first=0;
   if(estepm < stepm){    jmin=1e+5;
     printf ("Problem %d lower than %d\n",estepm, stepm);    jmax=-1;
   }    jmean=0.;
   else  hstepm=estepm;      for(i=1; i<=imx; i++){
   /* For example we decided to compute the life expectancy with the smallest unit */      mi=0;
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.      m=firstpass;
      nhstepm is the number of hstepm from age to agelim      while(s[m][i] <= nlstate){
      nstepm is the number of stepm from age to agelin.        if(s[m][i]>=1)
      Look at hpijx to understand the reason of that which relies in memory size          mw[++mi][i]=m;
      and note for a fixed period like k years */        if(m >=lastpass)
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          break;
      survival function given by stepm (the optimization length). Unfortunately it        else
      means that if the survival funtion is printed only each two years of age and if          m++;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same      }/* end while */
      results. So we changed our mind and took the option of the best precision.      if (s[m][i] > nlstate){
   */        mi++;     /* Death is another wave */
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        /* if(mi==0)  never been interviewed correctly before death */
   agelim = AGESUP;           /* Only death is a correct wave */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        mw[mi][i]=m;
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      }
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      wav[i]=mi;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      if(mi==0){
     gp=matrix(0,nhstepm,1,nlstate);        if(first==0){
     gm=matrix(0,nhstepm,1,nlstate);          printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
           first=1;
     for(theta=1; theta <=npar; theta++){        }
       for(i=1; i<=npar; i++){ /* Computes gradient */        if(first==1){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
       }        }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        } /* end mi==0 */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    } /* End individuals */
   
       if (popbased==1) {    for(i=1; i<=imx; i++){
         for(i=1; i<=nlstate;i++)      for(mi=1; mi<wav[i];mi++){
           prlim[i][i]=probs[(int)age][i][ij];        if (stepm <=0)
       }          dh[mi][i]=1;
          else{
       for(j=1; j<= nlstate; j++){          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
         for(h=0; h<=nhstepm; h++){            if (agedc[i] < 2*AGESUP) {
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];            if(j==0) j=1;  /* Survives at least one month after exam */
         }            k=k+1;
       }            if (j >= jmax) jmax=j;
                if (j <= jmin) jmin=j;
       for(i=1; i<=npar; i++) /* Computes gradient */            sum=sum+j;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            /*if (j<0) printf("j=%d num=%d \n",j,i);*/
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            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]);
              }
       if (popbased==1) {          }
         for(i=1; i<=nlstate;i++)          else{
           prlim[i][i]=probs[(int)age][i][ij];            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
       }            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             k=k+1;
       for(j=1; j<= nlstate; j++){            if (j >= jmax) jmax=j;
         for(h=0; h<=nhstepm; h++){            else if (j <= jmin)jmin=j;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
         }            if(j<0)printf("Error! Negative delay (%d) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       }            sum=sum+j;
           }
       for(j=1; j<= nlstate; j++)          jk= j/stepm;
         for(h=0; h<=nhstepm; h++){          jl= j -jk*stepm;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          ju= j -(jk+1)*stepm;
         }          if(mle <=1){ 
     } /* End theta */            if(jl==0){
               dh[mi][i]=jk;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);              bh[mi][i]=0;
             }else{ /* We want a negative bias in order to only have interpolation ie
     for(h=0; h<=nhstepm; h++)                    * at the price of an extra matrix product in likelihood */
       for(j=1; j<=nlstate;j++)              dh[mi][i]=jk+1;
         for(theta=1; theta <=npar; theta++)              bh[mi][i]=ju;
           trgradg[h][j][theta]=gradg[h][theta][j];            }
           }else{
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */            if(jl <= -ju){
     for(i=1;i<=nlstate;i++)              dh[mi][i]=jk;
       for(j=1;j<=nlstate;j++)              bh[mi][i]=jl;       /* bias is positive if real duration
         vareij[i][j][(int)age] =0.;                                   * is higher than the multiple of stepm and negative otherwise.
                                    */
     for(h=0;h<=nhstepm;h++){            }
       for(k=0;k<=nhstepm;k++){            else{
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);              dh[mi][i]=jk+1;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);              bh[mi][i]=ju;
         for(i=1;i<=nlstate;i++)            }
           for(j=1;j<=nlstate;j++)            if(dh[mi][i]==0){
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;              dh[mi][i]=1; /* At least one step */
       }              bh[mi][i]=ju; /* At least one step */
     }              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
             }
     fprintf(ficresvij,"%.0f ",age );          }
     for(i=1; i<=nlstate;i++)        } /* end if mle */
       for(j=1; j<=nlstate;j++){      } /* end wave */
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);    }
       }    jmean=sum/k;
     fprintf(ficresvij,"\n");    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     free_matrix(gp,0,nhstepm,1,nlstate);    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     free_matrix(gm,0,nhstepm,1,nlstate);   }
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);  
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);  /*********** Tricode ****************************/
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  void tricode(int *Tvar, int **nbcode, int imx)
   } /* End age */  {
      
   free_vector(xp,1,npar);    int Ndum[20],ij=1, k, j, i, maxncov=19;
   free_matrix(doldm,1,nlstate,1,npar);    int cptcode=0;
   free_matrix(dnewm,1,nlstate,1,nlstate);    cptcoveff=0; 
    
 }    for (k=0; k<maxncov; k++) Ndum[k]=0;
     for (k=1; k<=7; k++) ncodemax[k]=0;
 /************ Variance of prevlim ******************/  
 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)    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
 {      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
   /* Variance of prevalence limit */                                 modality*/ 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
   double **newm;        Ndum[ij]++; /*store the modality */
   double **dnewm,**doldm;        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   int i, j, nhstepm, hstepm;        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
   int k, cptcode;                                         Tvar[j]. If V=sex and male is 0 and 
   double *xp;                                         female is 1, then  cptcode=1.*/
   double *gp, *gm;      }
   double **gradg, **trgradg;  
   double age,agelim;      for (i=0; i<=cptcode; i++) {
   int theta;        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 */
          }
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");  
   fprintf(ficresvpl,"# Age");      ij=1; 
   for(i=1; i<=nlstate;i++)      for (i=1; i<=ncodemax[j]; i++) {
       fprintf(ficresvpl," %1d-%1d",i,i);        for (k=0; k<= maxncov; k++) {
   fprintf(ficresvpl,"\n");          if (Ndum[k] != 0) {
             nbcode[Tvar[j]][ij]=k; 
   xp=vector(1,npar);            /* 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; */
   dnewm=matrix(1,nlstate,1,npar);            
   doldm=matrix(1,nlstate,1,nlstate);            ij++;
            }
   hstepm=1*YEARM; /* Every year of age */          if (ij > ncodemax[j]) break; 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        }  
   agelim = AGESUP;      } 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    }  
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  
     if (stepm >= YEARM) hstepm=1;   for (k=0; k< maxncov; k++) Ndum[k]=0;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
     gradg=matrix(1,npar,1,nlstate);   for (i=1; i<=ncovmodel-2; i++) { 
     gp=vector(1,nlstate);     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     gm=vector(1,nlstate);     ij=Tvar[i];
      Ndum[ij]++;
     for(theta=1; theta <=npar; theta++){   }
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);   ij=1;
       }   for (i=1; i<= maxncov; i++) {
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);     if((Ndum[i]!=0) && (i<=ncovcol)){
       for(i=1;i<=nlstate;i++)       Tvaraff[ij]=i; /*For printing */
         gp[i] = prlim[i][i];       ij++;
         }
       for(i=1; i<=npar; i++) /* Computes gradient */   }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);   
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);   cptcoveff=ij-1; /*Number of simple covariates*/
       for(i=1;i<=nlstate;i++)  }
         gm[i] = prlim[i][i];  
   /*********** Health Expectancies ****************/
       for(i=1;i<=nlstate;i++)  
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];  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 )
     } /* End theta */  
   {
     trgradg =matrix(1,nlstate,1,npar);    /* Health expectancies */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     for(j=1; j<=nlstate;j++)    double age, agelim, hf;
       for(theta=1; theta <=npar; theta++)    double ***p3mat,***varhe;
         trgradg[j][theta]=gradg[theta][j];    double **dnewm,**doldm;
     double *xp;
     for(i=1;i<=nlstate;i++)    double **gp, **gm;
       varpl[i][(int)age] =0.;    double ***gradg, ***trgradg;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    int theta;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);  
     for(i=1;i<=nlstate;i++)    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    xp=vector(1,npar);
     dnewm=matrix(1,nlstate*nlstate,1,npar);
     fprintf(ficresvpl,"%.0f ",age );    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     for(i=1; i<=nlstate;i++)    
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    fprintf(ficreseij,"# Health expectancies\n");
     fprintf(ficresvpl,"\n");    fprintf(ficreseij,"# Age");
     free_vector(gp,1,nlstate);    for(i=1; i<=nlstate;i++)
     free_vector(gm,1,nlstate);      for(j=1; j<=nlstate;j++)
     free_matrix(gradg,1,npar,1,nlstate);        fprintf(ficreseij," %1d-%1d (SE)",i,j);
     free_matrix(trgradg,1,nlstate,1,npar);    fprintf(ficreseij,"\n");
   } /* End age */  
     if(estepm < stepm){
   free_vector(xp,1,npar);      printf ("Problem %d lower than %d\n",estepm, stepm);
   free_matrix(doldm,1,nlstate,1,npar);    }
   free_matrix(dnewm,1,nlstate,1,nlstate);    else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
 }     * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
 /************ Variance of one-step probabilities  ******************/     * we are calculating an estimate of the Life Expectancy assuming a linear 
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)     * progression in between and thus overestimating or underestimating according
 {     * to the curvature of the survival function. If, for the same date, we 
   int i, j, i1, k1, j1, z1;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   int k=0, cptcode;     * to compare the new estimate of Life expectancy with the same linear 
   double **dnewm,**doldm;     * hypothesis. A more precise result, taking into account a more precise
   double *xp;     * curvature will be obtained if estepm is as small as stepm. */
   double *gp, *gm;  
   double **gradg, **trgradg;    /* For example we decided to compute the life expectancy with the smallest unit */
   double age,agelim, cov[NCOVMAX];    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   int theta;       nhstepm is the number of hstepm from age to agelim 
   char fileresprob[FILENAMELENGTH];       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
   strcpy(fileresprob,"prob");       and note for a fixed period like estepm months */
   strcat(fileresprob,fileres);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {       survival function given by stepm (the optimization length). Unfortunately it
     printf("Problem with resultfile: %s\n", fileresprob);       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 
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);       results. So we changed our mind and took the option of the best precision.
      */
 fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   fprintf(ficresprob,"# Age");  
   for(i=1; i<=nlstate;i++)    agelim=AGESUP;
     for(j=1; j<=(nlstate+ndeath);j++)    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);      /* nhstepm age range expressed in number of stepm */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); 
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   fprintf(ficresprob,"\n");      /* if (stepm >= YEARM) hstepm=1;*/
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   xp=vector(1,npar);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      gp=matrix(0,nhstepm,1,nlstate*nlstate);
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));      gm=matrix(0,nhstepm,1,nlstate*nlstate);
    
   cov[1]=1;      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   j=cptcoveff;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   j1=0;   
   for(k1=1; k1<=1;k1++){  
     for(i1=1; i1<=ncodemax[k1];i1++){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     j1++;  
       /* Computing Variances of health expectancies */
     if  (cptcovn>0) {  
       fprintf(ficresprob, "\n#********** Variable ");       for(theta=1; theta <=npar; theta++){
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        for(i=1; i<=npar; i++){ 
       fprintf(ficresprob, "**********\n#");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     }        }
            hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       for (age=bage; age<=fage; age ++){    
         cov[2]=age;        cptj=0;
         for (k=1; k<=cptcovn;k++) {        for(j=1; j<= nlstate; j++){
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];          for(i=1; i<=nlstate; i++){
                      cptj=cptj+1;
         }            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/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]]];          }
                }
         gradg=matrix(1,npar,1,9);       
         trgradg=matrix(1,9,1,npar);       
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        for(i=1; i<=npar; i++) 
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          xp[i] = x[i] - (i==theta ?delti[theta]:0);
            hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         for(theta=1; theta <=npar; theta++){        
           for(i=1; i<=npar; i++)        cptj=0;
             xp[i] = x[i] + (i==theta ?delti[theta]:0);        for(j=1; j<= nlstate; j++){
                    for(i=1;i<=nlstate;i++){
           pmij(pmmij,cov,ncovmodel,xp,nlstate);            cptj=cptj+1;
                      for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
           k=0;  
           for(i=1; i<= (nlstate+ndeath); i++){              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
             for(j=1; j<=(nlstate+ndeath);j++){            }
               k=k+1;          }
               gp[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];
           for(i=1; i<=npar; i++)          }
             xp[i] = x[i] - (i==theta ?delti[theta]:0);       } 
         
           pmij(pmmij,cov,ncovmodel,xp,nlstate);  /* End theta */
           k=0;  
           for(i=1; i<=(nlstate+ndeath); i++){       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
             for(j=1; j<=(nlstate+ndeath);j++){  
               k=k+1;       for(h=0; h<=nhstepm-1; h++)
               gm[k]=pmmij[i][j];        for(j=1; j<=nlstate*nlstate;j++)
             }          for(theta=1; theta <=npar; theta++)
           }            trgradg[h][j][theta]=gradg[h][theta][j];
             
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)  
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];         for(i=1;i<=nlstate*nlstate;i++)
         }        for(j=1;j<=nlstate*nlstate;j++)
           varhe[i][j][(int)age] =0.;
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)  
           for(theta=1; theta <=npar; theta++)       printf("%d|",(int)age);fflush(stdout);
             trgradg[j][theta]=gradg[theta][j];       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
               for(h=0;h<=nhstepm-1;h++){
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);        for(k=0;k<=nhstepm-1;k++){
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          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]);
         pmij(pmmij,cov,ncovmodel,x,nlstate);          for(i=1;i<=nlstate*nlstate;i++)
                    for(j=1;j<=nlstate*nlstate;j++)
         k=0;              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
         for(i=1; i<=(nlstate+ndeath); i++){        }
           for(j=1; j<=(nlstate+ndeath);j++){      }
             k=k+1;      /* Computing expectancies */
             gm[k]=pmmij[i][j];      for(i=1; i<=nlstate;i++)
           }        for(j=1; j<=nlstate;j++)
         }          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
                  eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
      /*printf("\n%d ",(int)age);            
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){  /* 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]);*/
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));  
      }*/          }
   
         fprintf(ficresprob,"\n%d ",(int)age);      fprintf(ficreseij,"%3.0f",age );
       cptj=0;
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)      for(i=1; i<=nlstate;i++)
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));        for(j=1; j<=nlstate;j++){
            cptj++;
       }          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
     }        }
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));      fprintf(ficreseij,"\n");
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));     
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   free_vector(xp,1,npar);      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   fclose(ficresprob);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      }
 }    printf("\n");
     fprintf(ficlog,"\n");
 /******************* Printing html file ***********/  
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \    free_vector(xp,1,npar);
  int lastpass, int stepm, int weightopt, char model[],\    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
  char version[], int popforecast, int estepm ){  }
   int jj1, k1, i1, cpt;  
   FILE *fichtm;  /************ Variance ******************/
   /*char optionfilehtm[FILENAMELENGTH];*/  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)
   {
   strcpy(optionfilehtm,optionfile);    /* Variance of health expectancies */
   strcat(optionfilehtm,".htm");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    /* double **newm;*/
     printf("Problem with %s \n",optionfilehtm), exit(0);    double **dnewm,**doldm;
   }    double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n    int k, cptcode;
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n    double *xp;
 \n    double **gp, **gm;  /* for var eij */
 Total number of observations=%d <br>\n    double ***gradg, ***trgradg; /*for var eij */
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n    double **gradgp, **trgradgp; /* for var p point j */
 <hr  size=\"2\" color=\"#EC5E5E\">    double *gpp, *gmp; /* for var p point j */
  <ul><li>Outputs files<br>\n    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n    double ***p3mat;
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n    double age,agelim, hf;
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    double ***mobaverage;
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n    int theta;
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n    char digit[4];
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,estepm,fileres,fileres);    char digitp[25];
   
  fprintf(fichtm,"\n    char fileresprobmorprev[FILENAMELENGTH];
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n  
   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n    if(popbased==1){
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n      if(mobilav!=0)
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n        strcpy(digitp,"-populbased-mobilav-");
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);      else strcpy(digitp,"-populbased-nomobil-");
     }
  if(popforecast==1) fprintf(fichtm,"\n    else 
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n      strcpy(digitp,"-stablbased-");
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n  
         <br>",fileres,fileres,fileres,fileres);    if (mobilav!=0) {
  else      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    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 (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
 fprintf(fichtm," <li>Graphs</li><p>");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
  m=cptcoveff;      }
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    }
   
  jj1=0;    strcpy(fileresprobmorprev,"prmorprev"); 
  for(k1=1; k1<=m;k1++){    sprintf(digit,"%-d",ij);
    for(i1=1; i1<=ncodemax[k1];i1++){    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
        jj1++;    strcat(fileresprobmorprev,digit); /* Tvar to be done */
        if (cptcovn > 0) {    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    strcat(fileresprobmorprev,fileres);
          for (cpt=1; cpt<=cptcoveff;cpt++)    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
        }    }
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
        for(cpt=1; cpt<nlstate;cpt++){    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(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
        }      fprintf(ficresprobmorprev," p.%-d SE",j);
     for(cpt=1; cpt<=nlstate;cpt++) {      for(i=1; i<=nlstate;i++)
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
 interval) in state (%d): v%s%d%d.gif <br>    }  
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      fprintf(ficresprobmorprev,"\n");
      }    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
      for(cpt=1; cpt<=nlstate;cpt++) {      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      exit(0);
      }    }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    else{
 health expectancies in states (1) and (2): e%s%d.gif<br>      fprintf(ficgp,"\n# Routine varevsij");
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    }
 fprintf(fichtm,"\n</body>");    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
    }      printf("Problem with html file: %s\n", optionfilehtm);
    }      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
 fclose(fichtm);      exit(0);
 }    }
     else{
 /******************* Gnuplot file **************/      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");
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
     }
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
   strcpy(optionfilegnuplot,optionfilefiname);    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");
   strcat(optionfilegnuplot,".gp.txt");    fprintf(ficresvij,"# Age");
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    for(i=1; i<=nlstate;i++)
     printf("Problem with file %s",optionfilegnuplot);      for(j=1; j<=nlstate;j++)
   }        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     fprintf(ficresvij,"\n");
 #ifdef windows  
     fprintf(ficgp,"cd \"%s\" \n",pathc);    xp=vector(1,npar);
 #endif    dnewm=matrix(1,nlstate,1,npar);
 m=pow(2,cptcoveff);    doldm=matrix(1,nlstate,1,nlstate);
      dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
  /* 1eme*/    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   for (cpt=1; cpt<= nlstate ; cpt ++) {  
    for (k1=1; k1<= m ; k1 ++) {    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);    gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
 for (i=1; i<= nlstate ; i ++) {    
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    if(estepm < stepm){
   else fprintf(ficgp," \%%*lf (\%%*lf)");      printf ("Problem %d lower than %d\n",estepm, stepm);
 }    }
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    else  hstepm=estepm;   
     for (i=1; i<= nlstate ; i ++) {    /* For example we decided to compute the life expectancy with the smallest unit */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   else fprintf(ficgp," \%%*lf (\%%*lf)");       nhstepm is the number of hstepm from age to agelim 
 }       nstepm is the number of stepm from age to agelin. 
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);       Look at hpijx to understand the reason of that which relies in memory size
      for (i=1; i<= nlstate ; i ++) {       and note for a fixed period like k years */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   else fprintf(ficgp," \%%*lf (\%%*lf)");       survival function given by stepm (the optimization length). Unfortunately it
 }         means that if the survival funtion is printed every two years of age and if
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));       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.
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    */
    }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   }    agelim = AGESUP;
   /*2 eme*/    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   for (k1=1; k1<= m ; k1 ++) {      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
     for (i=1; i<= nlstate+1 ; i ++) {      gp=matrix(0,nhstepm,1,nlstate);
       k=2*i;      gm=matrix(0,nhstepm,1,nlstate);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      for(theta=1; theta <=npar; theta++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
 }            xp[i] = x[i] + (i==theta ?delti[theta]:0);
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        }
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       for (j=1; j<= nlstate+1 ; j ++) {  
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        if (popbased==1) {
         else fprintf(ficgp," \%%*lf (\%%*lf)");          if(mobilav ==0){
 }              for(i=1; i<=nlstate;i++)
       fprintf(ficgp,"\" t\"\" w l 0,");              prlim[i][i]=probs[(int)age][i][ij];
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);          }else{ /* mobilav */ 
       for (j=1; j<= nlstate+1 ; j ++) {            for(i=1; i<=nlstate;i++)
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              prlim[i][i]=mobaverage[(int)age][i][ij];
   else fprintf(ficgp," \%%*lf (\%%*lf)");          }
 }          }
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    
       else fprintf(ficgp,"\" t\"\" w l 0,");        for(j=1; j<= nlstate; j++){
     }          for(h=0; h<=nhstepm; h++){
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   }              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
            }
   /*3eme*/        }
         /* This for computing probability of death (h=1 means
   for (k1=1; k1<= m ; k1 ++) {           computed over hstepm matrices product = hstepm*stepm months) 
     for (cpt=1; cpt<= nlstate ; cpt ++) {           as a weighted average of prlim.
       k=2+nlstate*(2*cpt-2);        */
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");            gpp[j] += prlim[i][i]*p3mat[i][j][1];
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);        }    
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);        /* end probability of death */
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");  
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
 */        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       for (i=1; i< nlstate ; i ++) {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         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);   
         if (popbased==1) {
       }          if(mobilav ==0){
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            for(i=1; i<=nlstate;i++)
     }              prlim[i][i]=probs[(int)age][i][ij];
     }          }else{ /* mobilav */ 
              for(i=1; i<=nlstate;i++)
   /* CV preval stat */              prlim[i][i]=mobaverage[(int)age][i][ij];
     for (k1=1; k1<= m ; k1 ++) {          }
     for (cpt=1; cpt<nlstate ; cpt ++) {        }
       k=3;  
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);        for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
       for (i=1; i< nlstate ; i ++)            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
         fprintf(ficgp,"+$%d",k+i+1);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);          }
              }
       l=3+(nlstate+ndeath)*cpt;        /* This for computing probability of death (h=1 means
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);           computed over hstepm matrices product = hstepm*stepm months) 
       for (i=1; i< nlstate ; i ++) {           as a weighted average of prlim.
         l=3+(nlstate+ndeath)*cpt;        */
         fprintf(ficgp,"+$%d",l+i+1);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
       }          for(i=1,gmp[j]=0.; i<= nlstate; i++)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);             gmp[j] += prlim[i][i]*p3mat[i][j][1];
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        }    
     }        /* end probability of death */
   }    
          for(j=1; j<= nlstate; j++) /* vareij */
   /* proba elementaires */          for(h=0; h<=nhstepm; h++){
    for(i=1,jk=1; i <=nlstate; i++){            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     for(k=1; k <=(nlstate+ndeath); k++){          }
       if (k != i) {  
         for(j=1; j <=ncovmodel; j++){        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
                  gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);        }
           jk++;  
           fprintf(ficgp,"\n");      } /* End theta */
         }  
       }      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
     }  
     }      for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
     for(jk=1; jk <=m; jk++) {          for(theta=1; theta <=npar; theta++)
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);            trgradg[h][j][theta]=gradg[h][theta][j];
    i=1;  
    for(k2=1; k2<=nlstate; k2++) {      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
      k3=i;        for(theta=1; theta <=npar; theta++)
      for(k=1; k<=(nlstate+ndeath); k++) {          trgradgp[j][theta]=gradgp[theta][j];
        if (k != k2){    
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);  
 ij=1;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         for(j=3; j <=ncovmodel; j++) {      for(i=1;i<=nlstate;i++)
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        for(j=1;j<=nlstate;j++)
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          vareij[i][j][(int)age] =0.;
             ij++;  
           }      for(h=0;h<=nhstepm;h++){
           else        for(k=0;k<=nhstepm;k++){
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
         }          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           fprintf(ficgp,")/(1");          for(i=1;i<=nlstate;i++)
                    for(j=1;j<=nlstate;j++)
         for(k1=1; k1 <=nlstate; k1++){                vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);        }
 ij=1;      }
           for(j=3; j <=ncovmodel; j++){    
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      /* pptj */
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
             ij++;      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
           }      for(j=nlstate+1;j<=nlstate+ndeath;j++)
           else        for(i=nlstate+1;i<=nlstate+ndeath;i++)
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          varppt[j][i]=doldmp[j][i];
           }      /* end ppptj */
           fprintf(ficgp,")");      /*  x centered again */
         }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");   
         i=i+ncovmodel;      if (popbased==1) {
        }        if(mobilav ==0){
      }          for(i=1; i<=nlstate;i++)
    }            prlim[i][i]=probs[(int)age][i][ij];
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);        }else{ /* mobilav */ 
    }          for(i=1; i<=nlstate;i++)
                prlim[i][i]=mobaverage[(int)age][i][ij];
   fclose(ficgp);        }
 }  /* end gnuplot */      }
                
       /* This for computing probability of death (h=1 means
 /*************** Moving average **************/         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){         as a weighted average of prlim.
       */
   int i, cpt, cptcod;      for(j=nlstate+1;j<=nlstate+ndeath;j++){
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
       for (i=1; i<=nlstate;i++)          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)      }    
           mobaverage[(int)agedeb][i][cptcod]=0.;      /* end probability of death */
      
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for (i=1; i<=nlstate;i++){      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
           for (cpt=0;cpt<=4;cpt++){        for(i=1; i<=nlstate;i++){
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
           }        }
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;      } 
         }      fprintf(ficresprobmorprev,"\n");
       }  
     }      fprintf(ficresvij,"%.0f ",age );
          for(i=1; i<=nlstate;i++)
 }        for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
 /************** Forecasting ******************/      fprintf(ficresvij,"\n");
 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){      free_matrix(gp,0,nhstepm,1,nlstate);
        free_matrix(gm,0,nhstepm,1,nlstate);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   int *popage;      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   double *popeffectif,*popcount;    } /* End age */
   double ***p3mat;    free_vector(gpp,nlstate+1,nlstate+ndeath);
   char fileresf[FILENAMELENGTH];    free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
  agelim=AGESUP;    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
    /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
    /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   strcpy(fileresf,"f");  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   strcat(fileresf,fileres);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
   if((ficresf=fopen(fileresf,"w"))==NULL) {    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
     printf("Problem with forecast resultfile: %s\n", fileresf);    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);
   printf("Computing forecasting: result on file '%s' \n", fileresf);    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  */
     fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
   if (mobilav==1) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    free_vector(xp,1,npar);
     movingaverage(agedeb, fage, ageminpar, mobaverage);    free_matrix(doldm,1,nlstate,1,nlstate);
   }    free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   if (stepm<=12) stepsize=1;    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   agelim=AGESUP;    fclose(ficresprobmorprev);
      fclose(ficgp);
   hstepm=1;    fclose(fichtm);
   hstepm=hstepm/stepm;  }  
   yp1=modf(dateintmean,&yp);  
   anprojmean=yp;  /************ Variance of prevlim ******************/
   yp2=modf((yp1*12),&yp);  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)
   mprojmean=yp;  {
   yp1=modf((yp2*30.5),&yp);    /* Variance of prevalence limit */
   jprojmean=yp;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   if(jprojmean==0) jprojmean=1;    double **newm;
   if(mprojmean==0) jprojmean=1;    double **dnewm,**doldm;
      int i, j, nhstepm, hstepm;
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    int k, cptcode;
      double *xp;
   for(cptcov=1;cptcov<=i2;cptcov++){    double *gp, *gm;
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    double **gradg, **trgradg;
       k=k+1;    double age,agelim;
       fprintf(ficresf,"\n#******");    int theta;
       for(j=1;j<=cptcoveff;j++) {     
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
       }    fprintf(ficresvpl,"# Age");
       fprintf(ficresf,"******\n");    for(i=1; i<=nlstate;i++)
       fprintf(ficresf,"# StartingAge FinalAge");        fprintf(ficresvpl," %1d-%1d",i,i);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    fprintf(ficresvpl,"\n");
        
          xp=vector(1,npar);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    dnewm=matrix(1,nlstate,1,npar);
         fprintf(ficresf,"\n");    doldm=matrix(1,nlstate,1,nlstate);
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      
     hstepm=1*YEARM; /* Every year of age */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    agelim = AGESUP;
           nhstepm = nhstepm/hstepm;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      if (stepm >= YEARM) hstepm=1;
           oldm=oldms;savm=savms;      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        gradg=matrix(1,npar,1,nlstate);
              gp=vector(1,nlstate);
           for (h=0; h<=nhstepm; h++){      gm=vector(1,nlstate);
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);      for(theta=1; theta <=npar; theta++){
             }        for(i=1; i<=npar; i++){ /* Computes gradient */
             for(j=1; j<=nlstate+ndeath;j++) {          xp[i] = x[i] + (i==theta ?delti[theta]:0);
               kk1=0.;kk2=0;        }
               for(i=1; i<=nlstate;i++) {                      prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                 if (mobilav==1)        for(i=1;i<=nlstate;i++)
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          gp[i] = prlim[i][i];
                 else {      
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        for(i=1; i<=npar; i++) /* Computes gradient */
                 }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
                        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
               }        for(i=1;i<=nlstate;i++)
               if (h==(int)(calagedate+12*cpt)){          gm[i] = prlim[i][i];
                 fprintf(ficresf," %.3f", kk1);  
                                for(i=1;i<=nlstate;i++)
               }          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
             }      } /* End theta */
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      trgradg =matrix(1,nlstate,1,npar);
         }  
       }      for(j=1; j<=nlstate;j++)
     }        for(theta=1; theta <=npar; theta++)
   }          trgradg[j][theta]=gradg[theta][j];
          
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
   fclose(ficresf);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
 }      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
 /************** 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] = doldm[i][i]; /* Covariances are useless */
    
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      fprintf(ficresvpl,"%.0f ",age );
   int *popage;      for(i=1; i<=nlstate;i++)
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   double *popeffectif,*popcount;      fprintf(ficresvpl,"\n");
   double ***p3mat,***tabpop,***tabpopprev;      free_vector(gp,1,nlstate);
   char filerespop[FILENAMELENGTH];      free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      free_matrix(trgradg,1,nlstate,1,npar);
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    } /* End age */
   agelim=AGESUP;  
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    free_vector(xp,1,npar);
      free_matrix(doldm,1,nlstate,1,npar);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    free_matrix(dnewm,1,nlstate,1,nlstate);
    
    }
   strcpy(filerespop,"pop");  
   strcat(filerespop,fileres);  /************ Variance of one-step probabilities  ******************/
   if((ficrespop=fopen(filerespop,"w"))==NULL) {  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
     printf("Problem with forecast resultfile: %s\n", filerespop);  {
   }    int i, j=0,  i1, k1, l1, t, tj;
   printf("Computing forecasting: result on file '%s' \n", filerespop);    int k2, l2, j1,  z1;
     int k=0,l, cptcode;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   if (mobilav==1) {    double **dnewm,**doldm;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double *xp;
     movingaverage(agedeb, fage, ageminpar, mobaverage);    double *gp, *gm;
   }    double **gradg, **trgradg;
     double **mu;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    double age,agelim, cov[NCOVMAX];
   if (stepm<=12) stepsize=1;    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
      int theta;
   agelim=AGESUP;    char fileresprob[FILENAMELENGTH];
      char fileresprobcov[FILENAMELENGTH];
   hstepm=1;    char fileresprobcor[FILENAMELENGTH];
   hstepm=hstepm/stepm;  
      double ***varpij;
   if (popforecast==1) {  
     if((ficpop=fopen(popfile,"r"))==NULL) {    strcpy(fileresprob,"prob"); 
       printf("Problem with population file : %s\n",popfile);exit(0);    strcat(fileresprob,fileres);
     }    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     popage=ivector(0,AGESUP);      printf("Problem with resultfile: %s\n", fileresprob);
     popeffectif=vector(0,AGESUP);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     popcount=vector(0,AGESUP);    }
        strcpy(fileresprobcov,"probcov"); 
     i=1;      strcat(fileresprobcov,fileres);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
          printf("Problem with resultfile: %s\n", fileresprobcov);
     imx=i;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    }
   }    strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
   for(cptcov=1;cptcov<=i2;cptcov++){    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      printf("Problem with resultfile: %s\n", fileresprobcor);
       k=k+1;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficrespop,"\n#******");    }
       for(j=1;j<=cptcoveff;j++) {    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       }    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       fprintf(ficrespop,"******\n");    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       fprintf(ficrespop,"# Age");    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       if (popforecast==1)  fprintf(ficrespop," [Population]");    
          fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
       for (cpt=0; cpt<=0;cpt++) {    fprintf(ficresprob,"# Age");
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
            fprintf(ficresprobcov,"# Age");
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    fprintf(ficresprobcov,"# Age");
           nhstepm = nhstepm/hstepm;  
            
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for(i=1; i<=nlstate;i++)
           oldm=oldms;savm=savms;      for(j=1; j<=(nlstate+ndeath);j++){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          fprintf(ficresprob," p%1d-%1d (SE)",i,j);
                fprintf(ficresprobcov," p%1d-%1d ",i,j);
           for (h=0; h<=nhstepm; h++){        fprintf(ficresprobcor," p%1d-%1d ",i,j);
             if (h==(int) (calagedate+YEARM*cpt)) {      }  
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);   /* fprintf(ficresprob,"\n");
             }    fprintf(ficresprobcov,"\n");
             for(j=1; j<=nlstate+ndeath;j++) {    fprintf(ficresprobcor,"\n");
               kk1=0.;kk2=0;   */
               for(i=1; i<=nlstate;i++) {                 xp=vector(1,npar);
                 if (mobilav==1)    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
                 else {    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
                 }    first=1;
               }    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
               if (h==(int)(calagedate+12*cpt)){      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
                   /*fprintf(ficrespop," %.3f", kk1);      exit(0);
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/    }
               }    else{
             }      fprintf(ficgp,"\n# Routine varprob");
             for(i=1; i<=nlstate;i++){    }
               kk1=0.;    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
                 for(j=1; j<=nlstate;j++){      printf("Problem with html file: %s\n", optionfilehtm);
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
                 }      exit(0);
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    }
             }    else{
       fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)      fprintf(fichtm,"\n");
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);  
           }      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      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");
       }  
      }
   /******/  
     cov[1]=1;
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    tj=cptcoveff;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      if (cptcovn<1) {tj=1;ncodemax[1]=1;}
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    j1=0;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    for(t=1; t<=tj;t++){
           nhstepm = nhstepm/hstepm;      for(i1=1; i1<=ncodemax[t];i1++){ 
                  j1++;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        if  (cptcovn>0) {
           oldm=oldms;savm=savms;          fprintf(ficresprob, "\n#********** Variable "); 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           for (h=0; h<=nhstepm; h++){          fprintf(ficresprob, "**********\n#\n");
             if (h==(int) (calagedate+YEARM*cpt)) {          fprintf(ficresprobcov, "\n#********** Variable "); 
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
             }          fprintf(ficresprobcov, "**********\n#\n");
             for(j=1; j<=nlstate+ndeath;j++) {          
               kk1=0.;kk2=0;          fprintf(ficgp, "\n#********** Variable "); 
               for(i=1; i<=nlstate;i++) {                        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];              fprintf(ficgp, "**********\n#\n");
               }          
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);          
             }          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]]);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
         }          
       }          fprintf(ficresprobcor, "\n#********** Variable ");    
    }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   }          fprintf(ficresprobcor, "**********\n#");    
          }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        
         for (age=bage; age<=fage; age ++){ 
   if (popforecast==1) {          cov[2]=age;
     free_ivector(popage,0,AGESUP);          for (k=1; k<=cptcovn;k++) {
     free_vector(popeffectif,0,AGESUP);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     free_vector(popcount,0,AGESUP);          }
   }          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for (k=1; k<=cptcovprod;k++)
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   fclose(ficrespop);          
 }          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
 /***********************************************/          gp=vector(1,(nlstate)*(nlstate+ndeath));
 /**************** Main Program *****************/          gm=vector(1,(nlstate)*(nlstate+ndeath));
 /***********************************************/      
           for(theta=1; theta <=npar; theta++){
 int main(int argc, char *argv[])            for(i=1; i<=npar; i++)
 {              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   double agedeb, agefin,hf;            
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;            k=0;
             for(i=1; i<= (nlstate); i++){
   double fret;              for(j=1; j<=(nlstate+ndeath);j++){
   double **xi,tmp,delta;                k=k+1;
                 gp[k]=pmmij[i][j];
   double dum; /* Dummy variable */              }
   double ***p3mat;            }
   int *indx;            
   char line[MAXLINE], linepar[MAXLINE];            for(i=1; i<=npar; i++)
   char title[MAXLINE];              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];      
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];            pmij(pmmij,cov,ncovmodel,xp,nlstate);
              k=0;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];            for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
   char filerest[FILENAMELENGTH];                k=k+1;
   char fileregp[FILENAMELENGTH];                gm[k]=pmmij[i][j];
   char popfile[FILENAMELENGTH];              }
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];            }
   int firstobs=1, lastobs=10;       
   int sdeb, sfin; /* Status at beginning and end */            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
   int c,  h , cpt,l;              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
   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(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   int mobilav=0,popforecast=0;            for(theta=1; theta <=npar; theta++)
   int hstepm, nhstepm;              trgradg[j][theta]=gradg[theta][j];
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;          
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   double bage, fage, age, agelim, agebase;          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   double ftolpl=FTOL;          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   double **prlim;          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
   double *severity;          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   double ***param; /* Matrix of parameters */          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   double  *p;  
   double **matcov; /* Matrix of covariance */          pmij(pmmij,cov,ncovmodel,x,nlstate);
   double ***delti3; /* Scale */          
   double *delti; /* Scale */          k=0;
   double ***eij, ***vareij;          for(i=1; i<=(nlstate); i++){
   double **varpl; /* Variances of prevalence limits by age */            for(j=1; j<=(nlstate+ndeath);j++){
   double *epj, vepp;              k=k+1;
   double kk1, kk2;              mu[k][(int) age]=pmmij[i][j];
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;            }
            }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   char version[80]="Imach version 0.8a1, June 2003, INED-EUROREVES ";            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   char *alph[]={"a","a","b","c","d","e"}, str[4];              varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
   char z[1]="c", occ;            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
 #include <sys/time.h>            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
 #include <time.h>            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];            }*/
    
   /* long total_usecs;          fprintf(ficresprob,"\n%d ",(int)age);
   struct timeval start_time, end_time;          fprintf(ficresprobcov,"\n%d ",(int)age);
            fprintf(ficresprobcor,"\n%d ",(int)age);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */  
   getcwd(pathcd, size);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
   printf("\n%s",version);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   if(argc <=1){            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
     printf("\nEnter the parameter file name: ");            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     scanf("%s",pathtot);          }
   }          i=0;
   else{          for (k=1; k<=(nlstate);k++){
     strcpy(pathtot,argv[1]);            for (l=1; l<=(nlstate+ndeath);l++){ 
   }              i=i++;
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   /*cygwin_split_path(pathtot,path,optionfile);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/              for (j=1; j<=i;j++){
   /* cutv(path,optionfile,pathtot,'\\');*/                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);              }
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);            }
   chdir(path);          }/* end of loop for state */
   replace(pathc,path);        } /* end of loop for age */
   
 /*-------- arguments in the command line --------*/        /* Confidence intervalle of pij  */
         /*
   strcpy(fileres,"r");          fprintf(ficgp,"\nset noparametric;unset label");
   strcat(fileres, optionfilefiname);          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   strcat(fileres,".txt");    /* Other files have txt extension */          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
   /*---------arguments file --------*/          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
     printf("Problem with optionfile %s\n",optionfile);        */
     goto end;  
   }        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
   strcpy(filereso,"o");        for (k2=1; k2<=(nlstate);k2++){
   strcat(filereso,fileres);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
   if((ficparo=fopen(filereso,"w"))==NULL) {            if(l2==k2) continue;
     printf("Problem with Output resultfile: %s\n", filereso);goto end;            j=(k2-1)*(nlstate+ndeath)+l2;
   }            for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
   /* Reads comments: lines beginning with '#' */                if(l1==k1) continue;
   while((c=getc(ficpar))=='#' && c!= EOF){                i=(k1-1)*(nlstate+ndeath)+l1;
     ungetc(c,ficpar);                if(i<=j) continue;
     fgets(line, MAXLINE, ficpar);                for (age=bage; age<=fage; age ++){ 
     puts(line);                  if ((int)age %5==0){
     fputs(line,ficparo);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   }                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   ungetc(c,ficpar);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
   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);                    mu2=mu[j][(int) age]/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);                    c12=cv12/sqrt(v1*v2);
   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);                    /* Computing eigen value of matrix of covariance */
 while((c=getc(ficpar))=='#' && c!= EOF){                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     ungetc(c,ficpar);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     fgets(line, MAXLINE, ficpar);                    /* Eigen vectors */
     puts(line);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
     fputs(line,ficparo);                    /*v21=sqrt(1.-v11*v11); *//* error */
   }                    v21=(lc1-v1)/cv12*v11;
   ungetc(c,ficpar);                    v12=-v21;
                      v22=v11;
                        tnalp=v21/v11;
   covar=matrix(0,NCOVMAX,1,n);                    if(first1==1){
   cptcovn=0;                      first1=0;
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;                      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);
                     }
   ncovmodel=2+cptcovn;                    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);
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */                    /*printf(fignu*/
                      /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
   /* Read guess parameters */                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   /* Reads comments: lines beginning with '#' */                    if(first==1){
   while((c=getc(ficpar))=='#' && c!= EOF){                      first=0;
     ungetc(c,ficpar);                      fprintf(ficgp,"\nset parametric;unset label");
     fgets(line, MAXLINE, 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);
     puts(line);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     fputs(line,ficparo);                      fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
   }                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
   ungetc(c,ficpar);                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                        fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     for(i=1; i <=nlstate; i++)                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     for(j=1; j <=nlstate+ndeath-1; j++){                      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,"%1d%1d",&i1,&j1);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
       fprintf(ficparo,"%1d%1d",i1,j1);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
       printf("%1d%1d",i,j);                    }else{
       for(k=1; k<=ncovmodel;k++){                      first=0;
         fscanf(ficpar," %lf",&param[i][j][k]);                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
         printf(" %lf",param[i][j][k]);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
         fprintf(ficparo," %lf",param[i][j][k]);                      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",\
       fscanf(ficpar,"\n");                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
       printf("\n");                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
       fprintf(ficparo,"\n");                    }/* if first */
     }                  } /* age mod 5 */
                  } /* end loop age */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
                 first=1;
   p=param[1][1];              } /*l12 */
              } /* k12 */
   /* Reads comments: lines beginning with '#' */          } /*l1 */
   while((c=getc(ficpar))=='#' && c!= EOF){        }/* k1 */
     ungetc(c,ficpar);      } /* loop covariates */
     fgets(line, MAXLINE, ficpar);    }
     puts(line);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     fputs(line,ficparo);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   }    free_vector(xp,1,npar);
   ungetc(c,ficpar);    fclose(ficresprob);
     fclose(ficresprobcov);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    fclose(ficresprobcor);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    fclose(ficgp);
   for(i=1; i <=nlstate; i++){    fclose(fichtm);
     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);  /******************* Printing html file ***********/
       for(k=1; k<=ncovmodel;k++){  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
         fscanf(ficpar,"%le",&delti3[i][j][k]);                    int lastpass, int stepm, int weightopt, char model[],\
         printf(" %le",delti3[i][j][k]);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
         fprintf(ficparo," %le",delti3[i][j][k]);                    int popforecast, int estepm ,\
       }                    double jprev1, double mprev1,double anprev1, \
       fscanf(ficpar,"\n");                    double jprev2, double mprev2,double anprev2){
       printf("\n");    int jj1, k1, i1, cpt;
       fprintf(ficparo,"\n");    /*char optionfilehtm[FILENAMELENGTH];*/
     }    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
   }      printf("Problem with %s \n",optionfilehtm), exit(0);
   delti=delti3[1][1];      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
      }
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
     ungetc(c,ficpar);   - 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
     fgets(line, MAXLINE, ficpar);   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
     puts(line);   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
     fputs(line,ficparo);   - Life expectancies by age and initial health status (estepm=%2d months): 
   }     <a href=\"e%s\">e%s</a> <br>\n</li>", \
   ungetc(c,ficpar);    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
    
   matcov=matrix(1,npar,1,npar);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   for(i=1; i <=npar; i++){  
     fscanf(ficpar,"%s",&str);   m=cptcoveff;
     printf("%s",str);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     fprintf(ficparo,"%s",str);  
     for(j=1; j <=i; j++){   jj1=0;
       fscanf(ficpar," %le",&matcov[i][j]);   for(k1=1; k1<=m;k1++){
       printf(" %.5le",matcov[i][j]);     for(i1=1; i1<=ncodemax[k1];i1++){
       fprintf(ficparo," %.5le",matcov[i][j]);       jj1++;
     }       if (cptcovn > 0) {
     fscanf(ficpar,"\n");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     printf("\n");         for (cpt=1; cpt<=cptcoveff;cpt++) 
     fprintf(ficparo,"\n");           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   }         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   for(i=1; i <=npar; i++)       }
     for(j=i+1;j<=npar;j++)       /* Pij */
       matcov[i][j]=matcov[j][i];       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: pe%s%d1.png<br>
      <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
   printf("\n");       /* 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>
   <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
     /*-------- Rewriting paramater file ----------*/         /* Stable prevalence in each health state */
      strcpy(rfileres,"r");    /* "Rparameterfile */         for(cpt=1; cpt<nlstate;cpt++){
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
      strcat(rfileres,".");    /* */  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
      strcat(rfileres,optionfilext);    /* Other files have txt extension */         }
     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,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
     }  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
     fprintf(ficres,"#%s\n",version);       }
           fprintf(fichtm,"\n<br>- Total life expectancy by age and
     /*-------- data file ----------*/  health expectancies in states (1) and (2): e%s%d.png<br>
     if((fic=fopen(datafile,"r"))==NULL)    {  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
       printf("Problem with datafile: %s\n", datafile);goto end;     } /* end i1 */
     }   }/* End k1 */
    fprintf(fichtm,"</ul>");
     n= lastobs;  
     severity = vector(1,maxwav);  
     outcome=imatrix(1,maxwav+1,1,n);   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
     num=ivector(1,n);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
     moisnais=vector(1,n);   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
     annais=vector(1,n);   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
     moisdc=vector(1,n);   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
     andc=vector(1,n);   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
     agedc=vector(1,n);   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
     cod=ivector(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);
     weight=vector(1,n);  
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */  /*  if(popforecast==1) fprintf(fichtm,"\n */
     mint=matrix(1,maxwav,1,n);  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
     anint=matrix(1,maxwav,1,n);  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
     s=imatrix(1,maxwav+1,1,n);  /*      <br>",fileres,fileres,fileres,fileres); */
     adl=imatrix(1,maxwav+1,1,n);      /*  else  */
     tab=ivector(1,NCOVMAX);  /*    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); */
     ncodemax=ivector(1,8);  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
     i=1;   m=cptcoveff;
     while (fgets(line, MAXLINE, fic) != NULL)    {   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       if ((i >= firstobs) && (i <=lastobs)) {  
           jj1=0;
         for (j=maxwav;j>=1;j--){   for(k1=1; k1<=m;k1++){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);     for(i1=1; i1<=ncodemax[k1];i1++){
           strcpy(line,stra);       jj1++;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);       if (cptcovn > 0) {
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
         }         for (cpt=1; cpt<=cptcoveff;cpt++) 
                   fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);       }
        for(cpt=1; cpt<=nlstate;cpt++) {
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);         fprintf(fichtm,"<br>- Observed and period prevalence (with confident
         cutv(stra, strb,line,' '); moisnais[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);  
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);       }
         for (j=ncovcol;j>=1;j--){     } /* end i1 */
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);   }/* End k1 */
         }   fprintf(fichtm,"</ul>");
         num[i]=atol(stra);  fclose(fichtm);
          }
         /*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;}*/  /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
         i=i+1;  
       }    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     }    int ng;
     /* printf("ii=%d", ij);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
        scanf("%d",i);*/      printf("Problem with file %s",optionfilegnuplot);
   imx=i-1; /* Number of individuals */      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
     }
   /* for (i=1; i<=imx; i++){  
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    /*#ifdef windows */
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;      fprintf(ficgp,"cd \"%s\" \n",pathc);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;      /*#endif */
     }*/  m=pow(2,cptcoveff);
    /*  for (i=1; i<=imx; i++){    
      if (s[4][i]==9)  s[4][i]=-1;   /* 1eme*/
      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 (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) {
         fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
   /* Calculation of the number of parameter from char model*/       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);
   Tvar=ivector(1,15);  
   Tprod=ivector(1,15);       for (i=1; i<= nlstate ; i ++) {
   Tvaraff=ivector(1,15);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   Tvard=imatrix(1,15,1,2);         else fprintf(ficgp," \%%*lf (\%%*lf)");
   Tage=ivector(1,15);             }
           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);
   if (strlen(model) >1){       for (i=1; i<= nlstate ; i ++) {
     j=0, j1=0, k1=1, k2=1;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     j=nbocc(model,'+');         else fprintf(ficgp," \%%*lf (\%%*lf)");
     j1=nbocc(model,'*');       } 
     cptcovn=j+1;       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
     cptcovprod=j1;       for (i=1; i<= nlstate ; i ++) {
             if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     strcpy(modelsav,model);         else fprintf(ficgp," \%%*lf (\%%*lf)");
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){       }  
       printf("Error. Non available option model=%s ",model);       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
       goto end;     }
     }    }
        /*2 eme*/
     for(i=(j+1); i>=1;i--){    
       cutv(stra,strb,modelsav,'+');    for (k1=1; k1<= m ; k1 ++) { 
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       /*scanf("%d",i);*/      
       if (strchr(strb,'*')) {      for (i=1; i<= nlstate+1 ; i ++) {
         cutv(strd,strc,strb,'*');        k=2*i;
         if (strcmp(strc,"age")==0) {        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
           cptcovprod--;        for (j=1; j<= nlstate+1 ; j ++) {
           cutv(strb,stre,strd,'V');          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           Tvar[i]=atoi(stre);          else fprintf(ficgp," \%%*lf (\%%*lf)");
           cptcovage++;        }   
             Tage[cptcovage]=i;        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
             /*printf("stre=%s ", stre);*/        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         }        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
         else if (strcmp(strd,"age")==0) {        for (j=1; j<= nlstate+1 ; j ++) {
           cptcovprod--;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           cutv(strb,stre,strc,'V');          else fprintf(ficgp," \%%*lf (\%%*lf)");
           Tvar[i]=atoi(stre);        }   
           cptcovage++;        fprintf(ficgp,"\" t\"\" w l 0,");
           Tage[cptcovage]=i;        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
         }        for (j=1; j<= nlstate+1 ; j ++) {
         else {          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           cutv(strb,stre,strc,'V');          else fprintf(ficgp," \%%*lf (\%%*lf)");
           Tvar[i]=ncovcol+k1;        }   
           cutv(strb,strc,strd,'V');        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
           Tprod[k1]=i;        else fprintf(ficgp,"\" t\"\" w l 0,");
           Tvard[k1][1]=atoi(strc);      }
           Tvard[k1][2]=atoi(stre);    }
           Tvar[cptcovn+k2]=Tvard[k1][1];    
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    /*3eme*/
           for (k=1; k<=lastobs;k++)    
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    for (k1=1; k1<= m ; k1 ++) { 
           k1++;      for (cpt=1; cpt<= nlstate ; cpt ++) {
           k2=k2+2;        k=2+nlstate*(2*cpt-2);
         }        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
       }        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
       else {        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
        /*  scanf("%d",i);*/          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
       cutv(strd,strc,strb,'V');          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
       Tvar[i]=atoi(strc);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
       }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
       strcpy(modelsav,stra);            
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);        */
         scanf("%d",i);*/        for (i=1; i< nlstate ; i ++) {
     }          fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
 }          
          } 
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);      }
   printf("cptcovprod=%d ", cptcovprod);    }
   scanf("%d ",i);*/    
     fclose(fic);    /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
     /*  if(mle==1){*/      for (cpt=1; cpt<=nlstate ; cpt ++) {
     if (weightopt != 1) { /* Maximisation without weights*/        k=3;
       for(i=1;i<=n;i++) weight[i]=1.0;        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     }        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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
     /*-calculation of age at interview from date of interview and age at death -*/        
     agev=matrix(1,maxwav,1,imx);        for (i=1; i<= nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
     for (i=1; i<=imx; i++) {        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
       for(m=2; (m<= maxwav); m++) {        
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){        l=3+(nlstate+ndeath)*cpt;
          anint[m][i]=9999;        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
          s[m][i]=-1;        for (i=1; i< nlstate ; i ++) {
        }          l=3+(nlstate+ndeath)*cpt;
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;          fprintf(ficgp,"+$%d",l+i+1);
       }        }
     }        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     for (i=1; i<=imx; i++)  {    }  
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    
       for(m=1; (m<= maxwav); m++){    /* proba elementaires */
         if(s[m][i] >0){    for(i=1,jk=1; i <=nlstate; i++){
           if (s[m][i] >= nlstate+1) {      for(k=1; k <=(nlstate+ndeath); k++){
             if(agedc[i]>0)        if (k != i) {
               if(moisdc[i]!=99 && andc[i]!=9999)          for(j=1; j <=ncovmodel; j++){
                 agev[m][i]=agedc[i];            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/            jk++; 
            else {            fprintf(ficgp,"\n");
               if (andc[i]!=9999){          }
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        }
               agev[m][i]=-1;      }
               }     }
             }  
           }     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
           else if(s[m][i] !=9){ /* Should no more exist */       for(jk=1; jk <=m; jk++) {
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
             if(mint[m][i]==99 || anint[m][i]==9999)         if (ng==2)
               agev[m][i]=1;           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
             else if(agev[m][i] <agemin){         else
               agemin=agev[m][i];           fprintf(ficgp,"\nset title \"Probability\"\n");
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
             }         i=1;
             else if(agev[m][i] >agemax){         for(k2=1; k2<=nlstate; k2++) {
               agemax=agev[m][i];           k3=i;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/           for(k=1; k<=(nlstate+ndeath); k++) {
             }             if (k != k2){
             /*agev[m][i]=anint[m][i]-annais[i];*/               if(ng==2)
             /*   agev[m][i] = age[i]+2*m;*/                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
           }               else
           else { /* =9 */                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
             agev[m][i]=1;               ij=1;
             s[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]]]);
         else /*= 0 Unknown */                   ij++;
           agev[m][i]=1;                 }
       }                 else
                       fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
     }               }
     for (i=1; i<=imx; i++)  {               fprintf(ficgp,")/(1");
       for(m=1; (m<= maxwav); m++){               
         if (s[m][i] > (nlstate+ndeath)) {               for(k1=1; k1 <=nlstate; k1++){   
           printf("Error: Wrong value in nlstate or ndeath\n");                   fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
           goto end;                 ij=1;
         }                 for(j=3; j <=ncovmodel; j++){
       }                   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++;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);                   }
                    else
     free_vector(severity,1,maxwav);                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
     free_imatrix(outcome,1,maxwav+1,1,n);                 }
     free_vector(moisnais,1,n);                 fprintf(ficgp,")");
     free_vector(annais,1,n);               }
     /* free_matrix(mint,1,maxwav,1,n);               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
        free_matrix(anint,1,maxwav,1,n);*/               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
     free_vector(moisdc,1,n);               i=i+ncovmodel;
     free_vector(andc,1,n);             }
            } /* end k */
             } /* end k2 */
     wav=ivector(1,imx);       } /* end jk */
     dh=imatrix(1,lastpass-firstpass+1,1,imx);     } /* end ng */
     mw=imatrix(1,lastpass-firstpass+1,1,imx);     fclose(ficgp); 
      }  /* end gnuplot */
     /* Concatenates waves */  
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
       Tcode=ivector(1,100);  
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    int i, cpt, cptcod;
       ncodemax[1]=1;    int modcovmax =1;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    int mobilavrange, mob;
          double age;
    codtab=imatrix(1,100,1,10);  
    h=0;    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
    m=pow(2,cptcoveff);                             a covariate has 2 modalities */
      if (cptcovn<1) modcovmax=1; /* At least 1 pass */
    for(k=1;k<=cptcoveff; k++){  
      for(i=1; i <=(m/pow(2,k));i++){    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
        for(j=1; j <= ncodemax[k]; j++){      if(mobilav==1) mobilavrange=5; /* default */
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){      else mobilavrange=mobilav;
            h++;      for (age=bage; age<=fage; age++)
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;        for (i=1; i<=nlstate;i++)
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/          for (cptcod=1;cptcod<=modcovmax;cptcod++)
          }            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
        }      /* We keep the original values on the extreme ages bage, fage and for 
      }         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
    }         we use a 5 terms etc. until the borders are no more concerned. 
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);      */ 
       codtab[1][2]=1;codtab[2][2]=2; */      for (mob=3;mob <=mobilavrange;mob=mob+2){
    /* for(i=1; i <=m ;i++){        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
       for(k=1; k <=cptcovn; k++){          for (i=1; i<=nlstate;i++){
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);            for (cptcod=1;cptcod<=modcovmax;cptcod++){
       }              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
       printf("\n");                for (cpt=1;cpt<=(mob-1)/2;cpt++){
       }                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
       scanf("%d",i);*/                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                    }
    /* Calculates basic frequencies. Computes observed prevalence at single age              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
        and prints on file fileres'p'. */            }
           }
            }/* end age */
          }/* end mob */
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    }else return -1;
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    return 0;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  }/* End movingaverage */
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
        /************** Forecasting ******************/
     /* For Powell, parameters are in a vector p[] starting at p[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){
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    /* proj1, year, month, day of starting projection 
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */       agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
     if(mle==1){       anproj2 year of en of projection (same day and month as proj1).
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    */
     }    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
        int *popage;
     /*--------- results files --------------*/    double agec; /* generic age */
     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);    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
      double *popeffectif,*popcount;
     double ***p3mat;
    jk=1;    double ***mobaverage;
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    char fileresf[FILENAMELENGTH];
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  
    for(i=1,jk=1; i <=nlstate; i++){    agelim=AGESUP;
      for(k=1; k <=(nlstate+ndeath); k++){    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
        if (k != i)   
          {    strcpy(fileresf,"f"); 
            printf("%d%d ",i,k);    strcat(fileresf,fileres);
            fprintf(ficres,"%1d%1d ",i,k);    if((ficresf=fopen(fileresf,"w"))==NULL) {
            for(j=1; j <=ncovmodel; j++){      printf("Problem with forecast resultfile: %s\n", fileresf);
              printf("%f ",p[jk]);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
              fprintf(ficres,"%f ",p[jk]);    }
              jk++;    printf("Computing forecasting: result on file '%s' \n", fileresf);
            }    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
            printf("\n");  
            fprintf(ficres,"\n");    if (cptcoveff==0) ncodemax[cptcoveff]=1;
          }  
      }    if (mobilav!=0) {
    }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  if(mle==1){      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
     /* Computing hessian and covariance matrix */        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     ftolhess=ftol; /* Usually correct */        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     hesscov(matcov, p, npar, delti, ftolhess, func);      }
  }    }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");  
     printf("# Scales (for hessian or gradient estimation)\n");    stepsize=(int) (stepm+YEARM-1)/YEARM;
      for(i=1,jk=1; i <=nlstate; i++){    if (stepm<=12) stepsize=1;
       for(j=1; j <=nlstate+ndeath; j++){    if(estepm < stepm){
         if (j!=i) {      printf ("Problem %d lower than %d\n",estepm, stepm);
           fprintf(ficres,"%1d%1d",i,j);    }
           printf("%1d%1d",i,j);    else  hstepm=estepm;   
           for(k=1; k<=ncovmodel;k++){  
             printf(" %.5e",delti[jk]);    hstepm=hstepm/stepm; 
             fprintf(ficres," %.5e",delti[jk]);    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
             jk++;                                 fractional in yp1 */
           }    anprojmean=yp;
           printf("\n");    yp2=modf((yp1*12),&yp);
           fprintf(ficres,"\n");    mprojmean=yp;
         }    yp1=modf((yp2*30.5),&yp);
       }    jprojmean=yp;
      }    if(jprojmean==0) jprojmean=1;
        if(mprojmean==0) jprojmean=1;
     k=1;  
     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");    i1=cptcoveff;
     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 (cptcovn < 1){i1=1;}
     for(i=1;i<=npar;i++){    
       /*  if (k>nlstate) k=1;    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
       i1=(i-1)/(ncovmodel*nlstate)+1;    
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    fprintf(ficresf,"#****** Routine prevforecast **\n");
       printf("%s%d%d",alph[k],i1,tab[i]);*/  
       fprintf(ficres,"%3d",i);  /*            if (h==(int)(YEARM*yearp)){ */
       printf("%3d",i);    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(j=1; j<=i;j++){      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         fprintf(ficres," %.5e",matcov[i][j]);        k=k+1;
         printf(" %.5e",matcov[i][j]);        fprintf(ficresf,"\n#******");
       }        for(j=1;j<=cptcoveff;j++) {
       fprintf(ficres,"\n");          fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       printf("\n");        }
       k++;        fprintf(ficresf,"******\n");
     }        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
            for(j=1; j<=nlstate+ndeath;j++){ 
     while((c=getc(ficpar))=='#' && c!= EOF){          for(i=1; i<=nlstate;i++)              
       ungetc(c,ficpar);            fprintf(ficresf," p%d%d",i,j);
       fgets(line, MAXLINE, ficpar);          fprintf(ficresf," p.%d",j);
       puts(line);        }
       fputs(line,ficparo);        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
     }          fprintf(ficresf,"\n");
     ungetc(c,ficpar);          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
     estepm=0;  
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);          for (agec=fage; agec>=(ageminpar-1); agec--){ 
     if (estepm==0 || estepm < stepm) estepm=stepm;            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
     if (fage <= 2) {            nhstepm = nhstepm/hstepm; 
       bage = ageminpar;            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fage = agemaxpar;            oldm=oldms;savm=savms;
     }            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
              
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");            for (h=0; h<=nhstepm; h++){
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);              if (h*hstepm/YEARM*stepm ==yearp) {
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                fprintf(ficresf,"\n");
                  for(j=1;j<=cptcoveff;j++) 
     while((c=getc(ficpar))=='#' && c!= EOF){                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
     ungetc(c,ficpar);                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
     fgets(line, MAXLINE, ficpar);              } 
     puts(line);              for(j=1; j<=nlstate+ndeath;j++) {
     fputs(line,ficparo);                ppij=0.;
   }                for(i=1; i<=nlstate;i++) {
   ungetc(c,ficpar);                  if (mobilav==1) 
                      ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);                  else {
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                  }
                        if (h*hstepm/YEARM*stepm== yearp) {
   while((c=getc(ficpar))=='#' && c!= EOF){                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
     ungetc(c,ficpar);                  }
     fgets(line, MAXLINE, ficpar);                } /* end i */
     puts(line);                if (h*hstepm/YEARM*stepm==yearp) {
     fputs(line,ficparo);                  fprintf(ficresf," %.3f", ppij);
   }                }
   ungetc(c,ficpar);              }/* end j */
              } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    dateprev1=anprev1+mprev1/12.+jprev1/365.;          } /* end agec */
    dateprev2=anprev2+mprev2/12.+jprev2/365.;        } /* end yearp */
       } /* end cptcod */
   fscanf(ficpar,"pop_based=%d\n",&popbased);    } /* end  cptcov */
   fprintf(ficparo,"pop_based=%d\n",popbased);           
   fprintf(ficres,"pop_based=%d\n",popbased);      if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    
   while((c=getc(ficpar))=='#' && c!= EOF){    fclose(ficresf);
     ungetc(c,ficpar);  }
     fgets(line, MAXLINE, ficpar);  
     puts(line);  /************** Forecasting *****not tested NB*************/
     fputs(line,ficparo);  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){
   }    
   ungetc(c,ficpar);    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
   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);    double calagedatem, agelim, kk1, kk2;
 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);    double *popeffectif,*popcount;
 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);    double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
 while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fgets(line, MAXLINE, ficpar);    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     puts(line);    agelim=AGESUP;
     fputs(line,ficparo);    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
   }    
   ungetc(c,ficpar);    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
   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);    strcpy(filerespop,"pop"); 
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
 /*------------ gnuplot -------------*/    }
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);    printf("Computing forecasting: result on file '%s' \n", filerespop);
      fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
 /*------------ free_vector  -------------*/  
  chdir(path);    if (cptcoveff==0) ncodemax[cptcoveff]=1;
    
  free_ivector(wav,1,imx);    if (mobilav!=0) {
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);        if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
  free_ivector(num,1,n);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
  free_vector(agedc,1,n);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/      }
  fclose(ficparo);    }
  fclose(ficres);  
     stepsize=(int) (stepm+YEARM-1)/YEARM;
 /*--------- index.htm --------*/    if (stepm<=12) stepsize=1;
     
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);    agelim=AGESUP;
     
      hstepm=1;
   /*--------------- Prevalence limit --------------*/    hstepm=hstepm/stepm; 
      
   strcpy(filerespl,"pl");    if (popforecast==1) {
   strcat(filerespl,fileres);      if((ficpop=fopen(popfile,"r"))==NULL) {
   if((ficrespl=fopen(filerespl,"w"))==NULL) {        printf("Problem with population file : %s\n",popfile);exit(0);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
   }      } 
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      popage=ivector(0,AGESUP);
   fprintf(ficrespl,"#Prevalence limit\n");      popeffectif=vector(0,AGESUP);
   fprintf(ficrespl,"#Age ");      popcount=vector(0,AGESUP);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      
   fprintf(ficrespl,"\n");      i=1;   
        while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
   prlim=matrix(1,nlstate,1,nlstate);     
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      imx=i;
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
   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(cptcov=1,k=0;cptcov<=i2;cptcov++){
   k=0;     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   agebase=ageminpar;        k=k+1;
   agelim=agemaxpar;        fprintf(ficrespop,"\n#******");
   ftolpl=1.e-10;        for(j=1;j<=cptcoveff;j++) {
   i1=cptcoveff;          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   if (cptcovn < 1){i1=1;}        }
         fprintf(ficrespop,"******\n");
   for(cptcov=1;cptcov<=i1;cptcov++){        fprintf(ficrespop,"# Age");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         k=k+1;        if (popforecast==1)  fprintf(ficrespop," [Population]");
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/        
         fprintf(ficrespl,"\n#******");        for (cpt=0; cpt<=0;cpt++) { 
         for(j=1;j<=cptcoveff;j++)          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          
         fprintf(ficrespl,"******\n");          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
                    nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
         for (age=agebase; age<=agelim; age++){            nhstepm = nhstepm/hstepm; 
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            
           fprintf(ficrespl,"%.0f",age );            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           for(i=1; i<=nlstate;i++)            oldm=oldms;savm=savms;
           fprintf(ficrespl," %.5f", prlim[i][i]);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespl,"\n");          
         }            for (h=0; h<=nhstepm; h++){
       }              if (h==(int) (calagedatem+YEARM*cpt)) {
     }                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
   fclose(ficrespl);              } 
               for(j=1; j<=nlstate+ndeath;j++) {
   /*------------- h Pij x at various ages ------------*/                kk1=0.;kk2=0;
                  for(i=1; i<=nlstate;i++) {              
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);                  if (mobilav==1) 
   if((ficrespij=fopen(filerespij,"w"))==NULL) {                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;                  else {
   }                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
   printf("Computing pij: result on file '%s' \n", filerespij);                  }
                  }
   stepsize=(int) (stepm+YEARM-1)/YEARM;                if (h==(int)(calagedatem+12*cpt)){
   /*if (stepm<=24) stepsize=2;*/                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
   agelim=AGESUP;                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
   hstepm=stepsize*YEARM; /* Every year of age */                }
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */              }
                for(i=1; i<=nlstate;i++){
   k=0;                kk1=0.;
   for(cptcov=1;cptcov<=i1;cptcov++){                  for(j=1; j<=nlstate;j++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
       k=k+1;                  }
         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(j=1;j<=cptcoveff;j++)              }
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespij,"******\n");              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                        fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */            }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          }
           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,"# Age");  
           for(i=1; i<=nlstate;i++)        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
             for(j=1; j<=nlstate+ndeath;j++)          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
               fprintf(ficrespij," %1d-%1d",i,j);          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
           fprintf(ficrespij,"\n");            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
            for (h=0; h<=nhstepm; h++){            nhstepm = nhstepm/hstepm; 
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );            
             for(i=1; i<=nlstate;i++)            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
               for(j=1; j<=nlstate+ndeath;j++)            oldm=oldms;savm=savms;
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"\n");            for (h=0; h<=nhstepm; h++){
              }              if (h==(int) (calagedatem+YEARM*cpt)) {
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
           fprintf(ficrespij,"\n");              } 
         }              for(j=1; j<=nlstate+ndeath;j++) {
     }                kk1=0.;kk2=0;
   }                for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);                }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
   fclose(ficrespij);              }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /*---------- Forecasting ------------------*/          }
   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);    }
   }   
   else{    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     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 (popforecast==1) {
   }      free_ivector(popage,0,AGESUP);
        free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
   /*---------- Health expectancies and variances ------------*/    }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   strcpy(filerest,"t");    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   strcat(filerest,fileres);    fclose(ficrespop);
   if((ficrest=fopen(filerest,"w"))==NULL) {  }
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;  
   }  /***********************************************/
   printf("Computing Total LEs with variances: file '%s' \n", filerest);  /**************** Main Program *****************/
   /***********************************************/
   
   strcpy(filerese,"e");  int main(int argc, char *argv[])
   strcat(filerese,fileres);  {
   if((ficreseij=fopen(filerese,"w"))==NULL) {    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
   }    double agedeb, agefin,hf;
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
  strcpy(fileresv,"v");    double fret;
   strcat(fileresv,fileres);    double **xi,tmp,delta;
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    double dum; /* Dummy variable */
   }    double ***p3mat;
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    double ***mobaverage;
   calagedate=-1;    int *indx;
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    char line[MAXLINE], linepar[MAXLINE];
     char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
   k=0;    int firstobs=1, lastobs=10;
   for(cptcov=1;cptcov<=i1;cptcov++){    int sdeb, sfin; /* Status at beginning and end */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    int c,  h , cpt,l;
       k=k+1;    int ju,jl, mi;
       fprintf(ficrest,"\n#****** ");    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
       for(j=1;j<=cptcoveff;j++)    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
       fprintf(ficrest,"******\n");    int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
       fprintf(ficreseij,"\n#****** ");    double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
       for(j=1;j<=cptcoveff;j++)    double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficreseij,"******\n");    double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
       fprintf(ficresvij,"\n#****** ");    double **prlim;
       for(j=1;j<=cptcoveff;j++)    double *severity;
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double ***param; /* Matrix of parameters */
       fprintf(ficresvij,"******\n");    double  *p;
     double **matcov; /* Matrix of covariance */
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    double ***delti3; /* Scale */
       oldm=oldms;savm=savms;    double *delti; /* Scale */
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);      double ***eij, ***vareij;
      double **varpl; /* Variances of prevalence limits by age */
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    double *epj, vepp;
       oldm=oldms;savm=savms;    double kk1, kk2;
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
      
     char *alph[]={"a","a","b","c","d","e"}, str[4];
    
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");  
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    char z[1]="c", occ;
       fprintf(ficrest,"\n");  #include <sys/time.h>
   #include <time.h>
       epj=vector(1,nlstate+1);    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
       for(age=bage; age <=fage ;age++){   
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    /* long total_usecs;
         if (popbased==1) {       struct timeval start_time, end_time;
           for(i=1; i<=nlstate;i++)    
             prlim[i][i]=probs[(int)age][i][k];       gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
         }    getcwd(pathcd, size);
          
         fprintf(ficrest," %4.0f",age);    printf("\n%s\n%s",version,fullversion);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    if(argc <=1){
           for(i=1, epj[j]=0.;i <=nlstate;i++) {      printf("\nEnter the parameter file name: ");
             epj[j] += prlim[i][i]*eij[i][j][(int)age];      scanf("%s",pathtot);
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    }
           }    else{
           epj[nlstate+1] +=epj[j];      strcpy(pathtot,argv[1]);
         }    }
     /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
         for(i=1, vepp=0.;i <=nlstate;i++)    /*cygwin_split_path(pathtot,path,optionfile);
           for(j=1;j <=nlstate;j++)      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
             vepp += vareij[i][j][(int)age];    /* cutv(path,optionfile,pathtot,'\\');*/
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));  
         for(j=1;j <=nlstate;j++){    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
         }    chdir(path);
         fprintf(ficrest,"\n");    replace(pathc,path);
       }  
     }    /*-------- arguments in the command line --------*/
   }  
 free_matrix(mint,1,maxwav,1,n);    /* Log file */
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    strcat(filelog, optionfilefiname);
     free_vector(weight,1,n);    strcat(filelog,".log");    /* */
   fclose(ficreseij);    if((ficlog=fopen(filelog,"w"))==NULL)    {
   fclose(ficresvij);      printf("Problem with logfile %s\n",filelog);
   fclose(ficrest);      goto end;
   fclose(ficpar);    }
   free_vector(epj,1,nlstate+1);    fprintf(ficlog,"Log filename:%s\n",filelog);
      fprintf(ficlog,"\n%s",version);
   /*------- Variance limit prevalence------*/      fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   strcpy(fileresvpl,"vpl");    fflush(ficlog);
   strcat(fileresvpl,fileres);  
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    /* */
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    strcpy(fileres,"r");
     exit(0);    strcat(fileres, optionfilefiname);
   }    strcat(fileres,".txt");    /* Other files have txt extension */
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  
     /*---------arguments file --------*/
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){    if((ficpar=fopen(optionfile,"r"))==NULL)    {
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      printf("Problem with optionfile %s\n",optionfile);
       k=k+1;      fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fprintf(ficresvpl,"\n#****** ");      goto end;
       for(j=1;j<=cptcoveff;j++)    }
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficresvpl,"******\n");    strcpy(filereso,"o");
          strcat(filereso,fileres);
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    if((ficparo=fopen(filereso,"w"))==NULL) {
       oldm=oldms;savm=savms;      printf("Problem with Output resultfile: %s\n", filereso);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
     }      goto end;
  }    }
   
   fclose(ficresvpl);    /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
   /*---------- End : free ----------------*/      ungetc(c,ficpar);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      fgets(line, MAXLINE, ficpar);
        puts(line);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      fputs(line,ficparo);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    }
      ungetc(c,ficpar);
    
   free_matrix(pmmij,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(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    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_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    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(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    while((c=getc(ficpar))=='#' && c!= EOF){
        ungetc(c,ficpar);
   free_matrix(matcov,1,npar,1,npar);      fgets(line, MAXLINE, ficpar);
   free_vector(delti,1,npar);      puts(line);
   free_matrix(agev,1,maxwav,1,imx);      fputs(line,ficparo);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    }
     ungetc(c,ficpar);
   if(erreur >0)    
     printf("End of Imach with error or warning %d\n",erreur);     
   else   printf("End of Imach\n");    covar=matrix(0,NCOVMAX,1,n); 
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
      if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   /* 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);*/    ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
   /*------ End -----------*/    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     
     /* Read guess parameters */
  end:    /* Reads comments: lines beginning with '#' */
   /* chdir(pathcd);*/    while((c=getc(ficpar))=='#' && c!= EOF){
  /*system("wgnuplot graph.plt");*/      ungetc(c,ficpar);
  /*system("../gp37mgw/wgnuplot graph.plt");*/      fgets(line, MAXLINE, ficpar);
  /*system("cd ../gp37mgw");*/      puts(line);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/      fputs(line,ficparo);
  strcpy(plotcmd,GNUPLOTPROGRAM);    }
  strcat(plotcmd," ");    ungetc(c,ficpar);
  strcat(plotcmd,optionfilegnuplot);    
  system(plotcmd);    param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++)
  /*#ifdef windows*/      for(j=1; j <=nlstate+ndeath-1; j++){
   while (z[0] != 'q') {        fscanf(ficpar,"%1d%1d",&i1,&j1);
     /* chdir(path); */        fprintf(ficparo,"%1d%1d",i1,j1);
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");        if(mle==1)
     scanf("%s",z);          printf("%1d%1d",i,j);
     if (z[0] == 'c') system("./imach");        fprintf(ficlog,"%1d%1d",i,j);
     else if (z[0] == 'e') system(optionfilehtm);        for(k=1; k<=ncovmodel;k++){
     else if (z[0] == 'g') system(plotcmd);          fscanf(ficpar," %lf",&param[i][j][k]);
     else if (z[0] == 'q') exit(0);          if(mle==1){
   }            printf(" %lf",param[i][j][k]);
   /*#endif */            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.1.41.2.2  
changed lines
  Added in v.1.81

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