Diff for /imach/src/imach.c between versions 1.45 and 1.74

version 1.45, 2002/05/24 16:34:18 version 1.74, 2003/05/02 18:51:41
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain     Interpolated Markov Chain
   
   Short summary of the programme:    Short summary of the programme:
      
   This program computes Healthy Life Expectancies from    This program computes Healthy Life Expectancies from
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   first survey ("cross") where individuals from different ages are    first survey ("cross") where individuals from different ages are
   interviewed on their health status or degree of disability (in the    interviewed on their health status or degree of disability (in the
   case of a health survey which is our main interest) -2- at least a    case of a health survey which is our main interest) -2- at least a
   second wave of interviews ("longitudinal") which measure each change    second wave of interviews ("longitudinal") which measure each change
   (if any) in individual health status.  Health expectancies are    (if any) in individual health status.  Health expectancies are
   computed from the time spent in each health state according to a    computed from the time spent in each health state according to a
   model. More health states you consider, more time is necessary to reach the    model. More health states you consider, more time is necessary to reach the
   Maximum Likelihood of the parameters involved in the model.  The    Maximum Likelihood of the parameters involved in the model.  The
   simplest model is the multinomial logistic model where pij is the    simplest model is the multinomial logistic model where pij is the
   probability to be observed in state j at the second wave    probability to be observed in state j at the second wave
   conditional to be observed in state i at the first wave. Therefore    conditional to be observed in state i at the first wave. Therefore
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   'age' is age and 'sex' is a covariate. If you want to have a more    'age' is age and 'sex' is a covariate. If you want to have a more
   complex model than "constant and age", you should modify the program    complex model than "constant and age", you should modify the program
   where the markup *Covariates have to be included here again* invites    where the markup *Covariates have to be included here again* invites
   you to do it.  More covariates you add, slower the    you to do it.  More covariates you add, slower the
   convergence.    convergence.
   
   The advantage of this computer programme, compared to a simple    The advantage of this computer programme, compared to a simple
   multinomial logistic model, is clear when the delay between waves is not    multinomial logistic model, is clear when the delay between waves is not
   identical for each individual. Also, if a individual missed an    identical for each individual. Also, if a individual missed an
   intermediate interview, the information is lost, but taken into    intermediate interview, the information is lost, but taken into
   account using an interpolation or extrapolation.      account using an interpolation or extrapolation.  
   
   hPijx is the probability to be observed in state i at age x+h    hPijx is the probability to be observed in state i at age x+h
   conditional to the observed state i at age x. The delay 'h' can be    conditional to the observed state i at age x. The delay 'h' can be
   split into an exact number (nh*stepm) of unobserved intermediate    split into an exact number (nh*stepm) of unobserved intermediate
   states. This elementary transition (by month or quarter trimester,    states. This elementary transition (by month, quarter,
   semester or year) is model as a multinomial logistic.  The hPx    semester or year) is modelled as a multinomial logistic.  The hPx
   matrix is simply the matrix product of nh*stepm elementary matrices    matrix is simply the matrix product of nh*stepm elementary matrices
   and the contribution of each individual to the likelihood is simply    and the contribution of each individual to the likelihood is simply
   hPijx.    hPijx.
   
   Also this programme outputs the covariance matrix of the parameters but also    Also this programme outputs the covariance matrix of the parameters but also
   of the life expectancies. It also computes the prevalence limits.    of the life expectancies. It also computes the stable prevalence. 
      
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
            Institut national d'études démographiques, Paris.             Institut national d'études démographiques, Paris.
   This software have been partly granted by Euro-REVES, a concerted action    This software have been partly granted by Euro-REVES, a concerted action
   from the European Union.    from the European Union.
   It is copyrighted identically to a GNU software product, ie programme and    It is copyrighted identically to a GNU software product, ie programme and
   software can be distributed freely for non commercial use. Latest version    software can be distributed freely for non commercial use. Latest version
   can be accessed at http://euroreves.ined.fr/imach .    can be accessed at http://euroreves.ined.fr/imach .
   **********************************************************************/  
      Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #include <math.h>    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #include <stdio.h>    
 #include <stdlib.h>    **********************************************************************/
 #include <unistd.h>  /*
     main
 #define MAXLINE 256    read parameterfile
 #define GNUPLOTPROGRAM "gnuplot"    read datafile
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    concatwav
 #define FILENAMELENGTH 80    if (mle >= 1)
 /*#define DEBUG*/      mlikeli
 #define windows    print results files
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    if mle==1 
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */       computes hessian
     read end of parameter file: agemin, agemax, bage, fage, estepm
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */        begin-prev-date,...
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    open gnuplot file
     open html file
 #define NINTERVMAX 8    stable prevalence
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */     for age prevalim()
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    h Pij x
 #define NCOVMAX 8 /* Maximum number of covariates */    variance of p varprob
 #define MAXN 20000    forecasting if prevfcast==1 prevforecast call prevalence()
 #define YEARM 12. /* Number of months per year */    health expectancies
 #define AGESUP 130    Variance-covariance of DFLE
 #define AGEBASE 40    prevalence()
      movingaverage()
     varevsij() 
 int erreur; /* Error number */    if popbased==1 varevsij(,popbased)
 int nvar;    total life expectancies
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Variance of stable prevalence
 int npar=NPARMAX;   end
 int nlstate=2; /* Number of live states */  */
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;  
    
 int *wav; /* Number of waves for this individuual 0 is possible */  #include <math.h>
 int maxwav; /* Maxim number of waves */  #include <stdio.h>
 int jmin, jmax; /* min, max spacing between 2 waves */  #include <stdlib.h>
 int mle, weightopt;  #include <unistd.h>
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  #define MAXLINE 256
 double jmean; /* Mean space between 2 waves */  #define GNUPLOTPROGRAM "gnuplot"
 double **oldm, **newm, **savm; /* Working pointers to matrices */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  #define FILENAMELENGTH 80
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  /*#define DEBUG*/
 FILE *ficgp,*ficresprob,*ficpop;  #define windows
 FILE *ficreseij;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   char filerese[FILENAMELENGTH];  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
  FILE  *ficresvij;  
   char fileresv[FILENAMELENGTH];  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
  FILE  *ficresvpl;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   char fileresvpl[FILENAMELENGTH];  
   #define NINTERVMAX 8
 #define NR_END 1  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #define FREE_ARG char*  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #define FTOL 1.0e-10  #define NCOVMAX 8 /* Maximum number of covariates */
   #define MAXN 20000
 #define NRANSI  #define YEARM 12. /* Number of months per year */
 #define ITMAX 200  #define AGESUP 130
   #define AGEBASE 40
 #define TOL 2.0e-4  #ifdef windows
   #define DIRSEPARATOR '\\'
 #define CGOLD 0.3819660  #define ODIRSEPARATOR '/'
 #define ZEPS 1.0e-10  #else
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  #define DIRSEPARATOR '/'
   #define ODIRSEPARATOR '\\'
 #define GOLD 1.618034  #endif
 #define GLIMIT 100.0  
 #define TINY 1.0e-20  char version[80]="Imach version 0.95, February 2003, INED-EUROREVES ";
   int erreur; /* Error number */
 static double maxarg1,maxarg2;  int nvar;
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  int npar=NPARMAX;
    int nlstate=2; /* Number of live states */
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  int ndeath=1; /* Number of dead states */
 #define rint(a) floor(a+0.5)  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int popbased=0;
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  int *wav; /* Number of waves for this individuual 0 is possible */
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  int maxwav; /* Maxim number of waves */
   int jmin, jmax; /* min, max spacing between 2 waves */
 int imx;  int mle, weightopt;
 int stepm;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 /* Stepm, step in month: minimum step interpolation*/  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 int estepm;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  double jmean; /* Mean space between 2 waves */
   double **oldm, **newm, **savm; /* Working pointers to matrices */
 int m,nb;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  FILE *ficlog;
 double **pmmij, ***probs, ***mobaverage;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 double dateintmean=0;  FILE *ficresprobmorprev;
   FILE *fichtm; /* Html File */
 double *weight;  FILE *ficreseij;
 int **s; /* Status */  char filerese[FILENAMELENGTH];
 double *agedc, **covar, idx;  FILE  *ficresvij;
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  char fileresv[FILENAMELENGTH];
   FILE  *ficresvpl;
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  char fileresvpl[FILENAMELENGTH];
 double ftolhess; /* Tolerance for computing hessian */  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 /**************** split *************************/  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
    char *s;                             /* pointer */  char filelog[FILENAMELENGTH]; /* Log file */
    int  l1, l2;                         /* length counters */  char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
    l1 = strlen( path );                 /* length of path */  char popfile[FILENAMELENGTH];
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
 #ifdef windows  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
    s = strrchr( path, '\\' );           /* find last / */  
 #else  #define NR_END 1
    s = strrchr( path, '/' );            /* find last / */  #define FREE_ARG char*
 #endif  #define FTOL 1.0e-10
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */  #define NRANSI 
       extern char       *getwd( );  #define ITMAX 200 
   
       if ( getwd( dirc ) == NULL ) {  #define TOL 2.0e-4 
 #else  
       extern char       *getcwd( );  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 #endif  
          return( GLOCK_ERROR_GETCWD );  #define GOLD 1.618034 
       }  #define GLIMIT 100.0 
       strcpy( name, path );             /* we've got it */  #define TINY 1.0e-20 
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */  static double maxarg1,maxarg2;
       l2 = strlen( s );                 /* length of filename */  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       strcpy( name, s );                /* save file name */    
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
       dirc[l1-l2] = 0;                  /* add zero */  #define rint(a) floor(a+0.5)
    }  
    l1 = strlen( dirc );                 /* length of directory */  static double sqrarg;
 #ifdef windows  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 #else  
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  int imx; 
 #endif  int stepm;
    s = strrchr( name, '.' );            /* find last / */  /* Stepm, step in month: minimum step interpolation*/
    s++;  
    strcpy(ext,s);                       /* save extension */  int estepm;
    l1= strlen( name);  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
    l2= strlen( s)+1;  
    strncpy( finame, name, l1-l2);  int m,nb;
    finame[l1-l2]= 0;  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
    return( 0 );                         /* we're done */  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 }  double **pmmij, ***probs;
   double dateintmean=0;
   
 /******************************************/  double *weight;
   int **s; /* Status */
 void replace(char *s, char*t)  double *agedc, **covar, idx;
 {  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   int i;  
   int lg=20;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   i=0;  double ftolhess; /* Tolerance for computing hessian */
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {  /**************** split *************************/
     (s[i] = t[i]);  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     if (t[i]== '\\') s[i]='/';  {
   }    char  *ss;                            /* pointer */
 }    int   l1, l2;                         /* length counters */
   
 int nbocc(char *s, char occ)    l1 = strlen(path );                   /* length of path */
 {    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   int i,j=0;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   int lg=20;    if ( ss == NULL ) {                   /* no directory, so use current */
   i=0;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   lg=strlen(s);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   for(i=0; i<= lg; i++) {      /* get current working directory */
   if  (s[i] == occ ) j++;      /*    extern  char* getcwd ( char *buf , int len);*/
   }      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   return j;        return( GLOCK_ERROR_GETCWD );
 }      }
       strcpy( name, path );               /* we've got it */
 void cutv(char *u,char *v, char*t, char occ)    } else {                              /* strip direcotry from path */
 {      ss++;                               /* after this, the filename */
   int i,lg,j,p=0;      l2 = strlen( ss );                  /* length of filename */
   i=0;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   for(j=0; j<=strlen(t)-1; j++) {      strcpy( name, ss );         /* save file name */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   }      dirc[l1-l2] = 0;                    /* add zero */
     }
   lg=strlen(t);    l1 = strlen( dirc );                  /* length of directory */
   for(j=0; j<p; j++) {  #ifdef windows
     (u[j] = t[j]);    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   }  #else
      u[p]='\0';    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   #endif
    for(j=0; j<= lg; j++) {    ss = strrchr( name, '.' );            /* find last / */
     if (j>=(p+1))(v[j-p-1] = t[j]);    ss++;
   }    strcpy(ext,ss);                       /* save extension */
 }    l1= strlen( name);
     l2= strlen(ss)+1;
 /********************** nrerror ********************/    strncpy( finame, name, l1-l2);
     finame[l1-l2]= 0;
 void nrerror(char error_text[])    return( 0 );                          /* we're done */
 {  }
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);  
   exit(1);  /******************************************/
 }  
 /*********************** vector *******************/  void replace(char *s, char*t)
 double *vector(int nl, int nh)  {
 {    int i;
   double *v;    int lg=20;
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    i=0;
   if (!v) nrerror("allocation failure in vector");    lg=strlen(t);
   return v-nl+NR_END;    for(i=0; i<= lg; i++) {
 }      (s[i] = t[i]);
       if (t[i]== '\\') s[i]='/';
 /************************ free vector ******************/    }
 void free_vector(double*v, int nl, int nh)  }
 {  
   free((FREE_ARG)(v+nl-NR_END));  int nbocc(char *s, char occ)
 }  {
     int i,j=0;
 /************************ivector *******************************/    int lg=20;
 int *ivector(long nl,long nh)    i=0;
 {    lg=strlen(s);
   int *v;    for(i=0; i<= lg; i++) {
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    if  (s[i] == occ ) j++;
   if (!v) nrerror("allocation failure in ivector");    }
   return v-nl+NR_END;    return j;
 }  }
   
 /******************free ivector **************************/  void cutv(char *u,char *v, char*t, char occ)
 void free_ivector(int *v, long nl, long nh)  {
 {    /* cuts string t into u and v where u is ended by char occ excluding it
   free((FREE_ARG)(v+nl-NR_END));       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 }       gives u="abcedf" and v="ghi2j" */
     int i,lg,j,p=0;
 /******************* imatrix *******************************/    i=0;
 int **imatrix(long nrl, long nrh, long ncl, long nch)    for(j=0; j<=strlen(t)-1; j++) {
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 {    }
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;    lg=strlen(t);
      for(j=0; j<p; j++) {
   /* allocate pointers to rows */      (u[j] = t[j]);
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    }
   if (!m) nrerror("allocation failure 1 in matrix()");       u[p]='\0';
   m += NR_END;  
   m -= nrl;     for(j=0; j<= lg; j++) {
        if (j>=(p+1))(v[j-p-1] = t[j]);
      }
   /* allocate rows and set pointers to them */  }
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  /********************** nrerror ********************/
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  void nrerror(char error_text[])
    {
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    fprintf(stderr,"ERREUR ...\n");
      fprintf(stderr,"%s\n",error_text);
   /* return pointer to array of pointers to rows */    exit(EXIT_FAILURE);
   return m;  }
 }  /*********************** vector *******************/
   double *vector(int nl, int nh)
 /****************** free_imatrix *************************/  {
 void free_imatrix(m,nrl,nrh,ncl,nch)    double *v;
       int **m;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       long nch,ncl,nrh,nrl;    if (!v) nrerror("allocation failure in vector");
      /* free an int matrix allocated by imatrix() */    return v-nl+NR_END;
 {  }
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));  /************************ free vector ******************/
 }  void free_vector(double*v, int nl, int nh)
   {
 /******************* matrix *******************************/    free((FREE_ARG)(v+nl-NR_END));
 double **matrix(long nrl, long nrh, long ncl, long nch)  }
 {  
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  /************************ivector *******************************/
   double **m;  int *ivector(long nl,long nh)
   {
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    int *v;
   if (!m) nrerror("allocation failure 1 in matrix()");    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   m += NR_END;    if (!v) nrerror("allocation failure in ivector");
   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 ivector **************************/
   m[nrl] += NR_END;  void free_ivector(int *v, long nl, long 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;  
 }  /******************* imatrix *******************************/
   int **imatrix(long nrl, long nrh, long ncl, long nch) 
 /*************************free matrix ************************/       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  { 
 {    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    int **m; 
   free((FREE_ARG)(m+nrl-NR_END));    
 }    /* allocate pointers to rows */ 
     m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 /******************* ma3x *******************************/    if (!m) nrerror("allocation failure 1 in matrix()"); 
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    m += NR_END; 
 {    m -= nrl; 
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    
   double ***m;    
     /* allocate rows and set pointers to them */ 
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   if (!m) nrerror("allocation failure 1 in matrix()");    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   m += NR_END;    m[nrl] += NR_END; 
   m -= nrl;    m[nrl] -= ncl; 
     
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    
   m[nrl] += NR_END;    /* return pointer to array of pointers to rows */ 
   m[nrl] -= ncl;    return m; 
   } 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   /****************** free_imatrix *************************/
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  void free_imatrix(m,nrl,nrh,ncl,nch)
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");        int **m;
   m[nrl][ncl] += NR_END;        long nch,ncl,nrh,nrl; 
   m[nrl][ncl] -= nll;       /* free an int matrix allocated by imatrix() */ 
   for (j=ncl+1; j<=nch; j++)  { 
     m[nrl][j]=m[nrl][j-1]+nlay;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
      free((FREE_ARG) (m+nrl-NR_END)); 
   for (i=nrl+1; i<=nrh; i++) {  } 
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)  /******************* matrix *******************************/
       m[i][j]=m[i][j-1]+nlay;  double **matrix(long nrl, long nrh, long ncl, long nch)
   }  {
   return m;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 }    double **m;
   
 /*************************free ma3x ************************/    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    if (!m) nrerror("allocation failure 1 in matrix()");
 {    m += NR_END;
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    m -= nrl;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
 /***************** f1dim *************************/    m[nrl] -= ncl;
 extern int ncom;  
 extern double *pcom,*xicom;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 extern double (*nrfunc)(double []);    return m;
      /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
 double f1dim(double x)     */
 {  }
   int j;  
   double f;  /*************************free matrix ************************/
   double *xt;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
    {
   xt=vector(1,ncom);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    free((FREE_ARG)(m+nrl-NR_END));
   f=(*nrfunc)(xt);  }
   free_vector(xt,1,ncom);  
   return f;  /******************* ma3x *******************************/
 }  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   {
 /*****************brent *************************/    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    double ***m;
 {  
   int iter;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double a,b,d,etemp;    if (!m) nrerror("allocation failure 1 in matrix()");
   double fu,fv,fw,fx;    m += NR_END;
   double ftemp;    m -= nrl;
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
      if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   a=(ax < cx ? ax : cx);    m[nrl] += NR_END;
   b=(ax > cx ? ax : cx);    m[nrl] -= ncl;
   x=w=v=bx;  
   fw=fv=fx=(*f)(x);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   for (iter=1;iter<=ITMAX;iter++) {  
     xm=0.5*(a+b);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    m[nrl][ncl] += NR_END;
     printf(".");fflush(stdout);    m[nrl][ncl] -= nll;
 #ifdef DEBUG    for (j=ncl+1; j<=nch; j++) 
     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);      m[nrl][j]=m[nrl][j-1]+nlay;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    
 #endif    for (i=nrl+1; i<=nrh; i++) {
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       *xmin=x;      for (j=ncl+1; j<=nch; j++) 
       return fx;        m[i][j]=m[i][j-1]+nlay;
     }    }
     ftemp=fu;    return m; 
     if (fabs(e) > tol1) {    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       r=(x-w)*(fx-fv);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       q=(x-v)*(fx-fw);    */
       p=(x-v)*q-(x-w)*r;  }
       q=2.0*(q-r);  
       if (q > 0.0) p = -p;  /*************************free ma3x ************************/
       q=fabs(q);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       etemp=e;  {
       e=d;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    free((FREE_ARG)(m+nrl-NR_END));
       else {  }
         d=p/q;  
         u=x+d;  /***************** f1dim *************************/
         if (u-a < tol2 || b-u < tol2)  extern int ncom; 
           d=SIGN(tol1,xm-x);  extern double *pcom,*xicom;
       }  extern double (*nrfunc)(double []); 
     } else {   
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  double f1dim(double x) 
     }  { 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    int j; 
     fu=(*f)(u);    double f;
     if (fu <= fx) {    double *xt; 
       if (u >= x) a=x; else b=x;   
       SHFT(v,w,x,u)    xt=vector(1,ncom); 
         SHFT(fv,fw,fx,fu)    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
         } else {    f=(*nrfunc)(xt); 
           if (u < x) a=u; else b=u;    free_vector(xt,1,ncom); 
           if (fu <= fw || w == x) {    return f; 
             v=w;  } 
             w=u;  
             fv=fw;  /*****************brent *************************/
             fw=fu;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
           } else if (fu <= fv || v == x || v == w) {  { 
             v=u;    int iter; 
             fv=fu;    double a,b,d,etemp;
           }    double fu,fv,fw,fx;
         }    double ftemp;
   }    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   nrerror("Too many iterations in brent");    double e=0.0; 
   *xmin=x;   
   return fx;    a=(ax < cx ? ax : cx); 
 }    b=(ax > cx ? ax : cx); 
     x=w=v=bx; 
 /****************** mnbrak ***********************/    fw=fv=fx=(*f)(x); 
     for (iter=1;iter<=ITMAX;iter++) { 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,      xm=0.5*(a+b); 
             double (*func)(double))      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
 {      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   double ulim,u,r,q, dum;      printf(".");fflush(stdout);
   double fu;      fprintf(ficlog,".");fflush(ficlog);
    #ifdef DEBUG
   *fa=(*func)(*ax);      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);
   *fb=(*func)(*bx);      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 (*fb > *fa) {      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     SHFT(dum,*ax,*bx,dum)  #endif
       SHFT(dum,*fb,*fa,dum)      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       }        *xmin=x; 
   *cx=(*bx)+GOLD*(*bx-*ax);        return fx; 
   *fc=(*func)(*cx);      } 
   while (*fb > *fc) {      ftemp=fu;
     r=(*bx-*ax)*(*fb-*fc);      if (fabs(e) > tol1) { 
     q=(*bx-*cx)*(*fb-*fa);        r=(x-w)*(fx-fv); 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/        q=(x-v)*(fx-fw); 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));        p=(x-v)*q-(x-w)*r; 
     ulim=(*bx)+GLIMIT*(*cx-*bx);        q=2.0*(q-r); 
     if ((*bx-u)*(u-*cx) > 0.0) {        if (q > 0.0) p = -p; 
       fu=(*func)(u);        q=fabs(q); 
     } else if ((*cx-u)*(u-ulim) > 0.0) {        etemp=e; 
       fu=(*func)(u);        e=d; 
       if (fu < *fc) {        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
           SHFT(*fb,*fc,fu,(*func)(u))        else { 
           }          d=p/q; 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {          u=x+d; 
       u=ulim;          if (u-a < tol2 || b-u < tol2) 
       fu=(*func)(u);            d=SIGN(tol1,xm-x); 
     } else {        } 
       u=(*cx)+GOLD*(*cx-*bx);      } else { 
       fu=(*func)(u);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     }      } 
     SHFT(*ax,*bx,*cx,u)      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       SHFT(*fa,*fb,*fc,fu)      fu=(*f)(u); 
       }      if (fu <= fx) { 
 }        if (u >= x) a=x; else b=x; 
         SHFT(v,w,x,u) 
 /*************** linmin ************************/          SHFT(fv,fw,fx,fu) 
           } else { 
 int ncom;            if (u < x) a=u; else b=u; 
 double *pcom,*xicom;            if (fu <= fw || w == x) { 
 double (*nrfunc)(double []);              v=w; 
                w=u; 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))              fv=fw; 
 {              fw=fu; 
   double brent(double ax, double bx, double cx,            } else if (fu <= fv || v == x || v == w) { 
                double (*f)(double), double tol, double *xmin);              v=u; 
   double f1dim(double x);              fv=fu; 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,            } 
               double *fc, double (*func)(double));          } 
   int j;    } 
   double xx,xmin,bx,ax;    nrerror("Too many iterations in brent"); 
   double fx,fb,fa;    *xmin=x; 
      return fx; 
   ncom=n;  } 
   pcom=vector(1,n);  
   xicom=vector(1,n);  /****************** mnbrak ***********************/
   nrfunc=func;  
   for (j=1;j<=n;j++) {  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     pcom[j]=p[j];              double (*func)(double)) 
     xicom[j]=xi[j];  { 
   }    double ulim,u,r,q, dum;
   ax=0.0;    double fu; 
   xx=1.0;   
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    *fa=(*func)(*ax); 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    *fb=(*func)(*bx); 
 #ifdef DEBUG    if (*fb > *fa) { 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      SHFT(dum,*ax,*bx,dum) 
 #endif        SHFT(dum,*fb,*fa,dum) 
   for (j=1;j<=n;j++) {        } 
     xi[j] *= xmin;    *cx=(*bx)+GOLD*(*bx-*ax); 
     p[j] += xi[j];    *fc=(*func)(*cx); 
   }    while (*fb > *fc) { 
   free_vector(xicom,1,n);      r=(*bx-*ax)*(*fb-*fc); 
   free_vector(pcom,1,n);      q=(*bx-*cx)*(*fb-*fa); 
 }      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 /*************** powell ************************/      ulim=(*bx)+GLIMIT*(*cx-*bx); 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      if ((*bx-u)*(u-*cx) > 0.0) { 
             double (*func)(double []))        fu=(*func)(u); 
 {      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   void linmin(double p[], double xi[], int n, double *fret,        fu=(*func)(u); 
               double (*func)(double []));        if (fu < *fc) { 
   int i,ibig,j;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   double del,t,*pt,*ptt,*xit;            SHFT(*fb,*fc,fu,(*func)(u)) 
   double fp,fptt;            } 
   double *xits;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   pt=vector(1,n);        u=ulim; 
   ptt=vector(1,n);        fu=(*func)(u); 
   xit=vector(1,n);      } else { 
   xits=vector(1,n);        u=(*cx)+GOLD*(*cx-*bx); 
   *fret=(*func)(p);        fu=(*func)(u); 
   for (j=1;j<=n;j++) pt[j]=p[j];      } 
   for (*iter=1;;++(*iter)) {      SHFT(*ax,*bx,*cx,u) 
     fp=(*fret);        SHFT(*fa,*fb,*fc,fu) 
     ibig=0;        } 
     del=0.0;  } 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  
     for (i=1;i<=n;i++)  /*************** linmin ************************/
       printf(" %d %.12f",i, p[i]);  
     printf("\n");  int ncom; 
     for (i=1;i<=n;i++) {  double *pcom,*xicom;
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  double (*nrfunc)(double []); 
       fptt=(*fret);   
 #ifdef DEBUG  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       printf("fret=%lf \n",*fret);  { 
 #endif    double brent(double ax, double bx, double cx, 
       printf("%d",i);fflush(stdout);                 double (*f)(double), double tol, double *xmin); 
       linmin(p,xit,n,fret,func);    double f1dim(double x); 
       if (fabs(fptt-(*fret)) > del) {    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
         del=fabs(fptt-(*fret));                double *fc, double (*func)(double)); 
         ibig=i;    int j; 
       }    double xx,xmin,bx,ax; 
 #ifdef DEBUG    double fx,fb,fa;
       printf("%d %.12e",i,(*fret));   
       for (j=1;j<=n;j++) {    ncom=n; 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    pcom=vector(1,n); 
         printf(" x(%d)=%.12e",j,xit[j]);    xicom=vector(1,n); 
       }    nrfunc=func; 
       for(j=1;j<=n;j++)    for (j=1;j<=n;j++) { 
         printf(" p=%.12e",p[j]);      pcom[j]=p[j]; 
       printf("\n");      xicom[j]=xi[j]; 
 #endif    } 
     }    ax=0.0; 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    xx=1.0; 
 #ifdef DEBUG    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       int k[2],l;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       k[0]=1;  #ifdef DEBUG
       k[1]=-1;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       printf("Max: %.12e",(*func)(p));    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       for (j=1;j<=n;j++)  #endif
         printf(" %.12e",p[j]);    for (j=1;j<=n;j++) { 
       printf("\n");      xi[j] *= xmin; 
       for(l=0;l<=1;l++) {      p[j] += xi[j]; 
         for (j=1;j<=n;j++) {    } 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    free_vector(xicom,1,n); 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    free_vector(pcom,1,n); 
         }  } 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  
       }  /*************** powell ************************/
 #endif  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
               double (*func)(double [])) 
   { 
       free_vector(xit,1,n);    void linmin(double p[], double xi[], int n, double *fret, 
       free_vector(xits,1,n);                double (*func)(double [])); 
       free_vector(ptt,1,n);    int i,ibig,j; 
       free_vector(pt,1,n);    double del,t,*pt,*ptt,*xit;
       return;    double fp,fptt;
     }    double *xits;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    pt=vector(1,n); 
     for (j=1;j<=n;j++) {    ptt=vector(1,n); 
       ptt[j]=2.0*p[j]-pt[j];    xit=vector(1,n); 
       xit[j]=p[j]-pt[j];    xits=vector(1,n); 
       pt[j]=p[j];    *fret=(*func)(p); 
     }    for (j=1;j<=n;j++) pt[j]=p[j]; 
     fptt=(*func)(ptt);    for (*iter=1;;++(*iter)) { 
     if (fptt < fp) {      fp=(*fret); 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);      ibig=0; 
       if (t < 0.0) {      del=0.0; 
         linmin(p,xit,n,fret,func);      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
         for (j=1;j<=n;j++) {      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
           xi[j][ibig]=xi[j][n];      for (i=1;i<=n;i++) 
           xi[j][n]=xit[j];        printf(" %d %.12f",i, p[i]);
         }      fprintf(ficlog," %d %.12f",i, p[i]);
 #ifdef DEBUG      printf("\n");
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      fprintf(ficlog,"\n");
         for(j=1;j<=n;j++)      for (i=1;i<=n;i++) { 
           printf(" %.12e",xit[j]);        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         printf("\n");        fptt=(*fret); 
 #endif  #ifdef DEBUG
       }        printf("fret=%lf \n",*fret);
     }        fprintf(ficlog,"fret=%lf \n",*fret);
   }  #endif
 }        printf("%d",i);fflush(stdout);
         fprintf(ficlog,"%d",i);fflush(ficlog);
 /**** Prevalence limit ****************/        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)          del=fabs(fptt-(*fret)); 
 {          ibig=i; 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit        } 
      matrix by transitions matrix until convergence is reached */  #ifdef DEBUG
         printf("%d %.12e",i,(*fret));
   int i, ii,j,k;        fprintf(ficlog,"%d %.12e",i,(*fret));
   double min, max, maxmin, maxmax,sumnew=0.;        for (j=1;j<=n;j++) {
   double **matprod2();          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   double **out, cov[NCOVMAX], **pmij();          printf(" x(%d)=%.12e",j,xit[j]);
   double **newm;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   double agefin, delaymax=50 ; /* Max number of years to converge */        }
         for(j=1;j<=n;j++) {
   for (ii=1;ii<=nlstate+ndeath;ii++)          printf(" p=%.12e",p[j]);
     for (j=1;j<=nlstate+ndeath;j++){          fprintf(ficlog," p=%.12e",p[j]);
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        }
     }        printf("\n");
         fprintf(ficlog,"\n");
    cov[1]=1.;  #endif
        } 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  #ifdef DEBUG
     newm=savm;        int k[2],l;
     /* Covariates have to be included here again */        k[0]=1;
      cov[2]=agefin;        k[1]=-1;
          printf("Max: %.12e",(*func)(p));
       for (k=1; k<=cptcovn;k++) {        fprintf(ficlog,"Max: %.12e",(*func)(p));
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        for (j=1;j<=n;j++) {
         /*      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(" %.12e",p[j]);
       }          fprintf(ficlog," %.12e",p[j]);
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        }
       for (k=1; k<=cptcovprod;k++)        printf("\n");
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        fprintf(ficlog,"\n");
         for(l=0;l<=1;l++) {
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/          for (j=1;j<=n;j++) {
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
           }
     savm=oldm;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     oldm=newm;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     maxmax=0.;        }
     for(j=1;j<=nlstate;j++){  #endif
       min=1.;  
       max=0.;  
       for(i=1; i<=nlstate; i++) {        free_vector(xit,1,n); 
         sumnew=0;        free_vector(xits,1,n); 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        free_vector(ptt,1,n); 
         prlim[i][j]= newm[i][j]/(1-sumnew);        free_vector(pt,1,n); 
         max=FMAX(max,prlim[i][j]);        return; 
         min=FMIN(min,prlim[i][j]);      } 
       }      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       maxmin=max-min;      for (j=1;j<=n;j++) { 
       maxmax=FMAX(maxmax,maxmin);        ptt[j]=2.0*p[j]-pt[j]; 
     }        xit[j]=p[j]-pt[j]; 
     if(maxmax < ftolpl){        pt[j]=p[j]; 
       return prlim;      } 
     }      fptt=(*func)(ptt); 
   }      if (fptt < fp) { 
 }        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         if (t < 0.0) { 
 /*************** transition probabilities ***************/          linmin(p,xit,n,fret,func); 
           for (j=1;j<=n;j++) { 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )            xi[j][ibig]=xi[j][n]; 
 {            xi[j][n]=xit[j]; 
   double s1, s2;          }
   /*double t34;*/  #ifdef DEBUG
   int i,j,j1, nc, ii, jj;          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(i=1; i<= nlstate; i++){          for(j=1;j<=n;j++){
     for(j=1; j<i;j++){            printf(" %.12e",xit[j]);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){            fprintf(ficlog," %.12e",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("\n");
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/          fprintf(ficlog,"\n");
       }  #endif
       ps[i][j]=s2;        }
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/      } 
     }    } 
     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];  /**** Prevalence limit (stable prevalence)  ****************/
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  
       }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       ps[i][j]=s2;  {
     }    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   }       matrix by transitions matrix until convergence is reached */
     /*ps[3][2]=1;*/  
     int i, ii,j,k;
   for(i=1; i<= nlstate; i++){    double min, max, maxmin, maxmax,sumnew=0.;
      s1=0;    double **matprod2();
     for(j=1; j<i; j++)    double **out, cov[NCOVMAX], **pmij();
       s1+=exp(ps[i][j]);    double **newm;
     for(j=i+1; j<=nlstate+ndeath; j++)    double agefin, delaymax=50 ; /* Max number of years to converge */
       s1+=exp(ps[i][j]);  
     ps[i][i]=1./(s1+1.);    for (ii=1;ii<=nlstate+ndeath;ii++)
     for(j=1; j<i; j++)      for (j=1;j<=nlstate+ndeath;j++){
       ps[i][j]= exp(ps[i][j])*ps[i][i];        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(j=i+1; j<=nlstate+ndeath; j++)      }
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */     cov[1]=1.;
   } /* end i */   
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     for(jj=1; jj<= nlstate+ndeath; jj++){      newm=savm;
       ps[ii][jj]=0;      /* Covariates have to be included here again */
       ps[ii][ii]=1;       cov[2]=agefin;
     }    
   }        for (k=1; k<=cptcovn;k++) {
           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]]);*/
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        }
     for(jj=1; jj<= nlstate+ndeath; jj++){        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
      printf("%lf ",ps[ii][jj]);        for (k=1; k<=cptcovprod;k++)
    }          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     printf("\n ");  
     }        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     printf("\n ");printf("%lf ",cov[2]);*/        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
 /*        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   for(i=1; i<= npar; i++) printf("%f ",x[i]);      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   goto end;*/  
     return ps;      savm=oldm;
 }      oldm=newm;
       maxmax=0.;
 /**************** Product of 2 matrices ******************/      for(j=1;j<=nlstate;j++){
         min=1.;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        max=0.;
 {        for(i=1; i<=nlstate; i++) {
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times          sumnew=0;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   /* in, b, out are matrice of pointers which should have been initialized          prlim[i][j]= newm[i][j]/(1-sumnew);
      before: only the contents of out is modified. The function returns          max=FMAX(max,prlim[i][j]);
      a pointer to pointers identical to out */          min=FMIN(min,prlim[i][j]);
   long i, j, k;        }
   for(i=nrl; i<= nrh; i++)        maxmin=max-min;
     for(k=ncolol; k<=ncoloh; k++)        maxmax=FMAX(maxmax,maxmin);
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      }
         out[i][k] +=in[i][j]*b[j][k];      if(maxmax < ftolpl){
         return prlim;
   return out;      }
 }    }
   }
   
 /************* Higher Matrix Product ***************/  /*************** transition probabilities ***************/ 
   
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 {  {
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    double s1, s2;
      duration (i.e. until    /*double t34;*/
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    int i,j,j1, nc, ii, jj;
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  
      (typically every 2 years instead of every month which is too big).      for(i=1; i<= nlstate; i++){
      Model is determined by parameters x and covariates have to be      for(j=1; j<i;j++){
      included manually here.        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
           /*s2 += param[i][j][nc]*cov[nc];*/
      */          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
           /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
   int i, j, d, h, k;        }
   double **out, cov[NCOVMAX];        ps[i][j]=s2;
   double **newm;        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
       }
   /* Hstepm could be zero and should return the unit matrix */      for(j=i+1; j<=nlstate+ndeath;j++){
   for (i=1;i<=nlstate+ndeath;i++)        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     for (j=1;j<=nlstate+ndeath;j++){          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       oldm[i][j]=(i==j ? 1.0 : 0.0);          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
       po[i][j][0]=(i==j ? 1.0 : 0.0);        }
     }        ps[i][j]=s2;
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      }
   for(h=1; h <=nhstepm; h++){    }
     for(d=1; d <=hstepm; d++){      /*ps[3][2]=1;*/
       newm=savm;  
       /* Covariates have to be included here again */    for(i=1; i<= nlstate; i++){
       cov[1]=1.;       s1=0;
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      for(j=1; j<i; j++)
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        s1+=exp(ps[i][j]);
       for (k=1; k<=cptcovage;k++)      for(j=i+1; j<=nlstate+ndeath; j++)
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        s1+=exp(ps[i][j]);
       for (k=1; k<=cptcovprod;k++)      ps[i][i]=1./(s1+1.);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      for(j=1; j<i; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];
       for(j=i+1; j<=nlstate+ndeath; j++)
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        ps[i][j]= exp(ps[i][j])*ps[i][i];
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    } /* end i */
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  
       savm=oldm;    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       oldm=newm;      for(jj=1; jj<= nlstate+ndeath; jj++){
     }        ps[ii][jj]=0;
     for(i=1; i<=nlstate+ndeath; i++)        ps[ii][ii]=1;
       for(j=1;j<=nlstate+ndeath;j++) {      }
         po[i][j][h]=newm[i][j];    }
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  
          */  
       }    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   } /* end h */      for(jj=1; jj<= nlstate+ndeath; jj++){
   return po;       printf("%lf ",ps[ii][jj]);
 }     }
       printf("\n ");
       }
 /*************** log-likelihood *************/      printf("\n ");printf("%lf ",cov[2]);*/
 double func( double *x)  /*
 {    for(i=1; i<= npar; i++) printf("%f ",x[i]);
   int i, ii, j, k, mi, d, kk;    goto end;*/
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      return ps;
   double **out;  }
   double sw; /* Sum of weights */  
   double lli; /* Individual log likelihood */  /**************** Product of 2 matrices ******************/
   long ipmx;  
   /*extern weight */  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   /* We are differentiating ll according to initial status */  {
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   /*for(i=1;i<imx;i++)       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     printf(" %d\n",s[4][i]);    /* in, b, out are matrice of pointers which should have been initialized 
   */       before: only the contents of out is modified. The function returns
   cov[1]=1.;       a pointer to pointers identical to out */
     long i, j, k;
   for(k=1; k<=nlstate; k++) ll[k]=0.;    for(i=nrl; i<= nrh; i++)
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      for(k=ncolol; k<=ncoloh; k++)
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     for(mi=1; mi<= wav[i]-1; mi++){          out[i][k] +=in[i][j]*b[j][k];
       for (ii=1;ii<=nlstate+ndeath;ii++)  
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    return out;
       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++) {  /************* Higher Matrix Product ***************/
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  
         }  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
          {
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    /* Computes the transition matrix starting at age 'age' over 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));       'nhstepm*hstepm*stepm' months (i.e. until
         savm=oldm;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         oldm=newm;       nhstepm*hstepm matrices. 
               Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
               (typically every 2 years instead of every month which is too big 
       } /* end mult */       for the memory).
             Model is determined by parameters x and covariates have to be 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);       included manually here. 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  
       ipmx +=1;       */
       sw += weight[i];  
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    int i, j, d, h, k;
     } /* end of wave */    double **out, cov[NCOVMAX];
   } /* end of individual */    double **newm;
   
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    /* Hstepm could be zero and should return the unit matrix */
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    for (i=1;i<=nlstate+ndeath;i++)
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      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];    xi=matrix(1,npar,1,npar);
      for (i=1;i<=npar;i++)
   pp=vector(1,nlstate);      for (j=1;j<=npar;j++)
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        xi[i][j]=(i==j ? 1.0 : 0.0);
   strcpy(fileresp,"p");    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   strcat(fileresp,fileres);    powell(p,xi,npar,ftol,&iter,&fret,func);
   if((ficresp=fopen(fileresp,"w"))==NULL) {  
     printf("Problem with prevalence resultfile: %s\n", fileresp);     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     exit(0);    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   }    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  
   j1=0;  }
    
   j=cptcoveff;  /**** Computes Hessian and covariance matrix ***/
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
    {
   for(k1=1; k1<=j;k1++){    double  **a,**y,*x,pd;
     for(i1=1; i1<=ncodemax[k1];i1++){    double **hess;
       j1++;    int i, j,jk;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    int *indx;
         scanf("%d", i);*/  
       for (i=-1; i<=nlstate+ndeath; i++)      double hessii(double p[], double delta, int theta, double delti[]);
         for (jk=-1; jk<=nlstate+ndeath; jk++)      double hessij(double p[], double delti[], int i, int j);
           for(m=agemin; m <= agemax+3; m++)    void lubksb(double **a, int npar, int *indx, double b[]) ;
             freq[i][jk][m]=0;    void ludcmp(double **a, int npar, int *indx, double *d) ;
        
       dateintsum=0;    hess=matrix(1,npar,1,npar);
       k2cpt=0;  
       for (i=1; i<=imx; i++) {    printf("\nCalculation of the hessian matrix. Wait...\n");
         bool=1;    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         if  (cptcovn>0) {    for (i=1;i<=npar;i++){
           for (z1=1; z1<=cptcoveff; z1++)      printf("%d",i);fflush(stdout);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      fprintf(ficlog,"%d",i);fflush(ficlog);
               bool=0;      hess[i][i]=hessii(p,ftolhess,i,delti);
         }      /*printf(" %f ",p[i]);*/
         if (bool==1) {      /*printf(" %lf ",hess[i][i]);*/
           for(m=firstpass; m<=lastpass; m++){    }
             k2=anint[m][i]+(mint[m][i]/12.);    
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    for (i=1;i<=npar;i++) {
               if(agev[m][i]==0) agev[m][i]=agemax+1;      for (j=1;j<=npar;j++)  {
               if(agev[m][i]==1) agev[m][i]=agemax+2;        if (j>i) { 
               if (m<lastpass) {          printf(".%d%d",i,j);fflush(stdout);
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          hess[i][j]=hessij(p,delti,i,j);
               }          hess[j][i]=hess[i][j];    
                        /*printf(" %lf ",hess[i][j]);*/
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        }
                 dateintsum=dateintsum+k2;      }
                 k2cpt++;    }
               }    printf("\n");
             }    fprintf(ficlog,"\n");
           }  
         }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       }    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
            
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    a=matrix(1,npar,1,npar);
     y=matrix(1,npar,1,npar);
       if  (cptcovn>0) {    x=vector(1,npar);
         fprintf(ficresp, "\n#********** Variable ");    indx=ivector(1,npar);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    for (i=1;i<=npar;i++)
         fprintf(ficresp, "**********\n#");      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
       }    ludcmp(a,npar,indx,&pd);
       for(i=1; i<=nlstate;i++)  
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    for (j=1;j<=npar;j++) {
       fprintf(ficresp, "\n");      for (i=1;i<=npar;i++) x[i]=0;
            x[j]=1;
       for(i=(int)agemin; i <= (int)agemax+3; i++){      lubksb(a,npar,indx,x);
         if(i==(int)agemax+3)      for (i=1;i<=npar;i++){ 
           printf("Total");        matcov[i][j]=x[i];
         else      }
           printf("Age %d", i);    }
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=-1, 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(jk=1; jk <=nlstate ; jk++){      for (j=1;j<=npar;j++) { 
           for(m=-1, pos=0; m <=0 ; m++)        printf("%.3e ",hess[i][j]);
             pos += freq[jk][m][i];        fprintf(ficlog,"%.3e ",hess[i][j]);
           if(pp[jk]>=1.e-10)      }
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      printf("\n");
           else      fprintf(ficlog,"\n");
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    }
         }  
     /* Recompute Inverse */
         for(jk=1; jk <=nlstate ; jk++){    for (i=1;i<=npar;i++)
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
             pp[jk] += freq[jk][m][i];    ludcmp(a,npar,indx,&pd);
         }  
     /*  printf("\n#Hessian matrix recomputed#\n");
         for(jk=1,pos=0; jk <=nlstate ; jk++)  
           pos += pp[jk];    for (j=1;j<=npar;j++) {
         for(jk=1; jk <=nlstate ; jk++){      for (i=1;i<=npar;i++) x[i]=0;
           if(pos>=1.e-5)      x[j]=1;
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      lubksb(a,npar,indx,x);
           else      for (i=1;i<=npar;i++){ 
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        y[i][j]=x[i];
           if( i <= (int) agemax){        printf("%.3e ",y[i][j]);
             if(pos>=1.e-5){        fprintf(ficlog,"%.3e ",y[i][j]);
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);      }
               probs[i][jk][j1]= pp[jk]/pos;      printf("\n");
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/      fprintf(ficlog,"\n");
             }    }
             else    */
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);  
           }    free_matrix(a,1,npar,1,npar);
         }    free_matrix(y,1,npar,1,npar);
            free_vector(x,1,npar);
         for(jk=-1; jk <=nlstate+ndeath; jk++)    free_ivector(indx,1,npar);
           for(m=-1; m <=nlstate+ndeath; m++)    free_matrix(hess,1,npar,1,npar);
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  
         if(i <= (int) agemax)  
           fprintf(ficresp,"\n");  }
         printf("\n");  
       }  /*************** hessian matrix ****************/
     }  double hessii( double x[], double delta, int theta, double delti[])
   }  {
   dateintmean=dateintsum/k2cpt;    int i;
      int l=1, lmax=20;
   fclose(ficresp);    double k1,k2;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    double p2[NPARMAX+1];
   free_vector(pp,1,nlstate);    double res;
      double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   /* End of Freq */    double fx;
 }    int k=0,kmax=10;
     double l1;
 /************ 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)    fx=func(x);
 {  /* Some frequencies */    for (i=1;i<=npar;i++) p2[i]=x[i];
      for(l=0 ; l <=lmax; l++){
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      l1=pow(10,l);
   double ***freq; /* Frequencies */      delts=delt;
   double *pp;      for(k=1 ; k <kmax; k=k+1){
   double pos, k2;        delt = delta*(l1*k);
         p2[theta]=x[theta] +delt;
   pp=vector(1,nlstate);        k1=func(p2)-fx;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        p2[theta]=x[theta]-delt;
          k2=func(p2)-fx;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        /*res= (k1-2.0*fx+k2)/delt/delt; */
   j1=0;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
          
   j=cptcoveff;  #ifdef DEBUG
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
          fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   for(k1=1; k1<=j;k1++){  #endif
     for(i1=1; i1<=ncodemax[k1];i1++){        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
       j1++;        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
                k=kmax;
       for (i=-1; i<=nlstate+ndeath; i++)          }
         for (jk=-1; jk<=nlstate+ndeath; jk++)          else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           for(m=agemin; m <= agemax+3; m++)          k=kmax; l=lmax*10.;
             freq[i][jk][m]=0;        }
              else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       for (i=1; i<=imx; i++) {          delts=delt;
         bool=1;        }
         if  (cptcovn>0) {      }
           for (z1=1; z1<=cptcoveff; z1++)    }
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    delti[theta]=delts;
               bool=0;    return res; 
         }    
         if (bool==1) {  }
           for(m=firstpass; m<=lastpass; m++){  
             k2=anint[m][i]+(mint[m][i]/12.);  double hessij( double x[], double delti[], int thetai,int thetaj)
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  {
               if(agev[m][i]==0) agev[m][i]=agemax+1;    int i;
               if(agev[m][i]==1) agev[m][i]=agemax+2;    int l=1, l1, lmax=20;
               if (m<lastpass) {    double k1,k2,k3,k4,res,fx;
                 if (calagedate>0)    double p2[NPARMAX+1];
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    int k;
                 else  
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    fx=func(x);
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];    for (k=1; k<=2; k++) {
               }      for (i=1;i<=npar;i++) p2[i]=x[i];
             }      p2[thetai]=x[thetai]+delti[thetai]/k;
           }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         }      k1=func(p2)-fx;
       }    
       for(i=(int)agemin; i <= (int)agemax+3; i++){      p2[thetai]=x[thetai]+delti[thetai]/k;
         for(jk=1; jk <=nlstate ; jk++){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      k2=func(p2)-fx;
             pp[jk] += freq[jk][m][i];    
         }      p2[thetai]=x[thetai]-delti[thetai]/k;
         for(jk=1; jk <=nlstate ; jk++){      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
           for(m=-1, pos=0; m <=0 ; m++)      k3=func(p2)-fx;
             pos += freq[jk][m][i];    
         }      p2[thetai]=x[thetai]-delti[thetai]/k;
              p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         for(jk=1; jk <=nlstate ; jk++){      k4=func(p2)-fx;
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
             pp[jk] += freq[jk][m][i];  #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);
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];  #endif
            }
         for(jk=1; jk <=nlstate ; jk++){        return res;
           if( i <= (int) agemax){  }
             if(pos>=1.e-5){  
               probs[i][jk][j1]= pp[jk]/pos;  /************** Inverse of matrix **************/
             }  void ludcmp(double **a, int n, int *indx, double *d) 
           }  { 
         }    int i,imax,j,k; 
            double big,dum,sum,temp; 
       }    double *vv; 
     }   
   }    vv=vector(1,n); 
     *d=1.0; 
      for (i=1;i<=n;i++) { 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      big=0.0; 
   free_vector(pp,1,nlstate);      for (j=1;j<=n;j++) 
          if ((temp=fabs(a[i][j])) > big) big=temp; 
 }  /* End of Freq */      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       vv[i]=1.0/big; 
 /************* Waves Concatenation ***************/    } 
     for (j=1;j<=n;j++) { 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      for (i=1;i<j;i++) { 
 {        sum=a[i][j]; 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
      Death is a valid wave (if date is known).        a[i][j]=sum; 
      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]      big=0.0; 
      and mw[mi+1][i]. dh depends on stepm.      for (i=j;i<=n;i++) { 
      */        sum=a[i][j]; 
         for (k=1;k<j;k++) 
   int i, mi, m;          sum -= a[i][k]*a[k][j]; 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        a[i][j]=sum; 
      double sum=0., jmean=0.;*/        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           big=dum; 
   int j, k=0,jk, ju, jl;          imax=i; 
   double sum=0.;        } 
   jmin=1e+5;      } 
   jmax=-1;      if (j != imax) { 
   jmean=0.;        for (k=1;k<=n;k++) { 
   for(i=1; i<=imx; i++){          dum=a[imax][k]; 
     mi=0;          a[imax][k]=a[j][k]; 
     m=firstpass;          a[j][k]=dum; 
     while(s[m][i] <= nlstate){        } 
       if(s[m][i]>=1)        *d = -(*d); 
         mw[++mi][i]=m;        vv[imax]=vv[j]; 
       if(m >=lastpass)      } 
         break;      indx[j]=imax; 
       else      if (a[j][j] == 0.0) a[j][j]=TINY; 
         m++;      if (j != n) { 
     }/* end while */        dum=1.0/(a[j][j]); 
     if (s[m][i] > nlstate){        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       mi++;     /* Death is another wave */      } 
       /* if(mi==0)  never been interviewed correctly before death */    } 
          /* Only death is a correct wave */    free_vector(vv,1,n);  /* Doesn't work */
       mw[mi][i]=m;  ;
     }  } 
   
     wav[i]=mi;  void lubksb(double **a, int n, int *indx, double b[]) 
     if(mi==0)  { 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    int i,ii=0,ip,j; 
   }    double sum; 
    
   for(i=1; i<=imx; i++){    for (i=1;i<=n;i++) { 
     for(mi=1; mi<wav[i];mi++){      ip=indx[i]; 
       if (stepm <=0)      sum=b[ip]; 
         dh[mi][i]=1;      b[ip]=b[i]; 
       else{      if (ii) 
         if (s[mw[mi+1][i]][i] > nlstate) {        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
           if (agedc[i] < 2*AGESUP) {      else if (sum) ii=i; 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);      b[i]=sum; 
           if(j==0) j=1;  /* Survives at least one month after exam */    } 
           k=k+1;    for (i=n;i>=1;i--) { 
           if (j >= jmax) jmax=j;      sum=b[i]; 
           if (j <= jmin) jmin=j;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
           sum=sum+j;      b[i]=sum/a[i][i]; 
           /*if (j<0) printf("j=%d num=%d \n",j,i); */    } 
           }  } 
         }  
         else{  /************ Frequencies ********************/
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));  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)
           k=k+1;  {  /* Some frequencies */
           if (j >= jmax) jmax=j;    
           else if (j <= jmin)jmin=j;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    int first;
           sum=sum+j;    double ***freq; /* Frequencies */
         }    double *pp, **prop;
         jk= j/stepm;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
         jl= j -jk*stepm;    FILE *ficresp;
         ju= j -(jk+1)*stepm;    char fileresp[FILENAMELENGTH];
         if(jl <= -ju)    
           dh[mi][i]=jk;    pp=vector(1,nlstate);
         else    prop=matrix(1,nlstate,iagemin,iagemax+3);
           dh[mi][i]=jk+1;    strcpy(fileresp,"p");
         if(dh[mi][i]==0)    strcat(fileresp,fileres);
           dh[mi][i]=1; /* At least one step */    if((ficresp=fopen(fileresp,"w"))==NULL) {
       }      printf("Problem with prevalence resultfile: %s\n", fileresp);
     }      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   }      exit(0);
   jmean=sum/k;    }
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
  }    j1=0;
 /*********** Tricode ****************************/    
 void tricode(int *Tvar, int **nbcode, int imx)    j=cptcoveff;
 {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   int Ndum[20],ij=1, k, j, i;  
   int cptcode=0;    first=1;
   cptcoveff=0;  
      for(k1=1; k1<=j;k1++){
   for (k=0; k<19; k++) Ndum[k]=0;      for(i1=1; i1<=ncodemax[k1];i1++){
   for (k=1; k<=7; k++) ncodemax[k]=0;        j1++;
         /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          scanf("%d", i);*/
     for (i=1; i<=imx; i++) {        for (i=-1; i<=nlstate+ndeath; i++)  
       ij=(int)(covar[Tvar[j]][i]);          for (jk=-1; jk<=nlstate+ndeath; jk++)  
       Ndum[ij]++;            for(m=iagemin; m <= iagemax+3; m++)
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/              freq[i][jk][m]=0;
       if (ij > cptcode) cptcode=ij;  
     }      for (i=1; i<=nlstate; i++)  
         for(m=iagemin; m <= iagemax+3; m++)
     for (i=0; i<=cptcode; i++) {          prop[i][m]=0;
       if(Ndum[i]!=0) ncodemax[j]++;        
     }        dateintsum=0;
     ij=1;        k2cpt=0;
         for (i=1; i<=imx; i++) {
           bool=1;
     for (i=1; i<=ncodemax[j]; i++) {          if  (cptcovn>0) {
       for (k=0; k<=19; k++) {            for (z1=1; z1<=cptcoveff; z1++) 
         if (Ndum[k] != 0) {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
           nbcode[Tvar[j]][ij]=k;                bool=0;
                    }
           ij++;          if (bool==1){
         }            for(m=firstpass; m<=lastpass; m++){
         if (ij > ncodemax[j]) break;              k2=anint[m][i]+(mint[m][i]/12.);
       }                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];
  for (k=0; k<19; k++) Ndum[k]=0;                if (m<lastpass) {
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
  for (i=1; i<=ncovmodel-2; i++) {                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
       ij=Tvar[i];                }
       Ndum[ij]++;                
     }                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   dateintsum=dateintsum+k2;
  ij=1;                  k2cpt++;
  for (i=1; i<=10; i++) {                }
    if((Ndum[i]!=0) && (i<=ncovcol)){              }
      Tvaraff[ij]=i;            }
      ij++;          }
    }        }
  }         
          fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
     cptcoveff=ij-1;  
 }        if  (cptcovn>0) {
           fprintf(ficresp, "\n#********** Variable "); 
 /*********** Health Expectancies ****************/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresp, "**********\n#");
 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 )        }
         for(i=1; i<=nlstate;i++) 
 {          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   /* Health expectancies */        fprintf(ficresp, "\n");
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;        
   double age, agelim, hf;        for(i=iagemin; i <= iagemax+3; i++){
   double ***p3mat,***varhe;          if(i==iagemax+3){
   double **dnewm,**doldm;            fprintf(ficlog,"Total");
   double *xp;          }else{
   double **gp, **gm;            if(first==1){
   double ***gradg, ***trgradg;              first=0;
   int theta;              printf("See log file for details...\n");
             }
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);            fprintf(ficlog,"Age %d", i);
   xp=vector(1,npar);          }
   dnewm=matrix(1,nlstate*2,1,npar);          for(jk=1; jk <=nlstate ; jk++){
   doldm=matrix(1,nlstate*2,1,nlstate*2);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
                pp[jk] += freq[jk][m][i]; 
   fprintf(ficreseij,"# Health expectancies\n");          }
   fprintf(ficreseij,"# Age");          for(jk=1; jk <=nlstate ; jk++){
   for(i=1; i<=nlstate;i++)            for(m=-1, pos=0; m <=0 ; m++)
     for(j=1; j<=nlstate;j++)              pos += freq[jk][m][i];
       fprintf(ficreseij," %1d-%1d (SE)",i,j);            if(pp[jk]>=1.e-10){
   fprintf(ficreseij,"\n");              if(first==1){
               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   if(estepm < stepm){              }
     printf ("Problem %d lower than %d\n",estepm, stepm);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   }            }else{
   else  hstepm=estepm;                if(first==1)
   /* We compute the life expectancy from trapezoids spaced every estepm months                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
    * This is mainly to measure the difference between two models: for example              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
    * if stepm=24 months pijx are given only every 2 years and by summing them            }
    * we are calculating an estimate of the Life Expectancy assuming a linear          }
    * progression inbetween and thus overestimating or underestimating according  
    * 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=0, pp[jk]=0; m <=nlstate+ndeath; m++)
    * to compare the new estimate of Life expectancy with the same linear              pp[jk] += freq[jk][m][i];
    * hypothesis. A more precise result, taking into account a more precise          }       
    * curvature will be obtained if estepm is as small as stepm. */          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
             pos += pp[jk];
   /* For example we decided to compute the life expectancy with the smallest unit */            posprop += prop[jk][i];
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.          }
      nhstepm is the number of hstepm from age to agelim          for(jk=1; jk <=nlstate ; jk++){
      nstepm is the number of stepm from age to agelin.            if(pos>=1.e-5){
      Look at hpijx to understand the reason of that which relies in memory size              if(first==1)
      and note for a fixed period like estepm months */                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
      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              if(first==1)
      you sum them up and add 1 year (area under the trapezoids) you won't get the same                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
      results. So we changed our mind and took the option of the best precision.              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   */            }
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */            if( i <= iagemax){
               if(pos>=1.e-5){
   agelim=AGESUP;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */                probs[i][jk][j1]= pp[jk]/pos;
     /* nhstepm age range expressed in number of stepm */                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     nstepm=(int) rint((agelim-age)*YEARM/stepm);              }
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */              else
     /* if (stepm >= YEARM) hstepm=1;*/                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */            }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);          
     gp=matrix(0,nhstepm,1,nlstate*2);          for(jk=-1; jk <=nlstate+ndeath; jk++)
     gm=matrix(0,nhstepm,1,nlstate*2);            for(m=-1; m <=nlstate+ndeath; m++)
               if(freq[jk][m][i] !=0 ) {
     /* Computed by stepm unit matrices, product of hstepm matrices, stored              if(first==1)
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);                  fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
                }
           if(i <= iagemax)
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */            fprintf(ficresp,"\n");
           if(first==1)
     /* Computing Variances of health expectancies */            printf("Others in log...\n");
           fprintf(ficlog,"\n");
      for(theta=1; theta <=npar; theta++){        }
       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, gp[h][cptj]=0.; h<=nhstepm-1; h++){  }
             gp[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).
       for(i=1; i<=npar; i++)       We still use firstpass and lastpass as another selection.
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);     
          int i, m, jk, k1, i1, j1, bool, z1,z2,j;
       cptj=0;    double ***freq; /* Frequencies */
       for(j=1; j<= nlstate; j++){    double *pp, **prop;
         for(i=1;i<=nlstate;i++){    double pos,posprop; 
           cptj=cptj+1;    double  y2; /* in fractional years */
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){    int iagemin, iagemax;
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;  
           }    iagemin= (int) agemin;
         }    iagemax= (int) agemax;
       }    /*pp=vector(1,nlstate);*/
          prop=matrix(1,nlstate,iagemin,iagemax+3); 
        /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     j1=0;
       for(j=1; j<= nlstate*2; j++)    
         for(h=0; h<=nhstepm-1; h++){    j=cptcoveff;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         }    
     for(k1=1; k1<=j;k1++){
      }      for(i1=1; i1<=ncodemax[k1];i1++){
            j1++;
 /* End theta */        
         for (i=1; i<=nlstate; i++)  
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);          for(m=iagemin; m <= iagemax+3; m++)
             prop[i][m]=0.0;
      for(h=0; h<=nhstepm-1; h++)       
       for(j=1; j<=nlstate*2;j++)        for (i=1; i<=imx; i++) { /* Each individual */
         for(theta=1; theta <=npar; theta++)          bool=1;
         trgradg[h][j][theta]=gradg[h][theta][j];          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
      for(i=1;i<=nlstate*2;i++)                bool=0;
       for(j=1;j<=nlstate*2;j++)          } 
         varhe[i][j][(int)age] =0.;          if (bool==1) { 
             for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
      printf("%d|",(int)age);fflush(stdout);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     for(h=0;h<=nhstepm-1;h++){              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
       for(k=0;k<=nhstepm-1;k++){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
         for(i=1;i<=nlstate*2;i++)                if (s[m][i]>0 && s[m][i]<=nlstate) { 
           for(j=1;j<=nlstate*2;j++)                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
       }                  prop[s[m][i]][iagemax+3] += weight[i]; 
     }                } 
               }
                  } /* end selection of waves */
     /* Computing expectancies */          }
     for(i=1; i<=nlstate;i++)        }
       for(j=1; j<=nlstate;j++)        for(i=iagemin; i <= iagemax+3; i++){  
         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;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
                      posprop += prop[jk][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]);*/          } 
   
         }          for(jk=1; jk <=nlstate ; jk++){     
             if( i <=  iagemax){ 
     fprintf(ficreseij,"%3.0f",age );              if(posprop>=1.e-5){ 
     cptj=0;                probs[i][jk][j1]= prop[jk][i]/posprop;
     for(i=1; i<=nlstate;i++)              } 
       for(j=1; j<=nlstate;j++){            } 
         cptj++;          }/* end jk */ 
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );        }/* end i */ 
       }      } /* end i1 */
     fprintf(ficreseij,"\n");    } /* end k1 */
        
     free_matrix(gm,0,nhstepm,1,nlstate*2);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     free_matrix(gp,0,nhstepm,1,nlstate*2);    /*free_vector(pp,1,nlstate);*/
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);  }  /* End of prevalence */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   }  /************* Waves Concatenation ***************/
   free_vector(xp,1,npar);  
   free_matrix(dnewm,1,nlstate*2,1,npar);  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)
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);  {
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
 }       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
 /************ Variance ******************/       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][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)       and mw[mi+1][i]. dh depends on stepm.
 {       */
   /* Variance of health expectancies */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    int i, mi, m;
   double **newm;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   double **dnewm,**doldm;       double sum=0., jmean=0.;*/
   int i, j, nhstepm, hstepm, h, nstepm ;    int first;
   int k, cptcode;    int j, k=0,jk, ju, jl;
   double *xp;    double sum=0.;
   double **gp, **gm;    first=0;
   double ***gradg, ***trgradg;    jmin=1e+5;
   double ***p3mat;    jmax=-1;
   double age,agelim, hf;    jmean=0.;
   int theta;    for(i=1; i<=imx; i++){
       mi=0;
   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");      m=firstpass;
   fprintf(ficresvij,"# Age");      while(s[m][i] <= nlstate){
   for(i=1; i<=nlstate;i++)        if(s[m][i]>=1)
     for(j=1; j<=nlstate;j++)          mw[++mi][i]=m;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        if(m >=lastpass)
   fprintf(ficresvij,"\n");          break;
         else
   xp=vector(1,npar);          m++;
   dnewm=matrix(1,nlstate,1,npar);      }/* end while */
   doldm=matrix(1,nlstate,1,nlstate);      if (s[m][i] > nlstate){
          mi++;     /* Death is another wave */
   if(estepm < stepm){        /* if(mi==0)  never been interviewed correctly before death */
     printf ("Problem %d lower than %d\n",estepm, stepm);           /* Only death is a correct wave */
   }        mw[mi][i]=m;
   else  hstepm=estepm;        }
   /* For example we decided to compute the life expectancy with the smallest unit */  
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.      wav[i]=mi;
      nhstepm is the number of hstepm from age to agelim      if(mi==0){
      nstepm is the number of stepm from age to agelin.        if(first==0){
      Look at hpijx to understand the reason of that which relies in memory size          printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
      and note for a fixed period like k years */          first=1;
   /* 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        if(first==1){
      means that if the survival funtion is printed only each two years of age and if          fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
      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.      } /* end mi==0 */
   */    }
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */  
   agelim = AGESUP;    for(i=1; i<=imx; i++){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      for(mi=1; mi<wav[i];mi++){
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        if (stepm <=0)
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */          dh[mi][i]=1;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        else{
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          if (s[mw[mi+1][i]][i] > nlstate) {
     gp=matrix(0,nhstepm,1,nlstate);            if (agedc[i] < 2*AGESUP) {
     gm=matrix(0,nhstepm,1,nlstate);            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
             if(j==0) j=1;  /* Survives at least one month after exam */
     for(theta=1; theta <=npar; theta++){            k=k+1;
       for(i=1; i<=npar; i++){ /* Computes gradient */            if (j >= jmax) jmax=j;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            if (j <= jmin) jmin=j;
       }            sum=sum+j;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              /*if (j<0) printf("j=%d num=%d \n",j,i); */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
       if (popbased==1) {            }
         for(i=1; i<=nlstate;i++)          }
           prlim[i][i]=probs[(int)age][i][ij];          else{
       }            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);*/
       for(j=1; j<= nlstate; j++){            k=k+1;
         for(h=0; h<=nhstepm; h++){            if (j >= jmax) jmax=j;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)            else if (j <= jmin)jmin=j;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
         }            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
       }            sum=sum+j;
              }
       for(i=1; i<=npar; i++) /* Computes gradient */          jk= j/stepm;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          jl= j -jk*stepm;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            ju= j -(jk+1)*stepm;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          if(mle <=1){ 
              if(jl==0){
       if (popbased==1) {              dh[mi][i]=jk;
         for(i=1; i<=nlstate;i++)              bh[mi][i]=0;
           prlim[i][i]=probs[(int)age][i][ij];            }else{ /* We want a negative bias in order to only have interpolation ie
       }                    * at the price of an extra matrix product in likelihood */
               dh[mi][i]=jk+1;
       for(j=1; j<= nlstate; j++){              bh[mi][i]=ju;
         for(h=0; h<=nhstepm; h++){            }
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          }else{
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];            if(jl <= -ju){
         }              dh[mi][i]=jk;
       }              bh[mi][i]=jl;       /* bias is positive if real duration
                                    * is higher than the multiple of stepm and negative otherwise.
       for(j=1; j<= nlstate; j++)                                   */
         for(h=0; h<=nhstepm; h++){            }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            else{
         }              dh[mi][i]=jk+1;
     } /* End theta */              bh[mi][i]=ju;
             }
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);            if(dh[mi][i]==0){
               dh[mi][i]=1; /* At least one step */
     for(h=0; h<=nhstepm; h++)              bh[mi][i]=ju; /* At least one step */
       for(j=1; j<=nlstate;j++)              /*  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);*/
         for(theta=1; theta <=npar; theta++)            }
           trgradg[h][j][theta]=gradg[h][theta][j];          }
         } /* end if mle */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      } /* end wave */
     for(i=1;i<=nlstate;i++)    }
       for(j=1;j<=nlstate;j++)    jmean=sum/k;
         vareij[i][j][(int)age] =0.;    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     for(h=0;h<=nhstepm;h++){   }
       for(k=0;k<=nhstepm;k++){  
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);  /*********** Tricode ****************************/
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);  void tricode(int *Tvar, int **nbcode, int imx)
         for(i=1;i<=nlstate;i++)  {
           for(j=1;j<=nlstate;j++)    
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;    int Ndum[20],ij=1, k, j, i, maxncov=19;
       }    int cptcode=0;
     }    cptcoveff=0; 
    
     fprintf(ficresvij,"%.0f ",age );    for (k=0; k<maxncov; k++) Ndum[k]=0;
     for(i=1; i<=nlstate;i++)    for (k=1; k<=7; k++) ncodemax[k]=0;
       for(j=1; j<=nlstate;j++){  
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
       }      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
     fprintf(ficresvij,"\n");                                 modality*/ 
     free_matrix(gp,0,nhstepm,1,nlstate);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
     free_matrix(gm,0,nhstepm,1,nlstate);        Ndum[ij]++; /*store the modality */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                                         Tvar[j]. If V=sex and male is 0 and 
   } /* End age */                                         female is 1, then  cptcode=1.*/
        }
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);      for (i=0; i<=cptcode; i++) {
   free_matrix(dnewm,1,nlstate,1,nlstate);        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 */
       }
 }  
       ij=1; 
 /************ Variance of prevlim ******************/      for (i=1; i<=ncodemax[j]; i++) {
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)        for (k=0; k<= maxncov; k++) {
 {          if (Ndum[k] != 0) {
   /* Variance of prevalence limit */            nbcode[Tvar[j]][ij]=k; 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            /* 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; */
   double **newm;            
   double **dnewm,**doldm;            ij++;
   int i, j, nhstepm, hstepm;          }
   int k, cptcode;          if (ij > ncodemax[j]) break; 
   double *xp;        }  
   double *gp, *gm;      } 
   double **gradg, **trgradg;    }  
   double age,agelim;  
   int theta;   for (k=0; k< maxncov; k++) Ndum[k]=0;
      
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");   for (i=1; i<=ncovmodel-2; i++) { 
   fprintf(ficresvpl,"# Age");     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
   for(i=1; i<=nlstate;i++)     ij=Tvar[i];
       fprintf(ficresvpl," %1d-%1d",i,i);     Ndum[ij]++;
   fprintf(ficresvpl,"\n");   }
   
   xp=vector(1,npar);   ij=1;
   dnewm=matrix(1,nlstate,1,npar);   for (i=1; i<= maxncov; i++) {
   doldm=matrix(1,nlstate,1,nlstate);     if((Ndum[i]!=0) && (i<=ncovcol)){
         Tvaraff[ij]=i; /*For printing */
   hstepm=1*YEARM; /* Every year of age */       ij++;
   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 */   cptcoveff=ij-1; /*Number of simple covariates*/
     if (stepm >= YEARM) hstepm=1;  }
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
     gradg=matrix(1,npar,1,nlstate);  /*********** Health Expectancies ****************/
     gp=vector(1,nlstate);  
     gm=vector(1,nlstate);  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 )
   
     for(theta=1; theta <=npar; theta++){  {
       for(i=1; i<=npar; i++){ /* Computes gradient */    /* Health expectancies */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
       }    double age, agelim, hf;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double ***p3mat,***varhe;
       for(i=1;i<=nlstate;i++)    double **dnewm,**doldm;
         gp[i] = prlim[i][i];    double *xp;
        double **gp, **gm;
       for(i=1; i<=npar; i++) /* Computes gradient */    double ***gradg, ***trgradg;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    int theta;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
         gm[i] = prlim[i][i];    xp=vector(1,npar);
     dnewm=matrix(1,nlstate*nlstate,1,npar);
       for(i=1;i<=nlstate;i++)    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    
     } /* End theta */    fprintf(ficreseij,"# Health expectancies\n");
     fprintf(ficreseij,"# Age");
     trgradg =matrix(1,nlstate,1,npar);    for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
     for(j=1; j<=nlstate;j++)        fprintf(ficreseij," %1d-%1d (SE)",i,j);
       for(theta=1; theta <=npar; theta++)    fprintf(ficreseij,"\n");
         trgradg[j][theta]=gradg[theta][j];  
     if(estepm < stepm){
     for(i=1;i<=nlstate;i++)      printf ("Problem %d lower than %d\n",estepm, stepm);
       varpl[i][(int)age] =0.;    }
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    else  hstepm=estepm;   
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    /* We compute the life expectancy from trapezoids spaced every estepm months
     for(i=1;i<=nlstate;i++)     * This is mainly to measure the difference between two models: for example
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */     * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear 
     fprintf(ficresvpl,"%.0f ",age );     * progression in between and thus overestimating or underestimating according
     for(i=1; i<=nlstate;i++)     * to the curvature of the survival function. If, for the same date, we 
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));     * estimate the model with stepm=1 month, we can keep estepm to 24 months
     fprintf(ficresvpl,"\n");     * to compare the new estimate of Life expectancy with the same linear 
     free_vector(gp,1,nlstate);     * hypothesis. A more precise result, taking into account a more precise
     free_vector(gm,1,nlstate);     * curvature will be obtained if estepm is as small as stepm. */
     free_matrix(gradg,1,npar,1,nlstate);  
     free_matrix(trgradg,1,nlstate,1,npar);    /* For example we decided to compute the life expectancy with the smallest unit */
   } /* End age */    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
   free_vector(xp,1,npar);       nstepm is the number of stepm from age to agelin. 
   free_matrix(doldm,1,nlstate,1,npar);       Look at hpijx to understand the reason of that which relies in memory size
   free_matrix(dnewm,1,nlstate,1,nlstate);       and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 }       survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
 /************ Variance of one-step probabilities  ******************/       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)       results. So we changed our mind and took the option of the best precision.
 {    */
   int i, j, i1, k1, j1, z1;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   int k=0, cptcode;  
   double **dnewm,**doldm;    agelim=AGESUP;
   double *xp;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   double *gp, *gm;      /* nhstepm age range expressed in number of stepm */
   double **gradg, **trgradg;      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   double age,agelim, cov[NCOVMAX];      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   int theta;      /* if (stepm >= YEARM) hstepm=1;*/
   char fileresprob[FILENAMELENGTH];      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   strcpy(fileresprob,"prob");      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   strcat(fileresprob,fileres);      gp=matrix(0,nhstepm,1,nlstate*nlstate);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {      gm=matrix(0,nhstepm,1,nlstate*nlstate);
     printf("Problem with resultfile: %s\n", fileresprob);  
   }      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
        hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
 fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");   
   fprintf(ficresprob,"# Age");  
   for(i=1; i<=nlstate;i++)      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     for(j=1; j<=(nlstate+ndeath);j++)  
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);      /* Computing Variances of health expectancies */
   
        for(theta=1; theta <=npar; theta++){
   fprintf(ficresprob,"\n");        for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
   xp=vector(1,npar);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));        cptj=0;
          for(j=1; j<= nlstate; j++){
   cov[1]=1;          for(i=1; i<=nlstate; i++){
   j=cptcoveff;            cptj=cptj+1;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
   j1=0;              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   for(k1=1; k1<=1;k1++){            }
     for(i1=1; i1<=ncodemax[k1];i1++){          }
     j1++;        }
        
     if  (cptcovn>0) {       
       fprintf(ficresprob, "\n#********** Variable ");        for(i=1; i<=npar; i++) 
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       fprintf(ficresprob, "**********\n#");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     }        
            cptj=0;
       for (age=bage; age<=fage; age ++){        for(j=1; j<= nlstate; j++){
         cov[2]=age;          for(i=1;i<=nlstate;i++){
         for (k=1; k<=cptcovn;k++) {            cptj=cptj+1;
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
                        gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
         }            }
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          }
         for (k=1; k<=cptcovprod;k++)        }
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        for(j=1; j<= nlstate*nlstate; j++)
                  for(h=0; h<=nhstepm-1; h++){
         gradg=matrix(1,npar,1,9);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
         trgradg=matrix(1,9,1,npar);          }
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));       } 
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));     
      /* End theta */
         for(theta=1; theta <=npar; theta++){  
           for(i=1; i<=npar; i++)       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
             xp[i] = x[i] + (i==theta ?delti[theta]:0);  
                 for(h=0; h<=nhstepm-1; h++)
           pmij(pmmij,cov,ncovmodel,xp,nlstate);        for(j=1; j<=nlstate*nlstate;j++)
                    for(theta=1; theta <=npar; theta++)
           k=0;            trgradg[h][j][theta]=gradg[h][theta][j];
           for(i=1; i<= (nlstate+ndeath); i++){       
             for(j=1; j<=(nlstate+ndeath);j++){  
               k=k+1;       for(i=1;i<=nlstate*nlstate;i++)
               gp[k]=pmmij[i][j];        for(j=1;j<=nlstate*nlstate;j++)
             }          varhe[i][j][(int)age] =0.;
           }  
                 printf("%d|",(int)age);fflush(stdout);
           for(i=1; i<=npar; i++)       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
             xp[i] = x[i] - (i==theta ?delti[theta]:0);       for(h=0;h<=nhstepm-1;h++){
            for(k=0;k<=nhstepm-1;k++){
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           k=0;          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           for(i=1; i<=(nlstate+ndeath); i++){          for(i=1;i<=nlstate*nlstate;i++)
             for(j=1; j<=(nlstate+ndeath);j++){            for(j=1;j<=nlstate*nlstate;j++)
               k=k+1;              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
               gm[k]=pmmij[i][j];        }
             }      }
           }      /* Computing expectancies */
            for(i=1; i<=nlstate;i++)
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)        for(j=1; j<=nlstate;j++)
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];            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;
             
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
           for(theta=1; theta <=npar; theta++)  
             trgradg[j][theta]=gradg[theta][j];          }
          
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);      fprintf(ficreseij,"%3.0f",age );
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);      cptj=0;
              for(i=1; i<=nlstate;i++)
         pmij(pmmij,cov,ncovmodel,x,nlstate);        for(j=1; j<=nlstate;j++){
                  cptj++;
         k=0;          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
         for(i=1; i<=(nlstate+ndeath); i++){        }
           for(j=1; j<=(nlstate+ndeath);j++){      fprintf(ficreseij,"\n");
             k=k+1;     
             gm[k]=pmmij[i][j];      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
           }      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
         }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
            free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
      /*printf("\n%d ",(int)age);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    }
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    printf("\n");
      }*/    fprintf(ficlog,"\n");
   
         fprintf(ficresprob,"\n%d ",(int)age);    free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*nlstate,1,npar);
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
    }
       }  
     }  /************ Variance ******************/
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));  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)
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));  {
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    /* Variance of health expectancies */
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   }    /* double **newm;*/
   free_vector(xp,1,npar);    double **dnewm,**doldm;
   fclose(ficresprob);    double **dnewmp,**doldmp;
      int i, j, nhstepm, hstepm, h, nstepm ;
 }    int k, cptcode;
     double *xp;
     double **gp, **gm;  /* for var eij */
 /******************* Printing html file ***********/    double ***gradg, ***trgradg; /*for var eij */
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \    double **gradgp, **trgradgp; /* for var p point j */
                   int lastpass, int stepm, int weightopt, char model[],\    double *gpp, *gmp; /* for var p point j */
                   int imx,int jmin, int jmax, double jmeanint,char optionfile[], \    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
                   char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\    double ***p3mat;
                   char version[], int popforecast, int estepm ,\    double age,agelim, hf;
                   double jprev1, double mprev1,double anprev1, \    double ***mobaverage;
                   double jprev2, double mprev2,double anprev2){    int theta;
   int jj1, k1, i1, cpt;    char digit[4];
   FILE *fichtm;    char digitp[25];
   /*char optionfilehtm[FILENAMELENGTH];*/  
     char fileresprobmorprev[FILENAMELENGTH];
   strcpy(optionfilehtm,optionfile);  
   strcat(optionfilehtm,".htm");    if(popbased==1){
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {      if(mobilav!=0)
     printf("Problem with %s \n",optionfilehtm), exit(0);        strcpy(digitp,"-populbased-mobilav-");
   }      else strcpy(digitp,"-populbased-nomobil-");
     }
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n    else 
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n      strcpy(digitp,"-stablbased-");
 \n  
 Total number of observations=%d <br>\n    if (mobilav!=0) {
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 <hr  size=\"2\" color=\"#EC5E5E\">      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
  <ul><li>Parameter files<br>\n        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n        printf(" Error in movingaverage mobilav=%d\n",mobilav);
  - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);      }
     }
    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n  
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n    strcpy(fileresprobmorprev,"prmorprev"); 
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n    sprintf(digit,"%-d",ij);
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
  - Life expectancies by age and initial health status (estepm=%2d months):    strcat(fileresprobmorprev,digit); /* Tvar to be done */
    <a href=\"e%s\">e%s</a> <br>\n</li>", \    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);    strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n      printf("Problem with resultfile: %s\n", fileresprobmorprev);
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n    }
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
  if(popforecast==1) fprintf(fichtm,"\n    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n      fprintf(ficresprobmorprev," p.%-d SE",j);
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n      for(i=1; i<=nlstate;i++)
         <br>",fileres,fileres,fileres,fileres);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
  else    }  
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);    fprintf(ficresprobmorprev,"\n");
 fprintf(fichtm," <li>Graphs</li><p>");    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
  m=cptcoveff;      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      exit(0);
     }
  jj1=0;    else{
  for(k1=1; k1<=m;k1++){      fprintf(ficgp,"\n# Routine varevsij");
    for(i1=1; i1<=ncodemax[k1];i1++){    }
      jj1++;    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
      if (cptcovn > 0) {      printf("Problem with html file: %s\n", optionfilehtm);
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
        for (cpt=1; cpt<=cptcoveff;cpt++)      exit(0);
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    }
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    else{
      }      fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
      /* Pij */      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
      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);        varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      /* 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>    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");
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    fprintf(ficresvij,"# Age");
        /* Stable prevalence in each health state */    for(i=1; i<=nlstate;i++)
        for(cpt=1; cpt<nlstate;cpt++){      for(j=1; j<=nlstate;j++)
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    fprintf(ficresvij,"\n");
        }  
     for(cpt=1; cpt<=nlstate;cpt++) {    xp=vector(1,npar);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    dnewm=matrix(1,nlstate,1,npar);
 interval) in state (%d): v%s%d%d.png <br>    doldm=matrix(1,nlstate,1,nlstate);
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
      }    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      for(cpt=1; cpt<=nlstate;cpt++) {  
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    gpp=vector(nlstate+1,nlstate+ndeath);
      }    gmp=vector(nlstate+1,nlstate+ndeath);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
 health expectancies in states (1) and (2): e%s%d.png<br>    
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    if(estepm < stepm){
 fprintf(fichtm,"\n</body>");      printf ("Problem %d lower than %d\n",estepm, stepm);
    }    }
  }    else  hstepm=estepm;   
 fclose(fichtm);    /* For example we decided to compute the life expectancy with the smallest unit */
 }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
 /******************* Gnuplot file **************/       nstepm is the number of stepm from age to agelin. 
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like k years */
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   int ng;       survival function given by stepm (the optimization length). Unfortunately it
   strcpy(optionfilegnuplot,optionfilefiname);       means that if the survival funtion is printed every two years of age and if
   strcat(optionfilegnuplot,".gp.txt");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {       results. So we changed our mind and took the option of the best precision.
     printf("Problem with file %s",optionfilegnuplot);    */
   }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
 #ifdef windows    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     fprintf(ficgp,"cd \"%s\" \n",pathc);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
 #endif      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 m=pow(2,cptcoveff);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
  /* 1eme*/      gp=matrix(0,nhstepm,1,nlstate);
   for (cpt=1; cpt<= nlstate ; cpt ++) {      gm=matrix(0,nhstepm,1,nlstate);
    for (k1=1; k1<= m ; k1 ++) {  
   
 #ifdef windows      for(theta=1; theta <=npar; theta++){
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
      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);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 #endif        }
 #ifdef unix        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);  
 #endif        if (popbased==1) {
           if(mobilav ==0){
 for (i=1; i<= nlstate ; i ++) {            for(i=1; i<=nlstate;i++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              prlim[i][i]=probs[(int)age][i][ij];
   else fprintf(ficgp," \%%*lf (\%%*lf)");          }else{ /* mobilav */ 
 }            for(i=1; i<=nlstate;i++)
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);              prlim[i][i]=mobaverage[(int)age][i][ij];
     for (i=1; i<= nlstate ; i ++) {          }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        }
   else fprintf(ficgp," \%%*lf (\%%*lf)");    
 }        for(j=1; j<= nlstate; j++){
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          for(h=0; h<=nhstepm; h++){
      for (i=1; i<= nlstate ; i ++) {            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   else fprintf(ficgp," \%%*lf (\%%*lf)");          }
 }          }
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        /* This for computing probability of death (h=1 means
 #ifdef unix           computed over hstepm matrices product = hstepm*stepm months) 
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");           as a weighted average of prlim.
 #endif        */
    }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   }          for(i=1,gpp[j]=0.; i<= nlstate; i++)
   /*2 eme*/            gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
   for (k1=1; k1<= m ; k1 ++) {        /* end probability of death */
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);  
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
              xp[i] = x[i] - (i==theta ?delti[theta]:0);
     for (i=1; i<= nlstate+1 ; i ++) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       k=2*i;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);   
       for (j=1; j<= nlstate+1 ; j ++) {        if (popbased==1) {
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          if(mobilav ==0){
   else fprintf(ficgp," \%%*lf (\%%*lf)");            for(i=1; i<=nlstate;i++)
 }                prlim[i][i]=probs[(int)age][i][ij];
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          }else{ /* mobilav */ 
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);            for(i=1; i<=nlstate;i++)
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);              prlim[i][i]=mobaverage[(int)age][i][ij];
       for (j=1; j<= nlstate+1 ; j ++) {          }
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        }
         else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }          for(j=1; j<= nlstate; j++){
       fprintf(ficgp,"\" t\"\" w l 0,");          for(h=0; h<=nhstepm; h++){
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
       for (j=1; j<= nlstate+1 ; j ++) {              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          }
   else fprintf(ficgp," \%%*lf (\%%*lf)");        }
 }          /* This for computing probability of death (h=1 means
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");           computed over hstepm matrices product = hstepm*stepm months) 
       else fprintf(ficgp,"\" t\"\" w l 0,");           as a weighted average of prlim.
     }        */
   }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
            for(i=1,gmp[j]=0.; i<= nlstate; i++)
   /*3eme*/           gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
   for (k1=1; k1<= m ; k1 ++) {        /* end probability of death */
     for (cpt=1; cpt<= nlstate ; cpt ++) {  
       k=2+nlstate*(2*cpt-2);        for(j=1; j<= nlstate; j++) /* vareij */
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          for(h=0; h<=nhstepm; h++){
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);          }
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");  
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");        }
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);  
       } /* End theta */
 */  
       for (i=1; i< nlstate ; i ++) {      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);  
       for(h=0; h<=nhstepm; h++) /* veij */
       }        for(j=1; j<=nlstate;j++)
     }          for(theta=1; theta <=npar; theta++)
   }            trgradg[h][j][theta]=gradg[h][theta][j];
    
   /* CV preval stat */      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     for (k1=1; k1<= m ; k1 ++) {        for(theta=1; theta <=npar; theta++)
     for (cpt=1; cpt<nlstate ; cpt ++) {          trgradgp[j][theta]=gradgp[theta][j];
       k=3;    
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
       for (i=1; i< nlstate ; i ++)        for(j=1;j<=nlstate;j++)
         fprintf(ficgp,"+$%d",k+i+1);          vareij[i][j][(int)age] =0.;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);  
            for(h=0;h<=nhstepm;h++){
       l=3+(nlstate+ndeath)*cpt;        for(k=0;k<=nhstepm;k++){
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
       for (i=1; i< nlstate ; i ++) {          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
         l=3+(nlstate+ndeath)*cpt;          for(i=1;i<=nlstate;i++)
         fprintf(ficgp,"+$%d",l+i+1);            for(j=1;j<=nlstate;j++)
       }              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);          }
     }      }
   }      
        /* pptj */
   /* proba elementaires */      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
    for(i=1,jk=1; i <=nlstate; i++){      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
     for(k=1; k <=(nlstate+ndeath); k++){      for(j=nlstate+1;j<=nlstate+ndeath;j++)
       if (k != i) {        for(i=nlstate+1;i<=nlstate+ndeath;i++)
         for(j=1; j <=ncovmodel; j++){          varppt[j][i]=doldmp[j][i];
              /* end ppptj */
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);      /*  x centered again */
           jk++;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
           fprintf(ficgp,"\n");      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
         }   
       }      if (popbased==1) {
     }        if(mobilav ==0){
    }          for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/        }else{ /* mobilav */ 
      for(jk=1; jk <=m; jk++) {          for(i=1; i<=nlstate;i++)
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);            prlim[i][i]=mobaverage[(int)age][i][ij];
        if (ng==2)        }
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");      }
        else               
          fprintf(ficgp,"\nset title \"Probability\"\n");      /* This for computing probability of death (h=1 means
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
        i=1;         as a weighted average of prlim.
        for(k2=1; k2<=nlstate; k2++) {      */
          k3=i;      for(j=nlstate+1;j<=nlstate+ndeath;j++){
          for(k=1; k<=(nlstate+ndeath); k++) {        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
            if (k != k2){          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
              if(ng==2)      }    
                fprintf(ficgp," %f*exp(p%d+p%d*x",stepm/YEARM,i,i+1);      /* end probability of death */
              else  
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
              ij=1;      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
              for(j=3; j <=ncovmodel; j++) {        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        for(i=1; i<=nlstate;i++){
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
                  ij++;        }
                }      } 
                else      fprintf(ficresprobmorprev,"\n");
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  
              }      fprintf(ficresvij,"%.0f ",age );
              fprintf(ficgp,")/(1");      for(i=1; i<=nlstate;i++)
                      for(j=1; j<=nlstate;j++){
              for(k1=1; k1 <=nlstate; k1++){            fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);        }
                ij=1;      fprintf(ficresvij,"\n");
                for(j=3; j <=ncovmodel; j++){      free_matrix(gp,0,nhstepm,1,nlstate);
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      free_matrix(gm,0,nhstepm,1,nlstate);
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
                    ij++;      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
                  }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                  else    } /* End age */
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    free_vector(gpp,nlstate+1,nlstate+ndeath);
                }    free_vector(gmp,nlstate+1,nlstate+ndeath);
                fprintf(ficgp,")");    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
              }    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
              i=i+ncovmodel;    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); */
        }  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
      }    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
    }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
    fclose(ficgp);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
 }  /* end gnuplot */    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
     /*  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);
 /*************** Moving average **************/  */
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
   
   int i, cpt, cptcod;    free_vector(xp,1,npar);
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    free_matrix(doldm,1,nlstate,1,nlstate);
       for (i=1; i<=nlstate;i++)    free_matrix(dnewm,1,nlstate,1,npar);
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           mobaverage[(int)agedeb][i][cptcod]=0.;    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
        free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for (i=1; i<=nlstate;i++){    fclose(ficresprobmorprev);
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    fclose(ficgp);
           for (cpt=0;cpt<=4;cpt++){    fclose(fichtm);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];  }  
           }  
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;  /************ 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)
       }  {
     }    /* Variance of prevalence limit */
        /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
 }    double **newm;
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
 /************** Forecasting ******************/    int k, cptcode;
 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){    double *xp;
      double *gp, *gm;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    double **gradg, **trgradg;
   int *popage;    double age,agelim;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    int theta;
   double *popeffectif,*popcount;     
   double ***p3mat;    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
   char fileresf[FILENAMELENGTH];    fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
  agelim=AGESUP;        fprintf(ficresvpl," %1d-%1d",i,i);
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    fprintf(ficresvpl,"\n");
   
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    xp=vector(1,npar);
      dnewm=matrix(1,nlstate,1,npar);
      doldm=matrix(1,nlstate,1,nlstate);
   strcpy(fileresf,"f");    
   strcat(fileresf,fileres);    hstepm=1*YEARM; /* Every year of age */
   if((ficresf=fopen(fileresf,"w"))==NULL) {    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     printf("Problem with forecast resultfile: %s\n", fileresf);    agelim = AGESUP;
   }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   printf("Computing forecasting: result on file '%s' \n", fileresf);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
   if (mobilav==1) {      gp=vector(1,nlstate);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      gm=vector(1,nlstate);
     movingaverage(agedeb, fage, ageminpar, mobaverage);  
   }      for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
   stepsize=(int) (stepm+YEARM-1)/YEARM;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   if (stepm<=12) stepsize=1;        }
          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   agelim=AGESUP;        for(i=1;i<=nlstate;i++)
            gp[i] = prlim[i][i];
   hstepm=1;      
   hstepm=hstepm/stepm;        for(i=1; i<=npar; i++) /* Computes gradient */
   yp1=modf(dateintmean,&yp);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   anprojmean=yp;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   yp2=modf((yp1*12),&yp);        for(i=1;i<=nlstate;i++)
   mprojmean=yp;          gm[i] = prlim[i][i];
   yp1=modf((yp2*30.5),&yp);  
   jprojmean=yp;        for(i=1;i<=nlstate;i++)
   if(jprojmean==0) jprojmean=1;          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   if(mprojmean==0) jprojmean=1;      } /* End theta */
    
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);      trgradg =matrix(1,nlstate,1,npar);
    
   for(cptcov=1;cptcov<=i2;cptcov++){      for(j=1; j<=nlstate;j++)
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        for(theta=1; theta <=npar; theta++)
       k=k+1;          trgradg[j][theta]=gradg[theta][j];
       fprintf(ficresf,"\n#******");  
       for(j=1;j<=cptcoveff;j++) {      for(i=1;i<=nlstate;i++)
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        varpl[i][(int)age] =0.;
       }      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       fprintf(ficresf,"******\n");      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       fprintf(ficresf,"# StartingAge FinalAge");      for(i=1;i<=nlstate;i++)
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
        
            fprintf(ficresvpl,"%.0f ",age );
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {      for(i=1; i<=nlstate;i++)
         fprintf(ficresf,"\n");        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);        fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      free_vector(gm,1,nlstate);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      free_matrix(gradg,1,npar,1,nlstate);
           nhstepm = nhstepm/hstepm;      free_matrix(trgradg,1,nlstate,1,npar);
              } /* End age */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;    free_vector(xp,1,npar);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      free_matrix(doldm,1,nlstate,1,npar);
            free_matrix(dnewm,1,nlstate,1,nlstate);
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {  }
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);  
             }  /************ Variance of one-step probabilities  ******************/
             for(j=1; j<=nlstate+ndeath;j++) {  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
               kk1=0.;kk2=0;  {
               for(i=1; i<=nlstate;i++) {                  int i, j=0,  i1, k1, l1, t, tj;
                 if (mobilav==1)    int k2, l2, j1,  z1;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    int k=0,l, cptcode;
                 else {    int first=1, first1;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
                 }    double **dnewm,**doldm;
                    double *xp;
               }    double *gp, *gm;
               if (h==(int)(calagedate+12*cpt)){    double **gradg, **trgradg;
                 fprintf(ficresf," %.3f", kk1);    double **mu;
                            double age,agelim, cov[NCOVMAX];
               }    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
             }    int theta;
           }    char fileresprob[FILENAMELENGTH];
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    char fileresprobcov[FILENAMELENGTH];
         }    char fileresprobcor[FILENAMELENGTH];
       }  
     }    double ***varpij;
   }  
            strcpy(fileresprob,"prob"); 
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   fclose(ficresf);      printf("Problem with resultfile: %s\n", fileresprob);
 }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
 /************** Forecasting ******************/    }
 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){    strcpy(fileresprobcov,"probcov"); 
      strcat(fileresprobcov,fileres);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   int *popage;      printf("Problem with resultfile: %s\n", fileresprobcov);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   double *popeffectif,*popcount;    }
   double ***p3mat,***tabpop,***tabpopprev;    strcpy(fileresprobcor,"probcor"); 
   char filerespop[FILENAMELENGTH];    strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      printf("Problem with resultfile: %s\n", fileresprobcor);
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   agelim=AGESUP;    }
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
      fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
      fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
      printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   strcpy(filerespop,"pop");    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   strcat(filerespop,fileres);    
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     printf("Problem with forecast resultfile: %s\n", filerespop);    fprintf(ficresprob,"# Age");
   }    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   printf("Computing forecasting: result on file '%s' \n", filerespop);    fprintf(ficresprobcov,"# Age");
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    fprintf(ficresprobcov,"# Age");
   
   if (mobilav==1) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    for(i=1; i<=nlstate;i++)
     movingaverage(agedeb, fage, ageminpar, mobaverage);      for(j=1; j<=(nlstate+ndeath);j++){
   }        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
   stepsize=(int) (stepm+YEARM-1)/YEARM;        fprintf(ficresprobcor," p%1d-%1d ",i,j);
   if (stepm<=12) stepsize=1;      }  
     /* fprintf(ficresprob,"\n");
   agelim=AGESUP;    fprintf(ficresprobcov,"\n");
      fprintf(ficresprobcor,"\n");
   hstepm=1;   */
   hstepm=hstepm/stepm;   xp=vector(1,npar);
      dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   if (popforecast==1) {    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     if((ficpop=fopen(popfile,"r"))==NULL) {    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
       printf("Problem with population file : %s\n",popfile);exit(0);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     }    first=1;
     popage=ivector(0,AGESUP);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
     popeffectif=vector(0,AGESUP);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
     popcount=vector(0,AGESUP);      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
          exit(0);
     i=1;      }
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    else{
          fprintf(ficgp,"\n# Routine varprob");
     imx=i;    }
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   }      printf("Problem with html file: %s\n", optionfilehtm);
       fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   for(cptcov=1;cptcov<=i2;cptcov++){      exit(0);
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    }
       k=k+1;    else{
       fprintf(ficrespop,"\n#******");      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
       for(j=1;j<=cptcoveff;j++) {      fprintf(fichtm,"\n");
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       }      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
       fprintf(ficrespop,"******\n");      fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
       fprintf(ficrespop,"# Age");      fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);  
       if (popforecast==1)  fprintf(ficrespop," [Population]");    }
        
       for (cpt=0; cpt<=0;cpt++) {    cov[1]=1;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      tj=cptcoveff;
            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]]);
                  fprintf(ficresprob, "**********\n#\n");
           for (h=0; h<=nhstepm; h++){          fprintf(ficresprobcov, "\n#********** Variable "); 
             if (h==(int) (calagedate+YEARM*cpt)) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          fprintf(ficresprobcov, "**********\n#\n");
             }          
             for(j=1; j<=nlstate+ndeath;j++) {          fprintf(ficgp, "\n#********** Variable "); 
               kk1=0.;kk2=0;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
               for(i=1; i<=nlstate;i++) {                        fprintf(ficgp, "**********\n#\n");
                 if (mobilav==1)          
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          
                 else {          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                 }          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
               }          
               if (h==(int)(calagedate+12*cpt)){          fprintf(ficresprobcor, "\n#********** Variable ");    
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                   /*fprintf(ficrespop," %.3f", kk1);          fprintf(ficresprobcor, "**********\n#");    
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/        }
               }        
             }        for (age=bage; age<=fage; age ++){ 
             for(i=1; i<=nlstate;i++){          cov[2]=age;
               kk1=0.;          for (k=1; k<=cptcovn;k++) {
                 for(j=1; j<=nlstate;j++){            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];          }
                 }          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];          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]]];
           
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           }          gp=vector(1,(nlstate)*(nlstate+ndeath));
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          gm=vector(1,(nlstate)*(nlstate+ndeath));
         }      
       }          for(theta=1; theta <=npar; theta++){
              for(i=1; i<=npar; i++)
   /******/              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {            pmij(pmmij,cov,ncovmodel,xp,nlstate);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);              
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){            k=0;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            for(i=1; i<= (nlstate); i++){
           nhstepm = nhstepm/hstepm;              for(j=1; j<=(nlstate+ndeath);j++){
                          k=k+1;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                gp[k]=pmmij[i][j];
           oldm=oldms;savm=savms;              }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              }
           for (h=0; h<=nhstepm; h++){            
             if (h==(int) (calagedate+YEARM*cpt)) {            for(i=1; i<=npar; i++)
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
             }      
             for(j=1; j<=nlstate+ndeath;j++) {            pmij(pmmij,cov,ncovmodel,xp,nlstate);
               kk1=0.;kk2=0;            k=0;
               for(i=1; i<=nlstate;i++) {                          for(i=1; i<=(nlstate); i++){
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                  for(j=1; j<=(nlstate+ndeath);j++){
               }                k=k+1;
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);                gm[k]=pmmij[i][j];
             }              }
           }            }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       
         }            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
       }              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
    }          }
   }  
            for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
   if (popforecast==1) {          
     free_ivector(popage,0,AGESUP);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
     free_vector(popeffectif,0,AGESUP);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
     free_vector(popcount,0,AGESUP);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   }          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   fclose(ficrespop);  
 }          pmij(pmmij,cov,ncovmodel,x,nlstate);
           
 /***********************************************/          k=0;
 /**************** Main Program *****************/          for(i=1; i<=(nlstate); i++){
 /***********************************************/            for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
 int main(int argc, char *argv[])              mu[k][(int) age]=pmmij[i][j];
 {            }
           }
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   double agedeb, agefin,hf;            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;              varpij[i][j][(int)age] = doldm[i][j];
   
   double fret;          /*printf("\n%d ",(int)age);
   double **xi,tmp,delta;            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   double dum; /* Dummy variable */            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   double ***p3mat;            }*/
   int *indx;  
   char line[MAXLINE], linepar[MAXLINE];          fprintf(ficresprob,"\n%d ",(int)age);
   char title[MAXLINE];          fprintf(ficresprobcov,"\n%d ",(int)age);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];          fprintf(ficresprobcor,"\n%d ",(int)age);
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];  
            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   char filerest[FILENAMELENGTH];            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   char fileregp[FILENAMELENGTH];            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
   char popfile[FILENAMELENGTH];          }
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];          i=0;
   int firstobs=1, lastobs=10;          for (k=1; k<=(nlstate);k++){
   int sdeb, sfin; /* Status at beginning and end */            for (l=1; l<=(nlstate+ndeath);l++){ 
   int c,  h , cpt,l;              i=i++;
   int ju,jl, mi;              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;              for (j=1; j<=i;j++){
   int mobilav=0,popforecast=0;                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   int hstepm, nhstepm;                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;              }
             }
   double bage, fage, age, agelim, agebase;          }/* end of loop for state */
   double ftolpl=FTOL;        } /* end of loop for age */
   double **prlim;  
   double *severity;        /* Confidence intervalle of pij  */
   double ***param; /* Matrix of parameters */        /*
   double  *p;          fprintf(ficgp,"\nset noparametric;unset label");
   double **matcov; /* Matrix of covariance */          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   double ***delti3; /* Scale */          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   double *delti; /* Scale */          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);
   double ***eij, ***vareij;          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   double **varpl; /* Variances of prevalence limits by age */          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
   double *epj, vepp;          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
   double kk1, kk2;        */
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;  
          /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
   char version[80]="Imach version 0.8f, May 2002, INED-EUROREVES ";        for (k2=1; k2<=(nlstate);k2++){
   char *alph[]={"a","a","b","c","d","e"}, str[4];          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
   char z[1]="c", occ;            for (k1=1; k1<=(nlstate);k1++){
 #include <sys/time.h>              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
 #include <time.h>                if(l1==k1) continue;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];                i=(k1-1)*(nlstate+ndeath)+l1;
                  if(i<=j) continue;
   /* long total_usecs;                for (age=bage; age<=fage; age ++){ 
   struct timeval start_time, end_time;                  if ((int)age %5==0){
                      v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   getcwd(pathcd, size);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
   printf("\n%s",version);                    mu2=mu[j][(int) age]/stepm*YEARM;
   if(argc <=1){                    c12=cv12/sqrt(v1*v2);
     printf("\nEnter the parameter file name: ");                    /* Computing eigen value of matrix of covariance */
     scanf("%s",pathtot);                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   }                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   else{                    /* Eigen vectors */
     strcpy(pathtot,argv[1]);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
   }                    /*v21=sqrt(1.-v11*v11); *//* error */
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/                    v21=(lc1-v1)/cv12*v11;
   /*cygwin_split_path(pathtot,path,optionfile);                    v12=-v21;
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/                    v22=v11;
   /* cutv(path,optionfile,pathtot,'\\');*/                    tnalp=v21/v11;
                     if(first1==1){
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);                      first1=0;
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);                      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);
   chdir(path);                    }
   replace(pathc,path);                    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);
                     /*printf(fignu*/
 /*-------- arguments in the command line --------*/                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   strcpy(fileres,"r");                    if(first==1){
   strcat(fileres, optionfilefiname);                      first=0;
   strcat(fileres,".txt");    /* Other files have txt extension */                      fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
   /*---------arguments file --------*/                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       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);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
     printf("Problem with optionfile %s\n",optionfile);                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
     goto end;                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
   }                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   strcpy(filereso,"o");                      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",\
   strcat(filereso,fileres);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   if((ficparo=fopen(filereso,"w"))==NULL) {                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     printf("Problem with Output resultfile: %s\n", filereso);goto end;                    }else{
   }                      first=0;
                       fprintf(fichtm," %d (%.3f),",(int) age, c12);
   /* Reads comments: lines beginning with '#' */                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   while((c=getc(ficpar))=='#' && c!= EOF){                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     ungetc(c,ficpar);                      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",\
     fgets(line, MAXLINE, ficpar);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     puts(line);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     fputs(line,ficparo);                    }/* if first */
   }                  } /* age mod 5 */
   ungetc(c,ficpar);                } /* end loop age */
                 fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
   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);                first=1;
   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);              } /*l12 */
   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);            } /* k12 */
 while((c=getc(ficpar))=='#' && c!= EOF){          } /*l1 */
     ungetc(c,ficpar);        }/* k1 */
     fgets(line, MAXLINE, ficpar);      } /* loop covariates */
     puts(line);    }
     fputs(line,ficparo);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   }    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   ungetc(c,ficpar);    free_vector(xp,1,npar);
      fclose(ficresprob);
        fclose(ficresprobcov);
   covar=matrix(0,NCOVMAX,1,n);    fclose(ficresprobcor);
   cptcovn=0;    fclose(ficgp);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    fclose(fichtm);
   }
   ncovmodel=2+cptcovn;  
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  
    /******************* Printing html file ***********/
   /* Read guess parameters */  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
   /* Reads comments: lines beginning with '#' */                    int lastpass, int stepm, int weightopt, char model[],\
   while((c=getc(ficpar))=='#' && c!= EOF){                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
     ungetc(c,ficpar);                    int popforecast, int estepm ,\
     fgets(line, MAXLINE, ficpar);                    double jprev1, double mprev1,double anprev1, \
     puts(line);                    double jprev2, double mprev2,double anprev2){
     fputs(line,ficparo);    int jj1, k1, i1, cpt;
   }    /*char optionfilehtm[FILENAMELENGTH];*/
   ungetc(c,ficpar);    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
        printf("Problem with %s \n",optionfilehtm), exit(0);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
     for(i=1; i <=nlstate; i++)    }
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
       fprintf(ficparo,"%1d%1d",i1,j1);   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
       printf("%1d%1d",i,j);   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
       for(k=1; k<=ncovmodel;k++){   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
         fscanf(ficpar," %lf",&param[i][j][k]);   - Life expectancies by age and initial health status (estepm=%2d months): 
         printf(" %lf",param[i][j][k]);     <a href=\"e%s\">e%s</a> <br>\n</li>", \
         fprintf(ficparo," %lf",param[i][j][k]);    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
       }  
       fscanf(ficpar,"\n");  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
       printf("\n");  
       fprintf(ficparo,"\n");   m=cptcoveff;
     }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
    
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;   jj1=0;
    for(k1=1; k1<=m;k1++){
   p=param[1][1];     for(i1=1; i1<=ncodemax[k1];i1++){
         jj1++;
   /* Reads comments: lines beginning with '#' */       if (cptcovn > 0) {
   while((c=getc(ficpar))=='#' && c!= EOF){         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     ungetc(c,ficpar);         for (cpt=1; cpt<=cptcoveff;cpt++) 
     fgets(line, MAXLINE, ficpar);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     puts(line);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     fputs(line,ficparo);       }
   }       /* Pij */
   ungetc(c,ficpar);       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);     
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);       /* Quasi-incidences */
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */       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>
   for(i=1; i <=nlstate; i++){  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
     for(j=1; j <=nlstate+ndeath-1; j++){         /* Stable prevalence in each health state */
       fscanf(ficpar,"%1d%1d",&i1,&j1);         for(cpt=1; cpt<nlstate;cpt++){
       printf("%1d%1d",i,j);           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
       fprintf(ficparo,"%1d%1d",i1,j1);  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
       for(k=1; k<=ncovmodel;k++){         }
         fscanf(ficpar,"%le",&delti3[i][j][k]);       for(cpt=1; cpt<=nlstate;cpt++) {
         printf(" %le",delti3[i][j][k]);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
         fprintf(ficparo," %le",delti3[i][j][k]);  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
       }       }
       fscanf(ficpar,"\n");       fprintf(fichtm,"\n<br>- Total life expectancy by age and
       printf("\n");  health expectancies in states (1) and (2): e%s%d.png<br>
       fprintf(ficparo,"\n");  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
     }     } /* end i1 */
   }   }/* End k1 */
   delti=delti3[1][1];   fprintf(fichtm,"</ul>");
    
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
     ungetc(c,ficpar);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
     fgets(line, MAXLINE, ficpar);   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
     puts(line);   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
     fputs(line,ficparo);   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
   }   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
   ungetc(c,ficpar);   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
     - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
   matcov=matrix(1,npar,1,npar);  
   for(i=1; i <=npar; i++){   if(popforecast==1) fprintf(fichtm,"\n
     fscanf(ficpar,"%s",&str);   - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
     printf("%s",str);   - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
     fprintf(ficparo,"%s",str);          <br>",fileres,fileres,fileres,fileres);
     for(j=1; j <=i; j++){   else 
       fscanf(ficpar," %le",&matcov[i][j]);     fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
       printf(" %.5le",matcov[i][j]);  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
       fprintf(ficparo," %.5le",matcov[i][j]);  
     }   m=cptcoveff;
     fscanf(ficpar,"\n");   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     printf("\n");  
     fprintf(ficparo,"\n");   jj1=0;
   }   for(k1=1; k1<=m;k1++){
   for(i=1; i <=npar; i++)     for(i1=1; i1<=ncodemax[k1];i1++){
     for(j=i+1;j<=npar;j++)       jj1++;
       matcov[i][j]=matcov[j][i];       if (cptcovn > 0) {
             fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   printf("\n");         for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     /*-------- Rewriting paramater file ----------*/       }
      strcpy(rfileres,"r");    /* "Rparameterfile */       for(cpt=1; cpt<=nlstate;cpt++) {
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/         fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
      strcat(rfileres,".");    /* */  interval) in state (%d): v%s%d%d.png <br>
      strcat(rfileres,optionfilext);    /* Other files have txt extension */  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
     if((ficres =fopen(rfileres,"w"))==NULL) {       }
       printf("Problem writing new parameter file: %s\n", fileres);goto end;     } /* end i1 */
     }   }/* End k1 */
     fprintf(ficres,"#%s\n",version);   fprintf(fichtm,"</ul>");
      fclose(fichtm);
     /*-------- data file ----------*/  }
     if((fic=fopen(datafile,"r"))==NULL)    {  
       printf("Problem with datafile: %s\n", datafile);goto end;  /******************* Gnuplot file **************/
     }  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     n= lastobs;    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     severity = vector(1,maxwav);    int ng;
     outcome=imatrix(1,maxwav+1,1,n);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
     num=ivector(1,n);      printf("Problem with file %s",optionfilegnuplot);
     moisnais=vector(1,n);      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
     annais=vector(1,n);    }
     moisdc=vector(1,n);  
     andc=vector(1,n);    /*#ifdef windows */
     agedc=vector(1,n);      fprintf(ficgp,"cd \"%s\" \n",pathc);
     cod=ivector(1,n);      /*#endif */
     weight=vector(1,n);  m=pow(2,cptcoveff);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    
     mint=matrix(1,maxwav,1,n);   /* 1eme*/
     anint=matrix(1,maxwav,1,n);    for (cpt=1; cpt<= nlstate ; cpt ++) {
     s=imatrix(1,maxwav+1,1,n);     for (k1=1; k1<= m ; k1 ++) {
     adl=imatrix(1,maxwav+1,1,n);           fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     tab=ivector(1,NCOVMAX);       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);
     ncodemax=ivector(1,8);  
        for (i=1; i<= nlstate ; i ++) {
     i=1;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     while (fgets(line, MAXLINE, fic) != NULL)    {         else fprintf(ficgp," \%%*lf (\%%*lf)");
       if ((i >= firstobs) && (i <=lastobs)) {       }
               fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
         for (j=maxwav;j>=1;j--){       for (i=1; i<= nlstate ; i ++) {
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
           strcpy(line,stra);         else fprintf(ficgp," \%%*lf (\%%*lf)");
           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);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
         }       for (i=1; i<= nlstate ; i ++) {
                 if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);         else fprintf(ficgp," \%%*lf (\%%*lf)");
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);       }  
        fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);     }
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    }
     /*2 eme*/
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    
         for (j=ncovcol;j>=1;j--){    for (k1=1; k1<= m ; k1 ++) { 
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
         }      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
         num[i]=atol(stra);      
              for (i=1; i<= nlstate+1 ; i ++) {
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){        k=2*i;
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
         i=i+1;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       }          else fprintf(ficgp," \%%*lf (\%%*lf)");
     }        }   
     /* printf("ii=%d", ij);        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
        scanf("%d",i);*/        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
   imx=i-1; /* Number of individuals */        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 ++) {
   /* for (i=1; i<=imx; i++){          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;          else fprintf(ficgp," \%%*lf (\%%*lf)");
     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;        fprintf(ficgp,"\" t\"\" w l 0,");
     }*/        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
    /*  for (i=1; i<=imx; i++){        for (j=1; j<= nlstate+1 ; j ++) {
      if (s[4][i]==9)  s[4][i]=-1;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/          else fprintf(ficgp," \%%*lf (\%%*lf)");
          }   
          if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
   /* Calculation of the number of parameter from char model*/        else fprintf(ficgp,"\" t\"\" w l 0,");
   Tvar=ivector(1,15);      }
   Tprod=ivector(1,15);    }
   Tvaraff=ivector(1,15);    
   Tvard=imatrix(1,15,1,2);    /*3eme*/
   Tage=ivector(1,15);          
        for (k1=1; k1<= m ; k1 ++) { 
   if (strlen(model) >1){      for (cpt=1; cpt<= nlstate ; cpt ++) {
     j=0, j1=0, k1=1, k2=1;        k=2+nlstate*(2*cpt-2);
     j=nbocc(model,'+');        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     j1=nbocc(model,'*');        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
     cptcovn=j+1;        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     cptcovprod=j1;          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
              fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     strcpy(modelsav,model);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
       printf("Error. Non available option model=%s ",model);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
       goto end;          
     }        */
            for (i=1; i< nlstate ; i ++) {
     for(i=(j+1); i>=1;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);
       cutv(stra,strb,modelsav,'+');          
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);        } 
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      }
       /*scanf("%d",i);*/    }
       if (strchr(strb,'*')) {    
         cutv(strd,strc,strb,'*');    /* CV preval stat */
         if (strcmp(strc,"age")==0) {    for (k1=1; k1<= m ; k1 ++) { 
           cptcovprod--;      for (cpt=1; cpt<nlstate ; cpt ++) {
           cutv(strb,stre,strd,'V');        k=3;
           Tvar[i]=atoi(stre);        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
           cptcovage++;        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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
             Tage[cptcovage]=i;        
             /*printf("stre=%s ", stre);*/        for (i=1; i< nlstate ; i ++)
         }          fprintf(ficgp,"+$%d",k+i+1);
         else if (strcmp(strd,"age")==0) {        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
           cptcovprod--;        
           cutv(strb,stre,strc,'V');        l=3+(nlstate+ndeath)*cpt;
           Tvar[i]=atoi(stre);        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
           cptcovage++;        for (i=1; i< nlstate ; i ++) {
           Tage[cptcovage]=i;          l=3+(nlstate+ndeath)*cpt;
         }          fprintf(ficgp,"+$%d",l+i+1);
         else {        }
           cutv(strb,stre,strc,'V');        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
           Tvar[i]=ncovcol+k1;      } 
           cutv(strb,strc,strd,'V');    }  
           Tprod[k1]=i;    
           Tvard[k1][1]=atoi(strc);    /* proba elementaires */
           Tvard[k1][2]=atoi(stre);    for(i=1,jk=1; i <=nlstate; i++){
           Tvar[cptcovn+k2]=Tvard[k1][1];      for(k=1; k <=(nlstate+ndeath); k++){
           Tvar[cptcovn+k2+1]=Tvard[k1][2];        if (k != i) {
           for (k=1; k<=lastobs;k++)          for(j=1; j <=ncovmodel; j++){
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
           k1++;            jk++; 
           k2=k2+2;            fprintf(ficgp,"\n");
         }          }
       }        }
       else {      }
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/     }
        /*  scanf("%d",i);*/  
       cutv(strd,strc,strb,'V');     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
       Tvar[i]=atoi(strc);       for(jk=1; jk <=m; jk++) {
       }         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
       strcpy(modelsav,stra);           if (ng==2)
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
         scanf("%d",i);*/         else
     }           fprintf(ficgp,"\nset title \"Probability\"\n");
 }         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
           i=1;
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);         for(k2=1; k2<=nlstate; k2++) {
   printf("cptcovprod=%d ", cptcovprod);           k3=i;
   scanf("%d ",i);*/           for(k=1; k<=(nlstate+ndeath); k++) {
     fclose(fic);             if (k != k2){
                if(ng==2)
     /*  if(mle==1){*/                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
     if (weightopt != 1) { /* Maximisation without weights*/               else
       for(i=1;i<=n;i++) weight[i]=1.0;                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
     }               ij=1;
     /*-calculation of age at interview from date of interview and age at death -*/               for(j=3; j <=ncovmodel; j++) {
     agev=matrix(1,maxwav,1,imx);                 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]]]);
     for (i=1; i<=imx; i++) {                   ij++;
       for(m=2; (m<= maxwav); m++) {                 }
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){                 else
          anint[m][i]=9999;                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
          s[m][i]=-1;               }
        }               fprintf(ficgp,")/(1");
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;               
       }               for(k1=1; k1 <=nlstate; k1++){   
     }                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
     for (i=1; i<=imx; i++)  {                 for(j=3; j <=ncovmodel; j++){
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
       for(m=1; (m<= maxwav); m++){                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
         if(s[m][i] >0){                     ij++;
           if (s[m][i] >= nlstate+1) {                   }
             if(agedc[i]>0)                   else
               if(moisdc[i]!=99 && andc[i]!=9999)                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                 agev[m][i]=agedc[i];                 }
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/                 fprintf(ficgp,")");
            else {               }
               if (andc[i]!=9999){               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
               agev[m][i]=-1;               i=i+ncovmodel;
               }             }
             }           } /* end k */
           }         } /* end k2 */
           else if(s[m][i] !=9){ /* Should no more exist */       } /* end jk */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);     } /* end ng */
             if(mint[m][i]==99 || anint[m][i]==9999)     fclose(ficgp); 
               agev[m][i]=1;  }  /* end gnuplot */
             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);*/  /*************** Moving average **************/
             }  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
             else if(agev[m][i] >agemax){  
               agemax=agev[m][i];    int i, cpt, cptcod;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    int modcovmax =1;
             }    int mobilavrange, mob;
             /*agev[m][i]=anint[m][i]-annais[i];*/    double age;
             /*   agev[m][i] = age[i]+2*m;*/  
           }    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
           else { /* =9 */                             a covariate has 2 modalities */
             agev[m][i]=1;    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
             s[m][i]=-1;  
           }    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
         }      if(mobilav==1) mobilavrange=5; /* default */
         else /*= 0 Unknown */      else mobilavrange=mobilav;
           agev[m][i]=1;      for (age=bage; age<=fage; age++)
       }        for (i=1; i<=nlstate;i++)
              for (cptcod=1;cptcod<=modcovmax;cptcod++)
     }            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
     for (i=1; i<=imx; i++)  {      /* We keep the original values on the extreme ages bage, fage and for 
       for(m=1; (m<= maxwav); m++){         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
         if (s[m][i] > (nlstate+ndeath)) {         we use a 5 terms etc. until the borders are no more concerned. 
           printf("Error: Wrong value in nlstate or ndeath\n");        */ 
           goto end;      for (mob=3;mob <=mobilavrange;mob=mob+2){
         }        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
       }          for (i=1; i<=nlstate;i++){
     }            for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);                for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
     free_vector(severity,1,maxwav);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
     free_imatrix(outcome,1,maxwav+1,1,n);                }
     free_vector(moisnais,1,n);              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
     free_vector(annais,1,n);            }
     /* free_matrix(mint,1,maxwav,1,n);          }
        free_matrix(anint,1,maxwav,1,n);*/        }/* end age */
     free_vector(moisdc,1,n);      }/* end mob */
     free_vector(andc,1,n);    }else return -1;
     return 0;
      }/* End movingaverage */
     wav=ivector(1,imx);  
     dh=imatrix(1,lastpass-firstpass+1,1,imx);  
     mw=imatrix(1,lastpass-firstpass+1,1,imx);  /************** Forecasting ******************/
      prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* Concatenates waves */    /* proj1, year, month, day of starting projection 
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);       agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
       Tcode=ivector(1,100);    */
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
       ncodemax[1]=1;    int *popage;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    double agec; /* generic age */
          double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
    codtab=imatrix(1,100,1,10);    double *popeffectif,*popcount;
    h=0;    double ***p3mat;
    m=pow(2,cptcoveff);    double ***mobaverage;
      char fileresf[FILENAMELENGTH];
    for(k=1;k<=cptcoveff; k++){  
      for(i=1; i <=(m/pow(2,k));i++){    agelim=AGESUP;
        for(j=1; j <= ncodemax[k]; j++){    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){   
            h++;    strcpy(fileresf,"f"); 
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;    strcat(fileresf,fileres);
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/    if((ficresf=fopen(fileresf,"w"))==NULL) {
          }      printf("Problem with forecast resultfile: %s\n", fileresf);
        }      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
      }    }
    }    printf("Computing forecasting: result on file '%s' \n", fileresf);
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
       codtab[1][2]=1;codtab[2][2]=2; */  
    /* for(i=1; i <=m ;i++){    if (cptcoveff==0) ncodemax[cptcoveff]=1;
       for(k=1; k <=cptcovn; k++){  
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);    if (mobilav!=0) {
       }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       printf("\n");      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
       }        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       scanf("%d",i);*/        printf(" Error in movingaverage mobilav=%d\n",mobilav);
          }
    /* Calculates basic frequencies. Computes observed prevalence at single age    }
        and prints on file fileres'p'. */  
     stepsize=(int) (stepm+YEARM-1)/YEARM;
        if (stepm<=12) stepsize=1;
        if(estepm < stepm){
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      printf ("Problem %d lower than %d\n",estepm, stepm);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    }
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    else  hstepm=estepm;   
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    hstepm=hstepm/stepm; 
          yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
     /* For Powell, parameters are in a vector p[] starting at p[1]                                 fractional in yp1 */
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    anprojmean=yp;
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     if(mle==1){    yp1=modf((yp2*30.5),&yp);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    jprojmean=yp;
     }    if(jprojmean==0) jprojmean=1;
        if(mprojmean==0) jprojmean=1;
     /*--------- 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);    i1=cptcoveff;
      if (cptcovn < 1){i1=1;}
     
    jk=1;    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    fprintf(ficresf,"#****** Routine prevforecast **\n");
    for(i=1,jk=1; i <=nlstate; i++){  
      for(k=1; k <=(nlstate+ndeath); k++){    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
        if (k != i)      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
          {        k=k+1;
            printf("%d%d ",i,k);        fprintf(ficresf,"\n#******");
            fprintf(ficres,"%1d%1d ",i,k);        for(j=1;j<=cptcoveff;j++) {
            for(j=1; j <=ncovmodel; j++){          fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
              printf("%f ",p[jk]);        }
              fprintf(ficres,"%f ",p[jk]);        fprintf(ficresf,"******\n");
              jk++;        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
            }        for(j=1; j<=nlstate+ndeath;j++){ 
            printf("\n");          for(i=1; i<=nlstate;i++)              
            fprintf(ficres,"\n");            fprintf(ficresf," p%d%d",i,j);
          }          fprintf(ficresf," p.%d",j);
      }        }
    }        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
  if(mle==1){          fprintf(ficresf,"\n");
     /* Computing hessian and covariance matrix */          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
     ftolhess=ftol; /* Usually correct */  
     hesscov(matcov, p, npar, delti, ftolhess, func);          for (agec=fage; agec>=(ageminpar-1); agec--){ 
  }            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");            nhstepm = nhstepm/hstepm; 
     printf("# Scales (for hessian or gradient estimation)\n");            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      for(i=1,jk=1; i <=nlstate; i++){            oldm=oldms;savm=savms;
       for(j=1; j <=nlstate+ndeath; j++){            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
         if (j!=i) {          
           fprintf(ficres,"%1d%1d",i,j);            for (h=0; h<=nhstepm; h++){
           printf("%1d%1d",i,j);              if (h==(int) (YEARM*yearp)) {
           for(k=1; k<=ncovmodel;k++){                fprintf(ficresf,"\n");
             printf(" %.5e",delti[jk]);                for(j=1;j<=cptcoveff;j++) 
             fprintf(ficres," %.5e",delti[jk]);                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             jk++;                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
           }              } 
           printf("\n");              for(j=1; j<=nlstate+ndeath;j++) {
           fprintf(ficres,"\n");                ppij=0.;
         }                for(i=1; i<=nlstate;i++) {
       }                  if (mobilav==1) 
      }                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                      else {
     k=1;                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
     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");                  }
     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 (h==(int)(YEARM*yearp))
     for(i=1;i<=npar;i++){                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
       /*  if (k>nlstate) k=1;                }
       i1=(i-1)/(ncovmodel*nlstate)+1;                if (h==(int)(YEARM*yearp)){
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);                  fprintf(ficresf," %.3f", ppij);
       printf("%s%d%d",alph[k],i1,tab[i]);*/                }
       fprintf(ficres,"%3d",i);              }
       printf("%3d",i);            }
       for(j=1; j<=i;j++){            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(ficres," %.5e",matcov[i][j]);          }
         printf(" %.5e",matcov[i][j]);        }
       }      }
       fprintf(ficres,"\n");    }
       printf("\n");         
       k++;    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  
        fclose(ficresf);
     while((c=getc(ficpar))=='#' && c!= EOF){  }
       ungetc(c,ficpar);  
       fgets(line, MAXLINE, ficpar);  /************** Forecasting *****not tested NB*************/
       puts(line);  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){
       fputs(line,ficparo);    
     }    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     ungetc(c,ficpar);    int *popage;
     estepm=0;    double calagedatem, agelim, kk1, kk2;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);    double *popeffectif,*popcount;
     if (estepm==0 || estepm < stepm) estepm=stepm;    double ***p3mat,***tabpop,***tabpopprev;
     if (fage <= 2) {    double ***mobaverage;
       bage = ageminpar;    char filerespop[FILENAMELENGTH];
       fage = agemaxpar;  
     }    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    agelim=AGESUP;
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    
      prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     while((c=getc(ficpar))=='#' && c!= EOF){    
     ungetc(c,ficpar);    
     fgets(line, MAXLINE, ficpar);    strcpy(filerespop,"pop"); 
     puts(line);    strcat(filerespop,fileres);
     fputs(line,ficparo);    if((ficrespop=fopen(filerespop,"w"))==NULL) {
   }      printf("Problem with forecast resultfile: %s\n", filerespop);
   ungetc(c,ficpar);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
      }
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    printf("Computing forecasting: result on file '%s' \n", filerespop);
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  
          if (cptcoveff==0) ncodemax[cptcoveff]=1;
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    if (mobilav!=0) {
     fgets(line, MAXLINE, ficpar);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     puts(line);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
     fputs(line,ficparo);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   }        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   ungetc(c,ficpar);      }
      }
   
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    stepsize=(int) (stepm+YEARM-1)/YEARM;
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    if (stepm<=12) stepsize=1;
     
   fscanf(ficpar,"pop_based=%d\n",&popbased);    agelim=AGESUP;
   fprintf(ficparo,"pop_based=%d\n",popbased);      
   fprintf(ficres,"pop_based=%d\n",popbased);      hstepm=1;
      hstepm=hstepm/stepm; 
   while((c=getc(ficpar))=='#' && c!= EOF){    
     ungetc(c,ficpar);    if (popforecast==1) {
     fgets(line, MAXLINE, ficpar);      if((ficpop=fopen(popfile,"r"))==NULL) {
     puts(line);        printf("Problem with population file : %s\n",popfile);exit(0);
     fputs(line,ficparo);        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
   }      } 
   ungetc(c,ficpar);      popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
   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);      popcount=vector(0,AGESUP);
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);      
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);      i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
 while((c=getc(ficpar))=='#' && c!= EOF){      imx=i;
     ungetc(c,ficpar);      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     fgets(line, MAXLINE, ficpar);    }
     puts(line);  
     fputs(line,ficparo);    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
   }     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   ungetc(c,ficpar);        k=k+1;
         fprintf(ficrespop,"\n#******");
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);        for(j=1;j<=cptcoveff;j++) {
   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(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);        }
         fprintf(ficrespop,"******\n");
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
 /*------------ gnuplot -------------*/        if (popforecast==1)  fprintf(ficrespop," [Population]");
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);        
          for (cpt=0; cpt<=0;cpt++) { 
 /*------------ free_vector  -------------*/          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
  chdir(path);          
            for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
  free_ivector(wav,1,imx);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);            nhstepm = nhstepm/hstepm; 
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);              
  free_ivector(num,1,n);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  free_vector(agedc,1,n);            oldm=oldms;savm=savms;
  /*free_matrix(covar,1,NCOVMAX,1,n);*/            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
  fclose(ficparo);          
  fclose(ficres);            for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
 /*--------- index.htm --------*/                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);              for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                  for(i=1; i<=nlstate;i++) {              
   /*--------------- Prevalence limit --------------*/                  if (mobilav==1) 
                      kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
   strcpy(filerespl,"pl");                  else {
   strcat(filerespl,fileres);                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
   if((ficrespl=fopen(filerespl,"w"))==NULL) {                  }
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;                }
   }                if (h==(int)(calagedatem+12*cpt)){
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
   fprintf(ficrespl,"#Prevalence limit\n");                    /*fprintf(ficrespop," %.3f", kk1);
   fprintf(ficrespl,"#Age ");                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);                }
   fprintf(ficrespl,"\n");              }
                for(i=1; i<=nlstate;i++){
   prlim=matrix(1,nlstate,1,nlstate);                kk1=0.;
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                  for(j=1; j<=nlstate;j++){
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                  }
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */              }
   k=0;  
   agebase=ageminpar;              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
   agelim=agemaxpar;                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
   ftolpl=1.e-10;            }
   i1=cptcoveff;            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if (cptcovn < 1){i1=1;}          }
         }
   for(cptcov=1;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]);*/        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
         fprintf(ficrespl,"\n#******");          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
         for(j=1;j<=cptcoveff;j++)          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
         fprintf(ficrespl,"******\n");            nhstepm = nhstepm/hstepm; 
                    
         for (age=agebase; age<=agelim; age++){            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            oldm=oldms;savm=savms;
           fprintf(ficrespl,"%.0f",age );            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           for(i=1; i<=nlstate;i++)            for (h=0; h<=nhstepm; h++){
           fprintf(ficrespl," %.5f", prlim[i][i]);              if (h==(int) (calagedatem+YEARM*cpt)) {
           fprintf(ficrespl,"\n");                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
         }              } 
       }              for(j=1; j<=nlstate+ndeath;j++) {
     }                kk1=0.;kk2=0;
   fclose(ficrespl);                for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
   /*------------- h Pij x at various ages ------------*/                }
                  if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);              }
   if((ficrespij=fopen(filerespij,"w"))==NULL) {            }
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }          }
   printf("Computing pij: result on file '%s' \n", filerespij);        }
       } 
   stepsize=(int) (stepm+YEARM-1)/YEARM;    }
   /*if (stepm<=24) stepsize=2;*/   
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   agelim=AGESUP;  
   hstepm=stepsize*YEARM; /* Every year of age */    if (popforecast==1) {
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */      free_ivector(popage,0,AGESUP);
        free_vector(popeffectif,0,AGESUP);
   k=0;      free_vector(popcount,0,AGESUP);
   for(cptcov=1;cptcov<=i1;cptcov++){    }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       k=k+1;    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         fprintf(ficrespij,"\n#****** ");    fclose(ficrespop);
         for(j=1;j<=cptcoveff;j++)  }
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespij,"******\n");  /***********************************************/
          /**************** Main Program *****************/
         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 */  int main(int argc, char *argv[])
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  {
           oldm=oldms;savm=savms;    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
           fprintf(ficrespij,"# Age");    double agedeb, agefin,hf;
           for(i=1; i<=nlstate;i++)    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
             for(j=1; j<=nlstate+ndeath;j++)  
               fprintf(ficrespij," %1d-%1d",i,j);    double fret;
           fprintf(ficrespij,"\n");    double **xi,tmp,delta;
            for (h=0; h<=nhstepm; h++){  
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    double dum; /* Dummy variable */
             for(i=1; i<=nlstate;i++)    double ***p3mat;
               for(j=1; j<=nlstate+ndeath;j++)    double ***mobaverage;
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    int *indx;
             fprintf(ficrespij,"\n");    char line[MAXLINE], linepar[MAXLINE];
              }    char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int firstobs=1, lastobs=10;
           fprintf(ficrespij,"\n");    int sdeb, sfin; /* Status at beginning and end */
         }    int c,  h , cpt,l;
     }    int ju,jl, mi;
   }    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
   fclose(ficrespij);    int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   /*---------- Forecasting ------------------*/  
   if((stepm == 1) && (strcmp(model,".")==0)){    double bage, fage, age, agelim, agebase;
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    double ftolpl=FTOL;
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    double **prlim;
   }    double *severity;
   else{    double ***param; /* Matrix of parameters */
     erreur=108;    double  *p;
     printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);    double **matcov; /* Matrix of covariance */
   }    double ***delti3; /* Scale */
      double *delti; /* Scale */
     double ***eij, ***vareij;
   /*---------- Health expectancies and variances ------------*/    double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
   strcpy(filerest,"t");    double kk1, kk2;
   strcat(filerest,fileres);    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   if((ficrest=fopen(filerest,"w"))==NULL) {  
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    char *alph[]={"a","a","b","c","d","e"}, str[4];
   }  
   printf("Computing Total LEs with variances: file '%s' \n", filerest);  
     char z[1]="c", occ;
   #include <sys/time.h>
   strcpy(filerese,"e");  #include <time.h>
   strcat(filerese,fileres);    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
   if((ficreseij=fopen(filerese,"w"))==NULL) {   
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    /* long total_usecs;
   }       struct timeval start_time, end_time;
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    
        gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
  strcpy(fileresv,"v");    getcwd(pathcd, size);
   strcat(fileresv,fileres);  
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    printf("\n%s",version);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    if(argc <=1){
   }      printf("\nEnter the parameter file name: ");
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      scanf("%s",pathtot);
   calagedate=-1;    }
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    else{
       strcpy(pathtot,argv[1]);
   k=0;    }
   for(cptcov=1;cptcov<=i1;cptcov++){    /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    /*cygwin_split_path(pathtot,path,optionfile);
       k=k+1;      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
       fprintf(ficrest,"\n#****** ");    /* cutv(path,optionfile,pathtot,'\\');*/
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
       fprintf(ficrest,"******\n");    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
       fprintf(ficreseij,"\n#****** ");    replace(pathc,path);
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /*-------- arguments in the command line --------*/
       fprintf(ficreseij,"******\n");  
     /* Log file */
       fprintf(ficresvij,"\n#****** ");    strcat(filelog, optionfilefiname);
       for(j=1;j<=cptcoveff;j++)    strcat(filelog,".log");    /* */
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    if((ficlog=fopen(filelog,"w"))==NULL)    {
       fprintf(ficresvij,"******\n");      printf("Problem with logfile %s\n",filelog);
       goto end;
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    }
       oldm=oldms;savm=savms;    fprintf(ficlog,"Log filename:%s\n",filelog);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);      fprintf(ficlog,"\n%s",version);
      fprintf(ficlog,"\nEnter the parameter file name: ");
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
       oldm=oldms;savm=savms;    fflush(ficlog);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);  
        /* */
     strcpy(fileres,"r");
      strcat(fileres, optionfilefiname);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    strcat(fileres,".txt");    /* Other files have txt extension */
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);  
       fprintf(ficrest,"\n");    /*---------arguments file --------*/
   
       epj=vector(1,nlstate+1);    if((ficpar=fopen(optionfile,"r"))==NULL)    {
       for(age=bage; age <=fage ;age++){      printf("Problem with optionfile %s\n",optionfile);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
         if (popbased==1) {      goto end;
           for(i=1; i<=nlstate;i++)    }
             prlim[i][i]=probs[(int)age][i][k];  
         }    strcpy(filereso,"o");
            strcat(filereso,fileres);
         fprintf(ficrest," %4.0f",age);    if((ficparo=fopen(filereso,"w"))==NULL) {
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){      printf("Problem with Output resultfile: %s\n", filereso);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
             epj[j] += prlim[i][i]*eij[i][j][(int)age];      goto end;
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    }
           }  
           epj[nlstate+1] +=epj[j];    /* Reads comments: lines beginning with '#' */
         }    while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
         for(i=1, vepp=0.;i <=nlstate;i++)      fgets(line, MAXLINE, ficpar);
           for(j=1;j <=nlstate;j++)      puts(line);
             vepp += vareij[i][j][(int)age];      fputs(line,ficparo);
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    }
         for(j=1;j <=nlstate;j++){    ungetc(c,ficpar);
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));  
         }    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);
         fprintf(ficrest,"\n");    printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
       }    fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     }    while((c=getc(ficpar))=='#' && c!= EOF){
   }      ungetc(c,ficpar);
 free_matrix(mint,1,maxwav,1,n);      fgets(line, MAXLINE, ficpar);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);      puts(line);
     free_vector(weight,1,n);      fputs(line,ficparo);
   fclose(ficreseij);    }
   fclose(ficresvij);    ungetc(c,ficpar);
   fclose(ficrest);    
   fclose(ficpar);     
   free_vector(epj,1,nlstate+1);    covar=matrix(0,NCOVMAX,1,n); 
      cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
   /*------- Variance limit prevalence------*/      if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
   strcpy(fileresvpl,"vpl");    ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
   strcat(fileresvpl,fileres);    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    /* Read guess parameters */
     exit(0);    /* Reads comments: lines beginning with '#' */
   }    while((c=getc(ficpar))=='#' && c!= EOF){
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);      ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
   k=0;      puts(line);
   for(cptcov=1;cptcov<=i1;cptcov++){      fputs(line,ficparo);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    }
       k=k+1;    ungetc(c,ficpar);
       fprintf(ficresvpl,"\n#****** ");    
       for(j=1;j<=cptcoveff;j++)    param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    for(i=1; i <=nlstate; i++)
       fprintf(ficresvpl,"******\n");      for(j=1; j <=nlstate+ndeath-1; j++){
              fscanf(ficpar,"%1d%1d",&i1,&j1);
       varpl=matrix(1,nlstate,(int) bage, (int) fage);        fprintf(ficparo,"%1d%1d",i1,j1);
       oldm=oldms;savm=savms;        if(mle==1)
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          printf("%1d%1d",i,j);
     }        fprintf(ficlog,"%1d%1d",i,j);
  }        for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
   fclose(ficresvpl);          if(mle==1){
             printf(" %lf",param[i][j][k]);
   /*---------- End : free ----------------*/            fprintf(ficlog," %lf",param[i][j][k]);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);          }
            else
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);            fprintf(ficlog," %lf",param[i][j][k]);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);          fprintf(ficparo," %lf",param[i][j][k]);
          }
          fscanf(ficpar,"\n");
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);        if(mle==1)
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);          printf("\n");
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);        fprintf(ficlog,"\n");
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);        fprintf(ficparo,"\n");
        }
   free_matrix(matcov,1,npar,1,npar);    
   free_vector(delti,1,npar);    npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   free_matrix(agev,1,maxwav,1,imx);  
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    p=param[1][1];
     
   if(erreur >0)    /* Reads comments: lines beginning with '#' */
     printf("End of Imach with error or warning %d\n",erreur);    while((c=getc(ficpar))=='#' && c!= EOF){
   else   printf("End of Imach\n");      ungetc(c,ficpar);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      fgets(line, MAXLINE, ficpar);
        puts(line);
   /* 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);*/      fputs(line,ficparo);
   /*printf("Total time was %d uSec.\n", total_usecs);*/    }
   /*------ End -----------*/    ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
  end:    /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
 #ifdef windows    for(i=1; i <=nlstate; i++){
   /* chdir(pathcd);*/      for(j=1; j <=nlstate+ndeath-1; j++){
 #endif        fscanf(ficpar,"%1d%1d",&i1,&j1);
  /*system("wgnuplot graph.plt");*/        printf("%1d%1d",i,j);
  /*system("../gp37mgw/wgnuplot graph.plt");*/        fprintf(ficparo,"%1d%1d",i1,j1);
  /*system("cd ../gp37mgw");*/        for(k=1; k<=ncovmodel;k++){
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/          fscanf(ficpar,"%le",&delti3[i][j][k]);
  strcpy(plotcmd,GNUPLOTPROGRAM);          printf(" %le",delti3[i][j][k]);
  strcat(plotcmd," ");          fprintf(ficparo," %le",delti3[i][j][k]);
  strcat(plotcmd,optionfilegnuplot);        }
  system(plotcmd);        fscanf(ficpar,"\n");
         printf("\n");
 #ifdef windows        fprintf(ficparo,"\n");
   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: ");    delti=delti3[1][1];
     scanf("%s",z);  
     if (z[0] == 'c') system("./imach");  
     else if (z[0] == 'e') system(optionfilehtm);    /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     else if (z[0] == 'g') system(plotcmd);    
     else if (z[0] == 'q') exit(0);    /* Reads comments: lines beginning with '#' */
   }    while((c=getc(ficpar))=='#' && c!= EOF){
 #endif      ungetc(c,ficpar);
 }      fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
           fprintf(ficlog," %.5le",matcov[i][j]);
         }
         else
           fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=ivector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if(moisdc[i]!=99 && andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if (andc[i]!=9999){
                   printf("Warning negative age at death: %d line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if(mint[m][i]==99 || anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
   
       pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     jk=1;
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) 
           {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
       }
     }
     if(mle==1){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle==1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     fclose(ficgp);
     printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfile);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
   \n
   Total number of observations=%d <br>\n
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
   <hr  size=\"2\" color=\"#EC5E5E\">
    <ul><li><h4>Parameter files</h4>\n
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
    - Log file of the run: <a href=\"%s\">%s</a><br>\n
    - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
      fclose(fichtm);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     chdir(path);
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_ivector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     /*  fclose(fichtm);*/
     /*  fclose(ficgp);*/ /* ALready done */
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     
     /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
     /*printf("Total time was %d uSec.\n", total_usecs);*/
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting: %s\n",plotcmd);fflush(stdout);
     system(plotcmd);
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   

Removed from v.1.45  
changed lines
  Added in v.1.74


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