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version 1.35, 2002/03/26 17:08:39 version 1.71, 2003/03/28 13:32:54
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
   probabibility to be observed in state j at the second wave    probability to be observed in state j at the second wave
   conditional to be observed in state i at the first wave. Therefore    conditional to be observed in state i at the first wave. Therefore
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   'age' is age and 'sex' is a covariate. If you want to have a more    'age' is age and 'sex' is a covariate. If you want to have a more
   complex model than "constant and age", you should modify the program    complex model than "constant and age", you should modify the program
   where the markup *Covariates have to be included here again* invites    where the markup *Covariates have to be included here again* invites
   you to do it.  More covariates you add, slower the    you to do it.  More covariates you add, slower the
   convergence.    convergence.
   
   The advantage of this computer programme, compared to a simple    The advantage of this computer programme, compared to a simple
   multinomial logistic model, is clear when the delay between waves is not    multinomial logistic model, is clear when the delay between waves is not
   identical for each individual. Also, if a individual missed an    identical for each individual. Also, if a individual missed an
   intermediate interview, the information is lost, but taken into    intermediate interview, the information is lost, but taken into
   account using an interpolation or extrapolation.      account using an interpolation or extrapolation.  
   
   hPijx is the probability to be observed in state i at age x+h    hPijx is the probability to be observed in state i at age x+h
   conditional to the observed state i at age x. The delay 'h' can be    conditional to the observed state i at age x. The delay 'h' can be
   split into an exact number (nh*stepm) of unobserved intermediate    split into an exact number (nh*stepm) of unobserved intermediate
   states. This elementary transition (by month or quarter trimester,    states. This elementary transition (by month, quarter,
   semester or year) is model as a multinomial logistic.  The hPx    semester or year) is modelled as a multinomial logistic.  The hPx
   matrix is simply the matrix product of nh*stepm elementary matrices    matrix is simply the matrix product of nh*stepm elementary matrices
   and the contribution of each individual to the likelihood is simply    and the contribution of each individual to the likelihood is simply
   hPijx.    hPijx.
   
   Also this programme outputs the covariance matrix of the parameters but also    Also this programme outputs the covariance matrix of the parameters but also
   of the life expectancies. It also computes the prevalence limits.    of the life expectancies. It also computes the stable prevalence. 
      
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
            Institut national d'études démographiques, Paris.             Institut national d'études démographiques, Paris.
   This software have been partly granted by Euro-REVES, a concerted action    This software have been partly granted by Euro-REVES, a concerted action
   from the European Union.    from the European Union.
   It is copyrighted identically to a GNU software product, ie programme and    It is copyrighted identically to a GNU software product, ie programme and
   software can be distributed freely for non commercial use. Latest version    software can be distributed freely for non commercial use. Latest version
   can be accessed at http://euroreves.ined.fr/imach .    can be accessed at http://euroreves.ined.fr/imach .
   **********************************************************************/    **********************************************************************/
     
 #include <math.h>  #include <math.h>
 #include <stdio.h>  #include <stdio.h>
 #include <stdlib.h>  #include <stdlib.h>
 #include <unistd.h>  #include <unistd.h>
   
 #define MAXLINE 256  #define MAXLINE 256
 #define GNUPLOTPROGRAM "wgnuplot"  #define GNUPLOTPROGRAM "gnuplot"
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define FILENAMELENGTH 80  #define FILENAMELENGTH 80
 /*#define DEBUG*/  /*#define DEBUG*/
 #define windows  #define windows
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
 #define NINTERVMAX 8  #define NINTERVMAX 8
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #define NCOVMAX 8 /* Maximum number of covariates */  #define NCOVMAX 8 /* Maximum number of covariates */
 #define MAXN 20000  #define MAXN 20000
 #define YEARM 12. /* Number of months per year */  #define YEARM 12. /* Number of months per year */
 #define AGESUP 130  #define AGESUP 130
 #define AGEBASE 40  #define AGEBASE 40
   #ifdef windows
   #define DIRSEPARATOR '\\'
 int erreur; /* Error number */  #define ODIRSEPARATOR '/'
 int nvar;  #else
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  #define DIRSEPARATOR '/'
 int npar=NPARMAX;  #define ODIRSEPARATOR '\\'
 int nlstate=2; /* Number of live states */  #endif
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  char version[80]="Imach version 0.92, February 2003, INED-EUROREVES ";
 int popbased=0;  int erreur; /* Error number */
   int nvar;
 int *wav; /* Number of waves for this individuual 0 is possible */  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 int maxwav; /* Maxim number of waves */  int npar=NPARMAX;
 int jmin, jmax; /* min, max spacing between 2 waves */  int nlstate=2; /* Number of live states */
 int mle, weightopt;  int ndeath=1; /* Number of dead states */
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  int popbased=0;
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */  int *wav; /* Number of waves for this individuual 0 is possible */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  int maxwav; /* Maxim number of waves */
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  int jmin, jmax; /* min, max spacing between 2 waves */
 FILE *ficgp,*ficresprob,*ficpop;  int mle, weightopt;
 FILE *ficreseij;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   char filerese[FILENAMELENGTH];  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
  FILE  *ficresvij;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   char fileresv[FILENAMELENGTH];             * wave mi and wave mi+1 is not an exact multiple of stepm. */
  FILE  *ficresvpl;  double jmean; /* Mean space between 2 waves */
   char fileresvpl[FILENAMELENGTH];  double **oldm, **newm, **savm; /* Working pointers to matrices */
   double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 #define NR_END 1  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 #define FREE_ARG char*  FILE *ficlog;
 #define FTOL 1.0e-10  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
 #define NRANSI  FILE *fichtm; /* Html File */
 #define ITMAX 200  FILE *ficreseij;
   char filerese[FILENAMELENGTH];
 #define TOL 2.0e-4  FILE  *ficresvij;
   char fileresv[FILENAMELENGTH];
 #define CGOLD 0.3819660  FILE  *ficresvpl;
 #define ZEPS 1.0e-10  char fileresvpl[FILENAMELENGTH];
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 #define GOLD 1.618034  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 #define GLIMIT 100.0  
 #define TINY 1.0e-20  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   char filelog[FILENAMELENGTH]; /* Log file */
 static double maxarg1,maxarg2;  char filerest[FILENAMELENGTH];
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  char fileregp[FILENAMELENGTH];
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  char popfile[FILENAMELENGTH];
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
 #define rint(a) floor(a+0.5)  
   #define NR_END 1
 static double sqrarg;  #define FREE_ARG char*
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  #define FTOL 1.0e-10
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
   #define NRANSI 
 int imx;  #define ITMAX 200 
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/  #define TOL 2.0e-4 
   
 int m,nb;  #define CGOLD 0.3819660 
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  #define ZEPS 1.0e-10 
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 double **pmmij, ***probs, ***mobaverage;  
 double dateintmean=0;  #define GOLD 1.618034 
   #define GLIMIT 100.0 
 double *weight;  #define TINY 1.0e-20 
 int **s; /* Status */  
 double *agedc, **covar, idx;  static double maxarg1,maxarg2;
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    
 double ftolhess; /* Tolerance for computing hessian */  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   #define rint(a) floor(a+0.5)
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  static double sqrarg;
 {  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
    char *s;                             /* pointer */  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
    int  l1, l2;                         /* length counters */  
   int imx; 
    l1 = strlen( path );                 /* length of path */  int stepm;
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  /* Stepm, step in month: minimum step interpolation*/
 #ifdef windows  
    s = strrchr( path, '\\' );           /* find last / */  int estepm;
 #else  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
    s = strrchr( path, '/' );            /* find last / */  
 #endif  int m,nb;
    if ( s == NULL ) {                   /* no directory, so use current */  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 #if     defined(__bsd__)                /* get current working directory */  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       extern char       *getwd( );  double **pmmij, ***probs;
   double dateintmean=0;
       if ( getwd( dirc ) == NULL ) {  
 #else  double *weight;
       extern char       *getcwd( );  int **s; /* Status */
   double *agedc, **covar, idx;
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 #endif  
          return( GLOCK_ERROR_GETCWD );  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
       }  double ftolhess; /* Tolerance for computing hessian */
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */  /**************** split *************************/
       s++;                              /* after this, the filename */  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
       l2 = strlen( s );                 /* length of filename */  {
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    char  *ss;                            /* pointer */
       strcpy( name, s );                /* save file name */    int   l1, l2;                         /* length counters */
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */    l1 = strlen(path );                   /* length of path */
    }    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
    l1 = strlen( dirc );                 /* length of directory */    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
 #ifdef windows    if ( ss == NULL ) {                   /* no directory, so use current */
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 #else        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  #if     defined(__bsd__)                /* get current working directory */
 #endif      extern char *getwd( );
    s = strrchr( name, '.' );            /* find last / */  
    s++;      if ( getwd( dirc ) == NULL ) {
    strcpy(ext,s);                       /* save extension */  #else
    l1= strlen( name);      extern char *getcwd( );
    l2= strlen( s)+1;  
    strncpy( finame, name, l1-l2);      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
    finame[l1-l2]= 0;  #endif
    return( 0 );                         /* we're done */        return( GLOCK_ERROR_GETCWD );
 }      }
       strcpy( name, path );               /* we've got it */
     } else {                              /* strip direcotry from path */
 /******************************************/      ss++;                               /* after this, the filename */
       l2 = strlen( ss );                  /* length of filename */
 void replace(char *s, char*t)      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 {      strcpy( name, ss );         /* save file name */
   int i;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   int lg=20;      dirc[l1-l2] = 0;                    /* add zero */
   i=0;    }
   lg=strlen(t);    l1 = strlen( dirc );                  /* length of directory */
   for(i=0; i<= lg; i++) {  #ifdef windows
     (s[i] = t[i]);    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
     if (t[i]== '\\') s[i]='/';  #else
   }    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
 }  #endif
     ss = strrchr( name, '.' );            /* find last / */
 int nbocc(char *s, char occ)    ss++;
 {    strcpy(ext,ss);                       /* save extension */
   int i,j=0;    l1= strlen( name);
   int lg=20;    l2= strlen(ss)+1;
   i=0;    strncpy( finame, name, l1-l2);
   lg=strlen(s);    finame[l1-l2]= 0;
   for(i=0; i<= lg; i++) {    return( 0 );                          /* we're done */
   if  (s[i] == occ ) j++;  }
   }  
   return j;  
 }  /******************************************/
   
 void cutv(char *u,char *v, char*t, char occ)  void replace(char *s, char*t)
 {  {
   int i,lg,j,p=0;    int i;
   i=0;    int lg=20;
   for(j=0; j<=strlen(t)-1; j++) {    i=0;
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    lg=strlen(t);
   }    for(i=0; i<= lg; i++) {
       (s[i] = t[i]);
   lg=strlen(t);      if (t[i]== '\\') s[i]='/';
   for(j=0; j<p; j++) {    }
     (u[j] = t[j]);  }
   }  
      u[p]='\0';  int nbocc(char *s, char occ)
   {
    for(j=0; j<= lg; j++) {    int i,j=0;
     if (j>=(p+1))(v[j-p-1] = t[j]);    int lg=20;
   }    i=0;
 }    lg=strlen(s);
     for(i=0; i<= lg; i++) {
 /********************** nrerror ********************/    if  (s[i] == occ ) j++;
     }
 void nrerror(char error_text[])    return j;
 {  }
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);  void cutv(char *u,char *v, char*t, char occ)
   exit(1);  {
 }    /* cuts string t into u and v where u is ended by char occ excluding it
 /*********************** vector *******************/       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 double *vector(int nl, int nh)       gives u="abcedf" and v="ghi2j" */
 {    int i,lg,j,p=0;
   double *v;    i=0;
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    for(j=0; j<=strlen(t)-1; j++) {
   if (!v) nrerror("allocation failure in vector");      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   return v-nl+NR_END;    }
 }  
     lg=strlen(t);
 /************************ free vector ******************/    for(j=0; j<p; j++) {
 void free_vector(double*v, int nl, int nh)      (u[j] = t[j]);
 {    }
   free((FREE_ARG)(v+nl-NR_END));       u[p]='\0';
 }  
      for(j=0; j<= lg; j++) {
 /************************ivector *******************************/      if (j>=(p+1))(v[j-p-1] = t[j]);
 int *ivector(long nl,long nh)    }
 {  }
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  /********************** nrerror ********************/
   if (!v) nrerror("allocation failure in ivector");  
   return v-nl+NR_END;  void nrerror(char error_text[])
 }  {
     fprintf(stderr,"ERREUR ...\n");
 /******************free ivector **************************/    fprintf(stderr,"%s\n",error_text);
 void free_ivector(int *v, long nl, long nh)    exit(EXIT_FAILURE);
 {  }
   free((FREE_ARG)(v+nl-NR_END));  /*********************** vector *******************/
 }  double *vector(int nl, int nh)
   {
 /******************* imatrix *******************************/    double *v;
 int **imatrix(long nrl, long nrh, long ncl, long nch)    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    if (!v) nrerror("allocation failure in vector");
 {    return v-nl+NR_END;
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  }
   int **m;  
    /************************ free vector ******************/
   /* allocate pointers to rows */  void free_vector(double*v, int nl, int nh)
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  {
   if (!m) nrerror("allocation failure 1 in matrix()");    free((FREE_ARG)(v+nl-NR_END));
   m += NR_END;  }
   m -= nrl;  
    /************************ivector *******************************/
    int *ivector(long nl,long nh)
   /* allocate rows and set pointers to them */  {
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    int *v;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   m[nrl] += NR_END;    if (!v) nrerror("allocation failure in ivector");
   m[nrl] -= ncl;    return v-nl+NR_END;
    }
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
    /******************free ivector **************************/
   /* return pointer to array of pointers to rows */  void free_ivector(int *v, long nl, long nh)
   return m;  {
 }    free((FREE_ARG)(v+nl-NR_END));
   }
 /****************** free_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)  /******************* imatrix *******************************/
       int **m;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       long nch,ncl,nrh,nrl;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
      /* free an int matrix allocated by imatrix() */  { 
 {    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*))); 
 /******************* matrix *******************************/    if (!m) nrerror("allocation failure 1 in matrix()"); 
 double **matrix(long nrl, long nrh, long ncl, long nch)    m += NR_END; 
 {    m -= nrl; 
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+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;  
   return m;  /****************** free_imatrix *************************/
 }  void free_imatrix(m,nrl,nrh,ncl,nch)
         int **m;
 /*************************free matrix ************************/        long nch,ncl,nrh,nrl; 
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)       /* free an int matrix allocated by imatrix() */ 
 {  { 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   free((FREE_ARG)(m+nrl-NR_END));    free((FREE_ARG) (m+nrl-NR_END)); 
 }  } 
   
 /******************* ma3x *******************************/  /******************* matrix *******************************/
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  double **matrix(long nrl, long nrh, long ncl, long nch)
 {  {
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   double ***m;    double **m;
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   if (!m) nrerror("allocation failure 1 in matrix()");    if (!m) nrerror("allocation failure 1 in matrix()");
   m += NR_END;    m += NR_END;
   m -= nrl;    m -= nrl;
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   m[nrl] += NR_END;    m[nrl] += NR_END;
   m[nrl] -= ncl;    m[nrl] -= ncl;
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     return m;
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  }
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;  /*************************free matrix ************************/
   m[nrl][ncl] -= nll;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   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++)  /******************* ma3x *******************************/
       m[i][j]=m[i][j-1]+nlay;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   }  {
   return m;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+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 []);  
      m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 double f1dim(double x)    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
 {    m[nrl][ncl] += NR_END;
   int j;    m[nrl][ncl] -= nll;
   double f;    for (j=ncl+1; j<=nch; j++) 
   double *xt;      m[nrl][j]=m[nrl][j-1]+nlay;
      
   xt=vector(1,ncom);    for (i=nrl+1; i<=nrh; i++) {
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   f=(*nrfunc)(xt);      for (j=ncl+1; j<=nch; j++) 
   free_vector(xt,1,ncom);        m[i][j]=m[i][j-1]+nlay;
   return f;    }
 }    return m;
   }
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  /*************************free ma3x ************************/
 {  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   int iter;  {
   double a,b,d,etemp;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   double fu,fv,fw,fx;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double ftemp;    free((FREE_ARG)(m+nrl-NR_END));
   double p,q,r,tol1,tol2,u,v,w,x,xm;  }
   double e=0.0;  
    /***************** f1dim *************************/
   a=(ax < cx ? ax : cx);  extern int ncom; 
   b=(ax > cx ? ax : cx);  extern double *pcom,*xicom;
   x=w=v=bx;  extern double (*nrfunc)(double []); 
   fw=fv=fx=(*f)(x);   
   for (iter=1;iter<=ITMAX;iter++) {  double f1dim(double x) 
     xm=0.5*(a+b);  { 
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    int j; 
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    double f;
     printf(".");fflush(stdout);    double *xt; 
 #ifdef DEBUG   
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    xt=vector(1,ncom); 
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
 #endif    f=(*nrfunc)(xt); 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    free_vector(xt,1,ncom); 
       *xmin=x;    return f; 
       return fx;  } 
     }  
     ftemp=fu;  /*****************brent *************************/
     if (fabs(e) > tol1) {  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       r=(x-w)*(fx-fv);  { 
       q=(x-v)*(fx-fw);    int iter; 
       p=(x-v)*q-(x-w)*r;    double a,b,d,etemp;
       q=2.0*(q-r);    double fu,fv,fw,fx;
       if (q > 0.0) p = -p;    double ftemp;
       q=fabs(q);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       etemp=e;    double e=0.0; 
       e=d;   
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    a=(ax < cx ? ax : cx); 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    b=(ax > cx ? ax : cx); 
       else {    x=w=v=bx; 
         d=p/q;    fw=fv=fx=(*f)(x); 
         u=x+d;    for (iter=1;iter<=ITMAX;iter++) { 
         if (u-a < tol2 || b-u < tol2)      xm=0.5*(a+b); 
           d=SIGN(tol1,xm-x);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       }      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     } else {      printf(".");fflush(stdout);
       d=CGOLD*(e=(x >= xm ? a-x : b-x));      fprintf(ficlog,".");fflush(ficlog);
     }  #ifdef DEBUG
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));      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);
     fu=(*f)(u);      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 (fu <= fx) {      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       if (u >= x) a=x; else b=x;  #endif
       SHFT(v,w,x,u)      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         SHFT(fv,fw,fx,fu)        *xmin=x; 
         } else {        return fx; 
           if (u < x) a=u; else b=u;      } 
           if (fu <= fw || w == x) {      ftemp=fu;
             v=w;      if (fabs(e) > tol1) { 
             w=u;        r=(x-w)*(fx-fv); 
             fv=fw;        q=(x-v)*(fx-fw); 
             fw=fu;        p=(x-v)*q-(x-w)*r; 
           } else if (fu <= fv || v == x || v == w) {        q=2.0*(q-r); 
             v=u;        if (q > 0.0) p = -p; 
             fv=fu;        q=fabs(q); 
           }        etemp=e; 
         }        e=d; 
   }        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   nrerror("Too many iterations in brent");          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   *xmin=x;        else { 
   return fx;          d=p/q; 
 }          u=x+d; 
           if (u-a < tol2 || b-u < tol2) 
 /****************** mnbrak ***********************/            d=SIGN(tol1,xm-x); 
         } 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,      } else { 
             double (*func)(double))        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 {      } 
   double ulim,u,r,q, dum;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   double fu;      fu=(*f)(u); 
        if (fu <= fx) { 
   *fa=(*func)(*ax);        if (u >= x) a=x; else b=x; 
   *fb=(*func)(*bx);        SHFT(v,w,x,u) 
   if (*fb > *fa) {          SHFT(fv,fw,fx,fu) 
     SHFT(dum,*ax,*bx,dum)          } else { 
       SHFT(dum,*fb,*fa,dum)            if (u < x) a=u; else b=u; 
       }            if (fu <= fw || w == x) { 
   *cx=(*bx)+GOLD*(*bx-*ax);              v=w; 
   *fc=(*func)(*cx);              w=u; 
   while (*fb > *fc) {              fv=fw; 
     r=(*bx-*ax)*(*fb-*fc);              fw=fu; 
     q=(*bx-*cx)*(*fb-*fa);            } else if (fu <= fv || v == x || v == w) { 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/              v=u; 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));              fv=fu; 
     ulim=(*bx)+GLIMIT*(*cx-*bx);            } 
     if ((*bx-u)*(u-*cx) > 0.0) {          } 
       fu=(*func)(u);    } 
     } else if ((*cx-u)*(u-ulim) > 0.0) {    nrerror("Too many iterations in brent"); 
       fu=(*func)(u);    *xmin=x; 
       if (fu < *fc) {    return fx; 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  } 
           SHFT(*fb,*fc,fu,(*func)(u))  
           }  /****************** mnbrak ***********************/
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       fu=(*func)(u);              double (*func)(double)) 
     } else {  { 
       u=(*cx)+GOLD*(*cx-*bx);    double ulim,u,r,q, dum;
       fu=(*func)(u);    double fu; 
     }   
     SHFT(*ax,*bx,*cx,u)    *fa=(*func)(*ax); 
       SHFT(*fa,*fb,*fc,fu)    *fb=(*func)(*bx); 
       }    if (*fb > *fa) { 
 }      SHFT(dum,*ax,*bx,dum) 
         SHFT(dum,*fb,*fa,dum) 
 /*************** linmin ************************/        } 
     *cx=(*bx)+GOLD*(*bx-*ax); 
 int ncom;    *fc=(*func)(*cx); 
 double *pcom,*xicom;    while (*fb > *fc) { 
 double (*nrfunc)(double []);      r=(*bx-*ax)*(*fb-*fc); 
        q=(*bx-*cx)*(*fb-*fa); 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 {        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   double brent(double ax, double bx, double cx,      ulim=(*bx)+GLIMIT*(*cx-*bx); 
                double (*f)(double), double tol, double *xmin);      if ((*bx-u)*(u-*cx) > 0.0) { 
   double f1dim(double x);        fu=(*func)(u); 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,      } else if ((*cx-u)*(u-ulim) > 0.0) { 
               double *fc, double (*func)(double));        fu=(*func)(u); 
   int j;        if (fu < *fc) { 
   double xx,xmin,bx,ax;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   double fx,fb,fa;            SHFT(*fb,*fc,fu,(*func)(u)) 
              } 
   ncom=n;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   pcom=vector(1,n);        u=ulim; 
   xicom=vector(1,n);        fu=(*func)(u); 
   nrfunc=func;      } else { 
   for (j=1;j<=n;j++) {        u=(*cx)+GOLD*(*cx-*bx); 
     pcom[j]=p[j];        fu=(*func)(u); 
     xicom[j]=xi[j];      } 
   }      SHFT(*ax,*bx,*cx,u) 
   ax=0.0;        SHFT(*fa,*fb,*fc,fu) 
   xx=1.0;        } 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  } 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  
 #ifdef DEBUG  /*************** linmin ************************/
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  
 #endif  int ncom; 
   for (j=1;j<=n;j++) {  double *pcom,*xicom;
     xi[j] *= xmin;  double (*nrfunc)(double []); 
     p[j] += xi[j];   
   }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   free_vector(xicom,1,n);  { 
   free_vector(pcom,1,n);    double brent(double ax, double bx, double cx, 
 }                 double (*f)(double), double tol, double *xmin); 
     double f1dim(double x); 
 /*************** powell ************************/    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,                double *fc, double (*func)(double)); 
             double (*func)(double []))    int j; 
 {    double xx,xmin,bx,ax; 
   void linmin(double p[], double xi[], int n, double *fret,    double fx,fb,fa;
               double (*func)(double []));   
   int i,ibig,j;    ncom=n; 
   double del,t,*pt,*ptt,*xit;    pcom=vector(1,n); 
   double fp,fptt;    xicom=vector(1,n); 
   double *xits;    nrfunc=func; 
   pt=vector(1,n);    for (j=1;j<=n;j++) { 
   ptt=vector(1,n);      pcom[j]=p[j]; 
   xit=vector(1,n);      xicom[j]=xi[j]; 
   xits=vector(1,n);    } 
   *fret=(*func)(p);    ax=0.0; 
   for (j=1;j<=n;j++) pt[j]=p[j];    xx=1.0; 
   for (*iter=1;;++(*iter)) {    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     fp=(*fret);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     ibig=0;  #ifdef DEBUG
     del=0.0;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     for (i=1;i<=n;i++)  #endif
       printf(" %d %.12f",i, p[i]);    for (j=1;j<=n;j++) { 
     printf("\n");      xi[j] *= xmin; 
     for (i=1;i<=n;i++) {      p[j] += xi[j]; 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    } 
       fptt=(*fret);    free_vector(xicom,1,n); 
 #ifdef DEBUG    free_vector(pcom,1,n); 
       printf("fret=%lf \n",*fret);  } 
 #endif  
       printf("%d",i);fflush(stdout);  /*************** powell ************************/
       linmin(p,xit,n,fret,func);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       if (fabs(fptt-(*fret)) > del) {              double (*func)(double [])) 
         del=fabs(fptt-(*fret));  { 
         ibig=i;    void linmin(double p[], double xi[], int n, double *fret, 
       }                double (*func)(double [])); 
 #ifdef DEBUG    int i,ibig,j; 
       printf("%d %.12e",i,(*fret));    double del,t,*pt,*ptt,*xit;
       for (j=1;j<=n;j++) {    double fp,fptt;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    double *xits;
         printf(" x(%d)=%.12e",j,xit[j]);    pt=vector(1,n); 
       }    ptt=vector(1,n); 
       for(j=1;j<=n;j++)    xit=vector(1,n); 
         printf(" p=%.12e",p[j]);    xits=vector(1,n); 
       printf("\n");    *fret=(*func)(p); 
 #endif    for (j=1;j<=n;j++) pt[j]=p[j]; 
     }    for (*iter=1;;++(*iter)) { 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      fp=(*fret); 
 #ifdef DEBUG      ibig=0; 
       int k[2],l;      del=0.0; 
       k[0]=1;      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       k[1]=-1;      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       printf("Max: %.12e",(*func)(p));      for (i=1;i<=n;i++) 
       for (j=1;j<=n;j++)        printf(" %d %.12f",i, p[i]);
         printf(" %.12e",p[j]);      fprintf(ficlog," %d %.12f",i, p[i]);
       printf("\n");      printf("\n");
       for(l=0;l<=1;l++) {      fprintf(ficlog,"\n");
         for (j=1;j<=n;j++) {      for (i=1;i<=n;i++) { 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);        fptt=(*fret); 
         }  #ifdef DEBUG
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));        printf("fret=%lf \n",*fret);
       }        fprintf(ficlog,"fret=%lf \n",*fret);
 #endif  #endif
         printf("%d",i);fflush(stdout);
         fprintf(ficlog,"%d",i);fflush(ficlog);
       free_vector(xit,1,n);        linmin(p,xit,n,fret,func); 
       free_vector(xits,1,n);        if (fabs(fptt-(*fret)) > del) { 
       free_vector(ptt,1,n);          del=fabs(fptt-(*fret)); 
       free_vector(pt,1,n);          ibig=i; 
       return;        } 
     }  #ifdef DEBUG
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");        printf("%d %.12e",i,(*fret));
     for (j=1;j<=n;j++) {        fprintf(ficlog,"%d %.12e",i,(*fret));
       ptt[j]=2.0*p[j]-pt[j];        for (j=1;j<=n;j++) {
       xit[j]=p[j]-pt[j];          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       pt[j]=p[j];          printf(" x(%d)=%.12e",j,xit[j]);
     }          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     fptt=(*func)(ptt);        }
     if (fptt < fp) {        for(j=1;j<=n;j++) {
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);          printf(" p=%.12e",p[j]);
       if (t < 0.0) {          fprintf(ficlog," p=%.12e",p[j]);
         linmin(p,xit,n,fret,func);        }
         for (j=1;j<=n;j++) {        printf("\n");
           xi[j][ibig]=xi[j][n];        fprintf(ficlog,"\n");
           xi[j][n]=xit[j];  #endif
         }      } 
 #ifdef DEBUG      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  #ifdef DEBUG
         for(j=1;j<=n;j++)        int k[2],l;
           printf(" %.12e",xit[j]);        k[0]=1;
         printf("\n");        k[1]=-1;
 #endif        printf("Max: %.12e",(*func)(p));
       }        fprintf(ficlog,"Max: %.12e",(*func)(p));
     }        for (j=1;j<=n;j++) {
   }          printf(" %.12e",p[j]);
 }          fprintf(ficlog," %.12e",p[j]);
         }
 /**** Prevalence limit ****************/        printf("\n");
         fprintf(ficlog,"\n");
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)        for(l=0;l<=1;l++) {
 {          for (j=1;j<=n;j++) {
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
      matrix by transitions matrix until convergence is reached */            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
             fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   int i, ii,j,k;          }
   double min, max, maxmin, maxmax,sumnew=0.;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   double **matprod2();          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   double **out, cov[NCOVMAX], **pmij();        }
   double **newm;  #endif
   double agefin, delaymax=50 ; /* Max number of years to converge */  
   
   for (ii=1;ii<=nlstate+ndeath;ii++)        free_vector(xit,1,n); 
     for (j=1;j<=nlstate+ndeath;j++){        free_vector(xits,1,n); 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        free_vector(ptt,1,n); 
     }        free_vector(pt,1,n); 
         return; 
    cov[1]=1.;      } 
        if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      for (j=1;j<=n;j++) { 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        ptt[j]=2.0*p[j]-pt[j]; 
     newm=savm;        xit[j]=p[j]-pt[j]; 
     /* Covariates have to be included here again */        pt[j]=p[j]; 
      cov[2]=agefin;      } 
        fptt=(*func)(ptt); 
       for (k=1; k<=cptcovn;k++) {      if (fptt < fp) { 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         /*      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]]);*/        if (t < 0.0) { 
       }          linmin(p,xit,n,fret,func); 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          for (j=1;j<=n;j++) { 
       for (k=1; k<=cptcovprod;k++)            xi[j][ibig]=xi[j][n]; 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];            xi[j][n]=xit[j]; 
           }
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  #ifdef DEBUG
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);          for(j=1;j<=n;j++){
             printf(" %.12e",xit[j]);
     savm=oldm;            fprintf(ficlog," %.12e",xit[j]);
     oldm=newm;          }
     maxmax=0.;          printf("\n");
     for(j=1;j<=nlstate;j++){          fprintf(ficlog,"\n");
       min=1.;  #endif
       max=0.;        }
       for(i=1; i<=nlstate; i++) {      } 
         sumnew=0;    } 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  } 
         prlim[i][j]= newm[i][j]/(1-sumnew);  
         max=FMAX(max,prlim[i][j]);  /**** Prevalence limit (stable prevalence)  ****************/
         min=FMIN(min,prlim[i][j]);  
       }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       maxmin=max-min;  {
       maxmax=FMAX(maxmax,maxmin);    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     }       matrix by transitions matrix until convergence is reached */
     if(maxmax < ftolpl){  
       return prlim;    int i, ii,j,k;
     }    double min, max, maxmin, maxmax,sumnew=0.;
   }    double **matprod2();
 }    double **out, cov[NCOVMAX], **pmij();
     double **newm;
 /*************** transition probabilities ***************/    double agefin, delaymax=50 ; /* Max number of years to converge */
   
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    for (ii=1;ii<=nlstate+ndeath;ii++)
 {      for (j=1;j<=nlstate+ndeath;j++){
   double s1, s2;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   /*double t34;*/      }
   int i,j,j1, nc, ii, jj;  
      cov[1]=1.;
     for(i=1; i<= nlstate; i++){   
     for(j=1; j<i;j++){   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
         /*s2 += param[i][j][nc]*cov[nc];*/      newm=savm;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      /* Covariates have to be included here again */
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/       cov[2]=agefin;
       }    
       ps[i][j]=s2;        for (k=1; k<=cptcovn;k++) {
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/          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(j=i+1; j<=nlstate+ndeath;j++){        }
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        for (k=1; k<=cptcovprod;k++)
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       }  
       ps[i][j]=s2;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     }        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   }        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     /*ps[3][2]=1;*/      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   
   for(i=1; i<= nlstate; i++){      savm=oldm;
      s1=0;      oldm=newm;
     for(j=1; j<i; j++)      maxmax=0.;
       s1+=exp(ps[i][j]);      for(j=1;j<=nlstate;j++){
     for(j=i+1; j<=nlstate+ndeath; j++)        min=1.;
       s1+=exp(ps[i][j]);        max=0.;
     ps[i][i]=1./(s1+1.);        for(i=1; i<=nlstate; i++) {
     for(j=1; j<i; j++)          sumnew=0;
       ps[i][j]= exp(ps[i][j])*ps[i][i];          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     for(j=i+1; j<=nlstate+ndeath; j++)          prlim[i][j]= newm[i][j]/(1-sumnew);
       ps[i][j]= exp(ps[i][j])*ps[i][i];          max=FMAX(max,prlim[i][j]);
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */          min=FMIN(min,prlim[i][j]);
   } /* end i */        }
         maxmin=max-min;
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){        maxmax=FMAX(maxmax,maxmin);
     for(jj=1; jj<= nlstate+ndeath; jj++){      }
       ps[ii][jj]=0;      if(maxmax < ftolpl){
       ps[ii][ii]=1;        return prlim;
     }      }
   }    }
   }
   
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  /*************** transition probabilities ***************/ 
     for(jj=1; jj<= nlstate+ndeath; jj++){  
      printf("%lf ",ps[ii][jj]);  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
    }  {
     printf("\n ");    double s1, s2;
     }    /*double t34;*/
     printf("\n ");printf("%lf ",cov[2]);*/    int i,j,j1, nc, ii, jj;
 /*  
   for(i=1; i<= npar; i++) printf("%f ",x[i]);      for(i=1; i<= nlstate; i++){
   goto end;*/      for(j=1; j<i;j++){
     return ps;        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];
 /**************** Product of 2 matrices ******************/          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
         }
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        ps[i][j]=s2;
 {        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times      }
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      for(j=i+1; j<=nlstate+ndeath;j++){
   /* in, b, out are matrice of pointers which should have been initialized        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
      before: only the contents of out is modified. The function returns          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
      a pointer to pointers identical to out */          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   long i, j, k;        }
   for(i=nrl; i<= nrh; i++)        ps[i][j]=s2;
     for(k=ncolol; k<=ncoloh; k++)      }
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    }
         out[i][k] +=in[i][j]*b[j][k];      /*ps[3][2]=1;*/
   
   return out;    for(i=1; i<= nlstate; i++){
 }       s1=0;
       for(j=1; j<i; j++)
         s1+=exp(ps[i][j]);
 /************* Higher Matrix Product ***************/      for(j=i+1; j<=nlstate+ndeath; j++)
         s1+=exp(ps[i][j]);
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      ps[i][i]=1./(s1+1.);
 {      for(j=1; j<i; j++)
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month        ps[i][j]= exp(ps[i][j])*ps[i][i];
      duration (i.e. until      for(j=i+1; j<=nlstate+ndeath; j++)
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        ps[i][j]= exp(ps[i][j])*ps[i][i];
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
      (typically every 2 years instead of every month which is too big).    } /* end i */
      Model is determined by parameters x and covariates have to be  
      included manually here.    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       for(jj=1; jj<= nlstate+ndeath; jj++){
      */        ps[ii][jj]=0;
         ps[ii][ii]=1;
   int i, j, d, h, k;      }
   double **out, cov[NCOVMAX];    }
   double **newm;  
   
   /* Hstepm could be zero and should return the unit matrix */    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   for (i=1;i<=nlstate+ndeath;i++)      for(jj=1; jj<= nlstate+ndeath; jj++){
     for (j=1;j<=nlstate+ndeath;j++){       printf("%lf ",ps[ii][jj]);
       oldm[i][j]=(i==j ? 1.0 : 0.0);     }
       po[i][j][0]=(i==j ? 1.0 : 0.0);      printf("\n ");
     }      }
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      printf("\n ");printf("%lf ",cov[2]);*/
   for(h=1; h <=nhstepm; h++){  /*
     for(d=1; d <=hstepm; d++){    for(i=1; i<= npar; i++) printf("%f ",x[i]);
       newm=savm;    goto end;*/
       /* Covariates have to be included here again */      return ps;
       cov[1]=1.;  }
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  /**************** Product of 2 matrices ******************/
       for (k=1; k<=cptcovage;k++)  
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
       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]]];    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
        b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     /* in, b, out are matrice of pointers which should have been initialized 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/       before: only the contents of out is modified. The function returns
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/       a pointer to pointers identical to out */
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    long i, j, k;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    for(i=nrl; i<= nrh; i++)
       savm=oldm;      for(k=ncolol; k<=ncoloh; k++)
       oldm=newm;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     }          out[i][k] +=in[i][j]*b[j][k];
     for(i=1; i<=nlstate+ndeath; i++)  
       for(j=1;j<=nlstate+ndeath;j++) {    return out;
         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]);  
          */  
       }  /************* Higher Matrix Product ***************/
   } /* end h */  
   return po;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
 }  {
     /* Computes the transition matrix starting at age 'age' over 
        'nhstepm*hstepm*stepm' months (i.e. until
 /*************** log-likelihood *************/       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
 double func( double *x)       nhstepm*hstepm matrices. 
 {       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   int i, ii, j, k, mi, d, kk;       (typically every 2 years instead of every month which is too big 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];       for the memory).
   double **out;       Model is determined by parameters x and covariates have to be 
   double sw; /* Sum of weights */       included manually here. 
   double lli; /* Individual log likelihood */  
   long ipmx;       */
   /*extern weight */  
   /* We are differentiating ll according to initial status */    int i, j, d, h, k;
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    double **out, cov[NCOVMAX];
   /*for(i=1;i<imx;i++)    double **newm;
     printf(" %d\n",s[4][i]);  
   */    /* Hstepm could be zero and should return the unit matrix */
   cov[1]=1.;    for (i=1;i<=nlstate+ndeath;i++)
       for (j=1;j<=nlstate+ndeath;j++){
   for(k=1; k<=nlstate; k++) ll[k]=0.;        oldm[i][j]=(i==j ? 1.0 : 0.0);
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        po[i][j][0]=(i==j ? 1.0 : 0.0);
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      }
     for(mi=1; mi<= wav[i]-1; mi++){    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       for (ii=1;ii<=nlstate+ndeath;ii++)    for(h=1; h <=nhstepm; h++){
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      for(d=1; d <=hstepm; d++){
       for(d=0; d<dh[mi][i]; d++){        newm=savm;
         newm=savm;        /* Covariates have to be included here again */
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;        cov[1]=1.;
         for (kk=1; kk<=cptcovage;kk++) {        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         }        for (k=1; k<=cptcovage;k++)
                  cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        for (k=1; k<=cptcovprod;k++)
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         savm=oldm;  
         oldm=newm;  
                /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
                /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
       } /* end mult */        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                           pmij(pmmij,cov,ncovmodel,x,nlstate));
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        savm=oldm;
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        oldm=newm;
       ipmx +=1;      }
       sw += weight[i];      for(i=1; i<=nlstate+ndeath; i++)
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        for(j=1;j<=nlstate+ndeath;j++) {
     } /* end of wave */          po[i][j][h]=newm[i][j];
   } /* end of individual */          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
            */
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        }
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    } /* end h */
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    return po;
   return -l;  }
 }  
   
   /*************** log-likelihood *************/
 /*********** Maximum Likelihood Estimation ***************/  double func( double *x)
   {
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    int i, ii, j, k, mi, d, kk;
 {    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   int i,j, iter;    double **out;
   double **xi,*delti;    double sw; /* Sum of weights */
   double fret;    double lli; /* Individual log likelihood */
   xi=matrix(1,npar,1,npar);    int s1, s2;
   for (i=1;i<=npar;i++)    double bbh, survp;
     for (j=1;j<=npar;j++)    long ipmx;
       xi[i][j]=(i==j ? 1.0 : 0.0);    /*extern weight */
   printf("Powell\n");    /* We are differentiating ll according to initial status */
   powell(p,xi,npar,ftol,&iter,&fret,func);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      printf(" %d\n",s[4][i]);
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    */
     cov[1]=1.;
 }  
     for(k=1; k<=nlstate; k++) ll[k]=0.;
 /**** Computes Hessian and covariance matrix ***/  
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    if(mle==1){
 {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double  **a,**y,*x,pd;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double **hess;        for(mi=1; mi<= wav[i]-1; mi++){
   int i, j,jk;          for (ii=1;ii<=nlstate+ndeath;ii++)
   int *indx;            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double hessii(double p[], double delta, int theta, double delti[]);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double hessij(double p[], double delti[], int i, int j);            }
   void lubksb(double **a, int npar, int *indx, double b[]) ;          for(d=0; d<dh[mi][i]; d++){
   void ludcmp(double **a, int npar, int *indx, double *d) ;            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   hess=matrix(1,npar,1,npar);            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   printf("\nCalculation of the hessian matrix. Wait...\n");            }
   for (i=1;i<=npar;i++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     printf("%d",i);fflush(stdout);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     hess[i][i]=hessii(p,ftolhess,i,delti);            savm=oldm;
     /*printf(" %f ",p[i]);*/            oldm=newm;
     /*printf(" %lf ",hess[i][i]);*/          } /* end mult */
   }        
            /*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 
       if (j>i) {           * (in months) between two waves is not a multiple of stepm, we rounded to 
         printf(".%d%d",i,j);fflush(stdout);           * the nearest (and in case of equal distance, to the lowest) interval but now
         hess[i][j]=hessij(p,delti,i,j);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
         hess[j][i]=hess[i][j];               * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
         /*printf(" %lf ",hess[i][j]);*/           * probability in order to take into account the bias as a fraction of the way
       }           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     }           * -stepm/2 to stepm/2 .
   }           * For stepm=1 the results are the same as for previous versions of Imach.
   printf("\n");           * For stepm > 1 the results are less biased than in previous versions. 
            */
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");          s1=s[mw[mi][i]][i];
            s2=s[mw[mi+1][i]][i];
   a=matrix(1,npar,1,npar);          bbh=(double)bh[mi][i]/(double)stepm; 
   y=matrix(1,npar,1,npar);          /* bias is positive if real duration
   x=vector(1,npar);           * is higher than the multiple of stepm and negative otherwise.
   indx=ivector(1,npar);           */
   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]));*/
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];          if( s2 > nlstate){ 
   ludcmp(a,npar,indx,&pd);            /* 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 
   for (j=1;j<=npar;j++) {               step unit time, which is also the differences between probability to die before dh 
     for (i=1;i<=npar;i++) x[i]=0;               and probability to die before dh-stepm . 
     x[j]=1;               In version up to 0.92 likelihood was computed
     lubksb(a,npar,indx,x);          as if date of death was unknown. Death was treated as any other
     for (i=1;i<=npar;i++){          health state: the date of the interview describes the actual state
       matcov[i][j]=x[i];          and not the date of a change in health state. The former idea was
     }          to consider that at each interview the state was recorded
   }          (healthy, disable or death) and IMaCh was corrected; but when we
           introduced the exact date of death then we should have modified
   printf("\n#Hessian matrix#\n");          the contribution of an exact death to the likelihood. This new
   for (i=1;i<=npar;i++) {          contribution is smaller and very dependent of the step unit
     for (j=1;j<=npar;j++) {          stepm. It is no more the probability to die between last interview
       printf("%.3e ",hess[i][j]);          and month of death but the probability to survive from last
     }          interview up to one month before death multiplied by the
     printf("\n");          probability to die within a month. Thanks to Chris
   }          Jackson for correcting this bug.  Former versions increased
           mortality artificially. The bad side is that we add another loop
   /* Recompute Inverse */          which slows down the processing. The difference can be up to 10%
   for (i=1;i<=npar;i++)          lower mortality.
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];            */
   ludcmp(a,npar,indx,&pd);            lli=log(out[s1][s2] - savm[s1][s2]);
           }else{
   /*  printf("\n#Hessian matrix recomputed#\n");            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
             /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
   for (j=1;j<=npar;j++) {          } 
     for (i=1;i<=npar;i++) x[i]=0;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     x[j]=1;          /*if(lli ==000.0)*/
     lubksb(a,npar,indx,x);          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
     for (i=1;i<=npar;i++){          ipmx +=1;
       y[i][j]=x[i];          sw += weight[i];
       printf("%.3e ",y[i][j]);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }        } /* end of wave */
     printf("\n");      } /* end of individual */
   }    }  else if(mle==2){
   */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   free_matrix(a,1,npar,1,npar);        for(mi=1; mi<= wav[i]-1; mi++){
   free_matrix(y,1,npar,1,npar);          for (ii=1;ii<=nlstate+ndeath;ii++)
   free_vector(x,1,npar);            for (j=1;j<=nlstate+ndeath;j++){
   free_ivector(indx,1,npar);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_matrix(hess,1,npar,1,npar);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
           for(d=0; d<=dh[mi][i]; d++){
 }            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 /*************** hessian matrix ****************/            for (kk=1; kk<=cptcovage;kk++) {
 double hessii( double x[], double delta, int theta, double delti[])              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 {            }
   int i;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int l=1, lmax=20;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double k1,k2;            savm=oldm;
   double p2[NPARMAX+1];            oldm=newm;
   double res;          } /* end mult */
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        
   double fx;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   int k=0,kmax=10;          /* But now since version 0.9 we anticipate for bias and large stepm.
   double l1;           * 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 
   fx=func(x);           * the nearest (and in case of equal distance, to the lowest) interval but now
   for (i=1;i<=npar;i++) p2[i]=x[i];           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   for(l=0 ; l <=lmax; l++){           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     l1=pow(10,l);           * probability in order to take into account the bias as a fraction of the way
     delts=delt;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     for(k=1 ; k <kmax; k=k+1){           * -stepm/2 to stepm/2 .
       delt = delta*(l1*k);           * For stepm=1 the results are the same as for previous versions of Imach.
       p2[theta]=x[theta] +delt;           * For stepm > 1 the results are less biased than in previous versions. 
       k1=func(p2)-fx;           */
       p2[theta]=x[theta]-delt;          s1=s[mw[mi][i]][i];
       k2=func(p2)-fx;          s2=s[mw[mi+1][i]][i];
       /*res= (k1-2.0*fx+k2)/delt/delt; */          bbh=(double)bh[mi][i]/(double)stepm; 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          /* bias is positive if real duration
                 * is higher than the multiple of stepm and negative otherwise.
 #ifdef DEBUG           */
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);          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 */
 #endif          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          /*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 */
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         k=kmax;          /*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); */
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          ipmx +=1;
         k=kmax; l=lmax*10.;          sw += weight[i];
       }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){        } /* end of wave */
         delts=delt;      } /* end of individual */
       }    }  else if(mle==3){  /* exponential inter-extrapolation */
     }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   delti[theta]=delts;        for(mi=1; mi<= wav[i]-1; mi++){
   return res;          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
 }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
 double hessij( double x[], double delti[], int thetai,int thetaj)            }
 {          for(d=0; d<dh[mi][i]; d++){
   int i;            newm=savm;
   int l=1, l1, lmax=20;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double k1,k2,k3,k4,res,fx;            for (kk=1; kk<=cptcovage;kk++) {
   double p2[NPARMAX+1];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int k;            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   fx=func(x);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   for (k=1; k<=2; k++) {            savm=oldm;
     for (i=1;i<=npar;i++) p2[i]=x[i];            oldm=newm;
     p2[thetai]=x[thetai]+delti[thetai]/k;          } /* end mult */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        
     k1=func(p2)-fx;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
            /* But now since version 0.9 we anticipate for bias and large stepm.
     p2[thetai]=x[thetai]+delti[thetai]/k;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;           * (in months) between two waves is not a multiple of stepm, we rounded to 
     k2=func(p2)-fx;           * 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
     p2[thetai]=x[thetai]-delti[thetai]/k;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;           * probability in order to take into account the bias as a fraction of the way
     k3=func(p2)-fx;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
             * -stepm/2 to stepm/2 .
     p2[thetai]=x[thetai]-delti[thetai]/k;           * For stepm=1 the results are the same as for previous versions of Imach.
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;           * For stepm > 1 the results are less biased than in previous versions. 
     k4=func(p2)-fx;           */
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          s1=s[mw[mi][i]][i];
 #ifdef DEBUG          s2=s[mw[mi+1][i]][i];
     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);          bbh=(double)bh[mi][i]/(double)stepm; 
 #endif          /* bias is positive if real duration
   }           * is higher than the multiple of stepm and negative otherwise.
   return res;           */
 }          /* 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 */
 /************** Inverse of matrix **************/          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 void ludcmp(double **a, int n, int *indx, double *d)          /*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); */
   int i,imax,j,k;          ipmx +=1;
   double big,dum,sum,temp;          sw += weight[i];
   double *vv;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          } /* end of wave */
   vv=vector(1,n);      } /* end of individual */
   *d=1.0;    }else{  /* ml=4 no inter-extrapolation */
   for (i=1;i<=n;i++) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     big=0.0;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     for (j=1;j<=n;j++)        for(mi=1; mi<= wav[i]-1; mi++){
       if ((temp=fabs(a[i][j])) > big) big=temp;          for (ii=1;ii<=nlstate+ndeath;ii++)
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");            for (j=1;j<=nlstate+ndeath;j++){
     vv[i]=1.0/big;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (j=1;j<=n;j++) {            }
     for (i=1;i<j;i++) {          for(d=0; d<dh[mi][i]; d++){
       sum=a[i][j];            newm=savm;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       a[i][j]=sum;            for (kk=1; kk<=cptcovage;kk++) {
     }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     big=0.0;            }
     for (i=j;i<=n;i++) {          
       sum=a[i][j];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for (k=1;k<j;k++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         sum -= a[i][k]*a[k][j];            savm=oldm;
       a[i][j]=sum;            oldm=newm;
       if ( (dum=vv[i]*fabs(sum)) >= big) {          } /* end mult */
         big=dum;        
         imax=i;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       }          ipmx +=1;
     }          sw += weight[i];
     if (j != imax) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for (k=1;k<=n;k++) {        } /* end of wave */
         dum=a[imax][k];      } /* end of individual */
         a[imax][k]=a[j][k];    } /* End of if */
         a[j][k]=dum;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       *d = -(*d);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       vv[imax]=vv[j];    return -l;
     }  }
     indx[j]=imax;  
     if (a[j][j] == 0.0) a[j][j]=TINY;  
     if (j != n) {  /*********** Maximum Likelihood Estimation ***************/
       dum=1.0/(a[j][j]);  
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
     }  {
   }    int i,j, iter;
   free_vector(vv,1,n);  /* Doesn't work */    double **xi,*delti;
 ;    double fret;
 }    xi=matrix(1,npar,1,npar);
     for (i=1;i<=npar;i++)
 void lubksb(double **a, int n, int *indx, double b[])      for (j=1;j<=npar;j++)
 {        xi[i][j]=(i==j ? 1.0 : 0.0);
   int i,ii=0,ip,j;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   double sum;    powell(p,xi,npar,ftol,&iter,&fret,func);
    
   for (i=1;i<=n;i++) {     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     ip=indx[i];    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     sum=b[ip];    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     b[ip]=b[i];  
     if (ii)  }
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  
     else if (sum) ii=i;  /**** Computes Hessian and covariance matrix ***/
     b[i]=sum;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   }  {
   for (i=n;i>=1;i--) {    double  **a,**y,*x,pd;
     sum=b[i];    double **hess;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    int i, j,jk;
     b[i]=sum/a[i][i];    int *indx;
   }  
 }    double hessii(double p[], double delta, int theta, double delti[]);
     double hessij(double p[], double delti[], int i, int j);
 /************ Frequencies ********************/    void lubksb(double **a, int npar, int *indx, double b[]) ;
 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)    void ludcmp(double **a, int npar, int *indx, double *d) ;
 {  /* Some frequencies */  
      hess=matrix(1,npar,1,npar);
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  
   double ***freq; /* Frequencies */    printf("\nCalculation of the hessian matrix. Wait...\n");
   double *pp;    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   double pos, k2, dateintsum=0,k2cpt=0;    for (i=1;i<=npar;i++){
   FILE *ficresp;      printf("%d",i);fflush(stdout);
   char fileresp[FILENAMELENGTH];      fprintf(ficlog,"%d",i);fflush(ficlog);
        hess[i][i]=hessii(p,ftolhess,i,delti);
   pp=vector(1,nlstate);      /*printf(" %f ",p[i]);*/
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      /*printf(" %lf ",hess[i][i]);*/
   strcpy(fileresp,"p");    }
   strcat(fileresp,fileres);    
   if((ficresp=fopen(fileresp,"w"))==NULL) {    for (i=1;i<=npar;i++) {
     printf("Problem with prevalence resultfile: %s\n", fileresp);      for (j=1;j<=npar;j++)  {
     exit(0);        if (j>i) { 
   }          printf(".%d%d",i,j);fflush(stdout);
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   j1=0;          hess[i][j]=hessij(p,delti,i,j);
            hess[j][i]=hess[i][j];    
   j=cptcoveff;          /*printf(" %lf ",hess[i][j]);*/
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        }
        }
   for(k1=1; k1<=j;k1++){    }
     for(i1=1; i1<=ncodemax[k1];i1++){    printf("\n");
       j1++;    fprintf(ficlog,"\n");
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  
         scanf("%d", i);*/    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       for (i=-1; i<=nlstate+ndeath; i++)      fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
         for (jk=-1; jk<=nlstate+ndeath; jk++)      
           for(m=agemin; m <= agemax+3; m++)    a=matrix(1,npar,1,npar);
             freq[i][jk][m]=0;    y=matrix(1,npar,1,npar);
          x=vector(1,npar);
       dateintsum=0;    indx=ivector(1,npar);
       k2cpt=0;    for (i=1;i<=npar;i++)
       for (i=1; i<=imx; i++) {      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
         bool=1;    ludcmp(a,npar,indx,&pd);
         if  (cptcovn>0) {  
           for (z1=1; z1<=cptcoveff; z1++)    for (j=1;j<=npar;j++) {
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      for (i=1;i<=npar;i++) x[i]=0;
               bool=0;      x[j]=1;
         }      lubksb(a,npar,indx,x);
         if (bool==1) {      for (i=1;i<=npar;i++){ 
           for(m=firstpass; m<=lastpass; m++){        matcov[i][j]=x[i];
             k2=anint[m][i]+(mint[m][i]/12.);      }
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    }
               if(agev[m][i]==0) agev[m][i]=agemax+1;  
               if(agev[m][i]==1) agev[m][i]=agemax+2;    printf("\n#Hessian matrix#\n");
               if (m<lastpass) {    fprintf(ficlog,"\n#Hessian matrix#\n");
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    for (i=1;i<=npar;i++) { 
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      for (j=1;j<=npar;j++) { 
               }        printf("%.3e ",hess[i][j]);
                      fprintf(ficlog,"%.3e ",hess[i][j]);
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {      }
                 dateintsum=dateintsum+k2;      printf("\n");
                 k2cpt++;      fprintf(ficlog,"\n");
               }    }
             }  
           }    /* Recompute Inverse */
         }    for (i=1;i<=npar;i++)
       }      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
            ludcmp(a,npar,indx,&pd);
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  
     /*  printf("\n#Hessian matrix recomputed#\n");
       if  (cptcovn>0) {  
         fprintf(ficresp, "\n#********** Variable ");    for (j=1;j<=npar;j++) {
         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++) x[i]=0;
         fprintf(ficresp, "**********\n#");      x[j]=1;
       }      lubksb(a,npar,indx,x);
       for(i=1; i<=nlstate;i++)      for (i=1;i<=npar;i++){ 
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        y[i][j]=x[i];
       fprintf(ficresp, "\n");        printf("%.3e ",y[i][j]);
              fprintf(ficlog,"%.3e ",y[i][j]);
       for(i=(int)agemin; i <= (int)agemax+3; i++){      }
         if(i==(int)agemax+3)      printf("\n");
           printf("Total");      fprintf(ficlog,"\n");
         else    }
           printf("Age %d", i);    */
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    free_matrix(a,1,npar,1,npar);
             pp[jk] += freq[jk][m][i];    free_matrix(y,1,npar,1,npar);
         }    free_vector(x,1,npar);
         for(jk=1; jk <=nlstate ; jk++){    free_ivector(indx,1,npar);
           for(m=-1, pos=0; m <=0 ; m++)    free_matrix(hess,1,npar,1,npar);
             pos += freq[jk][m][i];  
           if(pp[jk]>=1.e-10)  
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  }
           else  
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  /*************** hessian matrix ****************/
         }  double hessii( double x[], double delta, int theta, double delti[])
   {
         for(jk=1; jk <=nlstate ; jk++){    int i;
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    int l=1, lmax=20;
             pp[jk] += freq[jk][m][i];    double k1,k2;
         }    double p2[NPARMAX+1];
     double res;
         for(jk=1,pos=0; jk <=nlstate ; jk++)    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
           pos += pp[jk];    double fx;
         for(jk=1; jk <=nlstate ; jk++){    int k=0,kmax=10;
           if(pos>=1.e-5)    double l1;
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  
           else    fx=func(x);
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    for (i=1;i<=npar;i++) p2[i]=x[i];
           if( i <= (int) agemax){    for(l=0 ; l <=lmax; l++){
             if(pos>=1.e-5){      l1=pow(10,l);
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);      delts=delt;
               probs[i][jk][j1]= pp[jk]/pos;      for(k=1 ; k <kmax; k=k+1){
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/        delt = delta*(l1*k);
             }        p2[theta]=x[theta] +delt;
             else        k1=func(p2)-fx;
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        p2[theta]=x[theta]-delt;
           }        k2=func(p2)-fx;
         }        /*res= (k1-2.0*fx+k2)/delt/delt; */
                res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         for(jk=-1; jk <=nlstate+ndeath; jk++)        
           for(m=-1; m <=nlstate+ndeath; m++)  #ifdef DEBUG
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         if(i <= (int) agemax)        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);
           fprintf(ficresp,"\n");  #endif
         printf("\n");        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
       }        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     }          k=kmax;
   }        }
   dateintmean=dateintsum/k2cpt;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
            k=kmax; l=lmax*10.;
   fclose(ficresp);        }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   free_vector(pp,1,nlstate);          delts=delt;
          }
   /* End of Freq */      }
 }    }
     delti[theta]=delts;
 /************ Prevalence ********************/    return res; 
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)    
 {  /* Some frequencies */  }
    
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  double hessij( double x[], double delti[], int thetai,int thetaj)
   double ***freq; /* Frequencies */  {
   double *pp;    int i;
   double pos, k2;    int l=1, l1, lmax=20;
     double k1,k2,k3,k4,res,fx;
   pp=vector(1,nlstate);    double p2[NPARMAX+1];
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    int k;
    
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    fx=func(x);
   j1=0;    for (k=1; k<=2; k++) {
        for (i=1;i<=npar;i++) p2[i]=x[i];
   j=cptcoveff;      p2[thetai]=x[thetai]+delti[thetai]/k;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
        k1=func(p2)-fx;
  for(k1=1; k1<=j;k1++){    
     for(i1=1; i1<=ncodemax[k1];i1++){      p2[thetai]=x[thetai]+delti[thetai]/k;
       j1++;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
        k2=func(p2)-fx;
       for (i=-1; i<=nlstate+ndeath; i++)      
         for (jk=-1; jk<=nlstate+ndeath; jk++)        p2[thetai]=x[thetai]-delti[thetai]/k;
           for(m=agemin; m <= agemax+3; m++)      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
             freq[i][jk][m]=0;      k3=func(p2)-fx;
          
       for (i=1; i<=imx; i++) {      p2[thetai]=x[thetai]-delti[thetai]/k;
         bool=1;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         if  (cptcovn>0) {      k4=func(p2)-fx;
           for (z1=1; z1<=cptcoveff; z1++)      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  #ifdef DEBUG
               bool=0;      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);
         if (bool==1) {  #endif
           for(m=firstpass; m<=lastpass; m++){    }
             k2=anint[m][i]+(mint[m][i]/12.);    return res;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  }
               if(agev[m][i]==0) agev[m][i]=agemax+1;  
               if(agev[m][i]==1) agev[m][i]=agemax+2;  /************** Inverse of matrix **************/
               if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];  void ludcmp(double **a, int n, int *indx, double *d) 
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */  { 
             }    int i,imax,j,k; 
           }    double big,dum,sum,temp; 
         }    double *vv; 
       }   
         for(i=(int)agemin; i <= (int)agemax+3; i++){    vv=vector(1,n); 
           for(jk=1; jk <=nlstate ; jk++){    *d=1.0; 
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    for (i=1;i<=n;i++) { 
               pp[jk] += freq[jk][m][i];      big=0.0; 
           }      for (j=1;j<=n;j++) 
           for(jk=1; jk <=nlstate ; jk++){        if ((temp=fabs(a[i][j])) > big) big=temp; 
             for(m=-1, pos=0; m <=0 ; m++)      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
             pos += freq[jk][m][i];      vv[i]=1.0/big; 
         }    } 
            for (j=1;j<=n;j++) { 
          for(jk=1; jk <=nlstate ; jk++){      for (i=1;i<j;i++) { 
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        sum=a[i][j]; 
              pp[jk] += freq[jk][m][i];        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
          }        a[i][j]=sum; 
                } 
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      big=0.0; 
       for (i=j;i<=n;i++) { 
          for(jk=1; jk <=nlstate ; jk++){                  sum=a[i][j]; 
            if( i <= (int) agemax){        for (k=1;k<j;k++) 
              if(pos>=1.e-5){          sum -= a[i][k]*a[k][j]; 
                probs[i][jk][j1]= pp[jk]/pos;        a[i][j]=sum; 
              }        if ( (dum=vv[i]*fabs(sum)) >= big) { 
            }          big=dum; 
          }          imax=i; 
                  } 
         }      } 
     }      if (j != imax) { 
   }        for (k=1;k<=n;k++) { 
            dum=a[imax][k]; 
            a[imax][k]=a[j][k]; 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          a[j][k]=dum; 
   free_vector(pp,1,nlstate);        } 
          *d = -(*d); 
 }  /* End of Freq */        vv[imax]=vv[j]; 
       } 
 /************* Waves Concatenation ***************/      indx[j]=imax; 
       if (a[j][j] == 0.0) a[j][j]=TINY; 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      if (j != n) { 
 {        dum=1.0/(a[j][j]); 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
      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    } 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    free_vector(vv,1,n);  /* Doesn't work */
      and mw[mi+1][i]. dh depends on stepm.  ;
      */  } 
   
   int i, mi, m;  void lubksb(double **a, int n, int *indx, double b[]) 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  { 
      double sum=0., jmean=0.;*/    int i,ii=0,ip,j; 
     double sum; 
   int j, k=0,jk, ju, jl;   
   double sum=0.;    for (i=1;i<=n;i++) { 
   jmin=1e+5;      ip=indx[i]; 
   jmax=-1;      sum=b[ip]; 
   jmean=0.;      b[ip]=b[i]; 
   for(i=1; i<=imx; i++){      if (ii) 
     mi=0;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     m=firstpass;      else if (sum) ii=i; 
     while(s[m][i] <= nlstate){      b[i]=sum; 
       if(s[m][i]>=1)    } 
         mw[++mi][i]=m;    for (i=n;i>=1;i--) { 
       if(m >=lastpass)      sum=b[i]; 
         break;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       else      b[i]=sum/a[i][i]; 
         m++;    } 
     }/* end while */  } 
     if (s[m][i] > nlstate){  
       mi++;     /* Death is another wave */  /************ Frequencies ********************/
       /* if(mi==0)  never been interviewed correctly before death */  void  freqsummary(char fileres[], int agemin, int agemax, 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)
          /* Only death is a correct wave */  {  /* Some frequencies */
       mw[mi][i]=m;    
     }    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     int first;
     wav[i]=mi;    double ***freq; /* Frequencies */
     if(mi==0)    double *pp;
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    double pos, k2, dateintsum=0,k2cpt=0;
   }    FILE *ficresp;
     char fileresp[FILENAMELENGTH];
   for(i=1; i<=imx; i++){    
     for(mi=1; mi<wav[i];mi++){    pp=vector(1,nlstate);
       if (stepm <=0)    probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
         dh[mi][i]=1;    strcpy(fileresp,"p");
       else{    strcat(fileresp,fileres);
         if (s[mw[mi+1][i]][i] > nlstate) {    if((ficresp=fopen(fileresp,"w"))==NULL) {
           if (agedc[i] < 2*AGESUP) {      printf("Problem with prevalence resultfile: %s\n", fileresp);
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
           if(j==0) j=1;  /* Survives at least one month after exam */      exit(0);
           k=k+1;    }
           if (j >= jmax) jmax=j;    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
           if (j <= jmin) jmin=j;    j1=0;
           sum=sum+j;    
           /*if (j<0) printf("j=%d num=%d \n",j,i); */    j=cptcoveff;
           }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         }  
         else{    first=1;
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));  
           k=k+1;    for(k1=1; k1<=j;k1++){
           if (j >= jmax) jmax=j;      for(i1=1; i1<=ncodemax[k1];i1++){
           else if (j <= jmin)jmin=j;        j1++;
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           sum=sum+j;          scanf("%d", i);*/
         }        for (i=-1; i<=nlstate+ndeath; i++)  
         jk= j/stepm;          for (jk=-1; jk<=nlstate+ndeath; jk++)  
         jl= j -jk*stepm;            for(m=agemin; m <= agemax+3; m++)
         ju= j -(jk+1)*stepm;              freq[i][jk][m]=0;
         if(jl <= -ju)        
           dh[mi][i]=jk;        dateintsum=0;
         else        k2cpt=0;
           dh[mi][i]=jk+1;        for (i=1; i<=imx; i++) {
         if(dh[mi][i]==0)          bool=1;
           dh[mi][i]=1; /* At least one step */          if  (cptcovn>0) {
       }            for (z1=1; z1<=cptcoveff; z1++) 
     }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   }                bool=0;
   jmean=sum/k;          }
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          if (bool==1){
  }            for(m=firstpass; m<=lastpass; m++){
 /*********** Tricode ****************************/              k2=anint[m][i]+(mint[m][i]/12.);
 void tricode(int *Tvar, int **nbcode, int imx)              if ((k2>=dateprev1) && (k2<=dateprev2)) {
 {                if(agev[m][i]==0) agev[m][i]=agemax+1;
   int Ndum[20],ij=1, k, j, i;                if(agev[m][i]==1) agev[m][i]=agemax+2;
   int cptcode=0;                if (m<lastpass) {
   cptcoveff=0;                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                    freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
   for (k=0; k<19; k++) Ndum[k]=0;                }
   for (k=1; k<=7; k++) ncodemax[k]=0;                
                 if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {                  dateintsum=dateintsum+k2;
     for (i=1; i<=imx; i++) {                  k2cpt++;
       ij=(int)(covar[Tvar[j]][i]);                }
       Ndum[ij]++;              }
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/            }
       if (ij > cptcode) cptcode=ij;          }
     }        }
          
     for (i=0; i<=cptcode; i++) {        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
       if(Ndum[i]!=0) ncodemax[j]++;  
     }        if  (cptcovn>0) {
     ij=1;          fprintf(ficresp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresp, "**********\n#");
     for (i=1; i<=ncodemax[j]; i++) {        }
       for (k=0; k<=19; k++) {        for(i=1; i<=nlstate;i++) 
         if (Ndum[k] != 0) {          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
           nbcode[Tvar[j]][ij]=k;        fprintf(ficresp, "\n");
           /*     printf("nbcodeaaaaaaaaaaa=%d Tvar[j]=%d ij=%d j=%d",nbcode[Tvar[j]][ij],Tvar[j],ij,j);*/        
           ij++;        for(i=(int)agemin; i <= (int)agemax+3; i++){
         }          if(i==(int)agemax+3){
         if (ij > ncodemax[j]) break;            fprintf(ficlog,"Total");
       }            }else{
     }            if(first==1){
   }                first=0;
               printf("See log file for details...\n");
  for (k=0; k<19; k++) Ndum[k]=0;            }
             fprintf(ficlog,"Age %d", i);
  for (i=1; i<=ncovmodel-2; i++) {          }
       ij=Tvar[i];          for(jk=1; jk <=nlstate ; jk++){
       Ndum[ij]++;            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     }              pp[jk] += freq[jk][m][i]; 
           }
  ij=1;          for(jk=1; jk <=nlstate ; jk++){
  for (i=1; i<=10; i++) {            for(m=-1, pos=0; m <=0 ; m++)
    if((Ndum[i]!=0) && (i<=ncovcol)){              pos += freq[jk][m][i];
      Tvaraff[ij]=i;            if(pp[jk]>=1.e-10){
      ij++;              if(first==1){
    }              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
  }              }
                fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     cptcoveff=ij-1;            }else{
 }              if(first==1)
                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 /*********** Health Expectancies ****************/              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             }
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)          }
 {  
   /* Health expectancies */          for(jk=1; jk <=nlstate ; jk++){
   int i, j, nhstepm, hstepm, h, nstepm, k;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   double age, agelim, hf;              pp[jk] += freq[jk][m][i];
   double ***p3mat;          }
    
   fprintf(ficreseij,"# Health expectancies\n");          for(jk=1,pos=0; jk <=nlstate ; jk++)
   fprintf(ficreseij,"# Age");            pos += pp[jk];
   for(i=1; i<=nlstate;i++)          for(jk=1; jk <=nlstate ; jk++){
     for(j=1; j<=nlstate;j++)            if(pos>=1.e-5){
       fprintf(ficreseij," %1d-%1d",i,j);              if(first==1)
   fprintf(ficreseij,"\n");                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
               fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   k=1;             /* For example stepm=6 months */            }else{
   hstepm=k*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */              if(first==1)
   hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
      nhstepm is the number of hstepm from age to agelim            }
      nstepm is the number of stepm from age to agelin.            if( i <= (int) agemax){
      Look at hpijx to understand the reason of that which relies in memory size              if(pos>=1.e-5){
      and note for a fixed period like k years */                fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the                probs[i][jk][j1]= pp[jk]/pos;
      survival function given by stepm (the optimization length). Unfortunately it                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
      means that if the survival funtion is printed only each two years of age and if              }
      you sum them up and add 1 year (area under the trapezoids) you won't get the same              else
      results. So we changed our mind and took the option of the best precision.                fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
   */            }
   hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */          }
           
   agelim=AGESUP;          for(jk=-1; jk <=nlstate+ndeath; jk++)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            for(m=-1; m <=nlstate+ndeath; m++)
     /* nhstepm age range expressed in number of stepm */              if(freq[jk][m][i] !=0 ) {
     nstepm=(int) rint((agelim-age)*YEARM/stepm);              if(first==1)
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     /* if (stepm >= YEARM) hstepm=1;*/                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */              }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          if(i <= (int) agemax)
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            fprintf(ficresp,"\n");
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          if(first==1)
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);              printf("Others in log...\n");
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */          fprintf(ficlog,"\n");
     for(i=1; i<=nlstate;i++)        }
       for(j=1; j<=nlstate;j++)      }
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    }
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;    dateintmean=dateintsum/k2cpt; 
           /* 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]);*/   
         }    fclose(ficresp);
     fprintf(ficreseij,"%3.0f",age );    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
     for(i=1; i<=nlstate;i++)    free_vector(pp,1,nlstate);
       for(j=1; j<=nlstate;j++){    
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);    /* End of Freq */
       }  }
     fprintf(ficreseij,"\n");  
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /************ 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, int firstpass, int lastpass)
 }  {  
     /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
 /************ Variance ******************/       in each health status at the date of interview (if between dateprev1 and dateprev2).
 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)       We still use firstpass and lastpass as another selection.
 {    */
   /* Variance of health expectancies */   
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   double **newm;    double ***freq; /* Frequencies */
   double **dnewm,**doldm;    double *pp;
   int i, j, nhstepm, hstepm, h, nstepm, kk;    double pos; 
   int k, cptcode;    double  y2; /* in fractional years */
   double *xp;  
   double **gp, **gm;    pp=vector(1,nlstate);
   double ***gradg, ***trgradg;    
   double ***p3mat;    freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
   double age,agelim, hf;    j1=0;
   int theta;    
     j=cptcoveff;
    fprintf(ficresvij,"# Covariances of life expectancies\n");    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   fprintf(ficresvij,"# Age");    
   for(i=1; i<=nlstate;i++)    for(k1=1; k1<=j;k1++){
     for(j=1; j<=nlstate;j++)      for(i1=1; i1<=ncodemax[k1];i1++){
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        j1++;
   fprintf(ficresvij,"\n");        
         for (i=-1; i<=nlstate+ndeath; i++)  
   xp=vector(1,npar);          for (jk=-1; jk<=nlstate+ndeath; jk++)  
   dnewm=matrix(1,nlstate,1,npar);            for(m=agemin; m <= agemax+3; m++)
   doldm=matrix(1,nlstate,1,nlstate);              freq[i][jk][m]=0;
         
   kk=1;             /* For example stepm=6 months */        for (i=1; i<=imx; i++) { /* Each individual */
   hstepm=kk*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */          bool=1;
   hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */          if  (cptcovn>0) {
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.            for (z1=1; z1<=cptcoveff; z1++) 
      nhstepm is the number of hstepm from age to agelim              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
      nstepm is the number of stepm from age to agelin.                bool=0;
      Look at hpijx to understand the reason of that which relies in memory size          } 
      and note for a fixed period like k years */          if (bool==1) { 
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
      survival function given by stepm (the optimization length). Unfortunately it              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
      means that if the survival funtion is printed only each two years of age and if              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
      you sum them up and add 1 year (area under the trapezoids) you won't get the same                if(agev[m][i]==0) agev[m][i]=agemax+1;
      results. So we changed our mind and took the option of the best precision.                if(agev[m][i]==1) agev[m][i]=agemax+2;
   */                if (m<lastpass) {
   hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   agelim = AGESUP;                  freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */                }
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */              }
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */            } /* end selection of waves */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);        }
     gp=matrix(0,nhstepm,1,nlstate);        for(i=(int)agemin; i <= (int)agemax+3; i++){ 
     gm=matrix(0,nhstepm,1,nlstate);          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     for(theta=1; theta <=npar; theta++){              pp[jk] += freq[jk][m][i]; 
       for(i=1; i<=npar; i++){ /* Computes gradient */          }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          for(jk=1; jk <=nlstate ; jk++){
       }            for(m=-1, pos=0; m <=0 ; m++)
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                pos += freq[jk][m][i];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          }
           
       if (popbased==1) {          for(jk=1; jk <=nlstate ; jk++){
         for(i=1; i<=nlstate;i++)            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
           prlim[i][i]=probs[(int)age][i][ij];              pp[jk] += freq[jk][m][i];
       }          }
            
       for(j=1; j<= nlstate; j++){          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
         for(h=0; h<=nhstepm; h++){          
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          for(jk=1; jk <=nlstate ; jk++){    
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];            if( i <= (int) agemax){
         }              if(pos>=1.e-5){
       }                probs[i][jk][j1]= pp[jk]/pos;
                  }
       for(i=1; i<=npar; i++) /* Computes gradient */            }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          }/* end jk */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          }/* end i */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      } /* end i1 */
      } /* end k1 */
       if (popbased==1) {  
         for(i=1; i<=nlstate;i++)    
           prlim[i][i]=probs[(int)age][i][ij];    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
       }    free_vector(pp,1,nlstate);
     
       for(j=1; j<= nlstate; j++){  }  /* End of Freq */
         for(h=0; h<=nhstepm; h++){  
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)  /************* Waves Concatenation ***************/
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];  
         }  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)
       }  {
     /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
       for(j=1; j<= nlstate; j++)       Death is a valid wave (if date is known).
         for(h=0; h<=nhstepm; h++){       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
         }       and mw[mi+1][i]. dh depends on stepm.
     } /* End theta */       */
   
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    int i, mi, m;
     /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     for(h=0; h<=nhstepm; h++)       double sum=0., jmean=0.;*/
       for(j=1; j<=nlstate;j++)    int first;
         for(theta=1; theta <=npar; theta++)    int j, k=0,jk, ju, jl;
           trgradg[h][j][theta]=gradg[h][theta][j];    double sum=0.;
     first=0;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    jmin=1e+5;
     for(i=1;i<=nlstate;i++)    jmax=-1;
       for(j=1;j<=nlstate;j++)    jmean=0.;
         vareij[i][j][(int)age] =0.;    for(i=1; i<=imx; i++){
       mi=0;
     for(h=0;h<=nhstepm;h++){      m=firstpass;
       for(k=0;k<=nhstepm;k++){      while(s[m][i] <= nlstate){
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);        if(s[m][i]>=1)
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          mw[++mi][i]=m;
         for(i=1;i<=nlstate;i++)        if(m >=lastpass)
           for(j=1;j<=nlstate;j++)          break;
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;        else
       }          m++;
     }      }/* end while */
       if (s[m][i] > nlstate){
     fprintf(ficresvij,"%.0f ",age );        mi++;     /* Death is another wave */
     for(i=1; i<=nlstate;i++)        /* if(mi==0)  never been interviewed correctly before death */
       for(j=1; j<=nlstate;j++){           /* Only death is a correct wave */
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);        mw[mi][i]=m;
       }      }
     fprintf(ficresvij,"\n");  
     free_matrix(gp,0,nhstepm,1,nlstate);      wav[i]=mi;
     free_matrix(gm,0,nhstepm,1,nlstate);      if(mi==0){
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        if(first==0){
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          first=1;
   } /* End age */        }
          if(first==1){
   free_vector(xp,1,npar);          fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
   free_matrix(doldm,1,nlstate,1,npar);        }
   free_matrix(dnewm,1,nlstate,1,nlstate);      } /* end mi==0 */
     }
 }  
     for(i=1; i<=imx; i++){
 /************ Variance of prevlim ******************/      for(mi=1; mi<wav[i];mi++){
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)        if (stepm <=0)
 {          dh[mi][i]=1;
   /* Variance of prevalence limit */        else{
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          if (s[mw[mi+1][i]][i] > nlstate) {
   double **newm;            if (agedc[i] < 2*AGESUP) {
   double **dnewm,**doldm;            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   int i, j, nhstepm, hstepm;            if(j==0) j=1;  /* Survives at least one month after exam */
   int k, cptcode;            k=k+1;
   double *xp;            if (j >= jmax) jmax=j;
   double *gp, *gm;            if (j <= jmin) jmin=j;
   double **gradg, **trgradg;            sum=sum+j;
   double age,agelim;            /*if (j<0) printf("j=%d num=%d \n",j,i); */
   int theta;            /*      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]);*/
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");            }
   fprintf(ficresvpl,"# Age");          }
   for(i=1; i<=nlstate;i++)          else{
       fprintf(ficresvpl," %1d-%1d",i,i);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   fprintf(ficresvpl,"\n");            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             k=k+1;
   xp=vector(1,npar);            if (j >= jmax) jmax=j;
   dnewm=matrix(1,nlstate,1,npar);            else if (j <= jmin)jmin=j;
   doldm=matrix(1,nlstate,1,nlstate);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
              sum=sum+j;
   hstepm=1*YEARM; /* Every year of age */          }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          jk= j/stepm;
   agelim = AGESUP;          jl= j -jk*stepm;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          ju= j -(jk+1)*stepm;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          if(mle <=1){ 
     if (stepm >= YEARM) hstepm=1;            if(jl==0){
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */              dh[mi][i]=jk;
     gradg=matrix(1,npar,1,nlstate);              bh[mi][i]=0;
     gp=vector(1,nlstate);            }else{ /* We want a negative bias in order to only have interpolation ie
     gm=vector(1,nlstate);                    * at the price of an extra matrix product in likelihood */
               dh[mi][i]=jk+1;
     for(theta=1; theta <=npar; theta++){              bh[mi][i]=ju;
       for(i=1; i<=npar; i++){ /* Computes gradient */            }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          }else{
       }            if(jl <= -ju){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              dh[mi][i]=jk;
       for(i=1;i<=nlstate;i++)              bh[mi][i]=jl;       /* bias is positive if real duration
         gp[i] = prlim[i][i];                                   * is higher than the multiple of stepm and negative otherwise.
                                       */
       for(i=1; i<=npar; i++) /* Computes gradient */            }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            else{
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              dh[mi][i]=jk+1;
       for(i=1;i<=nlstate;i++)              bh[mi][i]=ju;
         gm[i] = prlim[i][i];            }
             if(dh[mi][i]==0){
       for(i=1;i<=nlstate;i++)              dh[mi][i]=1; /* At least one step */
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];              bh[mi][i]=ju; /* At least one step */
     } /* End theta */              /*  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);*/
             }
     trgradg =matrix(1,nlstate,1,npar);          }
         } /* end if mle */
     for(j=1; j<=nlstate;j++)      } /* end wave */
       for(theta=1; theta <=npar; theta++)    }
         trgradg[j][theta]=gradg[theta][j];    jmean=sum/k;
     printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     for(i=1;i<=nlstate;i++)    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
       varpl[i][(int)age] =0.;   }
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);  
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);  /*********** Tricode ****************************/
     for(i=1;i<=nlstate;i++)  void tricode(int *Tvar, int **nbcode, int imx)
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */  {
     
     fprintf(ficresvpl,"%.0f ",age );    int Ndum[20],ij=1, k, j, i, maxncov=19;
     for(i=1; i<=nlstate;i++)    int cptcode=0;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    cptcoveff=0; 
     fprintf(ficresvpl,"\n");   
     free_vector(gp,1,nlstate);    for (k=0; k<maxncov; k++) Ndum[k]=0;
     free_vector(gm,1,nlstate);    for (k=1; k<=7; k++) ncodemax[k]=0;
     free_matrix(gradg,1,npar,1,nlstate);  
     free_matrix(trgradg,1,nlstate,1,npar);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   } /* End age */      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                  modality*/ 
   free_vector(xp,1,npar);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
   free_matrix(doldm,1,nlstate,1,npar);        Ndum[ij]++; /*store the modality */
   free_matrix(dnewm,1,nlstate,1,nlstate);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
 }                                         Tvar[j]. If V=sex and male is 0 and 
                                          female is 1, then  cptcode=1.*/
 /************ Variance of one-step probabilities  ******************/      }
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)  
 {      for (i=0; i<=cptcode; i++) {
   int i, j;        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 */
   int k=0, cptcode;      }
   double **dnewm,**doldm;  
   double *xp;      ij=1; 
   double *gp, *gm;      for (i=1; i<=ncodemax[j]; i++) {
   double **gradg, **trgradg;        for (k=0; k<= maxncov; k++) {
   double age,agelim, cov[NCOVMAX];          if (Ndum[k] != 0) {
   int theta;            nbcode[Tvar[j]][ij]=k; 
   char fileresprob[FILENAMELENGTH];            /* 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; */
             
   strcpy(fileresprob,"prob");            ij++;
   strcat(fileresprob,fileres);          }
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {          if (ij > ncodemax[j]) break; 
     printf("Problem with resultfile: %s\n", fileresprob);        }  
   }      } 
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);    }  
    
    for (k=0; k< maxncov; k++) Ndum[k]=0;
   xp=vector(1,npar);  
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);   for (i=1; i<=ncovmodel-2; i++) { 
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
       ij=Tvar[i];
   cov[1]=1;     Ndum[ij]++;
   for (age=bage; age<=fage; age ++){   }
     cov[2]=age;  
     gradg=matrix(1,npar,1,9);   ij=1;
     trgradg=matrix(1,9,1,npar);   for (i=1; i<= maxncov; i++) {
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));     if((Ndum[i]!=0) && (i<=ncovcol)){
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));       Tvaraff[ij]=i; /*For printing */
           ij++;
     for(theta=1; theta <=npar; theta++){     }
       for(i=1; i<=npar; i++)   }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);   
         cptcoveff=ij-1; /*Number of simple covariates*/
       pmij(pmmij,cov,ncovmodel,xp,nlstate);  }
      
       k=0;  /*********** Health Expectancies ****************/
       for(i=1; i<= (nlstate+ndeath); i++){  
         for(j=1; j<=(nlstate+ndeath);j++){  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 )
            k=k+1;  
           gp[k]=pmmij[i][j];  {
         }    /* Health expectancies */
       }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     double age, agelim, hf;
       for(i=1; i<=npar; i++)    double ***p3mat,***varhe;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    double **dnewm,**doldm;
        double *xp;
     double **gp, **gm;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    double ***gradg, ***trgradg;
       k=0;    int theta;
       for(i=1; i<=(nlstate+ndeath); i++){  
         for(j=1; j<=(nlstate+ndeath);j++){    varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
           k=k+1;    xp=vector(1,npar);
           gm[k]=pmmij[i][j];    dnewm=matrix(1,nlstate*2,1,npar);
         }    doldm=matrix(1,nlstate*2,1,nlstate*2);
       }    
          fprintf(ficreseij,"# Health expectancies\n");
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    fprintf(ficreseij,"# Age");
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      for(i=1; i<=nlstate;i++)
     }      for(j=1; j<=nlstate;j++)
         fprintf(ficreseij," %1d-%1d (SE)",i,j);
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    fprintf(ficreseij,"\n");
       for(theta=1; theta <=npar; theta++)  
       trgradg[j][theta]=gradg[theta][j];    if(estepm < stepm){
        printf ("Problem %d lower than %d\n",estepm, stepm);
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    }
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
      pmij(pmmij,cov,ncovmodel,x,nlstate);     * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
      k=0;     * we are calculating an estimate of the Life Expectancy assuming a linear 
      for(i=1; i<=(nlstate+ndeath); i++){     * progression in between and thus overestimating or underestimating according
        for(j=1; j<=(nlstate+ndeath);j++){     * to the curvature of the survival function. If, for the same date, we 
          k=k+1;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
          gm[k]=pmmij[i][j];     * to compare the new estimate of Life expectancy with the same linear 
         }     * hypothesis. A more precise result, taking into account a more precise
      }     * curvature will be obtained if estepm is as small as stepm. */
        
      /*printf("\n%d ",(int)age);    /* For example we decided to compute the life expectancy with the smallest unit */
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);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 
        nstepm is the number of stepm from age to agelin. 
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));       Look at hpijx to understand the reason of that which relies in memory size
      }*/       and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   fprintf(ficresprob,"\n%d ",(int)age);       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
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);       results. So we changed our mind and took the option of the best precision.
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    */
   }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    agelim=AGESUP;
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      /* nhstepm age range expressed in number of stepm */
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
 }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
  free_vector(xp,1,npar);      /* if (stepm >= YEARM) hstepm=1;*/
 fclose(ficresprob);      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);
 /******************* Printing html file ***********/      gm=matrix(0,nhstepm,1,nlstate*2);
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \  
  int lastpass, int stepm, int weightopt, char model[],\      /* Computed by stepm unit matrices, product of hstepm matrices, stored
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
  char version[], int popforecast ){   
   int jj1, k1, i1, cpt;  
   FILE *fichtm;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   /*char optionfilehtm[FILENAMELENGTH];*/  
       /* Computing Variances of health expectancies */
   strcpy(optionfilehtm,optionfile);  
   strcat(optionfilehtm,".htm");       for(theta=1; theta <=npar; theta++){
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {        for(i=1; i<=npar; i++){ 
     printf("Problem with %s \n",optionfilehtm), exit(0);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   }        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
  fprintf(fichtm,"<body> <font size=\"2\">Imach, Version %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        cptj=0;
 \n        for(j=1; j<= nlstate; j++){
 Total number of observations=%d <br>\n          for(i=1; i<=nlstate; i++){
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n            cptj=cptj+1;
 <hr  size=\"2\" color=\"#EC5E5E\">            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
  <ul><li>Outputs files<br>\n              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n            }
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n          }
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n        }
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n       
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n       
  - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);        for(i=1; i<=npar; i++) 
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
  fprintf(fichtm,"\n        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n        
  - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>\n        cptj=0;
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n        for(j=1; j<= nlstate; j++){
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres);          for(i=1;i<=nlstate;i++){
             cptj=cptj+1;
  if(popforecast==1) fprintf(fichtm,"\n            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n            }
         <br>",fileres,fileres,fileres,fileres);          }
  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);        for(j=1; j<= nlstate*2; j++)
 fprintf(fichtm," <li>Graphs</li><p>");          for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
  m=cptcoveff;          }
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}       } 
      
  jj1=0;  /* End theta */
  for(k1=1; k1<=m;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){       trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
        jj1++;  
        if (cptcovn > 0) {       for(h=0; h<=nhstepm-1; h++)
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        for(j=1; j<=nlstate*2;j++)
          for (cpt=1; cpt<=cptcoveff;cpt++)          for(theta=1; theta <=npar; theta++)
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);            trgradg[h][j][theta]=gradg[h][theta][j];
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");       
        }  
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>       for(i=1;i<=nlstate*2;i++)
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            for(j=1;j<=nlstate*2;j++)
        for(cpt=1; cpt<nlstate;cpt++){          varhe[i][j][(int)age] =0.;
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>  
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);       printf("%d|",(int)age);fflush(stdout);
        }       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     for(cpt=1; cpt<=nlstate;cpt++) {       for(h=0;h<=nhstepm-1;h++){
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident        for(k=0;k<=nhstepm-1;k++){
 interval) in state (%d): v%s%d%d.gif <br>          matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
      }          for(i=1;i<=nlstate*2;i++)
      for(cpt=1; cpt<=nlstate;cpt++) {            for(j=1;j<=nlstate*2;j++)
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        }
      }      }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and      /* Computing expectancies */
 health expectancies in states (1) and (2): e%s%d.gif<br>      for(i=1; i<=nlstate;i++)
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        for(j=1; j<=nlstate;j++)
 fprintf(fichtm,"\n</body>");          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;
    }            
 fclose(fichtm);  /* 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]);*/
 }  
           }
 /******************* Gnuplot file **************/  
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){      fprintf(ficreseij,"%3.0f",age );
       cptj=0;
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
   strcpy(optionfilegnuplot,optionfilefiname);          cptj++;
   strcat(optionfilegnuplot,".gp.txt");          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {        }
     printf("Problem with file %s",optionfilegnuplot);      fprintf(ficreseij,"\n");
   }     
       free_matrix(gm,0,nhstepm,1,nlstate*2);
 #ifdef windows      free_matrix(gp,0,nhstepm,1,nlstate*2);
     fprintf(ficgp,"cd \"%s\" \n",pathc);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
 #endif      free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
 m=pow(2,cptcoveff);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      }
  /* 1eme*/    printf("\n");
   for (cpt=1; cpt<= nlstate ; cpt ++) {    fprintf(ficlog,"\n");
    for (k1=1; k1<= m ; k1 ++) {  
     free_vector(xp,1,npar);
 #ifdef windows    free_matrix(dnewm,1,nlstate*2,1,npar);
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);    free_matrix(doldm,1,nlstate*2,1,nlstate*2);
 #endif    free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
 #ifdef unix  }
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);  
 #endif  /************ Variance ******************/
   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)
 for (i=1; i<= nlstate ; i ++) {  {
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    /* Variance of health expectancies */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
 }    /* double **newm;*/
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    double **dnewm,**doldm;
     for (i=1; i<= nlstate ; i ++) {    double **dnewmp,**doldmp;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    int i, j, nhstepm, hstepm, h, nstepm ;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    int k, cptcode;
 }    double *xp;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    double **gp, **gm;  /* for var eij */
      for (i=1; i<= nlstate ; i ++) {    double ***gradg, ***trgradg; /*for var eij */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    double **gradgp, **trgradgp; /* for var p point j */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double *gpp, *gmp; /* for var p point j */
 }      double **varppt; /* for var p point j nlstate to nlstate+ndeath */
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    double ***p3mat;
 #ifdef unix    double age,agelim, hf;
 fprintf(ficgp,"\nset ter gif small size 400,300");    double ***mobaverage;
 #endif    int theta;
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    char digit[4];
    }    char digitp[25];
   }  
   /*2 eme*/    char fileresprobmorprev[FILENAMELENGTH];
   
   for (k1=1; k1<= m ; k1 ++) {    if(popbased==1){
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);      if(mobilav!=0)
            strcpy(digitp,"-populbased-mobilav-");
     for (i=1; i<= nlstate+1 ; i ++) {      else strcpy(digitp,"-populbased-nomobil-");
       k=2*i;    }
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    else 
       for (j=1; j<= nlstate+1 ; j ++) {      strcpy(digitp,"-stablbased-");
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    if (mobilav!=0) {
 }        mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       for (j=1; j<= nlstate+1 ; j ++) {      }
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    }
         else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      strcpy(fileresprobmorprev,"prmorprev"); 
       fprintf(ficgp,"\" t\"\" w l 0,");    sprintf(digit,"%-d",ij);
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
       for (j=1; j<= nlstate+1 ; j ++) {    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    strcat(fileresprobmorprev,fileres);
 }      if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       else fprintf(ficgp,"\" t\"\" w l 0,");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }    }
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   }    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
      fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
   /*3eme*/    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   for (k1=1; k1<= m ; k1 ++) {      fprintf(ficresprobmorprev," p.%-d SE",j);
     for (cpt=1; cpt<= nlstate ; cpt ++) {      for(i=1; i<=nlstate;i++)
       k=2+nlstate*(cpt-1);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    }  
       for (i=1; i< nlstate ; i ++) {    fprintf(ficresprobmorprev,"\n");
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       }      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
     }      exit(0);
     }    }
      else{
   /* CV preval stat */      fprintf(ficgp,"\n# Routine varevsij");
     for (k1=1; k1<= m ; k1 ++) {    }
     for (cpt=1; cpt<nlstate ; cpt ++) {    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
       k=3;      printf("Problem with html file: %s\n", optionfilehtm);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
       exit(0);
       for (i=1; i< nlstate ; i ++)    }
         fprintf(ficgp,"+$%d",k+i+1);    else{
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);      fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
            fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
       l=3+(nlstate+ndeath)*cpt;    }
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       for (i=1; i< nlstate ; i ++) {  
         l=3+(nlstate+ndeath)*cpt;    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
         fprintf(ficgp,"+$%d",l+i+1);    fprintf(ficresvij,"# Age");
       }    for(i=1; i<=nlstate;i++)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);        for(j=1; j<=nlstate;j++)
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     }    fprintf(ficresvij,"\n");
   }    
      xp=vector(1,npar);
   /* proba elementaires */    dnewm=matrix(1,nlstate,1,npar);
    for(i=1,jk=1; i <=nlstate; i++){    doldm=matrix(1,nlstate,1,nlstate);
     for(k=1; k <=(nlstate+ndeath); k++){    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
       if (k != i) {    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         for(j=1; j <=ncovmodel; j++){  
            gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    gpp=vector(nlstate+1,nlstate+ndeath);
           jk++;    gmp=vector(nlstate+1,nlstate+ndeath);
           fprintf(ficgp,"\n");    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
         }    
       }    if(estepm < stepm){
     }      printf ("Problem %d lower than %d\n",estepm, stepm);
     }    }
     else  hstepm=estepm;   
     for(jk=1; jk <=m; jk++) {    /* For example we decided to compute the life expectancy with the smallest unit */
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
    i=1;       nhstepm is the number of hstepm from age to agelim 
    for(k2=1; k2<=nlstate; k2++) {       nstepm is the number of stepm from age to agelin. 
      k3=i;       Look at hpijx to understand the reason of that which relies in memory size
      for(k=1; k<=(nlstate+ndeath); k++) {       and note for a fixed period like k years */
        if (k != k2){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);       survival function given by stepm (the optimization length). Unfortunately it
 ij=1;       means that if the survival funtion is printed every two years of age and if
         for(j=3; j <=ncovmodel; j++) {       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {       results. So we changed our mind and took the option of the best precision.
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    */
             ij++;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           }    agelim = AGESUP;
           else    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         }      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
           fprintf(ficgp,")/(1");      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
              gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
         for(k1=1; k1 <=nlstate; k1++){        gp=matrix(0,nhstepm,1,nlstate);
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);      gm=matrix(0,nhstepm,1,nlstate);
 ij=1;  
           for(j=3; j <=ncovmodel; j++){  
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      for(theta=1; theta <=npar; theta++){
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
             ij++;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           }        }
           else        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           }  
           fprintf(ficgp,")");        if (popbased==1) {
         }          if(mobilav ==0){
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);            for(i=1; i<=nlstate;i++)
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");              prlim[i][i]=probs[(int)age][i][ij];
         i=i+ncovmodel;          }else{ /* mobilav */ 
        }            for(i=1; i<=nlstate;i++)
      }              prlim[i][i]=mobaverage[(int)age][i][ij];
    }          }
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);        }
    }    
            for(j=1; j<= nlstate; j++){
   fclose(ficgp);          for(h=0; h<=nhstepm; h++){
 }  /* end gnuplot */            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
 /*************** Moving average **************/        }
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
   int i, cpt, cptcod;           as a weighted average of prlim.
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)        */
       for (i=1; i<=nlstate;i++)        for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          for(i=1,gpp[j]=0.; i<= nlstate; i++)
           mobaverage[(int)agedeb][i][cptcod]=0.;            gpp[j] += prlim[i][i]*p3mat[i][j][1];
            }    
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){        /* end probability of death */
       for (i=1; i<=nlstate;i++){  
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           for (cpt=0;cpt<=4;cpt++){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;   
         }        if (popbased==1) {
       }          if(mobilav ==0){
     }            for(i=1; i<=nlstate;i++)
                  prlim[i][i]=probs[(int)age][i][ij];
 }          }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
 /************** Forecasting ******************/          }
 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){        }
    
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        for(j=1; j<= nlstate; j++){
   int *popage;          for(h=0; h<=nhstepm; h++){
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   double *popeffectif,*popcount;              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   double ***p3mat;          }
   char fileresf[FILENAMELENGTH];        }
         /* This for computing probability of death (h=1 means
  agelim=AGESUP;           computed over hstepm matrices product = hstepm*stepm months) 
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;           as a weighted average of prlim.
         */
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
            for(i=1,gmp[j]=0.; i<= nlstate; i++)
             gmp[j] += prlim[i][i]*p3mat[i][j][1];
   strcpy(fileresf,"f");        }    
   strcat(fileresf,fileres);        /* end probability of death */
   if((ficresf=fopen(fileresf,"w"))==NULL) {  
     printf("Problem with forecast resultfile: %s\n", fileresf);        for(j=1; j<= nlstate; j++) /* vareij */
   }          for(h=0; h<=nhstepm; h++){
   printf("Computing forecasting: result on file '%s' \n", fileresf);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   if (mobilav==1) {          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        }
     movingaverage(agedeb, fage, ageminpar, mobaverage);  
   }      } /* End theta */
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   if (stepm<=12) stepsize=1;  
        for(h=0; h<=nhstepm; h++) /* veij */
   agelim=AGESUP;        for(j=1; j<=nlstate;j++)
            for(theta=1; theta <=npar; theta++)
   hstepm=1;            trgradg[h][j][theta]=gradg[h][theta][j];
   hstepm=hstepm/stepm;  
   yp1=modf(dateintmean,&yp);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   anprojmean=yp;        for(theta=1; theta <=npar; theta++)
   yp2=modf((yp1*12),&yp);          trgradgp[j][theta]=gradgp[theta][j];
   mprojmean=yp;    
   yp1=modf((yp2*30.5),&yp);  
   jprojmean=yp;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   if(jprojmean==0) jprojmean=1;      for(i=1;i<=nlstate;i++)
   if(mprojmean==0) jprojmean=1;        for(j=1;j<=nlstate;j++)
            vareij[i][j][(int)age] =0.;
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);  
        for(h=0;h<=nhstepm;h++){
   for(cptcov=1;cptcov<=i2;cptcov++){        for(k=0;k<=nhstepm;k++){
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
       k=k+1;          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
       fprintf(ficresf,"\n#******");          for(i=1;i<=nlstate;i++)
       for(j=1;j<=cptcoveff;j++) {            for(j=1;j<=nlstate;j++)
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       }        }
       fprintf(ficresf,"******\n");      }
       fprintf(ficresf,"# StartingAge FinalAge");    
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);      /* pptj */
            matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
            matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {      for(j=nlstate+1;j<=nlstate+ndeath;j++)
         fprintf(ficresf,"\n");        for(i=nlstate+1;i<=nlstate+ndeath;i++)
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);            varppt[j][i]=doldmp[j][i];
       /* end ppptj */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      /*  x centered again */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
           nhstepm = nhstepm/hstepm;      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
             
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      if (popbased==1) {
           oldm=oldms;savm=savms;        if(mobilav ==0){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            for(i=1; i<=nlstate;i++)
                    prlim[i][i]=probs[(int)age][i][ij];
           for (h=0; h<=nhstepm; h++){        }else{ /* mobilav */ 
             if (h==(int) (calagedate+YEARM*cpt)) {          for(i=1; i<=nlstate;i++)
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);            prlim[i][i]=mobaverage[(int)age][i][ij];
             }        }
             for(j=1; j<=nlstate+ndeath;j++) {      }
               kk1=0.;kk2=0;               
               for(i=1; i<=nlstate;i++) {                    /* This for computing probability of death (h=1 means
                 if (mobilav==1)         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];         as a weighted average of prlim.
                 else {      */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      for(j=nlstate+1;j<=nlstate+ndeath;j++){
                 }        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
                          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
               }      }    
               if (h==(int)(calagedate+12*cpt)){      /* end probability of death */
                 fprintf(ficresf," %.3f", kk1);  
                              fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
               }      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
             }        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
           }        for(i=1; i<=nlstate;i++){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }        }
       }      } 
     }      fprintf(ficresprobmorprev,"\n");
   }  
              fprintf(ficresvij,"%.0f ",age );
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
   fclose(ficresf);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
 }        }
 /************** Forecasting ******************/      fprintf(ficresvij,"\n");
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){      free_matrix(gp,0,nhstepm,1,nlstate);
        free_matrix(gm,0,nhstepm,1,nlstate);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   int *popage;      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   double *popeffectif,*popcount;    } /* End age */
   double ***p3mat,***tabpop,***tabpopprev;    free_vector(gpp,nlstate+1,nlstate+ndeath);
   char filerespop[FILENAMELENGTH];    free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
   agelim=AGESUP;    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    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); */
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  /*   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);
   strcpy(filerespop,"pop");    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
   strcat(filerespop,fileres);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
     printf("Problem with forecast resultfile: %s\n", filerespop);    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);
   printf("Computing forecasting: result on file '%s' \n", filerespop);  */
     fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
     free_vector(xp,1,npar);
   if (mobilav==1) {    free_matrix(doldm,1,nlstate,1,nlstate);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    free_matrix(dnewm,1,nlstate,1,npar);
     movingaverage(agedeb, fage, ageminpar, mobaverage);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   }    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   if (stepm<=12) stepsize=1;    fclose(ficresprobmorprev);
      fclose(ficgp);
   agelim=AGESUP;    fclose(fichtm);
    }  
   hstepm=1;  
   hstepm=hstepm/stepm;  /************ 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)
   if (popforecast==1) {  {
     if((ficpop=fopen(popfile,"r"))==NULL) {    /* Variance of prevalence limit */
       printf("Problem with population file : %s\n",popfile);exit(0);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     }    double **newm;
     popage=ivector(0,AGESUP);    double **dnewm,**doldm;
     popeffectif=vector(0,AGESUP);    int i, j, nhstepm, hstepm;
     popcount=vector(0,AGESUP);    int k, cptcode;
        double *xp;
     i=1;      double *gp, *gm;
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    double **gradg, **trgradg;
        double age,agelim;
     imx=i;    int theta;
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];     
   }    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
     fprintf(ficresvpl,"# Age");
   for(cptcov=1;cptcov<=i2;cptcov++){    for(i=1; i<=nlstate;i++)
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        fprintf(ficresvpl," %1d-%1d",i,i);
       k=k+1;    fprintf(ficresvpl,"\n");
       fprintf(ficrespop,"\n#******");  
       for(j=1;j<=cptcoveff;j++) {    xp=vector(1,npar);
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    dnewm=matrix(1,nlstate,1,npar);
       }    doldm=matrix(1,nlstate,1,nlstate);
       fprintf(ficrespop,"******\n");    
       fprintf(ficrespop,"# Age");    hstepm=1*YEARM; /* Every year of age */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
       if (popforecast==1)  fprintf(ficrespop," [Population]");    agelim = AGESUP;
          for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       for (cpt=0; cpt<=0;cpt++) {      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);        if (stepm >= YEARM) hstepm=1;
              nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      gradg=matrix(1,npar,1,nlstate);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      gp=vector(1,nlstate);
           nhstepm = nhstepm/hstepm;      gm=vector(1,nlstate);
            
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for(theta=1; theta <=npar; theta++){
           oldm=oldms;savm=savms;        for(i=1; i<=npar; i++){ /* Computes gradient */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            xp[i] = x[i] + (i==theta ?delti[theta]:0);
                }
           for (h=0; h<=nhstepm; h++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
             if (h==(int) (calagedate+YEARM*cpt)) {        for(i=1;i<=nlstate;i++)
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          gp[i] = prlim[i][i];
             }      
             for(j=1; j<=nlstate+ndeath;j++) {        for(i=1; i<=npar; i++) /* Computes gradient */
               kk1=0.;kk2=0;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
               for(i=1; i<=nlstate;i++) {                      prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                 if (mobilav==1)        for(i=1;i<=nlstate;i++)
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          gm[i] = prlim[i][i];
                 else {  
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        for(i=1;i<=nlstate;i++)
                 }          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
               }      } /* End theta */
               if (h==(int)(calagedate+12*cpt)){  
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      trgradg =matrix(1,nlstate,1,npar);
                   /*fprintf(ficrespop," %.3f", kk1);  
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/      for(j=1; j<=nlstate;j++)
               }        for(theta=1; theta <=npar; theta++)
             }          trgradg[j][theta]=gradg[theta][j];
             for(i=1; i<=nlstate;i++){  
               kk1=0.;      for(i=1;i<=nlstate;i++)
                 for(j=1; j<=nlstate;j++){        varpl[i][(int)age] =0.;
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
                 }      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];      for(i=1;i<=nlstate;i++)
             }        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)      fprintf(ficresvpl,"%.0f ",age );
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);      for(i=1; i<=nlstate;i++)
           }        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fprintf(ficresvpl,"\n");
         }      free_vector(gp,1,nlstate);
       }      free_vector(gm,1,nlstate);
        free_matrix(gradg,1,npar,1,nlstate);
   /******/      free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {  
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      free_vector(xp,1,npar);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    free_matrix(doldm,1,nlstate,1,npar);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    free_matrix(dnewm,1,nlstate,1,nlstate);
           nhstepm = nhstepm/hstepm;  
            }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;  /************ Variance of one-step probabilities  ******************/
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
           for (h=0; h<=nhstepm; h++){  {
             if (h==(int) (calagedate+YEARM*cpt)) {    int i, j=0,  i1, k1, l1, t, tj;
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    int k2, l2, j1,  z1;
             }    int k=0,l, cptcode;
             for(j=1; j<=nlstate+ndeath;j++) {    int first=1, first1;
               kk1=0.;kk2=0;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
               for(i=1; i<=nlstate;i++) {                  double **dnewm,**doldm;
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        double *xp;
               }    double *gp, *gm;
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    double **gradg, **trgradg;
             }    double **mu;
           }    double age,agelim, cov[NCOVMAX];
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
         }    int theta;
       }    char fileresprob[FILENAMELENGTH];
    }    char fileresprobcov[FILENAMELENGTH];
   }    char fileresprobcor[FILENAMELENGTH];
    
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double ***varpij;
   
   if (popforecast==1) {    strcpy(fileresprob,"prob"); 
     free_ivector(popage,0,AGESUP);    strcat(fileresprob,fileres);
     free_vector(popeffectif,0,AGESUP);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     free_vector(popcount,0,AGESUP);      printf("Problem with resultfile: %s\n", fileresprob);
   }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    }
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    strcpy(fileresprobcov,"probcov"); 
   fclose(ficrespop);    strcat(fileresprobcov,fileres);
 }    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
 /***********************************************/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
 /**************** Main Program *****************/    }
 /***********************************************/    strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
 int main(int argc, char *argv[])    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
 {      printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    }
   double agedeb, agefin,hf;    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   double fret;    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   double **xi,tmp,delta;    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   double dum; /* Dummy variable */    
   double ***p3mat;    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   int *indx;    fprintf(ficresprob,"# Age");
   char line[MAXLINE], linepar[MAXLINE];    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   char title[MAXLINE];    fprintf(ficresprobcov,"# Age");
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    fprintf(ficresprobcov,"# Age");
    
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  
     for(i=1; i<=nlstate;i++)
   char filerest[FILENAMELENGTH];      for(j=1; j<=(nlstate+ndeath);j++){
   char fileregp[FILENAMELENGTH];        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   char popfile[FILENAMELENGTH];        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];        fprintf(ficresprobcor," p%1d-%1d ",i,j);
   int firstobs=1, lastobs=10;      }  
   int sdeb, sfin; /* Status at beginning and end */   /* fprintf(ficresprob,"\n");
   int c,  h , cpt,l;    fprintf(ficresprobcov,"\n");
   int ju,jl, mi;    fprintf(ficresprobcor,"\n");
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;   */
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;   xp=vector(1,npar);
   int mobilav=0,popforecast=0;    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   int hstepm, nhstepm;    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
   double bage, fage, age, agelim, agebase;    first=1;
   double ftolpl=FTOL;    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   double **prlim;      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   double *severity;      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
   double ***param; /* Matrix of parameters */      exit(0);
   double  *p;    }
   double **matcov; /* Matrix of covariance */    else{
   double ***delti3; /* Scale */      fprintf(ficgp,"\n# Routine varprob");
   double *delti; /* Scale */    }
   double ***eij, ***vareij;    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   double **varpl; /* Variances of prevalence limits by age */      printf("Problem with html file: %s\n", optionfilehtm);
   double *epj, vepp;      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   double kk1, kk2;      exit(0);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    }
      else{
       fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   char version[80]="Imach version 0.8a, March 2002, INED-EUROREVES ";      fprintf(fichtm,"\n");
   char *alph[]={"a","a","b","c","d","e"}, str[4];  
       fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
       fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
   char z[1]="c", occ;      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");
 #include <sys/time.h>  
 #include <time.h>    }
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  
      cov[1]=1;
   /* long total_usecs;    tj=cptcoveff;
   struct timeval start_time, end_time;    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
      j1=0;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    for(t=1; t<=tj;t++){
   getcwd(pathcd, size);      for(i1=1; i1<=ncodemax[t];i1++){ 
         j1++;
   printf("\n%s",version);        if  (cptcovn>0) {
   if(argc <=1){          fprintf(ficresprob, "\n#********** Variable "); 
     printf("\nEnter the parameter file name: ");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     scanf("%s",pathtot);          fprintf(ficresprob, "**********\n#\n");
   }          fprintf(ficresprobcov, "\n#********** Variable "); 
   else{          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     strcpy(pathtot,argv[1]);          fprintf(ficresprobcov, "**********\n#\n");
   }          
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/          fprintf(ficgp, "\n#********** Variable "); 
   /*cygwin_split_path(pathtot,path,optionfile);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/          fprintf(ficgp, "**********\n#\n");
   /* cutv(path,optionfile,pathtot,'\\');*/          
           
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   chdir(path);          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
   replace(pathc,path);          
           fprintf(ficresprobcor, "\n#********** Variable ");    
 /*-------- arguments in the command line --------*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
   strcpy(fileres,"r");        }
   strcat(fileres, optionfilefiname);        
   strcat(fileres,".txt");    /* Other files have txt extension */        for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
   /*---------arguments file --------*/          for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
   if((ficpar=fopen(optionfile,"r"))==NULL)    {          }
     printf("Problem with optionfile %s\n",optionfile);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     goto end;          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]]];
           
   strcpy(filereso,"o");          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   strcat(filereso,fileres);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   if((ficparo=fopen(filereso,"w"))==NULL) {          gp=vector(1,(nlstate)*(nlstate+ndeath));
     printf("Problem with Output resultfile: %s\n", filereso);goto end;          gm=vector(1,(nlstate)*(nlstate+ndeath));
   }      
           for(theta=1; theta <=npar; theta++){
   /* Reads comments: lines beginning with '#' */            for(i=1; i<=npar; i++)
   while((c=getc(ficpar))=='#' && c!= EOF){              xp[i] = x[i] + (i==theta ?delti[theta]:0);
     ungetc(c,ficpar);            
     fgets(line, MAXLINE, ficpar);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     puts(line);            
     fputs(line,ficparo);            k=0;
   }            for(i=1; i<= (nlstate); i++){
   ungetc(c,ficpar);              for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
   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);                gp[k]=pmmij[i][j];
   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);            for(i=1; i<=npar; i++)
     fgets(line, MAXLINE, ficpar);              xp[i] = x[i] - (i==theta ?delti[theta]:0);
     puts(line);      
     fputs(line,ficparo);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   }            k=0;
   ungetc(c,ficpar);            for(i=1; i<=(nlstate); i++){
                for(j=1; j<=(nlstate+ndeath);j++){
                    k=k+1;
   covar=matrix(0,NCOVMAX,1,n);                gm[k]=pmmij[i][j];
   cptcovn=0;              }
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;            }
        
   ncovmodel=2+cptcovn;            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */              gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
            }
   /* Read guess parameters */  
   /* Reads comments: lines beginning with '#' */          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   while((c=getc(ficpar))=='#' && c!= EOF){            for(theta=1; theta <=npar; theta++)
     ungetc(c,ficpar);              trgradg[j][theta]=gradg[theta][j];
     fgets(line, MAXLINE, ficpar);          
     puts(line);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
     fputs(line,ficparo);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   }          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   ungetc(c,ficpar);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
            free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     for(i=1; i <=nlstate; i++)  
     for(j=1; j <=nlstate+ndeath-1; j++){          pmij(pmmij,cov,ncovmodel,x,nlstate);
       fscanf(ficpar,"%1d%1d",&i1,&j1);          
       fprintf(ficparo,"%1d%1d",i1,j1);          k=0;
       printf("%1d%1d",i,j);          for(i=1; i<=(nlstate); i++){
       for(k=1; k<=ncovmodel;k++){            for(j=1; j<=(nlstate+ndeath);j++){
         fscanf(ficpar," %lf",&param[i][j][k]);              k=k+1;
         printf(" %lf",param[i][j][k]);              mu[k][(int) age]=pmmij[i][j];
         fprintf(ficparo," %lf",param[i][j][k]);            }
       }          }
       fscanf(ficpar,"\n");          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
       printf("\n");            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
       fprintf(ficparo,"\n");              varpij[i][j][(int)age] = doldm[i][j];
     }  
            /*printf("\n%d ",(int)age);
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;            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]));
   p=param[1][1];            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
              }*/
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficresprob,"\n%d ",(int)age);
     ungetc(c,ficpar);          fprintf(ficresprobcov,"\n%d ",(int)age);
     fgets(line, MAXLINE, ficpar);          fprintf(ficresprobcor,"\n%d ",(int)age);
     puts(line);  
     fputs(line,ficparo);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
   }            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
   ungetc(c,ficpar);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */          }
   for(i=1; i <=nlstate; i++){          i=0;
     for(j=1; j <=nlstate+ndeath-1; j++){          for (k=1; k<=(nlstate);k++){
       fscanf(ficpar,"%1d%1d",&i1,&j1);            for (l=1; l<=(nlstate+ndeath);l++){ 
       printf("%1d%1d",i,j);              i=i++;
       fprintf(ficparo,"%1d%1d",i1,j1);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
       for(k=1; k<=ncovmodel;k++){              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
         fscanf(ficpar,"%le",&delti3[i][j][k]);              for (j=1; j<=i;j++){
         printf(" %le",delti3[i][j][k]);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
         fprintf(ficparo," %le",delti3[i][j][k]);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
       }              }
       fscanf(ficpar,"\n");            }
       printf("\n");          }/* end of loop for state */
       fprintf(ficparo,"\n");        } /* end of loop for age */
     }  
   }        /* Confidence intervalle of pij  */
   delti=delti3[1][1];        /*
            fprintf(ficgp,"\nset noparametric;unset label");
   /* Reads comments: lines beginning with '#' */          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     ungetc(c,ficpar);          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);
     fgets(line, MAXLINE, ficpar);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
     puts(line);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
     fputs(line,ficparo);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
   }        */
   ungetc(c,ficpar);  
          /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
   matcov=matrix(1,npar,1,npar);        first1=1;
   for(i=1; i <=npar; i++){        for (k2=1; k2<=(nlstate);k2++){
     fscanf(ficpar,"%s",&str);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
     printf("%s",str);            if(l2==k2) continue;
     fprintf(ficparo,"%s",str);            j=(k2-1)*(nlstate+ndeath)+l2;
     for(j=1; j <=i; j++){            for (k1=1; k1<=(nlstate);k1++){
       fscanf(ficpar," %le",&matcov[i][j]);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
       printf(" %.5le",matcov[i][j]);                if(l1==k1) continue;
       fprintf(ficparo," %.5le",matcov[i][j]);                i=(k1-1)*(nlstate+ndeath)+l1;
     }                if(i<=j) continue;
     fscanf(ficpar,"\n");                for (age=bage; age<=fage; age ++){ 
     printf("\n");                  if ((int)age %5==0){
     fprintf(ficparo,"\n");                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   }                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   for(i=1; i <=npar; i++)                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
     for(j=i+1;j<=npar;j++)                    mu1=mu[i][(int) age]/stepm*YEARM ;
       matcov[i][j]=matcov[j][i];                    mu2=mu[j][(int) age]/stepm*YEARM;
                        c12=cv12/sqrt(v1*v2);
   printf("\n");                    /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     /*-------- Rewriting paramater file ----------*/                    /* Eigen vectors */
      strcpy(rfileres,"r");    /* "Rparameterfile */                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/                    /*v21=sqrt(1.-v11*v11); *//* error */
      strcat(rfileres,".");    /* */                    v21=(lc1-v1)/cv12*v11;
      strcat(rfileres,optionfilext);    /* Other files have txt extension */                    v12=-v21;
     if((ficres =fopen(rfileres,"w"))==NULL) {                    v22=v11;
       printf("Problem writing new parameter file: %s\n", fileres);goto end;                    tnalp=v21/v11;
     }                    if(first1==1){
     fprintf(ficres,"#%s\n",version);                      first1=0;
                          printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
     /*-------- data file ----------*/                    }
     if((fic=fopen(datafile,"r"))==NULL)    {                    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("Problem with datafile: %s\n", datafile);goto end;                    /*printf(fignu*/
     }                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
     n= lastobs;                    if(first==1){
     severity = vector(1,maxwav);                      first=0;
     outcome=imatrix(1,maxwav+1,1,n);                      fprintf(ficgp,"\nset parametric;unset label");
     num=ivector(1,n);                      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);
     moisnais=vector(1,n);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     annais=vector(1,n);                      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);
     moisdc=vector(1,n);                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
     andc=vector(1,n);                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
     agedc=vector(1,n);                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
     cod=ivector(1,n);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     weight=vector(1,n);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */                      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",\
     mint=matrix(1,maxwav,1,n);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     anint=matrix(1,maxwav,1,n);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     s=imatrix(1,maxwav+1,1,n);                    }else{
     adl=imatrix(1,maxwav+1,1,n);                          first=0;
     tab=ivector(1,NCOVMAX);                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
     ncodemax=ivector(1,8);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     i=1;                      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",\
     while (fgets(line, MAXLINE, fic) != NULL)    {                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
       if ((i >= firstobs) && (i <=lastobs)) {                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                            }/* if first */
         for (j=maxwav;j>=1;j--){                  } /* age mod 5 */
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);                } /* end loop age */
           strcpy(line,stra);                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                first=1;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);              } /*l12 */
         }            } /* k12 */
                  } /*l1 */
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        }/* k1 */
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      } /* loop covariates */
     }
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_vector(xp,1,npar);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    fclose(ficresprob);
         for (j=ncovcol;j>=1;j--){    fclose(ficresprobcov);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    fclose(ficresprobcor);
         }    fclose(ficgp);
         num[i]=atol(stra);    fclose(fichtm);
          }
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){  
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/  
   /******************* Printing html file ***********/
         i=i+1;  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
       }                    int lastpass, int stepm, int weightopt, char model[],\
     }                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
     /* printf("ii=%d", ij);                    int popforecast, int estepm ,\
        scanf("%d",i);*/                    double jprev1, double mprev1,double anprev1, \
   imx=i-1; /* Number of individuals */                    double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   /* for (i=1; i<=imx; i++){    /*char optionfilehtm[FILENAMELENGTH];*/
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;      printf("Problem with %s \n",optionfilehtm), exit(0);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
     }*/    }
    
   /* for (i=1; i<=imx; i++){     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
      if (s[4][i]==9)  s[4][i]=-1;   - 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("%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]));}   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
   */   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
     - Life expectancies by age and initial health status (estepm=%2d months): 
   /* Calculation of the number of parameter from char model*/     <a href=\"e%s\">e%s</a> <br>\n</li>", \
   Tvar=ivector(1,15);    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
   Tprod=ivector(1,15);  
   Tvaraff=ivector(1,15);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   Tvard=imatrix(1,15,1,2);  
   Tage=ivector(1,15);         m=cptcoveff;
       if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   if (strlen(model) >1){  
     j=0, j1=0, k1=1, k2=1;   jj1=0;
     j=nbocc(model,'+');   for(k1=1; k1<=m;k1++){
     j1=nbocc(model,'*');     for(i1=1; i1<=ncodemax[k1];i1++){
     cptcovn=j+1;       jj1++;
     cptcovprod=j1;       if (cptcovn > 0) {
             fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     strcpy(modelsav,model);         for (cpt=1; cpt<=cptcoveff;cpt++) 
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
       printf("Error. Non available option model=%s ",model);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
       goto end;       }
     }       /* Pij */
           fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>
     for(i=(j+1); i>=1;i--){  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
       cutv(stra,strb,modelsav,'+');       /* Quasi-incidences */
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
       /*scanf("%d",i);*/         /* Stable prevalence in each health state */
       if (strchr(strb,'*')) {         for(cpt=1; cpt<nlstate;cpt++){
         cutv(strd,strc,strb,'*');           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
         if (strcmp(strc,"age")==0) {  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
           cptcovprod--;         }
           cutv(strb,stre,strd,'V');       for(cpt=1; cpt<=nlstate;cpt++) {
           Tvar[i]=atoi(stre);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
           cptcovage++;  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
             Tage[cptcovage]=i;       }
             /*printf("stre=%s ", stre);*/       fprintf(fichtm,"\n<br>- Total life expectancy by age and
         }  health expectancies in states (1) and (2): e%s%d.png<br>
         else if (strcmp(strd,"age")==0) {  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
           cptcovprod--;     } /* end i1 */
           cutv(strb,stre,strc,'V');   }/* End k1 */
           Tvar[i]=atoi(stre);   fprintf(fichtm,"</ul>");
           cptcovage++;  
           Tage[cptcovage]=i;  
         }   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
         else {   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
           cutv(strb,stre,strc,'V');   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
           Tvar[i]=ncovcol+k1;   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
           cutv(strb,strc,strd,'V');   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
           Tprod[k1]=i;   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
           Tvard[k1][1]=atoi(strc);   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
           Tvard[k1][2]=atoi(stre);   - 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);
           Tvar[cptcovn+k2]=Tvard[k1][1];  
           Tvar[cptcovn+k2+1]=Tvard[k1][2];   if(popforecast==1) fprintf(fichtm,"\n
           for (k=1; k<=lastobs;k++)   - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];   - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
           k1++;          <br>",fileres,fileres,fileres,fileres);
           k2=k2+2;   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(fichtm," <ul><li><b>Graphs</b></li><p>");
       else {  
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/   m=cptcoveff;
        /*  scanf("%d",i);*/   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       cutv(strd,strc,strb,'V');  
       Tvar[i]=atoi(strc);   jj1=0;
       }   for(k1=1; k1<=m;k1++){
       strcpy(modelsav,stra);       for(i1=1; i1<=ncodemax[k1];i1++){
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);       jj1++;
         scanf("%d",i);*/       if (cptcovn > 0) {
     }         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
 }         for (cpt=1; cpt<=cptcoveff;cpt++) 
             fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   printf("cptcovprod=%d ", cptcovprod);       }
   scanf("%d ",i);*/       for(cpt=1; cpt<=nlstate;cpt++) {
     fclose(fic);         fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
   interval) in state (%d): v%s%d%d.png <br>
     /*  if(mle==1){*/  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
     if (weightopt != 1) { /* Maximisation without weights*/       }
       for(i=1;i<=n;i++) weight[i]=1.0;     } /* end i1 */
     }   }/* End k1 */
     /*-calculation of age at interview from date of interview and age at death -*/   fprintf(fichtm,"</ul>");
     agev=matrix(1,maxwav,1,imx);  fclose(fichtm);
   }
     for (i=1; i<=imx; i++) {  
       for(m=2; (m<= maxwav); m++) {  /******************* Gnuplot file **************/
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
          anint[m][i]=9999;  
          s[m][i]=-1;    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
        }    int ng;
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       }      printf("Problem with file %s",optionfilegnuplot);
     }      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
     }
     for (i=1; i<=imx; i++)  {  
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    /*#ifdef windows */
       for(m=1; (m<= maxwav); m++){      fprintf(ficgp,"cd \"%s\" \n",pathc);
         if(s[m][i] >0){      /*#endif */
           if (s[m][i] >= nlstate+1) {  m=pow(2,cptcoveff);
             if(agedc[i]>0)    
               if(moisdc[i]!=99 && andc[i]!=9999)   /* 1eme*/
                 agev[m][i]=agedc[i];    for (cpt=1; cpt<= nlstate ; cpt ++) {
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/     for (k1=1; k1<= m ; k1 ++) {
            else {       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
               if (andc[i]!=9999){       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);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  
               agev[m][i]=-1;       for (i=1; i<= nlstate ; i ++) {
               }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
             }         else fprintf(ficgp," \%%*lf (\%%*lf)");
           }       }
           else if(s[m][i] !=9){ /* Should no more exist */       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);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);       for (i=1; i<= nlstate ; i ++) {
             if(mint[m][i]==99 || anint[m][i]==9999)         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
               agev[m][i]=1;         else fprintf(ficgp," \%%*lf (\%%*lf)");
             else if(agev[m][i] <agemin){       } 
               agemin=agev[m][i];       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/       for (i=1; i<= nlstate ; i ++) {
             }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
             else if(agev[m][i] >agemax){         else fprintf(ficgp," \%%*lf (\%%*lf)");
               agemax=agev[m][i];       }  
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
             }     }
             /*agev[m][i]=anint[m][i]-annais[i];*/    }
             /*   agev[m][i] = age[i]+2*m;*/    /*2 eme*/
           }    
           else { /* =9 */    for (k1=1; k1<= m ; k1 ++) { 
             agev[m][i]=1;      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
             s[m][i]=-1;      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
           }      
         }      for (i=1; i<= nlstate+1 ; i ++) {
         else /*= 0 Unknown */        k=2*i;
           agev[m][i]=1;        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
       }        for (j=1; j<= nlstate+1 ; j ++) {
              if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     }          else fprintf(ficgp," \%%*lf (\%%*lf)");
     for (i=1; i<=imx; i++)  {        }   
       for(m=1; (m<= maxwav); m++){        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         if (s[m][i] > (nlstate+ndeath)) {        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
           printf("Error: Wrong value in nlstate or ndeath\n");          fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
           goto end;        for (j=1; j<= nlstate+1 ; j ++) {
         }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       }          else fprintf(ficgp," \%%*lf (\%%*lf)");
     }        }   
         fprintf(ficgp,"\" t\"\" w l 0,");
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);        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 ++) {
     free_vector(severity,1,maxwav);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     free_imatrix(outcome,1,maxwav+1,1,n);          else fprintf(ficgp," \%%*lf (\%%*lf)");
     free_vector(moisnais,1,n);        }   
     free_vector(annais,1,n);        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
     /* free_matrix(mint,1,maxwav,1,n);        else fprintf(ficgp,"\" t\"\" w l 0,");
        free_matrix(anint,1,maxwav,1,n);*/      }
     free_vector(moisdc,1,n);    }
     free_vector(andc,1,n);    
     /*3eme*/
        
     wav=ivector(1,imx);    for (k1=1; k1<= m ; k1 ++) { 
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      for (cpt=1; cpt<= nlstate ; cpt ++) {
     mw=imatrix(1,lastpass-firstpass+1,1,imx);        k=2+nlstate*(2*cpt-2);
            fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     /* Concatenates waves */        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);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);        /*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);
       Tcode=ivector(1,100);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
       ncodemax[1]=1;          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);          
              */
    codtab=imatrix(1,100,1,10);        for (i=1; i< nlstate ; i ++) {
    h=0;          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);
    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++){    /* CV preval stat */
            h++;    for (k1=1; k1<= m ; k1 ++) { 
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;      for (cpt=1; cpt<nlstate ; cpt ++) {
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/        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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
      }        
    }        for (i=1; i< nlstate ; i ++)
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);          fprintf(ficgp,"+$%d",k+i+1);
       codtab[1][2]=1;codtab[2][2]=2; */        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
    /* for(i=1; i <=m ;i++){        
       for(k=1; k <=cptcovn; k++){        l=3+(nlstate+ndeath)*cpt;
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
       }        for (i=1; i< nlstate ; i ++) {
       printf("\n");          l=3+(nlstate+ndeath)*cpt;
       }          fprintf(ficgp,"+$%d",l+i+1);
       scanf("%d",i);*/        }
            fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
    /* Calculates basic frequencies. Computes observed prevalence at single age      } 
        and prints on file fileres'p'. */    }  
     
        /* proba elementaires */
        for(i=1,jk=1; i <=nlstate; i++){
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for(k=1; k <=(nlstate+ndeath); k++){
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        if (k != i) {
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for(j=1; j <=ncovmodel; j++){
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            jk++; 
                  fprintf(ficgp,"\n");
     /* 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){  
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
     }       for(jk=1; jk <=m; jk++) {
             fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
     /*--------- results files --------------*/         if (ng==2)
     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);           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
           else
            fprintf(ficgp,"\nset title \"Probability\"\n");
    jk=1;         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");         i=1;
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");         for(k2=1; k2<=nlstate; k2++) {
    for(i=1,jk=1; i <=nlstate; i++){           k3=i;
      for(k=1; k <=(nlstate+ndeath); k++){           for(k=1; k<=(nlstate+ndeath); k++) {
        if (k != i)             if (k != k2){
          {               if(ng==2)
            printf("%d%d ",i,k);                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
            fprintf(ficres,"%1d%1d ",i,k);               else
            for(j=1; j <=ncovmodel; j++){                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
              printf("%f ",p[jk]);               ij=1;
              fprintf(ficres,"%f ",p[jk]);               for(j=3; j <=ncovmodel; j++) {
              jk++;                 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]]]);
            printf("\n");                   ij++;
            fprintf(ficres,"\n");                 }
          }                 else
      }                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
    }               }
  if(mle==1){               fprintf(ficgp,")/(1");
     /* Computing hessian and covariance matrix */               
     ftolhess=ftol; /* Usually correct */               for(k1=1; k1 <=nlstate; k1++){   
     hesscov(matcov, p, npar, delti, ftolhess, func);                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
  }                 ij=1;
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");                 for(j=3; j <=ncovmodel; j++){
     printf("# Scales (for hessian or gradient estimation)\n");                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
      for(i=1,jk=1; i <=nlstate; i++){                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
       for(j=1; j <=nlstate+ndeath; j++){                     ij++;
         if (j!=i) {                   }
           fprintf(ficres,"%1d%1d",i,j);                   else
           printf("%1d%1d",i,j);                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
           for(k=1; k<=ncovmodel;k++){                 }
             printf(" %.5e",delti[jk]);                 fprintf(ficgp,")");
             fprintf(ficres," %.5e",delti[jk]);               }
             jk++;               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
           }               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
           printf("\n");               i=i+ncovmodel;
           fprintf(ficres,"\n");             }
         }           } /* end k */
       }         } /* end k2 */
      }       } /* end jk */
         } /* end ng */
     k=1;     fclose(ficgp); 
     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");  }  /* end gnuplot */
     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");  
     for(i=1;i<=npar;i++){  
       /*  if (k>nlstate) k=1;  /*************** Moving average **************/
       i1=(i-1)/(ncovmodel*nlstate)+1;  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);  
       printf("%s%d%d",alph[k],i1,tab[i]);*/    int i, cpt, cptcod;
       fprintf(ficres,"%3d",i);    int modcovmax =1;
       printf("%3d",i);    int mobilavrange, mob;
       for(j=1; j<=i;j++){    double age;
         fprintf(ficres," %.5e",matcov[i][j]);  
         printf(" %.5e",matcov[i][j]);    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
       }                             a covariate has 2 modalities */
       fprintf(ficres,"\n");    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
       printf("\n");  
       k++;    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
     }      if(mobilav==1) mobilavrange=5; /* default */
          else mobilavrange=mobilav;
     while((c=getc(ficpar))=='#' && c!= EOF){      for (age=bage; age<=fage; age++)
       ungetc(c,ficpar);        for (i=1; i<=nlstate;i++)
       fgets(line, MAXLINE, ficpar);          for (cptcod=1;cptcod<=modcovmax;cptcod++)
       puts(line);            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       fputs(line,ficparo);      /* We keep the original values on the extreme ages bage, fage and for 
     }         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
     ungetc(c,ficpar);         we use a 5 terms etc. until the borders are no more concerned. 
        */ 
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&ageminpar,&agemaxpar, &bage, &fage);      for (mob=3;mob <=mobilavrange;mob=mob+2){
            for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
     if (fage <= 2) {          for (i=1; i<=nlstate;i++){
       bage = ageminpar;            for (cptcod=1;cptcod<=modcovmax;cptcod++){
       fage = agemaxpar;              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
     }                for (cpt=1;cpt<=(mob-1)/2;cpt++){
                      mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",ageminpar,agemaxpar,bage,fage);                }
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",ageminpar,agemaxpar,bage,fage);              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
              }
     while((c=getc(ficpar))=='#' && c!= EOF){          }
     ungetc(c,ficpar);        }/* end age */
     fgets(line, MAXLINE, ficpar);      }/* end mob */
     puts(line);    }else return -1;
     fputs(line,ficparo);    return 0;
   }  }/* End movingaverage */
   ungetc(c,ficpar);  
    
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);  /************** Forecasting ******************/
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    /* proj1, year, month, day of starting projection 
             agemin, agemax range of age
   while((c=getc(ficpar))=='#' && c!= EOF){       dateprev1 dateprev2 range of dates during which prevalence is computed
     ungetc(c,ficpar);       anproj2 year of en of projection (same day and month as proj1).
     fgets(line, MAXLINE, ficpar);    */
     puts(line);    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h;
     fputs(line,ficparo);    int *popage;
   }    double agec; /* generic age */
   ungetc(c,ficpar);    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
      double *popeffectif,*popcount;
     double ***p3mat;
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    double ***mobaverage;
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    char fileresf[FILENAMELENGTH];
   
   fscanf(ficpar,"pop_based=%d\n",&popbased);    agelim=AGESUP;
   fprintf(ficparo,"pop_based=%d\n",popbased);      prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   fprintf(ficres,"pop_based=%d\n",popbased);     
      strcpy(fileresf,"f"); 
   while((c=getc(ficpar))=='#' && c!= EOF){    strcat(fileresf,fileres);
     ungetc(c,ficpar);    if((ficresf=fopen(fileresf,"w"))==NULL) {
     fgets(line, MAXLINE, ficpar);      printf("Problem with forecast resultfile: %s\n", fileresf);
     puts(line);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     fputs(line,ficparo);    }
   }    printf("Computing forecasting: result on file '%s' \n", fileresf);
   ungetc(c,ficpar);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
   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);    if (cptcoveff==0) ncodemax[cptcoveff]=1;
 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);    if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
 while((c=getc(ficpar))=='#' && c!= EOF){        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     ungetc(c,ficpar);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     fgets(line, MAXLINE, ficpar);      }
     puts(line);    }
     fputs(line,ficparo);  
   }    stepsize=(int) (stepm+YEARM-1)/YEARM;
   ungetc(c,ficpar);    if (stepm<=12) stepsize=1;
     
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);    hstepm=1;
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    hstepm=hstepm/stepm; 
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    anprojmean=yp;
     yp2=modf((yp1*12),&yp);
 /*------------ gnuplot -------------*/    mprojmean=yp;
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);    yp1=modf((yp2*30.5),&yp);
      jprojmean=yp;
 /*------------ free_vector  -------------*/    if(jprojmean==0) jprojmean=1;
  chdir(path);    if(mprojmean==0) jprojmean=1;
      
  free_ivector(wav,1,imx);    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      fprintf(ficresf,"#****** Routine prevforecast **\n");
  free_ivector(num,1,n);    for(cptcov=1, k=0;cptcov<=cptcoveff;cptcov++){
  free_vector(agedc,1,n);      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
  /*free_matrix(covar,1,NCOVMAX,1,n);*/        k=k+1;
  fclose(ficparo);        fprintf(ficresf,"\n#******");
  fclose(ficres);        for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
 /*--------- index.htm --------*/        }
         fprintf(ficresf,"******\n");
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast);        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
            for(i=1; i<=nlstate;i++)              
   /*--------------- Prevalence limit --------------*/            fprintf(ficresf," p%d%d",i,j);
            fprintf(ficresf," p.%d",j);
   strcpy(filerespl,"pl");        }
   strcat(filerespl,fileres);        for (yearp=0; yearp<=(anproj2-anproj1);yearp++) { 
   if((ficrespl=fopen(filerespl,"w"))==NULL) {          fprintf(ficresf,"\n");
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   }  
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);          for (agec=fage; agec>=(ageminpar-1); agec--){ 
   fprintf(ficrespl,"#Prevalence limit\n");            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
   fprintf(ficrespl,"#Age ");            nhstepm = nhstepm/hstepm; 
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fprintf(ficrespl,"\n");            oldm=oldms;savm=savms;
              hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
   prlim=matrix(1,nlstate,1,nlstate);          
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            for (h=0; h<=nhstepm; h++){
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              if (h==(int) (YEARM*yearp)) {
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                fprintf(ficresf,"\n");
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                for(j=1;j<=cptcoveff;j++) 
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   k=0;                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
   agebase=ageminpar;              } 
   agelim=agemaxpar;              for(j=1; j<=nlstate+ndeath;j++) {
   ftolpl=1.e-10;                ppij=0.;
   i1=cptcoveff;                for(i=1; i<=nlstate;i++) {
   if (cptcovn < 1){i1=1;}                  if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
   for(cptcov=1;cptcov<=i1;cptcov++){                  else {
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
         k=k+1;                  }
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/                  if (h==(int)(YEARM*yearp))
         fprintf(ficrespl,"\n#******");                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
         for(j=1;j<=cptcoveff;j++)                }
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                if (h==(int)(YEARM*yearp)){
         fprintf(ficrespl,"******\n");                  fprintf(ficresf," %.3f", ppij);
                        }
         for (age=agebase; age<=agelim; age++){              }
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            }
           fprintf(ficrespl,"%.0f",age );            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           for(i=1; i<=nlstate;i++)          }
           fprintf(ficrespl," %.5f", prlim[i][i]);        }
           fprintf(ficrespl,"\n");      }
         }    }
       }         
     }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   fclose(ficrespl);  
     fclose(ficresf);
   /*------------- h Pij x at various ages ------------*/  }
    
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  /************** Forecasting *****not tested NB*************/
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  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){
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    
   }    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
   printf("Computing pij: result on file '%s' \n", filerespij);    int *popage;
      double calagedatem, agelim, kk1, kk2;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    double *popeffectif,*popcount;
   /*if (stepm<=24) stepsize=2;*/    double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
   agelim=AGESUP;    char filerespop[FILENAMELENGTH];
   hstepm=stepsize*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   k=0;    agelim=AGESUP;
   for(cptcov=1;cptcov<=i1;cptcov++){    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    
       k=k+1;    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
         fprintf(ficrespij,"\n#****** ");    
         for(j=1;j<=cptcoveff;j++)    
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    strcpy(filerespop,"pop"); 
         fprintf(ficrespij,"******\n");    strcat(filerespop,fileres);
            if((ficrespop=fopen(filerespop,"w"))==NULL) {
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */      printf("Problem with forecast resultfile: %s\n", filerespop);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    printf("Computing forecasting: result on file '%s' \n", filerespop);
           oldm=oldms;savm=savms;    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
           fprintf(ficrespij,"# Age");    if (cptcoveff==0) ncodemax[cptcoveff]=1;
           for(i=1; i<=nlstate;i++)  
             for(j=1; j<=nlstate+ndeath;j++)    if (mobilav!=0) {
               fprintf(ficrespij," %1d-%1d",i,j);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           fprintf(ficrespij,"\n");      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
           for (h=0; h<=nhstepm; h++){        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );        printf(" Error in movingaverage mobilav=%d\n",mobilav);
             for(i=1; i<=nlstate;i++)      }
               for(j=1; j<=nlstate+ndeath;j++)    }
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  
             fprintf(ficrespij,"\n");    stepsize=(int) (stepm+YEARM-1)/YEARM;
           }    if (stepm<=12) stepsize=1;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
           fprintf(ficrespij,"\n");    agelim=AGESUP;
         }    
     }    hstepm=1;
   }    hstepm=hstepm/stepm; 
     
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/    if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
   fclose(ficrespij);        printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
   /*---------- Forecasting ------------------*/      popage=ivector(0,AGESUP);
   if((stepm == 1) && (strcmp(model,".")==0)){      popeffectif=vector(0,AGESUP);
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);      popcount=vector(0,AGESUP);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);      
     free_matrix(mint,1,maxwav,1,n);      i=1;   
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
     free_vector(weight,1,n);}     
   else{      imx=i;
     erreur=108;      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     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);    }
   }  
      for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   /*---------- Health expectancies and variances ------------*/        k=k+1;
         fprintf(ficrespop,"\n#******");
   strcpy(filerest,"t");        for(j=1;j<=cptcoveff;j++) {
   strcat(filerest,fileres);          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   if((ficrest=fopen(filerest,"w"))==NULL) {        }
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;        fprintf(ficrespop,"******\n");
   }        fprintf(ficrespop,"# Age");
   printf("Computing Total LEs with variances: file '%s' \n", filerest);        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
   strcpy(filerese,"e");        for (cpt=0; cpt<=0;cpt++) { 
   strcat(filerese,fileres);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
   if((ficreseij=fopen(filerese,"w"))==NULL) {          
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
   }            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);            nhstepm = nhstepm/hstepm; 
             
  strcpy(fileresv,"v");            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   strcat(fileresv,fileres);            oldm=oldms;savm=savms;
   if((ficresvij=fopen(fileresv,"w"))==NULL) {            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);          
   }            for (h=0; h<=nhstepm; h++){
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);              if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
   k=0;              } 
   for(cptcov=1;cptcov<=i1;cptcov++){              for(j=1; j<=nlstate+ndeath;j++) {
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                kk1=0.;kk2=0;
       k=k+1;                for(i=1; i<=nlstate;i++) {              
       fprintf(ficrest,"\n#****** ");                  if (mobilav==1) 
       for(j=1;j<=cptcoveff;j++)                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                  else {
       fprintf(ficrest,"******\n");                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
       fprintf(ficreseij,"\n#****** ");                }
       for(j=1;j<=cptcoveff;j++)                if (h==(int)(calagedatem+12*cpt)){
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
       fprintf(ficreseij,"******\n");                    /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
       fprintf(ficresvij,"\n#****** ");                }
       for(j=1;j<=cptcoveff;j++)              }
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              for(i=1; i<=nlstate;i++){
       fprintf(ficresvij,"******\n");                kk1=0.;
                   for(j=1; j<=nlstate;j++){
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
       oldm=oldms;savm=savms;                  }
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);                      tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);              }
       oldm=oldms;savm=savms;  
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                    fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
              free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       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++){        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
         if (popbased==1) {          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
           for(i=1; i<=nlstate;i++)            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             prlim[i][i]=probs[(int)age][i][k];            nhstepm = nhstepm/hstepm; 
         }            
                    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(ficrest," %4.0f",age);            oldm=oldms;savm=savms;
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           for(i=1, epj[j]=0.;i <=nlstate;i++) {            for (h=0; h<=nhstepm; h++){
             epj[j] += prlim[i][i]*eij[i][j][(int)age];              if (h==(int) (calagedatem+YEARM*cpt)) {
           }                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
           epj[nlstate+1] +=epj[j];              } 
         }              for(j=1; j<=nlstate+ndeath;j++) {
         for(i=1, vepp=0.;i <=nlstate;i++)                kk1=0.;kk2=0;
           for(j=1;j <=nlstate;j++)                for(i=1; i<=nlstate;i++) {              
             vepp += vareij[i][j][(int)age];                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
         fprintf(ficrest," %7.2f (%7.2f)", epj[nlstate+1],sqrt(vepp));                }
         for(j=1;j <=nlstate;j++){                if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
           fprintf(ficrest," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age]));              }
         }            }
         fprintf(ficrest,"\n");            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       }          }
     }        }
   }     } 
     }
   fclose(ficreseij);   
   fclose(ficresvij);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   fclose(ficrest);  
   fclose(ficpar);    if (popforecast==1) {
   free_vector(epj,1,nlstate+1);      free_ivector(popage,0,AGESUP);
        free_vector(popeffectif,0,AGESUP);
   /*------- Variance limit prevalence------*/        free_vector(popcount,0,AGESUP);
     }
   strcpy(fileresvpl,"vpl");    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   strcat(fileresvpl,fileres);    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    fclose(ficrespop);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  }
     exit(0);  
   }  /***********************************************/
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  /**************** Main Program *****************/
   /***********************************************/
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){  int main(int argc, char *argv[])
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  {
       k=k+1;    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
       fprintf(ficresvpl,"\n#****** ");    int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
       for(j=1;j<=cptcoveff;j++)    double agedeb, agefin,hf;
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
       fprintf(ficresvpl,"******\n");  
          double fret;
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    double **xi,tmp,delta;
       oldm=oldms;savm=savms;  
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    double dum; /* Dummy variable */
     }    double ***p3mat;
  }    double ***mobaverage;
     int *indx;
   fclose(ficresvpl);    char line[MAXLINE], linepar[MAXLINE];
     char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
   /*---------- End : free ----------------*/    int firstobs=1, lastobs=10;
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    int sdeb, sfin; /* Status at beginning and end */
      int c,  h , cpt,l;
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    int ju,jl, mi;
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
      int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
      int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    int mobilav=0,popforecast=0;
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    int hstepm, nhstepm;
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);  
      double bage, fage, age, agelim, agebase;
   free_matrix(matcov,1,npar,1,npar);    double ftolpl=FTOL;
   free_vector(delti,1,npar);    double **prlim;
   free_matrix(agev,1,maxwav,1,imx);    double *severity;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    double ***param; /* Matrix of parameters */
     double  *p;
   if(erreur >0)    double **matcov; /* Matrix of covariance */
     printf("End of Imach with error or warning %d\n",erreur);    double ***delti3; /* Scale */
   else   printf("End of Imach\n");    double *delti; /* Scale */
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    double ***eij, ***vareij;
      double **varpl; /* Variances of prevalence limits by age */
   /* 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);*/    double *epj, vepp;
   /*printf("Total time was %d uSec.\n", total_usecs);*/    double kk1, kk2;
   /*------ End -----------*/    double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
  end:  
 #ifdef windows  
   /* chdir(pathcd);*/    char z[1]="c", occ;
 #endif  #include <sys/time.h>
  /*system("wgnuplot graph.plt");*/  #include <time.h>
  /*system("../gp37mgw/wgnuplot graph.plt");*/    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
  /*system("cd ../gp37mgw");*/   
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    /* long total_usecs;
  strcpy(plotcmd,GNUPLOTPROGRAM);       struct timeval start_time, end_time;
  strcat(plotcmd," ");    
  strcat(plotcmd,optionfilegnuplot);       gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
  system(plotcmd);    getcwd(pathcd, size);
   
 #ifdef windows    printf("\n%s",version);
   while (z[0] != 'q') {    if(argc <=1){
     /* chdir(path); */      printf("\nEnter the parameter file name: ");
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");      scanf("%s",pathtot);
     scanf("%s",z);    }
     if (z[0] == 'c') system("./imach");    else{
     else if (z[0] == 'e') system(optionfilehtm);      strcpy(pathtot,argv[1]);
     else if (z[0] == 'g') system(plotcmd);    }
     else if (z[0] == 'q') exit(0);    /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
   }    /*cygwin_split_path(pathtot,path,optionfile);
 #endif      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
 }    /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     replace(pathc,path);
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s",version);
     fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     fflush(ficlog);
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       goto end;
     }
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) {
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     
     /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++)
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)
           printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){
             printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
           }
           else
             fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);
         }
         fscanf(ficpar,"\n");
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     delti=delti3[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
           fprintf(ficlog," %.5le",matcov[i][j]);
         }
         else
           fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=ivector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if ((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);
   
     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, (int) bage, (int) 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);
         if (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);
   
     prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, 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_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_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);
   
     fprintf(fichtm,"\n</body>");
     fclose(fichtm);
     fclose(ficgp);
     
   
     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.1.35  
changed lines
  Added in v.1.71

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