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version 1.26, 2002/02/27 15:42:00 version 1.68, 2003/02/04 12:40:59
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 "..\\gp37mgw\\wgnuplot"  #define GNUPLOTPROGRAM "gnuplot"
 #define FILENAMELENGTH 80  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 /*#define DEBUG*/  #define FILENAMELENGTH 80
 #define windows  /*#define DEBUG*/
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  #define windows
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  #define NINTERVMAX 8
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #define NCOVMAX 8 /* Maximum number of covariates */  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #define MAXN 20000  #define NCOVMAX 8 /* Maximum number of covariates */
 #define YEARM 12. /* Number of months per year */  #define MAXN 20000
 #define AGESUP 130  #define YEARM 12. /* Number of months per year */
 #define AGEBASE 40  #define AGESUP 130
   #define AGEBASE 40
   #ifdef windows
 int erreur; /* Error number */  #define DIRSEPARATOR '\\'
 int nvar;  #define ODIRSEPARATOR '/'
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  #else
 int npar=NPARMAX;  #define DIRSEPARATOR '/'
 int nlstate=2; /* Number of live states */  #define ODIRSEPARATOR '\\'
 int ndeath=1; /* Number of dead states */  #endif
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;  char version[80]="Imach version 0.91, November 2002, INED-EUROREVES ";
   int erreur; /* Error number */
 int *wav; /* Number of waves for this individuual 0 is possible */  int nvar;
 int maxwav; /* Maxim number of waves */  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 int jmin, jmax; /* min, max spacing between 2 waves */  int npar=NPARMAX;
 int mle, weightopt;  int nlstate=2; /* Number of live states */
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  int ndeath=1; /* Number of dead states */
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 double jmean; /* Mean space between 2 waves */  int popbased=0;
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  int *wav; /* Number of waves for this individuual 0 is possible */
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;  int maxwav; /* Maxim number of waves */
 FILE *ficgp,*ficresprob,*ficpop;  int jmin, jmax; /* min, max spacing between 2 waves */
 FILE *ficreseij;  int mle, weightopt;
   char filerese[FILENAMELENGTH];  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
  FILE  *ficresvij;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   char fileresv[FILENAMELENGTH];  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
  FILE  *ficresvpl;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   char fileresvpl[FILENAMELENGTH];  double jmean; /* Mean space between 2 waves */
   double **oldm, **newm, **savm; /* Working pointers to matrices */
 #define NR_END 1  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 #define FREE_ARG char*  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 #define FTOL 1.0e-10  FILE *ficlog;
   FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 #define NRANSI  FILE *ficresprobmorprev;
 #define ITMAX 200  FILE *fichtm; /* Html File */
   FILE *ficreseij;
 #define TOL 2.0e-4  char filerese[FILENAMELENGTH];
   FILE  *ficresvij;
 #define CGOLD 0.3819660  char fileresv[FILENAMELENGTH];
 #define ZEPS 1.0e-10  FILE  *ficresvpl;
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  char fileresvpl[FILENAMELENGTH];
   char title[MAXLINE];
 #define GOLD 1.618034  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 #define GLIMIT 100.0  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 #define TINY 1.0e-20  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 static double maxarg1,maxarg2;  char filelog[FILENAMELENGTH]; /* Log file */
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  char filerest[FILENAMELENGTH];
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  char fileregp[FILENAMELENGTH];
    char popfile[FILENAMELENGTH];
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
   
 static double sqrarg;  #define NR_END 1
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  #define FREE_ARG char*
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  #define FTOL 1.0e-10
   
 int imx;  #define NRANSI 
 int stepm;  #define ITMAX 200 
 /* Stepm, step in month: minimum step interpolation*/  
   #define TOL 2.0e-4 
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  #define CGOLD 0.3819660 
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  #define ZEPS 1.0e-10 
 double **pmmij, ***probs, ***mobaverage;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 double dateintmean=0;  
   #define GOLD 1.618034 
 double *weight;  #define GLIMIT 100.0 
 int **s; /* Status */  #define TINY 1.0e-20 
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  static double maxarg1,maxarg2;
   #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 double ftolhess; /* Tolerance for computing hessian */    
   #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 /**************** split *************************/  #define rint(a) floor(a+0.5)
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {  static double sqrarg;
    char *s;                             /* pointer */  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
    int  l1, l2;                         /* length counters */  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   
    l1 = strlen( path );                 /* length of path */  int imx; 
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  int stepm;
 #ifdef windows  /* Stepm, step in month: minimum step interpolation*/
    s = strrchr( path, '\\' );           /* find last / */  
 #else  int estepm;
    s = strrchr( path, '/' );            /* find last / */  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 #endif  
    if ( s == NULL ) {                   /* no directory, so use current */  int m,nb;
 #if     defined(__bsd__)                /* get current working directory */  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
       extern char       *getwd( );  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double **pmmij, ***probs;
       if ( getwd( dirc ) == NULL ) {  double dateintmean=0;
 #else  
       extern char       *getcwd( );  double *weight;
   int **s; /* Status */
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  double *agedc, **covar, idx;
 #endif  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
          return( GLOCK_ERROR_GETCWD );  
       }  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
       strcpy( name, path );             /* we've got it */  double ftolhess; /* Tolerance for computing hessian */
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */  /**************** split *************************/
       l2 = strlen( s );                 /* length of filename */  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  {
       strcpy( name, s );                /* save file name */    char  *ss;                            /* pointer */
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    int   l1, l2;                         /* length counters */
       dirc[l1-l2] = 0;                  /* add zero */  
    }    l1 = strlen(path );                   /* length of path */
    l1 = strlen( dirc );                 /* length of directory */    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 #ifdef windows    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    if ( ss == NULL ) {                   /* no directory, so use current */
 #else      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 #endif  #if     defined(__bsd__)                /* get current working directory */
    s = strrchr( name, '.' );            /* find last / */      extern char *getwd( );
    s++;  
    strcpy(ext,s);                       /* save extension */      if ( getwd( dirc ) == NULL ) {
    l1= strlen( name);  #else
    l2= strlen( s)+1;      extern char *getcwd( );
    strncpy( finame, name, l1-l2);  
    finame[l1-l2]= 0;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
    return( 0 );                         /* we're done */  #endif
 }        return( GLOCK_ERROR_GETCWD );
       }
       strcpy( name, path );               /* we've got it */
 /******************************************/    } else {                              /* strip direcotry from path */
       ss++;                               /* after this, the filename */
 void replace(char *s, char*t)      l2 = strlen( ss );                  /* length of filename */
 {      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   int i;      strcpy( name, ss );         /* save file name */
   int lg=20;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   i=0;      dirc[l1-l2] = 0;                    /* add zero */
   lg=strlen(t);    }
   for(i=0; i<= lg; i++) {    l1 = strlen( dirc );                  /* length of directory */
     (s[i] = t[i]);  #ifdef windows
     if (t[i]== '\\') s[i]='/';    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   }  #else
 }    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   #endif
 int nbocc(char *s, char occ)    ss = strrchr( name, '.' );            /* find last / */
 {    ss++;
   int i,j=0;    strcpy(ext,ss);                       /* save extension */
   int lg=20;    l1= strlen( name);
   i=0;    l2= strlen(ss)+1;
   lg=strlen(s);    strncpy( finame, name, l1-l2);
   for(i=0; i<= lg; i++) {    finame[l1-l2]= 0;
   if  (s[i] == occ ) j++;    return( 0 );                          /* we're done */
   }  }
   return j;  
 }  
   /******************************************/
 void cutv(char *u,char *v, char*t, char occ)  
 {  void replace(char *s, char*t)
   int i,lg,j,p=0;  {
   i=0;    int i;
   for(j=0; j<=strlen(t)-1; j++) {    int lg=20;
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    i=0;
   }    lg=strlen(t);
     for(i=0; i<= lg; i++) {
   lg=strlen(t);      (s[i] = t[i]);
   for(j=0; j<p; j++) {      if (t[i]== '\\') s[i]='/';
     (u[j] = t[j]);    }
   }  }
      u[p]='\0';  
   int nbocc(char *s, char occ)
    for(j=0; j<= lg; j++) {  {
     if (j>=(p+1))(v[j-p-1] = t[j]);    int i,j=0;
   }    int lg=20;
 }    i=0;
     lg=strlen(s);
 /********************** nrerror ********************/    for(i=0; i<= lg; i++) {
     if  (s[i] == occ ) j++;
 void nrerror(char error_text[])    }
 {    return j;
   fprintf(stderr,"ERREUR ...\n");  }
   fprintf(stderr,"%s\n",error_text);  
   exit(1);  void cutv(char *u,char *v, char*t, char occ)
 }  {
 /*********************** vector *******************/    /* cuts string t into u and v where u is ended by char occ excluding it
 double *vector(int nl, int nh)       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 {       gives u="abcedf" and v="ghi2j" */
   double *v;    int i,lg,j,p=0;
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    i=0;
   if (!v) nrerror("allocation failure in vector");    for(j=0; j<=strlen(t)-1; j++) {
   return v-nl+NR_END;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 }    }
   
 /************************ free vector ******************/    lg=strlen(t);
 void free_vector(double*v, int nl, int nh)    for(j=0; j<p; j++) {
 {      (u[j] = t[j]);
   free((FREE_ARG)(v+nl-NR_END));    }
 }       u[p]='\0';
   
 /************************ivector *******************************/     for(j=0; j<= lg; j++) {
 int *ivector(long nl,long nh)      if (j>=(p+1))(v[j-p-1] = t[j]);
 {    }
   int *v;  }
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");  /********************** nrerror ********************/
   return v-nl+NR_END;  
 }  void nrerror(char error_text[])
   {
 /******************free ivector **************************/    fprintf(stderr,"ERREUR ...\n");
 void free_ivector(int *v, long nl, long nh)    fprintf(stderr,"%s\n",error_text);
 {    exit(EXIT_FAILURE);
   free((FREE_ARG)(v+nl-NR_END));  }
 }  /*********************** vector *******************/
   double *vector(int nl, int nh)
 /******************* imatrix *******************************/  {
 int **imatrix(long nrl, long nrh, long ncl, long nch)    double *v;
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 {    if (!v) nrerror("allocation failure in vector");
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    return v-nl+NR_END;
   int **m;  }
    
   /* allocate pointers to rows */  /************************ free vector ******************/
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  void free_vector(double*v, int nl, int nh)
   if (!m) nrerror("allocation failure 1 in matrix()");  {
   m += NR_END;    free((FREE_ARG)(v+nl-NR_END));
   m -= nrl;  }
    
    /************************ivector *******************************/
   /* allocate rows and set pointers to them */  int *ivector(long nl,long nh)
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  {
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    int *v;
   m[nrl] += NR_END;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   m[nrl] -= ncl;    if (!v) nrerror("allocation failure in ivector");
      return v-nl+NR_END;
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  }
    
   /* return pointer to array of pointers to rows */  /******************free ivector **************************/
   return m;  void free_ivector(int *v, long nl, long nh)
 }  {
     free((FREE_ARG)(v+nl-NR_END));
 /****************** free_imatrix *************************/  }
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;  /******************* imatrix *******************************/
       long nch,ncl,nrh,nrl;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
      /* free an int matrix allocated by imatrix() */       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 {  { 
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   free((FREE_ARG) (m+nrl-NR_END));    int **m; 
 }    
     /* allocate pointers to rows */ 
 /******************* matrix *******************************/    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 double **matrix(long nrl, long nrh, long ncl, long nch)    if (!m) nrerror("allocation failure 1 in matrix()"); 
 {    m += NR_END; 
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    m -= nrl; 
   double **m;    
     
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    /* allocate rows and set pointers to them */ 
   if (!m) nrerror("allocation failure 1 in matrix()");    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   m += NR_END;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   m -= nrl;    m[nrl] += NR_END; 
     m[nrl] -= ncl; 
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   m[nrl] += NR_END;    
   m[nrl] -= ncl;    /* return pointer to array of pointers to rows */ 
     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)
 /*************************free matrix ************************/        int **m;
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)        long nch,ncl,nrh,nrl; 
 {       /* free an int matrix allocated by imatrix() */ 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  { 
   free((FREE_ARG)(m+nrl-NR_END));    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 }    free((FREE_ARG) (m+nrl-NR_END)); 
   } 
 /******************* ma3x *******************************/  
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  /******************* matrix *******************************/
 {  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;  {
   double ***m;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     double **m;
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   m += NR_END;    if (!m) nrerror("allocation failure 1 in matrix()");
   m -= nrl;    m += NR_END;
     m -= nrl;
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   m[nrl] += NR_END;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   m[nrl] -= ncl;    m[nrl] += NR_END;
     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;
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    return m;
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  }
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;  /*************************free matrix ************************/
   for (j=ncl+1; j<=nch; j++)  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     m[nrl][j]=m[nrl][j-1]+nlay;  {
      free((FREE_ARG)(m[nrl]+ncl-NR_END));
   for (i=nrl+1; i<=nrh; i++) {    free((FREE_ARG)(m+nrl-NR_END));
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  }
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;  /******************* ma3x *******************************/
   }  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 ************************/  
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 {    if (!m) nrerror("allocation failure 1 in matrix()");
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    m += NR_END;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    m -= nrl;
   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()");
 /***************** f1dim *************************/    m[nrl] += NR_END;
 extern int ncom;    m[nrl] -= ncl;
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
    
 double f1dim(double x)    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 {    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   int j;    m[nrl][ncl] += NR_END;
   double f;    m[nrl][ncl] -= nll;
   double *xt;    for (j=ncl+1; j<=nch; j++) 
        m[nrl][j]=m[nrl][j-1]+nlay;
   xt=vector(1,ncom);    
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    for (i=nrl+1; i<=nrh; i++) {
   f=(*nrfunc)(xt);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   free_vector(xt,1,ncom);      for (j=ncl+1; j<=nch; j++) 
   return f;        m[i][j]=m[i][j-1]+nlay;
 }    }
     return m;
 /*****************brent *************************/  }
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  
 {  /*************************free ma3x ************************/
   int iter;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   double a,b,d,etemp;  {
   double fu,fv,fw,fx;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   double ftemp;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double p,q,r,tol1,tol2,u,v,w,x,xm;    free((FREE_ARG)(m+nrl-NR_END));
   double e=0.0;  }
    
   a=(ax < cx ? ax : cx);  /***************** f1dim *************************/
   b=(ax > cx ? ax : cx);  extern int ncom; 
   x=w=v=bx;  extern double *pcom,*xicom;
   fw=fv=fx=(*f)(x);  extern double (*nrfunc)(double []); 
   for (iter=1;iter<=ITMAX;iter++) {   
     xm=0.5*(a+b);  double f1dim(double x) 
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  { 
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    int j; 
     printf(".");fflush(stdout);    double f;
 #ifdef DEBUG    double *xt; 
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);   
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    xt=vector(1,ncom); 
 #endif    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    f=(*nrfunc)(xt); 
       *xmin=x;    free_vector(xt,1,ncom); 
       return fx;    return f; 
     }  } 
     ftemp=fu;  
     if (fabs(e) > tol1) {  /*****************brent *************************/
       r=(x-w)*(fx-fv);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       q=(x-v)*(fx-fw);  { 
       p=(x-v)*q-(x-w)*r;    int iter; 
       q=2.0*(q-r);    double a,b,d,etemp;
       if (q > 0.0) p = -p;    double fu,fv,fw,fx;
       q=fabs(q);    double ftemp;
       etemp=e;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       e=d;    double e=0.0; 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))   
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    a=(ax < cx ? ax : cx); 
       else {    b=(ax > cx ? ax : cx); 
         d=p/q;    x=w=v=bx; 
         u=x+d;    fw=fv=fx=(*f)(x); 
         if (u-a < tol2 || b-u < tol2)    for (iter=1;iter<=ITMAX;iter++) { 
           d=SIGN(tol1,xm-x);      xm=0.5*(a+b); 
       }      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     } else {      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       d=CGOLD*(e=(x >= xm ? a-x : b-x));      printf(".");fflush(stdout);
     }      fprintf(ficlog,".");fflush(ficlog);
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  #ifdef DEBUG
     fu=(*f)(u);      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     if (fu <= fx) {      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 (u >= x) a=x; else b=x;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       SHFT(v,w,x,u)  #endif
         SHFT(fv,fw,fx,fu)      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         } else {        *xmin=x; 
           if (u < x) a=u; else b=u;        return fx; 
           if (fu <= fw || w == x) {      } 
             v=w;      ftemp=fu;
             w=u;      if (fabs(e) > tol1) { 
             fv=fw;        r=(x-w)*(fx-fv); 
             fw=fu;        q=(x-v)*(fx-fw); 
           } else if (fu <= fv || v == x || v == w) {        p=(x-v)*q-(x-w)*r; 
             v=u;        q=2.0*(q-r); 
             fv=fu;        if (q > 0.0) p = -p; 
           }        q=fabs(q); 
         }        etemp=e; 
   }        e=d; 
   nrerror("Too many iterations in brent");        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   *xmin=x;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   return fx;        else { 
 }          d=p/q; 
           u=x+d; 
 /****************** mnbrak ***********************/          if (u-a < tol2 || b-u < tol2) 
             d=SIGN(tol1,xm-x); 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,        } 
             double (*func)(double))      } else { 
 {        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   double ulim,u,r,q, dum;      } 
   double fu;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
        fu=(*f)(u); 
   *fa=(*func)(*ax);      if (fu <= fx) { 
   *fb=(*func)(*bx);        if (u >= x) a=x; else b=x; 
   if (*fb > *fa) {        SHFT(v,w,x,u) 
     SHFT(dum,*ax,*bx,dum)          SHFT(fv,fw,fx,fu) 
       SHFT(dum,*fb,*fa,dum)          } else { 
       }            if (u < x) a=u; else b=u; 
   *cx=(*bx)+GOLD*(*bx-*ax);            if (fu <= fw || w == x) { 
   *fc=(*func)(*cx);              v=w; 
   while (*fb > *fc) {              w=u; 
     r=(*bx-*ax)*(*fb-*fc);              fv=fw; 
     q=(*bx-*cx)*(*fb-*fa);              fw=fu; 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/            } else if (fu <= fv || v == x || v == w) { 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));              v=u; 
     ulim=(*bx)+GLIMIT*(*cx-*bx);              fv=fu; 
     if ((*bx-u)*(u-*cx) > 0.0) {            } 
       fu=(*func)(u);          } 
     } else if ((*cx-u)*(u-ulim) > 0.0) {    } 
       fu=(*func)(u);    nrerror("Too many iterations in brent"); 
       if (fu < *fc) {    *xmin=x; 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    return fx; 
           SHFT(*fb,*fc,fu,(*func)(u))  } 
           }  
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  /****************** mnbrak ***********************/
       u=ulim;  
       fu=(*func)(u);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     } else {              double (*func)(double)) 
       u=(*cx)+GOLD*(*cx-*bx);  { 
       fu=(*func)(u);    double ulim,u,r,q, dum;
     }    double fu; 
     SHFT(*ax,*bx,*cx,u)   
       SHFT(*fa,*fb,*fc,fu)    *fa=(*func)(*ax); 
       }    *fb=(*func)(*bx); 
 }    if (*fb > *fa) { 
       SHFT(dum,*ax,*bx,dum) 
 /*************** linmin ************************/        SHFT(dum,*fb,*fa,dum) 
         } 
 int ncom;    *cx=(*bx)+GOLD*(*bx-*ax); 
 double *pcom,*xicom;    *fc=(*func)(*cx); 
 double (*nrfunc)(double []);    while (*fb > *fc) { 
        r=(*bx-*ax)*(*fb-*fc); 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))      q=(*bx-*cx)*(*fb-*fa); 
 {      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   double brent(double ax, double bx, double cx,        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
                double (*f)(double), double tol, double *xmin);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   double f1dim(double x);      if ((*bx-u)*(u-*cx) > 0.0) { 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,        fu=(*func)(u); 
               double *fc, double (*func)(double));      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   int j;        fu=(*func)(u); 
   double xx,xmin,bx,ax;        if (fu < *fc) { 
   double fx,fb,fa;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
              SHFT(*fb,*fc,fu,(*func)(u)) 
   ncom=n;            } 
   pcom=vector(1,n);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   xicom=vector(1,n);        u=ulim; 
   nrfunc=func;        fu=(*func)(u); 
   for (j=1;j<=n;j++) {      } else { 
     pcom[j]=p[j];        u=(*cx)+GOLD*(*cx-*bx); 
     xicom[j]=xi[j];        fu=(*func)(u); 
   }      } 
   ax=0.0;      SHFT(*ax,*bx,*cx,u) 
   xx=1.0;        SHFT(*fa,*fb,*fc,fu) 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);        } 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  } 
 #ifdef DEBUG  
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  /*************** linmin ************************/
 #endif  
   for (j=1;j<=n;j++) {  int ncom; 
     xi[j] *= xmin;  double *pcom,*xicom;
     p[j] += xi[j];  double (*nrfunc)(double []); 
   }   
   free_vector(xicom,1,n);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   free_vector(pcom,1,n);  { 
 }    double brent(double ax, double bx, double cx, 
                  double (*f)(double), double tol, double *xmin); 
 /*************** powell ************************/    double f1dim(double x); 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
             double (*func)(double []))                double *fc, double (*func)(double)); 
 {    int j; 
   void linmin(double p[], double xi[], int n, double *fret,    double xx,xmin,bx,ax; 
               double (*func)(double []));    double fx,fb,fa;
   int i,ibig,j;   
   double del,t,*pt,*ptt,*xit;    ncom=n; 
   double fp,fptt;    pcom=vector(1,n); 
   double *xits;    xicom=vector(1,n); 
   pt=vector(1,n);    nrfunc=func; 
   ptt=vector(1,n);    for (j=1;j<=n;j++) { 
   xit=vector(1,n);      pcom[j]=p[j]; 
   xits=vector(1,n);      xicom[j]=xi[j]; 
   *fret=(*func)(p);    } 
   for (j=1;j<=n;j++) pt[j]=p[j];    ax=0.0; 
   for (*iter=1;;++(*iter)) {    xx=1.0; 
     fp=(*fret);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     ibig=0;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     del=0.0;  #ifdef DEBUG
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     for (i=1;i<=n;i++)    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       printf(" %d %.12f",i, p[i]);  #endif
     printf("\n");    for (j=1;j<=n;j++) { 
     for (i=1;i<=n;i++) {      xi[j] *= xmin; 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];      p[j] += xi[j]; 
       fptt=(*fret);    } 
 #ifdef DEBUG    free_vector(xicom,1,n); 
       printf("fret=%lf \n",*fret);    free_vector(pcom,1,n); 
 #endif  } 
       printf("%d",i);fflush(stdout);  
       linmin(p,xit,n,fret,func);  /*************** powell ************************/
       if (fabs(fptt-(*fret)) > del) {  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
         del=fabs(fptt-(*fret));              double (*func)(double [])) 
         ibig=i;  { 
       }    void linmin(double p[], double xi[], int n, double *fret, 
 #ifdef DEBUG                double (*func)(double [])); 
       printf("%d %.12e",i,(*fret));    int i,ibig,j; 
       for (j=1;j<=n;j++) {    double del,t,*pt,*ptt,*xit;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    double fp,fptt;
         printf(" x(%d)=%.12e",j,xit[j]);    double *xits;
       }    pt=vector(1,n); 
       for(j=1;j<=n;j++)    ptt=vector(1,n); 
         printf(" p=%.12e",p[j]);    xit=vector(1,n); 
       printf("\n");    xits=vector(1,n); 
 #endif    *fret=(*func)(p); 
     }    for (j=1;j<=n;j++) pt[j]=p[j]; 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    for (*iter=1;;++(*iter)) { 
 #ifdef DEBUG      fp=(*fret); 
       int k[2],l;      ibig=0; 
       k[0]=1;      del=0.0; 
       k[1]=-1;      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       printf("Max: %.12e",(*func)(p));      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       for (j=1;j<=n;j++)      for (i=1;i<=n;i++) 
         printf(" %.12e",p[j]);        printf(" %d %.12f",i, p[i]);
       printf("\n");      fprintf(ficlog," %d %.12f",i, p[i]);
       for(l=0;l<=1;l++) {      printf("\n");
         for (j=1;j<=n;j++) {      fprintf(ficlog,"\n");
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];      for (i=1;i<=n;i++) { 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         }        fptt=(*fret); 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  #ifdef DEBUG
       }        printf("fret=%lf \n",*fret);
 #endif        fprintf(ficlog,"fret=%lf \n",*fret);
   #endif
         printf("%d",i);fflush(stdout);
       free_vector(xit,1,n);        fprintf(ficlog,"%d",i);fflush(ficlog);
       free_vector(xits,1,n);        linmin(p,xit,n,fret,func); 
       free_vector(ptt,1,n);        if (fabs(fptt-(*fret)) > del) { 
       free_vector(pt,1,n);          del=fabs(fptt-(*fret)); 
       return;          ibig=i; 
     }        } 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  #ifdef DEBUG
     for (j=1;j<=n;j++) {        printf("%d %.12e",i,(*fret));
       ptt[j]=2.0*p[j]-pt[j];        fprintf(ficlog,"%d %.12e",i,(*fret));
       xit[j]=p[j]-pt[j];        for (j=1;j<=n;j++) {
       pt[j]=p[j];          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     }          printf(" x(%d)=%.12e",j,xit[j]);
     fptt=(*func)(ptt);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     if (fptt < fp) {        }
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);        for(j=1;j<=n;j++) {
       if (t < 0.0) {          printf(" p=%.12e",p[j]);
         linmin(p,xit,n,fret,func);          fprintf(ficlog," p=%.12e",p[j]);
         for (j=1;j<=n;j++) {        }
           xi[j][ibig]=xi[j][n];        printf("\n");
           xi[j][n]=xit[j];        fprintf(ficlog,"\n");
         }  #endif
 #ifdef DEBUG      } 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
         for(j=1;j<=n;j++)  #ifdef DEBUG
           printf(" %.12e",xit[j]);        int k[2],l;
         printf("\n");        k[0]=1;
 #endif        k[1]=-1;
       }        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");
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)        fprintf(ficlog,"\n");
 {        for(l=0;l<=1;l++) {
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit          for (j=1;j<=n;j++) {
      matrix by transitions matrix until convergence is reached */            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
             printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   int i, ii,j,k;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   double min, max, maxmin, maxmax,sumnew=0.;          }
   double **matprod2();          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   double **out, cov[NCOVMAX], **pmij();          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   double **newm;        }
   double agefin, delaymax=50 ; /* Max number of years to converge */  #endif
   
   for (ii=1;ii<=nlstate+ndeath;ii++)  
     for (j=1;j<=nlstate+ndeath;j++){        free_vector(xit,1,n); 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        free_vector(xits,1,n); 
     }        free_vector(ptt,1,n); 
         free_vector(pt,1,n); 
    cov[1]=1.;        return; 
        } 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){      for (j=1;j<=n;j++) { 
     newm=savm;        ptt[j]=2.0*p[j]-pt[j]; 
     /* Covariates have to be included here again */        xit[j]=p[j]-pt[j]; 
      cov[2]=agefin;        pt[j]=p[j]; 
        } 
       for (k=1; k<=cptcovn;k++) {      fptt=(*func)(ptt); 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      if (fptt < fp) { 
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       }        if (t < 0.0) { 
       for (k=1; k<=cptcovage;k++)          linmin(p,xit,n,fret,func); 
         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);
           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=-2 lli=out[1][1]+out[1][2];*/
   ludcmp(a,npar,indx,&pd);          if (s2==-2) {
             for (j=1,survp=0. ; j<=nlstate; j++) 
   for (j=1;j<=npar;j++) {              survp += out[s1][j];
     for (i=1;i<=npar;i++) x[i]=0;            lli= survp;
     x[j]=1;          }
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){          else
       matcov[i][j]=x[i];          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));  /* linear interpolation */
     }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   }          /*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); */
   printf("\n#Hessian matrix#\n");          ipmx +=1;
   for (i=1;i<=npar;i++) {          sw += weight[i];
     for (j=1;j<=npar;j++) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       printf("%.3e ",hess[i][j]);        } /* end of wave */
     }      } /* end of individual */
     printf("\n");    }  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];
   /* Recompute Inverse */        for(mi=1; mi<= wav[i]-1; mi++){
   for (i=1;i<=npar;i++)          for (ii=1;ii<=nlstate+ndeath;ii++)
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];            for (j=1;j<=nlstate+ndeath;j++){
   ludcmp(a,npar,indx,&pd);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
   /*  printf("\n#Hessian matrix recomputed#\n");            }
           for(d=0; d<=dh[mi][i]; d++){
   for (j=1;j<=npar;j++) {            newm=savm;
     for (i=1;i<=npar;i++) x[i]=0;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     x[j]=1;            for (kk=1; kk<=cptcovage;kk++) {
     lubksb(a,npar,indx,x);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for (i=1;i<=npar;i++){            }
       y[i][j]=x[i];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       printf("%.3e ",y[i][j]);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }            savm=oldm;
     printf("\n");            oldm=newm;
   }          } /* end mult */
   */        
           /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   free_matrix(a,1,npar,1,npar);          /* But now since version 0.9 we anticipate for bias and large stepm.
   free_matrix(y,1,npar,1,npar);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   free_vector(x,1,npar);           * (in months) between two waves is not a multiple of stepm, we rounded to 
   free_ivector(indx,1,npar);           * the nearest (and in case of equal distance, to the lowest) interval but now
   free_matrix(hess,1,npar,1,npar);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
            * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
            * probability in order to take into account the bias as a fraction of the way
 }           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
            * -stepm/2 to stepm/2 .
 /*************** hessian matrix ****************/           * For stepm=1 the results are the same as for previous versions of Imach.
 double hessii( double x[], double delta, int theta, double delti[])           * For stepm > 1 the results are less biased than in previous versions. 
 {           */
   int i;          s1=s[mw[mi][i]][i];
   int l=1, lmax=20;          s2=s[mw[mi+1][i]][i];
   double k1,k2;          bbh=(double)bh[mi][i]/(double)stepm; 
   double p2[NPARMAX+1];          /* bias is positive if real duration
   double res;           * is higher than the multiple of stepm and negative otherwise.
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;           */
   double 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 */
   int k=0,kmax=10;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   double l1;          /*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 */
           /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   fx=func(x);          /*if(lli ==000.0)*/
   for (i=1;i<=npar;i++) p2[i]=x[i];          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   for(l=0 ; l <=lmax; l++){          ipmx +=1;
     l1=pow(10,l);          sw += weight[i];
     delts=delt;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(k=1 ; k <kmax; k=k+1){        } /* end of wave */
       delt = delta*(l1*k);      } /* end of individual */
       p2[theta]=x[theta] +delt;    }  else if(mle==3){  /* exponential inter-extrapolation */
       k1=func(p2)-fx;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       p2[theta]=x[theta]-delt;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       k2=func(p2)-fx;        for(mi=1; mi<= wav[i]-1; mi++){
       /*res= (k1-2.0*fx+k2)/delt/delt; */          for (ii=1;ii<=nlstate+ndeath;ii++)
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */            for (j=1;j<=nlstate+ndeath;j++){
                    oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 #ifdef DEBUG              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);            }
 #endif          for(d=0; d<dh[mi][i]; d++){
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */            newm=savm;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         k=kmax;            for (kk=1; kk<=cptcovage;kk++) {
       }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */            }
         k=kmax; l=lmax*10.;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){            savm=oldm;
         delts=delt;            oldm=newm;
       }          } /* end mult */
     }        
   }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   delti[theta]=delts;          /* But now since version 0.9 we anticipate for bias and large stepm.
   return res;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
             * (in months) between two waves is not a multiple of stepm, we rounded to 
 }           * the nearest (and in case of equal distance, to the lowest) interval but now
            * we keep into memory the bias bh[mi][i] and also the previous matrix product
 double hessij( double x[], double delti[], int thetai,int thetaj)           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
 {           * probability in order to take into account the bias as a fraction of the way
   int i;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   int l=1, l1, lmax=20;           * -stepm/2 to stepm/2 .
   double k1,k2,k3,k4,res,fx;           * For stepm=1 the results are the same as for previous versions of Imach.
   double p2[NPARMAX+1];           * For stepm > 1 the results are less biased than in previous versions. 
   int k;           */
           s1=s[mw[mi][i]][i];
   fx=func(x);          s2=s[mw[mi+1][i]][i];
   for (k=1; k<=2; k++) {          bbh=(double)bh[mi][i]/(double)stepm; 
     for (i=1;i<=npar;i++) p2[i]=x[i];          /* bias is positive if real duration
     p2[thetai]=x[thetai]+delti[thetai]/k;           * is higher than the multiple of stepm and negative otherwise.
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;           */
     k1=func(p2)-fx;          /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
            lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
     p2[thetai]=x[thetai]+delti[thetai]/k;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          /*if(lli ==000.0)*/
     k2=func(p2)-fx;          /*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); */
            ipmx +=1;
     p2[thetai]=x[thetai]-delti[thetai]/k;          sw += weight[i];
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     k3=func(p2)-fx;        } /* end of wave */
        } /* end of individual */
     p2[thetai]=x[thetai]-delti[thetai]/k;    }else{  /* ml=4 no inter-extrapolation */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     k4=func(p2)-fx;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        for(mi=1; mi<= wav[i]-1; mi++){
 #ifdef DEBUG          for (ii=1;ii<=nlstate+ndeath;ii++)
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);            for (j=1;j<=nlstate+ndeath;j++){
 #endif              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   return res;            }
 }          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
 /************** Inverse of matrix **************/            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 void ludcmp(double **a, int n, int *indx, double *d)            for (kk=1; kk<=cptcovage;kk++) {
 {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int i,imax,j,k;            }
   double big,dum,sum,temp;          
   double *vv;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   vv=vector(1,n);            savm=oldm;
   *d=1.0;            oldm=newm;
   for (i=1;i<=n;i++) {          } /* end mult */
     big=0.0;        
     for (j=1;j<=n;j++)          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       if ((temp=fabs(a[i][j])) > big) big=temp;          ipmx +=1;
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          sw += weight[i];
     vv[i]=1.0/big;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   }        } /* end of wave */
   for (j=1;j<=n;j++) {      } /* end of individual */
     for (i=1;i<j;i++) {    } /* End of if */
       sum=a[i][j];    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       a[i][j]=sum;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     }    return -l;
     big=0.0;  }
     for (i=j;i<=n;i++) {  
       sum=a[i][j];  
       for (k=1;k<j;k++)  /*********** Maximum Likelihood Estimation ***************/
         sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       if ( (dum=vv[i]*fabs(sum)) >= big) {  {
         big=dum;    int i,j, iter;
         imax=i;    double **xi,*delti;
       }    double fret;
     }    xi=matrix(1,npar,1,npar);
     if (j != imax) {    for (i=1;i<=npar;i++)
       for (k=1;k<=n;k++) {      for (j=1;j<=npar;j++)
         dum=a[imax][k];        xi[i][j]=(i==j ? 1.0 : 0.0);
         a[imax][k]=a[j][k];    printf("Powell\n");  fprintf(ficlog,"Powell\n");
         a[j][k]=dum;    powell(p,xi,npar,ftol,&iter,&fret,func);
       }  
       *d = -(*d);     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
       vv[imax]=vv[j];    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     }    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     indx[j]=imax;  
     if (a[j][j] == 0.0) a[j][j]=TINY;  }
     if (j != n) {  
       dum=1.0/(a[j][j]);  /**** Computes Hessian and covariance matrix ***/
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     }  {
   }    double  **a,**y,*x,pd;
   free_vector(vv,1,n);  /* Doesn't work */    double **hess;
 ;    int i, j,jk;
 }    int *indx;
   
 void lubksb(double **a, int n, int *indx, double b[])    double hessii(double p[], double delta, int theta, double delti[]);
 {    double hessij(double p[], double delti[], int i, int j);
   int i,ii=0,ip,j;    void lubksb(double **a, int npar, int *indx, double b[]) ;
   double sum;    void ludcmp(double **a, int npar, int *indx, double *d) ;
    
   for (i=1;i<=n;i++) {    hess=matrix(1,npar,1,npar);
     ip=indx[i];  
     sum=b[ip];    printf("\nCalculation of the hessian matrix. Wait...\n");
     b[ip]=b[i];    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     if (ii)    for (i=1;i<=npar;i++){
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];      printf("%d",i);fflush(stdout);
     else if (sum) ii=i;      fprintf(ficlog,"%d",i);fflush(ficlog);
     b[i]=sum;      hess[i][i]=hessii(p,ftolhess,i,delti);
   }      /*printf(" %f ",p[i]);*/
   for (i=n;i>=1;i--) {      /*printf(" %lf ",hess[i][i]);*/
     sum=b[i];    }
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    
     b[i]=sum/a[i][i];    for (i=1;i<=npar;i++) {
   }      for (j=1;j<=npar;j++)  {
 }        if (j>i) { 
           printf(".%d%d",i,j);fflush(stdout);
 /************ Frequencies ********************/          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
 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)          hess[i][j]=hessij(p,delti,i,j);
 {  /* Some frequencies */          hess[j][i]=hess[i][j];    
            /*printf(" %lf ",hess[i][j]);*/
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;        }
   double ***freq; /* Frequencies */      }
   double *pp;    }
   double pos, k2, dateintsum=0,k2cpt=0;    printf("\n");
   FILE *ficresp;    fprintf(ficlog,"\n");
   char fileresp[FILENAMELENGTH];  
     printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   pp=vector(1,nlstate);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    
   strcpy(fileresp,"p");    a=matrix(1,npar,1,npar);
   strcat(fileresp,fileres);    y=matrix(1,npar,1,npar);
   if((ficresp=fopen(fileresp,"w"))==NULL) {    x=vector(1,npar);
     printf("Problem with prevalence resultfile: %s\n", fileresp);    indx=ivector(1,npar);
     exit(0);    for (i=1;i<=npar;i++)
   }      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    ludcmp(a,npar,indx,&pd);
   j1=0;  
     for (j=1;j<=npar;j++) {
   j=cptcoveff;      for (i=1;i<=npar;i++) x[i]=0;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      x[j]=1;
       lubksb(a,npar,indx,x);
   for(k1=1; k1<=j;k1++){      for (i=1;i<=npar;i++){ 
    for(i1=1; i1<=ncodemax[k1];i1++){        matcov[i][j]=x[i];
        j1++;      }
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    }
          scanf("%d", i);*/  
         for (i=-1; i<=nlstate+ndeath; i++)      printf("\n#Hessian matrix#\n");
          for (jk=-1; jk<=nlstate+ndeath; jk++)      fprintf(ficlog,"\n#Hessian matrix#\n");
            for(m=agemin; m <= agemax+3; m++)    for (i=1;i<=npar;i++) { 
              freq[i][jk][m]=0;      for (j=1;j<=npar;j++) { 
         printf("%.3e ",hess[i][j]);
         dateintsum=0;        fprintf(ficlog,"%.3e ",hess[i][j]);
         k2cpt=0;      }
        for (i=1; i<=imx; i++) {      printf("\n");
          bool=1;      fprintf(ficlog,"\n");
          if  (cptcovn>0) {    }
            for (z1=1; z1<=cptcoveff; z1++)  
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    /* Recompute Inverse */
                bool=0;    for (i=1;i<=npar;i++)
          }      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
          if (bool==1) {    ludcmp(a,npar,indx,&pd);
            for(m=firstpass; m<=lastpass; m++){  
              k2=anint[m][i]+(mint[m][i]/12.);    /*  printf("\n#Hessian matrix recomputed#\n");
              if ((k2>=dateprev1) && (k2<=dateprev2)) {  
                if(agev[m][i]==0) agev[m][i]=agemax+1;    for (j=1;j<=npar;j++) {
                if(agev[m][i]==1) agev[m][i]=agemax+2;      for (i=1;i<=npar;i++) x[i]=0;
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      x[j]=1;
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      lubksb(a,npar,indx,x);
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {      for (i=1;i<=npar;i++){ 
                  dateintsum=dateintsum+k2;        y[i][j]=x[i];
                  k2cpt++;        printf("%.3e ",y[i][j]);
                }        fprintf(ficlog,"%.3e ",y[i][j]);
       }
              }      printf("\n");
            }      fprintf(ficlog,"\n");
          }    }
        }    */
          
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    free_matrix(a,1,npar,1,npar);
     free_matrix(y,1,npar,1,npar);
         if  (cptcovn>0) {    free_vector(x,1,npar);
          fprintf(ficresp, "\n#********** Variable ");    free_ivector(indx,1,npar);
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    free_matrix(hess,1,npar,1,npar);
        fprintf(ficresp, "**********\n#");  
         }  
        for(i=1; i<=nlstate;i++)  }
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  
        fprintf(ficresp, "\n");  /*************** hessian matrix ****************/
          double hessii( double x[], double delta, int theta, double delti[])
   for(i=(int)agemin; i <= (int)agemax+3; i++){  {
     if(i==(int)agemax+3)    int i;
       printf("Total");    int l=1, lmax=20;
     else    double k1,k2;
       printf("Age %d", i);    double p2[NPARMAX+1];
     for(jk=1; jk <=nlstate ; jk++){    double res;
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
         pp[jk] += freq[jk][m][i];    double fx;
     }    int k=0,kmax=10;
     for(jk=1; jk <=nlstate ; jk++){    double l1;
       for(m=-1, pos=0; m <=0 ; m++)  
         pos += freq[jk][m][i];    fx=func(x);
       if(pp[jk]>=1.e-10)    for (i=1;i<=npar;i++) p2[i]=x[i];
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    for(l=0 ; l <=lmax; l++){
       else      l1=pow(10,l);
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      delts=delt;
     }      for(k=1 ; k <kmax; k=k+1){
         delt = delta*(l1*k);
      for(jk=1; jk <=nlstate ; jk++){        p2[theta]=x[theta] +delt;
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        k1=func(p2)-fx;
         pp[jk] += freq[jk][m][i];        p2[theta]=x[theta]-delt;
      }        k2=func(p2)-fx;
         /*res= (k1-2.0*fx+k2)/delt/delt; */
     for(jk=1,pos=0; jk <=nlstate ; jk++)        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
       pos += pp[jk];        
     for(jk=1; jk <=nlstate ; jk++){  #ifdef DEBUG
       if(pos>=1.e-5)        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);
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        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);
       else  #endif
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
       if( i <= (int) agemax){        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         if(pos>=1.e-5){          k=kmax;
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        }
           probs[i][jk][j1]= pp[jk]/pos;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/          k=kmax; l=lmax*10.;
         }        }
       else        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          delts=delt;
       }        }
     }      }
     for(jk=-1; jk <=nlstate+ndeath; jk++)    }
       for(m=-1; m <=nlstate+ndeath; m++)    delti[theta]=delts;
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    return res; 
     if(i <= (int) agemax)    
       fprintf(ficresp,"\n");  }
     printf("\n");  
     }  double hessij( double x[], double delti[], int thetai,int thetaj)
     }  {
  }    int i;
   dateintmean=dateintsum/k2cpt;    int l=1, l1, lmax=20;
      double k1,k2,k3,k4,res,fx;
   fclose(ficresp);    double p2[NPARMAX+1];
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    int k;
   free_vector(pp,1,nlstate);  
     fx=func(x);
   /* End of Freq */    for (k=1; k<=2; k++) {
 }      for (i=1;i<=npar;i++) p2[i]=x[i];
       p2[thetai]=x[thetai]+delti[thetai]/k;
 /************ Prevalence ********************/      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
 void prevalence(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 calagedate)      k1=func(p2)-fx;
 {  /* Some frequencies */    
        p2[thetai]=x[thetai]+delti[thetai]/k;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   double ***freq; /* Frequencies */      k2=func(p2)-fx;
   double *pp;    
   double pos, k2;      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   pp=vector(1,nlstate);      k3=func(p2)-fx;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    
        p2[thetai]=x[thetai]-delti[thetai]/k;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   j1=0;      k4=func(p2)-fx;
        res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   j=cptcoveff;  #ifdef DEBUG
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
        fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
  for(k1=1; k1<=j;k1++){  #endif
     for(i1=1; i1<=ncodemax[k1];i1++){    }
       j1++;    return res;
    }
       for (i=-1; i<=nlstate+ndeath; i++)    
         for (jk=-1; jk<=nlstate+ndeath; jk++)    /************** Inverse of matrix **************/
           for(m=agemin; m <= agemax+3; m++)  void ludcmp(double **a, int n, int *indx, double *d) 
             freq[i][jk][m]=0;  { 
          int i,imax,j,k; 
       for (i=1; i<=imx; i++) {    double big,dum,sum,temp; 
         bool=1;    double *vv; 
         if  (cptcovn>0) {   
           for (z1=1; z1<=cptcoveff; z1++)    vv=vector(1,n); 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    *d=1.0; 
               bool=0;    for (i=1;i<=n;i++) { 
         }      big=0.0; 
         if (bool==1) {      for (j=1;j<=n;j++) 
           for(m=firstpass; m<=lastpass; m++){        if ((temp=fabs(a[i][j])) > big) big=temp; 
             k2=anint[m][i]+(mint[m][i]/12.);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      vv[i]=1.0/big; 
               if(agev[m][i]==0) agev[m][i]=agemax+1;    } 
               if(agev[m][i]==1) agev[m][i]=agemax+2;    for (j=1;j<=n;j++) { 
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];      for (i=1;i<j;i++) { 
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];          sum=a[i][j]; 
             }        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
           }        a[i][j]=sum; 
         }      } 
       }      big=0.0; 
            for (i=j;i<=n;i++) { 
         for(i=(int)agemin; i <= (int)agemax+3; i++){        sum=a[i][j]; 
           for(jk=1; jk <=nlstate ; jk++){        for (k=1;k<j;k++) 
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          sum -= a[i][k]*a[k][j]; 
               pp[jk] += freq[jk][m][i];        a[i][j]=sum; 
           }        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           for(jk=1; jk <=nlstate ; jk++){          big=dum; 
             for(m=-1, pos=0; m <=0 ; m++)          imax=i; 
             pos += freq[jk][m][i];        } 
         }      } 
              if (j != imax) { 
          for(jk=1; jk <=nlstate ; jk++){        for (k=1;k<=n;k++) { 
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          dum=a[imax][k]; 
              pp[jk] += freq[jk][m][i];          a[imax][k]=a[j][k]; 
          }          a[j][k]=dum; 
                  } 
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        *d = -(*d); 
         vv[imax]=vv[j]; 
          for(jk=1; jk <=nlstate ; jk++){                } 
            if( i <= (int) agemax){      indx[j]=imax; 
              if(pos>=1.e-5){      if (a[j][j] == 0.0) a[j][j]=TINY; 
                probs[i][jk][j1]= pp[jk]/pos;      if (j != n) { 
              }        dum=1.0/(a[j][j]); 
            }        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
          }      } 
              } 
         }    free_vector(vv,1,n);  /* Doesn't work */
     }  ;
   }  } 
    
    void lubksb(double **a, int n, int *indx, double b[]) 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  { 
   free_vector(pp,1,nlstate);    int i,ii=0,ip,j; 
      double sum; 
 }  /* End of Freq */   
     for (i=1;i<=n;i++) { 
 /************* Waves Concatenation ***************/      ip=indx[i]; 
       sum=b[ip]; 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      b[ip]=b[i]; 
 {      if (ii) 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
      Death is a valid wave (if date is known).      else if (sum) ii=i; 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      b[i]=sum; 
      dh[m][i] of 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.    for (i=n;i>=1;i--) { 
      */      sum=b[i]; 
       for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   int i, mi, m;      b[i]=sum/a[i][i]; 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    } 
      double sum=0., jmean=0.;*/  } 
   
   int j, k=0,jk, ju, jl;  /************ Frequencies ********************/
   double sum=0.;  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)
   jmin=1e+5;  {  /* Some frequencies */
   jmax=-1;    
   jmean=0.;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   for(i=1; i<=imx; i++){    int first;
     mi=0;    double ***freq; /* Frequencies */
     m=firstpass;    double *pp;
     while(s[m][i] <= nlstate){    double pos, k2, dateintsum=0,k2cpt=0;
       if(s[m][i]>=1)    FILE *ficresp;
         mw[++mi][i]=m;    char fileresp[FILENAMELENGTH];
       if(m >=lastpass)    
         break;    pp=vector(1,nlstate);
       else    probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
         m++;    strcpy(fileresp,"p");
     }/* end while */    strcat(fileresp,fileres);
     if (s[m][i] > nlstate){    if((ficresp=fopen(fileresp,"w"))==NULL) {
       mi++;     /* Death is another wave */      printf("Problem with prevalence resultfile: %s\n", fileresp);
       /* if(mi==0)  never been interviewed correctly before death */      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
          /* Only death is a correct wave */      exit(0);
       mw[mi][i]=m;    }
     }    freq= ma3x(-2,nlstate+ndeath,-2,nlstate+ndeath,agemin,agemax+3);
     j1=0;
     wav[i]=mi;    
     if(mi==0)    j=cptcoveff;
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   }  
     first=1;
   for(i=1; i<=imx; i++){  
     for(mi=1; mi<wav[i];mi++){    for(k1=1; k1<=j;k1++){
       if (stepm <=0)      for(i1=1; i1<=ncodemax[k1];i1++){
         dh[mi][i]=1;        j1++;
       else{        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
         if (s[mw[mi+1][i]][i] > nlstate) {          scanf("%d", i);*/
           if (agedc[i] < 2*AGESUP) {        for (i=-1; i<=nlstate+ndeath; i++)  
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          for (jk=-1; jk<=nlstate+ndeath; jk++)  
           if(j==0) j=1;  /* Survives at least one month after exam */            for(m=agemin; m <= agemax+3; m++)
           k=k+1;              freq[i][jk][m]=0;
           if (j >= jmax) jmax=j;        
           if (j <= jmin) jmin=j;        dateintsum=0;
           sum=sum+j;        k2cpt=0;
           /* if (j<10) printf("j=%d num=%d ",j,i); */        for (i=1; i<=imx; i++) {
           }          bool=1;
         }          if  (cptcovn>0) {
         else{            for (z1=1; z1<=cptcoveff; z1++) 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
           k=k+1;                bool=0;
           if (j >= jmax) jmax=j;          }
           else if (j <= jmin)jmin=j;          if (bool==1){
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */            for(m=firstpass; m<=lastpass; m++){
           sum=sum+j;              k2=anint[m][i]+(mint[m][i]/12.);
         }              if ((k2>=dateprev1) && (k2<=dateprev2)) {
         jk= j/stepm;                if(agev[m][i]==0) agev[m][i]=agemax+1;
         jl= j -jk*stepm;                if(agev[m][i]==1) agev[m][i]=agemax+2;
         ju= j -(jk+1)*stepm;                if (m<lastpass) {
         if(jl <= -ju)                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
           dh[mi][i]=jk;                  freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
         else                }
           dh[mi][i]=jk+1;                
         if(dh[mi][i]==0)                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
           dh[mi][i]=1; /* At least one step */                  dateintsum=dateintsum+k2;
       }                  k2cpt++;
     }                }
   }              }
   jmean=sum/k;            }
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          }
  }        }
 /*********** Tricode ****************************/         
 void tricode(int *Tvar, int **nbcode, int imx)        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
 {  
   int Ndum[20],ij=1, k, j, i;        if  (cptcovn>0) {
   int cptcode=0;          fprintf(ficresp, "\n#********** Variable "); 
   cptcoveff=0;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficresp, "**********\n#");
   for (k=0; k<19; k++) Ndum[k]=0;        }
   for (k=1; k<=7; k++) ncodemax[k]=0;        for(i=1; i<=nlstate;i++) 
           fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        fprintf(ficresp, "\n");
     for (i=1; i<=imx; i++) {        
       ij=(int)(covar[Tvar[j]][i]);        for(i=(int)agemin; i <= (int)agemax+3; i++){
       Ndum[ij]++;          if(i==(int)agemax+3){
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/            fprintf(ficlog,"Total");
       if (ij > cptcode) cptcode=ij;          }else{
     }            if(first==1){
               first=0;
     for (i=0; i<=cptcode; i++) {              printf("See log file for details...\n");
       if(Ndum[i]!=0) ncodemax[j]++;            }
     }            fprintf(ficlog,"Age %d", i);
     ij=1;          }
           for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     for (i=1; i<=ncodemax[j]; i++) {              pp[jk] += freq[jk][m][i]; 
       for (k=0; k<=19; k++) {          }
         if (Ndum[k] != 0) {          for(jk=1; jk <=nlstate ; jk++){
           nbcode[Tvar[j]][ij]=k;            for(m=-1, pos=0; m <=0 ; m++)
           ij++;              pos += freq[jk][m][i];
         }            if(pp[jk]>=1.e-10){
         if (ij > ncodemax[j]) break;              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]);
             }else{
  for (k=0; k<19; k++) Ndum[k]=0;              if(first==1)
                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
  for (i=1; i<=ncovmodel-2; i++) {              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       ij=Tvar[i];            }
       Ndum[ij]++;          }
     }  
           for(jk=1; jk <=nlstate ; jk++){
  ij=1;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
  for (i=1; i<=10; i++) {              pp[jk] += freq[jk][m][i];
    if((Ndum[i]!=0) && (i<=ncov)){          }
      Tvaraff[ij]=i;  
      ij++;          for(jk=1,pos=0; jk <=nlstate ; jk++)
    }            pos += pp[jk];
  }          for(jk=1; jk <=nlstate ; jk++){
              if(pos>=1.e-5){
     cptcoveff=ij-1;              if(first==1)
 }                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);
 /*********** Health Expectancies ****************/            }else{
               if(first==1)
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 {              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   /* Health expectancies */            }
   int i, j, nhstepm, hstepm, h;            if( i <= (int) agemax){
   double age, agelim,hf;              if(pos>=1.e-5){
   double ***p3mat;                fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
                  probs[i][jk][j1]= pp[jk]/pos;
   fprintf(ficreseij,"# Health expectancies\n");                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   fprintf(ficreseij,"# Age");              }
   for(i=1; i<=nlstate;i++)              else
     for(j=1; j<=nlstate;j++)                fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
       fprintf(ficreseij," %1d-%1d",i,j);            }
   fprintf(ficreseij,"\n");          }
           
   hstepm=1*YEARM; /*  Every j years of age (in month) */          for(jk=-2; jk <=nlstate+ndeath; jk++)
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            for(m=-2; m <=nlstate+ndeath; m++)
               if(freq[jk][m][i] !=0 ) {
   agelim=AGESUP;              if(first==1)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     /* nhstepm age range expressed in number of stepm */                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);              }
     /* Typically if 20 years = 20*12/6=40 stepm */          if(i <= (int) agemax)
     if (stepm >= YEARM) hstepm=1;            fprintf(ficresp,"\n");
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */          if(first==1)
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            printf("Others in log...\n");
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          fprintf(ficlog,"\n");
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        }
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);        }
     }
     dateintmean=dateintsum/k2cpt; 
     for(i=1; i<=nlstate;i++)   
       for(j=1; j<=nlstate;j++)    fclose(ficresp);
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){    free_ma3x(freq,-2,nlstate+ndeath,-2,nlstate+ndeath,(int) agemin,(int) agemax+3);
           eij[i][j][(int)age] +=p3mat[i][j][h];    free_vector(pp,1,nlstate);
         }    
        /* End of Freq */
     hf=1;  }
     if (stepm >= YEARM) hf=stepm/YEARM;  
     fprintf(ficreseij,"%.0f",age );  /************ Prevalence ********************/
     for(i=1; i<=nlstate;i++)  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)
       for(j=1; j<=nlstate;j++){  {  /* Some frequencies */
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);   
       }    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     fprintf(ficreseij,"\n");    double ***freq; /* Frequencies */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double *pp;
   }    double pos, k2;
 }  
     pp=vector(1,nlstate);
 /************ Variance ******************/    
 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)    freq=ma3x(-2,nlstate+ndeath,-2,nlstate+ndeath,agemin,agemax+3);
 {    j1=0;
   /* Variance of health expectancies */    
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    j=cptcoveff;
   double **newm;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   double **dnewm,**doldm;    
   int i, j, nhstepm, hstepm, h;    for(k1=1; k1<=j;k1++){
   int k, cptcode;      for(i1=1; i1<=ncodemax[k1];i1++){
   double *xp;        j1++;
   double **gp, **gm;        
   double ***gradg, ***trgradg;        for (i=-2; i<=nlstate+ndeath; i++)  
   double ***p3mat;          for (jk=-2; jk<=nlstate+ndeath; jk++)  
   double age,agelim;            for(m=agemin; m <= agemax+3; m++)
   int theta;              freq[i][jk][m]=0;
        
    fprintf(ficresvij,"# Covariances of life expectancies\n");        for (i=1; i<=imx; i++) {
   fprintf(ficresvij,"# Age");          bool=1;
   for(i=1; i<=nlstate;i++)          if  (cptcovn>0) {
     for(j=1; j<=nlstate;j++)            for (z1=1; z1<=cptcoveff; z1++) 
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   fprintf(ficresvij,"\n");                bool=0;
           } 
   xp=vector(1,npar);          if (bool==1) { 
   dnewm=matrix(1,nlstate,1,npar);            for(m=firstpass; m<=lastpass; m++){
   doldm=matrix(1,nlstate,1,nlstate);              k2=anint[m][i]+(mint[m][i]/12.);
                if ((k2>=dateprev1) && (k2<=dateprev2)) {
   hstepm=1*YEARM; /* Every year of age */                if(agev[m][i]==0) agev[m][i]=agemax+1;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */                if(agev[m][i]==1) agev[m][i]=agemax+2;
   agelim = AGESUP;                if (m<lastpass) {
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */                  if (calagedate>0) 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                    freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
     if (stepm >= YEARM) hstepm=1;                  else
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */                    freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                  freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);                }
     gp=matrix(0,nhstepm,1,nlstate);              }
     gm=matrix(0,nhstepm,1,nlstate);            }
           }
     for(theta=1; theta <=npar; theta++){        }
       for(i=1; i<=npar; i++){ /* Computes gradient */        for(i=(int)agemin; i <= (int)agemax+3; i++){ 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          for(jk=1; jk <=nlstate ; jk++){
       }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                pp[jk] += freq[jk][m][i]; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          }
           for(jk=1; jk <=nlstate ; jk++){
       if (popbased==1) {            for(m=-1, pos=0; m <=0 ; m++)
         for(i=1; i<=nlstate;i++)              pos += freq[jk][m][i];
           prlim[i][i]=probs[(int)age][i][ij];          }
       }          
            for(jk=1; jk <=nlstate ; jk++){
       for(j=1; j<= nlstate; j++){            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
         for(h=0; h<=nhstepm; h++){              pp[jk] += freq[jk][m][i];
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          }
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];          
         }          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
       }          
              for(jk=1; jk <=nlstate ; jk++){    
       for(i=1; i<=npar; i++) /* Computes gradient */            if( i <= (int) agemax){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);              if(pos>=1.e-5){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                  probs[i][jk][j1]= pp[jk]/pos;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              }
              }
       if (popbased==1) {          }/* end jk */
         for(i=1; i<=nlstate;i++)        }/* end i */
           prlim[i][i]=probs[(int)age][i][ij];      } /* end i1 */
       }    } /* end k1 */
   
       for(j=1; j<= nlstate; j++){    
         for(h=0; h<=nhstepm; h++){    free_ma3x(freq,-2,nlstate+ndeath,-2,nlstate+ndeath,(int) agemin,(int) agemax+3);
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    free_vector(pp,1,nlstate);
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    
         }  }  /* End of Freq */
       }  
   /************* Waves Concatenation ***************/
       for(j=1; j<= nlstate; j++)  
         for(h=0; h<=nhstepm; 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)
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  {
         }    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     } /* End theta */       Death is a valid wave (if date is known).
        mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);       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.
     for(h=0; h<=nhstepm; h++)       */
       for(j=1; j<=nlstate;j++)  
         for(theta=1; theta <=npar; theta++)    int i, mi, m;
           trgradg[h][j][theta]=gradg[h][theta][j];    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
        double sum=0., jmean=0.;*/
     for(i=1;i<=nlstate;i++)    int first;
       for(j=1;j<=nlstate;j++)    int j, k=0,jk, ju, jl;
         vareij[i][j][(int)age] =0.;    double sum=0.;
     for(h=0;h<=nhstepm;h++){    first=0;
       for(k=0;k<=nhstepm;k++){    jmin=1e+5;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    jmax=-1;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    jmean=0.;
         for(i=1;i<=nlstate;i++)    for(i=1; i<=imx; i++){
           for(j=1;j<=nlstate;j++)      mi=0;
             vareij[i][j][(int)age] += doldm[i][j];      m=firstpass;
       }      while(s[m][i] <= nlstate){
     }        if(s[m][i]>=1 || s[m][i]==-2)
     h=1;          mw[++mi][i]=m;
     if (stepm >= YEARM) h=stepm/YEARM;        if(m >=lastpass)
     fprintf(ficresvij,"%.0f ",age );          break;
     for(i=1; i<=nlstate;i++)        else
       for(j=1; j<=nlstate;j++){          m++;
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);      }/* end while */
       }      if (s[m][i] > nlstate){
     fprintf(ficresvij,"\n");        mi++;     /* Death is another wave */
     free_matrix(gp,0,nhstepm,1,nlstate);        /* if(mi==0)  never been interviewed correctly before death */
     free_matrix(gm,0,nhstepm,1,nlstate);           /* Only death is a correct wave */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        mw[mi][i]=m;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   } /* End age */      wav[i]=mi;
        if(mi==0){
   free_vector(xp,1,npar);        if(first==0){
   free_matrix(doldm,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_matrix(dnewm,1,nlstate,1,nlstate);          first=1;
         }
 }        if(first==1){
           fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
 /************ 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)      } /* end mi==0 */
 {    }
   /* Variance of prevalence limit */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    for(i=1; i<=imx; i++){
   double **newm;      for(mi=1; mi<wav[i];mi++){
   double **dnewm,**doldm;        if (stepm <=0)
   int i, j, nhstepm, hstepm;          dh[mi][i]=1;
   int k, cptcode;        else{
   double *xp;          if (s[mw[mi+1][i]][i] > nlstate) {
   double *gp, *gm;            if (agedc[i] < 2*AGESUP) {
   double **gradg, **trgradg;            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   double age,agelim;            if(j==0) j=1;  /* Survives at least one month after exam */
   int theta;            k=k+1;
                if (j >= jmax) jmax=j;
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");            if (j <= jmin) jmin=j;
   fprintf(ficresvpl,"# Age");            sum=sum+j;
   for(i=1; i<=nlstate;i++)            /*if (j<0) printf("j=%d num=%d \n",j,i); */
       fprintf(ficresvpl," %1d-%1d",i,i);            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   fprintf(ficresvpl,"\n");            }
           }
   xp=vector(1,npar);          else{
   dnewm=matrix(1,nlstate,1,npar);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   doldm=matrix(1,nlstate,1,nlstate);            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
              k=k+1;
   hstepm=1*YEARM; /* Every year of age */            if (j >= jmax) jmax=j;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            else if (j <= jmin)jmin=j;
   agelim = AGESUP;            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            sum=sum+j;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          }
     if (stepm >= YEARM) hstepm=1;          jk= j/stepm;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          jl= j -jk*stepm;
     gradg=matrix(1,npar,1,nlstate);          ju= j -(jk+1)*stepm;
     gp=vector(1,nlstate);          if(mle <=1){ 
     gm=vector(1,nlstate);            if(jl==0){
               dh[mi][i]=jk;
     for(theta=1; theta <=npar; theta++){              bh[mi][i]=0;
       for(i=1; i<=npar; i++){ /* Computes gradient */            }else{ /* We want a negative bias in order to only have interpolation ie
         xp[i] = x[i] + (i==theta ?delti[theta]:0);                    * at the price of an extra matrix product in likelihood */
       }              dh[mi][i]=jk+1;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              bh[mi][i]=ju;
       for(i=1;i<=nlstate;i++)            }
         gp[i] = prlim[i][i];          }else{
                if(jl <= -ju){
       for(i=1; i<=npar; i++) /* Computes gradient */              dh[mi][i]=jk;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);              bh[mi][i]=jl;       /* bias is positive if real duration
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);                                   * is higher than the multiple of stepm and negative otherwise.
       for(i=1;i<=nlstate;i++)                                   */
         gm[i] = prlim[i][i];            }
             else{
       for(i=1;i<=nlstate;i++)              dh[mi][i]=jk+1;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];              bh[mi][i]=ju;
     } /* End theta */            }
             if(dh[mi][i]==0){
     trgradg =matrix(1,nlstate,1,npar);              dh[mi][i]=1; /* At least one step */
               bh[mi][i]=ju; /* At least one step */
     for(j=1; j<=nlstate;j++)              printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);
       for(theta=1; theta <=npar; theta++)            }
         trgradg[j][theta]=gradg[theta][j];          }
         } /* end if mle */
     for(i=1;i<=nlstate;i++)      } /* end wave */
       varpl[i][(int)age] =0.;    }
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    jmean=sum/k;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    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] = doldm[i][i]; /* Covariances are useless */   }
   
     fprintf(ficresvpl,"%.0f ",age );  /*********** Tricode ****************************/
     for(i=1; i<=nlstate;i++)  void tricode(int *Tvar, int **nbcode, int imx)
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  {
     fprintf(ficresvpl,"\n");    
     free_vector(gp,1,nlstate);    int Ndum[20],ij=1, k, j, i, maxncov=19;
     free_vector(gm,1,nlstate);    int cptcode=0;
     free_matrix(gradg,1,npar,1,nlstate);    cptcoveff=0; 
     free_matrix(trgradg,1,nlstate,1,npar);   
   } /* End age */    for (k=0; k<maxncov; k++) Ndum[k]=0;
     for (k=1; k<=7; k++) ncodemax[k]=0;
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   free_matrix(dnewm,1,nlstate,1,nlstate);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                  modality*/ 
 }        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
         Ndum[ij]++; /*store the modality */
 /************ Variance of one-step probabilities  ******************/        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
 {                                         Tvar[j]. If V=sex and male is 0 and 
   int i, j;                                         female is 1, then  cptcode=1.*/
   int k=0, cptcode;      }
   double **dnewm,**doldm;  
   double *xp;      for (i=0; i<=cptcode; i++) {
   double *gp, *gm;        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 */
   double **gradg, **trgradg;      }
   double age,agelim, cov[NCOVMAX];  
   int theta;      ij=1; 
   char fileresprob[FILENAMELENGTH];      for (i=1; i<=ncodemax[j]; i++) {
         for (k=0; k<= maxncov; k++) {
   strcpy(fileresprob,"prob");          if (Ndum[k] != 0) {
   strcat(fileresprob,fileres);            nbcode[Tvar[j]][ij]=k; 
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {            /* 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; */
     printf("Problem with resultfile: %s\n", fileresprob);            
   }            ij++;
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);          }
            if (ij > ncodemax[j]) break; 
         }  
   xp=vector(1,npar);      } 
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    }  
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));  
     for (k=0; k< maxncov; k++) Ndum[k]=0;
   cov[1]=1;  
   for (age=bage; age<=fage; age ++){   for (i=1; i<=ncovmodel-2; i++) { 
     cov[2]=age;     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     gradg=matrix(1,npar,1,9);     ij=Tvar[i];
     trgradg=matrix(1,9,1,npar);     Ndum[ij]++;
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));   }
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  
       ij=1;
     for(theta=1; theta <=npar; theta++){   for (i=1; i<= maxncov; i++) {
       for(i=1; i<=npar; i++)     if((Ndum[i]!=0) && (i<=ncovcol)){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);       Tvaraff[ij]=i; /*For printing */
             ij++;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);     }
       }
       k=0;   
       for(i=1; i<= (nlstate+ndeath); i++){   cptcoveff=ij-1; /*Number of simple covariates*/
         for(j=1; j<=(nlstate+ndeath);j++){  }
            k=k+1;  
           gp[k]=pmmij[i][j];  /*********** Health Expectancies ****************/
         }  
       }  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
   
       for(i=1; i<=npar; i++)  {
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    /* Health expectancies */
        int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     double age, agelim, hf;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    double ***p3mat,***varhe;
       k=0;    double **dnewm,**doldm;
       for(i=1; i<=(nlstate+ndeath); i++){    double *xp;
         for(j=1; j<=(nlstate+ndeath);j++){    double **gp, **gm;
           k=k+1;    double ***gradg, ***trgradg;
           gm[k]=pmmij[i][j];    int theta;
         }  
       }    varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
          xp=vector(1,npar);
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    dnewm=matrix(1,nlstate*2,1,npar);
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      doldm=matrix(1,nlstate*2,1,nlstate*2);
     }    
     fprintf(ficreseij,"# Health expectancies\n");
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    fprintf(ficreseij,"# Age");
       for(theta=1; theta <=npar; theta++)    for(i=1; i<=nlstate;i++)
       trgradg[j][theta]=gradg[theta][j];      for(j=1; j<=nlstate;j++)
          fprintf(ficreseij," %1d-%1d (SE)",i,j);
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    fprintf(ficreseij,"\n");
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);  
     if(estepm < stepm){
      pmij(pmmij,cov,ncovmodel,x,nlstate);      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
      k=0;    else  hstepm=estepm;   
      for(i=1; i<=(nlstate+ndeath); i++){    /* We compute the life expectancy from trapezoids spaced every estepm months
        for(j=1; j<=(nlstate+ndeath);j++){     * This is mainly to measure the difference between two models: for example
          k=k+1;     * if stepm=24 months pijx are given only every 2 years and by summing them
          gm[k]=pmmij[i][j];     * we are calculating an estimate of the Life Expectancy assuming a linear 
         }     * progression in between and thus overestimating or underestimating according
      }     * to the curvature of the survival function. If, for the same date, we 
           * estimate the model with stepm=1 month, we can keep estepm to 24 months
      /*printf("\n%d ",(int)age);     * to compare the new estimate of Life expectancy with the same linear 
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){     * hypothesis. A more precise result, taking into account a more precise
             * curvature will be obtained if estepm is as small as stepm. */
   
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    /* For example we decided to compute the life expectancy with the smallest unit */
      }*/    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
   fprintf(ficresprob,"\n%d ",(int)age);       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){       and note for a fixed period like estepm months */
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);       survival function given by stepm (the optimization length). Unfortunately it
   }       means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));       results. So we changed our mind and took the option of the best precision.
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    */
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
 }    agelim=AGESUP;
  free_vector(xp,1,npar);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 fclose(ficresprob);      /* nhstepm age range expressed in number of stepm */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); 
 }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
 /******************* Printing html file ***********/      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 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 optionfile[],char optionfilehtm[] ){      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   int jj1, k1, i1, cpt;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
   FILE *fichtm;      gp=matrix(0,nhstepm,1,nlstate*2);
   /*char optionfilehtm[FILENAMELENGTH];*/      gm=matrix(0,nhstepm,1,nlstate*2);
   
   strcpy(optionfilehtm,optionfile);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   strcat(optionfilehtm,".htm");         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
     printf("Problem with %s \n",optionfilehtm), exit(0);   
   }  
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">  
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>      /* Computing Variances of health expectancies */
   
 Total number of observations=%d <br>       for(theta=1; theta <=npar; theta++){
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>        for(i=1; i<=npar; i++){ 
 <hr  size=\"2\" color=\"#EC5E5E\">          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 <li>Outputs files<br><br>\n        }
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>    
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>        cptj=0;
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>        for(j=1; j<= nlstate; j++){
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>          for(i=1; i<=nlstate; i++){
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>            cptj=cptj+1;
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>            }
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>          }
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);        }
         
 fprintf(fichtm," <li>Graphs</li><p>");       
         for(i=1; i<=npar; i++) 
  m=cptcoveff;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         
  jj1=0;        cptj=0;
  for(k1=1; k1<=m;k1++){        for(j=1; j<= nlstate; j++){
    for(i1=1; i1<=ncodemax[k1];i1++){          for(i=1;i<=nlstate;i++){
        jj1++;            cptj=cptj+1;
        if (cptcovn > 0) {            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
          for (cpt=1; cpt<=cptcoveff;cpt++)            }
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);          }
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");        }
        }        for(j=1; j<= nlstate*2; j++)
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>          for(h=0; h<=nhstepm-1; h++){
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
        for(cpt=1; cpt<nlstate;cpt++){          }
          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);     
        }  /* End theta */
     for(cpt=1; cpt<=nlstate;cpt++) {  
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident       trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
 interval) in state (%d): v%s%d%d.gif <br>  
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);         for(h=0; h<=nhstepm-1; h++)
      }        for(j=1; j<=nlstate*2;j++)
      for(cpt=1; cpt<=nlstate;cpt++) {          for(theta=1; theta <=npar; theta++)
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>            trgradg[h][j][theta]=gradg[h][theta][j];
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);       
      }  
      fprintf(fichtm,"\n<br>- Total life expectancy by age and       for(i=1;i<=nlstate*2;i++)
 health expectancies in states (1) and (2): e%s%d.gif<br>        for(j=1;j<=nlstate*2;j++)
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          varhe[i][j][(int)age] =0.;
 fprintf(fichtm,"\n</body>");  
    }       printf("%d|",(int)age);fflush(stdout);
    }       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
 fclose(fichtm);       for(h=0;h<=nhstepm-1;h++){
 }        for(k=0;k<=nhstepm-1;k++){
           matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
 /******************* Gnuplot file **************/          matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemax, double fage , char pathc[], double p[]){          for(i=1;i<=nlstate*2;i++)
             for(j=1;j<=nlstate*2;j++)
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
   strcpy(optionfilegnuplot,optionfilefiname);      }
   strcat(optionfilegnuplot,".plt");      /* Computing expectancies */
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {      for(i=1; i<=nlstate;i++)
     printf("Problem with file %s",optionfilegnuplot);        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;
 #ifdef windows            
     fprintf(ficgp,"cd \"%s\" \n",pathc);  /* 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]);*/
 #endif  
 m=pow(2,cptcoveff);          }
    
  /* 1eme*/      fprintf(ficreseij,"%3.0f",age );
   for (cpt=1; cpt<= nlstate ; cpt ++) {      cptj=0;
    for (k1=1; k1<= m ; k1 ++) {      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
 #ifdef windows          cptj++;
     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",agemin,fage,fileres,k1-1,k1-1);          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
 #endif        }
 #ifdef unix      fprintf(ficreseij,"\n");
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);     
 #endif      free_matrix(gm,0,nhstepm,1,nlstate*2);
       free_matrix(gp,0,nhstepm,1,nlstate*2);
 for (i=1; i<= nlstate ; i ++) {      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 }    }
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    printf("\n");
     for (i=1; i<= nlstate ; i ++) {    fprintf(ficlog,"\n");
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    free_vector(xp,1,npar);
 }    free_matrix(dnewm,1,nlstate*2,1,npar);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    free_matrix(doldm,1,nlstate*2,1,nlstate*2);
      for (i=1; i<= nlstate ; i ++) {    free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  }
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }    /************ Variance ******************/
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));  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)
 #ifdef unix  {
 fprintf(ficgp,"\nset ter gif small size 400,300");    /* Variance of health expectancies */
 #endif    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    /* double **newm;*/
    }    double **dnewm,**doldm;
   }    double **dnewmp,**doldmp;
   /*2 eme*/    int i, j, nhstepm, hstepm, h, nstepm ;
     int k, cptcode;
   for (k1=1; k1<= m ; k1 ++) {    double *xp;
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);    double **gp, **gm;  /* for var eij */
        double ***gradg, ***trgradg; /*for var eij */
     for (i=1; i<= nlstate+1 ; i ++) {    double **gradgp, **trgradgp; /* for var p point j */
       k=2*i;    double *gpp, *gmp; /* for var p point j */
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
       for (j=1; j<= nlstate+1 ; j ++) {    double ***p3mat;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    double age,agelim, hf;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double ***mobaverage;
 }      int theta;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    char digit[4];
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    char digitp[25];
     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 ++) {    char fileresprobmorprev[FILENAMELENGTH];
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
         else fprintf(ficgp," \%%*lf (\%%*lf)");    if(popbased==1){
 }        if(mobilav!=0)
       fprintf(ficgp,"\" t\"\" w l 0,");        strcpy(digitp,"-populbased-mobilav-");
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      else strcpy(digitp,"-populbased-nomobil-");
       for (j=1; j<= nlstate+1 ; j ++) {    }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    else 
   else fprintf(ficgp," \%%*lf (\%%*lf)");      strcpy(digitp,"-stablbased-");
 }    
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    if (mobilav!=0) {
       else fprintf(ficgp,"\" t\"\" w l 0,");      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   }        printf(" Error in movingaverage mobilav=%d\n",mobilav);
        }
   /*3eme*/    }
   
   for (k1=1; k1<= m ; k1 ++) {    strcpy(fileresprobmorprev,"prmorprev"); 
     for (cpt=1; cpt<= nlstate ; cpt ++) {    sprintf(digit,"%-d",ij);
       k=2+nlstate*(cpt-1);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
       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",agemin,fage,fileres,k1-1,k1-1,k,cpt);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
       for (i=1; i< nlstate ; i ++) {    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
         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);    strcat(fileresprobmorprev,fileres);
       }    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
     }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }    }
      printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   /* CV preval stat */    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     for (k1=1; k1<= m ; k1 ++) {    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);
     for (cpt=1; cpt<nlstate ; cpt ++) {    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
       k=3;    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);      fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
       for (i=1; i< nlstate ; i ++)        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
         fprintf(ficgp,"+$%d",k+i+1);    }  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    fprintf(ficresprobmorprev,"\n");
          if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       l=3+(nlstate+ndeath)*cpt;      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
       for (i=1; i< nlstate ; i ++) {      exit(0);
         l=3+(nlstate+ndeath)*cpt;    }
         fprintf(ficgp,"+$%d",l+i+1);    else{
       }      fprintf(ficgp,"\n# Routine varevsij");
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      }
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
     }      printf("Problem with html file: %s\n", optionfilehtm);
   }        fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
        exit(0);
   /* proba elementaires */    }
    for(i=1,jk=1; i <=nlstate; i++){    else{
     for(k=1; k <=(nlstate+ndeath); k++){      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");
       if (k != i) {      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
         for(j=1; j <=ncovmodel; j++){    }
            varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);  
           jk++;    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,"\n");    fprintf(ficresvij,"# Age");
         }    for(i=1; i<=nlstate;i++)
       }      for(j=1; j<=nlstate;j++)
     }        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     }    fprintf(ficresvij,"\n");
   
     for(jk=1; jk <=m; jk++) {    xp=vector(1,npar);
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    dnewm=matrix(1,nlstate,1,npar);
    i=1;    doldm=matrix(1,nlstate,1,nlstate);
    for(k2=1; k2<=nlstate; k2++) {    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
      k3=i;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      for(k=1; k<=(nlstate+ndeath); k++) {  
        if (k != k2){    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    gpp=vector(nlstate+1,nlstate+ndeath);
 ij=1;    gmp=vector(nlstate+1,nlstate+ndeath);
         for(j=3; j <=ncovmodel; j++) {    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    if(estepm < stepm){
             ij++;      printf ("Problem %d lower than %d\n",estepm, stepm);
           }    }
           else    else  hstepm=estepm;   
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    /* For example we decided to compute the life expectancy with the smallest unit */
         }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           fprintf(ficgp,")/(1");       nhstepm is the number of hstepm from age to agelim 
               nstepm is the number of stepm from age to agelin. 
         for(k1=1; k1 <=nlstate; k1++){         Look at hpijx to understand the reason of that which relies in memory size
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);       and note for a fixed period like k years */
 ij=1;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           for(j=3; j <=ncovmodel; j++){       survival function given by stepm (the optimization length). Unfortunately it
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {       means that if the survival funtion is printed every two years of age and if
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
             ij++;       results. So we changed our mind and took the option of the best precision.
           }    */
           else    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    agelim = AGESUP;
           }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
           fprintf(ficgp,")");      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,") t \"p%d%d\" ", k2,k);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
         i=i+ncovmodel;      gp=matrix(0,nhstepm,1,nlstate);
        }      gm=matrix(0,nhstepm,1,nlstate);
      }  
    }  
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);      for(theta=1; theta <=npar; theta++){
    }        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
              xp[i] = x[i] + (i==theta ?delti[theta]:0);
   fclose(ficgp);        }
 }  /* end gnuplot */        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
 /*************** Moving average **************/        if (popbased==1) {
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){          if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
   int i, cpt, cptcod;              prlim[i][i]=probs[(int)age][i][ij];
     for (agedeb=agemin; agedeb<=fage; agedeb++)          }else{ /* mobilav */ 
       for (i=1; i<=nlstate;i++)            for(i=1; i<=nlstate;i++)
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)              prlim[i][i]=mobaverage[(int)age][i][ij];
           mobaverage[(int)agedeb][i][cptcod]=0.;          }
            }
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){    
       for (i=1; i<=nlstate;i++){        for(j=1; j<= nlstate; j++){
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          for(h=0; h<=nhstepm; h++){
           for (cpt=0;cpt<=4;cpt++){            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }          }
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;        }
         }        /* This for computing probability of death (h=1 means
       }           computed over hstepm matrices product = hstepm*stepm months) 
     }           as a weighted average of prlim.
            */
 }        for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
 /***********************************************/            gpp[j] += prlim[i][i]*p3mat[i][j][1];
 /**************** Main Program *****************/        }    
 /***********************************************/        /* end probability of death */
   
 int main(int argc, char *argv[])        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
 {          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   double agedeb, agefin,hf;   
   double agemin=1.e20, agemax=-1.e20;        if (popbased==1) {
           if(mobilav ==0){
   double fret;            for(i=1; i<=nlstate;i++)
   double **xi,tmp,delta;              prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
   double dum; /* Dummy variable */            for(i=1; i<=nlstate;i++)
   double ***p3mat;              prlim[i][i]=mobaverage[(int)age][i][ij];
   int *indx;          }
   char line[MAXLINE], linepar[MAXLINE];        }
   char title[MAXLINE];  
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];        for(j=1; j<= nlstate; j++){
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];          for(h=0; h<=nhstepm; h++){
              for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
   char filerest[FILENAMELENGTH];        }
   char fileregp[FILENAMELENGTH];        /* This for computing probability of death (h=1 means
   char popfile[FILENAMELENGTH];           computed over hstepm matrices product = hstepm*stepm months) 
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];           as a weighted average of prlim.
   int firstobs=1, lastobs=10;        */
   int sdeb, sfin; /* Status at beginning and end */        for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
   int c,  h , cpt,l;          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   int ju,jl, mi;           gmp[j] += prlim[i][i]*p3mat[i][j][1];
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;        }    
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;        /* end probability of death */
   int mobilav=0,popforecast=0;  
   int hstepm, nhstepm;        for(j=1; j<= nlstate; j++) /* vareij */
   int *popage;/*boolprev=0 if date and zero if wave*/          for(h=0; h<=nhstepm; h++){
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   double bage, fage, age, agelim, agebase;  
   double ftolpl=FTOL;        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   double **prlim;          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   double *severity;        }
   double ***param; /* Matrix of parameters */  
   double  *p;      } /* End theta */
   double **matcov; /* Matrix of covariance */  
   double ***delti3; /* Scale */      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   double *delti; /* Scale */  
   double ***eij, ***vareij;      for(h=0; h<=nhstepm; h++) /* veij */
   double **varpl; /* Variances of prevalence limits by age */        for(j=1; j<=nlstate;j++)
   double *epj, vepp;          for(theta=1; theta <=npar; theta++)
   double kk1, kk2;            trgradg[h][j][theta]=gradg[h][theta][j];
   double *popeffectif,*popcount;  
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   double yp,yp1,yp2;        for(theta=1; theta <=npar; theta++) {
           trgradgp[j][theta]=gradgp[theta][j];
   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";        }
   char *alph[]={"a","a","b","c","d","e"}, str[4];  
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
   char z[1]="c", occ;        for(j=1;j<=nlstate;j++)
 #include <sys/time.h>          vareij[i][j][(int)age] =0.;
 #include <time.h>  
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      for(h=0;h<=nhstepm;h++){
          for(k=0;k<=nhstepm;k++){
   /* long total_usecs;          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   struct timeval start_time, end_time;          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
            for(i=1;i<=nlstate;i++)
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */            for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
   printf("\n%s",version);      }
   if(argc <=1){  
     printf("\nEnter the parameter file name: ");      /* pptj */
     scanf("%s",pathtot);      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);
   else{   
     strcpy(pathtot,argv[1]);     for(j=nlstate+1;j<=nlstate+ndeath;j++)
   }       for(i=nlstate+1;i<=nlstate+ndeath;i++){
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/          varppt[j][i]=doldmp[j][i];
   /*cygwin_split_path(pathtot,path,optionfile);       }
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/  
   /* cutv(path,optionfile,pathtot,'\\');*/      /* end ppptj */
       /*  x centered again */
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   chdir(path);   
   replace(pathc,path);      if (popbased==1) {
         if(mobilav ==0){
 /*-------- arguments in the command line --------*/          for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
   strcpy(fileres,"r");        }else{ /* mobilav */ 
   strcat(fileres, optionfilefiname);          for(i=1; i<=nlstate;i++)
   strcat(fileres,".txt");    /* Other files have txt extension */            prlim[i][i]=mobaverage[(int)age][i][ij];
         }
   /*---------arguments file --------*/      }
       
   if((ficpar=fopen(optionfile,"r"))==NULL)    {      /* This for computing probability of death (h=1 means
     printf("Problem with optionfile %s\n",optionfile);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
     goto end;         as a weighted average of prlim.
   }      */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
   strcpy(filereso,"o");        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   strcat(filereso,fileres);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   if((ficparo=fopen(filereso,"w"))==NULL) {      }    
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      /* end probability of death */
   }  
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   /* Reads comments: lines beginning with '#' */      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   while((c=getc(ficpar))=='#' && c!= EOF){        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     ungetc(c,ficpar);        for(i=1; i<=nlstate;i++){
     fgets(line, MAXLINE, ficpar);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     puts(line);        }
     fputs(line,ficparo);      } 
   }      fprintf(ficresprobmorprev,"\n");
   ungetc(c,ficpar);  
       fprintf(ficresvij,"%.0f ",age );
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);      for(i=1; i<=nlstate;i++)
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);        for(j=1; j<=nlstate;j++){
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
 while((c=getc(ficpar))=='#' && c!= EOF){        }
     ungetc(c,ficpar);      fprintf(ficresvij,"\n");
     fgets(line, MAXLINE, ficpar);      free_matrix(gp,0,nhstepm,1,nlstate);
     puts(line);      free_matrix(gm,0,nhstepm,1,nlstate);
     fputs(line,ficparo);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   }      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
   ungetc(c,ficpar);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      } /* End age */
        free_vector(gpp,nlstate+1,nlstate+ndeath);
   covar=matrix(0,NCOVMAX,1,n);    free_vector(gmp,nlstate+1,nlstate+ndeath);
   cptcovn=0;    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
   ncovmodel=2+cptcovn;    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    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); */
   /* Read guess parameters */  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /* Reads comments: lines beginning with '#' */  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
     ungetc(c,ficpar);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
     fgets(line, MAXLINE, ficpar);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
     puts(line);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
     fputs(line,ficparo);    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", estepm,digitp,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);
   ungetc(c,ficpar);  */
      fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
     for(i=1; i <=nlstate; i++)    free_vector(xp,1,npar);
     for(j=1; j <=nlstate+ndeath-1; j++){    free_matrix(doldm,1,nlstate,1,nlstate);
       fscanf(ficpar,"%1d%1d",&i1,&j1);    free_matrix(dnewm,1,nlstate,1,npar);
       fprintf(ficparo,"%1d%1d",i1,j1);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       printf("%1d%1d",i,j);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
       for(k=1; k<=ncovmodel;k++){    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         fscanf(ficpar," %lf",&param[i][j][k]);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         printf(" %lf",param[i][j][k]);    fclose(ficresprobmorprev);
         fprintf(ficparo," %lf",param[i][j][k]);    fclose(ficgp);
       }    fclose(fichtm);
       fscanf(ficpar,"\n");  }
       printf("\n");  
       fprintf(ficparo,"\n");  /************ 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)
    {
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   p=param[1][1];    double **newm;
      double **dnewm,**doldm;
   /* Reads comments: lines beginning with '#' */    int i, j, nhstepm, hstepm;
   while((c=getc(ficpar))=='#' && c!= EOF){    int k, cptcode;
     ungetc(c,ficpar);    double *xp;
     fgets(line, MAXLINE, ficpar);    double *gp, *gm;
     puts(line);    double **gradg, **trgradg;
     fputs(line,ficparo);    double age,agelim;
   }    int theta;
   ungetc(c,ficpar);     
     fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    fprintf(ficresvpl,"# Age");
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    for(i=1; i<=nlstate;i++)
   for(i=1; i <=nlstate; i++){        fprintf(ficresvpl," %1d-%1d",i,i);
     for(j=1; j <=nlstate+ndeath-1; j++){    fprintf(ficresvpl,"\n");
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       printf("%1d%1d",i,j);    xp=vector(1,npar);
       fprintf(ficparo,"%1d%1d",i1,j1);    dnewm=matrix(1,nlstate,1,npar);
       for(k=1; k<=ncovmodel;k++){    doldm=matrix(1,nlstate,1,nlstate);
         fscanf(ficpar,"%le",&delti3[i][j][k]);    
         printf(" %le",delti3[i][j][k]);    hstepm=1*YEARM; /* Every year of age */
         fprintf(ficparo," %le",delti3[i][j][k]);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
       }    agelim = AGESUP;
       fscanf(ficpar,"\n");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       printf("\n");      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       fprintf(ficparo,"\n");      if (stepm >= YEARM) hstepm=1;
     }      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   }      gradg=matrix(1,npar,1,nlstate);
   delti=delti3[1][1];      gp=vector(1,nlstate);
        gm=vector(1,nlstate);
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){      for(theta=1; theta <=npar; theta++){
     ungetc(c,ficpar);        for(i=1; i<=npar; i++){ /* Computes gradient */
     fgets(line, MAXLINE, ficpar);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     puts(line);        }
     fputs(line,ficparo);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   }        for(i=1;i<=nlstate;i++)
   ungetc(c,ficpar);          gp[i] = prlim[i][i];
        
   matcov=matrix(1,npar,1,npar);        for(i=1; i<=npar; i++) /* Computes gradient */
   for(i=1; i <=npar; i++){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     fscanf(ficpar,"%s",&str);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     printf("%s",str);        for(i=1;i<=nlstate;i++)
     fprintf(ficparo,"%s",str);          gm[i] = prlim[i][i];
     for(j=1; j <=i; j++){  
       fscanf(ficpar," %le",&matcov[i][j]);        for(i=1;i<=nlstate;i++)
       printf(" %.5le",matcov[i][j]);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       fprintf(ficparo," %.5le",matcov[i][j]);      } /* End theta */
     }  
     fscanf(ficpar,"\n");      trgradg =matrix(1,nlstate,1,npar);
     printf("\n");  
     fprintf(ficparo,"\n");      for(j=1; j<=nlstate;j++)
   }        for(theta=1; theta <=npar; theta++)
   for(i=1; i <=npar; i++)          trgradg[j][theta]=gradg[theta][j];
     for(j=i+1;j<=npar;j++)  
       matcov[i][j]=matcov[j][i];      for(i=1;i<=nlstate;i++)
            varpl[i][(int)age] =0.;
   printf("\n");      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
     /*-------- data file ----------*/        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
     if((ficres =fopen(fileres,"w"))==NULL) {  
       printf("Problem with resultfile: %s\n", fileres);goto end;      fprintf(ficresvpl,"%.0f ",age );
     }      for(i=1; i<=nlstate;i++)
     fprintf(ficres,"#%s\n",version);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
          fprintf(ficresvpl,"\n");
     if((fic=fopen(datafile,"r"))==NULL)    {      free_vector(gp,1,nlstate);
       printf("Problem with datafile: %s\n", datafile);goto end;      free_vector(gm,1,nlstate);
     }      free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     n= lastobs;    } /* End age */
     severity = vector(1,maxwav);  
     outcome=imatrix(1,maxwav+1,1,n);    free_vector(xp,1,npar);
     num=ivector(1,n);    free_matrix(doldm,1,nlstate,1,npar);
     moisnais=vector(1,n);    free_matrix(dnewm,1,nlstate,1,nlstate);
     annais=vector(1,n);  
     moisdc=vector(1,n);  }
     andc=vector(1,n);  
     agedc=vector(1,n);  /************ Variance of one-step probabilities  ******************/
     cod=ivector(1,n);  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
     weight=vector(1,n);  {
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    int i, j=0,  i1, k1, l1, t, tj;
     mint=matrix(1,maxwav,1,n);    int k2, l2, j1,  z1;
     anint=matrix(1,maxwav,1,n);    int k=0,l, cptcode;
     s=imatrix(1,maxwav+1,1,n);    int first=1, first1;
     adl=imatrix(1,maxwav+1,1,n);        double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     tab=ivector(1,NCOVMAX);    double **dnewm,**doldm;
     ncodemax=ivector(1,8);    double *xp;
     double *gp, *gm;
     i=1;    double **gradg, **trgradg;
     while (fgets(line, MAXLINE, fic) != NULL)    {    double **mu;
       if ((i >= firstobs) && (i <=lastobs)) {    double age,agelim, cov[NCOVMAX];
            double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
         for (j=maxwav;j>=1;j--){    int theta;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    char fileresprob[FILENAMELENGTH];
           strcpy(line,stra);    char fileresprobcov[FILENAMELENGTH];
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    char fileresprobcor[FILENAMELENGTH];
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }    double ***varpij;
          
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    strcpy(fileresprob,"prob"); 
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);      printf("Problem with resultfile: %s\n", fileresprob);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    strcpy(fileresprobcov,"probcov"); 
         for (j=ncov;j>=1;j--){    strcat(fileresprobcov,fileres);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
         }      printf("Problem with resultfile: %s\n", fileresprobcov);
         num[i]=atol(stra);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
            }
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    strcpy(fileresprobcor,"probcor"); 
           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;}*/    strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
         i=i+1;      printf("Problem with resultfile: %s\n", fileresprobcor);
       }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }    }
     /* printf("ii=%d", ij);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
        scanf("%d",i);*/    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   imx=i-1; /* Number of individuals */    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   /* for (i=1; i<=imx; i++){    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     }    fprintf(ficresprob,"# Age");
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     for (i=1; i<=imx; i++)    fprintf(ficresprobcov,"# Age");
     if (covar[1][i]==0) 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]));*/    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcov,"# Age");
   /* Calculation of the number of parameter from char model*/  
   Tvar=ivector(1,15);  
   Tprod=ivector(1,15);    for(i=1; i<=nlstate;i++)
   Tvaraff=ivector(1,15);      for(j=1; j<=(nlstate+ndeath);j++){
   Tvard=imatrix(1,15,1,2);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   Tage=ivector(1,15);              fprintf(ficresprobcov," p%1d-%1d ",i,j);
            fprintf(ficresprobcor," p%1d-%1d ",i,j);
   if (strlen(model) >1){      }  
     j=0, j1=0, k1=1, k2=1;    fprintf(ficresprob,"\n");
     j=nbocc(model,'+');    fprintf(ficresprobcov,"\n");
     j1=nbocc(model,'*');    fprintf(ficresprobcor,"\n");
     cptcovn=j+1;    xp=vector(1,npar);
     cptcovprod=j1;    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
        doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
        mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     strcpy(modelsav,model);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    first=1;
       printf("Error. Non available option model=%s ",model);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       goto end;      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
     }      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
          exit(0);
     for(i=(j+1); i>=1;i--){    }
       cutv(stra,strb,modelsav,'+');    else{
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);      fprintf(ficgp,"\n# Routine varprob");
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    }
       /*scanf("%d",i);*/    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
       if (strchr(strb,'*')) {      printf("Problem with html file: %s\n", optionfilehtm);
         cutv(strd,strc,strb,'*');      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
         if (strcmp(strc,"age")==0) {      exit(0);
           cptcovprod--;    }
           cutv(strb,stre,strd,'V');    else{
           Tvar[i]=atoi(stre);      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
           cptcovage++;      fprintf(fichtm,"\n");
             Tage[cptcovage]=i;  
             /*printf("stre=%s ", stre);*/      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");
         else if (strcmp(strd,"age")==0) {      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");
           cptcovprod--;  
           cutv(strb,stre,strc,'V');    }
           Tvar[i]=atoi(stre);  
           cptcovage++;    cov[1]=1;
           Tage[cptcovage]=i;    tj=cptcoveff;
         }    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
         else {    j1=0;
           cutv(strb,stre,strc,'V');    for(t=1; t<=tj;t++){
           Tvar[i]=ncov+k1;      for(i1=1; i1<=ncodemax[t];i1++){ 
           cutv(strb,strc,strd,'V');        j1++;
           Tprod[k1]=i;        if  (cptcovn>0) {
           Tvard[k1][1]=atoi(strc);          fprintf(ficresprob, "\n#********** Variable "); 
           Tvard[k1][2]=atoi(stre);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           Tvar[cptcovn+k2]=Tvard[k1][1];          fprintf(ficresprob, "**********\n#");
           Tvar[cptcovn+k2+1]=Tvard[k1][2];          fprintf(ficresprobcov, "\n#********** Variable "); 
           for (k=1; k<=lastobs;k++)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];          fprintf(ficresprobcov, "**********\n#");
           k1++;          
           k2=k2+2;          fprintf(ficgp, "\n#********** Variable "); 
         }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       }          fprintf(ficgp, "**********\n#");
       else {          
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/          
        /*  scanf("%d",i);*/          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
       cutv(strd,strc,strb,'V');          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       Tvar[i]=atoi(strc);          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
       }          
       strcpy(modelsav,stra);            fprintf(ficresprobcor, "\n#********** Variable ");    
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         scanf("%d",i);*/          fprintf(ficgp, "**********\n#");    
     }        }
 }        
          for (age=bage; age<=fage; age ++){ 
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);          cov[2]=age;
   printf("cptcovprod=%d ", cptcovprod);          for (k=1; k<=cptcovn;k++) {
   scanf("%d ",i);*/            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     fclose(fic);          }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     /*  if(mle==1){*/          for (k=1; k<=cptcovprod;k++)
     if (weightopt != 1) { /* Maximisation without weights*/            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       for(i=1;i<=n;i++) weight[i]=1.0;          
     }          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
     /*-calculation of age at interview from date of interview and age at death -*/          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     agev=matrix(1,maxwav,1,imx);          gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
    for (i=1; i<=imx; i++)      
      for(m=2; (m<= maxwav); m++)          for(theta=1; theta <=npar; theta++){
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){            for(i=1; i<=npar; i++)
          anint[m][i]=9999;              xp[i] = x[i] + (i==theta ?delti[theta]:0);
          s[m][i]=-1;            
        }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
                
     for (i=1; i<=imx; i++)  {            k=0;
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);            for(i=1; i<= (nlstate); i++){
       for(m=1; (m<= maxwav); m++){              for(j=1; j<=(nlstate+ndeath);j++){
         if(s[m][i] >0){                k=k+1;
           if (s[m][i] == nlstate+1) {                gp[k]=pmmij[i][j];
             if(agedc[i]>0)              }
               if(moisdc[i]!=99 && andc[i]!=9999)            }
               agev[m][i]=agedc[i];            
             else {            for(i=1; i<=npar; i++)
               if (andc[i]!=9999){              xp[i] = x[i] - (i==theta ?delti[theta]:0);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);      
               agev[m][i]=-1;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
               }            k=0;
             }            for(i=1; i<=(nlstate); i++){
           }              for(j=1; j<=(nlstate+ndeath);j++){
           else if(s[m][i] !=9){ /* Should no more exist */                k=k+1;
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);                gm[k]=pmmij[i][j];
             if(mint[m][i]==99 || anint[m][i]==9999)              }
               agev[m][i]=1;            }
             else if(agev[m][i] <agemin){       
               agemin=agev[m][i];            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/              gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
             }          }
             else if(agev[m][i] >agemax){  
               agemax=agev[m][i];          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/            for(theta=1; theta <=npar; theta++)
             }              trgradg[j][theta]=gradg[theta][j];
             /*agev[m][i]=anint[m][i]-annais[i];*/          
             /*   agev[m][i] = age[i]+2*m;*/          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           }          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           else { /* =9 */          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
             agev[m][i]=1;          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
             s[m][i]=-1;          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           }          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         }  
         else /*= 0 Unknown */          pmij(pmmij,cov,ncovmodel,x,nlstate);
           agev[m][i]=1;          
       }          k=0;
              for(i=1; i<=(nlstate); i++){
     }            for(j=1; j<=(nlstate+ndeath);j++){
     for (i=1; i<=imx; i++)  {              k=k+1;
       for(m=1; (m<= maxwav); m++){              mu[k][(int) age]=pmmij[i][j];
         if (s[m][i] > (nlstate+ndeath)) {            }
           printf("Error: Wrong value in nlstate or ndeath\n");            }
           goto end;          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
         }            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
       }              varpij[i][j][(int)age] = doldm[i][j];
     }  
           /*printf("\n%d ",(int)age);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);            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]));
     free_vector(severity,1,maxwav);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     free_imatrix(outcome,1,maxwav+1,1,n);            }*/
     free_vector(moisnais,1,n);  
     free_vector(annais,1,n);          fprintf(ficresprob,"\n%d ",(int)age);
     /* free_matrix(mint,1,maxwav,1,n);          fprintf(ficresprobcov,"\n%d ",(int)age);
        free_matrix(anint,1,maxwav,1,n);*/          fprintf(ficresprobcor,"\n%d ",(int)age);
     free_vector(moisdc,1,n);  
     free_vector(andc,1,n);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
              for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     wav=ivector(1,imx);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          }
              i=0;
     /* Concatenates waves */          for (k=1; k<=(nlstate);k++){
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);            for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
       Tcode=ivector(1,100);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);              for (j=1; j<=i;j++){
       ncodemax[1]=1;                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
                    }
    codtab=imatrix(1,100,1,10);            }
    h=0;          }/* end of loop for state */
    m=pow(2,cptcoveff);        } /* end of loop for age */
    
    for(k=1;k<=cptcoveff; k++){        /* Confidence intervalle of pij  */
      for(i=1; i <=(m/pow(2,k));i++){        /*
        for(j=1; j <= ncodemax[k]; j++){          fprintf(ficgp,"\nset noparametric;unset label");
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
            h++;          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
            if (h>m) h=1;codtab[h][k]=j;          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);
          }          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
        }          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
      }          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
    }        */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
    /*for(i=1; i <=m ;i++){        first1=1;
      for(k=1; k <=cptcovn; k++){        for (k2=1; k2<=(nlstate);k2++){
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
      }            if(l2==k2) continue;
      printf("\n");            j=(k2-1)*(nlstate+ndeath)+l2;
    }            for (k1=1; k1<=(nlstate);k1++){
    scanf("%d",i);*/              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                    if(l1==k1) continue;
    /* Calculates basic frequencies. Computes observed prevalence at single age                i=(k1-1)*(nlstate+ndeath)+l1;
        and prints on file fileres'p'. */                if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                      if ((int)age %5==0){
                        v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    mu1=mu[i][(int) age]/stepm*YEARM ;
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    mu2=mu[j][(int) age]/stepm*YEARM;
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */                    c12=cv12/sqrt(v1*v2);
                          /* Computing eigen value of matrix of covariance */
     /* For Powell, parameters are in a vector p[] starting at p[1]                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */                    /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
     if(mle==1){                    /*v21=sqrt(1.-v11*v11); *//* error */
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);                    v21=(lc1-v1)/cv12*v11;
     }                    v12=-v21;
                        v22=v11;
     /*--------- results files --------------*/                    tnalp=v21/v11;
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);                    if(first1==1){
                        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);
    jk=1;                    }
    fprintf(ficres,"# Parameters\n");                    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("# Parameters\n");                    /*printf(fignu*/
    for(i=1,jk=1; i <=nlstate; i++){                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
      for(k=1; k <=(nlstate+ndeath); k++){                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
        if (k != i)                    if(first==1){
          {                      first=0;
            printf("%d%d ",i,k);                      fprintf(ficgp,"\nset parametric;unset label");
            fprintf(ficres,"%1d%1d ",i,k);                      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);
            for(j=1; j <=ncovmodel; j++){                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
              printf("%f ",p[jk]);                      fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
              fprintf(ficres,"%f ",p[jk]);                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
              jk++;                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
            }                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
            printf("\n");                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
            fprintf(ficres,"\n");                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
          }                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
      }                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
    }                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
  if(mle==1){                    }else{
     /* Computing hessian and covariance matrix */                      first=0;
     ftolhess=ftol; /* Usually correct */                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
     hesscov(matcov, p, npar, delti, ftolhess, func);                      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);
     fprintf(ficres,"# Scales\n");                      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",\
     printf("# Scales\n");                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
      for(i=1,jk=1; i <=nlstate; i++){                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
       for(j=1; j <=nlstate+ndeath; j++){                    }/* if first */
         if (j!=i) {                  } /* age mod 5 */
           fprintf(ficres,"%1d%1d",i,j);                } /* end loop age */
           printf("%1d%1d",i,j);                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
           for(k=1; k<=ncovmodel;k++){                first=1;
             printf(" %.5e",delti[jk]);              } /*l12 */
             fprintf(ficres," %.5e",delti[jk]);            } /* k12 */
             jk++;          } /*l1 */
           }        }/* k1 */
           printf("\n");      } /* loop covariates */
           fprintf(ficres,"\n");    }
         }    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
       }    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
      }    free_vector(xp,1,npar);
        fclose(ficresprob);
     k=1;    fclose(ficresprobcov);
     fprintf(ficres,"# Covariance\n");    fclose(ficresprobcor);
     printf("# Covariance\n");    fclose(ficgp);
     for(i=1;i<=npar;i++){    fclose(fichtm);
       /*  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]);*/  /******************* Printing html file ***********/
       fprintf(ficres,"%3d",i);  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
       printf("%3d",i);                    int lastpass, int stepm, int weightopt, char model[],\
       for(j=1; j<=i;j++){                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
         fprintf(ficres," %.5e",matcov[i][j]);                    int popforecast, int estepm ,\
         printf(" %.5e",matcov[i][j]);                    double jprev1, double mprev1,double anprev1, \
       }                    double jprev2, double mprev2,double anprev2){
       fprintf(ficres,"\n");    int jj1, k1, i1, cpt;
       printf("\n");    /*char optionfilehtm[FILENAMELENGTH];*/
       k++;    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
     }      printf("Problem with %s \n",optionfilehtm), exit(0);
          fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
     while((c=getc(ficpar))=='#' && c!= EOF){    }
       ungetc(c,ficpar);  
       fgets(line, MAXLINE, ficpar);     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
       puts(line);   - 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
       fputs(line,ficparo);   - 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
     ungetc(c,ficpar);   - Life expectancies by age and initial health status (estepm=%2d months): 
       <a href=\"e%s\">e%s</a> <br>\n</li>", \
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
      
     if (fage <= 2) {  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
       bage = agemin;  
       fage = agemax;   m=cptcoveff;
     }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");   jj1=0;
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);   for(k1=1; k1<=m;k1++){
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);     for(i1=1; i1<=ncodemax[k1];i1++){
         jj1++;
     while((c=getc(ficpar))=='#' && c!= EOF){       if (cptcovn > 0) {
     ungetc(c,ficpar);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     fgets(line, MAXLINE, ficpar);         for (cpt=1; cpt<=cptcoveff;cpt++) 
     puts(line);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     fputs(line,ficparo);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   }       }
   ungetc(c,ficpar);       /* 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>
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);       /* Quasi-incidences */
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
        <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
   while((c=getc(ficpar))=='#' && c!= EOF){         /* Stable prevalence in each health state */
     ungetc(c,ficpar);         for(cpt=1; cpt<nlstate;cpt++){
     fgets(line, MAXLINE, ficpar);           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
     puts(line);  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
     fputs(line,ficparo);         }
   }       for(cpt=1; cpt<=nlstate;cpt++) {
   ungetc(c,ficpar);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
    <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
        }
    dateprev1=anprev1+mprev1/12.+jprev1/365.;       fprintf(fichtm,"\n<br>- Total life expectancy by age and
    dateprev2=anprev2+mprev2/12.+jprev2/365.;  health expectancies in states (1) and (2): e%s%d.png<br>
   <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
   fscanf(ficpar,"pop_based=%d\n",&popbased);     } /* end i1 */
    fprintf(ficparo,"pop_based=%d\n",popbased);     }/* End k1 */
    fprintf(ficres,"pop_based=%d\n",popbased);     fprintf(fichtm,"</ul>");
   
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
     fgets(line, MAXLINE, ficpar);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
     puts(line);   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
     fputs(line,ficparo);   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
   }   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
   ungetc(c,ficpar);   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);   - 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);
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);  
    if(popforecast==1) fprintf(fichtm,"\n
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);   - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
    - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
 /*------------ gnuplot -------------*/          <br>",fileres,fileres,fileres,fileres);
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemax,fage, pathc,p);   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);
 /*------------ free_vector  -------------*/  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
  chdir(path);  
     m=cptcoveff;
  free_ivector(wav,1,imx);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);     jj1=0;
  free_ivector(num,1,n);   for(k1=1; k1<=m;k1++){
  free_vector(agedc,1,n);     for(i1=1; i1<=ncodemax[k1];i1++){
  /*free_matrix(covar,1,NCOVMAX,1,n);*/       jj1++;
  fclose(ficparo);       if (cptcovn > 0) {
  fclose(ficres);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
           for (cpt=1; cpt<=cptcoveff;cpt++) 
   /* Reads comments: lines beginning with '#' */           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   while((c=getc(ficpar))=='#' && c!= EOF){         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     ungetc(c,ficpar);       }
     fgets(line, MAXLINE, ficpar);       for(cpt=1; cpt<=nlstate;cpt++) {
     puts(line);         fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
     fputs(line,ficparo);  interval) in state (%d): v%s%d%d.png <br>
   }  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
   ungetc(c,ficpar);       }
       } /* end i1 */
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);   }/* End k1 */
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);   fprintf(fichtm,"</ul>");
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);  fclose(fichtm);
 /*--------- index.htm --------*/  }
   
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm);  /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
    
   /*--------------- Prevalence limit --------------*/    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
      int ng;
   strcpy(filerespl,"pl");    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   strcat(filerespl,fileres);      printf("Problem with file %s",optionfilegnuplot);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    }
   }  
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    /*#ifdef windows */
   fprintf(ficrespl,"#Prevalence limit\n");      fprintf(ficgp,"cd \"%s\" \n",pathc);
   fprintf(ficrespl,"#Age ");      /*#endif */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  m=pow(2,cptcoveff);
   fprintf(ficrespl,"\n");    
     /* 1eme*/
   prlim=matrix(1,nlstate,1,nlstate);    for (cpt=1; cpt<= nlstate ; cpt ++) {
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */     for (k1=1; k1<= m ; k1 ++) {
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       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);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */       for (i=1; i<= nlstate ; i ++) {
   k=0;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   agebase=agemin;         else fprintf(ficgp," \%%*lf (\%%*lf)");
   agelim=agemax;       }
   ftolpl=1.e-10;       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
   i1=cptcoveff;       for (i=1; i<= nlstate ; i ++) {
   if (cptcovn < 1){i1=1;}         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
   for(cptcov=1;cptcov<=i1;cptcov++){       } 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); 
         k=k+1;       for (i=1; i<= nlstate ; i ++) {
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         fprintf(ficrespl,"\n#******");         else fprintf(ficgp," \%%*lf (\%%*lf)");
         for(j=1;j<=cptcoveff;j++)       }  
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
         fprintf(ficrespl,"******\n");     }
            }
         for (age=agebase; age<=agelim; age++){    /*2 eme*/
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    
           fprintf(ficrespl,"%.0f",age );    for (k1=1; k1<= m ; k1 ++) { 
           for(i=1; i<=nlstate;i++)      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
           fprintf(ficrespl," %.5f", prlim[i][i]);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
           fprintf(ficrespl,"\n");      
         }      for (i=1; i<= nlstate+1 ; i ++) {
       }        k=2*i;
     }        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
   fclose(ficrespl);        for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   /*------------- h Pij x at various ages ------------*/          else fprintf(ficgp," \%%*lf (\%%*lf)");
          }   
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
   if((ficrespij=fopen(filerespij,"w"))==NULL) {        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;        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 ++) {
   printf("Computing pij: result on file '%s' \n", filerespij);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
            else fprintf(ficgp," \%%*lf (\%%*lf)");
   stepsize=(int) (stepm+YEARM-1)/YEARM;        }   
   /*if (stepm<=24) stepsize=2;*/        fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
   agelim=AGESUP;        for (j=1; j<= nlstate+1 ; j ++) {
   hstepm=stepsize*YEARM; /* Every year of age */          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          else fprintf(ficgp," \%%*lf (\%%*lf)");
          }   
   k=0;        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
   for(cptcov=1;cptcov<=i1;cptcov++){        else fprintf(ficgp,"\" t\"\" w l 0,");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      }
       k=k+1;    }
         fprintf(ficrespij,"\n#****** ");    
         for(j=1;j<=cptcoveff;j++)    /*3eme*/
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    
         fprintf(ficrespij,"******\n");    for (k1=1; k1<= m ; k1 ++) { 
              for (cpt=1; cpt<= nlstate ; cpt ++) {
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */        k=2+nlstate*(2*cpt-2);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           oldm=oldms;savm=savms;          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficrespij,"# Age");          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for(i=1; i<=nlstate;i++)          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
             for(j=1; j<=nlstate+ndeath;j++)          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
               fprintf(ficrespij," %1d-%1d",i,j);          
           fprintf(ficrespij,"\n");        */
           for (h=0; h<=nhstepm; h++){        for (i=1; i< nlstate ; i ++) {
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );          fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
             for(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);    /* CV preval stat */
           fprintf(ficrespij,"\n");    for (k1=1; k1<= m ; k1 ++) { 
         }      for (cpt=1; cpt<nlstate ; cpt ++) {
     }        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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/        
         for (i=1; i< nlstate ; i ++)
   fclose(ficrespij);          fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
   if(stepm == 1) {        
   /*---------- Forecasting ------------------*/        l=3+(nlstate+ndeath)*cpt;
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
            l=3+(nlstate+ndeath)*cpt;
            fprintf(ficgp,"+$%d",l+i+1);
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
        } 
   strcpy(fileresf,"f");    }  
   strcat(fileresf,fileres);    
   if((ficresf=fopen(fileresf,"w"))==NULL) {    /* proba elementaires */
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;    for(i=1,jk=1; i <=nlstate; i++){
   }      for(k=1; k <=(nlstate+ndeath); k++){
   printf("Computing forecasting: result on file '%s' \n", fileresf);        if (k != i) {
            for(j=1; j <=ncovmodel; j++){
   free_matrix(mint,1,maxwav,1,n);            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
   free_matrix(anint,1,maxwav,1,n);            jk++; 
             fprintf(ficgp,"\n");
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          }
         }
   if (mobilav==1) {      }
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     }
     movingaverage(agedeb, fage, agemin, mobaverage);  
   }     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
   stepsize=(int) (stepm+YEARM-1)/YEARM;         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
   if (stepm<=12) stepsize=1;         if (ng==2)
             fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
   agelim=AGESUP;         else
             fprintf(ficgp,"\nset title \"Probability\"\n");
   hstepm=1;         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
   hstepm=hstepm/stepm;         i=1;
   yp1=modf(dateintmean,&yp);         for(k2=1; k2<=nlstate; k2++) {
   anprojmean=yp;           k3=i;
   yp2=modf((yp1*12),&yp);           for(k=1; k<=(nlstate+ndeath); k++) {
   mprojmean=yp;             if (k != k2){
   yp1=modf((yp2*30.5),&yp);               if(ng==2)
   jprojmean=yp;                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
   if(jprojmean==0) jprojmean=1;               else
   if(mprojmean==0) jprojmean=1;                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                 ij=1;
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);               for(j=3; j <=ncovmodel; j++) {
                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   if (popforecast==1) {                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
     if((ficpop=fopen(popfile,"r"))==NULL)    {                   ij++;
       printf("Problem with population file : %s\n",popfile);goto end;                 }
     }                 else
     popage=ivector(0,AGESUP);                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
     popeffectif=vector(0,AGESUP);               }
     popcount=vector(0,AGESUP);               fprintf(ficgp,")/(1");
                   
     i=1;                 for(k1=1; k1 <=nlstate; k1++){   
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
       {                 ij=1;
         i=i+1;                 for(j=3; j <=ncovmodel; j++){
       }                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
     imx=i;                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                         ij++;
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];                   }
   }                   else
                       fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   for(cptcov=1;cptcov<=i1;cptcov++){                 }
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                 fprintf(ficgp,")");
       k=k+1;               }
       fprintf(ficresf,"\n#******");               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
       for(j=1;j<=cptcoveff;j++) {               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);               i=i+ncovmodel;
       }             }
       fprintf(ficresf,"******\n");           } /* end k */
       fprintf(ficresf,"# StartingAge FinalAge");         } /* end k2 */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);       } /* end jk */
       if (popforecast==1)  fprintf(ficresf," [Population]");     } /* end ng */
           fclose(ficgp); 
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {  }  /* end gnuplot */
         fprintf(ficresf,"\n");  
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);    
          /*************** Moving average **************/
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;    int i, cpt, cptcod;
              int modcovmax =1;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int mobilavrange, mob;
           oldm=oldms;savm=savms;    double age;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
            modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
           for (h=0; h<=nhstepm; h++){                             a covariate has 2 modalities */
             if (h==(int) (calagedate+YEARM*cpt)) {    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);  
             }    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
             for(j=1; j<=nlstate+ndeath;j++) {      if(mobilav==1) mobilavrange=5; /* default */
               kk1=0.;kk2=0;      else mobilavrange=mobilav;
               for(i=1; i<=nlstate;i++) {                    for (age=bage; age<=fage; age++)
                 if (mobilav==1)        for (i=1; i<=nlstate;i++)
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          for (cptcod=1;cptcod<=modcovmax;cptcod++)
                 else {            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      /* We keep the original values on the extreme ages bage, fage and for 
                 }         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
                 if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];         we use a 5 terms etc. until the borders are no more concerned. 
               }      */ 
               if (h==(int)(calagedate+12*cpt)){      for (mob=3;mob <=mobilavrange;mob=mob+2){
                 fprintf(ficresf," %.3f", kk1);        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
                        for (i=1; i<=nlstate;i++){
                 if (popforecast==1) fprintf(ficresf," [%.f]", kk2);            for (cptcod=1;cptcod<=modcovmax;cptcod++){
               }              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];
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
         }                }
       }              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
     }            }
   }          }
                }/* end age */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      }/* end mob */
     }else return -1;
   if (popforecast==1) {    return 0;
     free_ivector(popage,0,AGESUP);  }/* End movingaverage */
     free_vector(popeffectif,0,AGESUP);  
     free_vector(popcount,0,AGESUP);  
   }  /************** 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){
   free_imatrix(s,1,maxwav+1,1,n);    
   free_vector(weight,1,n);    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
   fclose(ficresf);    int *popage;
   }    double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
   /* End forecasting */    double ***p3mat;
   else{    double ***mobaverage;
     erreur=108;    char fileresf[FILENAMELENGTH];
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);  
   }   agelim=AGESUP;
     calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
    
   /*---------- Health expectancies and variances ------------*/    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
    
   strcpy(filerest,"t");   
   strcat(filerest,fileres);    strcpy(fileresf,"f"); 
   if((ficrest=fopen(filerest,"w"))==NULL) {    strcat(fileresf,fileres);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    if((ficresf=fopen(fileresf,"w"))==NULL) {
   }      printf("Problem with forecast resultfile: %s\n", fileresf);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
   strcpy(filerese,"e");    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   strcat(filerese,fileres);  
   if((ficreseij=fopen(filerese,"w"))==NULL) {    if (cptcoveff==0) ncodemax[cptcoveff]=1;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  
   }    if (mobilav!=0) {
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
  strcpy(fileresv,"v");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   strcat(fileresv,fileres);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {      }
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    }
   }  
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
   k=0;    
   for(cptcov=1;cptcov<=i1;cptcov++){    agelim=AGESUP;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    
       k=k+1;    hstepm=1;
       fprintf(ficrest,"\n#****** ");    hstepm=hstepm/stepm; 
       for(j=1;j<=cptcoveff;j++)    yp1=modf(dateintmean,&yp);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    anprojmean=yp;
       fprintf(ficrest,"******\n");    yp2=modf((yp1*12),&yp);
     mprojmean=yp;
       fprintf(ficreseij,"\n#****** ");    yp1=modf((yp2*30.5),&yp);
       for(j=1;j<=cptcoveff;j++)    jprojmean=yp;
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    if(jprojmean==0) jprojmean=1;
       fprintf(ficreseij,"******\n");    if(mprojmean==0) jprojmean=1;
     
       fprintf(ficresvij,"\n#****** ");    fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean); 
       for(j=1;j<=cptcoveff;j++)    
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    for(cptcov=1;cptcov<=i2;cptcov++){
       fprintf(ficresvij,"******\n");      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        fprintf(ficresf,"\n#******");
       oldm=oldms;savm=savms;        for(j=1;j<=cptcoveff;j++) {
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);            fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        }
       oldm=oldms;savm=savms;        fprintf(ficresf,"******\n");
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        fprintf(ficresf,"# StartingAge FinalAge");
            for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
         
          
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");        for (cpt=0; cpt<=(anproj2-anproj1);cpt++) { 
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);          fprintf(ficresf,"\n");
       fprintf(ficrest,"\n");          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);   
   
       hf=1;          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
       if (stepm >= YEARM) hf=stepm/YEARM;            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
       epj=vector(1,nlstate+1);            nhstepm = nhstepm/hstepm; 
       for(age=bage; age <=fage ;age++){            
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         if (popbased==1) {            oldm=oldms;savm=savms;
           for(i=1; i<=nlstate;i++)            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             prlim[i][i]=probs[(int)age][i][k];          
         }            for (h=0; h<=nhstepm; h++){
                      if (h==(int) (calagedate+YEARM*cpt)) {
         fprintf(ficrest," %.0f",age);                fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){              } 
           for(i=1, epj[j]=0.;i <=nlstate;i++) {              for(j=1; j<=nlstate+ndeath;j++) {
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];                kk1=0.;kk2=0;
           }                for(i=1; i<=nlstate;i++) {              
           epj[nlstate+1] +=epj[j];                  if (mobilav==1) 
         }                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
         for(i=1, vepp=0.;i <=nlstate;i++)                  else {
           for(j=1;j <=nlstate;j++)                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
             vepp += vareij[i][j][(int)age];                  }
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));                  
         for(j=1;j <=nlstate;j++){                }
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));                if (h==(int)(calagedate+12*cpt)){
         }                  fprintf(ficresf," %.3f", kk1);
         fprintf(ficrest,"\n");                          
       }                }
     }              }
   }            }
                    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                  }
         }
       }
  fclose(ficreseij);    }
  fclose(ficresvij);         
   fclose(ficrest);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   fclose(ficpar);  
   free_vector(epj,1,nlstate+1);    fclose(ficresf);
   /*  scanf("%d ",i); */  }
    /************** Forecasting ******************/
   /*------- Variance limit prevalence------*/    populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
 strcpy(fileresvpl,"vpl");    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
   strcat(fileresvpl,fileres);    int *popage;
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    double calagedate, agelim, kk1, kk2;
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    double *popeffectif,*popcount;
     exit(0);    double ***p3mat,***tabpop,***tabpopprev;
   }    double ***mobaverage;
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    char filerespop[FILENAMELENGTH];
   
  k=0;    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  for(cptcov=1;cptcov<=i1;cptcov++){    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    agelim=AGESUP;
      k=k+1;    calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
      fprintf(ficresvpl,"\n#****** ");    
      for(j=1;j<=cptcoveff;j++)    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    
      fprintf(ficresvpl,"******\n");    
          strcpy(filerespop,"pop"); 
      varpl=matrix(1,nlstate,(int) bage, (int) fage);    strcat(filerespop,fileres);
      oldm=oldms;savm=savms;    if((ficrespop=fopen(filerespop,"w"))==NULL) {
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      printf("Problem with forecast resultfile: %s\n", filerespop);
    }      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
  }    }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
   fclose(ficresvpl);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
   /*---------- End : free ----------------*/    if (cptcoveff==0) ncodemax[cptcoveff]=1;
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  
      if (mobilav!=0) {
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
          fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
          printf(" Error in movingaverage mobilav=%d\n",mobilav);
   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);    stepsize=(int) (stepm+YEARM-1)/YEARM;
      if (stepm<=12) stepsize=1;
   free_matrix(matcov,1,npar,1,npar);    
   free_vector(delti,1,npar);    agelim=AGESUP;
   free_matrix(agev,1,maxwav,1,imx);    
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    hstepm=1;
     hstepm=hstepm/stepm; 
   if(erreur >0)    
     printf("End of Imach with error %d\n",erreur);    if (popforecast==1) {
   else   printf("End of Imach\n");      if((ficpop=fopen(popfile,"r"))==NULL) {
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */        printf("Problem with population file : %s\n",popfile);exit(0);
          fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
   /* 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);*/      popage=ivector(0,AGESUP);
   /*------ End -----------*/      popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
  end:      i=1;   
 #ifdef windows      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
   /* chdir(pathcd);*/     
 #endif      imx=i;
  /*system("wgnuplot graph.plt");*/      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
  /*system("../gp37mgw/wgnuplot graph.plt");*/    }
  /*system("cd ../gp37mgw");*/  
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    for(cptcov=1;cptcov<=i2;cptcov++){
  strcpy(plotcmd,GNUPLOTPROGRAM);     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
  strcat(plotcmd," ");        k=k+1;
  strcat(plotcmd,optionfilegnuplot);        fprintf(ficrespop,"\n#******");
  system(plotcmd);        for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
 #ifdef windows        }
   while (z[0] != 'q') {        fprintf(ficrespop,"******\n");
     chdir(path);        fprintf(ficrespop,"# Age");
     printf("\nType e to edit output files, c to start again, and q for exiting: ");        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
     scanf("%s",z);        if (popforecast==1)  fprintf(ficrespop," [Population]");
     if (z[0] == 'c') system("./imach");        
     else if (z[0] == 'e') {        for (cpt=0; cpt<=0;cpt++) { 
       chdir(path);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
       system(optionfilehtm);          
     }          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
     else if (z[0] == 'q') exit(0);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   }            nhstepm = nhstepm/hstepm; 
 #endif            
 }            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);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedate+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedate+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedate+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);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             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);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedate+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1); 
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   }
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     char z[1]="c", occ;
   #include <sys/time.h>
   #include <time.h>
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
    
     /* long total_usecs;
        struct timeval start_time, end_time;
     
        gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     getcwd(pathcd, size);
   
     printf("\n%s",version);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     replace(pathc,path);
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s",version);
     fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     fflush(ficlog);
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       goto end;
     }
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) {
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     
     /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++)
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)
           printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){
             printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
           }
           else
             fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);
         }
         fscanf(ficpar,"\n");
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     delti=delti3[1][1];
     
     /* 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]));}*/
     
    
     /* 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=1; (m<= maxwav); m++){
         if(s[m][i] >0 || s[m][i]==-2){
           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){ /* Should no more exist */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if(mint[m][i]==99 || anint[m][i]==9999)
               agev[m][i]=1;
             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=1; (m<= maxwav); 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;
         }
       }
     }
   
     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);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+mprev1/12.+jprev1/365.;
     dateprev2=anprev2+mprev2/12.+jprev2/365.;
   
     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,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);
     fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
     fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,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(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*/
   
     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,"# Age");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %f %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)){
       prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
       if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
     } 
     else{
       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);
   
     calagedate=-1;
   
     prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
   
     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.1.26  
changed lines
  Added in v.1.68

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