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version 1.33, 2002/03/12 22:13:38 version 1.57, 2002/07/25 07:37:44
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 or quarter trimester,
   semester or year) is model as a multinomial logistic.  The hPx    semester or year) is model 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 0.8k, July 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,*ficrespop;  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];  double jmean; /* Mean space between 2 waves */
  FILE  *ficresvpl;  double **oldm, **newm, **savm; /* Working pointers to matrices */
   char fileresvpl[FILENAMELENGTH];  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 #define NR_END 1  FILE *ficlog;
 #define FREE_ARG char*  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 #define FTOL 1.0e-10  FILE *ficresprobmorprev;
   FILE *fichtm; /* Html File */
 #define NRANSI  FILE *ficreseij;
 #define ITMAX 200  char filerese[FILENAMELENGTH];
   FILE  *ficresvij;
 #define TOL 2.0e-4  char fileresv[FILENAMELENGTH];
   FILE  *ficresvpl;
 #define CGOLD 0.3819660  char fileresvpl[FILENAMELENGTH];
 #define ZEPS 1.0e-10  char title[MAXLINE];
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 #define GOLD 1.618034  
 #define GLIMIT 100.0  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 #define TINY 1.0e-20  char filelog[FILENAMELENGTH]; /* Log file */
   char filerest[FILENAMELENGTH];
 static double maxarg1,maxarg2;  char fileregp[FILENAMELENGTH];
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  char popfile[FILENAMELENGTH];
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
    char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)  #define NR_END 1
   #define FREE_ARG char*
 static double sqrarg;  #define FTOL 1.0e-10
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  #define NRANSI 
   #define ITMAX 200 
 int imx;  
 int stepm;  #define TOL 2.0e-4 
 /* Stepm, step in month: minimum step interpolation*/  
   #define CGOLD 0.3819660 
 int m,nb;  #define ZEPS 1.0e-10 
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;  #define GOLD 1.618034 
 double dateintmean=0;  #define GLIMIT 100.0 
   #define TINY 1.0e-20 
 double *weight;  
 int **s; /* Status */  static double maxarg1,maxarg2;
 double *agedc, **covar, idx;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 double ftolhess; /* Tolerance for computing hessian */  #define rint(a) floor(a+0.5)
   
 /**************** split *************************/  static double sqrarg;
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 {  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */  int imx; 
   int stepm;
    l1 = strlen( path );                 /* length of path */  /* Stepm, step in month: minimum step interpolation*/
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
 #ifdef windows  int estepm;
    s = strrchr( path, '\\' );           /* find last / */  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 #else  
    s = strrchr( path, '/' );            /* find last / */  int m,nb;
 #endif  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
    if ( s == NULL ) {                   /* no directory, so use current */  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 #if     defined(__bsd__)                /* get current working directory */  double **pmmij, ***probs;
       extern char       *getwd( );  double dateintmean=0;
   
       if ( getwd( dirc ) == NULL ) {  double *weight;
 #else  int **s; /* Status */
       extern char       *getcwd( );  double *agedc, **covar, idx;
   int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
          return( GLOCK_ERROR_GETCWD );  double ftolhess; /* Tolerance for computing hessian */
       }  
       strcpy( name, path );             /* we've got it */  /**************** split *************************/
    } else {                             /* strip direcotry from path */  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
       s++;                              /* after this, the filename */  {
       l2 = strlen( s );                 /* length of filename */     char *s;                             /* pointer */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );     int  l1, l2;                         /* length counters */
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */     l1 = strlen( path );                 /* length of path */
       dirc[l1-l2] = 0;                  /* add zero */     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
    }     s= strrchr( path, DIRSEPARATOR );            /* find last / */
    l1 = strlen( dirc );                 /* length of directory */     if ( s == NULL ) {                   /* no directory, so use current */
 #ifdef windows       /*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);*/
 #else  #if     defined(__bsd__)                /* get current working directory */
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }        extern char       *getwd( );
 #endif  
    s = strrchr( name, '.' );            /* find last / */        if ( getwd( dirc ) == NULL ) {
    s++;  #else
    strcpy(ext,s);                       /* save extension */        extern char       *getcwd( );
    l1= strlen( name);  
    l2= strlen( s)+1;        if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
    strncpy( finame, name, l1-l2);  #endif
    finame[l1-l2]= 0;           return( GLOCK_ERROR_GETCWD );
    return( 0 );                         /* we're done */        }
 }        strcpy( name, path );             /* we've got it */
      } else {                             /* strip direcotry from path */
         s++;                              /* after this, the filename */
 /******************************************/        l2 = strlen( s );                 /* length of filename */
         if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 void replace(char *s, char*t)        strcpy( name, s );                /* save file name */
 {        strncpy( dirc, path, l1 - l2 );   /* now the directory */
   int i;        dirc[l1-l2] = 0;                  /* add zero */
   int lg=20;     }
   i=0;     l1 = strlen( dirc );                 /* length of directory */
   lg=strlen(t);  #ifdef windows
   for(i=0; i<= lg; i++) {     if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
     (s[i] = t[i]);  #else
     if (t[i]== '\\') s[i]='/';     if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   }  #endif
 }     s = strrchr( name, '.' );            /* find last / */
      s++;
 int nbocc(char *s, char occ)     strcpy(ext,s);                       /* save extension */
 {     l1= strlen( name);
   int i,j=0;     l2= strlen( s)+1;
   int lg=20;     strncpy( finame, name, l1-l2);
   i=0;     finame[l1-l2]= 0;
   lg=strlen(s);     return( 0 );                         /* we're done */
   for(i=0; i<= lg; i++) {  }
   if  (s[i] == occ ) j++;  
   }  
   return j;  /******************************************/
 }  
   void replace(char *s, char*t)
 void cutv(char *u,char *v, char*t, char occ)  {
 {    int i;
   int i,lg,j,p=0;    int lg=20;
   i=0;    i=0;
   for(j=0; j<=strlen(t)-1; j++) {    lg=strlen(t);
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    for(i=0; i<= lg; i++) {
   }      (s[i] = t[i]);
       if (t[i]== '\\') s[i]='/';
   lg=strlen(t);    }
   for(j=0; j<p; j++) {  }
     (u[j] = t[j]);  
   }  int nbocc(char *s, char occ)
      u[p]='\0';  {
     int i,j=0;
    for(j=0; j<= lg; j++) {    int lg=20;
     if (j>=(p+1))(v[j-p-1] = t[j]);    i=0;
   }    lg=strlen(s);
 }    for(i=0; i<= lg; i++) {
     if  (s[i] == occ ) j++;
 /********************** nrerror ********************/    }
     return j;
 void nrerror(char error_text[])  }
 {  
   fprintf(stderr,"ERREUR ...\n");  void cutv(char *u,char *v, char*t, char occ)
   fprintf(stderr,"%s\n",error_text);  {
   exit(1);    /* cuts string t into u and v where u is ended by char occ excluding it
 }       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 /*********************** vector *******************/       gives u="abcedf" and v="ghi2j" */
 double *vector(int nl, int nh)    int i,lg,j,p=0;
 {    i=0;
   double *v;    for(j=0; j<=strlen(t)-1; j++) {
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   if (!v) nrerror("allocation failure in vector");    }
   return v-nl+NR_END;  
 }    lg=strlen(t);
     for(j=0; j<p; j++) {
 /************************ free vector ******************/      (u[j] = t[j]);
 void free_vector(double*v, int nl, int nh)    }
 {       u[p]='\0';
   free((FREE_ARG)(v+nl-NR_END));  
 }     for(j=0; j<= lg; j++) {
       if (j>=(p+1))(v[j-p-1] = t[j]);
 /************************ivector *******************************/    }
 int *ivector(long nl,long nh)  }
 {  
   int *v;  /********************** nrerror ********************/
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");  void nrerror(char error_text[])
   return v-nl+NR_END;  {
 }    fprintf(stderr,"ERREUR ...\n");
     fprintf(stderr,"%s\n",error_text);
 /******************free ivector **************************/    exit(1);
 void free_ivector(int *v, long nl, long nh)  }
 {  /*********************** vector *******************/
   free((FREE_ARG)(v+nl-NR_END));  double *vector(int nl, int nh)
 }  {
     double *v;
 /******************* imatrix *******************************/    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 int **imatrix(long nrl, long nrh, long ncl, long nch)    if (!v) nrerror("allocation failure in vector");
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    return v-nl+NR_END;
 {  }
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;  /************************ free vector ******************/
    void free_vector(double*v, int nl, int nh)
   /* allocate pointers to rows */  {
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    free((FREE_ARG)(v+nl-NR_END));
   if (!m) nrerror("allocation failure 1 in matrix()");  }
   m += NR_END;  
   m -= nrl;  /************************ivector *******************************/
    int *ivector(long nl,long nh)
    {
   /* allocate rows and set pointers to them */    int *v;
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    if (!v) nrerror("allocation failure in ivector");
   m[nrl] += NR_END;    return v-nl+NR_END;
   m[nrl] -= ncl;  }
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  /******************free ivector **************************/
    void free_ivector(int *v, long nl, long nh)
   /* return pointer to array of pointers to rows */  {
   return m;    free((FREE_ARG)(v+nl-NR_END));
 }  }
   
 /****************** free_imatrix *************************/  /******************* imatrix *******************************/
 void free_imatrix(m,nrl,nrh,ncl,nch)  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       int **m;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       long nch,ncl,nrh,nrl;  { 
      /* free an int matrix allocated by imatrix() */    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
 {    int **m; 
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    
   free((FREE_ARG) (m+nrl-NR_END));    /* allocate pointers to rows */ 
 }    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     if (!m) nrerror("allocation failure 1 in matrix()"); 
 /******************* matrix *******************************/    m += NR_END; 
 double **matrix(long nrl, long nrh, long ncl, long nch)    m -= nrl; 
 {    
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    
   double **m;    /* allocate rows and set pointers to them */ 
     m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   if (!m) nrerror("allocation failure 1 in matrix()");    m[nrl] += NR_END; 
   m += NR_END;    m[nrl] -= ncl; 
   m -= nrl;    
     for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    /* return pointer to array of pointers to rows */ 
   m[nrl] += NR_END;    return m; 
   m[nrl] -= ncl;  } 
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  /****************** free_imatrix *************************/
   return m;  void free_imatrix(m,nrl,nrh,ncl,nch)
 }        int **m;
         long nch,ncl,nrh,nrl; 
 /*************************free matrix ************************/       /* free an int matrix allocated by imatrix() */ 
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  { 
 {    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    free((FREE_ARG) (m+nrl-NR_END)); 
   free((FREE_ARG)(m+nrl-NR_END));  } 
 }  
   /******************* matrix *******************************/
 /******************* ma3x *******************************/  double **matrix(long nrl, long nrh, long ncl, long nch)
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  {
 {    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    double **m;
   double ***m;  
     m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    if (!m) nrerror("allocation failure 1 in matrix()");
   if (!m) nrerror("allocation failure 1 in matrix()");    m += NR_END;
   m += NR_END;    m -= nrl;
   m -= nrl;  
     m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    m[nrl] += NR_END;
   m[nrl] += NR_END;    m[nrl] -= ncl;
   m[nrl] -= ncl;  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    return m;
   }
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  /*************************free matrix ************************/
   m[nrl][ncl] += NR_END;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   m[nrl][ncl] -= nll;  {
   for (j=ncl+1; j<=nch; j++)    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     m[nrl][j]=m[nrl][j-1]+nlay;    free((FREE_ARG)(m+nrl-NR_END));
    }
   for (i=nrl+1; i<=nrh; i++) {  
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  /******************* ma3x *******************************/
     for (j=ncl+1; j<=nch; j++)  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       m[i][j]=m[i][j-1]+nlay;  {
   }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   return m;    double ***m;
 }  
     m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 /*************************free ma3x ************************/    if (!m) nrerror("allocation failure 1 in matrix()");
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    m += NR_END;
 {    m -= nrl;
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   free((FREE_ARG)(m+nrl-NR_END));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 }    m[nrl] += NR_END;
     m[nrl] -= ncl;
 /***************** f1dim *************************/  
 extern int ncom;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
      if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
 double f1dim(double x)    m[nrl][ncl] += NR_END;
 {    m[nrl][ncl] -= nll;
   int j;    for (j=ncl+1; j<=nch; j++) 
   double f;      m[nrl][j]=m[nrl][j-1]+nlay;
   double *xt;    
      for (i=nrl+1; i<=nrh; i++) {
   xt=vector(1,ncom);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];      for (j=ncl+1; j<=nch; j++) 
   f=(*nrfunc)(xt);        m[i][j]=m[i][j-1]+nlay;
   free_vector(xt,1,ncom);    }
   return f;    return m;
 }  }
   
 /*****************brent *************************/  /*************************free ma3x ************************/
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 {  {
   int iter;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   double a,b,d,etemp;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double fu,fv,fw,fx;    free((FREE_ARG)(m+nrl-NR_END));
   double ftemp;  }
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;  /***************** f1dim *************************/
    extern int ncom; 
   a=(ax < cx ? ax : cx);  extern double *pcom,*xicom;
   b=(ax > cx ? ax : cx);  extern double (*nrfunc)(double []); 
   x=w=v=bx;   
   fw=fv=fx=(*f)(x);  double f1dim(double x) 
   for (iter=1;iter<=ITMAX;iter++) {  { 
     xm=0.5*(a+b);    int j; 
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    double f;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    double *xt; 
     printf(".");fflush(stdout);   
 #ifdef DEBUG    xt=vector(1,ncom); 
     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);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    f=(*nrfunc)(xt); 
 #endif    free_vector(xt,1,ncom); 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    return f; 
       *xmin=x;  } 
       return fx;  
     }  /*****************brent *************************/
     ftemp=fu;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     if (fabs(e) > tol1) {  { 
       r=(x-w)*(fx-fv);    int iter; 
       q=(x-v)*(fx-fw);    double a,b,d,etemp;
       p=(x-v)*q-(x-w)*r;    double fu,fv,fw,fx;
       q=2.0*(q-r);    double ftemp;
       if (q > 0.0) p = -p;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       q=fabs(q);    double e=0.0; 
       etemp=e;   
       e=d;    a=(ax < cx ? ax : cx); 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    b=(ax > cx ? ax : cx); 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    x=w=v=bx; 
       else {    fw=fv=fx=(*f)(x); 
         d=p/q;    for (iter=1;iter<=ITMAX;iter++) { 
         u=x+d;      xm=0.5*(a+b); 
         if (u-a < tol2 || b-u < tol2)      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
           d=SIGN(tol1,xm-x);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       }      printf(".");fflush(stdout);
     } else {      fprintf(ficlog,".");fflush(ficlog);
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  #ifdef DEBUG
     }      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));      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);
     fu=(*f)(u);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     if (fu <= fx) {  #endif
       if (u >= x) a=x; else b=x;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       SHFT(v,w,x,u)        *xmin=x; 
         SHFT(fv,fw,fx,fu)        return fx; 
         } else {      } 
           if (u < x) a=u; else b=u;      ftemp=fu;
           if (fu <= fw || w == x) {      if (fabs(e) > tol1) { 
             v=w;        r=(x-w)*(fx-fv); 
             w=u;        q=(x-v)*(fx-fw); 
             fv=fw;        p=(x-v)*q-(x-w)*r; 
             fw=fu;        q=2.0*(q-r); 
           } else if (fu <= fv || v == x || v == w) {        if (q > 0.0) p = -p; 
             v=u;        q=fabs(q); 
             fv=fu;        etemp=e; 
           }        e=d; 
         }        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)); 
   nrerror("Too many iterations in brent");        else { 
   *xmin=x;          d=p/q; 
   return fx;          u=x+d; 
 }          if (u-a < tol2 || b-u < tol2) 
             d=SIGN(tol1,xm-x); 
 /****************** mnbrak ***********************/        } 
       } else { 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
             double (*func)(double))      } 
 {      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   double ulim,u,r,q, dum;      fu=(*f)(u); 
   double fu;      if (fu <= fx) { 
          if (u >= x) a=x; else b=x; 
   *fa=(*func)(*ax);        SHFT(v,w,x,u) 
   *fb=(*func)(*bx);          SHFT(fv,fw,fx,fu) 
   if (*fb > *fa) {          } else { 
     SHFT(dum,*ax,*bx,dum)            if (u < x) a=u; else b=u; 
       SHFT(dum,*fb,*fa,dum)            if (fu <= fw || w == x) { 
       }              v=w; 
   *cx=(*bx)+GOLD*(*bx-*ax);              w=u; 
   *fc=(*func)(*cx);              fv=fw; 
   while (*fb > *fc) {              fw=fu; 
     r=(*bx-*ax)*(*fb-*fc);            } else if (fu <= fv || v == x || v == w) { 
     q=(*bx-*cx)*(*fb-*fa);              v=u; 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/              fv=fu; 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));            } 
     ulim=(*bx)+GLIMIT*(*cx-*bx);          } 
     if ((*bx-u)*(u-*cx) > 0.0) {    } 
       fu=(*func)(u);    nrerror("Too many iterations in brent"); 
     } else if ((*cx-u)*(u-ulim) > 0.0) {    *xmin=x; 
       fu=(*func)(u);    return fx; 
       if (fu < *fc) {  } 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))  /****************** mnbrak ***********************/
           }  
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       u=ulim;              double (*func)(double)) 
       fu=(*func)(u);  { 
     } else {    double ulim,u,r,q, dum;
       u=(*cx)+GOLD*(*cx-*bx);    double fu; 
       fu=(*func)(u);   
     }    *fa=(*func)(*ax); 
     SHFT(*ax,*bx,*cx,u)    *fb=(*func)(*bx); 
       SHFT(*fa,*fb,*fc,fu)    if (*fb > *fa) { 
       }      SHFT(dum,*ax,*bx,dum) 
 }        SHFT(dum,*fb,*fa,dum) 
         } 
 /*************** linmin ************************/    *cx=(*bx)+GOLD*(*bx-*ax); 
     *fc=(*func)(*cx); 
 int ncom;    while (*fb > *fc) { 
 double *pcom,*xicom;      r=(*bx-*ax)*(*fb-*fc); 
 double (*nrfunc)(double []);      q=(*bx-*cx)*(*fb-*fa); 
        u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 {      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   double brent(double ax, double bx, double cx,      if ((*bx-u)*(u-*cx) > 0.0) { 
                double (*f)(double), double tol, double *xmin);        fu=(*func)(u); 
   double f1dim(double x);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,        fu=(*func)(u); 
               double *fc, double (*func)(double));        if (fu < *fc) { 
   int j;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   double xx,xmin,bx,ax;            SHFT(*fb,*fc,fu,(*func)(u)) 
   double fx,fb,fa;            } 
        } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   ncom=n;        u=ulim; 
   pcom=vector(1,n);        fu=(*func)(u); 
   xicom=vector(1,n);      } else { 
   nrfunc=func;        u=(*cx)+GOLD*(*cx-*bx); 
   for (j=1;j<=n;j++) {        fu=(*func)(u); 
     pcom[j]=p[j];      } 
     xicom[j]=xi[j];      SHFT(*ax,*bx,*cx,u) 
   }        SHFT(*fa,*fb,*fc,fu) 
   ax=0.0;        } 
   xx=1.0;  } 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  /*************** linmin ************************/
 #ifdef DEBUG  
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  int ncom; 
 #endif  double *pcom,*xicom;
   for (j=1;j<=n;j++) {  double (*nrfunc)(double []); 
     xi[j] *= xmin;   
     p[j] += xi[j];  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   }  { 
   free_vector(xicom,1,n);    double brent(double ax, double bx, double cx, 
   free_vector(pcom,1,n);                 double (*f)(double), double tol, double *xmin); 
 }    double f1dim(double x); 
     void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
 /*************** powell ************************/                double *fc, double (*func)(double)); 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    int j; 
             double (*func)(double []))    double xx,xmin,bx,ax; 
 {    double fx,fb,fa;
   void linmin(double p[], double xi[], int n, double *fret,   
               double (*func)(double []));    ncom=n; 
   int i,ibig,j;    pcom=vector(1,n); 
   double del,t,*pt,*ptt,*xit;    xicom=vector(1,n); 
   double fp,fptt;    nrfunc=func; 
   double *xits;    for (j=1;j<=n;j++) { 
   pt=vector(1,n);      pcom[j]=p[j]; 
   ptt=vector(1,n);      xicom[j]=xi[j]; 
   xit=vector(1,n);    } 
   xits=vector(1,n);    ax=0.0; 
   *fret=(*func)(p);    xx=1.0; 
   for (j=1;j<=n;j++) pt[j]=p[j];    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   for (*iter=1;;++(*iter)) {    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     fp=(*fret);  #ifdef DEBUG
     ibig=0;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     del=0.0;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  #endif
     for (i=1;i<=n;i++)    for (j=1;j<=n;j++) { 
       printf(" %d %.12f",i, p[i]);      xi[j] *= xmin; 
     printf("\n");      p[j] += xi[j]; 
     for (i=1;i<=n;i++) {    } 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    free_vector(xicom,1,n); 
       fptt=(*fret);    free_vector(pcom,1,n); 
 #ifdef DEBUG  } 
       printf("fret=%lf \n",*fret);  
 #endif  /*************** powell ************************/
       printf("%d",i);fflush(stdout);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       linmin(p,xit,n,fret,func);              double (*func)(double [])) 
       if (fabs(fptt-(*fret)) > del) {  { 
         del=fabs(fptt-(*fret));    void linmin(double p[], double xi[], int n, double *fret, 
         ibig=i;                double (*func)(double [])); 
       }    int i,ibig,j; 
 #ifdef DEBUG    double del,t,*pt,*ptt,*xit;
       printf("%d %.12e",i,(*fret));    double fp,fptt;
       for (j=1;j<=n;j++) {    double *xits;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    pt=vector(1,n); 
         printf(" x(%d)=%.12e",j,xit[j]);    ptt=vector(1,n); 
       }    xit=vector(1,n); 
       for(j=1;j<=n;j++)    xits=vector(1,n); 
         printf(" p=%.12e",p[j]);    *fret=(*func)(p); 
       printf("\n");    for (j=1;j<=n;j++) pt[j]=p[j]; 
 #endif    for (*iter=1;;++(*iter)) { 
     }      fp=(*fret); 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      ibig=0; 
 #ifdef DEBUG      del=0.0; 
       int k[2],l;      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       k[0]=1;      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       k[1]=-1;      for (i=1;i<=n;i++) 
       printf("Max: %.12e",(*func)(p));        printf(" %d %.12f",i, p[i]);
       for (j=1;j<=n;j++)      fprintf(ficlog," %d %.12f",i, p[i]);
         printf(" %.12e",p[j]);      printf("\n");
       printf("\n");      fprintf(ficlog,"\n");
       for(l=0;l<=1;l++) {      for (i=1;i<=n;i++) { 
         for (j=1;j<=n;j++) {        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];        fptt=(*fret); 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  #ifdef DEBUG
         }        printf("fret=%lf \n",*fret);
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));        fprintf(ficlog,"fret=%lf \n",*fret);
       }  #endif
 #endif        printf("%d",i);fflush(stdout);
         fprintf(ficlog,"%d",i);fflush(ficlog);
         linmin(p,xit,n,fret,func); 
       free_vector(xit,1,n);        if (fabs(fptt-(*fret)) > del) { 
       free_vector(xits,1,n);          del=fabs(fptt-(*fret)); 
       free_vector(ptt,1,n);          ibig=i; 
       free_vector(pt,1,n);        } 
       return;  #ifdef DEBUG
     }        printf("%d %.12e",i,(*fret));
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");        fprintf(ficlog,"%d %.12e",i,(*fret));
     for (j=1;j<=n;j++) {        for (j=1;j<=n;j++) {
       ptt[j]=2.0*p[j]-pt[j];          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       xit[j]=p[j]-pt[j];          printf(" x(%d)=%.12e",j,xit[j]);
       pt[j]=p[j];          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     }        }
     fptt=(*func)(ptt);        for(j=1;j<=n;j++) {
     if (fptt < fp) {          printf(" p=%.12e",p[j]);
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);          fprintf(ficlog," p=%.12e",p[j]);
       if (t < 0.0) {        }
         linmin(p,xit,n,fret,func);        printf("\n");
         for (j=1;j<=n;j++) {        fprintf(ficlog,"\n");
           xi[j][ibig]=xi[j][n];  #endif
           xi[j][n]=xit[j];      } 
         }      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
 #ifdef DEBUG  #ifdef DEBUG
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);        int k[2],l;
         for(j=1;j<=n;j++)        k[0]=1;
           printf(" %.12e",xit[j]);        k[1]=-1;
         printf("\n");        printf("Max: %.12e",(*func)(p));
 #endif        fprintf(ficlog,"Max: %.12e",(*func)(p));
       }        for (j=1;j<=n;j++) {
     }          printf(" %.12e",p[j]);
   }          fprintf(ficlog," %.12e",p[j]);
 }        }
         printf("\n");
 /**** Prevalence limit ****************/        fprintf(ficlog,"\n");
         for(l=0;l<=1;l++) {
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)          for (j=1;j<=n;j++) {
 {            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
      matrix by transitions matrix until convergence is reached */            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
           }
   int i, ii,j,k;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   double min, max, maxmin, maxmax,sumnew=0.;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   double **matprod2();        }
   double **out, cov[NCOVMAX], **pmij();  #endif
   double **newm;  
   double agefin, delaymax=50 ; /* Max number of years to converge */  
         free_vector(xit,1,n); 
   for (ii=1;ii<=nlstate+ndeath;ii++)        free_vector(xits,1,n); 
     for (j=1;j<=nlstate+ndeath;j++){        free_vector(ptt,1,n); 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        free_vector(pt,1,n); 
     }        return; 
       } 
    cov[1]=1.;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
        for (j=1;j<=n;j++) { 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        ptt[j]=2.0*p[j]-pt[j]; 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        xit[j]=p[j]-pt[j]; 
     newm=savm;        pt[j]=p[j]; 
     /* Covariates have to be included here again */      } 
      cov[2]=agefin;      fptt=(*func)(ptt); 
        if (fptt < fp) { 
       for (k=1; k<=cptcovn;k++) {        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        if (t < 0.0) { 
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/          linmin(p,xit,n,fret,func); 
       }          for (j=1;j<=n;j++) { 
       for (k=1; k<=cptcovage;k++)            xi[j][ibig]=xi[j][n]; 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];            xi[j][n]=xit[j]; 
       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]]];  #ifdef DEBUG
           printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/          for(j=1;j<=n;j++){
             printf(" %.12e",xit[j]);
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);            fprintf(ficlog," %.12e",xit[j]);
           }
     savm=oldm;          printf("\n");
     oldm=newm;          fprintf(ficlog,"\n");
     maxmax=0.;  #endif
     for(j=1;j<=nlstate;j++){        }
       min=1.;      } 
       max=0.;    } 
       for(i=1; i<=nlstate; i++) {  } 
         sumnew=0;  
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  /**** Prevalence limit (stable prevalence)  ****************/
         prlim[i][j]= newm[i][j]/(1-sumnew);  
         max=FMAX(max,prlim[i][j]);  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
         min=FMIN(min,prlim[i][j]);  {
       }    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       maxmin=max-min;       matrix by transitions matrix until convergence is reached */
       maxmax=FMAX(maxmax,maxmin);  
     }    int i, ii,j,k;
     if(maxmax < ftolpl){    double min, max, maxmin, maxmax,sumnew=0.;
       return prlim;    double **matprod2();
     }    double **out, cov[NCOVMAX], **pmij();
   }    double **newm;
 }    double agefin, delaymax=50 ; /* Max number of years to converge */
   
 /*************** transition probabilities ***************/    for (ii=1;ii<=nlstate+ndeath;ii++)
       for (j=1;j<=nlstate+ndeath;j++){
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 {      }
   double s1, s2;  
   /*double t34;*/     cov[1]=1.;
   int i,j,j1, nc, ii, jj;   
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(i=1; i<= nlstate; i++){    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     for(j=1; j<i;j++){      newm=savm;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      /* Covariates have to be included here again */
         /*s2 += param[i][j][nc]*cov[nc];*/       cov[2]=agefin;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/        for (k=1; k<=cptcovn;k++) {
       }          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       ps[i][j]=s2;          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        }
     }        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for(j=i+1; j<=nlstate+ndeath;j++){        for (k=1; k<=cptcovprod;k++)
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/        /*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]);*/
       ps[i][j]=s2;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     }      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   }  
     /*ps[3][2]=1;*/      savm=oldm;
       oldm=newm;
   for(i=1; i<= nlstate; i++){      maxmax=0.;
      s1=0;      for(j=1;j<=nlstate;j++){
     for(j=1; j<i; j++)        min=1.;
       s1+=exp(ps[i][j]);        max=0.;
     for(j=i+1; j<=nlstate+ndeath; j++)        for(i=1; i<=nlstate; i++) {
       s1+=exp(ps[i][j]);          sumnew=0;
     ps[i][i]=1./(s1+1.);          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     for(j=1; j<i; 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]);
     for(j=i+1; j<=nlstate+ndeath; j++)          min=FMIN(min,prlim[i][j]);
       ps[i][j]= exp(ps[i][j])*ps[i][i];        }
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        maxmin=max-min;
   } /* end i */        maxmax=FMAX(maxmax,maxmin);
       }
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      if(maxmax < ftolpl){
     for(jj=1; jj<= nlstate+ndeath; jj++){        return prlim;
       ps[ii][jj]=0;      }
       ps[ii][ii]=1;    }
     }  }
   }  
   /*************** transition probabilities ***************/ 
   
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     for(jj=1; jj<= nlstate+ndeath; jj++){  {
      printf("%lf ",ps[ii][jj]);    double s1, s2;
    }    /*double t34;*/
     printf("\n ");    int i,j,j1, nc, ii, jj;
     }  
     printf("\n ");printf("%lf ",cov[2]);*/      for(i=1; i<= nlstate; i++){
 /*      for(j=1; j<i;j++){
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   goto end;*/          /*s2 += param[i][j][nc]*cov[nc];*/
     return ps;          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
 }          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
         }
 /**************** Product of 2 matrices ******************/        ps[i][j]=s2;
         /*printf("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)      }
 {      for(j=i+1; j<=nlstate+ndeath;j++){
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   /* in, b, out are matrice of pointers which should have been initialized          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
      before: only the contents of out is modified. The function returns        }
      a pointer to pointers identical to out */        ps[i][j]=s2;
   long i, j, k;      }
   for(i=nrl; i<= nrh; i++)    }
     for(k=ncolol; k<=ncoloh; k++)      /*ps[3][2]=1;*/
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  
         out[i][k] +=in[i][j]*b[j][k];    for(i=1; i<= nlstate; i++){
        s1=0;
   return out;      for(j=1; j<i; j++)
 }        s1+=exp(ps[i][j]);
       for(j=i+1; j<=nlstate+ndeath; j++)
         s1+=exp(ps[i][j]);
 /************* Higher Matrix Product ***************/      ps[i][i]=1./(s1+1.);
       for(j=1; j<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][j]= exp(ps[i][j])*ps[i][i];
 {      for(j=i+1; j<=nlstate+ndeath; 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      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    } /* end i */
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  
      (typically every 2 years instead of every month which is too big).    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
      Model is determined by parameters x and covariates have to be      for(jj=1; jj<= nlstate+ndeath; jj++){
      included manually here.        ps[ii][jj]=0;
         ps[ii][ii]=1;
      */      }
     }
   int i, j, d, h, k;  
   double **out, cov[NCOVMAX];  
   double **newm;    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
       for(jj=1; jj<= nlstate+ndeath; jj++){
   /* Hstepm could be zero and should return the unit matrix */       printf("%lf ",ps[ii][jj]);
   for (i=1;i<=nlstate+ndeath;i++)     }
     for (j=1;j<=nlstate+ndeath;j++){      printf("\n ");
       oldm[i][j]=(i==j ? 1.0 : 0.0);      }
       po[i][j][0]=(i==j ? 1.0 : 0.0);      printf("\n ");printf("%lf ",cov[2]);*/
     }  /*
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    for(i=1; i<= npar; i++) printf("%f ",x[i]);
   for(h=1; h <=nhstepm; h++){    goto end;*/
     for(d=1; d <=hstepm; d++){      return ps;
       newm=savm;  }
       /* Covariates have to be included here again */  
       cov[1]=1.;  /**************** Product of 2 matrices ******************/
       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]]];  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
       for (k=1; k<=cptcovage;k++)  {
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       for (k=1; k<=cptcovprod;k++)       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    /* in, b, out are matrice of pointers which should have been initialized 
        before: only the contents of out is modified. The function returns
        a pointer to pointers identical to out */
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    long i, j, k;
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    for(i=nrl; i<= nrh; i++)
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      for(k=ncolol; k<=ncoloh; k++)
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        for(j=ncl,out[i][k]=0.; j<=nch; j++)
       savm=oldm;          out[i][k] +=in[i][j]*b[j][k];
       oldm=newm;  
     }    return out;
     for(i=1; i<=nlstate+ndeath; i++)  }
       for(j=1;j<=nlstate+ndeath;j++) {  
         po[i][j][h]=newm[i][j];  
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  /************* Higher Matrix Product ***************/
          */  
       }  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   } /* end h */  {
   return po;    /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month 
 }       duration (i.e. until
        age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices. 
        Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
 /*************** log-likelihood *************/       (typically every 2 years instead of every month which is too big).
 double func( double *x)       Model is determined by parameters x and covariates have to be 
 {       included manually here. 
   int i, ii, j, k, mi, d, kk;  
   double l, ll[NLSTATEMAX], cov[NCOVMAX];       */
   double **out;  
   double sw; /* Sum of weights */    int i, j, d, h, k;
   double lli; /* Individual log likelihood */    double **out, cov[NCOVMAX];
   long ipmx;    double **newm;
   /*extern weight */  
   /* We are differentiating ll according to initial status */    /* Hstepm could be zero and should return the unit matrix */
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    for (i=1;i<=nlstate+ndeath;i++)
   /*for(i=1;i<imx;i++)      for (j=1;j<=nlstate+ndeath;j++){
     printf(" %d\n",s[4][i]);        oldm[i][j]=(i==j ? 1.0 : 0.0);
   */        po[i][j][0]=(i==j ? 1.0 : 0.0);
   cov[1]=1.;      }
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   for(k=1; k<=nlstate; k++) ll[k]=0.;    for(h=1; h <=nhstepm; h++){
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      for(d=1; d <=hstepm; d++){
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        newm=savm;
     for(mi=1; mi<= wav[i]-1; mi++){        /* Covariates have to be included here again */
       for (ii=1;ii<=nlstate+ndeath;ii++)        cov[1]=1.;
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       for(d=0; d<dh[mi][i]; d++){        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         newm=savm;        for (k=1; k<=cptcovage;k++)
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (kk=1; kk<=cptcovage;kk++) {        for (k=1; k<=cptcovprod;k++)
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         }  
          
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         savm=oldm;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
         oldm=newm;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
                savm=oldm;
                oldm=newm;
       } /* end mult */      }
            for(i=1; i<=nlstate+ndeath; i++)
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        for(j=1;j<=nlstate+ndeath;j++) {
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/          po[i][j][h]=newm[i][j];
       ipmx +=1;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
       sw += weight[i];           */
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        }
     } /* end of wave */    } /* end h */
   } /* end of individual */    return po;
   }
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  /*************** log-likelihood *************/
   return -l;  double func( double *x)
 }  {
     int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX], cov[NCOVMAX];
 /*********** Maximum Likelihood Estimation ***************/    double **out;
     double sw; /* Sum of weights */
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    double lli; /* Individual log likelihood */
 {    long ipmx;
   int i,j, iter;    /*extern weight */
   double **xi,*delti;    /* We are differentiating ll according to initial status */
   double fret;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   xi=matrix(1,npar,1,npar);    /*for(i=1;i<imx;i++) 
   for (i=1;i<=npar;i++)      printf(" %d\n",s[4][i]);
     for (j=1;j<=npar;j++)    */
       xi[i][j]=(i==j ? 1.0 : 0.0);    cov[1]=1.;
   printf("Powell\n");  
   powell(p,xi,npar,ftol,&iter,&fret,func);    for(k=1; k<=nlstate; k++) ll[k]=0.;
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      for(mi=1; mi<= wav[i]-1; mi++){
         for (ii=1;ii<=nlstate+ndeath;ii++)
 }          for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         for(d=0; d<dh[mi][i]; d++){
 /**** Computes Hessian and covariance matrix ***/          newm=savm;
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 {          for (kk=1; kk<=cptcovage;kk++) {
   double  **a,**y,*x,pd;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double **hess;          }
   int i, j,jk;          
   int *indx;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double hessii(double p[], double delta, int theta, double delti[]);          savm=oldm;
   double hessij(double p[], double delti[], int i, int j);          oldm=newm;
   void lubksb(double **a, int npar, int *indx, double b[]) ;          
   void ludcmp(double **a, int npar, int *indx, double *d) ;          
         } /* end mult */
   hess=matrix(1,npar,1,npar);        
         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
   printf("\nCalculation of the hessian matrix. Wait...\n");        /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
   for (i=1;i<=npar;i++){        ipmx +=1;
     printf("%d",i);fflush(stdout);        sw += weight[i];
     hess[i][i]=hessii(p,ftolhess,i,delti);        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     /*printf(" %f ",p[i]);*/      } /* end of wave */
     /*printf(" %lf ",hess[i][i]);*/    } /* end of individual */
   }  
      for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   for (i=1;i<=npar;i++) {    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     for (j=1;j<=npar;j++)  {    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       if (j>i) {    return -l;
         printf(".%d%d",i,j);fflush(stdout);  }
         hess[i][j]=hessij(p,delti,i,j);  
         hess[j][i]=hess[i][j];      
         /*printf(" %lf ",hess[i][j]);*/  /*********** Maximum Likelihood Estimation ***************/
       }  
     }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   }  {
   printf("\n");    int i,j, iter;
     double **xi,*delti;
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    double fret;
      xi=matrix(1,npar,1,npar);
   a=matrix(1,npar,1,npar);    for (i=1;i<=npar;i++)
   y=matrix(1,npar,1,npar);      for (j=1;j<=npar;j++)
   x=vector(1,npar);        xi[i][j]=(i==j ? 1.0 : 0.0);
   indx=ivector(1,npar);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   for (i=1;i<=npar;i++)    powell(p,xi,npar,ftol,&iter,&fret,func);
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  
   ludcmp(a,npar,indx,&pd);     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   for (j=1;j<=npar;j++) {    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;  }
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){  /**** Computes Hessian and covariance matrix ***/
       matcov[i][j]=x[i];  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     }  {
   }    double  **a,**y,*x,pd;
     double **hess;
   printf("\n#Hessian matrix#\n");    int i, j,jk;
   for (i=1;i<=npar;i++) {    int *indx;
     for (j=1;j<=npar;j++) {  
       printf("%.3e ",hess[i][j]);    double hessii(double p[], double delta, int theta, double delti[]);
     }    double hessij(double p[], double delti[], int i, int j);
     printf("\n");    void lubksb(double **a, int npar, int *indx, double b[]) ;
   }    void ludcmp(double **a, int npar, int *indx, double *d) ;
   
   /* Recompute Inverse */    hess=matrix(1,npar,1,npar);
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    printf("\nCalculation of the hessian matrix. Wait...\n");
   ludcmp(a,npar,indx,&pd);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     for (i=1;i<=npar;i++){
   /*  printf("\n#Hessian matrix recomputed#\n");      printf("%d",i);fflush(stdout);
       fprintf(ficlog,"%d",i);fflush(ficlog);
   for (j=1;j<=npar;j++) {      hess[i][i]=hessii(p,ftolhess,i,delti);
     for (i=1;i<=npar;i++) x[i]=0;      /*printf(" %f ",p[i]);*/
     x[j]=1;      /*printf(" %lf ",hess[i][i]);*/
     lubksb(a,npar,indx,x);    }
     for (i=1;i<=npar;i++){    
       y[i][j]=x[i];    for (i=1;i<=npar;i++) {
       printf("%.3e ",y[i][j]);      for (j=1;j<=npar;j++)  {
     }        if (j>i) { 
     printf("\n");          printf(".%d%d",i,j);fflush(stdout);
   }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   */          hess[i][j]=hessij(p,delti,i,j);
           hess[j][i]=hess[i][j];    
   free_matrix(a,1,npar,1,npar);          /*printf(" %lf ",hess[i][j]);*/
   free_matrix(y,1,npar,1,npar);        }
   free_vector(x,1,npar);      }
   free_ivector(indx,1,npar);    }
   free_matrix(hess,1,npar,1,npar);    printf("\n");
     fprintf(ficlog,"\n");
   
 }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
 /*************** hessian matrix ****************/    
 double hessii( double x[], double delta, int theta, double delti[])    a=matrix(1,npar,1,npar);
 {    y=matrix(1,npar,1,npar);
   int i;    x=vector(1,npar);
   int l=1, lmax=20;    indx=ivector(1,npar);
   double k1,k2;    for (i=1;i<=npar;i++)
   double p2[NPARMAX+1];      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   double res;    ludcmp(a,npar,indx,&pd);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  
   double fx;    for (j=1;j<=npar;j++) {
   int k=0,kmax=10;      for (i=1;i<=npar;i++) x[i]=0;
   double l1;      x[j]=1;
       lubksb(a,npar,indx,x);
   fx=func(x);      for (i=1;i<=npar;i++){ 
   for (i=1;i<=npar;i++) p2[i]=x[i];        matcov[i][j]=x[i];
   for(l=0 ; l <=lmax; l++){      }
     l1=pow(10,l);    }
     delts=delt;  
     for(k=1 ; k <kmax; k=k+1){    printf("\n#Hessian matrix#\n");
       delt = delta*(l1*k);    fprintf(ficlog,"\n#Hessian matrix#\n");
       p2[theta]=x[theta] +delt;    for (i=1;i<=npar;i++) { 
       k1=func(p2)-fx;      for (j=1;j<=npar;j++) { 
       p2[theta]=x[theta]-delt;        printf("%.3e ",hess[i][j]);
       k2=func(p2)-fx;        fprintf(ficlog,"%.3e ",hess[i][j]);
       /*res= (k1-2.0*fx+k2)/delt/delt; */      }
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */      printf("\n");
            fprintf(ficlog,"\n");
 #ifdef DEBUG    }
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);  
 #endif    /* Recompute Inverse */
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    for (i=1;i<=npar;i++)
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
         k=kmax;    ludcmp(a,npar,indx,&pd);
       }  
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    /*  printf("\n#Hessian matrix recomputed#\n");
         k=kmax; l=lmax*10.;  
       }    for (j=1;j<=npar;j++) {
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      for (i=1;i<=npar;i++) x[i]=0;
         delts=delt;      x[j]=1;
       }      lubksb(a,npar,indx,x);
     }      for (i=1;i<=npar;i++){ 
   }        y[i][j]=x[i];
   delti[theta]=delts;        printf("%.3e ",y[i][j]);
   return res;        fprintf(ficlog,"%.3e ",y[i][j]);
        }
 }      printf("\n");
       fprintf(ficlog,"\n");
 double hessij( double x[], double delti[], int thetai,int thetaj)    }
 {    */
   int i;  
   int l=1, l1, lmax=20;    free_matrix(a,1,npar,1,npar);
   double k1,k2,k3,k4,res,fx;    free_matrix(y,1,npar,1,npar);
   double p2[NPARMAX+1];    free_vector(x,1,npar);
   int k;    free_ivector(indx,1,npar);
     free_matrix(hess,1,npar,1,npar);
   fx=func(x);  
   for (k=1; k<=2; k++) {  
     for (i=1;i<=npar;i++) p2[i]=x[i];  }
     p2[thetai]=x[thetai]+delti[thetai]/k;  
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  /*************** hessian matrix ****************/
     k1=func(p2)-fx;  double hessii( double x[], double delta, int theta, double delti[])
    {
     p2[thetai]=x[thetai]+delti[thetai]/k;    int i;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    int l=1, lmax=20;
     k2=func(p2)-fx;    double k1,k2;
      double p2[NPARMAX+1];
     p2[thetai]=x[thetai]-delti[thetai]/k;    double res;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     k3=func(p2)-fx;    double fx;
      int k=0,kmax=10;
     p2[thetai]=x[thetai]-delti[thetai]/k;    double l1;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k4=func(p2)-fx;    fx=func(x);
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    for (i=1;i<=npar;i++) p2[i]=x[i];
 #ifdef DEBUG    for(l=0 ; l <=lmax; l++){
     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);      l1=pow(10,l);
 #endif      delts=delt;
   }      for(k=1 ; k <kmax; k=k+1){
   return res;        delt = delta*(l1*k);
 }        p2[theta]=x[theta] +delt;
         k1=func(p2)-fx;
 /************** Inverse of matrix **************/        p2[theta]=x[theta]-delt;
 void ludcmp(double **a, int n, int *indx, double *d)        k2=func(p2)-fx;
 {        /*res= (k1-2.0*fx+k2)/delt/delt; */
   int i,imax,j,k;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   double big,dum,sum,temp;        
   double *vv;  #ifdef DEBUG
          printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   vv=vector(1,n);        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);
   *d=1.0;  #endif
   for (i=1;i<=n;i++) {        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     big=0.0;        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     for (j=1;j<=n;j++)          k=kmax;
       if ((temp=fabs(a[i][j])) > big) big=temp;        }
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     vv[i]=1.0/big;          k=kmax; l=lmax*10.;
   }        }
   for (j=1;j<=n;j++) {        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     for (i=1;i<j;i++) {          delts=delt;
       sum=a[i][j];        }
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];      }
       a[i][j]=sum;    }
     }    delti[theta]=delts;
     big=0.0;    return res; 
     for (i=j;i<=n;i++) {    
       sum=a[i][j];  }
       for (k=1;k<j;k++)  
         sum -= a[i][k]*a[k][j];  double hessij( double x[], double delti[], int thetai,int thetaj)
       a[i][j]=sum;  {
       if ( (dum=vv[i]*fabs(sum)) >= big) {    int i;
         big=dum;    int l=1, l1, lmax=20;
         imax=i;    double k1,k2,k3,k4,res,fx;
       }    double p2[NPARMAX+1];
     }    int k;
     if (j != imax) {  
       for (k=1;k<=n;k++) {    fx=func(x);
         dum=a[imax][k];    for (k=1; k<=2; k++) {
         a[imax][k]=a[j][k];      for (i=1;i<=npar;i++) p2[i]=x[i];
         a[j][k]=dum;      p2[thetai]=x[thetai]+delti[thetai]/k;
       }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       *d = -(*d);      k1=func(p2)-fx;
       vv[imax]=vv[j];    
     }      p2[thetai]=x[thetai]+delti[thetai]/k;
     indx[j]=imax;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     if (a[j][j] == 0.0) a[j][j]=TINY;      k2=func(p2)-fx;
     if (j != n) {    
       dum=1.0/(a[j][j]);      p2[thetai]=x[thetai]-delti[thetai]/k;
       for (i=j+1;i<=n;i++) a[i][j] *= dum;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     }      k3=func(p2)-fx;
   }    
   free_vector(vv,1,n);  /* Doesn't work */      p2[thetai]=x[thetai]-delti[thetai]/k;
 ;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 }      k4=func(p2)-fx;
       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
 void lubksb(double **a, int n, int *indx, double b[])  #ifdef DEBUG
 {      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   int i,ii=0,ip,j;      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);
   double sum;  #endif
      }
   for (i=1;i<=n;i++) {    return res;
     ip=indx[i];  }
     sum=b[ip];  
     b[ip]=b[i];  /************** Inverse of matrix **************/
     if (ii)  void ludcmp(double **a, int n, int *indx, double *d) 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  { 
     else if (sum) ii=i;    int i,imax,j,k; 
     b[i]=sum;    double big,dum,sum,temp; 
   }    double *vv; 
   for (i=n;i>=1;i--) {   
     sum=b[i];    vv=vector(1,n); 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    *d=1.0; 
     b[i]=sum/a[i][i];    for (i=1;i<=n;i++) { 
   }      big=0.0; 
 }      for (j=1;j<=n;j++) 
         if ((temp=fabs(a[i][j])) > big) big=temp; 
 /************ Frequencies ********************/      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
 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)      vv[i]=1.0/big; 
 {  /* Some frequencies */    } 
      for (j=1;j<=n;j++) { 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;      for (i=1;i<j;i++) { 
   double ***freq; /* Frequencies */        sum=a[i][j]; 
   double *pp;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   double pos, k2, dateintsum=0,k2cpt=0;        a[i][j]=sum; 
   FILE *ficresp;      } 
   char fileresp[FILENAMELENGTH];      big=0.0; 
        for (i=j;i<=n;i++) { 
   pp=vector(1,nlstate);        sum=a[i][j]; 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        for (k=1;k<j;k++) 
   strcpy(fileresp,"p");          sum -= a[i][k]*a[k][j]; 
   strcat(fileresp,fileres);        a[i][j]=sum; 
   if((ficresp=fopen(fileresp,"w"))==NULL) {        if ( (dum=vv[i]*fabs(sum)) >= big) { 
     printf("Problem with prevalence resultfile: %s\n", fileresp);          big=dum; 
     exit(0);          imax=i; 
   }        } 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      } 
   j1=0;      if (j != imax) { 
         for (k=1;k<=n;k++) { 
   j=cptcoveff;          dum=a[imax][k]; 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          a[imax][k]=a[j][k]; 
           a[j][k]=dum; 
   for(k1=1; k1<=j;k1++){        } 
    for(i1=1; i1<=ncodemax[k1];i1++){        *d = -(*d); 
        j1++;        vv[imax]=vv[j]; 
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);      } 
          scanf("%d", i);*/      indx[j]=imax; 
         for (i=-1; i<=nlstate+ndeath; i++)        if (a[j][j] == 0.0) a[j][j]=TINY; 
          for (jk=-1; jk<=nlstate+ndeath; jk++)        if (j != n) { 
            for(m=agemin; m <= agemax+3; m++)        dum=1.0/(a[j][j]); 
              freq[i][jk][m]=0;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       } 
         dateintsum=0;    } 
         k2cpt=0;    free_vector(vv,1,n);  /* Doesn't work */
        for (i=1; i<=imx; i++) {  ;
          bool=1;  } 
          if  (cptcovn>0) {  
            for (z1=1; z1<=cptcoveff; z1++)  void lubksb(double **a, int n, int *indx, double b[]) 
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  { 
                bool=0;    int i,ii=0,ip,j; 
          }    double sum; 
          if (bool==1) {   
            for(m=firstpass; m<=lastpass; m++){    for (i=1;i<=n;i++) { 
              k2=anint[m][i]+(mint[m][i]/12.);      ip=indx[i]; 
              if ((k2>=dateprev1) && (k2<=dateprev2)) {      sum=b[ip]; 
                if(agev[m][i]==0) agev[m][i]=agemax+1;      b[ip]=b[i]; 
                if(agev[m][i]==1) agev[m][i]=agemax+2;      if (ii) 
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      else if (sum) ii=i; 
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {      b[i]=sum; 
                  dateintsum=dateintsum+k2;    } 
                  k2cpt++;    for (i=n;i>=1;i--) { 
                }      sum=b[i]; 
       for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
              }      b[i]=sum/a[i][i]; 
            }    } 
          }  } 
        }  
          /************ Frequencies ********************/
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
   {  /* Some frequencies */
         if  (cptcovn>0) {    
          fprintf(ficresp, "\n#********** Variable ");    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    int first;
        fprintf(ficresp, "**********\n#");    double ***freq; /* Frequencies */
         }    double *pp;
        for(i=1; i<=nlstate;i++)    double pos, k2, dateintsum=0,k2cpt=0;
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    FILE *ficresp;
        fprintf(ficresp, "\n");    char fileresp[FILENAMELENGTH];
            
   for(i=(int)agemin; i <= (int)agemax+3; i++){    pp=vector(1,nlstate);
     if(i==(int)agemax+3)    probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       printf("Total");    strcpy(fileresp,"p");
     else    strcat(fileresp,fileres);
       printf("Age %d", i);    if((ficresp=fopen(fileresp,"w"))==NULL) {
     for(jk=1; jk <=nlstate ; jk++){      printf("Problem with prevalence resultfile: %s\n", fileresp);
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
         pp[jk] += freq[jk][m][i];      exit(0);
     }    }
     for(jk=1; jk <=nlstate ; jk++){    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
       for(m=-1, pos=0; m <=0 ; m++)    j1=0;
         pos += freq[jk][m][i];    
       if(pp[jk]>=1.e-10)    j=cptcoveff;
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       else  
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    first=1;
     }  
     for(k1=1; k1<=j;k1++){
      for(jk=1; jk <=nlstate ; jk++){      for(i1=1; i1<=ncodemax[k1];i1++){
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        j1++;
         pp[jk] += freq[jk][m][i];        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
      }          scanf("%d", i);*/
         for (i=-1; i<=nlstate+ndeath; i++)  
     for(jk=1,pos=0; jk <=nlstate ; jk++)          for (jk=-1; jk<=nlstate+ndeath; jk++)  
       pos += pp[jk];            for(m=agemin; m <= agemax+3; m++)
     for(jk=1; jk <=nlstate ; jk++){              freq[i][jk][m]=0;
       if(pos>=1.e-5)        
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        dateintsum=0;
       else        k2cpt=0;
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        for (i=1; i<=imx; i++) {
       if( i <= (int) agemax){          bool=1;
         if(pos>=1.e-5){          if  (cptcovn>0) {
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);            for (z1=1; z1<=cptcoveff; z1++) 
           probs[i][jk][j1]= pp[jk]/pos;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/                bool=0;
         }          }
       else          if (bool==1) {
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);            for(m=firstpass; m<=lastpass; m++){
       }              k2=anint[m][i]+(mint[m][i]/12.);
     }              if ((k2>=dateprev1) && (k2<=dateprev2)) {
     for(jk=-1; jk <=nlstate+ndeath; jk++)                if(agev[m][i]==0) agev[m][i]=agemax+1;
       for(m=-1; m <=nlstate+ndeath; m++)                if(agev[m][i]==1) agev[m][i]=agemax+2;
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);                if (m<lastpass) {
     if(i <= (int) agemax)                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
       fprintf(ficresp,"\n");                  freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
     printf("\n");                }
     }                
     }                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
  }                  dateintsum=dateintsum+k2;
   dateintmean=dateintsum/k2cpt;                  k2cpt++;
                  }
   fclose(ficresp);              }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            }
   free_vector(pp,1,nlstate);          }
         }
   /* End of Freq */         
 }        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
 /************ Prevalence ********************/        if  (cptcovn>0) {
 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)          fprintf(ficresp, "\n#********** Variable "); 
 {  /* Some frequencies */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficresp, "**********\n#");
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        }
   double ***freq; /* Frequencies */        for(i=1; i<=nlstate;i++) 
   double *pp;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   double pos, k2;        fprintf(ficresp, "\n");
         
   pp=vector(1,nlstate);        for(i=(int)agemin; i <= (int)agemax+3; i++){
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          if(i==(int)agemax+3){
              fprintf(ficlog,"Total");
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          }else{
   j1=0;            if(first==1){
                first=0;
   j=cptcoveff;              printf("See log file for details...\n");
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            }
              fprintf(ficlog,"Age %d", i);
  for(k1=1; k1<=j;k1++){          }
     for(i1=1; i1<=ncodemax[k1];i1++){          for(jk=1; jk <=nlstate ; jk++){
       j1++;            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
                pp[jk] += freq[jk][m][i]; 
       for (i=-1; i<=nlstate+ndeath; i++)            }
         for (jk=-1; jk<=nlstate+ndeath; jk++)            for(jk=1; jk <=nlstate ; jk++){
           for(m=agemin; m <= agemax+3; m++)            for(m=-1, pos=0; m <=0 ; m++)
             freq[i][jk][m]=0;              pos += freq[jk][m][i];
                  if(pp[jk]>=1.e-10){
       for (i=1; i<=imx; i++) {              if(first==1){
         bool=1;              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         if  (cptcovn>0) {              }
           for (z1=1; z1<=cptcoveff; z1++)              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])            }else{
               bool=0;              if(first==1)
         }                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         if (bool==1) {              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
           for(m=firstpass; m<=lastpass; m++){            }
             k2=anint[m][i]+(mint[m][i]/12.);          }
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  
               if(agev[m][i]==0) agev[m][i]=agemax+1;          for(jk=1; jk <=nlstate ; jk++){
               if(agev[m][i]==1) agev[m][i]=agemax+2;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];              pp[jk] += freq[jk][m][i];
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */          }
             }  
           }          for(jk=1,pos=0; jk <=nlstate ; jk++)
         }            pos += pp[jk];
       }          for(jk=1; jk <=nlstate ; jk++){
         for(i=(int)agemin; i <= (int)agemax+3; i++){            if(pos>=1.e-5){
           for(jk=1; jk <=nlstate ; jk++){              if(first==1)
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
               pp[jk] += freq[jk][m][i];              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
           }            }else{
           for(jk=1; jk <=nlstate ; jk++){              if(first==1)
             for(m=-1, pos=0; m <=0 ; m++)                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             pos += freq[jk][m][i];              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         }            }
                    if( i <= (int) agemax){
          for(jk=1; jk <=nlstate ; jk++){              if(pos>=1.e-5){
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)                fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
              pp[jk] += freq[jk][m][i];                probs[i][jk][j1]= pp[jk]/pos;
          }                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
                        }
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];              else
                 fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
          for(jk=1; jk <=nlstate ; jk++){                      }
            if( i <= (int) agemax){          }
              if(pos>=1.e-5){          
                probs[i][jk][j1]= pp[jk]/pos;          for(jk=-1; jk <=nlstate+ndeath; jk++)
              }            for(m=-1; m <=nlstate+ndeath; m++)
            }              if(freq[jk][m][i] !=0 ) {
          }              if(first==1)
                          printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
         }                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     }              }
   }          if(i <= (int) agemax)
              fprintf(ficresp,"\n");
            if(first==1)
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            printf("Others in log...\n");
   free_vector(pp,1,nlstate);          fprintf(ficlog,"\n");
          }
 }  /* End of Freq */      }
     }
 /************* Waves Concatenation ***************/    dateintmean=dateintsum/k2cpt; 
    
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    fclose(ficresp);
 {    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    free_vector(pp,1,nlstate);
      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    /* End of Freq */
      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.  
      */  /************ Prevalence ********************/
   void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
   int i, mi, m;  {  /* Some frequencies */
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;   
      double sum=0., jmean=0.;*/    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     double ***freq; /* Frequencies */
   int j, k=0,jk, ju, jl;    double *pp;
   double sum=0.;    double pos, k2;
   jmin=1e+5;  
   jmax=-1;    pp=vector(1,nlstate);
   jmean=0.;    
   for(i=1; i<=imx; i++){    freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
     mi=0;    j1=0;
     m=firstpass;    
     while(s[m][i] <= nlstate){    j=cptcoveff;
       if(s[m][i]>=1)    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         mw[++mi][i]=m;    
       if(m >=lastpass)    for(k1=1; k1<=j;k1++){
         break;      for(i1=1; i1<=ncodemax[k1];i1++){
       else        j1++;
         m++;        
     }/* end while */        for (i=-1; i<=nlstate+ndeath; i++)  
     if (s[m][i] > nlstate){          for (jk=-1; jk<=nlstate+ndeath; jk++)  
       mi++;     /* Death is another wave */            for(m=agemin; m <= agemax+3; m++)
       /* if(mi==0)  never been interviewed correctly before death */              freq[i][jk][m]=0;
          /* Only death is a correct wave */       
       mw[mi][i]=m;        for (i=1; i<=imx; i++) {
     }          bool=1;
           if  (cptcovn>0) {
     wav[i]=mi;            for (z1=1; z1<=cptcoveff; z1++) 
     if(mi==0)              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);                bool=0;
   }          } 
           if (bool==1) { 
   for(i=1; i<=imx; i++){            for(m=firstpass; m<=lastpass; m++){
     for(mi=1; mi<wav[i];mi++){              k2=anint[m][i]+(mint[m][i]/12.);
       if (stepm <=0)              if ((k2>=dateprev1) && (k2<=dateprev2)) {
         dh[mi][i]=1;                if(agev[m][i]==0) agev[m][i]=agemax+1;
       else{                if(agev[m][i]==1) agev[m][i]=agemax+2;
         if (s[mw[mi+1][i]][i] > nlstate) {                if (m<lastpass) {
           if (agedc[i] < 2*AGESUP) {                  if (calagedate>0) 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);                    freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
           if(j==0) j=1;  /* Survives at least one month after exam */                  else
           k=k+1;                    freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
           if (j >= jmax) jmax=j;                  freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; 
           if (j <= jmin) jmin=j;                }
           sum=sum+j;              }
           /*if (j<0) printf("j=%d num=%d \n",j,i); */            }
           }          }
         }        }
         else{        for(i=(int)agemin; i <= (int)agemax+3; i++){ 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          for(jk=1; jk <=nlstate ; jk++){
           k=k+1;            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
           if (j >= jmax) jmax=j;              pp[jk] += freq[jk][m][i]; 
           else if (j <= jmin)jmin=j;          }
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          for(jk=1; jk <=nlstate ; jk++){
           sum=sum+j;            for(m=-1, pos=0; m <=0 ; m++)
         }              pos += freq[jk][m][i];
         jk= j/stepm;          }
         jl= j -jk*stepm;          
         ju= j -(jk+1)*stepm;          for(jk=1; jk <=nlstate ; jk++){
         if(jl <= -ju)            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
           dh[mi][i]=jk;              pp[jk] += freq[jk][m][i];
         else          }
           dh[mi][i]=jk+1;          
         if(dh[mi][i]==0)          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
           dh[mi][i]=1; /* At least one step */          
       }          for(jk=1; jk <=nlstate ; jk++){    
     }            if( i <= (int) agemax){
   }              if(pos>=1.e-5){
   jmean=sum/k;                probs[i][jk][j1]= pp[jk]/pos;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);              }
  }            }
 /*********** Tricode ****************************/          }/* end jk */
 void tricode(int *Tvar, int **nbcode, int imx)        }/* end i */
 {      } /* end i1 */
   int Ndum[20],ij=1, k, j, i;    } /* end k1 */
   int cptcode=0;  
   cptcoveff=0;    
      free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
   for (k=0; k<19; k++) Ndum[k]=0;    free_vector(pp,1,nlstate);
   for (k=1; k<=7; k++) ncodemax[k]=0;    
   }  /* End of Freq */
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  
     for (i=1; i<=imx; i++) {  /************* Waves Concatenation ***************/
       ij=(int)(covar[Tvar[j]][i]);  
       Ndum[ij]++;  void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  {
       if (ij > cptcode) cptcode=ij;    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     }       Death is a valid wave (if date is known).
        mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     for (i=0; i<=cptcode; i++) {       dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]
       if(Ndum[i]!=0) ncodemax[j]++;       and mw[mi+1][i]. dh depends on stepm.
     }       */
     ij=1;  
     int i, mi, m;
     /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     for (i=1; i<=ncodemax[j]; i++) {       double sum=0., jmean=0.;*/
       for (k=0; k<=19; k++) {    int first;
         if (Ndum[k] != 0) {    int j, k=0,jk, ju, jl;
           nbcode[Tvar[j]][ij]=k;    double sum=0.;
           ij++;    first=0;
         }    jmin=1e+5;
         if (ij > ncodemax[j]) break;    jmax=-1;
       }      jmean=0.;
     }    for(i=1; i<=imx; i++){
   }        mi=0;
       m=firstpass;
  for (k=0; k<19; k++) Ndum[k]=0;      while(s[m][i] <= nlstate){
         if(s[m][i]>=1)
  for (i=1; i<=ncovmodel-2; i++) {          mw[++mi][i]=m;
       ij=Tvar[i];        if(m >=lastpass)
       Ndum[ij]++;          break;
     }        else
           m++;
  ij=1;      }/* end while */
  for (i=1; i<=10; i++) {      if (s[m][i] > nlstate){
    if((Ndum[i]!=0) && (i<=ncov)){        mi++;     /* Death is another wave */
      Tvaraff[ij]=i;        /* if(mi==0)  never been interviewed correctly before death */
      ij++;           /* Only death is a correct wave */
    }        mw[mi][i]=m;
  }      }
    
     cptcoveff=ij-1;      wav[i]=mi;
 }      if(mi==0){
         if(first==0){
 /*********** Health Expectancies ****************/          printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
           first=1;
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)        }
 {        if(first==1){
   /* Health expectancies */          fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
   int i, j, nhstepm, hstepm, h, nstepm, k;        }
   double age, agelim,hf;      } /* end mi==0 */
   double ***p3mat;    }
    
   fprintf(ficreseij,"# Health expectancies\n");    for(i=1; i<=imx; i++){
   fprintf(ficreseij,"# Age");      for(mi=1; mi<wav[i];mi++){
   for(i=1; i<=nlstate;i++)        if (stepm <=0)
     for(j=1; j<=nlstate;j++)          dh[mi][i]=1;
       fprintf(ficreseij," %1d-%1d",i,j);        else{
   fprintf(ficreseij,"\n");          if (s[mw[mi+1][i]][i] > nlstate) {
             if (agedc[i] < 2*AGESUP) {
   k=1;             /* For example stepm=6 months */            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   hstepm=k*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */            if(j==0) j=1;  /* Survives at least one month after exam */
   hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */            k=k+1;
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.            if (j >= jmax) jmax=j;
      nhstepm is the number of hstepm from age to agelim            if (j <= jmin) jmin=j;
      nstepm is the number of stepm from age to agelin.            sum=sum+j;
      Look at hpijx to understand the reason of that which relies in memory size            /*if (j<0) printf("j=%d num=%d \n",j,i); */
      and note for a fixed period like k years */            }
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          }
      survival function given by stepm (the optimization length). Unfortunately it          else{
      means that if the survival funtion is printed only each two years of age and if            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
      you sum them up and add 1 year (area under the trapezoids) you won't get the same            k=k+1;
      results. So we changed our mind and took the option of the best precision.            if (j >= jmax) jmax=j;
   */            else if (j <= jmin)jmin=j;
   hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             sum=sum+j;
   agelim=AGESUP;          }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          jk= j/stepm;
     /* nhstepm age range expressed in number of stepm */          jl= j -jk*stepm;
     nstepm=(int) rint((agelim-age)*YEARM/stepm);          ju= j -(jk+1)*stepm;
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */          if(jl <= -ju)
     /* if (stepm >= YEARM) hstepm=1;*/            dh[mi][i]=jk;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */          else
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            dh[mi][i]=jk+1;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          if(dh[mi][i]==0)
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */            dh[mi][i]=1; /* At least one step */
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          }
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      }
     for(i=1; i<=nlstate;i++)    }
       for(j=1; j<=nlstate;j++)    jmean=sum/k;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
           /* 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]);*/   }
         }  
     fprintf(ficreseij,"%3.0f",age );  /*********** Tricode ****************************/
     for(i=1; i<=nlstate;i++)  void tricode(int *Tvar, int **nbcode, int imx)
       for(j=1; j<=nlstate;j++){  {
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);    int Ndum[20],ij=1, k, j, i;
       }    int cptcode=0;
     fprintf(ficreseij,"\n");    cptcoveff=0; 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   
   }    for (k=0; k<19; k++) Ndum[k]=0;
 }    for (k=1; k<=7; k++) ncodemax[k]=0;
   
 /************ Variance ******************/    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
 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)      for (i=1; i<=imx; i++) {
 {        ij=(int)(covar[Tvar[j]][i]);
   /* Variance of health expectancies */        Ndum[ij]++; 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   double **newm;        if (ij > cptcode) cptcode=ij; 
   double **dnewm,**doldm;      }
   int i, j, nhstepm, hstepm, h;  
   int k, cptcode;      for (i=0; i<=cptcode; i++) {
   double *xp;        if(Ndum[i]!=0) ncodemax[j]++;
   double **gp, **gm;      }
   double ***gradg, ***trgradg;      ij=1; 
   double ***p3mat;  
   double age,agelim;  
   int theta;      for (i=1; i<=ncodemax[j]; i++) {
         for (k=0; k<=19; k++) {
    fprintf(ficresvij,"# Covariances of life expectancies\n");          if (Ndum[k] != 0) {
   fprintf(ficresvij,"# Age");            nbcode[Tvar[j]][ij]=k; 
   for(i=1; i<=nlstate;i++)            
     for(j=1; j<=nlstate;j++)            ij++;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          }
   fprintf(ficresvij,"\n");          if (ij > ncodemax[j]) break; 
         }  
   xp=vector(1,npar);      } 
   dnewm=matrix(1,nlstate,1,npar);    }  
   doldm=matrix(1,nlstate,1,nlstate);  
     for (k=0; k<19; k++) Ndum[k]=0;
   hstepm=1*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */   for (i=1; i<=ncovmodel-2; i++) {
   agelim = AGESUP;     ij=Tvar[i];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */     Ndum[ij]++; 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */   }
     if (stepm >= YEARM) hstepm=1;  
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */   ij=1;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   for (i=1; i<=10; i++) {
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);     if((Ndum[i]!=0) && (i<=ncovcol)){
     gp=matrix(0,nhstepm,1,nlstate);       Tvaraff[ij]=i; 
     gm=matrix(0,nhstepm,1,nlstate);       ij++;
      }
     for(theta=1; theta <=npar; theta++){   }
       for(i=1; i<=npar; i++){ /* Computes gradient */   
         xp[i] = x[i] + (i==theta ?delti[theta]:0);   cptcoveff=ij-1;
       }  }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  /*********** Health Expectancies ****************/
   
       if (popbased==1) {  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
         for(i=1; i<=nlstate;i++)  
           prlim[i][i]=probs[(int)age][i][ij];  {
       }    /* Health expectancies */
      int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
       for(j=1; j<= nlstate; j++){    double age, agelim, hf;
         for(h=0; h<=nhstepm; h++){    double ***p3mat,***varhe;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    double **dnewm,**doldm;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    double *xp;
         }    double **gp, **gm;
       }    double ***gradg, ***trgradg;
        int theta;
       for(i=1; i<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      xp=vector(1,npar);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    dnewm=matrix(1,nlstate*2,1,npar);
      doldm=matrix(1,nlstate*2,1,nlstate*2);
       if (popbased==1) {    
         for(i=1; i<=nlstate;i++)    fprintf(ficreseij,"# Health expectancies\n");
           prlim[i][i]=probs[(int)age][i][ij];    fprintf(ficreseij,"# Age");
       }    for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
       for(j=1; j<= nlstate; j++){        fprintf(ficreseij," %1d-%1d (SE)",i,j);
         for(h=0; h<=nhstepm; h++){    fprintf(ficreseij,"\n");
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)  
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    if(estepm < stepm){
         }      printf ("Problem %d lower than %d\n",estepm, stepm);
       }    }
     else  hstepm=estepm;   
       for(j=1; j<= nlstate; j++)    /* We compute the life expectancy from trapezoids spaced every estepm months
         for(h=0; h<=nhstepm; h++){     * This is mainly to measure the difference between two models: for example
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];     * if stepm=24 months pijx are given only every 2 years and by summing them
         }     * we are calculating an estimate of the Life Expectancy assuming a linear 
     } /* End theta */     * progression inbetween and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
     for(h=0; h<=nhstepm; h++)     * hypothesis. A more precise result, taking into account a more precise
       for(j=1; j<=nlstate;j++)     * curvature will be obtained if estepm is as small as stepm. */
         for(theta=1; theta <=npar; theta++)  
           trgradg[h][j][theta]=gradg[h][theta][j];    /* 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. 
     for(i=1;i<=nlstate;i++)       nhstepm is the number of hstepm from age to agelim 
       for(j=1;j<=nlstate;j++)       nstepm is the number of stepm from age to agelin. 
         vareij[i][j][(int)age] =0.;       Look at hpijx to understand the reason of that which relies in memory size
     for(h=0;h<=nhstepm;h++){       and note for a fixed period like estepm months */
       for(k=0;k<=nhstepm;k++){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);       survival function given by stepm (the optimization length). Unfortunately it
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);       means that if the survival funtion is printed only each two years of age and if
         for(i=1;i<=nlstate;i++)       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           for(j=1;j<=nlstate;j++)       results. So we changed our mind and took the option of the best precision.
             vareij[i][j][(int)age] += doldm[i][j];    */
       }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     }  
     h=1;    agelim=AGESUP;
     if (stepm >= YEARM) h=stepm/YEARM;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     fprintf(ficresvij,"%.0f ",age );      /* nhstepm age range expressed in number of stepm */
     for(i=1; i<=nlstate;i++)      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
       for(j=1; j<=nlstate;j++){      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);      /* if (stepm >= YEARM) hstepm=1;*/
       }      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     fprintf(ficresvij,"\n");      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_matrix(gp,0,nhstepm,1,nlstate);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
     free_matrix(gm,0,nhstepm,1,nlstate);      gp=matrix(0,nhstepm,1,nlstate*2);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      gm=matrix(0,nhstepm,1,nlstate*2);
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);  
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   } /* End age */         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
        hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   free_vector(xp,1,npar);   
   free_matrix(doldm,1,nlstate,1,npar);  
   free_matrix(dnewm,1,nlstate,1,nlstate);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
 }      /* Computing Variances of health expectancies */
   
 /************ Variance of prevlim ******************/       for(theta=1; theta <=npar; theta++){
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)        for(i=1; i<=npar; i++){ 
 {          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   /* Variance of prevalence limit */        }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   double **newm;    
   double **dnewm,**doldm;        cptj=0;
   int i, j, nhstepm, hstepm;        for(j=1; j<= nlstate; j++){
   int k, cptcode;          for(i=1; i<=nlstate; i++){
   double *xp;            cptj=cptj+1;
   double *gp, *gm;            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
   double **gradg, **trgradg;              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   double age,agelim;            }
   int theta;          }
            }
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");       
   fprintf(ficresvpl,"# Age");       
   for(i=1; i<=nlstate;i++)        for(i=1; i<=npar; i++) 
       fprintf(ficresvpl," %1d-%1d",i,i);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   fprintf(ficresvpl,"\n");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         
   xp=vector(1,npar);        cptj=0;
   dnewm=matrix(1,nlstate,1,npar);        for(j=1; j<= nlstate; j++){
   doldm=matrix(1,nlstate,1,nlstate);          for(i=1;i<=nlstate;i++){
              cptj=cptj+1;
   hstepm=1*YEARM; /* Every year of age */            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   agelim = AGESUP;            }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        }
     if (stepm >= YEARM) hstepm=1;        for(j=1; j<= nlstate*2; j++)
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          for(h=0; h<=nhstepm-1; h++){
     gradg=matrix(1,npar,1,nlstate);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     gp=vector(1,nlstate);          }
     gm=vector(1,nlstate);       } 
      
     for(theta=1; theta <=npar; theta++){  /* End theta */
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);       trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
       }  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);       for(h=0; h<=nhstepm-1; h++)
       for(i=1;i<=nlstate;i++)        for(j=1; j<=nlstate*2;j++)
         gp[i] = prlim[i][i];          for(theta=1; theta <=npar; theta++)
                trgradg[h][j][theta]=gradg[h][theta][j];
       for(i=1; i<=npar; i++) /* Computes gradient */       
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);       for(i=1;i<=nlstate*2;i++)
       for(i=1;i<=nlstate;i++)        for(j=1;j<=nlstate*2;j++)
         gm[i] = prlim[i][i];          varhe[i][j][(int)age] =0.;
   
       for(i=1;i<=nlstate;i++)       printf("%d|",(int)age);fflush(stdout);
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     } /* End theta */       for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
     trgradg =matrix(1,nlstate,1,npar);          matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
     for(j=1; j<=nlstate;j++)          for(i=1;i<=nlstate*2;i++)
       for(theta=1; theta <=npar; theta++)            for(j=1;j<=nlstate*2;j++)
         trgradg[j][theta]=gradg[theta][j];              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
     for(i=1;i<=nlstate;i++)      }
       varpl[i][(int)age] =0.;      /* Computing expectancies */
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      for(i=1; i<=nlstate;i++)
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        for(j=1; j<=nlstate;j++)
     for(i=1;i<=nlstate;i++)          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             
     fprintf(ficresvpl,"%.0f ",age );  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
     for(i=1; i<=nlstate;i++)  
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));          }
     fprintf(ficresvpl,"\n");  
     free_vector(gp,1,nlstate);      fprintf(ficreseij,"%3.0f",age );
     free_vector(gm,1,nlstate);      cptj=0;
     free_matrix(gradg,1,npar,1,nlstate);      for(i=1; i<=nlstate;i++)
     free_matrix(trgradg,1,nlstate,1,npar);        for(j=1; j<=nlstate;j++){
   } /* End age */          cptj++;
           fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   free_vector(xp,1,npar);        }
   free_matrix(doldm,1,nlstate,1,npar);      fprintf(ficreseij,"\n");
   free_matrix(dnewm,1,nlstate,1,nlstate);     
       free_matrix(gm,0,nhstepm,1,nlstate*2);
 }      free_matrix(gp,0,nhstepm,1,nlstate*2);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
 /************ Variance of one-step probabilities  ******************/      free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 {    }
   int i, j;    printf("\n");
   int k=0, cptcode;    fprintf(ficlog,"\n");
   double **dnewm,**doldm;  
   double *xp;    free_vector(xp,1,npar);
   double *gp, *gm;    free_matrix(dnewm,1,nlstate*2,1,npar);
   double **gradg, **trgradg;    free_matrix(doldm,1,nlstate*2,1,nlstate*2);
   double age,agelim, cov[NCOVMAX];    free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
   int theta;  }
   char fileresprob[FILENAMELENGTH];  
   /************ Variance ******************/
   strcpy(fileresprob,"prob");  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)
   strcat(fileresprob,fileres);  {
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    /* Variance of health expectancies */
     printf("Problem with resultfile: %s\n", fileresprob);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   }    /* double **newm;*/
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);    double **dnewm,**doldm;
      double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
   xp=vector(1,npar);    int k, cptcode;
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    double *xp;
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    double **gp, **gm;  /* for var eij */
      double ***gradg, ***trgradg; /*for var eij */
   cov[1]=1;    double **gradgp, **trgradgp; /* for var p point j */
   for (age=bage; age<=fage; age ++){    double *gpp, *gmp; /* for var p point j */
     cov[2]=age;    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     gradg=matrix(1,npar,1,9);    double ***p3mat;
     trgradg=matrix(1,9,1,npar);    double age,agelim, hf;
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    double ***mobaverage;
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    int theta;
        char digit[4];
     for(theta=1; theta <=npar; theta++){    char digitp[25];
       for(i=1; i<=npar; i++)  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    char fileresprobmorprev[FILENAMELENGTH];
        
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    if(popbased==1){
          if(mobilav==1)
       k=0;        strcpy(digitp,"-populbased-mobilav-");
       for(i=1; i<= (nlstate+ndeath); i++){      else strcpy(digitp,"-populbased-nomobil-");
         for(j=1; j<=(nlstate+ndeath);j++){    }
            k=k+1;    else 
           gp[k]=pmmij[i][j];      strcpy(digitp,"-stablbased-");
         }  
       }    if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1; i<=npar; i++)      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
            printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    }
       k=0;  
       for(i=1; i<=(nlstate+ndeath); i++){    strcpy(fileresprobmorprev,"prmorprev"); 
         for(j=1; j<=(nlstate+ndeath);j++){    sprintf(digit,"%-d",ij);
           k=k+1;    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
           gm[k]=pmmij[i][j];    strcat(fileresprobmorprev,digit); /* Tvar to be done */
         }    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
       }    strcat(fileresprobmorprev,fileres);
          if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)      printf("Problem with resultfile: %s\n", fileresprobmorprev);
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }    }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       for(theta=1; theta <=npar; theta++)    fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");
       trgradg[j][theta]=gradg[theta][j];    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);      fprintf(ficresprobmorprev," p.%-d SE",j);
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);      for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
      pmij(pmmij,cov,ncovmodel,x,nlstate);    }  
     fprintf(ficresprobmorprev,"\n");
      k=0;    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
      for(i=1; i<=(nlstate+ndeath); i++){      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
        for(j=1; j<=(nlstate+ndeath);j++){      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
          k=k+1;      exit(0);
          gm[k]=pmmij[i][j];    }
         }    else{
      }      fprintf(ficgp,"\n# Routine varevsij");
          }
      /*printf("\n%d ",(int)age);    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      printf("Problem with html file: %s\n", optionfilehtm);
              fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
       exit(0);
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    }
      }*/    else{
       fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
   fprintf(ficresprob,"\n%d ",(int)age);      fprintf(fichtm,"\n<br>%s (à revoir) <br>\n",digitp);
     }
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    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(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));      for(j=1; j<=nlstate;j++)
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    fprintf(ficresvij,"\n");
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
 }    xp=vector(1,npar);
  free_vector(xp,1,npar);    dnewm=matrix(1,nlstate,1,npar);
 fclose(ficresprob);    doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
 }    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
 /******************* Printing html file ***********/    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
 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[],char rfileres[] ){    gpp=vector(nlstate+1,nlstate+ndeath);
   int jj1, k1, i1, cpt;    gmp=vector(nlstate+1,nlstate+ndeath);
   FILE *fichtm;    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   /*char optionfilehtm[FILENAMELENGTH];*/    
     if(estepm < stepm){
   strcpy(optionfilehtm,optionfile);      printf ("Problem %d lower than %d\n",estepm, stepm);
   strcat(optionfilehtm,".htm");    }
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    else  hstepm=estepm;   
     printf("Problem with %s \n",optionfilehtm), exit(0);    /* 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(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.71e </font> <hr size=\"2\" color=\"#EC5E5E\">       nstepm is the number of stepm from age to agelin. 
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like k years */
 Total number of observations=%d <br>    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>       survival function given by stepm (the optimization length). Unfortunately it
 <hr  size=\"2\" color=\"#EC5E5E\">       means that if the survival funtion is printed only each two years of age and if
 <li>Outputs files<br><br>\n       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n       results. So we changed our mind and took the option of the best precision.
 - 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>    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>    agelim = AGESUP;
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>      gp=matrix(0,nhstepm,1,nlstate);
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>      gm=matrix(0,nhstepm,1,nlstate);
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,rfileres,rfileres,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(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
  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;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
  for(k1=1; k1<=m;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){        if (popbased==1) {
        jj1++;          if(mobilav ==0){
        if (cptcovn > 0) {            for(i=1; i<=nlstate;i++)
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");              prlim[i][i]=probs[(int)age][i][ij];
          for (cpt=1; cpt<=cptcoveff;cpt++)          }else{ /* mobilav */ 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);            for(i=1; i<=nlstate;i++)
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");              prlim[i][i]=mobaverage[(int)age][i][ij];
        }          }
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>        }
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        
        for(cpt=1; cpt<nlstate;cpt++){        for(j=1; j<= nlstate; j++){
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>          for(h=0; h<=nhstepm; h++){
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
        }              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
     for(cpt=1; cpt<=nlstate;cpt++) {          }
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident        }
 interval) in state (%d): v%s%d%d.gif <br>        /* This for computing forces of mortality (h=1)as a weighted average */
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
      }          for(i=1; i<= nlstate; i++)
      for(cpt=1; cpt<=nlstate;cpt++) {            gpp[j] += prlim[i][i]*p3mat[i][j][1];
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>        }    
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        /* end force of mortality */
      }  
      fprintf(fichtm,"\n<br>- Total life expectancy by age and        for(i=1; i<=npar; i++) /* Computes gradient */
 health expectancies in states (1) and (2): e%s%d.gif<br>          xp[i] = x[i] - (i==theta ?delti[theta]:0);
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 fprintf(fichtm,"\n</body>");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    }   
    }        if (popbased==1) {
 fclose(fichtm);          if(mobilav ==0){
 }            for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
 /******************* Gnuplot file **************/          }else{ /* mobilav */ 
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){            for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;          }
         }
   strcpy(optionfilegnuplot,optionfilefiname);  
   strcat(optionfilegnuplot,".plt");        for(j=1; j<= nlstate; j++){
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {          for(h=0; h<=nhstepm; h++){
     printf("Problem with file %s",optionfilegnuplot);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   }              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
 #ifdef windows        }
     fprintf(ficgp,"cd \"%s\" \n",pathc);        /* This for computing force of mortality (h=1)as a weighted average */
 #endif        for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
 m=pow(2,cptcoveff);          for(i=1; i<= nlstate; i++)
              gmp[j] += prlim[i][i]*p3mat[i][j][1];
  /* 1eme*/        }    
   for (cpt=1; cpt<= nlstate ; cpt ++) {        /* end force of mortality */
    for (k1=1; k1<= m ; k1 ++) {  
         for(j=1; j<= nlstate; j++) /* vareij */
 #ifdef windows          for(h=0; h<=nhstepm; h++){
     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);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
 #endif          }
 #ifdef unix        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
 #endif        }
   
 for (i=1; i<= nlstate ; i ++) {      } /* End theta */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
 }  
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);      for(h=0; h<=nhstepm; h++) /* veij */
     for (i=1; i<= nlstate ; i ++) {        for(j=1; j<=nlstate;j++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          for(theta=1; theta <=npar; theta++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");            trgradg[h][j][theta]=gradg[h][theta][j];
 }  
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
      for (i=1; i<= nlstate ; i ++) {        for(theta=1; theta <=npar; theta++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          trgradgp[j][theta]=gradgp[theta][j];
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }        hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      for(i=1;i<=nlstate;i++)
 #ifdef unix        for(j=1;j<=nlstate;j++)
 fprintf(ficgp,"\nset ter gif small size 400,300");          vareij[i][j][(int)age] =0.;
 #endif  
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      for(h=0;h<=nhstepm;h++){
    }        for(k=0;k<=nhstepm;k++){
   }          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   /*2 eme*/          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
   for (k1=1; k1<= m ; k1 ++) {            for(j=1;j<=nlstate;j++)
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
            }
     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);      /* pptj */
       for (j=1; j<= nlstate+1 ; j ++) {      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for(j=nlstate+1;j<=nlstate+ndeath;j++)
 }          for(i=nlstate+1;i<=nlstate+ndeath;i++)
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          varppt[j][i]=doldmp[j][i];
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);      /* end ppptj */
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       for (j=1; j<= nlstate+1 ; j ++) {      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");   
         else fprintf(ficgp," \%%*lf (\%%*lf)");      if (popbased==1) {
 }          if(mobilav ==0){
       fprintf(ficgp,"\" t\"\" w l 0,");          for(i=1; i<=nlstate;i++)
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);            prlim[i][i]=probs[(int)age][i][ij];
       for (j=1; j<= nlstate+1 ; j ++) {        }else{ /* mobilav */ 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          for(i=1; i<=nlstate;i++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");            prlim[i][i]=mobaverage[(int)age][i][ij];
 }          }
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");      }
       else fprintf(ficgp,"\" t\"\" w l 0,");      
     }      /* This for computing force of mortality (h=1)as a weighted average */
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);      for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
   }        for(i=1; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   /*3eme*/      }    
       /* end force of mortality */
   for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<= nlstate ; cpt ++) {      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       k=2+nlstate*(cpt-1);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
       for (i=1; i< nlstate ; i ++) {        for(i=1; i<=nlstate;i++){
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
       }        }
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      } 
     }      fprintf(ficresprobmorprev,"\n");
     }  
        fprintf(ficresvij,"%.0f ",age );
   /* CV preval stat */      for(i=1; i<=nlstate;i++)
     for (k1=1; k1<= m ; k1 ++) {        for(j=1; j<=nlstate;j++){
     for (cpt=1; cpt<nlstate ; cpt ++) {          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       k=3;        }
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);      fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       for (i=1; i< nlstate ; i ++)      free_matrix(gm,0,nhstepm,1,nlstate);
         fprintf(ficgp,"+$%d",k+i+1);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       l=3+(nlstate+ndeath)*cpt;    } /* End age */
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    free_vector(gpp,nlstate+1,nlstate+ndeath);
       for (i=1; i< nlstate ; i ++) {    free_vector(gmp,nlstate+1,nlstate+ndeath);
         l=3+(nlstate+ndeath)*cpt;    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
         fprintf(ficgp,"+$%d",l+i+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");
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
     }    fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);
   }      fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);
      fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);
   /* proba elementaires */    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
    for(i=1,jk=1; i <=nlstate; i++){    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);
     for(k=1; k <=(nlstate+ndeath); k++){    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
       if (k != i) {  */
         for(j=1; j <=ncovmodel; j++){    fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
          
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    free_vector(xp,1,npar);
           jk++;    free_matrix(doldm,1,nlstate,1,nlstate);
           fprintf(ficgp,"\n");    free_matrix(dnewm,1,nlstate,1,npar);
         }    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       }    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     }    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     for(jk=1; jk <=m; jk++) {    fclose(ficgp);
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);    fclose(fichtm);
    i=1;  }
    for(k2=1; k2<=nlstate; k2++) {  
      k3=i;  /************ Variance of prevlim ******************/
      for(k=1; k<=(nlstate+ndeath); k++) {  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
        if (k != k2){  {
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    /* Variance of prevalence limit */
 ij=1;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
         for(j=3; j <=ncovmodel; j++) {    double **newm;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    double **dnewm,**doldm;
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    int i, j, nhstepm, hstepm;
             ij++;    int k, cptcode;
           }    double *xp;
           else    double *gp, *gm;
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    double **gradg, **trgradg;
         }    double age,agelim;
           fprintf(ficgp,")/(1");    int theta;
             
         for(k1=1; k1 <=nlstate; k1++){      fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    fprintf(ficresvpl,"# Age");
 ij=1;    for(i=1; i<=nlstate;i++)
           for(j=3; j <=ncovmodel; j++){        fprintf(ficresvpl," %1d-%1d",i,i);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    fprintf(ficresvpl,"\n");
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  
             ij++;    xp=vector(1,npar);
           }    dnewm=matrix(1,nlstate,1,npar);
           else    doldm=matrix(1,nlstate,1,nlstate);
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    
           }    hstepm=1*YEARM; /* Every year of age */
           fprintf(ficgp,")");    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
         }    agelim = AGESUP;
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         i=i+ncovmodel;      if (stepm >= YEARM) hstepm=1;
        }      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
      }      gradg=matrix(1,npar,1,nlstate);
    }      gp=vector(1,nlstate);
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);      gm=vector(1,nlstate);
    }  
          for(theta=1; theta <=npar; theta++){
   fclose(ficgp);        for(i=1; i<=npar; i++){ /* Computes gradient */
 }  /* end gnuplot */          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 /*************** Moving average **************/        for(i=1;i<=nlstate;i++)
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){          gp[i] = prlim[i][i];
       
   int i, cpt, cptcod;        for(i=1; i<=npar; i++) /* Computes gradient */
     for (agedeb=agemin; agedeb<=fage; agedeb++)          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       for (i=1; i<=nlstate;i++)        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        for(i=1;i<=nlstate;i++)
           mobaverage[(int)agedeb][i][cptcod]=0.;          gm[i] = prlim[i][i];
      
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){        for(i=1;i<=nlstate;i++)
       for (i=1; i<=nlstate;i++){          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      } /* End theta */
           for (cpt=0;cpt<=4;cpt++){  
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];      trgradg =matrix(1,nlstate,1,npar);
           }  
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;      for(j=1; j<=nlstate;j++)
         }        for(theta=1; theta <=npar; theta++)
       }          trgradg[j][theta]=gradg[theta][j];
     }  
          for(i=1;i<=nlstate;i++)
 }        varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
 /************** Forecasting ******************/      for(i=1;i<=nlstate;i++)
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
    
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      fprintf(ficresvpl,"%.0f ",age );
   int *popage;      for(i=1; i<=nlstate;i++)
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   double *popeffectif,*popcount;      fprintf(ficresvpl,"\n");
   double ***p3mat;      free_vector(gp,1,nlstate);
   char fileresf[FILENAMELENGTH];      free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
  agelim=AGESUP;      free_matrix(trgradg,1,nlstate,1,npar);
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    } /* End age */
   
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    free_vector(xp,1,npar);
      free_matrix(doldm,1,nlstate,1,npar);
      free_matrix(dnewm,1,nlstate,1,nlstate);
   strcpy(fileresf,"f");  
   strcat(fileresf,fileres);  }
   if((ficresf=fopen(fileresf,"w"))==NULL) {  
     printf("Problem with forecast resultfile: %s\n", fileresf);  /************ Variance of one-step probabilities  ******************/
   }  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
   printf("Computing forecasting: result on file '%s' \n", fileresf);  {
     int i, j=0,  i1, k1, l1, t, tj;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    int k2, l2, j1,  z1;
     int k=0,l, cptcode;
   if (mobilav==1) {    int first=1, first1;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     movingaverage(agedeb, fage, agemin, mobaverage);    double **dnewm,**doldm;
   }    double *xp;
     double *gp, *gm;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    double **gradg, **trgradg;
   if (stepm<=12) stepsize=1;    double **mu;
      double age,agelim, cov[NCOVMAX];
   agelim=AGESUP;    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
      int theta;
   hstepm=1;    char fileresprob[FILENAMELENGTH];
   hstepm=hstepm/stepm;    char fileresprobcov[FILENAMELENGTH];
   yp1=modf(dateintmean,&yp);    char fileresprobcor[FILENAMELENGTH];
   anprojmean=yp;  
   yp2=modf((yp1*12),&yp);    double ***varpij;
   mprojmean=yp;  
   yp1=modf((yp2*30.5),&yp);    strcpy(fileresprob,"prob"); 
   jprojmean=yp;    strcat(fileresprob,fileres);
   if(jprojmean==0) jprojmean=1;    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   if(mprojmean==0) jprojmean=1;      printf("Problem with resultfile: %s\n", fileresprob);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    }
      strcpy(fileresprobcov,"probcov"); 
   for(cptcov=1;cptcov<=i2;cptcov++){    strcat(fileresprobcov,fileres);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       k=k+1;      printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficresf,"\n#******");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
       for(j=1;j<=cptcoveff;j++) {    }
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    strcpy(fileresprobcor,"probcor"); 
       }    strcat(fileresprobcor,fileres);
       fprintf(ficresf,"******\n");    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       fprintf(ficresf,"# StartingAge FinalAge");      printf("Problem with resultfile: %s\n", fileresprobcor);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
          }
          printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
         fprintf(ficresf,"\n");    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    
           nhstepm = nhstepm/hstepm;    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
              fprintf(ficresprob,"# Age");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
           oldm=oldms;savm=savms;    fprintf(ficresprobcov,"# Age");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
            fprintf(ficresprobcov,"# Age");
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);    for(i=1; i<=nlstate;i++)
             }      for(j=1; j<=(nlstate+ndeath);j++){
             for(j=1; j<=nlstate+ndeath;j++) {        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
               kk1=0.;kk2=0;        fprintf(ficresprobcov," p%1d-%1d ",i,j);
               for(i=1; i<=nlstate;i++) {                      fprintf(ficresprobcor," p%1d-%1d ",i,j);
                 if (mobilav==1)      }  
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    fprintf(ficresprob,"\n");
                 else {    fprintf(ficresprobcov,"\n");
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    fprintf(ficresprobcor,"\n");
                 }    xp=vector(1,npar);
                    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
               }    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
               if (h==(int)(calagedate+12*cpt)){    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
                 fprintf(ficresf," %.3f", kk1);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
                            first=1;
               }    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
             }      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
           }      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      exit(0);
         }    }
       }    else{
     }      fprintf(ficgp,"\n# Routine varprob");
   }    }
            if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      printf("Problem with html file: %s\n", optionfilehtm);
       fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   fclose(ficresf);      exit(0);
 }    }
 /************** Forecasting ******************/    else{
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
        fprintf(fichtm,"\n");
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  
   int *popage;      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      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");
   double *popeffectif,*popcount;      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");
   double ***p3mat,***tabpop,***tabpopprev;  
   char filerespop[FILENAMELENGTH];    }
   
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    cov[1]=1;
   agelim=AGESUP;    tj=cptcoveff;
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
      j1=0;
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    for(t=1; t<=tj;t++){
        for(i1=1; i1<=ncodemax[t];i1++){ 
          j1++;
   strcpy(filerespop,"pop");        
   strcat(filerespop,fileres);        if  (cptcovn>0) {
   if((ficrespop=fopen(filerespop,"w"))==NULL) {          fprintf(ficresprob, "\n#********** Variable "); 
     printf("Problem with forecast resultfile: %s\n", filerespop);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   }          fprintf(ficresprob, "**********\n#");
   printf("Computing forecasting: result on file '%s' \n", filerespop);          fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          fprintf(ficresprobcov, "**********\n#");
           
   if (mobilav==1) {          fprintf(ficgp, "\n#********** Variable "); 
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     movingaverage(agedeb, fage, agemin, mobaverage);          fprintf(ficgp, "**********\n#");
   }          
           
   stepsize=(int) (stepm+YEARM-1)/YEARM;          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   if (stepm<=12) stepsize=1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
   agelim=AGESUP;          
            fprintf(ficresprobcor, "\n#********** Variable ");    
   hstepm=1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   hstepm=hstepm/stepm;          fprintf(ficgp, "**********\n#");    
          }
   if (popforecast==1) {        
     if((ficpop=fopen(popfile,"r"))==NULL) {        for (age=bage; age<=fage; age ++){ 
       printf("Problem with population file : %s\n",popfile);exit(0);          cov[2]=age;
     }          for (k=1; k<=cptcovn;k++) {
     popage=ivector(0,AGESUP);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     popeffectif=vector(0,AGESUP);          }
     popcount=vector(0,AGESUP);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
              for (k=1; k<=cptcovprod;k++)
     i=1;              cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;          
              gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
     imx=i;          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];          gp=vector(1,(nlstate)*(nlstate+ndeath));
   }          gm=vector(1,(nlstate)*(nlstate+ndeath));
       
   for(cptcov=1;cptcov<=i2;cptcov++){          for(theta=1; theta <=npar; theta++){
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            for(i=1; i<=npar; i++)
       k=k+1;              xp[i] = x[i] + (i==theta ?delti[theta]:0);
       fprintf(ficrespop,"\n#******");            
       for(j=1;j<=cptcoveff;j++) {            pmij(pmmij,cov,ncovmodel,xp,nlstate);
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            
       }            k=0;
       fprintf(ficrespop,"******\n");            for(i=1; i<= (nlstate); i++){
       fprintf(ficrespop,"# Age");              for(j=1; j<=(nlstate+ndeath);j++){
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);                k=k+1;
       if (popforecast==1)  fprintf(ficrespop," [Population]");                gp[k]=pmmij[i][j];
                    }
       for (cpt=0; cpt<=0;cpt++) {            }
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);              
                    for(i=1; i<=npar; i++)
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){              xp[i] = x[i] - (i==theta ?delti[theta]:0);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      
           nhstepm = nhstepm/hstepm;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
                      k=0;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for(i=1; i<=(nlstate); i++){
           oldm=oldms;savm=savms;              for(j=1; j<=(nlstate+ndeath);j++){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                  k=k+1;
                        gm[k]=pmmij[i][j];
           for (h=0; h<=nhstepm; h++){              }
             if (h==(int) (calagedate+YEARM*cpt)) {            }
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);       
             }            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
             for(j=1; j<=nlstate+ndeath;j++) {              gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
               kk1=0.;kk2=0;          }
               for(i=1; i<=nlstate;i++) {                
                 if (mobilav==1)          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];            for(theta=1; theta <=npar; theta++)
                 else {              trgradg[j][theta]=gradg[theta][j];
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          
                 }          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);
               if (h==(int)(calagedate+12*cpt)){          
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;          pmij(pmmij,cov,ncovmodel,x,nlstate);
                   /*fprintf(ficrespop," %.3f", kk1);          
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/          k=0;
               }          for(i=1; i<=(nlstate); i++){
             }            for(j=1; j<=(nlstate+ndeath);j++){
             for(i=1; i<=nlstate;i++){              k=k+1;
               kk1=0.;              mu[k][(int) age]=pmmij[i][j];
                 for(j=1; j<=nlstate;j++){            }
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];          }
                 }          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
             }              varpij[i][j][(int)age] = doldm[i][j];
   
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)          /*printf("\n%d ",(int)age);
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);       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_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);         fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
         }       }*/
       }  
            fprintf(ficresprob,"\n%d ",(int)age);
   /******/          fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {  
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
           nhstepm = nhstepm/hstepm;            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
                      fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
           oldm=oldms;savm=savms;          i=0;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            for (k=1; k<=(nlstate);k++){
           for (h=0; h<=nhstepm; h++){            for (l=1; l<=(nlstate+ndeath);l++){ 
             if (h==(int) (calagedate+YEARM*cpt)) {              i=i++;
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
             }              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
             for(j=1; j<=nlstate+ndeath;j++) {              for (j=1; j<=i;j++){
               kk1=0.;kk2=0;                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
               for(i=1; i<=nlstate;i++) {                              fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                  }
               }            }
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);          }/* end of loop for state */
             }        } /* end of loop for age */
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        /* Confidence intervalle of pij  */
         }        /*
       }        fprintf(ficgp,"\nset noparametric;unset label");
    }        fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   }        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
   if (popforecast==1) {        fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
     free_ivector(popage,0,AGESUP);        */
     free_vector(popeffectif,0,AGESUP);  
     free_vector(popcount,0,AGESUP);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
   }        first1=1;
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for (k2=1; k2<=(nlstate);k2++){
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
   fclose(ficrespop);            if(l2==k2) continue;
 }            j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
 /***********************************************/              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
 /**************** Main Program *****************/                if(l1==k1) continue;
 /***********************************************/                i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
 int main(int argc, char *argv[])                for (age=bage; age<=fage; age ++){ 
 {                  if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   double agedeb, agefin,hf;                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;                    mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
   double fret;                    c12=cv12/sqrt(v1*v2);
   double **xi,tmp,delta;                    /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   double dum; /* Dummy variable */                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   double ***p3mat;                    /* Eigen vectors */
   int *indx;                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
   char line[MAXLINE], linepar[MAXLINE];                    /*v21=sqrt(1.-v11*v11); *//* error */
   char title[MAXLINE];                    v21=(lc1-v1)/cv12*v11;
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];                    v12=-v21;
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];                    v22=v11;
                      tnalp=v21/v11;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];                    if(first1==1){
                       first1=0;
   char filerest[FILENAMELENGTH];                      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);
   char fileregp[FILENAMELENGTH];                    }
   char popfile[FILENAMELENGTH];                    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);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];                    /*printf(fignu*/
   int firstobs=1, lastobs=10;                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
   int sdeb, sfin; /* Status at beginning and end */                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   int c,  h , cpt,l;                    if(first==1){
   int ju,jl, mi;                      first=0;
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;                      fprintf(ficgp,"\nset parametric;unset label");
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;                      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);
   int mobilav=0,popforecast=0;                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   int hstepm, nhstepm;                      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);
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
                       fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
   double bage, fage, age, agelim, agebase;                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
   double ftolpl=FTOL;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   double **prlim;                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   double *severity;                      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",\
   double ***param; /* Matrix of parameters */                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   double  *p;                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   double **matcov; /* Matrix of covariance */                    }else{
   double ***delti3; /* Scale */                      first=0;
   double *delti; /* Scale */                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
   double ***eij, ***vareij;                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   double **varpl; /* Variances of prevalence limits by age */                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   double *epj, vepp;                      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",\
   double kk1, kk2;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                      }/* if first */
                   } /* age mod 5 */
   char version[80]="Imach version 0.71e, March 2002, INED-EUROREVES ";                } /* end loop age */
   char *alph[]={"a","a","b","c","d","e"}, str[4];                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
   char z[1]="c", occ;            } /* k12 */
 #include <sys/time.h>          } /*l1 */
 #include <time.h>        }/* k1 */
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      } /* loop covariates */
        free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   /* long total_usecs;      free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   struct timeval start_time, end_time;      free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
        free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     }
   printf("\n%s",version);    free_vector(xp,1,npar);
   if(argc <=1){    fclose(ficresprob);
     printf("\nEnter the parameter file name: ");    fclose(ficresprobcov);
     scanf("%s",pathtot);    fclose(ficresprobcor);
   }    fclose(ficgp);
   else{    fclose(fichtm);
     strcpy(pathtot,argv[1]);  }
   }  
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/  
   /*cygwin_split_path(pathtot,path,optionfile);  /******************* Printing html file ***********/
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
   /* cutv(path,optionfile,pathtot,'\\');*/                    int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);                    int popforecast, int estepm ,\
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);                    double jprev1, double mprev1,double anprev1, \
   chdir(path);                    double jprev2, double mprev2,double anprev2){
   replace(pathc,path);    int jj1, k1, i1, cpt;
     /*char optionfilehtm[FILENAMELENGTH];*/
 /*-------- arguments in the command line --------*/    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
   strcpy(fileres,"r");      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
   strcat(fileres, optionfilefiname);    }
   strcat(fileres,".txt");    /* Other files have txt extension */  
      fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
   /*---------arguments file --------*/   - 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
    - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
   if((ficpar=fopen(optionfile,"r"))==NULL)    {   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
     printf("Problem with optionfile %s\n",optionfile);   - Life expectancies by age and initial health status (estepm=%2d months): 
     goto end;     <a href=\"e%s\">e%s</a> <br>\n</li>", \
   }    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
   
   strcpy(filereso,"o");  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   strcat(filereso,fileres);  
   if((ficparo=fopen(filereso,"w"))==NULL) {   m=cptcoveff;
     printf("Problem with Output resultfile: %s\n", filereso);goto end;   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   }  
    jj1=0;
   /* Reads comments: lines beginning with '#' */   for(k1=1; k1<=m;k1++){
   while((c=getc(ficpar))=='#' && c!= EOF){     for(i1=1; i1<=ncodemax[k1];i1++){
     ungetc(c,ficpar);       jj1++;
     fgets(line, MAXLINE, ficpar);       if (cptcovn > 0) {
     puts(line);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     fputs(line,ficparo);         for (cpt=1; cpt<=cptcoveff;cpt++) 
   }           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   ungetc(c,ficpar);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
   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);       /* Pij */
   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);       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>
   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);  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
 while((c=getc(ficpar))=='#' && c!= EOF){       /* Quasi-incidences */
     ungetc(c,ficpar);       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>
     fgets(line, MAXLINE, ficpar);  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
     puts(line);         /* Stable prevalence in each health state */
     fputs(line,ficparo);         for(cpt=1; cpt<nlstate;cpt++){
   }           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
   ungetc(c,ficpar);  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
           }
           for(cpt=1; cpt<=nlstate;cpt++) {
   covar=matrix(0,NCOVMAX,1,n);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
   cptcovn=0;  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;       }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and
   ncovmodel=2+cptcovn;  health expectancies in states (1) and (2): e%s%d.png<br>
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
       } /* end i1 */
   /* Read guess parameters */   }/* End k1 */
   /* Reads comments: lines beginning with '#' */   fprintf(fichtm,"</ul>");
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
     puts(line);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
     fputs(line,ficparo);   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
   }   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
   ungetc(c,ficpar);   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
     - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
     for(i=1; i <=nlstate; i++)   - 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);
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);   if(popforecast==1) fprintf(fichtm,"\n
       fprintf(ficparo,"%1d%1d",i1,j1);   - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
       printf("%1d%1d",i,j);   - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
       for(k=1; k<=ncovmodel;k++){          <br>",fileres,fileres,fileres,fileres);
         fscanf(ficpar," %lf",&param[i][j][k]);   else 
         printf(" %lf",param[i][j][k]);     fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
         fprintf(ficparo," %lf",param[i][j][k]);  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
       }  
       fscanf(ficpar,"\n");   m=cptcoveff;
       printf("\n");   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       fprintf(ficparo,"\n");  
     }   jj1=0;
     for(k1=1; k1<=m;k1++){
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;     for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
   p=param[1][1];       if (cptcovn > 0) {
           fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   /* Reads comments: lines beginning with '#' */         for (cpt=1; cpt<=cptcoveff;cpt++) 
   while((c=getc(ficpar))=='#' && c!= EOF){           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     ungetc(c,ficpar);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     fgets(line, MAXLINE, ficpar);       }
     puts(line);       for(cpt=1; cpt<=nlstate;cpt++) {
     fputs(line,ficparo);         fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
   }  interval) in state (%d): v%s%d%d.png <br>
   ungetc(c,ficpar);  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
        }
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);     } /* end i1 */
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */   }/* End k1 */
   for(i=1; i <=nlstate; i++){   fprintf(fichtm,"</ul>");
     for(j=1; j <=nlstate+ndeath-1; j++){  fclose(fichtm);
       fscanf(ficpar,"%1d%1d",&i1,&j1);  }
       printf("%1d%1d",i,j);  
       fprintf(ficparo,"%1d%1d",i1,j1);  /******************* Gnuplot file **************/
       for(k=1; k<=ncovmodel;k++){  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
         fscanf(ficpar,"%le",&delti3[i][j][k]);  
         printf(" %le",delti3[i][j][k]);    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
         fprintf(ficparo," %le",delti3[i][j][k]);    int ng;
       }    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       fscanf(ficpar,"\n");      printf("Problem with file %s",optionfilegnuplot);
       printf("\n");      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
       fprintf(ficparo,"\n");    }
     }  
   }    /*#ifdef windows */
   delti=delti3[1][1];      fprintf(ficgp,"cd \"%s\" \n",pathc);
        /*#endif */
   /* Reads comments: lines beginning with '#' */  m=pow(2,cptcoveff);
   while((c=getc(ficpar))=='#' && c!= EOF){    
     ungetc(c,ficpar);   /* 1eme*/
     fgets(line, MAXLINE, ficpar);    for (cpt=1; cpt<= nlstate ; cpt ++) {
     puts(line);     for (k1=1; k1<= m ; k1 ++) {
     fputs(line,ficparo);       fprintf(ficgp,"\nset out \"v%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] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
   ungetc(c,ficpar);  
         for (i=1; i<= nlstate ; i ++) {
   matcov=matrix(1,npar,1,npar);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   for(i=1; i <=npar; i++){         else fprintf(ficgp," \%%*lf (\%%*lf)");
     fscanf(ficpar,"%s",&str);       }
     printf("%s",str);       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
     fprintf(ficparo,"%s",str);       for (i=1; i<= nlstate ; i ++) {
     for(j=1; j <=i; j++){         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       fscanf(ficpar," %le",&matcov[i][j]);         else fprintf(ficgp," \%%*lf (\%%*lf)");
       printf(" %.5le",matcov[i][j]);       } 
       fprintf(ficparo," %.5le",matcov[i][j]);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); 
     }       for (i=1; i<= nlstate ; i ++) {
     fscanf(ficpar,"\n");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     printf("\n");         else fprintf(ficgp," \%%*lf (\%%*lf)");
     fprintf(ficparo,"\n");       }  
   }       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
   for(i=1; i <=npar; i++)     }
     for(j=i+1;j<=npar;j++)    }
       matcov[i][j]=matcov[j][i];    /*2 eme*/
        
   printf("\n");    for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
     /*-------- Rewriting paramater file ----------*/      
      strcpy(rfileres,"r");    /* "Rparameterfile */      for (i=1; i<= nlstate+1 ; i ++) {
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/        k=2*i;
      strcat(rfileres,".");    /* */        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
      strcat(rfileres,optionfilext);    /* Other files have txt extension */        for (j=1; j<= nlstate+1 ; j ++) {
     if((ficres =fopen(rfileres,"w"))==NULL) {          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       printf("Problem writing new parameter file: %s\n", fileres);goto end;          else fprintf(ficgp," \%%*lf (\%%*lf)");
     }        }   
     fprintf(ficres,"#%s\n",version);        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
            else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
     /*-------- data file ----------*/        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
     if((fic=fopen(datafile,"r"))==NULL)    {        for (j=1; j<= nlstate+1 ; j ++) {
       printf("Problem with datafile: %s\n", datafile);goto end;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     }          else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
     n= lastobs;        fprintf(ficgp,"\" t\"\" w l 0,");
     severity = vector(1,maxwav);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
     outcome=imatrix(1,maxwav+1,1,n);        for (j=1; j<= nlstate+1 ; j ++) {
     num=ivector(1,n);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     moisnais=vector(1,n);          else fprintf(ficgp," \%%*lf (\%%*lf)");
     annais=vector(1,n);        }   
     moisdc=vector(1,n);        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
     andc=vector(1,n);        else fprintf(ficgp,"\" t\"\" w l 0,");
     agedc=vector(1,n);      }
     cod=ivector(1,n);    }
     weight=vector(1,n);    
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    /*3eme*/
     mint=matrix(1,maxwav,1,n);    
     anint=matrix(1,maxwav,1,n);    for (k1=1; k1<= m ; k1 ++) { 
     s=imatrix(1,maxwav+1,1,n);      for (cpt=1; cpt<= nlstate ; cpt ++) {
     adl=imatrix(1,maxwav+1,1,n);            k=2+nlstate*(2*cpt-2);
     tab=ivector(1,NCOVMAX);        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     ncodemax=ivector(1,8);        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     i=1;          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     while (fgets(line, MAXLINE, fic) != NULL)    {          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
       if ((i >= firstobs) && (i <=lastobs)) {          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
                  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
         for (j=maxwav;j>=1;j--){          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           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);        for (i=1; i< nlstate ; i ++) {
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
         }          
                } 
         cutv(stra, strb,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);    /* CV preval stat */
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<nlstate ; cpt ++) {
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);        k=3;
         for (j=ncov;j>=1;j--){        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
         }        
         num[i]=atol(stra);        for (i=1; i< nlstate ; i ++)
                  fprintf(ficgp,"+$%d",k+i+1);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+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])); ij=ij+1;}*/        
         l=3+(nlstate+ndeath)*cpt;
         i=i+1;        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
       }        for (i=1; i< nlstate ; i ++) {
     }          l=3+(nlstate+ndeath)*cpt;
     /* printf("ii=%d", ij);          fprintf(ficgp,"+$%d",l+i+1);
        scanf("%d",i);*/        }
   imx=i-1; /* Number of individuals */        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
   /* 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;    /* proba elementaires */
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    for(i=1,jk=1; i <=nlstate; i++){
     }      for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
     for (i=1; i<=imx; i++)          for(j=1; j <=ncovmodel; j++){
     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(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
   /* Calculation of the number of parameter from char model*/            fprintf(ficgp,"\n");
   Tvar=ivector(1,15);          }
   Tprod=ivector(1,15);        }
   Tvaraff=ivector(1,15);      }
   Tvard=imatrix(1,15,1,2);     }
   Tage=ivector(1,15);        
         for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
   if (strlen(model) >1){       for(jk=1; jk <=m; jk++) {
     j=0, j1=0, k1=1, k2=1;         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
     j=nbocc(model,'+');         if (ng==2)
     j1=nbocc(model,'*');           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
     cptcovn=j+1;         else
     cptcovprod=j1;           fprintf(ficgp,"\nset title \"Probability\"\n");
             fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
             i=1;
     strcpy(modelsav,model);         for(k2=1; k2<=nlstate; k2++) {
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){           k3=i;
       printf("Error. Non available option model=%s ",model);           for(k=1; k<=(nlstate+ndeath); k++) {
       goto end;             if (k != k2){
     }               if(ng==2)
                     fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
     for(i=(j+1); i>=1;i--){               else
       cutv(stra,strb,modelsav,'+');                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);               ij=1;
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/               for(j=3; j <=ncovmodel; j++) {
       /*scanf("%d",i);*/                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
       if (strchr(strb,'*')) {                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
         cutv(strd,strc,strb,'*');                   ij++;
         if (strcmp(strc,"age")==0) {                 }
           cptcovprod--;                 else
           cutv(strb,stre,strd,'V');                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
           Tvar[i]=atoi(stre);               }
           cptcovage++;               fprintf(ficgp,")/(1");
             Tage[cptcovage]=i;               
             /*printf("stre=%s ", stre);*/               for(k1=1; k1 <=nlstate; k1++){   
         }                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
         else if (strcmp(strd,"age")==0) {                 ij=1;
           cptcovprod--;                 for(j=3; j <=ncovmodel; j++){
           cutv(strb,stre,strc,'V');                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
           Tvar[i]=atoi(stre);                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
           cptcovage++;                     ij++;
           Tage[cptcovage]=i;                   }
         }                   else
         else {                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
           cutv(strb,stre,strc,'V');                 }
           Tvar[i]=ncov+k1;                 fprintf(ficgp,")");
           cutv(strb,strc,strd,'V');               }
           Tprod[k1]=i;               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
           Tvard[k1][1]=atoi(strc);               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
           Tvard[k1][2]=atoi(stre);               i=i+ncovmodel;
           Tvar[cptcovn+k2]=Tvard[k1][1];             }
           Tvar[cptcovn+k2+1]=Tvard[k1][2];           } /* end k */
           for (k=1; k<=lastobs;k++)         } /* end k2 */
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];       } /* end jk */
           k1++;     } /* end ng */
           k2=k2+2;     fclose(ficgp); 
         }  }  /* end gnuplot */
       }  
       else {  
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/  /*************** Moving average **************/
        /*  scanf("%d",i);*/  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
       cutv(strd,strc,strb,'V');  
       Tvar[i]=atoi(strc);    int i, cpt, cptcod;
       }    int mobilavrange, mob;
       strcpy(modelsav,stra);      double age;
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
         scanf("%d",i);*/      if(mobilav==1) mobilavrange=5; /* default */
     }      else mobilavrange=mobilav;
 }      for (age=bage; age<=fage; age++)
          for (i=1; i<=nlstate;i++)
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);          for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
   printf("cptcovprod=%d ", cptcovprod);            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
   scanf("%d ",i);*/      /* We keep the original values on the extreme ages bage, fage and for 
     fclose(fic);         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
     /*  if(mle==1){*/      */ 
     if (weightopt != 1) { /* Maximisation without weights*/      for (mob=3;mob <=mobilavrange;mob=mob+2){
       for(i=1;i<=n;i++) weight[i]=1.0;        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
     }          for (i=1; i<=nlstate;i++){
     /*-calculation of age at interview from date of interview and age at death -*/            for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
     agev=matrix(1,maxwav,1,imx);              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
    for (i=1; i<=imx; i++)                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
      for(m=2; (m<= maxwav); m++)                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){                }
          anint[m][i]=9999;              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
          s[m][i]=-1;            }
        }          }
            }/* end age */
     for (i=1; i<=imx; i++)  {      }/* end mob */
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    }else return -1;
       for(m=1; (m<= maxwav); m++){    return 0;
         if(s[m][i] >0){  }/* End movingaverage */
           if (s[m][i] == nlstate+1) {  
             if(agedc[i]>0)  
               if(moisdc[i]!=99 && andc[i]!=9999)  /************** Forecasting ******************/
               agev[m][i]=agedc[i];  prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){
             else {    
               if (andc[i]!=9999){    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    int *popage;
               agev[m][i]=-1;    double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
               }    double *popeffectif,*popcount;
             }    double ***p3mat;
           }    double ***mobaverage;
           else if(s[m][i] !=9){ /* Should no more exist */    char fileresf[FILENAMELENGTH];
             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)   agelim=AGESUP;
               agev[m][i]=1;  calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
             else if(agev[m][i] <agemin){  
               agemin=agev[m][i];    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
               /*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){    strcpy(fileresf,"f"); 
               agemax=agev[m][i];    strcat(fileresf,fileres);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    if((ficresf=fopen(fileresf,"w"))==NULL) {
             }      printf("Problem with forecast resultfile: %s\n", fileresf);
             /*agev[m][i]=anint[m][i]-annais[i];*/      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
             /*   agev[m][i] = age[i]+2*m;*/    }
           }    printf("Computing forecasting: result on file '%s' \n", fileresf);
           else { /* =9 */    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
             agev[m][i]=1;  
             s[m][i]=-1;    if (cptcoveff==0) ncodemax[cptcoveff]=1;
           }  
         }    if (mobilav!=0) {
         else /*= 0 Unknown */      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           agev[m][i]=1;      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);
     }      }
     for (i=1; i<=imx; i++)  {    }
       for(m=1; (m<= maxwav); m++){  
         if (s[m][i] > (nlstate+ndeath)) {    stepsize=(int) (stepm+YEARM-1)/YEARM;
           printf("Error: Wrong value in nlstate or ndeath\n");      if (stepm<=12) stepsize=1;
           goto end;    
         }    agelim=AGESUP;
       }    
     }    hstepm=1;
     hstepm=hstepm/stepm; 
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    yp1=modf(dateintmean,&yp);
     anprojmean=yp;
     free_vector(severity,1,maxwav);    yp2=modf((yp1*12),&yp);
     free_imatrix(outcome,1,maxwav+1,1,n);    mprojmean=yp;
     free_vector(moisnais,1,n);    yp1=modf((yp2*30.5),&yp);
     free_vector(annais,1,n);    jprojmean=yp;
     /* free_matrix(mint,1,maxwav,1,n);    if(jprojmean==0) jprojmean=1;
        free_matrix(anint,1,maxwav,1,n);*/    if(mprojmean==0) jprojmean=1;
     free_vector(moisdc,1,n);    
     free_vector(andc,1,n);    fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean); 
     
        for(cptcov=1;cptcov<=i2;cptcov++){
     wav=ivector(1,imx);      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
     dh=imatrix(1,lastpass-firstpass+1,1,imx);        k=k+1;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);        fprintf(ficresf,"\n#******");
            for(j=1;j<=cptcoveff;j++) {
     /* Concatenates waves */          fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);        }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# StartingAge FinalAge");
       Tcode=ivector(1,100);        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);        
       ncodemax[1]=1;        
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);        for (cpt=0; cpt<=(anproj2-anproj1);cpt++) { 
                fprintf(ficresf,"\n");
    codtab=imatrix(1,100,1,10);          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);   
    h=0;  
    m=pow(2,cptcoveff);          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
              nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
    for(k=1;k<=cptcoveff; k++){            nhstepm = nhstepm/hstepm; 
      for(i=1; i <=(m/pow(2,k));i++){            
        for(j=1; j <= ncodemax[k]; j++){            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){            oldm=oldms;savm=savms;
            h++;            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
            if (h>m) h=1;codtab[h][k]=j;          
          }            for (h=0; h<=nhstepm; h++){
        }              if (h==(int) (calagedate+YEARM*cpt)) {
      }                fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
    }              } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
    /*for(i=1; i <=m ;i++){                for(i=1; i<=nlstate;i++) {              
      for(k=1; k <=cptcovn; k++){                  if (mobilav==1) 
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
      }                  else {
      printf("\n");                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
    }                  }
    scanf("%d",i);*/                  
                    }
    /* Calculates basic frequencies. Computes observed prevalence at single age                if (h==(int)(calagedate+12*cpt)){
        and prints on file fileres'p'. */                  fprintf(ficresf," %.3f", kk1);
                           
                    }
                  }
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            }
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     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] */    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */  
     fclose(ficresf);
     if(mle==1){  }
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  /************** Forecasting ******************/
     }  populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
        
     /*--------- results files --------------*/    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     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= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, weightopt,model);    int *popage;
      double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
    jk=1;    double ***p3mat,***tabpop,***tabpopprev;
    fprintf(ficres,"# Parameters\n");    double ***mobaverage;
    printf("# Parameters\n");    char filerespop[FILENAMELENGTH];
    for(i=1,jk=1; i <=nlstate; i++){  
      for(k=1; k <=(nlstate+ndeath); k++){    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        if (k != i)    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
          {    agelim=AGESUP;
            printf("%d%d ",i,k);    calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
            fprintf(ficres,"%1d%1d ",i,k);    
            for(j=1; j <=ncovmodel; j++){    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
              printf("%f ",p[jk]);    
              fprintf(ficres,"%f ",p[jk]);    
              jk++;    strcpy(filerespop,"pop"); 
            }    strcat(filerespop,fileres);
            printf("\n");    if((ficrespop=fopen(filerespop,"w"))==NULL) {
            fprintf(ficres,"\n");      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);
  if(mle==1){    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
     /* Computing hessian and covariance matrix */  
     ftolhess=ftol; /* Usually correct */    if (cptcoveff==0) ncodemax[cptcoveff]=1;
     hesscov(matcov, p, npar, delti, ftolhess, func);  
  }    if (mobilav!=0) {
     fprintf(ficres,"# Scales\n");      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     printf("# Scales\n");      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
      for(i=1,jk=1; i <=nlstate; i++){        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       for(j=1; j <=nlstate+ndeath; j++){        printf(" Error in movingaverage mobilav=%d\n",mobilav);
         if (j!=i) {      }
           fprintf(ficres,"%1d%1d",i,j);    }
           printf("%1d%1d",i,j);  
           for(k=1; k<=ncovmodel;k++){    stepsize=(int) (stepm+YEARM-1)/YEARM;
             printf(" %.5e",delti[jk]);    if (stepm<=12) stepsize=1;
             fprintf(ficres," %.5e",delti[jk]);    
             jk++;    agelim=AGESUP;
           }    
           printf("\n");    hstepm=1;
           fprintf(ficres,"\n");    hstepm=hstepm/stepm; 
         }    
       }    if (popforecast==1) {
      }      if((ficpop=fopen(popfile,"r"))==NULL) {
            printf("Problem with population file : %s\n",popfile);exit(0);
     k=1;        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
     fprintf(ficres,"# Covariance\n");      } 
     printf("# Covariance\n");      popage=ivector(0,AGESUP);
     for(i=1;i<=npar;i++){      popeffectif=vector(0,AGESUP);
       /*  if (k>nlstate) k=1;      popcount=vector(0,AGESUP);
       i1=(i-1)/(ncovmodel*nlstate)+1;      
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);      i=1;   
       printf("%s%d%d",alph[k],i1,tab[i]);*/      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
       fprintf(ficres,"%3d",i);     
       printf("%3d",i);      imx=i;
       for(j=1; j<=i;j++){      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
         fprintf(ficres," %.5e",matcov[i][j]);    }
         printf(" %.5e",matcov[i][j]);  
       }    for(cptcov=1;cptcov<=i2;cptcov++){
       fprintf(ficres,"\n");     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
       printf("\n");        k=k+1;
       k++;        fprintf(ficrespop,"\n#******");
     }        for(j=1;j<=cptcoveff;j++) {
              fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
     while((c=getc(ficpar))=='#' && c!= EOF){        }
       ungetc(c,ficpar);        fprintf(ficrespop,"******\n");
       fgets(line, MAXLINE, ficpar);        fprintf(ficrespop,"# Age");
       puts(line);        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
       fputs(line,ficparo);        if (popforecast==1)  fprintf(ficrespop," [Population]");
     }        
     ungetc(c,ficpar);        for (cpt=0; cpt<=0;cpt++) { 
            fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);          
              for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
     if (fage <= 2) {            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
       bage = agemin;            nhstepm = nhstepm/hstepm; 
       fage = agemaxpar;            
     }            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                oldm=oldms;savm=savms;
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);          
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);            for (h=0; h<=nhstepm; h++){
                if (h==(int) (calagedate+YEARM*cpt)) {
     while((c=getc(ficpar))=='#' && c!= EOF){                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
     ungetc(c,ficpar);              } 
     fgets(line, MAXLINE, ficpar);              for(j=1; j<=nlstate+ndeath;j++) {
     puts(line);                kk1=0.;kk2=0;
     fputs(line,ficparo);                for(i=1; i<=nlstate;i++) {              
   }                  if (mobilav==1) 
   ungetc(c,ficpar);                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                    else {
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                  }
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                }
                      if (h==(int)(calagedate+12*cpt)){
   while((c=getc(ficpar))=='#' && c!= EOF){                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
     ungetc(c,ficpar);                    /*fprintf(ficrespop," %.3f", kk1);
     fgets(line, MAXLINE, ficpar);                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
     puts(line);                }
     fputs(line,ficparo);              }
   }              for(i=1; i<=nlstate;i++){
   ungetc(c,ficpar);                kk1=0.;
                    for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
    dateprev1=anprev1+mprev1/12.+jprev1/365.;                  }
    dateprev2=anprev2+mprev2/12.+jprev2/365.;                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   fscanf(ficpar,"pop_based=%d\n",&popbased);  
   fprintf(ficparo,"pop_based=%d\n",popbased);                if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) 
   fprintf(ficres,"pop_based=%d\n",popbased);                  fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
              }
   while((c=getc(ficpar))=='#' && c!= EOF){            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);        }
     puts(line);   
     fputs(line,ficparo);    /******/
   }  
   ungetc(c,ficpar);        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);            nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 while((c=getc(ficpar))=='#' && c!= EOF){            oldm=oldms;savm=savms;
     ungetc(c,ficpar);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
     fgets(line, MAXLINE, ficpar);            for (h=0; h<=nhstepm; h++){
     puts(line);              if (h==(int) (calagedate+YEARM*cpt)) {
     fputs(line,ficparo);                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
   }              } 
   ungetc(c,ficpar);              for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);                for(i=1; i<=nlstate;i++) {              
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);                }
                 if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1); 
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);              }
             }
 /*------------ gnuplot -------------*/            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);          }
          }
 /*------------ free_vector  -------------*/     } 
  chdir(path);    }
     
  free_ivector(wav,1,imx);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      if (popforecast==1) {
  free_ivector(num,1,n);      free_ivector(popage,0,AGESUP);
  free_vector(agedc,1,n);      free_vector(popeffectif,0,AGESUP);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/      free_vector(popcount,0,AGESUP);
  fclose(ficparo);    }
  fclose(ficres);    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 /*--------- index.htm --------*/    fclose(ficrespop);
   }
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres);  
   /***********************************************/
    /**************** Main Program *****************/
   /*--------------- Prevalence limit --------------*/  /***********************************************/
    
   strcpy(filerespl,"pl");  int main(int argc, char *argv[])
   strcat(filerespl,fileres);  {
   if((ficrespl=fopen(filerespl,"w"))==NULL) {  
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
   }    double agedeb, agefin,hf;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   fprintf(ficrespl,"#Prevalence limit\n");  
   fprintf(ficrespl,"#Age ");    double fret;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    double **xi,tmp,delta;
   fprintf(ficrespl,"\n");  
      double dum; /* Dummy variable */
   prlim=matrix(1,nlstate,1,nlstate);    double ***p3mat;
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double ***mobaverage;
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int *indx;
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    char line[MAXLINE], linepar[MAXLINE];
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    int firstobs=1, lastobs=10;
   k=0;    int sdeb, sfin; /* Status at beginning and end */
   agebase=agemin;    int c,  h , cpt,l;
   agelim=agemaxpar;    int ju,jl, mi;
   ftolpl=1.e-10;    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
   i1=cptcoveff;    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab; 
   if (cptcovn < 1){i1=1;}    int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
   for(cptcov=1;cptcov<=i1;cptcov++){    double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
         k=k+1;    double bage, fage, age, agelim, agebase;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    double ftolpl=FTOL;
         fprintf(ficrespl,"\n#******");    double **prlim;
         for(j=1;j<=cptcoveff;j++)    double *severity;
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double ***param; /* Matrix of parameters */
         fprintf(ficrespl,"******\n");    double  *p;
            double **matcov; /* Matrix of covariance */
         for (age=agebase; age<=agelim; age++){    double ***delti3; /* Scale */
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    double *delti; /* Scale */
           fprintf(ficrespl,"%.0f",age );    double ***eij, ***vareij;
           for(i=1; i<=nlstate;i++)    double **varpl; /* Variances of prevalence limits by age */
           fprintf(ficrespl," %.5f", prlim[i][i]);    double *epj, vepp;
           fprintf(ficrespl,"\n");    double kk1, kk2;
         }    double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
       }    
     }  
   fclose(ficrespl);    char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   /*------------- h Pij x at various ages ------------*/  
      char z[1]="c", occ;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  #include <sys/time.h>
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  #include <time.h>
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
   }   
   printf("Computing pij: result on file '%s' \n", filerespij);    /* long total_usecs;
      struct timeval start_time, end_time;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    
   /*if (stepm<=24) stepsize=2;*/    gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     getcwd(pathcd, size);
   agelim=AGESUP;  
   hstepm=stepsize*YEARM; /* Every year of age */    printf("\n%s",version);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    if(argc <=1){
        printf("\nEnter the parameter file name: ");
   k=0;      scanf("%s",pathtot);
   for(cptcov=1;cptcov<=i1;cptcov++){    }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    else{
       k=k+1;      strcpy(pathtot,argv[1]);
         fprintf(ficrespij,"\n#****** ");    }
         for(j=1;j<=cptcoveff;j++)    /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /*cygwin_split_path(pathtot,path,optionfile);
         fprintf(ficrespij,"******\n");      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
            /* cutv(path,optionfile,pathtot,'\\');*/
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */     printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    chdir(path);
           oldm=oldms;savm=savms;    replace(pathc,path);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
           fprintf(ficrespij,"# Age");  /*-------- arguments in the command line --------*/
           for(i=1; i<=nlstate;i++)  
             for(j=1; j<=nlstate+ndeath;j++)    /* Log file */
               fprintf(ficrespij," %1d-%1d",i,j);    strcat(filelog, optionfilefiname);
           fprintf(ficrespij,"\n");    strcat(filelog,".log");    /* */
           for (h=0; h<=nhstepm; h++){    if((ficlog=fopen(filelog,"w"))==NULL)    {
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );      printf("Problem with logfile %s\n",filelog);
             for(i=1; i<=nlstate;i++)      goto end;
               for(j=1; j<=nlstate+ndeath;j++)    }
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    fprintf(ficlog,"Log filename:%s\n",filelog);
             fprintf(ficrespij,"\n");    fprintf(ficlog,"\n%s",version);
           }    fprintf(ficlog,"\nEnter the parameter file name: ");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
           fprintf(ficrespij,"\n");    fflush(ficlog);
         }  
     }    /* */
   }    strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/    strcat(fileres,".txt");    /* Other files have txt extension */
   
   fclose(ficrespij);    /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
   /*---------- Forecasting ------------------*/      printf("Problem with optionfile %s\n",optionfile);
   if((stepm == 1) && (strcmp(model,".")==0)){      fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);      goto end;
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    }
     free_matrix(mint,1,maxwav,1,n);  
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    strcpy(filereso,"o");
     free_vector(weight,1,n);}    strcat(filereso,fileres);
   else{    if((ficparo=fopen(filereso,"w"))==NULL) {
     erreur=108;      printf("Problem with Output resultfile: %s\n", filereso);
     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,"Problem with Output resultfile: %s\n", filereso);
   }      goto end;
      }
   
   /*---------- Health expectancies and variances ------------*/    /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
   strcpy(filerest,"t");      ungetc(c,ficpar);
   strcat(filerest,fileres);      fgets(line, MAXLINE, ficpar);
   if((ficrest=fopen(filerest,"w"))==NULL) {      puts(line);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      fputs(line,ficparo);
   }    }
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    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);
   strcpy(filerese,"e");    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);
   strcat(filerese,fileres);    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);
   if((ficreseij=fopen(filerese,"w"))==NULL) {  while((c=getc(ficpar))=='#' && c!= EOF){
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      ungetc(c,ficpar);
   }      fgets(line, MAXLINE, ficpar);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      puts(line);
       fputs(line,ficparo);
  strcpy(fileresv,"v");    }
   strcat(fileresv,fileres);    ungetc(c,ficpar);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);     
   }    covar=matrix(0,NCOVMAX,1,n); 
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    cptcovn=0; 
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){    ncovmodel=2+cptcovn;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
       k=k+1;    
       fprintf(ficrest,"\n#****** ");    /* Read guess parameters */
       for(j=1;j<=cptcoveff;j++)    /* Reads comments: lines beginning with '#' */
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    while((c=getc(ficpar))=='#' && c!= EOF){
       fprintf(ficrest,"******\n");      ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       fprintf(ficreseij,"\n#****** ");      puts(line);
       for(j=1;j<=cptcoveff;j++)      fputs(line,ficparo);
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    }
       fprintf(ficreseij,"******\n");    ungetc(c,ficpar);
     
       fprintf(ficresvij,"\n#****** ");    param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(j=1;j<=cptcoveff;j++)      for(i=1; i <=nlstate; i++)
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);      for(j=1; j <=nlstate+ndeath-1; j++){
       fprintf(ficresvij,"******\n");        fscanf(ficpar,"%1d%1d",&i1,&j1);
         fprintf(ficparo,"%1d%1d",i1,j1);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        if(mle==1)
       oldm=oldms;savm=savms;          printf("%1d%1d",i,j);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);          fprintf(ficlog,"%1d%1d",i,j);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        for(k=1; k<=ncovmodel;k++){
       oldm=oldms;savm=savms;          fscanf(ficpar," %lf",&param[i][j][k]);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          if(mle==1){
                printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
            }
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");          else
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);            fprintf(ficlog," %lf",param[i][j][k]);
       fprintf(ficrest,"\n");          fprintf(ficparo," %lf",param[i][j][k]);
         }
       epj=vector(1,nlstate+1);        fscanf(ficpar,"\n");
       for(age=bage; age <=fage ;age++){        if(mle==1)
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          printf("\n");
         if (popbased==1) {        fprintf(ficlog,"\n");
           for(i=1; i<=nlstate;i++)        fprintf(ficparo,"\n");
             prlim[i][i]=probs[(int)age][i][k];      }
         }    
              npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
         fprintf(ficrest," %4.0f",age);  
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    p=param[1][1];
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    /* Reads comments: lines beginning with '#' */
           }    while((c=getc(ficpar))=='#' && c!= EOF){
           epj[nlstate+1] +=epj[j];      ungetc(c,ficpar);
         }      fgets(line, MAXLINE, ficpar);
         for(i=1, vepp=0.;i <=nlstate;i++)      puts(line);
           for(j=1;j <=nlstate;j++)      fputs(line,ficparo);
             vepp += vareij[i][j][(int)age];    }
         fprintf(ficrest," %7.2f (%7.2f)", epj[nlstate+1],sqrt(vepp));    ungetc(c,ficpar);
         for(j=1;j <=nlstate;j++){  
           fprintf(ficrest," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age]));    delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
         }    delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
         fprintf(ficrest,"\n");    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);
   fclose(ficreseij);        for(k=1; k<=ncovmodel;k++){
   fclose(ficresvij);          fscanf(ficpar,"%le",&delti3[i][j][k]);
   fclose(ficrest);          printf(" %le",delti3[i][j][k]);
   fclose(ficpar);          fprintf(ficparo," %le",delti3[i][j][k]);
   free_vector(epj,1,nlstate+1);        }
          fscanf(ficpar,"\n");
   /*------- Variance limit prevalence------*/          printf("\n");
         fprintf(ficparo,"\n");
   strcpy(fileresvpl,"vpl");      }
   strcat(fileresvpl,fileres);    }
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    delti=delti3[1][1];
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    
     exit(0);    /* Reads comments: lines beginning with '#' */
   }    while((c=getc(ficpar))=='#' && c!= EOF){
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);      ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
   k=0;      puts(line);
   for(cptcov=1;cptcov<=i1;cptcov++){      fputs(line,ficparo);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    }
       k=k+1;    ungetc(c,ficpar);
       fprintf(ficresvpl,"\n#****** ");    
       for(j=1;j<=cptcoveff;j++)    matcov=matrix(1,npar,1,npar);
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    for(i=1; i <=npar; i++){
       fprintf(ficresvpl,"******\n");      fscanf(ficpar,"%s",&str);
            if(mle==1)
       varpl=matrix(1,nlstate,(int) bage, (int) fage);        printf("%s",str);
       oldm=oldms;savm=savms;      fprintf(ficlog,"%s",str);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      fprintf(ficparo,"%s",str);
     }      for(j=1; j <=i; j++){
  }        fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
   fclose(ficresvpl);          printf(" %.5le",matcov[i][j]);
           fprintf(ficlog," %.5le",matcov[i][j]);
   /*---------- End : free ----------------*/        }
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);        else
            fprintf(ficlog," %.5le",matcov[i][j]);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);        fprintf(ficparo," %.5le",matcov[i][j]);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);      }
        fscanf(ficpar,"\n");
        if(mle==1)
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);        printf("\n");
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      fprintf(ficlog,"\n");
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      fprintf(ficparo,"\n");
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    }
      for(i=1; i <=npar; i++)
   free_matrix(matcov,1,npar,1,npar);      for(j=i+1;j<=npar;j++)
   free_vector(delti,1,npar);        matcov[i][j]=matcov[j][i];
   free_matrix(agev,1,maxwav,1,imx);     
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    if(mle==1)
       printf("\n");
   if(erreur >0)    fprintf(ficlog,"\n");
     printf("End of Imach with error %d\n",erreur);  
   else   printf("End of Imach\n");  
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      /*-------- Rewriting paramater file ----------*/
         strcpy(rfileres,"r");    /* "Rparameterfile */
   /* 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);*/       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
   /*printf("Total time was %d uSec.\n", total_usecs);*/       strcat(rfileres,".");    /* */
   /*------ End -----------*/       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;
  end:        fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
 #ifdef windows      }
   /* chdir(pathcd);*/      fprintf(ficres,"#%s\n",version);
 #endif      
  /*system("wgnuplot graph.plt");*/      /*-------- data file ----------*/
  /*system("../gp37mgw/wgnuplot graph.plt");*/      if((fic=fopen(datafile,"r"))==NULL)    {
  /*system("cd ../gp37mgw");*/        printf("Problem with datafile: %s\n", datafile);goto end;
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/        fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
  strcpy(plotcmd,GNUPLOTPROGRAM);      }
  strcat(plotcmd," ");  
  strcat(plotcmd,optionfilegnuplot);      n= lastobs;
  system(plotcmd);      severity = vector(1,maxwav);
       outcome=imatrix(1,maxwav+1,1,n);
 #ifdef windows      num=ivector(1,n);
   while (z[0] != 'q') {      moisnais=vector(1,n);
     chdir(path);      annais=vector(1,n);
     printf("\nType e to edit output files, c to start again, and q for exiting: ");      moisdc=vector(1,n);
     scanf("%s",z);      andc=vector(1,n);
     if (z[0] == 'c') system("./imach");      agedc=vector(1,n);
     else if (z[0] == 'e') {      cod=ivector(1,n);
       chdir(path);      weight=vector(1,n);
       system(optionfilehtm);      for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     }      mint=matrix(1,maxwav,1,n);
     else if (z[0] == 'q') exit(0);      anint=matrix(1,maxwav,1,n);
   }      s=imatrix(1,maxwav+1,1,n);
 #endif      adl=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){
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+');
       j1=nbocc(model,'*');
       cptcovn=j+1;
       cptcovprod=j1;
       
       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;
       }
       
       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 analyze 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 */
     
     /* 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){
             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);
       mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
       /* Concatenates waves */
         concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
   
         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);
      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){
       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");
          }
        }
      }
      
      k=1;
      fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
      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;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,Tvar,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(mw,1,lastpass-firstpass+1,1,imx);   
    free_ivector(num,1,n);
    free_vector(agedc,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);
     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 */
     k=0;
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
           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*/
   
     k=0;
     for(cptcov=1;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);
       }
     }
   
     k=0;
     for(cptcov=1;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_matrix(mint,1,maxwav,1,n);
       free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
       free_vector(weight,1,n);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     free_vector(epj,1,nlstate+1);
     
     /*------- 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);
   
     k=0;
     for(cptcov=1;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);
       }
    }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
     
     free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
     free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
     
     
     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(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);
   
     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.1.33  
changed lines
  Added in v.1.57

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