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version 1.41.2.2, 2003/06/13 07:45:28 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
   probability to be observed in state j at the second wave    probability to be observed in state j at the second wave
   conditional to be observed in state i at the first wave. Therefore    conditional to be observed in state i at the first wave. Therefore
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   'age' is age and 'sex' is a covariate. If you want to have a more    'age' is age and 'sex' is a covariate. If you want to have a more
   complex model than "constant and age", you should modify the program    complex model than "constant and age", you should modify the program
   where the markup *Covariates have to be included here again* invites    where the markup *Covariates have to be included here again* invites
   you to do it.  More covariates you add, slower the    you to do it.  More covariates you add, slower the
   convergence.    convergence.
   
   The advantage of this computer programme, compared to a simple    The advantage of this computer programme, compared to a simple
   multinomial logistic model, is clear when the delay between waves is not    multinomial logistic model, is clear when the delay between waves is not
   identical for each individual. Also, if a individual missed an    identical for each individual. Also, if a individual missed an
   intermediate interview, the information is lost, but taken into    intermediate interview, the information is lost, but taken into
   account using an interpolation or extrapolation.      account using an interpolation or extrapolation.  
   
   hPijx is the probability to be observed in state i at age x+h    hPijx is the probability to be observed in state i at age x+h
   conditional to the observed state i at age x. The delay 'h' can be    conditional to the observed state i at age x. The delay 'h' can be
   split into an exact number (nh*stepm) of unobserved intermediate    split into an exact number (nh*stepm) of unobserved intermediate
   states. This elementary transition (by month or quarter trimester,    states. This elementary transition (by month 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 "wgnuplot"  #define GNUPLOTPROGRAM "gnuplot"
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define FILENAMELENGTH 80  #define FILENAMELENGTH 80
 /*#define DEBUG*/  /*#define DEBUG*/
   #define windows
 /*#define windows*/  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
   #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
   #define NINTERVMAX 8
 #define NINTERVMAX 8  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  #define NCOVMAX 8 /* Maximum number of covariates */
 #define NCOVMAX 8 /* Maximum number of covariates */  #define MAXN 20000
 #define MAXN 20000  #define YEARM 12. /* Number of months per year */
 #define YEARM 12. /* Number of months per year */  #define AGESUP 130
 #define AGESUP 130  #define AGEBASE 40
 #define AGEBASE 40  #ifdef windows
   #define DIRSEPARATOR '\\'
   #define ODIRSEPARATOR '/'
 int erreur; /* Error number */  #else
 int nvar;  #define DIRSEPARATOR '/'
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  #define ODIRSEPARATOR '\\'
 int npar=NPARMAX;  #endif
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */  char version[80]="Imach version 0.8k, July 2002, INED-EUROREVES ";
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  int erreur; /* Error number */
 int popbased=0;  int nvar;
   int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 int *wav; /* Number of waves for this individuual 0 is possible */  int npar=NPARMAX;
 int maxwav; /* Maxim number of waves */  int nlstate=2; /* Number of live states */
 int jmin, jmax; /* min, max spacing between 2 waves */  int ndeath=1; /* Number of dead states */
 int mle, weightopt;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  int popbased=0;
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double jmean; /* Mean space between 2 waves */  int *wav; /* Number of waves for this individuual 0 is possible */
 double **oldm, **newm, **savm; /* Working pointers to matrices */  int maxwav; /* Maxim number of waves */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  int jmin, jmax; /* min, max spacing between 2 waves */
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  int mle, weightopt;
 FILE *ficgp,*ficresprob,*ficpop;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 FILE *ficreseij;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   char filerese[FILENAMELENGTH];  double jmean; /* Mean space between 2 waves */
  FILE  *ficresvij;  double **oldm, **newm, **savm; /* Working pointers to matrices */
   char fileresv[FILENAMELENGTH];  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
  FILE  *ficresvpl;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   char fileresvpl[FILENAMELENGTH];  FILE *ficlog;
   FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 #define NR_END 1  FILE *ficresprobmorprev;
 #define FREE_ARG char*  FILE *fichtm; /* Html File */
 #define FTOL 1.0e-10  FILE *ficreseij;
   char filerese[FILENAMELENGTH];
 #define NRANSI  FILE  *ficresvij;
 #define ITMAX 200  char fileresv[FILENAMELENGTH];
   FILE  *ficresvpl;
 #define TOL 2.0e-4  char fileresvpl[FILENAMELENGTH];
   char title[MAXLINE];
 #define CGOLD 0.3819660  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 #define ZEPS 1.0e-10  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 #define GOLD 1.618034  char filelog[FILENAMELENGTH]; /* Log file */
 #define GLIMIT 100.0  char filerest[FILENAMELENGTH];
 #define TINY 1.0e-20  char fileregp[FILENAMELENGTH];
   char popfile[FILENAMELENGTH];
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
    #define NR_END 1
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  #define FREE_ARG char*
 #define rint(a) floor(a+0.5)  #define FTOL 1.0e-10
   
 static double sqrarg;  #define NRANSI 
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  #define ITMAX 200 
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
   #define TOL 2.0e-4 
 int imx;  
 int stepm;  #define CGOLD 0.3819660 
 /* Stepm, step in month: minimum step interpolation*/  #define ZEPS 1.0e-10 
   #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 int estepm;  
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  #define GOLD 1.618034 
   #define GLIMIT 100.0 
 int m,nb;  #define TINY 1.0e-20 
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  static double maxarg1,maxarg2;
 double **pmmij, ***probs, ***mobaverage;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 double dateintmean=0;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     
 double *weight;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 int **s; /* Status */  #define rint(a) floor(a+0.5)
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  static double sqrarg;
   #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 double ftolhess; /* Tolerance for computing hessian */  
   int imx; 
 /**************** split *************************/  int stepm;
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  /* Stepm, step in month: minimum step interpolation*/
 {  
    char *s;                             /* pointer */  int estepm;
    int  l1, l2;                         /* length counters */  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   
    l1 = strlen( path );                 /* length of path */  int m,nb;
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 #ifdef windows  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
    s = strrchr( path, '\\' );           /* find last / */  double **pmmij, ***probs;
 #else  double dateintmean=0;
    s = strrchr( path, '/' );            /* find last / */  
 #endif  double *weight;
    if ( s == NULL ) {                   /* no directory, so use current */  int **s; /* Status */
 #if     defined(__bsd__)                /* get current working directory */  double *agedc, **covar, idx;
       extern char       *getwd( );  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   
       if ( getwd( dirc ) == NULL ) {  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 #else  double ftolhess; /* Tolerance for computing hessian */
       extern char       *getcwd( );  
   /**************** split *************************/
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 #endif  {
          return( GLOCK_ERROR_GETCWD );     char *s;                             /* pointer */
       }     int  l1, l2;                         /* length counters */
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */     l1 = strlen( path );                 /* length of path */
       s++;                              /* after this, the filename */     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       l2 = strlen( s );                 /* length of filename */     s= strrchr( path, DIRSEPARATOR );            /* find last / */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );     if ( s == NULL ) {                   /* no directory, so use current */
       strcpy( name, s );                /* save file name */       /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       strncpy( dirc, path, l1 - l2 );   /* now the directory */         printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       dirc[l1-l2] = 0;                  /* add zero */  #if     defined(__bsd__)                /* get current working directory */
    }        extern char       *getwd( );
    l1 = strlen( dirc );                 /* length of directory */  
 #ifdef windows        if ( getwd( dirc ) == NULL ) {
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  #else
 #else        extern char       *getcwd( );
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif        if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
    s = strrchr( name, '.' );            /* find last / */  #endif
    s++;           return( GLOCK_ERROR_GETCWD );
    strcpy(ext,s);                       /* save extension */        }
    l1= strlen( name);        strcpy( name, path );             /* we've got it */
    l2= strlen( s)+1;     } else {                             /* strip direcotry from path */
    strncpy( finame, name, l1-l2);        s++;                              /* after this, the filename */
    finame[l1-l2]= 0;        l2 = strlen( s );                 /* length of filename */
    return( 0 );                         /* we're done */        if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 }        strcpy( name, s );                /* save file name */
         strncpy( dirc, path, l1 - l2 );   /* now the directory */
         dirc[l1-l2] = 0;                  /* add zero */
 /******************************************/     }
      l1 = strlen( dirc );                 /* length of directory */
 void replace(char *s, char*t)  #ifdef windows
 {     if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   int i;  #else
   int lg=20;     if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   i=0;  #endif
   lg=strlen(t);     s = strrchr( name, '.' );            /* find last / */
   for(i=0; i<= lg; i++) {     s++;
     (s[i] = t[i]);     strcpy(ext,s);                       /* save extension */
     if (t[i]== '\\') s[i]='/';     l1= strlen( name);
   }     l2= strlen( s)+1;
 }     strncpy( finame, name, l1-l2);
      finame[l1-l2]= 0;
 int nbocc(char *s, char occ)     return( 0 );                         /* we're done */
 {  }
   int i,j=0;  
   int lg=20;  
   i=0;  /******************************************/
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {  void replace(char *s, char*t)
   if  (s[i] == occ ) j++;  {
   }    int i;
   return j;    int lg=20;
 }    i=0;
     lg=strlen(t);
 void cutv(char *u,char *v, char*t, char occ)    for(i=0; i<= lg; i++) {
 {      (s[i] = t[i]);
   int i,lg,j,p=0;      if (t[i]== '\\') s[i]='/';
   i=0;    }
   for(j=0; j<=strlen(t)-1; j++) {  }
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }  int nbocc(char *s, char occ)
   {
   lg=strlen(t);    int i,j=0;
   for(j=0; j<p; j++) {    int lg=20;
     (u[j] = t[j]);    i=0;
   }    lg=strlen(s);
      u[p]='\0';    for(i=0; i<= lg; i++) {
     if  (s[i] == occ ) j++;
    for(j=0; j<= lg; j++) {    }
     if (j>=(p+1))(v[j-p-1] = t[j]);    return j;
   }  }
 }  
   void cutv(char *u,char *v, char*t, char occ)
 /********************** nrerror ********************/  {
     /* cuts string t into u and v where u is ended by char occ excluding it
 void nrerror(char error_text[])       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 {       gives u="abcedf" and v="ghi2j" */
   fprintf(stderr,"ERREUR ...\n");    int i,lg,j,p=0;
   fprintf(stderr,"%s\n",error_text);    i=0;
   exit(1);    for(j=0; j<=strlen(t)-1; j++) {
 }      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 /*********************** vector *******************/    }
 double *vector(int nl, int nh)  
 {    lg=strlen(t);
   double *v;    for(j=0; j<p; j++) {
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));      (u[j] = t[j]);
   if (!v) nrerror("allocation failure in vector");    }
   return v-nl+NR_END;       u[p]='\0';
 }  
      for(j=0; j<= lg; j++) {
 /************************ free vector ******************/      if (j>=(p+1))(v[j-p-1] = t[j]);
 void free_vector(double*v, int nl, int nh)    }
 {  }
   free((FREE_ARG)(v+nl-NR_END));  
 }  /********************** nrerror ********************/
   
 /************************ivector *******************************/  void nrerror(char error_text[])
 int *ivector(long nl,long nh)  {
 {    fprintf(stderr,"ERREUR ...\n");
   int *v;    fprintf(stderr,"%s\n",error_text);
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    exit(1);
   if (!v) nrerror("allocation failure in ivector");  }
   return v-nl+NR_END;  /*********************** vector *******************/
 }  double *vector(int nl, int nh)
   {
 /******************free ivector **************************/    double *v;
 void free_ivector(int *v, long nl, long nh)    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 {    if (!v) nrerror("allocation failure in vector");
   free((FREE_ARG)(v+nl-NR_END));    return v-nl+NR_END;
 }  }
   
 /******************* imatrix *******************************/  /************************ free vector ******************/
 int **imatrix(long nrl, long nrh, long ncl, long nch)  void free_vector(double*v, int nl, int nh)
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  {
 {    free((FREE_ARG)(v+nl-NR_END));
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  }
   int **m;  
    /************************ivector *******************************/
   /* allocate pointers to rows */  int *ivector(long nl,long nh)
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  {
   if (!m) nrerror("allocation failure 1 in matrix()");    int *v;
   m += NR_END;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   m -= nrl;    if (!v) nrerror("allocation failure in ivector");
      return v-nl+NR_END;
    }
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  /******************free ivector **************************/
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  void free_ivector(int *v, long nl, long nh)
   m[nrl] += NR_END;  {
   m[nrl] -= ncl;    free((FREE_ARG)(v+nl-NR_END));
    }
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
    /******************* imatrix *******************************/
   /* return pointer to array of pointers to rows */  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   return m;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 }  { 
     long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
 /****************** free_imatrix *************************/    int **m; 
 void free_imatrix(m,nrl,nrh,ncl,nch)    
       int **m;    /* allocate pointers to rows */ 
       long nch,ncl,nrh,nrl;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
      /* free an int matrix allocated by imatrix() */    if (!m) nrerror("allocation failure 1 in matrix()"); 
 {    m += NR_END; 
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    m -= nrl; 
   free((FREE_ARG) (m+nrl-NR_END));    
 }    
     /* allocate rows and set pointers to them */ 
 /******************* matrix *******************************/    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
 double **matrix(long nrl, long nrh, long ncl, long nch)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
 {    m[nrl] += NR_END; 
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    m[nrl] -= ncl; 
   double **m;    
     for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    
   if (!m) nrerror("allocation failure 1 in matrix()");    /* return pointer to array of pointers to rows */ 
   m += NR_END;    return m; 
   m -= nrl;  } 
   
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  /****************** free_imatrix *************************/
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  void free_imatrix(m,nrl,nrh,ncl,nch)
   m[nrl] += NR_END;        int **m;
   m[nrl] -= ncl;        long nch,ncl,nrh,nrl; 
        /* free an int matrix allocated by imatrix() */ 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  { 
   return m;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 }    free((FREE_ARG) (m+nrl-NR_END)); 
   } 
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  /******************* matrix *******************************/
 {  double **matrix(long nrl, long nrh, long ncl, long nch)
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  {
   free((FREE_ARG)(m+nrl-NR_END));    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 }    double **m;
   
 /******************* ma3x *******************************/    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    if (!m) nrerror("allocation failure 1 in matrix()");
 {    m += NR_END;
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    m -= nrl;
   double ***m;  
     m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   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)));    return m;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  }
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  /*************************free matrix ************************/
   void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  {
     free((FREE_ARG)(m[nrl]+ncl-NR_END));
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    free((FREE_ARG)(m+nrl-NR_END));
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  }
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;  /******************* ma3x *******************************/
   for (j=ncl+1; j<=nch; j++)  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     m[nrl][j]=m[nrl][j-1]+nlay;  {
      long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   for (i=nrl+1; i<=nrh; i++) {    double ***m;
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       m[i][j]=m[i][j-1]+nlay;    if (!m) nrerror("allocation failure 1 in matrix()");
   }    m += NR_END;
   return m;    m -= nrl;
 }  
     m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 /*************************free ma3x ************************/    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    m[nrl] += NR_END;
 {    m[nrl] -= ncl;
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   free((FREE_ARG)(m+nrl-NR_END));  
 }    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
 /***************** f1dim *************************/    m[nrl][ncl] += NR_END;
 extern int ncom;    m[nrl][ncl] -= nll;
 extern double *pcom,*xicom;    for (j=ncl+1; j<=nch; j++) 
 extern double (*nrfunc)(double []);      m[nrl][j]=m[nrl][j-1]+nlay;
      
 double f1dim(double x)    for (i=nrl+1; i<=nrh; i++) {
 {      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   int j;      for (j=ncl+1; j<=nch; j++) 
   double f;        m[i][j]=m[i][j-1]+nlay;
   double *xt;    }
      return m;
   xt=vector(1,ncom);  }
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  
   f=(*nrfunc)(xt);  /*************************free ma3x ************************/
   free_vector(xt,1,ncom);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   return f;  {
 }    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     free((FREE_ARG)(m[nrl]+ncl-NR_END));
 /*****************brent *************************/    free((FREE_ARG)(m+nrl-NR_END));
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  }
 {  
   int iter;  /***************** f1dim *************************/
   double a,b,d,etemp;  extern int ncom; 
   double fu,fv,fw,fx;  extern double *pcom,*xicom;
   double ftemp;  extern double (*nrfunc)(double []); 
   double p,q,r,tol1,tol2,u,v,w,x,xm;   
   double e=0.0;  double f1dim(double x) 
    { 
   a=(ax < cx ? ax : cx);    int j; 
   b=(ax > cx ? ax : cx);    double f;
   x=w=v=bx;    double *xt; 
   fw=fv=fx=(*f)(x);   
   for (iter=1;iter<=ITMAX;iter++) {    xt=vector(1,ncom); 
     xm=0.5*(a+b);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    f=(*nrfunc)(xt); 
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    free_vector(xt,1,ncom); 
     printf(".");fflush(stdout);    return f; 
 #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);  
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  /*****************brent *************************/
 #endif  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  { 
       *xmin=x;    int iter; 
       return fx;    double a,b,d,etemp;
     }    double fu,fv,fw,fx;
     ftemp=fu;    double ftemp;
     if (fabs(e) > tol1) {    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       r=(x-w)*(fx-fv);    double e=0.0; 
       q=(x-v)*(fx-fw);   
       p=(x-v)*q-(x-w)*r;    a=(ax < cx ? ax : cx); 
       q=2.0*(q-r);    b=(ax > cx ? ax : cx); 
       if (q > 0.0) p = -p;    x=w=v=bx; 
       q=fabs(q);    fw=fv=fx=(*f)(x); 
       etemp=e;    for (iter=1;iter<=ITMAX;iter++) { 
       e=d;      xm=0.5*(a+b); 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       else {      printf(".");fflush(stdout);
         d=p/q;      fprintf(ficlog,".");fflush(ficlog);
         u=x+d;  #ifdef DEBUG
         if (u-a < tol2 || b-u < tol2)      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);
           d=SIGN(tol1,xm-x);      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       }      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     } else {  #endif
       d=CGOLD*(e=(x >= xm ? a-x : b-x));      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     }        *xmin=x; 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));        return fx; 
     fu=(*f)(u);      } 
     if (fu <= fx) {      ftemp=fu;
       if (u >= x) a=x; else b=x;      if (fabs(e) > tol1) { 
       SHFT(v,w,x,u)        r=(x-w)*(fx-fv); 
         SHFT(fv,fw,fx,fu)        q=(x-v)*(fx-fw); 
         } else {        p=(x-v)*q-(x-w)*r; 
           if (u < x) a=u; else b=u;        q=2.0*(q-r); 
           if (fu <= fw || w == x) {        if (q > 0.0) p = -p; 
             v=w;        q=fabs(q); 
             w=u;        etemp=e; 
             fv=fw;        e=d; 
             fw=fu;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
           } else if (fu <= fv || v == x || v == w) {          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
             v=u;        else { 
             fv=fu;          d=p/q; 
           }          u=x+d; 
         }          if (u-a < tol2 || b-u < tol2) 
   }            d=SIGN(tol1,xm-x); 
   nrerror("Too many iterations in brent");        } 
   *xmin=x;      } else { 
   return fx;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 }      } 
       u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
 /****************** mnbrak ***********************/      fu=(*f)(u); 
       if (fu <= fx) { 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,        if (u >= x) a=x; else b=x; 
             double (*func)(double))        SHFT(v,w,x,u) 
 {          SHFT(fv,fw,fx,fu) 
   double ulim,u,r,q, dum;          } else { 
   double fu;            if (u < x) a=u; else b=u; 
              if (fu <= fw || w == x) { 
   *fa=(*func)(*ax);              v=w; 
   *fb=(*func)(*bx);              w=u; 
   if (*fb > *fa) {              fv=fw; 
     SHFT(dum,*ax,*bx,dum)              fw=fu; 
       SHFT(dum,*fb,*fa,dum)            } else if (fu <= fv || v == x || v == w) { 
       }              v=u; 
   *cx=(*bx)+GOLD*(*bx-*ax);              fv=fu; 
   *fc=(*func)(*cx);            } 
   while (*fb > *fc) {          } 
     r=(*bx-*ax)*(*fb-*fc);    } 
     q=(*bx-*cx)*(*fb-*fa);    nrerror("Too many iterations in brent"); 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    *xmin=x; 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    return fx; 
     ulim=(*bx)+GLIMIT*(*cx-*bx);  } 
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);  /****************** mnbrak ***********************/
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       if (fu < *fc) {              double (*func)(double)) 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  { 
           SHFT(*fb,*fc,fu,(*func)(u))    double ulim,u,r,q, dum;
           }    double fu; 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {   
       u=ulim;    *fa=(*func)(*ax); 
       fu=(*func)(u);    *fb=(*func)(*bx); 
     } else {    if (*fb > *fa) { 
       u=(*cx)+GOLD*(*cx-*bx);      SHFT(dum,*ax,*bx,dum) 
       fu=(*func)(u);        SHFT(dum,*fb,*fa,dum) 
     }        } 
     SHFT(*ax,*bx,*cx,u)    *cx=(*bx)+GOLD*(*bx-*ax); 
       SHFT(*fa,*fb,*fc,fu)    *fc=(*func)(*cx); 
       }    while (*fb > *fc) { 
 }      r=(*bx-*ax)*(*fb-*fc); 
       q=(*bx-*cx)*(*fb-*fa); 
 /*************** linmin ************************/      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 int ncom;      ulim=(*bx)+GLIMIT*(*cx-*bx); 
 double *pcom,*xicom;      if ((*bx-u)*(u-*cx) > 0.0) { 
 double (*nrfunc)(double []);        fu=(*func)(u); 
        } else if ((*cx-u)*(u-ulim) > 0.0) { 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))        fu=(*func)(u); 
 {        if (fu < *fc) { 
   double brent(double ax, double bx, double cx,          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
                double (*f)(double), double tol, double *xmin);            SHFT(*fb,*fc,fu,(*func)(u)) 
   double f1dim(double x);            } 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
               double *fc, double (*func)(double));        u=ulim; 
   int j;        fu=(*func)(u); 
   double xx,xmin,bx,ax;      } else { 
   double fx,fb,fa;        u=(*cx)+GOLD*(*cx-*bx); 
          fu=(*func)(u); 
   ncom=n;      } 
   pcom=vector(1,n);      SHFT(*ax,*bx,*cx,u) 
   xicom=vector(1,n);        SHFT(*fa,*fb,*fc,fu) 
   nrfunc=func;        } 
   for (j=1;j<=n;j++) {  } 
     pcom[j]=p[j];  
     xicom[j]=xi[j];  /*************** linmin ************************/
   }  
   ax=0.0;  int ncom; 
   xx=1.0;  double *pcom,*xicom;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  double (*nrfunc)(double []); 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);   
 #ifdef DEBUG  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  { 
 #endif    double brent(double ax, double bx, double cx, 
   for (j=1;j<=n;j++) {                 double (*f)(double), double tol, double *xmin); 
     xi[j] *= xmin;    double f1dim(double x); 
     p[j] += xi[j];    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   }                double *fc, double (*func)(double)); 
   free_vector(xicom,1,n);    int j; 
   free_vector(pcom,1,n);    double xx,xmin,bx,ax; 
 }    double fx,fb,fa;
    
 /*************** powell ************************/    ncom=n; 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    pcom=vector(1,n); 
             double (*func)(double []))    xicom=vector(1,n); 
 {    nrfunc=func; 
   void linmin(double p[], double xi[], int n, double *fret,    for (j=1;j<=n;j++) { 
               double (*func)(double []));      pcom[j]=p[j]; 
   int i,ibig,j;      xicom[j]=xi[j]; 
   double del,t,*pt,*ptt,*xit;    } 
   double fp,fptt;    ax=0.0; 
   double *xits;    xx=1.0; 
   pt=vector(1,n);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   ptt=vector(1,n);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   xit=vector(1,n);  #ifdef DEBUG
   xits=vector(1,n);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   *fret=(*func)(p);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   for (j=1;j<=n;j++) pt[j]=p[j];  #endif
   for (*iter=1;;++(*iter)) {    for (j=1;j<=n;j++) { 
     fp=(*fret);      xi[j] *= xmin; 
     ibig=0;      p[j] += xi[j]; 
     del=0.0;    } 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    free_vector(xicom,1,n); 
     for (i=1;i<=n;i++)    free_vector(pcom,1,n); 
       printf(" %d %.12f",i, p[i]);  } 
     printf("\n");  
     for (i=1;i<=n;i++) {  /*************** powell ************************/
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       fptt=(*fret);              double (*func)(double [])) 
 #ifdef DEBUG  { 
       printf("fret=%lf \n",*fret);    void linmin(double p[], double xi[], int n, double *fret, 
 #endif                double (*func)(double [])); 
       printf("%d",i);fflush(stdout);    int i,ibig,j; 
       linmin(p,xit,n,fret,func);    double del,t,*pt,*ptt,*xit;
       if (fabs(fptt-(*fret)) > del) {    double fp,fptt;
         del=fabs(fptt-(*fret));    double *xits;
         ibig=i;    pt=vector(1,n); 
       }    ptt=vector(1,n); 
 #ifdef DEBUG    xit=vector(1,n); 
       printf("%d %.12e",i,(*fret));    xits=vector(1,n); 
       for (j=1;j<=n;j++) {    *fret=(*func)(p); 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    for (j=1;j<=n;j++) pt[j]=p[j]; 
         printf(" x(%d)=%.12e",j,xit[j]);    for (*iter=1;;++(*iter)) { 
       }      fp=(*fret); 
       for(j=1;j<=n;j++)      ibig=0; 
         printf(" p=%.12e",p[j]);      del=0.0; 
       printf("\n");      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
 #endif      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
     }      for (i=1;i<=n;i++) 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {        printf(" %d %.12f",i, p[i]);
 #ifdef DEBUG      fprintf(ficlog," %d %.12f",i, p[i]);
       int k[2],l;      printf("\n");
       k[0]=1;      fprintf(ficlog,"\n");
       k[1]=-1;      for (i=1;i<=n;i++) { 
       printf("Max: %.12e",(*func)(p));        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       for (j=1;j<=n;j++)        fptt=(*fret); 
         printf(" %.12e",p[j]);  #ifdef DEBUG
       printf("\n");        printf("fret=%lf \n",*fret);
       for(l=0;l<=1;l++) {        fprintf(ficlog,"fret=%lf \n",*fret);
         for (j=1;j<=n;j++) {  #endif
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];        printf("%d",i);fflush(stdout);
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);        fprintf(ficlog,"%d",i);fflush(ficlog);
         }        linmin(p,xit,n,fret,func); 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));        if (fabs(fptt-(*fret)) > del) { 
       }          del=fabs(fptt-(*fret)); 
 #endif          ibig=i; 
         } 
   #ifdef DEBUG
       free_vector(xit,1,n);        printf("%d %.12e",i,(*fret));
       free_vector(xits,1,n);        fprintf(ficlog,"%d %.12e",i,(*fret));
       free_vector(ptt,1,n);        for (j=1;j<=n;j++) {
       free_vector(pt,1,n);          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       return;          printf(" x(%d)=%.12e",j,xit[j]);
     }          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");        }
     for (j=1;j<=n;j++) {        for(j=1;j<=n;j++) {
       ptt[j]=2.0*p[j]-pt[j];          printf(" p=%.12e",p[j]);
       xit[j]=p[j]-pt[j];          fprintf(ficlog," p=%.12e",p[j]);
       pt[j]=p[j];        }
     }        printf("\n");
     fptt=(*func)(ptt);        fprintf(ficlog,"\n");
     if (fptt < fp) {  #endif
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);      } 
       if (t < 0.0) {      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
         linmin(p,xit,n,fret,func);  #ifdef DEBUG
         for (j=1;j<=n;j++) {        int k[2],l;
           xi[j][ibig]=xi[j][n];        k[0]=1;
           xi[j][n]=xit[j];        k[1]=-1;
         }        printf("Max: %.12e",(*func)(p));
 #ifdef DEBUG        fprintf(ficlog,"Max: %.12e",(*func)(p));
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);        for (j=1;j<=n;j++) {
         for(j=1;j<=n;j++)          printf(" %.12e",p[j]);
           printf(" %.12e",xit[j]);          fprintf(ficlog," %.12e",p[j]);
         printf("\n");        }
 #endif        printf("\n");
       }        fprintf(ficlog,"\n");
     }        for(l=0;l<=1;l++) {
   }          for (j=1;j<=n;j++) {
 }            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
             printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 /**** Prevalence limit ****************/            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
           }
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 {          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit        }
      matrix by transitions matrix until convergence is reached */  #endif
   
   int i, ii,j,k;  
   double min, max, maxmin, maxmax,sumnew=0.;        free_vector(xit,1,n); 
   double **matprod2();        free_vector(xits,1,n); 
   double **out, cov[NCOVMAX], **pmij();        free_vector(ptt,1,n); 
   double **newm;        free_vector(pt,1,n); 
   double agefin, delaymax=50 ; /* Max number of years to converge */        return; 
       } 
   for (ii=1;ii<=nlstate+ndeath;ii++)      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     for (j=1;j<=nlstate+ndeath;j++){      for (j=1;j<=n;j++) { 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        ptt[j]=2.0*p[j]-pt[j]; 
     }        xit[j]=p[j]-pt[j]; 
         pt[j]=p[j]; 
    cov[1]=1.;      } 
        fptt=(*func)(ptt); 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      if (fptt < fp) { 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     newm=savm;        if (t < 0.0) { 
     /* Covariates have to be included here again */          linmin(p,xit,n,fret,func); 
      cov[2]=agefin;          for (j=1;j<=n;j++) { 
              xi[j][ibig]=xi[j][n]; 
       for (k=1; k<=cptcovn;k++) {            xi[j][n]=xit[j]; 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];          }
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/  #ifdef DEBUG
       }          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       for (k=1; k<=cptcovprod;k++)          for(j=1;j<=n;j++){
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];            printf(" %.12e",xit[j]);
             fprintf(ficlog," %.12e",xit[j]);
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/          }
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/          printf("\n");
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/          fprintf(ficlog,"\n");
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  #endif
         }
     savm=oldm;      } 
     oldm=newm;    } 
     maxmax=0.;  } 
     for(j=1;j<=nlstate;j++){  
       min=1.;  /**** Prevalence limit (stable prevalence)  ****************/
       max=0.;  
       for(i=1; i<=nlstate; i++) {  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
         sumnew=0;  {
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
         prlim[i][j]= newm[i][j]/(1-sumnew);       matrix by transitions matrix until convergence is reached */
         max=FMAX(max,prlim[i][j]);  
         min=FMIN(min,prlim[i][j]);    int i, ii,j,k;
       }    double min, max, maxmin, maxmax,sumnew=0.;
       maxmin=max-min;    double **matprod2();
       maxmax=FMAX(maxmax,maxmin);    double **out, cov[NCOVMAX], **pmij();
     }    double **newm;
     if(maxmax < ftolpl){    double agefin, delaymax=50 ; /* Max number of years to converge */
       return prlim;  
     }    for (ii=1;ii<=nlstate+ndeath;ii++)
   }      for (j=1;j<=nlstate+ndeath;j++){
 }        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }
 /*************** transition probabilities ***************/  
      cov[1]=1.;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )   
 {   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   double s1, s2;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   /*double t34;*/      newm=savm;
   int i,j,j1, nc, ii, jj;      /* Covariates have to be included here again */
        cov[2]=agefin;
     for(i=1; i<= nlstate; i++){    
     for(j=1; j<i;j++){        for (k=1; k<=cptcovn;k++) {
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         /*s2 += param[i][j][nc]*cov[nc];*/          /*      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]]);*/
         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<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       }        for (k=1; k<=cptcovprod;k++)
       ps[i][j]=s2;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  
     }        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     for(j=i+1; j<=nlstate+ndeath;j++){        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  
       }      savm=oldm;
       ps[i][j]=s2;      oldm=newm;
     }      maxmax=0.;
   }      for(j=1;j<=nlstate;j++){
     /*ps[3][2]=1;*/        min=1.;
         max=0.;
   for(i=1; i<= nlstate; i++){        for(i=1; i<=nlstate; i++) {
      s1=0;          sumnew=0;
     for(j=1; j<i; j++)          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       s1+=exp(ps[i][j]);          prlim[i][j]= newm[i][j]/(1-sumnew);
     for(j=i+1; j<=nlstate+ndeath; j++)          max=FMAX(max,prlim[i][j]);
       s1+=exp(ps[i][j]);          min=FMIN(min,prlim[i][j]);
     ps[i][i]=1./(s1+1.);        }
     for(j=1; j<i; j++)        maxmin=max-min;
       ps[i][j]= exp(ps[i][j])*ps[i][i];        maxmax=FMAX(maxmax,maxmin);
     for(j=i+1; j<=nlstate+ndeath; j++)      }
       ps[i][j]= exp(ps[i][j])*ps[i][i];      if(maxmax < ftolpl){
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        return prlim;
   } /* end i */      }
     }
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  }
     for(jj=1; jj<= nlstate+ndeath; jj++){  
       ps[ii][jj]=0;  /*************** transition probabilities ***************/ 
       ps[ii][ii]=1;  
     }  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   }  {
     double s1, s2;
     /*double t34;*/
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    int i,j,j1, nc, ii, jj;
     for(jj=1; jj<= nlstate+ndeath; jj++){  
      printf("%lf ",ps[ii][jj]);      for(i=1; i<= nlstate; i++){
    }      for(j=1; j<i;j++){
     printf("\n ");        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     }          /*s2 += param[i][j][nc]*cov[nc];*/
     printf("\n ");printf("%lf ",cov[2]);*/          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(i=1; i<= npar; i++) printf("%f ",x[i]);        }
   goto end;*/        ps[i][j]=s2;
     return ps;        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
 }      }
       for(j=i+1; j<=nlstate+ndeath;j++){
 /**************** Product of 2 matrices ******************/        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
 {        }
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        ps[i][j]=s2;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      }
   /* in, b, out are matrice of pointers which should have been initialized    }
      before: only the contents of out is modified. The function returns      /*ps[3][2]=1;*/
      a pointer to pointers identical to out */  
   long i, j, k;    for(i=1; i<= nlstate; i++){
   for(i=nrl; i<= nrh; i++)       s1=0;
     for(k=ncolol; k<=ncoloh; k++)      for(j=1; j<i; j++)
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        s1+=exp(ps[i][j]);
         out[i][k] +=in[i][j]*b[j][k];      for(j=i+1; j<=nlstate+ndeath; j++)
         s1+=exp(ps[i][j]);
   return out;      ps[i][i]=1./(s1+1.);
 }      for(j=1; j<i; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];
       for(j=i+1; j<=nlstate+ndeath; j++)
 /************* Higher Matrix Product ***************/        ps[i][j]= exp(ps[i][j])*ps[i][i];
       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    } /* end i */
 {  
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
      duration (i.e. until      for(jj=1; jj<= nlstate+ndeath; jj++){
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        ps[ii][jj]=0;
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        ps[ii][ii]=1;
      (typically every 2 years instead of every month which is too big).      }
      Model is determined by parameters x and covariates have to be    }
      included manually here.  
   
      */    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
       for(jj=1; jj<= nlstate+ndeath; jj++){
   int i, j, d, h, k;       printf("%lf ",ps[ii][jj]);
   double **out, cov[NCOVMAX];     }
   double **newm;      printf("\n ");
       }
   /* Hstepm could be zero and should return the unit matrix */      printf("\n ");printf("%lf ",cov[2]);*/
   for (i=1;i<=nlstate+ndeath;i++)  /*
     for (j=1;j<=nlstate+ndeath;j++){    for(i=1; i<= npar; i++) printf("%f ",x[i]);
       oldm[i][j]=(i==j ? 1.0 : 0.0);    goto end;*/
       po[i][j][0]=(i==j ? 1.0 : 0.0);      return ps;
     }  }
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(h=1; h <=nhstepm; h++){  /**************** Product of 2 matrices ******************/
     for(d=1; d <=hstepm; d++){  
       newm=savm;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
       /* Covariates have to be included here again */  {
       cov[1]=1.;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    /* in, b, out are matrice of pointers which should have been initialized 
       for (k=1; k<=cptcovage;k++)       before: only the contents of out is modified. The function returns
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];       a pointer to pointers identical to out */
       for (k=1; k<=cptcovprod;k++)    long i, j, k;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    for(i=nrl; i<= nrh; i++)
       for(k=ncolol; k<=ncoloh; k++)
         for(j=ncl,out[i][k]=0.; j<=nch; j++)
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/          out[i][k] +=in[i][j]*b[j][k];
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    return out;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  }
       savm=oldm;  
       oldm=newm;  
     }  /************* Higher Matrix Product ***************/
     for(i=1; i<=nlstate+ndeath; i++)  
       for(j=1;j<=nlstate+ndeath;j++) {  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
         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]);    /* 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. 
   } /* end h */       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   return po;       (typically every 2 years instead of every month which is too big).
 }       Model is determined by parameters x and covariates have to be 
        included manually here. 
   
 /*************** log-likelihood *************/       */
 double func( double *x)  
 {    int i, j, d, h, k;
   int i, ii, j, k, mi, d, kk;    double **out, cov[NCOVMAX];
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    double **newm;
   double **out;  
   double sw; /* Sum of weights */    /* Hstepm could be zero and should return the unit matrix */
   double lli; /* Individual log likelihood */    for (i=1;i<=nlstate+ndeath;i++)
   int s1, s2;      for (j=1;j<=nlstate+ndeath;j++){
   long ipmx;        oldm[i][j]=(i==j ? 1.0 : 0.0);
   /*extern weight */        po[i][j][0]=(i==j ? 1.0 : 0.0);
   /* We are differentiating ll according to initial status */      }
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   /*for(i=1;i<imx;i++)    for(h=1; h <=nhstepm; h++){
     printf(" %d\n",s[4][i]);      for(d=1; d <=hstepm; d++){
   */        newm=savm;
   cov[1]=1.;        /* Covariates have to be included here again */
         cov[1]=1.;
   for(k=1; k<=nlstate; k++) ll[k]=0.;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        for (k=1; k<=cptcovage;k++)
     for(mi=1; mi<= wav[i]-1; mi++){          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       for (ii=1;ii<=nlstate+ndeath;ii++)        for (k=1; k<=cptcovprod;k++)
         for (j=1;j<=nlstate+ndeath;j++){          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           oldm[ii][j]=(ii==j ? 1.0 : 0.0);  
           savm[ii][j]=(ii==j ? 1.0 : 0.0);  
         }        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       for(d=0; d<dh[mi][i]; d++){        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         newm=savm;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         for (kk=1; kk<=cptcovage;kk++) {        savm=oldm;
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        oldm=newm;
         }      }
              for(i=1; i<=nlstate+ndeath; i++)
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        for(j=1;j<=nlstate+ndeath;j++) {
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));          po[i][j][h]=newm[i][j];
         savm=oldm;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
         oldm=newm;           */
                }
            } /* end h */
       } /* end mult */    return po;
        }
       s1=s[mw[mi][i]][i];  
       s2=s[mw[mi+1][i]][i];  
       if( s2 > nlstate){  /*************** log-likelihood *************/
         /* i.e. if s2 is a death state and if the date of death is known then the contribution  double func( double *x)
            to the likelihood is the probability to die between last step unit time and current  {
            step unit time, which is also the differences between probability to die before dh    int i, ii, j, k, mi, d, kk;
            and probability to die before dh-stepm .    double l, ll[NLSTATEMAX], cov[NCOVMAX];
            In version up to 0.92 likelihood was computed    double **out;
            as if date of death was unknown. Death was treated as any other    double sw; /* Sum of weights */
            health state: the date of the interview describes the actual state    double lli; /* Individual log likelihood */
            and not the date of a change in health state. The former idea was    long ipmx;
            to consider that at each interview the state was recorded    /*extern weight */
            (healthy, disable or death) and IMaCh was corrected; but when we    /* We are differentiating ll according to initial status */
            introduced the exact date of death then we should have modified    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
            the contribution of an exact death to the likelihood. This new    /*for(i=1;i<imx;i++) 
            contribution is smaller and very dependent of the step unit      printf(" %d\n",s[4][i]);
            stepm. It is no more the probability to die between last interview    */
            and month of death but the probability to survive from last    cov[1]=1.;
            interview up to one month before death multiplied by the  
            probability to die within a month. Thanks to Chris    for(k=1; k<=nlstate; k++) ll[k]=0.;
            Jackson for correcting this bug.  Former versions increased    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
            mortality artificially. The bad side is that we add another loop      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
            which slows down the processing. The difference can be up to 10%      for(mi=1; mi<= wav[i]-1; mi++){
            lower mortality.        for (ii=1;ii<=nlstate+ndeath;ii++)
         */          for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         lli=log(out[s1][s2] - savm[s1][s2]);        for(d=0; d<dh[mi][i]; d++){
       }else{          newm=savm;
         lli=log(out[s1][s2]); /* or     lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); */          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/          for (kk=1; kk<=cptcovage;kk++) {
       }            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       ipmx +=1;          }
       sw += weight[i];          
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d lli=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],lli,weight[i],out[s1][s2],savm[s1][s2]);*/                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     } /* end of wave */          savm=oldm;
   } /* end of individual */          oldm=newm;
           
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];          
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */        } /* end mult */
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        
   /*exit(0);*/        lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
   return -l;        /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
 }        ipmx +=1;
         sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 /*********** Maximum Likelihood Estimation ***************/      } /* end of wave */
     } /* end of individual */
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  
 {    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   int i,j, iter;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   double **xi,*delti;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   double fret;    return -l;
   xi=matrix(1,npar,1,npar);  }
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++)  
       xi[i][j]=(i==j ? 1.0 : 0.0);  /*********** Maximum Likelihood Estimation ***************/
   printf("Powell\n");  
   powell(p,xi,npar,ftol,&iter,&fret,func);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   {
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    int i,j, iter;
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    double **xi,*delti;
     double fret;
 }    xi=matrix(1,npar,1,npar);
     for (i=1;i<=npar;i++)
 /**** Computes Hessian and covariance matrix ***/      for (j=1;j<=npar;j++)
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        xi[i][j]=(i==j ? 1.0 : 0.0);
 {    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   double  **a,**y,*x,pd;    powell(p,xi,npar,ftol,&iter,&fret,func);
   double **hess;  
   int i, j,jk;     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   int *indx;    fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   double hessii(double p[], double delta, int theta, double delti[]);  
   double hessij(double p[], double delti[], int i, int j);  }
   void lubksb(double **a, int npar, int *indx, double b[]) ;  
   void ludcmp(double **a, int npar, int *indx, double *d) ;  /**** Computes Hessian and covariance matrix ***/
   void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   hess=matrix(1,npar,1,npar);  {
     double  **a,**y,*x,pd;
   printf("\nCalculation of the hessian matrix. Wait...\n");    double **hess;
   for (i=1;i<=npar;i++){    int i, j,jk;
     printf("%d",i);fflush(stdout);    int *indx;
     hess[i][i]=hessii(p,ftolhess,i,delti);  
     /*printf(" %f ",p[i]);*/    double hessii(double p[], double delta, int theta, double delti[]);
     /*printf(" %lf ",hess[i][i]);*/    double hessij(double p[], double delti[], int i, int j);
   }    void lubksb(double **a, int npar, int *indx, double b[]) ;
      void ludcmp(double **a, int npar, int *indx, double *d) ;
   for (i=1;i<=npar;i++) {  
     for (j=1;j<=npar;j++)  {    hess=matrix(1,npar,1,npar);
       if (j>i) {  
         printf(".%d%d",i,j);fflush(stdout);    printf("\nCalculation of the hessian matrix. Wait...\n");
         hess[i][j]=hessij(p,delti,i,j);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         hess[j][i]=hess[i][j];        for (i=1;i<=npar;i++){
         /*printf(" %lf ",hess[i][j]);*/      printf("%d",i);fflush(stdout);
       }      fprintf(ficlog,"%d",i);fflush(ficlog);
     }      hess[i][i]=hessii(p,ftolhess,i,delti);
   }      /*printf(" %f ",p[i]);*/
   printf("\n");      /*printf(" %lf ",hess[i][i]);*/
     }
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    
      for (i=1;i<=npar;i++) {
   a=matrix(1,npar,1,npar);      for (j=1;j<=npar;j++)  {
   y=matrix(1,npar,1,npar);        if (j>i) { 
   x=vector(1,npar);          printf(".%d%d",i,j);fflush(stdout);
   indx=ivector(1,npar);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   for (i=1;i<=npar;i++)          hess[i][j]=hessij(p,delti,i,j);
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];          hess[j][i]=hess[i][j];    
   ludcmp(a,npar,indx,&pd);          /*printf(" %lf ",hess[i][j]);*/
         }
   for (j=1;j<=npar;j++) {      }
     for (i=1;i<=npar;i++) x[i]=0;    }
     x[j]=1;    printf("\n");
     lubksb(a,npar,indx,x);    fprintf(ficlog,"\n");
     for (i=1;i<=npar;i++){  
       matcov[i][j]=x[i];    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     }    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   }    
     a=matrix(1,npar,1,npar);
   printf("\n#Hessian matrix#\n");    y=matrix(1,npar,1,npar);
   for (i=1;i<=npar;i++) {    x=vector(1,npar);
     for (j=1;j<=npar;j++) {    indx=ivector(1,npar);
       printf("%.3e ",hess[i][j]);    for (i=1;i<=npar;i++)
     }      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     printf("\n");    ludcmp(a,npar,indx,&pd);
   }  
     for (j=1;j<=npar;j++) {
   /* Recompute Inverse */      for (i=1;i<=npar;i++) x[i]=0;
   for (i=1;i<=npar;i++)      x[j]=1;
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];      lubksb(a,npar,indx,x);
   ludcmp(a,npar,indx,&pd);      for (i=1;i<=npar;i++){ 
         matcov[i][j]=x[i];
   /*  printf("\n#Hessian matrix recomputed#\n");      }
     }
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;    printf("\n#Hessian matrix#\n");
     x[j]=1;    fprintf(ficlog,"\n#Hessian matrix#\n");
     lubksb(a,npar,indx,x);    for (i=1;i<=npar;i++) { 
     for (i=1;i<=npar;i++){      for (j=1;j<=npar;j++) { 
       y[i][j]=x[i];        printf("%.3e ",hess[i][j]);
       printf("%.3e ",y[i][j]);        fprintf(ficlog,"%.3e ",hess[i][j]);
     }      }
     printf("\n");      printf("\n");
   }      fprintf(ficlog,"\n");
   */    }
   
   free_matrix(a,1,npar,1,npar);    /* Recompute Inverse */
   free_matrix(y,1,npar,1,npar);    for (i=1;i<=npar;i++)
   free_vector(x,1,npar);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   free_ivector(indx,1,npar);    ludcmp(a,npar,indx,&pd);
   free_matrix(hess,1,npar,1,npar);  
     /*  printf("\n#Hessian matrix recomputed#\n");
   
 }    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
 /*************** hessian matrix ****************/      x[j]=1;
 double hessii( double x[], double delta, int theta, double delti[])      lubksb(a,npar,indx,x);
 {      for (i=1;i<=npar;i++){ 
   int i;        y[i][j]=x[i];
   int l=1, lmax=20;        printf("%.3e ",y[i][j]);
   double k1,k2;        fprintf(ficlog,"%.3e ",y[i][j]);
   double p2[NPARMAX+1];      }
   double res;      printf("\n");
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      fprintf(ficlog,"\n");
   double fx;    }
   int k=0,kmax=10;    */
   double l1;  
     free_matrix(a,1,npar,1,npar);
   fx=func(x);    free_matrix(y,1,npar,1,npar);
   for (i=1;i<=npar;i++) p2[i]=x[i];    free_vector(x,1,npar);
   for(l=0 ; l <=lmax; l++){    free_ivector(indx,1,npar);
     l1=pow(10,l);    free_matrix(hess,1,npar,1,npar);
     delts=delt;  
     for(k=1 ; k <kmax; k=k+1){  
       delt = delta*(l1*k);  }
       p2[theta]=x[theta] +delt;  
       k1=func(p2)-fx;  /*************** hessian matrix ****************/
       p2[theta]=x[theta]-delt;  double hessii( double x[], double delta, int theta, double delti[])
       k2=func(p2)-fx;  {
       /*res= (k1-2.0*fx+k2)/delt/delt; */    int i;
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    int l=1, lmax=20;
          double k1,k2;
 #ifdef DEBUG    double p2[NPARMAX+1];
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);    double res;
 #endif    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    double fx;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    int k=0,kmax=10;
         k=kmax;    double l1;
       }  
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    fx=func(x);
         k=kmax; l=lmax*10.;    for (i=1;i<=npar;i++) p2[i]=x[i];
       }    for(l=0 ; l <=lmax; l++){
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      l1=pow(10,l);
         delts=delt;      delts=delt;
       }      for(k=1 ; k <kmax; k=k+1){
     }        delt = delta*(l1*k);
   }        p2[theta]=x[theta] +delt;
   delti[theta]=delts;        k1=func(p2)-fx;
   return res;        p2[theta]=x[theta]-delt;
          k2=func(p2)-fx;
 }        /*res= (k1-2.0*fx+k2)/delt/delt; */
         res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
 double hessij( double x[], double delti[], int thetai,int thetaj)        
 {  #ifdef DEBUG
   int i;        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   int l=1, l1, lmax=20;        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);
   double k1,k2,k3,k4,res,fx;  #endif
   double p2[NPARMAX+1];        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   int k;        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           k=kmax;
   fx=func(x);        }
   for (k=1; k<=2; k++) {        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     for (i=1;i<=npar;i++) p2[i]=x[i];          k=kmax; l=lmax*10.;
     p2[thetai]=x[thetai]+delti[thetai]/k;        }
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     k1=func(p2)-fx;          delts=delt;
          }
     p2[thetai]=x[thetai]+delti[thetai]/k;      }
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    }
     k2=func(p2)-fx;    delti[theta]=delts;
      return res; 
     p2[thetai]=x[thetai]-delti[thetai]/k;    
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  }
     k3=func(p2)-fx;  
    double hessij( double x[], double delti[], int thetai,int thetaj)
     p2[thetai]=x[thetai]-delti[thetai]/k;  {
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    int i;
     k4=func(p2)-fx;    int l=1, l1, lmax=20;
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    double k1,k2,k3,k4,res,fx;
 #ifdef DEBUG    double p2[NPARMAX+1];
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);    int k;
 #endif  
   }    fx=func(x);
   return res;    for (k=1; k<=2; k++) {
 }      for (i=1;i<=npar;i++) p2[i]=x[i];
       p2[thetai]=x[thetai]+delti[thetai]/k;
 /************** Inverse of matrix **************/      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
 void ludcmp(double **a, int n, int *indx, double *d)      k1=func(p2)-fx;
 {    
   int i,imax,j,k;      p2[thetai]=x[thetai]+delti[thetai]/k;
   double big,dum,sum,temp;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   double *vv;      k2=func(p2)-fx;
      
   vv=vector(1,n);      p2[thetai]=x[thetai]-delti[thetai]/k;
   *d=1.0;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   for (i=1;i<=n;i++) {      k3=func(p2)-fx;
     big=0.0;    
     for (j=1;j<=n;j++)      p2[thetai]=x[thetai]-delti[thetai]/k;
       if ((temp=fabs(a[i][j])) > big) big=temp;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");      k4=func(p2)-fx;
     vv[i]=1.0/big;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   }  #ifdef DEBUG
   for (j=1;j<=n;j++) {      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     for (i=1;i<j;i++) {      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);
       sum=a[i][j];  #endif
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    }
       a[i][j]=sum;    return res;
     }  }
     big=0.0;  
     for (i=j;i<=n;i++) {  /************** Inverse of matrix **************/
       sum=a[i][j];  void ludcmp(double **a, int n, int *indx, double *d) 
       for (k=1;k<j;k++)  { 
         sum -= a[i][k]*a[k][j];    int i,imax,j,k; 
       a[i][j]=sum;    double big,dum,sum,temp; 
       if ( (dum=vv[i]*fabs(sum)) >= big) {    double *vv; 
         big=dum;   
         imax=i;    vv=vector(1,n); 
       }    *d=1.0; 
     }    for (i=1;i<=n;i++) { 
     if (j != imax) {      big=0.0; 
       for (k=1;k<=n;k++) {      for (j=1;j<=n;j++) 
         dum=a[imax][k];        if ((temp=fabs(a[i][j])) > big) big=temp; 
         a[imax][k]=a[j][k];      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
         a[j][k]=dum;      vv[i]=1.0/big; 
       }    } 
       *d = -(*d);    for (j=1;j<=n;j++) { 
       vv[imax]=vv[j];      for (i=1;i<j;i++) { 
     }        sum=a[i][j]; 
     indx[j]=imax;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     if (a[j][j] == 0.0) a[j][j]=TINY;        a[i][j]=sum; 
     if (j != n) {      } 
       dum=1.0/(a[j][j]);      big=0.0; 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;      for (i=j;i<=n;i++) { 
     }        sum=a[i][j]; 
   }        for (k=1;k<j;k++) 
   free_vector(vv,1,n);  /* Doesn't work */          sum -= a[i][k]*a[k][j]; 
 ;        a[i][j]=sum; 
 }        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           big=dum; 
 void lubksb(double **a, int n, int *indx, double b[])          imax=i; 
 {        } 
   int i,ii=0,ip,j;      } 
   double sum;      if (j != imax) { 
          for (k=1;k<=n;k++) { 
   for (i=1;i<=n;i++) {          dum=a[imax][k]; 
     ip=indx[i];          a[imax][k]=a[j][k]; 
     sum=b[ip];          a[j][k]=dum; 
     b[ip]=b[i];        } 
     if (ii)        *d = -(*d); 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        vv[imax]=vv[j]; 
     else if (sum) ii=i;      } 
     b[i]=sum;      indx[j]=imax; 
   }      if (a[j][j] == 0.0) a[j][j]=TINY; 
   for (i=n;i>=1;i--) {      if (j != n) { 
     sum=b[i];        dum=1.0/(a[j][j]); 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     b[i]=sum/a[i][i];      } 
   }    } 
 }    free_vector(vv,1,n);  /* Doesn't work */
   ;
 /************ Frequencies ********************/  } 
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)  
 {  /* Some frequencies */  void lubksb(double **a, int n, int *indx, double b[]) 
    { 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    int i,ii=0,ip,j; 
   double ***freq; /* Frequencies */    double sum; 
   double *pp;   
   double pos, k2, dateintsum=0,k2cpt=0;    for (i=1;i<=n;i++) { 
   FILE *ficresp;      ip=indx[i]; 
   char fileresp[FILENAMELENGTH];      sum=b[ip]; 
        b[ip]=b[i]; 
   pp=vector(1,nlstate);      if (ii) 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   strcpy(fileresp,"p");      else if (sum) ii=i; 
   strcat(fileresp,fileres);      b[i]=sum; 
   if((ficresp=fopen(fileresp,"w"))==NULL) {    } 
     printf("Problem with prevalence resultfile: %s\n", fileresp);    for (i=n;i>=1;i--) { 
     exit(0);      sum=b[i]; 
   }      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      b[i]=sum/a[i][i]; 
   j1=0;    } 
    } 
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  /************ Frequencies ********************/
    void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
   for(k1=1; k1<=j;k1++){  {  /* Some frequencies */
     for(i1=1; i1<=ncodemax[k1];i1++){    
       j1++;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    int first;
         scanf("%d", i);*/    double ***freq; /* Frequencies */
       for (i=-1; i<=nlstate+ndeath; i++)      double *pp;
         for (jk=-1; jk<=nlstate+ndeath; jk++)      double pos, k2, dateintsum=0,k2cpt=0;
           for(m=agemin; m <= agemax+3; m++)    FILE *ficresp;
             freq[i][jk][m]=0;    char fileresp[FILENAMELENGTH];
          
       dateintsum=0;    pp=vector(1,nlstate);
       k2cpt=0;    probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for (i=1; i<=imx; i++) {    strcpy(fileresp,"p");
         bool=1;    strcat(fileresp,fileres);
         if  (cptcovn>0) {    if((ficresp=fopen(fileresp,"w"))==NULL) {
           for (z1=1; z1<=cptcoveff; z1++)      printf("Problem with prevalence resultfile: %s\n", fileresp);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
               bool=0;      exit(0);
         }    }
         if (bool==1) {    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
           for(m=firstpass; m<=lastpass; m++){    j1=0;
             k2=anint[m][i]+(mint[m][i]/12.);    
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    j=cptcoveff;
               if(agev[m][i]==0) agev[m][i]=agemax+1;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
               if(agev[m][i]==1) agev[m][i]=agemax+2;  
               if (m<lastpass) {    first=1;
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    for(k1=1; k1<=j;k1++){
               }      for(i1=1; i1<=ncodemax[k1];i1++){
                      j1++;
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
                 dateintsum=dateintsum+k2;          scanf("%d", i);*/
                 k2cpt++;        for (i=-1; i<=nlstate+ndeath; i++)  
               }          for (jk=-1; jk<=nlstate+ndeath; jk++)  
             }            for(m=agemin; m <= agemax+3; m++)
           }              freq[i][jk][m]=0;
         }        
       }        dateintsum=0;
                k2cpt=0;
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        for (i=1; i<=imx; i++) {
           bool=1;
       if  (cptcovn>0) {          if  (cptcovn>0) {
         fprintf(ficresp, "\n#********** Variable ");            for (z1=1; z1<=cptcoveff; z1++) 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
         fprintf(ficresp, "**********\n#");                bool=0;
       }          }
       for(i=1; i<=nlstate;i++)          if (bool==1) {
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);            for(m=firstpass; m<=lastpass; m++){
       fprintf(ficresp, "\n");              k2=anint[m][i]+(mint[m][i]/12.);
                    if ((k2>=dateprev1) && (k2<=dateprev2)) {
       for(i=(int)agemin; i <= (int)agemax+3; i++){                if(agev[m][i]==0) agev[m][i]=agemax+1;
         if(i==(int)agemax+3)                if(agev[m][i]==1) agev[m][i]=agemax+2;
           printf("Total");                if (m<lastpass) {
         else                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
           printf("Age %d", i);                  freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
         for(jk=1; jk <=nlstate ; jk++){                }
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)                
             pp[jk] += freq[jk][m][i];                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
         }                  dateintsum=dateintsum+k2;
         for(jk=1; jk <=nlstate ; jk++){                  k2cpt++;
           for(m=-1, pos=0; m <=0 ; m++)                }
             pos += freq[jk][m][i];              }
           if(pp[jk]>=1.e-10)            }
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          }
           else        }
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);         
         }        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
         for(jk=1; jk <=nlstate ; jk++){        if  (cptcovn>0) {
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          fprintf(ficresp, "\n#********** Variable "); 
             pp[jk] += freq[jk][m][i];          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         }          fprintf(ficresp, "**********\n#");
         }
         for(jk=1,pos=0; jk <=nlstate ; jk++)        for(i=1; i<=nlstate;i++) 
           pos += pp[jk];          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         for(jk=1; jk <=nlstate ; jk++){        fprintf(ficresp, "\n");
           if(pos>=1.e-5)        
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        for(i=(int)agemin; i <= (int)agemax+3; i++){
           else          if(i==(int)agemax+3){
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);            fprintf(ficlog,"Total");
           if( i <= (int) agemax){          }else{
             if(pos>=1.e-5){            if(first==1){
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);              first=0;
               probs[i][jk][j1]= pp[jk]/pos;              printf("See log file for details...\n");
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/            }
             }            fprintf(ficlog,"Age %d", i);
             else          }
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          for(jk=1; jk <=nlstate ; jk++){
           }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
         }              pp[jk] += freq[jk][m][i]; 
                  }
         for(jk=-1; jk <=nlstate+ndeath; jk++)          for(jk=1; jk <=nlstate ; jk++){
           for(m=-1; m <=nlstate+ndeath; m++)            for(m=-1, pos=0; m <=0 ; m++)
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);              pos += freq[jk][m][i];
         if(i <= (int) agemax)            if(pp[jk]>=1.e-10){
           fprintf(ficresp,"\n");              if(first==1){
         printf("\n");              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       }              }
     }              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   }            }else{
   dateintmean=dateintsum/k2cpt;              if(first==1)
                  printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   fclose(ficresp);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            }
   free_vector(pp,1,nlstate);          }
    
   /* End of Freq */          for(jk=1; jk <=nlstate ; jk++){
 }            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
               pp[jk] += freq[jk][m][i];
 /************ 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)  
 {  /* Some frequencies */          for(jk=1,pos=0; jk <=nlstate ; jk++)
              pos += pp[jk];
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          for(jk=1; jk <=nlstate ; jk++){
   double ***freq; /* Frequencies */            if(pos>=1.e-5){
   double *pp;              if(first==1)
   double pos, k2;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
               fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   pp=vector(1,nlstate);            }else{
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);              if(first==1)
                  printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   j1=0;            }
              if( i <= (int) agemax){
   j=cptcoveff;              if(pos>=1.e-5){
   if (cptcovn<1) {j=1;ncodemax[1]=1;}                fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
                  probs[i][jk][j1]= pp[jk]/pos;
  for(k1=1; k1<=j;k1++){                /*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(i1=1; i1<=ncodemax[k1];i1++){              }
       j1++;              else
                  fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
       for (i=-1; i<=nlstate+ndeath; i++)              }
         for (jk=-1; jk<=nlstate+ndeath; jk++)            }
           for(m=agemin; m <= agemax+3; m++)          
             freq[i][jk][m]=0;          for(jk=-1; jk <=nlstate+ndeath; jk++)
                  for(m=-1; m <=nlstate+ndeath; m++)
       for (i=1; i<=imx; i++) {              if(freq[jk][m][i] !=0 ) {
         bool=1;              if(first==1)
         if  (cptcovn>0) {                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
           for (z1=1; z1<=cptcoveff; z1++)                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])              }
               bool=0;          if(i <= (int) agemax)
         }            fprintf(ficresp,"\n");
         if (bool==1) {          if(first==1)
           for(m=firstpass; m<=lastpass; m++){            printf("Others in log...\n");
             k2=anint[m][i]+(mint[m][i]/12.);          fprintf(ficlog,"\n");
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        }
               if(agev[m][i]==0) agev[m][i]=agemax+1;      }
               if(agev[m][i]==1) agev[m][i]=agemax+2;    }
               if (m<lastpass)    dateintmean=dateintsum/k2cpt; 
                 if (calagedate>0) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];   
               else    fclose(ficresp);
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
                freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];    free_vector(pp,1,nlstate);
             }    
           }    /* End of Freq */
         }  }
       }  
         for(i=(int)agemin; i <= (int)agemax+3; i++){  /************ Prevalence ********************/
           for(jk=1; jk <=nlstate ; jk++){  void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  {  /* Some frequencies */
               pp[jk] += freq[jk][m][i];   
           }    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
           for(jk=1; jk <=nlstate ; jk++){    double ***freq; /* Frequencies */
             for(m=-1, pos=0; m <=0 ; m++)    double *pp;
             pos += freq[jk][m][i];    double pos, k2;
         }  
            pp=vector(1,nlstate);
          for(jk=1; jk <=nlstate ; jk++){    
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
              pp[jk] += freq[jk][m][i];    j1=0;
          }    
              j=cptcoveff;
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     
          for(jk=1; jk <=nlstate ; jk++){              for(k1=1; k1<=j;k1++){
            if( i <= (int) agemax){      for(i1=1; i1<=ncodemax[k1];i1++){
              if(pos>=1.e-5){        j1++;
                probs[i][jk][j1]= pp[jk]/pos;        
              }        for (i=-1; i<=nlstate+ndeath; i++)  
            }          for (jk=-1; jk<=nlstate+ndeath; jk++)  
          }            for(m=agemin; m <= agemax+3; m++)
                        freq[i][jk][m]=0;
         }       
     }        for (i=1; i<=imx; i++) {
   }          bool=1;
           if  (cptcovn>0) {
              for (z1=1; z1<=cptcoveff; z1++) 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   free_vector(pp,1,nlstate);                bool=0;
            } 
 }  /* End of Freq */          if (bool==1) { 
             for(m=firstpass; m<=lastpass; m++){
 /************* Waves Concatenation ***************/              k2=anint[m][i]+(mint[m][i]/12.);
               if ((k2>=dateprev1) && (k2<=dateprev2)) {
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)                if(agev[m][i]==0) agev[m][i]=agemax+1;
 {                if(agev[m][i]==1) agev[m][i]=agemax+2;
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.                if (m<lastpass) {
      Death is a valid wave (if date is known).                  if (calagedate>0) 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i                    freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]                  else
      and mw[mi+1][i]. dh depends on stepm.                    freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
      */                  freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; 
                 }
   int i, mi, m;              }
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;            }
      double sum=0., jmean=0.;*/          }
         }
   int j, k=0,jk, ju, jl;        for(i=(int)agemin; i <= (int)agemax+3; i++){ 
   double sum=0.;          for(jk=1; jk <=nlstate ; jk++){
   jmin=1e+5;            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   jmax=-1;              pp[jk] += freq[jk][m][i]; 
   jmean=0.;          }
   for(i=1; i<=imx; i++){          for(jk=1; jk <=nlstate ; jk++){
     mi=0;            for(m=-1, pos=0; m <=0 ; m++)
     m=firstpass;              pos += freq[jk][m][i];
     while(s[m][i] <= nlstate){          }
       if(s[m][i]>=1)          
         mw[++mi][i]=m;          for(jk=1; jk <=nlstate ; jk++){
       if(m >=lastpass)            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
         break;              pp[jk] += freq[jk][m][i];
       else          }
         m++;          
     }/* end while */          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
     if (s[m][i] > nlstate){          
       mi++;     /* Death is another wave */          for(jk=1; jk <=nlstate ; jk++){    
       /* if(mi==0)  never been interviewed correctly before death */            if( i <= (int) agemax){
          /* Only death is a correct wave */              if(pos>=1.e-5){
       mw[mi][i]=m;                probs[i][jk][j1]= pp[jk]/pos;
     }              }
             }
     wav[i]=mi;          }/* end jk */
     if(mi==0)        }/* end i */
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);      } /* end i1 */
   }    } /* end k1 */
   
   for(i=1; i<=imx; i++){    
     for(mi=1; mi<wav[i];mi++){    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
       if (stepm <=0)    free_vector(pp,1,nlstate);
         dh[mi][i]=1;    
       else{  }  /* End of Freq */
         if (s[mw[mi+1][i]][i] > nlstate) {  
           if (agedc[i] < 2*AGESUP) {  /************* Waves Concatenation ***************/
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  
           if(j==0) j=1;  /* Survives at least one month after exam */  void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
           k=k+1;  {
           if (j >= jmax) jmax=j;    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
           if (j <= jmin) jmin=j;       Death is a valid wave (if date is known).
           sum=sum+j;       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
           /*if (j<0) printf("j=%d num=%d \n",j,i); */       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.
         }       */
         else{  
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    int i, mi, m;
           k=k+1;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
           if (j >= jmax) jmax=j;       double sum=0., jmean=0.;*/
           else if (j <= jmin)jmin=j;    int first;
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    int j, k=0,jk, ju, jl;
           sum=sum+j;    double sum=0.;
         }    first=0;
         jk= j/stepm;    jmin=1e+5;
         jl= j -jk*stepm;    jmax=-1;
         ju= j -(jk+1)*stepm;    jmean=0.;
         if(jl <= -ju)    for(i=1; i<=imx; i++){
           dh[mi][i]=jk;      mi=0;
         else      m=firstpass;
           dh[mi][i]=jk+1;      while(s[m][i] <= nlstate){
         if(dh[mi][i]==0)        if(s[m][i]>=1)
           dh[mi][i]=1; /* At least one step */          mw[++mi][i]=m;
       }        if(m >=lastpass)
     }          break;
   }        else
   jmean=sum/k;          m++;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);      }/* end while */
  }      if (s[m][i] > nlstate){
 /*********** Tricode ****************************/        mi++;     /* Death is another wave */
 void tricode(int *Tvar, int **nbcode, int imx)        /* if(mi==0)  never been interviewed correctly before death */
 {           /* Only death is a correct wave */
   int Ndum[20],ij=1, k, j, i;        mw[mi][i]=m;
   int cptcode=0;      }
   cptcoveff=0;  
        wav[i]=mi;
   for (k=0; k<19; k++) Ndum[k]=0;      if(mi==0){
   for (k=1; k<=7; k++) ncodemax[k]=0;        if(first==0){
           printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          first=1;
     for (i=1; i<=imx; i++) {        }
       ij=(int)(covar[Tvar[j]][i]);        if(first==1){
       Ndum[ij]++;          fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        }
       if (ij > cptcode) cptcode=ij;      } /* end mi==0 */
     }    }
   
     for (i=0; i<=cptcode; i++) {    for(i=1; i<=imx; i++){
       if(Ndum[i]!=0) ncodemax[j]++;      for(mi=1; mi<wav[i];mi++){
     }        if (stepm <=0)
     ij=1;          dh[mi][i]=1;
         else{
           if (s[mw[mi+1][i]][i] > nlstate) {
     for (i=1; i<=ncodemax[j]; i++) {            if (agedc[i] < 2*AGESUP) {
       for (k=0; k<=19; k++) {            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
         if (Ndum[k] != 0) {            if(j==0) j=1;  /* Survives at least one month after exam */
           nbcode[Tvar[j]][ij]=k;            k=k+1;
                      if (j >= jmax) jmax=j;
           ij++;            if (j <= jmin) jmin=j;
         }            sum=sum+j;
         if (ij > ncodemax[j]) break;            /*if (j<0) printf("j=%d num=%d \n",j,i); */
       }              }
     }          }
   }            else{
             j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
  for (k=0; k<19; k++) Ndum[k]=0;            k=k+1;
             if (j >= jmax) jmax=j;
  for (i=1; i<=ncovmodel-2; i++) {            else if (j <= jmin)jmin=j;
       ij=Tvar[i];            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       Ndum[ij]++;            sum=sum+j;
     }          }
           jk= j/stepm;
  ij=1;          jl= j -jk*stepm;
  for (i=1; i<=10; i++) {          ju= j -(jk+1)*stepm;
    if((Ndum[i]!=0) && (i<=ncovcol)){          if(jl <= -ju)
      Tvaraff[ij]=i;            dh[mi][i]=jk;
      ij++;          else
    }            dh[mi][i]=jk+1;
  }          if(dh[mi][i]==0)
              dh[mi][i]=1; /* At least one step */
     cptcoveff=ij-1;        }
 }      }
     }
 /*********** Health Expectancies ****************/    jmean=sum/k;
     printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
 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 )    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
    }
 {  
   /* Health expectancies */  /*********** Tricode ****************************/
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;  void tricode(int *Tvar, int **nbcode, int imx)
   double age, agelim, hf;  {
   double ***p3mat,***varhe;    int Ndum[20],ij=1, k, j, i;
   double **dnewm,**doldm;    int cptcode=0;
   double *xp;    cptcoveff=0; 
   double **gp, **gm;   
   double ***gradg, ***trgradg;    for (k=0; k<19; k++) Ndum[k]=0;
   int theta;    for (k=1; k<=7; k++) ncodemax[k]=0;
   
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   xp=vector(1,npar);      for (i=1; i<=imx; i++) {
   dnewm=matrix(1,nlstate*2,1,npar);        ij=(int)(covar[Tvar[j]][i]);
   doldm=matrix(1,nlstate*2,1,nlstate*2);        Ndum[ij]++; 
          /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   fprintf(ficreseij,"# Health expectancies\n");        if (ij > cptcode) cptcode=ij; 
   fprintf(ficreseij,"# Age");      }
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=nlstate;j++)      for (i=0; i<=cptcode; i++) {
       fprintf(ficreseij," %1d-%1d (SE)",i,j);        if(Ndum[i]!=0) ncodemax[j]++;
   fprintf(ficreseij,"\n");      }
       ij=1; 
   if(estepm < stepm){  
     printf ("Problem %d lower than %d\n",estepm, stepm);  
   }      for (i=1; i<=ncodemax[j]; i++) {
   else  hstepm=estepm;          for (k=0; k<=19; k++) {
   /* We compute the life expectancy from trapezoids spaced every estepm months          if (Ndum[k] != 0) {
    * This is mainly to measure the difference between two models: for example            nbcode[Tvar[j]][ij]=k; 
    * 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            ij++;
    * progression inbetween and thus overestimating or underestimating according          }
    * to the curvature of the survival function. If, for the same date, we          if (ij > ncodemax[j]) break; 
    * 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      } 
    * hypothesis. A more precise result, taking into account a more precise    }  
    * curvature will be obtained if estepm is as small as stepm. */  
    for (k=0; k<19; k++) Ndum[k]=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.   for (i=1; i<=ncovmodel-2; i++) {
      nhstepm is the number of hstepm from age to agelim     ij=Tvar[i];
      nstepm is the number of stepm from age to agelin.     Ndum[ij]++; 
      Look at hpijx to understand the reason of that which relies in memory size   }
      and note for a fixed period like estepm months */  
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the   ij=1;
      survival function given by stepm (the optimization length). Unfortunately it   for (i=1; i<=10; i++) {
      means that if the survival funtion is printed only each two years of age and if     if((Ndum[i]!=0) && (i<=ncovcol)){
      you sum them up and add 1 year (area under the trapezoids) you won't get the same       Tvaraff[ij]=i; 
      results. So we changed our mind and took the option of the best precision.       ij++;
   */     }
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */   }
    
   agelim=AGESUP;   cptcoveff=ij-1;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  }
     /* nhstepm age range expressed in number of stepm */  
     nstepm=(int) rint((agelim-age)*YEARM/stepm);  /*********** Health Expectancies ****************/
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */  
     /* if (stepm >= YEARM) hstepm=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 )
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  {
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);    /* Health expectancies */
     gp=matrix(0,nhstepm,1,nlstate*2);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     gm=matrix(0,nhstepm,1,nlstate*2);    double age, agelim, hf;
     double ***p3mat,***varhe;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    double **dnewm,**doldm;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    double *xp;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      double **gp, **gm;
      double ***gradg, ***trgradg;
     int theta;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  
     varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
     /* Computing Variances of health expectancies */    xp=vector(1,npar);
     dnewm=matrix(1,nlstate*2,1,npar);
      for(theta=1; theta <=npar; theta++){    doldm=matrix(1,nlstate*2,1,nlstate*2);
       for(i=1; i<=npar; i++){    
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    fprintf(ficreseij,"# Health expectancies\n");
       }    fprintf(ficreseij,"# Age");
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++)
       cptj=0;        fprintf(ficreseij," %1d-%1d (SE)",i,j);
       for(j=1; j<= nlstate; j++){    fprintf(ficreseij,"\n");
         for(i=1; i<=nlstate; i++){  
           cptj=cptj+1;    if(estepm < stepm){
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){      printf ("Problem %d lower than %d\n",estepm, stepm);
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    }
           }    else  hstepm=estepm;   
         }    /* We compute the life expectancy from trapezoids spaced every estepm months
       }     * This is mainly to measure the difference between two models: for example
           * if stepm=24 months pijx are given only every 2 years and by summing them
           * we are calculating an estimate of the Life Expectancy assuming a linear 
       for(i=1; i<=npar; i++)     * progression inbetween and thus overestimating or underestimating according
         xp[i] = x[i] - (i==theta ?delti[theta]:0);     * to the curvature of the survival function. If, for the same date, we 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);       * 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 
       cptj=0;     * 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(i=1;i<=nlstate;i++){  
           cptj=cptj+1;    /* For example we decided to compute the life expectancy with the smallest unit */
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;       nhstepm is the number of hstepm from age to agelim 
           }       nstepm is the number of stepm from age to agelin. 
         }       Look at hpijx to understand the reason of that which relies in memory size
       }       and note for a fixed period like estepm months */
          /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
       for(j=1; j<= nlstate*2; j++)       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         for(h=0; h<=nhstepm-1; h++){       results. So we changed our mind and took the option of the best precision.
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    */
         }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
      }    agelim=AGESUP;
        for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 /* End theta */      /* nhstepm age range expressed in number of stepm */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); 
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
      for(h=0; h<=nhstepm-1; h++)      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       for(j=1; j<=nlstate*2;j++)      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         for(theta=1; theta <=npar; theta++)      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
         trgradg[h][j][theta]=gradg[h][theta][j];      gp=matrix(0,nhstepm,1,nlstate*2);
       gm=matrix(0,nhstepm,1,nlstate*2);
   
      for(i=1;i<=nlstate*2;i++)      /* Computed by stepm unit matrices, product of hstepm matrices, stored
       for(j=1;j<=nlstate*2;j++)         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
         varhe[i][j][(int)age] =0.;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
    
     for(h=0;h<=nhstepm-1;h++){  
       for(k=0;k<=nhstepm-1;k++){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         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]);      /* Computing Variances of health expectancies */
         for(i=1;i<=nlstate*2;i++)  
           for(j=1;j<=nlstate*2;j++)       for(theta=1; theta <=npar; theta++){
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;        for(i=1; i<=npar; i++){ 
       }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     }        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
          
     /* Computing expectancies */        cptj=0;
     for(i=1; i<=nlstate;i++)        for(j=1; j<= nlstate; j++){
       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++){            cptj=cptj+1;
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
                        gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
 /* 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 );       
     cptj=0;        for(i=1; i<=npar; i++) 
     for(i=1; i<=nlstate;i++)          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       for(j=1; j<=nlstate;j++){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         cptj++;        
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );        cptj=0;
       }        for(j=1; j<= nlstate; j++){
     fprintf(ficreseij,"\n");          for(i=1;i<=nlstate;i++){
                cptj=cptj+1;
     free_matrix(gm,0,nhstepm,1,nlstate*2);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
     free_matrix(gp,0,nhstepm,1,nlstate*2);              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);            }
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);          }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
   }        for(j=1; j<= nlstate*2; j++)
   free_vector(xp,1,npar);          for(h=0; h<=nhstepm-1; h++){
   free_matrix(dnewm,1,nlstate*2,1,npar);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);          }
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);       } 
 }     
   /* End theta */
 /************ Variance ******************/  
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)       trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
 {  
   /* Variance of health expectancies */       for(h=0; h<=nhstepm-1; h++)
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        for(j=1; j<=nlstate*2;j++)
   double **newm;          for(theta=1; theta <=npar; theta++)
   double **dnewm,**doldm;            trgradg[h][j][theta]=gradg[h][theta][j];
   int i, j, nhstepm, hstepm, h, nstepm ;       
   int k, cptcode;  
   double *xp;       for(i=1;i<=nlstate*2;i++)
   double **gp, **gm;        for(j=1;j<=nlstate*2;j++)
   double ***gradg, ***trgradg;          varhe[i][j][(int)age] =0.;
   double ***p3mat;  
   double age,agelim, hf;       printf("%d|",(int)age);fflush(stdout);
   int theta;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(h=0;h<=nhstepm-1;h++){
    fprintf(ficresvij,"# Covariances of life expectancies\n");        for(k=0;k<=nhstepm-1;k++){
   fprintf(ficresvij,"# Age");          matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
   for(i=1; i<=nlstate;i++)          matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
     for(j=1; j<=nlstate;j++)          for(i=1;i<=nlstate*2;i++)
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);            for(j=1;j<=nlstate*2;j++)
   fprintf(ficresvij,"\n");              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
   xp=vector(1,npar);      }
   dnewm=matrix(1,nlstate,1,npar);      /* Computing expectancies */
   doldm=matrix(1,nlstate,1,nlstate);      for(i=1; i<=nlstate;i++)
          for(j=1; j<=nlstate;j++)
   if(estepm < stepm){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     printf ("Problem %d lower than %d\n",estepm, stepm);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   }            
   else  hstepm=estepm;    /* 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 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  
      nstepm is the number of stepm from age to agelin.      fprintf(ficreseij,"%3.0f",age );
      Look at hpijx to understand the reason of that which relies in memory size      cptj=0;
      and note for a fixed period like k years */      for(i=1; i<=nlstate;i++)
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        for(j=1; j<=nlstate;j++){
      survival function given by stepm (the optimization length). Unfortunately it          cptj++;
      means that if the survival funtion is printed only each two years of age and if          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
      you sum them up and add 1 year (area under the trapezoids) you won't get the same        }
      results. So we changed our mind and took the option of the best precision.      fprintf(ficreseij,"\n");
   */     
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */      free_matrix(gm,0,nhstepm,1,nlstate*2);
   agelim = AGESUP;      free_matrix(gp,0,nhstepm,1,nlstate*2);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    printf("\n");
     gp=matrix(0,nhstepm,1,nlstate);    fprintf(ficlog,"\n");
     gm=matrix(0,nhstepm,1,nlstate);  
     free_vector(xp,1,npar);
     for(theta=1; theta <=npar; theta++){    free_matrix(dnewm,1,nlstate*2,1,npar);
       for(i=1; i<=npar; i++){ /* Computes gradient */    free_matrix(doldm,1,nlstate*2,1,nlstate*2);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
       }  }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  /************ Variance ******************/
   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
       if (popbased==1) {  {
         for(i=1; i<=nlstate;i++)    /* Variance of health expectancies */
           prlim[i][i]=probs[(int)age][i][ij];    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
       }    /* double **newm;*/
      double **dnewm,**doldm;
       for(j=1; j<= nlstate; j++){    double **dnewmp,**doldmp;
         for(h=0; h<=nhstepm; h++){    int i, j, nhstepm, hstepm, h, nstepm ;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    int k, cptcode;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    double *xp;
         }    double **gp, **gm;  /* for var eij */
       }    double ***gradg, ***trgradg; /*for var eij */
        double **gradgp, **trgradgp; /* for var p point j */
       for(i=1; i<=npar; i++) /* Computes gradient */    double *gpp, *gmp; /* for var p point j */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      double ***p3mat;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double age,agelim, hf;
      double ***mobaverage;
       if (popbased==1) {    int theta;
         for(i=1; i<=nlstate;i++)    char digit[4];
           prlim[i][i]=probs[(int)age][i][ij];    char digitp[25];
       }  
     char fileresprobmorprev[FILENAMELENGTH];
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){    if(popbased==1){
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      if(mobilav==1)
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        strcpy(digitp,"-populbased-mobilav-");
         }      else strcpy(digitp,"-populbased-nomobil-");
       }    }
     else 
       for(j=1; j<= nlstate; j++)      strcpy(digitp,"-stablbased-");
         for(h=0; h<=nhstepm; h++){  
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    if (mobilav!=0) {
         }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     } /* End theta */      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     for(h=0; h<=nhstepm; h++)    }
       for(j=1; j<=nlstate;j++)  
         for(theta=1; theta <=npar; theta++)    strcpy(fileresprobmorprev,"prmorprev"); 
           trgradg[h][j][theta]=gradg[h][theta][j];    sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     for(i=1;i<=nlstate;i++)    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
       for(j=1;j<=nlstate;j++)    strcat(fileresprobmorprev,fileres);
         vareij[i][j][(int)age] =0.;    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
     for(h=0;h<=nhstepm;h++){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
       for(k=0;k<=nhstepm;k++){    }
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         for(i=1;i<=nlstate;i++)    fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");
           for(j=1;j<=nlstate;j++)    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       }      fprintf(ficresprobmorprev," p.%-d SE",j);
     }      for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     fprintf(ficresvij,"%.0f ",age );    }  
     for(i=1; i<=nlstate;i++)    fprintf(ficresprobmorprev,"\n");
       for(j=1; j<=nlstate;j++){    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
       }      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
     fprintf(ficresvij,"\n");      exit(0);
     free_matrix(gp,0,nhstepm,1,nlstate);    }
     free_matrix(gm,0,nhstepm,1,nlstate);    else{
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      fprintf(ficgp,"\n# Routine varevsij");
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   } /* End age */      printf("Problem with html file: %s\n", optionfilehtm);
        fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   free_vector(xp,1,npar);      exit(0);
   free_matrix(doldm,1,nlstate,1,npar);    }
   free_matrix(dnewm,1,nlstate,1,nlstate);    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(fichtm,"\n<br>%s (à revoir) <br>\n",digitp);
     }
 /************ Variance of prevlim ******************/    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 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)  
 {    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");
   /* Variance of prevalence limit */    fprintf(ficresvij,"# Age");
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    for(i=1; i<=nlstate;i++)
   double **newm;      for(j=1; j<=nlstate;j++)
   double **dnewm,**doldm;        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   int i, j, nhstepm, hstepm;    fprintf(ficresvij,"\n");
   int k, cptcode;  
   double *xp;    xp=vector(1,npar);
   double *gp, *gm;    dnewm=matrix(1,nlstate,1,npar);
   double **gradg, **trgradg;    doldm=matrix(1,nlstate,1,nlstate);
   double age,agelim;    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   int theta;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   fprintf(ficresvpl,"# Age");    gpp=vector(nlstate+1,nlstate+ndeath);
   for(i=1; i<=nlstate;i++)    gmp=vector(nlstate+1,nlstate+ndeath);
       fprintf(ficresvpl," %1d-%1d",i,i);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   fprintf(ficresvpl,"\n");    
     if(estepm < stepm){
   xp=vector(1,npar);      printf ("Problem %d lower than %d\n",estepm, stepm);
   dnewm=matrix(1,nlstate,1,npar);    }
   doldm=matrix(1,nlstate,1,nlstate);    else  hstepm=estepm;   
      /* For example we decided to compute the life expectancy with the smallest unit */
   hstepm=1*YEARM; /* Every year of age */    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */       nhstepm is the number of hstepm from age to agelim 
   agelim = AGESUP;       nstepm is the number of stepm from age to agelin. 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */       Look at hpijx to understand the reason of that which relies in memory size
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */       and note for a fixed period like k years */
     if (stepm >= YEARM) hstepm=1;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */       survival function given by stepm (the optimization length). Unfortunately it
     gradg=matrix(1,npar,1,nlstate);       means that if the survival funtion is printed only each two years of age and if
     gp=vector(1,nlstate);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     gm=vector(1,nlstate);       results. So we changed our mind and took the option of the best precision.
     */
     for(theta=1; theta <=npar; theta++){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       for(i=1; i<=npar; i++){ /* Computes gradient */    agelim = AGESUP;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       }      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       for(i=1;i<=nlstate;i++)      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         gp[i] = prlim[i][i];      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
          gp=matrix(0,nhstepm,1,nlstate);
       for(i=1; i<=npar; i++) /* Computes gradient */      gm=matrix(0,nhstepm,1,nlstate);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)      for(theta=1; theta <=npar; theta++){
         gm[i] = prlim[i][i];        for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
       for(i=1;i<=nlstate;i++)        }
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     } /* End theta */        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
     trgradg =matrix(1,nlstate,1,npar);        if (popbased==1) {
           if(mobilav ==0){
     for(j=1; j<=nlstate;j++)            for(i=1; i<=nlstate;i++)
       for(theta=1; theta <=npar; theta++)              prlim[i][i]=probs[(int)age][i][ij];
         trgradg[j][theta]=gradg[theta][j];          }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
     for(i=1;i<=nlstate;i++)              prlim[i][i]=mobaverage[(int)age][i][ij];
       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);    
     for(i=1;i<=nlstate;i++)        for(j=1; j<= nlstate; j++){
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
     fprintf(ficresvpl,"%.0f ",age );              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
     for(i=1; i<=nlstate;i++)          }
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        }
     fprintf(ficresvpl,"\n");        /* This for computing forces of mortality (h=1)as a weighted average */
     free_vector(gp,1,nlstate);        for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
     free_vector(gm,1,nlstate);          for(i=1; i<= nlstate; i++)
     free_matrix(gradg,1,npar,1,nlstate);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     free_matrix(trgradg,1,nlstate,1,npar);        }    
   } /* End age */        /* end force of mortality */
   
   free_vector(xp,1,npar);        for(i=1; i<=npar; i++) /* Computes gradient */
   free_matrix(doldm,1,nlstate,1,npar);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   free_matrix(dnewm,1,nlstate,1,nlstate);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 }   
         if (popbased==1) {
 /************ Variance of one-step probabilities  ******************/          if(mobilav ==0){
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)            for(i=1; i<=nlstate;i++)
 {              prlim[i][i]=probs[(int)age][i][ij];
   int i, j, i1, k1, j1, z1;          }else{ /* mobilav */ 
   int k=0, cptcode;            for(i=1; i<=nlstate;i++)
   double **dnewm,**doldm;              prlim[i][i]=mobaverage[(int)age][i][ij];
   double *xp;          }
   double *gp, *gm;        }
   double **gradg, **trgradg;  
   double age,agelim, cov[NCOVMAX];        for(j=1; j<= nlstate; j++){
   int theta;          for(h=0; h<=nhstepm; h++){
   char fileresprob[FILENAMELENGTH];            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   strcpy(fileresprob,"prob");          }
   strcat(fileresprob,fileres);        }
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        /* This for computing force of mortality (h=1)as a weighted average */
     printf("Problem with resultfile: %s\n", fileresprob);        for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
   }          for(i=1; i<= nlstate; i++)
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);            gmp[j] += prlim[i][i]*p3mat[i][j][1];
          }    
 fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");        /* end force of mortality */
   fprintf(ficresprob,"# Age");  
   for(i=1; i<=nlstate;i++)        for(j=1; j<= nlstate; j++) /* vareij */
     for(j=1; j<=(nlstate+ndeath);j++)          for(h=0; h<=nhstepm; h++){
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   fprintf(ficresprob,"\n");          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
   xp=vector(1,npar);      } /* End theta */
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
    
   cov[1]=1;      for(h=0; h<=nhstepm; h++) /* veij */
   j=cptcoveff;        for(j=1; j<=nlstate;j++)
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          for(theta=1; theta <=npar; theta++)
   j1=0;            trgradg[h][j][theta]=gradg[h][theta][j];
   for(k1=1; k1<=1;k1++){  
     for(i1=1; i1<=ncodemax[k1];i1++){      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     j1++;        for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     if  (cptcovn>0) {  
       fprintf(ficresprob, "\n#********** Variable ");      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      for(i=1;i<=nlstate;i++)
       fprintf(ficresprob, "**********\n#");        for(j=1;j<=nlstate;j++)
     }          vareij[i][j][(int)age] =0.;
      
       for (age=bage; age<=fage; age ++){      for(h=0;h<=nhstepm;h++){
         cov[2]=age;        for(k=0;k<=nhstepm;k++){
         for (k=1; k<=cptcovn;k++) {          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
                    for(i=1;i<=nlstate;i++)
         }            for(j=1;j<=nlstate;j++)
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         for (k=1; k<=cptcovprod;k++)        }
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      }
          
         gradg=matrix(1,npar,1,9);      /* pptj */
         trgradg=matrix(1,9,1,npar);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      for(j=nlstate+1;j<=nlstate+ndeath;j++)
            for(i=nlstate+1;i<=nlstate+ndeath;i++)
         for(theta=1; theta <=npar; theta++){          varppt[j][i]=doldmp[j][i];
           for(i=1; i<=npar; i++)      /* end ppptj */
             xp[i] = x[i] + (i==theta ?delti[theta]:0);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
                prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
           pmij(pmmij,cov,ncovmodel,xp,nlstate);   
                if (popbased==1) {
           k=0;        if(mobilav ==0){
           for(i=1; i<= (nlstate+ndeath); i++){          for(i=1; i<=nlstate;i++)
             for(j=1; j<=(nlstate+ndeath);j++){            prlim[i][i]=probs[(int)age][i][ij];
               k=k+1;        }else{ /* mobilav */ 
               gp[k]=pmmij[i][j];          for(i=1; i<=nlstate;i++)
             }            prlim[i][i]=mobaverage[(int)age][i][ij];
           }        }
                }
           for(i=1; i<=npar; i++)      
             xp[i] = x[i] - (i==theta ?delti[theta]:0);      /* This for computing force of mortality (h=1)as a weighted average */
          for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
           pmij(pmmij,cov,ncovmodel,xp,nlstate);        for(i=1; i<= nlstate; i++)
           k=0;          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
           for(i=1; i<=(nlstate+ndeath); i++){      }    
             for(j=1; j<=(nlstate+ndeath);j++){      /* end force of mortality */
               k=k+1;  
               gm[k]=pmmij[i][j];      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
             }      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
           }        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
              for(i=1; i<=nlstate;i++){
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];          }
         }      } 
       fprintf(ficresprobmorprev,"\n");
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)  
           for(theta=1; theta <=npar; theta++)      fprintf(ficresvij,"%.0f ",age );
             trgradg[j][theta]=gradg[theta][j];      for(i=1; i<=nlstate;i++)
                for(j=1; j<=nlstate;j++){
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);        }
              fprintf(ficresvij,"\n");
         pmij(pmmij,cov,ncovmodel,x,nlstate);      free_matrix(gp,0,nhstepm,1,nlstate);
              free_matrix(gm,0,nhstepm,1,nlstate);
         k=0;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
         for(i=1; i<=(nlstate+ndeath); i++){      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
           for(j=1; j<=(nlstate+ndeath);j++){      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             k=k+1;    } /* End age */
             gm[k]=pmmij[i][j];    free_vector(gpp,nlstate+1,nlstate+ndeath);
           }    free_vector(gmp,nlstate+1,nlstate+ndeath);
         }    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
          free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
      /*printf("\n%d ",(int)age);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    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(ficresprob,"\n%d ",(int)age);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));    /*  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);
    */
       }    fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
     }  
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    free_vector(xp,1,npar);
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   }    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   free_vector(xp,1,npar);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   fclose(ficresprob);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      fclose(ficresprobmorprev);
 }    fclose(ficgp);
     fclose(fichtm);
 /******************* Printing html file ***********/  }
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \  
  int lastpass, int stepm, int weightopt, char model[],\  /************ Variance of prevlim ******************/
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \  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)
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\  {
  char version[], int popforecast, int estepm ){    /* Variance of prevalence limit */
   int jj1, k1, i1, cpt;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   FILE *fichtm;    double **newm;
   /*char optionfilehtm[FILENAMELENGTH];*/    double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
   strcpy(optionfilehtm,optionfile);    int k, cptcode;
   strcat(optionfilehtm,".htm");    double *xp;
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    double *gp, *gm;
     printf("Problem with %s \n",optionfilehtm), exit(0);    double **gradg, **trgradg;
   }    double age,agelim;
     int theta;
  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    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
 \n    fprintf(ficresvpl,"# Age");
 Total number of observations=%d <br>\n    for(i=1; i<=nlstate;i++)
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n        fprintf(ficresvpl," %1d-%1d",i,i);
 <hr  size=\"2\" color=\"#EC5E5E\">    fprintf(ficresvpl,"\n");
  <ul><li>Outputs files<br>\n  
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n    xp=vector(1,npar);
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n    dnewm=matrix(1,nlstate,1,npar);
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    doldm=matrix(1,nlstate,1,nlstate);
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n    
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n    hstepm=1*YEARM; /* Every year of age */
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,estepm,fileres,fileres);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
  fprintf(fichtm,"\n    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n      if (stepm >= YEARM) hstepm=1;
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n      gradg=matrix(1,npar,1,nlstate);
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);      gp=vector(1,nlstate);
       gm=vector(1,nlstate);
  if(popforecast==1) fprintf(fichtm,"\n  
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n      for(theta=1; theta <=npar; theta++){
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n        for(i=1; i<=npar; i++){ /* Computes gradient */
         <br>",fileres,fileres,fileres,fileres);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
  else        }
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 fprintf(fichtm," <li>Graphs</li><p>");        for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
  m=cptcoveff;      
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
  jj1=0;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
  for(k1=1; k1<=m;k1++){        for(i=1;i<=nlstate;i++)
    for(i1=1; i1<=ncodemax[k1];i1++){          gm[i] = prlim[i][i];
        jj1++;  
        if (cptcovn > 0) {        for(i=1;i<=nlstate;i++)
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
          for (cpt=1; cpt<=cptcoveff;cpt++)      } /* End theta */
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);  
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");      trgradg =matrix(1,nlstate,1,npar);
        }  
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>      for(j=1; j<=nlstate;j++)
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            for(theta=1; theta <=npar; theta++)
        for(cpt=1; cpt<nlstate;cpt++){          trgradg[j][theta]=gradg[theta][j];
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>  
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      for(i=1;i<=nlstate;i++)
        }        varpl[i][(int)age] =0.;
     for(cpt=1; cpt<=nlstate;cpt++) {      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
 interval) in state (%d): v%s%d%d.gif <br>      for(i=1;i<=nlstate;i++)
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
      }  
      for(cpt=1; cpt<=nlstate;cpt++) {      fprintf(ficresvpl,"%.0f ",age );
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>      for(i=1; i<=nlstate;i++)
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
      }      fprintf(ficresvpl,"\n");
      fprintf(fichtm,"\n<br>- Total life expectancy by age and      free_vector(gp,1,nlstate);
 health expectancies in states (1) and (2): e%s%d.gif<br>      free_vector(gm,1,nlstate);
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      free_matrix(gradg,1,npar,1,nlstate);
 fprintf(fichtm,"\n</body>");      free_matrix(trgradg,1,nlstate,1,npar);
    }    } /* End age */
    }  
 fclose(fichtm);    free_vector(xp,1,npar);
 }    free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
 /******************* Gnuplot file **************/  
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  }
   
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;  /************ 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)
   strcpy(optionfilegnuplot,optionfilefiname);  {
   strcat(optionfilegnuplot,".gp.txt");    int i, j=0,  i1, k1, l1, t, tj;
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    int k2, l2, j1,  z1;
     printf("Problem with file %s",optionfilegnuplot);    int k=0,l, cptcode;
   }    int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
 #ifdef windows    double **dnewm,**doldm;
     fprintf(ficgp,"cd \"%s\" \n",pathc);    double *xp;
 #endif    double *gp, *gm;
 m=pow(2,cptcoveff);    double **gradg, **trgradg;
      double **mu;
  /* 1eme*/    double age,agelim, cov[NCOVMAX];
   for (cpt=1; cpt<= nlstate ; cpt ++) {    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
    for (k1=1; k1<= m ; k1 ++) {    int theta;
     char fileresprob[FILENAMELENGTH];
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);    char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
 for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    double ***varpij;
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }    strcpy(fileresprob,"prob"); 
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    strcat(fileresprob,fileres);
     for (i=1; i<= nlstate ; i ++) {    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      printf("Problem with resultfile: %s\n", fileresprob);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
 }    }
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    strcpy(fileresprobcov,"probcov"); 
      for (i=1; i<= nlstate ; i ++) {    strcat(fileresprobcov,fileres);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   else fprintf(ficgp," \%%*lf (\%%*lf)");      printf("Problem with resultfile: %s\n", fileresprobcov);
 }        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    }
     strcpy(fileresprobcor,"probcor"); 
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    strcat(fileresprobcor,fileres);
    }    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", fileresprobcor);
   /*2 eme*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
   for (k1=1; k1<= m ; k1 ++) {    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
        printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     for (i=1; i<= nlstate+1 ; i ++) {    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       k=2*i;    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       for (j=1; j<= nlstate+1 ; j ++) {    
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");    fprintf(ficresprob,"# Age");
 }      fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    fprintf(ficresprobcov,"# Age");
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    fprintf(ficresprobcov,"# Age");
       for (j=1; j<= nlstate+1 ; j ++) {  
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
         else fprintf(ficgp," \%%*lf (\%%*lf)");    for(i=1; i<=nlstate;i++)
 }        for(j=1; j<=(nlstate+ndeath);j++){
       fprintf(ficgp,"\" t\"\" w l 0,");        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
       for (j=1; j<= nlstate+1 ; j ++) {        fprintf(ficresprobcor," p%1d-%1d ",i,j);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      }  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    fprintf(ficresprob,"\n");
 }      fprintf(ficresprobcov,"\n");
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    fprintf(ficresprobcor,"\n");
       else fprintf(ficgp,"\" t\"\" w l 0,");    xp=vector(1,npar);
     }    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   }    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
      varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
   /*3eme*/    first=1;
     if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   for (k1=1; k1<= m ; k1 ++) {      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
     for (cpt=1; cpt<= nlstate ; cpt ++) {      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
       k=2+nlstate*(2*cpt-2);      exit(0);
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    }
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    else{
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");      fprintf(ficgp,"\n# Routine varprob");
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    }
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");      printf("Problem with html file: %s\n", optionfilehtm);
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
       exit(0);
 */    }
       for (i=1; i< nlstate ; i ++) {    else{
         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);      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
       fprintf(fichtm,"\n");
       }  
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
     }      fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     }      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");
    
   /* CV preval stat */    }
     for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<nlstate ; cpt ++) {   
       k=3;    cov[1]=1;
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);    tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
       for (i=1; i< nlstate ; i ++)    j1=0;
         fprintf(ficgp,"+$%d",k+i+1);    for(t=1; t<=tj;t++){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);      for(i1=1; i1<=ncodemax[t];i1++){ 
              j1++;
       l=3+(nlstate+ndeath)*cpt;        
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        if  (cptcovn>0) {
       for (i=1; i< nlstate ; i ++) {          fprintf(ficresprob, "\n#********** Variable "); 
         l=3+(nlstate+ndeath)*cpt;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fprintf(ficgp,"+$%d",l+i+1);          fprintf(ficresprob, "**********\n#");
       }          fprintf(ficresprobcov, "\n#********** Variable "); 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          fprintf(ficresprobcov, "**********\n#");
     }          
   }            fprintf(ficgp, "\n#********** Variable "); 
            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   /* proba elementaires */          fprintf(ficgp, "**********\n#");
    for(i=1,jk=1; i <=nlstate; i++){          
     for(k=1; k <=(nlstate+ndeath); k++){          
       if (k != i) {          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
         for(j=1; j <=ncovmodel; j++){          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\">");
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);          
           jk++;          fprintf(ficresprobcor, "\n#********** Variable ");    
           fprintf(ficgp,"\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         }          fprintf(ficgp, "**********\n#");    
       }        }
     }        
     }        for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
     for(jk=1; jk <=m; jk++) {          for (k=1; k<=cptcovn;k++) {
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
    i=1;          }
    for(k2=1; k2<=nlstate; k2++) {          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
      k3=i;          for (k=1; k<=cptcovprod;k++)
      for(k=1; k<=(nlstate+ndeath); k++) {            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
        if (k != k2){          
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
 ij=1;          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         for(j=3; j <=ncovmodel; j++) {          gp=vector(1,(nlstate)*(nlstate+ndeath));
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          gm=vector(1,(nlstate)*(nlstate+ndeath));
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      
             ij++;          for(theta=1; theta <=npar; theta++){
           }            for(i=1; i<=npar; i++)
           else              xp[i] = x[i] + (i==theta ?delti[theta]:0);
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            
         }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
           fprintf(ficgp,")/(1");            
                    k=0;
         for(k1=1; k1 <=nlstate; k1++){              for(i=1; i<= (nlstate); i++){
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);              for(j=1; j<=(nlstate+ndeath);j++){
 ij=1;                k=k+1;
           for(j=3; j <=ncovmodel; j++){                gp[k]=pmmij[i][j];
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              }
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            }
             ij++;            
           }            for(i=1; i<=npar; i++)
           else              xp[i] = x[i] - (i==theta ?delti[theta]:0);
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      
           }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
           fprintf(ficgp,")");            k=0;
         }            for(i=1; i<=(nlstate); i++){
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);              for(j=1; j<=(nlstate+ndeath);j++){
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");                k=k+1;
         i=i+ncovmodel;                gm[k]=pmmij[i][j];
        }              }
      }            }
    }       
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
    }              gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
              }
   fclose(ficgp);  
 }  /* end gnuplot */          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
 /*************** Moving average **************/          
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){          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);
   int i, cpt, cptcod;          
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)          pmij(pmmij,cov,ncovmodel,x,nlstate);
       for (i=1; i<=nlstate;i++)          
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          k=0;
           mobaverage[(int)agedeb][i][cptcod]=0.;          for(i=1; i<=(nlstate); i++){
                for(j=1; j<=(nlstate+ndeath);j++){
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){              k=k+1;
       for (i=1; i<=nlstate;i++){              mu[k][(int) age]=pmmij[i][j];
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            }
           for (cpt=0;cpt<=4;cpt++){          }
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
           }            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;              varpij[i][j][(int)age] = doldm[i][j];
         }  
       }          /*printf("\n%d ",(int)age);
     }       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]));
 }         fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
        }*/
   
 /************** Forecasting ******************/          fprintf(ficresprob,"\n%d ",(int)age);
 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){          fprintf(ficresprobcov,"\n%d ",(int)age);
            fprintf(ficresprobcor,"\n%d ",(int)age);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  
   int *popage;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
   double *popeffectif,*popcount;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   double ***p3mat;            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   char fileresf[FILENAMELENGTH];            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
  agelim=AGESUP;          i=0;
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;          for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);              i=i++;
                fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
                fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
   strcpy(fileresf,"f");              for (j=1; j<=i;j++){
   strcat(fileresf,fileres);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   if((ficresf=fopen(fileresf,"w"))==NULL) {                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
     printf("Problem with forecast resultfile: %s\n", fileresf);              }
   }            }
   printf("Computing forecasting: result on file '%s' \n", fileresf);          }/* end of loop for state */
         } /* end of loop for age */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
         /* Confidence intervalle of pij  */
   if (mobilav==1) {        /*
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        fprintf(ficgp,"\nset noparametric;unset label");
     movingaverage(agedeb, fage, ageminpar, mobaverage);        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);
   stepsize=(int) (stepm+YEARM-1)/YEARM;        fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   if (stepm<=12) stepsize=1;        fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
   agelim=AGESUP;        */
    
   hstepm=1;        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
   hstepm=hstepm/stepm;        first1=1;
   yp1=modf(dateintmean,&yp);        for (k2=1; k2<=(nlstate);k2++){
   anprojmean=yp;          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
   yp2=modf((yp1*12),&yp);            if(l2==k2) continue;
   mprojmean=yp;            j=(k2-1)*(nlstate+ndeath)+l2;
   yp1=modf((yp2*30.5),&yp);            for (k1=1; k1<=(nlstate);k1++){
   jprojmean=yp;              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
   if(jprojmean==0) jprojmean=1;                if(l1==k1) continue;
   if(mprojmean==0) jprojmean=1;                i=(k1-1)*(nlstate+ndeath)+l1;
                  if(i<=j) continue;
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);                for (age=bage; age<=fage; age ++){ 
                    if ((int)age %5==0){
   for(cptcov=1;cptcov<=i2;cptcov++){                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
       k=k+1;                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
       fprintf(ficresf,"\n#******");                    mu1=mu[i][(int) age]/stepm*YEARM ;
       for(j=1;j<=cptcoveff;j++) {                    mu2=mu[j][(int) age]/stepm*YEARM;
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    c12=cv12/sqrt(v1*v2);
       }                    /* Computing eigen value of matrix of covariance */
       fprintf(ficresf,"******\n");                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       fprintf(ficresf,"# StartingAge FinalAge");                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);                    /* Eigen vectors */
                          v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                          /*v21=sqrt(1.-v11*v11); *//* error */
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {                    v21=(lc1-v1)/cv12*v11;
         fprintf(ficresf,"\n");                    v12=-v21;
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);                      v22=v11;
                     tnalp=v21/v11;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){                    if(first1==1){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);                      first1=0;
           nhstepm = nhstepm/hstepm;                      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);
                              }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                    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);
           oldm=oldms;savm=savms;                    /*printf(fignu*/
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                      /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                            /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
           for (h=0; h<=nhstepm; h++){                    if(first==1){
             if (h==(int) (calagedate+YEARM*cpt)) {                      first=0;
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);                      fprintf(ficgp,"\nset parametric;unset label");
             }                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
             for(j=1; j<=nlstate+ndeath;j++) {                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
               kk1=0.;kk2=0;                      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);
               for(i=1; i<=nlstate;i++) {                                    fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
                 if (mobilav==1)                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
                 else {                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                 }                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
               }                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
               if (h==(int)(calagedate+12*cpt)){                    }else{
                 fprintf(ficresf," %.3f", kk1);                      first=0;
                                              fprintf(fichtm," %d (%.3f),",(int) age, c12);
               }                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
             }                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
           }                      fprintf(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",\
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
         }                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
       }                    }/* if first */
     }                  } /* age mod 5 */
   }                } /* end loop age */
                        fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                first=1;
               } /*l12 */
   fclose(ficresf);            } /* k12 */
 }          } /*l1 */
 /************** Forecasting ******************/        }/* k1 */
 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){      } /* loop covariates */
        free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   int *popage;      free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   double *popeffectif,*popcount;      free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   double ***p3mat,***tabpop,***tabpopprev;      free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   char filerespop[FILENAMELENGTH];    }
     free_vector(xp,1,npar);
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fclose(ficresprob);
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fclose(ficresprobcov);
   agelim=AGESUP;    fclose(ficresprobcor);
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    fclose(ficgp);
      fclose(fichtm);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  }
    
    
   strcpy(filerespop,"pop");  /******************* Printing html file ***********/
   strcat(filerespop,fileres);  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
   if((ficrespop=fopen(filerespop,"w"))==NULL) {                    int lastpass, int stepm, int weightopt, char model[],\
     printf("Problem with forecast resultfile: %s\n", filerespop);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   }                    int popforecast, int estepm ,\
   printf("Computing forecasting: result on file '%s' \n", filerespop);                    double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    int jj1, k1, i1, cpt;
     /*char optionfilehtm[FILENAMELENGTH];*/
   if (mobilav==1) {    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      printf("Problem with %s \n",optionfilehtm), exit(0);
     movingaverage(agedeb, fage, ageminpar, mobaverage);      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
   }    }
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
   if (stepm<=12) stepsize=1;   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
     - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
   agelim=AGESUP;   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
     - Life expectancies by age and initial health status (estepm=%2d months): 
   hstepm=1;     <a href=\"e%s\">e%s</a> <br>\n</li>", \
   hstepm=hstepm/stepm;    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
    
   if (popforecast==1) {  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
     if((ficpop=fopen(popfile,"r"))==NULL) {  
       printf("Problem with population file : %s\n",popfile);exit(0);   m=cptcoveff;
     }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     popage=ivector(0,AGESUP);  
     popeffectif=vector(0,AGESUP);   jj1=0;
     popcount=vector(0,AGESUP);   for(k1=1; k1<=m;k1++){
         for(i1=1; i1<=ncodemax[k1];i1++){
     i=1;         jj1++;
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;       if (cptcovn > 0) {
             fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     imx=i;         for (cpt=1; cpt<=cptcoveff;cpt++) 
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   }         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
   for(cptcov=1;cptcov<=i2;cptcov++){       /* Pij */
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){       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>
       k=k+1;  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
       fprintf(ficrespop,"\n#******");       /* Quasi-incidences */
       for(j=1;j<=cptcoveff;j++) {       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
       }         /* Stable prevalence in each health state */
       fprintf(ficrespop,"******\n");         for(cpt=1; cpt<nlstate;cpt++){
       fprintf(ficrespop,"# Age");           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
       if (popforecast==1)  fprintf(ficrespop," [Population]");         }
             for(cpt=1; cpt<=nlstate;cpt++) {
       for (cpt=0; cpt<=0;cpt++) {          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
               }
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){       fprintf(fichtm,"\n<br>- Total life expectancy by age and
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  health expectancies in states (1) and (2): e%s%d.png<br>
           nhstepm = nhstepm/hstepm;  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
               } /* end i1 */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   }/* End k1 */
           oldm=oldms;savm=savms;   fprintf(fichtm,"</ul>");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
          
           for (h=0; h<=nhstepm; h++){   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
             if (h==(int) (calagedate+YEARM*cpt)) {   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);   - 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
             for(j=1; j<=nlstate+ndeath;j++) {   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
               kk1=0.;kk2=0;   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
               for(i=1; i<=nlstate;i++) {                 - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
                 if (mobilav==1)   - 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);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  
                 else {   if(popforecast==1) fprintf(fichtm,"\n
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];   - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
                 }   - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
               }          <br>",fileres,fileres,fileres,fileres);
               if (h==(int)(calagedate+12*cpt)){   else 
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;     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(ficrespop," %.3f", kk1);  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/  
               }   m=cptcoveff;
             }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
             for(i=1; i<=nlstate;i++){  
               kk1=0.;   jj1=0;
                 for(j=1; j<=nlstate;j++){   for(k1=1; k1<=m;k1++){
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];     for(i1=1; i1<=ncodemax[k1];i1++){
                 }       jj1++;
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];       if (cptcovn > 0) {
             }         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
           }       }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       for(cpt=1; cpt<=nlstate;cpt++) {
         }         fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
       }  interval) in state (%d): v%s%d%d.png <br>
    <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
   /******/       }
      } /* end i1 */
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {   }/* End k1 */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);     fprintf(fichtm,"</ul>");
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  fclose(fichtm);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  }
           nhstepm = nhstepm/hstepm;  
            /******************* Gnuplot file **************/
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
           for (h=0; h<=nhstepm; h++){    int ng;
             if (h==(int) (calagedate+YEARM*cpt)) {    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      printf("Problem with file %s",optionfilegnuplot);
             }      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
             for(j=1; j<=nlstate+ndeath;j++) {    }
               kk1=0.;kk2=0;  
               for(i=1; i<=nlstate;i++) {                  /*#ifdef windows */
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];          fprintf(ficgp,"cd \"%s\" \n",pathc);
               }      /*#endif */
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);  m=pow(2,cptcoveff);
             }    
           }   /* 1eme*/
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for (cpt=1; cpt<= nlstate ; cpt ++) {
         }     for (k1=1; k1<= m ; k1 ++) {
       }       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
    }       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);
   }  
         for (i=1; i<= nlstate ; i ++) {
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
   if (popforecast==1) {       }
     free_ivector(popage,0,AGESUP);       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
     free_vector(popeffectif,0,AGESUP);       for (i=1; i<= nlstate ; i ++) {
     free_vector(popcount,0,AGESUP);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   }         else fprintf(ficgp," \%%*lf (\%%*lf)");
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       } 
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); 
   fclose(ficrespop);       for (i=1; i<= nlstate ; i ++) {
 }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
 /***********************************************/       }  
 /**************** Main Program *****************/       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
 /***********************************************/     }
     }
 int main(int argc, char *argv[])    /*2 eme*/
 {    
     for (k1=1; k1<= m ; k1 ++) { 
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
   double agedeb, agefin,hf;      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;      
       for (i=1; i<= nlstate+1 ; i ++) {
   double fret;        k=2*i;
   double **xi,tmp,delta;        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
   double dum; /* Dummy variable */          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   double ***p3mat;          else fprintf(ficgp," \%%*lf (\%%*lf)");
   int *indx;        }   
   char line[MAXLINE], linepar[MAXLINE];        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
   char title[MAXLINE];        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];        for (j=1; j<= nlstate+1 ; j ++) {
            if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];          else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
   char filerest[FILENAMELENGTH];        fprintf(ficgp,"\" t\"\" w l 0,");
   char fileregp[FILENAMELENGTH];        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
   char popfile[FILENAMELENGTH];        for (j=1; j<= nlstate+1 ; j ++) {
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   int firstobs=1, lastobs=10;          else fprintf(ficgp," \%%*lf (\%%*lf)");
   int sdeb, sfin; /* Status at beginning and end */        }   
   int c,  h , cpt,l;        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
   int ju,jl, mi;        else fprintf(ficgp,"\" t\"\" w l 0,");
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      }
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    }
   int mobilav=0,popforecast=0;    
   int hstepm, nhstepm;    /*3eme*/
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;    
     for (k1=1; k1<= m ; k1 ++) { 
   double bage, fage, age, agelim, agebase;      for (cpt=1; cpt<= nlstate ; cpt ++) {
   double ftolpl=FTOL;        k=2+nlstate*(2*cpt-2);
   double **prlim;        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
   double *severity;        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
   double ***param; /* Matrix of parameters */        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   double  *p;          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
   double **matcov; /* Matrix of covariance */          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   double ***delti3; /* Scale */          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   double *delti; /* Scale */          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
   double ***eij, ***vareij;          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   double **varpl; /* Variances of prevalence limits by age */          
   double *epj, vepp;        */
   double kk1, kk2;        for (i=1; i< nlstate ; i ++) {
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;          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);
            
         } 
   char version[80]="Imach version 0.8a1, June 2003, INED-EUROREVES ";      }
   char *alph[]={"a","a","b","c","d","e"}, str[4];    }
     
     /* CV preval stat */
   char z[1]="c", occ;    for (k1=1; k1<= m ; k1 ++) { 
 #include <sys/time.h>      for (cpt=1; cpt<nlstate ; cpt ++) {
 #include <time.h>        k=3;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
   /* long total_usecs;        
   struct timeval start_time, end_time;        for (i=1; i< nlstate ; i ++)
            fprintf(ficgp,"+$%d",k+i+1);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
   getcwd(pathcd, size);        
         l=3+(nlstate+ndeath)*cpt;
   printf("\n%s",version);        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
   if(argc <=1){        for (i=1; i< nlstate ; i ++) {
     printf("\nEnter the parameter file name: ");          l=3+(nlstate+ndeath)*cpt;
     scanf("%s",pathtot);          fprintf(ficgp,"+$%d",l+i+1);
   }        }
   else{        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
     strcpy(pathtot,argv[1]);      } 
   }    }  
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    
   /*cygwin_split_path(pathtot,path,optionfile);    /* proba elementaires */
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    for(i=1,jk=1; i <=nlstate; i++){
   /* cutv(path,optionfile,pathtot,'\\');*/      for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);          for(j=1; j <=ncovmodel; j++){
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
   chdir(path);            jk++; 
   replace(pathc,path);            fprintf(ficgp,"\n");
           }
 /*-------- arguments in the command line --------*/        }
       }
   strcpy(fileres,"r");     }
   strcat(fileres, optionfilefiname);  
   strcat(fileres,".txt");    /* Other files have txt extension */     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
   /*---------arguments file --------*/         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
          if (ng==2)
   if((ficpar=fopen(optionfile,"r"))==NULL)    {           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
     printf("Problem with optionfile %s\n",optionfile);         else
     goto end;           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(filereso,"o");         for(k2=1; k2<=nlstate; k2++) {
   strcat(filereso,fileres);           k3=i;
   if((ficparo=fopen(filereso,"w"))==NULL) {           for(k=1; k<=(nlstate+ndeath); k++) {
     printf("Problem with Output resultfile: %s\n", filereso);goto end;             if (k != k2){
   }               if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
   /* Reads comments: lines beginning with '#' */               else
   while((c=getc(ficpar))=='#' && c!= EOF){                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
     ungetc(c,ficpar);               ij=1;
     fgets(line, MAXLINE, ficpar);               for(j=3; j <=ncovmodel; j++) {
     puts(line);                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
     fputs(line,ficparo);                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   }                   ij++;
   ungetc(c,ficpar);                 }
                  else
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);               }
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);               fprintf(ficgp,")/(1");
 while((c=getc(ficpar))=='#' && c!= EOF){               
     ungetc(c,ficpar);               for(k1=1; k1 <=nlstate; k1++){   
     fgets(line, MAXLINE, ficpar);                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
     puts(line);                 ij=1;
     fputs(line,ficparo);                 for(j=3; j <=ncovmodel; j++){
   }                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   ungetc(c,ficpar);                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                       ij++;
                       }
   covar=matrix(0,NCOVMAX,1,n);                   else
   cptcovn=0;                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;                 }
                  fprintf(ficgp,")");
   ncovmodel=2+cptcovn;               }
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                 if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
   /* Read guess parameters */               i=i+ncovmodel;
   /* Reads comments: lines beginning with '#' */             }
   while((c=getc(ficpar))=='#' && c!= EOF){           } /* end k */
     ungetc(c,ficpar);         } /* end k2 */
     fgets(line, MAXLINE, ficpar);       } /* end jk */
     puts(line);     } /* end ng */
     fputs(line,ficparo);     fclose(ficgp); 
   }  }  /* end gnuplot */
   ungetc(c,ficpar);  
    
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  /*************** Moving average **************/
     for(i=1; i <=nlstate; i++)  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);    int i, cpt, cptcod;
       fprintf(ficparo,"%1d%1d",i1,j1);    int mobilavrange, mob;
       printf("%1d%1d",i,j);    double age;
       for(k=1; k<=ncovmodel;k++){    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
         fscanf(ficpar," %lf",&param[i][j][k]);      if(mobilav==1) mobilavrange=5; /* default */
         printf(" %lf",param[i][j][k]);      else mobilavrange=mobilav;
         fprintf(ficparo," %lf",param[i][j][k]);      for (age=bage; age<=fage; age++)
       }        for (i=1; i<=nlstate;i++)
       fscanf(ficpar,"\n");          for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
       printf("\n");            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       fprintf(ficparo,"\n");      /* We keep the original values on the extreme ages bage, fage and for 
     }         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
           we use a 5 terms etc. until the borders are no more concerned. 
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
   p=param[1][1];        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
            for (i=1; i<=nlstate;i++){
   /* Reads comments: lines beginning with '#' */            for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   while((c=getc(ficpar))=='#' && c!= EOF){              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
     ungetc(c,ficpar);                for (cpt=1;cpt<=(mob-1)/2;cpt++){
     fgets(line, MAXLINE, ficpar);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
     puts(line);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
     fputs(line,ficparo);                }
   }              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
   ungetc(c,ficpar);            }
           }
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        }/* end age */
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      }/* end mob */
   for(i=1; i <=nlstate; i++){    }else return -1;
     for(j=1; j <=nlstate+ndeath-1; j++){    return 0;
       fscanf(ficpar,"%1d%1d",&i1,&j1);  }/* End movingaverage */
       printf("%1d%1d",i,j);  
       fprintf(ficparo,"%1d%1d",i1,j1);  
       for(k=1; k<=ncovmodel;k++){  /************** Forecasting ******************/
         fscanf(ficpar,"%le",&delti3[i][j][k]);  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){
         printf(" %le",delti3[i][j][k]);    
         fprintf(ficparo," %le",delti3[i][j][k]);    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
       }    int *popage;
       fscanf(ficpar,"\n");    double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
       printf("\n");    double *popeffectif,*popcount;
       fprintf(ficparo,"\n");    double ***p3mat;
     }    double ***mobaverage;
   }    char fileresf[FILENAMELENGTH];
   delti=delti3[1][1];  
     agelim=AGESUP;
   /* Reads comments: lines beginning with '#' */  calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
     fgets(line, MAXLINE, ficpar);   
     puts(line);   
     fputs(line,ficparo);    strcpy(fileresf,"f"); 
   }    strcat(fileresf,fileres);
   ungetc(c,ficpar);    if((ficresf=fopen(fileresf,"w"))==NULL) {
        printf("Problem with forecast resultfile: %s\n", fileresf);
   matcov=matrix(1,npar,1,npar);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
   for(i=1; i <=npar; i++){    }
     fscanf(ficpar,"%s",&str);    printf("Computing forecasting: result on file '%s' \n", fileresf);
     printf("%s",str);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficparo,"%s",str);  
     for(j=1; j <=i; j++){    if (cptcoveff==0) ncodemax[cptcoveff]=1;
       fscanf(ficpar," %le",&matcov[i][j]);  
       printf(" %.5le",matcov[i][j]);    if (mobilav!=0) {
       fprintf(ficparo," %.5le",matcov[i][j]);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
     fscanf(ficpar,"\n");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     printf("\n");        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     fprintf(ficparo,"\n");      }
   }    }
   for(i=1; i <=npar; i++)  
     for(j=i+1;j<=npar;j++)    stepsize=(int) (stepm+YEARM-1)/YEARM;
       matcov[i][j]=matcov[j][i];    if (stepm<=12) stepsize=1;
        
   printf("\n");    agelim=AGESUP;
     
     hstepm=1;
     /*-------- Rewriting paramater file ----------*/    hstepm=hstepm/stepm; 
      strcpy(rfileres,"r");    /* "Rparameterfile */    yp1=modf(dateintmean,&yp);
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    anprojmean=yp;
      strcat(rfileres,".");    /* */    yp2=modf((yp1*12),&yp);
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    mprojmean=yp;
     if((ficres =fopen(rfileres,"w"))==NULL) {    yp1=modf((yp2*30.5),&yp);
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    jprojmean=yp;
     }    if(jprojmean==0) jprojmean=1;
     fprintf(ficres,"#%s\n",version);    if(mprojmean==0) jprojmean=1;
        
     /*-------- data file ----------*/    fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean); 
     if((fic=fopen(datafile,"r"))==NULL)    {    
       printf("Problem with datafile: %s\n", datafile);goto end;    for(cptcov=1;cptcov<=i2;cptcov++){
     }      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
     n= lastobs;        fprintf(ficresf,"\n#******");
     severity = vector(1,maxwav);        for(j=1;j<=cptcoveff;j++) {
     outcome=imatrix(1,maxwav+1,1,n);          fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
     num=ivector(1,n);        }
     moisnais=vector(1,n);        fprintf(ficresf,"******\n");
     annais=vector(1,n);        fprintf(ficresf,"# StartingAge FinalAge");
     moisdc=vector(1,n);        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
     andc=vector(1,n);        
     agedc=vector(1,n);        
     cod=ivector(1,n);        for (cpt=0; cpt<=(anproj2-anproj1);cpt++) { 
     weight=vector(1,n);          fprintf(ficresf,"\n");
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);   
     mint=matrix(1,maxwav,1,n);  
     anint=matrix(1,maxwav,1,n);          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
     s=imatrix(1,maxwav+1,1,n);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
     adl=imatrix(1,maxwav+1,1,n);                nhstepm = nhstepm/hstepm; 
     tab=ivector(1,NCOVMAX);            
     ncodemax=ivector(1,8);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
     i=1;            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
     while (fgets(line, MAXLINE, fic) != NULL)    {          
       if ((i >= firstobs) && (i <=lastobs)) {            for (h=0; h<=nhstepm; h++){
                      if (h==(int) (calagedate+YEARM*cpt)) {
         for (j=maxwav;j>=1;j--){                fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);              } 
           strcpy(line,stra);              for(j=1; j<=nlstate+ndeath;j++) {
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                kk1=0.;kk2=0;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                for(i=1; i<=nlstate;i++) {              
         }                  if (mobilav==1) 
                            kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);                  else {
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);                  
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);                }
                 if (h==(int)(calagedate+12*cpt)){
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);                  fprintf(ficresf," %.3f", kk1);
         for (j=ncovcol;j>=1;j--){                          
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);                }
         }              }
         num[i]=atol(stra);            }
                    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         /*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;    }
       }         
     }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     /* printf("ii=%d", ij);  
        scanf("%d",i);*/    fclose(ficresf);
   imx=i-1; /* Number of individuals */  }
   /************** Forecasting ******************/
   /* for (i=1; i<=imx; i++){  populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     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;    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    int *popage;
     }*/    double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
    /*  for (i=1; i<=imx; i++){    double *popeffectif,*popcount;
      if (s[4][i]==9)  s[4][i]=-1;    double ***p3mat,***tabpop,***tabpopprev;
      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]));}*/    double ***mobaverage;
      char filerespop[FILENAMELENGTH];
    
   /* Calculation of the number of parameter from char model*/    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   Tvar=ivector(1,15);    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   Tprod=ivector(1,15);    agelim=AGESUP;
   Tvaraff=ivector(1,15);    calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
   Tvard=imatrix(1,15,1,2);    
   Tage=ivector(1,15);          prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
        
   if (strlen(model) >1){    
     j=0, j1=0, k1=1, k2=1;    strcpy(filerespop,"pop"); 
     j=nbocc(model,'+');    strcat(filerespop,fileres);
     j1=nbocc(model,'*');    if((ficrespop=fopen(filerespop,"w"))==NULL) {
     cptcovn=j+1;      printf("Problem with forecast resultfile: %s\n", filerespop);
     cptcovprod=j1;      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
        }
     strcpy(modelsav,model);    printf("Computing forecasting: result on file '%s' \n", filerespop);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
       printf("Error. Non available option model=%s ",model);  
       goto end;    if (cptcoveff==0) ncodemax[cptcoveff]=1;
     }  
        if (mobilav!=0) {
     for(i=(j+1); i>=1;i--){      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       cutv(stra,strb,modelsav,'+');      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       /*scanf("%d",i);*/      }
       if (strchr(strb,'*')) {    }
         cutv(strd,strc,strb,'*');  
         if (strcmp(strc,"age")==0) {    stepsize=(int) (stepm+YEARM-1)/YEARM;
           cptcovprod--;    if (stepm<=12) stepsize=1;
           cutv(strb,stre,strd,'V');    
           Tvar[i]=atoi(stre);    agelim=AGESUP;
           cptcovage++;    
             Tage[cptcovage]=i;    hstepm=1;
             /*printf("stre=%s ", stre);*/    hstepm=hstepm/stepm; 
         }    
         else if (strcmp(strd,"age")==0) {    if (popforecast==1) {
           cptcovprod--;      if((ficpop=fopen(popfile,"r"))==NULL) {
           cutv(strb,stre,strc,'V');        printf("Problem with population file : %s\n",popfile);exit(0);
           Tvar[i]=atoi(stre);        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
           cptcovage++;      } 
           Tage[cptcovage]=i;      popage=ivector(0,AGESUP);
         }      popeffectif=vector(0,AGESUP);
         else {      popcount=vector(0,AGESUP);
           cutv(strb,stre,strc,'V');      
           Tvar[i]=ncovcol+k1;      i=1;   
           cutv(strb,strc,strd,'V');      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
           Tprod[k1]=i;     
           Tvard[k1][1]=atoi(strc);      imx=i;
           Tvard[k1][2]=atoi(stre);      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
           Tvar[cptcovn+k2]=Tvard[k1][1];    }
           Tvar[cptcovn+k2+1]=Tvard[k1][2];  
           for (k=1; k<=lastobs;k++)    for(cptcov=1;cptcov<=i2;cptcov++){
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
           k1++;        k=k+1;
           k2=k2+2;        fprintf(ficrespop,"\n#******");
         }        for(j=1;j<=cptcoveff;j++) {
       }          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       else {        }
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/        fprintf(ficrespop,"******\n");
        /*  scanf("%d",i);*/        fprintf(ficrespop,"# Age");
       cutv(strd,strc,strb,'V');        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
       Tvar[i]=atoi(strc);        if (popforecast==1)  fprintf(ficrespop," [Population]");
       }        
       strcpy(modelsav,stra);          for (cpt=0; cpt<=0;cpt++) { 
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
         scanf("%d",i);*/          
     }          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
 }            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
              nhstepm = nhstepm/hstepm; 
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);            
   printf("cptcovprod=%d ", cptcovprod);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   scanf("%d ",i);*/            oldm=oldms;savm=savms;
     fclose(fic);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
     /*  if(mle==1){*/            for (h=0; h<=nhstepm; h++){
     if (weightopt != 1) { /* Maximisation without weights*/              if (h==(int) (calagedate+YEARM*cpt)) {
       for(i=1;i<=n;i++) weight[i]=1.0;                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
     }              } 
     /*-calculation of age at interview from date of interview and age at death -*/              for(j=1; j<=nlstate+ndeath;j++) {
     agev=matrix(1,maxwav,1,imx);                kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
     for (i=1; i<=imx; i++) {                  if (mobilav==1) 
       for(m=2; (m<= maxwav); m++) {                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){                  else {
          anint[m][i]=9999;                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
          s[m][i]=-1;                  }
        }                }
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;                if (h==(int)(calagedate+12*cpt)){
       }                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
     }                    /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
     for (i=1; i<=imx; i++)  {                }
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);              }
       for(m=1; (m<= maxwav); m++){              for(i=1; i<=nlstate;i++){
         if(s[m][i] >0){                kk1=0.;
           if (s[m][i] >= nlstate+1) {                  for(j=1; j<=nlstate;j++){
             if(agedc[i]>0)                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
               if(moisdc[i]!=99 && andc[i]!=9999)                  }
                 agev[m][i]=agedc[i];                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/              }
            else {  
               if (andc[i]!=9999){              if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) 
               printf("Warning negative age at death: %d line:%d\n",num[i],i);                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
               agev[m][i]=-1;            }
               }            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             }          }
           }        }
           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;        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
             else if(agev[m][i] <agemin){          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
               agemin=agev[m][i];          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             }            nhstepm = nhstepm/hstepm; 
             else if(agev[m][i] >agemax){            
               agemax=agev[m][i];            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/            oldm=oldms;savm=savms;
             }            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             /*agev[m][i]=anint[m][i]-annais[i];*/            for (h=0; h<=nhstepm; h++){
             /*   agev[m][i] = age[i]+2*m;*/              if (h==(int) (calagedate+YEARM*cpt)) {
           }                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
           else { /* =9 */              } 
             agev[m][i]=1;              for(j=1; j<=nlstate+ndeath;j++) {
             s[m][i]=-1;                kk1=0.;kk2=0;
           }                for(i=1; i<=nlstate;i++) {              
         }                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
         else /*= 0 Unknown */                }
           agev[m][i]=1;                if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1); 
       }              }
                }
     }            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     for (i=1; i<=imx; i++)  {          }
       for(m=1; (m<= maxwav); m++){        }
         if (s[m][i] > (nlstate+ndeath)) {     } 
           printf("Error: Wrong value in nlstate or ndeath\n");      }
           goto end;   
         }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       }  
     }    if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);      free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     free_vector(severity,1,maxwav);    }
     free_imatrix(outcome,1,maxwav+1,1,n);    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_vector(moisnais,1,n);    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_vector(annais,1,n);    fclose(ficrespop);
     /* free_matrix(mint,1,maxwav,1,n);  }
        free_matrix(anint,1,maxwav,1,n);*/  
     free_vector(moisdc,1,n);  /***********************************************/
     free_vector(andc,1,n);  /**************** Main Program *****************/
   /***********************************************/
      
     wav=ivector(1,imx);  int main(int argc, char *argv[])
     dh=imatrix(1,lastpass-firstpass+1,1,imx);  {
     mw=imatrix(1,lastpass-firstpass+1,1,imx);  
        int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
     /* Concatenates waves */    double agedeb, agefin,hf;
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
       Tcode=ivector(1,100);    double **xi,tmp,delta;
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);  
       ncodemax[1]=1;    double dum; /* Dummy variable */
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    double ***p3mat;
          double ***mobaverage;
    codtab=imatrix(1,100,1,10);    int *indx;
    h=0;    char line[MAXLINE], linepar[MAXLINE];
    m=pow(2,cptcoveff);    char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
      int firstobs=1, lastobs=10;
    for(k=1;k<=cptcoveff; k++){    int sdeb, sfin; /* Status at beginning and end */
      for(i=1; i <=(m/pow(2,k));i++){    int c,  h , cpt,l;
        for(j=1; j <= ncodemax[k]; j++){    int ju,jl, mi;
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
            h++;    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab; 
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;    int mobilav=0,popforecast=0;
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/    int hstepm, nhstepm;
          }    double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
        }  
      }    double bage, fage, age, agelim, agebase;
    }    double ftolpl=FTOL;
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    double **prlim;
       codtab[1][2]=1;codtab[2][2]=2; */    double *severity;
    /* for(i=1; i <=m ;i++){    double ***param; /* Matrix of parameters */
       for(k=1; k <=cptcovn; k++){    double  *p;
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);    double **matcov; /* Matrix of covariance */
       }    double ***delti3; /* Scale */
       printf("\n");    double *delti; /* Scale */
       }    double ***eij, ***vareij;
       scanf("%d",i);*/    double **varpl; /* Variances of prevalence limits by age */
        double *epj, vepp;
    /* Calculates basic frequencies. Computes observed prevalence at single age    double kk1, kk2;
        and prints on file fileres'p'. */    double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
     
      
        char *alph[]={"a","a","b","c","d","e"}, str[4];
     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 */    char z[1]="c", occ;
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  #include <sys/time.h>
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  #include <time.h>
          char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     /* 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] */    /* long total_usecs;
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    struct timeval start_time, end_time;
     
     if(mle==1){    gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    getcwd(pathcd, size);
     }  
        printf("\n%s",version);
     /*--------- results files --------------*/    if(argc <=1){
     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);      printf("\nEnter the parameter file name: ");
        scanf("%s",pathtot);
     }
    jk=1;    else{
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      strcpy(pathtot,argv[1]);
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    }
    for(i=1,jk=1; i <=nlstate; i++){    /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
      for(k=1; k <=(nlstate+ndeath); k++){    /*cygwin_split_path(pathtot,path,optionfile);
        if (k != i)      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
          {    /* cutv(path,optionfile,pathtot,'\\');*/
            printf("%d%d ",i,k);  
            fprintf(ficres,"%1d%1d ",i,k);    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
            for(j=1; j <=ncovmodel; j++){     printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
              printf("%f ",p[jk]);    chdir(path);
              fprintf(ficres,"%f ",p[jk]);    replace(pathc,path);
              jk++;  
            }  /*-------- arguments in the command line --------*/
            printf("\n");  
            fprintf(ficres,"\n");    /* Log file */
          }    strcat(filelog, optionfilefiname);
      }    strcat(filelog,".log");    /* */
    }    if((ficlog=fopen(filelog,"w"))==NULL)    {
  if(mle==1){      printf("Problem with logfile %s\n",filelog);
     /* Computing hessian and covariance matrix */      goto end;
     ftolhess=ftol; /* Usually correct */    }
     hesscov(matcov, p, npar, delti, ftolhess, func);    fprintf(ficlog,"Log filename:%s\n",filelog);
  }    fprintf(ficlog,"\n%s",version);
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    fprintf(ficlog,"\nEnter the parameter file name: ");
     printf("# Scales (for hessian or gradient estimation)\n");    fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
      for(i=1,jk=1; i <=nlstate; i++){    fflush(ficlog);
       for(j=1; j <=nlstate+ndeath; j++){  
         if (j!=i) {    /* */
           fprintf(ficres,"%1d%1d",i,j);    strcpy(fileres,"r");
           printf("%1d%1d",i,j);    strcat(fileres, optionfilefiname);
           for(k=1; k<=ncovmodel;k++){    strcat(fileres,".txt");    /* Other files have txt extension */
             printf(" %.5e",delti[jk]);  
             fprintf(ficres," %.5e",delti[jk]);    /*---------arguments file --------*/
             jk++;  
           }    if((ficpar=fopen(optionfile,"r"))==NULL)    {
           printf("\n");      printf("Problem with optionfile %s\n",optionfile);
           fprintf(ficres,"\n");      fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
         }      goto end;
       }    }
      }  
        strcpy(filereso,"o");
     k=1;    strcat(filereso,fileres);
     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((ficparo=fopen(filereso,"w"))==NULL) {
     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");      printf("Problem with Output resultfile: %s\n", filereso);
     for(i=1;i<=npar;i++){      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       /*  if (k>nlstate) k=1;      goto end;
       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]);*/    /* Reads comments: lines beginning with '#' */
       fprintf(ficres,"%3d",i);    while((c=getc(ficpar))=='#' && c!= EOF){
       printf("%3d",i);      ungetc(c,ficpar);
       for(j=1; j<=i;j++){      fgets(line, MAXLINE, ficpar);
         fprintf(ficres," %.5e",matcov[i][j]);      puts(line);
         printf(" %.5e",matcov[i][j]);      fputs(line,ficparo);
       }    }
       fprintf(ficres,"\n");    ungetc(c,ficpar);
       printf("\n");  
       k++;    fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     }    printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
        fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     while((c=getc(ficpar))=='#' && c!= EOF){  while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);      ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);      fgets(line, MAXLINE, ficpar);
       puts(line);      puts(line);
       fputs(line,ficparo);      fputs(line,ficparo);
     }    }
     ungetc(c,ficpar);    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;    covar=matrix(0,NCOVMAX,1,n); 
     if (fage <= 2) {    cptcovn=0; 
       bage = ageminpar;    if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
       fage = agemaxpar;  
     }    ncovmodel=2+cptcovn;
        nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     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);    /* Read guess parameters */
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    /* Reads comments: lines beginning with '#' */
      while((c=getc(ficpar))=='#' && c!= EOF){
     while((c=getc(ficpar))=='#' && c!= EOF){      ungetc(c,ficpar);
     ungetc(c,ficpar);      fgets(line, MAXLINE, ficpar);
     fgets(line, MAXLINE, ficpar);      puts(line);
     puts(line);      fputs(line,ficparo);
     fputs(line,ficparo);    }
   }    ungetc(c,ficpar);
   ungetc(c,ficpar);    
      param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);      for(i=1; i <=nlstate; i++)
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      for(j=1; j <=nlstate+ndeath-1; j++){
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        fscanf(ficpar,"%1d%1d",&i1,&j1);
              fprintf(ficparo,"%1d%1d",i1,j1);
   while((c=getc(ficpar))=='#' && c!= EOF){        if(mle==1)
     ungetc(c,ficpar);          printf("%1d%1d",i,j);
     fgets(line, MAXLINE, ficpar);        fprintf(ficlog,"%1d%1d",i,j);
     puts(line);        for(k=1; k<=ncovmodel;k++){
     fputs(line,ficparo);          fscanf(ficpar," %lf",&param[i][j][k]);
   }          if(mle==1){
   ungetc(c,ficpar);            printf(" %lf",param[i][j][k]);
              fprintf(ficlog," %lf",param[i][j][k]);
           }
    dateprev1=anprev1+mprev1/12.+jprev1/365.;          else
    dateprev2=anprev2+mprev2/12.+jprev2/365.;            fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);
   fscanf(ficpar,"pop_based=%d\n",&popbased);        }
   fprintf(ficparo,"pop_based=%d\n",popbased);          fscanf(ficpar,"\n");
   fprintf(ficres,"pop_based=%d\n",popbased);          if(mle==1)
            printf("\n");
   while((c=getc(ficpar))=='#' && c!= EOF){        fprintf(ficlog,"\n");
     ungetc(c,ficpar);        fprintf(ficparo,"\n");
     fgets(line, MAXLINE, ficpar);      }
     puts(line);    
     fputs(line,ficparo);      npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
   }  
   ungetc(c,ficpar);    p=param[1][1];
     
   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);    /* Reads comments: lines beginning with '#' */
 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);    while((c=getc(ficpar))=='#' && c!= EOF){
 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);      ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
 while((c=getc(ficpar))=='#' && c!= EOF){      fputs(line,ficparo);
     ungetc(c,ficpar);    }
     fgets(line, MAXLINE, ficpar);    ungetc(c,ficpar);
     puts(line);  
     fputs(line,ficparo);    delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
   }    delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
   ungetc(c,ficpar);    for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);        fscanf(ficpar,"%1d%1d",&i1,&j1);
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);        printf("%1d%1d",i,j);
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);        fprintf(ficparo,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
 /*------------ gnuplot -------------*/          fprintf(ficparo," %le",delti3[i][j][k]);
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);        }
          fscanf(ficpar,"\n");
 /*------------ free_vector  -------------*/        printf("\n");
  chdir(path);        fprintf(ficparo,"\n");
        }
  free_ivector(wav,1,imx);    }
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    delti=delti3[1][1];
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      
  free_ivector(num,1,n);    /* Reads comments: lines beginning with '#' */
  free_vector(agedc,1,n);    while((c=getc(ficpar))=='#' && c!= EOF){
  /*free_matrix(covar,1,NCOVMAX,1,n);*/      ungetc(c,ficpar);
  fclose(ficparo);      fgets(line, MAXLINE, ficpar);
  fclose(ficres);      puts(line);
       fputs(line,ficparo);
 /*--------- index.htm --------*/    }
     ungetc(c,ficpar);
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);    
     matcov=matrix(1,npar,1,npar);
      for(i=1; i <=npar; i++){
   /*--------------- Prevalence limit --------------*/      fscanf(ficpar,"%s",&str);
        if(mle==1)
   strcpy(filerespl,"pl");        printf("%s",str);
   strcat(filerespl,fileres);      fprintf(ficlog,"%s",str);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {      fprintf(ficparo,"%s",str);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;      for(j=1; j <=i; j++){
   }        fscanf(ficpar," %le",&matcov[i][j]);
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);        if(mle==1){
   fprintf(ficrespl,"#Prevalence limit\n");          printf(" %.5le",matcov[i][j]);
   fprintf(ficrespl,"#Age ");          fprintf(ficlog," %.5le",matcov[i][j]);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);        }
   fprintf(ficrespl,"\n");        else
            fprintf(ficlog," %.5le",matcov[i][j]);
   prlim=matrix(1,nlstate,1,nlstate);        fprintf(ficparo," %.5le",matcov[i][j]);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      }
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      fscanf(ficpar,"\n");
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      if(mle==1)
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        printf("\n");
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      fprintf(ficlog,"\n");
   k=0;      fprintf(ficparo,"\n");
   agebase=ageminpar;    }
   agelim=agemaxpar;    for(i=1; i <=npar; i++)
   ftolpl=1.e-10;      for(j=i+1;j<=npar;j++)
   i1=cptcoveff;        matcov[i][j]=matcov[j][i];
   if (cptcovn < 1){i1=1;}     
     if(mle==1)
   for(cptcov=1;cptcov<=i1;cptcov++){      printf("\n");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficlog,"\n");
         k=k+1;  
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  
         fprintf(ficrespl,"\n#******");      /*-------- Rewriting paramater file ----------*/
         for(j=1;j<=cptcoveff;j++)       strcpy(rfileres,"r");    /* "Rparameterfile */
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
         fprintf(ficrespl,"******\n");       strcat(rfileres,".");    /* */
               strcat(rfileres,optionfilext);    /* Other files have txt extension */
         for (age=agebase; age<=agelim; age++){      if((ficres =fopen(rfileres,"w"))==NULL) {
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        printf("Problem writing new parameter file: %s\n", fileres);goto end;
           fprintf(ficrespl,"%.0f",age );        fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
           for(i=1; i<=nlstate;i++)      }
           fprintf(ficrespl," %.5f", prlim[i][i]);      fprintf(ficres,"#%s\n",version);
           fprintf(ficrespl,"\n");      
         }      /*-------- data file ----------*/
       }      if((fic=fopen(datafile,"r"))==NULL)    {
     }        printf("Problem with datafile: %s\n", datafile);goto end;
   fclose(ficrespl);        fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
       }
   /*------------- h Pij x at various ages ------------*/  
        n= lastobs;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);      severity = vector(1,maxwav);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {      outcome=imatrix(1,maxwav+1,1,n);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;      num=ivector(1,n);
   }      moisnais=vector(1,n);
   printf("Computing pij: result on file '%s' \n", filerespij);      annais=vector(1,n);
        moisdc=vector(1,n);
   stepsize=(int) (stepm+YEARM-1)/YEARM;      andc=vector(1,n);
   /*if (stepm<=24) stepsize=2;*/      agedc=vector(1,n);
       cod=ivector(1,n);
   agelim=AGESUP;      weight=vector(1,n);
   hstepm=stepsize*YEARM; /* Every year of age */      for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */      mint=matrix(1,maxwav,1,n);
        anint=matrix(1,maxwav,1,n);
   k=0;      s=imatrix(1,maxwav+1,1,n);
   for(cptcov=1;cptcov<=i1;cptcov++){      adl=imatrix(1,maxwav+1,1,n);    
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      tab=ivector(1,NCOVMAX);
       k=k+1;      ncodemax=ivector(1,8);
         fprintf(ficrespij,"\n#****** ");  
         for(j=1;j<=cptcoveff;j++)      i=1;
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      while (fgets(line, MAXLINE, fic) != NULL)    {
         fprintf(ficrespij,"******\n");        if ((i >= firstobs) && (i <=lastobs)) {
                  
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          for (j=maxwav;j>=1;j--){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            strcpy(line,stra);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           oldm=oldms;savm=savms;            cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            }
           fprintf(ficrespij,"# Age");          
           for(i=1; i<=nlstate;i++)          cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
             for(j=1; j<=nlstate+ndeath;j++)          cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
               fprintf(ficrespij," %1d-%1d",i,j);  
           fprintf(ficrespij,"\n");          cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
            for (h=0; h<=nhstepm; h++){          cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  
             for(i=1; i<=nlstate;i++)          cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
               for(j=1; j<=nlstate+ndeath;j++)          for (j=ncovcol;j>=1;j--){
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);            cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
             fprintf(ficrespij,"\n");          } 
              }          num[i]=atol(stra);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          
           fprintf(ficrespij,"\n");          /*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;
         }
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);      } 
       /* printf("ii=%d", ij);
   fclose(ficrespij);         scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
   /*---------- Forecasting ------------------*/    /* for (i=1; i<=imx; i++){
   if((stepm == 1) && (strcmp(model,".")==0)){      if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);      if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);      if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
   }      }*/
   else{     /*  for (i=1; i<=imx; i++){
     erreur=108;       if (s[4][i]==9)  s[4][i]=-1; 
     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);       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*/
   /*---------- Health expectancies and variances ------------*/    Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
   strcpy(filerest,"t");    Tvaraff=ivector(1,15); 
   strcat(filerest,fileres);    Tvard=imatrix(1,15,1,2);
   if((ficrest=fopen(filerest,"w"))==NULL) {    Tage=ivector(1,15);      
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;     
   }    if (strlen(model) >1){
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+');
       j1=nbocc(model,'*');
   strcpy(filerese,"e");      cptcovn=j+1;
   strcat(filerese,fileres);      cptcovprod=j1;
   if((ficreseij=fopen(filerese,"w"))==NULL) {      
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      strcpy(modelsav,model); 
   }      if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);        printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
  strcpy(fileresv,"v");        goto end;
   strcat(fileresv,fileres);      }
   if((ficresvij=fopen(fileresv,"w"))==NULL) {      
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);      for(i=(j+1); i>=1;i--){
   }        cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);        if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */
   calagedate=-1;        /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
   k=0;          cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
   for(cptcov=1;cptcov<=i1;cptcov++){          if (strcmp(strc,"age")==0) { /* Vn*age */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            cptcovprod--;
       k=k+1;            cutv(strb,stre,strd,'V');
       fprintf(ficrest,"\n#****** ");            Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
       for(j=1;j<=cptcoveff;j++)            cptcovage++;
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              Tage[cptcovage]=i;
       fprintf(ficrest,"******\n");              /*printf("stre=%s ", stre);*/
           }
       fprintf(ficreseij,"\n#****** ");          else if (strcmp(strd,"age")==0) { /* or age*Vn */
       for(j=1;j<=cptcoveff;j++)            cptcovprod--;
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            cutv(strb,stre,strc,'V');
       fprintf(ficreseij,"******\n");            Tvar[i]=atoi(stre);
             cptcovage++;
       fprintf(ficresvij,"\n#****** ");            Tage[cptcovage]=i;
       for(j=1;j<=cptcoveff;j++)          }
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          else {  /* Age is not in the model */
       fprintf(ficresvij,"******\n");            cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);            cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
       oldm=oldms;savm=savms;            Tprod[k1]=i;
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);              Tvard[k1][1]=atoi(strc); /* m*/
              Tvard[k1][2]=atoi(stre); /* n */
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);            Tvar[cptcovn+k2]=Tvard[k1][1];
       oldm=oldms;savm=savms;            Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);            for (k=1; k<=lastobs;k++) 
                  covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
              k2=k2+2;
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");          }
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);        }
       fprintf(ficrest,"\n");        else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
       epj=vector(1,nlstate+1);         /*  scanf("%d",i);*/
       for(age=bage; age <=fage ;age++){        cutv(strd,strc,strb,'V');
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        Tvar[i]=atoi(strc);
         if (popbased==1) {        }
           for(i=1; i<=nlstate;i++)        strcpy(modelsav,stra);  
             prlim[i][i]=probs[(int)age][i][k];        /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
         }          scanf("%d",i);*/
              } /* end of loop + */
         fprintf(ficrest," %4.0f",age);    } /* end model */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    printf("cptcovprod=%d ", cptcovprod);
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
           }    scanf("%d ",i);*/
           epj[nlstate+1] +=epj[j];      fclose(fic);
         }  
       /*  if(mle==1){*/
         for(i=1, vepp=0.;i <=nlstate;i++)      if (weightopt != 1) { /* Maximisation without weights*/
           for(j=1;j <=nlstate;j++)        for(i=1;i<=n;i++) weight[i]=1.0;
             vepp += vareij[i][j][(int)age];      }
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));      /*-calculation of age at interview from date of interview and age at death -*/
         for(j=1;j <=nlstate;j++){      agev=matrix(1,maxwav,1,imx);
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));  
         }      for (i=1; i<=imx; i++) {
         fprintf(ficrest,"\n");        for(m=2; (m<= maxwav); m++) {
       }         if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
     }           anint[m][i]=9999;
   }           s[m][i]=-1;
 free_matrix(mint,1,maxwav,1,n);         }
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);       if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
     free_vector(weight,1,n);        }
   fclose(ficreseij);      }
   fclose(ficresvij);  
   fclose(ficrest);      for (i=1; i<=imx; i++)  {
   fclose(ficpar);        agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
   free_vector(epj,1,nlstate+1);        for(m=1; (m<= maxwav); m++){
            if(s[m][i] >0){
   /*------- Variance limit prevalence------*/              if (s[m][i] >= nlstate+1) {
               if(agedc[i]>0)
   strcpy(fileresvpl,"vpl");                if(moisdc[i]!=99 && andc[i]!=9999)
   strcat(fileresvpl,fileres);                  agev[m][i]=agedc[i];
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {              /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);             else {
     exit(0);                if (andc[i]!=9999){
   }                printf("Warning negative age at death: %d line:%d\n",num[i],i);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);                fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
                 agev[m][i]=-1;
   k=0;                }
   for(cptcov=1;cptcov<=i1;cptcov++){              }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            }
       k=k+1;            else if(s[m][i] !=9){ /* Should no more exist */
       fprintf(ficresvpl,"\n#****** ");              agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
       for(j=1;j<=cptcoveff;j++)              if(mint[m][i]==99 || anint[m][i]==9999)
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                agev[m][i]=1;
       fprintf(ficresvpl,"******\n");              else if(agev[m][i] <agemin){ 
                      agemin=agev[m][i];
       varpl=matrix(1,nlstate,(int) bage, (int) fage);                /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
       oldm=oldms;savm=savms;              }
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);              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);*/
               }
   fclose(ficresvpl);              /*agev[m][i]=anint[m][i]-annais[i];*/
               /*   agev[m][i] = age[i]+2*m;*/
   /*---------- End : free ----------------*/            }
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);            else { /* =9 */
                agev[m][i]=1;
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);              s[m][i]=-1;
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);            }
            }
            else /*= 0 Unknown */
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);            agev[m][i]=1;
   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);      }
        for (i=1; i<=imx; i++)  {
   free_matrix(matcov,1,npar,1,npar);        for(m=1; (m<= maxwav); m++){
   free_vector(delti,1,npar);          if (s[m][i] > (nlstate+ndeath)) {
   free_matrix(agev,1,maxwav,1,imx);            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);   
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);            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;
   if(erreur >0)          }
     printf("End of Imach with error or warning %d\n",erreur);        }
   else   printf("End of Imach\n");      }
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */  
    printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
   /* 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);*/   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   /*printf("Total time was %d uSec.\n", total_usecs);*/  
   /*------ End -----------*/      free_vector(severity,1,maxwav);
       free_imatrix(outcome,1,maxwav+1,1,n);
       free_vector(moisnais,1,n);
  end:      free_vector(annais,1,n);
   /* chdir(pathcd);*/      /* free_matrix(mint,1,maxwav,1,n);
  /*system("wgnuplot graph.plt");*/         free_matrix(anint,1,maxwav,1,n);*/
  /*system("../gp37mgw/wgnuplot graph.plt");*/      free_vector(moisdc,1,n);
  /*system("cd ../gp37mgw");*/      free_vector(andc,1,n);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/  
  strcpy(plotcmd,GNUPLOTPROGRAM);     
  strcat(plotcmd," ");      wav=ivector(1,imx);
  strcat(plotcmd,optionfilegnuplot);      dh=imatrix(1,lastpass-firstpass+1,1,imx);
  system(plotcmd);      mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
  /*#ifdef windows*/      /* Concatenates waves */
   while (z[0] != 'q') {        concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* chdir(path); */  
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");  
     scanf("%s",z);        Tcode=ivector(1,100);
     if (z[0] == 'c') system("./imach");        nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     else if (z[0] == 'e') system(optionfilehtm);        ncodemax[1]=1;
     else if (z[0] == 'g') system(plotcmd);        if (cptcovn > 0) tricode(Tvar,nbcode,imx);
     else if (z[0] == 'q') exit(0);        
   }     codtab=imatrix(1,100,1,10);
   /*#endif */     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.1.41.2.2  
changed lines
  Added in v.1.57

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