[BACK]Return to imach.c CVS log [TXT] [DIR] Up to [Local Repository] / imach / src

Diff for /imach/src/imach.c between versions 1.35 and 1.65

version 1.35, 2002/03/26 17:08:39 version 1.65, 2002/12/11 16:58:19
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain     Interpolated Markov Chain
   
   Short summary of the programme:    Short summary of the programme:
      
   This program computes Healthy Life Expectancies from    This program computes Healthy Life Expectancies from
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   first survey ("cross") where individuals from different ages are    first survey ("cross") where individuals from different ages are
   interviewed on their health status or degree of disability (in the    interviewed on their health status or degree of disability (in the
   case of a health survey which is our main interest) -2- at least a    case of a health survey which is our main interest) -2- at least a
   second wave of interviews ("longitudinal") which measure each change    second wave of interviews ("longitudinal") which measure each change
   (if any) in individual health status.  Health expectancies are    (if any) in individual health status.  Health expectancies are
   computed from the time spent in each health state according to a    computed from the time spent in each health state according to a
   model. More health states you consider, more time is necessary to reach the    model. More health states you consider, more time is necessary to reach the
   Maximum Likelihood of the parameters involved in the model.  The    Maximum Likelihood of the parameters involved in the model.  The
   simplest model is the multinomial logistic model where pij is the    simplest model is the multinomial logistic model where pij is the
   probabibility to be observed in state j at the second wave    probability to be observed in state j at the second wave
   conditional to be observed in state i at the first wave. Therefore    conditional to be observed in state i at the first wave. Therefore
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   'age' is age and 'sex' is a covariate. If you want to have a more    'age' is age and 'sex' is a covariate. If you want to have a more
   complex model than "constant and age", you should modify the program    complex model than "constant and age", you should modify the program
   where the markup *Covariates have to be included here again* invites    where the markup *Covariates have to be included here again* invites
   you to do it.  More covariates you add, slower the    you to do it.  More covariates you add, slower the
   convergence.    convergence.
   
   The advantage of this computer programme, compared to a simple    The advantage of this computer programme, compared to a simple
   multinomial logistic model, is clear when the delay between waves is not    multinomial logistic model, is clear when the delay between waves is not
   identical for each individual. Also, if a individual missed an    identical for each individual. Also, if a individual missed an
   intermediate interview, the information is lost, but taken into    intermediate interview, the information is lost, but taken into
   account using an interpolation or extrapolation.      account using an interpolation or extrapolation.  
   
   hPijx is the probability to be observed in state i at age x+h    hPijx is the probability to be observed in state i at age x+h
   conditional to the observed state i at age x. The delay 'h' can be    conditional to the observed state i at age x. The delay 'h' can be
   split into an exact number (nh*stepm) of unobserved intermediate    split into an exact number (nh*stepm) of unobserved intermediate
   states. This elementary transition (by month or quarter trimester,    states. This elementary transition (by month or quarter trimester,
   semester or year) is model as a multinomial logistic.  The hPx    semester or year) is model as a multinomial logistic.  The hPx
   matrix is simply the matrix product of nh*stepm elementary matrices    matrix is simply the matrix product of nh*stepm elementary matrices
   and the contribution of each individual to the likelihood is simply    and the contribution of each individual to the likelihood is simply
   hPijx.    hPijx.
   
   Also this programme outputs the covariance matrix of the parameters but also    Also this programme outputs the covariance matrix of the parameters but also
   of the life expectancies. It also computes the prevalence limits.    of the life expectancies. It also computes the stable prevalence. 
      
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
            Institut national d'études démographiques, Paris.             Institut national d'études démographiques, Paris.
   This software have been partly granted by Euro-REVES, a concerted action    This software have been partly granted by Euro-REVES, a concerted action
   from the European Union.    from the European Union.
   It is copyrighted identically to a GNU software product, ie programme and    It is copyrighted identically to a GNU software product, ie programme and
   software can be distributed freely for non commercial use. Latest version    software can be distributed freely for non commercial use. Latest version
   can be accessed at http://euroreves.ined.fr/imach .    can be accessed at http://euroreves.ined.fr/imach .
   **********************************************************************/    **********************************************************************/
     
 #include <math.h>  #include <math.h>
 #include <stdio.h>  #include <stdio.h>
 #include <stdlib.h>  #include <stdlib.h>
 #include <unistd.h>  #include <unistd.h>
   
 #define MAXLINE 256  #define MAXLINE 256
 #define GNUPLOTPROGRAM "wgnuplot"  #define GNUPLOTPROGRAM "gnuplot"
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define FILENAMELENGTH 80  #define FILENAMELENGTH 80
 /*#define DEBUG*/  /*#define DEBUG*/
 #define windows  #define windows
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
 #define NINTERVMAX 8  #define NINTERVMAX 8
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #define NCOVMAX 8 /* Maximum number of covariates */  #define NCOVMAX 8 /* Maximum number of covariates */
 #define MAXN 20000  #define MAXN 20000
 #define YEARM 12. /* Number of months per year */  #define YEARM 12. /* Number of months per year */
 #define AGESUP 130  #define AGESUP 130
 #define AGEBASE 40  #define AGEBASE 40
   #ifdef windows
   #define DIRSEPARATOR '\\'
 int erreur; /* Error number */  #define ODIRSEPARATOR '/'
 int nvar;  #else
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  #define DIRSEPARATOR '/'
 int npar=NPARMAX;  #define ODIRSEPARATOR '\\'
 int nlstate=2; /* Number of live states */  #endif
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  char version[80]="Imach version 0.9, November 2002, INED-EUROREVES ";
 int popbased=0;  int erreur; /* Error number */
   int nvar;
 int *wav; /* Number of waves for this individuual 0 is possible */  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 int maxwav; /* Maxim number of waves */  int npar=NPARMAX;
 int jmin, jmax; /* min, max spacing between 2 waves */  int nlstate=2; /* Number of live states */
 int mle, weightopt;  int ndeath=1; /* Number of dead states */
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  int popbased=0;
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */  int *wav; /* Number of waves for this individuual 0 is possible */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  int maxwav; /* Maxim number of waves */
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  int jmin, jmax; /* min, max spacing between 2 waves */
 FILE *ficgp,*ficresprob,*ficpop;  int mle, weightopt;
 FILE *ficreseij;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   char filerese[FILENAMELENGTH];  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
  FILE  *ficresvij;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   char fileresv[FILENAMELENGTH];             * wave mi and wave mi+1 is not an exact multiple of stepm. */
  FILE  *ficresvpl;  double jmean; /* Mean space between 2 waves */
   char fileresvpl[FILENAMELENGTH];  double **oldm, **newm, **savm; /* Working pointers to matrices */
   double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 #define NR_END 1  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 #define FREE_ARG char*  FILE *ficlog;
 #define FTOL 1.0e-10  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
 #define NRANSI  FILE *fichtm; /* Html File */
 #define ITMAX 200  FILE *ficreseij;
   char filerese[FILENAMELENGTH];
 #define TOL 2.0e-4  FILE  *ficresvij;
   char fileresv[FILENAMELENGTH];
 #define CGOLD 0.3819660  FILE  *ficresvpl;
 #define ZEPS 1.0e-10  char fileresvpl[FILENAMELENGTH];
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 #define GOLD 1.618034  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 #define GLIMIT 100.0  
 #define TINY 1.0e-20  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   char filelog[FILENAMELENGTH]; /* Log file */
 static double maxarg1,maxarg2;  char filerest[FILENAMELENGTH];
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  char fileregp[FILENAMELENGTH];
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  char popfile[FILENAMELENGTH];
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
 #define rint(a) floor(a+0.5)  
   #define NR_END 1
 static double sqrarg;  #define FREE_ARG char*
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  #define FTOL 1.0e-10
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
   #define NRANSI 
 int imx;  #define ITMAX 200 
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/  #define TOL 2.0e-4 
   
 int m,nb;  #define CGOLD 0.3819660 
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  #define ZEPS 1.0e-10 
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 double **pmmij, ***probs, ***mobaverage;  
 double dateintmean=0;  #define GOLD 1.618034 
   #define GLIMIT 100.0 
 double *weight;  #define TINY 1.0e-20 
 int **s; /* Status */  
 double *agedc, **covar, idx;  static double maxarg1,maxarg2;
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    
 double ftolhess; /* Tolerance for computing hessian */  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   #define rint(a) floor(a+0.5)
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  static double sqrarg;
 {  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
    char *s;                             /* pointer */  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
    int  l1, l2;                         /* length counters */  
   int imx; 
    l1 = strlen( path );                 /* length of path */  int stepm;
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  /* Stepm, step in month: minimum step interpolation*/
 #ifdef windows  
    s = strrchr( path, '\\' );           /* find last / */  int estepm;
 #else  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
    s = strrchr( path, '/' );            /* find last / */  
 #endif  int m,nb;
    if ( s == NULL ) {                   /* no directory, so use current */  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 #if     defined(__bsd__)                /* get current working directory */  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       extern char       *getwd( );  double **pmmij, ***probs;
   double dateintmean=0;
       if ( getwd( dirc ) == NULL ) {  
 #else  double *weight;
       extern char       *getcwd( );  int **s; /* Status */
   double *agedc, **covar, idx;
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 #endif  
          return( GLOCK_ERROR_GETCWD );  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
       }  double ftolhess; /* Tolerance for computing hessian */
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */  /**************** split *************************/
       s++;                              /* after this, the filename */  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
       l2 = strlen( s );                 /* length of filename */  {
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    char  *ss;                            /* pointer */
       strcpy( name, s );                /* save file name */    int   l1, l2;                         /* length counters */
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */    l1 = strlen(path );                   /* length of path */
    }    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
    l1 = strlen( dirc );                 /* length of directory */    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
 #ifdef windows    if ( ss == NULL ) {                   /* no directory, so use current */
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 #else        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  #if     defined(__bsd__)                /* get current working directory */
 #endif      extern char *getwd( );
    s = strrchr( name, '.' );            /* find last / */  
    s++;      if ( getwd( dirc ) == NULL ) {
    strcpy(ext,s);                       /* save extension */  #else
    l1= strlen( name);      extern char *getcwd( );
    l2= strlen( s)+1;  
    strncpy( finame, name, l1-l2);      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
    finame[l1-l2]= 0;  #endif
    return( 0 );                         /* we're done */        return( GLOCK_ERROR_GETCWD );
 }      }
       strcpy( name, path );               /* we've got it */
     } else {                              /* strip direcotry from path */
 /******************************************/      ss++;                               /* after this, the filename */
       l2 = strlen( ss );                  /* length of filename */
 void replace(char *s, char*t)      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 {      strcpy( name, ss );         /* save file name */
   int i;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   int lg=20;      dirc[l1-l2] = 0;                    /* add zero */
   i=0;    }
   lg=strlen(t);    l1 = strlen( dirc );                  /* length of directory */
   for(i=0; i<= lg; i++) {  #ifdef windows
     (s[i] = t[i]);    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
     if (t[i]== '\\') s[i]='/';  #else
   }    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
 }  #endif
     ss = strrchr( name, '.' );            /* find last / */
 int nbocc(char *s, char occ)    ss++;
 {    strcpy(ext,ss);                       /* save extension */
   int i,j=0;    l1= strlen( name);
   int lg=20;    l2= strlen(ss)+1;
   i=0;    strncpy( finame, name, l1-l2);
   lg=strlen(s);    finame[l1-l2]= 0;
   for(i=0; i<= lg; i++) {    return( 0 );                          /* we're done */
   if  (s[i] == occ ) j++;  }
   }  
   return j;  
 }  /******************************************/
   
 void cutv(char *u,char *v, char*t, char occ)  void replace(char *s, char*t)
 {  {
   int i,lg,j,p=0;    int i;
   i=0;    int lg=20;
   for(j=0; j<=strlen(t)-1; j++) {    i=0;
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    lg=strlen(t);
   }    for(i=0; i<= lg; i++) {
       (s[i] = t[i]);
   lg=strlen(t);      if (t[i]== '\\') s[i]='/';
   for(j=0; j<p; j++) {    }
     (u[j] = t[j]);  }
   }  
      u[p]='\0';  int nbocc(char *s, char occ)
   {
    for(j=0; j<= lg; j++) {    int i,j=0;
     if (j>=(p+1))(v[j-p-1] = t[j]);    int lg=20;
   }    i=0;
 }    lg=strlen(s);
     for(i=0; i<= lg; i++) {
 /********************** nrerror ********************/    if  (s[i] == occ ) j++;
     }
 void nrerror(char error_text[])    return j;
 {  }
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);  void cutv(char *u,char *v, char*t, char occ)
   exit(1);  {
 }    /* cuts string t into u and v where u is ended by char occ excluding it
 /*********************** vector *******************/       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 double *vector(int nl, int nh)       gives u="abcedf" and v="ghi2j" */
 {    int i,lg,j,p=0;
   double *v;    i=0;
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    for(j=0; j<=strlen(t)-1; j++) {
   if (!v) nrerror("allocation failure in vector");      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   return v-nl+NR_END;    }
 }  
     lg=strlen(t);
 /************************ free vector ******************/    for(j=0; j<p; j++) {
 void free_vector(double*v, int nl, int nh)      (u[j] = t[j]);
 {    }
   free((FREE_ARG)(v+nl-NR_END));       u[p]='\0';
 }  
      for(j=0; j<= lg; j++) {
 /************************ivector *******************************/      if (j>=(p+1))(v[j-p-1] = t[j]);
 int *ivector(long nl,long nh)    }
 {  }
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  /********************** nrerror ********************/
   if (!v) nrerror("allocation failure in ivector");  
   return v-nl+NR_END;  void nrerror(char error_text[])
 }  {
     fprintf(stderr,"ERREUR ...\n");
 /******************free ivector **************************/    fprintf(stderr,"%s\n",error_text);
 void free_ivector(int *v, long nl, long nh)    exit(EXIT_FAILURE);
 {  }
   free((FREE_ARG)(v+nl-NR_END));  /*********************** vector *******************/
 }  double *vector(int nl, int nh)
   {
 /******************* imatrix *******************************/    double *v;
 int **imatrix(long nrl, long nrh, long ncl, long nch)    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    if (!v) nrerror("allocation failure in vector");
 {    return v-nl+NR_END;
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  }
   int **m;  
    /************************ free vector ******************/
   /* allocate pointers to rows */  void free_vector(double*v, int nl, int nh)
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  {
   if (!m) nrerror("allocation failure 1 in matrix()");    free((FREE_ARG)(v+nl-NR_END));
   m += NR_END;  }
   m -= nrl;  
    /************************ivector *******************************/
    int *ivector(long nl,long nh)
   /* allocate rows and set pointers to them */  {
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    int *v;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   m[nrl] += NR_END;    if (!v) nrerror("allocation failure in ivector");
   m[nrl] -= ncl;    return v-nl+NR_END;
    }
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
    /******************free ivector **************************/
   /* return pointer to array of pointers to rows */  void free_ivector(int *v, long nl, long nh)
   return m;  {
 }    free((FREE_ARG)(v+nl-NR_END));
   }
 /****************** free_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)  /******************* imatrix *******************************/
       int **m;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       long nch,ncl,nrh,nrl;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
      /* free an int matrix allocated by imatrix() */  { 
 {    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    int **m; 
   free((FREE_ARG) (m+nrl-NR_END));    
 }    /* allocate pointers to rows */ 
     m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 /******************* matrix *******************************/    if (!m) nrerror("allocation failure 1 in matrix()"); 
 double **matrix(long nrl, long nrh, long ncl, long nch)    m += NR_END; 
 {    m -= nrl; 
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    
   double **m;    
     /* allocate rows and set pointers to them */ 
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   if (!m) nrerror("allocation failure 1 in matrix()");    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   m += NR_END;    m[nrl] += NR_END; 
   m -= nrl;    m[nrl] -= ncl; 
     
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    
   m[nrl] += NR_END;    /* return pointer to array of pointers to rows */ 
   m[nrl] -= ncl;    return m; 
   } 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;  /****************** free_imatrix *************************/
 }  void free_imatrix(m,nrl,nrh,ncl,nch)
         int **m;
 /*************************free matrix ************************/        long nch,ncl,nrh,nrl; 
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)       /* free an int matrix allocated by imatrix() */ 
 {  { 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   free((FREE_ARG)(m+nrl-NR_END));    free((FREE_ARG) (m+nrl-NR_END)); 
 }  } 
   
 /******************* ma3x *******************************/  /******************* matrix *******************************/
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  double **matrix(long nrl, long nrh, long ncl, long nch)
 {  {
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   double ***m;    double **m;
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   if (!m) nrerror("allocation failure 1 in matrix()");    if (!m) nrerror("allocation failure 1 in matrix()");
   m += NR_END;    m += NR_END;
   m -= nrl;    m -= nrl;
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   m[nrl] += NR_END;    m[nrl] += NR_END;
   m[nrl] -= ncl;    m[nrl] -= ncl;
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     return m;
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  }
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;  /*************************free matrix ************************/
   m[nrl][ncl] -= nll;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   for (j=ncl+1; j<=nch; j++)  {
     m[nrl][j]=m[nrl][j-1]+nlay;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
      free((FREE_ARG)(m+nrl-NR_END));
   for (i=nrl+1; i<=nrh; i++) {  }
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)  /******************* ma3x *******************************/
       m[i][j]=m[i][j-1]+nlay;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   }  {
   return m;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
 }    double ***m;
   
 /*************************free ma3x ************************/    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    if (!m) nrerror("allocation failure 1 in matrix()");
 {    m += NR_END;
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    m -= nrl;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
 /***************** f1dim *************************/    m[nrl] -= ncl;
 extern int ncom;  
 extern double *pcom,*xicom;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 extern double (*nrfunc)(double []);  
      m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 double f1dim(double x)    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
 {    m[nrl][ncl] += NR_END;
   int j;    m[nrl][ncl] -= nll;
   double f;    for (j=ncl+1; j<=nch; j++) 
   double *xt;      m[nrl][j]=m[nrl][j-1]+nlay;
      
   xt=vector(1,ncom);    for (i=nrl+1; i<=nrh; i++) {
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   f=(*nrfunc)(xt);      for (j=ncl+1; j<=nch; j++) 
   free_vector(xt,1,ncom);        m[i][j]=m[i][j-1]+nlay;
   return f;    }
 }    return m;
   }
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  /*************************free ma3x ************************/
 {  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   int iter;  {
   double a,b,d,etemp;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   double fu,fv,fw,fx;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double ftemp;    free((FREE_ARG)(m+nrl-NR_END));
   double p,q,r,tol1,tol2,u,v,w,x,xm;  }
   double e=0.0;  
    /***************** f1dim *************************/
   a=(ax < cx ? ax : cx);  extern int ncom; 
   b=(ax > cx ? ax : cx);  extern double *pcom,*xicom;
   x=w=v=bx;  extern double (*nrfunc)(double []); 
   fw=fv=fx=(*f)(x);   
   for (iter=1;iter<=ITMAX;iter++) {  double f1dim(double x) 
     xm=0.5*(a+b);  { 
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    int j; 
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    double f;
     printf(".");fflush(stdout);    double *xt; 
 #ifdef DEBUG   
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    xt=vector(1,ncom); 
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
 #endif    f=(*nrfunc)(xt); 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    free_vector(xt,1,ncom); 
       *xmin=x;    return f; 
       return fx;  } 
     }  
     ftemp=fu;  /*****************brent *************************/
     if (fabs(e) > tol1) {  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       r=(x-w)*(fx-fv);  { 
       q=(x-v)*(fx-fw);    int iter; 
       p=(x-v)*q-(x-w)*r;    double a,b,d,etemp;
       q=2.0*(q-r);    double fu,fv,fw,fx;
       if (q > 0.0) p = -p;    double ftemp;
       q=fabs(q);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       etemp=e;    double e=0.0; 
       e=d;   
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    a=(ax < cx ? ax : cx); 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    b=(ax > cx ? ax : cx); 
       else {    x=w=v=bx; 
         d=p/q;    fw=fv=fx=(*f)(x); 
         u=x+d;    for (iter=1;iter<=ITMAX;iter++) { 
         if (u-a < tol2 || b-u < tol2)      xm=0.5*(a+b); 
           d=SIGN(tol1,xm-x);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       }      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     } else {      printf(".");fflush(stdout);
       d=CGOLD*(e=(x >= xm ? a-x : b-x));      fprintf(ficlog,".");fflush(ficlog);
     }  #ifdef DEBUG
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     fu=(*f)(u);      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     if (fu <= fx) {      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       if (u >= x) a=x; else b=x;  #endif
       SHFT(v,w,x,u)      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         SHFT(fv,fw,fx,fu)        *xmin=x; 
         } else {        return fx; 
           if (u < x) a=u; else b=u;      } 
           if (fu <= fw || w == x) {      ftemp=fu;
             v=w;      if (fabs(e) > tol1) { 
             w=u;        r=(x-w)*(fx-fv); 
             fv=fw;        q=(x-v)*(fx-fw); 
             fw=fu;        p=(x-v)*q-(x-w)*r; 
           } else if (fu <= fv || v == x || v == w) {        q=2.0*(q-r); 
             v=u;        if (q > 0.0) p = -p; 
             fv=fu;        q=fabs(q); 
           }        etemp=e; 
         }        e=d; 
   }        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   nrerror("Too many iterations in brent");          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   *xmin=x;        else { 
   return fx;          d=p/q; 
 }          u=x+d; 
           if (u-a < tol2 || b-u < tol2) 
 /****************** mnbrak ***********************/            d=SIGN(tol1,xm-x); 
         } 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,      } else { 
             double (*func)(double))        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 {      } 
   double ulim,u,r,q, dum;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   double fu;      fu=(*f)(u); 
        if (fu <= fx) { 
   *fa=(*func)(*ax);        if (u >= x) a=x; else b=x; 
   *fb=(*func)(*bx);        SHFT(v,w,x,u) 
   if (*fb > *fa) {          SHFT(fv,fw,fx,fu) 
     SHFT(dum,*ax,*bx,dum)          } else { 
       SHFT(dum,*fb,*fa,dum)            if (u < x) a=u; else b=u; 
       }            if (fu <= fw || w == x) { 
   *cx=(*bx)+GOLD*(*bx-*ax);              v=w; 
   *fc=(*func)(*cx);              w=u; 
   while (*fb > *fc) {              fv=fw; 
     r=(*bx-*ax)*(*fb-*fc);              fw=fu; 
     q=(*bx-*cx)*(*fb-*fa);            } else if (fu <= fv || v == x || v == w) { 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/              v=u; 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));              fv=fu; 
     ulim=(*bx)+GLIMIT*(*cx-*bx);            } 
     if ((*bx-u)*(u-*cx) > 0.0) {          } 
       fu=(*func)(u);    } 
     } else if ((*cx-u)*(u-ulim) > 0.0) {    nrerror("Too many iterations in brent"); 
       fu=(*func)(u);    *xmin=x; 
       if (fu < *fc) {    return fx; 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  } 
           SHFT(*fb,*fc,fu,(*func)(u))  
           }  /****************** mnbrak ***********************/
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       fu=(*func)(u);              double (*func)(double)) 
     } else {  { 
       u=(*cx)+GOLD*(*cx-*bx);    double ulim,u,r,q, dum;
       fu=(*func)(u);    double fu; 
     }   
     SHFT(*ax,*bx,*cx,u)    *fa=(*func)(*ax); 
       SHFT(*fa,*fb,*fc,fu)    *fb=(*func)(*bx); 
       }    if (*fb > *fa) { 
 }      SHFT(dum,*ax,*bx,dum) 
         SHFT(dum,*fb,*fa,dum) 
 /*************** linmin ************************/        } 
     *cx=(*bx)+GOLD*(*bx-*ax); 
 int ncom;    *fc=(*func)(*cx); 
 double *pcom,*xicom;    while (*fb > *fc) { 
 double (*nrfunc)(double []);      r=(*bx-*ax)*(*fb-*fc); 
        q=(*bx-*cx)*(*fb-*fa); 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 {        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   double brent(double ax, double bx, double cx,      ulim=(*bx)+GLIMIT*(*cx-*bx); 
                double (*f)(double), double tol, double *xmin);      if ((*bx-u)*(u-*cx) > 0.0) { 
   double f1dim(double x);        fu=(*func)(u); 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,      } else if ((*cx-u)*(u-ulim) > 0.0) { 
               double *fc, double (*func)(double));        fu=(*func)(u); 
   int j;        if (fu < *fc) { 
   double xx,xmin,bx,ax;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   double fx,fb,fa;            SHFT(*fb,*fc,fu,(*func)(u)) 
              } 
   ncom=n;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   pcom=vector(1,n);        u=ulim; 
   xicom=vector(1,n);        fu=(*func)(u); 
   nrfunc=func;      } else { 
   for (j=1;j<=n;j++) {        u=(*cx)+GOLD*(*cx-*bx); 
     pcom[j]=p[j];        fu=(*func)(u); 
     xicom[j]=xi[j];      } 
   }      SHFT(*ax,*bx,*cx,u) 
   ax=0.0;        SHFT(*fa,*fb,*fc,fu) 
   xx=1.0;        } 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  } 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  
 #ifdef DEBUG  /*************** linmin ************************/
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  
 #endif  int ncom; 
   for (j=1;j<=n;j++) {  double *pcom,*xicom;
     xi[j] *= xmin;  double (*nrfunc)(double []); 
     p[j] += xi[j];   
   }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   free_vector(xicom,1,n);  { 
   free_vector(pcom,1,n);    double brent(double ax, double bx, double cx, 
 }                 double (*f)(double), double tol, double *xmin); 
     double f1dim(double x); 
 /*************** powell ************************/    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,                double *fc, double (*func)(double)); 
             double (*func)(double []))    int j; 
 {    double xx,xmin,bx,ax; 
   void linmin(double p[], double xi[], int n, double *fret,    double fx,fb,fa;
               double (*func)(double []));   
   int i,ibig,j;    ncom=n; 
   double del,t,*pt,*ptt,*xit;    pcom=vector(1,n); 
   double fp,fptt;    xicom=vector(1,n); 
   double *xits;    nrfunc=func; 
   pt=vector(1,n);    for (j=1;j<=n;j++) { 
   ptt=vector(1,n);      pcom[j]=p[j]; 
   xit=vector(1,n);      xicom[j]=xi[j]; 
   xits=vector(1,n);    } 
   *fret=(*func)(p);    ax=0.0; 
   for (j=1;j<=n;j++) pt[j]=p[j];    xx=1.0; 
   for (*iter=1;;++(*iter)) {    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     fp=(*fret);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     ibig=0;  #ifdef DEBUG
     del=0.0;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     for (i=1;i<=n;i++)  #endif
       printf(" %d %.12f",i, p[i]);    for (j=1;j<=n;j++) { 
     printf("\n");      xi[j] *= xmin; 
     for (i=1;i<=n;i++) {      p[j] += xi[j]; 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    } 
       fptt=(*fret);    free_vector(xicom,1,n); 
 #ifdef DEBUG    free_vector(pcom,1,n); 
       printf("fret=%lf \n",*fret);  } 
 #endif  
       printf("%d",i);fflush(stdout);  /*************** powell ************************/
       linmin(p,xit,n,fret,func);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       if (fabs(fptt-(*fret)) > del) {              double (*func)(double [])) 
         del=fabs(fptt-(*fret));  { 
         ibig=i;    void linmin(double p[], double xi[], int n, double *fret, 
       }                double (*func)(double [])); 
 #ifdef DEBUG    int i,ibig,j; 
       printf("%d %.12e",i,(*fret));    double del,t,*pt,*ptt,*xit;
       for (j=1;j<=n;j++) {    double fp,fptt;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    double *xits;
         printf(" x(%d)=%.12e",j,xit[j]);    pt=vector(1,n); 
       }    ptt=vector(1,n); 
       for(j=1;j<=n;j++)    xit=vector(1,n); 
         printf(" p=%.12e",p[j]);    xits=vector(1,n); 
       printf("\n");    *fret=(*func)(p); 
 #endif    for (j=1;j<=n;j++) pt[j]=p[j]; 
     }    for (*iter=1;;++(*iter)) { 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      fp=(*fret); 
 #ifdef DEBUG      ibig=0; 
       int k[2],l;      del=0.0; 
       k[0]=1;      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       k[1]=-1;      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       printf("Max: %.12e",(*func)(p));      for (i=1;i<=n;i++) 
       for (j=1;j<=n;j++)        printf(" %d %.12f",i, p[i]);
         printf(" %.12e",p[j]);      fprintf(ficlog," %d %.12f",i, p[i]);
       printf("\n");      printf("\n");
       for(l=0;l<=1;l++) {      fprintf(ficlog,"\n");
         for (j=1;j<=n;j++) {      for (i=1;i<=n;i++) { 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);        fptt=(*fret); 
         }  #ifdef DEBUG
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));        printf("fret=%lf \n",*fret);
       }        fprintf(ficlog,"fret=%lf \n",*fret);
 #endif  #endif
         printf("%d",i);fflush(stdout);
         fprintf(ficlog,"%d",i);fflush(ficlog);
       free_vector(xit,1,n);        linmin(p,xit,n,fret,func); 
       free_vector(xits,1,n);        if (fabs(fptt-(*fret)) > del) { 
       free_vector(ptt,1,n);          del=fabs(fptt-(*fret)); 
       free_vector(pt,1,n);          ibig=i; 
       return;        } 
     }  #ifdef DEBUG
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");        printf("%d %.12e",i,(*fret));
     for (j=1;j<=n;j++) {        fprintf(ficlog,"%d %.12e",i,(*fret));
       ptt[j]=2.0*p[j]-pt[j];        for (j=1;j<=n;j++) {
       xit[j]=p[j]-pt[j];          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       pt[j]=p[j];          printf(" x(%d)=%.12e",j,xit[j]);
     }          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     fptt=(*func)(ptt);        }
     if (fptt < fp) {        for(j=1;j<=n;j++) {
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);          printf(" p=%.12e",p[j]);
       if (t < 0.0) {          fprintf(ficlog," p=%.12e",p[j]);
         linmin(p,xit,n,fret,func);        }
         for (j=1;j<=n;j++) {        printf("\n");
           xi[j][ibig]=xi[j][n];        fprintf(ficlog,"\n");
           xi[j][n]=xit[j];  #endif
         }      } 
 #ifdef DEBUG      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  #ifdef DEBUG
         for(j=1;j<=n;j++)        int k[2],l;
           printf(" %.12e",xit[j]);        k[0]=1;
         printf("\n");        k[1]=-1;
 #endif        printf("Max: %.12e",(*func)(p));
       }        fprintf(ficlog,"Max: %.12e",(*func)(p));
     }        for (j=1;j<=n;j++) {
   }          printf(" %.12e",p[j]);
 }          fprintf(ficlog," %.12e",p[j]);
         }
 /**** Prevalence limit ****************/        printf("\n");
         fprintf(ficlog,"\n");
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)        for(l=0;l<=1;l++) {
 {          for (j=1;j<=n;j++) {
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
      matrix by transitions matrix until convergence is reached */            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
             fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   int i, ii,j,k;          }
   double min, max, maxmin, maxmax,sumnew=0.;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   double **matprod2();          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   double **out, cov[NCOVMAX], **pmij();        }
   double **newm;  #endif
   double agefin, delaymax=50 ; /* Max number of years to converge */  
   
   for (ii=1;ii<=nlstate+ndeath;ii++)        free_vector(xit,1,n); 
     for (j=1;j<=nlstate+ndeath;j++){        free_vector(xits,1,n); 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        free_vector(ptt,1,n); 
     }        free_vector(pt,1,n); 
         return; 
    cov[1]=1.;      } 
        if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      for (j=1;j<=n;j++) { 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        ptt[j]=2.0*p[j]-pt[j]; 
     newm=savm;        xit[j]=p[j]-pt[j]; 
     /* Covariates have to be included here again */        pt[j]=p[j]; 
      cov[2]=agefin;      } 
        fptt=(*func)(ptt); 
       for (k=1; k<=cptcovn;k++) {      if (fptt < fp) { 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/        if (t < 0.0) { 
       }          linmin(p,xit,n,fret,func); 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          for (j=1;j<=n;j++) { 
       for (k=1; k<=cptcovprod;k++)            xi[j][ibig]=xi[j][n]; 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];            xi[j][n]=xit[j]; 
           }
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  #ifdef DEBUG
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);          for(j=1;j<=n;j++){
             printf(" %.12e",xit[j]);
     savm=oldm;            fprintf(ficlog," %.12e",xit[j]);
     oldm=newm;          }
     maxmax=0.;          printf("\n");
     for(j=1;j<=nlstate;j++){          fprintf(ficlog,"\n");
       min=1.;  #endif
       max=0.;        }
       for(i=1; i<=nlstate; i++) {      } 
         sumnew=0;    } 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  } 
         prlim[i][j]= newm[i][j]/(1-sumnew);  
         max=FMAX(max,prlim[i][j]);  /**** Prevalence limit (stable prevalence)  ****************/
         min=FMIN(min,prlim[i][j]);  
       }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       maxmin=max-min;  {
       maxmax=FMAX(maxmax,maxmin);    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     }       matrix by transitions matrix until convergence is reached */
     if(maxmax < ftolpl){  
       return prlim;    int i, ii,j,k;
     }    double min, max, maxmin, maxmax,sumnew=0.;
   }    double **matprod2();
 }    double **out, cov[NCOVMAX], **pmij();
     double **newm;
 /*************** transition probabilities ***************/    double agefin, delaymax=50 ; /* Max number of years to converge */
   
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    for (ii=1;ii<=nlstate+ndeath;ii++)
 {      for (j=1;j<=nlstate+ndeath;j++){
   double s1, s2;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   /*double t34;*/      }
   int i,j,j1, nc, ii, jj;  
      cov[1]=1.;
     for(i=1; i<= nlstate; i++){   
     for(j=1; j<i;j++){   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
         /*s2 += param[i][j][nc]*cov[nc];*/      newm=savm;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      /* Covariates have to be included here again */
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/       cov[2]=agefin;
       }    
       ps[i][j]=s2;        for (k=1; k<=cptcovn;k++) {
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     }          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
     for(j=i+1; j<=nlstate+ndeath;j++){        }
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        for (k=1; k<=cptcovprod;k++)
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       }  
       ps[i][j]=s2;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     }        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   }        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     /*ps[3][2]=1;*/      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   
   for(i=1; i<= nlstate; i++){      savm=oldm;
      s1=0;      oldm=newm;
     for(j=1; j<i; j++)      maxmax=0.;
       s1+=exp(ps[i][j]);      for(j=1;j<=nlstate;j++){
     for(j=i+1; j<=nlstate+ndeath; j++)        min=1.;
       s1+=exp(ps[i][j]);        max=0.;
     ps[i][i]=1./(s1+1.);        for(i=1; i<=nlstate; i++) {
     for(j=1; j<i; j++)          sumnew=0;
       ps[i][j]= exp(ps[i][j])*ps[i][i];          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     for(j=i+1; j<=nlstate+ndeath; j++)          prlim[i][j]= newm[i][j]/(1-sumnew);
       ps[i][j]= exp(ps[i][j])*ps[i][i];          max=FMAX(max,prlim[i][j]);
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */          min=FMIN(min,prlim[i][j]);
   } /* end i */        }
         maxmin=max-min;
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){        maxmax=FMAX(maxmax,maxmin);
     for(jj=1; jj<= nlstate+ndeath; jj++){      }
       ps[ii][jj]=0;      if(maxmax < ftolpl){
       ps[ii][ii]=1;        return prlim;
     }      }
   }    }
   }
   
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  /*************** transition probabilities ***************/ 
     for(jj=1; jj<= nlstate+ndeath; jj++){  
      printf("%lf ",ps[ii][jj]);  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
    }  {
     printf("\n ");    double s1, s2;
     }    /*double t34;*/
     printf("\n ");printf("%lf ",cov[2]);*/    int i,j,j1, nc, ii, jj;
 /*  
   for(i=1; i<= npar; i++) printf("%f ",x[i]);      for(i=1; i<= nlstate; i++){
   goto end;*/      for(j=1; j<i;j++){
     return ps;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 }          /*s2 += param[i][j][nc]*cov[nc];*/
           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
 /**************** Product of 2 matrices ******************/          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
         }
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        ps[i][j]=s2;
 {        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times      }
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      for(j=i+1; j<=nlstate+ndeath;j++){
   /* in, b, out are matrice of pointers which should have been initialized        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
      before: only the contents of out is modified. The function returns          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
      a pointer to pointers identical to out */          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   long i, j, k;        }
   for(i=nrl; i<= nrh; i++)        ps[i][j]=s2;
     for(k=ncolol; k<=ncoloh; k++)      }
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    }
         out[i][k] +=in[i][j]*b[j][k];      /*ps[3][2]=1;*/
   
   return out;    for(i=1; i<= nlstate; i++){
 }       s1=0;
       for(j=1; j<i; j++)
         s1+=exp(ps[i][j]);
 /************* Higher Matrix Product ***************/      for(j=i+1; j<=nlstate+ndeath; j++)
         s1+=exp(ps[i][j]);
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      ps[i][i]=1./(s1+1.);
 {      for(j=1; j<i; j++)
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month        ps[i][j]= exp(ps[i][j])*ps[i][i];
      duration (i.e. until      for(j=i+1; j<=nlstate+ndeath; j++)
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        ps[i][j]= exp(ps[i][j])*ps[i][i];
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
      (typically every 2 years instead of every month which is too big).    } /* end i */
      Model is determined by parameters x and covariates have to be  
      included manually here.    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       for(jj=1; jj<= nlstate+ndeath; jj++){
      */        ps[ii][jj]=0;
         ps[ii][ii]=1;
   int i, j, d, h, k;      }
   double **out, cov[NCOVMAX];    }
   double **newm;  
   
   /* Hstepm could be zero and should return the unit matrix */    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   for (i=1;i<=nlstate+ndeath;i++)      for(jj=1; jj<= nlstate+ndeath; jj++){
     for (j=1;j<=nlstate+ndeath;j++){       printf("%lf ",ps[ii][jj]);
       oldm[i][j]=(i==j ? 1.0 : 0.0);     }
       po[i][j][0]=(i==j ? 1.0 : 0.0);      printf("\n ");
     }      }
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      printf("\n ");printf("%lf ",cov[2]);*/
   for(h=1; h <=nhstepm; h++){  /*
     for(d=1; d <=hstepm; d++){    for(i=1; i<= npar; i++) printf("%f ",x[i]);
       newm=savm;    goto end;*/
       /* Covariates have to be included here again */      return ps;
       cov[1]=1.;  }
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  /**************** Product of 2 matrices ******************/
       for (k=1; k<=cptcovage;k++)  
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
       for (k=1; k<=cptcovprod;k++)  {
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
        b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     /* in, b, out are matrice of pointers which should have been initialized 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/       before: only the contents of out is modified. The function returns
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/       a pointer to pointers identical to out */
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    long i, j, k;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    for(i=nrl; i<= nrh; i++)
       savm=oldm;      for(k=ncolol; k<=ncoloh; k++)
       oldm=newm;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     }          out[i][k] +=in[i][j]*b[j][k];
     for(i=1; i<=nlstate+ndeath; i++)  
       for(j=1;j<=nlstate+ndeath;j++) {    return out;
         po[i][j][h]=newm[i][j];  }
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  
          */  
       }  /************* Higher Matrix Product ***************/
   } /* end h */  
   return po;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
 }  {
     /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month 
        duration (i.e. until
 /*************** log-likelihood *************/       age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices. 
 double func( double *x)       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
 {       (typically every 2 years instead of every month which is too big).
   int i, ii, j, k, mi, d, kk;       Model is determined by parameters x and covariates have to be 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];       included manually here. 
   double **out;  
   double sw; /* Sum of weights */       */
   double lli; /* Individual log likelihood */  
   long ipmx;    int i, j, d, h, k;
   /*extern weight */    double **out, cov[NCOVMAX];
   /* We are differentiating ll according to initial status */    double **newm;
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  
   /*for(i=1;i<imx;i++)    /* Hstepm could be zero and should return the unit matrix */
     printf(" %d\n",s[4][i]);    for (i=1;i<=nlstate+ndeath;i++)
   */      for (j=1;j<=nlstate+ndeath;j++){
   cov[1]=1.;        oldm[i][j]=(i==j ? 1.0 : 0.0);
         po[i][j][0]=(i==j ? 1.0 : 0.0);
   for(k=1; k<=nlstate; k++) ll[k]=0.;      }
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    for(h=1; h <=nhstepm; h++){
     for(mi=1; mi<= wav[i]-1; mi++){      for(d=1; d <=hstepm; d++){
       for (ii=1;ii<=nlstate+ndeath;ii++)        newm=savm;
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        /* Covariates have to be included here again */
       for(d=0; d<dh[mi][i]; d++){        cov[1]=1.;
         newm=savm;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         for (kk=1; kk<=cptcovage;kk++) {        for (k=1; k<=cptcovage;k++)
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         }        for (k=1; k<=cptcovprod;k++)
                  cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  
         savm=oldm;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         oldm=newm;        /*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, 
                             pmij(pmmij,cov,ncovmodel,x,nlstate));
       } /* end mult */        savm=oldm;
              oldm=newm;
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);      }
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/      for(i=1; i<=nlstate+ndeath; i++)
       ipmx +=1;        for(j=1;j<=nlstate+ndeath;j++) {
       sw += weight[i];          po[i][j][h]=newm[i][j];
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
     } /* end of wave */           */
   } /* end of individual */        }
     } /* end h */
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    return po;
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  }
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  
   return -l;  
 }  /*************** log-likelihood *************/
   double func( double *x)
   {
 /*********** Maximum Likelihood Estimation ***************/    int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX], cov[NCOVMAX];
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    double **out;
 {    double sw; /* Sum of weights */
   int i,j, iter;    double lli; /* Individual log likelihood */
   double **xi,*delti;    int s1, s2;
   double fret;    double bbh;
   xi=matrix(1,npar,1,npar);    long ipmx;
   for (i=1;i<=npar;i++)    /*extern weight */
     for (j=1;j<=npar;j++)    /* We are differentiating ll according to initial status */
       xi[i][j]=(i==j ? 1.0 : 0.0);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   printf("Powell\n");    /*for(i=1;i<imx;i++) 
   powell(p,xi,npar,ftol,&iter,&fret,func);      printf(" %d\n",s[4][i]);
     */
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    cov[1]=1.;
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  
     for(k=1; k<=nlstate; k++) ll[k]=0.;
 }  
     if(mle==1){
 /**** Computes Hessian and covariance matrix ***/      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 {        for(mi=1; mi<= wav[i]-1; mi++){
   double  **a,**y,*x,pd;          for (ii=1;ii<=nlstate+ndeath;ii++)
   double **hess;            for (j=1;j<=nlstate+ndeath;j++){
   int i, j,jk;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int *indx;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
   double hessii(double p[], double delta, int theta, double delti[]);          for(d=0; d<dh[mi][i]; d++){
   double hessij(double p[], double delti[], int i, int j);            newm=savm;
   void lubksb(double **a, int npar, int *indx, double b[]) ;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   void ludcmp(double **a, int npar, int *indx, double *d) ;            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   hess=matrix(1,npar,1,npar);            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   printf("\nCalculation of the hessian matrix. Wait...\n");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   for (i=1;i<=npar;i++){            savm=oldm;
     printf("%d",i);fflush(stdout);            oldm=newm;
     hess[i][i]=hessii(p,ftolhess,i,delti);          } /* end mult */
     /*printf(" %f ",p[i]);*/        
     /*printf(" %lf ",hess[i][i]);*/          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   }          /* But now since version 0.9 we anticipate for bias and large stepm.
             * If stepm is larger than one month (smallest stepm) and if the exact delay 
   for (i=1;i<=npar;i++) {           * (in months) between two waves is not a multiple of stepm, we rounded to 
     for (j=1;j<=npar;j++)  {           * the nearest (and in case of equal distance, to the lowest) interval but now
       if (j>i) {           * we keep into memory the bias bh[mi][i] and also the previous matrix product
         printf(".%d%d",i,j);fflush(stdout);           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
         hess[i][j]=hessij(p,delti,i,j);           * probability in order to take into account the bias as a fraction of the way
         hess[j][i]=hess[i][j];               * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
         /*printf(" %lf ",hess[i][j]);*/           * -stepm/2 to stepm/2 .
       }           * For stepm=1 the results are the same as for previous versions of Imach.
     }           * For stepm > 1 the results are less biased than in previous versions. 
   }           */
   printf("\n");          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");          bbh=(double)bh[mi][i]/(double)stepm; 
            /* bias is positive if real duration
   a=matrix(1,npar,1,npar);           * is higher than the multiple of stepm and negative otherwise.
   y=matrix(1,npar,1,npar);           */
   x=vector(1,npar);          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   indx=ivector(1,npar);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));  /* linear interpolation */
   for (i=1;i<=npar;i++)          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];          /*if(lli ==000.0)*/
   ludcmp(a,npar,indx,&pd);          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
           ipmx +=1;
   for (j=1;j<=npar;j++) {          sw += weight[i];
     for (i=1;i<=npar;i++) x[i]=0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     x[j]=1;        } /* end of wave */
     lubksb(a,npar,indx,x);      } /* end of individual */
     for (i=1;i<=npar;i++){    }  else if(mle==2){
       matcov[i][j]=x[i];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   }        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
   printf("\n#Hessian matrix#\n");            for (j=1;j<=nlstate+ndeath;j++){
   for (i=1;i<=npar;i++) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (j=1;j<=npar;j++) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       printf("%.3e ",hess[i][j]);            }
     }          for(d=0; d<=dh[mi][i]; d++){
     printf("\n");            newm=savm;
   }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
   /* Recompute Inverse */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   for (i=1;i<=npar;i++)            }
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   ludcmp(a,npar,indx,&pd);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   /*  printf("\n#Hessian matrix recomputed#\n");            oldm=newm;
           } /* end mult */
   for (j=1;j<=npar;j++) {        
     for (i=1;i<=npar;i++) x[i]=0;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     x[j]=1;          /* But now since version 0.9 we anticipate for bias and large stepm.
     lubksb(a,npar,indx,x);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     for (i=1;i<=npar;i++){           * (in months) between two waves is not a multiple of stepm, we rounded to 
       y[i][j]=x[i];           * the nearest (and in case of equal distance, to the lowest) interval but now
       printf("%.3e ",y[i][j]);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     }           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     printf("\n");           * probability in order to take into account the bias as a fraction of the way
   }           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   */           * -stepm/2 to stepm/2 .
            * For stepm=1 the results are the same as for previous versions of Imach.
   free_matrix(a,1,npar,1,npar);           * For stepm > 1 the results are less biased than in previous versions. 
   free_matrix(y,1,npar,1,npar);           */
   free_vector(x,1,npar);          s1=s[mw[mi][i]][i];
   free_ivector(indx,1,npar);          s2=s[mw[mi+1][i]][i];
   free_matrix(hess,1,npar,1,npar);          bbh=(double)bh[mi][i]/(double)stepm; 
           /* bias is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
 }           */
           lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
 /*************** hessian matrix ****************/          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
 double hessii( double x[], double delta, int theta, double delti[])          /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
 {          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   int i;          /*if(lli ==000.0)*/
   int l=1, lmax=20;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   double k1,k2;          ipmx +=1;
   double p2[NPARMAX+1];          sw += weight[i];
   double res;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        } /* end of wave */
   double fx;      } /* end of individual */
   int k=0,kmax=10;    }  else if(mle==3){  /* exponential inter-extrapolation */
   double l1;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   fx=func(x);        for(mi=1; mi<= wav[i]-1; mi++){
   for (i=1;i<=npar;i++) p2[i]=x[i];          for (ii=1;ii<=nlstate+ndeath;ii++)
   for(l=0 ; l <=lmax; l++){            for (j=1;j<=nlstate+ndeath;j++){
     l1=pow(10,l);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     delts=delt;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(k=1 ; k <kmax; k=k+1){            }
       delt = delta*(l1*k);          for(d=0; d<dh[mi][i]; d++){
       p2[theta]=x[theta] +delt;            newm=savm;
       k1=func(p2)-fx;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       p2[theta]=x[theta]-delt;            for (kk=1; kk<=cptcovage;kk++) {
       k2=func(p2)-fx;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       /*res= (k1-2.0*fx+k2)/delt/delt; */            }
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                               1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 #ifdef DEBUG            savm=oldm;
       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);            oldm=newm;
 #endif          } /* end mult */
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         k=kmax;          /* But now since version 0.9 we anticipate for bias and large stepm.
       }           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */           * (in months) between two waves is not a multiple of stepm, we rounded to 
         k=kmax; l=lmax*10.;           * the nearest (and in case of equal distance, to the lowest) interval but now
       }           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
         delts=delt;           * probability in order to take into account the bias as a fraction of the way
       }           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     }           * -stepm/2 to stepm/2 .
   }           * For stepm=1 the results are the same as for previous versions of Imach.
   delti[theta]=delts;           * For stepm > 1 the results are less biased than in previous versions. 
   return res;           */
            s1=s[mw[mi][i]][i];
 }          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
 double hessij( double x[], double delti[], int thetai,int thetaj)          /* bias is positive if real duration
 {           * is higher than the multiple of stepm and negative otherwise.
   int i;           */
   int l=1, l1, lmax=20;          /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
   double k1,k2,k3,k4,res,fx;          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   double p2[NPARMAX+1];          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   int k;          /*if(lli ==000.0)*/
           /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   fx=func(x);          ipmx +=1;
   for (k=1; k<=2; k++) {          sw += weight[i];
     for (i=1;i<=npar;i++) p2[i]=x[i];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     p2[thetai]=x[thetai]+delti[thetai]/k;        } /* end of wave */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      } /* end of individual */
     k1=func(p2)-fx;    }else{  /* ml=4 no inter-extrapolation */
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     p2[thetai]=x[thetai]+delti[thetai]/k;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        for(mi=1; mi<= wav[i]-1; mi++){
     k2=func(p2)-fx;          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
     p2[thetai]=x[thetai]-delti[thetai]/k;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     k3=func(p2)-fx;            }
            for(d=0; d<dh[mi][i]; d++){
     p2[thetai]=x[thetai]-delti[thetai]/k;            newm=savm;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     k4=func(p2)-fx;            for (kk=1; kk<=cptcovage;kk++) {
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 #ifdef DEBUG            }
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);          
 #endif            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   return res;            savm=oldm;
 }            oldm=newm;
           } /* end mult */
 /************** Inverse of matrix **************/        
 void ludcmp(double **a, int n, int *indx, double *d)          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
 {          ipmx +=1;
   int i,imax,j,k;          sw += weight[i];
   double big,dum,sum,temp;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double *vv;        } /* end of wave */
        } /* end of individual */
   vv=vector(1,n);    } /* End of if */
   *d=1.0;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   for (i=1;i<=n;i++) {    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     big=0.0;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     for (j=1;j<=n;j++)    return -l;
       if ((temp=fabs(a[i][j])) > big) big=temp;  }
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  
     vv[i]=1.0/big;  
   }  /*********** Maximum Likelihood Estimation ***************/
   for (j=1;j<=n;j++) {  
     for (i=1;i<j;i++) {  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       sum=a[i][j];  {
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    int i,j, iter;
       a[i][j]=sum;    double **xi,*delti;
     }    double fret;
     big=0.0;    xi=matrix(1,npar,1,npar);
     for (i=j;i<=n;i++) {    for (i=1;i<=npar;i++)
       sum=a[i][j];      for (j=1;j<=npar;j++)
       for (k=1;k<j;k++)        xi[i][j]=(i==j ? 1.0 : 0.0);
         sum -= a[i][k]*a[k][j];    printf("Powell\n");  fprintf(ficlog,"Powell\n");
       a[i][j]=sum;    powell(p,xi,npar,ftol,&iter,&fret,func);
       if ( (dum=vv[i]*fabs(sum)) >= big) {  
         big=dum;     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
         imax=i;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       }    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     }  
     if (j != imax) {  }
       for (k=1;k<=n;k++) {  
         dum=a[imax][k];  /**** Computes Hessian and covariance matrix ***/
         a[imax][k]=a[j][k];  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
         a[j][k]=dum;  {
       }    double  **a,**y,*x,pd;
       *d = -(*d);    double **hess;
       vv[imax]=vv[j];    int i, j,jk;
     }    int *indx;
     indx[j]=imax;  
     if (a[j][j] == 0.0) a[j][j]=TINY;    double hessii(double p[], double delta, int theta, double delti[]);
     if (j != n) {    double hessij(double p[], double delti[], int i, int j);
       dum=1.0/(a[j][j]);    void lubksb(double **a, int npar, int *indx, double b[]) ;
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    void ludcmp(double **a, int npar, int *indx, double *d) ;
     }  
   }    hess=matrix(1,npar,1,npar);
   free_vector(vv,1,n);  /* Doesn't work */  
 ;    printf("\nCalculation of the hessian matrix. Wait...\n");
 }    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     for (i=1;i<=npar;i++){
 void lubksb(double **a, int n, int *indx, double b[])      printf("%d",i);fflush(stdout);
 {      fprintf(ficlog,"%d",i);fflush(ficlog);
   int i,ii=0,ip,j;      hess[i][i]=hessii(p,ftolhess,i,delti);
   double sum;      /*printf(" %f ",p[i]);*/
        /*printf(" %lf ",hess[i][i]);*/
   for (i=1;i<=n;i++) {    }
     ip=indx[i];    
     sum=b[ip];    for (i=1;i<=npar;i++) {
     b[ip]=b[i];      for (j=1;j<=npar;j++)  {
     if (ii)        if (j>i) { 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          printf(".%d%d",i,j);fflush(stdout);
     else if (sum) ii=i;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     b[i]=sum;          hess[i][j]=hessij(p,delti,i,j);
   }          hess[j][i]=hess[i][j];    
   for (i=n;i>=1;i--) {          /*printf(" %lf ",hess[i][j]);*/
     sum=b[i];        }
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];      }
     b[i]=sum/a[i][i];    }
   }    printf("\n");
 }    fprintf(ficlog,"\n");
   
 /************ Frequencies ********************/    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
 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)    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
 {  /* Some frequencies */    
      a=matrix(1,npar,1,npar);
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    y=matrix(1,npar,1,npar);
   double ***freq; /* Frequencies */    x=vector(1,npar);
   double *pp;    indx=ivector(1,npar);
   double pos, k2, dateintsum=0,k2cpt=0;    for (i=1;i<=npar;i++)
   FILE *ficresp;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   char fileresp[FILENAMELENGTH];    ludcmp(a,npar,indx,&pd);
    
   pp=vector(1,nlstate);    for (j=1;j<=npar;j++) {
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      for (i=1;i<=npar;i++) x[i]=0;
   strcpy(fileresp,"p");      x[j]=1;
   strcat(fileresp,fileres);      lubksb(a,npar,indx,x);
   if((ficresp=fopen(fileresp,"w"))==NULL) {      for (i=1;i<=npar;i++){ 
     printf("Problem with prevalence resultfile: %s\n", fileresp);        matcov[i][j]=x[i];
     exit(0);      }
   }    }
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  
   j1=0;    printf("\n#Hessian matrix#\n");
      fprintf(ficlog,"\n#Hessian matrix#\n");
   j=cptcoveff;    for (i=1;i<=npar;i++) { 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      for (j=1;j<=npar;j++) { 
          printf("%.3e ",hess[i][j]);
   for(k1=1; k1<=j;k1++){        fprintf(ficlog,"%.3e ",hess[i][j]);
     for(i1=1; i1<=ncodemax[k1];i1++){      }
       j1++;      printf("\n");
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);      fprintf(ficlog,"\n");
         scanf("%d", i);*/    }
       for (i=-1; i<=nlstate+ndeath; i++)    
         for (jk=-1; jk<=nlstate+ndeath; jk++)      /* Recompute Inverse */
           for(m=agemin; m <= agemax+3; m++)    for (i=1;i<=npar;i++)
             freq[i][jk][m]=0;      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
          ludcmp(a,npar,indx,&pd);
       dateintsum=0;  
       k2cpt=0;    /*  printf("\n#Hessian matrix recomputed#\n");
       for (i=1; i<=imx; i++) {  
         bool=1;    for (j=1;j<=npar;j++) {
         if  (cptcovn>0) {      for (i=1;i<=npar;i++) x[i]=0;
           for (z1=1; z1<=cptcoveff; z1++)      x[j]=1;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      lubksb(a,npar,indx,x);
               bool=0;      for (i=1;i<=npar;i++){ 
         }        y[i][j]=x[i];
         if (bool==1) {        printf("%.3e ",y[i][j]);
           for(m=firstpass; m<=lastpass; m++){        fprintf(ficlog,"%.3e ",y[i][j]);
             k2=anint[m][i]+(mint[m][i]/12.);      }
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      printf("\n");
               if(agev[m][i]==0) agev[m][i]=agemax+1;      fprintf(ficlog,"\n");
               if(agev[m][i]==1) agev[m][i]=agemax+2;    }
               if (m<lastpass) {    */
                 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];    free_matrix(a,1,npar,1,npar);
               }    free_matrix(y,1,npar,1,npar);
                  free_vector(x,1,npar);
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    free_ivector(indx,1,npar);
                 dateintsum=dateintsum+k2;    free_matrix(hess,1,npar,1,npar);
                 k2cpt++;  
               }  
             }  }
           }  
         }  /*************** hessian matrix ****************/
       }  double hessii( double x[], double delta, int theta, double delti[])
          {
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    int i;
     int l=1, lmax=20;
       if  (cptcovn>0) {    double k1,k2;
         fprintf(ficresp, "\n#********** Variable ");    double p2[NPARMAX+1];
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    double res;
         fprintf(ficresp, "**********\n#");    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       }    double fx;
       for(i=1; i<=nlstate;i++)    int k=0,kmax=10;
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    double l1;
       fprintf(ficresp, "\n");  
          fx=func(x);
       for(i=(int)agemin; i <= (int)agemax+3; i++){    for (i=1;i<=npar;i++) p2[i]=x[i];
         if(i==(int)agemax+3)    for(l=0 ; l <=lmax; l++){
           printf("Total");      l1=pow(10,l);
         else      delts=delt;
           printf("Age %d", i);      for(k=1 ; k <kmax; k=k+1){
         for(jk=1; jk <=nlstate ; jk++){        delt = delta*(l1*k);
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        p2[theta]=x[theta] +delt;
             pp[jk] += freq[jk][m][i];        k1=func(p2)-fx;
         }        p2[theta]=x[theta]-delt;
         for(jk=1; jk <=nlstate ; jk++){        k2=func(p2)-fx;
           for(m=-1, pos=0; m <=0 ; m++)        /*res= (k1-2.0*fx+k2)/delt/delt; */
             pos += freq[jk][m][i];        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
           if(pp[jk]>=1.e-10)        
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  #ifdef DEBUG
           else        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        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);
         }  #endif
         /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         for(jk=1; jk <=nlstate ; jk++){        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          k=kmax;
             pp[jk] += freq[jk][m][i];        }
         }        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           k=kmax; l=lmax*10.;
         for(jk=1,pos=0; jk <=nlstate ; jk++)        }
           pos += pp[jk];        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
         for(jk=1; jk <=nlstate ; jk++){          delts=delt;
           if(pos>=1.e-5)        }
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      }
           else    }
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    delti[theta]=delts;
           if( i <= (int) agemax){    return res; 
             if(pos>=1.e-5){    
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  }
               probs[i][jk][j1]= pp[jk]/pos;  
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/  double hessij( double x[], double delti[], int thetai,int thetaj)
             }  {
             else    int i;
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    int l=1, l1, lmax=20;
           }    double k1,k2,k3,k4,res,fx;
         }    double p2[NPARMAX+1];
            int k;
         for(jk=-1; jk <=nlstate+ndeath; jk++)  
           for(m=-1; m <=nlstate+ndeath; m++)    fx=func(x);
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    for (k=1; k<=2; k++) {
         if(i <= (int) agemax)      for (i=1;i<=npar;i++) p2[i]=x[i];
           fprintf(ficresp,"\n");      p2[thetai]=x[thetai]+delti[thetai]/k;
         printf("\n");      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       }      k1=func(p2)-fx;
     }    
   }      p2[thetai]=x[thetai]+delti[thetai]/k;
   dateintmean=dateintsum/k2cpt;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
        k2=func(p2)-fx;
   fclose(ficresp);    
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      p2[thetai]=x[thetai]-delti[thetai]/k;
   free_vector(pp,1,nlstate);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
        k3=func(p2)-fx;
   /* End of Freq */    
 }      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 /************ Prevalence ********************/      k4=func(p2)-fx;
 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)      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
 {  /* Some frequencies */  #ifdef DEBUG
        printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   double ***freq; /* Frequencies */  #endif
   double *pp;    }
   double pos, k2;    return res;
   }
   pp=vector(1,nlstate);  
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  /************** Inverse of matrix **************/
    void ludcmp(double **a, int n, int *indx, double *d) 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  { 
   j1=0;    int i,imax,j,k; 
      double big,dum,sum,temp; 
   j=cptcoveff;    double *vv; 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}   
      vv=vector(1,n); 
  for(k1=1; k1<=j;k1++){    *d=1.0; 
     for(i1=1; i1<=ncodemax[k1];i1++){    for (i=1;i<=n;i++) { 
       j1++;      big=0.0; 
        for (j=1;j<=n;j++) 
       for (i=-1; i<=nlstate+ndeath; i++)          if ((temp=fabs(a[i][j])) > big) big=temp; 
         for (jk=-1; jk<=nlstate+ndeath; jk++)        if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
           for(m=agemin; m <= agemax+3; m++)      vv[i]=1.0/big; 
             freq[i][jk][m]=0;    } 
          for (j=1;j<=n;j++) { 
       for (i=1; i<=imx; i++) {      for (i=1;i<j;i++) { 
         bool=1;        sum=a[i][j]; 
         if  (cptcovn>0) {        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
           for (z1=1; z1<=cptcoveff; z1++)        a[i][j]=sum; 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      } 
               bool=0;      big=0.0; 
         }      for (i=j;i<=n;i++) { 
         if (bool==1) {        sum=a[i][j]; 
           for(m=firstpass; m<=lastpass; m++){        for (k=1;k<j;k++) 
             k2=anint[m][i]+(mint[m][i]/12.);          sum -= a[i][k]*a[k][j]; 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        a[i][j]=sum; 
               if(agev[m][i]==0) agev[m][i]=agemax+1;        if ( (dum=vv[i]*fabs(sum)) >= big) { 
               if(agev[m][i]==1) agev[m][i]=agemax+2;          big=dum; 
               if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          imax=i; 
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */        } 
             }      } 
           }      if (j != imax) { 
         }        for (k=1;k<=n;k++) { 
       }          dum=a[imax][k]; 
         for(i=(int)agemin; i <= (int)agemax+3; i++){          a[imax][k]=a[j][k]; 
           for(jk=1; jk <=nlstate ; jk++){          a[j][k]=dum; 
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        } 
               pp[jk] += freq[jk][m][i];        *d = -(*d); 
           }        vv[imax]=vv[j]; 
           for(jk=1; jk <=nlstate ; jk++){      } 
             for(m=-1, pos=0; m <=0 ; m++)      indx[j]=imax; 
             pos += freq[jk][m][i];      if (a[j][j] == 0.0) a[j][j]=TINY; 
         }      if (j != n) { 
                dum=1.0/(a[j][j]); 
          for(jk=1; jk <=nlstate ; jk++){        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      } 
              pp[jk] += freq[jk][m][i];    } 
          }    free_vector(vv,1,n);  /* Doesn't work */
            ;
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];  } 
   
          for(jk=1; jk <=nlstate ; jk++){            void lubksb(double **a, int n, int *indx, double b[]) 
            if( i <= (int) agemax){  { 
              if(pos>=1.e-5){    int i,ii=0,ip,j; 
                probs[i][jk][j1]= pp[jk]/pos;    double sum; 
              }   
            }    for (i=1;i<=n;i++) { 
          }      ip=indx[i]; 
                sum=b[ip]; 
         }      b[ip]=b[i]; 
     }      if (ii) 
   }        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
        else if (sum) ii=i; 
        b[i]=sum; 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    } 
   free_vector(pp,1,nlstate);    for (i=n;i>=1;i--) { 
        sum=b[i]; 
 }  /* End of Freq */      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       b[i]=sum/a[i][i]; 
 /************* Waves Concatenation ***************/    } 
   } 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  
 {  /************ Frequencies ********************/
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
      Death is a valid wave (if date is known).  {  /* Some frequencies */
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
      and mw[mi+1][i]. dh depends on stepm.    int first;
      */    double ***freq; /* Frequencies */
     double *pp;
   int i, mi, m;    double pos, k2, dateintsum=0,k2cpt=0;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    FILE *ficresp;
      double sum=0., jmean=0.;*/    char fileresp[FILENAMELENGTH];
     
   int j, k=0,jk, ju, jl;    pp=vector(1,nlstate);
   double sum=0.;    probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   jmin=1e+5;    strcpy(fileresp,"p");
   jmax=-1;    strcat(fileresp,fileres);
   jmean=0.;    if((ficresp=fopen(fileresp,"w"))==NULL) {
   for(i=1; i<=imx; i++){      printf("Problem with prevalence resultfile: %s\n", fileresp);
     mi=0;      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     m=firstpass;      exit(0);
     while(s[m][i] <= nlstate){    }
       if(s[m][i]>=1)    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
         mw[++mi][i]=m;    j1=0;
       if(m >=lastpass)    
         break;    j=cptcoveff;
       else    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         m++;  
     }/* end while */    first=1;
     if (s[m][i] > nlstate){  
       mi++;     /* Death is another wave */    for(k1=1; k1<=j;k1++){
       /* if(mi==0)  never been interviewed correctly before death */      for(i1=1; i1<=ncodemax[k1];i1++){
          /* Only death is a correct wave */        j1++;
       mw[mi][i]=m;        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     }          scanf("%d", i);*/
         for (i=-1; i<=nlstate+ndeath; i++)  
     wav[i]=mi;          for (jk=-1; jk<=nlstate+ndeath; jk++)  
     if(mi==0)            for(m=agemin; m <= agemax+3; m++)
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);              freq[i][jk][m]=0;
   }        
         dateintsum=0;
   for(i=1; i<=imx; i++){        k2cpt=0;
     for(mi=1; mi<wav[i];mi++){        for (i=1; i<=imx; i++) {
       if (stepm <=0)          bool=1;
         dh[mi][i]=1;          if  (cptcovn>0) {
       else{            for (z1=1; z1<=cptcoveff; z1++) 
         if (s[mw[mi+1][i]][i] > nlstate) {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
           if (agedc[i] < 2*AGESUP) {                bool=0;
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          }
           if(j==0) j=1;  /* Survives at least one month after exam */          if (bool==1){
           k=k+1;            for(m=firstpass; m<=lastpass; m++){
           if (j >= jmax) jmax=j;              k2=anint[m][i]+(mint[m][i]/12.);
           if (j <= jmin) jmin=j;              if ((k2>=dateprev1) && (k2<=dateprev2)) {
           sum=sum+j;                if(agev[m][i]==0) agev[m][i]=agemax+1;
           /*if (j<0) printf("j=%d num=%d \n",j,i); */                if(agev[m][i]==1) agev[m][i]=agemax+2;
           }                if (m<lastpass) {
         }                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
         else{                  freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));                }
           k=k+1;                
           if (j >= jmax) jmax=j;                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
           else if (j <= jmin)jmin=j;                  dateintsum=dateintsum+k2;
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */                  k2cpt++;
           sum=sum+j;                }
         }              }
         jk= j/stepm;            }
         jl= j -jk*stepm;          }
         ju= j -(jk+1)*stepm;        }
         if(jl <= -ju)         
           dh[mi][i]=jk;        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
         else  
           dh[mi][i]=jk+1;        if  (cptcovn>0) {
         if(dh[mi][i]==0)          fprintf(ficresp, "\n#********** Variable "); 
           dh[mi][i]=1; /* At least one step */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       }          fprintf(ficresp, "**********\n#");
     }        }
   }        for(i=1; i<=nlstate;i++) 
   jmean=sum/k;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        fprintf(ficresp, "\n");
  }        
 /*********** Tricode ****************************/        for(i=(int)agemin; i <= (int)agemax+3; i++){
 void tricode(int *Tvar, int **nbcode, int imx)          if(i==(int)agemax+3){
 {            fprintf(ficlog,"Total");
   int Ndum[20],ij=1, k, j, i;          }else{
   int cptcode=0;            if(first==1){
   cptcoveff=0;              first=0;
                printf("See log file for details...\n");
   for (k=0; k<19; k++) Ndum[k]=0;            }
   for (k=1; k<=7; k++) ncodemax[k]=0;            fprintf(ficlog,"Age %d", i);
           }
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          for(jk=1; jk <=nlstate ; jk++){
     for (i=1; i<=imx; i++) {            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       ij=(int)(covar[Tvar[j]][i]);              pp[jk] += freq[jk][m][i]; 
       Ndum[ij]++;          }
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          for(jk=1; jk <=nlstate ; jk++){
       if (ij > cptcode) cptcode=ij;            for(m=-1, pos=0; m <=0 ; m++)
     }              pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
     for (i=0; i<=cptcode; i++) {              if(first==1){
       if(Ndum[i]!=0) ncodemax[j]++;              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     }              }
     ij=1;              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             }else{
               if(first==1)
     for (i=1; i<=ncodemax[j]; i++) {                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       for (k=0; k<=19; k++) {              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         if (Ndum[k] != 0) {            }
           nbcode[Tvar[j]][ij]=k;          }
           /*     printf("nbcodeaaaaaaaaaaa=%d Tvar[j]=%d ij=%d j=%d",nbcode[Tvar[j]][ij],Tvar[j],ij,j);*/  
           ij++;          for(jk=1; jk <=nlstate ; jk++){
         }            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
         if (ij > ncodemax[j]) break;              pp[jk] += freq[jk][m][i];
       }            }
     }  
   }            for(jk=1,pos=0; jk <=nlstate ; jk++)
             pos += pp[jk];
  for (k=0; k<19; k++) Ndum[k]=0;          for(jk=1; jk <=nlstate ; jk++){
             if(pos>=1.e-5){
  for (i=1; i<=ncovmodel-2; i++) {              if(first==1)
       ij=Tvar[i];                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       Ndum[ij]++;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     }            }else{
               if(first==1)
  ij=1;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
  for (i=1; i<=10; i++) {              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
    if((Ndum[i]!=0) && (i<=ncovcol)){            }
      Tvaraff[ij]=i;            if( i <= (int) agemax){
      ij++;              if(pos>=1.e-5){
    }                fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
  }                probs[i][jk][j1]= pp[jk]/pos;
                  /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     cptcoveff=ij-1;              }
 }              else
                 fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
 /*********** Health Expectancies ****************/            }
           }
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)          
 {          for(jk=-1; jk <=nlstate+ndeath; jk++)
   /* Health expectancies */            for(m=-1; m <=nlstate+ndeath; m++)
   int i, j, nhstepm, hstepm, h, nstepm, k;              if(freq[jk][m][i] !=0 ) {
   double age, agelim, hf;              if(first==1)
   double ***p3mat;                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                  fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   fprintf(ficreseij,"# Health expectancies\n");              }
   fprintf(ficreseij,"# Age");          if(i <= (int) agemax)
   for(i=1; i<=nlstate;i++)            fprintf(ficresp,"\n");
     for(j=1; j<=nlstate;j++)          if(first==1)
       fprintf(ficreseij," %1d-%1d",i,j);            printf("Others in log...\n");
   fprintf(ficreseij,"\n");          fprintf(ficlog,"\n");
         }
   k=1;             /* For example stepm=6 months */      }
   hstepm=k*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */    }
   hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */    dateintmean=dateintsum/k2cpt; 
   /* 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    fclose(ficresp);
      nstepm is the number of stepm from age to agelin.    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
      Look at hpijx to understand the reason of that which relies in memory size    free_vector(pp,1,nlstate);
      and note for a fixed period like k years */    
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    /* End of Freq */
      survival function given by stepm (the optimization length). Unfortunately it  }
      means that if the survival funtion is printed only each two years of age and if  
      you sum them up and add 1 year (area under the trapezoids) you won't get the same  /************ Prevalence ********************/
      results. So we changed our mind and took the option of the best precision.  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 */
   hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */   
     int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   agelim=AGESUP;    double ***freq; /* Frequencies */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    double *pp;
     /* nhstepm age range expressed in number of stepm */    double pos, k2;
     nstepm=(int) rint((agelim-age)*YEARM/stepm);  
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    pp=vector(1,nlstate);
     /* if (stepm >= YEARM) hstepm=1;*/    
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    j1=0;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    j=cptcoveff;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      if (cptcovn<1) {j=1;ncodemax[1]=1;}
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    
     for(i=1; i<=nlstate;i++)    for(k1=1; k1<=j;k1++){
       for(j=1; j<=nlstate;j++)      for(i1=1; i1<=ncodemax[k1];i1++){
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){        j1++;
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;        
           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/        for (i=-1; i<=nlstate+ndeath; i++)  
         }          for (jk=-1; jk<=nlstate+ndeath; jk++)  
     fprintf(ficreseij,"%3.0f",age );            for(m=agemin; m <= agemax+3; m++)
     for(i=1; i<=nlstate;i++)              freq[i][jk][m]=0;
       for(j=1; j<=nlstate;j++){       
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);        for (i=1; i<=imx; i++) {
       }          bool=1;
     fprintf(ficreseij,"\n");          if  (cptcovn>0) {
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for (z1=1; z1<=cptcoveff; z1++) 
   }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
 }                bool=0;
           } 
 /************ Variance ******************/          if (bool==1) { 
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)            for(m=firstpass; m<=lastpass; m++){
 {              k2=anint[m][i]+(mint[m][i]/12.);
   /* Variance of health expectancies */              if ((k2>=dateprev1) && (k2<=dateprev2)) {
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/                if(agev[m][i]==0) agev[m][i]=agemax+1;
   double **newm;                if(agev[m][i]==1) agev[m][i]=agemax+2;
   double **dnewm,**doldm;                if (m<lastpass) {
   int i, j, nhstepm, hstepm, h, nstepm, kk;                  if (calagedate>0) 
   int k, cptcode;                    freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
   double *xp;                  else
   double **gp, **gm;                    freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   double ***gradg, ***trgradg;                  freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; 
   double ***p3mat;                }
   double age,agelim, hf;              }
   int theta;            }
           }
    fprintf(ficresvij,"# Covariances of life expectancies\n");        }
   fprintf(ficresvij,"# Age");        for(i=(int)agemin; i <= (int)agemax+3; i++){ 
   for(i=1; i<=nlstate;i++)          for(jk=1; jk <=nlstate ; jk++){
     for(j=1; j<=nlstate;j++)            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);              pp[jk] += freq[jk][m][i]; 
   fprintf(ficresvij,"\n");          }
           for(jk=1; jk <=nlstate ; jk++){
   xp=vector(1,npar);            for(m=-1, pos=0; m <=0 ; m++)
   dnewm=matrix(1,nlstate,1,npar);              pos += freq[jk][m][i];
   doldm=matrix(1,nlstate,1,nlstate);          }
            
   kk=1;             /* For example stepm=6 months */          for(jk=1; jk <=nlstate ; jk++){
   hstepm=kk*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */              pp[jk] += freq[jk][m][i];
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.          }
      nhstepm is the number of hstepm from age to agelim          
      nstepm is the number of stepm from age to agelin.          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
      Look at hpijx to understand the reason of that which relies in memory size          
      and note for a fixed period like k years */          for(jk=1; jk <=nlstate ; jk++){    
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the            if( i <= (int) agemax){
      survival function given by stepm (the optimization length). Unfortunately it              if(pos>=1.e-5){
      means that if the survival funtion is printed only each two years of age and if                probs[i][jk][j1]= pp[jk]/pos;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same              }
      results. So we changed our mind and took the option of the best precision.            }
   */          }/* end jk */
   hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */        }/* end i */
   agelim = AGESUP;      } /* end i1 */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    } /* end k1 */
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    free_vector(pp,1,nlstate);
     gp=matrix(0,nhstepm,1,nlstate);    
     gm=matrix(0,nhstepm,1,nlstate);  }  /* End of Freq */
   
     for(theta=1; theta <=npar; theta++){  /************* Waves Concatenation ***************/
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
       }  {
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);       Death is a valid wave (if date is known).
        mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
       if (popbased==1) {       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
         for(i=1; i<=nlstate;i++)       and mw[mi+1][i]. dh depends on stepm.
           prlim[i][i]=probs[(int)age][i][ij];       */
       }  
      int i, mi, m;
       for(j=1; j<= nlstate; j++){    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
         for(h=0; h<=nhstepm; h++){       double sum=0., jmean=0.;*/
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    int first;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    int j, k=0,jk, ju, jl;
         }    double sum=0.;
       }    first=0;
        jmin=1e+5;
       for(i=1; i<=npar; i++) /* Computes gradient */    jmax=-1;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    jmean=0.;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      for(i=1; i<=imx; i++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      mi=0;
        m=firstpass;
       if (popbased==1) {      while(s[m][i] <= nlstate){
         for(i=1; i<=nlstate;i++)        if(s[m][i]>=1)
           prlim[i][i]=probs[(int)age][i][ij];          mw[++mi][i]=m;
       }        if(m >=lastpass)
           break;
       for(j=1; j<= nlstate; j++){        else
         for(h=0; h<=nhstepm; h++){          m++;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      }/* end while */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];      if (s[m][i] > nlstate){
         }        mi++;     /* Death is another wave */
       }        /* if(mi==0)  never been interviewed correctly before death */
            /* Only death is a correct wave */
       for(j=1; j<= nlstate; j++)        mw[mi][i]=m;
         for(h=0; h<=nhstepm; h++){      }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  
         }      wav[i]=mi;
     } /* End theta */      if(mi==0){
         if(first==0){
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
           first=1;
     for(h=0; h<=nhstepm; h++)        }
       for(j=1; j<=nlstate;j++)        if(first==1){
         for(theta=1; theta <=npar; theta++)          fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
           trgradg[h][j][theta]=gradg[h][theta][j];        }
       } /* end mi==0 */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    }
     for(i=1;i<=nlstate;i++)  
       for(j=1;j<=nlstate;j++)    for(i=1; i<=imx; i++){
         vareij[i][j][(int)age] =0.;      for(mi=1; mi<wav[i];mi++){
         if (stepm <=0)
     for(h=0;h<=nhstepm;h++){          dh[mi][i]=1;
       for(k=0;k<=nhstepm;k++){        else{
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          if (s[mw[mi+1][i]][i] > nlstate) {
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);            if (agedc[i] < 2*AGESUP) {
         for(i=1;i<=nlstate;i++)            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
           for(j=1;j<=nlstate;j++)            if(j==0) j=1;  /* Survives at least one month after exam */
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;            k=k+1;
       }            if (j >= jmax) jmax=j;
     }            if (j <= jmin) jmin=j;
             sum=sum+j;
     fprintf(ficresvij,"%.0f ",age );            /*if (j<0) printf("j=%d num=%d \n",j,i); */
     for(i=1; i<=nlstate;i++)            }
       for(j=1; j<=nlstate;j++){          }
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);          else{
       }            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     fprintf(ficresvij,"\n");            k=k+1;
     free_matrix(gp,0,nhstepm,1,nlstate);            if (j >= jmax) jmax=j;
     free_matrix(gm,0,nhstepm,1,nlstate);            else if (j <= jmin)jmin=j;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);            sum=sum+j;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
   } /* End age */          jk= j/stepm;
            jl= j -jk*stepm;
   free_vector(xp,1,npar);          ju= j -(jk+1)*stepm;
   free_matrix(doldm,1,nlstate,1,npar);          if(mle <=1){ 
   free_matrix(dnewm,1,nlstate,1,nlstate);            if(jl==0){
               dh[mi][i]=jk;
 }              bh[mi][i]=0;
             }else{ /* We want a negative bias in order to only have interpolation ie
 /************ Variance of prevlim ******************/                    * at the price of an extra matrix product in likelihood */
 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)              dh[mi][i]=jk+1;
 {              bh[mi][i]=ju;
   /* Variance of prevalence limit */            }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          }else{
   double **newm;            if(jl <= -ju){
   double **dnewm,**doldm;              dh[mi][i]=jk;
   int i, j, nhstepm, hstepm;              bh[mi][i]=jl;       /* bias is positive if real duration
   int k, cptcode;                                   * is higher than the multiple of stepm and negative otherwise.
   double *xp;                                   */
   double *gp, *gm;            }
   double **gradg, **trgradg;            else{
   double age,agelim;              dh[mi][i]=jk+1;
   int theta;              bh[mi][i]=ju;
                }
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");            if(dh[mi][i]==0){
   fprintf(ficresvpl,"# Age");              dh[mi][i]=1; /* At least one step */
   for(i=1; i<=nlstate;i++)              bh[mi][i]=ju; /* At least one step */
       fprintf(ficresvpl," %1d-%1d",i,i);              printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);
   fprintf(ficresvpl,"\n");            }
             if(i==298 || i==287 || i==763 ||i==1061)printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d",bh[mi][i],ju,jl,dh[mi][i],jk,stepm);
   xp=vector(1,npar);          }
   dnewm=matrix(1,nlstate,1,npar);        } /* end if mle */
   doldm=matrix(1,nlstate,1,nlstate);      } /* end wave */
      }
   hstepm=1*YEARM; /* Every year of age */    jmean=sum/k;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   agelim = AGESUP;    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */   }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  
     if (stepm >= YEARM) hstepm=1;  /*********** Tricode ****************************/
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  void tricode(int *Tvar, int **nbcode, int imx)
     gradg=matrix(1,npar,1,nlstate);  {
     gp=vector(1,nlstate);    
     gm=vector(1,nlstate);    int Ndum[20],ij=1, k, j, i, maxncov=19;
     int cptcode=0;
     for(theta=1; theta <=npar; theta++){    cptcoveff=0; 
       for(i=1; i<=npar; i++){ /* Computes gradient */   
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    for (k=0; k<maxncov; k++) Ndum[k]=0;
       }    for (k=1; k<=7; k++) ncodemax[k]=0;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
         gp[i] = prlim[i][i];      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                     modality*/ 
       for(i=1; i<=npar; i++) /* Computes gradient */        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        Ndum[ij]++; /*store the modality */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       for(i=1;i<=nlstate;i++)        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
         gm[i] = prlim[i][i];                                         Tvar[j]. If V=sex and male is 0 and 
                                          female is 1, then  cptcode=1.*/
       for(i=1;i<=nlstate;i++)      }
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];  
     } /* End theta */      for (i=0; i<=cptcode; i++) {
         if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
     trgradg =matrix(1,nlstate,1,npar);      }
   
     for(j=1; j<=nlstate;j++)      ij=1; 
       for(theta=1; theta <=npar; theta++)      for (i=1; i<=ncodemax[j]; i++) {
         trgradg[j][theta]=gradg[theta][j];        for (k=0; k<= maxncov; k++) {
           if (Ndum[k] != 0) {
     for(i=1;i<=nlstate;i++)            nbcode[Tvar[j]][ij]=k; 
       varpl[i][(int)age] =0.;            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);            
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);            ij++;
     for(i=1;i<=nlstate;i++)          }
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          if (ij > ncodemax[j]) break; 
         }  
     fprintf(ficresvpl,"%.0f ",age );      } 
     for(i=1; i<=nlstate;i++)    }  
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  
     fprintf(ficresvpl,"\n");   for (k=0; k< maxncov; k++) Ndum[k]=0;
     free_vector(gp,1,nlstate);  
     free_vector(gm,1,nlstate);   for (i=1; i<=ncovmodel-2; i++) { 
     free_matrix(gradg,1,npar,1,nlstate);     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     free_matrix(trgradg,1,nlstate,1,npar);     ij=Tvar[i];
   } /* End age */     Ndum[ij]++;
    }
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);   ij=1;
   free_matrix(dnewm,1,nlstate,1,nlstate);   for (i=1; i<= maxncov; i++) {
      if((Ndum[i]!=0) && (i<=ncovcol)){
 }       Tvaraff[ij]=i; /*For printing */
        ij++;
 /************ Variance of one-step probabilities  ******************/     }
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)   }
 {   
   int i, j;   cptcoveff=ij-1; /*Number of simple covariates*/
   int k=0, cptcode;  }
   double **dnewm,**doldm;  
   double *xp;  /*********** Health Expectancies ****************/
   double *gp, *gm;  
   double **gradg, **trgradg;  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 )
   double age,agelim, cov[NCOVMAX];  
   int theta;  {
   char fileresprob[FILENAMELENGTH];    /* Health expectancies */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
   strcpy(fileresprob,"prob");    double age, agelim, hf;
   strcat(fileresprob,fileres);    double ***p3mat,***varhe;
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    double **dnewm,**doldm;
     printf("Problem with resultfile: %s\n", fileresprob);    double *xp;
   }    double **gp, **gm;
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);    double ***gradg, ***trgradg;
      int theta;
   
   xp=vector(1,npar);    varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    xp=vector(1,npar);
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    dnewm=matrix(1,nlstate*2,1,npar);
      doldm=matrix(1,nlstate*2,1,nlstate*2);
   cov[1]=1;    
   for (age=bage; age<=fage; age ++){    fprintf(ficreseij,"# Health expectancies\n");
     cov[2]=age;    fprintf(ficreseij,"# Age");
     gradg=matrix(1,npar,1,9);    for(i=1; i<=nlstate;i++)
     trgradg=matrix(1,9,1,npar);      for(j=1; j<=nlstate;j++)
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        fprintf(ficreseij," %1d-%1d (SE)",i,j);
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    fprintf(ficreseij,"\n");
      
     for(theta=1; theta <=npar; theta++){    if(estepm < stepm){
       for(i=1; i<=npar; i++)      printf ("Problem %d lower than %d\n",estepm, stepm);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    }
          else  hstepm=estepm;   
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    /* We compute the life expectancy from trapezoids spaced every estepm months
         * This is mainly to measure the difference between two models: for example
       k=0;     * if stepm=24 months pijx are given only every 2 years and by summing them
       for(i=1; i<= (nlstate+ndeath); i++){     * we are calculating an estimate of the Life Expectancy assuming a linear 
         for(j=1; j<=(nlstate+ndeath);j++){     * progression inbetween and thus overestimating or underestimating according
            k=k+1;     * to the curvature of the survival function. If, for the same date, we 
           gp[k]=pmmij[i][j];     * 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(i=1; i<=npar; i++)  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    /* For example we decided to compute the life expectancy with the smallest unit */
        /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);       nstepm is the number of stepm from age to agelin. 
       k=0;       Look at hpijx to understand the reason of that which relies in memory size
       for(i=1; i<=(nlstate+ndeath); i++){       and note for a fixed period like estepm months */
         for(j=1; j<=(nlstate+ndeath);j++){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           k=k+1;       survival function given by stepm (the optimization length). Unfortunately it
           gm[k]=pmmij[i][j];       means that if the survival funtion is printed only each two years of age and if
         }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       }       results. So we changed our mind and took the option of the best precision.
          */
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];    
     }    agelim=AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)      /* nhstepm age range expressed in number of stepm */
       for(theta=1; theta <=npar; theta++)      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
       trgradg[j][theta]=gradg[theta][j];      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
        /* if (stepm >= YEARM) hstepm=1;*/
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
      pmij(pmmij,cov,ncovmodel,x,nlstate);      gp=matrix(0,nhstepm,1,nlstate*2);
       gm=matrix(0,nhstepm,1,nlstate*2);
      k=0;  
      for(i=1; i<=(nlstate+ndeath); i++){      /* Computed by stepm unit matrices, product of hstepm matrices, stored
        for(j=1; j<=(nlstate+ndeath);j++){         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
          k=k+1;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
          gm[k]=pmmij[i][j];   
         }  
      }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
        
      /*printf("\n%d ",(int)age);      /* Computing Variances of health expectancies */
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){  
               for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));          xp[i] = x[i] + (i==theta ?delti[theta]:0);
      }*/        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   fprintf(ficresprob,"\n%d ",(int)age);    
         cptj=0;
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        for(j=1; j<= nlstate; j++){
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);          for(i=1; i<=nlstate; i++){
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);            cptj=cptj+1;
   }            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
               gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));            }
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));          }
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        }
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);       
 }       
  free_vector(xp,1,npar);        for(i=1; i<=npar; i++) 
 fclose(ficresprob);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 }        
         cptj=0;
 /******************* Printing html file ***********/        for(j=1; j<= nlstate; j++){
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \          for(i=1;i<=nlstate;i++){
  int lastpass, int stepm, int weightopt, char model[],\            cptj=cptj+1;
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
  char version[], int popforecast ){            }
   int jj1, k1, i1, cpt;          }
   FILE *fichtm;        }
   /*char optionfilehtm[FILENAMELENGTH];*/        for(j=1; j<= nlstate*2; j++)
           for(h=0; h<=nhstepm-1; h++){
   strcpy(optionfilehtm,optionfile);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   strcat(optionfilehtm,".htm");          }
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {       } 
     printf("Problem with %s \n",optionfilehtm), exit(0);     
   }  /* End theta */
   
  fprintf(fichtm,"<body> <font size=\"2\">Imach, Version %s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n       trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n  
 \n       for(h=0; h<=nhstepm-1; h++)
 Total number of observations=%d <br>\n        for(j=1; j<=nlstate*2;j++)
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n          for(theta=1; theta <=npar; theta++)
 <hr  size=\"2\" color=\"#EC5E5E\">            trgradg[h][j][theta]=gradg[h][theta][j];
  <ul><li>Outputs files<br>\n       
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n  
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n       for(i=1;i<=nlstate*2;i++)
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n        for(j=1;j<=nlstate*2;j++)
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n          varhe[i][j][(int)age] =0.;
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n  
  - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);       printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
  fprintf(fichtm,"\n       for(h=0;h<=nhstepm-1;h++){
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n        for(k=0;k<=nhstepm-1;k++){
  - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>\n          matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n          matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres);          for(i=1;i<=nlstate*2;i++)
             for(j=1;j<=nlstate*2;j++)
  if(popforecast==1) fprintf(fichtm,"\n              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
  - 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);      /* Computing expectancies */
  else      for(i=1; i<=nlstate;i++)
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);        for(j=1; j<=nlstate;j++)
 fprintf(fichtm," <li>Graphs</li><p>");          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
  m=cptcoveff;            
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  /* 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]);*/
   
  jj1=0;          }
  for(k1=1; k1<=m;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){      fprintf(ficreseij,"%3.0f",age );
        jj1++;      cptj=0;
        if (cptcovn > 0) {      for(i=1; i<=nlstate;i++)
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        for(j=1; j<=nlstate;j++){
          for (cpt=1; cpt<=cptcoveff;cpt++)          cptj++;
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");        }
        }      fprintf(ficreseij,"\n");
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>     
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          free_matrix(gm,0,nhstepm,1,nlstate*2);
        for(cpt=1; cpt<nlstate;cpt++){      free_matrix(gp,0,nhstepm,1,nlstate*2);
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
        }      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    printf("\n");
 interval) in state (%d): v%s%d%d.gif <br>    fprintf(ficlog,"\n");
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    
      }    free_vector(xp,1,npar);
      for(cpt=1; cpt<=nlstate;cpt++) {    free_matrix(dnewm,1,nlstate*2,1,npar);
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    free_matrix(doldm,1,nlstate*2,1,nlstate*2);
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
      }  }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and  
 health expectancies in states (1) and (2): e%s%d.gif<br>  /************ Variance ******************/
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);  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)
 fprintf(fichtm,"\n</body>");  {
    }    /* Variance of health expectancies */
    }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
 fclose(fichtm);    /* double **newm;*/
 }    double **dnewm,**doldm;
     double **dnewmp,**doldmp;
 /******************* Gnuplot file **************/    int i, j, nhstepm, hstepm, h, nstepm ;
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){    int k, cptcode;
     double *xp;
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
   strcpy(optionfilegnuplot,optionfilefiname);    double **gradgp, **trgradgp; /* for var p point j */
   strcat(optionfilegnuplot,".gp.txt");    double *gpp, *gmp; /* for var p point j */
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     printf("Problem with file %s",optionfilegnuplot);    double ***p3mat;
   }    double age,agelim, hf;
     double ***mobaverage;
 #ifdef windows    int theta;
     fprintf(ficgp,"cd \"%s\" \n",pathc);    char digit[4];
 #endif    char digitp[25];
 m=pow(2,cptcoveff);  
      char fileresprobmorprev[FILENAMELENGTH];
  /* 1eme*/  
   for (cpt=1; cpt<= nlstate ; cpt ++) {    if(popbased==1){
    for (k1=1; k1<= m ; k1 ++) {      if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
 #ifdef windows      else strcpy(digitp,"-populbased-nomobil-");
     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);    }
 #endif    else 
 #ifdef unix      strcpy(digitp,"-stablbased-");
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);  
 #endif    if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 for (i=1; i<= nlstate ; i ++) {      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   else fprintf(ficgp," \%%*lf (\%%*lf)");        printf(" Error in movingaverage mobilav=%d\n",mobilav);
 }      }
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    }
     for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    strcpy(fileresprobmorprev,"prmorprev"); 
   else fprintf(ficgp," \%%*lf (\%%*lf)");    sprintf(digit,"%-d",ij);
 }    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
      for (i=1; i<= nlstate ; i ++) {    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    strcat(fileresprobmorprev,fileres);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
 }        printf("Problem with resultfile: %s\n", fileresprobmorprev);
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
 #ifdef unix    }
 fprintf(ficgp,"\nset ter gif small size 400,300");    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
 #endif    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");
    }    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   }    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   /*2 eme*/      fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
   for (k1=1; k1<= m ; k1 ++) {        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);    }  
        fprintf(ficresprobmorprev,"\n");
     for (i=1; i<= nlstate+1 ; i ++) {    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       k=2*i;      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
       for (j=1; j<= nlstate+1 ; j ++) {      exit(0);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    }
   else fprintf(ficgp," \%%*lf (\%%*lf)");    else{
 }        fprintf(ficgp,"\n# Routine varevsij");
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    }
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);      printf("Problem with html file: %s\n", optionfilehtm);
       for (j=1; j<= nlstate+1 ; j ++) {      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      exit(0);
         else fprintf(ficgp," \%%*lf (\%%*lf)");    }
 }      else{
       fprintf(ficgp,"\" t\"\" w l 0,");      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(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      fprintf(fichtm,"\n<br>%s (à revoir) <br>\n",digitp);
       for (j=1; j<= nlstate+1 ; j ++) {    }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      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");
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    fprintf(ficresvij,"# Age");
       else fprintf(ficgp,"\" t\"\" w l 0,");    for(i=1; i<=nlstate;i++)
     }      for(j=1; j<=nlstate;j++)
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   }    fprintf(ficresvij,"\n");
    
   /*3eme*/    xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
   for (k1=1; k1<= m ; k1 ++) {    doldm=matrix(1,nlstate,1,nlstate);
     for (cpt=1; cpt<= nlstate ; cpt ++) {    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
       k=2+nlstate*(cpt-1);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);  
       for (i=1; i< nlstate ; i ++) {    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);    gpp=vector(nlstate+1,nlstate+ndeath);
       }    gmp=vector(nlstate+1,nlstate+ndeath);
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     }    
     }    if(estepm < stepm){
        printf ("Problem %d lower than %d\n",estepm, stepm);
   /* CV preval stat */    }
     for (k1=1; k1<= m ; k1 ++) {    else  hstepm=estepm;   
     for (cpt=1; cpt<nlstate ; cpt ++) {    /* For example we decided to compute the life expectancy with the smallest unit */
       k=3;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
       for (i=1; i< nlstate ; i ++)       Look at hpijx to understand the reason of that which relies in memory size
         fprintf(ficgp,"+$%d",k+i+1);       and note for a fixed period like k years */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
             survival function given by stepm (the optimization length). Unfortunately it
       l=3+(nlstate+ndeath)*cpt;       means that if the survival funtion is printed only each two years of age and if
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       for (i=1; i< nlstate ; i ++) {       results. So we changed our mind and took the option of the best precision.
         l=3+(nlstate+ndeath)*cpt;    */
         fprintf(ficgp,"+$%d",l+i+1);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       }    agelim = AGESUP;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     }      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   }        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   /* proba elementaires */      gp=matrix(0,nhstepm,1,nlstate);
    for(i=1,jk=1; i <=nlstate; i++){      gm=matrix(0,nhstepm,1,nlstate);
     for(k=1; k <=(nlstate+ndeath); k++){  
       if (k != i) {  
         for(j=1; j <=ncovmodel; j++){      for(theta=1; theta <=npar; theta++){
                for(i=1; i<=npar; i++){ /* Computes gradient */
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           jk++;        }
           fprintf(ficgp,"\n");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       }  
     }        if (popbased==1) {
     }          if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
     for(jk=1; jk <=m; jk++) {              prlim[i][i]=probs[(int)age][i][ij];
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);          }else{ /* mobilav */ 
    i=1;            for(i=1; i<=nlstate;i++)
    for(k2=1; k2<=nlstate; k2++) {              prlim[i][i]=mobaverage[(int)age][i][ij];
      k3=i;          }
      for(k=1; k<=(nlstate+ndeath); k++) {        }
        if (k != k2){    
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);        for(j=1; j<= nlstate; j++){
 ij=1;          for(h=0; h<=nhstepm; h++){
         for(j=3; j <=ncovmodel; j++) {            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          }
             ij++;        }
           }        /* This for computing forces of mortality (h=1)as a weighted average */
           else        for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          for(i=1; i<= nlstate; i++)
         }            gpp[j] += prlim[i][i]*p3mat[i][j][1];
           fprintf(ficgp,")/(1");        }    
                /* end force of mortality */
         for(k1=1; k1 <=nlstate; k1++){    
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);        for(i=1; i<=npar; i++) /* Computes gradient */
 ij=1;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           for(j=3; j <=ncovmodel; j++){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);   
             ij++;        if (popbased==1) {
           }          if(mobilav ==0){
           else            for(i=1; i<=nlstate;i++)
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              prlim[i][i]=probs[(int)age][i][ij];
           }          }else{ /* mobilav */ 
           fprintf(ficgp,")");            for(i=1; i<=nlstate;i++)
         }              prlim[i][i]=mobaverage[(int)age][i][ij];
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);          }
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");        }
         i=i+ncovmodel;  
        }        for(j=1; j<= nlstate; j++){
      }          for(h=0; h<=nhstepm; h++){
    }            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
    }          }
            }
   fclose(ficgp);        /* This for computing force of mortality (h=1)as a weighted average */
 }  /* end gnuplot */        for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
           for(i=1; i<= nlstate; i++)
             gmp[j] += prlim[i][i]*p3mat[i][j][1];
 /*************** Moving average **************/        }    
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){        /* end force of mortality */
   
   int i, cpt, cptcod;        for(j=1; j<= nlstate; j++) /* vareij */
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)          for(h=0; h<=nhstepm; h++){
       for (i=1; i<=nlstate;i++)            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          }
           mobaverage[(int)agedeb][i][cptcod]=0.;        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
              gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){        }
       for (i=1; i<=nlstate;i++){  
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      } /* End theta */
           for (cpt=0;cpt<=4;cpt++){  
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
           }  
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;      for(h=0; h<=nhstepm; h++) /* veij */
         }        for(j=1; j<=nlstate;j++)
       }          for(theta=1; theta <=npar; theta++)
     }            trgradg[h][j][theta]=gradg[h][theta][j];
      
 }      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
 /************** Forecasting ******************/  
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
        for(i=1;i<=nlstate;i++)
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        for(j=1;j<=nlstate;j++)
   int *popage;          vareij[i][j][(int)age] =0.;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  
   double *popeffectif,*popcount;      for(h=0;h<=nhstepm;h++){
   double ***p3mat;        for(k=0;k<=nhstepm;k++){
   char fileresf[FILENAMELENGTH];          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
  agelim=AGESUP;          for(i=1;i<=nlstate;i++)
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;            for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        }
        }
    
   strcpy(fileresf,"f");      /* pptj */
   strcat(fileresf,fileres);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   if((ficresf=fopen(fileresf,"w"))==NULL) {      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
     printf("Problem with forecast resultfile: %s\n", fileresf);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   }        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   printf("Computing forecasting: result on file '%s' \n", fileresf);          varppt[j][i]=doldmp[j][i];
       /* end ppptj */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   if (mobilav==1) {   
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      if (popbased==1) {
     movingaverage(agedeb, fage, ageminpar, mobaverage);        if(mobilav ==0){
   }          for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
   stepsize=(int) (stepm+YEARM-1)/YEARM;        }else{ /* mobilav */ 
   if (stepm<=12) stepsize=1;          for(i=1; i<=nlstate;i++)
              prlim[i][i]=mobaverage[(int)age][i][ij];
   agelim=AGESUP;        }
        }
   hstepm=1;      
   hstepm=hstepm/stepm;      /* This for computing force of mortality (h=1)as a weighted average */
   yp1=modf(dateintmean,&yp);      for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
   anprojmean=yp;        for(i=1; i<= nlstate; i++)
   yp2=modf((yp1*12),&yp);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   mprojmean=yp;      }    
   yp1=modf((yp2*30.5),&yp);      /* end force of mortality */
   jprojmean=yp;  
   if(jprojmean==0) jprojmean=1;      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   if(mprojmean==0) jprojmean=1;      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
          fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);        for(i=1; i<=nlstate;i++){
            fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   for(cptcov=1;cptcov<=i2;cptcov++){        }
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      } 
       k=k+1;      fprintf(ficresprobmorprev,"\n");
       fprintf(ficresf,"\n#******");  
       for(j=1;j<=cptcoveff;j++) {      fprintf(ficresvij,"%.0f ",age );
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for(i=1; i<=nlstate;i++)
       }        for(j=1; j<=nlstate;j++){
       fprintf(ficresf,"******\n");          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       fprintf(ficresf,"# StartingAge FinalAge");        }
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);      fprintf(ficresvij,"\n");
            free_matrix(gp,0,nhstepm,1,nlstate);
            free_matrix(gm,0,nhstepm,1,nlstate);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
         fprintf(ficresf,"\n");      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    free_vector(gpp,nlstate+1,nlstate+ndeath);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    free_vector(gmp,nlstate+1,nlstate+ndeath);
           nhstepm = nhstepm/hstepm;    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
              free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
           oldm=oldms;savm=savms;    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      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);
           for (h=0; h<=nhstepm; h++){    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);
             if (h==(int) (calagedate+YEARM*cpt)) {    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
             }    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);
             for(j=1; j<=nlstate+ndeath;j++) {    /*  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);
               kk1=0.;kk2=0;  */
               for(i=1; i<=nlstate;i++) {                  fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
                 if (mobilav==1)  
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    free_vector(xp,1,npar);
                 else {    free_matrix(doldm,1,nlstate,1,nlstate);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    free_matrix(dnewm,1,nlstate,1,npar);
                 }    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
               }    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
               if (h==(int)(calagedate+12*cpt)){    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                 fprintf(ficresf," %.3f", kk1);    fclose(ficresprobmorprev);
                            fclose(ficgp);
               }    fclose(fichtm);
             }  }
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /************ Variance of prevlim ******************/
         }  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
       }  {
     }    /* Variance of prevalence limit */
   }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
            double **newm;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
   fclose(ficresf);    int k, cptcode;
 }    double *xp;
 /************** Forecasting ******************/    double *gp, *gm;
 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){    double **gradg, **trgradg;
      double age,agelim;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    int theta;
   int *popage;     
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
   double *popeffectif,*popcount;    fprintf(ficresvpl,"# Age");
   double ***p3mat,***tabpop,***tabpopprev;    for(i=1; i<=nlstate;i++)
   char filerespop[FILENAMELENGTH];        fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    xp=vector(1,npar);
   agelim=AGESUP;    dnewm=matrix(1,nlstate,1,npar);
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    doldm=matrix(1,nlstate,1,nlstate);
      
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    hstepm=1*YEARM; /* Every year of age */
      hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
      agelim = AGESUP;
   strcpy(filerespop,"pop");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   strcat(filerespop,fileres);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   if((ficrespop=fopen(filerespop,"w"))==NULL) {      if (stepm >= YEARM) hstepm=1;
     printf("Problem with forecast resultfile: %s\n", filerespop);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   }      gradg=matrix(1,npar,1,nlstate);
   printf("Computing forecasting: result on file '%s' \n", filerespop);      gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
       for(theta=1; theta <=npar; theta++){
   if (mobilav==1) {        for(i=1; i<=npar; i++){ /* Computes gradient */
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     movingaverage(agedeb, fage, ageminpar, mobaverage);        }
   }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
   stepsize=(int) (stepm+YEARM-1)/YEARM;          gp[i] = prlim[i][i];
   if (stepm<=12) stepsize=1;      
          for(i=1; i<=npar; i++) /* Computes gradient */
   agelim=AGESUP;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   hstepm=1;        for(i=1;i<=nlstate;i++)
   hstepm=hstepm/stepm;          gm[i] = prlim[i][i];
    
   if (popforecast==1) {        for(i=1;i<=nlstate;i++)
     if((ficpop=fopen(popfile,"r"))==NULL) {          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       printf("Problem with population file : %s\n",popfile);exit(0);      } /* End theta */
     }  
     popage=ivector(0,AGESUP);      trgradg =matrix(1,nlstate,1,npar);
     popeffectif=vector(0,AGESUP);  
     popcount=vector(0,AGESUP);      for(j=1; j<=nlstate;j++)
            for(theta=1; theta <=npar; theta++)
     i=1;            trgradg[j][theta]=gradg[theta][j];
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;  
          for(i=1;i<=nlstate;i++)
     imx=i;        varpl[i][(int)age] =0.;
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      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(cptcov=1;cptcov<=i2;cptcov++){        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
       k=k+1;      fprintf(ficresvpl,"%.0f ",age );
       fprintf(ficrespop,"\n#******");      for(i=1; i<=nlstate;i++)
       for(j=1;j<=cptcoveff;j++) {        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      fprintf(ficresvpl,"\n");
       }      free_vector(gp,1,nlstate);
       fprintf(ficrespop,"******\n");      free_vector(gm,1,nlstate);
       fprintf(ficrespop,"# Age");      free_matrix(gradg,1,npar,1,nlstate);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);      free_matrix(trgradg,1,nlstate,1,npar);
       if (popforecast==1)  fprintf(ficrespop," [Population]");    } /* End age */
        
       for (cpt=0; cpt<=0;cpt++) {    free_vector(xp,1,npar);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      free_matrix(doldm,1,nlstate,1,npar);
            free_matrix(dnewm,1,nlstate,1,nlstate);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  }
           nhstepm = nhstepm/hstepm;  
            /************ Variance of one-step probabilities  ******************/
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
           oldm=oldms;savm=savms;  {
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      int i, j=0,  i1, k1, l1, t, tj;
            int k2, l2, j1,  z1;
           for (h=0; h<=nhstepm; h++){    int k=0,l, cptcode;
             if (h==(int) (calagedate+YEARM*cpt)) {    int first=1, first1;
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
             }    double **dnewm,**doldm;
             for(j=1; j<=nlstate+ndeath;j++) {    double *xp;
               kk1=0.;kk2=0;    double *gp, *gm;
               for(i=1; i<=nlstate;i++) {                  double **gradg, **trgradg;
                 if (mobilav==1)    double **mu;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    double age,agelim, cov[NCOVMAX];
                 else {    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    int theta;
                 }    char fileresprob[FILENAMELENGTH];
               }    char fileresprobcov[FILENAMELENGTH];
               if (h==(int)(calagedate+12*cpt)){    char fileresprobcor[FILENAMELENGTH];
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;  
                   /*fprintf(ficrespop," %.3f", kk1);    double ***varpij;
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/  
               }    strcpy(fileresprob,"prob"); 
             }    strcat(fileresprob,fileres);
             for(i=1; i<=nlstate;i++){    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
               kk1=0.;      printf("Problem with resultfile: %s\n", fileresprob);
                 for(j=1; j<=nlstate;j++){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    }
                 }    strcpy(fileresprobcov,"probcov"); 
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    strcat(fileresprobcov,fileres);
             }    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    }
           }    strcpy(fileresprobcor,"probcor"); 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    strcat(fileresprobcor,fileres);
         }    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       }      printf("Problem with resultfile: %s\n", fileresprobcor);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   /******/    }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
           nhstepm = nhstepm/hstepm;    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
              
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
           oldm=oldms;savm=savms;    fprintf(ficresprob,"# Age");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
           for (h=0; h<=nhstepm; h++){    fprintf(ficresprobcov,"# Age");
             if (h==(int) (calagedate+YEARM*cpt)) {    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    fprintf(ficresprobcov,"# Age");
             }  
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;    for(i=1; i<=nlstate;i++)
               for(i=1; i<=nlstate;i++) {                    for(j=1; j<=(nlstate+ndeath);j++){
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];            fprintf(ficresprob," p%1d-%1d (SE)",i,j);
               }        fprintf(ficresprobcov," p%1d-%1d ",i,j);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
             }      }  
           }    fprintf(ficresprob,"\n");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficresprobcov,"\n");
         }    fprintf(ficresprobcor,"\n");
       }    xp=vector(1,npar);
    }    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   }    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
      mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
   if (popforecast==1) {    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
     free_ivector(popage,0,AGESUP);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
     free_vector(popeffectif,0,AGESUP);      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
     free_vector(popcount,0,AGESUP);      exit(0);
   }    }
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    else{
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      fprintf(ficgp,"\n# Routine varprob");
   fclose(ficrespop);    }
 }    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
       printf("Problem with html file: %s\n", optionfilehtm);
 /***********************************************/      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
 /**************** Main Program *****************/      exit(0);
 /***********************************************/    }
     else{
 int main(int argc, char *argv[])      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
 {      fprintf(fichtm,"\n");
   
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
   double agedeb, agefin,hf;      fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;      fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
   
   double fret;    }
   double **xi,tmp,delta;  
     cov[1]=1;
   double dum; /* Dummy variable */    tj=cptcoveff;
   double ***p3mat;    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   int *indx;    j1=0;
   char line[MAXLINE], linepar[MAXLINE];    for(t=1; t<=tj;t++){
   char title[MAXLINE];      for(i1=1; i1<=ncodemax[t];i1++){ 
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];        j1++;
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];        if  (cptcovn>0) {
            fprintf(ficresprob, "\n#********** Variable "); 
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#");
   char filerest[FILENAMELENGTH];          fprintf(ficresprobcov, "\n#********** Variable "); 
   char fileregp[FILENAMELENGTH];          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   char popfile[FILENAMELENGTH];          fprintf(ficresprobcov, "**********\n#");
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];          
   int firstobs=1, lastobs=10;          fprintf(ficgp, "\n#********** Variable "); 
   int sdeb, sfin; /* Status at beginning and end */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   int c,  h , cpt,l;          fprintf(ficgp, "**********\n#");
   int ju,jl, mi;          
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;          
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   int mobilav=0,popforecast=0;          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   int hstepm, nhstepm;          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;          
           fprintf(ficresprobcor, "\n#********** Variable ");    
   double bage, fage, age, agelim, agebase;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   double ftolpl=FTOL;          fprintf(ficgp, "**********\n#");    
   double **prlim;        }
   double *severity;        
   double ***param; /* Matrix of parameters */        for (age=bage; age<=fage; age ++){ 
   double  *p;          cov[2]=age;
   double **matcov; /* Matrix of covariance */          for (k=1; k<=cptcovn;k++) {
   double ***delti3; /* Scale */            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
   double *delti; /* Scale */          }
   double ***eij, ***vareij;          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   double **varpl; /* Variances of prevalence limits by age */          for (k=1; k<=cptcovprod;k++)
   double *epj, vepp;            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   double kk1, kk2;          
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
            trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           gp=vector(1,(nlstate)*(nlstate+ndeath));
   char version[80]="Imach version 0.8a, March 2002, INED-EUROREVES ";          gm=vector(1,(nlstate)*(nlstate+ndeath));
   char *alph[]={"a","a","b","c","d","e"}, str[4];      
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
   char z[1]="c", occ;              xp[i] = x[i] + (i==theta ?delti[theta]:0);
 #include <sys/time.h>            
 #include <time.h>            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];            
              k=0;
   /* long total_usecs;            for(i=1; i<= (nlstate); i++){
   struct timeval start_time, end_time;              for(j=1; j<=(nlstate+ndeath);j++){
                  k=k+1;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */                gp[k]=pmmij[i][j];
   getcwd(pathcd, size);              }
             }
   printf("\n%s",version);            
   if(argc <=1){            for(i=1; i<=npar; i++)
     printf("\nEnter the parameter file name: ");              xp[i] = x[i] - (i==theta ?delti[theta]:0);
     scanf("%s",pathtot);      
   }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   else{            k=0;
     strcpy(pathtot,argv[1]);            for(i=1; i<=(nlstate); i++){
   }              for(j=1; j<=(nlstate+ndeath);j++){
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/                k=k+1;
   /*cygwin_split_path(pathtot,path,optionfile);                gm[k]=pmmij[i][j];
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/              }
   /* cutv(path,optionfile,pathtot,'\\');*/            }
        
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);              gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
   chdir(path);          }
   replace(pathc,path);  
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
 /*-------- arguments in the command line --------*/            for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
   strcpy(fileres,"r");          
   strcat(fileres, optionfilefiname);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   strcat(fileres,".txt");    /* Other files have txt extension */          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   /*---------arguments file --------*/          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     printf("Problem with optionfile %s\n",optionfile);  
     goto end;          pmij(pmmij,cov,ncovmodel,x,nlstate);
   }          
           k=0;
   strcpy(filereso,"o");          for(i=1; i<=(nlstate); i++){
   strcat(filereso,fileres);            for(j=1; j<=(nlstate+ndeath);j++){
   if((ficparo=fopen(filereso,"w"))==NULL) {              k=k+1;
     printf("Problem with Output resultfile: %s\n", filereso);goto end;              mu[k][(int) age]=pmmij[i][j];
   }            }
           }
   /* Reads comments: lines beginning with '#' */          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   while((c=getc(ficpar))=='#' && c!= EOF){            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
     ungetc(c,ficpar);              varpij[i][j][(int)age] = doldm[i][j];
     fgets(line, MAXLINE, ficpar);  
     puts(line);          /*printf("\n%d ",(int)age);
     fputs(line,ficparo);            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]));
   ungetc(c,ficpar);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   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);  
   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(ficresprob,"\n%d ",(int)age);
   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(ficresprobcov,"\n%d ",(int)age);
 while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficresprobcor,"\n%d ",(int)age);
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
     puts(line);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
     fputs(line,ficparo);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   }            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   ungetc(c,ficpar);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
            }
              i=0;
   covar=matrix(0,NCOVMAX,1,n);          for (k=1; k<=(nlstate);k++){
   cptcovn=0;            for (l=1; l<=(nlstate+ndeath);l++){ 
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;              i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   ncovmodel=2+cptcovn;              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */              for (j=1; j<=i;j++){
                  fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   /* Read guess parameters */                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
   /* Reads comments: lines beginning with '#' */              }
   while((c=getc(ficpar))=='#' && c!= EOF){            }
     ungetc(c,ficpar);          }/* end of loop for state */
     fgets(line, MAXLINE, ficpar);        } /* end of loop for age */
     puts(line);  
     fputs(line,ficparo);        /* Confidence intervalle of pij  */
   }        /*
   ungetc(c,ficpar);          fprintf(ficgp,"\nset noparametric;unset label");
            fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     for(i=1; i <=nlstate; i++)          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);
     for(j=1; j <=nlstate+ndeath-1; j++){          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
       fscanf(ficpar,"%1d%1d",&i1,&j1);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
       fprintf(ficparo,"%1d%1d",i1,j1);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
       printf("%1d%1d",i,j);        */
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar," %lf",&param[i][j][k]);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         printf(" %lf",param[i][j][k]);        first1=1;
         fprintf(ficparo," %lf",param[i][j][k]);        for (k2=1; k2<=(nlstate);k2++){
       }          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
       fscanf(ficpar,"\n");            if(l2==k2) continue;
       printf("\n");            j=(k2-1)*(nlstate+ndeath)+l2;
       fprintf(ficparo,"\n");            for (k1=1; k1<=(nlstate);k1++){
     }              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                  if(l1==k1) continue;
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;                i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
   p=param[1][1];                for (age=bage; age<=fage; age ++){ 
                    if ((int)age %5==0){
   /* Reads comments: lines beginning with '#' */                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   while((c=getc(ficpar))=='#' && c!= EOF){                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
     ungetc(c,ficpar);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
     fgets(line, MAXLINE, ficpar);                    mu1=mu[i][(int) age]/stepm*YEARM ;
     puts(line);                    mu2=mu[j][(int) age]/stepm*YEARM;
     fputs(line,ficparo);                    c12=cv12/sqrt(v1*v2);
   }                    /* Computing eigen value of matrix of covariance */
   ungetc(c,ficpar);                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);                    /* Eigen vectors */
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
   for(i=1; i <=nlstate; i++){                    /*v21=sqrt(1.-v11*v11); *//* error */
     for(j=1; j <=nlstate+ndeath-1; j++){                    v21=(lc1-v1)/cv12*v11;
       fscanf(ficpar,"%1d%1d",&i1,&j1);                    v12=-v21;
       printf("%1d%1d",i,j);                    v22=v11;
       fprintf(ficparo,"%1d%1d",i1,j1);                    tnalp=v21/v11;
       for(k=1; k<=ncovmodel;k++){                    if(first1==1){
         fscanf(ficpar,"%le",&delti3[i][j][k]);                      first1=0;
         printf(" %le",delti3[i][j][k]);                      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);
         fprintf(ficparo," %le",delti3[i][j][k]);                    }
       }                    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);
       fscanf(ficpar,"\n");                    /*printf(fignu*/
       printf("\n");                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
       fprintf(ficparo,"\n");                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
     }                    if(first==1){
   }                      first=0;
   delti=delti3[1][1];                      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);
   /* Reads comments: lines beginning with '#' */                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   while((c=getc(ficpar))=='#' && c!= EOF){                      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);
     ungetc(c,ficpar);                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
     fgets(line, MAXLINE, ficpar);                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
     puts(line);                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
     fputs(line,ficparo);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   }                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   ungetc(c,ficpar);                      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),\
   matcov=matrix(1,npar,1,npar);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   for(i=1; i <=npar; i++){                    }else{
     fscanf(ficpar,"%s",&str);                      first=0;
     printf("%s",str);                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
     fprintf(ficparo,"%s",str);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     for(j=1; j <=i; j++){                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
       fscanf(ficpar," %le",&matcov[i][j]);                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
       printf(" %.5le",matcov[i][j]);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
       fprintf(ficparo," %.5le",matcov[i][j]);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     }                    }/* if first */
     fscanf(ficpar,"\n");                  } /* age mod 5 */
     printf("\n");                } /* end loop age */
     fprintf(ficparo,"\n");                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
   }                first=1;
   for(i=1; i <=npar; i++)              } /*l12 */
     for(j=i+1;j<=npar;j++)            } /* k12 */
       matcov[i][j]=matcov[j][i];          } /*l1 */
            }/* k1 */
   printf("\n");      } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     /*-------- Rewriting paramater file ----------*/    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
      strcpy(rfileres,"r");    /* "Rparameterfile */    free_vector(xp,1,npar);
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    fclose(ficresprob);
      strcat(rfileres,".");    /* */    fclose(ficresprobcov);
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    fclose(ficresprobcor);
     if((ficres =fopen(rfileres,"w"))==NULL) {    fclose(ficgp);
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    fclose(fichtm);
     }  }
     fprintf(ficres,"#%s\n",version);  
      
     /*-------- data file ----------*/  /******************* Printing html file ***********/
     if((fic=fopen(datafile,"r"))==NULL)    {  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
       printf("Problem with datafile: %s\n", datafile);goto end;                    int lastpass, int stepm, int weightopt, char model[],\
     }                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
     n= lastobs;                    double jprev1, double mprev1,double anprev1, \
     severity = vector(1,maxwav);                    double jprev2, double mprev2,double anprev2){
     outcome=imatrix(1,maxwav+1,1,n);    int jj1, k1, i1, cpt;
     num=ivector(1,n);    /*char optionfilehtm[FILENAMELENGTH];*/
     moisnais=vector(1,n);    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
     annais=vector(1,n);      printf("Problem with %s \n",optionfilehtm), exit(0);
     moisdc=vector(1,n);      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
     andc=vector(1,n);    }
     agedc=vector(1,n);  
     cod=ivector(1,n);     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
     weight=vector(1,n);   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
     mint=matrix(1,maxwav,1,n);   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
     anint=matrix(1,maxwav,1,n);   - Life expectancies by age and initial health status (estepm=%2d months): 
     s=imatrix(1,maxwav+1,1,n);     <a href=\"e%s\">e%s</a> <br>\n</li>", \
     adl=imatrix(1,maxwav+1,1,n);        jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
     tab=ivector(1,NCOVMAX);  
     ncodemax=ivector(1,8);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
     i=1;   m=cptcoveff;
     while (fgets(line, MAXLINE, fic) != NULL)    {   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       if ((i >= firstobs) && (i <=lastobs)) {  
           jj1=0;
         for (j=maxwav;j>=1;j--){   for(k1=1; k1<=m;k1++){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);     for(i1=1; i1<=ncodemax[k1];i1++){
           strcpy(line,stra);       jj1++;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);       if (cptcovn > 0) {
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
         }         for (cpt=1; cpt<=cptcoveff;cpt++) 
                   fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);       }
        /* Pij */
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);       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>
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
        /* Quasi-incidences */
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
         for (j=ncovcol;j>=1;j--){  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);         /* Stable prevalence in each health state */
         }         for(cpt=1; cpt<nlstate;cpt++){
         num[i]=atol(stra);           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
          <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
         /*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;}*/       for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
         i=i+1;  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
       }       }
     }       fprintf(fichtm,"\n<br>- Total life expectancy by age and
     /* printf("ii=%d", ij);  health expectancies in states (1) and (2): e%s%d.png<br>
        scanf("%d",i);*/  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
   imx=i-1; /* Number of individuals */     } /* end i1 */
    }/* End k1 */
   /* for (i=1; i<=imx; i++){   fprintf(fichtm,"</ul>");
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;  
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;  
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
     }*/   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
     - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
   /* for (i=1; i<=imx; i++){   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
      if (s[4][i]==9)  s[4][i]=-1;   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
   */   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
     - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
   /* Calculation of the number of parameter from char model*/  
   Tvar=ivector(1,15);   if(popforecast==1) fprintf(fichtm,"\n
   Tprod=ivector(1,15);   - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
   Tvaraff=ivector(1,15);   - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
   Tvard=imatrix(1,15,1,2);          <br>",fileres,fileres,fileres,fileres);
   Tage=ivector(1,15);         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);
   if (strlen(model) >1){  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
     j=0, j1=0, k1=1, k2=1;  
     j=nbocc(model,'+');   m=cptcoveff;
     j1=nbocc(model,'*');   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     cptcovn=j+1;  
     cptcovprod=j1;   jj1=0;
       for(k1=1; k1<=m;k1++){
     strcpy(modelsav,model);     for(i1=1; i1<=ncodemax[k1];i1++){
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){       jj1++;
       printf("Error. Non available option model=%s ",model);       if (cptcovn > 0) {
       goto end;         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     }         for (cpt=1; cpt<=cptcoveff;cpt++) 
               fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     for(i=(j+1); i>=1;i--){         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
       cutv(stra,strb,modelsav,'+');       }
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);       for(cpt=1; cpt<=nlstate;cpt++) {
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/         fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
       /*scanf("%d",i);*/  interval) in state (%d): v%s%d%d.png <br>
       if (strchr(strb,'*')) {  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
         cutv(strd,strc,strb,'*');       }
         if (strcmp(strc,"age")==0) {     } /* end i1 */
           cptcovprod--;   }/* End k1 */
           cutv(strb,stre,strd,'V');   fprintf(fichtm,"</ul>");
           Tvar[i]=atoi(stre);  fclose(fichtm);
           cptcovage++;  }
             Tage[cptcovage]=i;  
             /*printf("stre=%s ", stre);*/  /******************* Gnuplot file **************/
         }  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
         else if (strcmp(strd,"age")==0) {  
           cptcovprod--;    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
           cutv(strb,stre,strc,'V');    int ng;
           Tvar[i]=atoi(stre);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
           cptcovage++;      printf("Problem with file %s",optionfilegnuplot);
           Tage[cptcovage]=i;      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
         }    }
         else {  
           cutv(strb,stre,strc,'V');    /*#ifdef windows */
           Tvar[i]=ncovcol+k1;      fprintf(ficgp,"cd \"%s\" \n",pathc);
           cutv(strb,strc,strd,'V');      /*#endif */
           Tprod[k1]=i;  m=pow(2,cptcoveff);
           Tvard[k1][1]=atoi(strc);    
           Tvard[k1][2]=atoi(stre);   /* 1eme*/
           Tvar[cptcovn+k2]=Tvard[k1][1];    for (cpt=1; cpt<= nlstate ; cpt ++) {
           Tvar[cptcovn+k2+1]=Tvard[k1][2];     for (k1=1; k1<= m ; k1 ++) {
           for (k=1; k<=lastobs;k++)       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];       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);
           k1++;  
           k2=k2+2;       for (i=1; i<= nlstate ; i ++) {
         }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       }         else fprintf(ficgp," \%%*lf (\%%*lf)");
       else {       }
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
        /*  scanf("%d",i);*/       for (i=1; i<= nlstate ; i ++) {
       cutv(strd,strc,strb,'V');         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       Tvar[i]=atoi(strc);         else fprintf(ficgp," \%%*lf (\%%*lf)");
       }       } 
       strcpy(modelsav,stra);         fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); 
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);       for (i=1; i<= nlstate ; i ++) {
         scanf("%d",i);*/         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     }         else fprintf(ficgp," \%%*lf (\%%*lf)");
 }       }  
         fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);     }
   printf("cptcovprod=%d ", cptcovprod);    }
   scanf("%d ",i);*/    /*2 eme*/
     fclose(fic);    
     for (k1=1; k1<= m ; k1 ++) { 
     /*  if(mle==1){*/      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
     if (weightopt != 1) { /* Maximisation without weights*/      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       for(i=1;i<=n;i++) weight[i]=1.0;      
     }      for (i=1; i<= nlstate+1 ; i ++) {
     /*-calculation of age at interview from date of interview and age at death -*/        k=2*i;
     agev=matrix(1,maxwav,1,imx);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
     for (i=1; i<=imx; i++) {          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       for(m=2; (m<= maxwav); m++) {          else fprintf(ficgp," \%%*lf (\%%*lf)");
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){        }   
          anint[m][i]=9999;        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
          s[m][i]=-1;        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
        }        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;        for (j=1; j<= nlstate+1 ; j ++) {
       }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     }          else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
     for (i=1; i<=imx; i++)  {        fprintf(ficgp,"\" t\"\" w l 0,");
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
       for(m=1; (m<= maxwav); m++){        for (j=1; j<= nlstate+1 ; j ++) {
         if(s[m][i] >0){          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           if (s[m][i] >= nlstate+1) {          else fprintf(ficgp," \%%*lf (\%%*lf)");
             if(agedc[i]>0)        }   
               if(moisdc[i]!=99 && andc[i]!=9999)        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
                 agev[m][i]=agedc[i];        else fprintf(ficgp,"\" t\"\" w l 0,");
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/      }
            else {    }
               if (andc[i]!=9999){    
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    /*3eme*/
               agev[m][i]=-1;    
               }    for (k1=1; k1<= m ; k1 ++) { 
             }      for (cpt=1; cpt<= nlstate ; cpt ++) {
           }        k=2+nlstate*(2*cpt-2);
           else if(s[m][i] !=9){ /* Should no more exist */        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
             if(mint[m][i]==99 || anint[m][i]==9999)        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
               agev[m][i]=1;          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
             else if(agev[m][i] <agemin){          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
               agemin=agev[m][i];          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
             }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
             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);*/        for (i=1; i< nlstate ; i ++) {
             }          fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
             /*agev[m][i]=anint[m][i]-annais[i];*/          
             /*   agev[m][i] = age[i]+2*m;*/        } 
           }      }
           else { /* =9 */    }
             agev[m][i]=1;    
             s[m][i]=-1;    /* CV preval stat */
           }    for (k1=1; k1<= m ; k1 ++) { 
         }      for (cpt=1; cpt<nlstate ; cpt ++) {
         else /*= 0 Unknown */        k=3;
           agev[m][i]=1;        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
       }        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
            
     }        for (i=1; i< nlstate ; i ++)
     for (i=1; i<=imx; i++)  {          fprintf(ficgp,"+$%d",k+i+1);
       for(m=1; (m<= maxwav); m++){        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         if (s[m][i] > (nlstate+ndeath)) {        
           printf("Error: Wrong value in nlstate or ndeath\n");          l=3+(nlstate+ndeath)*cpt;
           goto end;        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
         }        for (i=1; i< nlstate ; i ++) {
       }          l=3+(nlstate+ndeath)*cpt;
     }          fprintf(ficgp,"+$%d",l+i+1);
         }
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     free_vector(severity,1,maxwav);    }  
     free_imatrix(outcome,1,maxwav+1,1,n);    
     free_vector(moisnais,1,n);    /* proba elementaires */
     free_vector(annais,1,n);    for(i=1,jk=1; i <=nlstate; i++){
     /* free_matrix(mint,1,maxwav,1,n);      for(k=1; k <=(nlstate+ndeath); k++){
        free_matrix(anint,1,maxwav,1,n);*/        if (k != i) {
     free_vector(moisdc,1,n);          for(j=1; j <=ncovmodel; j++){
     free_vector(andc,1,n);            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
                fprintf(ficgp,"\n");
     wav=ivector(1,imx);          }
     dh=imatrix(1,lastpass-firstpass+1,1,imx);        }
     mw=imatrix(1,lastpass-firstpass+1,1,imx);      }
         }
     /* Concatenates waves */  
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
       Tcode=ivector(1,100);         if (ng==2)
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
       ncodemax[1]=1;         else
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);           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);
    codtab=imatrix(1,100,1,10);         i=1;
    h=0;         for(k2=1; k2<=nlstate; k2++) {
    m=pow(2,cptcoveff);           k3=i;
             for(k=1; k<=(nlstate+ndeath); k++) {
    for(k=1;k<=cptcoveff; k++){             if (k != k2){
      for(i=1; i <=(m/pow(2,k));i++){               if(ng==2)
        for(j=1; j <= ncodemax[k]; j++){                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){               else
            h++;                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;               ij=1;
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/               for(j=3; j <=ncovmodel; j++) {
          }                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
        }                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
      }                   ij++;
    }                 }
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);                 else
       codtab[1][2]=1;codtab[2][2]=2; */                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
    /* for(i=1; i <=m ;i++){               }
       for(k=1; k <=cptcovn; k++){               fprintf(ficgp,")/(1");
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);               
       }               for(k1=1; k1 <=nlstate; k1++){   
       printf("\n");                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
       }                 ij=1;
       scanf("%d",i);*/                 for(j=3; j <=ncovmodel; j++){
                       if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
    /* Calculates basic frequencies. Computes observed prevalence at single age                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
        and prints on file fileres'p'. */                     ij++;
                    }
                       else
                         fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                 }
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                 fprintf(ficgp,")");
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */               }
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                     i=i+ncovmodel;
     /* 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] */           } /* end k */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */         } /* end k2 */
        } /* end jk */
     if(mle==1){     } /* end ng */
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);     fclose(ficgp); 
     }  }  /* end gnuplot */
      
     /*--------- 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);  /*************** Moving average **************/
    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
    jk=1;    int i, cpt, cptcod;
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    int modcovmax =1;
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    int mobilavrange, mob;
    for(i=1,jk=1; i <=nlstate; i++){    double age;
      for(k=1; k <=(nlstate+ndeath); k++){  
        if (k != i)    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
          {                             a covariate has 2 modalities */
            printf("%d%d ",i,k);    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
            fprintf(ficres,"%1d%1d ",i,k);  
            for(j=1; j <=ncovmodel; j++){    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
              printf("%f ",p[jk]);      if(mobilav==1) mobilavrange=5; /* default */
              fprintf(ficres,"%f ",p[jk]);      else mobilavrange=mobilav;
              jk++;      for (age=bage; age<=fage; age++)
            }        for (i=1; i<=nlstate;i++)
            printf("\n");          for (cptcod=1;cptcod<=modcovmax;cptcod++)
            fprintf(ficres,"\n");            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
          }      /* We keep the original values on the extreme ages bage, fage and for 
      }         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
    }         we use a 5 terms etc. until the borders are no more concerned. 
  if(mle==1){      */ 
     /* Computing hessian and covariance matrix */      for (mob=3;mob <=mobilavrange;mob=mob+2){
     ftolhess=ftol; /* Usually correct */        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
     hesscov(matcov, p, npar, delti, ftolhess, func);          for (i=1; i<=nlstate;i++){
  }            for (cptcod=1;cptcod<=modcovmax;cptcod++){
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
     printf("# Scales (for hessian or gradient estimation)\n");                for (cpt=1;cpt<=(mob-1)/2;cpt++){
      for(i=1,jk=1; i <=nlstate; i++){                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
       for(j=1; j <=nlstate+ndeath; j++){                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
         if (j!=i) {                }
           fprintf(ficres,"%1d%1d",i,j);              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
           printf("%1d%1d",i,j);            }
           for(k=1; k<=ncovmodel;k++){          }
             printf(" %.5e",delti[jk]);        }/* end age */
             fprintf(ficres," %.5e",delti[jk]);      }/* end mob */
             jk++;    }else return -1;
           }    return 0;
           printf("\n");  }/* End movingaverage */
           fprintf(ficres,"\n");  
         }  
       }  /************** Forecasting ******************/
      }  prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){
        
     k=1;    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     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");    int *popage;
     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");    double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     for(i=1;i<=npar;i++){    double *popeffectif,*popcount;
       /*  if (k>nlstate) k=1;    double ***p3mat;
       i1=(i-1)/(ncovmodel*nlstate)+1;    double ***mobaverage;
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    char fileresf[FILENAMELENGTH];
       printf("%s%d%d",alph[k],i1,tab[i]);*/  
       fprintf(ficres,"%3d",i);   agelim=AGESUP;
       printf("%3d",i);   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
       for(j=1; j<=i;j++){  
         fprintf(ficres," %.5e",matcov[i][j]);    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
         printf(" %.5e",matcov[i][j]);   
       }   
       fprintf(ficres,"\n");    strcpy(fileresf,"f"); 
       printf("\n");    strcat(fileresf,fileres);
       k++;    if((ficresf=fopen(fileresf,"w"))==NULL) {
     }      printf("Problem with forecast resultfile: %s\n", fileresf);
          fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     while((c=getc(ficpar))=='#' && c!= EOF){    }
       ungetc(c,ficpar);    printf("Computing forecasting: result on file '%s' \n", fileresf);
       fgets(line, MAXLINE, ficpar);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
       puts(line);  
       fputs(line,ficparo);    if (cptcoveff==0) ncodemax[cptcoveff]=1;
     }  
     ungetc(c,ficpar);    if (mobilav!=0) {
        mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&ageminpar,&agemaxpar, &bage, &fage);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
            fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     if (fage <= 2) {        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       bage = ageminpar;      }
       fage = agemaxpar;    }
     }  
        stepsize=(int) (stepm+YEARM-1)/YEARM;
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    if (stepm<=12) stepsize=1;
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",ageminpar,agemaxpar,bage,fage);    
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",ageminpar,agemaxpar,bage,fage);    agelim=AGESUP;
      
     while((c=getc(ficpar))=='#' && c!= EOF){    hstepm=1;
     ungetc(c,ficpar);    hstepm=hstepm/stepm; 
     fgets(line, MAXLINE, ficpar);    yp1=modf(dateintmean,&yp);
     puts(line);    anprojmean=yp;
     fputs(line,ficparo);    yp2=modf((yp1*12),&yp);
   }    mprojmean=yp;
   ungetc(c,ficpar);    yp1=modf((yp2*30.5),&yp);
      jprojmean=yp;
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    if(jprojmean==0) jprojmean=1;
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    if(mprojmean==0) jprojmean=1;
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    
          fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean); 
   while((c=getc(ficpar))=='#' && c!= EOF){    
     ungetc(c,ficpar);    for(cptcov=1;cptcov<=i2;cptcov++){
     fgets(line, MAXLINE, ficpar);      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
     puts(line);        k=k+1;
     fputs(line,ficparo);        fprintf(ficresf,"\n#******");
   }        for(j=1;j<=cptcoveff;j++) {
   ungetc(c,ficpar);          fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
          }
         fprintf(ficresf,"******\n");
    dateprev1=anprev1+mprev1/12.+jprev1/365.;        fprintf(ficresf,"# StartingAge FinalAge");
    dateprev2=anprev2+mprev2/12.+jprev2/365.;        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
         
   fscanf(ficpar,"pop_based=%d\n",&popbased);        
   fprintf(ficparo,"pop_based=%d\n",popbased);          for (cpt=0; cpt<=(anproj2-anproj1);cpt++) { 
   fprintf(ficres,"pop_based=%d\n",popbased);            fprintf(ficresf,"\n");
            fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);   
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
     fgets(line, MAXLINE, ficpar);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
     puts(line);            nhstepm = nhstepm/hstepm; 
     fputs(line,ficparo);            
   }            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   ungetc(c,ficpar);            oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
   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);          
 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);            for (h=0; h<=nhstepm; h++){
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);              if (h==(int) (calagedate+YEARM*cpt)) {
                 fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
               } 
 while((c=getc(ficpar))=='#' && c!= EOF){              for(j=1; j<=nlstate+ndeath;j++) {
     ungetc(c,ficpar);                kk1=0.;kk2=0;
     fgets(line, MAXLINE, ficpar);                for(i=1; i<=nlstate;i++) {              
     puts(line);                  if (mobilav==1) 
     fputs(line,ficparo);                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
   }                  else {
   ungetc(c,ficpar);                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
   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);                if (h==(int)(calagedate+12*cpt)){
                   fprintf(ficresf," %.3f", kk1);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                          
                 }
 /*------------ gnuplot -------------*/              }
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);            }
              free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 /*------------ 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);      if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  free_ivector(num,1,n);  
  free_vector(agedc,1,n);    fclose(ficresf);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/  }
  fclose(ficparo);  /************** Forecasting ******************/
  fclose(ficres);  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){
     
 /*--------- index.htm --------*/    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast);    double calagedate, agelim, kk1, kk2;
     double *popeffectif,*popcount;
      double ***p3mat,***tabpop,***tabpopprev;
   /*--------------- Prevalence limit --------------*/    double ***mobaverage;
      char filerespop[FILENAMELENGTH];
   strcpy(filerespl,"pl");  
   strcat(filerespl,fileres);    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    agelim=AGESUP;
   }    calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    
   fprintf(ficrespl,"#Prevalence limit\n");    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
   fprintf(ficrespl,"#Age ");    
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    
   fprintf(ficrespl,"\n");    strcpy(filerespop,"pop"); 
      strcat(filerespop,fileres);
   prlim=matrix(1,nlstate,1,nlstate);    if((ficrespop=fopen(filerespop,"w"))==NULL) {
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      printf("Problem with forecast resultfile: %s\n", filerespop);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    }
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    printf("Computing forecasting: result on file '%s' \n", filerespop);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   k=0;  
   agebase=ageminpar;    if (cptcoveff==0) ncodemax[cptcoveff]=1;
   agelim=agemaxpar;  
   ftolpl=1.e-10;    if (mobilav!=0) {
   i1=cptcoveff;      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   if (cptcovn < 1){i1=1;}      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   for(cptcov=1;cptcov<=i1;cptcov++){        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     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#******");    stepsize=(int) (stepm+YEARM-1)/YEARM;
         for(j=1;j<=cptcoveff;j++)    if (stepm<=12) stepsize=1;
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    
         fprintf(ficrespl,"******\n");    agelim=AGESUP;
            
         for (age=agebase; age<=agelim; age++){    hstepm=1;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    hstepm=hstepm/stepm; 
           fprintf(ficrespl,"%.0f",age );    
           for(i=1; i<=nlstate;i++)    if (popforecast==1) {
           fprintf(ficrespl," %.5f", prlim[i][i]);      if((ficpop=fopen(popfile,"r"))==NULL) {
           fprintf(ficrespl,"\n");        printf("Problem with population file : %s\n",popfile);exit(0);
         }        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       }      } 
     }      popage=ivector(0,AGESUP);
   fclose(ficrespl);      popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
   /*------------- h Pij x at various ages ------------*/      
        i=1;   
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
   if((ficrespij=fopen(filerespij,"w"))==NULL) {     
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;      imx=i;
   }      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
   printf("Computing pij: result on file '%s' \n", filerespij);    }
    
   stepsize=(int) (stepm+YEARM-1)/YEARM;    for(cptcov=1;cptcov<=i2;cptcov++){
   /*if (stepm<=24) stepsize=2;*/     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
   agelim=AGESUP;        fprintf(ficrespop,"\n#******");
   hstepm=stepsize*YEARM; /* Every year of age */        for(j=1;j<=cptcoveff;j++) {
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
          }
   k=0;        fprintf(ficrespop,"******\n");
   for(cptcov=1;cptcov<=i1;cptcov++){        fprintf(ficrespop,"# Age");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
       k=k+1;        if (popforecast==1)  fprintf(ficrespop," [Population]");
         fprintf(ficrespij,"\n#****** ");        
         for(j=1;j<=cptcoveff;j++)        for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
         fprintf(ficrespij,"******\n");          
                  for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            nhstepm = nhstepm/hstepm; 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;            oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Age");          
           for(i=1; i<=nlstate;i++)            for (h=0; h<=nhstepm; h++){
             for(j=1; j<=nlstate+ndeath;j++)              if (h==(int) (calagedate+YEARM*cpt)) {
               fprintf(ficrespij," %1d-%1d",i,j);                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
           fprintf(ficrespij,"\n");              } 
           for (h=0; h<=nhstepm; h++){              for(j=1; j<=nlstate+ndeath;j++) {
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );                kk1=0.;kk2=0;
             for(i=1; i<=nlstate;i++)                for(i=1; i<=nlstate;i++) {              
               for(j=1; j<=nlstate+ndeath;j++)                  if (mobilav==1) 
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
             fprintf(ficrespij,"\n");                  else {
           }                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                  }
           fprintf(ficrespij,"\n");                }
         }                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]);*/
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/                }
               }
   fclose(ficrespij);              for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
   /*---------- Forecasting ------------------*/                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
   if((stepm == 1) && (strcmp(model,".")==0)){                  }
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);              }
     free_matrix(mint,1,maxwav,1,n);  
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);              if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) 
     free_vector(weight,1,n);}                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
   else{            }
     erreur=108;            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     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);          }
   }        }
     
     /******/
   /*---------- Health expectancies and variances ------------*/  
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
   strcpy(filerest,"t");          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
   strcat(filerest,fileres);          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
   if((ficrest=fopen(filerest,"w"))==NULL) {            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;            nhstepm = nhstepm/hstepm; 
   }            
   printf("Computing Total LEs with variances: file '%s' \n", filerest);            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);  
   strcpy(filerese,"e");            for (h=0; h<=nhstepm; h++){
   strcat(filerese,fileres);              if (h==(int) (calagedate+YEARM*cpt)) {
   if((ficreseij=fopen(filerese,"w"))==NULL) {                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);              } 
   }              for(j=1; j<=nlstate+ndeath;j++) {
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);                kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
  strcpy(fileresv,"v");                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
   strcat(fileresv,fileres);                }
   if((ficresvij=fopen(fileresv,"w"))==NULL) {                if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1); 
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);              }
   }            }
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
   k=0;        }
   for(cptcov=1;cptcov<=i1;cptcov++){     } 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    }
       k=k+1;   
       fprintf(ficrest,"\n#****** ");    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    if (popforecast==1) {
       fprintf(ficrest,"******\n");      free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       fprintf(ficreseij,"\n#****** ");      free_vector(popcount,0,AGESUP);
       for(j=1;j<=cptcoveff;j++)    }
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       fprintf(ficreseij,"******\n");    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
       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");  /**************** Main Program *****************/
   /***********************************************/
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;  int main(int argc, char *argv[])
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);    {
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
       oldm=oldms;savm=savms;    int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    double agedeb, agefin,hf;
        double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
      double fret;
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    double **xi,tmp,delta;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);  
       fprintf(ficrest,"\n");    double dum; /* Dummy variable */
     double ***p3mat;
       epj=vector(1,nlstate+1);    double ***mobaverage;
       for(age=bage; age <=fage ;age++){    int *indx;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    char line[MAXLINE], linepar[MAXLINE];
         if (popbased==1) {    char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
           for(i=1; i<=nlstate;i++)    int firstobs=1, lastobs=10;
             prlim[i][i]=probs[(int)age][i][k];    int sdeb, sfin; /* Status at beginning and end */
         }    int c,  h , cpt,l;
            int ju,jl, mi;
         fprintf(ficrest," %4.0f",age);    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    int mobilav=0,popforecast=0;
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    int hstepm, nhstepm;
           }    double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
           epj[nlstate+1] +=epj[j];  
         }    double bage, fage, age, agelim, agebase;
         for(i=1, vepp=0.;i <=nlstate;i++)    double ftolpl=FTOL;
           for(j=1;j <=nlstate;j++)    double **prlim;
             vepp += vareij[i][j][(int)age];    double *severity;
         fprintf(ficrest," %7.2f (%7.2f)", epj[nlstate+1],sqrt(vepp));    double ***param; /* Matrix of parameters */
         for(j=1;j <=nlstate;j++){    double  *p;
           fprintf(ficrest," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age]));    double **matcov; /* Matrix of covariance */
         }    double ***delti3; /* Scale */
         fprintf(ficrest,"\n");    double *delti; /* Scale */
       }    double ***eij, ***vareij;
     }    double **varpl; /* Variances of prevalence limits by age */
   }    double *epj, vepp;
     double kk1, kk2;
   fclose(ficreseij);    double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
   fclose(ficresvij);  
   fclose(ficrest);    char *alph[]={"a","a","b","c","d","e"}, str[4];
   fclose(ficpar);  
   free_vector(epj,1,nlstate+1);  
      char z[1]="c", occ;
   /*------- Variance limit prevalence------*/    #include <sys/time.h>
   #include <time.h>
   strcpy(fileresvpl,"vpl");    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
   strcat(fileresvpl,fileres);   
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    /* long total_usecs;
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);       struct timeval start_time, end_time;
     exit(0);    
   }       gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    getcwd(pathcd, size);
   
   k=0;    printf("\n%s",version);
   for(cptcov=1;cptcov<=i1;cptcov++){    if(argc <=1){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      printf("\nEnter the parameter file name: ");
       k=k+1;      scanf("%s",pathtot);
       fprintf(ficresvpl,"\n#****** ");    }
       for(j=1;j<=cptcoveff;j++)    else{
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      strcpy(pathtot,argv[1]);
       fprintf(ficresvpl,"******\n");    }
          /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    /*cygwin_split_path(pathtot,path,optionfile);
       oldm=oldms;savm=savms;      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    /* cutv(path,optionfile,pathtot,'\\');*/
     }  
  }    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   fclose(ficresvpl);    chdir(path);
     replace(pathc,path);
   /*---------- End : free ----------------*/  
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    /*-------- arguments in the command line --------*/
    
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    /* Log file */
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    strcat(filelog, optionfilefiname);
      strcat(filelog,".log");    /* */
      if((ficlog=fopen(filelog,"w"))==NULL)    {
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      printf("Problem with logfile %s\n",filelog);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      goto end;
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    }
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    fprintf(ficlog,"Log filename:%s\n",filelog);
      fprintf(ficlog,"\n%s",version);
   free_matrix(matcov,1,npar,1,npar);    fprintf(ficlog,"\nEnter the parameter file name: ");
   free_vector(delti,1,npar);    fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   free_matrix(agev,1,maxwav,1,imx);    fflush(ficlog);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);  
     /* */
   if(erreur >0)    strcpy(fileres,"r");
     printf("End of Imach with error or warning %d\n",erreur);    strcat(fileres, optionfilefiname);
   else   printf("End of Imach\n");    strcat(fileres,".txt");    /* Other files have txt extension */
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */  
      /*---------arguments file --------*/
   /* 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);*/    if((ficpar=fopen(optionfile,"r"))==NULL)    {
   /*------ End -----------*/      printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       goto end;
  end:    }
 #ifdef windows  
   /* chdir(pathcd);*/    strcpy(filereso,"o");
 #endif    strcat(filereso,fileres);
  /*system("wgnuplot graph.plt");*/    if((ficparo=fopen(filereso,"w"))==NULL) {
  /*system("../gp37mgw/wgnuplot graph.plt");*/      printf("Problem with Output resultfile: %s\n", filereso);
  /*system("cd ../gp37mgw");*/      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/      goto end;
  strcpy(plotcmd,GNUPLOTPROGRAM);    }
  strcat(plotcmd," ");  
  strcat(plotcmd,optionfilegnuplot);    /* Reads comments: lines beginning with '#' */
  system(plotcmd);    while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
 #ifdef windows      fgets(line, MAXLINE, ficpar);
   while (z[0] != 'q') {      puts(line);
     /* chdir(path); */      fputs(line,ficparo);
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    }
     scanf("%s",z);    ungetc(c,ficpar);
     if (z[0] == 'c') system("./imach");  
     else if (z[0] == 'e') system(optionfilehtm);    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);
     else if (z[0] == 'g') system(plotcmd);    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);
     else if (z[0] == 'q') exit(0);    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){
 #endif      ungetc(c,ficpar);
 }      fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     
     /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++)
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)
           printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){
             printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
           }
           else
             fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);
         }
         fscanf(ficpar,"\n");
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     delti=delti3[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
           fprintf(ficlog," %.5le",matcov[i][j]);
         }
         else
           fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=ivector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=1; (m<= maxwav); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if(moisdc[i]!=99 && andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if (andc[i]!=9999){
                   printf("Warning negative age at death: %d line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Should no more exist */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if(mint[m][i]==99 || anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=1; (m<= maxwav); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
   
       pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     jk=1;
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) 
           {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
       }
     }
     if(mle==1){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle==1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+mprev1/12.+jprev1/365.;
     dateprev2=anprev2+mprev2/12.+jprev2/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);
     fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
     fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
   
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     fclose(ficgp);
     printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfile);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
   \n
   Total number of observations=%d <br>\n
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
   <hr  size=\"2\" color=\"#EC5E5E\">
    <ul><li><h4>Parameter files</h4>\n
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
    - Log file of the run: <a href=\"%s\">%s</a><br>\n
    - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
     fclose(fichtm);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     chdir(path);
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_ivector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f",age );
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Age");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
   
     /*---------- Forecasting ------------------*/
     if((stepm == 1) && (strcmp(model,".")==0)){
       prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
       if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
     } 
     else{
       erreur=108;
       printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
       fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     calagedate=-1;
   
     prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     free_vector(delti,1,npar);
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     fprintf(fichtm,"\n</body>");
     fclose(fichtm);
     fclose(ficgp);
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     
     /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
     /*printf("Total time was %d uSec.\n", total_usecs);*/
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting: %s\n",plotcmd);fflush(stdout);
     system(plotcmd);
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   
Removed from v.1.35  
changed lines
  Added in v.1.65

FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>