Diff for /imach/src/imach.c between versions 1.35 and 1.58

version 1.35, 2002/03/26 17:08:39 version 1.58, 2002/07/26 12:29:55
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 0.8k, July 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;  double jmean; /* Mean space between 2 waves */
   char fileresv[FILENAMELENGTH];  double **oldm, **newm, **savm; /* Working pointers to matrices */
  FILE  *ficresvpl;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   char fileresvpl[FILENAMELENGTH];  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   FILE *ficlog;
 #define NR_END 1  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 #define FREE_ARG char*  FILE *ficresprobmorprev;
 #define FTOL 1.0e-10  FILE *fichtm; /* Html File */
   FILE *ficreseij;
 #define NRANSI  char filerese[FILENAMELENGTH];
 #define ITMAX 200  FILE  *ficresvij;
   char fileresv[FILENAMELENGTH];
 #define TOL 2.0e-4  FILE  *ficresvpl;
   char fileresvpl[FILENAMELENGTH];
 #define CGOLD 0.3819660  char title[MAXLINE];
 #define ZEPS 1.0e-10  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   
 #define GOLD 1.618034  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 #define GLIMIT 100.0  char filelog[FILENAMELENGTH]; /* Log file */
 #define TINY 1.0e-20  char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
 static double maxarg1,maxarg2;  char popfile[FILENAMELENGTH];
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  #define NR_END 1
 #define rint(a) floor(a+0.5)  #define FREE_ARG char*
   #define FTOL 1.0e-10
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  #define NRANSI 
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  #define ITMAX 200 
   
 int imx;  #define TOL 2.0e-4 
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
 int m,nb;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  #define GOLD 1.618034 
 double **pmmij, ***probs, ***mobaverage;  #define GLIMIT 100.0 
 double dateintmean=0;  #define TINY 1.0e-20 
   
 double *weight;  static double maxarg1,maxarg2;
 int **s; /* Status */  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 double *agedc, **covar, idx;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    
   #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  #define rint(a) floor(a+0.5)
 double ftolhess; /* Tolerance for computing hessian */  
   static double sqrarg;
 /**************** split *************************/  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 {  
    char *s;                             /* pointer */  int imx; 
    int  l1, l2;                         /* length counters */  int stepm;
   /* Stepm, step in month: minimum step interpolation*/
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  int estepm;
 #ifdef windows  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
    s = strrchr( path, '\\' );           /* find last / */  
 #else  int m,nb;
    s = strrchr( path, '/' );            /* find last / */  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 #endif  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
    if ( s == NULL ) {                   /* no directory, so use current */  double **pmmij, ***probs;
 #if     defined(__bsd__)                /* get current working directory */  double dateintmean=0;
       extern char       *getwd( );  
   double *weight;
       if ( getwd( dirc ) == NULL ) {  int **s; /* Status */
 #else  double *agedc, **covar, idx;
       extern char       *getcwd( );  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 #endif  double ftolhess; /* Tolerance for computing hessian */
          return( GLOCK_ERROR_GETCWD );  
       }  /**************** split *************************/
       strcpy( name, path );             /* we've got it */  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
    } else {                             /* strip direcotry from path */  {
       s++;                              /* after this, the filename */     char *s;                             /* pointer */
       l2 = strlen( s );                 /* length of filename */     int  l1, l2;                         /* length counters */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */     l1 = strlen( path );                 /* length of path */
       strncpy( dirc, path, l1 - l2 );   /* now the directory */     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       dirc[l1-l2] = 0;                  /* add zero */     s= strrchr( path, DIRSEPARATOR );            /* find last / */
    }     if ( s == NULL ) {                   /* no directory, so use current */
    l1 = strlen( dirc );                 /* length of directory */       /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 #ifdef windows         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 */
 #else        extern char       *getwd( );
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif        if ( getwd( dirc ) == NULL ) {
    s = strrchr( name, '.' );            /* find last / */  #else
    s++;        extern char       *getcwd( );
    strcpy(ext,s);                       /* save extension */  
    l1= strlen( name);        if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
    l2= strlen( s)+1;  #endif
    strncpy( finame, name, l1-l2);           return( GLOCK_ERROR_GETCWD );
    finame[l1-l2]= 0;        }
    return( 0 );                         /* we're done */        strcpy( name, path );             /* we've got it */
 }     } else {                             /* strip direcotry from path */
         s++;                              /* after this, the filename */
         l2 = strlen( s );                 /* length of filename */
 /******************************************/        if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
         strcpy( name, s );                /* save file name */
 void replace(char *s, char*t)        strncpy( dirc, path, l1 - l2 );   /* now the directory */
 {        dirc[l1-l2] = 0;                  /* add zero */
   int i;     }
   int lg=20;     l1 = strlen( dirc );                 /* length of directory */
   i=0;  #ifdef windows
   lg=strlen(t);     if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   for(i=0; i<= lg; i++) {  #else
     (s[i] = t[i]);     if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
     if (t[i]== '\\') s[i]='/';  #endif
   }     s = strrchr( name, '.' );            /* find last / */
 }     s++;
      strcpy(ext,s);                       /* save extension */
 int nbocc(char *s, char occ)     l1= strlen( name);
 {     l2= strlen( s)+1;
   int i,j=0;     strncpy( finame, name, l1-l2);
   int lg=20;     finame[l1-l2]= 0;
   i=0;     return( 0 );                         /* we're done */
   lg=strlen(s);  }
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;  
   }  /******************************************/
   return j;  
 }  void replace(char *s, char*t)
   {
 void cutv(char *u,char *v, char*t, char occ)    int i;
 {    int lg=20;
   int i,lg,j,p=0;    i=0;
   i=0;    lg=strlen(t);
   for(j=0; j<=strlen(t)-1; j++) {    for(i=0; i<= lg; i++) {
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;      (s[i] = t[i]);
   }      if (t[i]== '\\') s[i]='/';
     }
   lg=strlen(t);  }
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);  int nbocc(char *s, char occ)
   }  {
      u[p]='\0';    int i,j=0;
     int lg=20;
    for(j=0; j<= lg; j++) {    i=0;
     if (j>=(p+1))(v[j-p-1] = t[j]);    lg=strlen(s);
   }    for(i=0; i<= lg; i++) {
 }    if  (s[i] == occ ) j++;
     }
 /********************** nrerror ********************/    return j;
   }
 void nrerror(char error_text[])  
 {  void cutv(char *u,char *v, char*t, char occ)
   fprintf(stderr,"ERREUR ...\n");  {
   fprintf(stderr,"%s\n",error_text);    /* cuts string t into u and v where u is ended by char occ excluding it
   exit(1);       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 }       gives u="abcedf" and v="ghi2j" */
 /*********************** vector *******************/    int i,lg,j,p=0;
 double *vector(int nl, int nh)    i=0;
 {    for(j=0; j<=strlen(t)-1; j++) {
   double *v;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    }
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;    lg=strlen(t);
 }    for(j=0; j<p; j++) {
       (u[j] = t[j]);
 /************************ free vector ******************/    }
 void free_vector(double*v, int nl, int nh)       u[p]='\0';
 {  
   free((FREE_ARG)(v+nl-NR_END));     for(j=0; j<= lg; j++) {
 }      if (j>=(p+1))(v[j-p-1] = t[j]);
     }
 /************************ivector *******************************/  }
 int *ivector(long nl,long nh)  
 {  /********************** nrerror ********************/
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  void nrerror(char error_text[])
   if (!v) nrerror("allocation failure in ivector");  {
   return v-nl+NR_END;    fprintf(stderr,"ERREUR ...\n");
 }    fprintf(stderr,"%s\n",error_text);
     exit(1);
 /******************free ivector **************************/  }
 void free_ivector(int *v, long nl, long nh)  /*********************** vector *******************/
 {  double *vector(int nl, int nh)
   free((FREE_ARG)(v+nl-NR_END));  {
 }    double *v;
     v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 /******************* imatrix *******************************/    if (!v) nrerror("allocation failure in vector");
 int **imatrix(long nrl, long nrh, long ncl, long nch)    return v-nl+NR_END;
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  }
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  /************************ free vector ******************/
   int **m;  void free_vector(double*v, int nl, int nh)
    {
   /* allocate pointers to rows */    free((FREE_ARG)(v+nl-NR_END));
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  }
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  /************************ivector *******************************/
   m -= nrl;  int *ivector(long nl,long nh)
    {
      int *v;
   /* allocate rows and set pointers to them */    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    if (!v) nrerror("allocation failure in ivector");
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    return v-nl+NR_END;
   m[nrl] += NR_END;  }
   m[nrl] -= ncl;  
    /******************free ivector **************************/
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  void free_ivector(int *v, long nl, long nh)
    {
   /* return pointer to array of pointers to rows */    free((FREE_ARG)(v+nl-NR_END));
   return m;  }
 }  
   /******************* imatrix *******************************/
 /****************** free_imatrix *************************/  int **imatrix(long nrl, long nrh, long ncl, long nch) 
 void free_imatrix(m,nrl,nrh,ncl,nch)       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       int **m;  { 
       long nch,ncl,nrh,nrl;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
      /* free an int matrix allocated by imatrix() */    int **m; 
 {    
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    /* allocate pointers to rows */ 
   free((FREE_ARG) (m+nrl-NR_END));    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 }    if (!m) nrerror("allocation failure 1 in matrix()"); 
     m += NR_END; 
 /******************* matrix *******************************/    m -= nrl; 
 double **matrix(long nrl, long nrh, long ncl, long nch)    
 {    
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    /* allocate rows and set pointers to them */ 
   double **m;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    m[nrl] += NR_END; 
   if (!m) nrerror("allocation failure 1 in matrix()");    m[nrl] -= ncl; 
   m += NR_END;    
   m -= nrl;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    /* return pointer to array of pointers to rows */ 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    return m; 
   m[nrl] += NR_END;  } 
   m[nrl] -= ncl;  
   /****************** free_imatrix *************************/
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  void free_imatrix(m,nrl,nrh,ncl,nch)
   return m;        int **m;
 }        long nch,ncl,nrh,nrl; 
        /* free an int matrix allocated by imatrix() */ 
 /*************************free matrix ************************/  { 
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 {    free((FREE_ARG) (m+nrl-NR_END)); 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  } 
   free((FREE_ARG)(m+nrl-NR_END));  
 }  /******************* matrix *******************************/
   double **matrix(long nrl, long nrh, long ncl, long nch)
 /******************* ma3x *******************************/  {
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 {    double **m;
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    m += NR_END;
   if (!m) nrerror("allocation failure 1 in matrix()");    m -= nrl;
   m += NR_END;  
   m -= nrl;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    m[nrl] += NR_END;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    m[nrl] -= ncl;
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     return m;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  }
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  /*************************free matrix ************************/
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   m[nrl][ncl] += NR_END;  {
   m[nrl][ncl] -= nll;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   for (j=ncl+1; j<=nch; j++)    free((FREE_ARG)(m+nrl-NR_END));
     m[nrl][j]=m[nrl][j-1]+nlay;  }
    
   for (i=nrl+1; i<=nrh; i++) {  /******************* ma3x *******************************/
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     for (j=ncl+1; j<=nch; j++)  {
       m[i][j]=m[i][j-1]+nlay;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   }    double ***m;
   return m;  
 }    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
 /*************************free ma3x ************************/    m += NR_END;
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    m -= nrl;
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   free((FREE_ARG)(m+nrl-NR_END));    m[nrl] += NR_END;
 }    m[nrl] -= ncl;
   
 /***************** f1dim *************************/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 extern int ncom;  
 extern double *pcom,*xicom;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 extern double (*nrfunc)(double []);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
      m[nrl][ncl] += NR_END;
 double f1dim(double x)    m[nrl][ncl] -= nll;
 {    for (j=ncl+1; j<=nch; j++) 
   int j;      m[nrl][j]=m[nrl][j-1]+nlay;
   double f;    
   double *xt;    for (i=nrl+1; i<=nrh; i++) {
        m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   xt=vector(1,ncom);      for (j=ncl+1; j<=nch; j++) 
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];        m[i][j]=m[i][j-1]+nlay;
   f=(*nrfunc)(xt);    }
   free_vector(xt,1,ncom);    return m;
   return f;  }
 }  
   /*************************free ma3x ************************/
 /*****************brent *************************/  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  {
 {    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   int iter;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double a,b,d,etemp;    free((FREE_ARG)(m+nrl-NR_END));
   double fu,fv,fw,fx;  }
   double ftemp;  
   double p,q,r,tol1,tol2,u,v,w,x,xm;  /***************** f1dim *************************/
   double e=0.0;  extern int ncom; 
    extern double *pcom,*xicom;
   a=(ax < cx ? ax : cx);  extern double (*nrfunc)(double []); 
   b=(ax > cx ? ax : cx);   
   x=w=v=bx;  double f1dim(double x) 
   fw=fv=fx=(*f)(x);  { 
   for (iter=1;iter<=ITMAX;iter++) {    int j; 
     xm=0.5*(a+b);    double f;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    double *xt; 
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/   
     printf(".");fflush(stdout);    xt=vector(1,ncom); 
 #ifdef DEBUG    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     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);    f=(*nrfunc)(xt); 
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    free_vector(xt,1,ncom); 
 #endif    return f; 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  } 
       *xmin=x;  
       return fx;  /*****************brent *************************/
     }  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     ftemp=fu;  { 
     if (fabs(e) > tol1) {    int iter; 
       r=(x-w)*(fx-fv);    double a,b,d,etemp;
       q=(x-v)*(fx-fw);    double fu,fv,fw,fx;
       p=(x-v)*q-(x-w)*r;    double ftemp;
       q=2.0*(q-r);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       if (q > 0.0) p = -p;    double e=0.0; 
       q=fabs(q);   
       etemp=e;    a=(ax < cx ? ax : cx); 
       e=d;    b=(ax > cx ? ax : cx); 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    x=w=v=bx; 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    fw=fv=fx=(*f)(x); 
       else {    for (iter=1;iter<=ITMAX;iter++) { 
         d=p/q;      xm=0.5*(a+b); 
         u=x+d;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
         if (u-a < tol2 || b-u < tol2)      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
           d=SIGN(tol1,xm-x);      printf(".");fflush(stdout);
       }      fprintf(ficlog,".");fflush(ficlog);
     } else {  #ifdef DEBUG
       d=CGOLD*(e=(x >= xm ? a-x : b-x));      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);
     }      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);
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     fu=(*f)(u);  #endif
     if (fu <= fx) {      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       if (u >= x) a=x; else b=x;        *xmin=x; 
       SHFT(v,w,x,u)        return fx; 
         SHFT(fv,fw,fx,fu)      } 
         } else {      ftemp=fu;
           if (u < x) a=u; else b=u;      if (fabs(e) > tol1) { 
           if (fu <= fw || w == x) {        r=(x-w)*(fx-fv); 
             v=w;        q=(x-v)*(fx-fw); 
             w=u;        p=(x-v)*q-(x-w)*r; 
             fv=fw;        q=2.0*(q-r); 
             fw=fu;        if (q > 0.0) p = -p; 
           } else if (fu <= fv || v == x || v == w) {        q=fabs(q); 
             v=u;        etemp=e; 
             fv=fu;        e=d; 
           }        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
         }          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   }        else { 
   nrerror("Too many iterations in brent");          d=p/q; 
   *xmin=x;          u=x+d; 
   return fx;          if (u-a < tol2 || b-u < tol2) 
 }            d=SIGN(tol1,xm-x); 
         } 
 /****************** mnbrak ***********************/      } else { 
         d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,      } 
             double (*func)(double))      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
 {      fu=(*f)(u); 
   double ulim,u,r,q, dum;      if (fu <= fx) { 
   double fu;        if (u >= x) a=x; else b=x; 
          SHFT(v,w,x,u) 
   *fa=(*func)(*ax);          SHFT(fv,fw,fx,fu) 
   *fb=(*func)(*bx);          } else { 
   if (*fb > *fa) {            if (u < x) a=u; else b=u; 
     SHFT(dum,*ax,*bx,dum)            if (fu <= fw || w == x) { 
       SHFT(dum,*fb,*fa,dum)              v=w; 
       }              w=u; 
   *cx=(*bx)+GOLD*(*bx-*ax);              fv=fw; 
   *fc=(*func)(*cx);              fw=fu; 
   while (*fb > *fc) {            } else if (fu <= fv || v == x || v == w) { 
     r=(*bx-*ax)*(*fb-*fc);              v=u; 
     q=(*bx-*cx)*(*fb-*fa);              fv=fu; 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/            } 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));          } 
     ulim=(*bx)+GLIMIT*(*cx-*bx);    } 
     if ((*bx-u)*(u-*cx) > 0.0) {    nrerror("Too many iterations in brent"); 
       fu=(*func)(u);    *xmin=x; 
     } else if ((*cx-u)*(u-ulim) > 0.0) {    return fx; 
       fu=(*func)(u);  } 
       if (fu < *fc) {  
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  /****************** mnbrak ***********************/
           SHFT(*fb,*fc,fu,(*func)(u))  
           }  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {              double (*func)(double)) 
       u=ulim;  { 
       fu=(*func)(u);    double ulim,u,r,q, dum;
     } else {    double fu; 
       u=(*cx)+GOLD*(*cx-*bx);   
       fu=(*func)(u);    *fa=(*func)(*ax); 
     }    *fb=(*func)(*bx); 
     SHFT(*ax,*bx,*cx,u)    if (*fb > *fa) { 
       SHFT(*fa,*fb,*fc,fu)      SHFT(dum,*ax,*bx,dum) 
       }        SHFT(dum,*fb,*fa,dum) 
 }        } 
     *cx=(*bx)+GOLD*(*bx-*ax); 
 /*************** linmin ************************/    *fc=(*func)(*cx); 
     while (*fb > *fc) { 
 int ncom;      r=(*bx-*ax)*(*fb-*fc); 
 double *pcom,*xicom;      q=(*bx-*cx)*(*fb-*fa); 
 double (*nrfunc)(double []);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
          (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))      ulim=(*bx)+GLIMIT*(*cx-*bx); 
 {      if ((*bx-u)*(u-*cx) > 0.0) { 
   double brent(double ax, double bx, double cx,        fu=(*func)(u); 
                double (*f)(double), double tol, double *xmin);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   double f1dim(double x);        fu=(*func)(u); 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,        if (fu < *fc) { 
               double *fc, double (*func)(double));          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   int j;            SHFT(*fb,*fc,fu,(*func)(u)) 
   double xx,xmin,bx,ax;            } 
   double fx,fb,fa;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
          u=ulim; 
   ncom=n;        fu=(*func)(u); 
   pcom=vector(1,n);      } else { 
   xicom=vector(1,n);        u=(*cx)+GOLD*(*cx-*bx); 
   nrfunc=func;        fu=(*func)(u); 
   for (j=1;j<=n;j++) {      } 
     pcom[j]=p[j];      SHFT(*ax,*bx,*cx,u) 
     xicom[j]=xi[j];        SHFT(*fa,*fb,*fc,fu) 
   }        } 
   ax=0.0;  } 
   xx=1.0;  
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /*************** linmin ************************/
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  
 #ifdef DEBUG  int ncom; 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  double *pcom,*xicom;
 #endif  double (*nrfunc)(double []); 
   for (j=1;j<=n;j++) {   
     xi[j] *= xmin;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     p[j] += xi[j];  { 
   }    double brent(double ax, double bx, double cx, 
   free_vector(xicom,1,n);                 double (*f)(double), double tol, double *xmin); 
   free_vector(pcom,1,n);    double f1dim(double x); 
 }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                 double *fc, double (*func)(double)); 
 /*************** powell ************************/    int j; 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    double xx,xmin,bx,ax; 
             double (*func)(double []))    double fx,fb,fa;
 {   
   void linmin(double p[], double xi[], int n, double *fret,    ncom=n; 
               double (*func)(double []));    pcom=vector(1,n); 
   int i,ibig,j;    xicom=vector(1,n); 
   double del,t,*pt,*ptt,*xit;    nrfunc=func; 
   double fp,fptt;    for (j=1;j<=n;j++) { 
   double *xits;      pcom[j]=p[j]; 
   pt=vector(1,n);      xicom[j]=xi[j]; 
   ptt=vector(1,n);    } 
   xit=vector(1,n);    ax=0.0; 
   xits=vector(1,n);    xx=1.0; 
   *fret=(*func)(p);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   for (j=1;j<=n;j++) pt[j]=p[j];    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   for (*iter=1;;++(*iter)) {  #ifdef DEBUG
     fp=(*fret);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     ibig=0;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     del=0.0;  #endif
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    for (j=1;j<=n;j++) { 
     for (i=1;i<=n;i++)      xi[j] *= xmin; 
       printf(" %d %.12f",i, p[i]);      p[j] += xi[j]; 
     printf("\n");    } 
     for (i=1;i<=n;i++) {    free_vector(xicom,1,n); 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    free_vector(pcom,1,n); 
       fptt=(*fret);  } 
 #ifdef DEBUG  
       printf("fret=%lf \n",*fret);  /*************** powell ************************/
 #endif  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       printf("%d",i);fflush(stdout);              double (*func)(double [])) 
       linmin(p,xit,n,fret,func);  { 
       if (fabs(fptt-(*fret)) > del) {    void linmin(double p[], double xi[], int n, double *fret, 
         del=fabs(fptt-(*fret));                double (*func)(double [])); 
         ibig=i;    int i,ibig,j; 
       }    double del,t,*pt,*ptt,*xit;
 #ifdef DEBUG    double fp,fptt;
       printf("%d %.12e",i,(*fret));    double *xits;
       for (j=1;j<=n;j++) {    pt=vector(1,n); 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    ptt=vector(1,n); 
         printf(" x(%d)=%.12e",j,xit[j]);    xit=vector(1,n); 
       }    xits=vector(1,n); 
       for(j=1;j<=n;j++)    *fret=(*func)(p); 
         printf(" p=%.12e",p[j]);    for (j=1;j<=n;j++) pt[j]=p[j]; 
       printf("\n");    for (*iter=1;;++(*iter)) { 
 #endif      fp=(*fret); 
     }      ibig=0; 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      del=0.0; 
 #ifdef DEBUG      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       int k[2],l;      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       k[0]=1;      for (i=1;i<=n;i++) 
       k[1]=-1;        printf(" %d %.12f",i, p[i]);
       printf("Max: %.12e",(*func)(p));      fprintf(ficlog," %d %.12f",i, p[i]);
       for (j=1;j<=n;j++)      printf("\n");
         printf(" %.12e",p[j]);      fprintf(ficlog,"\n");
       printf("\n");      for (i=1;i<=n;i++) { 
       for(l=0;l<=1;l++) {        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         for (j=1;j<=n;j++) {        fptt=(*fret); 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  #ifdef DEBUG
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);        printf("fret=%lf \n",*fret);
         }        fprintf(ficlog,"fret=%lf \n",*fret);
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  #endif
       }        printf("%d",i);fflush(stdout);
 #endif        fprintf(ficlog,"%d",i);fflush(ficlog);
         linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
       free_vector(xit,1,n);          del=fabs(fptt-(*fret)); 
       free_vector(xits,1,n);          ibig=i; 
       free_vector(ptt,1,n);        } 
       free_vector(pt,1,n);  #ifdef DEBUG
       return;        printf("%d %.12e",i,(*fret));
     }        fprintf(ficlog,"%d %.12e",i,(*fret));
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");        for (j=1;j<=n;j++) {
     for (j=1;j<=n;j++) {          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       ptt[j]=2.0*p[j]-pt[j];          printf(" x(%d)=%.12e",j,xit[j]);
       xit[j]=p[j]-pt[j];          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       pt[j]=p[j];        }
     }        for(j=1;j<=n;j++) {
     fptt=(*func)(ptt);          printf(" p=%.12e",p[j]);
     if (fptt < fp) {          fprintf(ficlog," p=%.12e",p[j]);
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);        }
       if (t < 0.0) {        printf("\n");
         linmin(p,xit,n,fret,func);        fprintf(ficlog,"\n");
         for (j=1;j<=n;j++) {  #endif
           xi[j][ibig]=xi[j][n];      } 
           xi[j][n]=xit[j];      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
         }  #ifdef DEBUG
 #ifdef DEBUG        int k[2],l;
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);        k[0]=1;
         for(j=1;j<=n;j++)        k[1]=-1;
           printf(" %.12e",xit[j]);        printf("Max: %.12e",(*func)(p));
         printf("\n");        fprintf(ficlog,"Max: %.12e",(*func)(p));
 #endif        for (j=1;j<=n;j++) {
       }          printf(" %.12e",p[j]);
     }          fprintf(ficlog," %.12e",p[j]);
   }        }
 }        printf("\n");
         fprintf(ficlog,"\n");
 /**** Prevalence limit ****************/        for(l=0;l<=1;l++) {
           for (j=1;j<=n;j++) {
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
 {            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
      matrix by transitions matrix until convergence is reached */          }
           printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   int i, ii,j,k;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   double min, max, maxmin, maxmax,sumnew=0.;        }
   double **matprod2();  #endif
   double **out, cov[NCOVMAX], **pmij();  
   double **newm;  
   double agefin, delaymax=50 ; /* Max number of years to converge */        free_vector(xit,1,n); 
         free_vector(xits,1,n); 
   for (ii=1;ii<=nlstate+ndeath;ii++)        free_vector(ptt,1,n); 
     for (j=1;j<=nlstate+ndeath;j++){        free_vector(pt,1,n); 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        return; 
     }      } 
       if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
    cov[1]=1.;      for (j=1;j<=n;j++) { 
          ptt[j]=2.0*p[j]-pt[j]; 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        xit[j]=p[j]-pt[j]; 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        pt[j]=p[j]; 
     newm=savm;      } 
     /* Covariates have to be included here again */      fptt=(*func)(ptt); 
      cov[2]=agefin;      if (fptt < fp) { 
          t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       for (k=1; k<=cptcovn;k++) {        if (t < 0.0) { 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];          linmin(p,xit,n,fret,func); 
         /*      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=1;j<=n;j++) { 
       }            xi[j][ibig]=xi[j][n]; 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];            xi[j][n]=xit[j]; 
       for (k=1; k<=cptcovprod;k++)          }
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  #ifdef DEBUG
           printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/          for(j=1;j<=n;j++){
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/            printf(" %.12e",xit[j]);
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);            fprintf(ficlog," %.12e",xit[j]);
           }
     savm=oldm;          printf("\n");
     oldm=newm;          fprintf(ficlog,"\n");
     maxmax=0.;  #endif
     for(j=1;j<=nlstate;j++){        }
       min=1.;      } 
       max=0.;    } 
       for(i=1; i<=nlstate; i++) {  } 
         sumnew=0;  
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  /**** Prevalence limit (stable prevalence)  ****************/
         prlim[i][j]= newm[i][j]/(1-sumnew);  
         max=FMAX(max,prlim[i][j]);  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
         min=FMIN(min,prlim[i][j]);  {
       }    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       maxmin=max-min;       matrix by transitions matrix until convergence is reached */
       maxmax=FMAX(maxmax,maxmin);  
     }    int i, ii,j,k;
     if(maxmax < ftolpl){    double min, max, maxmin, maxmax,sumnew=0.;
       return prlim;    double **matprod2();
     }    double **out, cov[NCOVMAX], **pmij();
   }    double **newm;
 }    double agefin, delaymax=50 ; /* Max number of years to converge */
   
 /*************** transition probabilities ***************/    for (ii=1;ii<=nlstate+ndeath;ii++)
       for (j=1;j<=nlstate+ndeath;j++){
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 {      }
   double s1, s2;  
   /*double t34;*/     cov[1]=1.;
   int i,j,j1, nc, ii, jj;   
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(i=1; i<= nlstate; i++){    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     for(j=1; j<i;j++){      newm=savm;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      /* Covariates have to be included here again */
         /*s2 += param[i][j][nc]*cov[nc];*/       cov[2]=agefin;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/        for (k=1; k<=cptcovn;k++) {
       }          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       ps[i][j]=s2;          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        }
     }        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for(j=i+1; j<=nlstate+ndeath;j++){        for (k=1; k<=cptcovprod;k++)
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       }        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
       ps[i][j]=s2;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     }      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   }  
     /*ps[3][2]=1;*/      savm=oldm;
       oldm=newm;
   for(i=1; i<= nlstate; i++){      maxmax=0.;
      s1=0;      for(j=1;j<=nlstate;j++){
     for(j=1; j<i; j++)        min=1.;
       s1+=exp(ps[i][j]);        max=0.;
     for(j=i+1; j<=nlstate+ndeath; j++)        for(i=1; i<=nlstate; i++) {
       s1+=exp(ps[i][j]);          sumnew=0;
     ps[i][i]=1./(s1+1.);          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     for(j=1; j<i; j++)          prlim[i][j]= newm[i][j]/(1-sumnew);
       ps[i][j]= exp(ps[i][j])*ps[i][i];          max=FMAX(max,prlim[i][j]);
     for(j=i+1; j<=nlstate+ndeath; j++)          min=FMIN(min,prlim[i][j]);
       ps[i][j]= exp(ps[i][j])*ps[i][i];        }
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        maxmin=max-min;
   } /* end i */        maxmax=FMAX(maxmax,maxmin);
       }
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      if(maxmax < ftolpl){
     for(jj=1; jj<= nlstate+ndeath; jj++){        return prlim;
       ps[ii][jj]=0;      }
       ps[ii][ii]=1;    }
     }  }
   }  
   /*************** transition probabilities ***************/ 
   
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     for(jj=1; jj<= nlstate+ndeath; jj++){  {
      printf("%lf ",ps[ii][jj]);    double s1, s2;
    }    /*double t34;*/
     printf("\n ");    int i,j,j1, nc, ii, jj;
     }  
     printf("\n ");printf("%lf ",cov[2]);*/      for(i=1; i<= nlstate; i++){
 /*      for(j=1; j<i;j++){
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   goto end;*/          /*s2 += param[i][j][nc]*cov[nc];*/
     return ps;          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
 }          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
         }
 /**************** Product of 2 matrices ******************/        ps[i][j]=s2;
         /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      }
 {      for(j=i+1; j<=nlstate+ndeath;j++){
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   /* in, b, out are matrice of pointers which should have been initialized          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
      before: only the contents of out is modified. The function returns        }
      a pointer to pointers identical to out */        ps[i][j]=s2;
   long i, j, k;      }
   for(i=nrl; i<= nrh; i++)    }
     for(k=ncolol; k<=ncoloh; k++)      /*ps[3][2]=1;*/
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  
         out[i][k] +=in[i][j]*b[j][k];    for(i=1; i<= nlstate; i++){
        s1=0;
   return out;      for(j=1; j<i; j++)
 }        s1+=exp(ps[i][j]);
       for(j=i+1; j<=nlstate+ndeath; j++)
         s1+=exp(ps[i][j]);
 /************* Higher Matrix Product ***************/      ps[i][i]=1./(s1+1.);
       for(j=1; j<i; j++)
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )        ps[i][j]= exp(ps[i][j])*ps[i][i];
 {      for(j=i+1; j<=nlstate+ndeath; j++)
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month        ps[i][j]= exp(ps[i][j])*ps[i][i];
      duration (i.e. until      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    } /* end i */
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  
      (typically every 2 years instead of every month which is too big).    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
      Model is determined by parameters x and covariates have to be      for(jj=1; jj<= nlstate+ndeath; jj++){
      included manually here.        ps[ii][jj]=0;
         ps[ii][ii]=1;
      */      }
     }
   int i, j, d, h, k;  
   double **out, cov[NCOVMAX];  
   double **newm;    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
       for(jj=1; jj<= nlstate+ndeath; jj++){
   /* Hstepm could be zero and should return the unit matrix */       printf("%lf ",ps[ii][jj]);
   for (i=1;i<=nlstate+ndeath;i++)     }
     for (j=1;j<=nlstate+ndeath;j++){      printf("\n ");
       oldm[i][j]=(i==j ? 1.0 : 0.0);      }
       po[i][j][0]=(i==j ? 1.0 : 0.0);      printf("\n ");printf("%lf ",cov[2]);*/
     }  /*
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    for(i=1; i<= npar; i++) printf("%f ",x[i]);
   for(h=1; h <=nhstepm; h++){    goto end;*/
     for(d=1; d <=hstepm; d++){      return ps;
       newm=savm;  }
       /* Covariates have to be included here again */  
       cov[1]=1.;  /**************** Product of 2 matrices ******************/
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
       for (k=1; k<=cptcovage;k++)  {
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       for (k=1; k<=cptcovprod;k++)       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    /* in, b, out are matrice of pointers which should have been initialized 
        before: only the contents of out is modified. The function returns
        a pointer to pointers identical to out */
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    long i, j, k;
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    for(i=nrl; i<= nrh; i++)
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      for(k=ncolol; k<=ncoloh; k++)
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        for(j=ncl,out[i][k]=0.; j<=nch; j++)
       savm=oldm;          out[i][k] +=in[i][j]*b[j][k];
       oldm=newm;  
     }    return out;
     for(i=1; i<=nlstate+ndeath; i++)  }
       for(j=1;j<=nlstate+ndeath;j++) {  
         po[i][j][h]=newm[i][j];  
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  /************* Higher Matrix Product ***************/
          */  
       }  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   } /* end h */  {
   return po;    /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month 
 }       duration (i.e. until
        age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices. 
        Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
 /*************** log-likelihood *************/       (typically every 2 years instead of every month which is too big).
 double func( double *x)       Model is determined by parameters x and covariates have to be 
 {       included manually here. 
   int i, ii, j, k, mi, d, kk;  
   double l, ll[NLSTATEMAX], cov[NCOVMAX];       */
   double **out;  
   double sw; /* Sum of weights */    int i, j, d, h, k;
   double lli; /* Individual log likelihood */    double **out, cov[NCOVMAX];
   long ipmx;    double **newm;
   /*extern weight */  
   /* We are differentiating ll according to initial status */    /* Hstepm could be zero and should return the unit matrix */
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    for (i=1;i<=nlstate+ndeath;i++)
   /*for(i=1;i<imx;i++)      for (j=1;j<=nlstate+ndeath;j++){
     printf(" %d\n",s[4][i]);        oldm[i][j]=(i==j ? 1.0 : 0.0);
   */        po[i][j][0]=(i==j ? 1.0 : 0.0);
   cov[1]=1.;      }
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   for(k=1; k<=nlstate; k++) ll[k]=0.;    for(h=1; h <=nhstepm; h++){
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      for(d=1; d <=hstepm; d++){
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        newm=savm;
     for(mi=1; mi<= wav[i]-1; mi++){        /* Covariates have to be included here again */
       for (ii=1;ii<=nlstate+ndeath;ii++)        cov[1]=1.;
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       for(d=0; d<dh[mi][i]; d++){        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         newm=savm;        for (k=1; k<=cptcovage;k++)
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (kk=1; kk<=cptcovage;kk++) {        for (k=1; k<=cptcovprod;k++)
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         }  
          
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         savm=oldm;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
         oldm=newm;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
                savm=oldm;
                oldm=newm;
       } /* end mult */      }
            for(i=1; i<=nlstate+ndeath; i++)
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        for(j=1;j<=nlstate+ndeath;j++) {
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/          po[i][j][h]=newm[i][j];
       ipmx +=1;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
       sw += weight[i];           */
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        }
     } /* end of wave */    } /* end h */
   } /* end of individual */    return po;
   }
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  /*************** log-likelihood *************/
   return -l;  double func( double *x)
 }  {
     int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX], cov[NCOVMAX];
 /*********** Maximum Likelihood Estimation ***************/    double **out;
     double sw; /* Sum of weights */
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    double lli; /* Individual log likelihood */
 {    long ipmx;
   int i,j, iter;    /*extern weight */
   double **xi,*delti;    /* We are differentiating ll according to initial status */
   double fret;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   xi=matrix(1,npar,1,npar);    /*for(i=1;i<imx;i++) 
   for (i=1;i<=npar;i++)      printf(" %d\n",s[4][i]);
     for (j=1;j<=npar;j++)    */
       xi[i][j]=(i==j ? 1.0 : 0.0);    cov[1]=1.;
   printf("Powell\n");  
   powell(p,xi,npar,ftol,&iter,&fret,func);    for(k=1; k<=nlstate; k++) ll[k]=0.;
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      for(mi=1; mi<= wav[i]-1; mi++){
         for (ii=1;ii<=nlstate+ndeath;ii++)
 }          for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         for(d=0; d<dh[mi][i]; d++){
 /**** Computes Hessian and covariance matrix ***/          newm=savm;
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 {          for (kk=1; kk<=cptcovage;kk++) {
   double  **a,**y,*x,pd;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double **hess;          }
   int i, j,jk;          
   int *indx;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double hessii(double p[], double delta, int theta, double delti[]);          savm=oldm;
   double hessij(double p[], double delti[], int i, int j);          oldm=newm;
   void lubksb(double **a, int npar, int *indx, double b[]) ;          
   void ludcmp(double **a, int npar, int *indx, double *d) ;          
         } /* end mult */
   hess=matrix(1,npar,1,npar);        
         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
   printf("\nCalculation of the hessian matrix. Wait...\n");        /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
   for (i=1;i<=npar;i++){        ipmx +=1;
     printf("%d",i);fflush(stdout);        sw += weight[i];
     hess[i][i]=hessii(p,ftolhess,i,delti);        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     /*printf(" %f ",p[i]);*/      } /* end of wave */
     /*printf(" %lf ",hess[i][i]);*/    } /* end of individual */
   }  
      for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   for (i=1;i<=npar;i++) {    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     for (j=1;j<=npar;j++)  {    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       if (j>i) {    return -l;
         printf(".%d%d",i,j);fflush(stdout);  }
         hess[i][j]=hessij(p,delti,i,j);  
         hess[j][i]=hess[i][j];      
         /*printf(" %lf ",hess[i][j]);*/  /*********** Maximum Likelihood Estimation ***************/
       }  
     }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   }  {
   printf("\n");    int i,j, iter;
     double **xi,*delti;
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    double fret;
      xi=matrix(1,npar,1,npar);
   a=matrix(1,npar,1,npar);    for (i=1;i<=npar;i++)
   y=matrix(1,npar,1,npar);      for (j=1;j<=npar;j++)
   x=vector(1,npar);        xi[i][j]=(i==j ? 1.0 : 0.0);
   indx=ivector(1,npar);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   for (i=1;i<=npar;i++)    powell(p,xi,npar,ftol,&iter,&fret,func);
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  
   ludcmp(a,npar,indx,&pd);     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   for (j=1;j<=npar;j++) {    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;  }
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){  /**** Computes Hessian and covariance matrix ***/
       matcov[i][j]=x[i];  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     }  {
   }    double  **a,**y,*x,pd;
     double **hess;
   printf("\n#Hessian matrix#\n");    int i, j,jk;
   for (i=1;i<=npar;i++) {    int *indx;
     for (j=1;j<=npar;j++) {  
       printf("%.3e ",hess[i][j]);    double hessii(double p[], double delta, int theta, double delti[]);
     }    double hessij(double p[], double delti[], int i, int j);
     printf("\n");    void lubksb(double **a, int npar, int *indx, double b[]) ;
   }    void ludcmp(double **a, int npar, int *indx, double *d) ;
   
   /* Recompute Inverse */    hess=matrix(1,npar,1,npar);
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    printf("\nCalculation of the hessian matrix. Wait...\n");
   ludcmp(a,npar,indx,&pd);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     for (i=1;i<=npar;i++){
   /*  printf("\n#Hessian matrix recomputed#\n");      printf("%d",i);fflush(stdout);
       fprintf(ficlog,"%d",i);fflush(ficlog);
   for (j=1;j<=npar;j++) {      hess[i][i]=hessii(p,ftolhess,i,delti);
     for (i=1;i<=npar;i++) x[i]=0;      /*printf(" %f ",p[i]);*/
     x[j]=1;      /*printf(" %lf ",hess[i][i]);*/
     lubksb(a,npar,indx,x);    }
     for (i=1;i<=npar;i++){    
       y[i][j]=x[i];    for (i=1;i<=npar;i++) {
       printf("%.3e ",y[i][j]);      for (j=1;j<=npar;j++)  {
     }        if (j>i) { 
     printf("\n");          printf(".%d%d",i,j);fflush(stdout);
   }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   */          hess[i][j]=hessij(p,delti,i,j);
           hess[j][i]=hess[i][j];    
   free_matrix(a,1,npar,1,npar);          /*printf(" %lf ",hess[i][j]);*/
   free_matrix(y,1,npar,1,npar);        }
   free_vector(x,1,npar);      }
   free_ivector(indx,1,npar);    }
   free_matrix(hess,1,npar,1,npar);    printf("\n");
     fprintf(ficlog,"\n");
   
 }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
 /*************** hessian matrix ****************/    
 double hessii( double x[], double delta, int theta, double delti[])    a=matrix(1,npar,1,npar);
 {    y=matrix(1,npar,1,npar);
   int i;    x=vector(1,npar);
   int l=1, lmax=20;    indx=ivector(1,npar);
   double k1,k2;    for (i=1;i<=npar;i++)
   double p2[NPARMAX+1];      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   double res;    ludcmp(a,npar,indx,&pd);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  
   double fx;    for (j=1;j<=npar;j++) {
   int k=0,kmax=10;      for (i=1;i<=npar;i++) x[i]=0;
   double l1;      x[j]=1;
       lubksb(a,npar,indx,x);
   fx=func(x);      for (i=1;i<=npar;i++){ 
   for (i=1;i<=npar;i++) p2[i]=x[i];        matcov[i][j]=x[i];
   for(l=0 ; l <=lmax; l++){      }
     l1=pow(10,l);    }
     delts=delt;  
     for(k=1 ; k <kmax; k=k+1){    printf("\n#Hessian matrix#\n");
       delt = delta*(l1*k);    fprintf(ficlog,"\n#Hessian matrix#\n");
       p2[theta]=x[theta] +delt;    for (i=1;i<=npar;i++) { 
       k1=func(p2)-fx;      for (j=1;j<=npar;j++) { 
       p2[theta]=x[theta]-delt;        printf("%.3e ",hess[i][j]);
       k2=func(p2)-fx;        fprintf(ficlog,"%.3e ",hess[i][j]);
       /*res= (k1-2.0*fx+k2)/delt/delt; */      }
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */      printf("\n");
            fprintf(ficlog,"\n");
 #ifdef DEBUG    }
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);  
 #endif    /* Recompute Inverse */
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    for (i=1;i<=npar;i++)
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
         k=kmax;    ludcmp(a,npar,indx,&pd);
       }  
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    /*  printf("\n#Hessian matrix recomputed#\n");
         k=kmax; l=lmax*10.;  
       }    for (j=1;j<=npar;j++) {
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      for (i=1;i<=npar;i++) x[i]=0;
         delts=delt;      x[j]=1;
       }      lubksb(a,npar,indx,x);
     }      for (i=1;i<=npar;i++){ 
   }        y[i][j]=x[i];
   delti[theta]=delts;        printf("%.3e ",y[i][j]);
   return res;        fprintf(ficlog,"%.3e ",y[i][j]);
        }
 }      printf("\n");
       fprintf(ficlog,"\n");
 double hessij( double x[], double delti[], int thetai,int thetaj)    }
 {    */
   int i;  
   int l=1, l1, lmax=20;    free_matrix(a,1,npar,1,npar);
   double k1,k2,k3,k4,res,fx;    free_matrix(y,1,npar,1,npar);
   double p2[NPARMAX+1];    free_vector(x,1,npar);
   int k;    free_ivector(indx,1,npar);
     free_matrix(hess,1,npar,1,npar);
   fx=func(x);  
   for (k=1; k<=2; k++) {  
     for (i=1;i<=npar;i++) p2[i]=x[i];  }
     p2[thetai]=x[thetai]+delti[thetai]/k;  
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  /*************** hessian matrix ****************/
     k1=func(p2)-fx;  double hessii( double x[], double delta, int theta, double delti[])
    {
     p2[thetai]=x[thetai]+delti[thetai]/k;    int i;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    int l=1, lmax=20;
     k2=func(p2)-fx;    double k1,k2;
      double p2[NPARMAX+1];
     p2[thetai]=x[thetai]-delti[thetai]/k;    double res;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     k3=func(p2)-fx;    double fx;
      int k=0,kmax=10;
     p2[thetai]=x[thetai]-delti[thetai]/k;    double l1;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k4=func(p2)-fx;    fx=func(x);
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    for (i=1;i<=npar;i++) p2[i]=x[i];
 #ifdef DEBUG    for(l=0 ; l <=lmax; l++){
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);      l1=pow(10,l);
 #endif      delts=delt;
   }      for(k=1 ; k <kmax; k=k+1){
   return res;        delt = delta*(l1*k);
 }        p2[theta]=x[theta] +delt;
         k1=func(p2)-fx;
 /************** Inverse of matrix **************/        p2[theta]=x[theta]-delt;
 void ludcmp(double **a, int n, int *indx, double *d)        k2=func(p2)-fx;
 {        /*res= (k1-2.0*fx+k2)/delt/delt; */
   int i,imax,j,k;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   double big,dum,sum,temp;        
   double *vv;  #ifdef DEBUG
          printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   vv=vector(1,n);        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   *d=1.0;  #endif
   for (i=1;i<=n;i++) {        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     big=0.0;        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     for (j=1;j<=n;j++)          k=kmax;
       if ((temp=fabs(a[i][j])) > big) big=temp;        }
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     vv[i]=1.0/big;          k=kmax; l=lmax*10.;
   }        }
   for (j=1;j<=n;j++) {        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     for (i=1;i<j;i++) {          delts=delt;
       sum=a[i][j];        }
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];      }
       a[i][j]=sum;    }
     }    delti[theta]=delts;
     big=0.0;    return res; 
     for (i=j;i<=n;i++) {    
       sum=a[i][j];  }
       for (k=1;k<j;k++)  
         sum -= a[i][k]*a[k][j];  double hessij( double x[], double delti[], int thetai,int thetaj)
       a[i][j]=sum;  {
       if ( (dum=vv[i]*fabs(sum)) >= big) {    int i;
         big=dum;    int l=1, l1, lmax=20;
         imax=i;    double k1,k2,k3,k4,res,fx;
       }    double p2[NPARMAX+1];
     }    int k;
     if (j != imax) {  
       for (k=1;k<=n;k++) {    fx=func(x);
         dum=a[imax][k];    for (k=1; k<=2; k++) {
         a[imax][k]=a[j][k];      for (i=1;i<=npar;i++) p2[i]=x[i];
         a[j][k]=dum;      p2[thetai]=x[thetai]+delti[thetai]/k;
       }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       *d = -(*d);      k1=func(p2)-fx;
       vv[imax]=vv[j];    
     }      p2[thetai]=x[thetai]+delti[thetai]/k;
     indx[j]=imax;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     if (a[j][j] == 0.0) a[j][j]=TINY;      k2=func(p2)-fx;
     if (j != n) {    
       dum=1.0/(a[j][j]);      p2[thetai]=x[thetai]-delti[thetai]/k;
       for (i=j+1;i<=n;i++) a[i][j] *= dum;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     }      k3=func(p2)-fx;
   }    
   free_vector(vv,1,n);  /* Doesn't work */      p2[thetai]=x[thetai]-delti[thetai]/k;
 ;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 }      k4=func(p2)-fx;
       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
 void lubksb(double **a, int n, int *indx, double b[])  #ifdef DEBUG
 {      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   int i,ii=0,ip,j;      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   double sum;  #endif
      }
   for (i=1;i<=n;i++) {    return res;
     ip=indx[i];  }
     sum=b[ip];  
     b[ip]=b[i];  /************** Inverse of matrix **************/
     if (ii)  void ludcmp(double **a, int n, int *indx, double *d) 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  { 
     else if (sum) ii=i;    int i,imax,j,k; 
     b[i]=sum;    double big,dum,sum,temp; 
   }    double *vv; 
   for (i=n;i>=1;i--) {   
     sum=b[i];    vv=vector(1,n); 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    *d=1.0; 
     b[i]=sum/a[i][i];    for (i=1;i<=n;i++) { 
   }      big=0.0; 
 }      for (j=1;j<=n;j++) 
         if ((temp=fabs(a[i][j])) > big) big=temp; 
 /************ Frequencies ********************/      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)      vv[i]=1.0/big; 
 {  /* Some frequencies */    } 
      for (j=1;j<=n;j++) { 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;      for (i=1;i<j;i++) { 
   double ***freq; /* Frequencies */        sum=a[i][j]; 
   double *pp;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   double pos, k2, dateintsum=0,k2cpt=0;        a[i][j]=sum; 
   FILE *ficresp;      } 
   char fileresp[FILENAMELENGTH];      big=0.0; 
        for (i=j;i<=n;i++) { 
   pp=vector(1,nlstate);        sum=a[i][j]; 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        for (k=1;k<j;k++) 
   strcpy(fileresp,"p");          sum -= a[i][k]*a[k][j]; 
   strcat(fileresp,fileres);        a[i][j]=sum; 
   if((ficresp=fopen(fileresp,"w"))==NULL) {        if ( (dum=vv[i]*fabs(sum)) >= big) { 
     printf("Problem with prevalence resultfile: %s\n", fileresp);          big=dum; 
     exit(0);          imax=i; 
   }        } 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      } 
   j1=0;      if (j != imax) { 
          for (k=1;k<=n;k++) { 
   j=cptcoveff;          dum=a[imax][k]; 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          a[imax][k]=a[j][k]; 
            a[j][k]=dum; 
   for(k1=1; k1<=j;k1++){        } 
     for(i1=1; i1<=ncodemax[k1];i1++){        *d = -(*d); 
       j1++;        vv[imax]=vv[j]; 
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);      } 
         scanf("%d", i);*/      indx[j]=imax; 
       for (i=-1; i<=nlstate+ndeath; i++)        if (a[j][j] == 0.0) a[j][j]=TINY; 
         for (jk=-1; jk<=nlstate+ndeath; jk++)        if (j != n) { 
           for(m=agemin; m <= agemax+3; m++)        dum=1.0/(a[j][j]); 
             freq[i][jk][m]=0;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
            } 
       dateintsum=0;    } 
       k2cpt=0;    free_vector(vv,1,n);  /* Doesn't work */
       for (i=1; i<=imx; i++) {  ;
         bool=1;  } 
         if  (cptcovn>0) {  
           for (z1=1; z1<=cptcoveff; z1++)  void lubksb(double **a, int n, int *indx, double b[]) 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  { 
               bool=0;    int i,ii=0,ip,j; 
         }    double sum; 
         if (bool==1) {   
           for(m=firstpass; m<=lastpass; m++){    for (i=1;i<=n;i++) { 
             k2=anint[m][i]+(mint[m][i]/12.);      ip=indx[i]; 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      sum=b[ip]; 
               if(agev[m][i]==0) agev[m][i]=agemax+1;      b[ip]=b[i]; 
               if(agev[m][i]==1) agev[m][i]=agemax+2;      if (ii) 
               if (m<lastpass) {        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      else if (sum) ii=i; 
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      b[i]=sum; 
               }    } 
                  for (i=n;i>=1;i--) { 
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {      sum=b[i]; 
                 dateintsum=dateintsum+k2;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
                 k2cpt++;      b[i]=sum/a[i][i]; 
               }    } 
             }  } 
           }  
         }  /************ Frequencies ********************/
       }  void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
          {  /* Some frequencies */
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    
     int i, m, jk, k1,i1, j1, bool, z1,z2,j;
       if  (cptcovn>0) {    int first;
         fprintf(ficresp, "\n#********** Variable ");    double ***freq; /* Frequencies */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    double *pp;
         fprintf(ficresp, "**********\n#");    double pos, k2, dateintsum=0,k2cpt=0;
       }    FILE *ficresp;
       for(i=1; i<=nlstate;i++)    char fileresp[FILENAMELENGTH];
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    
       fprintf(ficresp, "\n");    pp=vector(1,nlstate);
          probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=(int)agemin; i <= (int)agemax+3; i++){    strcpy(fileresp,"p");
         if(i==(int)agemax+3)    strcat(fileresp,fileres);
           printf("Total");    if((ficresp=fopen(fileresp,"w"))==NULL) {
         else      printf("Problem with prevalence resultfile: %s\n", fileresp);
           printf("Age %d", i);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
         for(jk=1; jk <=nlstate ; jk++){      exit(0);
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    }
             pp[jk] += freq[jk][m][i];    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
         }    j1=0;
         for(jk=1; jk <=nlstate ; jk++){    
           for(m=-1, pos=0; m <=0 ; m++)    j=cptcoveff;
             pos += freq[jk][m][i];    if (cptcovn<1) {j=1;ncodemax[1]=1;}
           if(pp[jk]>=1.e-10)  
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    first=1;
           else  
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    for(k1=1; k1<=j;k1++){
         }      for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
         for(jk=1; jk <=nlstate ; jk++){        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          scanf("%d", i);*/
             pp[jk] += freq[jk][m][i];        for (i=-1; i<=nlstate+ndeath; i++)  
         }          for (jk=-1; jk<=nlstate+ndeath; jk++)  
             for(m=agemin; m <= agemax+3; m++)
         for(jk=1,pos=0; jk <=nlstate ; jk++)              freq[i][jk][m]=0;
           pos += pp[jk];        
         for(jk=1; jk <=nlstate ; jk++){        dateintsum=0;
           if(pos>=1.e-5)        k2cpt=0;
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        for (i=1; i<=imx; i++) {
           else          bool=1;
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          if  (cptcovn>0) {
           if( i <= (int) agemax){            for (z1=1; z1<=cptcoveff; z1++) 
             if(pos>=1.e-5){              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);                bool=0;
               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]);*/          if (bool==1){
             }            for(m=firstpass; m<=lastpass; m++){
             else              k2=anint[m][i]+(mint[m][i]/12.);
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);              if ((k2>=dateprev1) && (k2<=dateprev2)) {
           }                if(agev[m][i]==0) agev[m][i]=agemax+1;
         }                if(agev[m][i]==1) agev[m][i]=agemax+2;
                        if (m<lastpass) {
         for(jk=-1; jk <=nlstate+ndeath; jk++)                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
           for(m=-1; m <=nlstate+ndeath; m++)                  freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);                }
         if(i <= (int) agemax)                
           fprintf(ficresp,"\n");                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
         printf("\n");                  dateintsum=dateintsum+k2;
       }                  k2cpt++;
     }                }
   }              }
   dateintmean=dateintsum/k2cpt;            }
            }
   fclose(ficresp);        }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);         
   free_vector(pp,1,nlstate);        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
    
   /* End of Freq */        if  (cptcovn>0) {
 }          fprintf(ficresp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 /************ Prevalence ********************/          fprintf(ficresp, "**********\n#");
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)        }
 {  /* Some frequencies */        for(i=1; i<=nlstate;i++) 
            fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        fprintf(ficresp, "\n");
   double ***freq; /* Frequencies */        
   double *pp;        for(i=(int)agemin; i <= (int)agemax+3; i++){
   double pos, k2;          if(i==(int)agemax+3){
             fprintf(ficlog,"Total");
   pp=vector(1,nlstate);          }else{
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            if(first==1){
                first=0;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);              printf("See log file for details...\n");
   j1=0;            }
              fprintf(ficlog,"Age %d", i);
   j=cptcoveff;          }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          for(jk=1; jk <=nlstate ; jk++){
              for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
  for(k1=1; k1<=j;k1++){              pp[jk] += freq[jk][m][i]; 
     for(i1=1; i1<=ncodemax[k1];i1++){          }
       j1++;          for(jk=1; jk <=nlstate ; jk++){
              for(m=-1, pos=0; m <=0 ; m++)
       for (i=-1; i<=nlstate+ndeath; i++)                pos += freq[jk][m][i];
         for (jk=-1; jk<=nlstate+ndeath; jk++)              if(pp[jk]>=1.e-10){
           for(m=agemin; m <= agemax+3; m++)              if(first==1){
             freq[i][jk][m]=0;              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                    }
       for (i=1; i<=imx; i++) {              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         bool=1;            }else{
         if  (cptcovn>0) {              if(first==1)
           for (z1=1; z1<=cptcoveff; z1++)                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
               bool=0;            }
         }          }
         if (bool==1) {  
           for(m=firstpass; m<=lastpass; m++){          for(jk=1; jk <=nlstate ; jk++){
             k2=anint[m][i]+(mint[m][i]/12.);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
             if ((k2>=dateprev1) && (k2<=dateprev2)) {              pp[jk] += freq[jk][m][i];
               if(agev[m][i]==0) agev[m][i]=agemax+1;          }
               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]+1-((int)calagedate %12)/12.)] += weight[i];          for(jk=1,pos=0; jk <=nlstate ; jk++)
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */            pos += pp[jk];
             }          for(jk=1; jk <=nlstate ; jk++){
           }            if(pos>=1.e-5){
         }              if(first==1)
       }                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         for(i=(int)agemin; i <= (int)agemax+3; i++){              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
           for(jk=1; jk <=nlstate ; jk++){            }else{
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)              if(first==1)
               pp[jk] += freq[jk][m][i];                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
           }              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
           for(jk=1; jk <=nlstate ; jk++){            }
             for(m=-1, pos=0; m <=0 ; m++)            if( i <= (int) agemax){
             pos += freq[jk][m][i];              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;
          for(jk=1; jk <=nlstate ; jk++){                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)              }
              pp[jk] += freq[jk][m][i];              else
          }                fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
                      }
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          }
           
          for(jk=1; jk <=nlstate ; jk++){                    for(jk=-1; jk <=nlstate+ndeath; jk++)
            if( i <= (int) agemax){            for(m=-1; m <=nlstate+ndeath; m++)
              if(pos>=1.e-5){              if(freq[jk][m][i] !=0 ) {
                probs[i][jk][j1]= pp[jk]/pos;              if(first==1)
              }                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
            }                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
          }              }
                    if(i <= (int) agemax)
         }            fprintf(ficresp,"\n");
     }          if(first==1)
   }            printf("Others in log...\n");
            fprintf(ficlog,"\n");
          }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      }
   free_vector(pp,1,nlstate);    }
      dateintmean=dateintsum/k2cpt; 
 }  /* End of Freq */   
     fclose(ficresp);
 /************* Waves Concatenation ***************/    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
     free_vector(pp,1,nlstate);
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    
 {    /* End of Freq */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  }
      Death is a valid wave (if date is known).  
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  /************ Prevalence ********************/
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
      and mw[mi+1][i]. dh depends on stepm.  {  /* Some frequencies */
      */   
     int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   int i, mi, m;    double ***freq; /* Frequencies */
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    double *pp;
      double sum=0., jmean=0.;*/    double pos, k2;
   
   int j, k=0,jk, ju, jl;    pp=vector(1,nlstate);
   double sum=0.;    
   jmin=1e+5;    freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
   jmax=-1;    j1=0;
   jmean=0.;    
   for(i=1; i<=imx; i++){    j=cptcoveff;
     mi=0;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     m=firstpass;    
     while(s[m][i] <= nlstate){    for(k1=1; k1<=j;k1++){
       if(s[m][i]>=1)      for(i1=1; i1<=ncodemax[k1];i1++){
         mw[++mi][i]=m;        j1++;
       if(m >=lastpass)        
         break;        for (i=-1; i<=nlstate+ndeath; i++)  
       else          for (jk=-1; jk<=nlstate+ndeath; jk++)  
         m++;            for(m=agemin; m <= agemax+3; m++)
     }/* end while */              freq[i][jk][m]=0;
     if (s[m][i] > nlstate){       
       mi++;     /* Death is another wave */        for (i=1; i<=imx; i++) {
       /* if(mi==0)  never been interviewed correctly before death */          bool=1;
          /* Only death is a correct wave */          if  (cptcovn>0) {
       mw[mi][i]=m;            for (z1=1; z1<=cptcoveff; z1++) 
     }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                 bool=0;
     wav[i]=mi;          } 
     if(mi==0)          if (bool==1) { 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);            for(m=firstpass; m<=lastpass; m++){
   }              k2=anint[m][i]+(mint[m][i]/12.);
               if ((k2>=dateprev1) && (k2<=dateprev2)) {
   for(i=1; i<=imx; i++){                if(agev[m][i]==0) agev[m][i]=agemax+1;
     for(mi=1; mi<wav[i];mi++){                if(agev[m][i]==1) agev[m][i]=agemax+2;
       if (stepm <=0)                if (m<lastpass) {
         dh[mi][i]=1;                  if (calagedate>0) 
       else{                    freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
         if (s[mw[mi+1][i]][i] > nlstate) {                  else
           if (agedc[i] < 2*AGESUP) {                    freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);                  freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; 
           if(j==0) j=1;  /* Survives at least one month after exam */                }
           k=k+1;              }
           if (j >= jmax) jmax=j;            }
           if (j <= jmin) jmin=j;          }
           sum=sum+j;        }
           /*if (j<0) printf("j=%d num=%d \n",j,i); */        for(i=(int)agemin; i <= (int)agemax+3; i++){ 
           }          for(jk=1; jk <=nlstate ; jk++){
         }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
         else{              pp[jk] += freq[jk][m][i]; 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          }
           k=k+1;          for(jk=1; jk <=nlstate ; jk++){
           if (j >= jmax) jmax=j;            for(m=-1, pos=0; m <=0 ; m++)
           else if (j <= jmin)jmin=j;              pos += freq[jk][m][i];
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          }
           sum=sum+j;          
         }          for(jk=1; jk <=nlstate ; jk++){
         jk= j/stepm;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
         jl= j -jk*stepm;              pp[jk] += freq[jk][m][i];
         ju= j -(jk+1)*stepm;          }
         if(jl <= -ju)          
           dh[mi][i]=jk;          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
         else          
           dh[mi][i]=jk+1;          for(jk=1; jk <=nlstate ; jk++){    
         if(dh[mi][i]==0)            if( i <= (int) agemax){
           dh[mi][i]=1; /* At least one step */              if(pos>=1.e-5){
       }                probs[i][jk][j1]= pp[jk]/pos;
     }              }
   }            }
   jmean=sum/k;          }/* end jk */
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        }/* end i */
  }      } /* end i1 */
 /*********** Tricode ****************************/    } /* end k1 */
 void tricode(int *Tvar, int **nbcode, int imx)  
 {    
   int Ndum[20],ij=1, k, j, i;    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
   int cptcode=0;    free_vector(pp,1,nlstate);
   cptcoveff=0;    
    }  /* End of Freq */
   for (k=0; k<19; k++) Ndum[k]=0;  
   for (k=1; k<=7; k++) ncodemax[k]=0;  /************* Waves Concatenation ***************/
   
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
     for (i=1; i<=imx; i++) {  {
       ij=(int)(covar[Tvar[j]][i]);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
       Ndum[ij]++;       Death is a valid wave (if date is known).
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
       if (ij > cptcode) cptcode=ij;       dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]
     }       and mw[mi+1][i]. dh depends on stepm.
        */
     for (i=0; i<=cptcode; i++) {  
       if(Ndum[i]!=0) ncodemax[j]++;    int i, mi, m;
     }    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     ij=1;       double sum=0., jmean=0.;*/
     int first;
     int j, k=0,jk, ju, jl;
     for (i=1; i<=ncodemax[j]; i++) {    double sum=0.;
       for (k=0; k<=19; k++) {    first=0;
         if (Ndum[k] != 0) {    jmin=1e+5;
           nbcode[Tvar[j]][ij]=k;    jmax=-1;
           /*     printf("nbcodeaaaaaaaaaaa=%d Tvar[j]=%d ij=%d j=%d",nbcode[Tvar[j]][ij],Tvar[j],ij,j);*/    jmean=0.;
           ij++;    for(i=1; i<=imx; i++){
         }      mi=0;
         if (ij > ncodemax[j]) break;      m=firstpass;
       }        while(s[m][i] <= nlstate){
     }        if(s[m][i]>=1)
   }            mw[++mi][i]=m;
         if(m >=lastpass)
  for (k=0; k<19; k++) Ndum[k]=0;          break;
         else
  for (i=1; i<=ncovmodel-2; i++) {          m++;
       ij=Tvar[i];      }/* end while */
       Ndum[ij]++;      if (s[m][i] > nlstate){
     }        mi++;     /* Death is another wave */
         /* if(mi==0)  never been interviewed correctly before death */
  ij=1;           /* Only death is a correct wave */
  for (i=1; i<=10; i++) {        mw[mi][i]=m;
    if((Ndum[i]!=0) && (i<=ncovcol)){      }
      Tvaraff[ij]=i;  
      ij++;      wav[i]=mi;
    }      if(mi==0){
  }        if(first==0){
            printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
     cptcoveff=ij-1;          first=1;
 }        }
         if(first==1){
 /*********** Health Expectancies ****************/          fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
         }
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)      } /* end mi==0 */
 {    }
   /* Health expectancies */  
   int i, j, nhstepm, hstepm, h, nstepm, k;    for(i=1; i<=imx; i++){
   double age, agelim, hf;      for(mi=1; mi<wav[i];mi++){
   double ***p3mat;        if (stepm <=0)
            dh[mi][i]=1;
   fprintf(ficreseij,"# Health expectancies\n");        else{
   fprintf(ficreseij,"# Age");          if (s[mw[mi+1][i]][i] > nlstate) {
   for(i=1; i<=nlstate;i++)            if (agedc[i] < 2*AGESUP) {
     for(j=1; j<=nlstate;j++)            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
       fprintf(ficreseij," %1d-%1d",i,j);            if(j==0) j=1;  /* Survives at least one month after exam */
   fprintf(ficreseij,"\n");            k=k+1;
             if (j >= jmax) jmax=j;
   k=1;             /* For example stepm=6 months */            if (j <= jmin) jmin=j;
   hstepm=k*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */            sum=sum+j;
   hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */            /*if (j<0) printf("j=%d num=%d \n",j,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.          else{
      Look at hpijx to understand the reason of that which relies in memory size            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
      and note for a fixed period like k years */            k=k+1;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the            if (j >= jmax) jmax=j;
      survival function given by stepm (the optimization length). Unfortunately it            else if (j <= jmin)jmin=j;
      means that if the survival funtion is printed only each two years of age and if            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
      you sum them up and add 1 year (area under the trapezoids) you won't get the same            sum=sum+j;
      results. So we changed our mind and took the option of the best precision.          }
   */          jk= j/stepm;
   hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */          jl= j -jk*stepm;
           ju= j -(jk+1)*stepm;
   agelim=AGESUP;          if(jl <= -ju)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            dh[mi][i]=jk;
     /* nhstepm age range expressed in number of stepm */          else
     nstepm=(int) rint((agelim-age)*YEARM/stepm);            dh[mi][i]=jk+1;
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */          if(dh[mi][i]==0)
     /* if (stepm >= YEARM) hstepm=1;*/            dh[mi][i]=1; /* At least one step */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */        }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      }
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    }
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    jmean=sum/k;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     for(i=1; i<=nlstate;i++)   }
       for(j=1; j<=nlstate;j++)  
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){  /*********** Tricode ****************************/
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;  void tricode(int *Tvar, int **nbcode, int imx)
           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/  {
         }    
     fprintf(ficreseij,"%3.0f",age );    int Ndum[20],ij=1, k, j, i, maxncov=19;
     for(i=1; i<=nlstate;i++)    int cptcode=0;
       for(j=1; j<=nlstate;j++){    cptcoveff=0; 
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);   
       }    for (k=0; k<maxncov; k++) Ndum[k]=0;
     fprintf(ficreseij,"\n");    for (k=1; k<=7; k++) ncodemax[k]=0;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   }    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
 }      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                  modality*/ 
 /************ Variance ******************/        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
 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)        Ndum[ij]++; /*store the modality */
 {        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   /* Variance of health expectancies */        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/                                         Tvar[j]. If V=sex and male is 0 and 
   double **newm;                                         female is 1, then  cptcode=1.*/
   double **dnewm,**doldm;      }
   int i, j, nhstepm, hstepm, h, nstepm, kk;  
   int k, cptcode;      for (i=0; i<=cptcode; i++) {
   double *xp;        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
   double **gp, **gm;      }
   double ***gradg, ***trgradg;  
   double ***p3mat;      ij=1; 
   double age,agelim, hf;      for (i=1; i<=ncodemax[j]; i++) {
   int theta;        for (k=0; k<= maxncov; k++) {
           if (Ndum[k] != 0) {
    fprintf(ficresvij,"# Covariances of life expectancies\n");            nbcode[Tvar[j]][ij]=k; 
   fprintf(ficresvij,"# Age");            /* 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; */
   for(i=1; i<=nlstate;i++)            
     for(j=1; j<=nlstate;j++)            ij++;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          }
   fprintf(ficresvij,"\n");          if (ij > ncodemax[j]) break; 
         }  
   xp=vector(1,npar);      } 
   dnewm=matrix(1,nlstate,1,npar);    }  
   doldm=matrix(1,nlstate,1,nlstate);  
     for (k=0; k< maxncov; k++) Ndum[k]=0;
   kk=1;             /* For example stepm=6 months */  
   hstepm=kk*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */   for (i=1; i<=ncovmodel-2; i++) { 
   hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.     ij=Tvar[i];
      nhstepm is the number of hstepm from age to agelim     Ndum[ij]++;
      nstepm is the number of stepm from age to agelin.   }
      Look at hpijx to understand the reason of that which relies in memory size  
      and note for a fixed period like k years */   ij=1;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the   for (i=1; i<= maxncov; i++) {
      survival function given by stepm (the optimization length). Unfortunately it     if((Ndum[i]!=0) && (i<=ncovcol)){
      means that if the survival funtion is printed only each two years of age and if       Tvaraff[ij]=i; /*For printing */
      you sum them up and add 1 year (area under the trapezoids) you won't get the same       ij++;
      results. So we changed our mind and took the option of the best precision.     }
   */   }
   hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */   
   agelim = AGESUP;   cptcoveff=ij-1; /*Number of simple covariates*/
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  }
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  /*********** Health Expectancies ****************/
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);  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 )
     gp=matrix(0,nhstepm,1,nlstate);  
     gm=matrix(0,nhstepm,1,nlstate);  {
     /* Health expectancies */
     for(theta=1; theta <=npar; theta++){    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
       for(i=1; i<=npar; i++){ /* Computes gradient */    double age, agelim, hf;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    double ***p3mat,***varhe;
       }    double **dnewm,**doldm;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      double *xp;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double **gp, **gm;
     double ***gradg, ***trgradg;
       if (popbased==1) {    int theta;
         for(i=1; i<=nlstate;i++)  
           prlim[i][i]=probs[(int)age][i][ij];    varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
       }    xp=vector(1,npar);
      dnewm=matrix(1,nlstate*2,1,npar);
       for(j=1; j<= nlstate; j++){    doldm=matrix(1,nlstate*2,1,nlstate*2);
         for(h=0; h<=nhstepm; h++){    
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    fprintf(ficreseij,"# Health expectancies\n");
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    fprintf(ficreseij,"# Age");
         }    for(i=1; i<=nlstate;i++)
       }      for(j=1; j<=nlstate;j++)
            fprintf(ficreseij," %1d-%1d (SE)",i,j);
       for(i=1; i<=npar; i++) /* Computes gradient */    fprintf(ficreseij,"\n");
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      if(estepm < stepm){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      printf ("Problem %d lower than %d\n",estepm, stepm);
      }
       if (popbased==1) {    else  hstepm=estepm;   
         for(i=1; i<=nlstate;i++)    /* We compute the life expectancy from trapezoids spaced every estepm months
           prlim[i][i]=probs[(int)age][i][ij];     * This is mainly to measure the difference between two models: for example
       }     * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear 
       for(j=1; j<= nlstate; j++){     * progression inbetween and thus overestimating or underestimating according
         for(h=0; h<=nhstepm; h++){     * to the curvature of the survival function. If, for the same date, we 
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)     * estimate the model with stepm=1 month, we can keep estepm to 24 months
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];     * 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(j=1; j<= nlstate; j++)    /* For example we decided to compute the life expectancy with the smallest unit */
         for(h=0; h<=nhstepm; h++){    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];       nhstepm is the number of hstepm from age to agelim 
         }       nstepm is the number of stepm from age to agelin. 
     } /* End theta */       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    /* 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
     for(h=0; h<=nhstepm; h++)       means that if the survival funtion is printed only each two years of age and if
       for(j=1; j<=nlstate;j++)       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         for(theta=1; theta <=npar; theta++)       results. So we changed our mind and took the option of the best precision.
           trgradg[h][j][theta]=gradg[h][theta][j];    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  
     for(i=1;i<=nlstate;i++)    agelim=AGESUP;
       for(j=1;j<=nlstate;j++)    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         vareij[i][j][(int)age] =0.;      /* nhstepm age range expressed in number of stepm */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); 
     for(h=0;h<=nhstepm;h++){      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       for(k=0;k<=nhstepm;k++){      /* if (stepm >= YEARM) hstepm=1;*/
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         for(i=1;i<=nlstate;i++)      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
           for(j=1;j<=nlstate;j++)      gp=matrix(0,nhstepm,1,nlstate*2);
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;      gm=matrix(0,nhstepm,1,nlstate*2);
       }  
     }      /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     fprintf(ficresvij,"%.0f ",age );      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
     for(i=1; i<=nlstate;i++)   
       for(j=1; j<=nlstate;j++){  
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       }  
     fprintf(ficresvij,"\n");      /* Computing Variances of health expectancies */
     free_matrix(gp,0,nhstepm,1,nlstate);  
     free_matrix(gm,0,nhstepm,1,nlstate);       for(theta=1; theta <=npar; theta++){
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        for(i=1; i<=npar; i++){ 
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
   } /* End age */        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
      
   free_vector(xp,1,npar);        cptj=0;
   free_matrix(doldm,1,nlstate,1,npar);        for(j=1; j<= nlstate; j++){
   free_matrix(dnewm,1,nlstate,1,nlstate);          for(i=1; i<=nlstate; 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.;
 /************ 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;        for(i=1; i<=npar; i++) 
   double **dnewm,**doldm;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   int i, j, nhstepm, hstepm;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   int k, cptcode;        
   double *xp;        cptj=0;
   double *gp, *gm;        for(j=1; j<= nlstate; j++){
   double **gradg, **trgradg;          for(i=1;i<=nlstate;i++){
   double age,agelim;            cptj=cptj+1;
   int theta;            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
                  gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");            }
   fprintf(ficresvpl,"# Age");          }
   for(i=1; i<=nlstate;i++)        }
       fprintf(ficresvpl," %1d-%1d",i,i);        for(j=1; j<= nlstate*2; j++)
   fprintf(ficresvpl,"\n");          for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   xp=vector(1,npar);          }
   dnewm=matrix(1,nlstate,1,npar);       } 
   doldm=matrix(1,nlstate,1,nlstate);     
    /* End theta */
   hstepm=1*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */       trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
   agelim = AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */       for(h=0; h<=nhstepm-1; h++)
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        for(j=1; j<=nlstate*2;j++)
     if (stepm >= YEARM) hstepm=1;          for(theta=1; theta <=npar; theta++)
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            trgradg[h][j][theta]=gradg[h][theta][j];
     gradg=matrix(1,npar,1,nlstate);       
     gp=vector(1,nlstate);  
     gm=vector(1,nlstate);       for(i=1;i<=nlstate*2;i++)
         for(j=1;j<=nlstate*2;j++)
     for(theta=1; theta <=npar; theta++){          varhe[i][j][(int)age] =0.;
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);       printf("%d|",(int)age);fflush(stdout);
       }       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);       for(h=0;h<=nhstepm-1;h++){
       for(i=1;i<=nlstate;i++)        for(k=0;k<=nhstepm-1;k++){
         gp[i] = prlim[i][i];          matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
              matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
       for(i=1; i<=npar; i++) /* Computes gradient */          for(i=1;i<=nlstate*2;i++)
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            for(j=1;j<=nlstate*2;j++)
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
       for(i=1;i<=nlstate;i++)        }
         gm[i] = prlim[i][i];      }
       /* Computing expectancies */
       for(i=1;i<=nlstate;i++)      for(i=1; i<=nlstate;i++)
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        for(j=1; j<=nlstate;j++)
     } /* End theta */          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;
     trgradg =matrix(1,nlstate,1,npar);            
   /* 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(j=1; j<=nlstate;j++)  
       for(theta=1; theta <=npar; theta++)          }
         trgradg[j][theta]=gradg[theta][j];  
       fprintf(ficreseij,"%3.0f",age );
     for(i=1;i<=nlstate;i++)      cptj=0;
       varpl[i][(int)age] =0.;      for(i=1; i<=nlstate;i++)
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);        for(j=1; j<=nlstate;j++){
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          cptj++;
     for(i=1;i<=nlstate;i++)          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        }
       fprintf(ficreseij,"\n");
     fprintf(ficresvpl,"%.0f ",age );     
     for(i=1; i<=nlstate;i++)      free_matrix(gm,0,nhstepm,1,nlstate*2);
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));      free_matrix(gp,0,nhstepm,1,nlstate*2);
     fprintf(ficresvpl,"\n");      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
     free_vector(gp,1,nlstate);      free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
     free_vector(gm,1,nlstate);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_matrix(gradg,1,npar,1,nlstate);    }
     free_matrix(trgradg,1,nlstate,1,npar);    printf("\n");
   } /* End age */    fprintf(ficlog,"\n");
   
   free_vector(xp,1,npar);    free_vector(xp,1,npar);
   free_matrix(doldm,1,nlstate,1,npar);    free_matrix(dnewm,1,nlstate*2,1,npar);
   free_matrix(dnewm,1,nlstate,1,nlstate);    free_matrix(doldm,1,nlstate*2,1,nlstate*2);
     free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
 }  }
   
 /************ Variance of one-step probabilities  ******************/  /************ Variance ******************/
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)  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)
 {  {
   int i, j;    /* Variance of health expectancies */
   int k=0, cptcode;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   double **dnewm,**doldm;    /* double **newm;*/
   double *xp;    double **dnewm,**doldm;
   double *gp, *gm;    double **dnewmp,**doldmp;
   double **gradg, **trgradg;    int i, j, nhstepm, hstepm, h, nstepm ;
   double age,agelim, cov[NCOVMAX];    int k, cptcode;
   int theta;    double *xp;
   char fileresprob[FILENAMELENGTH];    double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
   strcpy(fileresprob,"prob");    double **gradgp, **trgradgp; /* for var p point j */
   strcat(fileresprob,fileres);    double *gpp, *gmp; /* for var p point j */
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     printf("Problem with resultfile: %s\n", fileresprob);    double ***p3mat;
   }    double age,agelim, hf;
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);    double ***mobaverage;
      int theta;
     char digit[4];
   xp=vector(1,npar);    char digitp[25];
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    char fileresprobmorprev[FILENAMELENGTH];
    
   cov[1]=1;    if(popbased==1){
   for (age=bage; age<=fage; age ++){      if(mobilav!=0)
     cov[2]=age;        strcpy(digitp,"-populbased-mobilav-");
     gradg=matrix(1,npar,1,9);      else strcpy(digitp,"-populbased-nomobil-");
     trgradg=matrix(1,9,1,npar);    }
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    else 
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      strcpy(digitp,"-stablbased-");
      
     for(theta=1; theta <=npar; theta++){    if (mobilav!=0) {
       for(i=1; i<=npar; i++)      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
              fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       pmij(pmmij,cov,ncovmodel,xp,nlstate);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
          }
       k=0;    }
       for(i=1; i<= (nlstate+ndeath); i++){  
         for(j=1; j<=(nlstate+ndeath);j++){    strcpy(fileresprobmorprev,"prmorprev"); 
            k=k+1;    sprintf(digit,"%-d",ij);
           gp[k]=pmmij[i][j];    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
         }    strcat(fileresprobmorprev,digit); /* Tvar to be done */
       }    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
       for(i=1; i<=npar; i++)    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
          fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       k=0;    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       for(i=1; i<=(nlstate+ndeath); i++){    fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");
         for(j=1; j<=(nlstate+ndeath);j++){    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
           k=k+1;    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
           gm[k]=pmmij[i][j];      fprintf(ficresprobmorprev," p.%-d SE",j);
         }      for(i=1; i<=nlstate;i++)
       }        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
          }  
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    fprintf(ficresprobmorprev,"\n");
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
     }      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
       fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)      exit(0);
       for(theta=1; theta <=npar; theta++)    }
       trgradg[j][theta]=gradg[theta][j];    else{
        fprintf(ficgp,"\n# Routine varevsij");
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    }
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
       printf("Problem with html file: %s\n", optionfilehtm);
      pmij(pmmij,cov,ncovmodel,x,nlstate);      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
       exit(0);
      k=0;    }
      for(i=1; i<=(nlstate+ndeath); i++){    else{
        for(j=1; j<=(nlstate+ndeath);j++){      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");
          k=k+1;      fprintf(fichtm,"\n<br>%s (à revoir) <br>\n",digitp);
          gm[k]=pmmij[i][j];    }
         }    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      }  
          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");
      /*printf("\n%d ",(int)age);    fprintf(ficresvij,"# Age");
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    for(i=1; i<=nlstate;i++)
              for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    fprintf(ficresvij,"\n");
      }*/  
     xp=vector(1,npar);
   fprintf(ficresprob,"\n%d ",(int)age);    dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  
   }    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    gmp=vector(nlstate+1,nlstate+ndeath);
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    if(estepm < stepm){
 }      printf ("Problem %d lower than %d\n",estepm, stepm);
  free_vector(xp,1,npar);    }
 fclose(ficresprob);    else  hstepm=estepm;   
     /* 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 
 /******************* Printing html file ***********/       nstepm is the number of stepm from age to agelin. 
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \       Look at hpijx to understand the reason of that which relies in memory size
  int lastpass, int stepm, int weightopt, char model[],\       and note for a fixed period like k years */
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\       survival function given by stepm (the optimization length). Unfortunately it
  char version[], int popforecast ){       means that if the survival funtion is printed only each two years of age and if
   int jj1, k1, i1, cpt;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   FILE *fichtm;       results. So we changed our mind and took the option of the best precision.
   /*char optionfilehtm[FILENAMELENGTH];*/    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   strcpy(optionfilehtm,optionfile);    agelim = AGESUP;
   strcat(optionfilehtm,".htm");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     printf("Problem with %s \n",optionfilehtm), exit(0);      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);
  fprintf(fichtm,"<body> <font size=\"2\">Imach, Version %s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n      gp=matrix(0,nhstepm,1,nlstate);
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n      gm=matrix(0,nhstepm,1,nlstate);
 \n  
 Total number of observations=%d <br>\n  
 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\">        for(i=1; i<=npar; i++){ /* Computes gradient */
  <ul><li>Outputs files<br>\n          xp[i] = x[i] + (i==theta ?delti[theta]:0);
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n        }
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n  
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n        if (popbased==1) {
  - 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);          if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
  fprintf(fichtm,"\n              prlim[i][i]=probs[(int)age][i][ij];
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n          }else{ /* mobilav */ 
  - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>\n            for(i=1; i<=nlstate;i++)
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n              prlim[i][i]=mobaverage[(int)age][i][ij];
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres);          }
         }
  if(popforecast==1) fprintf(fichtm,"\n    
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n        for(j=1; j<= nlstate; j++){
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n          for(h=0; h<=nhstepm; h++){
         <br>",fileres,fileres,fileres,fileres);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
  else              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);          }
 fprintf(fichtm," <li>Graphs</li><p>");        }
         /* This for computing forces of mortality (h=1)as a weighted average */
  m=cptcoveff;        for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}          for(i=1; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
  jj1=0;        }    
  for(k1=1; k1<=m;k1++){        /* end force of mortality */
    for(i1=1; i1<=ncodemax[k1];i1++){  
        jj1++;        for(i=1; i<=npar; i++) /* Computes gradient */
        if (cptcovn > 0) {          xp[i] = x[i] - (i==theta ?delti[theta]:0);
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
          for (cpt=1; cpt<=cptcoveff;cpt++)        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);   
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");        if (popbased==1) {
        }          if(mobilav ==0){
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>            for(i=1; i<=nlstate;i++)
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                  prlim[i][i]=probs[(int)age][i][ij];
        for(cpt=1; cpt<nlstate;cpt++){          }else{ /* mobilav */ 
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>            for(i=1; i<=nlstate;i++)
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);              prlim[i][i]=mobaverage[(int)age][i][ij];
        }          }
     for(cpt=1; cpt<=nlstate;cpt++) {        }
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident  
 interval) in state (%d): v%s%d%d.gif <br>        for(j=1; j<= nlstate; j++){
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            for(h=0; h<=nhstepm; h++){
      }            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
      for(cpt=1; cpt<=nlstate;cpt++) {              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>          }
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        }
      }        /* This for computing force of mortality (h=1)as a weighted average */
      fprintf(fichtm,"\n<br>- Total life expectancy by age and        for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
 health expectancies in states (1) and (2): e%s%d.gif<br>          for(i=1; i<= nlstate; i++)
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            gmp[j] += prlim[i][i]*p3mat[i][j][1];
 fprintf(fichtm,"\n</body>");        }    
    }        /* end force of mortality */
    }  
 fclose(fichtm);        for(j=1; j<= nlstate; j++) /* vareij */
 }          for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
 /******************* Gnuplot file **************/          }
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;        }
   
   strcpy(optionfilegnuplot,optionfilefiname);      } /* End theta */
   strcat(optionfilegnuplot,".gp.txt");  
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
     printf("Problem with file %s",optionfilegnuplot);  
   }      for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
 #ifdef windows          for(theta=1; theta <=npar; theta++)
     fprintf(ficgp,"cd \"%s\" \n",pathc);            trgradg[h][j][theta]=gradg[h][theta][j];
 #endif  
 m=pow(2,cptcoveff);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
          for(theta=1; theta <=npar; theta++)
  /* 1eme*/          trgradgp[j][theta]=gradgp[theta][j];
   for (cpt=1; cpt<= nlstate ; cpt ++) {  
    for (k1=1; k1<= m ; k1 ++) {      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
 #ifdef windows        for(j=1;j<=nlstate;j++)
     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);          vareij[i][j][(int)age] =0.;
 #endif  
 #ifdef unix      for(h=0;h<=nhstepm;h++){
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);        for(k=0;k<=nhstepm;k++){
 #endif          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
 for (i=1; i<= nlstate ; i ++) {          for(i=1;i<=nlstate;i++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            for(j=1;j<=nlstate;j++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
 }        }
     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)");      /* pptj */
   else fprintf(ficgp," \%%*lf (\%%*lf)");      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
 }      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
      for (i=1; i<= nlstate ; i ++) {        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          varppt[j][i]=doldmp[j][i];
   else fprintf(ficgp," \%%*lf (\%%*lf)");      /* end ppptj */
 }        hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
 #ifdef unix   
 fprintf(ficgp,"\nset ter gif small size 400,300");      if (popbased==1) {
 #endif        if(mobilav ==0){
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          for(i=1; i<=nlstate;i++)
    }            prlim[i][i]=probs[(int)age][i][ij];
   }        }else{ /* mobilav */ 
   /*2 eme*/          for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
   for (k1=1; k1<= m ; k1 ++) {        }
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);      }
          
     for (i=1; i<= nlstate+1 ; i ++) {      /* This for computing force of mortality (h=1)as a weighted average */
       k=2*i;      for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);        for(i=1; i<= nlstate; i++)
       for (j=1; j<= nlstate+1 ; j ++) {          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      }    
   else fprintf(ficgp," \%%*lf (\%%*lf)");      /* end force of mortality */
 }    
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
       for (j=1; j<= nlstate+1 ; j ++) {        for(i=1; i<=nlstate;i++){
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         else fprintf(ficgp," \%%*lf (\%%*lf)");        }
 }        } 
       fprintf(ficgp,"\" t\"\" w l 0,");      fprintf(ficresprobmorprev,"\n");
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {      fprintf(ficresvij,"%.0f ",age );
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      for(i=1; i<=nlstate;i++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(j=1; j<=nlstate;j++){
 }            fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        }
       else fprintf(ficgp,"\" t\"\" w l 0,");      fprintf(ficresvij,"\n");
     }      free_matrix(gp,0,nhstepm,1,nlstate);
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);      free_matrix(gm,0,nhstepm,1,nlstate);
   }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
        free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
   /*3eme*/      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
   for (k1=1; k1<= m ; k1 ++) {    free_vector(gpp,nlstate+1,nlstate+ndeath);
     for (cpt=1; cpt<= nlstate ; cpt ++) {    free_vector(gmp,nlstate+1,nlstate+ndeath);
       k=2+nlstate*(cpt-1);    free_matrix(gradgp,1,npar,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);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       for (i=1; i< nlstate ; i ++) {    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
         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);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
       }    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);
     }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);
     }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);
      fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
   /* CV preval stat */    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);
     for (k1=1; k1<= m ; k1 ++) {    /*  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);
     for (cpt=1; cpt<nlstate ; cpt ++) {  */
       k=3;    fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);  
     free_vector(xp,1,npar);
       for (i=1; i< nlstate ; i ++)    free_matrix(doldm,1,nlstate,1,nlstate);
         fprintf(ficgp,"+$%d",k+i+1);    free_matrix(dnewm,1,nlstate,1,npar);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
          free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
       l=3+(nlstate+ndeath)*cpt;    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for (i=1; i< nlstate ; i ++) {    fclose(ficresprobmorprev);
         l=3+(nlstate+ndeath)*cpt;    fclose(ficgp);
         fprintf(ficgp,"+$%d",l+i+1);    fclose(fichtm);
       }  }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);    
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  /************ 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 */
   /* proba elementaires */    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
    for(i=1,jk=1; i <=nlstate; i++){    double **newm;
     for(k=1; k <=(nlstate+ndeath); k++){    double **dnewm,**doldm;
       if (k != i) {    int i, j, nhstepm, hstepm;
         for(j=1; j <=ncovmodel; j++){    int k, cptcode;
            double *xp;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    double *gp, *gm;
           jk++;    double **gradg, **trgradg;
           fprintf(ficgp,"\n");    double age,agelim;
         }    int theta;
       }     
     }    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
     }    fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
     for(jk=1; jk <=m; jk++) {        fprintf(ficresvpl," %1d-%1d",i,i);
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);    fprintf(ficresvpl,"\n");
    i=1;  
    for(k2=1; k2<=nlstate; k2++) {    xp=vector(1,npar);
      k3=i;    dnewm=matrix(1,nlstate,1,npar);
      for(k=1; k<=(nlstate+ndeath); k++) {    doldm=matrix(1,nlstate,1,nlstate);
        if (k != k2){    
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    hstepm=1*YEARM; /* Every year of age */
 ij=1;    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
         for(j=3; j <=ncovmodel; j++) {    agelim = AGESUP;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             ij++;      if (stepm >= YEARM) hstepm=1;
           }      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
           else      gradg=matrix(1,npar,1,nlstate);
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      gp=vector(1,nlstate);
         }      gm=vector(1,nlstate);
           fprintf(ficgp,")/(1");  
              for(theta=1; theta <=npar; theta++){
         for(k1=1; k1 <=nlstate; k1++){          for(i=1; i<=npar; i++){ /* Computes gradient */
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 ij=1;        }
           for(j=3; j <=ncovmodel; j++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        for(i=1;i<=nlstate;i++)
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          gp[i] = prlim[i][i];
             ij++;      
           }        for(i=1; i<=npar; i++) /* Computes gradient */
           else          xp[i] = x[i] - (i==theta ?delti[theta]:0);
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           }        for(i=1;i<=nlstate;i++)
           fprintf(ficgp,")");          gm[i] = prlim[i][i];
         }  
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);        for(i=1;i<=nlstate;i++)
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
         i=i+ncovmodel;      } /* End theta */
        }  
      }      trgradg =matrix(1,nlstate,1,npar);
    }  
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);      for(j=1; j<=nlstate;j++)
    }        for(theta=1; theta <=npar; theta++)
              trgradg[j][theta]=gradg[theta][j];
   fclose(ficgp);  
 }  /* end gnuplot */      for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
 /*************** Moving average **************/      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){      for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   int i, cpt, cptcod;  
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)      fprintf(ficresvpl,"%.0f ",age );
       for (i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++)
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
           mobaverage[(int)agedeb][i][cptcod]=0.;      fprintf(ficresvpl,"\n");
          free_vector(gp,1,nlstate);
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){      free_vector(gm,1,nlstate);
       for (i=1; i<=nlstate;i++){      free_matrix(gradg,1,npar,1,nlstate);
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      free_matrix(trgradg,1,nlstate,1,npar);
           for (cpt=0;cpt<=4;cpt++){    } /* End age */
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];  
           }    free_vector(xp,1,npar);
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    free_matrix(doldm,1,nlstate,1,npar);
         }    free_matrix(dnewm,1,nlstate,1,nlstate);
       }  
     }  }
      
 }  /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
   {
 /************** Forecasting ******************/    int i, j=0,  i1, k1, l1, t, tj;
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){    int k2, l2, j1,  z1;
      int k=0,l, cptcode;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    int first=1, first1;
   int *popage;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    double **dnewm,**doldm;
   double *popeffectif,*popcount;    double *xp;
   double ***p3mat;    double *gp, *gm;
   char fileresf[FILENAMELENGTH];    double **gradg, **trgradg;
     double **mu;
  agelim=AGESUP;    double age,agelim, cov[NCOVMAX];
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    char fileresprob[FILENAMELENGTH];
      char fileresprobcov[FILENAMELENGTH];
      char fileresprobcor[FILENAMELENGTH];
   strcpy(fileresf,"f");  
   strcat(fileresf,fileres);    double ***varpij;
   if((ficresf=fopen(fileresf,"w"))==NULL) {  
     printf("Problem with forecast resultfile: %s\n", fileresf);    strcpy(fileresprob,"prob"); 
   }    strcat(fileresprob,fileres);
   printf("Computing forecasting: result on file '%s' \n", fileresf);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
   if (mobilav==1) {    strcpy(fileresprobcov,"probcov"); 
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    strcat(fileresprobcov,fileres);
     movingaverage(agedeb, fage, ageminpar, mobaverage);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    }
   if (stepm<=12) stepsize=1;    strcpy(fileresprobcor,"probcor"); 
      strcat(fileresprobcor,fileres);
   agelim=AGESUP;    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprobcor);
   hstepm=1;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   hstepm=hstepm/stepm;    }
   yp1=modf(dateintmean,&yp);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   anprojmean=yp;    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   yp2=modf((yp1*12),&yp);    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   mprojmean=yp;    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   yp1=modf((yp2*30.5),&yp);    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   jprojmean=yp;    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   if(jprojmean==0) jprojmean=1;    
   if(mprojmean==0) jprojmean=1;    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
      fprintf(ficresprob,"# Age");
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
      fprintf(ficresprobcov,"# Age");
   for(cptcov=1;cptcov<=i2;cptcov++){    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    fprintf(ficresprobcov,"# Age");
       k=k+1;  
       fprintf(ficresf,"\n#******");  
       for(j=1;j<=cptcoveff;j++) {    for(i=1; i<=nlstate;i++)
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for(j=1; j<=(nlstate+ndeath);j++){
       }        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
       fprintf(ficresf,"******\n");        fprintf(ficresprobcov," p%1d-%1d ",i,j);
       fprintf(ficresf,"# StartingAge FinalAge");        fprintf(ficresprobcor," p%1d-%1d ",i,j);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);      }  
          fprintf(ficresprob,"\n");
          fprintf(ficresprobcov,"\n");
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    fprintf(ficresprobcor,"\n");
         fprintf(ficresf,"\n");    xp=vector(1,npar);
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
           nhstepm = nhstepm/hstepm;    first=1;
              if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
           oldm=oldms;savm=savms;      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        exit(0);
            }
           for (h=0; h<=nhstepm; h++){    else{
             if (h==(int) (calagedate+YEARM*cpt)) {      fprintf(ficgp,"\n# Routine varprob");
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    }
             }    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
             for(j=1; j<=nlstate+ndeath;j++) {      printf("Problem with html file: %s\n", optionfilehtm);
               kk1=0.;kk2=0;      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
               for(i=1; i<=nlstate;i++) {                    exit(0);
                 if (mobilav==1)    }
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    else{
                 else {      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      fprintf(fichtm,"\n");
                 }  
                      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
               }      fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
               if (h==(int)(calagedate+12*cpt)){      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");
                 fprintf(ficresf," %.3f", kk1);  
                            }
               }  
             }   
           }    cov[1]=1;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    tj=cptcoveff;
         }    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
       }    j1=0;
     }    for(t=1; t<=tj;t++){
   }      for(i1=1; i1<=ncodemax[t];i1++){ 
                j1++;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        
         if  (cptcovn>0) {
   fclose(ficresf);          fprintf(ficresprob, "\n#********** Variable "); 
 }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 /************** Forecasting ******************/          fprintf(ficresprob, "**********\n#");
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){          fprintf(ficresprobcov, "\n#********** Variable "); 
            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          fprintf(ficresprobcov, "**********\n#");
   int *popage;          
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          fprintf(ficgp, "\n#********** Variable "); 
   double *popeffectif,*popcount;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   double ***p3mat,***tabpop,***tabpopprev;          fprintf(ficgp, "**********\n#");
   char filerespop[FILENAMELENGTH];          
           
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   agelim=AGESUP;          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;          
            fprintf(ficresprobcor, "\n#********** Variable ");    
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficgp, "**********\n#");    
          }
   strcpy(filerespop,"pop");        
   strcat(filerespop,fileres);        for (age=bage; age<=fage; age ++){ 
   if((ficrespop=fopen(filerespop,"w"))==NULL) {          cov[2]=age;
     printf("Problem with forecast resultfile: %s\n", filerespop);          for (k=1; k<=cptcovn;k++) {
   }            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
   printf("Computing forecasting: result on file '%s' \n", filerespop);          }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          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]]];
   if (mobilav==1) {          
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
     movingaverage(agedeb, fage, ageminpar, mobaverage);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   }          gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
   stepsize=(int) (stepm+YEARM-1)/YEARM;      
   if (stepm<=12) stepsize=1;          for(theta=1; theta <=npar; theta++){
              for(i=1; i<=npar; i++)
   agelim=AGESUP;              xp[i] = x[i] + (i==theta ?delti[theta]:0);
              
   hstepm=1;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   hstepm=hstepm/stepm;            
              k=0;
   if (popforecast==1) {            for(i=1; i<= (nlstate); i++){
     if((ficpop=fopen(popfile,"r"))==NULL) {              for(j=1; j<=(nlstate+ndeath);j++){
       printf("Problem with population file : %s\n",popfile);exit(0);                k=k+1;
     }                gp[k]=pmmij[i][j];
     popage=ivector(0,AGESUP);              }
     popeffectif=vector(0,AGESUP);            }
     popcount=vector(0,AGESUP);            
                for(i=1; i<=npar; i++)
     i=1;                xp[i] = x[i] - (i==theta ?delti[theta]:0);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;      
                pmij(pmmij,cov,ncovmodel,xp,nlstate);
     imx=i;            k=0;
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];            for(i=1; i<=(nlstate); i++){
   }              for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
   for(cptcov=1;cptcov<=i2;cptcov++){                gm[k]=pmmij[i][j];
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){              }
       k=k+1;            }
       fprintf(ficrespop,"\n#******");       
       for(j=1;j<=cptcoveff;j++) {            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
       }          }
       fprintf(ficrespop,"******\n");  
       fprintf(ficrespop,"# Age");          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);            for(theta=1; theta <=npar; theta++)
       if (popforecast==1)  fprintf(ficrespop," [Population]");              trgradg[j][theta]=gradg[theta][j];
                
       for (cpt=0; cpt<=0;cpt++) {          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
                  
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          pmij(pmmij,cov,ncovmodel,x,nlstate);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          
           nhstepm = nhstepm/hstepm;          k=0;
                    for(i=1; i<=(nlstate); i++){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for(j=1; j<=(nlstate+ndeath);j++){
           oldm=oldms;savm=savms;              k=k+1;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                mu[k][(int) age]=pmmij[i][j];
                    }
           for (h=0; h<=nhstepm; h++){          }
             if (h==(int) (calagedate+YEARM*cpt)) {          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
             }              varpij[i][j][(int)age] = doldm[i][j];
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;          /*printf("\n%d ",(int)age);
               for(i=1; i<=nlstate;i++) {                     for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                 if (mobilav==1)         printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];         fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                 else {       }*/
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  
                 }          fprintf(ficresprob,"\n%d ",(int)age);
               }          fprintf(ficresprobcov,"\n%d ",(int)age);
               if (h==(int)(calagedate+12*cpt)){          fprintf(ficresprobcor,"\n%d ",(int)age);
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;  
                   /*fprintf(ficrespop," %.3f", kk1);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
               }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             }            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             for(i=1; i<=nlstate;i++){            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
               kk1=0.;          }
                 for(j=1; j<=nlstate;j++){          i=0;
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];          for (k=1; k<=(nlstate);k++){
                 }            for (l=1; l<=(nlstate+ndeath);l++){ 
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];              i=i++;
             }              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)              for (j=1; j<=i;j++){
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
           }                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              }
         }            }
       }          }/* end of loop for state */
          } /* end of loop for age */
   /******/  
         /* Confidence intervalle of pij  */
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {        /*
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          fprintf(ficgp,"\nset noparametric;unset label");
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           nhstepm = nhstepm/hstepm;        fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
                  fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           oldm=oldms;savm=savms;        fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          */
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        first1=1;
             }        for (k2=1; k2<=(nlstate);k2++){
             for(j=1; j<=nlstate+ndeath;j++) {          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
               kk1=0.;kk2=0;            if(l2==k2) continue;
               for(i=1; i<=nlstate;i++) {                          j=(k2-1)*(nlstate+ndeath)+l2;
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                for (k1=1; k1<=(nlstate);k1++){
               }              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);                if(l1==k1) continue;
             }                i=(k1-1)*(nlstate+ndeath)+l1;
           }                if(i<=j) continue;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                for (age=bage; age<=fage; age ++){ 
         }                  if ((int)age %5==0){
       }                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
    }                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   }                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                      mu1=mu[i][(int) age]/stepm*YEARM ;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                    mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
   if (popforecast==1) {                    /* Computing eigen value of matrix of covariance */
     free_ivector(popage,0,AGESUP);                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     free_vector(popeffectif,0,AGESUP);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     free_vector(popcount,0,AGESUP);                    /* Eigen vectors */
   }                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                    /*v21=sqrt(1.-v11*v11); *//* error */
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                    v21=(lc1-v1)/cv12*v11;
   fclose(ficrespop);                    v12=-v21;
 }                    v22=v11;
                     tnalp=v21/v11;
 /***********************************************/                    if(first1==1){
 /**************** Main Program *****************/                      first1=0;
 /***********************************************/                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
 int main(int argc, char *argv[])                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
 {                    /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   double agedeb, agefin,hf;                    if(first==1){
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;                      first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
   double fret;                      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);
   double **xi,tmp,delta;                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
   double dum; /* Dummy variable */                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
   double ***p3mat;                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
   int *indx;                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
   char line[MAXLINE], linepar[MAXLINE];                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   char title[MAXLINE];                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];                      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",\
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                                mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];                    }else{
                       first=0;
   char filerest[FILENAMELENGTH];                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
   char fileregp[FILENAMELENGTH];                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   char popfile[FILENAMELENGTH];                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];                      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",\
   int firstobs=1, lastobs=10;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   int sdeb, sfin; /* Status at beginning and end */                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   int c,  h , cpt,l;                    }/* if first */
   int ju,jl, mi;                  } /* age mod 5 */
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;                } /* end loop age */
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
   int mobilav=0,popforecast=0;                first=1;
   int hstepm, nhstepm;              } /*l12 */
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;            } /* k12 */
           } /*l1 */
   double bage, fage, age, agelim, agebase;        }/* k1 */
   double ftolpl=FTOL;      } /* loop covariates */
   double **prlim;      free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   double *severity;      free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   double ***param; /* Matrix of parameters */      free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
   double  *p;      free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   double **matcov; /* Matrix of covariance */      free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   double ***delti3; /* Scale */      free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   double *delti; /* Scale */    }
   double ***eij, ***vareij;    free_vector(xp,1,npar);
   double **varpl; /* Variances of prevalence limits by age */    fclose(ficresprob);
   double *epj, vepp;    fclose(ficresprobcov);
   double kk1, kk2;    fclose(ficresprobcor);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    fclose(ficgp);
      fclose(fichtm);
   }
   char version[80]="Imach version 0.8a, March 2002, INED-EUROREVES ";  
   char *alph[]={"a","a","b","c","d","e"}, str[4];  
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
   char z[1]="c", occ;                    int lastpass, int stepm, int weightopt, char model[],\
 #include <sys/time.h>                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
 #include <time.h>                    int popforecast, int estepm ,\
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];                    double jprev1, double mprev1,double anprev1, \
                      double jprev2, double mprev2,double anprev2){
   /* long total_usecs;    int jj1, k1, i1, cpt;
   struct timeval start_time, end_time;    /*char optionfilehtm[FILENAMELENGTH];*/
      if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      printf("Problem with %s \n",optionfilehtm), exit(0);
   getcwd(pathcd, size);      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
     }
   printf("\n%s",version);  
   if(argc <=1){     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
     printf("\nEnter the parameter file name: ");   - 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
     scanf("%s",pathtot);   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
   }   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
   else{   - Life expectancies by age and initial health status (estepm=%2d months): 
     strcpy(pathtot,argv[1]);     <a href=\"e%s\">e%s</a> <br>\n</li>", \
   }    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/  
   /*cygwin_split_path(pathtot,path,optionfile);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/  
   /* cutv(path,optionfile,pathtot,'\\');*/   m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);  
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);   jj1=0;
   chdir(path);   for(k1=1; k1<=m;k1++){
   replace(pathc,path);     for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
 /*-------- arguments in the command line --------*/       if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   strcpy(fileres,"r");         for (cpt=1; cpt<=cptcoveff;cpt++) 
   strcat(fileres, optionfilefiname);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   strcat(fileres,".txt");    /* Other files have txt extension */         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
   /*---------arguments file --------*/       /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>
   if((ficpar=fopen(optionfile,"r"))==NULL)    {  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
     printf("Problem with optionfile %s\n",optionfile);       /* Quasi-incidences */
     goto end;       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
   }  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
          /* Stable prevalence in each health state */
   strcpy(filereso,"o");         for(cpt=1; cpt<nlstate;cpt++){
   strcat(filereso,fileres);           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
   if((ficparo=fopen(filereso,"w"))==NULL) {  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
     printf("Problem with Output resultfile: %s\n", filereso);goto end;         }
   }       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>
   /* Reads comments: lines beginning with '#' */  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
   while((c=getc(ficpar))=='#' && c!= EOF){       }
     ungetc(c,ficpar);       fprintf(fichtm,"\n<br>- Total life expectancy by age and
     fgets(line, MAXLINE, ficpar);  health expectancies in states (1) and (2): e%s%d.png<br>
     puts(line);  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
     fputs(line,ficparo);     } /* end i1 */
   }   }/* End k1 */
   ungetc(c,ficpar);   fprintf(fichtm,"</ul>");
   
   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(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
   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);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
 while((c=getc(ficpar))=='#' && c!= EOF){   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
     ungetc(c,ficpar);   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
     fgets(line, MAXLINE, ficpar);   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
     puts(line);   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
     fputs(line,ficparo);   - 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);
   ungetc(c,ficpar);  
     if(popforecast==1) fprintf(fichtm,"\n
       - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
   covar=matrix(0,NCOVMAX,1,n);   - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
   cptcovn=0;          <br>",fileres,fileres,fileres,fileres);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;   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);
   ncovmodel=2+cptcovn;  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  
     m=cptcoveff;
   /* Read guess parameters */   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){   jj1=0;
     ungetc(c,ficpar);   for(k1=1; k1<=m;k1++){
     fgets(line, MAXLINE, ficpar);     for(i1=1; i1<=ncodemax[k1];i1++){
     puts(line);       jj1++;
     fputs(line,ficparo);       if (cptcovn > 0) {
   }         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   ungetc(c,ficpar);         for (cpt=1; cpt<=cptcoveff;cpt++) 
             fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     for(i=1; i <=nlstate; i++)       }
     for(j=1; j <=nlstate+ndeath-1; j++){       for(cpt=1; cpt<=nlstate;cpt++) {
       fscanf(ficpar,"%1d%1d",&i1,&j1);         fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
       fprintf(ficparo,"%1d%1d",i1,j1);  interval) in state (%d): v%s%d%d.png <br>
       printf("%1d%1d",i,j);  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
       for(k=1; k<=ncovmodel;k++){       }
         fscanf(ficpar," %lf",&param[i][j][k]);     } /* end i1 */
         printf(" %lf",param[i][j][k]);   }/* End k1 */
         fprintf(ficparo," %lf",param[i][j][k]);   fprintf(fichtm,"</ul>");
       }  fclose(fichtm);
       fscanf(ficpar,"\n");  }
       printf("\n");  
       fprintf(ficparo,"\n");  /******************* Gnuplot file **************/
     }  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
    
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   p=param[1][1];    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
        printf("Problem with file %s",optionfilegnuplot);
   /* Reads comments: lines beginning with '#' */      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
   while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    /*#ifdef windows */
     puts(line);      fprintf(ficgp,"cd \"%s\" \n",pathc);
     fputs(line,ficparo);      /*#endif */
   }  m=pow(2,cptcoveff);
   ungetc(c,ficpar);    
    /* 1eme*/
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    for (cpt=1; cpt<= nlstate ; cpt ++) {
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */     for (k1=1; k1<= m ; k1 ++) {
   for(i=1; i <=nlstate; i++){       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     for(j=1; j <=nlstate+ndeath-1; j++){       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);
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       printf("%1d%1d",i,j);       for (i=1; i<= nlstate ; i ++) {
       fprintf(ficparo,"%1d%1d",i1,j1);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       for(k=1; k<=ncovmodel;k++){         else fprintf(ficgp," \%%*lf (\%%*lf)");
         fscanf(ficpar,"%le",&delti3[i][j][k]);       }
         printf(" %le",delti3[i][j][k]);       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
         fprintf(ficparo," %le",delti3[i][j][k]);       for (i=1; i<= nlstate ; i ++) {
       }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       fscanf(ficpar,"\n");         else fprintf(ficgp," \%%*lf (\%%*lf)");
       printf("\n");       } 
       fprintf(ficparo,"\n");       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); 
     }       for (i=1; i<= nlstate ; i ++) {
   }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   delti=delti3[1][1];         else fprintf(ficgp," \%%*lf (\%%*lf)");
         }  
   /* Reads comments: lines beginning with '#' */       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
   while((c=getc(ficpar))=='#' && c!= EOF){     }
     ungetc(c,ficpar);    }
     fgets(line, MAXLINE, ficpar);    /*2 eme*/
     puts(line);    
     fputs(line,ficparo);    for (k1=1; k1<= m ; k1 ++) { 
   }      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
   ungetc(c,ficpar);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
        
   matcov=matrix(1,npar,1,npar);      for (i=1; i<= nlstate+1 ; i ++) {
   for(i=1; i <=npar; i++){        k=2*i;
     fscanf(ficpar,"%s",&str);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
     printf("%s",str);        for (j=1; j<= nlstate+1 ; j ++) {
     fprintf(ficparo,"%s",str);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     for(j=1; j <=i; j++){          else fprintf(ficgp," \%%*lf (\%%*lf)");
       fscanf(ficpar," %le",&matcov[i][j]);        }   
       printf(" %.5le",matcov[i][j]);        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
       fprintf(ficparo," %.5le",matcov[i][j]);        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);
     fscanf(ficpar,"\n");        for (j=1; j<= nlstate+1 ; j ++) {
     printf("\n");          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     fprintf(ficparo,"\n");          else fprintf(ficgp," \%%*lf (\%%*lf)");
   }        }   
   for(i=1; i <=npar; i++)        fprintf(ficgp,"\" t\"\" w l 0,");
     for(j=i+1;j<=npar;j++)        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
       matcov[i][j]=matcov[j][i];        for (j=1; j<= nlstate+1 ; j ++) {
              if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   printf("\n");          else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
     /*-------- Rewriting paramater file ----------*/        else fprintf(ficgp,"\" t\"\" w l 0,");
      strcpy(rfileres,"r");    /* "Rparameterfile */      }
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    }
      strcat(rfileres,".");    /* */    
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    /*3eme*/
     if((ficres =fopen(rfileres,"w"))==NULL) {    
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    for (k1=1; k1<= m ; k1 ++) { 
     }      for (cpt=1; cpt<= nlstate ; cpt ++) {
     fprintf(ficres,"#%s\n",version);        k=2+nlstate*(2*cpt-2);
            fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     /*-------- data file ----------*/        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
     if((fic=fopen(datafile,"r"))==NULL)    {        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
       printf("Problem with datafile: %s\n", datafile);goto end;          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     n= lastobs;          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     severity = vector(1,maxwav);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     outcome=imatrix(1,maxwav+1,1,n);          
     num=ivector(1,n);        */
     moisnais=vector(1,n);        for (i=1; i< nlstate ; i ++) {
     annais=vector(1,n);          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);
     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 */    /* CV preval stat */
     mint=matrix(1,maxwav,1,n);    for (k1=1; k1<= m ; k1 ++) { 
     anint=matrix(1,maxwav,1,n);      for (cpt=1; cpt<nlstate ; cpt ++) {
     s=imatrix(1,maxwav+1,1,n);        k=3;
     adl=imatrix(1,maxwav+1,1,n);            fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     tab=ivector(1,NCOVMAX);        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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
     ncodemax=ivector(1,8);        
         for (i=1; i< nlstate ; i ++)
     i=1;          fprintf(ficgp,"+$%d",k+i+1);
     while (fgets(line, MAXLINE, fic) != NULL)    {        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
       if ((i >= firstobs) && (i <=lastobs)) {        
                l=3+(nlstate+ndeath)*cpt;
         for (j=maxwav;j>=1;j--){        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        for (i=1; i< nlstate ; i ++) {
           strcpy(line,stra);          l=3+(nlstate+ndeath)*cpt;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          fprintf(ficgp,"+$%d",l+i+1);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        }
         }        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
              } 
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    }  
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    
     /* proba elementaires */
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    for(i=1,jk=1; i <=nlstate; i++){
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);      for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);          for(j=1; j <=ncovmodel; j++){
         for (j=ncovcol;j>=1;j--){            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);            jk++; 
         }            fprintf(ficgp,"\n");
         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;     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); 
     /* printf("ii=%d", ij);         if (ng==2)
        scanf("%d",i);*/           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
   imx=i-1; /* Number of individuals */         else
            fprintf(ficgp,"\nset title \"Probability\"\n");
   /* for (i=1; i<=imx; i++){         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;         i=1;
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;         for(k2=1; k2<=nlstate; k2++) {
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;           k3=i;
     }*/           for(k=1; k<=(nlstate+ndeath); k++) {
               if (k != k2){
   /* for (i=1; i<=imx; i++){               if(ng==2)
      if (s[4][i]==9)  s[4][i]=-1;                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,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]));}               else
   */                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                 ij=1;
   /* Calculation of the number of parameter from char model*/               for(j=3; j <=ncovmodel; j++) {
   Tvar=ivector(1,15);                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   Tprod=ivector(1,15);                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   Tvaraff=ivector(1,15);                   ij++;
   Tvard=imatrix(1,15,1,2);                 }
   Tage=ivector(1,15);                       else
                       fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   if (strlen(model) >1){               }
     j=0, j1=0, k1=1, k2=1;               fprintf(ficgp,")/(1");
     j=nbocc(model,'+');               
     j1=nbocc(model,'*');               for(k1=1; k1 <=nlstate; k1++){   
     cptcovn=j+1;                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
     cptcovprod=j1;                 ij=1;
                     for(j=3; j <=ncovmodel; j++){
     strcpy(modelsav,model);                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
       printf("Error. Non available option model=%s ",model);                     ij++;
       goto end;                   }
     }                   else
                         fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
     for(i=(j+1); i>=1;i--){                 }
       cutv(stra,strb,modelsav,'+');                 fprintf(ficgp,")");
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);               }
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
       /*scanf("%d",i);*/               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
       if (strchr(strb,'*')) {               i=i+ncovmodel;
         cutv(strd,strc,strb,'*');             }
         if (strcmp(strc,"age")==0) {           } /* end k */
           cptcovprod--;         } /* end k2 */
           cutv(strb,stre,strd,'V');       } /* end jk */
           Tvar[i]=atoi(stre);     } /* end ng */
           cptcovage++;     fclose(ficgp); 
             Tage[cptcovage]=i;  }  /* end gnuplot */
             /*printf("stre=%s ", stre);*/  
         }  
         else if (strcmp(strd,"age")==0) {  /*************** Moving average **************/
           cptcovprod--;  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
           cutv(strb,stre,strc,'V');  
           Tvar[i]=atoi(stre);    int i, cpt, cptcod;
           cptcovage++;    int modcovmax =1;
           Tage[cptcovage]=i;    int mobilavrange, mob;
         }    double age;
         else {  
           cutv(strb,stre,strc,'V');    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
           Tvar[i]=ncovcol+k1;                             a covariate has 2 modalities */
           cutv(strb,strc,strd,'V');    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
           Tprod[k1]=i;  
           Tvard[k1][1]=atoi(strc);    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
           Tvard[k1][2]=atoi(stre);      if(mobilav==1) mobilavrange=5; /* default */
           Tvar[cptcovn+k2]=Tvard[k1][1];      else mobilavrange=mobilav;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];      for (age=bage; age<=fage; age++)
           for (k=1; k<=lastobs;k++)        for (i=1; i<=nlstate;i++)
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];          for (cptcod=1;cptcod<=modcovmax;cptcod++)
           k1++;            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
           k2=k2+2;      /* 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. 
       else {      */ 
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/      for (mob=3;mob <=mobilavrange;mob=mob+2){
        /*  scanf("%d",i);*/        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
       cutv(strd,strc,strb,'V');          for (i=1; i<=nlstate;i++){
       Tvar[i]=atoi(strc);            for (cptcod=1;cptcod<=modcovmax;cptcod++){
       }              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
       strcpy(modelsav,stra);                  for (cpt=1;cpt<=(mob-1)/2;cpt++){
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
         scanf("%d",i);*/                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
     }                }
 }              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
              }
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);          }
   printf("cptcovprod=%d ", cptcovprod);        }/* end age */
   scanf("%d ",i);*/      }/* end mob */
     fclose(fic);    }else return -1;
     return 0;
     /*  if(mle==1){*/  }/* End movingaverage */
     if (weightopt != 1) { /* Maximisation without weights*/  
       for(i=1;i<=n;i++) weight[i]=1.0;  
     }  /************** Forecasting ******************/
     /*-calculation of age at interview from date of interview and age at death -*/  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){
     agev=matrix(1,maxwav,1,imx);    
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     for (i=1; i<=imx; i++) {    int *popage;
       for(m=2; (m<= maxwav); m++) {    double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    double *popeffectif,*popcount;
          anint[m][i]=9999;    double ***p3mat;
          s[m][i]=-1;    double ***mobaverage;
        }    char fileresf[FILENAMELENGTH];
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;  
       }   agelim=AGESUP;
     }   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
   
     for (i=1; i<=imx; i++)  {    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);   
       for(m=1; (m<= maxwav); m++){   
         if(s[m][i] >0){    strcpy(fileresf,"f"); 
           if (s[m][i] >= nlstate+1) {    strcat(fileresf,fileres);
             if(agedc[i]>0)    if((ficresf=fopen(fileresf,"w"))==NULL) {
               if(moisdc[i]!=99 && andc[i]!=9999)      printf("Problem with forecast resultfile: %s\n", fileresf);
                 agev[m][i]=agedc[i];      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/    }
            else {    printf("Computing forecasting: result on file '%s' \n", fileresf);
               if (andc[i]!=9999){    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  
               agev[m][i]=-1;    if (cptcoveff==0) ncodemax[cptcoveff]=1;
               }  
             }    if (mobilav!=0) {
           }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           else if(s[m][i] !=9){ /* Should no more exist */      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
             if(mint[m][i]==99 || anint[m][i]==9999)        printf(" Error in movingaverage mobilav=%d\n",mobilav);
               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);*/    stepsize=(int) (stepm+YEARM-1)/YEARM;
             }    if (stepm<=12) stepsize=1;
             else if(agev[m][i] >agemax){    
               agemax=agev[m][i];    agelim=AGESUP;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    
             }    hstepm=1;
             /*agev[m][i]=anint[m][i]-annais[i];*/    hstepm=hstepm/stepm; 
             /*   agev[m][i] = age[i]+2*m;*/    yp1=modf(dateintmean,&yp);
           }    anprojmean=yp;
           else { /* =9 */    yp2=modf((yp1*12),&yp);
             agev[m][i]=1;    mprojmean=yp;
             s[m][i]=-1;    yp1=modf((yp2*30.5),&yp);
           }    jprojmean=yp;
         }    if(jprojmean==0) jprojmean=1;
         else /*= 0 Unknown */    if(mprojmean==0) jprojmean=1;
           agev[m][i]=1;    
       }    fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean); 
        
     }    for(cptcov=1;cptcov<=i2;cptcov++){
     for (i=1; i<=imx; i++)  {      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
       for(m=1; (m<= maxwav); m++){        k=k+1;
         if (s[m][i] > (nlstate+ndeath)) {        fprintf(ficresf,"\n#******");
           printf("Error: Wrong value in nlstate or ndeath\n");          for(j=1;j<=cptcoveff;j++) {
           goto end;          fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }        }
       }        fprintf(ficresf,"******\n");
     }        fprintf(ficresf,"# StartingAge FinalAge");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);        
         
     free_vector(severity,1,maxwav);        for (cpt=0; cpt<=(anproj2-anproj1);cpt++) { 
     free_imatrix(outcome,1,maxwav+1,1,n);          fprintf(ficresf,"\n");
     free_vector(moisnais,1,n);          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);   
     free_vector(annais,1,n);  
     /* free_matrix(mint,1,maxwav,1,n);          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
        free_matrix(anint,1,maxwav,1,n);*/            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
     free_vector(moisdc,1,n);            nhstepm = nhstepm/hstepm; 
     free_vector(andc,1,n);            
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                oldm=oldms;savm=savms;
     wav=ivector(1,imx);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
     dh=imatrix(1,lastpass-firstpass+1,1,imx);          
     mw=imatrix(1,lastpass-firstpass+1,1,imx);            for (h=0; h<=nhstepm; h++){
                  if (h==(int) (calagedate+YEARM*cpt)) {
     /* Concatenates waves */                fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);              } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
       Tcode=ivector(1,100);                for(i=1; i<=nlstate;i++) {              
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);                  if (mobilav==1) 
       ncodemax[1]=1;                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);                  else {
                          kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
    codtab=imatrix(1,100,1,10);                  }
    h=0;                  
    m=pow(2,cptcoveff);                }
                  if (h==(int)(calagedate+12*cpt)){
    for(k=1;k<=cptcoveff; k++){                  fprintf(ficresf," %.3f", kk1);
      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;            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
            /*  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]);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       codtab[1][2]=1;codtab[2][2]=2; */  
    /* for(i=1; i <=m ;i++){    fclose(ficresf);
       for(k=1; k <=cptcovn; k++){  }
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);  /************** Forecasting ******************/
       }  populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
       printf("\n");    
       }    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
       scanf("%d",i);*/    int *popage;
        double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
    /* Calculates basic frequencies. Computes observed prevalence at single age    double *popeffectif,*popcount;
        and prints on file fileres'p'. */    double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
        char filerespop[FILENAMELENGTH];
      
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    agelim=AGESUP;
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    
          prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
     /* 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) */    strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if(mle==1){    if((ficrespop=fopen(filerespop,"w"))==NULL) {
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);      printf("Problem with forecast resultfile: %s\n", filerespop);
     }      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
        }
     /*--------- results files --------------*/    printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
    
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
    jk=1;  
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    if (mobilav!=0) {
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    for(i=1,jk=1; i <=nlstate; i++){      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
      for(k=1; k <=(nlstate+ndeath); k++){        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
        if (k != i)        printf(" Error in movingaverage mobilav=%d\n",mobilav);
          {      }
            printf("%d%d ",i,k);    }
            fprintf(ficres,"%1d%1d ",i,k);  
            for(j=1; j <=ncovmodel; j++){    stepsize=(int) (stepm+YEARM-1)/YEARM;
              printf("%f ",p[jk]);    if (stepm<=12) stepsize=1;
              fprintf(ficres,"%f ",p[jk]);    
              jk++;    agelim=AGESUP;
            }    
            printf("\n");    hstepm=1;
            fprintf(ficres,"\n");    hstepm=hstepm/stepm; 
          }    
      }    if (popforecast==1) {
    }      if((ficpop=fopen(popfile,"r"))==NULL) {
  if(mle==1){        printf("Problem with population file : %s\n",popfile);exit(0);
     /* Computing hessian and covariance matrix */        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
     ftolhess=ftol; /* Usually correct */      } 
     hesscov(matcov, p, npar, delti, ftolhess, func);      popage=ivector(0,AGESUP);
  }      popeffectif=vector(0,AGESUP);
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");      popcount=vector(0,AGESUP);
     printf("# Scales (for hessian or gradient estimation)\n");      
      for(i=1,jk=1; i <=nlstate; i++){      i=1;   
       for(j=1; j <=nlstate+ndeath; j++){      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
         if (j!=i) {     
           fprintf(ficres,"%1d%1d",i,j);      imx=i;
           printf("%1d%1d",i,j);      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
           for(k=1; k<=ncovmodel;k++){    }
             printf(" %.5e",delti[jk]);  
             fprintf(ficres," %.5e",delti[jk]);    for(cptcov=1;cptcov<=i2;cptcov++){
             jk++;     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
           }        k=k+1;
           printf("\n");        fprintf(ficrespop,"\n#******");
           fprintf(ficres,"\n");        for(j=1;j<=cptcoveff;j++) {
         }          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       }        }
      }        fprintf(ficrespop,"******\n");
            fprintf(ficrespop,"# Age");
     k=1;        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
     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 (popforecast==1)  fprintf(ficrespop," [Population]");
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");        
     for(i=1;i<=npar;i++){        for (cpt=0; cpt<=0;cpt++) { 
       /*  if (k>nlstate) k=1;          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
       i1=(i-1)/(ncovmodel*nlstate)+1;          
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
       printf("%s%d%d",alph[k],i1,tab[i]);*/            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
       fprintf(ficres,"%3d",i);            nhstepm = nhstepm/hstepm; 
       printf("%3d",i);            
       for(j=1; j<=i;j++){            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(ficres," %.5e",matcov[i][j]);            oldm=oldms;savm=savms;
         printf(" %.5e",matcov[i][j]);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
       }          
       fprintf(ficres,"\n");            for (h=0; h<=nhstepm; h++){
       printf("\n");              if (h==(int) (calagedate+YEARM*cpt)) {
       k++;                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
     }              } 
                  for(j=1; j<=nlstate+ndeath;j++) {
     while((c=getc(ficpar))=='#' && c!= EOF){                kk1=0.;kk2=0;
       ungetc(c,ficpar);                for(i=1; i<=nlstate;i++) {              
       fgets(line, MAXLINE, ficpar);                  if (mobilav==1) 
       puts(line);                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
       fputs(line,ficparo);                  else {
     }                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
     ungetc(c,ficpar);                  }
                  }
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&ageminpar,&agemaxpar, &bage, &fage);                if (h==(int)(calagedate+12*cpt)){
                      tabpop[(int)(agedeb)][j][cptcod]=kk1;
     if (fage <= 2) {                    /*fprintf(ficrespop," %.3f", kk1);
       bage = ageminpar;                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
       fage = agemaxpar;                }
     }              }
                  for(i=1; i<=nlstate;i++){
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                kk1=0.;
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",ageminpar,agemaxpar,bage,fage);                  for(j=1; j<=nlstate;j++){
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",ageminpar,agemaxpar,bage,fage);                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                    }
     while((c=getc(ficpar))=='#' && c!= EOF){                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
     ungetc(c,ficpar);              }
     fgets(line, MAXLINE, ficpar);  
     puts(line);              if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) 
     fputs(line,ficparo);                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
   }            }
   ungetc(c,ficpar);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
            }
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);        }
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);   
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    /******/
        
   while((c=getc(ficpar))=='#' && c!= EOF){        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
     ungetc(c,ficpar);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
     fgets(line, MAXLINE, ficpar);          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
     puts(line);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
     fputs(line,ficparo);            nhstepm = nhstepm/hstepm; 
   }            
   ungetc(c,ficpar);            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);  
    dateprev1=anprev1+mprev1/12.+jprev1/365.;            for (h=0; h<=nhstepm; h++){
    dateprev2=anprev2+mprev2/12.+jprev2/365.;              if (h==(int) (calagedate+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
   fscanf(ficpar,"pop_based=%d\n",&popbased);              } 
   fprintf(ficparo,"pop_based=%d\n",popbased);                for(j=1; j<=nlstate+ndeath;j++) {
   fprintf(ficres,"pop_based=%d\n",popbased);                  kk1=0.;kk2=0;
                  for(i=1; i<=nlstate;i++) {              
   while((c=getc(ficpar))=='#' && c!= EOF){                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
     ungetc(c,ficpar);                }
     fgets(line, MAXLINE, ficpar);                if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1); 
     puts(line);              }
     fputs(line,ficparo);            }
   }            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   ungetc(c,ficpar);          }
         }
   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);    }
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);   
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
 while((c=getc(ficpar))=='#' && c!= EOF){    if (popforecast==1) {
     ungetc(c,ficpar);      free_ivector(popage,0,AGESUP);
     fgets(line, MAXLINE, ficpar);      free_vector(popeffectif,0,AGESUP);
     puts(line);      free_vector(popcount,0,AGESUP);
     fputs(line,ficparo);    }
   }    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   ungetc(c,ficpar);    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   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);  /***********************************************/
   /**************** Main Program *****************/
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  /***********************************************/
   
 /*------------ gnuplot -------------*/  int main(int argc, char *argv[])
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);  {
    
 /*------------ free_vector  -------------*/    int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
  chdir(path);    double agedeb, agefin,hf;
      double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
  free_ivector(wav,1,imx);  
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    double fret;
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      double **xi,tmp,delta;
  free_ivector(num,1,n);  
  free_vector(agedc,1,n);    double dum; /* Dummy variable */
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    double ***p3mat;
  fclose(ficparo);    double ***mobaverage;
  fclose(ficres);    int *indx;
     char line[MAXLINE], linepar[MAXLINE];
 /*--------- index.htm --------*/    char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
     int firstobs=1, lastobs=10;
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast);    int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
      int ju,jl, mi;
   /*--------------- Prevalence limit --------------*/    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
      int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab; 
   strcpy(filerespl,"pl");    int mobilav=0,popforecast=0;
   strcat(filerespl,fileres);    int hstepm, nhstepm;
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;  
   }    double bage, fage, age, agelim, agebase;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    double ftolpl=FTOL;
   fprintf(ficrespl,"#Prevalence limit\n");    double **prlim;
   fprintf(ficrespl,"#Age ");    double *severity;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    double ***param; /* Matrix of parameters */
   fprintf(ficrespl,"\n");    double  *p;
      double **matcov; /* Matrix of covariance */
   prlim=matrix(1,nlstate,1,nlstate);    double ***delti3; /* Scale */
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double *delti; /* Scale */
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double ***eij, ***vareij;
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double **varpl; /* Variances of prevalence limits by age */
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double *epj, vepp;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    double kk1, kk2;
   k=0;    double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
   agebase=ageminpar;    
   agelim=agemaxpar;  
   ftolpl=1.e-10;    char *alph[]={"a","a","b","c","d","e"}, str[4];
   i1=cptcoveff;  
   if (cptcovn < 1){i1=1;}  
     char z[1]="c", occ;
   for(cptcov=1;cptcov<=i1;cptcov++){  #include <sys/time.h>
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  #include <time.h>
         k=k+1;    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/   
         fprintf(ficrespl,"\n#******");    /* long total_usecs;
         for(j=1;j<=cptcoveff;j++)    struct timeval start_time, end_time;
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    
         fprintf(ficrespl,"******\n");    gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
            getcwd(pathcd, size);
         for (age=agebase; age<=agelim; age++){  
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    printf("\n%s",version);
           fprintf(ficrespl,"%.0f",age );    if(argc <=1){
           for(i=1; i<=nlstate;i++)      printf("\nEnter the parameter file name: ");
           fprintf(ficrespl," %.5f", prlim[i][i]);      scanf("%s",pathtot);
           fprintf(ficrespl,"\n");    }
         }    else{
       }      strcpy(pathtot,argv[1]);
     }    }
   fclose(ficrespl);    /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
   /*------------- h Pij x at various ages ------------*/      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
      /* cutv(path,optionfile,pathtot,'\\');*/
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;     printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   }    chdir(path);
   printf("Computing pij: result on file '%s' \n", filerespij);    replace(pathc,path);
    
   stepsize=(int) (stepm+YEARM-1)/YEARM;  /*-------- arguments in the command line --------*/
   /*if (stepm<=24) stepsize=2;*/  
     /* Log file */
   agelim=AGESUP;    strcat(filelog, optionfilefiname);
   hstepm=stepsize*YEARM; /* Every year of age */    strcat(filelog,".log");    /* */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    if((ficlog=fopen(filelog,"w"))==NULL)    {
        printf("Problem with logfile %s\n",filelog);
   k=0;      goto end;
   for(cptcov=1;cptcov<=i1;cptcov++){    }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficlog,"Log filename:%s\n",filelog);
       k=k+1;    fprintf(ficlog,"\n%s",version);
         fprintf(ficrespij,"\n#****** ");    fprintf(ficlog,"\nEnter the parameter file name: ");
         for(j=1;j<=cptcoveff;j++)    fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fflush(ficlog);
         fprintf(ficrespij,"******\n");  
            /* */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    strcpy(fileres,"r");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    strcat(fileres, optionfilefiname);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    strcat(fileres,".txt");    /* Other files have txt extension */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;    /*---------arguments file --------*/
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
           fprintf(ficrespij,"# Age");    if((ficpar=fopen(optionfile,"r"))==NULL)    {
           for(i=1; i<=nlstate;i++)      printf("Problem with optionfile %s\n",optionfile);
             for(j=1; j<=nlstate+ndeath;j++)      fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
               fprintf(ficrespij," %1d-%1d",i,j);      goto end;
           fprintf(ficrespij,"\n");    }
           for (h=0; h<=nhstepm; h++){  
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    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) {
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);      printf("Problem with Output resultfile: %s\n", filereso);
             fprintf(ficrespij,"\n");      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
           }      goto end;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    }
           fprintf(ficrespij,"\n");  
         }    /* Reads comments: lines beginning with '#' */
     }    while((c=getc(ficpar))=='#' && c!= EOF){
   }      ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/      puts(line);
       fputs(line,ficparo);
   fclose(ficrespij);    }
     ungetc(c,ficpar);
   
   /*---------- Forecasting ------------------*/    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);
   if((stepm == 1) && (strcmp(model,".")==0)){    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);
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);  while((c=getc(ficpar))=='#' && c!= EOF){
     free_matrix(mint,1,maxwav,1,n);      ungetc(c,ficpar);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);      fgets(line, MAXLINE, ficpar);
     free_vector(weight,1,n);}      puts(line);
   else{      fputs(line,ficparo);
     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);    ungetc(c,ficpar);
   }    
       
     covar=matrix(0,NCOVMAX,1,n); 
   /*---------- Health expectancies and variances ------------*/    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   strcpy(filerest,"t");  
   strcat(filerest,fileres);    ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
   if((ficrest=fopen(filerest,"w"))==NULL) {    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    
   }    /* Read guess parameters */
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
   strcpy(filerese,"e");      fgets(line, MAXLINE, ficpar);
   strcat(filerese,fileres);      puts(line);
   if((ficreseij=fopen(filerese,"w"))==NULL) {      fputs(line,ficparo);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    }
   }    ungetc(c,ficpar);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
  strcpy(fileresv,"v");      for(i=1; i <=nlstate; i++)
   strcat(fileresv,fileres);      for(j=1; j <=nlstate+ndeath-1; j++){
   if((ficresvij=fopen(fileresv,"w"))==NULL) {        fscanf(ficpar,"%1d%1d",&i1,&j1);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        fprintf(ficparo,"%1d%1d",i1,j1);
   }        if(mle==1)
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
   k=0;        for(k=1; k<=ncovmodel;k++){
   for(cptcov=1;cptcov<=i1;cptcov++){          fscanf(ficpar," %lf",&param[i][j][k]);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          if(mle==1){
       k=k+1;            printf(" %lf",param[i][j][k]);
       fprintf(ficrest,"\n#****** ");            fprintf(ficlog," %lf",param[i][j][k]);
       for(j=1;j<=cptcoveff;j++)          }
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          else
       fprintf(ficrest,"******\n");            fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);
       fprintf(ficreseij,"\n#****** ");        }
       for(j=1;j<=cptcoveff;j++)        fscanf(ficpar,"\n");
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        if(mle==1)
       fprintf(ficreseij,"******\n");          printf("\n");
         fprintf(ficlog,"\n");
       fprintf(ficresvij,"\n#****** ");        fprintf(ficparo,"\n");
       for(j=1;j<=cptcoveff;j++)      }
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    
       fprintf(ficresvij,"******\n");      npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    p=param[1][1];
       oldm=oldms;savm=savms;    
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      /* Reads comments: lines beginning with '#' */
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    while((c=getc(ficpar))=='#' && c!= EOF){
       oldm=oldms;savm=savms;      ungetc(c,ficpar);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      fgets(line, MAXLINE, ficpar);
          puts(line);
       fputs(line,ficparo);
      }
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    ungetc(c,ficpar);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);  
       fprintf(ficrest,"\n");    delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
       epj=vector(1,nlstate+1);    for(i=1; i <=nlstate; i++){
       for(age=bage; age <=fage ;age++){      for(j=1; j <=nlstate+ndeath-1; j++){
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        fscanf(ficpar,"%1d%1d",&i1,&j1);
         if (popbased==1) {        printf("%1d%1d",i,j);
           for(i=1; i<=nlstate;i++)        fprintf(ficparo,"%1d%1d",i1,j1);
             prlim[i][i]=probs[(int)age][i][k];        for(k=1; k<=ncovmodel;k++){
         }          fscanf(ficpar,"%le",&delti3[i][j][k]);
                  printf(" %le",delti3[i][j][k]);
         fprintf(ficrest," %4.0f",age);          fprintf(ficparo," %le",delti3[i][j][k]);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){        }
           for(i=1, epj[j]=0.;i <=nlstate;i++) {        fscanf(ficpar,"\n");
             epj[j] += prlim[i][i]*eij[i][j][(int)age];        printf("\n");
           }        fprintf(ficparo,"\n");
           epj[nlstate+1] +=epj[j];      }
         }    }
         for(i=1, vepp=0.;i <=nlstate;i++)    delti=delti3[1][1];
           for(j=1;j <=nlstate;j++)    
             vepp += vareij[i][j][(int)age];    /* Reads comments: lines beginning with '#' */
         fprintf(ficrest," %7.2f (%7.2f)", epj[nlstate+1],sqrt(vepp));    while((c=getc(ficpar))=='#' && c!= EOF){
         for(j=1;j <=nlstate;j++){      ungetc(c,ficpar);
           fprintf(ficrest," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age]));      fgets(line, MAXLINE, ficpar);
         }      puts(line);
         fprintf(ficrest,"\n");      fputs(line,ficparo);
       }    }
     }    ungetc(c,ficpar);
   }    
     matcov=matrix(1,npar,1,npar);
   fclose(ficreseij);    for(i=1; i <=npar; i++){
   fclose(ficresvij);      fscanf(ficpar,"%s",&str);
   fclose(ficrest);      if(mle==1)
   fclose(ficpar);        printf("%s",str);
   free_vector(epj,1,nlstate+1);      fprintf(ficlog,"%s",str);
        fprintf(ficparo,"%s",str);
   /*------- Variance limit prevalence------*/        for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
   strcpy(fileresvpl,"vpl");        if(mle==1){
   strcat(fileresvpl,fileres);          printf(" %.5le",matcov[i][j]);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {          fprintf(ficlog," %.5le",matcov[i][j]);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);        }
     exit(0);        else
   }          fprintf(ficlog," %.5le",matcov[i][j]);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);        fprintf(ficparo," %.5le",matcov[i][j]);
       }
   k=0;      fscanf(ficpar,"\n");
   for(cptcov=1;cptcov<=i1;cptcov++){      if(mle==1)
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        printf("\n");
       k=k+1;      fprintf(ficlog,"\n");
       fprintf(ficresvpl,"\n#****** ");      fprintf(ficparo,"\n");
       for(j=1;j<=cptcoveff;j++)    }
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    for(i=1; i <=npar; i++)
       fprintf(ficresvpl,"******\n");      for(j=i+1;j<=npar;j++)
              matcov[i][j]=matcov[j][i];
       varpl=matrix(1,nlstate,(int) bage, (int) fage);     
       oldm=oldms;savm=savms;    if(mle==1)
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      printf("\n");
     }    fprintf(ficlog,"\n");
  }  
   
   fclose(ficresvpl);      /*-------- Rewriting paramater file ----------*/
        strcpy(rfileres,"r");    /* "Rparameterfile */
   /*---------- End : free ----------------*/       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);       strcat(rfileres,".");    /* */
         strcat(rfileres,optionfilext);    /* Other files have txt extension */
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      if((ficres =fopen(rfileres,"w"))==NULL) {
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        printf("Problem writing new parameter file: %s\n", fileres);goto end;
          fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
        }
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      fprintf(ficres,"#%s\n",version);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      /*-------- data file ----------*/
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);      if((fic=fopen(datafile,"r"))==NULL)    {
          printf("Problem with datafile: %s\n", datafile);goto end;
   free_matrix(matcov,1,npar,1,npar);        fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
   free_vector(delti,1,npar);      }
   free_matrix(agev,1,maxwav,1,imx);  
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      n= lastobs;
       severity = vector(1,maxwav);
   if(erreur >0)      outcome=imatrix(1,maxwav+1,1,n);
     printf("End of Imach with error or warning %d\n",erreur);      num=ivector(1,n);
   else   printf("End of Imach\n");      moisnais=vector(1,n);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      annais=vector(1,n);
        moisdc=vector(1,n);
   /* 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);*/      andc=vector(1,n);
   /*printf("Total time was %d uSec.\n", total_usecs);*/      agedc=vector(1,n);
   /*------ End -----------*/      cod=ivector(1,n);
       weight=vector(1,n);
       for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
  end:      mint=matrix(1,maxwav,1,n);
 #ifdef windows      anint=matrix(1,maxwav,1,n);
   /* chdir(pathcd);*/      s=imatrix(1,maxwav+1,1,n);
 #endif      adl=imatrix(1,maxwav+1,1,n);    
  /*system("wgnuplot graph.plt");*/      tab=ivector(1,NCOVMAX);
  /*system("../gp37mgw/wgnuplot graph.plt");*/      ncodemax=ivector(1,8);
  /*system("cd ../gp37mgw");*/  
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/      i=1;
  strcpy(plotcmd,GNUPLOTPROGRAM);      while (fgets(line, MAXLINE, fic) != NULL)    {
  strcat(plotcmd," ");        if ((i >= firstobs) && (i <=lastobs)) {
  strcat(plotcmd,optionfilegnuplot);          
  system(plotcmd);          for (j=maxwav;j>=1;j--){
             cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
 #ifdef windows            strcpy(line,stra);
   while (z[0] != 'q') {            cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
     /* chdir(path); */            cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
     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");          cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
     else if (z[0] == 'e') system(optionfilehtm);          cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
     else if (z[0] == 'g') system(plotcmd);  
     else if (z[0] == 'q') exit(0);          cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
   }          cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
 #endif  
 }          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 fill 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 analyze it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*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);
       mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
       /* Concatenates waves */
         concatwav(wav, dh, 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){
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
      jk=1;
      fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
      printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
      fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
      for(i=1,jk=1; i <=nlstate; i++){
        for(k=1; k <=(nlstate+ndeath); k++){
          if (k != i) 
            {
              printf("%d%d ",i,k);
              fprintf(ficlog,"%d%d ",i,k);
              fprintf(ficres,"%1d%1d ",i,k);
              for(j=1; j <=ncovmodel; j++){
                printf("%f ",p[jk]);
                fprintf(ficlog,"%f ",p[jk]);
                fprintf(ficres,"%f ",p[jk]);
                jk++; 
              }
              printf("\n");
              fprintf(ficlog,"\n");
              fprintf(ficres,"\n");
            }
        }
      }
      if(mle==1){
        /* Computing hessian and covariance matrix */
        ftolhess=ftol; /* Usually correct */
        hesscov(matcov, p, npar, delti, ftolhess, func);
      }
      fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
      printf("# Scales (for hessian or gradient estimation)\n");
      fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
      for(i=1,jk=1; i <=nlstate; i++){
        for(j=1; j <=nlstate+ndeath; j++){
          if (j!=i) {
            fprintf(ficres,"%1d%1d",i,j);
            printf("%1d%1d",i,j);
            fprintf(ficlog,"%1d%1d",i,j);
            for(k=1; k<=ncovmodel;k++){
              printf(" %.5e",delti[jk]);
              fprintf(ficlog," %.5e",delti[jk]);
              fprintf(ficres," %.5e",delti[jk]);
              jk++;
            }
            printf("\n");
            fprintf(ficlog,"\n");
            fprintf(ficres,"\n");
          }
        }
      }
      
      k=1;
      fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
      if(mle==1)
        printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
      fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
      for(i=1;i<=npar;i++){
        /*  if (k>nlstate) k=1;
            i1=(i-1)/(ncovmodel*nlstate)+1; 
            fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
            printf("%s%d%d",alph[k],i1,tab[i]);*/
        fprintf(ficres,"%3d",i);
        if(mle==1)
          printf("%3d",i);
        fprintf(ficlog,"%3d",i);
        for(j=1; j<=i;j++){
          fprintf(ficres," %.5e",matcov[i][j]);
          if(mle==1)
            printf(" %.5e",matcov[i][j]);
          fprintf(ficlog," %.5e",matcov[i][j]);
        }
        fprintf(ficres,"\n");
        if(mle==1)
          printf("\n");
        fprintf(ficlog,"\n");
        k++;
      }
      
      while((c=getc(ficpar))=='#' && c!= EOF){
        ungetc(c,ficpar);
        fgets(line, MAXLINE, ficpar);
        puts(line);
        fputs(line,ficparo);
      }
      ungetc(c,ficpar);
      estepm=0;
      fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
      if (estepm==0 || estepm < stepm) estepm=stepm;
      if (fage <= 2) {
        bage = ageminpar;
        fage = agemaxpar;
      }
      
      fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
      fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
      while((c=getc(ficpar))=='#' && c!= EOF){
        ungetc(c,ficpar);
        fgets(line, MAXLINE, ficpar);
        puts(line);
        fputs(line,ficparo);
      }
      ungetc(c,ficpar);
     
      fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
      fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
      while((c=getc(ficpar))=='#' && c!= EOF){
        ungetc(c,ficpar);
        fgets(line, MAXLINE, ficpar);
        puts(line);
        fputs(line,ficparo);
      }
      ungetc(c,ficpar);
    
   
      dateprev1=anprev1+mprev1/12.+jprev1/365.;
      dateprev2=anprev2+mprev2/12.+jprev2/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);
   fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
   fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
   
   
   while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
   /*------------ gnuplot -------------*/
    strcpy(optionfilegnuplot,optionfilefiname);
    strcat(optionfilegnuplot,".gp");
    if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
      printf("Problem with file %s",optionfilegnuplot);
    }
    else{
      fprintf(ficgp,"\n# %s\n", version); 
      fprintf(ficgp,"# %s\n", optionfilegnuplot); 
      fprintf(ficgp,"set missing 'NaNq'\n");
   }
    fclose(ficgp);
    printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
   /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfile);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
   \n
   Total number of observations=%d <br>\n
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
   <hr  size=\"2\" color=\"#EC5E5E\">
    <ul><li><h4>Parameter files</h4>\n
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
    - Log file of the run: <a href=\"%s\">%s</a><br>\n
    - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
     fclose(fichtm);
   
    printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
   /*------------ free_vector  -------------*/
    chdir(path);
    
    free_ivector(wav,1,imx);
    free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
    free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
    free_ivector(num,1,n);
    free_vector(agedc,1,n);
    /*free_matrix(covar,1,NCOVMAX,1,n);*/
    fclose(ficparo);
    fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
     k=0;
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f",age );
             for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     k=0;
     for(cptcov=1;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Age");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
              for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
                }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
   
     /*---------- Forecasting ------------------*/
     if((stepm == 1) && (strcmp(model,".")==0)){
       prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
       if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
     } 
     else{
       erreur=108;
       printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
       fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     calagedate=-1;
   
     prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     k=0;
     for(cptcov=1;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
          }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
       }
     }
   free_matrix(mint,1,maxwav,1,n);
       free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
       free_vector(weight,1,n);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     free_vector(epj,1,nlstate+1);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     k=0;
     for(cptcov=1;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
        varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
       }
    }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
     
     free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
     free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
     
     
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
    
     free_matrix(matcov,1,npar,1,npar);
     free_vector(delti,1,npar);
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fprintf(fichtm,"\n</body>");
     fclose(fichtm);
     fclose(ficgp);
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     
     /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
     /*printf("Total time was %d uSec.\n", total_usecs);*/
     /*------ End -----------*/
   
   
    end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
    strcpy(plotcmd,GNUPLOTPROGRAM);
    strcat(plotcmd," ");
    strcat(plotcmd,optionfilegnuplot);
    printf("Starting: %s\n",plotcmd);fflush(stdout);
    system(plotcmd);
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   

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changed lines
  Added in v.1.58


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