Diff for /imach/src/imach.c between versions 1.41 and 1.62

version 1.41, 2002/05/07 15:53:01 version 1.62, 2002/11/20 07:56:21
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain     Interpolated Markov Chain
   
   Short summary of the programme:    Short summary of the programme:
      
   This program computes Healthy Life Expectancies from    This program computes Healthy Life Expectancies from
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   first survey ("cross") where individuals from different ages are    first survey ("cross") where individuals from different ages are
   interviewed on their health status or degree of disability (in the    interviewed on their health status or degree of disability (in the
   case of a health survey which is our main interest) -2- at least a    case of a health survey which is our main interest) -2- at least a
   second wave of interviews ("longitudinal") which measure each change    second wave of interviews ("longitudinal") which measure each change
   (if any) in individual health status.  Health expectancies are    (if any) in individual health status.  Health expectancies are
   computed from the time spent in each health state according to a    computed from the time spent in each health state according to a
   model. More health states you consider, more time is necessary to reach the    model. More health states you consider, more time is necessary to reach the
   Maximum Likelihood of the parameters involved in the model.  The    Maximum Likelihood of the parameters involved in the model.  The
   simplest model is the multinomial logistic model where pij is the    simplest model is the multinomial logistic model where pij is the
   probability to be observed in state j at the second wave    probability to be observed in state j at the second wave
   conditional to be observed in state i at the first wave. Therefore    conditional to be observed in state i at the first wave. Therefore
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   'age' is age and 'sex' is a covariate. If you want to have a more    'age' is age and 'sex' is a covariate. If you want to have a more
   complex model than "constant and age", you should modify the program    complex model than "constant and age", you should modify the program
   where the markup *Covariates have to be included here again* invites    where the markup *Covariates have to be included here again* invites
   you to do it.  More covariates you add, slower the    you to do it.  More covariates you add, slower the
   convergence.    convergence.
   
   The advantage of this computer programme, compared to a simple    The advantage of this computer programme, compared to a simple
   multinomial logistic model, is clear when the delay between waves is not    multinomial logistic model, is clear when the delay between waves is not
   identical for each individual. Also, if a individual missed an    identical for each individual. Also, if a individual missed an
   intermediate interview, the information is lost, but taken into    intermediate interview, the information is lost, but taken into
   account using an interpolation or extrapolation.      account using an interpolation or extrapolation.  
   
   hPijx is the probability to be observed in state i at age x+h    hPijx is the probability to be observed in state i at age x+h
   conditional to the observed state i at age x. The delay 'h' can be    conditional to the observed state i at age x. The delay 'h' can be
   split into an exact number (nh*stepm) of unobserved intermediate    split into an exact number (nh*stepm) of unobserved intermediate
   states. This elementary transition (by month or quarter trimester,    states. This elementary transition (by month or quarter trimester,
   semester or year) is model as a multinomial logistic.  The hPx    semester or year) is model as a multinomial logistic.  The hPx
   matrix is simply the matrix product of nh*stepm elementary matrices    matrix is simply the matrix product of nh*stepm elementary matrices
   and the contribution of each individual to the likelihood is simply    and the contribution of each individual to the likelihood is simply
   hPijx.    hPijx.
   
   Also this programme outputs the covariance matrix of the parameters but also    Also this programme outputs the covariance matrix of the parameters but also
   of the life expectancies. It also computes the prevalence limits.    of the life expectancies. It also computes the stable prevalence. 
      
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
            Institut national d'études démographiques, Paris.             Institut national d'études démographiques, Paris.
   This software have been partly granted by Euro-REVES, a concerted action    This software have been partly granted by Euro-REVES, a concerted action
   from the European Union.    from the European Union.
   It is copyrighted identically to a GNU software product, ie programme and    It is copyrighted identically to a GNU software product, ie programme and
   software can be distributed freely for non commercial use. Latest version    software can be distributed freely for non commercial use. Latest version
   can be accessed at http://euroreves.ined.fr/imach .    can be accessed at http://euroreves.ined.fr/imach .
   **********************************************************************/    **********************************************************************/
     
 #include <math.h>  #include <math.h>
 #include <stdio.h>  #include <stdio.h>
 #include <stdlib.h>  #include <stdlib.h>
 #include <unistd.h>  #include <unistd.h>
   
 #define MAXLINE 256  #define MAXLINE 256
 #define GNUPLOTPROGRAM "wgnuplot"  #define GNUPLOTPROGRAM "gnuplot"
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define FILENAMELENGTH 80  #define FILENAMELENGTH 80
 /*#define DEBUG*/  /*#define DEBUG*/
 #define windows  #define windows
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
 #define NINTERVMAX 8  #define NINTERVMAX 8
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #define NCOVMAX 8 /* Maximum number of covariates */  #define NCOVMAX 8 /* Maximum number of covariates */
 #define MAXN 20000  #define MAXN 20000
 #define YEARM 12. /* Number of months per year */  #define YEARM 12. /* Number of months per year */
 #define AGESUP 130  #define AGESUP 130
 #define AGEBASE 40  #define AGEBASE 40
   #ifdef windows
   #define DIRSEPARATOR '\\'
 int erreur; /* Error number */  #define ODIRSEPARATOR '/'
 int nvar;  #else
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  #define DIRSEPARATOR '/'
 int npar=NPARMAX;  #define ODIRSEPARATOR '\\'
 int nlstate=2; /* Number of live states */  #endif
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  char version[80]="Imach version 0.9, November 2002, INED-EUROREVES ";
 int popbased=0;  int erreur; /* Error number */
   int nvar;
 int *wav; /* Number of waves for this individuual 0 is possible */  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 int maxwav; /* Maxim number of waves */  int npar=NPARMAX;
 int jmin, jmax; /* min, max spacing between 2 waves */  int nlstate=2; /* Number of live states */
 int mle, weightopt;  int ndeath=1; /* Number of dead states */
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  int popbased=0;
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */  int *wav; /* Number of waves for this individuual 0 is possible */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  int maxwav; /* Maxim number of waves */
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  int jmin, jmax; /* min, max spacing between 2 waves */
 FILE *ficgp,*ficresprob,*ficpop;  int mle, weightopt;
 FILE *ficreseij;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   char filerese[FILENAMELENGTH];  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
  FILE  *ficresvij;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   char fileresv[FILENAMELENGTH];             * wave mi and wave mi+1 is not an exact multiple of stepm. */
  FILE  *ficresvpl;  double jmean; /* Mean space between 2 waves */
   char fileresvpl[FILENAMELENGTH];  double **oldm, **newm, **savm; /* Working pointers to matrices */
   double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 #define NR_END 1  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 #define FREE_ARG char*  FILE *ficlog;
 #define FTOL 1.0e-10  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
 #define NRANSI  FILE *fichtm; /* Html File */
 #define ITMAX 200  FILE *ficreseij;
   char filerese[FILENAMELENGTH];
 #define TOL 2.0e-4  FILE  *ficresvij;
   char fileresv[FILENAMELENGTH];
 #define CGOLD 0.3819660  FILE  *ficresvpl;
 #define ZEPS 1.0e-10  char fileresvpl[FILENAMELENGTH];
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 #define GOLD 1.618034  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 #define GLIMIT 100.0  
 #define TINY 1.0e-20  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   char filelog[FILENAMELENGTH]; /* Log file */
 static double maxarg1,maxarg2;  char filerest[FILENAMELENGTH];
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  char fileregp[FILENAMELENGTH];
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  char popfile[FILENAMELENGTH];
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
 #define rint(a) floor(a+0.5)  
   #define NR_END 1
 static double sqrarg;  #define FREE_ARG char*
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  #define FTOL 1.0e-10
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
   #define NRANSI 
 int imx;  #define ITMAX 200 
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/  #define TOL 2.0e-4 
   
 int estepm;  #define CGOLD 0.3819660 
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  #define ZEPS 1.0e-10 
   #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  #define GOLD 1.618034 
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  #define GLIMIT 100.0 
 double **pmmij, ***probs, ***mobaverage;  #define TINY 1.0e-20 
 double dateintmean=0;  
   static double maxarg1,maxarg2;
 double *weight;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 int **s; /* Status */  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 double *agedc, **covar, idx;    
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   #define rint(a) floor(a+0.5)
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */  static double sqrarg;
   #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 /**************** split *************************/  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {  int imx; 
    char *s;                             /* pointer */  int stepm;
    int  l1, l2;                         /* length counters */  /* Stepm, step in month: minimum step interpolation*/
   
    l1 = strlen( path );                 /* length of path */  int estepm;
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 #ifdef windows  
    s = strrchr( path, '\\' );           /* find last / */  int m,nb;
 #else  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
    s = strrchr( path, '/' );            /* find last / */  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 #endif  double **pmmij, ***probs;
    if ( s == NULL ) {                   /* no directory, so use current */  double dateintmean=0;
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );  double *weight;
   int **s; /* Status */
       if ( getwd( dirc ) == NULL ) {  double *agedc, **covar, idx;
 #else  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
       extern char       *getcwd( );  
   double ftol=FTOL; /* Tolerance for computing Max Likelihood */
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  double ftolhess; /* Tolerance for computing hessian */
 #endif  
          return( GLOCK_ERROR_GETCWD );  /**************** split *************************/
       }  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
       strcpy( name, path );             /* we've got it */  {
    } else {                             /* strip direcotry from path */    char  *ss;                            /* pointer */
       s++;                              /* after this, the filename */    int   l1, l2;                         /* length counters */
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    l1 = strlen(path );                   /* length of path */
       strcpy( name, s );                /* save file name */    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       dirc[l1-l2] = 0;                  /* add zero */    if ( ss == NULL ) {                   /* no directory, so use current */
    }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
    l1 = strlen( dirc );                 /* length of directory */        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 #ifdef windows  #if     defined(__bsd__)                /* get current working directory */
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }      extern char *getwd( );
 #else  
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }      if ( getwd( dirc ) == NULL ) {
 #endif  #else
    s = strrchr( name, '.' );            /* find last / */      extern char *getcwd( );
    s++;  
    strcpy(ext,s);                       /* save extension */      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
    l1= strlen( name);  #endif
    l2= strlen( s)+1;        return( GLOCK_ERROR_GETCWD );
    strncpy( finame, name, l1-l2);      }
    finame[l1-l2]= 0;      strcpy( name, path );               /* we've got it */
    return( 0 );                         /* we're done */    } else {                              /* strip direcotry from path */
 }      ss++;                               /* after this, the filename */
       l2 = strlen( ss );                  /* length of filename */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 /******************************************/      strcpy( name, ss );         /* save file name */
       strncpy( dirc, path, l1 - l2 );     /* now the directory */
 void replace(char *s, char*t)      dirc[l1-l2] = 0;                    /* add zero */
 {    }
   int i;    l1 = strlen( dirc );                  /* length of directory */
   int lg=20;  #ifdef windows
   i=0;    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   lg=strlen(t);  #else
   for(i=0; i<= lg; i++) {    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
     (s[i] = t[i]);  #endif
     if (t[i]== '\\') s[i]='/';    ss = strrchr( name, '.' );            /* find last / */
   }    ss++;
 }    strcpy(ext,ss);                       /* save extension */
     l1= strlen( name);
 int nbocc(char *s, char occ)    l2= strlen(ss)+1;
 {    strncpy( finame, name, l1-l2);
   int i,j=0;    finame[l1-l2]= 0;
   int lg=20;    return( 0 );                          /* we're done */
   i=0;  }
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;  /******************************************/
   }  
   return j;  void replace(char *s, char*t)
 }  {
     int i;
 void cutv(char *u,char *v, char*t, char occ)    int lg=20;
 {    i=0;
   int i,lg,j,p=0;    lg=strlen(t);
   i=0;    for(i=0; i<= lg; i++) {
   for(j=0; j<=strlen(t)-1; j++) {      (s[i] = t[i]);
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;      if (t[i]== '\\') s[i]='/';
   }    }
   }
   lg=strlen(t);  
   for(j=0; j<p; j++) {  int nbocc(char *s, char occ)
     (u[j] = t[j]);  {
   }    int i,j=0;
      u[p]='\0';    int lg=20;
     i=0;
    for(j=0; j<= lg; j++) {    lg=strlen(s);
     if (j>=(p+1))(v[j-p-1] = t[j]);    for(i=0; i<= lg; i++) {
   }    if  (s[i] == occ ) j++;
 }    }
     return j;
 /********************** nrerror ********************/  }
   
 void nrerror(char error_text[])  void cutv(char *u,char *v, char*t, char occ)
 {  {
   fprintf(stderr,"ERREUR ...\n");    /* cuts string t into u and v where u is ended by char occ excluding it
   fprintf(stderr,"%s\n",error_text);       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   exit(1);       gives u="abcedf" and v="ghi2j" */
 }    int i,lg,j,p=0;
 /*********************** vector *******************/    i=0;
 double *vector(int nl, int nh)    for(j=0; j<=strlen(t)-1; j++) {
 {      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   double *v;    }
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");    lg=strlen(t);
   return v-nl+NR_END;    for(j=0; j<p; j++) {
 }      (u[j] = t[j]);
     }
 /************************ free vector ******************/       u[p]='\0';
 void free_vector(double*v, int nl, int nh)  
 {     for(j=0; j<= lg; j++) {
   free((FREE_ARG)(v+nl-NR_END));      if (j>=(p+1))(v[j-p-1] = t[j]);
 }    }
   }
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)  /********************** nrerror ********************/
 {  
   int *v;  void nrerror(char error_text[])
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  {
   if (!v) nrerror("allocation failure in ivector");    fprintf(stderr,"ERREUR ...\n");
   return v-nl+NR_END;    fprintf(stderr,"%s\n",error_text);
 }    exit(EXIT_FAILURE);
   }
 /******************free ivector **************************/  /*********************** vector *******************/
 void free_ivector(int *v, long nl, long nh)  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)));
     if (!v) nrerror("allocation failure in vector");
 /******************* imatrix *******************************/    return v-nl+NR_END;
 int **imatrix(long nrl, long nrh, long ncl, long nch)  }
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {  /************************ free vector ******************/
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  void free_vector(double*v, int nl, int nh)
   int **m;  {
      free((FREE_ARG)(v+nl-NR_END));
   /* allocate pointers to rows */  }
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  /************************ivector *******************************/
   m += NR_END;  int *ivector(long nl,long nh)
   m -= nrl;  {
      int *v;
      v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   /* allocate rows and set pointers to them */    if (!v) nrerror("allocation failure in ivector");
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    return v-nl+NR_END;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  }
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  /******************free ivector **************************/
    void free_ivector(int *v, long nl, long nh)
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  {
      free((FREE_ARG)(v+nl-NR_END));
   /* return pointer to array of pointers to rows */  }
   return m;  
 }  /******************* imatrix *******************************/
   int **imatrix(long nrl, long nrh, long ncl, long nch) 
 /****************** free_imatrix *************************/       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 void free_imatrix(m,nrl,nrh,ncl,nch)  { 
       int **m;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       long nch,ncl,nrh,nrl;    int **m; 
      /* free an int matrix allocated by imatrix() */    
 {    /* allocate pointers to rows */ 
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   free((FREE_ARG) (m+nrl-NR_END));    if (!m) nrerror("allocation failure 1 in matrix()"); 
 }    m += NR_END; 
     m -= nrl; 
 /******************* matrix *******************************/    
 double **matrix(long nrl, long nrh, long ncl, long nch)    
 {    /* allocate rows and set pointers to them */ 
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   double **m;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     m[nrl] += NR_END; 
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    m[nrl] -= ncl; 
   if (!m) nrerror("allocation failure 1 in matrix()");    
   m += NR_END;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   m -= nrl;    
     /* return pointer to array of pointers to rows */ 
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    return m; 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  } 
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  /****************** free_imatrix *************************/
   void free_imatrix(m,nrl,nrh,ncl,nch)
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;        int **m;
   return m;        long nch,ncl,nrh,nrl; 
 }       /* free an int matrix allocated by imatrix() */ 
   { 
 /*************************free matrix ************************/    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    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 *******************************/    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    double **m;
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double ***m;    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    m -= nrl;
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   m -= nrl;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    m[nrl] -= ncl;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   m[nrl] -= ncl;    return m;
   }
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   /*************************free matrix ************************/
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  {
   m[nrl][ncl] += NR_END;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   m[nrl][ncl] -= nll;    free((FREE_ARG)(m+nrl-NR_END));
   for (j=ncl+1; j<=nch; j++)  }
     m[nrl][j]=m[nrl][j-1]+nlay;  
    /******************* ma3x *******************************/
   for (i=nrl+1; i<=nrh; i++) {  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  {
     for (j=ncl+1; j<=nch; j++)    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       m[i][j]=m[i][j-1]+nlay;    double ***m;
   }  
   return m;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 }    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
 /*************************free ma3x ************************/    m -= nrl;
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    m[nrl] += NR_END;
   free((FREE_ARG)(m+nrl-NR_END));    m[nrl] -= ncl;
 }  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 /***************** f1dim *************************/  
 extern int ncom;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 extern double *pcom,*xicom;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
 extern double (*nrfunc)(double []);    m[nrl][ncl] += NR_END;
      m[nrl][ncl] -= nll;
 double f1dim(double x)    for (j=ncl+1; j<=nch; j++) 
 {      m[nrl][j]=m[nrl][j-1]+nlay;
   int j;    
   double f;    for (i=nrl+1; i<=nrh; i++) {
   double *xt;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
        for (j=ncl+1; j<=nch; j++) 
   xt=vector(1,ncom);        m[i][j]=m[i][j-1]+nlay;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    }
   f=(*nrfunc)(xt);    return m;
   free_vector(xt,1,ncom);  }
   return f;  
 }  /*************************free ma3x ************************/
   void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 /*****************brent *************************/  {
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
 {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   int iter;    free((FREE_ARG)(m+nrl-NR_END));
   double a,b,d,etemp;  }
   double fu,fv,fw,fx;  
   double ftemp;  /***************** f1dim *************************/
   double p,q,r,tol1,tol2,u,v,w,x,xm;  extern int ncom; 
   double e=0.0;  extern double *pcom,*xicom;
    extern double (*nrfunc)(double []); 
   a=(ax < cx ? ax : cx);   
   b=(ax > cx ? ax : cx);  double f1dim(double x) 
   x=w=v=bx;  { 
   fw=fv=fx=(*f)(x);    int j; 
   for (iter=1;iter<=ITMAX;iter++) {    double f;
     xm=0.5*(a+b);    double *xt; 
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);   
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    xt=vector(1,ncom); 
     printf(".");fflush(stdout);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
 #ifdef DEBUG    f=(*nrfunc)(xt); 
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    free_vector(xt,1,ncom); 
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    return f; 
 #endif  } 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  
       *xmin=x;  /*****************brent *************************/
       return fx;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     }  { 
     ftemp=fu;    int iter; 
     if (fabs(e) > tol1) {    double a,b,d,etemp;
       r=(x-w)*(fx-fv);    double fu,fv,fw,fx;
       q=(x-v)*(fx-fw);    double ftemp;
       p=(x-v)*q-(x-w)*r;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       q=2.0*(q-r);    double e=0.0; 
       if (q > 0.0) p = -p;   
       q=fabs(q);    a=(ax < cx ? ax : cx); 
       etemp=e;    b=(ax > cx ? ax : cx); 
       e=d;    x=w=v=bx; 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    fw=fv=fx=(*f)(x); 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    for (iter=1;iter<=ITMAX;iter++) { 
       else {      xm=0.5*(a+b); 
         d=p/q;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
         u=x+d;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
         if (u-a < tol2 || b-u < tol2)      printf(".");fflush(stdout);
           d=SIGN(tol1,xm-x);      fprintf(ficlog,".");fflush(ficlog);
       }  #ifdef DEBUG
     } else {      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       d=CGOLD*(e=(x >= xm ? a-x : b-x));      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     }      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  #endif
     fu=(*f)(u);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     if (fu <= fx) {        *xmin=x; 
       if (u >= x) a=x; else b=x;        return fx; 
       SHFT(v,w,x,u)      } 
         SHFT(fv,fw,fx,fu)      ftemp=fu;
         } else {      if (fabs(e) > tol1) { 
           if (u < x) a=u; else b=u;        r=(x-w)*(fx-fv); 
           if (fu <= fw || w == x) {        q=(x-v)*(fx-fw); 
             v=w;        p=(x-v)*q-(x-w)*r; 
             w=u;        q=2.0*(q-r); 
             fv=fw;        if (q > 0.0) p = -p; 
             fw=fu;        q=fabs(q); 
           } else if (fu <= fv || v == x || v == w) {        etemp=e; 
             v=u;        e=d; 
             fv=fu;        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 { 
   }          d=p/q; 
   nrerror("Too many iterations in brent");          u=x+d; 
   *xmin=x;          if (u-a < tol2 || b-u < tol2) 
   return fx;            d=SIGN(tol1,xm-x); 
 }        } 
       } else { 
 /****************** mnbrak ***********************/        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       } 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
             double (*func)(double))      fu=(*f)(u); 
 {      if (fu <= fx) { 
   double ulim,u,r,q, dum;        if (u >= x) a=x; else b=x; 
   double fu;        SHFT(v,w,x,u) 
            SHFT(fv,fw,fx,fu) 
   *fa=(*func)(*ax);          } else { 
   *fb=(*func)(*bx);            if (u < x) a=u; else b=u; 
   if (*fb > *fa) {            if (fu <= fw || w == x) { 
     SHFT(dum,*ax,*bx,dum)              v=w; 
       SHFT(dum,*fb,*fa,dum)              w=u; 
       }              fv=fw; 
   *cx=(*bx)+GOLD*(*bx-*ax);              fw=fu; 
   *fc=(*func)(*cx);            } else if (fu <= fv || v == x || v == w) { 
   while (*fb > *fc) {              v=u; 
     r=(*bx-*ax)*(*fb-*fc);              fv=fu; 
     q=(*bx-*cx)*(*fb-*fa);            } 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/          } 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    } 
     ulim=(*bx)+GLIMIT*(*cx-*bx);    nrerror("Too many iterations in brent"); 
     if ((*bx-u)*(u-*cx) > 0.0) {    *xmin=x; 
       fu=(*func)(u);    return fx; 
     } else if ((*cx-u)*(u-ulim) > 0.0) {  } 
       fu=(*func)(u);  
       if (fu < *fc) {  /****************** mnbrak ***********************/
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
           }              double (*func)(double)) 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  { 
       u=ulim;    double ulim,u,r,q, dum;
       fu=(*func)(u);    double fu; 
     } else {   
       u=(*cx)+GOLD*(*cx-*bx);    *fa=(*func)(*ax); 
       fu=(*func)(u);    *fb=(*func)(*bx); 
     }    if (*fb > *fa) { 
     SHFT(*ax,*bx,*cx,u)      SHFT(dum,*ax,*bx,dum) 
       SHFT(*fa,*fb,*fc,fu)        SHFT(dum,*fb,*fa,dum) 
       }        } 
 }    *cx=(*bx)+GOLD*(*bx-*ax); 
     *fc=(*func)(*cx); 
 /*************** linmin ************************/    while (*fb > *fc) { 
       r=(*bx-*ax)*(*fb-*fc); 
 int ncom;      q=(*bx-*cx)*(*fb-*fa); 
 double *pcom,*xicom;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 double (*nrfunc)(double []);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
        ulim=(*bx)+GLIMIT*(*cx-*bx); 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))      if ((*bx-u)*(u-*cx) > 0.0) { 
 {        fu=(*func)(u); 
   double brent(double ax, double bx, double cx,      } else if ((*cx-u)*(u-ulim) > 0.0) { 
                double (*f)(double), double tol, double *xmin);        fu=(*func)(u); 
   double f1dim(double x);        if (fu < *fc) { 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
               double *fc, double (*func)(double));            SHFT(*fb,*fc,fu,(*func)(u)) 
   int j;            } 
   double xx,xmin,bx,ax;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   double fx,fb,fa;        u=ulim; 
          fu=(*func)(u); 
   ncom=n;      } else { 
   pcom=vector(1,n);        u=(*cx)+GOLD*(*cx-*bx); 
   xicom=vector(1,n);        fu=(*func)(u); 
   nrfunc=func;      } 
   for (j=1;j<=n;j++) {      SHFT(*ax,*bx,*cx,u) 
     pcom[j]=p[j];        SHFT(*fa,*fb,*fc,fu) 
     xicom[j]=xi[j];        } 
   }  } 
   ax=0.0;  
   xx=1.0;  /*************** linmin ************************/
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  int ncom; 
 #ifdef DEBUG  double *pcom,*xicom;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  double (*nrfunc)(double []); 
 #endif   
   for (j=1;j<=n;j++) {  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     xi[j] *= xmin;  { 
     p[j] += xi[j];    double brent(double ax, double bx, double cx, 
   }                 double (*f)(double), double tol, double *xmin); 
   free_vector(xicom,1,n);    double f1dim(double x); 
   free_vector(pcom,1,n);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
 }                double *fc, double (*func)(double)); 
     int j; 
 /*************** powell ************************/    double xx,xmin,bx,ax; 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    double fx,fb,fa;
             double (*func)(double []))   
 {    ncom=n; 
   void linmin(double p[], double xi[], int n, double *fret,    pcom=vector(1,n); 
               double (*func)(double []));    xicom=vector(1,n); 
   int i,ibig,j;    nrfunc=func; 
   double del,t,*pt,*ptt,*xit;    for (j=1;j<=n;j++) { 
   double fp,fptt;      pcom[j]=p[j]; 
   double *xits;      xicom[j]=xi[j]; 
   pt=vector(1,n);    } 
   ptt=vector(1,n);    ax=0.0; 
   xit=vector(1,n);    xx=1.0; 
   xits=vector(1,n);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   *fret=(*func)(p);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   for (j=1;j<=n;j++) pt[j]=p[j];  #ifdef DEBUG
   for (*iter=1;;++(*iter)) {    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     fp=(*fret);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     ibig=0;  #endif
     del=0.0;    for (j=1;j<=n;j++) { 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      xi[j] *= xmin; 
     for (i=1;i<=n;i++)      p[j] += xi[j]; 
       printf(" %d %.12f",i, p[i]);    } 
     printf("\n");    free_vector(xicom,1,n); 
     for (i=1;i<=n;i++) {    free_vector(pcom,1,n); 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  } 
       fptt=(*fret);  
 #ifdef DEBUG  /*************** powell ************************/
       printf("fret=%lf \n",*fret);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
 #endif              double (*func)(double [])) 
       printf("%d",i);fflush(stdout);  { 
       linmin(p,xit,n,fret,func);    void linmin(double p[], double xi[], int n, double *fret, 
       if (fabs(fptt-(*fret)) > del) {                double (*func)(double [])); 
         del=fabs(fptt-(*fret));    int i,ibig,j; 
         ibig=i;    double del,t,*pt,*ptt,*xit;
       }    double fp,fptt;
 #ifdef DEBUG    double *xits;
       printf("%d %.12e",i,(*fret));    pt=vector(1,n); 
       for (j=1;j<=n;j++) {    ptt=vector(1,n); 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    xit=vector(1,n); 
         printf(" x(%d)=%.12e",j,xit[j]);    xits=vector(1,n); 
       }    *fret=(*func)(p); 
       for(j=1;j<=n;j++)    for (j=1;j<=n;j++) pt[j]=p[j]; 
         printf(" p=%.12e",p[j]);    for (*iter=1;;++(*iter)) { 
       printf("\n");      fp=(*fret); 
 #endif      ibig=0; 
     }      del=0.0; 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
 #ifdef DEBUG      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       int k[2],l;      for (i=1;i<=n;i++) 
       k[0]=1;        printf(" %d %.12f",i, p[i]);
       k[1]=-1;      fprintf(ficlog," %d %.12f",i, p[i]);
       printf("Max: %.12e",(*func)(p));      printf("\n");
       for (j=1;j<=n;j++)      fprintf(ficlog,"\n");
         printf(" %.12e",p[j]);      for (i=1;i<=n;i++) { 
       printf("\n");        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       for(l=0;l<=1;l++) {        fptt=(*fret); 
         for (j=1;j<=n;j++) {  #ifdef DEBUG
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];        printf("fret=%lf \n",*fret);
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);        fprintf(ficlog,"fret=%lf \n",*fret);
         }  #endif
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));        printf("%d",i);fflush(stdout);
       }        fprintf(ficlog,"%d",i);fflush(ficlog);
 #endif        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
           del=fabs(fptt-(*fret)); 
       free_vector(xit,1,n);          ibig=i; 
       free_vector(xits,1,n);        } 
       free_vector(ptt,1,n);  #ifdef DEBUG
       free_vector(pt,1,n);        printf("%d %.12e",i,(*fret));
       return;        fprintf(ficlog,"%d %.12e",i,(*fret));
     }        for (j=1;j<=n;j++) {
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     for (j=1;j<=n;j++) {          printf(" x(%d)=%.12e",j,xit[j]);
       ptt[j]=2.0*p[j]-pt[j];          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       xit[j]=p[j]-pt[j];        }
       pt[j]=p[j];        for(j=1;j<=n;j++) {
     }          printf(" p=%.12e",p[j]);
     fptt=(*func)(ptt);          fprintf(ficlog," p=%.12e",p[j]);
     if (fptt < fp) {        }
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);        printf("\n");
       if (t < 0.0) {        fprintf(ficlog,"\n");
         linmin(p,xit,n,fret,func);  #endif
         for (j=1;j<=n;j++) {      } 
           xi[j][ibig]=xi[j][n];      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
           xi[j][n]=xit[j];  #ifdef DEBUG
         }        int k[2],l;
 #ifdef DEBUG        k[0]=1;
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);        k[1]=-1;
         for(j=1;j<=n;j++)        printf("Max: %.12e",(*func)(p));
           printf(" %.12e",xit[j]);        fprintf(ficlog,"Max: %.12e",(*func)(p));
         printf("\n");        for (j=1;j<=n;j++) {
 #endif          printf(" %.12e",p[j]);
       }          fprintf(ficlog," %.12e",p[j]);
     }        }
   }        printf("\n");
 }        fprintf(ficlog,"\n");
         for(l=0;l<=1;l++) {
 /**** Prevalence limit ****************/          for (j=1;j<=n;j++) {
             ptt[j]=p[j]+(p[j]-pt[j])*k[l];
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 {            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit          }
      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)));
           fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   int i, ii,j,k;        }
   double min, max, maxmin, maxmax,sumnew=0.;  #endif
   double **matprod2();  
   double **out, cov[NCOVMAX], **pmij();  
   double **newm;        free_vector(xit,1,n); 
   double agefin, delaymax=50 ; /* Max number of years to converge */        free_vector(xits,1,n); 
         free_vector(ptt,1,n); 
   for (ii=1;ii<=nlstate+ndeath;ii++)        free_vector(pt,1,n); 
     for (j=1;j<=nlstate+ndeath;j++){        return; 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      } 
     }      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (j=1;j<=n;j++) { 
    cov[1]=1.;        ptt[j]=2.0*p[j]-pt[j]; 
          xit[j]=p[j]-pt[j]; 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        pt[j]=p[j]; 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){      } 
     newm=savm;      fptt=(*func)(ptt); 
     /* Covariates have to be included here again */      if (fptt < fp) { 
      cov[2]=agefin;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
          if (t < 0.0) { 
       for (k=1; k<=cptcovn;k++) {          linmin(p,xit,n,fret,func); 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];          for (j=1;j<=n;j++) { 
         /*      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]]);*/            xi[j][ibig]=xi[j][n]; 
       }            xi[j][n]=xit[j]; 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          }
       for (k=1; k<=cptcovprod;k++)  #ifdef DEBUG
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/          for(j=1;j<=n;j++){
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/            printf(" %.12e",xit[j]);
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/            fprintf(ficlog," %.12e",xit[j]);
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);          }
           printf("\n");
     savm=oldm;          fprintf(ficlog,"\n");
     oldm=newm;  #endif
     maxmax=0.;        }
     for(j=1;j<=nlstate;j++){      } 
       min=1.;    } 
       max=0.;  } 
       for(i=1; i<=nlstate; i++) {  
         sumnew=0;  /**** Prevalence limit (stable prevalence)  ****************/
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  
         prlim[i][j]= newm[i][j]/(1-sumnew);  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
         max=FMAX(max,prlim[i][j]);  {
         min=FMIN(min,prlim[i][j]);    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       }       matrix by transitions matrix until convergence is reached */
       maxmin=max-min;  
       maxmax=FMAX(maxmax,maxmin);    int i, ii,j,k;
     }    double min, max, maxmin, maxmax,sumnew=0.;
     if(maxmax < ftolpl){    double **matprod2();
       return prlim;    double **out, cov[NCOVMAX], **pmij();
     }    double **newm;
   }    double agefin, delaymax=50 ; /* Max number of years to converge */
 }  
     for (ii=1;ii<=nlstate+ndeath;ii++)
 /*************** transition probabilities ***************/      for (j=1;j<=nlstate+ndeath;j++){
         oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )      }
 {  
   double s1, s2;     cov[1]=1.;
   /*double t34;*/   
   int i,j,j1, nc, ii, jj;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     for(i=1; i<= nlstate; i++){      newm=savm;
     for(j=1; j<i;j++){      /* Covariates have to be included here again */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){       cov[2]=agefin;
         /*s2 += param[i][j][nc]*cov[nc];*/    
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        for (k=1; k<=cptcovn;k++) {
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       }          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
       ps[i][j]=s2;        }
       /*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 (k=1; k<=cptcovprod;k++)
     for(j=i+1; j<=nlstate+ndeath;j++){          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
       }        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       ps[i][j]=s2;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
     }  
   }      savm=oldm;
     /*ps[3][2]=1;*/      oldm=newm;
       maxmax=0.;
   for(i=1; i<= nlstate; i++){      for(j=1;j<=nlstate;j++){
      s1=0;        min=1.;
     for(j=1; j<i; j++)        max=0.;
       s1+=exp(ps[i][j]);        for(i=1; i<=nlstate; i++) {
     for(j=i+1; j<=nlstate+ndeath; j++)          sumnew=0;
       s1+=exp(ps[i][j]);          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     ps[i][i]=1./(s1+1.);          prlim[i][j]= newm[i][j]/(1-sumnew);
     for(j=1; j<i; j++)          max=FMAX(max,prlim[i][j]);
       ps[i][j]= exp(ps[i][j])*ps[i][i];          min=FMIN(min,prlim[i][j]);
     for(j=i+1; j<=nlstate+ndeath; j++)        }
       ps[i][j]= exp(ps[i][j])*ps[i][i];        maxmin=max-min;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        maxmax=FMAX(maxmax,maxmin);
   } /* end i */      }
       if(maxmax < ftolpl){
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){        return prlim;
     for(jj=1; jj<= nlstate+ndeath; jj++){      }
       ps[ii][jj]=0;    }
       ps[ii][ii]=1;  }
     }  
   }  /*************** transition probabilities ***************/ 
   
   double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  {
     for(jj=1; jj<= nlstate+ndeath; jj++){    double s1, s2;
      printf("%lf ",ps[ii][jj]);    /*double t34;*/
    }    int i,j,j1, nc, ii, jj;
     printf("\n ");  
     }      for(i=1; i<= nlstate; i++){
     printf("\n ");printf("%lf ",cov[2]);*/      for(j=1; j<i;j++){
 /*        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   for(i=1; i<= npar; i++) printf("%f ",x[i]);          /*s2 += param[i][j][nc]*cov[nc];*/
   goto end;*/          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     return ps;          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
 }        }
         ps[i][j]=s2;
 /**************** Product of 2 matrices ******************/        /*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++){
 {        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   /* in, b, out are matrice of pointers which should have been initialized        }
      before: only the contents of out is modified. The function returns        ps[i][j]=s2;
      a pointer to pointers identical to out */      }
   long i, j, k;    }
   for(i=nrl; i<= nrh; i++)      /*ps[3][2]=1;*/
     for(k=ncolol; k<=ncoloh; k++)  
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    for(i=1; i<= nlstate; i++){
         out[i][k] +=in[i][j]*b[j][k];       s1=0;
       for(j=1; j<i; j++)
   return out;        s1+=exp(ps[i][j]);
 }      for(j=i+1; j<=nlstate+ndeath; j++)
         s1+=exp(ps[i][j]);
       ps[i][i]=1./(s1+1.);
 /************* Higher Matrix Product ***************/      for(j=1; j<i; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      for(j=i+1; j<=nlstate+ndeath; j++)
 {        ps[i][j]= exp(ps[i][j])*ps[i][i];
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
      duration (i.e. until    } /* end i */
      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    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
      (typically every 2 years instead of every month which is too big).      for(jj=1; jj<= nlstate+ndeath; jj++){
      Model is determined by parameters x and covariates have to be        ps[ii][jj]=0;
      included manually here.        ps[ii][ii]=1;
       }
      */    }
   
   int i, j, d, h, k;  
   double **out, cov[NCOVMAX];    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   double **newm;      for(jj=1; jj<= nlstate+ndeath; jj++){
        printf("%lf ",ps[ii][jj]);
   /* Hstepm could be zero and should return the unit matrix */     }
   for (i=1;i<=nlstate+ndeath;i++)      printf("\n ");
     for (j=1;j<=nlstate+ndeath;j++){      }
       oldm[i][j]=(i==j ? 1.0 : 0.0);      printf("\n ");printf("%lf ",cov[2]);*/
       po[i][j][0]=(i==j ? 1.0 : 0.0);  /*
     }    for(i=1; i<= npar; i++) printf("%f ",x[i]);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    goto end;*/
   for(h=1; h <=nhstepm; h++){      return ps;
     for(d=1; d <=hstepm; d++){  }
       newm=savm;  
       /* Covariates have to be included here again */  /**************** Product of 2 matrices ******************/
       cov[1]=1.;  
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  {
       for (k=1; k<=cptcovage;k++)    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       for (k=1; k<=cptcovprod;k++)    /* in, b, out are matrice of pointers which should have been initialized 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];       before: only the contents of out is modified. The function returns
        a pointer to pointers identical to out */
     long i, j, k;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    for(i=nrl; i<= nrh; i++)
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      for(k=ncolol; k<=ncoloh; k++)
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        for(j=ncl,out[i][k]=0.; j<=nch; j++)
                    pmij(pmmij,cov,ncovmodel,x,nlstate));          out[i][k] +=in[i][j]*b[j][k];
       savm=oldm;  
       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];  /************* Higher Matrix Product ***************/
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  
          */  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
       }  {
   } /* end h */    /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month 
   return po;       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 
        (typically every 2 years instead of every month which is too big).
 /*************** log-likelihood *************/       Model is determined by parameters x and covariates have to be 
 double func( double *x)       included manually here. 
 {  
   int i, ii, j, k, mi, d, kk;       */
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  
   double **out;    int i, j, d, h, k;
   double sw; /* Sum of weights */    double **out, cov[NCOVMAX];
   double lli; /* Individual log likelihood */    double **newm;
   long ipmx;  
   /*extern weight */    /* Hstepm could be zero and should return the unit matrix */
   /* We are differentiating ll according to initial status */    for (i=1;i<=nlstate+ndeath;i++)
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      for (j=1;j<=nlstate+ndeath;j++){
   /*for(i=1;i<imx;i++)        oldm[i][j]=(i==j ? 1.0 : 0.0);
     printf(" %d\n",s[4][i]);        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(h=1; h <=nhstepm; h++){
   for(k=1; k<=nlstate; k++) ll[k]=0.;      for(d=1; d <=hstepm; d++){
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        newm=savm;
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        /* Covariates have to be included here again */
     for(mi=1; mi<= wav[i]-1; mi++){        cov[1]=1.;
       for (ii=1;ii<=nlstate+ndeath;ii++)        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       for(d=0; d<dh[mi][i]; d++){        for (k=1; k<=cptcovage;k++)
         newm=savm;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;        for (k=1; k<=cptcovprod;k++)
         for (kk=1; kk<=cptcovage;kk++) {          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  
         }  
                /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
         savm=oldm;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         oldm=newm;        savm=oldm;
                oldm=newm;
              }
       } /* end mult */      for(i=1; i<=nlstate+ndeath; i++)
              for(j=1;j<=nlstate+ndeath;j++) {
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);          po[i][j][h]=newm[i][j];
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
       ipmx +=1;           */
       sw += weight[i];        }
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    } /* end h */
     } /* end of wave */    return po;
   } /* end of individual */  }
   
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  /*************** log-likelihood *************/
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  double func( double *x)
   return -l;  {
 }    int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX], cov[NCOVMAX];
     double **out;
 /*********** Maximum Likelihood Estimation ***************/    double sw; /* Sum of weights */
     double lli; /* Individual log likelihood */
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    int s1, s2;
 {    double bbh;
   int i,j, iter;    long ipmx;
   double **xi,*delti;    /*extern weight */
   double fret;    /* We are differentiating ll according to initial status */
   xi=matrix(1,npar,1,npar);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   for (i=1;i<=npar;i++)    /*for(i=1;i<imx;i++) 
     for (j=1;j<=npar;j++)      printf(" %d\n",s[4][i]);
       xi[i][j]=(i==j ? 1.0 : 0.0);    */
   printf("Powell\n");    cov[1]=1.;
   powell(p,xi,npar,ftol,&iter,&fret,func);  
     for(k=1; k<=nlstate; k++) ll[k]=0.;
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    if(mle==1){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
 /**** Computes Hessian and covariance matrix ***/          for (ii=1;ii<=nlstate+ndeath;ii++)
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))            for (j=1;j<=nlstate+ndeath;j++){
 {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double  **a,**y,*x,pd;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double **hess;            }
   int i, j,jk;          for(d=0; d<dh[mi][i]; d++){
   int *indx;            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double hessii(double p[], double delta, int theta, double delti[]);            for (kk=1; kk<=cptcovage;kk++) {
   double hessij(double p[], double delti[], int i, int j);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   void lubksb(double **a, int npar, int *indx, double b[]) ;            }
   void ludcmp(double **a, int npar, int *indx, double *d) ;          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   hess=matrix(1,npar,1,npar);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   printf("\nCalculation of the hessian matrix. Wait...\n");            oldm=newm;
   for (i=1;i<=npar;i++){          
     printf("%d",i);fflush(stdout);          
     hess[i][i]=hessii(p,ftolhess,i,delti);          } /* end mult */
     /*printf(" %f ",p[i]);*/        
     /*printf(" %lf ",hess[i][i]);*/          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   }          /* But now since version 0.9 we anticipate for bias and large stepm.
             * If stepm is larger than one month (smallest stepm) and if the exact delay 
   for (i=1;i<=npar;i++) {           * (in months) between two waves is not a multiple of stepm, we rounded to 
     for (j=1;j<=npar;j++)  {           * the nearest (and in case of equal distance, to the lowest) interval but now
       if (j>i) {           * we keep into memory the bias bh[mi][i] and also the previous matrix product
         printf(".%d%d",i,j);fflush(stdout);           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
         hess[i][j]=hessij(p,delti,i,j);           * probability in order to take into account the bias as a fraction of the way
         hess[j][i]=hess[i][j];               * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
         /*printf(" %lf ",hess[i][j]);*/           * -stepm/2 to stepm/2 .
       }           * For stepm=1 the results are the same as for previous versions of Imach.
     }           * For stepm > 1 the results are less biased than in previous versions. 
   }           */
   printf("\n");          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");          bbh=(double)bh[mi][i]/(double)stepm;
            lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));
   a=matrix(1,npar,1,npar);          /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-bbh)*out[s1][s2]));*/
   y=matrix(1,npar,1,npar);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   x=vector(1,npar);          /*if(lli ==000.0)*/
   indx=ivector(1,npar);          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   for (i=1;i<=npar;i++)          ipmx +=1;
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];          sw += weight[i];
   ludcmp(a,npar,indx,&pd);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
   for (j=1;j<=npar;j++) {      } /* end of individual */
     for (i=1;i<=npar;i++) x[i]=0;    }  else{ 
     x[j]=1;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     lubksb(a,npar,indx,x);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     for (i=1;i<=npar;i++){        for(mi=1; mi<= wav[i]-1; mi++){
       matcov[i][j]=x[i];          for (ii=1;ii<=nlstate+ndeath;ii++)
     }            for (j=1;j<=nlstate+ndeath;j++){
   }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
   printf("\n#Hessian matrix#\n");            }
   for (i=1;i<=npar;i++) {          for(d=0; d<dh[mi][i]; d++){
     for (j=1;j<=npar;j++) {            newm=savm;
       printf("%.3e ",hess[i][j]);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     }            for (kk=1; kk<=cptcovage;kk++) {
     printf("\n");              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   }            }
           
   /* Recompute Inverse */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   for (i=1;i<=npar;i++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];            savm=oldm;
   ludcmp(a,npar,indx,&pd);            oldm=newm;
           } /* end mult */
   /*  printf("\n#Hessian matrix recomputed#\n");        
           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   for (j=1;j<=npar;j++) {          ipmx +=1;
     for (i=1;i<=npar;i++) x[i]=0;          sw += weight[i];
     x[j]=1;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     lubksb(a,npar,indx,x);        } /* end of wave */
     for (i=1;i<=npar;i++){      } /* end of individual */
       y[i][j]=x[i];    } /* End of if */
       printf("%.3e ",y[i][j]);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     printf("\n");    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   }    return -l;
   */  }
   
   free_matrix(a,1,npar,1,npar);  
   free_matrix(y,1,npar,1,npar);  /*********** Maximum Likelihood Estimation ***************/
   free_vector(x,1,npar);  
   free_ivector(indx,1,npar);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   free_matrix(hess,1,npar,1,npar);  {
     int i,j, iter;
     double **xi,*delti;
 }    double fret;
     xi=matrix(1,npar,1,npar);
 /*************** hessian matrix ****************/    for (i=1;i<=npar;i++)
 double hessii( double x[], double delta, int theta, double delti[])      for (j=1;j<=npar;j++)
 {        xi[i][j]=(i==j ? 1.0 : 0.0);
   int i;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   int l=1, lmax=20;    powell(p,xi,npar,ftol,&iter,&fret,func);
   double k1,k2;  
   double p2[NPARMAX+1];     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   double res;    fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   double fx;  
   int k=0,kmax=10;  }
   double l1;  
   /**** Computes Hessian and covariance matrix ***/
   fx=func(x);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   for (i=1;i<=npar;i++) p2[i]=x[i];  {
   for(l=0 ; l <=lmax; l++){    double  **a,**y,*x,pd;
     l1=pow(10,l);    double **hess;
     delts=delt;    int i, j,jk;
     for(k=1 ; k <kmax; k=k+1){    int *indx;
       delt = delta*(l1*k);  
       p2[theta]=x[theta] +delt;    double hessii(double p[], double delta, int theta, double delti[]);
       k1=func(p2)-fx;    double hessij(double p[], double delti[], int i, int j);
       p2[theta]=x[theta]-delt;    void lubksb(double **a, int npar, int *indx, double b[]) ;
       k2=func(p2)-fx;    void ludcmp(double **a, int npar, int *indx, double *d) ;
       /*res= (k1-2.0*fx+k2)/delt/delt; */  
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    hess=matrix(1,npar,1,npar);
        
 #ifdef DEBUG    printf("\nCalculation of the hessian matrix. Wait...\n");
       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);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
 #endif    for (i=1;i<=npar;i++){
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */      printf("%d",i);fflush(stdout);
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){      fprintf(ficlog,"%d",i);fflush(ficlog);
         k=kmax;      hess[i][i]=hessii(p,ftolhess,i,delti);
       }      /*printf(" %f ",p[i]);*/
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      /*printf(" %lf ",hess[i][i]);*/
         k=kmax; l=lmax*10.;    }
       }    
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    for (i=1;i<=npar;i++) {
         delts=delt;      for (j=1;j<=npar;j++)  {
       }        if (j>i) { 
     }          printf(".%d%d",i,j);fflush(stdout);
   }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   delti[theta]=delts;          hess[i][j]=hessij(p,delti,i,j);
   return res;          hess[j][i]=hess[i][j];    
            /*printf(" %lf ",hess[i][j]);*/
 }        }
       }
 double hessij( double x[], double delti[], int thetai,int thetaj)    }
 {    printf("\n");
   int i;    fprintf(ficlog,"\n");
   int l=1, l1, lmax=20;  
   double k1,k2,k3,k4,res,fx;    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   double p2[NPARMAX+1];    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   int k;    
     a=matrix(1,npar,1,npar);
   fx=func(x);    y=matrix(1,npar,1,npar);
   for (k=1; k<=2; k++) {    x=vector(1,npar);
     for (i=1;i<=npar;i++) p2[i]=x[i];    indx=ivector(1,npar);
     p2[thetai]=x[thetai]+delti[thetai]/k;    for (i=1;i<=npar;i++)
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     k1=func(p2)-fx;    ludcmp(a,npar,indx,&pd);
    
     p2[thetai]=x[thetai]+delti[thetai]/k;    for (j=1;j<=npar;j++) {
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      for (i=1;i<=npar;i++) x[i]=0;
     k2=func(p2)-fx;      x[j]=1;
        lubksb(a,npar,indx,x);
     p2[thetai]=x[thetai]-delti[thetai]/k;      for (i=1;i<=npar;i++){ 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        matcov[i][j]=x[i];
     k3=func(p2)-fx;      }
      }
     p2[thetai]=x[thetai]-delti[thetai]/k;  
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    printf("\n#Hessian matrix#\n");
     k4=func(p2)-fx;    fprintf(ficlog,"\n#Hessian matrix#\n");
     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++) { 
 #ifdef DEBUG      for (j=1;j<=npar;j++) { 
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);        printf("%.3e ",hess[i][j]);
 #endif        fprintf(ficlog,"%.3e ",hess[i][j]);
   }      }
   return res;      printf("\n");
 }      fprintf(ficlog,"\n");
     }
 /************** Inverse of matrix **************/  
 void ludcmp(double **a, int n, int *indx, double *d)    /* Recompute Inverse */
 {    for (i=1;i<=npar;i++)
   int i,imax,j,k;      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   double big,dum,sum,temp;    ludcmp(a,npar,indx,&pd);
   double *vv;  
      /*  printf("\n#Hessian matrix recomputed#\n");
   vv=vector(1,n);  
   *d=1.0;    for (j=1;j<=npar;j++) {
   for (i=1;i<=n;i++) {      for (i=1;i<=npar;i++) x[i]=0;
     big=0.0;      x[j]=1;
     for (j=1;j<=n;j++)      lubksb(a,npar,indx,x);
       if ((temp=fabs(a[i][j])) > big) big=temp;      for (i=1;i<=npar;i++){ 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        y[i][j]=x[i];
     vv[i]=1.0/big;        printf("%.3e ",y[i][j]);
   }        fprintf(ficlog,"%.3e ",y[i][j]);
   for (j=1;j<=n;j++) {      }
     for (i=1;i<j;i++) {      printf("\n");
       sum=a[i][j];      fprintf(ficlog,"\n");
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    }
       a[i][j]=sum;    */
     }  
     big=0.0;    free_matrix(a,1,npar,1,npar);
     for (i=j;i<=n;i++) {    free_matrix(y,1,npar,1,npar);
       sum=a[i][j];    free_vector(x,1,npar);
       for (k=1;k<j;k++)    free_ivector(indx,1,npar);
         sum -= a[i][k]*a[k][j];    free_matrix(hess,1,npar,1,npar);
       a[i][j]=sum;  
       if ( (dum=vv[i]*fabs(sum)) >= big) {  
         big=dum;  }
         imax=i;  
       }  /*************** hessian matrix ****************/
     }  double hessii( double x[], double delta, int theta, double delti[])
     if (j != imax) {  {
       for (k=1;k<=n;k++) {    int i;
         dum=a[imax][k];    int l=1, lmax=20;
         a[imax][k]=a[j][k];    double k1,k2;
         a[j][k]=dum;    double p2[NPARMAX+1];
       }    double res;
       *d = -(*d);    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       vv[imax]=vv[j];    double fx;
     }    int k=0,kmax=10;
     indx[j]=imax;    double l1;
     if (a[j][j] == 0.0) a[j][j]=TINY;  
     if (j != n) {    fx=func(x);
       dum=1.0/(a[j][j]);    for (i=1;i<=npar;i++) p2[i]=x[i];
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    for(l=0 ; l <=lmax; l++){
     }      l1=pow(10,l);
   }      delts=delt;
   free_vector(vv,1,n);  /* Doesn't work */      for(k=1 ; k <kmax; k=k+1){
 ;        delt = delta*(l1*k);
 }        p2[theta]=x[theta] +delt;
         k1=func(p2)-fx;
 void lubksb(double **a, int n, int *indx, double b[])        p2[theta]=x[theta]-delt;
 {        k2=func(p2)-fx;
   int i,ii=0,ip,j;        /*res= (k1-2.0*fx+k2)/delt/delt; */
   double sum;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
          
   for (i=1;i<=n;i++) {  #ifdef DEBUG
     ip=indx[i];        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     sum=b[ip];        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);
     b[ip]=b[i];  #endif
     if (ii)        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     else if (sum) ii=i;          k=kmax;
     b[i]=sum;        }
   }        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   for (i=n;i>=1;i--) {          k=kmax; l=lmax*10.;
     sum=b[i];        }
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     b[i]=sum/a[i][i];          delts=delt;
   }        }
 }      }
     }
 /************ Frequencies ********************/    delti[theta]=delts;
 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)    return res; 
 {  /* Some frequencies */    
    }
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  
   double ***freq; /* Frequencies */  double hessij( double x[], double delti[], int thetai,int thetaj)
   double *pp;  {
   double pos, k2, dateintsum=0,k2cpt=0;    int i;
   FILE *ficresp;    int l=1, l1, lmax=20;
   char fileresp[FILENAMELENGTH];    double k1,k2,k3,k4,res,fx;
      double p2[NPARMAX+1];
   pp=vector(1,nlstate);    int k;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   strcpy(fileresp,"p");    fx=func(x);
   strcat(fileresp,fileres);    for (k=1; k<=2; k++) {
   if((ficresp=fopen(fileresp,"w"))==NULL) {      for (i=1;i<=npar;i++) p2[i]=x[i];
     printf("Problem with prevalence resultfile: %s\n", fileresp);      p2[thetai]=x[thetai]+delti[thetai]/k;
     exit(0);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   }      k1=func(p2)-fx;
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    
   j1=0;      p2[thetai]=x[thetai]+delti[thetai]/k;
        p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   j=cptcoveff;      k2=func(p2)-fx;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    
        p2[thetai]=x[thetai]-delti[thetai]/k;
   for(k1=1; k1<=j;k1++){      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     for(i1=1; i1<=ncodemax[k1];i1++){      k3=func(p2)-fx;
       j1++;    
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);      p2[thetai]=x[thetai]-delti[thetai]/k;
         scanf("%d", i);*/      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       for (i=-1; i<=nlstate+ndeath; i++)        k4=func(p2)-fx;
         for (jk=-1; jk<=nlstate+ndeath; jk++)        res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
           for(m=agemin; m <= agemax+3; m++)  #ifdef DEBUG
             freq[i][jk][m]=0;      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
            fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       dateintsum=0;  #endif
       k2cpt=0;    }
       for (i=1; i<=imx; i++) {    return res;
         bool=1;  }
         if  (cptcovn>0) {  
           for (z1=1; z1<=cptcoveff; z1++)  /************** Inverse of matrix **************/
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  void ludcmp(double **a, int n, int *indx, double *d) 
               bool=0;  { 
         }    int i,imax,j,k; 
         if (bool==1) {    double big,dum,sum,temp; 
           for(m=firstpass; m<=lastpass; m++){    double *vv; 
             k2=anint[m][i]+(mint[m][i]/12.);   
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    vv=vector(1,n); 
               if(agev[m][i]==0) agev[m][i]=agemax+1;    *d=1.0; 
               if(agev[m][i]==1) agev[m][i]=agemax+2;    for (i=1;i<=n;i++) { 
               if (m<lastpass) {      big=0.0; 
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      for (j=1;j<=n;j++) 
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        if ((temp=fabs(a[i][j])) > big) big=temp; 
               }      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
                    vv[i]=1.0/big; 
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    } 
                 dateintsum=dateintsum+k2;    for (j=1;j<=n;j++) { 
                 k2cpt++;      for (i=1;i<j;i++) { 
               }        sum=a[i][j]; 
             }        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
           }        a[i][j]=sum; 
         }      } 
       }      big=0.0; 
              for (i=j;i<=n;i++) { 
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        sum=a[i][j]; 
         for (k=1;k<j;k++) 
       if  (cptcovn>0) {          sum -= a[i][k]*a[k][j]; 
         fprintf(ficresp, "\n#********** Variable ");        a[i][j]=sum; 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
         fprintf(ficresp, "**********\n#");          big=dum; 
       }          imax=i; 
       for(i=1; i<=nlstate;i++)        } 
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      } 
       fprintf(ficresp, "\n");      if (j != imax) { 
              for (k=1;k<=n;k++) { 
       for(i=(int)agemin; i <= (int)agemax+3; i++){          dum=a[imax][k]; 
         if(i==(int)agemax+3)          a[imax][k]=a[j][k]; 
           printf("Total");          a[j][k]=dum; 
         else        } 
           printf("Age %d", i);        *d = -(*d); 
         for(jk=1; jk <=nlstate ; jk++){        vv[imax]=vv[j]; 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      } 
             pp[jk] += freq[jk][m][i];      indx[j]=imax; 
         }      if (a[j][j] == 0.0) a[j][j]=TINY; 
         for(jk=1; jk <=nlstate ; jk++){      if (j != n) { 
           for(m=-1, pos=0; m <=0 ; m++)        dum=1.0/(a[j][j]); 
             pos += freq[jk][m][i];        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
           if(pp[jk]>=1.e-10)      } 
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    } 
           else    free_vector(vv,1,n);  /* Doesn't work */
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  ;
         }  } 
   
         for(jk=1; jk <=nlstate ; jk++){  void lubksb(double **a, int n, int *indx, double b[]) 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  { 
             pp[jk] += freq[jk][m][i];    int i,ii=0,ip,j; 
         }    double sum; 
    
         for(jk=1,pos=0; jk <=nlstate ; jk++)    for (i=1;i<=n;i++) { 
           pos += pp[jk];      ip=indx[i]; 
         for(jk=1; jk <=nlstate ; jk++){      sum=b[ip]; 
           if(pos>=1.e-5)      b[ip]=b[i]; 
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      if (ii) 
           else        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      else if (sum) ii=i; 
           if( i <= (int) agemax){      b[i]=sum; 
             if(pos>=1.e-5){    } 
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    for (i=n;i>=1;i--) { 
               probs[i][jk][j1]= pp[jk]/pos;      sum=b[i]; 
               /*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 (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
             }      b[i]=sum/a[i][i]; 
             else    } 
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);  } 
           }  
         }  /************ Frequencies ********************/
          void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
         for(jk=-1; jk <=nlstate+ndeath; jk++)  {  /* Some frequencies */
           for(m=-1; m <=nlstate+ndeath; m++)    
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
         if(i <= (int) agemax)    int first;
           fprintf(ficresp,"\n");    double ***freq; /* Frequencies */
         printf("\n");    double *pp;
       }    double pos, k2, dateintsum=0,k2cpt=0;
     }    FILE *ficresp;
   }    char fileresp[FILENAMELENGTH];
   dateintmean=dateintsum/k2cpt;    
      pp=vector(1,nlstate);
   fclose(ficresp);    probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    strcpy(fileresp,"p");
   free_vector(pp,1,nlstate);    strcat(fileresp,fileres);
      if((ficresp=fopen(fileresp,"w"))==NULL) {
   /* End of Freq */      printf("Problem with prevalence resultfile: %s\n", fileresp);
 }      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       exit(0);
 /************ Prevalence ********************/    }
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
 {  /* Some frequencies */    j1=0;
      
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    j=cptcoveff;
   double ***freq; /* Frequencies */    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   double *pp;  
   double pos, k2;    first=1;
   
   pp=vector(1,nlstate);    for(k1=1; k1<=j;k1++){
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      for(i1=1; i1<=ncodemax[k1];i1++){
          j1++;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   j1=0;          scanf("%d", i);*/
          for (i=-1; i<=nlstate+ndeath; i++)  
   j=cptcoveff;          for (jk=-1; jk<=nlstate+ndeath; jk++)  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            for(m=agemin; m <= agemax+3; m++)
                freq[i][jk][m]=0;
  for(k1=1; k1<=j;k1++){        
     for(i1=1; i1<=ncodemax[k1];i1++){        dateintsum=0;
       j1++;        k2cpt=0;
          for (i=1; i<=imx; i++) {
       for (i=-1; i<=nlstate+ndeath; i++)            bool=1;
         for (jk=-1; jk<=nlstate+ndeath; jk++)            if  (cptcovn>0) {
           for(m=agemin; m <= agemax+3; m++)            for (z1=1; z1<=cptcoveff; z1++) 
             freq[i][jk][m]=0;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                      bool=0;
       for (i=1; i<=imx; i++) {          }
         bool=1;          if (bool==1){
         if  (cptcovn>0) {            for(m=firstpass; m<=lastpass; m++){
           for (z1=1; z1<=cptcoveff; z1++)              k2=anint[m][i]+(mint[m][i]/12.);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])              if ((k2>=dateprev1) && (k2<=dateprev2)) {
               bool=0;                if(agev[m][i]==0) agev[m][i]=agemax+1;
         }                if(agev[m][i]==1) agev[m][i]=agemax+2;
         if (bool==1) {                if (m<lastpass) {
           for(m=firstpass; m<=lastpass; m++){                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
             k2=anint[m][i]+(mint[m][i]/12.);                  freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
             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 ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
               if (m<lastpass)                  dateintsum=dateintsum+k2;
                 if (calagedate>0) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];                  k2cpt++;
               else                }
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];              }
                freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];            }
             }          }
           }        }
         }         
       }        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
         for(i=(int)agemin; i <= (int)agemax+3; i++){  
           for(jk=1; jk <=nlstate ; jk++){        if  (cptcovn>0) {
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          fprintf(ficresp, "\n#********** Variable "); 
               pp[jk] += freq[jk][m][i];          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           }          fprintf(ficresp, "**********\n#");
           for(jk=1; jk <=nlstate ; jk++){        }
             for(m=-1, pos=0; m <=0 ; m++)        for(i=1; i<=nlstate;i++) 
             pos += freq[jk][m][i];          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         }        fprintf(ficresp, "\n");
                
          for(jk=1; jk <=nlstate ; jk++){        for(i=(int)agemin; i <= (int)agemax+3; i++){
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          if(i==(int)agemax+3){
              pp[jk] += freq[jk][m][i];            fprintf(ficlog,"Total");
          }          }else{
                      if(first==1){
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];              first=0;
               printf("See log file for details...\n");
          for(jk=1; jk <=nlstate ; jk++){                      }
            if( i <= (int) agemax){            fprintf(ficlog,"Age %d", i);
              if(pos>=1.e-5){          }
                probs[i][jk][j1]= pp[jk]/pos;          for(jk=1; jk <=nlstate ; jk++){
              }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
            }              pp[jk] += freq[jk][m][i]; 
          }          }
                    for(jk=1; jk <=nlstate ; jk++){
         }            for(m=-1, pos=0; m <=0 ; m++)
     }              pos += freq[jk][m][i];
   }            if(pp[jk]>=1.e-10){
               if(first==1){
                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);              }
   free_vector(pp,1,nlstate);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
              }else{
 }  /* End of Freq */              if(first==1)
                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 /************* Waves Concatenation ***************/              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             }
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          }
 {  
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          for(jk=1; jk <=nlstate ; jk++){
      Death is a valid wave (if date is known).            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i              pp[jk] += freq[jk][m][i];
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          }
      and mw[mi+1][i]. dh depends on stepm.  
      */          for(jk=1,pos=0; jk <=nlstate ; jk++)
             pos += pp[jk];
   int i, mi, m;          for(jk=1; jk <=nlstate ; jk++){
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;            if(pos>=1.e-5){
      double sum=0., jmean=0.;*/              if(first==1)
                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   int j, k=0,jk, ju, jl;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   double sum=0.;            }else{
   jmin=1e+5;              if(first==1)
   jmax=-1;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   jmean=0.;              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   for(i=1; i<=imx; i++){            }
     mi=0;            if( i <= (int) agemax){
     m=firstpass;              if(pos>=1.e-5){
     while(s[m][i] <= nlstate){                fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
       if(s[m][i]>=1)                probs[i][jk][j1]= pp[jk]/pos;
         mw[++mi][i]=m;                /*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(m >=lastpass)              }
         break;              else
       else                fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
         m++;            }
     }/* end while */          }
     if (s[m][i] > nlstate){          
       mi++;     /* Death is another wave */          for(jk=-1; jk <=nlstate+ndeath; jk++)
       /* if(mi==0)  never been interviewed correctly before death */            for(m=-1; m <=nlstate+ndeath; m++)
          /* Only death is a correct wave */              if(freq[jk][m][i] !=0 ) {
       mw[mi][i]=m;              if(first==1)
     }                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                 fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     wav[i]=mi;              }
     if(mi==0)          if(i <= (int) agemax)
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);            fprintf(ficresp,"\n");
   }          if(first==1)
             printf("Others in log...\n");
   for(i=1; i<=imx; i++){          fprintf(ficlog,"\n");
     for(mi=1; mi<wav[i];mi++){        }
       if (stepm <=0)      }
         dh[mi][i]=1;    }
       else{    dateintmean=dateintsum/k2cpt; 
         if (s[mw[mi+1][i]][i] > nlstate) {   
           if (agedc[i] < 2*AGESUP) {    fclose(ficresp);
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
           if(j==0) j=1;  /* Survives at least one month after exam */    free_vector(pp,1,nlstate);
           k=k+1;    
           if (j >= jmax) jmax=j;    /* End of Freq */
           if (j <= jmin) jmin=j;  }
           sum=sum+j;  
           /*if (j<0) printf("j=%d num=%d \n",j,i); */  /************ Prevalence ********************/
           }  void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
         }  {  /* Some frequencies */
         else{   
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
           k=k+1;    double ***freq; /* Frequencies */
           if (j >= jmax) jmax=j;    double *pp;
           else if (j <= jmin)jmin=j;    double pos, k2;
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */  
           sum=sum+j;    pp=vector(1,nlstate);
         }    
         jk= j/stepm;    freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
         jl= j -jk*stepm;    j1=0;
         ju= j -(jk+1)*stepm;    
         if(jl <= -ju)    j=cptcoveff;
           dh[mi][i]=jk;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         else    
           dh[mi][i]=jk+1;    for(k1=1; k1<=j;k1++){
         if(dh[mi][i]==0)      for(i1=1; i1<=ncodemax[k1];i1++){
           dh[mi][i]=1; /* At least one step */        j1++;
       }        
     }        for (i=-1; i<=nlstate+ndeath; i++)  
   }          for (jk=-1; jk<=nlstate+ndeath; jk++)  
   jmean=sum/k;            for(m=agemin; m <= agemax+3; m++)
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);              freq[i][jk][m]=0;
  }       
 /*********** Tricode ****************************/        for (i=1; i<=imx; i++) {
 void tricode(int *Tvar, int **nbcode, int imx)          bool=1;
 {          if  (cptcovn>0) {
   int Ndum[20],ij=1, k, j, i;            for (z1=1; z1<=cptcoveff; z1++) 
   int cptcode=0;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   cptcoveff=0;                bool=0;
            } 
   for (k=0; k<19; k++) Ndum[k]=0;          if (bool==1) { 
   for (k=1; k<=7; k++) ncodemax[k]=0;            for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {              if ((k2>=dateprev1) && (k2<=dateprev2)) {
     for (i=1; i<=imx; i++) {                if(agev[m][i]==0) agev[m][i]=agemax+1;
       ij=(int)(covar[Tvar[j]][i]);                if(agev[m][i]==1) agev[m][i]=agemax+2;
       Ndum[ij]++;                if (m<lastpass) {
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/                  if (calagedate>0) 
       if (ij > cptcode) cptcode=ij;                    freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
     }                  else
                     freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     for (i=0; i<=cptcode; i++) {                  freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; 
       if(Ndum[i]!=0) ncodemax[j]++;                }
     }              }
     ij=1;            }
           }
         }
     for (i=1; i<=ncodemax[j]; i++) {        for(i=(int)agemin; i <= (int)agemax+3; i++){ 
       for (k=0; k<=19; k++) {          for(jk=1; jk <=nlstate ; jk++){
         if (Ndum[k] != 0) {            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
           nbcode[Tvar[j]][ij]=k;              pp[jk] += freq[jk][m][i]; 
                    }
           ij++;          for(jk=1; jk <=nlstate ; jk++){
         }            for(m=-1, pos=0; m <=0 ; m++)
         if (ij > ncodemax[j]) break;              pos += freq[jk][m][i];
       }            }
     }          
   }            for(jk=1; jk <=nlstate ; jk++){
             for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
  for (k=0; k<19; k++) Ndum[k]=0;              pp[jk] += freq[jk][m][i];
           }
  for (i=1; i<=ncovmodel-2; i++) {          
       ij=Tvar[i];          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
       Ndum[ij]++;          
     }          for(jk=1; jk <=nlstate ; jk++){    
             if( i <= (int) agemax){
  ij=1;              if(pos>=1.e-5){
  for (i=1; i<=10; i++) {                probs[i][jk][j1]= pp[jk]/pos;
    if((Ndum[i]!=0) && (i<=ncovcol)){              }
      Tvaraff[ij]=i;            }
      ij++;          }/* end jk */
    }        }/* end i */
  }      } /* end i1 */
      } /* end k1 */
     cptcoveff=ij-1;  
 }    
     free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
 /*********** Health Expectancies ****************/    free_vector(pp,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 )  }  /* End of Freq */
   
 {  /************* Waves Concatenation ***************/
   /* Health expectancies */  
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
   double age, agelim, hf;  {
   double ***p3mat,***varhe;    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   double **dnewm,**doldm;       Death is a valid wave (if date is known).
   double *xp;       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   double **gp, **gm;       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   double ***gradg, ***trgradg;       and mw[mi+1][i]. dh depends on stepm.
   int theta;       */
   
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);    int i, mi, m;
   xp=vector(1,npar);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   dnewm=matrix(1,nlstate*2,1,npar);       double sum=0., jmean=0.;*/
   doldm=matrix(1,nlstate*2,1,nlstate*2);    int first;
      int j, k=0,jk, ju, jl;
   fprintf(ficreseij,"# Health expectancies\n");    double sum=0.;
   fprintf(ficreseij,"# Age");    first=0;
   for(i=1; i<=nlstate;i++)    jmin=1e+5;
     for(j=1; j<=nlstate;j++)    jmax=-1;
       fprintf(ficreseij," %1d-%1d (SE)",i,j);    jmean=0.;
   fprintf(ficreseij,"\n");    for(i=1; i<=imx; i++){
       mi=0;
   if(estepm < stepm){      m=firstpass;
     printf ("Problem %d lower than %d\n",estepm, stepm);      while(s[m][i] <= nlstate){
   }        if(s[m][i]>=1)
   else  hstepm=estepm;            mw[++mi][i]=m;
   /* We compute the life expectancy from trapezoids spaced every estepm months        if(m >=lastpass)
    * This is mainly to measure the difference between two models: for example          break;
    * if stepm=24 months pijx are given only every 2 years and by summing them        else
    * we are calculating an estimate of the Life Expectancy assuming a linear          m++;
    * progression inbetween and thus overestimating or underestimating according      }/* end while */
    * to the curvature of the survival function. If, for the same date, we      if (s[m][i] > nlstate){
    * estimate the model with stepm=1 month, we can keep estepm to 24 months        mi++;     /* Death is another wave */
    * to compare the new estimate of Life expectancy with the same linear        /* if(mi==0)  never been interviewed correctly before death */
    * hypothesis. A more precise result, taking into account a more precise           /* Only death is a correct wave */
    * curvature will be obtained if estepm is as small as stepm. */        mw[mi][i]=m;
       }
   /* 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.      wav[i]=mi;
      nhstepm is the number of hstepm from age to agelim      if(mi==0){
      nstepm is the number of stepm from age to agelin.        if(first==0){
      Look at hpijx to understand the reason of that which relies in memory size          printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
      and note for a fixed period like estepm months */          first=1;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        }
      survival function given by stepm (the optimization length). Unfortunately it        if(first==1){
      means that if the survival funtion is printed only each two years of age and if          fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
      you sum them up and add 1 year (area under the trapezoids) you won't get the same        }
      results. So we changed our mind and took the option of the best precision.      } /* end mi==0 */
   */    }
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */  
     for(i=1; i<=imx; i++){
   agelim=AGESUP;      for(mi=1; mi<wav[i];mi++){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        if (stepm <=0)
     /* nhstepm age range expressed in number of stepm */          dh[mi][i]=1;
     nstepm=(int) rint((agelim-age)*YEARM/stepm);        else{
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */          if (s[mw[mi+1][i]][i] > nlstate) {
     /* if (stepm >= YEARM) hstepm=1;*/            if (agedc[i] < 2*AGESUP) {
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            if(j==0) j=1;  /* Survives at least one month after exam */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);            k=k+1;
     gp=matrix(0,nhstepm,1,nlstate*2);            if (j >= jmax) jmax=j;
     gm=matrix(0,nhstepm,1,nlstate*2);            if (j <= jmin) jmin=j;
             sum=sum+j;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            /*if (j<0) printf("j=%d num=%d \n",j,i); */
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */            }
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            }
            else{
             j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */            k=k+1;
             if (j >= jmax) jmax=j;
     /* Computing Variances of health expectancies */            else if (j <= jmin)jmin=j;
             /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
      for(theta=1; theta <=npar; theta++){            sum=sum+j;
       for(i=1; i<=npar; i++){          }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          jk= j/stepm;
       }          jl= j -jk*stepm;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            ju= j -(jk+1)*stepm;
            if(jl <= -ju){
       cptj=0;            dh[mi][i]=jk;
       for(j=1; j<= nlstate; j++){            bh[mi][i]=jl;
         for(i=1; i<=nlstate; i++){          }
           cptj=cptj+1;          else{
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){            dh[mi][i]=jk+1;
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;            bh[mi][i]=ju;
           }          }
         }          if(dh[mi][i]==0){
       }            dh[mi][i]=1; /* At least one step */
                  bh[mi][i]=ju; /* At least one step */
                  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);
       for(i=1; i<=npar; i++)          }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          if(i==298 || i==287 || i==763 ||i==1061)printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d",bh[mi][i],ju,jl,dh[mi][i],jk,stepm);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          }
            }
       cptj=0;    }
       for(j=1; j<= nlstate; j++){    jmean=sum/k;
         for(i=1;i<=nlstate;i++){    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
           cptj=cptj+1;    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){   }
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;  
           }  /*********** Tricode ****************************/
         }  void tricode(int *Tvar, int **nbcode, int imx)
       }  {
          
        int Ndum[20],ij=1, k, j, i, maxncov=19;
     int cptcode=0;
       for(j=1; j<= nlstate*2; j++)    cptcoveff=0; 
         for(h=0; h<=nhstepm-1; h++){   
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    for (k=0; k<maxncov; k++) Ndum[k]=0;
         }    for (k=1; k<=7; k++) ncodemax[k]=0;
   
      }    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
          for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
 /* End theta */                                 modality*/ 
         ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);        Ndum[ij]++; /*store the modality */
         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
      for(h=0; h<=nhstepm-1; h++)        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
       for(j=1; j<=nlstate*2;j++)                                         Tvar[j]. If V=sex and male is 0 and 
         for(theta=1; theta <=npar; theta++)                                         female is 1, then  cptcode=1.*/
         trgradg[h][j][theta]=gradg[h][theta][j];      }
   
       for (i=0; i<=cptcode; i++) {
      for(i=1;i<=nlstate*2;i++)        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
       for(j=1;j<=nlstate*2;j++)      }
         varhe[i][j][(int)age] =0.;  
       ij=1; 
     for(h=0;h<=nhstepm-1;h++){      for (i=1; i<=ncodemax[j]; i++) {
       for(k=0;k<=nhstepm-1;k++){        for (k=0; k<= maxncov; k++) {
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);          if (Ndum[k] != 0) {
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);            nbcode[Tvar[j]][ij]=k; 
         for(i=1;i<=nlstate*2;i++)            /* 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(j=1;j<=nlstate*2;j++)            
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;            ij++;
       }          }
     }          if (ij > ncodemax[j]) break; 
         }  
            } 
     /* Computing expectancies */    }  
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++)   for (k=0; k< maxncov; k++) Ndum[k]=0;
         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;   for (i=1; i<=ncovmodel-2; i++) { 
               /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
 /* 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]);*/     ij=Tvar[i];
      Ndum[ij]++;
         }   }
   
     fprintf(ficreseij,"%3.0f",age );   ij=1;
     cptj=0;   for (i=1; i<= maxncov; i++) {
     for(i=1; i<=nlstate;i++)     if((Ndum[i]!=0) && (i<=ncovcol)){
       for(j=1; j<=nlstate;j++){       Tvaraff[ij]=i; /*For printing */
         cptj++;       ij++;
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );     }
       }   }
     fprintf(ficreseij,"\n");   
       cptcoveff=ij-1; /*Number of simple covariates*/
     free_matrix(gm,0,nhstepm,1,nlstate*2);  }
     free_matrix(gp,0,nhstepm,1,nlstate*2);  
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);  /*********** Health Expectancies ****************/
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);  
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  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 )
   }  
   free_vector(xp,1,npar);  {
   free_matrix(dnewm,1,nlstate*2,1,npar);    /* Health expectancies */
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);    double age, agelim, hf;
 }    double ***p3mat,***varhe;
     double **dnewm,**doldm;
 /************ Variance ******************/    double *xp;
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)    double **gp, **gm;
 {    double ***gradg, ***trgradg;
   /* Variance of health expectancies */    int theta;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  
   double **newm;    varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
   double **dnewm,**doldm;    xp=vector(1,npar);
   int i, j, nhstepm, hstepm, h, nstepm ;    dnewm=matrix(1,nlstate*2,1,npar);
   int k, cptcode;    doldm=matrix(1,nlstate*2,1,nlstate*2);
   double *xp;    
   double **gp, **gm;    fprintf(ficreseij,"# Health expectancies\n");
   double ***gradg, ***trgradg;    fprintf(ficreseij,"# Age");
   double ***p3mat;    for(i=1; i<=nlstate;i++)
   double age,agelim, hf;      for(j=1; j<=nlstate;j++)
   int theta;        fprintf(ficreseij," %1d-%1d (SE)",i,j);
     fprintf(ficreseij,"\n");
    fprintf(ficresvij,"# Covariances of life expectancies\n");  
   fprintf(ficresvij,"# Age");    if(estepm < stepm){
   for(i=1; i<=nlstate;i++)      printf ("Problem %d lower than %d\n",estepm, stepm);
     for(j=1; j<=nlstate;j++)    }
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    else  hstepm=estepm;   
   fprintf(ficresvij,"\n");    /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
   xp=vector(1,npar);     * if stepm=24 months pijx are given only every 2 years and by summing them
   dnewm=matrix(1,nlstate,1,npar);     * we are calculating an estimate of the Life Expectancy assuming a linear 
   doldm=matrix(1,nlstate,1,nlstate);     * progression inbetween and thus overestimating or underestimating according
       * to the curvature of the survival function. If, for the same date, we 
   if(estepm < stepm){     * estimate the model with stepm=1 month, we can keep estepm to 24 months
     printf ("Problem %d lower than %d\n",estepm, stepm);     * to compare the new estimate of Life expectancy with the same linear 
   }     * hypothesis. A more precise result, taking into account a more precise
   else  hstepm=estepm;       * curvature will be obtained if estepm is as small as stepm. */
   /* For example we decided to compute the life expectancy with the smallest unit */  
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    /* For example we decided to compute the life expectancy with the smallest unit */
      nhstepm is the number of hstepm from age to agelim    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
      nstepm is the number of stepm from age to agelin.       nhstepm is the number of hstepm from age to agelim 
      Look at hpijx to understand the reason of that which relies in memory size       nstepm is the number of stepm from age to agelin. 
      and note for a fixed period like k years */       Look at hpijx to understand the reason of that which relies in memory size
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the       and note for a fixed period like estepm months */
      survival function given by stepm (the optimization length). Unfortunately it    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
      means that if the survival funtion is printed only each two years of age and if       survival function given by stepm (the optimization length). Unfortunately it
      you sum them up and add 1 year (area under the trapezoids) you won't get the same       means that if the survival funtion is printed only each two years of age and if
      results. So we changed our mind and took the option of the best precision.       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   */       results. So we changed our mind and took the option of the best precision.
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    */
   agelim = AGESUP;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    agelim=AGESUP;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      /* nhstepm age range expressed in number of stepm */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
     gp=matrix(0,nhstepm,1,nlstate);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     gm=matrix(0,nhstepm,1,nlstate);      /* if (stepm >= YEARM) hstepm=1;*/
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     for(theta=1; theta <=npar; theta++){      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       for(i=1; i<=npar; i++){ /* Computes gradient */      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      gp=matrix(0,nhstepm,1,nlstate*2);
       }      gm=matrix(0,nhstepm,1,nlstate*2);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       if (popbased==1) {      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
         for(i=1; i<=nlstate;i++)   
           prlim[i][i]=probs[(int)age][i][ij];  
       }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
    
       for(j=1; j<= nlstate; j++){      /* Computing Variances of health expectancies */
         for(h=0; h<=nhstepm; h++){  
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)       for(theta=1; theta <=npar; theta++){
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        for(i=1; i<=npar; i++){ 
         }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       }        }
            hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       for(i=1; i<=npar; i++) /* Computes gradient */    
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        cptj=0;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          for(j=1; j<= nlstate; j++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          for(i=1; i<=nlstate; i++){
              cptj=cptj+1;
       if (popbased==1) {            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
         for(i=1; i<=nlstate;i++)              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
           prlim[i][i]=probs[(int)age][i][ij];            }
       }          }
         }
       for(j=1; j<= nlstate; j++){       
         for(h=0; h<=nhstepm; h++){       
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        for(i=1; i<=npar; i++) 
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       }        
         cptj=0;
       for(j=1; j<= nlstate; j++)        for(j=1; j<= nlstate; j++){
         for(h=0; h<=nhstepm; h++){          for(i=1;i<=nlstate;i++){
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            cptj=cptj+1;
         }            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
     } /* End theta */              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
             }
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          }
         }
     for(h=0; h<=nhstepm; h++)        for(j=1; j<= nlstate*2; j++)
       for(j=1; j<=nlstate;j++)          for(h=0; h<=nhstepm-1; h++){
         for(theta=1; theta <=npar; theta++)            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           trgradg[h][j][theta]=gradg[h][theta][j];          }
        } 
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */     
     for(i=1;i<=nlstate;i++)  /* End theta */
       for(j=1;j<=nlstate;j++)  
         vareij[i][j][(int)age] =0.;       trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
   
     for(h=0;h<=nhstepm;h++){       for(h=0; h<=nhstepm-1; h++)
       for(k=0;k<=nhstepm;k++){        for(j=1; j<=nlstate*2;j++)
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          for(theta=1; theta <=npar; theta++)
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);            trgradg[h][j][theta]=gradg[h][theta][j];
         for(i=1;i<=nlstate;i++)       
           for(j=1;j<=nlstate;j++)  
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;       for(i=1;i<=nlstate*2;i++)
       }        for(j=1;j<=nlstate*2;j++)
     }          varhe[i][j][(int)age] =0.;
   
     fprintf(ficresvij,"%.0f ",age );       printf("%d|",(int)age);fflush(stdout);
     for(i=1; i<=nlstate;i++)       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       for(j=1; j<=nlstate;j++){       for(h=0;h<=nhstepm-1;h++){
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);        for(k=0;k<=nhstepm-1;k++){
       }          matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
     fprintf(ficresvij,"\n");          matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
     free_matrix(gp,0,nhstepm,1,nlstate);          for(i=1;i<=nlstate*2;i++)
     free_matrix(gm,0,nhstepm,1,nlstate);            for(j=1;j<=nlstate*2;j++)
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      }
   } /* End age */      /* Computing expectancies */
        for(i=1; i<=nlstate;i++)
   free_vector(xp,1,npar);        for(j=1; j<=nlstate;j++)
   free_matrix(doldm,1,nlstate,1,npar);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   free_matrix(dnewm,1,nlstate,1,nlstate);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             
 }  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
 /************ 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)  
 {      fprintf(ficreseij,"%3.0f",age );
   /* Variance of prevalence limit */      cptj=0;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      for(i=1; i<=nlstate;i++)
   double **newm;        for(j=1; j<=nlstate;j++){
   double **dnewm,**doldm;          cptj++;
   int i, j, nhstepm, hstepm;          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   int k, cptcode;        }
   double *xp;      fprintf(ficreseij,"\n");
   double *gp, *gm;     
   double **gradg, **trgradg;      free_matrix(gm,0,nhstepm,1,nlstate*2);
   double age,agelim;      free_matrix(gp,0,nhstepm,1,nlstate*2);
   int theta;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
          free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fprintf(ficresvpl,"# Age");    }
   for(i=1; i<=nlstate;i++)    printf("\n");
       fprintf(ficresvpl," %1d-%1d",i,i);    fprintf(ficlog,"\n");
   fprintf(ficresvpl,"\n");  
     free_vector(xp,1,npar);
   xp=vector(1,npar);    free_matrix(dnewm,1,nlstate*2,1,npar);
   dnewm=matrix(1,nlstate,1,npar);    free_matrix(doldm,1,nlstate*2,1,nlstate*2);
   doldm=matrix(1,nlstate,1,nlstate);    free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
    }
   hstepm=1*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  /************ Variance ******************/
   agelim = AGESUP;  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)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  {
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    /* Variance of health expectancies */
     if (stepm >= YEARM) hstepm=1;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    /* double **newm;*/
     gradg=matrix(1,npar,1,nlstate);    double **dnewm,**doldm;
     gp=vector(1,nlstate);    double **dnewmp,**doldmp;
     gm=vector(1,nlstate);    int i, j, nhstepm, hstepm, h, nstepm ;
     int k, cptcode;
     for(theta=1; theta <=npar; theta++){    double *xp;
       for(i=1; i<=npar; i++){ /* Computes gradient */    double **gp, **gm;  /* for var eij */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    double ***gradg, ***trgradg; /*for var eij */
       }    double **gradgp, **trgradgp; /* for var p point j */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double *gpp, *gmp; /* for var p point j */
       for(i=1;i<=nlstate;i++)    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
         gp[i] = prlim[i][i];    double ***p3mat;
        double age,agelim, hf;
       for(i=1; i<=npar; i++) /* Computes gradient */    double ***mobaverage;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    int theta;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    char digit[4];
       for(i=1;i<=nlstate;i++)    char digitp[25];
         gm[i] = prlim[i][i];  
     char fileresprobmorprev[FILENAMELENGTH];
       for(i=1;i<=nlstate;i++)  
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    if(popbased==1){
     } /* End theta */      if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
     trgradg =matrix(1,nlstate,1,npar);      else strcpy(digitp,"-populbased-nomobil-");
     }
     for(j=1; j<=nlstate;j++)    else 
       for(theta=1; theta <=npar; theta++)      strcpy(digitp,"-stablbased-");
         trgradg[j][theta]=gradg[theta][j];  
     if (mobilav!=0) {
     for(i=1;i<=nlstate;i++)      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       varpl[i][(int)age] =0.;      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     for(i=1;i<=nlstate;i++)      }
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    }
   
     fprintf(ficresvpl,"%.0f ",age );    strcpy(fileresprobmorprev,"prmorprev"); 
     for(i=1; i<=nlstate;i++)    sprintf(digit,"%-d",ij);
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     fprintf(ficresvpl,"\n");    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     free_vector(gp,1,nlstate);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     free_vector(gm,1,nlstate);    strcat(fileresprobmorprev,fileres);
     free_matrix(gradg,1,npar,1,nlstate);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     free_matrix(trgradg,1,nlstate,1,npar);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   } /* End age */      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
   free_vector(xp,1,npar);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   free_matrix(doldm,1,nlstate,1,npar);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   free_matrix(dnewm,1,nlstate,1,nlstate);    fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
 }    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
 /************ Variance of one-step probabilities  ******************/      for(i=1; i<=nlstate;i++)
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
 {    }  
   int i, j, i1, k1, j1, z1;    fprintf(ficresprobmorprev,"\n");
   int k=0, cptcode;    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   double **dnewm,**doldm;      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   double *xp;      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
   double *gp, *gm;      exit(0);
   double **gradg, **trgradg;    }
   double age,agelim, cov[NCOVMAX];    else{
   int theta;      fprintf(ficgp,"\n# Routine varevsij");
   char fileresprob[FILENAMELENGTH];    }
     if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   strcpy(fileresprob,"prob");      printf("Problem with html file: %s\n", optionfilehtm);
   strcat(fileresprob,fileres);      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {      exit(0);
     printf("Problem with resultfile: %s\n", fileresprob);    }
   }    else{
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);      fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
        fprintf(fichtm,"\n<br>%s (à revoir) <br>\n",digitp);
 fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");    }
   fprintf(ficresprob,"# Age");    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=(nlstate+ndeath);j++)    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);    fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
   fprintf(ficresprob,"\n");        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     fprintf(ficresvij,"\n");
   
   xp=vector(1,npar);    xp=vector(1,npar);
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    dnewm=matrix(1,nlstate,1,npar);
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    doldm=matrix(1,nlstate,1,nlstate);
      dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   cov[1]=1;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   j1=0;    gpp=vector(nlstate+1,nlstate+ndeath);
   for(k1=1; k1<=1;k1++){    gmp=vector(nlstate+1,nlstate+ndeath);
     for(i1=1; i1<=ncodemax[k1];i1++){    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     j1++;    
     if(estepm < stepm){
     if  (cptcovn>0) {      printf ("Problem %d lower than %d\n",estepm, stepm);
       fprintf(ficresprob, "\n#********** Variable ");    }
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    else  hstepm=estepm;   
       fprintf(ficresprob, "**********\n#");    /* 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 
       for (age=bage; age<=fage; age ++){       nstepm is the number of stepm from age to agelin. 
         cov[2]=age;       Look at hpijx to understand the reason of that which relies in memory size
         for (k=1; k<=cptcovn;k++) {       and note for a fixed period like k years */
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
                 survival function given by stepm (the optimization length). Unfortunately it
         }       means that if the survival funtion is printed only each two years of age and if
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         for (k=1; k<=cptcovprod;k++)       results. So we changed our mind and took the option of the best precision.
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    */
            hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         gradg=matrix(1,npar,1,9);    agelim = AGESUP;
         trgradg=matrix(1,9,1,npar);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         for(theta=1; theta <=npar; theta++){      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
           for(i=1; i<=npar; i++)      gp=matrix(0,nhstepm,1,nlstate);
             xp[i] = x[i] + (i==theta ?delti[theta]:0);      gm=matrix(0,nhstepm,1,nlstate);
            
           pmij(pmmij,cov,ncovmodel,xp,nlstate);  
                for(theta=1; theta <=npar; theta++){
           k=0;        for(i=1; i<=npar; i++){ /* Computes gradient */
           for(i=1; i<= (nlstate+ndeath); i++){          xp[i] = x[i] + (i==theta ?delti[theta]:0);
             for(j=1; j<=(nlstate+ndeath);j++){        }
               k=k+1;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
               gp[k]=pmmij[i][j];        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
             }  
           }        if (popbased==1) {
                    if(mobilav ==0){
           for(i=1; i<=npar; i++)            for(i=1; i<=nlstate;i++)
             xp[i] = x[i] - (i==theta ?delti[theta]:0);              prlim[i][i]=probs[(int)age][i][ij];
              }else{ /* mobilav */ 
           pmij(pmmij,cov,ncovmodel,xp,nlstate);            for(i=1; i<=nlstate;i++)
           k=0;              prlim[i][i]=mobaverage[(int)age][i][ij];
           for(i=1; i<=(nlstate+ndeath); i++){          }
             for(j=1; j<=(nlstate+ndeath);j++){        }
               k=k+1;    
               gm[k]=pmmij[i][j];        for(j=1; j<= nlstate; j++){
             }          for(h=0; h<=nhstepm; h++){
           }            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
                    gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)          }
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];          }
         }        /* This for computing forces of mortality (h=1)as a weighted average */
         for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)          for(i=1; i<= nlstate; i++)
           for(theta=1; theta <=npar; theta++)            gpp[j] += prlim[i][i]*p3mat[i][j][1];
             trgradg[j][theta]=gradg[theta][j];        }    
                /* end force of mortality */
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);  
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);        for(i=1; i<=npar; i++) /* Computes gradient */
                  xp[i] = x[i] - (i==theta ?delti[theta]:0);
         pmij(pmmij,cov,ncovmodel,x,nlstate);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         k=0;   
         for(i=1; i<=(nlstate+ndeath); i++){        if (popbased==1) {
           for(j=1; j<=(nlstate+ndeath);j++){          if(mobilav ==0){
             k=k+1;            for(i=1; i<=nlstate;i++)
             gm[k]=pmmij[i][j];              prlim[i][i]=probs[(int)age][i][ij];
           }          }else{ /* mobilav */ 
         }            for(i=1; i<=nlstate;i++)
                    prlim[i][i]=mobaverage[(int)age][i][ij];
      /*printf("\n%d ",(int)age);          }
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        }
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));  
      }*/        for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
         fprintf(ficresprob,"\n%d ",(int)age);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)          }
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));        }
          /* This for computing force of mortality (h=1)as a weighted average */
       }        for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
     }          for(i=1; i<= nlstate; i++)
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));            gmp[j] += prlim[i][i]*p3mat[i][j][1];
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));        }    
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        /* end force of mortality */
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
   }        for(j=1; j<= nlstate; j++) /* vareij */
   free_vector(xp,1,npar);          for(h=0; h<=nhstepm; h++){
   fclose(ficresprob);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
            }
 }        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
 /******************* Printing html file ***********/        }
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \  
  int lastpass, int stepm, int weightopt, char model[],\      } /* End theta */
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \  
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
  char version[], int popforecast, int estepm ){  
   int jj1, k1, i1, cpt;      for(h=0; h<=nhstepm; h++) /* veij */
   FILE *fichtm;        for(j=1; j<=nlstate;j++)
   /*char optionfilehtm[FILENAMELENGTH];*/          for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   strcpy(optionfilehtm,optionfile);  
   strcat(optionfilehtm,".htm");      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {        for(theta=1; theta <=npar; theta++)
     printf("Problem with %s \n",optionfilehtm), exit(0);          trgradgp[j][theta]=gradgp[theta][j];
   }  
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n      for(i=1;i<=nlstate;i++)
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n        for(j=1;j<=nlstate;j++)
 \n          vareij[i][j][(int)age] =0.;
 Total number of observations=%d <br>\n  
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n      for(h=0;h<=nhstepm;h++){
 <hr  size=\"2\" color=\"#EC5E5E\">        for(k=0;k<=nhstepm;k++){
  <ul><li>Outputs files<br>\n          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n          for(i=1;i<=nlstate;i++)
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n            for(j=1;j<=nlstate;j++)
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n        }
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,estepm,fileres,fileres);      }
   
  fprintf(fichtm,"\n      /* pptj */
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n      for(j=nlstate+1;j<=nlstate+ndeath;j++)
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n        for(i=nlstate+1;i<=nlstate+ndeath;i++)
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);          varppt[j][i]=doldmp[j][i];
       /* end ppptj */
  if(popforecast==1) fprintf(fichtm,"\n      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n   
         <br>",fileres,fileres,fileres,fileres);      if (popbased==1) {
  else        if(mobilav ==0){
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);          for(i=1; i<=nlstate;i++)
 fprintf(fichtm," <li>Graphs</li><p>");            prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
  m=cptcoveff;          for(i=1; i<=nlstate;i++)
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}            prlim[i][i]=mobaverage[(int)age][i][ij];
         }
  jj1=0;      }
  for(k1=1; k1<=m;k1++){      
    for(i1=1; i1<=ncodemax[k1];i1++){      /* This for computing force of mortality (h=1)as a weighted average */
        jj1++;      for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
        if (cptcovn > 0) {        for(i=1; i<= nlstate; i++)
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
          for (cpt=1; cpt<=cptcoveff;cpt++)      }    
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);      /* end force of mortality */
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");  
        }      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
        for(cpt=1; cpt<nlstate;cpt++){        for(i=1; i<=nlstate;i++){
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        }
        }      } 
     for(cpt=1; cpt<=nlstate;cpt++) {      fprintf(ficresprobmorprev,"\n");
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident  
 interval) in state (%d): v%s%d%d.gif <br>      fprintf(ficresvij,"%.0f ",age );
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        for(i=1; i<=nlstate;i++)
      }        for(j=1; j<=nlstate;j++){
      for(cpt=1; cpt<=nlstate;cpt++) {          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         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);      fprintf(ficresvij,"\n");
      }      free_matrix(gp,0,nhstepm,1,nlstate);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and      free_matrix(gm,0,nhstepm,1,nlstate);
 health expectancies in states (1) and (2): e%s%d.gif<br>      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
 fprintf(fichtm,"\n</body>");      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    }    } /* End age */
    }    free_vector(gpp,nlstate+1,nlstate+ndeath);
 fclose(fichtm);    free_vector(gmp,nlstate+1,nlstate+ndeath);
 }    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
 /******************* Gnuplot file **************/    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
 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++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    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);
   strcpy(optionfilegnuplot,optionfilefiname);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);
   strcat(optionfilegnuplot,".gp.txt");    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);
     printf("Problem with file %s",optionfilegnuplot);    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   }  */
     fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
 #ifdef windows  
     fprintf(ficgp,"cd \"%s\" \n",pathc);    free_vector(xp,1,npar);
 #endif    free_matrix(doldm,1,nlstate,1,nlstate);
 m=pow(2,cptcoveff);    free_matrix(dnewm,1,nlstate,1,npar);
      free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
  /* 1eme*/    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   for (cpt=1; cpt<= nlstate ; cpt ++) {    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    for (k1=1; k1<= m ; k1 ++) {    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
 #ifdef windows    fclose(ficgp);
     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);    fclose(fichtm);
 #endif  }
 #ifdef unix  
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);  /************ Variance of prevlim ******************/
 #endif  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
   {
 for (i=1; i<= nlstate ; i ++) {    /* Variance of prevalence limit */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double **newm;
 }    double **dnewm,**doldm;
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    int i, j, nhstepm, hstepm;
     for (i=1; i<= nlstate ; i ++) {    int k, cptcode;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    double *xp;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double *gp, *gm;
 }    double **gradg, **trgradg;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    double age,agelim;
      for (i=1; i<= nlstate ; i ++) {    int theta;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");     
   else fprintf(ficgp," \%%*lf (\%%*lf)");    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
 }      fprintf(ficresvpl,"# Age");
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    for(i=1; i<=nlstate;i++)
 #ifdef unix        fprintf(ficresvpl," %1d-%1d",i,i);
 fprintf(ficgp,"\nset ter gif small size 400,300");    fprintf(ficresvpl,"\n");
 #endif  
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    xp=vector(1,npar);
    }    dnewm=matrix(1,nlstate,1,npar);
   }    doldm=matrix(1,nlstate,1,nlstate);
   /*2 eme*/    
     hstepm=1*YEARM; /* Every year of age */
   for (k1=1; k1<= m ; k1 ++) {    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);    agelim = AGESUP;
        for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     for (i=1; i<= nlstate+1 ; i ++) {      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       k=2*i;      if (stepm >= YEARM) hstepm=1;
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       for (j=1; j<= nlstate+1 ; j ++) {      gradg=matrix(1,npar,1,nlstate);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      gp=vector(1,nlstate);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      gm=vector(1,nlstate);
 }    
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      for(theta=1; theta <=npar; theta++){
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        for(i=1; i<=npar; i++){ /* Computes gradient */
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       for (j=1; j<= nlstate+1 ; j ++) {        }
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         else fprintf(ficgp," \%%*lf (\%%*lf)");        for(i=1;i<=nlstate;i++)
 }            gp[i] = prlim[i][i];
       fprintf(ficgp,"\" t\"\" w l 0,");      
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);        for(i=1; i<=npar; i++) /* Computes gradient */
       for (j=1; j<= nlstate+1 ; j ++) {          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(i=1;i<=nlstate;i++)
 }            gm[i] = prlim[i][i];
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");  
       else fprintf(ficgp,"\" t\"\" w l 0,");        for(i=1;i<=nlstate;i++)
     }          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);      } /* End theta */
   }  
        trgradg =matrix(1,nlstate,1,npar);
   /*3eme*/  
       for(j=1; j<=nlstate;j++)
   for (k1=1; k1<= m ; k1 ++) {        for(theta=1; theta <=npar; theta++)
     for (cpt=1; cpt<= nlstate ; cpt ++) {          trgradg[j][theta]=gradg[theta][j];
       k=2+nlstate*(2*cpt-2);  
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);      for(i=1;i<=nlstate;i++)
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);        varpl[i][(int)age] =0.;
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);      for(i=1;i<=nlstate;i++)
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);  
       fprintf(ficresvpl,"%.0f ",age );
 */      for(i=1; i<=nlstate;i++)
       for (i=1; i< nlstate ; i ++) {        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);      fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       }      free_vector(gm,1,nlstate);
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      free_matrix(gradg,1,npar,1,nlstate);
     }      free_matrix(trgradg,1,nlstate,1,npar);
     }    } /* End age */
    
   /* CV preval stat */    free_vector(xp,1,npar);
     for (k1=1; k1<= m ; k1 ++) {    free_matrix(doldm,1,nlstate,1,npar);
     for (cpt=1; cpt<nlstate ; cpt ++) {    free_matrix(dnewm,1,nlstate,1,nlstate);
       k=3;  
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);  }
   
       for (i=1; i< nlstate ; i ++)  /************ Variance of one-step probabilities  ******************/
         fprintf(ficgp,"+$%d",k+i+1);  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);  {
          int i, j=0,  i1, k1, l1, t, tj;
       l=3+(nlstate+ndeath)*cpt;    int k2, l2, j1,  z1;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    int k=0,l, cptcode;
       for (i=1; i< nlstate ; i ++) {    int first=1, first1;
         l=3+(nlstate+ndeath)*cpt;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
         fprintf(ficgp,"+$%d",l+i+1);    double **dnewm,**doldm;
       }    double *xp;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      double *gp, *gm;
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    double **gradg, **trgradg;
     }    double **mu;
   }      double age,agelim, cov[NCOVMAX];
      double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   /* proba elementaires */    int theta;
    for(i=1,jk=1; i <=nlstate; i++){    char fileresprob[FILENAMELENGTH];
     for(k=1; k <=(nlstate+ndeath); k++){    char fileresprobcov[FILENAMELENGTH];
       if (k != i) {    char fileresprobcor[FILENAMELENGTH];
         for(j=1; j <=ncovmodel; j++){  
            double ***varpij;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);  
           jk++;    strcpy(fileresprob,"prob"); 
           fprintf(ficgp,"\n");    strcat(fileresprob,fileres);
         }    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       }      printf("Problem with resultfile: %s\n", fileresprob);
     }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }    }
     strcpy(fileresprobcov,"probcov"); 
     for(jk=1; jk <=m; jk++) {    strcat(fileresprobcov,fileres);
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
    i=1;      printf("Problem with resultfile: %s\n", fileresprobcov);
    for(k2=1; k2<=nlstate; k2++) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
      k3=i;    }
      for(k=1; k<=(nlstate+ndeath); k++) {    strcpy(fileresprobcor,"probcor"); 
        if (k != k2){    strcat(fileresprobcor,fileres);
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
 ij=1;      printf("Problem with resultfile: %s\n", fileresprobcor);
         for(j=3; j <=ncovmodel; j++) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    }
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
             ij++;    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
           }    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
           else    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
         }    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
           fprintf(ficgp,")/(1");    
            fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
         for(k1=1; k1 <=nlstate; k1++){      fprintf(ficresprob,"# Age");
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
 ij=1;    fprintf(ficresprobcov,"# Age");
           for(j=3; j <=ncovmodel; j++){    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    fprintf(ficresprobcov,"# Age");
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  
             ij++;  
           }    for(i=1; i<=nlstate;i++)
           else      for(j=1; j<=(nlstate+ndeath);j++){
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
           }        fprintf(ficresprobcov," p%1d-%1d ",i,j);
           fprintf(ficgp,")");        fprintf(ficresprobcor," p%1d-%1d ",i,j);
         }      }  
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    fprintf(ficresprob,"\n");
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    fprintf(ficresprobcov,"\n");
         i=i+ncovmodel;    fprintf(ficresprobcor,"\n");
        }    xp=vector(1,npar);
      }    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
    }    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
    }    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
        first=1;
   fclose(ficgp);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
 }  /* end gnuplot */      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
       fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
       exit(0);
 /*************** Moving average **************/    }
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    else{
       fprintf(ficgp,"\n# Routine varprob");
   int i, cpt, cptcod;    }
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
       for (i=1; i<=nlstate;i++)      printf("Problem with html file: %s\n", optionfilehtm);
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
           mobaverage[(int)agedeb][i][cptcod]=0.;      exit(0);
        }
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){    else{
       for (i=1; i<=nlstate;i++){      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      fprintf(fichtm,"\n");
           for (cpt=0;cpt<=4;cpt++){  
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];      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");
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;      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");
         }  
       }    }
     }  
        cov[1]=1;
 }    tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
 /************** Forecasting ******************/    for(t=1; t<=tj;t++){
 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){      for(i1=1; i1<=ncodemax[t];i1++){ 
          j1++;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        if  (cptcovn>0) {
   int *popage;          fprintf(ficresprob, "\n#********** Variable "); 
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   double *popeffectif,*popcount;          fprintf(ficresprob, "**********\n#");
   double ***p3mat;          fprintf(ficresprobcov, "\n#********** Variable "); 
   char fileresf[FILENAMELENGTH];          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#");
  agelim=AGESUP;          
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;          fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          fprintf(ficgp, "**********\n#");
            
            
   strcpy(fileresf,"f");          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   strcat(fileresf,fileres);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   if((ficresf=fopen(fileresf,"w"))==NULL) {          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     printf("Problem with forecast resultfile: %s\n", fileresf);          
   }          fprintf(ficresprobcor, "\n#********** Variable ");    
   printf("Computing forecasting: result on file '%s' \n", fileresf);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#");    
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        }
         
   if (mobilav==1) {        for (age=bage; age<=fage; age ++){ 
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          cov[2]=age;
     movingaverage(agedeb, fage, ageminpar, mobaverage);          for (k=1; k<=cptcovn;k++) {
   }            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }
   stepsize=(int) (stepm+YEARM-1)/YEARM;          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   if (stepm<=12) stepsize=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]]];
   agelim=AGESUP;          
            gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   hstepm=1;          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   hstepm=hstepm/stepm;          gp=vector(1,(nlstate)*(nlstate+ndeath));
   yp1=modf(dateintmean,&yp);          gm=vector(1,(nlstate)*(nlstate+ndeath));
   anprojmean=yp;      
   yp2=modf((yp1*12),&yp);          for(theta=1; theta <=npar; theta++){
   mprojmean=yp;            for(i=1; i<=npar; i++)
   yp1=modf((yp2*30.5),&yp);              xp[i] = x[i] + (i==theta ?delti[theta]:0);
   jprojmean=yp;            
   if(jprojmean==0) jprojmean=1;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   if(mprojmean==0) jprojmean=1;            
              k=0;
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);            for(i=1; i<= (nlstate); i++){
                for(j=1; j<=(nlstate+ndeath);j++){
   for(cptcov=1;cptcov<=i2;cptcov++){                k=k+1;
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                gp[k]=pmmij[i][j];
       k=k+1;              }
       fprintf(ficresf,"\n#******");            }
       for(j=1;j<=cptcoveff;j++) {            
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            for(i=1; i<=npar; i++)
       }              xp[i] = x[i] - (i==theta ?delti[theta]:0);
       fprintf(ficresf,"******\n");      
       fprintf(ficresf,"# StartingAge FinalAge");            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);            k=0;
                  for(i=1; i<=(nlstate); i++){
                    for(j=1; j<=(nlstate+ndeath);j++){
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {                k=k+1;
         fprintf(ficresf,"\n");                gm[k]=pmmij[i][j];
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);                }
             }
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){       
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
           nhstepm = nhstepm/hstepm;              gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
                    }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              for(theta=1; theta <=npar; theta++)
                      trgradg[j][theta]=gradg[theta][j];
           for (h=0; h<=nhstepm; h++){          
             if (h==(int) (calagedate+YEARM*cpt)) {          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
             }          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
             for(j=1; j<=nlstate+ndeath;j++) {          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
               kk1=0.;kk2=0;          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
               for(i=1; i<=nlstate;i++) {                        free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
                 if (mobilav==1)  
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          pmij(pmmij,cov,ncovmodel,x,nlstate);
                 else {          
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          k=0;
                 }          for(i=1; i<=(nlstate); i++){
                            for(j=1; j<=(nlstate+ndeath);j++){
               }              k=k+1;
               if (h==(int)(calagedate+12*cpt)){              mu[k][(int) age]=pmmij[i][j];
                 fprintf(ficresf," %.3f", kk1);            }
                                  }
               }          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             }            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
           }              varpij[i][j][(int)age] = doldm[i][j];
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }          /*printf("\n%d ",(int)age);
       }            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     }            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   }            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                    }*/
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
           fprintf(ficresprob,"\n%d ",(int)age);
   fclose(ficresf);          fprintf(ficresprobcov,"\n%d ",(int)age);
 }          fprintf(ficresprobcor,"\n%d ",(int)age);
 /************** 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){          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
              fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   int *popage;            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
   double *popeffectif,*popcount;          }
   double ***p3mat,***tabpop,***tabpopprev;          i=0;
   char filerespop[FILENAMELENGTH];          for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              i=i++;
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   agelim=AGESUP;              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;              for (j=1; j<=i;j++){
                  fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
                }
              }
   strcpy(filerespop,"pop");          }/* end of loop for state */
   strcat(filerespop,fileres);        } /* end of loop for age */
   if((ficrespop=fopen(filerespop,"w"))==NULL) {  
     printf("Problem with forecast resultfile: %s\n", filerespop);        /* Confidence intervalle of pij  */
   }        /*
   printf("Computing forecasting: result on file '%s' \n", filerespop);          fprintf(ficgp,"\nset noparametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
   if (mobilav==1) {          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
     movingaverage(agedeb, fage, ageminpar, mobaverage);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
   }        */
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
   if (stepm<=12) stepsize=1;        first1=1;
          for (k2=1; k2<=(nlstate);k2++){
   agelim=AGESUP;          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
              if(l2==k2) continue;
   hstepm=1;            j=(k2-1)*(nlstate+ndeath)+l2;
   hstepm=hstepm/stepm;            for (k1=1; k1<=(nlstate);k1++){
                for (l1=1; l1<=(nlstate+ndeath);l1++){ 
   if (popforecast==1) {                if(l1==k1) continue;
     if((ficpop=fopen(popfile,"r"))==NULL) {                i=(k1-1)*(nlstate+ndeath)+l1;
       printf("Problem with population file : %s\n",popfile);exit(0);                if(i<=j) continue;
     }                for (age=bage; age<=fage; age ++){ 
     popage=ivector(0,AGESUP);                  if ((int)age %5==0){
     popeffectif=vector(0,AGESUP);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
     popcount=vector(0,AGESUP);                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                        cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
     i=1;                      mu1=mu[i][(int) age]/stepm*YEARM ;
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;                    mu2=mu[j][(int) age]/stepm*YEARM;
                        c12=cv12/sqrt(v1*v2);
     imx=i;                    /* Computing eigen value of matrix of covariance */
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   }                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* Eigen vectors */
   for(cptcov=1;cptcov<=i2;cptcov++){                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                    /*v21=sqrt(1.-v11*v11); *//* error */
       k=k+1;                    v21=(lc1-v1)/cv12*v11;
       fprintf(ficrespop,"\n#******");                    v12=-v21;
       for(j=1;j<=cptcoveff;j++) {                    v22=v11;
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    tnalp=v21/v11;
       }                    if(first1==1){
       fprintf(ficrespop,"******\n");                      first1=0;
       fprintf(ficrespop,"# Age");                      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);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);                    }
       if (popforecast==1)  fprintf(ficrespop," [Population]");                    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*/
       for (cpt=0; cpt<=0;cpt++) {                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                      /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                            if(first==1){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){                      first=0;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);                      fprintf(ficgp,"\nset parametric;unset label");
           nhstepm = nhstepm/hstepm;                      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);
                                fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                      fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
           oldm=oldms;savm=savms;                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                        fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                              fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
           for (h=0; h<=nhstepm; h++){                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
             if (h==(int) (calagedate+YEARM*cpt)) {                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
             }                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
             for(j=1; j<=nlstate+ndeath;j++) {                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
               kk1=0.;kk2=0;                    }else{
               for(i=1; i<=nlstate;i++) {                                    first=0;
                 if (mobilav==1)                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                 else {                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];                      fprintf(ficgp,"\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",\
                 }                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
               }                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
               if (h==(int)(calagedate+12*cpt)){                    }/* if first */
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;                  } /* age mod 5 */
                   /*fprintf(ficrespop," %.3f", kk1);                } /* end loop age */
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
               }                first=1;
             }              } /*l12 */
             for(i=1; i<=nlstate;i++){            } /* k12 */
               kk1=0.;          } /*l1 */
                 for(j=1; j<=nlstate;j++){        }/* k1 */
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];      } /* loop covariates */
                 }    }
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
             }    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_vector(xp,1,npar);
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    fclose(ficresprob);
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    fclose(ficresprobcov);
           }    fclose(ficresprobcor);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fclose(ficgp);
         }    fclose(fichtm);
       }  }
    
   /******/  
   /******************* Printing html file ***********/
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                      int lastpass, int stepm, int weightopt, char model[],\
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);                    int popforecast, int estepm ,\
           nhstepm = nhstepm/hstepm;                    double jprev1, double mprev1,double anprev1, \
                              double jprev2, double mprev2,double anprev2){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int jj1, k1, i1, cpt;
           oldm=oldms;savm=savms;    /*char optionfilehtm[FILENAMELENGTH];*/
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
           for (h=0; h<=nhstepm; h++){      printf("Problem with %s \n",optionfilehtm), exit(0);
             if (h==(int) (calagedate+YEARM*cpt)) {      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    }
             }  
             for(j=1; j<=nlstate+ndeath;j++) {     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
               kk1=0.;kk2=0;   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
               for(i=1; i<=nlstate;i++) {                 - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];       - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
               }   - Life expectancies by age and initial health status (estepm=%2d months): 
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);     <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);
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
         }  
       }   m=cptcoveff;
    }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   }  
     jj1=0;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
   if (popforecast==1) {       jj1++;
     free_ivector(popage,0,AGESUP);       if (cptcovn > 0) {
     free_vector(popeffectif,0,AGESUP);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     free_vector(popcount,0,AGESUP);         for (cpt=1; cpt<=cptcoveff;cpt++) 
   }           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       }
   fclose(ficrespop);       /* 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>
   <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
 /***********************************************/       /* Quasi-incidences */
 /**************** Main Program *****************/       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 */
 int main(int argc, char *argv[])         for(cpt=1; cpt<nlstate;cpt++){
 {           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
   <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;         }
   double agedeb, agefin,hf;       for(cpt=1; cpt<=nlstate;cpt++) {
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
   <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
   double fret;       }
   double **xi,tmp,delta;       fprintf(fichtm,"\n<br>- Total life expectancy by age and
   health expectancies in states (1) and (2): e%s%d.png<br>
   double dum; /* Dummy variable */  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
   double ***p3mat;     } /* end i1 */
   int *indx;   }/* End k1 */
   char line[MAXLINE], linepar[MAXLINE];   fprintf(fichtm,"</ul>");
   char title[MAXLINE];  
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
     - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
    - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
   char filerest[FILENAMELENGTH];   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
   char fileregp[FILENAMELENGTH];   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
   char popfile[FILENAMELENGTH];   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];   - 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);
   int firstobs=1, lastobs=10;  
   int sdeb, sfin; /* Status at beginning and end */   if(popforecast==1) fprintf(fichtm,"\n
   int c,  h , cpt,l;   - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
   int ju,jl, mi;   - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;          <br>",fileres,fileres,fileres,fileres);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;   else 
   int mobilav=0,popforecast=0;     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);
   int hstepm, nhstepm;  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;  
    m=cptcoveff;
   double bage, fage, age, agelim, agebase;   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   double ftolpl=FTOL;  
   double **prlim;   jj1=0;
   double *severity;   for(k1=1; k1<=m;k1++){
   double ***param; /* Matrix of parameters */     for(i1=1; i1<=ncodemax[k1];i1++){
   double  *p;       jj1++;
   double **matcov; /* Matrix of covariance */       if (cptcovn > 0) {
   double ***delti3; /* Scale */         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   double *delti; /* Scale */         for (cpt=1; cpt<=cptcoveff;cpt++) 
   double ***eij, ***vareij;           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   double **varpl; /* Variances of prevalence limits by age */         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   double *epj, vepp;       }
   double kk1, kk2;       for(cpt=1; cpt<=nlstate;cpt++) {
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;         fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
    interval) in state (%d): v%s%d%d.png <br>
   <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
   char version[80]="Imach version 0.8a, May 2002, INED-EUROREVES ";       }
   char *alph[]={"a","a","b","c","d","e"}, str[4];     } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   char z[1]="c", occ;  fclose(fichtm);
 #include <sys/time.h>  }
 #include <time.h>  
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  /******************* Gnuplot file **************/
    void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   /* long total_usecs;  
   struct timeval start_time, end_time;    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
      int ng;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   getcwd(pathcd, size);      printf("Problem with file %s",optionfilegnuplot);
       fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
   printf("\n%s",version);    }
   if(argc <=1){  
     printf("\nEnter the parameter file name: ");    /*#ifdef windows */
     scanf("%s",pathtot);      fprintf(ficgp,"cd \"%s\" \n",pathc);
   }      /*#endif */
   else{  m=pow(2,cptcoveff);
     strcpy(pathtot,argv[1]);    
   }   /* 1eme*/
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    for (cpt=1; cpt<= nlstate ; cpt ++) {
   /*cygwin_split_path(pathtot,path,optionfile);     for (k1=1; k1<= m ; k1 ++) {
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
   /* cutv(path,optionfile,pathtot,'\\');*/       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);
   
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);       for (i=1; i<= nlstate ; i ++) {
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   chdir(path);         else fprintf(ficgp," \%%*lf (\%%*lf)");
   replace(pathc,path);       }
        fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
 /*-------- arguments in the command line --------*/       for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   strcpy(fileres,"r");         else fprintf(ficgp," \%%*lf (\%%*lf)");
   strcat(fileres, optionfilefiname);       } 
   strcat(fileres,".txt");    /* Other files have txt extension */       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
   /*---------arguments file --------*/         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
   if((ficpar=fopen(optionfile,"r"))==NULL)    {       }  
     printf("Problem with optionfile %s\n",optionfile);       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
     goto end;     }
   }    }
     /*2 eme*/
   strcpy(filereso,"o");    
   strcat(filereso,fileres);    for (k1=1; k1<= m ; k1 ++) { 
   if((ficparo=fopen(filereso,"w"))==NULL) {      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
   }      
       for (i=1; i<= nlstate+1 ; i ++) {
   /* Reads comments: lines beginning with '#' */        k=2*i;
   while((c=getc(ficpar))=='#' && c!= EOF){        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
     ungetc(c,ficpar);        for (j=1; j<= nlstate+1 ; j ++) {
     fgets(line, MAXLINE, ficpar);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     puts(line);          else fprintf(ficgp," \%%*lf (\%%*lf)");
     fputs(line,ficparo);        }   
   }        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
   ungetc(c,ficpar);        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,"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);        for (j=1; j<= nlstate+1 ; j ++) {
   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);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   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);          else fprintf(ficgp," \%%*lf (\%%*lf)");
 while((c=getc(ficpar))=='#' && c!= EOF){        }   
     ungetc(c,ficpar);        fprintf(ficgp,"\" t\"\" w l 0,");
     fgets(line, MAXLINE, ficpar);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
     puts(line);        for (j=1; j<= nlstate+1 ; j ++) {
     fputs(line,ficparo);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   }          else fprintf(ficgp," \%%*lf (\%%*lf)");
   ungetc(c,ficpar);        }   
          if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
            else fprintf(ficgp,"\" t\"\" w l 0,");
   covar=matrix(0,NCOVMAX,1,n);      }
   cptcovn=0;    }
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    
     /*3eme*/
   ncovmodel=2+cptcovn;    
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    for (k1=1; k1<= m ; k1 ++) { 
        for (cpt=1; cpt<= nlstate ; cpt ++) {
   /* Read guess parameters */        k=2+nlstate*(2*cpt-2);
   /* Reads comments: lines beginning with '#' */        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
   while((c=getc(ficpar))=='#' && c!= EOF){        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
     ungetc(c,ficpar);        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     fgets(line, MAXLINE, ficpar);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     puts(line);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     fputs(line,ficparo);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   }          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
   ungetc(c,ficpar);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
            
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        */
     for(i=1; i <=nlstate; i++)        for (i=1; i< nlstate ; i ++) {
     for(j=1; j <=nlstate+ndeath-1; j++){          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);
       fscanf(ficpar,"%1d%1d",&i1,&j1);          
       fprintf(ficparo,"%1d%1d",i1,j1);        } 
       printf("%1d%1d",i,j);      }
       for(k=1; k<=ncovmodel;k++){    }
         fscanf(ficpar," %lf",&param[i][j][k]);    
         printf(" %lf",param[i][j][k]);    /* CV preval stat */
         fprintf(ficparo," %lf",param[i][j][k]);    for (k1=1; k1<= m ; k1 ++) { 
       }      for (cpt=1; cpt<nlstate ; cpt ++) {
       fscanf(ficpar,"\n");        k=3;
       printf("\n");        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
       fprintf(ficparo,"\n");        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
     }        
          for (i=1; i< nlstate ; i ++)
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;          fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
   p=param[1][1];        
          l=3+(nlstate+ndeath)*cpt;
   /* Reads comments: lines beginning with '#' */        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
   while((c=getc(ficpar))=='#' && c!= EOF){        for (i=1; i< nlstate ; i ++) {
     ungetc(c,ficpar);          l=3+(nlstate+ndeath)*cpt;
     fgets(line, MAXLINE, ficpar);          fprintf(ficgp,"+$%d",l+i+1);
     puts(line);        }
     fputs(line,ficparo);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
   }      } 
   ungetc(c,ficpar);    }  
     
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    /* proba elementaires */
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    for(i=1,jk=1; i <=nlstate; i++){
   for(i=1; i <=nlstate; i++){      for(k=1; k <=(nlstate+ndeath); k++){
     for(j=1; j <=nlstate+ndeath-1; j++){        if (k != i) {
       fscanf(ficpar,"%1d%1d",&i1,&j1);          for(j=1; j <=ncovmodel; j++){
       printf("%1d%1d",i,j);            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
       fprintf(ficparo,"%1d%1d",i1,j1);            jk++; 
       for(k=1; k<=ncovmodel;k++){            fprintf(ficgp,"\n");
         fscanf(ficpar,"%le",&delti3[i][j][k]);          }
         printf(" %le",delti3[i][j][k]);        }
         fprintf(ficparo," %le",delti3[i][j][k]);      }
       }     }
       fscanf(ficpar,"\n");  
       printf("\n");     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
       fprintf(ficparo,"\n");       for(jk=1; jk <=m; jk++) {
     }         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
   }         if (ng==2)
   delti=delti3[1][1];           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
           else
   /* Reads comments: lines beginning with '#' */           fprintf(ficgp,"\nset title \"Probability\"\n");
   while((c=getc(ficpar))=='#' && c!= EOF){         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
     ungetc(c,ficpar);         i=1;
     fgets(line, MAXLINE, ficpar);         for(k2=1; k2<=nlstate; k2++) {
     puts(line);           k3=i;
     fputs(line,ficparo);           for(k=1; k<=(nlstate+ndeath); k++) {
   }             if (k != k2){
   ungetc(c,ficpar);               if(ng==2)
                   fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
   matcov=matrix(1,npar,1,npar);               else
   for(i=1; i <=npar; i++){                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
     fscanf(ficpar,"%s",&str);               ij=1;
     printf("%s",str);               for(j=3; j <=ncovmodel; j++) {
     fprintf(ficparo,"%s",str);                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
     for(j=1; j <=i; j++){                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
       fscanf(ficpar," %le",&matcov[i][j]);                   ij++;
       printf(" %.5le",matcov[i][j]);                 }
       fprintf(ficparo," %.5le",matcov[i][j]);                 else
     }                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
     fscanf(ficpar,"\n");               }
     printf("\n");               fprintf(ficgp,")/(1");
     fprintf(ficparo,"\n");               
   }               for(k1=1; k1 <=nlstate; k1++){   
   for(i=1; i <=npar; i++)                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
     for(j=i+1;j<=npar;j++)                 ij=1;
       matcov[i][j]=matcov[j][i];                 for(j=3; j <=ncovmodel; j++){
                       if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   printf("\n");                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
     /*-------- Rewriting paramater file ----------*/                   else
      strcpy(rfileres,"r");    /* "Rparameterfile */                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/                 }
      strcat(rfileres,".");    /* */                 fprintf(ficgp,")");
      strcat(rfileres,optionfilext);    /* Other files have txt extension */               }
     if((ficres =fopen(rfileres,"w"))==NULL) {               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
       printf("Problem writing new parameter file: %s\n", fileres);goto end;               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
     }               i=i+ncovmodel;
     fprintf(ficres,"#%s\n",version);             }
               } /* end k */
     /*-------- data file ----------*/         } /* end k2 */
     if((fic=fopen(datafile,"r"))==NULL)    {       } /* end jk */
       printf("Problem with datafile: %s\n", datafile);goto end;     } /* end ng */
     }     fclose(ficgp); 
   }  /* end gnuplot */
     n= lastobs;  
     severity = vector(1,maxwav);  
     outcome=imatrix(1,maxwav+1,1,n);  /*************** Moving average **************/
     num=ivector(1,n);  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
     moisnais=vector(1,n);  
     annais=vector(1,n);    int i, cpt, cptcod;
     moisdc=vector(1,n);    int modcovmax =1;
     andc=vector(1,n);    int mobilavrange, mob;
     agedc=vector(1,n);    double age;
     cod=ivector(1,n);  
     weight=vector(1,n);    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */                             a covariate has 2 modalities */
     mint=matrix(1,maxwav,1,n);    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
     anint=matrix(1,maxwav,1,n);  
     s=imatrix(1,maxwav+1,1,n);    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
     adl=imatrix(1,maxwav+1,1,n);          if(mobilav==1) mobilavrange=5; /* default */
     tab=ivector(1,NCOVMAX);      else mobilavrange=mobilav;
     ncodemax=ivector(1,8);      for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
     i=1;          for (cptcod=1;cptcod<=modcovmax;cptcod++)
     while (fgets(line, MAXLINE, fic) != NULL)    {            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       if ((i >= firstobs) && (i <=lastobs)) {      /* 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
         for (j=maxwav;j>=1;j--){         we use a 5 terms etc. until the borders are no more concerned. 
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);      */ 
           strcpy(line,stra);      for (mob=3;mob <=mobilavrange;mob=mob+2){
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          for (i=1; i<=nlstate;i++){
         }            for (cptcod=1;cptcod<=modcovmax;cptcod++){
                      mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);                for (cpt=1;cpt<=(mob-1)/2;cpt++){
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);                }
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);          }
         for (j=ncovcol;j>=1;j--){        }/* end age */
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      }/* end mob */
         }    }else return -1;
         num[i]=atol(stra);    return 0;
          }/* End movingaverage */
         /*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;}*/  
   /************** Forecasting ******************/
         i=i+1;  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 cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     /* printf("ii=%d", ij);    int *popage;
        scanf("%d",i);*/    double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
   imx=i-1; /* Number of individuals */    double *popeffectif,*popcount;
     double ***p3mat;
   /* for (i=1; i<=imx; i++){    double ***mobaverage;
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    char fileresf[FILENAMELENGTH];
     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;   agelim=AGESUP;
     }*/   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
    /*  for (i=1; i<=imx; i++){  
      if (s[4][i]==9)  s[4][i]=-1;    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
      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]));}*/   
     
      strcpy(fileresf,"f"); 
   /* Calculation of the number of parameter from char model*/    strcat(fileresf,fileres);
   Tvar=ivector(1,15);    if((ficresf=fopen(fileresf,"w"))==NULL) {
   Tprod=ivector(1,15);      printf("Problem with forecast resultfile: %s\n", fileresf);
   Tvaraff=ivector(1,15);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
   Tvard=imatrix(1,15,1,2);    }
   Tage=ivector(1,15);          printf("Computing forecasting: result on file '%s' \n", fileresf);
        fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   if (strlen(model) >1){  
     j=0, j1=0, k1=1, k2=1;    if (cptcoveff==0) ncodemax[cptcoveff]=1;
     j=nbocc(model,'+');  
     j1=nbocc(model,'*');    if (mobilav!=0) {
     cptcovn=j+1;      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     cptcovprod=j1;      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
            fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     strcpy(modelsav,model);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      }
       printf("Error. Non available option model=%s ",model);    }
       goto end;  
     }    stepsize=(int) (stepm+YEARM-1)/YEARM;
        if (stepm<=12) stepsize=1;
     for(i=(j+1); i>=1;i--){    
       cutv(stra,strb,modelsav,'+');    agelim=AGESUP;
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    hstepm=1;
       /*scanf("%d",i);*/    hstepm=hstepm/stepm; 
       if (strchr(strb,'*')) {    yp1=modf(dateintmean,&yp);
         cutv(strd,strc,strb,'*');    anprojmean=yp;
         if (strcmp(strc,"age")==0) {    yp2=modf((yp1*12),&yp);
           cptcovprod--;    mprojmean=yp;
           cutv(strb,stre,strd,'V');    yp1=modf((yp2*30.5),&yp);
           Tvar[i]=atoi(stre);    jprojmean=yp;
           cptcovage++;    if(jprojmean==0) jprojmean=1;
             Tage[cptcovage]=i;    if(mprojmean==0) jprojmean=1;
             /*printf("stre=%s ", stre);*/    
         }    fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean); 
         else if (strcmp(strd,"age")==0) {    
           cptcovprod--;    for(cptcov=1;cptcov<=i2;cptcov++){
           cutv(strb,stre,strc,'V');      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
           Tvar[i]=atoi(stre);        k=k+1;
           cptcovage++;        fprintf(ficresf,"\n#******");
           Tage[cptcovage]=i;        for(j=1;j<=cptcoveff;j++) {
         }          fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         else {        }
           cutv(strb,stre,strc,'V');        fprintf(ficresf,"******\n");
           Tvar[i]=ncovcol+k1;        fprintf(ficresf,"# StartingAge FinalAge");
           cutv(strb,strc,strd,'V');        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
           Tprod[k1]=i;        
           Tvard[k1][1]=atoi(strc);        
           Tvard[k1][2]=atoi(stre);        for (cpt=0; cpt<=(anproj2-anproj1);cpt++) { 
           Tvar[cptcovn+k2]=Tvard[k1][1];          fprintf(ficresf,"\n");
           Tvar[cptcovn+k2+1]=Tvard[k1][2];          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);   
           for (k=1; k<=lastobs;k++)  
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
           k1++;            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
           k2=k2+2;            nhstepm = nhstepm/hstepm; 
         }            
       }            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       else {            oldm=oldms;savm=savms;
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
        /*  scanf("%d",i);*/          
       cutv(strd,strc,strb,'V');            for (h=0; h<=nhstepm; h++){
       Tvar[i]=atoi(strc);              if (h==(int) (calagedate+YEARM*cpt)) {
       }                fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
       strcpy(modelsav,stra);                } 
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);              for(j=1; j<=nlstate+ndeath;j++) {
         scanf("%d",i);*/                kk1=0.;kk2=0;
     }                for(i=1; i<=nlstate;i++) {              
 }                  if (mobilav==1) 
                      kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);                  else {
   printf("cptcovprod=%d ", cptcovprod);                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
   scanf("%d ",i);*/                  }
     fclose(fic);                  
                 }
     /*  if(mle==1){*/                if (h==(int)(calagedate+12*cpt)){
     if (weightopt != 1) { /* Maximisation without weights*/                  fprintf(ficresf," %.3f", kk1);
       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);            }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     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 (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;  
       }    fclose(ficresf);
     }  }
   /************** Forecasting ******************/
     for (i=1; i<=imx; i++)  {  populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    
       for(m=1; (m<= maxwav); m++){    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
         if(s[m][i] >0){    int *popage;
           if (s[m][i] >= nlstate+1) {    double calagedate, agelim, kk1, kk2;
             if(agedc[i]>0)    double *popeffectif,*popcount;
               if(moisdc[i]!=99 && andc[i]!=9999)    double ***p3mat,***tabpop,***tabpopprev;
                 agev[m][i]=agedc[i];    double ***mobaverage;
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/    char filerespop[FILENAMELENGTH];
            else {  
               if (andc[i]!=9999){    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
               agev[m][i]=-1;    agelim=AGESUP;
               }    calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
             }    
           }    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
           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)    strcpy(filerespop,"pop"); 
               agev[m][i]=1;    strcat(filerespop,fileres);
             else if(agev[m][i] <agemin){    if((ficrespop=fopen(filerespop,"w"))==NULL) {
               agemin=agev[m][i];      printf("Problem with forecast resultfile: %s\n", filerespop);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
             }    }
             else if(agev[m][i] >agemax){    printf("Computing forecasting: result on file '%s' \n", filerespop);
               agemax=agev[m][i];    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  
             }    if (cptcoveff==0) ncodemax[cptcoveff]=1;
             /*agev[m][i]=anint[m][i]-annais[i];*/  
             /*   agev[m][i] = age[i]+2*m;*/    if (mobilav!=0) {
           }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           else { /* =9 */      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
             agev[m][i]=1;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
             s[m][i]=-1;        printf(" Error in movingaverage mobilav=%d\n",mobilav);
           }      }
         }    }
         else /*= 0 Unknown */  
           agev[m][i]=1;    stepsize=(int) (stepm+YEARM-1)/YEARM;
       }    if (stepm<=12) stepsize=1;
        
     }    agelim=AGESUP;
     for (i=1; i<=imx; i++)  {    
       for(m=1; (m<= maxwav); m++){    hstepm=1;
         if (s[m][i] > (nlstate+ndeath)) {    hstepm=hstepm/stepm; 
           printf("Error: Wrong value in nlstate or ndeath\n");      
           goto end;    if (popforecast==1) {
         }      if((ficpop=fopen(popfile,"r"))==NULL) {
       }        printf("Problem with population file : %s\n",popfile);exit(0);
     }        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);      popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
     free_vector(severity,1,maxwav);      popcount=vector(0,AGESUP);
     free_imatrix(outcome,1,maxwav+1,1,n);      
     free_vector(moisnais,1,n);      i=1;   
     free_vector(annais,1,n);      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
     /* free_matrix(mint,1,maxwav,1,n);     
        free_matrix(anint,1,maxwav,1,n);*/      imx=i;
     free_vector(moisdc,1,n);      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     free_vector(andc,1,n);    }
   
        for(cptcov=1;cptcov<=i2;cptcov++){
     wav=ivector(1,imx);     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
     dh=imatrix(1,lastpass-firstpass+1,1,imx);        k=k+1;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);        fprintf(ficrespop,"\n#******");
            for(j=1;j<=cptcoveff;j++) {
     /* Concatenates waves */          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);        }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
       Tcode=ivector(1,100);        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);        if (popforecast==1)  fprintf(ficrespop," [Population]");
       ncodemax[1]=1;        
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);        for (cpt=0; cpt<=0;cpt++) { 
                fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
    codtab=imatrix(1,100,1,10);          
    h=0;          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
    m=pow(2,cptcoveff);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
              nhstepm = nhstepm/hstepm; 
    for(k=1;k<=cptcoveff; k++){            
      for(i=1; i <=(m/pow(2,k));i++){            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        for(j=1; j <= ncodemax[k]; j++){            oldm=oldms;savm=savms;
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
            h++;          
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;            for (h=0; h<=nhstepm; h++){
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/              if (h==(int) (calagedate+YEARM*cpt)) {
          }                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
        }              } 
      }              for(j=1; j<=nlstate+ndeath;j++) {
    }                kk1=0.;kk2=0;
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);                for(i=1; i<=nlstate;i++) {              
       codtab[1][2]=1;codtab[2][2]=2; */                  if (mobilav==1) 
    /* for(i=1; i <=m ;i++){                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
       for(k=1; k <=cptcovn; k++){                  else {
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
       }                  }
       printf("\n");                }
       }                if (h==(int)(calagedate+12*cpt)){
       scanf("%d",i);*/                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
                        /*fprintf(ficrespop," %.3f", kk1);
    /* Calculates basic frequencies. Computes observed prevalence at single age                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
        and prints on file fileres'p'. */                }
               }
                  for(i=1; i<=nlstate;i++){
                    kk1=0.;
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                  for(j=1; j<=nlstate;j++){
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                  }
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */              }
        
     /* For Powell, parameters are in a vector p[] starting at p[1]              if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) 
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */            }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     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);        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
            fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
    jk=1;            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");            nhstepm = nhstepm/hstepm; 
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");            
    for(i=1,jk=1; i <=nlstate; i++){            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      for(k=1; k <=(nlstate+ndeath); k++){            oldm=oldms;savm=savms;
        if (k != i)            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
          {            for (h=0; h<=nhstepm; h++){
            printf("%d%d ",i,k);              if (h==(int) (calagedate+YEARM*cpt)) {
            fprintf(ficres,"%1d%1d ",i,k);                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
            for(j=1; j <=ncovmodel; j++){              } 
              printf("%f ",p[jk]);              for(j=1; j<=nlstate+ndeath;j++) {
              fprintf(ficres,"%f ",p[jk]);                kk1=0.;kk2=0;
              jk++;                for(i=1; i<=nlstate;i++) {              
            }                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
            printf("\n");                }
            fprintf(ficres,"\n");                if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1); 
          }              }
      }            }
    }            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  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");    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     printf("# Scales (for hessian or gradient estimation)\n");  
      for(i=1,jk=1; i <=nlstate; i++){    if (popforecast==1) {
       for(j=1; j <=nlstate+ndeath; j++){      free_ivector(popage,0,AGESUP);
         if (j!=i) {      free_vector(popeffectif,0,AGESUP);
           fprintf(ficres,"%1d%1d",i,j);      free_vector(popcount,0,AGESUP);
           printf("%1d%1d",i,j);    }
           for(k=1; k<=ncovmodel;k++){    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
             printf(" %.5e",delti[jk]);    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
             fprintf(ficres," %.5e",delti[jk]);    fclose(ficrespop);
             jk++;  }
           }  
           printf("\n");  /***********************************************/
           fprintf(ficres,"\n");  /**************** Main Program *****************/
         }  /***********************************************/
       }  
      }  int main(int argc, char *argv[])
      {
     k=1;    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");    int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");    double agedeb, agefin,hf;
     for(i=1;i<=npar;i++){    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
       /*  if (k>nlstate) k=1;  
       i1=(i-1)/(ncovmodel*nlstate)+1;    double fret;
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    double **xi,tmp,delta;
       printf("%s%d%d",alph[k],i1,tab[i]);*/  
       fprintf(ficres,"%3d",i);    double dum; /* Dummy variable */
       printf("%3d",i);    double ***p3mat;
       for(j=1; j<=i;j++){    double ***mobaverage;
         fprintf(ficres," %.5e",matcov[i][j]);    int *indx;
         printf(" %.5e",matcov[i][j]);    char line[MAXLINE], linepar[MAXLINE];
       }    char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
       fprintf(ficres,"\n");    int firstobs=1, lastobs=10;
       printf("\n");    int sdeb, sfin; /* Status at beginning and end */
       k++;    int c,  h , cpt,l;
     }    int ju,jl, mi;
        int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     while((c=getc(ficpar))=='#' && c!= EOF){    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
       ungetc(c,ficpar);    int mobilav=0,popforecast=0;
       fgets(line, MAXLINE, ficpar);    int hstepm, nhstepm;
       puts(line);    double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
       fputs(line,ficparo);  
     }    double bage, fage, age, agelim, agebase;
     ungetc(c,ficpar);    double ftolpl=FTOL;
     estepm=0;    double **prlim;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);    double *severity;
     if (estepm==0 || estepm < stepm) estepm=stepm;    double ***param; /* Matrix of parameters */
     if (fage <= 2) {    double  *p;
       bage = ageminpar;    double **matcov; /* Matrix of covariance */
       fage = agemaxpar;    double ***delti3; /* Scale */
     }    double *delti; /* Scale */
        double ***eij, ***vareij;
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    double **varpl; /* Variances of prevalence limits by age */
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    double *epj, vepp;
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    double kk1, kk2;
      double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
     while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    char *alph[]={"a","a","b","c","d","e"}, str[4];
     fgets(line, MAXLINE, ficpar);  
     puts(line);  
     fputs(line,ficparo);    char z[1]="c", occ;
   }  #include <sys/time.h>
   ungetc(c,ficpar);  #include <time.h>
      char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
   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);    /* long total_usecs;
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);       struct timeval start_time, end_time;
          
   while((c=getc(ficpar))=='#' && c!= EOF){       gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     ungetc(c,ficpar);    getcwd(pathcd, size);
     fgets(line, MAXLINE, ficpar);  
     puts(line);    printf("\n%s",version);
     fputs(line,ficparo);    if(argc <=1){
   }      printf("\nEnter the parameter file name: ");
   ungetc(c,ficpar);      scanf("%s",pathtot);
      }
     else{
    dateprev1=anprev1+mprev1/12.+jprev1/365.;      strcpy(pathtot,argv[1]);
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    }
     /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
   fscanf(ficpar,"pop_based=%d\n",&popbased);    /*cygwin_split_path(pathtot,path,optionfile);
   fprintf(ficparo,"pop_based=%d\n",popbased);        printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
   fprintf(ficres,"pop_based=%d\n",popbased);      /* cutv(path,optionfile,pathtot,'\\');*/
    
   while((c=getc(ficpar))=='#' && c!= EOF){    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     ungetc(c,ficpar);    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     fgets(line, MAXLINE, ficpar);    chdir(path);
     puts(line);    replace(pathc,path);
     fputs(line,ficparo);  
   }    /*-------- arguments in the command line --------*/
   ungetc(c,ficpar);  
     /* Log file */
   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);    strcat(filelog, optionfilefiname);
 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);    strcat(filelog,".log");    /* */
 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((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
 while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);    fprintf(ficlog,"Log filename:%s\n",filelog);
     fgets(line, MAXLINE, ficpar);    fprintf(ficlog,"\n%s",version);
     puts(line);    fprintf(ficlog,"\nEnter the parameter file name: ");
     fputs(line,ficparo);    fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   }    fflush(ficlog);
   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);    strcpy(fileres,"r");
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    strcat(fileres, optionfilefiname);
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    strcat(fileres,".txt");    /* Other files have txt extension */
   
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    /*---------arguments file --------*/
   
 /*------------ gnuplot -------------*/    if((ficpar=fopen(optionfile,"r"))==NULL)    {
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);      printf("Problem with optionfile %s\n",optionfile);
        fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
 /*------------ free_vector  -------------*/      goto end;
  chdir(path);    }
    
  free_ivector(wav,1,imx);    strcpy(filereso,"o");
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    strcat(filereso,fileres);
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      if((ficparo=fopen(filereso,"w"))==NULL) {
  free_ivector(num,1,n);      printf("Problem with Output resultfile: %s\n", filereso);
  free_vector(agedc,1,n);      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/      goto end;
  fclose(ficparo);    }
  fclose(ficres);  
     /* Reads comments: lines beginning with '#' */
 /*--------- index.htm --------*/    while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);      fgets(line, MAXLINE, ficpar);
       puts(line);
        fputs(line,ficparo);
   /*--------------- Prevalence limit --------------*/    }
      ungetc(c,ficpar);
   strcpy(filerespl,"pl");  
   strcat(filerespl,fileres);    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((ficrespl=fopen(filerespl,"w"))==NULL) {    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);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
   }    while((c=getc(ficpar))=='#' && c!= EOF){
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      ungetc(c,ficpar);
   fprintf(ficrespl,"#Prevalence limit\n");      fgets(line, MAXLINE, ficpar);
   fprintf(ficrespl,"#Age ");      puts(line);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      fputs(line,ficparo);
   fprintf(ficrespl,"\n");    }
      ungetc(c,ficpar);
   prlim=matrix(1,nlstate,1,nlstate);    
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */     
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    covar=matrix(0,NCOVMAX,1,n); 
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
   k=0;    ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
   agebase=ageminpar;    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
   agelim=agemaxpar;    
   ftolpl=1.e-10;    /* Read guess parameters */
   i1=cptcoveff;    /* Reads comments: lines beginning with '#' */
   if (cptcovn < 1){i1=1;}    while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
   for(cptcov=1;cptcov<=i1;cptcov++){      fgets(line, MAXLINE, ficpar);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      puts(line);
         k=k+1;      fputs(line,ficparo);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    }
         fprintf(ficrespl,"\n#******");    ungetc(c,ficpar);
         for(j=1;j<=cptcoveff;j++)    
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
         fprintf(ficrespl,"******\n");    for(i=1; i <=nlstate; i++)
              for(j=1; j <=nlstate+ndeath-1; j++){
         for (age=agebase; age<=agelim; age++){        fscanf(ficpar,"%1d%1d",&i1,&j1);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficrespl,"%.0f",age );        if(mle==1)
           for(i=1; i<=nlstate;i++)          printf("%1d%1d",i,j);
           fprintf(ficrespl," %.5f", prlim[i][i]);        fprintf(ficlog,"%1d%1d",i,j);
           fprintf(ficrespl,"\n");        for(k=1; k<=ncovmodel;k++){
         }          fscanf(ficpar," %lf",&param[i][j][k]);
       }          if(mle==1){
     }            printf(" %lf",param[i][j][k]);
   fclose(ficrespl);            fprintf(ficlog," %lf",param[i][j][k]);
           }
   /*------------- h Pij x at various ages ------------*/          else
              fprintf(ficlog," %lf",param[i][j][k]);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);          fprintf(ficparo," %lf",param[i][j][k]);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {        }
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;        fscanf(ficpar,"\n");
   }        if(mle==1)
   printf("Computing pij: result on file '%s' \n", filerespij);          printf("\n");
          fprintf(ficlog,"\n");
   stepsize=(int) (stepm+YEARM-1)/YEARM;        fprintf(ficparo,"\n");
   /*if (stepm<=24) stepsize=2;*/      }
     
   agelim=AGESUP;    npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   hstepm=stepsize*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    p=param[1][1];
      
   k=0;    /* Reads comments: lines beginning with '#' */
   for(cptcov=1;cptcov<=i1;cptcov++){    while((c=getc(ficpar))=='#' && c!= EOF){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      ungetc(c,ficpar);
       k=k+1;      fgets(line, MAXLINE, ficpar);
         fprintf(ficrespij,"\n#****** ");      puts(line);
         for(j=1;j<=cptcoveff;j++)      fputs(line,ficparo);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    }
         fprintf(ficrespij,"******\n");    ungetc(c,ficpar);
          
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    for(i=1; i <=nlstate; i++){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for(j=1; j <=nlstate+ndeath-1; j++){
           oldm=oldms;savm=savms;        fscanf(ficpar,"%1d%1d",&i1,&j1);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          printf("%1d%1d",i,j);
           fprintf(ficrespij,"# Age");        fprintf(ficparo,"%1d%1d",i1,j1);
           for(i=1; i<=nlstate;i++)        for(k=1; k<=ncovmodel;k++){
             for(j=1; j<=nlstate+ndeath;j++)          fscanf(ficpar,"%le",&delti3[i][j][k]);
               fprintf(ficrespij," %1d-%1d",i,j);          printf(" %le",delti3[i][j][k]);
           fprintf(ficrespij,"\n");          fprintf(ficparo," %le",delti3[i][j][k]);
            for (h=0; h<=nhstepm; h++){        }
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );        fscanf(ficpar,"\n");
             for(i=1; i<=nlstate;i++)        printf("\n");
               for(j=1; j<=nlstate+ndeath;j++)        fprintf(ficparo,"\n");
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);      }
             fprintf(ficrespij,"\n");    }
              }    delti=delti3[1][1];
           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);
       puts(line);
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);      fputs(line,ficparo);
     }
   fclose(ficrespij);    ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
   /*---------- Forecasting ------------------*/    for(i=1; i <=npar; i++){
   if((stepm == 1) && (strcmp(model,".")==0)){      fscanf(ficpar,"%s",&str);
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);      if(mle==1)
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);        printf("%s",str);
   }      fprintf(ficlog,"%s",str);
   else{      fprintf(ficparo,"%s",str);
     erreur=108;      for(j=1; j <=i; j++){
     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);        fscanf(ficpar," %le",&matcov[i][j]);
   }        if(mle==1){
            printf(" %.5le",matcov[i][j]);
           fprintf(ficlog," %.5le",matcov[i][j]);
   /*---------- Health expectancies and variances ------------*/        }
         else
   strcpy(filerest,"t");          fprintf(ficlog," %.5le",matcov[i][j]);
   strcat(filerest,fileres);        fprintf(ficparo," %.5le",matcov[i][j]);
   if((ficrest=fopen(filerest,"w"))==NULL) {      }
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      fscanf(ficpar,"\n");
   }      if(mle==1)
   printf("Computing Total LEs with variances: file '%s' \n", filerest);        printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
   strcpy(filerese,"e");    }
   strcat(filerese,fileres);    for(i=1; i <=npar; i++)
   if((ficreseij=fopen(filerese,"w"))==NULL) {      for(j=i+1;j<=npar;j++)
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        matcov[i][j]=matcov[j][i];
   }     
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    if(mle==1)
       printf("\n");
  strcpy(fileresv,"v");    fprintf(ficlog,"\n");
   strcat(fileresv,fileres);  
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    /*-------- Rewriting paramater file ----------*/
   }    strcpy(rfileres,"r");    /* "Rparameterfile */
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
   calagedate=-1;    strcat(rfileres,".");    /* */
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
   k=0;      printf("Problem writing new parameter file: %s\n", fileres);goto end;
   for(cptcov=1;cptcov<=i1;cptcov++){      fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    }
       k=k+1;    fprintf(ficres,"#%s\n",version);
       fprintf(ficrest,"\n#****** ");      
       for(j=1;j<=cptcoveff;j++)    /*-------- data file ----------*/
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    if((fic=fopen(datafile,"r"))==NULL)    {
       fprintf(ficrest,"******\n");      printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficreseij,"\n#****** ");    }
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    n= lastobs;
       fprintf(ficreseij,"******\n");    severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
       fprintf(ficresvij,"\n#****** ");    num=ivector(1,n);
       for(j=1;j<=cptcoveff;j++)    moisnais=vector(1,n);
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    annais=vector(1,n);
       fprintf(ficresvij,"******\n");    moisdc=vector(1,n);
     andc=vector(1,n);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    agedc=vector(1,n);
       oldm=oldms;savm=savms;    cod=ivector(1,n);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);      weight=vector(1,n);
      for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    mint=matrix(1,maxwav,1,n);
       oldm=oldms;savm=savms;    anint=matrix(1,maxwav,1,n);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);    s=imatrix(1,maxwav+1,1,n);
        tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
    
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    i=1;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    while (fgets(line, MAXLINE, fic) != NULL)    {
       fprintf(ficrest,"\n");      if ((i >= firstobs) && (i <=lastobs)) {
           
       epj=vector(1,nlstate+1);        for (j=maxwav;j>=1;j--){
       for(age=bage; age <=fage ;age++){          cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          strcpy(line,stra);
         if (popbased==1) {          cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           for(i=1; i<=nlstate;i++)          cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
             prlim[i][i]=probs[(int)age][i][k];        }
         }          
                cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         fprintf(ficrest," %4.0f",age);        cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  
           for(i=1, epj[j]=0.;i <=nlstate;i++) {        cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
             epj[j] += prlim[i][i]*eij[i][j][(int)age];        cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/  
           }        cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
           epj[nlstate+1] +=epj[j];        for (j=ncovcol;j>=1;j--){
         }          cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         for(i=1, vepp=0.;i <=nlstate;i++)        num[i]=atol(stra);
           for(j=1;j <=nlstate;j++)          
             vepp += vareij[i][j][(int)age];        /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));          printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
         for(j=1;j <=nlstate;j++){  
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));        i=i+1;
         }      }
         fprintf(ficrest,"\n");    }
       }    /* printf("ii=%d", ij);
     }       scanf("%d",i);*/
   }    imx=i-1; /* Number of individuals */
 free_matrix(mint,1,maxwav,1,n);  
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    /* for (i=1; i<=imx; i++){
     free_vector(weight,1,n);      if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
   fclose(ficreseij);      if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
   fclose(ficresvij);      if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
   fclose(ficrest);      }*/
   fclose(ficpar);     /*  for (i=1; i<=imx; i++){
   free_vector(epj,1,nlstate+1);       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]));}*/
   /*------- Variance limit prevalence------*/      
    
   strcpy(fileresvpl,"vpl");    /* Calculation of the number of parameter from char model*/
   strcat(fileresvpl,fileres);    Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    Tprod=ivector(1,15); 
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    Tvaraff=ivector(1,15); 
     exit(0);    Tvard=imatrix(1,15,1,2);
   }    Tage=ivector(1,15);      
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);     
     if (strlen(model) >1){ /* If there is at least 1 covariate */
   k=0;      j=0, j1=0, k1=1, k2=1;
   for(cptcov=1;cptcov<=i1;cptcov++){      j=nbocc(model,'+'); /* j=Number of '+' */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      j1=nbocc(model,'*'); /* j1=Number of '*' */
       k=k+1;      cptcovn=j+1; 
       fprintf(ficresvpl,"\n#****** ");      cptcovprod=j1; /*Number of products */
       for(j=1;j<=cptcoveff;j++)      
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      strcpy(modelsav,model); 
       fprintf(ficresvpl,"******\n");      if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
              printf("Error. Non available option model=%s ",model);
       varpl=matrix(1,nlstate,(int) bage, (int) fage);        fprintf(ficlog,"Error. Non available option model=%s ",model);
       oldm=oldms;savm=savms;        goto end;
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      }
     }      
  }      /* This loop fills the array Tvar from the string 'model'.*/
   
   fclose(ficresvpl);      for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
   /*---------- End : free ----------------*/        if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);        /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
          /*scanf("%d",i);*/
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);        if (strchr(strb,'*')) {  /* Model includes a product */
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);          cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
            if (strcmp(strc,"age")==0) { /* Vn*age */
              cptcovprod--;
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);            cutv(strb,stre,strd,'V');
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);            Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);            cptcovage++;
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);              Tage[cptcovage]=i;
                /*printf("stre=%s ", stre);*/
   free_matrix(matcov,1,npar,1,npar);          }
   free_vector(delti,1,npar);          else if (strcmp(strd,"age")==0) { /* or age*Vn */
   free_matrix(agev,1,maxwav,1,imx);            cptcovprod--;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);            cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
   if(erreur >0)            cptcovage++;
     printf("End of Imach with error or warning %d\n",erreur);            Tage[cptcovage]=i;
   else   printf("End of Imach\n");          }
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */          else {  /* Age is not in the model */
              cutv(strb,stre,strc,'V'); /* strc= Vn, stre is 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);*/            Tvar[i]=ncovcol+k1;
   /*printf("Total time was %d uSec.\n", total_usecs);*/            cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
   /*------ End -----------*/            Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
  end:            Tvar[cptcovn+k2]=Tvard[k1][1];
 #ifdef windows            Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
   /* chdir(pathcd);*/            for (k=1; k<=lastobs;k++) 
 #endif              covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
  /*system("wgnuplot graph.plt");*/            k1++;
  /*system("../gp37mgw/wgnuplot graph.plt");*/            k2=k2+2;
  /*system("cd ../gp37mgw");*/          }
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/        }
  strcpy(plotcmd,GNUPLOTPROGRAM);        else { /* no more sum */
  strcat(plotcmd," ");          /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
  strcat(plotcmd,optionfilegnuplot);         /*  scanf("%d",i);*/
  system(plotcmd);        cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
 #ifdef windows        }
   while (z[0] != 'q') {        strcpy(modelsav,stra);  
     /* chdir(path); */        /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");          scanf("%d",i);*/
     scanf("%s",z);      } /* end of loop + */
     if (z[0] == 'c') system("./imach");    } /* end model */
     else if (z[0] == 'e') system(optionfilehtm);    
     else if (z[0] == 'g') system(plotcmd);    /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
     else if (z[0] == 'q') exit(0);      If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   }  
 #endif    /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
 }    printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=1; (m<= maxwav); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if(moisdc[i]!=99 && andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if (andc[i]!=9999){
                   printf("Warning negative age at death: %d line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Should no more exist */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if(mint[m][i]==99 || anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=1; (m<= maxwav); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
   
       pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     jk=1;
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) 
           {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
       }
     }
     if(mle==1){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle==1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+mprev1/12.+jprev1/365.;
     dateprev2=anprev2+mprev2/12.+jprev2/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);
     fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
     fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
   
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     fclose(ficgp);
     printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfile);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
   \n
   Total number of observations=%d <br>\n
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
   <hr  size=\"2\" color=\"#EC5E5E\">
    <ul><li><h4>Parameter files</h4>\n
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
    - Log file of the run: <a href=\"%s\">%s</a><br>\n
    - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
     fclose(fichtm);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     chdir(path);
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_ivector(num,1,n);
     free_vector(agedc,1,n);
     free_matrix(covar,0,NCOVMAX,1,n);
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f",age );
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Age");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
   
     /*---------- Forecasting ------------------*/
     if((stepm == 1) && (strcmp(model,".")==0)){
       prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
       if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
     } 
     else{
       erreur=108;
       printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
       fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     calagedate=-1;
   
     prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
    
     free_matrix(matcov,1,npar,1,npar);
     free_vector(delti,1,npar);
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     fprintf(fichtm,"\n</body>");
     fclose(fichtm);
     fclose(ficgp);
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     
     /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
     /*printf("Total time was %d uSec.\n", total_usecs);*/
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting: %s\n",plotcmd);fflush(stdout);
     system(plotcmd);
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   

Removed from v.1.41  
changed lines
  Added in v.1.62


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