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version 1.41.2.1, 2003/06/12 10:43:20 version 1.74, 2003/05/02 18:51:41
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, quarter,
   semester or year) is model as a multinomial logistic.  The hPx    semester or year) is modelled 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 .
   **********************************************************************/  
      Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #include <math.h>    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #include <stdio.h>    
 #include <stdlib.h>    **********************************************************************/
 #include <unistd.h>  /*
     main
 #define MAXLINE 256    read parameterfile
 #define GNUPLOTPROGRAM "wgnuplot"    read datafile
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    concatwav
 #define FILENAMELENGTH 80    if (mle >= 1)
 /*#define DEBUG*/      mlikeli
     print results files
 /*#define windows*/    if mle==1 
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */       computes hessian
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    read end of parameter file: agemin, agemax, bage, fage, estepm
         begin-prev-date,...
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    open gnuplot file
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    open html file
     stable prevalence
 #define NINTERVMAX 8     for age prevalim()
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    h Pij x
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    variance of p varprob
 #define NCOVMAX 8 /* Maximum number of covariates */    forecasting if prevfcast==1 prevforecast call prevalence()
 #define MAXN 20000    health expectancies
 #define YEARM 12. /* Number of months per year */    Variance-covariance of DFLE
 #define AGESUP 130    prevalence()
 #define AGEBASE 40     movingaverage()
     varevsij() 
     if popbased==1 varevsij(,popbased)
 int erreur; /* Error number */    total life expectancies
 int nvar;    Variance of stable prevalence
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;   end
 int npar=NPARMAX;  */
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;   
   #include <math.h>
 int *wav; /* Number of waves for this individuual 0 is possible */  #include <stdio.h>
 int maxwav; /* Maxim number of waves */  #include <stdlib.h>
 int jmin, jmax; /* min, max spacing between 2 waves */  #include <unistd.h>
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  #define MAXLINE 256
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  #define GNUPLOTPROGRAM "gnuplot"
 double jmean; /* Mean space between 2 waves */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 double **oldm, **newm, **savm; /* Working pointers to matrices */  #define FILENAMELENGTH 80
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  /*#define DEBUG*/
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  #define windows
 FILE *ficgp,*ficresprob,*ficpop;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 FILE *ficreseij;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   char fileresv[FILENAMELENGTH];  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];  #define NINTERVMAX 8
   #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #define NR_END 1  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #define FREE_ARG char*  #define NCOVMAX 8 /* Maximum number of covariates */
 #define FTOL 1.0e-10  #define MAXN 20000
   #define YEARM 12. /* Number of months per year */
 #define NRANSI  #define AGESUP 130
 #define ITMAX 200  #define AGEBASE 40
   #ifdef windows
 #define TOL 2.0e-4  #define DIRSEPARATOR '\\'
   #define ODIRSEPARATOR '/'
 #define CGOLD 0.3819660  #else
 #define ZEPS 1.0e-10  #define DIRSEPARATOR '/'
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  #define ODIRSEPARATOR '\\'
   #endif
 #define GOLD 1.618034  
 #define GLIMIT 100.0  char version[80]="Imach version 0.95, February 2003, INED-EUROREVES ";
 #define TINY 1.0e-20  int erreur; /* Error number */
   int nvar;
 static double maxarg1,maxarg2;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  int npar=NPARMAX;
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  int nlstate=2; /* Number of live states */
    int ndeath=1; /* Number of dead states */
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 #define rint(a) floor(a+0.5)  int popbased=0;
   
 static double sqrarg;  int *wav; /* Number of waves for this individuual 0 is possible */
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  int maxwav; /* Maxim number of waves */
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  int jmin, jmax; /* min, max spacing between 2 waves */
   int mle, weightopt;
 int imx;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 int stepm;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 /* Stepm, step in month: minimum step interpolation*/  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
              * wave mi and wave mi+1 is not an exact multiple of stepm. */
 int estepm;  double jmean; /* Mean space between 2 waves */
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  double **oldm, **newm, **savm; /* Working pointers to matrices */
   double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 int m,nb;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  FILE *ficlog;
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 double **pmmij, ***probs, ***mobaverage;  FILE *ficresprobmorprev;
 double dateintmean=0;  FILE *fichtm; /* Html File */
   FILE *ficreseij;
 double *weight;  char filerese[FILENAMELENGTH];
 int **s; /* Status */  FILE  *ficresvij;
 double *agedc, **covar, idx;  char fileresv[FILENAMELENGTH];
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  FILE  *ficresvpl;
   char fileresvpl[FILENAMELENGTH];
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  char title[MAXLINE];
 double ftolhess; /* Tolerance for computing hessian */  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 {  char filelog[FILENAMELENGTH]; /* Log file */
    char *s;                             /* pointer */  char filerest[FILENAMELENGTH];
    int  l1, l2;                         /* length counters */  char fileregp[FILENAMELENGTH];
   char popfile[FILENAMELENGTH];
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
 #ifdef windows  
    s = strrchr( path, '\\' );           /* find last / */  #define NR_END 1
 #else  #define FREE_ARG char*
    s = strrchr( path, '/' );            /* find last / */  #define FTOL 1.0e-10
 #endif  
    if ( s == NULL ) {                   /* no directory, so use current */  #define NRANSI 
 #if     defined(__bsd__)                /* get current working directory */  #define ITMAX 200 
       extern char       *getwd( );  
   #define TOL 2.0e-4 
       if ( getwd( dirc ) == NULL ) {  
 #else  #define CGOLD 0.3819660 
       extern char       *getcwd( );  #define ZEPS 1.0e-10 
   #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif  #define GOLD 1.618034 
          return( GLOCK_ERROR_GETCWD );  #define GLIMIT 100.0 
       }  #define TINY 1.0e-20 
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */  static double maxarg1,maxarg2;
       s++;                              /* after this, the filename */  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       l2 = strlen( s );                 /* length of filename */  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    
       strcpy( name, s );                /* save file name */  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  #define rint(a) floor(a+0.5)
       dirc[l1-l2] = 0;                  /* add zero */  
    }  static double sqrarg;
    l1 = strlen( dirc );                 /* length of directory */  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 #ifdef windows  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else  int imx; 
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  int stepm;
 #endif  /* Stepm, step in month: minimum step interpolation*/
    s = strrchr( name, '.' );            /* find last / */  
    s++;  int estepm;
    strcpy(ext,s);                       /* save extension */  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
    l1= strlen( name);  
    l2= strlen( s)+1;  int m,nb;
    strncpy( finame, name, l1-l2);  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
    finame[l1-l2]= 0;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
    return( 0 );                         /* we're done */  double **pmmij, ***probs;
 }  double dateintmean=0;
   
   double *weight;
 /******************************************/  int **s; /* Status */
   double *agedc, **covar, idx;
 void replace(char *s, char*t)  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 {  
   int i;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   int lg=20;  double ftolhess; /* Tolerance for computing hessian */
   i=0;  
   lg=strlen(t);  /**************** split *************************/
   for(i=0; i<= lg; i++) {  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     (s[i] = t[i]);  {
     if (t[i]== '\\') s[i]='/';    char  *ss;                            /* pointer */
   }    int   l1, l2;                         /* length counters */
 }  
     l1 = strlen(path );                   /* length of path */
 int nbocc(char *s, char occ)    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 {    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   int i,j=0;    if ( ss == NULL ) {                   /* no directory, so use current */
   int lg=20;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   i=0;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   lg=strlen(s);      /* get current working directory */
   for(i=0; i<= lg; i++) {      /*    extern  char* getcwd ( char *buf , int len);*/
   if  (s[i] == occ ) j++;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   }        return( GLOCK_ERROR_GETCWD );
   return j;      }
 }      strcpy( name, path );               /* we've got it */
     } else {                              /* strip direcotry from path */
 void cutv(char *u,char *v, char*t, char occ)      ss++;                               /* after this, the filename */
 {      l2 = strlen( ss );                  /* length of filename */
   int i,lg,j,p=0;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   i=0;      strcpy( name, ss );         /* save file name */
   for(j=0; j<=strlen(t)-1; j++) {      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;      dirc[l1-l2] = 0;                    /* add zero */
   }    }
     l1 = strlen( dirc );                  /* length of directory */
   lg=strlen(t);  #ifdef windows
   for(j=0; j<p; j++) {    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
     (u[j] = t[j]);  #else
   }    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
      u[p]='\0';  #endif
     ss = strrchr( name, '.' );            /* find last / */
    for(j=0; j<= lg; j++) {    ss++;
     if (j>=(p+1))(v[j-p-1] = t[j]);    strcpy(ext,ss);                       /* save extension */
   }    l1= strlen( name);
 }    l2= strlen(ss)+1;
     strncpy( finame, name, l1-l2);
 /********************** nrerror ********************/    finame[l1-l2]= 0;
     return( 0 );                          /* we're done */
 void nrerror(char error_text[])  }
 {  
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);  /******************************************/
   exit(1);  
 }  void replace(char *s, char*t)
 /*********************** vector *******************/  {
 double *vector(int nl, int nh)    int i;
 {    int lg=20;
   double *v;    i=0;
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    lg=strlen(t);
   if (!v) nrerror("allocation failure in vector");    for(i=0; i<= lg; i++) {
   return v-nl+NR_END;      (s[i] = t[i]);
 }      if (t[i]== '\\') s[i]='/';
     }
 /************************ free vector ******************/  }
 void free_vector(double*v, int nl, int nh)  
 {  int nbocc(char *s, char occ)
   free((FREE_ARG)(v+nl-NR_END));  {
 }    int i,j=0;
     int lg=20;
 /************************ivector *******************************/    i=0;
 int *ivector(long nl,long nh)    lg=strlen(s);
 {    for(i=0; i<= lg; i++) {
   int *v;    if  (s[i] == occ ) j++;
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    }
   if (!v) nrerror("allocation failure in ivector");    return j;
   return v-nl+NR_END;  }
 }  
   void cutv(char *u,char *v, char*t, char occ)
 /******************free ivector **************************/  {
 void free_ivector(int *v, long nl, long nh)    /* cuts string t into u and v where u is ended by char occ excluding it
 {       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   free((FREE_ARG)(v+nl-NR_END));       gives u="abcedf" and v="ghi2j" */
 }    int i,lg,j,p=0;
     i=0;
 /******************* imatrix *******************************/    for(j=0; j<=strlen(t)-1; j++) {
 int **imatrix(long nrl, long nrh, long ncl, long nch)      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    }
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    lg=strlen(t);
   int **m;    for(j=0; j<p; j++) {
        (u[j] = t[j]);
   /* allocate pointers to rows */    }
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));       u[p]='\0';
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;     for(j=0; j<= lg; j++) {
   m -= nrl;      if (j>=(p+1))(v[j-p-1] = t[j]);
      }
    }
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  /********************** nrerror ********************/
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  void nrerror(char error_text[])
   m[nrl] -= ncl;  {
      fprintf(stderr,"ERREUR ...\n");
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    fprintf(stderr,"%s\n",error_text);
      exit(EXIT_FAILURE);
   /* return pointer to array of pointers to rows */  }
   return m;  /*********************** vector *******************/
 }  double *vector(int nl, int nh)
   {
 /****************** free_imatrix *************************/    double *v;
 void free_imatrix(m,nrl,nrh,ncl,nch)    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       int **m;    if (!v) nrerror("allocation failure in vector");
       long nch,ncl,nrh,nrl;    return v-nl+NR_END;
      /* free an int matrix allocated by imatrix() */  }
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  /************************ free vector ******************/
   free((FREE_ARG) (m+nrl-NR_END));  void free_vector(double*v, int nl, int nh)
 }  {
     free((FREE_ARG)(v+nl-NR_END));
 /******************* matrix *******************************/  }
 double **matrix(long nrl, long nrh, long ncl, long nch)  
 {  /************************ivector *******************************/
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  int *ivector(long nl,long nh)
   double **m;  {
     int *v;
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   if (!m) nrerror("allocation failure 1 in matrix()");    if (!v) nrerror("allocation failure in ivector");
   m += NR_END;    return v-nl+NR_END;
   m -= nrl;  }
   
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  /******************free ivector **************************/
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  void free_ivector(int *v, long nl, long nh)
   m[nrl] += NR_END;  {
   m[nrl] -= ncl;    free((FREE_ARG)(v+nl-NR_END));
   }
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;  /******************* imatrix *******************************/
 }  int **imatrix(long nrl, long nrh, long ncl, long nch) 
        /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 /*************************free matrix ************************/  { 
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
 {    int **m; 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    
   free((FREE_ARG)(m+nrl-NR_END));    /* allocate pointers to rows */ 
 }    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     if (!m) nrerror("allocation failure 1 in matrix()"); 
 /******************* ma3x *******************************/    m += NR_END; 
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    m -= nrl; 
 {    
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    
   double ***m;    /* allocate rows and set pointers to them */ 
     m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   if (!m) nrerror("allocation failure 1 in matrix()");    m[nrl] += NR_END; 
   m += NR_END;    m[nrl] -= ncl; 
   m -= nrl;    
     for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    /* return pointer to array of pointers to rows */ 
   m[nrl] += NR_END;    return m; 
   m[nrl] -= ncl;  } 
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  /****************** free_imatrix *************************/
   void free_imatrix(m,nrl,nrh,ncl,nch)
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));        int **m;
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");        long nch,ncl,nrh,nrl; 
   m[nrl][ncl] += NR_END;       /* free an int matrix allocated by imatrix() */ 
   m[nrl][ncl] -= nll;  { 
   for (j=ncl+1; j<=nch; j++)    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     m[nrl][j]=m[nrl][j-1]+nlay;    free((FREE_ARG) (m+nrl-NR_END)); 
    } 
   for (i=nrl+1; i<=nrh; i++) {  
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  /******************* matrix *******************************/
     for (j=ncl+1; j<=nch; j++)  double **matrix(long nrl, long nrh, long ncl, long nch)
       m[i][j]=m[i][j-1]+nlay;  {
   }    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   return m;    double **m;
 }  
     m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 /*************************free ma3x ************************/    if (!m) nrerror("allocation failure 1 in matrix()");
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    m += NR_END;
 {    m -= nrl;
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   free((FREE_ARG)(m+nrl-NR_END));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 }    m[nrl] += NR_END;
     m[nrl] -= ncl;
 /***************** f1dim *************************/  
 extern int ncom;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 extern double *pcom,*xicom;    return m;
 extern double (*nrfunc)(double []);    /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
       */
 double f1dim(double x)  }
 {  
   int j;  /*************************free matrix ************************/
   double f;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   double *xt;  {
      free((FREE_ARG)(m[nrl]+ncl-NR_END));
   xt=vector(1,ncom);    free((FREE_ARG)(m+nrl-NR_END));
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  }
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);  /******************* ma3x *******************************/
   return f;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
 }  {
     long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
 /*****************brent *************************/    double ***m;
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  
 {    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   int iter;    if (!m) nrerror("allocation failure 1 in matrix()");
   double a,b,d,etemp;    m += NR_END;
   double fu,fv,fw,fx;    m -= nrl;
   double ftemp;  
   double p,q,r,tol1,tol2,u,v,w,x,xm;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   double e=0.0;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
      m[nrl] += NR_END;
   a=(ax < cx ? ax : cx);    m[nrl] -= ncl;
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   fw=fv=fx=(*f)(x);  
   for (iter=1;iter<=ITMAX;iter++) {    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     xm=0.5*(a+b);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    m[nrl][ncl] += NR_END;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    m[nrl][ncl] -= nll;
     printf(".");fflush(stdout);    for (j=ncl+1; j<=nch; j++) 
 #ifdef DEBUG      m[nrl][j]=m[nrl][j-1]+nlay;
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    for (i=nrl+1; i<=nrh; i++) {
 #endif      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){      for (j=ncl+1; j<=nch; j++) 
       *xmin=x;        m[i][j]=m[i][j-1]+nlay;
       return fx;    }
     }    return m; 
     ftemp=fu;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     if (fabs(e) > tol1) {             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       r=(x-w)*(fx-fv);    */
       q=(x-v)*(fx-fw);  }
       p=(x-v)*q-(x-w)*r;  
       q=2.0*(q-r);  /*************************free ma3x ************************/
       if (q > 0.0) p = -p;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       q=fabs(q);  {
       etemp=e;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       e=d;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    free((FREE_ARG)(m+nrl-NR_END));
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  }
       else {  
         d=p/q;  /***************** f1dim *************************/
         u=x+d;  extern int ncom; 
         if (u-a < tol2 || b-u < tol2)  extern double *pcom,*xicom;
           d=SIGN(tol1,xm-x);  extern double (*nrfunc)(double []); 
       }   
     } else {  double f1dim(double x) 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  { 
     }    int j; 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    double f;
     fu=(*f)(u);    double *xt; 
     if (fu <= fx) {   
       if (u >= x) a=x; else b=x;    xt=vector(1,ncom); 
       SHFT(v,w,x,u)    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
         SHFT(fv,fw,fx,fu)    f=(*nrfunc)(xt); 
         } else {    free_vector(xt,1,ncom); 
           if (u < x) a=u; else b=u;    return f; 
           if (fu <= fw || w == x) {  } 
             v=w;  
             w=u;  /*****************brent *************************/
             fv=fw;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
             fw=fu;  { 
           } else if (fu <= fv || v == x || v == w) {    int iter; 
             v=u;    double a,b,d,etemp;
             fv=fu;    double fu,fv,fw,fx;
           }    double ftemp;
         }    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   }    double e=0.0; 
   nrerror("Too many iterations in brent");   
   *xmin=x;    a=(ax < cx ? ax : cx); 
   return fx;    b=(ax > cx ? ax : cx); 
 }    x=w=v=bx; 
     fw=fv=fx=(*f)(x); 
 /****************** mnbrak ***********************/    for (iter=1;iter<=ITMAX;iter++) { 
       xm=0.5*(a+b); 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
             double (*func)(double))      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
 {      printf(".");fflush(stdout);
   double ulim,u,r,q, dum;      fprintf(ficlog,".");fflush(ficlog);
   double fu;  #ifdef DEBUG
        printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   *fa=(*func)(*ax);      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);
   *fb=(*func)(*bx);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   if (*fb > *fa) {  #endif
     SHFT(dum,*ax,*bx,dum)      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       SHFT(dum,*fb,*fa,dum)        *xmin=x; 
       }        return fx; 
   *cx=(*bx)+GOLD*(*bx-*ax);      } 
   *fc=(*func)(*cx);      ftemp=fu;
   while (*fb > *fc) {      if (fabs(e) > tol1) { 
     r=(*bx-*ax)*(*fb-*fc);        r=(x-w)*(fx-fv); 
     q=(*bx-*cx)*(*fb-*fa);        q=(x-v)*(fx-fw); 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/        p=(x-v)*q-(x-w)*r; 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));        q=2.0*(q-r); 
     ulim=(*bx)+GLIMIT*(*cx-*bx);        if (q > 0.0) p = -p; 
     if ((*bx-u)*(u-*cx) > 0.0) {        q=fabs(q); 
       fu=(*func)(u);        etemp=e; 
     } else if ((*cx-u)*(u-ulim) > 0.0) {        e=d; 
       fu=(*func)(u);        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       if (fu < *fc) {          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))        else { 
           SHFT(*fb,*fc,fu,(*func)(u))          d=p/q; 
           }          u=x+d; 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {          if (u-a < tol2 || b-u < tol2) 
       u=ulim;            d=SIGN(tol1,xm-x); 
       fu=(*func)(u);        } 
     } else {      } else { 
       u=(*cx)+GOLD*(*cx-*bx);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       fu=(*func)(u);      } 
     }      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     SHFT(*ax,*bx,*cx,u)      fu=(*f)(u); 
       SHFT(*fa,*fb,*fc,fu)      if (fu <= fx) { 
       }        if (u >= x) a=x; else b=x; 
 }        SHFT(v,w,x,u) 
           SHFT(fv,fw,fx,fu) 
 /*************** linmin ************************/          } else { 
             if (u < x) a=u; else b=u; 
 int ncom;            if (fu <= fw || w == x) { 
 double *pcom,*xicom;              v=w; 
 double (*nrfunc)(double []);              w=u; 
                fv=fw; 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))              fw=fu; 
 {            } else if (fu <= fv || v == x || v == w) { 
   double brent(double ax, double bx, double cx,              v=u; 
                double (*f)(double), double tol, double *xmin);              fv=fu; 
   double f1dim(double x);            } 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,          } 
               double *fc, double (*func)(double));    } 
   int j;    nrerror("Too many iterations in brent"); 
   double xx,xmin,bx,ax;    *xmin=x; 
   double fx,fb,fa;    return fx; 
    } 
   ncom=n;  
   pcom=vector(1,n);  /****************** mnbrak ***********************/
   xicom=vector(1,n);  
   nrfunc=func;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   for (j=1;j<=n;j++) {              double (*func)(double)) 
     pcom[j]=p[j];  { 
     xicom[j]=xi[j];    double ulim,u,r,q, dum;
   }    double fu; 
   ax=0.0;   
   xx=1.0;    *fa=(*func)(*ax); 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    *fb=(*func)(*bx); 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    if (*fb > *fa) { 
 #ifdef DEBUG      SHFT(dum,*ax,*bx,dum) 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);        SHFT(dum,*fb,*fa,dum) 
 #endif        } 
   for (j=1;j<=n;j++) {    *cx=(*bx)+GOLD*(*bx-*ax); 
     xi[j] *= xmin;    *fc=(*func)(*cx); 
     p[j] += xi[j];    while (*fb > *fc) { 
   }      r=(*bx-*ax)*(*fb-*fc); 
   free_vector(xicom,1,n);      q=(*bx-*cx)*(*fb-*fa); 
   free_vector(pcom,1,n);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 }        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       ulim=(*bx)+GLIMIT*(*cx-*bx); 
 /*************** powell ************************/      if ((*bx-u)*(u-*cx) > 0.0) { 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,        fu=(*func)(u); 
             double (*func)(double []))      } else if ((*cx-u)*(u-ulim) > 0.0) { 
 {        fu=(*func)(u); 
   void linmin(double p[], double xi[], int n, double *fret,        if (fu < *fc) { 
               double (*func)(double []));          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   int i,ibig,j;            SHFT(*fb,*fc,fu,(*func)(u)) 
   double del,t,*pt,*ptt,*xit;            } 
   double fp,fptt;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   double *xits;        u=ulim; 
   pt=vector(1,n);        fu=(*func)(u); 
   ptt=vector(1,n);      } else { 
   xit=vector(1,n);        u=(*cx)+GOLD*(*cx-*bx); 
   xits=vector(1,n);        fu=(*func)(u); 
   *fret=(*func)(p);      } 
   for (j=1;j<=n;j++) pt[j]=p[j];      SHFT(*ax,*bx,*cx,u) 
   for (*iter=1;;++(*iter)) {        SHFT(*fa,*fb,*fc,fu) 
     fp=(*fret);        } 
     ibig=0;  } 
     del=0.0;  
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  /*************** linmin ************************/
     for (i=1;i<=n;i++)  
       printf(" %d %.12f",i, p[i]);  int ncom; 
     printf("\n");  double *pcom,*xicom;
     for (i=1;i<=n;i++) {  double (*nrfunc)(double []); 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];   
       fptt=(*fret);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
 #ifdef DEBUG  { 
       printf("fret=%lf \n",*fret);    double brent(double ax, double bx, double cx, 
 #endif                 double (*f)(double), double tol, double *xmin); 
       printf("%d",i);fflush(stdout);    double f1dim(double x); 
       linmin(p,xit,n,fret,func);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       if (fabs(fptt-(*fret)) > del) {                double *fc, double (*func)(double)); 
         del=fabs(fptt-(*fret));    int j; 
         ibig=i;    double xx,xmin,bx,ax; 
       }    double fx,fb,fa;
 #ifdef DEBUG   
       printf("%d %.12e",i,(*fret));    ncom=n; 
       for (j=1;j<=n;j++) {    pcom=vector(1,n); 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    xicom=vector(1,n); 
         printf(" x(%d)=%.12e",j,xit[j]);    nrfunc=func; 
       }    for (j=1;j<=n;j++) { 
       for(j=1;j<=n;j++)      pcom[j]=p[j]; 
         printf(" p=%.12e",p[j]);      xicom[j]=xi[j]; 
       printf("\n");    } 
 #endif    ax=0.0; 
     }    xx=1.0; 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
 #ifdef DEBUG    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       int k[2],l;  #ifdef DEBUG
       k[0]=1;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       k[1]=-1;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       printf("Max: %.12e",(*func)(p));  #endif
       for (j=1;j<=n;j++)    for (j=1;j<=n;j++) { 
         printf(" %.12e",p[j]);      xi[j] *= xmin; 
       printf("\n");      p[j] += xi[j]; 
       for(l=0;l<=1;l++) {    } 
         for (j=1;j<=n;j++) {    free_vector(xicom,1,n); 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    free_vector(pcom,1,n); 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  } 
         }  
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  /*************** powell ************************/
       }  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
 #endif              double (*func)(double [])) 
   { 
     void linmin(double p[], double xi[], int n, double *fret, 
       free_vector(xit,1,n);                double (*func)(double [])); 
       free_vector(xits,1,n);    int i,ibig,j; 
       free_vector(ptt,1,n);    double del,t,*pt,*ptt,*xit;
       free_vector(pt,1,n);    double fp,fptt;
       return;    double *xits;
     }    pt=vector(1,n); 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    ptt=vector(1,n); 
     for (j=1;j<=n;j++) {    xit=vector(1,n); 
       ptt[j]=2.0*p[j]-pt[j];    xits=vector(1,n); 
       xit[j]=p[j]-pt[j];    *fret=(*func)(p); 
       pt[j]=p[j];    for (j=1;j<=n;j++) pt[j]=p[j]; 
     }    for (*iter=1;;++(*iter)) { 
     fptt=(*func)(ptt);      fp=(*fret); 
     if (fptt < fp) {      ibig=0; 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);      del=0.0; 
       if (t < 0.0) {      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
         linmin(p,xit,n,fret,func);      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
         for (j=1;j<=n;j++) {      for (i=1;i<=n;i++) 
           xi[j][ibig]=xi[j][n];        printf(" %d %.12f",i, p[i]);
           xi[j][n]=xit[j];      fprintf(ficlog," %d %.12f",i, p[i]);
         }      printf("\n");
 #ifdef DEBUG      fprintf(ficlog,"\n");
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      for (i=1;i<=n;i++) { 
         for(j=1;j<=n;j++)        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
           printf(" %.12e",xit[j]);        fptt=(*fret); 
         printf("\n");  #ifdef DEBUG
 #endif        printf("fret=%lf \n",*fret);
       }        fprintf(ficlog,"fret=%lf \n",*fret);
     }  #endif
   }        printf("%d",i);fflush(stdout);
 }        fprintf(ficlog,"%d",i);fflush(ficlog);
         linmin(p,xit,n,fret,func); 
 /**** Prevalence limit ****************/        if (fabs(fptt-(*fret)) > del) { 
           del=fabs(fptt-(*fret)); 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)          ibig=i; 
 {        } 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  #ifdef DEBUG
      matrix by transitions matrix until convergence is reached */        printf("%d %.12e",i,(*fret));
         fprintf(ficlog,"%d %.12e",i,(*fret));
   int i, ii,j,k;        for (j=1;j<=n;j++) {
   double min, max, maxmin, maxmax,sumnew=0.;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   double **matprod2();          printf(" x(%d)=%.12e",j,xit[j]);
   double **out, cov[NCOVMAX], **pmij();          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   double **newm;        }
   double agefin, delaymax=50 ; /* Max number of years to converge */        for(j=1;j<=n;j++) {
           printf(" p=%.12e",p[j]);
   for (ii=1;ii<=nlstate+ndeath;ii++)          fprintf(ficlog," p=%.12e",p[j]);
     for (j=1;j<=nlstate+ndeath;j++){        }
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        printf("\n");
     }        fprintf(ficlog,"\n");
   #endif
    cov[1]=1.;      } 
        if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  #ifdef DEBUG
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        int k[2],l;
     newm=savm;        k[0]=1;
     /* Covariates have to be included here again */        k[1]=-1;
      cov[2]=agefin;        printf("Max: %.12e",(*func)(p));
          fprintf(ficlog,"Max: %.12e",(*func)(p));
       for (k=1; k<=cptcovn;k++) {        for (j=1;j<=n;j++) {
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];          printf(" %.12e",p[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]]);*/          fprintf(ficlog," %.12e",p[j]);
       }        }
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        printf("\n");
       for (k=1; k<=cptcovprod;k++)        fprintf(ficlog,"\n");
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        for(l=0;l<=1;l++) {
           for (j=1;j<=n;j++) {
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);          }
           printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     savm=oldm;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     oldm=newm;        }
     maxmax=0.;  #endif
     for(j=1;j<=nlstate;j++){  
       min=1.;  
       max=0.;        free_vector(xit,1,n); 
       for(i=1; i<=nlstate; i++) {        free_vector(xits,1,n); 
         sumnew=0;        free_vector(ptt,1,n); 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        free_vector(pt,1,n); 
         prlim[i][j]= newm[i][j]/(1-sumnew);        return; 
         max=FMAX(max,prlim[i][j]);      } 
         min=FMIN(min,prlim[i][j]);      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       }      for (j=1;j<=n;j++) { 
       maxmin=max-min;        ptt[j]=2.0*p[j]-pt[j]; 
       maxmax=FMAX(maxmax,maxmin);        xit[j]=p[j]-pt[j]; 
     }        pt[j]=p[j]; 
     if(maxmax < ftolpl){      } 
       return prlim;      fptt=(*func)(ptt); 
     }      if (fptt < fp) { 
   }        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
 }        if (t < 0.0) { 
           linmin(p,xit,n,fret,func); 
 /*************** transition probabilities ***************/          for (j=1;j<=n;j++) { 
             xi[j][ibig]=xi[j][n]; 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )            xi[j][n]=xit[j]; 
 {          }
   double s1, s2;  #ifdef DEBUG
   /*double t34;*/          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   int i,j,j1, nc, ii, jj;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           for(j=1;j<=n;j++){
     for(i=1; i<= nlstate; i++){            printf(" %.12e",xit[j]);
     for(j=1; j<i;j++){            fprintf(ficlog," %.12e",xit[j]);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){          }
         /*s2 += param[i][j][nc]*cov[nc];*/          printf("\n");
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];          fprintf(ficlog,"\n");
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  #endif
       }        }
       ps[i][j]=s2;      } 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    } 
     }  } 
     for(j=i+1; j<=nlstate+ndeath;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  /**** Prevalence limit (stable prevalence)  ****************/
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       }  {
       ps[i][j]=s2;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     }       matrix by transitions matrix until convergence is reached */
   }  
     /*ps[3][2]=1;*/    int i, ii,j,k;
     double min, max, maxmin, maxmax,sumnew=0.;
   for(i=1; i<= nlstate; i++){    double **matprod2();
      s1=0;    double **out, cov[NCOVMAX], **pmij();
     for(j=1; j<i; j++)    double **newm;
       s1+=exp(ps[i][j]);    double agefin, delaymax=50 ; /* Max number of years to converge */
     for(j=i+1; j<=nlstate+ndeath; j++)  
       s1+=exp(ps[i][j]);    for (ii=1;ii<=nlstate+ndeath;ii++)
     ps[i][i]=1./(s1+1.);      for (j=1;j<=nlstate+ndeath;j++){
     for(j=1; j<i; j++)        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       ps[i][j]= exp(ps[i][j])*ps[i][i];      }
     for(j=i+1; j<=nlstate+ndeath; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];     cov[1]=1.;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */   
   } /* end i */   /* 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(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      newm=savm;
     for(jj=1; jj<= nlstate+ndeath; jj++){      /* Covariates have to be included here again */
       ps[ii][jj]=0;       cov[2]=agefin;
       ps[ii][ii]=1;    
     }        for (k=1; k<=cptcovn;k++) {
   }          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
           /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
         }
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for(jj=1; jj<= nlstate+ndeath; jj++){        for (k=1; k<=cptcovprod;k++)
      printf("%lf ",ps[ii][jj]);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
    }  
     printf("\n ");        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     }        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     printf("\n ");printf("%lf ",cov[2]);*/        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
 /*      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  
   goto end;*/      savm=oldm;
     return ps;      oldm=newm;
 }      maxmax=0.;
       for(j=1;j<=nlstate;j++){
 /**************** Product of 2 matrices ******************/        min=1.;
         max=0.;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        for(i=1; i<=nlstate; i++) {
 {          sumnew=0;
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */          prlim[i][j]= newm[i][j]/(1-sumnew);
   /* in, b, out are matrice of pointers which should have been initialized          max=FMAX(max,prlim[i][j]);
      before: only the contents of out is modified. The function returns          min=FMIN(min,prlim[i][j]);
      a pointer to pointers identical to out */        }
   long i, j, k;        maxmin=max-min;
   for(i=nrl; i<= nrh; i++)        maxmax=FMAX(maxmax,maxmin);
     for(k=ncolol; k<=ncoloh; k++)      }
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      if(maxmax < ftolpl){
         out[i][k] +=in[i][j]*b[j][k];        return prlim;
       }
   return out;    }
 }  }
   
   /*************** transition probabilities ***************/ 
 /************* Higher Matrix Product ***************/  
   double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  {
 {    double s1, s2;
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    /*double t34;*/
      duration (i.e. until    int i,j,j1, nc, ii, jj;
      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(i=1; i<= nlstate; i++){
      (typically every 2 years instead of every month which is too big).      for(j=1; j<i;j++){
      Model is determined by parameters x and covariates have to be        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
      included manually here.          /*s2 += param[i][j][nc]*cov[nc];*/
           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
      */          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
         }
   int i, j, d, h, k;        ps[i][j]=s2;
   double **out, cov[NCOVMAX];        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
   double **newm;      }
       for(j=i+1; j<=nlstate+ndeath;j++){
   /* Hstepm could be zero and should return the unit matrix */        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   for (i=1;i<=nlstate+ndeath;i++)          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     for (j=1;j<=nlstate+ndeath;j++){          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
       oldm[i][j]=(i==j ? 1.0 : 0.0);        }
       po[i][j][0]=(i==j ? 1.0 : 0.0);        ps[i][j]=s2;
     }      }
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    }
   for(h=1; h <=nhstepm; h++){      /*ps[3][2]=1;*/
     for(d=1; d <=hstepm; d++){  
       newm=savm;    for(i=1; i<= nlstate; i++){
       /* Covariates have to be included here again */       s1=0;
       cov[1]=1.;      for(j=1; j<i; j++)
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        s1+=exp(ps[i][j]);
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      for(j=i+1; j<=nlstate+ndeath; j++)
       for (k=1; k<=cptcovage;k++)        s1+=exp(ps[i][j]);
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      ps[i][i]=1./(s1+1.);
       for (k=1; k<=cptcovprod;k++)      for(j=1; j<i; j++)
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        ps[i][j]= exp(ps[i][j])*ps[i][i];
       for(j=i+1; j<=nlstate+ndeath; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    } /* end i */
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       savm=oldm;      for(jj=1; jj<= nlstate+ndeath; jj++){
       oldm=newm;        ps[ii][jj]=0;
     }        ps[ii][ii]=1;
     for(i=1; i<=nlstate+ndeath; i++)      }
       for(j=1;j<=nlstate+ndeath;j++) {    }
         po[i][j][h]=newm[i][j];  
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  
          */    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
       }      for(jj=1; jj<= nlstate+ndeath; jj++){
   } /* end h */       printf("%lf ",ps[ii][jj]);
   return po;     }
 }      printf("\n ");
       }
       printf("\n ");printf("%lf ",cov[2]);*/
 /*************** log-likelihood *************/  /*
 double func( double *x)    for(i=1; i<= npar; i++) printf("%f ",x[i]);
 {    goto end;*/
   int i, ii, j, k, mi, d, kk;      return ps;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  }
   double **out;  
   double sw; /* Sum of weights */  /**************** Product of 2 matrices ******************/
   double lli; /* Individual log likelihood */  
   long ipmx;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   /*extern weight */  {
   /* We are differentiating ll according to initial status */    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   /*for(i=1;i<imx;i++)    /* in, b, out are matrice of pointers which should have been initialized 
     printf(" %d\n",s[4][i]);       before: only the contents of out is modified. The function returns
   */       a pointer to pointers identical to out */
   cov[1]=1.;    long i, j, k;
     for(i=nrl; i<= nrh; i++)
   for(k=1; k<=nlstate; k++) ll[k]=0.;      for(k=ncolol; k<=ncoloh; k++)
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];          out[i][k] +=in[i][j]*b[j][k];
     for(mi=1; mi<= wav[i]-1; mi++){  
       for (ii=1;ii<=nlstate+ndeath;ii++)    return out;
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  }
       for(d=0; d<dh[mi][i]; d++){  
         newm=savm;  
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  /************* Higher Matrix Product ***************/
         for (kk=1; kk<=cptcovage;kk++) {  
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
         }  {
            /* Computes the transition matrix starting at age 'age' over 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,       'nhstepm*hstepm*stepm' months (i.e. until
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         savm=oldm;       nhstepm*hstepm matrices. 
         oldm=newm;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
               (typically every 2 years instead of every month which is too big 
               for the memory).
       } /* end mult */       Model is determined by parameters x and covariates have to be 
             included manually here. 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/       */
       ipmx +=1;  
       sw += weight[i];    int i, j, d, h, k;
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    double **out, cov[NCOVMAX];
     } /* end of wave */    double **newm;
   } /* end of individual */  
     /* Hstepm could be zero and should return the unit matrix */
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    for (i=1;i<=nlstate+ndeath;i++)
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      for (j=1;j<=nlstate+ndeath;j++){
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        oldm[i][j]=(i==j ? 1.0 : 0.0);
   return -l;        po[i][j][0]=(i==j ? 1.0 : 0.0);
 }      }
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(h=1; h <=nhstepm; h++){
 /*********** Maximum Likelihood Estimation ***************/      for(d=1; d <=hstepm; d++){
         newm=savm;
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        /* Covariates have to be included here again */
 {        cov[1]=1.;
   int i,j, iter;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   double **xi,*delti;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   double fret;        for (k=1; k<=cptcovage;k++)
   xi=matrix(1,npar,1,npar);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   for (i=1;i<=npar;i++)        for (k=1; k<=cptcovprod;k++)
     for (j=1;j<=npar;j++)          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       xi[i][j]=(i==j ? 1.0 : 0.0);  
   printf("Powell\n");  
   powell(p,xi,npar,ftol,&iter,&fret,func);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         savm=oldm;
 }        oldm=newm;
       }
 /**** Computes Hessian and covariance matrix ***/      for(i=1; i<=nlstate+ndeath; i++)
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        for(j=1;j<=nlstate+ndeath;j++) {
 {          po[i][j][h]=newm[i][j];
   double  **a,**y,*x,pd;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
   double **hess;           */
   int i, j,jk;        }
   int *indx;    } /* end h */
     return po;
   double hessii(double p[], double delta, int theta, double delti[]);  }
   double hessij(double p[], double delti[], int i, int j);  
   void lubksb(double **a, int npar, int *indx, double b[]) ;  
   void ludcmp(double **a, int npar, int *indx, double *d) ;  /*************** log-likelihood *************/
   double func( double *x)
   hess=matrix(1,npar,1,npar);  {
     int i, ii, j, k, mi, d, kk;
   printf("\nCalculation of the hessian matrix. Wait...\n");    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   for (i=1;i<=npar;i++){    double **out;
     printf("%d",i);fflush(stdout);    double sw; /* Sum of weights */
     hess[i][i]=hessii(p,ftolhess,i,delti);    double lli; /* Individual log likelihood */
     /*printf(" %f ",p[i]);*/    int s1, s2;
     /*printf(" %lf ",hess[i][i]);*/    double bbh, survp;
   }    long ipmx;
      /*extern weight */
   for (i=1;i<=npar;i++) {    /* We are differentiating ll according to initial status */
     for (j=1;j<=npar;j++)  {    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       if (j>i) {    /*for(i=1;i<imx;i++) 
         printf(".%d%d",i,j);fflush(stdout);      printf(" %d\n",s[4][i]);
         hess[i][j]=hessij(p,delti,i,j);    */
         hess[j][i]=hess[i][j];        cov[1]=1.;
         /*printf(" %lf ",hess[i][j]);*/  
       }    for(k=1; k<=nlstate; k++) ll[k]=0.;
     }  
   }    if(mle==1){
   printf("\n");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        for(mi=1; mi<= wav[i]-1; mi++){
            for (ii=1;ii<=nlstate+ndeath;ii++)
   a=matrix(1,npar,1,npar);            for (j=1;j<=nlstate+ndeath;j++){
   y=matrix(1,npar,1,npar);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   x=vector(1,npar);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   indx=ivector(1,npar);            }
   for (i=1;i<=npar;i++)          for(d=0; d<dh[mi][i]; d++){
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];            newm=savm;
   ludcmp(a,npar,indx,&pd);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
   for (j=1;j<=npar;j++) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for (i=1;i<=npar;i++) x[i]=0;            }
     x[j]=1;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     lubksb(a,npar,indx,x);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for (i=1;i<=npar;i++){            savm=oldm;
       matcov[i][j]=x[i];            oldm=newm;
     }          } /* end mult */
   }        
           /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   printf("\n#Hessian matrix#\n");          /* But now since version 0.9 we anticipate for bias and large stepm.
   for (i=1;i<=npar;i++) {           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     for (j=1;j<=npar;j++) {           * (in months) between two waves is not a multiple of stepm, we rounded to 
       printf("%.3e ",hess[i][j]);           * the nearest (and in case of equal distance, to the lowest) interval but now
     }           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     printf("\n");           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   }           * probability in order to take into account the bias as a fraction of the way
            * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   /* Recompute Inverse */           * -stepm/2 to stepm/2 .
   for (i=1;i<=npar;i++)           * For stepm=1 the results are the same as for previous versions of Imach.
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];           * For stepm > 1 the results are less biased than in previous versions. 
   ludcmp(a,npar,indx,&pd);           */
           s1=s[mw[mi][i]][i];
   /*  printf("\n#Hessian matrix recomputed#\n");          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
   for (j=1;j<=npar;j++) {          /* bias is positive if real duration
     for (i=1;i<=npar;i++) x[i]=0;           * is higher than the multiple of stepm and negative otherwise.
     x[j]=1;           */
     lubksb(a,npar,indx,x);          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     for (i=1;i<=npar;i++){          if( s2 > nlstate){ 
       y[i][j]=x[i];            /* i.e. if s2 is a death state and if the date of death is known then the contribution
       printf("%.3e ",y[i][j]);               to the likelihood is the probability to die between last step unit time and current 
     }               step unit time, which is also the differences between probability to die before dh 
     printf("\n");               and probability to die before dh-stepm . 
   }               In version up to 0.92 likelihood was computed
   */          as if date of death was unknown. Death was treated as any other
           health state: the date of the interview describes the actual state
   free_matrix(a,1,npar,1,npar);          and not the date of a change in health state. The former idea was
   free_matrix(y,1,npar,1,npar);          to consider that at each interview the state was recorded
   free_vector(x,1,npar);          (healthy, disable or death) and IMaCh was corrected; but when we
   free_ivector(indx,1,npar);          introduced the exact date of death then we should have modified
   free_matrix(hess,1,npar,1,npar);          the contribution of an exact death to the likelihood. This new
           contribution is smaller and very dependent of the step unit
           stepm. It is no more the probability to die between last interview
 }          and month of death but the probability to survive from last
           interview up to one month before death multiplied by the
 /*************** hessian matrix ****************/          probability to die within a month. Thanks to Chris
 double hessii( double x[], double delta, int theta, double delti[])          Jackson for correcting this bug.  Former versions increased
 {          mortality artificially. The bad side is that we add another loop
   int i;          which slows down the processing. The difference can be up to 10%
   int l=1, lmax=20;          lower mortality.
   double k1,k2;            */
   double p2[NPARMAX+1];            lli=log(out[s1][s2] - savm[s1][s2]);
   double res;          }else{
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   double fx;            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
   int k=0,kmax=10;          } 
   double l1;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           /*if(lli ==000.0)*/
   fx=func(x);          /*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++) p2[i]=x[i];          ipmx +=1;
   for(l=0 ; l <=lmax; l++){          sw += weight[i];
     l1=pow(10,l);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     delts=delt;        } /* end of wave */
     for(k=1 ; k <kmax; k=k+1){      } /* end of individual */
       delt = delta*(l1*k);    }  else if(mle==2){
       p2[theta]=x[theta] +delt;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       k1=func(p2)-fx;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       p2[theta]=x[theta]-delt;        for(mi=1; mi<= wav[i]-1; mi++){
       k2=func(p2)-fx;          for (ii=1;ii<=nlstate+ndeath;ii++)
       /*res= (k1-2.0*fx+k2)/delt/delt; */            for (j=1;j<=nlstate+ndeath;j++){
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                    savm[ii][j]=(ii==j ? 1.0 : 0.0);
 #ifdef DEBUG            }
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);          for(d=0; d<=dh[mi][i]; d++){
 #endif            newm=savm;
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){            for (kk=1; kk<=cptcovage;kk++) {
         k=kmax;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       }            }
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         k=kmax; l=lmax*10.;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       }            savm=oldm;
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){            oldm=newm;
         delts=delt;          } /* end mult */
       }        
     }          /*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.
   delti[theta]=delts;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   return res;           * (in months) between two waves is not a multiple of stepm, we rounded to 
             * the nearest (and in case of equal distance, to the lowest) interval but now
 }           * we keep into memory the bias bh[mi][i] and also the previous matrix product
            * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
 double hessij( double x[], double delti[], int thetai,int thetaj)           * probability in order to take into account the bias as a fraction of the way
 {           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   int i;           * -stepm/2 to stepm/2 .
   int l=1, l1, lmax=20;           * For stepm=1 the results are the same as for previous versions of Imach.
   double k1,k2,k3,k4,res,fx;           * For stepm > 1 the results are less biased than in previous versions. 
   double p2[NPARMAX+1];           */
   int k;          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
   fx=func(x);          bbh=(double)bh[mi][i]/(double)stepm; 
   for (k=1; k<=2; k++) {          /* bias is positive if real duration
     for (i=1;i<=npar;i++) p2[i]=x[i];           * is higher than the multiple of stepm and negative otherwise.
     p2[thetai]=x[thetai]+delti[thetai]/k;           */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
     k1=func(p2)-fx;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
            /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
     p2[thetai]=x[thetai]+delti[thetai]/k;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          /*if(lli ==000.0)*/
     k2=func(p2)-fx;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
            ipmx +=1;
     p2[thetai]=x[thetai]-delti[thetai]/k;          sw += weight[i];
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     k3=func(p2)-fx;        } /* end of wave */
        } /* end of individual */
     p2[thetai]=x[thetai]-delti[thetai]/k;    }  else if(mle==3){  /* exponential inter-extrapolation */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     k4=func(p2)-fx;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        for(mi=1; mi<= wav[i]-1; mi++){
 #ifdef DEBUG          for (ii=1;ii<=nlstate+ndeath;ii++)
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);            for (j=1;j<=nlstate+ndeath;j++){
 #endif              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   return res;            }
 }          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
 /************** Inverse of matrix **************/            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 void ludcmp(double **a, int n, int *indx, double *d)            for (kk=1; kk<=cptcovage;kk++) {
 {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int i,imax,j,k;            }
   double big,dum,sum,temp;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double *vv;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              savm=oldm;
   vv=vector(1,n);            oldm=newm;
   *d=1.0;          } /* end mult */
   for (i=1;i<=n;i++) {        
     big=0.0;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     for (j=1;j<=n;j++)          /* But now since version 0.9 we anticipate for bias and large stepm.
       if ((temp=fabs(a[i][j])) > big) big=temp;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");           * (in months) between two waves is not a multiple of stepm, we rounded to 
     vv[i]=1.0/big;           * the nearest (and in case of equal distance, to the lowest) interval but now
   }           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   for (j=1;j<=n;j++) {           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     for (i=1;i<j;i++) {           * probability in order to take into account the bias as a fraction of the way
       sum=a[i][j];           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];           * -stepm/2 to stepm/2 .
       a[i][j]=sum;           * 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. 
     big=0.0;           */
     for (i=j;i<=n;i++) {          s1=s[mw[mi][i]][i];
       sum=a[i][j];          s2=s[mw[mi+1][i]][i];
       for (k=1;k<j;k++)          bbh=(double)bh[mi][i]/(double)stepm; 
         sum -= a[i][k]*a[k][j];          /* bias is positive if real duration
       a[i][j]=sum;           * is higher than the multiple of stepm and negative otherwise.
       if ( (dum=vv[i]*fabs(sum)) >= big) {           */
         big=dum;          /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
         imax=i;          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
       }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     }          /*if(lli ==000.0)*/
     if (j != imax) {          /*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 (k=1;k<=n;k++) {          ipmx +=1;
         dum=a[imax][k];          sw += weight[i];
         a[imax][k]=a[j][k];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         a[j][k]=dum;        } /* end of wave */
       }      } /* end of individual */
       *d = -(*d);    }else{  /* ml=4 no inter-extrapolation */
       vv[imax]=vv[j];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     indx[j]=imax;        for(mi=1; mi<= wav[i]-1; mi++){
     if (a[j][j] == 0.0) a[j][j]=TINY;          for (ii=1;ii<=nlstate+ndeath;ii++)
     if (j != n) {            for (j=1;j<=nlstate+ndeath;j++){
       dum=1.0/(a[j][j]);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for (i=j+1;i<=n;i++) a[i][j] *= dum;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     }            }
   }          for(d=0; d<dh[mi][i]; d++){
   free_vector(vv,1,n);  /* Doesn't work */            newm=savm;
 ;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 }            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 void lubksb(double **a, int n, int *indx, double b[])            }
 {          
   int i,ii=0,ip,j;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double sum;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              savm=oldm;
   for (i=1;i<=n;i++) {            oldm=newm;
     ip=indx[i];          } /* end mult */
     sum=b[ip];        
     b[ip]=b[i];          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     if (ii)          ipmx +=1;
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          sw += weight[i];
     else if (sum) ii=i;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     b[i]=sum;        } /* end of wave */
   }      } /* end of individual */
   for (i=n;i>=1;i--) {    } /* End of if */
     sum=b[i];    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     b[i]=sum/a[i][i];    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   }    return -l;
 }  }
   
 /************ Frequencies ********************/  
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)  /*********** Maximum Likelihood Estimation ***************/
 {  /* Some frequencies */  
    void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  {
   double ***freq; /* Frequencies */    int i,j, iter;
   double *pp;    double **xi;
   double pos, k2, dateintsum=0,k2cpt=0;    double fret;
   FILE *ficresp;    xi=matrix(1,npar,1,npar);
   char fileresp[FILENAMELENGTH];    for (i=1;i<=npar;i++)
        for (j=1;j<=npar;j++)
   pp=vector(1,nlstate);        xi[i][j]=(i==j ? 1.0 : 0.0);
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   strcpy(fileresp,"p");    powell(p,xi,npar,ftol,&iter,&fret,func);
   strcat(fileresp,fileres);  
   if((ficresp=fopen(fileresp,"w"))==NULL) {     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     printf("Problem with prevalence resultfile: %s\n", fileresp);    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     exit(0);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   }  
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  }
   j1=0;  
    /**** Computes Hessian and covariance matrix ***/
   j=cptcoveff;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  {
      double  **a,**y,*x,pd;
   for(k1=1; k1<=j;k1++){    double **hess;
     for(i1=1; i1<=ncodemax[k1];i1++){    int i, j,jk;
       j1++;    int *indx;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  
         scanf("%d", i);*/    double hessii(double p[], double delta, int theta, double delti[]);
       for (i=-1; i<=nlstate+ndeath; i++)      double hessij(double p[], double delti[], int i, int j);
         for (jk=-1; jk<=nlstate+ndeath; jk++)      void lubksb(double **a, int npar, int *indx, double b[]) ;
           for(m=agemin; m <= agemax+3; m++)    void ludcmp(double **a, int npar, int *indx, double *d) ;
             freq[i][jk][m]=0;  
          hess=matrix(1,npar,1,npar);
       dateintsum=0;  
       k2cpt=0;    printf("\nCalculation of the hessian matrix. Wait...\n");
       for (i=1; i<=imx; i++) {    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         bool=1;    for (i=1;i<=npar;i++){
         if  (cptcovn>0) {      printf("%d",i);fflush(stdout);
           for (z1=1; z1<=cptcoveff; z1++)      fprintf(ficlog,"%d",i);fflush(ficlog);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      hess[i][i]=hessii(p,ftolhess,i,delti);
               bool=0;      /*printf(" %f ",p[i]);*/
         }      /*printf(" %lf ",hess[i][i]);*/
         if (bool==1) {    }
           for(m=firstpass; m<=lastpass; m++){    
             k2=anint[m][i]+(mint[m][i]/12.);    for (i=1;i<=npar;i++) {
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      for (j=1;j<=npar;j++)  {
               if(agev[m][i]==0) agev[m][i]=agemax+1;        if (j>i) { 
               if(agev[m][i]==1) agev[m][i]=agemax+2;          printf(".%d%d",i,j);fflush(stdout);
               if (m<lastpass) {          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          hess[i][j]=hessij(p,delti,i,j);
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          hess[j][i]=hess[i][j];    
               }          /*printf(" %lf ",hess[i][j]);*/
                      }
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {      }
                 dateintsum=dateintsum+k2;    }
                 k2cpt++;    printf("\n");
               }    fprintf(ficlog,"\n");
             }  
           }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
         }    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       }    
            a=matrix(1,npar,1,npar);
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    y=matrix(1,npar,1,npar);
     x=vector(1,npar);
       if  (cptcovn>0) {    indx=ivector(1,npar);
         fprintf(ficresp, "\n#********** Variable ");    for (i=1;i<=npar;i++)
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
         fprintf(ficresp, "**********\n#");    ludcmp(a,npar,indx,&pd);
       }  
       for(i=1; i<=nlstate;i++)    for (j=1;j<=npar;j++) {
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      for (i=1;i<=npar;i++) x[i]=0;
       fprintf(ficresp, "\n");      x[j]=1;
            lubksb(a,npar,indx,x);
       for(i=(int)agemin; i <= (int)agemax+3; i++){      for (i=1;i<=npar;i++){ 
         if(i==(int)agemax+3)        matcov[i][j]=x[i];
           printf("Total");      }
         else    }
           printf("Age %d", i);  
         for(jk=1; jk <=nlstate ; jk++){    printf("\n#Hessian matrix#\n");
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    fprintf(ficlog,"\n#Hessian matrix#\n");
             pp[jk] += freq[jk][m][i];    for (i=1;i<=npar;i++) { 
         }      for (j=1;j<=npar;j++) { 
         for(jk=1; jk <=nlstate ; jk++){        printf("%.3e ",hess[i][j]);
           for(m=-1, pos=0; m <=0 ; m++)        fprintf(ficlog,"%.3e ",hess[i][j]);
             pos += freq[jk][m][i];      }
           if(pp[jk]>=1.e-10)      printf("\n");
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      fprintf(ficlog,"\n");
           else    }
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  
         }    /* Recompute Inverse */
     for (i=1;i<=npar;i++)
         for(jk=1; jk <=nlstate ; jk++){      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    ludcmp(a,npar,indx,&pd);
             pp[jk] += freq[jk][m][i];  
         }    /*  printf("\n#Hessian matrix recomputed#\n");
   
         for(jk=1,pos=0; jk <=nlstate ; jk++)    for (j=1;j<=npar;j++) {
           pos += pp[jk];      for (i=1;i<=npar;i++) x[i]=0;
         for(jk=1; jk <=nlstate ; jk++){      x[j]=1;
           if(pos>=1.e-5)      lubksb(a,npar,indx,x);
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      for (i=1;i<=npar;i++){ 
           else        y[i][j]=x[i];
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        printf("%.3e ",y[i][j]);
           if( i <= (int) agemax){        fprintf(ficlog,"%.3e ",y[i][j]);
             if(pos>=1.e-5){      }
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);      printf("\n");
               probs[i][jk][j1]= pp[jk]/pos;      fprintf(ficlog,"\n");
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/    }
             }    */
             else  
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    free_matrix(a,1,npar,1,npar);
           }    free_matrix(y,1,npar,1,npar);
         }    free_vector(x,1,npar);
            free_ivector(indx,1,npar);
         for(jk=-1; jk <=nlstate+ndeath; jk++)    free_matrix(hess,1,npar,1,npar);
           for(m=-1; m <=nlstate+ndeath; m++)  
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  
         if(i <= (int) agemax)  }
           fprintf(ficresp,"\n");  
         printf("\n");  /*************** hessian matrix ****************/
       }  double hessii( double x[], double delta, int theta, double delti[])
     }  {
   }    int i;
   dateintmean=dateintsum/k2cpt;    int l=1, lmax=20;
      double k1,k2;
   fclose(ficresp);    double p2[NPARMAX+1];
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    double res;
   free_vector(pp,1,nlstate);    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
      double fx;
   /* End of Freq */    int k=0,kmax=10;
 }    double l1;
   
 /************ Prevalence ********************/    fx=func(x);
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)    for (i=1;i<=npar;i++) p2[i]=x[i];
 {  /* Some frequencies */    for(l=0 ; l <=lmax; l++){
        l1=pow(10,l);
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      delts=delt;
   double ***freq; /* Frequencies */      for(k=1 ; k <kmax; k=k+1){
   double *pp;        delt = delta*(l1*k);
   double pos, k2;        p2[theta]=x[theta] +delt;
         k1=func(p2)-fx;
   pp=vector(1,nlstate);        p2[theta]=x[theta]-delt;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        k2=func(p2)-fx;
          /*res= (k1-2.0*fx+k2)/delt/delt; */
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   j1=0;        
    #ifdef DEBUG
   j=cptcoveff;        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);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
    #endif
  for(k1=1; k1<=j;k1++){        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     for(i1=1; i1<=ncodemax[k1];i1++){        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
       j1++;          k=kmax;
          }
       for (i=-1; i<=nlstate+ndeath; i++)          else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
         for (jk=-1; jk<=nlstate+ndeath; jk++)            k=kmax; l=lmax*10.;
           for(m=agemin; m <= agemax+3; m++)        }
             freq[i][jk][m]=0;        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
                delts=delt;
       for (i=1; i<=imx; i++) {        }
         bool=1;      }
         if  (cptcovn>0) {    }
           for (z1=1; z1<=cptcoveff; z1++)    delti[theta]=delts;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    return res; 
               bool=0;    
         }  }
         if (bool==1) {  
           for(m=firstpass; m<=lastpass; m++){  double hessij( double x[], double delti[], int thetai,int thetaj)
             k2=anint[m][i]+(mint[m][i]/12.);  {
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    int i;
               if(agev[m][i]==0) agev[m][i]=agemax+1;    int l=1, l1, lmax=20;
               if(agev[m][i]==1) agev[m][i]=agemax+2;    double k1,k2,k3,k4,res,fx;
               if (m<lastpass)    double p2[NPARMAX+1];
                 if (calagedate>0) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    int k;
               else  
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    fx=func(x);
                freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];    for (k=1; k<=2; k++) {
             }      for (i=1;i<=npar;i++) p2[i]=x[i];
           }      p2[thetai]=x[thetai]+delti[thetai]/k;
         }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       }      k1=func(p2)-fx;
         for(i=(int)agemin; i <= (int)agemax+3; i++){    
           for(jk=1; jk <=nlstate ; jk++){      p2[thetai]=x[thetai]+delti[thetai]/k;
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
               pp[jk] += freq[jk][m][i];      k2=func(p2)-fx;
           }    
           for(jk=1; jk <=nlstate ; jk++){      p2[thetai]=x[thetai]-delti[thetai]/k;
             for(m=-1, pos=0; m <=0 ; m++)      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
             pos += freq[jk][m][i];      k3=func(p2)-fx;
         }    
              p2[thetai]=x[thetai]-delti[thetai]/k;
          for(jk=1; jk <=nlstate ; jk++){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      k4=func(p2)-fx;
              pp[jk] += freq[jk][m][i];      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
          }  #ifdef DEBUG
                printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      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);
   #endif
          for(jk=1; jk <=nlstate ; jk++){              }
            if( i <= (int) agemax){    return res;
              if(pos>=1.e-5){  }
                probs[i][jk][j1]= pp[jk]/pos;  
              }  /************** Inverse of matrix **************/
            }  void ludcmp(double **a, int n, int *indx, double *d) 
          }  { 
              int i,imax,j,k; 
         }    double big,dum,sum,temp; 
     }    double *vv; 
   }   
     vv=vector(1,n); 
      *d=1.0; 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    for (i=1;i<=n;i++) { 
   free_vector(pp,1,nlstate);      big=0.0; 
        for (j=1;j<=n;j++) 
 }  /* End of Freq */        if ((temp=fabs(a[i][j])) > big) big=temp; 
       if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
 /************* Waves Concatenation ***************/      vv[i]=1.0/big; 
     } 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    for (j=1;j<=n;j++) { 
 {      for (i=1;i<j;i++) { 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        sum=a[i][j]; 
      Death is a valid wave (if date is known).        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i        a[i][j]=sum; 
      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.      big=0.0; 
      */      for (i=j;i<=n;i++) { 
         sum=a[i][j]; 
   int i, mi, m;        for (k=1;k<j;k++) 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          sum -= a[i][k]*a[k][j]; 
      double sum=0., jmean=0.;*/        a[i][j]=sum; 
         if ( (dum=vv[i]*fabs(sum)) >= big) { 
   int j, k=0,jk, ju, jl;          big=dum; 
   double sum=0.;          imax=i; 
   jmin=1e+5;        } 
   jmax=-1;      } 
   jmean=0.;      if (j != imax) { 
   for(i=1; i<=imx; i++){        for (k=1;k<=n;k++) { 
     mi=0;          dum=a[imax][k]; 
     m=firstpass;          a[imax][k]=a[j][k]; 
     while(s[m][i] <= nlstate){          a[j][k]=dum; 
       if(s[m][i]>=1)        } 
         mw[++mi][i]=m;        *d = -(*d); 
       if(m >=lastpass)        vv[imax]=vv[j]; 
         break;      } 
       else      indx[j]=imax; 
         m++;      if (a[j][j] == 0.0) a[j][j]=TINY; 
     }/* end while */      if (j != n) { 
     if (s[m][i] > nlstate){        dum=1.0/(a[j][j]); 
       mi++;     /* Death is another wave */        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       /* if(mi==0)  never been interviewed correctly before death */      } 
          /* Only death is a correct wave */    } 
       mw[mi][i]=m;    free_vector(vv,1,n);  /* Doesn't work */
     }  ;
   } 
     wav[i]=mi;  
     if(mi==0)  void lubksb(double **a, int n, int *indx, double b[]) 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  { 
   }    int i,ii=0,ip,j; 
     double sum; 
   for(i=1; i<=imx; i++){   
     for(mi=1; mi<wav[i];mi++){    for (i=1;i<=n;i++) { 
       if (stepm <=0)      ip=indx[i]; 
         dh[mi][i]=1;      sum=b[ip]; 
       else{      b[ip]=b[i]; 
         if (s[mw[mi+1][i]][i] > nlstate) {      if (ii) 
           if (agedc[i] < 2*AGESUP) {        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);      else if (sum) ii=i; 
           if(j==0) j=1;  /* Survives at least one month after exam */      b[i]=sum; 
           k=k+1;    } 
           if (j >= jmax) jmax=j;    for (i=n;i>=1;i--) { 
           if (j <= jmin) jmin=j;      sum=b[i]; 
           sum=sum+j;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
           /*if (j<0) printf("j=%d num=%d \n",j,i); */      b[i]=sum/a[i][i]; 
           }    } 
         }  } 
         else{  
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));  /************ Frequencies ********************/
           k=k+1;  void  freqsummary(char fileres[], int iagemin, int iagemax, 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)
           if (j >= jmax) jmax=j;  {  /* Some frequencies */
           else if (j <= jmin)jmin=j;    
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
           sum=sum+j;    int first;
         }    double ***freq; /* Frequencies */
         jk= j/stepm;    double *pp, **prop;
         jl= j -jk*stepm;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
         ju= j -(jk+1)*stepm;    FILE *ficresp;
         if(jl <= -ju)    char fileresp[FILENAMELENGTH];
           dh[mi][i]=jk;    
         else    pp=vector(1,nlstate);
           dh[mi][i]=jk+1;    prop=matrix(1,nlstate,iagemin,iagemax+3);
         if(dh[mi][i]==0)    strcpy(fileresp,"p");
           dh[mi][i]=1; /* At least one step */    strcat(fileresp,fileres);
       }    if((ficresp=fopen(fileresp,"w"))==NULL) {
     }      printf("Problem with prevalence resultfile: %s\n", fileresp);
   }      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   jmean=sum/k;      exit(0);
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    }
  }    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
 /*********** Tricode ****************************/    j1=0;
 void tricode(int *Tvar, int **nbcode, int imx)    
 {    j=cptcoveff;
   int Ndum[20],ij=1, k, j, i;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   int cptcode=0;  
   cptcoveff=0;    first=1;
    
   for (k=0; k<19; k++) Ndum[k]=0;    for(k1=1; k1<=j;k1++){
   for (k=1; k<=7; k++) ncodemax[k]=0;      for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     for (i=1; i<=imx; i++) {          scanf("%d", i);*/
       ij=(int)(covar[Tvar[j]][i]);        for (i=-1; i<=nlstate+ndeath; i++)  
       Ndum[ij]++;          for (jk=-1; jk<=nlstate+ndeath; jk++)  
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/            for(m=iagemin; m <= iagemax+3; m++)
       if (ij > cptcode) cptcode=ij;              freq[i][jk][m]=0;
     }  
       for (i=1; i<=nlstate; i++)  
     for (i=0; i<=cptcode; i++) {        for(m=iagemin; m <= iagemax+3; m++)
       if(Ndum[i]!=0) ncodemax[j]++;          prop[i][m]=0;
     }        
     ij=1;        dateintsum=0;
         k2cpt=0;
         for (i=1; i<=imx; i++) {
     for (i=1; i<=ncodemax[j]; i++) {          bool=1;
       for (k=0; k<=19; k++) {          if  (cptcovn>0) {
         if (Ndum[k] != 0) {            for (z1=1; z1<=cptcoveff; z1++) 
           nbcode[Tvar[j]][ij]=k;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                          bool=0;
           ij++;          }
         }          if (bool==1){
         if (ij > ncodemax[j]) break;            for(m=firstpass; m<=lastpass; m++){
       }                k2=anint[m][i]+(mint[m][i]/12.);
     }              if ((k2>=dateprev1) && (k2<=dateprev2)) {
   }                  if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
  for (k=0; k<19; k++) Ndum[k]=0;                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
                 if (m<lastpass) {
  for (i=1; i<=ncovmodel-2; i++) {                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
       ij=Tvar[i];                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
       Ndum[ij]++;                }
     }                
                 if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
  ij=1;                  dateintsum=dateintsum+k2;
  for (i=1; i<=10; i++) {                  k2cpt++;
    if((Ndum[i]!=0) && (i<=ncovcol)){                }
      Tvaraff[ij]=i;              }
      ij++;            }
    }          }
  }        }
           
     cptcoveff=ij-1;        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
 }  
         if  (cptcovn>0) {
 /*********** Health Expectancies ****************/          fprintf(ficresp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )          fprintf(ficresp, "**********\n#");
         }
 {        for(i=1; i<=nlstate;i++) 
   /* Health expectancies */          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;        fprintf(ficresp, "\n");
   double age, agelim, hf;        
   double ***p3mat,***varhe;        for(i=iagemin; i <= iagemax+3; i++){
   double **dnewm,**doldm;          if(i==iagemax+3){
   double *xp;            fprintf(ficlog,"Total");
   double **gp, **gm;          }else{
   double ***gradg, ***trgradg;            if(first==1){
   int theta;              first=0;
               printf("See log file for details...\n");
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);            }
   xp=vector(1,npar);            fprintf(ficlog,"Age %d", i);
   dnewm=matrix(1,nlstate*2,1,npar);          }
   doldm=matrix(1,nlstate*2,1,nlstate*2);          for(jk=1; jk <=nlstate ; jk++){
              for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   fprintf(ficreseij,"# Health expectancies\n");              pp[jk] += freq[jk][m][i]; 
   fprintf(ficreseij,"# Age");          }
   for(i=1; i<=nlstate;i++)          for(jk=1; jk <=nlstate ; jk++){
     for(j=1; j<=nlstate;j++)            for(m=-1, pos=0; m <=0 ; m++)
       fprintf(ficreseij," %1d-%1d (SE)",i,j);              pos += freq[jk][m][i];
   fprintf(ficreseij,"\n");            if(pp[jk]>=1.e-10){
               if(first==1){
   if(estepm < stepm){              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     printf ("Problem %d lower than %d\n",estepm, stepm);              }
   }              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   else  hstepm=estepm;              }else{
   /* We compute the life expectancy from trapezoids spaced every estepm months              if(first==1)
    * This is mainly to measure the difference between two models: for example                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
    * if stepm=24 months pijx are given only every 2 years and by summing them              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
    * we are calculating an estimate of the Life Expectancy assuming a linear            }
    * progression inbetween and thus overestimating or underestimating according          }
    * to the curvature of the survival function. If, for the same date, we  
    * estimate the model with stepm=1 month, we can keep estepm to 24 months          for(jk=1; jk <=nlstate ; jk++){
    * to compare the new estimate of Life expectancy with the same linear            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
    * hypothesis. A more precise result, taking into account a more precise              pp[jk] += freq[jk][m][i];
    * curvature will be obtained if estepm is as small as stepm. */          }       
           for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   /* For example we decided to compute the life expectancy with the smallest unit */            pos += pp[jk];
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.            posprop += prop[jk][i];
      nhstepm is the number of hstepm from age to agelim          }
      nstepm is the number of stepm from age to agelin.          for(jk=1; jk <=nlstate ; jk++){
      Look at hpijx to understand the reason of that which relies in memory size            if(pos>=1.e-5){
      and note for a fixed period like estepm months */              if(first==1)
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
      survival function given by stepm (the optimization length). Unfortunately it              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
      means that if the survival funtion is printed only each two years of age and if            }else{
      you sum them up and add 1 year (area under the trapezoids) you won't get the same              if(first==1)
      results. So we changed our mind and took the option of the best precision.                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   */              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */            }
             if( i <= iagemax){
   agelim=AGESUP;              if(pos>=1.e-5){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
     /* nhstepm age range expressed in number of stepm */                probs[i][jk][j1]= pp[jk]/pos;
     nstepm=(int) rint((agelim-age)*YEARM/stepm);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */              }
     /* if (stepm >= YEARM) hstepm=1;*/              else
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);          }
     gp=matrix(0,nhstepm,1,nlstate*2);          
     gm=matrix(0,nhstepm,1,nlstate*2);          for(jk=-1; jk <=nlstate+ndeath; jk++)
             for(m=-1; m <=nlstate+ndeath; m++)
     /* Computed by stepm unit matrices, product of hstepm matrices, stored              if(freq[jk][m][i] !=0 ) {
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */              if(first==1)
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);                  printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                  fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
               }
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */          if(i <= iagemax)
             fprintf(ficresp,"\n");
     /* Computing Variances of health expectancies */          if(first==1)
             printf("Others in log...\n");
      for(theta=1; theta <=npar; theta++){          fprintf(ficlog,"\n");
       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);      dateintmean=dateintsum/k2cpt; 
     
       cptj=0;    fclose(ficresp);
       for(j=1; j<= nlstate; j++){    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
         for(i=1; i<=nlstate; i++){    free_vector(pp,1,nlstate);
           cptj=cptj+1;    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){    /* End of Freq */
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;  }
           }  
         }  /************ Prevalence ********************/
       }  void prevalence(double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
        {  
          /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
       for(i=1; i<=npar; i++)       in each health status at the date of interview (if between dateprev1 and dateprev2).
         xp[i] = x[i] - (i==theta ?delti[theta]:0);       We still use firstpass and lastpass as another selection.
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      */
         
       cptj=0;    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
       for(j=1; j<= nlstate; j++){    double ***freq; /* Frequencies */
         for(i=1;i<=nlstate;i++){    double *pp, **prop;
           cptj=cptj+1;    double pos,posprop; 
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){    double  y2; /* in fractional years */
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    int iagemin, iagemax;
           }  
         }    iagemin= (int) agemin;
       }    iagemax= (int) agemax;
          /*pp=vector(1,nlstate);*/
        prop=matrix(1,nlstate,iagemin,iagemax+3); 
     /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
       for(j=1; j<= nlstate*2; j++)    j1=0;
         for(h=0; h<=nhstepm-1; h++){    
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    j=cptcoveff;
         }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     
      }    for(k1=1; k1<=j;k1++){
          for(i1=1; i1<=ncodemax[k1];i1++){
 /* End theta */        j1++;
         
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);        for (i=1; i<=nlstate; i++)  
           for(m=iagemin; m <= iagemax+3; m++)
      for(h=0; h<=nhstepm-1; h++)            prop[i][m]=0.0;
       for(j=1; j<=nlstate*2;j++)       
         for(theta=1; theta <=npar; theta++)        for (i=1; i<=imx; i++) { /* Each individual */
         trgradg[h][j][theta]=gradg[h][theta][j];          bool=1;
           if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
      for(i=1;i<=nlstate*2;i++)              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       for(j=1;j<=nlstate*2;j++)                bool=0;
         varhe[i][j][(int)age] =0.;          } 
           if (bool==1) { 
     for(h=0;h<=nhstepm-1;h++){            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
       for(k=0;k<=nhstepm-1;k++){              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         for(i=1;i<=nlstate*2;i++)                if(agev[m][i]==1) agev[m][i]=iagemax+2;
           for(j=1;j<=nlstate*2;j++)                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;                if (s[m][i]>0 && s[m][i]<=nlstate) { 
       }                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
     }                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                   prop[s[m][i]][iagemax+3] += weight[i]; 
                      } 
     /* Computing expectancies */              }
     for(i=1; i<=nlstate;i++)            } /* end selection of waves */
       for(j=1; j<=nlstate;j++)          }
         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=iagemin; i <= iagemax+3; i++){  
                    
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
             posprop += prop[jk][i]; 
         }          } 
   
     fprintf(ficreseij,"%3.0f",age );          for(jk=1; jk <=nlstate ; jk++){     
     cptj=0;            if( i <=  iagemax){ 
     for(i=1; i<=nlstate;i++)              if(posprop>=1.e-5){ 
       for(j=1; j<=nlstate;j++){                probs[i][jk][j1]= prop[jk][i]/posprop;
         cptj++;              } 
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );            } 
       }          }/* end jk */ 
     fprintf(ficreseij,"\n");        }/* end i */ 
          } /* end i1 */
     free_matrix(gm,0,nhstepm,1,nlstate*2);    } /* end k1 */
     free_matrix(gp,0,nhstepm,1,nlstate*2);    
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);    /*free_vector(pp,1,nlstate);*/
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  }  /* End of prevalence */
   free_vector(xp,1,npar);  
   free_matrix(dnewm,1,nlstate*2,1,npar);  /************* Waves Concatenation ***************/
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);  
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);  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)
 }  {
     /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
 /************ Variance ******************/       Death is a valid wave (if date is known).
 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)       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
 {       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   /* Variance of health expectancies */       and mw[mi+1][i]. dh depends on stepm.
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/       */
   double **newm;  
   double **dnewm,**doldm;    int i, mi, m;
   int i, j, nhstepm, hstepm, h, nstepm ;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   int k, cptcode;       double sum=0., jmean=0.;*/
   double *xp;    int first;
   double **gp, **gm;    int j, k=0,jk, ju, jl;
   double ***gradg, ***trgradg;    double sum=0.;
   double ***p3mat;    first=0;
   double age,agelim, hf;    jmin=1e+5;
   int theta;    jmax=-1;
     jmean=0.;
    fprintf(ficresvij,"# Covariances of life expectancies\n");    for(i=1; i<=imx; i++){
   fprintf(ficresvij,"# Age");      mi=0;
   for(i=1; i<=nlstate;i++)      m=firstpass;
     for(j=1; j<=nlstate;j++)      while(s[m][i] <= nlstate){
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        if(s[m][i]>=1)
   fprintf(ficresvij,"\n");          mw[++mi][i]=m;
         if(m >=lastpass)
   xp=vector(1,npar);          break;
   dnewm=matrix(1,nlstate,1,npar);        else
   doldm=matrix(1,nlstate,1,nlstate);          m++;
        }/* end while */
   if(estepm < stepm){      if (s[m][i] > nlstate){
     printf ("Problem %d lower than %d\n",estepm, stepm);        mi++;     /* Death is another wave */
   }        /* if(mi==0)  never been interviewed correctly before death */
   else  hstepm=estepm;             /* Only death is a correct wave */
   /* For example we decided to compute the life expectancy with the smallest unit */        mw[mi][i]=m;
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.      }
      nhstepm is the number of hstepm from age to agelim  
      nstepm is the number of stepm from age to agelin.      wav[i]=mi;
      Look at hpijx to understand the reason of that which relies in memory size      if(mi==0){
      and note for a fixed period like k years */        if(first==0){
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
      survival function given by stepm (the optimization length). Unfortunately it          first=1;
      means that if the survival funtion is printed only each two years of age and if        }
      you sum them up and add 1 year (area under the trapezoids) you won't get the same        if(first==1){
      results. So we changed our mind and took the option of the best precision.          fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
   */        }
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */      } /* end mi==0 */
   agelim = AGESUP;    }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    for(i=1; i<=imx; i++){
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      for(mi=1; mi<wav[i];mi++){
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        if (stepm <=0)
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          dh[mi][i]=1;
     gp=matrix(0,nhstepm,1,nlstate);        else{
     gm=matrix(0,nhstepm,1,nlstate);          if (s[mw[mi+1][i]][i] > nlstate) {
             if (agedc[i] < 2*AGESUP) {
     for(theta=1; theta <=npar; theta++){            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
       for(i=1; i<=npar; i++){ /* Computes gradient */            if(j==0) j=1;  /* Survives at least one month after exam */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            k=k+1;
       }            if (j >= jmax) jmax=j;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              if (j <= jmin) jmin=j;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            sum=sum+j;
             /*if (j<0) printf("j=%d num=%d \n",j,i); */
       if (popbased==1) {            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
         for(i=1; i<=nlstate;i++)            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
           prlim[i][i]=probs[(int)age][i][ij];            }
       }          }
            else{
       for(j=1; j<= nlstate; j++){            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
         for(h=0; h<=nhstepm; h++){            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)            k=k+1;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];            if (j >= jmax) jmax=j;
         }            else if (j <= jmin)jmin=j;
       }            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
                /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
       for(i=1; i<=npar; i++) /* Computes gradient */            sum=sum+j;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            jk= j/stepm;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          jl= j -jk*stepm;
            ju= j -(jk+1)*stepm;
       if (popbased==1) {          if(mle <=1){ 
         for(i=1; i<=nlstate;i++)            if(jl==0){
           prlim[i][i]=probs[(int)age][i][ij];              dh[mi][i]=jk;
       }              bh[mi][i]=0;
             }else{ /* We want a negative bias in order to only have interpolation ie
       for(j=1; j<= nlstate; j++){                    * at the price of an extra matrix product in likelihood */
         for(h=0; h<=nhstepm; h++){              dh[mi][i]=jk+1;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)              bh[mi][i]=ju;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];            }
         }          }else{
       }            if(jl <= -ju){
               dh[mi][i]=jk;
       for(j=1; j<= nlstate; j++)              bh[mi][i]=jl;       /* bias is positive if real duration
         for(h=0; h<=nhstepm; h++){                                   * is higher than the multiple of stepm and negative otherwise.
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];                                   */
         }            }
     } /* End theta */            else{
               dh[mi][i]=jk+1;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);              bh[mi][i]=ju;
             }
     for(h=0; h<=nhstepm; h++)            if(dh[mi][i]==0){
       for(j=1; j<=nlstate;j++)              dh[mi][i]=1; /* At least one step */
         for(theta=1; theta <=npar; theta++)              bh[mi][i]=ju; /* At least one step */
           trgradg[h][j][theta]=gradg[h][theta][j];              /*  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);*/
             }
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */          }
     for(i=1;i<=nlstate;i++)        } /* end if mle */
       for(j=1;j<=nlstate;j++)      } /* end wave */
         vareij[i][j][(int)age] =0.;    }
     jmean=sum/k;
     for(h=0;h<=nhstepm;h++){    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
       for(k=0;k<=nhstepm;k++){    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);   }
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);  
         for(i=1;i<=nlstate;i++)  /*********** Tricode ****************************/
           for(j=1;j<=nlstate;j++)  void tricode(int *Tvar, int **nbcode, int imx)
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;  {
       }    
     }    int Ndum[20],ij=1, k, j, i, maxncov=19;
     int cptcode=0;
     fprintf(ficresvij,"%.0f ",age );    cptcoveff=0; 
     for(i=1; i<=nlstate;i++)   
       for(j=1; j<=nlstate;j++){    for (k=0; k<maxncov; k++) Ndum[k]=0;
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);    for (k=1; k<=7; k++) ncodemax[k]=0;
       }  
     fprintf(ficresvij,"\n");    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     free_matrix(gp,0,nhstepm,1,nlstate);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
     free_matrix(gm,0,nhstepm,1,nlstate);                                 modality*/ 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        Ndum[ij]++; /*store the modality */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   } /* End age */        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
                                           Tvar[j]. If V=sex and male is 0 and 
   free_vector(xp,1,npar);                                         female is 1, then  cptcode=1.*/
   free_matrix(doldm,1,nlstate,1,npar);      }
   free_matrix(dnewm,1,nlstate,1,nlstate);  
       for (i=0; i<=cptcode; i++) {
 }        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
       }
 /************ 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)      ij=1; 
 {      for (i=1; i<=ncodemax[j]; i++) {
   /* Variance of prevalence limit */        for (k=0; k<= maxncov; k++) {
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          if (Ndum[k] != 0) {
   double **newm;            nbcode[Tvar[j]][ij]=k; 
   double **dnewm,**doldm;            /* 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; */
   int i, j, nhstepm, hstepm;            
   int k, cptcode;            ij++;
   double *xp;          }
   double *gp, *gm;          if (ij > ncodemax[j]) break; 
   double **gradg, **trgradg;        }  
   double age,agelim;      } 
   int theta;    }  
      
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");   for (k=0; k< maxncov; k++) Ndum[k]=0;
   fprintf(ficresvpl,"# Age");  
   for(i=1; i<=nlstate;i++)   for (i=1; i<=ncovmodel-2; i++) { 
       fprintf(ficresvpl," %1d-%1d",i,i);     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
   fprintf(ficresvpl,"\n");     ij=Tvar[i];
      Ndum[ij]++;
   xp=vector(1,npar);   }
   dnewm=matrix(1,nlstate,1,npar);  
   doldm=matrix(1,nlstate,1,nlstate);   ij=1;
     for (i=1; i<= maxncov; i++) {
   hstepm=1*YEARM; /* Every year of age */     if((Ndum[i]!=0) && (i<=ncovcol)){
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */       Tvaraff[ij]=i; /*For printing */
   agelim = AGESUP;       ij++;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */     }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */   }
     if (stepm >= YEARM) hstepm=1;   
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */   cptcoveff=ij-1; /*Number of simple covariates*/
     gradg=matrix(1,npar,1,nlstate);  }
     gp=vector(1,nlstate);  
     gm=vector(1,nlstate);  /*********** Health Expectancies ****************/
   
     for(theta=1; theta <=npar; theta++){  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  {
       }    /* Health expectancies */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
       for(i=1;i<=nlstate;i++)    double age, agelim, hf;
         gp[i] = prlim[i][i];    double ***p3mat,***varhe;
        double **dnewm,**doldm;
       for(i=1; i<=npar; i++) /* Computes gradient */    double *xp;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    double **gp, **gm;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double ***gradg, ***trgradg;
       for(i=1;i<=nlstate;i++)    int theta;
         gm[i] = prlim[i][i];  
     varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
       for(i=1;i<=nlstate;i++)    xp=vector(1,npar);
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    dnewm=matrix(1,nlstate*nlstate,1,npar);
     } /* End theta */    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     
     trgradg =matrix(1,nlstate,1,npar);    fprintf(ficreseij,"# Health expectancies\n");
     fprintf(ficreseij,"# Age");
     for(j=1; j<=nlstate;j++)    for(i=1; i<=nlstate;i++)
       for(theta=1; theta <=npar; theta++)      for(j=1; j<=nlstate;j++)
         trgradg[j][theta]=gradg[theta][j];        fprintf(ficreseij," %1d-%1d (SE)",i,j);
     fprintf(ficreseij,"\n");
     for(i=1;i<=nlstate;i++)  
       varpl[i][(int)age] =0.;    if(estepm < stepm){
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      printf ("Problem %d lower than %d\n",estepm, stepm);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    }
     for(i=1;i<=nlstate;i++)    else  hstepm=estepm;   
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
     fprintf(ficresvpl,"%.0f ",age );     * if stepm=24 months pijx are given only every 2 years and by summing them
     for(i=1; i<=nlstate;i++)     * we are calculating an estimate of the Life Expectancy assuming a linear 
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));     * progression in between and thus overestimating or underestimating according
     fprintf(ficresvpl,"\n");     * to the curvature of the survival function. If, for the same date, we 
     free_vector(gp,1,nlstate);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
     free_vector(gm,1,nlstate);     * to compare the new estimate of Life expectancy with the same linear 
     free_matrix(gradg,1,npar,1,nlstate);     * hypothesis. A more precise result, taking into account a more precise
     free_matrix(trgradg,1,nlstate,1,npar);     * curvature will be obtained if estepm is as small as stepm. */
   } /* End age */  
     /* For example we decided to compute the life expectancy with the smallest unit */
   free_vector(xp,1,npar);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   free_matrix(doldm,1,nlstate,1,npar);       nhstepm is the number of hstepm from age to agelim 
   free_matrix(dnewm,1,nlstate,1,nlstate);       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
 }       and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 /************ Variance of one-step probabilities  ******************/       survival function given by stepm (the optimization length). Unfortunately it
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)       means that if the survival funtion is printed only each two years of age and if
 {       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   int i, j, i1, k1, j1, z1;       results. So we changed our mind and took the option of the best precision.
   int k=0, cptcode;    */
   double **dnewm,**doldm;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   double *xp;  
   double *gp, *gm;    agelim=AGESUP;
   double **gradg, **trgradg;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   double age,agelim, cov[NCOVMAX];      /* nhstepm age range expressed in number of stepm */
   int theta;      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   char fileresprob[FILENAMELENGTH];      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
   strcpy(fileresprob,"prob");      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   strcat(fileresprob,fileres);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     printf("Problem with resultfile: %s\n", fileresprob);      gp=matrix(0,nhstepm,1,nlstate*nlstate);
   }      gm=matrix(0,nhstepm,1,nlstate*nlstate);
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);  
        /* Computed by stepm unit matrices, product of hstepm matrices, stored
 fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   fprintf(ficresprob,"# Age");      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   for(i=1; i<=nlstate;i++)   
     for(j=1; j<=(nlstate+ndeath);j++)  
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
       /* Computing Variances of health expectancies */
   fprintf(ficresprob,"\n");  
        for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
   xp=vector(1,npar);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        }
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
      
   cov[1]=1;        cptj=0;
   j=cptcoveff;        for(j=1; j<= nlstate; j++){
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          for(i=1; i<=nlstate; i++){
   j1=0;            cptj=cptj+1;
   for(k1=1; k1<=1;k1++){            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
     for(i1=1; i1<=ncodemax[k1];i1++){              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     j1++;            }
           }
     if  (cptcovn>0) {        }
       fprintf(ficresprob, "\n#********** Variable ");       
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);       
       fprintf(ficresprob, "**********\n#");        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 (age=bage; age<=fage; age ++){        
         cov[2]=age;        cptj=0;
         for (k=1; k<=cptcovn;k++) {        for(j=1; j<= nlstate; j++){
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];          for(i=1;i<=nlstate;i++){
                      cptj=cptj+1;
         }            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
         for (k=1; k<=cptcovprod;k++)            }
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          }
                }
         gradg=matrix(1,npar,1,9);        for(j=1; j<= nlstate*nlstate; j++)
         trgradg=matrix(1,9,1,npar);          for(h=0; h<=nhstepm-1; h++){
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          }
           } 
         for(theta=1; theta <=npar; theta++){     
           for(i=1; i<=npar; i++)  /* End theta */
             xp[i] = x[i] + (i==theta ?delti[theta]:0);  
                 trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
           pmij(pmmij,cov,ncovmodel,xp,nlstate);  
                 for(h=0; h<=nhstepm-1; h++)
           k=0;        for(j=1; j<=nlstate*nlstate;j++)
           for(i=1; i<= (nlstate+ndeath); i++){          for(theta=1; theta <=npar; theta++)
             for(j=1; j<=(nlstate+ndeath);j++){            trgradg[h][j][theta]=gradg[h][theta][j];
               k=k+1;       
               gp[k]=pmmij[i][j];  
             }       for(i=1;i<=nlstate*nlstate;i++)
           }        for(j=1;j<=nlstate*nlstate;j++)
                    varhe[i][j][(int)age] =0.;
           for(i=1; i<=npar; i++)  
             xp[i] = x[i] - (i==theta ?delti[theta]:0);       printf("%d|",(int)age);fflush(stdout);
           fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
           pmij(pmmij,cov,ncovmodel,xp,nlstate);       for(h=0;h<=nhstepm-1;h++){
           k=0;        for(k=0;k<=nhstepm-1;k++){
           for(i=1; i<=(nlstate+ndeath); i++){          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
             for(j=1; j<=(nlstate+ndeath);j++){          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
               k=k+1;          for(i=1;i<=nlstate*nlstate;i++)
               gm[k]=pmmij[i][j];            for(j=1;j<=nlstate*nlstate;j++)
             }              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
           }        }
            }
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)      /* Computing expectancies */
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];        for(i=1; i<=nlstate;i++)
         }        for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
           for(theta=1; theta <=npar; theta++)            
             trgradg[j][theta]=gradg[theta][j];  /* 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]);*/
          
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);          }
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);  
              fprintf(ficreseij,"%3.0f",age );
         pmij(pmmij,cov,ncovmodel,x,nlstate);      cptj=0;
              for(i=1; i<=nlstate;i++)
         k=0;        for(j=1; j<=nlstate;j++){
         for(i=1; i<=(nlstate+ndeath); i++){          cptj++;
           for(j=1; j<=(nlstate+ndeath);j++){          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
             k=k+1;        }
             gm[k]=pmmij[i][j];      fprintf(ficreseij,"\n");
           }     
         }      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
            free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
      /*printf("\n%d ",(int)age);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      }*/    }
     printf("\n");
         fprintf(ficresprob,"\n%d ",(int)age);    fprintf(ficlog,"\n");
   
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)    free_vector(xp,1,npar);
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
      free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
       }    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
     }  }
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));  
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));  /************ Variance ******************/
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  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)
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  {
   }    /* Variance of health expectancies */
   free_vector(xp,1,npar);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   fclose(ficresprob);    /* double **newm;*/
      double **dnewm,**doldm;
 }    double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
 /******************* Printing html file ***********/    int k, cptcode;
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \    double *xp;
  int lastpass, int stepm, int weightopt, char model[],\    double **gp, **gm;  /* for var eij */
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \    double ***gradg, ***trgradg; /*for var eij */
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\    double **gradgp, **trgradgp; /* for var p point j */
  char version[], int popforecast, int estepm ){    double *gpp, *gmp; /* for var p point j */
   int jj1, k1, i1, cpt;    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   FILE *fichtm;    double ***p3mat;
   /*char optionfilehtm[FILENAMELENGTH];*/    double age,agelim, hf;
     double ***mobaverage;
   strcpy(optionfilehtm,optionfile);    int theta;
   strcat(optionfilehtm,".htm");    char digit[4];
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    char digitp[25];
     printf("Problem with %s \n",optionfilehtm), exit(0);  
   }    char fileresprobmorprev[FILENAMELENGTH];
   
  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n    if(popbased==1){
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n      if(mobilav!=0)
 \n        strcpy(digitp,"-populbased-mobilav-");
 Total number of observations=%d <br>\n      else strcpy(digitp,"-populbased-nomobil-");
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n    }
 <hr  size=\"2\" color=\"#EC5E5E\">    else 
  <ul><li>Outputs files<br>\n      strcpy(digitp,"-stablbased-");
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n  
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n    if (mobilav!=0) {
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
  - 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);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
  fprintf(fichtm,"\n    }
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n  
   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n    strcpy(fileresprobmorprev,"prmorprev"); 
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n    sprintf(digit,"%-d",ij);
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
  - 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);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
  if(popforecast==1) fprintf(fichtm,"\n    strcat(fileresprobmorprev,fileres);
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n      printf("Problem with resultfile: %s\n", fileresprobmorprev);
         <br>",fileres,fileres,fileres,fileres);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
  else    }
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
 fprintf(fichtm," <li>Graphs</li><p>");    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
  m=cptcoveff;    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
  jj1=0;      for(i=1; i<=nlstate;i++)
  for(k1=1; k1<=m;k1++){        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
    for(i1=1; i1<=ncodemax[k1];i1++){    }  
        jj1++;    fprintf(ficresprobmorprev,"\n");
        if (cptcovn > 0) {    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
          for (cpt=1; cpt<=cptcoveff;cpt++)      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);      exit(0);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    }
        }    else{
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>      fprintf(ficgp,"\n# Routine varevsij");
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        }
        for(cpt=1; cpt<nlstate;cpt++){    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>      printf("Problem with html file: %s\n", optionfilehtm);
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
        }      exit(0);
     for(cpt=1; cpt<=nlstate;cpt++) {    }
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    else{
 interval) in state (%d): v%s%d%d.gif <br>      fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
      }    }
      for(cpt=1; cpt<=nlstate;cpt++) {    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         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,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
      }    fprintf(ficresvij,"# Age");
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    for(i=1; i<=nlstate;i++)
 health expectancies in states (1) and (2): e%s%d.gif<br>      for(j=1; j<=nlstate;j++)
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
 fprintf(fichtm,"\n</body>");    fprintf(ficresvij,"\n");
    }  
    }    xp=vector(1,npar);
 fclose(fichtm);    dnewm=matrix(1,nlstate,1,npar);
 }    doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
 /******************* Gnuplot file **************/    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
   strcpy(optionfilegnuplot,optionfilefiname);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   strcat(optionfilegnuplot,".gp.txt");    
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    if(estepm < stepm){
     printf("Problem with file %s",optionfilegnuplot);      printf ("Problem %d lower than %d\n",estepm, stepm);
   }    }
     else  hstepm=estepm;   
 #ifdef windows    /* For example we decided to compute the life expectancy with the smallest unit */
     fprintf(ficgp,"cd \"%s\" \n",pathc);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
 #endif       nhstepm is the number of hstepm from age to agelim 
 m=pow(2,cptcoveff);       nstepm is the number of stepm from age to agelin. 
         Look at hpijx to understand the reason of that which relies in memory size
  /* 1eme*/       and note for a fixed period like k years */
   for (cpt=1; cpt<= nlstate ; cpt ++) {    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
    for (k1=1; k1<= m ; k1 ++) {       survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed every two years of age and if
      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);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
 for (i=1; i<= nlstate ; i ++) {    */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   else fprintf(ficgp," \%%*lf (\%%*lf)");    agelim = AGESUP;
 }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     for (i=1; i<= nlstate ; i ++) {      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
 }      gp=matrix(0,nhstepm,1,nlstate);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      gm=matrix(0,nhstepm,1,nlstate);
      for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for(theta=1; theta <=npar; theta++){
 }          for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
    }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   }  
   /*2 eme*/        if (popbased==1) {
           if(mobilav ==0){
   for (k1=1; k1<= m ; k1 ++) {            for(i=1; i<=nlstate;i++)
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);              prlim[i][i]=probs[(int)age][i][ij];
              }else{ /* mobilav */ 
     for (i=1; i<= nlstate+1 ; i ++) {            for(i=1; i<=nlstate;i++)
       k=2*i;              prlim[i][i]=mobaverage[(int)age][i][ij];
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          }
       for (j=1; j<= nlstate+1 ; j ++) {        }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(j=1; j<= nlstate; j++){
 }            for(h=0; h<=nhstepm; h++){
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);          }
       for (j=1; j<= nlstate+1 ; j ++) {        }
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        /* This for computing probability of death (h=1 means
         else fprintf(ficgp," \%%*lf (\%%*lf)");           computed over hstepm matrices product = hstepm*stepm months) 
 }             as a weighted average of prlim.
       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(j=nlstate+1;j<=nlstate+ndeath;j++){
       for (j=1; j<= nlstate+1 ; j ++) {          for(i=1,gpp[j]=0.; i<= nlstate; i++)
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            gpp[j] += prlim[i][i]*p3mat[i][j][1];
   else fprintf(ficgp," \%%*lf (\%%*lf)");        }    
 }          /* end probability of death */
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");  
       else fprintf(ficgp,"\" t\"\" w l 0,");        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
     }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     
   /*3eme*/        if (popbased==1) {
           if(mobilav ==0){
   for (k1=1; k1<= m ; k1 ++) {            for(i=1; i<=nlstate;i++)
     for (cpt=1; cpt<= nlstate ; cpt ++) {              prlim[i][i]=probs[(int)age][i][ij];
       k=2+nlstate*(2*cpt-2);          }else{ /* mobilav */ 
       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);              prlim[i][i]=mobaverage[(int)age][i][ij];
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          }
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);        }
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);  
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");        for(j=1; j<= nlstate; j++){
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          for(h=0; h<=nhstepm; h++){
             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 ; i ++) {          }
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);        }
         /* This for computing probability of death (h=1 means
       }           computed over hstepm matrices product = hstepm*stepm months) 
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);           as a weighted average of prlim.
     }        */
     }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
            for(i=1,gmp[j]=0.; i<= nlstate; i++)
   /* CV preval stat */           gmp[j] += prlim[i][i]*p3mat[i][j][1];
     for (k1=1; k1<= m ; k1 ++) {        }    
     for (cpt=1; cpt<nlstate ; cpt ++) {        /* end probability of death */
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);        for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
       for (i=1; i< nlstate ; i ++)            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
         fprintf(ficgp,"+$%d",k+i+1);          }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);  
              for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
       l=3+(nlstate+ndeath)*cpt;          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        }
       for (i=1; i< nlstate ; i ++) {  
         l=3+(nlstate+ndeath)*cpt;      } /* End theta */
         fprintf(ficgp,"+$%d",l+i+1);  
       }      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);    
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      for(h=0; h<=nhstepm; h++) /* veij */
     }        for(j=1; j<=nlstate;j++)
   }            for(theta=1; theta <=npar; theta++)
              trgradg[h][j][theta]=gradg[h][theta][j];
   /* proba elementaires */  
    for(i=1,jk=1; i <=nlstate; i++){      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     for(k=1; k <=(nlstate+ndeath); k++){        for(theta=1; theta <=npar; theta++)
       if (k != i) {          trgradgp[j][theta]=gradgp[theta][j];
         for(j=1; j <=ncovmodel; j++){    
          
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           jk++;      for(i=1;i<=nlstate;i++)
           fprintf(ficgp,"\n");        for(j=1;j<=nlstate;j++)
         }          vareij[i][j][(int)age] =0.;
       }  
     }      for(h=0;h<=nhstepm;h++){
     }        for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
     for(jk=1; jk <=m; jk++) {          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);          for(i=1;i<=nlstate;i++)
    i=1;            for(j=1;j<=nlstate;j++)
    for(k2=1; k2<=nlstate; k2++) {              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
      k3=i;        }
      for(k=1; k<=(nlstate+ndeath); k++) {      }
        if (k != k2){    
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);      /* pptj */
 ij=1;      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
         for(j=3; j <=ncovmodel; j++) {      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      for(j=nlstate+1;j<=nlstate+ndeath;j++)
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
             ij++;          varppt[j][i]=doldmp[j][i];
           }      /* end ppptj */
           else      /*  x centered again */
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
         }      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
           fprintf(ficgp,")/(1");   
              if (popbased==1) {
         for(k1=1; k1 <=nlstate; k1++){          if(mobilav ==0){
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);          for(i=1; i<=nlstate;i++)
 ij=1;            prlim[i][i]=probs[(int)age][i][ij];
           for(j=3; j <=ncovmodel; j++){        }else{ /* mobilav */ 
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          for(i=1; i<=nlstate;i++)
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            prlim[i][i]=mobaverage[(int)age][i][ij];
             ij++;        }
           }      }
           else               
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      /* This for computing probability of death (h=1 means
           }         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
           fprintf(ficgp,")");         as a weighted average of prlim.
         }      */
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
         i=i+ncovmodel;          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
        }      }    
      }      /* end probability of death */
    }  
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
    }      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
            fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
   fclose(ficgp);        for(i=1; i<=nlstate;i++){
 }  /* end gnuplot */          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
 /*************** Moving average **************/      fprintf(ficresprobmorprev,"\n");
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){  
       fprintf(ficresvij,"%.0f ",age );
   int i, cpt, cptcod;      for(i=1; i<=nlstate;i++)
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)        for(j=1; j<=nlstate;j++){
       for (i=1; i<=nlstate;i++)          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        }
           mobaverage[(int)agedeb][i][cptcod]=0.;      fprintf(ficresvij,"\n");
          free_matrix(gp,0,nhstepm,1,nlstate);
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){      free_matrix(gm,0,nhstepm,1,nlstate);
       for (i=1; i<=nlstate;i++){      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
           for (cpt=0;cpt<=4;cpt++){      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    } /* End age */
           }    free_vector(gpp,nlstate+1,nlstate+ndeath);
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    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*/
     }    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
        /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
 }    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\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); */
 /************** Forecasting ******************/  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
      fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
   int *popage;    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
   double *popeffectif,*popcount;    /*  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);
   double ***p3mat;  */
   char fileresf[FILENAMELENGTH];    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
   
  agelim=AGESUP;    free_vector(xp,1,npar);
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
      free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   strcpy(fileresf,"f");    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   strcat(fileresf,fileres);    fclose(ficresprobmorprev);
   if((ficresf=fopen(fileresf,"w"))==NULL) {    fclose(ficgp);
     printf("Problem with forecast resultfile: %s\n", fileresf);    fclose(fichtm);
   }  }  
   printf("Computing forecasting: result on file '%s' \n", fileresf);  
   /************ Variance of prevlim ******************/
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
   {
   if (mobilav==1) {    /* Variance of prevalence limit */
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     movingaverage(agedeb, fage, ageminpar, mobaverage);    double **newm;
   }    double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    int k, cptcode;
   if (stepm<=12) stepsize=1;    double *xp;
      double *gp, *gm;
   agelim=AGESUP;    double **gradg, **trgradg;
      double age,agelim;
   hstepm=1;    int theta;
   hstepm=hstepm/stepm;     
   yp1=modf(dateintmean,&yp);    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
   anprojmean=yp;    fprintf(ficresvpl,"# Age");
   yp2=modf((yp1*12),&yp);    for(i=1; i<=nlstate;i++)
   mprojmean=yp;        fprintf(ficresvpl," %1d-%1d",i,i);
   yp1=modf((yp2*30.5),&yp);    fprintf(ficresvpl,"\n");
   jprojmean=yp;  
   if(jprojmean==0) jprojmean=1;    xp=vector(1,npar);
   if(mprojmean==0) jprojmean=1;    dnewm=matrix(1,nlstate,1,npar);
      doldm=matrix(1,nlstate,1,nlstate);
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    
      hstepm=1*YEARM; /* Every year of age */
   for(cptcov=1;cptcov<=i2;cptcov++){    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    agelim = AGESUP;
       k=k+1;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       fprintf(ficresf,"\n#******");      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       for(j=1;j<=cptcoveff;j++) {      if (stepm >= YEARM) hstepm=1;
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       }      gradg=matrix(1,npar,1,nlstate);
       fprintf(ficresf,"******\n");      gp=vector(1,nlstate);
       fprintf(ficresf,"# StartingAge FinalAge");      gm=vector(1,nlstate);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);  
            for(theta=1; theta <=npar; theta++){
              for(i=1; i<=npar; i++){ /* Computes gradient */
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         fprintf(ficresf,"\n");        }
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          gp[i] = prlim[i][i];
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      
           nhstepm = nhstepm/hstepm;        for(i=1; i<=npar; i++) /* Computes gradient */
                    xp[i] = x[i] - (i==theta ?delti[theta]:0);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           oldm=oldms;savm=savms;        for(i=1;i<=nlstate;i++)
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            gm[i] = prlim[i][i];
          
           for (h=0; h<=nhstepm; h++){        for(i=1;i<=nlstate;i++)
             if (h==(int) (calagedate+YEARM*cpt)) {          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);      } /* End theta */
             }  
             for(j=1; j<=nlstate+ndeath;j++) {      trgradg =matrix(1,nlstate,1,npar);
               kk1=0.;kk2=0;  
               for(i=1; i<=nlstate;i++) {                    for(j=1; j<=nlstate;j++)
                 if (mobilav==1)        for(theta=1; theta <=npar; theta++)
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          trgradg[j][theta]=gradg[theta][j];
                 else {  
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      for(i=1;i<=nlstate;i++)
                 }        varpl[i][(int)age] =0.;
                      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
               }      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
               if (h==(int)(calagedate+12*cpt)){      for(i=1;i<=nlstate;i++)
                 fprintf(ficresf," %.3f", kk1);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
                          
               }      fprintf(ficresvpl,"%.0f ",age );
             }      for(i=1; i<=nlstate;i++)
           }        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fprintf(ficresvpl,"\n");
         }      free_vector(gp,1,nlstate);
       }      free_vector(gm,1,nlstate);
     }      free_matrix(gradg,1,npar,1,nlstate);
   }      free_matrix(trgradg,1,nlstate,1,npar);
            } /* End age */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
     free_vector(xp,1,npar);
   fclose(ficresf);    free_matrix(doldm,1,nlstate,1,npar);
 }    free_matrix(dnewm,1,nlstate,1,nlstate);
 /************** 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){  }
    
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  /************ Variance of one-step probabilities  ******************/
   int *popage;  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  {
   double *popeffectif,*popcount;    int i, j=0,  i1, k1, l1, t, tj;
   double ***p3mat,***tabpop,***tabpopprev;    int k2, l2, j1,  z1;
   char filerespop[FILENAMELENGTH];    int k=0,l, cptcode;
     int first=1, first1;
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double **dnewm,**doldm;
   agelim=AGESUP;    double *xp;
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    double *gp, *gm;
      double **gradg, **trgradg;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    double **mu;
      double age,agelim, cov[NCOVMAX];
      double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   strcpy(filerespop,"pop");    int theta;
   strcat(filerespop,fileres);    char fileresprob[FILENAMELENGTH];
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    char fileresprobcov[FILENAMELENGTH];
     printf("Problem with forecast resultfile: %s\n", filerespop);    char fileresprobcor[FILENAMELENGTH];
   }  
   printf("Computing forecasting: result on file '%s' \n", filerespop);    double ***varpij;
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
   if (mobilav==1) {    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      printf("Problem with resultfile: %s\n", fileresprob);
     movingaverage(agedeb, fage, ageminpar, mobaverage);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   }    }
     strcpy(fileresprobcov,"probcov"); 
   stepsize=(int) (stepm+YEARM-1)/YEARM;    strcat(fileresprobcov,fileres);
   if (stepm<=12) stepsize=1;    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprobcov);
   agelim=AGESUP;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
      }
   hstepm=1;    strcpy(fileresprobcor,"probcor"); 
   hstepm=hstepm/stepm;    strcat(fileresprobcor,fileres);
      if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   if (popforecast==1) {      printf("Problem with resultfile: %s\n", fileresprobcor);
     if((ficpop=fopen(popfile,"r"))==NULL) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
       printf("Problem with population file : %s\n",popfile);exit(0);    }
     }    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     popage=ivector(0,AGESUP);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     popeffectif=vector(0,AGESUP);    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     popcount=vector(0,AGESUP);    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
        printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     i=1;      fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    
        fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     imx=i;    fprintf(ficresprob,"# Age");
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   }    fprintf(ficresprobcov,"# Age");
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   for(cptcov=1;cptcov<=i2;cptcov++){    fprintf(ficresprobcov,"# Age");
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
       k=k+1;  
       fprintf(ficrespop,"\n#******");    for(i=1; i<=nlstate;i++)
       for(j=1;j<=cptcoveff;j++) {      for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
       }        fprintf(ficresprobcov," p%1d-%1d ",i,j);
       fprintf(ficrespop,"******\n");        fprintf(ficresprobcor," p%1d-%1d ",i,j);
       fprintf(ficrespop,"# Age");      }  
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);   /* fprintf(ficresprob,"\n");
       if (popforecast==1)  fprintf(ficrespop," [Population]");    fprintf(ficresprobcov,"\n");
          fprintf(ficresprobcor,"\n");
       for (cpt=0; cpt<=0;cpt++) {   */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);     xp=vector(1,npar);
            dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
           nhstepm = nhstepm/hstepm;    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
              first=1;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
           oldm=oldms;savm=savms;      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
              exit(0);
           for (h=0; h<=nhstepm; h++){    }
             if (h==(int) (calagedate+YEARM*cpt)) {    else{
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      fprintf(ficgp,"\n# Routine varprob");
             }    }
             for(j=1; j<=nlstate+ndeath;j++) {    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
               kk1=0.;kk2=0;      printf("Problem with html file: %s\n", optionfilehtm);
               for(i=1; i<=nlstate;i++) {                    fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
                 if (mobilav==1)      exit(0);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    }
                 else {    else{
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
                 }      fprintf(fichtm,"\n");
               }  
               if (h==(int)(calagedate+12*cpt)){      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
                   /*fprintf(ficrespop," %.3f", kk1);      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");
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/  
               }    }
             }  
             for(i=1; i<=nlstate;i++){    cov[1]=1;
               kk1=0.;    tj=cptcoveff;
                 for(j=1; j<=nlstate;j++){    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    j1=0;
                 }    for(t=1; t<=tj;t++){
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];      for(i1=1; i1<=ncodemax[t];i1++){ 
             }        j1++;
         if  (cptcovn>0) {
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)          fprintf(ficresprob, "\n#********** Variable "); 
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           }          fprintf(ficresprob, "**********\n#\n");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficresprobcov, "\n#********** Variable "); 
         }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       }          fprintf(ficresprobcov, "**********\n#\n");
            
   /******/          fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {          fprintf(ficgp, "**********\n#\n");
         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--){          
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           nhstepm = nhstepm/hstepm;          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                    fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          
           oldm=oldms;savm=savms;          fprintf(ficresprobcor, "\n#********** Variable ");    
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           for (h=0; h<=nhstepm; h++){          fprintf(ficresprobcor, "**********\n#");    
             if (h==(int) (calagedate+YEARM*cpt)) {        }
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        
             }        for (age=bage; age<=fage; age ++){ 
             for(j=1; j<=nlstate+ndeath;j++) {          cov[2]=age;
               kk1=0.;kk2=0;          for (k=1; k<=cptcovn;k++) {
               for(i=1; i<=nlstate;i++) {                          cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];              }
               }          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);          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]]];
           }          
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
         }          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       }          gp=vector(1,(nlstate)*(nlstate+ndeath));
    }          gm=vector(1,(nlstate)*(nlstate+ndeath));
   }      
            for(theta=1; theta <=npar; theta++){
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
   if (popforecast==1) {            
     free_ivector(popage,0,AGESUP);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     free_vector(popeffectif,0,AGESUP);            
     free_vector(popcount,0,AGESUP);            k=0;
   }            for(i=1; i<= (nlstate); i++){
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              for(j=1; j<=(nlstate+ndeath);j++){
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                k=k+1;
   fclose(ficrespop);                gp[k]=pmmij[i][j];
 }              }
             }
 /***********************************************/            
 /**************** Main Program *****************/            for(i=1; i<=npar; i++)
 /***********************************************/              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
 int main(int argc, char *argv[])            pmij(pmmij,cov,ncovmodel,xp,nlstate);
 {            k=0;
             for(i=1; i<=(nlstate); i++){
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;              for(j=1; j<=(nlstate+ndeath);j++){
   double agedeb, agefin,hf;                k=k+1;
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;                gm[k]=pmmij[i][j];
               }
   double fret;            }
   double **xi,tmp,delta;       
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
   double dum; /* Dummy variable */              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
   double ***p3mat;          }
   int *indx;  
   char line[MAXLINE], linepar[MAXLINE];          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   char title[MAXLINE];            for(theta=1; theta <=npar; theta++)
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];              trgradg[j][theta]=gradg[theta][j];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];          
            matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   char filerest[FILENAMELENGTH];          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
   char fileregp[FILENAMELENGTH];          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   char popfile[FILENAMELENGTH];          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];  
   int firstobs=1, lastobs=10;          pmij(pmmij,cov,ncovmodel,x,nlstate);
   int sdeb, sfin; /* Status at beginning and end */          
   int c,  h , cpt,l;          k=0;
   int ju,jl, mi;          for(i=1; i<=(nlstate); i++){
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;            for(j=1; j<=(nlstate+ndeath);j++){
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;              k=k+1;
   int mobilav=0,popforecast=0;              mu[k][(int) age]=pmmij[i][j];
   int hstepm, nhstepm;            }
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;          }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   double bage, fage, age, agelim, agebase;            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   double ftolpl=FTOL;              varpij[i][j][(int)age] = doldm[i][j];
   double **prlim;  
   double *severity;          /*printf("\n%d ",(int)age);
   double ***param; /* Matrix of parameters */            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   double  *p;            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   double **matcov; /* Matrix of covariance */            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   double ***delti3; /* Scale */            }*/
   double *delti; /* Scale */  
   double ***eij, ***vareij;          fprintf(ficresprob,"\n%d ",(int)age);
   double **varpl; /* Variances of prevalence limits by age */          fprintf(ficresprobcov,"\n%d ",(int)age);
   double *epj, vepp;          fprintf(ficresprobcor,"\n%d ",(int)age);
   double kk1, kk2;  
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
              fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   char version[80]="Imach version 0.8a, May 2002, INED-EUROREVES ";            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   char *alph[]={"a","a","b","c","d","e"}, str[4];            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
   char z[1]="c", occ;          for (k=1; k<=(nlstate);k++){
 #include <sys/time.h>            for (l=1; l<=(nlstate+ndeath);l++){ 
 #include <time.h>              i=i++;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
                fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
   /* long total_usecs;              for (j=1; j<=i;j++){
   struct timeval start_time, end_time;                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                  fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */              }
   getcwd(pathcd, size);            }
           }/* end of loop for state */
   printf("\n%s",version);        } /* end of loop for age */
   if(argc <=1){  
     printf("\nEnter the parameter file name: ");        /* Confidence intervalle of pij  */
     scanf("%s",pathtot);        /*
   }          fprintf(ficgp,"\nset noparametric;unset label");
   else{          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
     strcpy(pathtot,argv[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(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   /*cygwin_split_path(pathtot,path,optionfile);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
   /* cutv(path,optionfile,pathtot,'\\');*/        */
   
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);        first1=1;
   chdir(path);        for (k2=1; k2<=(nlstate);k2++){
   replace(pathc,path);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
 /*-------- arguments in the command line --------*/            j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
   strcpy(fileres,"r");              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
   strcat(fileres, optionfilefiname);                if(l1==k1) continue;
   strcat(fileres,".txt");    /* Other files have txt extension */                i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
   /*---------arguments file --------*/                for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
   if((ficpar=fopen(optionfile,"r"))==NULL)    {                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
     printf("Problem with optionfile %s\n",optionfile);                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
     goto end;                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
   }                    mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
   strcpy(filereso,"o");                    c12=cv12/sqrt(v1*v2);
   strcat(filereso,fileres);                    /* Computing eigen value of matrix of covariance */
   if((ficparo=fopen(filereso,"w"))==NULL) {                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     printf("Problem with Output resultfile: %s\n", filereso);goto end;                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   }                    /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
   /* Reads comments: lines beginning with '#' */                    /*v21=sqrt(1.-v11*v11); *//* error */
   while((c=getc(ficpar))=='#' && c!= EOF){                    v21=(lc1-v1)/cv12*v11;
     ungetc(c,ficpar);                    v12=-v21;
     fgets(line, MAXLINE, ficpar);                    v22=v11;
     puts(line);                    tnalp=v21/v11;
     fputs(line,ficparo);                    if(first1==1){
   }                      first1=0;
   ungetc(c,ficpar);                      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);
                     }
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);                    fprintf(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("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(fignu*/
   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);                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
 while((c=getc(ficpar))=='#' && c!= EOF){                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
     ungetc(c,ficpar);                    if(first==1){
     fgets(line, MAXLINE, ficpar);                      first=0;
     puts(line);                      fprintf(ficgp,"\nset parametric;unset label");
     fputs(line,ficparo);                      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");
   ungetc(c,ficpar);                      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);
                        fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
                          fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
   covar=matrix(0,NCOVMAX,1,n);                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
   cptcovn=0;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
   ncovmodel=2+cptcovn;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                      }else{
   /* Read guess parameters */                      first=0;
   /* Reads comments: lines beginning with '#' */                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
   while((c=getc(ficpar))=='#' && c!= EOF){                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     ungetc(c,ficpar);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     fgets(line, MAXLINE, ficpar);                      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",\
     puts(line);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     fputs(line,ficparo);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   }                    }/* if first */
   ungetc(c,ficpar);                  } /* age mod 5 */
                  } /* end loop age */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
     for(i=1; i <=nlstate; i++)                first=1;
     for(j=1; j <=nlstate+ndeath-1; j++){              } /*l12 */
       fscanf(ficpar,"%1d%1d",&i1,&j1);            } /* k12 */
       fprintf(ficparo,"%1d%1d",i1,j1);          } /*l1 */
       printf("%1d%1d",i,j);        }/* k1 */
       for(k=1; k<=ncovmodel;k++){      } /* loop covariates */
         fscanf(ficpar," %lf",&param[i][j][k]);    }
         printf(" %lf",param[i][j][k]);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
         fprintf(ficparo," %lf",param[i][j][k]);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
       }    free_vector(xp,1,npar);
       fscanf(ficpar,"\n");    fclose(ficresprob);
       printf("\n");    fclose(ficresprobcov);
       fprintf(ficparo,"\n");    fclose(ficresprobcor);
     }    fclose(ficgp);
      fclose(fichtm);
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;  }
   
   p=param[1][1];  
    /******************* Printing html file ***********/
   /* Reads comments: lines beginning with '#' */  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
   while((c=getc(ficpar))=='#' && c!= EOF){                    int lastpass, int stepm, int weightopt, char model[],\
     ungetc(c,ficpar);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
     fgets(line, MAXLINE, ficpar);                    int popforecast, int estepm ,\
     puts(line);                    double jprev1, double mprev1,double anprev1, \
     fputs(line,ficparo);                    double jprev2, double mprev2,double anprev2){
   }    int jj1, k1, i1, cpt;
   ungetc(c,ficpar);    /*char optionfilehtm[FILENAMELENGTH];*/
     if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      printf("Problem with %s \n",optionfilehtm), exit(0);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
   for(i=1; i <=nlstate; i++){    }
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
       printf("%1d%1d",i,j);   - 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
       fprintf(ficparo,"%1d%1d",i1,j1);   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
       for(k=1; k<=ncovmodel;k++){   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
         fscanf(ficpar,"%le",&delti3[i][j][k]);   - Life expectancies by age and initial health status (estepm=%2d months): 
         printf(" %le",delti3[i][j][k]);     <a href=\"e%s\">e%s</a> <br>\n</li>", \
         fprintf(ficparo," %le",delti3[i][j][k]);    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
       }  
       fscanf(ficpar,"\n");  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
       printf("\n");  
       fprintf(ficparo,"\n");   m=cptcoveff;
     }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   }  
   delti=delti3[1][1];   jj1=0;
     for(k1=1; k1<=m;k1++){
   /* Reads comments: lines beginning with '#' */     for(i1=1; i1<=ncodemax[k1];i1++){
   while((c=getc(ficpar))=='#' && c!= EOF){       jj1++;
     ungetc(c,ficpar);       if (cptcovn > 0) {
     fgets(line, MAXLINE, ficpar);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     puts(line);         for (cpt=1; cpt<=cptcoveff;cpt++) 
     fputs(line,ficparo);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   }         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   ungetc(c,ficpar);       }
         /* Pij */
   matcov=matrix(1,npar,1,npar);       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>
   for(i=1; i <=npar; i++){  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
     fscanf(ficpar,"%s",&str);       /* Quasi-incidences */
     printf("%s",str);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
     fprintf(ficparo,"%s",str);  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
     for(j=1; j <=i; j++){         /* Stable prevalence in each health state */
       fscanf(ficpar," %le",&matcov[i][j]);         for(cpt=1; cpt<nlstate;cpt++){
       printf(" %.5le",matcov[i][j]);           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
       fprintf(ficparo," %.5le",matcov[i][j]);  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
     }         }
     fscanf(ficpar,"\n");       for(cpt=1; cpt<=nlstate;cpt++) {
     printf("\n");          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
     fprintf(ficparo,"\n");  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
   }       }
   for(i=1; i <=npar; i++)       fprintf(fichtm,"\n<br>- Total life expectancy by age and
     for(j=i+1;j<=npar;j++)  health expectancies in states (1) and (2): e%s%d.png<br>
       matcov[i][j]=matcov[j][i];  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
         } /* end i1 */
   printf("\n");   }/* End k1 */
    fprintf(fichtm,"</ul>");
   
     /*-------- Rewriting paramater file ----------*/  
      strcpy(rfileres,"r");    /* "Rparameterfile */   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
      strcat(rfileres,".");    /* */   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
      strcat(rfileres,optionfilext);    /* Other files have txt extension */   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
     if((ficres =fopen(rfileres,"w"))==NULL) {   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
       printf("Problem writing new parameter file: %s\n", fileres);goto end;   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
     }   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
     fprintf(ficres,"#%s\n",version);   - 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);
      
     /*-------- data file ----------*/   if(popforecast==1) fprintf(fichtm,"\n
     if((fic=fopen(datafile,"r"))==NULL)    {   - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
       printf("Problem with datafile: %s\n", datafile);goto end;   - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
     }          <br>",fileres,fileres,fileres,fileres);
    else 
     n= lastobs;     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);
     severity = vector(1,maxwav);  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
     outcome=imatrix(1,maxwav+1,1,n);  
     num=ivector(1,n);   m=cptcoveff;
     moisnais=vector(1,n);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     annais=vector(1,n);  
     moisdc=vector(1,n);   jj1=0;
     andc=vector(1,n);   for(k1=1; k1<=m;k1++){
     agedc=vector(1,n);     for(i1=1; i1<=ncodemax[k1];i1++){
     cod=ivector(1,n);       jj1++;
     weight=vector(1,n);       if (cptcovn > 0) {
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     mint=matrix(1,maxwav,1,n);         for (cpt=1; cpt<=cptcoveff;cpt++) 
     anint=matrix(1,maxwav,1,n);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     s=imatrix(1,maxwav+1,1,n);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     adl=imatrix(1,maxwav+1,1,n);           }
     tab=ivector(1,NCOVMAX);       for(cpt=1; cpt<=nlstate;cpt++) {
     ncodemax=ivector(1,8);         fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
   interval) in state (%d): v%s%d%d.png <br>
     i=1;  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
     while (fgets(line, MAXLINE, fic) != NULL)    {       }
       if ((i >= firstobs) && (i <=lastobs)) {     } /* end i1 */
           }/* End k1 */
         for (j=maxwav;j>=1;j--){   fprintf(fichtm,"</ul>");
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);  fclose(fichtm);
           strcpy(line,stra);  }
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  /******************* Gnuplot file **************/
         }  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
          
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    int ng;
     if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);      printf("Problem with file %s",optionfilegnuplot);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
     }
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);  
         for (j=ncovcol;j>=1;j--){    /*#ifdef windows */
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      fprintf(ficgp,"cd \"%s\" \n",pathc);
         }      /*#endif */
         num[i]=atol(stra);  m=pow(2,cptcoveff);
            
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){   /* 1eme*/
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/    for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
         i=i+1;       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
       }       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
     }  
     /* printf("ii=%d", ij);       for (i=1; i<= nlstate ; i ++) {
        scanf("%d",i);*/         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   imx=i-1; /* Number of individuals */         else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
   /* for (i=1; i<=imx; i++){       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;       for (i=1; i<= nlstate ; i ++) {
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;         else fprintf(ficgp," \%%*lf (\%%*lf)");
     }*/       } 
    /*  for (i=1; i<=imx; i++){       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
      if (s[4][i]==9)  s[4][i]=-1;       for (i=1; i<= nlstate ; i ++) {
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }  
   /* Calculation of the number of parameter from char model*/       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
   Tvar=ivector(1,15);     }
   Tprod=ivector(1,15);    }
   Tvaraff=ivector(1,15);    /*2 eme*/
   Tvard=imatrix(1,15,1,2);    
   Tage=ivector(1,15);          for (k1=1; k1<= m ; k1 ++) { 
          fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
   if (strlen(model) >1){      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
     j=0, j1=0, k1=1, k2=1;      
     j=nbocc(model,'+');      for (i=1; i<= nlstate+1 ; i ++) {
     j1=nbocc(model,'*');        k=2*i;
     cptcovn=j+1;        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
     cptcovprod=j1;        for (j=1; j<= nlstate+1 ; j ++) {
              if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     strcpy(modelsav,model);          else fprintf(ficgp," \%%*lf (\%%*lf)");
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){        }   
       printf("Error. Non available option model=%s ",model);        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
       goto end;        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);
            for (j=1; j<= nlstate+1 ; j ++) {
     for(i=(j+1); i>=1;i--){          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       cutv(stra,strb,modelsav,'+');          else fprintf(ficgp," \%%*lf (\%%*lf)");
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);        }   
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/        fprintf(ficgp,"\" t\"\" w l 0,");
       /*scanf("%d",i);*/        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
       if (strchr(strb,'*')) {        for (j=1; j<= nlstate+1 ; j ++) {
         cutv(strd,strc,strb,'*');          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
         if (strcmp(strc,"age")==0) {          else fprintf(ficgp," \%%*lf (\%%*lf)");
           cptcovprod--;        }   
           cutv(strb,stre,strd,'V');        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
           Tvar[i]=atoi(stre);        else fprintf(ficgp,"\" t\"\" w l 0,");
           cptcovage++;      }
             Tage[cptcovage]=i;    }
             /*printf("stre=%s ", stre);*/    
         }    /*3eme*/
         else if (strcmp(strd,"age")==0) {    
           cptcovprod--;    for (k1=1; k1<= m ; k1 ++) { 
           cutv(strb,stre,strc,'V');      for (cpt=1; cpt<= nlstate ; cpt ++) {
           Tvar[i]=atoi(stre);        k=2+nlstate*(2*cpt-2);
           cptcovage++;        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
           Tage[cptcovage]=i;        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
         }        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
         else {          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           cutv(strb,stre,strc,'V');          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           Tvar[i]=ncovcol+k1;          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           cutv(strb,strc,strd,'V');          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           Tprod[k1]=i;          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           Tvard[k1][1]=atoi(strc);          
           Tvard[k1][2]=atoi(stre);        */
           Tvar[cptcovn+k2]=Tvard[k1][1];        for (i=1; i< nlstate ; i ++) {
           Tvar[cptcovn+k2+1]=Tvard[k1][2];          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);
           for (k=1; k<=lastobs;k++)          
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];        } 
           k1++;      }
           k2=k2+2;    }
         }    
       }    /* CV preval stat */
       else {    for (k1=1; k1<= m ; k1 ++) { 
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/      for (cpt=1; cpt<nlstate ; cpt ++) {
        /*  scanf("%d",i);*/        k=3;
       cutv(strd,strc,strb,'V');        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
       Tvar[i]=atoi(strc);        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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
       }        
       strcpy(modelsav,stra);          for (i=1; i< nlstate ; i ++)
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);          fprintf(ficgp,"+$%d",k+i+1);
         scanf("%d",i);*/        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
     }        
 }        l=3+(nlstate+ndeath)*cpt;
          fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);        for (i=1; i< nlstate ; i ++) {
   printf("cptcovprod=%d ", cptcovprod);          l=3+(nlstate+ndeath)*cpt;
   scanf("%d ",i);*/          fprintf(ficgp,"+$%d",l+i+1);
     fclose(fic);        }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
     /*  if(mle==1){*/      } 
     if (weightopt != 1) { /* Maximisation without weights*/    }  
       for(i=1;i<=n;i++) weight[i]=1.0;    
     }    /* proba elementaires */
     /*-calculation of age at interview from date of interview and age at death -*/    for(i=1,jk=1; i <=nlstate; i++){
     agev=matrix(1,maxwav,1,imx);      for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
     for (i=1; i<=imx; i++) {          for(j=1; j <=ncovmodel; j++){
       for(m=2; (m<= maxwav); m++) {            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){            jk++; 
          anint[m][i]=9999;            fprintf(ficgp,"\n");
          s[m][i]=-1;          }
        }        }
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;      }
       }     }
     }  
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
     for (i=1; i<=imx; i++)  {       for(jk=1; jk <=m; jk++) {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
       for(m=1; (m<= maxwav); m++){         if (ng==2)
         if(s[m][i] >0){           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
           if (s[m][i] >= nlstate+1) {         else
             if(agedc[i]>0)           fprintf(ficgp,"\nset title \"Probability\"\n");
               if(moisdc[i]!=99 && andc[i]!=9999)         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
                 agev[m][i]=agedc[i];         i=1;
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/         for(k2=1; k2<=nlstate; k2++) {
            else {           k3=i;
               if (andc[i]!=9999){           for(k=1; k<=(nlstate+ndeath); k++) {
               printf("Warning negative age at death: %d line:%d\n",num[i],i);             if (k != k2){
               agev[m][i]=-1;               if(ng==2)
               }                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
             }               else
           }                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
           else if(s[m][i] !=9){ /* Should no more exist */               ij=1;
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);               for(j=3; j <=ncovmodel; j++) {
             if(mint[m][i]==99 || anint[m][i]==9999)                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
               agev[m][i]=1;                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
             else if(agev[m][i] <agemin){                   ij++;
               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
             }                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
             else if(agev[m][i] >agemax){               }
               agemax=agev[m][i];               fprintf(ficgp,")/(1");
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/               
             }               for(k1=1; k1 <=nlstate; k1++){   
             /*agev[m][i]=anint[m][i]-annais[i];*/                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
             /*   agev[m][i] = age[i]+2*m;*/                 ij=1;
           }                 for(j=3; j <=ncovmodel; j++){
           else { /* =9 */                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
             agev[m][i]=1;                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
             s[m][i]=-1;                     ij++;
           }                   }
         }                   else
         else /*= 0 Unknown */                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
           agev[m][i]=1;                 }
       }                 fprintf(ficgp,")");
                   }
     }               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
     for (i=1; i<=imx; i++)  {               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
       for(m=1; (m<= maxwav); m++){               i=i+ncovmodel;
         if (s[m][i] > (nlstate+ndeath)) {             }
           printf("Error: Wrong value in nlstate or ndeath\n");             } /* end k */
           goto end;         } /* end k2 */
         }       } /* end jk */
       }     } /* end ng */
     }     fclose(ficgp); 
   }  /* end gnuplot */
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);  
   
     free_vector(severity,1,maxwav);  /*************** Moving average **************/
     free_imatrix(outcome,1,maxwav+1,1,n);  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
     free_vector(moisnais,1,n);  
     free_vector(annais,1,n);    int i, cpt, cptcod;
     /* free_matrix(mint,1,maxwav,1,n);    int modcovmax =1;
        free_matrix(anint,1,maxwav,1,n);*/    int mobilavrange, mob;
     free_vector(moisdc,1,n);    double age;
     free_vector(andc,1,n);  
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                                 a covariate has 2 modalities */
     wav=ivector(1,imx);    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
     dh=imatrix(1,lastpass-firstpass+1,1,imx);  
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
          if(mobilav==1) mobilavrange=5; /* default */
     /* Concatenates waves */      else mobilavrange=mobilav;
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
       Tcode=ivector(1,100);            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);      /* We keep the original values on the extreme ages bage, fage and for 
       ncodemax[1]=1;         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);         we use a 5 terms etc. until the borders are no more concerned. 
            */ 
    codtab=imatrix(1,100,1,10);      for (mob=3;mob <=mobilavrange;mob=mob+2){
    h=0;        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
    m=pow(2,cptcoveff);          for (i=1; i<=nlstate;i++){
              for (cptcod=1;cptcod<=modcovmax;cptcod++){
    for(k=1;k<=cptcoveff; k++){              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
      for(i=1; i <=(m/pow(2,k));i++){                for (cpt=1;cpt<=(mob-1)/2;cpt++){
        for(j=1; j <= ncodemax[k]; j++){                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
            h++;                }
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/            }
          }          }
        }        }/* end age */
      }      }/* end mob */
    }    }else return -1;
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    return 0;
       codtab[1][2]=1;codtab[2][2]=2; */  }/* End movingaverage */
    /* 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);  /************** Forecasting ******************/
       }  prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
       printf("\n");    /* proj1, year, month, day of starting projection 
       }       agemin, agemax range of age
       scanf("%d",i);*/       dateprev1 dateprev2 range of dates during which prevalence is computed
           anproj2 year of en of projection (same day and month as proj1).
    /* Calculates basic frequencies. Computes observed prevalence at single age    */
        and prints on file fileres'p'. */    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
        double agec; /* generic age */
        double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double *popeffectif,*popcount;
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double ***p3mat;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double ***mobaverage;
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    char fileresf[FILENAMELENGTH];
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
          agelim=AGESUP;
     /* For Powell, parameters are in a vector p[] starting at p[1]    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */   
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if(mle==1){    if((ficresf=fopen(fileresf,"w"))==NULL) {
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);      printf("Problem with forecast resultfile: %s\n", fileresf);
     }      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
        }
     /*--------- results files --------------*/    printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
    
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
    jk=1;  
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    if (mobilav!=0) {
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    for(i=1,jk=1; i <=nlstate; i++){      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
      for(k=1; k <=(nlstate+ndeath); k++){        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
        if (k != i)        printf(" Error in movingaverage mobilav=%d\n",mobilav);
          {      }
            printf("%d%d ",i,k);    }
            fprintf(ficres,"%1d%1d ",i,k);  
            for(j=1; j <=ncovmodel; j++){    stepsize=(int) (stepm+YEARM-1)/YEARM;
              printf("%f ",p[jk]);    if (stepm<=12) stepsize=1;
              fprintf(ficres,"%f ",p[jk]);    if(estepm < stepm){
              jk++;      printf ("Problem %d lower than %d\n",estepm, stepm);
            }    }
            printf("\n");    else  hstepm=estepm;   
            fprintf(ficres,"\n");  
          }    hstepm=hstepm/stepm; 
      }    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
    }                                 fractional in yp1 */
  if(mle==1){    anprojmean=yp;
     /* Computing hessian and covariance matrix */    yp2=modf((yp1*12),&yp);
     ftolhess=ftol; /* Usually correct */    mprojmean=yp;
     hesscov(matcov, p, npar, delti, ftolhess, func);    yp1=modf((yp2*30.5),&yp);
  }    jprojmean=yp;
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    if(jprojmean==0) jprojmean=1;
     printf("# Scales (for hessian or gradient estimation)\n");    if(mprojmean==0) jprojmean=1;
      for(i=1,jk=1; i <=nlstate; i++){  
       for(j=1; j <=nlstate+ndeath; j++){    i1=cptcoveff;
         if (j!=i) {    if (cptcovn < 1){i1=1;}
           fprintf(ficres,"%1d%1d",i,j);    
           printf("%1d%1d",i,j);    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
           for(k=1; k<=ncovmodel;k++){    
             printf(" %.5e",delti[jk]);    fprintf(ficresf,"#****** Routine prevforecast **\n");
             fprintf(ficres," %.5e",delti[jk]);  
             jk++;    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
           }      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
           printf("\n");        k=k+1;
           fprintf(ficres,"\n");        fprintf(ficresf,"\n#******");
         }        for(j=1;j<=cptcoveff;j++) {
       }          fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
      }        }
            fprintf(ficresf,"******\n");
     k=1;        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
     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");        for(j=1; j<=nlstate+ndeath;j++){ 
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");          for(i=1; i<=nlstate;i++)              
     for(i=1;i<=npar;i++){            fprintf(ficresf," p%d%d",i,j);
       /*  if (k>nlstate) k=1;          fprintf(ficresf," p.%d",j);
       i1=(i-1)/(ncovmodel*nlstate)+1;        }
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
       printf("%s%d%d",alph[k],i1,tab[i]);*/          fprintf(ficresf,"\n");
       fprintf(ficres,"%3d",i);          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
       printf("%3d",i);  
       for(j=1; j<=i;j++){          for (agec=fage; agec>=(ageminpar-1); agec--){ 
         fprintf(ficres," %.5e",matcov[i][j]);            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
         printf(" %.5e",matcov[i][j]);            nhstepm = nhstepm/hstepm; 
       }            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficres,"\n");            oldm=oldms;savm=savms;
       printf("\n");            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
       k++;          
     }            for (h=0; h<=nhstepm; h++){
                  if (h==(int) (YEARM*yearp)) {
     while((c=getc(ficpar))=='#' && c!= EOF){                fprintf(ficresf,"\n");
       ungetc(c,ficpar);                for(j=1;j<=cptcoveff;j++) 
       fgets(line, MAXLINE, ficpar);                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       puts(line);                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
       fputs(line,ficparo);              } 
     }              for(j=1; j<=nlstate+ndeath;j++) {
     ungetc(c,ficpar);                ppij=0.;
     estepm=0;                for(i=1; i<=nlstate;i++) {
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);                  if (mobilav==1) 
     if (estepm==0 || estepm < stepm) estepm=stepm;                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
     if (fage <= 2) {                  else {
       bage = ageminpar;                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
       fage = agemaxpar;                  }
     }                  if (h==(int)(YEARM*yearp))
                        fprintf(ficresf," %.3f", p3mat[i][j][h]);
     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);                if (h==(int)(YEARM*yearp)){
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                  fprintf(ficresf," %.3f", ppij);
                  }
     while((c=getc(ficpar))=='#' && c!= EOF){              }
     ungetc(c,ficpar);            }
     fgets(line, MAXLINE, ficpar);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     puts(line);          }
     fputs(line,ficparo);        }
   }      }
   ungetc(c,ficpar);    }
           
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    fclose(ficresf);
        }
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  /************** Forecasting *****not tested NB*************/
     fgets(line, MAXLINE, ficpar);  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){
     puts(line);    
     fputs(line,ficparo);    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
   }    int *popage;
   ungetc(c,ficpar);    double calagedatem, agelim, kk1, kk2;
      double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    double ***mobaverage;
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    char filerespop[FILENAMELENGTH];
   
   fscanf(ficpar,"pop_based=%d\n",&popbased);    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   fprintf(ficparo,"pop_based=%d\n",popbased);      tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   fprintf(ficres,"pop_based=%d\n",popbased);      agelim=AGESUP;
      calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
   while((c=getc(ficpar))=='#' && c!= EOF){    
     ungetc(c,ficpar);    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     fgets(line, MAXLINE, ficpar);    
     puts(line);    
     fputs(line,ficparo);    strcpy(filerespop,"pop"); 
   }    strcat(filerespop,fileres);
   ungetc(c,ficpar);    if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);    }
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);    printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
 while((c=getc(ficpar))=='#' && c!= EOF){    if (cptcoveff==0) ncodemax[cptcoveff]=1;
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    if (mobilav!=0) {
     puts(line);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fputs(line,ficparo);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
   }        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   ungetc(c,ficpar);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
   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);    stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    
     agelim=AGESUP;
 /*------------ gnuplot -------------*/    
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);    hstepm=1;
      hstepm=hstepm/stepm; 
 /*------------ free_vector  -------------*/    
  chdir(path);    if (popforecast==1) {
        if((ficpop=fopen(popfile,"r"))==NULL) {
  free_ivector(wav,1,imx);        printf("Problem with population file : %s\n",popfile);exit(0);
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);        } 
  free_ivector(num,1,n);      popage=ivector(0,AGESUP);
  free_vector(agedc,1,n);      popeffectif=vector(0,AGESUP);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/      popcount=vector(0,AGESUP);
  fclose(ficparo);      
  fclose(ficres);      i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
 /*--------- index.htm --------*/     
       imx=i;
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
    
   /*--------------- Prevalence limit --------------*/    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   strcpy(filerespl,"pl");        k=k+1;
   strcat(filerespl,fileres);        fprintf(ficrespop,"\n#******");
   if((ficrespl=fopen(filerespl,"w"))==NULL) {        for(j=1;j<=cptcoveff;j++) {
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   }        }
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);        fprintf(ficrespop,"******\n");
   fprintf(ficrespl,"#Prevalence limit\n");        fprintf(ficrespop,"# Age");
   fprintf(ficrespl,"#Age ");        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);        if (popforecast==1)  fprintf(ficrespop," [Population]");
   fprintf(ficrespl,"\n");        
          for (cpt=0; cpt<=0;cpt++) { 
   prlim=matrix(1,nlstate,1,nlstate);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            nhstepm = nhstepm/hstepm; 
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            
   k=0;            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   agebase=ageminpar;            oldm=oldms;savm=savms;
   agelim=agemaxpar;            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
   ftolpl=1.e-10;          
   i1=cptcoveff;            for (h=0; h<=nhstepm; h++){
   if (cptcovn < 1){i1=1;}              if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
   for(cptcov=1;cptcov<=i1;cptcov++){              } 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              for(j=1; j<=nlstate+ndeath;j++) {
         k=k+1;                kk1=0.;kk2=0;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/                for(i=1; i<=nlstate;i++) {              
         fprintf(ficrespl,"\n#******");                  if (mobilav==1) 
         for(j=1;j<=cptcoveff;j++)                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                  else {
         fprintf(ficrespl,"******\n");                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                          }
         for (age=agebase; age<=agelim; age++){                }
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                if (h==(int)(calagedatem+12*cpt)){
           fprintf(ficrespl,"%.0f",age );                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
           for(i=1; i<=nlstate;i++)                    /*fprintf(ficrespop," %.3f", kk1);
           fprintf(ficrespl," %.5f", prlim[i][i]);                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
           fprintf(ficrespl,"\n");                }
         }              }
       }              for(i=1; i<=nlstate;i++){
     }                kk1=0.;
   fclose(ficrespl);                  for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
   /*------------- h Pij x at various ages ------------*/                  }
                      tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);              }
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
   }                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
   printf("Computing pij: result on file '%s' \n", filerespij);            }
              free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   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 */        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
            fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
   k=0;          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
   for(cptcov=1;cptcov<=i1;cptcov++){            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            nhstepm = nhstepm/hstepm; 
       k=k+1;            
         fprintf(ficrespij,"\n#****** ");            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         for(j=1;j<=cptcoveff;j++)            oldm=oldms;savm=savms;
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
         fprintf(ficrespij,"******\n");            for (h=0; h<=nhstepm; h++){
                      if (h==(int) (calagedatem+YEARM*cpt)) {
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */              } 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */              for(j=1; j<=nlstate+ndeath;j++) {
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                kk1=0.;kk2=0;
           oldm=oldms;savm=savms;                for(i=1; i<=nlstate;i++) {              
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                    kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
           fprintf(ficrespij,"# Age");                }
           for(i=1; i<=nlstate;i++)                if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
             for(j=1; j<=nlstate+ndeath;j++)              }
               fprintf(ficrespij," %1d-%1d",i,j);            }
           fprintf(ficrespij,"\n");            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
            for (h=0; h<=nhstepm; h++){          }
             fprintf(ficrespij,"%d %.0f %.0f",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");    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
              }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    if (popforecast==1) {
           fprintf(ficrespij,"\n");      free_ivector(popage,0,AGESUP);
         }      free_vector(popeffectif,0,AGESUP);
     }      free_vector(popcount,0,AGESUP);
   }    }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   fclose(ficrespij);  }
   
   /***********************************************/
   /*---------- Forecasting ------------------*/  /**************** Main Program *****************/
   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);  int main(int argc, char *argv[])
   }  {
   else{    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     erreur=108;    int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     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);    double agedeb, agefin,hf;
   }    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
    
     double fret;
   /*---------- Health expectancies and variances ------------*/    double **xi,tmp,delta;
   
   strcpy(filerest,"t");    double dum; /* Dummy variable */
   strcat(filerest,fileres);    double ***p3mat;
   if((ficrest=fopen(filerest,"w"))==NULL) {    double ***mobaverage;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    int *indx;
   }    char line[MAXLINE], linepar[MAXLINE];
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
   strcpy(filerese,"e");    int c,  h , cpt,l;
   strcat(filerese,fileres);    int ju,jl, mi;
   if((ficreseij=fopen(filerese,"w"))==NULL) {    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
   }    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
  strcpy(fileresv,"v");    double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
   strcat(fileresv,fileres);    double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    double bage, fage, age, agelim, agebase;
   }    double ftolpl=FTOL;
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    double **prlim;
   calagedate=-1;    double *severity;
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    double ***param; /* Matrix of parameters */
     double  *p;
   k=0;    double **matcov; /* Matrix of covariance */
   for(cptcov=1;cptcov<=i1;cptcov++){    double ***delti3; /* Scale */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    double *delti; /* Scale */
       k=k+1;    double ***eij, ***vareij;
       fprintf(ficrest,"\n#****** ");    double **varpl; /* Variances of prevalence limits by age */
       for(j=1;j<=cptcoveff;j++)    double *epj, vepp;
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double kk1, kk2;
       fprintf(ficrest,"******\n");    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   
       fprintf(ficreseij,"\n#****** ");    char *alph[]={"a","a","b","c","d","e"}, str[4];
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficreseij,"******\n");    char z[1]="c", occ;
   #include <sys/time.h>
       fprintf(ficresvij,"\n#****** ");  #include <time.h>
       for(j=1;j<=cptcoveff;j++)    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   
       fprintf(ficresvij,"******\n");    /* long total_usecs;
        struct timeval start_time, end_time;
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    
       oldm=oldms;savm=savms;       gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);      getcwd(pathcd, size);
    
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    printf("\n%s",version);
       oldm=oldms;savm=savms;    if(argc <=1){
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);      printf("\nEnter the parameter file name: ");
          scanf("%s",pathtot);
     }
      else{
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      strcpy(pathtot,argv[1]);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    }
       fprintf(ficrest,"\n");    /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       epj=vector(1,nlstate+1);      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
       for(age=bage; age <=fage ;age++){    /* cutv(path,optionfile,pathtot,'\\');*/
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  
         if (popbased==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);
             prlim[i][i]=probs[(int)age][i][k];    chdir(path);
         }    replace(pathc,path);
          
         fprintf(ficrest," %4.0f",age);    /*-------- arguments in the command line --------*/
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    /* Log file */
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    strcat(filelog, optionfilefiname);
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    strcat(filelog,".log");    /* */
           }    if((ficlog=fopen(filelog,"w"))==NULL)    {
           epj[nlstate+1] +=epj[j];      printf("Problem with logfile %s\n",filelog);
         }      goto end;
     }
         for(i=1, vepp=0.;i <=nlstate;i++)    fprintf(ficlog,"Log filename:%s\n",filelog);
           for(j=1;j <=nlstate;j++)    fprintf(ficlog,"\n%s",version);
             vepp += vareij[i][j][(int)age];    fprintf(ficlog,"\nEnter the parameter file name: ");
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
         for(j=1;j <=nlstate;j++){    fflush(ficlog);
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));  
         }    /* */
         fprintf(ficrest,"\n");    strcpy(fileres,"r");
       }    strcat(fileres, optionfilefiname);
     }    strcat(fileres,".txt");    /* Other files have txt extension */
   }  
 free_matrix(mint,1,maxwav,1,n);    /*---------arguments file --------*/
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);  
     free_vector(weight,1,n);    if((ficpar=fopen(optionfile,"r"))==NULL)    {
   fclose(ficreseij);      printf("Problem with optionfile %s\n",optionfile);
   fclose(ficresvij);      fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
   fclose(ficrest);      goto end;
   fclose(ficpar);    }
   free_vector(epj,1,nlstate+1);  
      strcpy(filereso,"o");
   /*------- Variance limit prevalence------*/      strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) {
   strcpy(fileresvpl,"vpl");      printf("Problem with Output resultfile: %s\n", filereso);
   strcat(fileresvpl,fileres);      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      goto end;
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    }
     exit(0);  
   }    /* Reads comments: lines beginning with '#' */
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
   k=0;      fgets(line, MAXLINE, ficpar);
   for(cptcov=1;cptcov<=i1;cptcov++){      puts(line);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      fputs(line,ficparo);
       k=k+1;    }
       fprintf(ficresvpl,"\n#****** ");    ungetc(c,ficpar);
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    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);
       fprintf(ficresvpl,"******\n");    printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
          fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    while((c=getc(ficpar))=='#' && c!= EOF){
       oldm=oldms;savm=savms;      ungetc(c,ficpar);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      fgets(line, MAXLINE, ficpar);
     }      puts(line);
  }      fputs(line,ficparo);
     }
   fclose(ficresvpl);    ungetc(c,ficpar);
     
   /*---------- End : free ----------------*/     
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    covar=matrix(0,NCOVMAX,1,n); 
      cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
      ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
      nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    /* Read guess parameters */
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    /* Reads comments: lines beginning with '#' */
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    while((c=getc(ficpar))=='#' && c!= EOF){
        ungetc(c,ficpar);
   free_matrix(matcov,1,npar,1,npar);      fgets(line, MAXLINE, ficpar);
   free_vector(delti,1,npar);      puts(line);
   free_matrix(agev,1,maxwav,1,imx);      fputs(line,ficparo);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    }
     ungetc(c,ficpar);
   if(erreur >0)    
     printf("End of Imach with error or warning %d\n",erreur);    param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
   else   printf("End of Imach\n");    for(i=1; i <=nlstate; i++)
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      for(j=1; j <=nlstate+ndeath-1; j++){
          fscanf(ficpar,"%1d%1d",&i1,&j1);
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/        fprintf(ficparo,"%1d%1d",i1,j1);
   /*printf("Total time was %d uSec.\n", total_usecs);*/        if(mle==1)
   /*------ End -----------*/          printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
  end:          fscanf(ficpar," %lf",&param[i][j][k]);
   /* chdir(pathcd);*/          if(mle==1){
  /*system("wgnuplot graph.plt");*/            printf(" %lf",param[i][j][k]);
  /*system("../gp37mgw/wgnuplot graph.plt");*/            fprintf(ficlog," %lf",param[i][j][k]);
  /*system("cd ../gp37mgw");*/          }
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/          else
  strcpy(plotcmd,GNUPLOTPROGRAM);            fprintf(ficlog," %lf",param[i][j][k]);
  strcat(plotcmd," ");          fprintf(ficparo," %lf",param[i][j][k]);
  strcat(plotcmd,optionfilegnuplot);        }
  system(plotcmd);        fscanf(ficpar,"\n");
         if(mle==1)
  /*#ifdef windows*/          printf("\n");
   while (z[0] != 'q') {        fprintf(ficlog,"\n");
     /* chdir(path); */        fprintf(ficparo,"\n");
     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");    npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
     else if (z[0] == 'e') system(optionfilehtm);  
     else if (z[0] == 'g') system(plotcmd);    p=param[1][1];
     else if (z[0] == 'q') exit(0);    
   }    /* Reads comments: lines beginning with '#' */
   /*#endif */    while((c=getc(ficpar))=='#' && c!= EOF){
 }      ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     delti=delti3[1][1];
   
   
     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
           fprintf(ficlog," %.5le",matcov[i][j]);
         }
         else
           fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=ivector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); 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){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             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=firstpass; (m<=lastpass); 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;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
     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);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"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+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/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,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year 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);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     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(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           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*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     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,"# Cov Agex agex+h hpijx with i,j=");
           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 %3.f %3.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, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (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);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     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_ma3x(probs,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);
   
     /*  fclose(fichtm);*/
     /*  fclose(ficgp);*/ /* ALready done */
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     
     /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
     /*printf("Total time was %d uSec.\n", total_usecs);*/
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting: %s\n",plotcmd);fflush(stdout);
     system(plotcmd);
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   
Removed from v.1.41.2.1  
changed lines
  Added in v.1.74

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